NEISSERIAL ANTIGENS

Description

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a Divisional application of U.S. patent application Ser. No. 12/653,954, filed, Dec. 18, 2009, which is a Divisional of U.S. patent application Ser. No. 10/864,684, filed Jun. 8, 2004, now U.S. Pat. No. 7,655,245, which is a continuation application of U.S. patent application Ser. No. 09/303,518, filed Apr. 30, 1999, now U.S. Pat. No. 6,914,131, which is a continuation-in-part of International Patent Application PCT/IB1998/001665, filed Oct. 9, 1998, from which applications priority is claimed pursuant to 35 U.S.C. §120. PCT/IB1998/001665 claims priority to Great Britain Patent Applications No. 9723516.2, filed Nov. 6, 1997; No. 9724190.5, filed Nov. 14, 1997; No. 9724386.9, filed Nov. 18, 1997; No. 9725158.1, filed Nov. 27, 1997; No. 9726147.3, filed Dec. 10, 1997; No. 9800759.4, filed Jan. 14, 1998; No. 9819016.8, filed Sep. 1, 1998. All of the above applications are incorporated herein by reference in their entirety.

SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE

The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: 223002099611SUBSEQLIST.txt, date recorded: Oct. 1, 2012, size: 2,099 KB).

This invention relates to antigens from Neisseria bacteria.

BACKGROUND ART

Neisseria meningitidis and Neisseria gonorrhoeae are non-motile, gram negative diplococci that are pathogenic in humans. N. meningitidis colonises the pharynx and causes meningitis (and, occasionally, septicaemia in the absence of meningitis); N. gonorrhoeae colonises the genital tract and causes gonorrhea. Although colonising different areas of the body and causing completely different diseases, the two pathogens are closely related, although one feature that clearly differentiates meningococcus from gonococcus is the presence of a polysaccharide capsule that is present in all pathogenic meningococci.

N. gonorrhoeae caused approximately 800,000 cases per year during the period 1983-1990 in the United States alone (chapter by Meitzner & Cohen, “Vaccines Against Gonococcal Infection”, In: New Generation Vaccines, 2nd edition, ed. Levine, Woodrow, Kaper, & Cobon, Marcel Dekker, New York, 1997, pp. 817-842). The disease causes significant morbidity but limited mortality. Vaccination against N. gonorrhoeae would be highly desirable, but repeated attempts have failed. The main candidate antigens for this vaccine are surface-exposed proteins such as pili, porins, opacity-associated proteins (Opas) and other surface-exposed proteins such as the Lip, Laz, IgA1 protease and transferrin-binding proteins. The lipooligosaccharide (LOS) has also been suggested as vaccine (Meitzner & Cohen, supra).

N. meningitidis causes both endemic and epidemic disease. In the United States the attack rate is 0.6-1 per 100,000 persons per year, and it can be much greater during outbreaks (see Lieberman et al. (1996) Safety and Immunogenicity of a Serogroups A/C Neisseria meningitidis Oligosaccharide-Protein Conjugate Vaccine in Young Children. JAMA 275(19):1499-1503; Schuchat et al (1997) Bacterial Meningitis in the United States in 1995. N Engl J Med 337(14):970-976). In developing countries, endemic disease rates are much higher and during epidemics incidence rates can reach 500 cases per 100,000 persons per year. Mortality is extremely high, at 10-20% in the United States, and much higher in developing countries. Following the introduction of the conjugate vaccine against Haemophilus influenzae, N. meningitidis is the major cause of bacterial meningitis at all ages in the United States (Schuchat et al (1997) supra).

Based on the organism's capsular polysaccharide, 12 serogroups of N. meningitidis have been identified. Group A is the pathogen most often implicated in epidemic disease in sub-Saharan Africa. Serogroups B and C are responsible for the vast majority of cases in the United States and in most developed countries. Serogroups W135 and Y are responsible for the rest of the cases in the United States and developed countries. The meningococcal vaccine currently in use is a tetravalent polysaccharide vaccine composed of serogroups A, C, Y and W135. Although efficacious in adolescents and adults, it induces a poor immune response and short duration of protection, and cannot be, used in infants [eg. Morbidity and Mortality weekly report, Vol. 46, No. RR-5 (1997)]. This is because polysaccharides are T-cell independent antigens that induce a weak immune response that cannot be boosted by repeated immunization. Following the success of the vaccination against H. influenzae, conjugate vaccines against serogroups A and C have been developed and are at the final stage of clinical testing (Zollinger W D “New and Improved Vaccines Against Meningococcal Disease” in: New Generation Vaccines, supra, pp. 469-488; Lieberman et al (1996) supra; Costantino et al (1992) Development and phase I clinical testing of a conjugate vaccine against meningococcus A and C. Vaccine 10:691-698).

Meningococcus B remains a problem, however. This serotype currently is responsible for approximately 50% of total meningitis in the United States, Europe, and South America. The polysaccharide approach cannot be used because the menB capsular polysaccharide is a polymer of α(2-8)-linked N-acetyl neuraminic acid that is also present in mammalian tissue. This results in tolerance to the antigen; indeed, if an immune response were elicited, it would be anti-self, and therefore undesirable. In order to avoid induction of autoimmunity and to induce a protective immune response, the capsular polysaccharide has, for instance, been chemically modified substituting the N-acetyl groups with N-propionyl groups, leaving the specific antigenicity unaltered (Romero & Outschoorn (1994) Current status of Meningococcal group B vaccine candidates: capsular or non-capsular? Clin Microbiol Rev 7(4):559-575).

Alternative approaches to menB vaccines have used complex mixtures of outer membrane proteins (OMPs), containing either the OMPs alone, or OMPs enriched in porins, or deleted of the class 4 OMPs that are believed to induce antibodies that block bactericidal activity. This approach produces vaccines that are not well characterized. They are able to protect against the homologous strain, but are not effective at large where there are many antigenic variants of the outer membrane proteins. To overcome the antigenic variability, multivalent vaccines containing up to nine different porins have been constructed (eg. Poolman J T (1992) Development of a meningococcal vaccine. Infect. Agents Dis. 4:13-28). Additional proteins to be used in outer membrane vaccines have been the opa and opc proteins, but none of these approaches have been able to overcome the antigenic variability (eg. Ala'Aldeen & Borriello (1996) The meningococcal transferrin-binding proteins 1 and 2 are both surface exposed and generate bactericidal antibodies capable of killing homologous and heterologous strains. Vaccine 14(1):49-53).

A certain amount of sequence data is available for meningococcal and gonoccocal genes and proteins (eg. EP-A-0467714, WO96/29412), but this is by no means complete. The provision of further sequences could provide an opportunity to identify secreted or surface-exposed proteins that are presumed targets for the immune system and which are not antigenically variable. For instance, some of the identified proteins could be components of efficacious vaccines against meningococcus B, some could be components of vaccines against all meningococcal serotypes, and others could be components of vaccines against all pathogenic Neisseriae.

THE INVENTION

The invention provides proteins comprising the Neisserial amino acid sequences disclosed in the examples. These sequences relate to N. meningitidis or N. gonorrhoeae.

It also provides proteins comprising sequences homologous (ie. having sequence identity) to the Neisserial amino acid sequences disclosed in the examples. Depending on the particular sequence, the degree of identity is preferably greater than 50% (eg. 65%, 80%, 90%, or more). These homologous proteins include mutants and allelic variants of the sequences disclosed in the examples. Typically, 50% identity or more between two proteins is considered to be an indication of functional equivalence. Identity between the proteins is preferably determined by the Smith-Waterman homology search algorithm as implemented in the MPSRCH program (Oxford Molecular), using an affine gap search with parameters gap open penalty=12 and gap extension penalty=1.

The invention further provides proteins comprising fragments of the Neisserial amino acid sequences disclosed in the examples. The fragments should comprise at least n consecutive amino acids from the sequences and, depending on the particular sequence, n is 7 or more (eg. 8, 10, 12, 14, 16, 18, 20 or more). Preferably the fragments comprise an epitope from the sequence.

The proteins of the invention can, of course, be prepared by various means (eg. recombinant expression, purification from cell culture, chemical synthesis etc.) and in various forms (eg. native, fusions etc.). They are preferably prepared in substantially pure or isolated form (ie. substantially free from other Neisserial or host cell proteins)

According to a further aspect, the invention provides antibodies which bind to these proteins. These may be polyclonal or monoclonal and may be produced by any suitable means.

According to a further aspect, the invention provides nucleic acid comprising the Neisserial nucleotide sequences disclosed in the examples. In addition, the invention provides nucleic acid comprising sequences homologous (ie. having sequence identity) to the Neisserial nucleotide sequences disclosed in the examples.

Furthermore, the invention provides nucleic acid which can hybridise to the Neisserial nucleic acid disclosed in the examples, preferably under “high stringency” conditions (eg. 65° C. in a 0.1×SSC, 0.5% SDS solution).

Nucleic acid comprising fragments of these sequences are also provided. These should comprise at least n consecutive nucleotides from the Neisserial sequences and, depending on the particular sequence, n is 10 or more (eg 12, 14, 15, 18, 20, 25, 30, 35, 40 or more).

According to a further aspect, the invention provides nucleic acid encoding the proteins and protein fragments of the invention.

It should also be appreciated that the invention provides nucleic acid comprising sequences complementary to those described above (eg. for antisense or probing purposes).

Nucleic acid according to the invention can, of course, be prepared in many ways (eg. by chemical synthesis, from genomic or cDNA libraries, from the organism itself etc.) and can take various forms (eg. single stranded, double stranded, vectors, probes etc.).

In addition, the term “nucleic acid” includes DNA and RNA, and also their analogues, such as those containing modified backbones, and also peptide nucleic acids (PNA) etc.

According to a further aspect, the invention provides vectors comprising nucleotide sequences of the invention (eg. expression vectors) and host cells transformed with such vectors.

According to a further aspect, the invention provides compositions comprising protein, antibody, and/or nucleic acid according to the invention. These compositions may be suitable as vaccines, for instance, or as diagnostic reagents, or as immunogenic compositions.

The invention also provides nucleic acid, protein, or antibody according to the invention for use as medicaments (eg. as vaccines) or as diagnostic reagents. It also provides the use of nucleic acid, protein, or antibody according to the invention in the manufacture of: (i) a medicament for treating or preventing infection due to Neisserial bacteria; (ii) a diagnostic reagent for detecting the presence of Neisserial bacteria or of antibodies raised against Neisserial bacteria; and/or (iii) a reagent which can raise antibodies against Neisserial bacteria. Said Neisserial bacteria may be any species or strain (such as N. gonorrhoeae, or any strain of N. meningitidis, such as strain A, strain B or strain C).

The invention also provides a method of treating a patient, comprising administering to the patient a therapeutically effective amount of nucleic acid, protein, and/or antibody according to the invention.

According to further aspects, the invention provides various processes.

A process for producing proteins of the invention is provided, comprising the step of culturing a host cell according to the invention under conditions which induce protein expression.

A process for producing protein or nucleic acid of the invention is provided, wherein the protein or nucleic acid is synthesised in part or in whole using chemical means.

A process for detecting polynucleotides of the invention is provided, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridizing conditions to form duplexes; and (b) detecting said duplexes.

A process for detecting proteins of the invention is provided, comprising the steps of: (a) contacting an antibody according to the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.

A summary of standard techniques and procedures which may be employed in order to perform the invention (eg. to utilise the disclosed sequences for vaccination or diagnostic purposes) follows. This summary is not a limitation on the invention but, rather, gives examples that may be used, but are not required.

General

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature eg. Sambrook Molecular Cloning; A Laboratory Manual, Second Edition (1989); DNA Cloning, Volumes I and ii (D. N Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed, 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription and Translation (B. D. Hames & S. J. Higgins eds. 1984); Animal Cell Culture (R. I. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide to Molecular Cloning (1984); the Methods in Enzymology series (Academic Press, Inc.), especially volumes 154 & 155; Gene Transfer Vectors for Mammalian Cells (J. H. Miller and M. P. Calm eds. 1987, Cold Spring Harbor Laboratory); Mayer and Walker, eds. (1987), Immunochemical Methods in Cell and Molecular Biology (Academic Press, London); Scopes, (1987) Protein Purification: Principles and Practice, Second Edition (Springer-Verlag, N.Y.), and Handbook of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell eds 1986).

Standard abbreviations for nucleotides and amino acids are used in this specification.

All publications, patents, and patent applications cited herein are incorporated in full by reference. In particular, the contents of UK patent applications 9723516.2, 9724190.5, 9724386.9, 9725158.1, 9726147.3, 9800759.4, and 9819016.8 are incorporated herein.

DEFINITIONS

A composition containing X is “substantially free of” Y when at least 85% by weight of the total X+Y in the composition is X. Preferably, X comprises at least about 90% by weight of the total of X+Y in the composition, more preferably at least about 95% or even 99% by weight.

The term “comprising” means “including” as well as “consisting” eg. a composition “comprising” X may consist exclusively of X or may include something additional to X, such as X+Y.

The term “heterologous” refers to two biological components that are not found together in nature. The components may be host cells, genes, or regulatory regions, such as promoters. Although the heterologous components are not found together in nature, they can function together, as when a promoter heterologous to a gene is operably linked to the gene. Another example is where a Neisserial sequence is heterologous to a mouse host cell. A further examples would be two epitopes from the same or different proteins which have been assembled in a single protein in an arrangement not found in nature.

An “origin of replication” is a polynucleotide sequence that initiates and regulates replication of polynucleotides, such as an expression vector. The origin of replication behaves as an autonomous unit of polynucleotide replication within a cell, capable of replication under its own control. An origin of replication may be needed for a vector to replicate in a particular host cell. With certain origins of replication, an expression vector can be reproduced at a high copy number in the presence of the appropriate proteins within the cell. Examples of origins are the autonomously replicating sequences, which are effective in yeast; and the viral T-antigen, effective in COS-7 cells.

A “mutant” sequence is defined as DNA, RNA or amino acid sequence differing from but having sequence identity with the native or disclosed sequence. Depending on the particular sequence, the degree of sequence identity between the native or disclosed sequence and the mutant sequence is preferably greater than 50% (eg. 60%, 70%, 80%, 90%, 95%, 99% or more, calculated using the Smith-Waterman algorithm as described above). As used herein, an “allelic variant” of a nucleic acid molecule, or region, for which nucleic acid sequence is provided herein is a nucleic acid molecule, or region, that occurs essentially at the same locus in the genome of another or second isolate, and that, due to natural variation caused by, for example, mutation or recombination, has a similar but not identical nucleic acid sequence. A coding region allelic variant typically encodes a protein having similar activity to that of the protein encoded by the gene to which it is being compared. An allelic variant can also comprise an alteration in the 5′ or 3′ untranslated regions of the gene, such as in regulatory control regions (eg. see U.S. Pat. No. 5,753,235).

Expression Systems

The Neisserial nucleotide sequences can be expressed in a variety of different expression systems; for example those used with mammalian cells, baculoviruses, plants, bacteria, and yeast.

i. Mammalian Systems

Mammalian expression systems are known in the art. A mammalian promoter is any DNA sequence capable of binding mammalian RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiating region, which is usually placed proximal to the 5′ end of the coding sequence, and a TATA box, usually located 25-30 base pairs (bp) upstream of the transcription initiation site. The TATA box is thought to direct RNA polymerase II to begin RNA synthesis at the correct site. A mammalian promoter will also contain an upstream promoter element, usually located within 100 to 200 bp upstream of the TATA box. An upstream promoter element determines the rate at which transcription is initiated and can act in either orientation [Sambrook et al. (1989) “Expression of Cloned Genes in Mammalian Cells.” In Molecular Cloning: A Laboratory Manual, 2nd ed.].

Mammalian viral genes are often highly expressed and have a broad host range; therefore sequences encoding mammalian viral genes provide particularly useful promoter sequences. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter (Ad MLP), and herpes simplex virus promoter. In addition, sequences derived from non-viral genes, such as the murine metallotheionein gene, also provide useful promoter sequences. Expression may be either constitutive or regulated (inducible), depending on the promoter can be induced with glucocorticoid in hormone-responsive cells.

The presence of an enhancer element (enhancer), combined with the promoter elements described above, will usually increase expression levels. An enhancer is a regulatory DNA sequence that can stimulate transcription up to 1000-fold when linked to homologous or heterologous promoters, with synthesis beginning at the normal RNA start site. Enhancers are also active when they are placed upstream or downstream from the transcription initiation site, in either normal or flipped orientation, or at a distance of more than 1000 nucleotides from the promoter [Maniatis et al. (1987) Science 236:1237; Alberts et al. (1989) Molecular Biology of the Cell, 2nd ed.]. Enhancer elements derived from viruses may be particularly useful, because they usually have a broader host range. Examples include the SV40 early gene enhancer [Dijkema et al (1985) EMBO J. 4:761] and the enhancer/promoters derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus [Gorman et al. (1982b) Proc. Natl. Acad. Sci. 79:6777] and from human cytomegalovirus [Boshart et al. (1985) Cell 41:521]. Additionally, some enhancers are regulatable and become active only in the presence of an inducer, such as a hormone or metal ion [Sassone-Corsi and Borelli (1986) Trends Genet. 2:215; Maniatis et al. (1987) Science 236:1237].

A DNA molecule may be expressed intracellularly in mammalian cells. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in mammalian cells. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell. The adenovirus triparite leader is an example of a leader sequence that provides for secretion of a foreign protein in mammalian cells.

Usually, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3′ to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. The 3′ terminus of the mature mRNA is formed by site-specific post-transcriptional cleavage and polyadenylation [Birnstiel et al. (1985) Cell 41:349; Proudfoot and Whitelaw (1988) “Termination and 3′ end processing of eukaryotic RNA. In Transcription and splicing (ed. B. D. Hames and D. M. Glover); Proudfoot (1989) Trends Biochem. Sci. 14:105]. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminater/polyadenylation signals include those derived from SV40 [Sambrook et al (1989) “Expression of cloned genes in cultured mammalian cells.” In Molecular Cloning: A Laboratory Manual].

Usually, the above described components, comprising a promoter, polyadenylation signal, and transcription termination sequence are put together into expression constructs. Enhancers, introns with functional splice donor and acceptor sites, and leader sequences may also be included in an expression construct, if desired. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as mammalian cells or bacteria. Mammalian replication systems include those derived from animal viruses, which require trans-acting factors to replicate. For example, plasmids containing the replication systems of papovaviruses, such as SV40 [Gluzman (1981) Cell 23:175] or polyomavirus, replicate to extremely high copy number in the presence of the appropriate viral T antigen. Additional examples of mammalian replicons include those derived from bovine papillomavirus and Epstein-Barr virus. Additionally, the replicon may have two replicaton systems, thus allowing it to be maintained, for example, in mammalian cells for expression and in a prokaryotic host for cloning and amplification. Examples of such mammalian-bacteria shuttle vectors include pMT2 [Kaufman et al. (1989) Mol. Cell. Biol. 9:946] and pHEBO [Shimizu et al. (1986) Mol. Cell. Biol. 6:1074].

The transformation procedure used depends upon the host to be transformed. Methods for introduction of heterologous polynucleotides into mammalian cells are known in the art and include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.

Mammalian cell lines available as hosts for expression are known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including but not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (eg. Hep G2), and a number of other cell lines.

ii. Baculovirus Systems

The polynucleotide encoding the protein can also be inserted into a suitable insect expression vector, and is operably linked to the control elements within that vector. Vector construction employs techniques which are known in the art. Generally, the components of the expression system include a transfer vector, usually a bacterial plasmid, which contains both a fragment of the baculovirus genome, and a convenient restriction site for insertion of the heterologous gene or genes to be expressed; a wild type baculovirus with a sequence homologous to the baculovirus-specific fragment in the transfer vector (this allows for the homologous recombination of the heterologous gene in to the baculovirus genome); and appropriate insect host cells and growth media.

After inserting the DNA sequence encoding the protein into the transfer vector, the vector and the wild type viral genome are transfected into an insect host cell where the vector and viral genome are allowed to recombine. The packaged recombinant virus is expressed and recombinant plaques are identified and purified. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego Calif. (“MaxBac” kit). These techniques are generally known to those skilled in the art and fully described in Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987) (hereinafter “Summers and Smith”).

Prior to inserting the DNA sequence encoding the protein into the baculovirus genome, the above described components, comprising a promoter, leader (if desired), coding sequence of interest, and transcription termination sequence, are usually assembled into an intermediate transplacement construct (transfer vector). This construct may contain a single gene and operably linked regulatory elements; multiple genes, each with its owned set of operably linked regulatory elements; or multiple genes, regulated by the same set of regulatory elements. Intermediate transplacement constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as a bacterium. The replicon will have a replication system, thus allowing it to be maintained in a suitable host for cloning and amplification.

Currently, the most commonly used transfer vector for introducing foreign genes into AcNPV is pAc373. Many other vectors, known to those of skill in the art, have also been designed. These include, for example, pVL985 (which alters the polyhedrin start codon from ATG to ATT, and which introduces a BamHI cloning site 32 basepairs downstream from the ATT; see Luckow and Summers, Virology (1989) 17:31.

The plasmid usually also contains the polyhedrin polyadenylation signal (Miller et al. (1988) Ann. Rev. Microbiol., 42:177) and a prokaryotic ampicillin-resistance (amp) gene and origin of replication for selection and propagation in E. coli.

Baculovirus transfer vectors usually contain a baculovirus promoter. A baculovirus promoter is any DNA sequence capable of binding a baculovirus RNA polymerase and initiating the downstream (5′ to 3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A baculovirus transfer vector may also have a second domain called an enhancer, which, if present, is usually distal to the structural gene. Expression may be either regulated or constitutive.

Structural genes, abundantly transcribed at late times in a viral infection cycle, provide particularly useful promoter sequences. Examples include sequences derived from the gene encoding the viral polyhedron protein, Friesen et al., (1986) “The Regulation of Baculovirus Gene Expression,” in: The Molecular Biology of Baculoviruses (ed. Walter Doerfler); EPO Publ. Nos. 127 839 and 155 476; and the gene encoding the p10 protein, Vlak et al., (1988), J. Gen. Virol. 69:765.

DNA encoding suitable signal sequences can be derived from genes for secreted insect or baculovirus proteins, such as the baculovirus polyhedrin gene (Carbonell et al. (1988) Gene, 73:409). Alternatively, since the signals for mammalian cell posttranslational modifications (such as signal peptide cleavage, proteolytic cleavage, and phosphorylation) appear to be recognized by insect cells, and the signals required for secretion and nuclear accumulation also appear to be conserved between the invertebrate cells and vertebrate cells, leaders of non-insect origin, such as those derived from genes encoding human α-interferon, Maeda et al., (1985), Nature 315:592; human gastrin-releasing peptide, Lebacq-Verheyden et al., (1988), Molec. Cell. Biol. 8:3129; human IL-2, Smith et al., (1985) Proc. Nat'l Acad. Sci. USA, 82:8404; mouse IL-3, (Miyajima et al., (1987) Gene 58:273; and human glucocerebrosidase, Martin et al. (1988) DNA, 7:99, can also be used to provide for secretion in insects.

A recombinant polypeptide or polyprotein may be expressed intracellularly or, if it is expressed with the proper regulatory sequences, it can be secreted. Good intracellular expression of nonfused foreign proteins usually requires heterologous genes that ideally have a short leader sequence containing suitable translation initiation signals preceding an ATG start signal. If desired, methionine at the N-terminus may be cleaved from the mature protein by in vitro incubation with cyanogen bromide.

Alternatively, recombinant polyproteins or proteins which are not naturally secreted can be secreted from the insect cell by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in insects. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the translocation of the protein into the endoplasmic reticulum.

After insertion of the DNA sequence and/or the gene encoding the expression product precursor of the protein, an insect cell host is co-transformed with the heterologous DNA of the transfer vector and the genomic DNA of wild type baculovirus—usually by co-transfection. The promoter and transcription termination sequence of the construct will usually comprise a 2-5 kb section of the baculovirus genome. Methods for introducing heterologous DNA into the desired site in the baculovirus virus are known in the art. (See Summers and Smith supra; Ju et al. (1987); Smith et al., Mol. Cell. Biol. (1983) 3:2156; and Luckow and Summers (1989)). For example, the insertion can be into a gene such as the polyhedrin gene, by homologous double crossover recombination; insertion can also be into a restriction enzyme site engineered into the desired baculovirus gene. Miller et al., (1989), Bioessays 4:91. The DNA sequence, when cloned in place of the polyhedrin gene in the expression vector, is flanked both 5′ and 3′ by polyhedrin-specific sequences and is positioned downstream of the polyhedrin promoter.

The newly formed baculovirus expression vector is subsequently packaged into an infectious recombinant baculovirus. Homologous recombination occurs at low frequency (between about 1% and about 5%); thus, the majority of the virus produced after cotransfection is still wild-type virus. Therefore, a method is necessary to identify recombinant viruses. An advantage of the expression system is a visual screen allowing recombinant viruses to be distinguished. The polyhedrin protein, which is produced by the native virus, is produced at very high levels in the nuclei of infected cells at late times after viral infection. Accumulated polyhedrin protein forms occlusion bodies that also contain embedded particles. These occlusion bodies, up to 15 μm in size, are highly refractile, giving them a bright shiny appearance that is readily visualized under the light microscope. Cells infected with recombinant viruses lack occlusion bodies. To distinguish recombinant virus from wild-type virus, the transfection supernatant is plagued onto a monolayer of insect cells by techniques known to those skilled in the art. Namely, the plaques are screened under the light microscope for the presence (indicative of wild-type virus) or absence (indicative of recombinant virus) of occlusion bodies. “Current Protocols in Microbiology” Vol. 2 (Ausubel et al. eds) at 16.8 (Supp. 10, 1990); Summers and Smith, supra; Miller et al. (1989).

Recombinant baculovirus expression vectors have been developed for infection into several insect cells. For example, recombinant baculoviruses have been developed for, inter alis: Aedes aegypti, Autographa californica, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda, and Trichoplusia ni (WO 89/046699; Carbonell et al., (1985) J. Virol. 56:153; Wright (1986) Nature 321:718; Smith et al., (1983) Mol. Cell. Biol. 3:2156; and see generally, Fraser, et al. (1989) In Vitro Cell. Dev. Biol. 25:225).

Cells and cell culture media are commercially available for both direct and fusion expression of heterologous polypeptides in a baculovirus/expression system; cell culture technology is generally known to those skilled in the art. See, eg. Summers and Smith supra.

The modified insect cells may then be grown in an appropriate nutrient medium, which allows for stable maintenance of the plasmid(s) present in the modified insect host. Where the expression product gene is under inducible control, the host may be grown to high density, and expression induced. Alternatively, where expression is constitutive, the product will be continuously expressed into the medium and the nutrient medium must be continuously circulated, while removing the product of interest and augmenting depleted nutrients. The product may be purified by such techniques as chromatography, eg. HPLC, affinity chromatography, ion exchange chromatography, etc.; electrophoresis; density gradient centrifugation; solvent extraction, or the like. As appropriate, the product may be further purified, as required, so as to remove substantially any insect proteins which are also secreted in the medium or result from lysis of insect cells, so as to provide a product which is at least substantially free of host debris, eg. proteins, lipids and polysaccharides.

In order to obtain protein expression, recombinant host cells derived from the transformants are incubated under conditions which allow expression of the recombinant protein encoding sequence. These conditions will vary, dependent upon the host cell selected. However, the conditions are readily ascertainable to those of ordinary skill in the art, based upon what is known in the art.

iii. Plant Systems

There are many plant cell culture and whole plant genetic expression systems known in the art. Exemplary plant cellular genetic expression systems include those described in patents, such as: U.S. Pat. No. 5,693,506; U.S. Pat. No. 5,659,122; and U.S. Pat. No. 5,608,143. Additional examples of genetic expression in plant cell culture has been described by Zenk, Phytochemistry 30:3861-3863 (1991). Descriptions of plant protein signal peptides may be found in addition to the references described above in Vaulcombe et al., Mol. Gen. Genet. 209:33-40 (1987); Chandler et al., Plant Molecular Biology 3:407-418 (1984); Rogers, J. Biol. Chem. 260:3731-3738 (1985); Rothstein et al., Gene 55:353-356 (1987); Whittier et al., Nucleic Acids Research 15:2515-2535 (1987); Wirsel et al., Molecular Microbiology 3:3-14 (1989); Yu et al., Gene 122:247-253 (1992). A description of the regulation of plant gene expression by the phytohormone, gibberellic acid and secreted enzymes induced by gibberellic acid can be found in R. L. Jones and J. MacMillin, Gibberellins: in: Advanced Plant Physiology, Malcolm B. Wilkins, ed., 1984 Pitman Publishing Limited, London, pp. 21-52. References that describe other metabolically-regulated genes: Sheen, Plant Cell, 2:1027-1038 (1990); Maas et al., EMBO J. 9:3447-3452 (1990); Benkel and Hickey, Proc. Natl. Acad. Sci. 84:1337-1339 (1987)

Typically, using techniques known in the art, a desired polynucleotide sequence is inserted into an expression cassette comprising genetic regulatory elements designed for operation in plants. The expression cassette is inserted into a desired expression vector with companion sequences upstream and downstream from the expression cassette suitable for expression in a plant host. The companion sequences will be of plasmid or viral origin and provide necessary characteristics to the vector to permit the vectors to move DNA from an original cloning host, such as bacteria, to the desired plant host. The basic bacterial/plant vector construct will preferably provide a broad host range prokaryote replication origin; a prokaryote selectable marker; and, for Agrobacterium transformations, T DNA sequences for Agrobacterium-mediated transfer to plant chromosomes. Where the heterologous gene is not readily amenable to detection, the construct will preferably also have a selectable marker gene suitable for determining if a plant cell has been transformed. A general review of suitable markers, for example for the members of the grass family, is found in Wilmink and Dons, 1993, Plant Mol. Biol. Reptr, 11(2):165-185.

Sequences suitable for permitting integration of the heterologous sequence into the plant genome are also recommended. These might include transposon sequences and the like for homologous recombination as well as Ti sequences which permit random insertion of a heterologous expression cassette into a plant genome. Suitable prokaryote selectable markers include resistance toward antibiotics such as ampicillin or tetracycline. Other DNA sequences encoding additional functions may also be present in the vector, as is known in the art.

The nucleic acid molecules of the subject invention may be included into an expression cassette for expression of the protein(s) of interest. Usually, there will be only one expression cassette, although two or more are feasible. The recombinant expression cassette will contain in addition to the heterologous protein encoding sequence the following elements, a promoter region, plant 5′ untranslated sequences, initiation codon depending upon whether or not the structural gene comes equipped with one, and a transcription and translation termination sequence. Unique restriction enzyme sites at the 5′ and 3′ ends of the cassette allow for easy insertion into a pre-existing vector.

A heterologous coding sequence may be for any protein relating to the present invention. The sequence encoding the protein of interest will encode a signal peptide which allows processing and translocation of the protein, as appropriate, and will usually lack any sequence which might result in the binding of the desired protein of the invention to a membrane. Since, for the most part, the transcriptional initiation region will be for a gene which is expressed and translocated during germination, by employing the signal peptide which provides for translocation, one may also provide for translocation of the protein of interest. In this way, the protein(s) of interest will be translocated from the cells in which they are expressed and may be efficiently harvested. Typically secretion in seeds are across the aleurone or scutellar epithelium layer into the endosperm of the seed. While it is not required that the protein be secreted from the cells in which the protein is produced, this facilitates the isolation and purification of the recombinant protein.

Since the ultimate expression of the desired gene product will be in a eucaryotic cell it is desirable to determine whether any portion of the cloned gene contains sequences which will be processed out as introns by the host's splicosome machinery. If so, site-directed mutagenesis of the “intron” region may be conducted to prevent losing a portion of the genetic message as a false intron code, Reed and Maniatis, Cell 41:95-105, 1985.

The vector can be microinjected directly into plant cells by use of micropipettes to mechanically transfer the recombinant DNA. Crossway, Mol. Gen. Genet, 202:179-185, 1985. The genetic material may also be transferred into the plant cell by using polyethylene glycol, Krens, et al., Nature, 296, 72-74, 1982. Another method of introduction of nucleic acid segments is high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface, Klein, et al., Nature, 327, 70-73, 1987 and Knudsen and Muller, 1991, Planta, 185:330-336 teaching particle bombardment of barley endosperm to create transgenic barley. Yet another method of introduction would be fusion of protoplasts with other entities, either minicells, cells, lysosomes or other fusible lipid-surfaced bodies, Fraley, et al., Proc. Natl. Acad. Sci. USA, 79, 1859-1863, 1982.

The vector may also be introduced into the plant cells by electroporation. (Fromm et al., Proc. Natl. Acad. Sci. USA 82:5824, 1985). In this technique, plant protoplasts are electroporated in the presence of plasmids containing the gene construct. Electrical impulses of high field strength reversibly permeabilize biomembranes allowing the introduction of the plasmids. Electroporated plant protoplasts reform the cell wall, divide, and form plant callus.

All plants from which protoplasts can be isolated and cultured to give whole regenerated plants can be transformed by the present invention so that whole plants are recovered which contain the transferred gene. It is known that practically all plants can be regenerated from cultured cells or tissues, including but not limited to all major species of sugarcane, sugar beet, cotton, fruit and other trees, legumes and vegetables. Some suitable plants include, for example, species from the genera Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersion, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Hererocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Lolium, Zea, Triticum, Sorghum, and Datura.

Means for regeneration vary from species to species of plants, but generally a suspension of transformed protoplasts containing copies of the heterologous gene is first provided. Callus tissue is formed and shoots may be induced from callus and subsequently rooted. Alternatively, embryo formation can be induced from the protoplast suspension. These embryos germinate as natural embryos to form plants. The culture media will generally contain various amino acids and hormones, such as auxin and cytokinins. It is also advantageous to add glutamic acid and proline to the medium, especially for such species as corn and alfalfa. Shoots and roots normally develop simultaneously. Efficient regeneration will depend on the medium, on the genotype, and on the history of the culture. If these three variables are controlled, then regeneration is fully reproducible and repeatable.

In some plant cell culture systems, the desired protein of the invention may be excreted or alternatively, the protein may be extracted from the whole plant. Where the desired protein of the invention is secreted into the medium, it may be collected. Alternatively, the embryos and embryoless-half seeds or other plant tissue may be mechanically disrupted to release any secreted protein between cells and tissues. The mixture may be suspended in a buffer solution to retrieve soluble proteins. Conventional protein isolation and purification methods will be then used to purify the recombinant protein. Parameters of time, temperature pH, oxygen, and volumes will be adjusted through routine methods to optimize expression and recovery of heterologous protein.

iv. Bacterial Systems

Bacterial expression techniques are known in the art. A bacterial promoter is any DNA sequence capable of binding bacterial RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A bacterial promoter may also have a second domain called an operator, that may overlap an adjacent RNA polymerase binding site at which RNA synthesis begins. The operator permits negative regulated (inducible) transcription, as a gene repressor protein may bind the operator and thereby inhibit transcription of a specific gene. Constitutive expression may occur in the absence of negative regulatory elements, such as the operator. In addition, positive regulation may be achieved by a gene activator protein binding sequence, which, if present is usually proximal (5′) to the RNA polymerase binding sequence. An example of a gene activator protein is the catabolite activator protein (CAP), which helps initiate transcription of the lac operon in Escherichia coli (E. coli) [Raibaud et al. (1984) Annu. Rev. Genet. 18:173]. Regulated expression may therefore be either positive or negative, thereby either enhancing or reducing transcription.

Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences. Examples include promoter sequences derived from sugar metabolizing enzymes, such as galactose, lactose (lac) [Chang et al. (1977) Nature 198:1056], and maltose. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp) [Goeddel et al. (1980) Nuc. Acids Res. 8:4057; Yelverton et al. (1981) Nucl. Acids Res. 9:731; U.S. Pat. No. 4,738,921; EP-A-0036776 and EP-A-0121775]. The g-laotamase (bla) promoter system [Weissmann (1981) “The cloning of interferon and other mistakes.” In Interferon 3 (ed. I. Gresser)], bacteriophage lambda PL [Shimatake et al. (1981) Nature 292:128] and T5 [U.S. Pat. No. 4,689,406] promoter systems also provide useful promoter sequences.

In addition, synthetic promoters which do not occur in nature also function as bacterial promoters. For example, transcription activation sequences of one bacterial or bacteriophage promoter may be joined with the operon sequences of another bacterial or bacteriophage promoter, creating a synthetic hybrid promoter [U.S. Pat. No. 4,551,433]. For example, the tac promoter is a hybrid trp-lac promoter comprised of both trp promoter and lac operon sequences that is regulated by the lac repressor [Amann et al. (1983) Gene 25:167; de Boer et al. (1983) Proc. Natl. Acad. Sci. 80:21].

Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. A naturally occurring promoter of non-bacterial origin can also be coupled with a compatible RNA polymerase to produce high levels of expression of some genes in prokaryotes. The bacteriophage T7 RNA polymerase/promoter system is an example of a coupled promoter system [Studier et al. (1986) J. Mol. Biol. 189:113; Tabor et al., (1985) Proc Natl. Acad. Sci. 82:1074]. In addition, a hybrid promoter can also be comprised of a bacteriophage promoter and an E. coli operator region (EPO-A-0 267 851).

In addition to a functioning promoter sequence, an efficient ribosome binding site is also useful for the expression of foreign genes in prokaryotes. In E. coli, the ribosome binding site is called the Shine-Dalgarno (SD) sequence and includes an initiation codon (ATG) and a sequence 3-9 nucleotides in length located 3-11 nucleotides upstream of the initiation codon [Shine et al. (1975) Nature 254:34]. The SD sequence is thought to promote binding of mRNA to the ribosome by the pairing of bases between the SD sequence and the 3′ and of E. coli 16S rRNA [Steitz et al: (1979) “Genetic signals and nucleotide sequences in messenger RNA.” In Biological Regulation and Development: Gene Expression (ed. R. F. Goldberger)]. To express eukaryotic genes and prokaryotic genes with weak ribosome-binding site [Sambrook et al. (1989) “Expression of cloned genes in Escherichia coli.” In Molecular Cloning: A Laboratory Manual].

A DNA molecule may be expressed intracellularly. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide or by either in vivo on in vitro incubation with a bacterial methionine N-terminal peptidase (EPO-A-0 219 237).

Fusion proteins provide an alternative to direct expression. Usually, a DNA sequence encoding the N-terminal portion of an endogenous bacterial protein, or other stable protein, is fused to the 5′ end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the bacteriophage lambda cell gene can be linked at the 5′ terminus of a foreign gene and expressed in bacteria. The resulting fusion protein preferably retains a site for a processing enzyme (factor Xa) to cleave the bacteriophage protein from the foreign gene [Nagai et al. (1984) Nature 309:810]. Fusion proteins can also be made with sequences from the lacZ [Jia et al. (1987) Gene 60:197], trpE [Allen et al. (1987) J. Biotechnol. 5:93; Makoff et al. (1989) J. Gen. Microbiol. 135:11], and Chey [EP-A-0 324 647] genes. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin specific processing-protease) to cleave the ubiquitin from the foreign protein. Through this method, native foreign protein can be isolated [Miller et al. (1989) Bio/Technology 7:698].

Alternatively, foreign proteins can also be secreted from the cell by creating chimeric DNA molecules that encode a fusion protein comprised of a signal peptide sequence fragment that provides for secretion of the foreign protein in bacteria [U.S. Pat. No. 4,336,336]. The signal sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell. The protein is either secreted into the growth media (gram-positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). Preferably there are processing sites, which can be cleaved either in vivo or in vitro encoded between the signal peptide fragment and the foreign gene.

DNA encoding suitable signal sequences can be derived from genes for secreted bacterial proteins, such as the E. coli outer membrane protein gene (ompA) [Masui et al. (1983), in: Experimental Manipulation of Gene Expression; Ghrayeb et al. (1984) EMBO J. 3:2437] and the E. coli alkaline phosphatase signal sequence (phoA) [Oka et al. (1985) Proc. Natl. Acad. Sci. 82:7212]. As an additional example, the signal sequence of the alpha-amylase gene from various Bacillus strains can be used to secrete heterologous proteins from B. subtilis [Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 244 042].

Usually, transcription termination sequences recognized by bacteria are regulatory regions located 3′ to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Transcription termination sequences frequently include DNA sequences of about 50 nucleotides capable of forming stem loop structures that aid in terminating transcription. Examples include transcription termination sequences derived from genes with strong promoters, such as the irp gene in E. coli as well as other biosynthetic genes.

Usually, the above described components, comprising a promoter, signal sequence (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as bacteria. The replicon will have a replication system, thus allowing it to be maintained in a prokaryotic host either for expression or for cloning and amplification. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably contain at least about 10, and more preferably at least about 20 plasmids. Either a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host.

Alternatively, the expression constructs can be integrated into the bacterial genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to the bacterial chromosome that allows the vector to integrate. Integrations appear to result from recombinations between homologous DNA in the vector and the bacterial chromosome. For example, integrating vectors constructed with DNA from various Bacillus strains integrate into the Bacillus chromosome (EP-A-0 127 328). Integrating vectors may also be comprised of bacteriophage of transposon sequences.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of bacterial strains that have been transformed. Selectable markers can be expressed in the bacterial host and may include genes which render bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin (neomycin), and tetracycline [Davies et al. (1978) Annu. Rev. Microbiol. 32:469]. Selectable markers may also include biosynthetic genes, such as those in the histidine, tryptophan, and leucine biosynthetic pathways.

Alternatively, some of the above described components can be put together in transformation vectors. Transformation vectors are usually comprised of a selectable market that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extra-chromosomal replicons or integrating vectors, have been developed for transformation into many bacteria. For example, expression vectors have been developed for, inter alfa, the following bacteria: Bacillus subtilis [Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541], Escherichia coli [Shimatake et al. (1981) Nature 292:128; Amann et al. (1985) Gene 40:183; Studier et al. (1986) J. Mol. Biol. 189:113; EP-A-0 036 776, EP-A-0 136 829 and EP-A-0 136 907], Streptococcus cremoris [Powell et al. (1988) Appl. Environ. Microbiol. 54:655]; Streptococcus lividans [Powell et al. (1988) Appl. Environ. Microbiol. 54:655], Streptomyces lividans [U.S. Pat. No. 4,745,056].

Methods of introducing exogenous DNA into bacterial hosts are well-known in the art, and usually include either the transformation of bacteria treated with CaCl₂ or other agents, such as divalent cations and DMSO. DNA can also be introduced into bacterial cells by electroporation. Transformation procedures usually vary with the bacterial specie to be transformed. See eg. [Masson et al. (1989) FEMS Microbiol. Lett. 60:273; Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541, Bacillus], [Miller et al. (1988) Proc. Natl. Acad. Sci. 85:856; Wang et al. (1990) J. Bacteriol. 172:949, Campylobacter], [Cohen et al. (1973) Proc. Natl. Acad. Sci. 69:2110; Dower et al. (1988) Nucleic Acids Res. 16:6127; Kushner (1978) “An improved method for transformation of Escherichia coli with ColE1-derived plasmids. In Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering (eds. H. W. Boyer and S. Nicosia); Mandel et al. (1970) J. Mol. Biol. 53:159; Taketo (1988) Biochim. Biophys. Acta 949:318; Escherichia], [Chassy et al. (1987) FEMS Microbiol. Lett. 44:173 Lactobacillus]; [Fiedler et al. (1988) Anal. Biochem 170:38, Pseudomonas]; [Augustin et al. (1990) FEMS Microbiol. Lett. 66:203, Staphylococcus], [Barany et al. (1980) J. Bacteriol. 144:698; Harlander (1987) “Transformation of Streptococcus lactis by electroporation, in: Streptococcal Genetics (ed. J. Ferretti and R. Curtiss III); Perry et al. (1981) Infect. Immun. 32:1295; Powell et al. (1988) Appl. Environ. Microbiol. 54:655; Somkuti et al. (1987) Proc. 4th Evr. Cong. Biotechnology 1:412, Streptococcus].

v. Yeast Expression

Yeast expression systems are also known to one of ordinary skill in the art. A yeast promoter is any DNA sequence capable of binding yeast RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site (the “TATA Box”) and a transcription initiation site. A yeast promoter may also have a second domain called an upstream activator sequence (UAS), which, if present, is usually distal to the structural gene. The UAS permits regulated (inducible) expression. Constitutive expression occurs in the absence of a UAS. Regulated expression may be either positive or negative, thereby either enhancing or reducing transcription.

Yeast is a fermenting organism with an active metabolic pathway, therefore sequences encoding enzymes in the metabolic pathway provide particularly useful promoter sequences. Examples include alcohol dehydrogenase (ADH) (EP-A-0 284 044), enolase, glucokinase, glucose-6-phosphate isomerase, glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH), hexokinase, phosphofructokinase, 3-phosphoglycerate mutase, and pyruvate kinase (PyK) (EPO-A-0 329 203). The yeast PHO5 gene, encoding acid phosphatase, also provides useful promoter sequences [Myanohara et al. (1983) Proc. Natl. Acad. Sci. USA 80:1).

In addition, synthetic promoters which do not occur in nature also function as yeast promoters. For example, UAS sequences of one yeast promoter may be joined with the transcription activation region of another yeast promoter, creating a synthetic hybrid promoter. Examples of such hybrid promoters include the ADH regulatory sequence linked to the GAP transcription activation region (U.S. Pat. Nos. 4,876,197 and 4,880,734). Other examples of hybrid promoters include promoters which consist of the regulatory sequences of either the ADH2, GAL4, GAL10, OR PHO5 genes, combined with the transcriptional activation region of a glycolytic enzyme gene such as GAP or PyK (EP-A-0 164 556). Furthermore, a yeast promoter can include naturally occurring promoters of non-yeast origin that have the ability to bind yeast RNA polymerase and initiate transcription. Examples of such promoters include, inter alia, [Cohen et al. (1980) Proc. Natl. Acad. Sci. USA 77:1078; Henikoff et al. (1981) Nature 283:835; Hollenberg et al. (1981) Curr. Topics Microbiol. Immunol. 96:119; Hollenberg et al. (1979) “The Expression of Bacterial Antibiotic Resistance Genes in the Yeast Saccharomyces cerevisiae,” in: Plasmids of Medical, Environmental and Commercial Importance (eds. K. N. Timmis and A. Puhler); Mercerau-Puigalon et al. (1980) Gene 11:163; Panthier et al. (1980) Curr. Genet. 2:109;].

A DNA molecule may be expressed intracellularly in yeast. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Fusion proteins provide an alternative for yeast expression systems, as well as in mammalian, baculovirus, and bacterial expression systems. Usually, a DNA sequence encoding the N-terminal portion of an endogenous yeast protein, or other stable protein, is fused to the 5′ end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the yeast or human superoxide dismutase (SOD) gene, can be linked at the 5′ terminus of a foreign gene and expressed in yeast. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. See eg. EP-A-0 196 056. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg, ubiquitin-specific processing protease) to cleave the ubiquitin from the foreign protein. Through this method, therefore, native foreign protein can be isolated (eg. WO88/024066).

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provide for secretion in yeast of the foreign protein. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell.

DNA encoding suitable signal sequences can be derived from genes for secreted yeast proteins, such as the yeast invertase gene (EP-A-0 012 873; JPO. 62,096,086) and the A-factor gene (U.S. Pat. No. 4,588,684). Alternatively, leaders of non-yeast origin, such as an interferon leader, exist that also provide for secretion in yeast (EP-A-0 060 057).

A preferred class of secretion leaders are those that employ a fragment of the yeast alpha-factor gene, which contains both a “pre” signal sequence, and a “pro” region. The types of alpha-factor fragments that can be employed include the full-length pre-pro alpha factor leader (about 83 amino acid residues) as well as truncated alpha-factor leaders (usually about 25 to about 50 amino acid residues) (U.S. Pat. Nos. 4,546,083 and 4,870,008; EP-A-0 324 274). Additional leaders employing an alpha-factor leader fragment that provides for secretion include hybrid alpha-factor leaders made with a presequence of a first yeast, but a pro-region from a second yeast alphafactor. (eg. see WO 89/02463.)

Usually, transcription termination sequences recognized by yeast are regulatory regions located 3′ to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminator sequence and other yeast-recognized termination sequences, such as those coding for glycolytic enzymes.

Usually, the above described components, comprising a promoter, leader (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as yeast or bacteria. The repl icon may have two replication systems, thus allowing it to be maintained, for example, in yeast for expression and in a prokaryotic host for cloning and amplification. Examples of such yeast-bacteria shuttle vectors include YEp24 [Botstein et al. (1979) Gene 8:17-24], pCl/1 [Brake et al. (1984) Proc. Natl. Acad. Sci. USA 81:4642-4646], and YRp17 [Stinchcomb et al. (1982) J. Mol. Biol. 158:157]. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably have at least about 10, and more preferably at least about 20. Enter a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host. See eg. Brake et al., supra.

Alternatively, the expression constructs can be integrated into the yeast genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to a yeast chromosome that allows the vector to integrate, and preferably contain two homologous sequences flanking the expression construct. Integrations appear to result from recombinations between homologous DNA in the vector and the yeast chromosome [Orr-Weaver et al. (1983) Methods in Enzymol. 101:228-245]. An integrating vector may be directed to a specific locus in yeast by selecting the appropriate homologous sequence for inclusion in the vector. See Orr-Weaver et al., supra. One or more expression construct may integrate, possibly affecting levels of recombinant protein produced [Rine et al. (1983) Proc. Natl. Acad. Sci. USA 80:6750]. The chromosomal sequences included in the vector can occur either as a single segment in the vector, which results in the integration of the entire vector, or two segments homologous to adjacent segments in the chromosome and flanking the expression construct in the vector, which can result in the stable integration of only the expression construct.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of yeast strains that have been transformed. Selectable markers may include biosynthetic genes that can be expressed in the yeast host, such as ADE2, HIS4, LEU2, TRP1, and ALG7, and the G418 resistance gene, which confer resistance in yeast cells to tunicamycin and G418, respectively. In addition, a suitable selectable marker may also provide yeast with the ability to grow in the presence of toxic compounds, such as metal. For example, the presence of CUP1 allows yeast to grow in the presence of copper ions [Butt et al. (1987) Microbiol, Rev. 51:351].

Alternatively, some of the above described components can be put together into transformation vectors. Transformation vectors are usually comprised of a selectable marker that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extrachromosomal replicons or integrating vectors, have been developed for transformation into many yeasts. For example, expression vectors have been developed for, inter alia, the following yeasts: Candida albicans [Kurtz, et al. (1986) Mol. Cell. Biol. 6:142], Candida maltosa [Kunze, et al. (1985) J. Basic Microbiol. 25:141]. Hansenula polymorpha [Gleeson, et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302], Kluyveromyces fragilis [Das, et al. (1984) J. Bacteriol. 158:1165], Kluyveromyces lactis [De Louvencourt et al. (1983) J. Bacteriol. 154:737; Van den Berg et al. (1990) Bio/Technology 8:135], Pichia guillerimondii [Kunze et al. (1985) J. Basic Microbiol. 25:141], Pichia pastoris [Cregg, et al. (1985) Mol. Cell. Biol. 5:3376; U.S. Pat. Nos. 4,837,148 and 4,929,555], Saccharomyces cerevisiae [Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75:1929; Ito et al. (1983) J. Bacteriol. 153:163], Schizosaccharomyces pombe [Beach and Nurse (1981) Nature 300:706], and Yarrowia lipolytica [Davidow, et al. (1985) Curr. Genet. 10:380471 Gaillardin, et al. (1985) Curr. Genet. 10:49].

Methods of introducing exogenous DNA into yeast hosts are well-known in the art, and usually include either the transformation of spheroplasts or of intact yeast cells treated with alkali cations. Transformation procedures usually vary with the yeast species to be transformed. See eg. [Kurtz et al. (1986) Mol. Cell. Biol. 6:142; Kunze et al. (1985) J. Basic Microbiol. 25:141; Candida]; [Gleeson et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302; Hansenula]; [Das et al. (1984) J. Bacteriol. 158:1165; De Louvencourt et al. (1983) J. Bacteriol. 154:1165; Van den Berg et al. (1990) Bio/Technology 8:135; Kluyveromyces]; [Cregg et al. (1985) Mol. Cell. Biol. 5:3376; Kunze et al. (1985) J. Basic Microbiol. 25:141; U.S. Pat. Nos. 4,837,148 and 4,929,555; Pichia]; [Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75; 1929; Ito et al. (1983) J. Bacteriol. 153:163 Saccharomyces]; [Beach and Nurse (1981) Nature 300:706; Schizosaccharomyces]; [Davidow et al. (1985) Curr. Genet. 10:39; Gaillardin et al. (1985) Curr. Genet. 10:49; Yarrowia].

Antibodies

As used herein, the term “antibody” refers to a polypeptide or group of polypeptides composed of at least one antibody combining site. An “antibody combining site” is the three-dimensional binding space with an internal surface shape and charge distribution complementary to the features of an epitope of an antigen, which allows a binding of the antibody with the antigen. “Antibody” includes, for example, vertebrate antibodies, hybrid antibodies, chimeric antibodies, humanised antibodies, altered antibodies, univalent antibodies, Fab proteins, and single domain antibodies.

Antibodies against the proteins of the invention are useful for affinity chromatography, immunoassays, and distinguishing/identifying Neisserial proteins.

Antibodies to the proteins of the invention, both polyclonal and monoclonal, may be prepared by conventional methods. In general, the protein is first used to immunize a suitable animal, preferably a mouse, rat, rabbit or goat. Rabbits and goats are preferred for the preparation of polyclonal sera due to the volume of serum obtainable, and the availability of labeled anti-rabbit and anti-goat antibodies. Immunization is generally performed by mixing or emulsifying the protein in saline, preferably in an adjuvant such as Freund's complete adjuvant, and injecting the mixture or emulsion parenterally (generally subcutaneously or intramuscularly): A dose of 50-200 μg/injection is typically sufficient. Immunization is generally boosted 2-6 weeks later with one or more injections of the protein in saline, preferably using Freund's incomplete adjuvant. One may alternatively generate antibodies by in vitro immunization using methods known in the art, which for the purposes of this invention is considered equivalent to in vivo immunization. Polyclonal antisera is obtained by bleeding the immunized animal into a glass or plastic container, incubating the blood at 25° C. for one hour, followed by incubating at 4° C. for 2-18 hours. The serum is recovered by centrifugation (eg. 1,000 g for 10 minutes). About 20-50 ml per bleed may be obtained from rabbits.

Monoclonal antibodies are prepared using the standard method of Kohler & Milstein [Nature (1975) 256:495-96], or a modification thereof. Typically, a mouse or rat is immunized as described above. However, rather than bleeding the animal to extract serum, the spleen (and optionally several large lymph nodes) is removed and dissociated into single cells. If desired, the spleen cells may be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to a plate or well coated with the protein antigen. B-cells expressing membrane-bound immunoglobulin specific for the antigen bind to the plate, and are not rinsed away with the rest of the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas, and are cultured in a selective medium (eg. hypoxanthine, aminopterin, thymidine medium, “HAT”). The resulting hybridomas are plated by limiting dilution, and are assayed for the production of antibodies which bind specifically to the immunizing antigen (and which do not bind to unrelated antigens). The selected MAb-secreting hybridomas are then cultured either in vitro (eg. in tissue culture bottles or hollow fiber reactors), or in vivo (as ascites in mice).

If desired, the antibodies (whether polyclonal or monoclonal) may be labeled using conventional techniques. Suitable labels include fluorophores, chromophores, radioactive atoms (particularly ³²P and ¹²⁵I), electron-dense reagents, enzymes, and ligands having specific binding partners. Enzymes are typically detected by their activity. For example, horseradish peroxidase is usually detected by its ability to convert 3,3′,5,5′-tetramethylbenzidine (TMB) to a blue pigment, quantifiable with a spectrophotometer. “Specific binding partner” refers to a protein capable of binding a ligand molecule with high specificity, as for example in the case of an antigen and a monoclonal antibody specific therefor. Other specific binding partners include biotin and avidin or streptavidin, IgG and protein A, and the numerous receptor-ligand couples known in the art. It should be understood that the above description is not meant to categorize the various labels into distinct classes, as the same label may serve in several different modes. For example, ¹²⁵I may serve as a radioactive label or as an electron-dense reagent. HRP may serve as enzyme or as antigen for a MAb. Further, one may combine various labels for desired effect. For example, MAbs and avidin also require labels in the practice of this invention: thus, one might label a MAb with biotin, and detect its presence with avidin labeled with ¹²⁵I, or with an anti-biotin MAb labeled with HRP. Other permutations and possibilities will be readily apparent to those of ordinary skill in the art, and are considered as equivalents within the scope of the instant invention.

Pharmaceutical Compositions

Pharmaceutical compositions can comprise either polypeptides, antibodies, or nucleic acid of the invention. The pharmaceutical compositions will comprise a therapeutically effective amount of either polypeptides, antibodies, or polynucleotides of the claimed invention.

The term “therapeutically effective amount” as used herein refers to an amount of a therapeutic agent to treat, ameliorate, or prevent a desired disease or condition, or to exhibit a detectable therapeutic or preventative effect. The effect can be detected by, for example, chemical markers or antigen levels. Therapeutic effects also include reduction in physical symptoms, such as decreased body temperature. The precise effective amount for a subject will depend upon the subject's size and health, the nature and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. Thus, it is not useful to specify an exact effective amount in advance. However, the effective amount for a given situation can be determined by routine experimentation and is within the judgement of the clinician.

For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.

A pharmaceutical composition can also contain a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” refers to a carrier for administration of a therapeutic agent, such as antibodies or a polypeptide, genes, and other therapeutic agents. The term refers to any pharmaceutical carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Suitable carriers may be large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, and inactive virus particles. Such carriers are well known to those of ordinary skill in the art.

Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable excipients is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).

Pharmaceutically acceptable carriers in therapeutic compositions may contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles. Typically, the therapeutic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Liposomes are included within the definition of a pharmaceutically acceptable carrier.

Delivery Methods

Once formulated, the compositions of the invention can be administered directly to the subject. The subjects to be treated can be animals; in particular, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Vaccines

Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or therapeutic (ie. to treat disease after infection).

Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination with “pharmaceutically acceptable carriers,” which include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates (such as oil droplets or liposomes), and inactive virus particles. Such carriers are well known to those of ordinary skill in the art. Additionally, these carriers may function as immunostimulating agents (“adjuvants”). Furthermore, the antigen or immunogen may be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, H. pylori, etc. pathogens.

Preferred adjuvants to enhance effectiveness of the composition include, but are not limited to: (1) aluminum salts (alum), such as aluminum hydroxide, aluminum phosphate, aluminum sulfate, etc; (2) oil-in-water emulsion formulations (with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall components), such as for example (a) MF59™ (WO 90/14837; Chapter 10 in Vaccine design: the subunit and adjuvant approach, eds. Powell & Newman, Plenum Press 1995), containing 5% Squalene, 0.5% Tween 80, and 0.5% Span 85 (optionally containing various amounts of MTP-PE (see below), although not required) formulated into submicron particles using a microfluidizer such as Model 110Y microfluidizer (Microfluidics, Newton, Mass.), (b) SAF, containing 10% Squalane, 0.4% Tween 80, 5% pluronic-blocked polymer L121, and thr-MDP (see below) either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion, and (c) Ribi™ adjuvant system (RAS), (Ribi Immunochem, Hamilton, Mont.) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (Detox™); (3) saponin adjuvants, such as Stimulon™ (Cambridge Bioscience, Worcester, Mass.) may be used or particles generated therefrom such as ISCOMs (immunostimulating complexes); (4) Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA); (5) cytokines, such as interleukins (eg. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (eg. gamma interferon), macrophage colony stimulating factor (M-CSF), tumor necrosis factor (TNF), etc; and (6) other substances that act as immunostimulating agents to enhance the effectiveness of the composition. Alum and MF59™ are preferred.

As mentioned above, muramyl peptides include, but are not limited to, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (MTP-PE), etc.

The immunogenic compositions (eg. the immunising antigen/immunogen/polypeptide/protein/nucleic acid, pharmaceutically acceptable carrier, and adjuvant) typically will contain diluents, such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.

Typically, the immunogenic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. The preparation also may be emulsified or encapsulated in liposomes for enhanced adjuvant effect, as discussed above under pharmaceutically acceptable carriers.

Immunogenic compositions used as vaccines comprise an immunologically effective amount of the antigenic or immunogenic polypeptides, as well as any other of the above-mentioned components, as needed. By “immunologically effective amount”, it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, the taxonomic group of individual to be treated (eg. nonhuman primate, primate, etc.), the capacity of the individual's immune system to synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.

The immunogenic compositions are conventionally administered parenterally, eg. by injection, either subcutaneously, intramuscularly, or transdermally/transcutaneously (eg. WO98/20734). Additional formulations suitable for other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Dosage treatment may be a single dose schedule or a multiple dose schedule. The vaccine may be administered in conjunction with other immunoregulatory agents.

As an alternative to protein-based vaccines, DNA vaccination may be employed [eg. Robinson & Torres (1997) Seminars in Immunology 9:271-283; Donnelly et al. (1997) Annu Rev Immunol 15:617-648; see later herein].

Gene Delivery Vehicles

Gene therapy vehicles for delivery of constructs including a coding sequence of a therapeutic of the invention, to be delivered to the mammal for expression in the mammal, can be administered either locally or systemically. These constructs can utilize viral or non-viral vector approaches in in vivo or ex vivo modality. Expression of such coding sequence can be induced using endogenous mammalian or heterologous promoters. Expression of the coding sequence in vivo can be either constitutive or regulated.

The invention includes gene delivery vehicles capable of expressing the contemplated nucleic acid sequences. The gene delivery vehicle is preferably a viral vector and, more preferably, a retroviral, adenoviral, adeno-associated viral (AAV), herpes viral, or alphavirus vector. The viral vector can also be an astrovirus, coronavirus, orthomyxovirus, papovavirus, paramyxovirus, parvovirus, picornavirus, poxvirus, or togavirus viral vector. See generally, Jolly (1994) Cancer Gene Therapy 1:51-64; Kimura (1994) Human Gene Therapy 5:845-852; Connelly (1995) Human Gene Therapy 6:185-193; and Kaplitt (1994) Nature Genetics 6:148-153.

Retroviral vectors are well known in the art and we contemplate that any retroviral gene therapy vector is employable in the invention, including B, C and D type retroviruses, xenotropic retroviruses (for example, NZB-X1, NZB-X2 and NZB9-1 (see O'Neill (1985) J. Virol. 53:160) polytropic retroviruses eg. MCF and MCF-M LV (see Kelly (1983) J. Virol. 45:291), spumaviruses and lentiviruses. See RNA Tumor Viruses, Second Edition, Cold Spring Harbor Laboratory, 1985.

Portions of the retroviral gene therapy vector may be derived from different retroviruses. For example, retrovector LTRs may be derived from a Murine Sarcoma Virus, a tRNA binding site from a Rous Sarcoma Virus, a packaging signal from a Murine Leukemia Virus, and an origin of second strand synthesis from an Avian Leukosis Virus.

These recombinant retroviral vectors may be used to generate transduction competent retroviral vector particles by introducing them into appropriate packaging cell lines (see U.S. Pat. No. 5,591,624). Retrovirus vectors can be constructed for site-specific integration into host cell DNA by incorporation of a chimeric integrase enzyme into the retroviral particle (see WO96/37626). It is preferable that the recombinant viral vector is a replication defective recombinant virus.

Packaging cell lines suitable for use with the above-described retrovirus vectors are well known in the art, are readily prepared (see WO95/30763 and WO92/05266), and can be used to create producer cell lines (also termed vector cell lines or “VCLs”) for the production of recombinant vector particles. Preferably, the packaging cell lines are made from human parent cells (eg. HT1080 cells) or mink parent cell lines, which eliminates inactivation in human serum.

Preferred retroviruses for the construction of retroviral gene therapy vectors include Avian Leukosis Virus, Bovine Leukemia, Virus, Murine Leukemia Virus, Mink-Cell Focus-Inducing Virus, Murine Sarcoma Virus, Reticuloendotheliosis Virus and Rous Sarcoma Virus. Particularly preferred Murine Leukemia Viruses include 4070A and 1504A (Hartley and Rowe (1976) J Virol 19:19-25), Abelson (ATCC No. VR-999), Friend (ATCC No. VR-245), Graffi, Gross (ATCC Nol VR-590), Kirsten, Harvey Sarcoma Virus and Rauscher (ATCC No. VR-998) and Moloney Murine Leukemia Virus (ATCC No. VR-190). Such retroviruses may be obtained from depositories or collections such as the American Type Culture Collection (“ATCC”) in Rockville, Md. or isolated from known sources using commonly available techniques.

Exemplary known retroviral gene therapy vectors employable in this invention include those described in patent applications GB2200651, EP0415731, EP0345242, EP0334301, WO89/02468; WO89/05349, WO89/09271, WO90/02806, WO90/07936, WO94/03622, WO93/25698, WO93/25234, WO93/11230, WO93/10218, WO91/02805, WO91/02825, WO95/07994, U.S. Pat. No. 5,219,740, U.S. Pat. No. 4,405,712, U.S. Pat. No. 4,861,719, U.S. Pat. No. 4,980,289, U.S. Pat. No. 4,777,127, U.S. Pat. No. 5,591,624. See also Vile (1993) Cancer Res 53:3860-3864; Vile (1993) Cancer Res 53:962-967; Ram (1993) Cancer Res 53 (1993) 83-88; Takamiya (1992) J Neurosci Res 33:493-503; Baba (1993) J Neurosurg 79:729-735; Mann (1983) Cell 33:153; Cane (1984) Proc Natl Acad Sci 81:6349; and Miller (1990) Human Gene Therapy 1.

Human adenoviral gene therapy vectors are also known in the art and employable in this invention. See, for example, Berkner (1988) Biotechniques 6:616 and Rosenfeld (1991) Science 252:431, and WO93/07283, WO93/06223, and WO93/07282. Exemplary known adenoviral gene therapy vectors employable in this invention include those described in the above referenced documents and in WO94/12649, WO93/03769, WO93/19191, WO94/28938, WO95/11984, WO95/00655, WO95/27071, WO95/29993, WO95/34671, WO96/05320, WO94/08026, WO94/11506, WO93/06223, WO94/24299, WO95/14102, WO95/24297, WO95/02697, WO94/28152, WO94/24299, WO95/09241, WO95/25807, WO95/05835, WO94/18922 and WO95/09654. Alternatively, administration of DNA linked to killed adenovirus as described in Curiel (1992) Hum. Gene Ther. 3:147-154 may be employed. The gene delivery vehicles of the invention also include adenovirus associated virus (AAV) vectors. Leading and preferred examples of such vectors for use in this invention are the AAV-2 based vectors disclosed in Srivastava, WO93/09239. Most preferred AAV vectors comprise the two AAV inverted terminal repeats in which the native D-sequences are modified by substitution of nucleotides, such that at least 5 native nucleotides and up to 18 native nucleotides, preferably at least 10 native nucleotides up to 18 native nucleotides, most preferably 10 native nucleotides are retained and the remaining nucleotides of the D-sequence are deleted or replaced with non-native nucleotides. The native D-sequences of the AAV inverted terminal repeats are sequences of 20 consecutive nucleotides in each AAV inverted terminal repeat (ie. there is one sequence at each end) which are not involved in HP formation. The non-native replacement nucleotide may be any nucleotide other than the nucleotide found in the native D-sequence in the same position. Other employable exemplary AAV vectors are pWP-19, pWN-1, both of which are disclosed in Nahreini (1993) Gene 124:257-262. Another example of such an AAV vector is psub201 (see Samulski (1987) J. Virol. 61:3096). Another exemplary AAV vector is the Double-D ITR vector. Construction of the Double-D ITR vector is disclosed in U.S. Pat. No. 5,478,745. Still other vectors are those disclosed in Carter U.S. Pat. No. 4,797,368 and Muzyczka U.S. Pat. No. 5,139,941, Chartejee U.S. Pat. No. 5,474,935, and Kotin WO94/288157. Yet a further example of an AAV vector employable in this invention is SSV9AFABTKneo, which contains the AFP enhancer and albumin promoter and directs expression predominantly in the liver. Its structure and construction are disclosed in Su (1996) Human Gene Therapy 7:463-470. Additional AAV gene therapy vectors are described in U.S. Pat. No. 5,354,678, U.S. Pat. No. 5,173,414, U.S. Pat. No. 5,139,941, and U.S. Pat. No. 5,252,479.

The gene therapy vectors of the invention also include herpes vectors. Leading and preferred examples are herpes simplex virus vectors containing a sequence encoding a thymidine kinase polypeptide such as those disclosed in U.S. Pat. No. 5,288,641 and EP0176170 (Roizman). Additional exemplary herpes simplex virus vectors include HFEWICP6-LacZ disclosed in WO95/04139 (Wistar Institute), pHSVlac described in Geller (1988) Science 241:1667-1669 and in WO90/09441 and WO92/07945, HSV Us3::pgC-lacZ described in Fink (1992) Human Gene Therapy 3:11-19 and HSV 7134, 2 RH 105 and GAL4 described in EP 0453242 (Breakefield), and those deposited with the ATCC as accession numbers ATCC VR-977 and ATCC VR-260.

Also contemplated are alpha virus gene therapy vectors that can be employed in this invention. Preferred alpha virus vectors are Sindbis viruses vectors. Togaviruses, Semliki Forest virus (ATCC VR-67; ATCC VR-1247), Middleberg virus (ATCC VR-370), Ross River virus (ATCC VR-373; ATCC VR-1246), Venezuelan equine encephalitis virus (ATCC VR923; ATCC VR-1250; ATCC VR-1249; ATCC VR-532), and those described in U.S. Pat. Nos. 5,091,309, 5,217,879, and WO92/10578. More particularly, those alpha virus vectors described in U.S. Ser. No. 08/405,627, filed Mar. 15, 1995, WO94/21792, WO92/10578, WO95/07994, U.S. Pat. No. 5,091,309 and U.S. Pat. No. 5,217,879 are employable. Such alpha viruses may be obtained from depositories or collections such as the ATCC in Rockville, Md. or isolated from known sources using commonly available techniques. Preferably, alphavirus vectors with reduced cytotoxicity are used (see U.S. Ser. No. 08/679,640).

DNA vector systems such as eukarytic layered expression systems are also useful for expressing the nucleic acids of the invention. See WO95/07994 for a detailed description of eukaryotic layered expression systems. Preferably, the eukaryotic layered expression systems of the invention are derived from alphavirus vectors and most preferably from Sindbis viral vectors.

Other viral vectors suitable for use in the present invention include those derived from poliovirus, for example ATCC VR-58 and those described in Evans, Nature 339 (1989)385 and Sabin (1973) J. Biol. Standardization 1:115; rhinovirus, for example ATCC VR-1110 and those described in Arnold (1990) J Cell Biochem L401; pox viruses such as canary pox virus or vaccinia virus, for example ATCC VR-111 and ATCC VR-2010 and those described in Fisher-Hoch (1989) Proc Nan Acad Sci 86:317; Flexner (1989) Ann NY Acad Sci 569:86, Flexner (1990) Vaccine 8:17; in U.S. Pat. No. 4,603,112 and U.S. Pat. No. 4,769,330 and WO89/01973; SV40 virus, for example ATCC VR-305 and those described in Mulligan (1979) Nature 277:108 and Madzak (1992) J Gen Virol 73:1533; influenza virus, for example ATCC VR-797 and recombinant influenza viruses made employing reverse genetics techniques as described in U.S. Pat. No. 5,166,057 and in Enami (1990) Proc Nall Acad Sci 87:3802-3805; Enami & Palese (1991) J Virol 65:2711-2713 and Luytjes (1989) Cell 59:110, (see also McMichael (1983) NEJ Med 309:13, and Yap (1978) Nature 273:238 and Nature (1979) 277:108); human immunodeficiency virus as described in EP-0386882 and in Buchschacher (1992) J. Virol. 66:2731; measles virus, for example ATCC VR-67 and VR-1247 and those described in EP-0440219; Aura virus, for example ATCC VR-368; Bebaru virus, for example ATCC VR-600 and ATCC VR-1240; Cabassou virus, for example ATCC VR-922; Chikungunya virus, for example ATCC VR-64 and ATCC VR-1241; Fort Morgan Virus, for example ATCC VR-924; Getah virus, for example ATCC VR-369 and ATCC VR-1243; Kyzylagach virus, for example ATCC VR-927; Mayaro virus, for example ATCC VR-66; Mucambo virus, for example ATCC VR-580 and ATCC VR-1244; Ndumu virus, for example ATCC VR-371; Pixuna virus, for example ATCC VR-372 and ATCC VR-1245; Tonate virus, for example ATCC VR-925; Triniti virus, for example ATCC VR-469; Una virus, for example ATCC VR-374; Whataroa virus, for example ATCC VR-926; Y-62-33 virus, for example ATCC VR-375; O'Nyong virus, Eastern encephalitis virus, for example ATCC VR-65 and ATCC VR-1242; Western encephalitis virus, for example ATCC VR-70, ATCC VR-1251, ATCC VR-622 and ATCC VR-1252; and coronavirus, for example ATCC VR-740 and those described in Hamre (1966) Proc Soc Exp Biol Med 121:190.

Delivery of the compositions of this invention into cells is not limited to the above mentioned viral vectors. Other delivery methods and media may be employed such as, for example, nucleic acid expression vectors, polycationic condensed DNA linked or unlinked to killed adenovirus alone, for example see U.S. Ser. No. 08/366,787, filed Dec. 30, 1994 and Curie] (1992) Hum Gene Titer 3:147-154 ligand linked DNA, for example see Wu (1989) J Biol Chem 264:16985-16987, eucaryotic cell delivery vehicles cells, for example see U.S. Ser. No. 08/240,030, filed May 9, 1994, and U.S. Ser. No. 08/404,796, deposition of photopolymerized hydrogel materials, hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655, ionizing radiation as described in U.S. Pat. No. 5,206,152 and in WO92/11033, nucleic charge neutralization or fusion with cell membranes. Additional approaches are described in Philip (1994) Mol Cell Biol 14:2411-2418 and in Woffendin (1994) Proc Natl Acad Sci 91:1581-1585.

Particle mediated gene transfer may be employed, for example see U.S. Ser. No. 60/023,867. Briefly, the sequence can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, as described in Wu & Wu (1987) J. Biol. Chem. 262:4429-4432, insulin as described in Hucked (1990) Biochem Pharmacol 40:253-263, galactose as described in Plank (1992) Bioconjugate Chem 3:533-539, lactose or transferrin.

Naked DNA may also be employed. Exemplary naked DNA introduction methods are described in WO 90/11092 and U.S. Pat. No. 5,580,859. Uptake efficiency may be improved using biodegradable latex beads. DNA coated latex beads are efficiently transported into cells after endocytosis initiation by the beads. The method may be improved further by treatment of the beads to increase hydrophobicity and thereby facilitate disruption of the endosome and release of the DNA into the cytoplasm.

Liposomes that can act as gene delivery vehicles are described in U.S. Pat. No. 5,422,120, WO95/13796, WO94/23697, WO91/14445 and EP-524,968. As described in U.S. Ser. No. 60/023,867, on non-viral delivery, the nucleic acid sequences encoding a polypeptide can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then be incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, insulin, galactose, lactose, or transferrin. Other delivery systems include the use of liposomes to encapsulate DNA comprising the gene under the control of a variety of tissue-specific or ubiquitously-active promoters. Further non-viral delivery suitable for use includes mechanical delivery systems such as the approach described in Woffendin et al (1994) Proc. Natl. Acad. Sci. USA 91(24):11581-11585. Moreover, the coding sequence and the product of expression of such can be delivered through deposition of photopolymerized hydrogel materials. Other conventional methods for gene delivery that can be used for delivery of the coding sequence include, for example, use of hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655; use of ionizing radiation for activating transferred gene, as described in U.S. Pat. No. 5,206,152 and WO92/11033

Exemplary liposome and polycationic gene delivery vehicles are those described in U.S. Pat. Nos. 5,422,120 and 4,762,915; in WO 95/13796; WO94/23697; and WO91/14445; in EP-0524968; and in Stryer, Biochemistry, pages 236-240 (1975) W.H. Freeman, San Francisco; Szoka (1980) Biochem Biophys Acta 600:1; Bayer (1979) Biochem Biophys Acta 550:464; Rivnay (1987) Meth Enzymol 149:119; Wang (1987) Proc Natl Acad Sci 84:7851; Plant (1989) Anal Biochem 176:420.

A polynucleotide composition can comprises therapeutically effective amount of a gene therapy vehicle, as the term is defined above. For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.

Delivery Methods

Once formulated, the polynucleotide compositions of the invention can be administered (1) directly to the subject; (2) delivered ex vivo, to cells derived from the subject; or (3) in vitro for expression of recombinant proteins. The subjects to be treated can be mammals or birds. Also, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Methods for the ex vivo delivery and reimplantation of transformed cells into a subject are known in the art and described in eg. WO93/14778. Examples of cells useful in ex vivo applications include, for example, stem cells, particularly hematopoetic, lymph cells, macrophages, dendritic cells, or tumor cells.

Generally, delivery of nucleic acids for both ex vivo and in vitro applications can be accomplished by the following procedures, for example, dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei, all well known in the art.

Polynucleotide and Polypeptide Pharmaceutical Compositions

In addition to the pharmaceutically acceptable carriers and salts described above, the following additional agents can be used with polynucleotide and/or polypeptide compositions.

A. Polypeptides

One example are polypeptides which include, without limitation: asioloorosomucoid (ASOR); transferrin; asialoglycoproteins; antibodies; antibody fragments; ferritin; interleukins; interferons, granulocyte, macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), stem cell factor and erythropoietin. Viral antigens, such as envelope proteins, can also be used. Also, proteins from other invasive organisms, such as the 17 amino acid peptide from the circumsporozoite protein of plasmodium falciparum known as RH.

B. Hormones, Vitamins, etc.

Other groups that can be included are, for example: hormones, steroids, androgens, estrogens, thyroid hormone, or vitamins, folic acid.

C. Polyalkylenes, Polysaccharides, etc.

Also, polyalkylene glycol can be included with the desired polynucleotides/polypeptides. In a preferred embodiment, the polyalkylene glycol is polyethlylene glycol. Iri addition, mono-, di-, or polysaccarides can be included. In a preferred embodiment of this aspect, the polysaccharide is dextran or DEAE-dextran. Also, chitosan and poly(lactide-co-glycolide)

D. Lipids, and Liposomes

The desired polynucleotide/polypeptide can also be encapsulated in lipids or packaged in liposomes prior to delivery to the subject or to cells derived therefrom.

Lipid encapsulation is generally accomplished using liposomes which are able to stably bind or entrap and retain nucleic acid. The ratio of condensed polynucleotide to lipid preparation can vary but will generally be around 1:1 (mg DNA:micromoles lipid), or more of lipid. For a review of the use of liposomes as carriers for delivery of nucleic acids, see, Hug and Sleight (1991) Biochim. Biophys. Acta. 1097:1-17; Straubinger (1983) Meth. Enzymol. 101:512-527.

Liposomal preparations for use in the present invention include cationic (positively charged), anionic (negatively charged) and neutral preparations. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Feigner (1987) Proc. Natl. Acad. Sci. USA 84:7413-7416); mRNA (Malone (1989) Proc. Natl. Acad. Sci. USA 86:6077-6081); and purified transcription factors (Debs (1990) J. Biol. Chem. 265:10189-10192), in functional form.

Cationic liposomes are readily available. For example, N[1-2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (DOTMA) liposomes are available under the trademark Lipofectin, from GIBCO BRL, Grand Island, N.Y. (See, also, Feigner supra). Other commercially available liposomes include transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic liposomes can be prepared from readily available materials using techniques well known in the art. See, eg. Szoka (1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; WO90/11092 fora description of the synthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes.

Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using readily available materials. Such materials include phosphatidyl choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE), among others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for making liposomes using these materials are well known in the art.

The liposomes can comprise multilammelar vesicles (MLVs), small unilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs). The various liposome-nucleic acid complexes are prepared using methods known in the art. See eg. Straubinger (1983) Meth. Immunol. 101:512-527; Szoka (1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; Papahadjopoulos (1975) Biochim. Biophys. Acta 394:483; Wilson (1979) Cell 17:77); Deamer & Bangham (1976) Biochim. Biophys. Ada 443:629; Ostro (1977) Biochem. Biophys. Res. Commun. 76:836; Fraley (1979) Proc. Natl. Acad. Sci. USA 76:3348); Enoch & Strittmatter (1979) Proc. Natl. Acad. Sci. USA 76:145; Fraley (1980) J. Biol. Chem. (1980) 255:10431; Szoka & Papahadjopoulos (1978) Proc. Natl. Acad. Sci. USA 75:145; and Schaefer-Ridder (1982) Science 215:166.

E. Lipoproteins

In addition, lipoproteins can be included with the polynucleotide/polypeptide to be delivered. Examples of lipoproteins to be utilized include: chylomicrons, HDL, IDL, LDL, and VLDL. Mutants, fragments, or fusions of these proteins can also be used. Also, modifications of naturally occurring lipoproteins can be used, such as acetylated LDL. These lipoproteins can target the delivery of polynucleotides to cells expressing lipoprotein receptors. Preferably, if lipoproteins are including with the polynucleotide to be delivered, no other targeting ligand is included in the composition.

Naturally occurring lipoproteins comprise a lipid and a protein portion. The protein portion are known as apoproteins. At the present, apoproteins A, B, C, D, and E have been isolated and identified. At least two of these contain several proteins, designated by Roman numerals, AI, AII, AIV; CI, CII, CIII.

A lipoprotein can comprise more than one apoprotein. For example, naturally occurring chylomicrons comprises of A, B, C, and E, over time these lipoproteins lose A and acquire C and E apoproteins. VLDL comprises A, B, C, and E apoproteins, LDL comprises apoprotein B; and HDL comprises apoproteins A, C, and E.

The amino acid of these apoproteins are known and are described in, for example, Breslow (1985) Annu Rev. Biochem 54:699; Law (1986) Adv. Exp Med. Biol. 151:162; Chen (1986) J Biol Chem 261:12918; Kane (1980) Proc Natl Acad Sci USA 77:2465; and Utermann (1984) Hum Genet 65:232.

Lipoproteins contain a variety of lipids including, triglycerides, cholesterol (free and esters), and phopholipids. The composition of the lipids varies in naturally occurring lipoproteins. For example, chylomicrons comprise mainly triglycerides. A more detailed description of the lipid content of naturally occurring lipoproteins can be found, for example, in Meth. Enzymol. 128 (1986). The composition of the lipids are chosen to aid in conformation of the apoprotein for receptor binding activity. The composition of lipids can also be chosen to facilitate hydrophobic interaction and association with the polynucleotide binding molecule.

Naturally occurring lipoproteins can be isolated from serum by ultracentrifugation, for instance. Such methods are described in Meth. Enzymol. (supra); Pitas (1980) J. Biochem. 255:5454-5460 and Mahey (1979) J. Clin. Invest 64:743-750. Lipoproteins can also be produced by in vitro or recombinant methods by expression of the apoprotein genes in a desired host cell. See, for example, Atkinson (1986) Annu Rev Biophys Chem 15:403 and Radding (1958) Biochim Biophys Acta 30: 443. Lipoproteins can also be purchased from commercial suppliers, such as Biomedical Techniologies, Inc., Stoughton, Mass., USA. Further description of lipoproteins can be found in Zuckermann et al. PCT/US97/14465.

F. Polycationic Agents

Polycationic agents can be included, with or without lipoprotein, in a composition with the desired polynucleotide/polypeptide to be delivered.

Polycationic agents, typically, exhibit a net positive charge at physiological relevant pH and are capable of neutralizing the electrical charge of nucleic acids to facilitate delivery to a desired location. These agents have both in vitro, ex vivo, and in vivo applications. Polycationic agents can be used to deliver nucleic acids to a living subject either intramuscularly, subcutaneously, etc.

The following are examples of useful polypeptides as polycationic agents: polylysine, polyarginine, polyornithine, and protamine. Other examples include histones, protamines, human serum albumin, DNA binding proteins, non-histone chromosomal proteins, coat proteins from DNA viruses, such as (X174, transcriptional factors also contain domains that bind DNA and therefore may be useful as nucleic aid condensing agents. Briefly, transcriptional factors such as C/CEBP, c-jun, c-fos, AP-1, AP-2, AP-3, CPF, Prot-1, Sp-1, Oct-1, Oct-2, CREP, and TFIID contain basic domains that bind DNA sequences.

Organic polycationic agents include: spermine, spermidine, and purtrescine.

The dimensions and of the physical properties of a polycationic agent can be extrapolated from the list above, to construct other polypeptide polycationic agents or to produce synthetic polycationic agents.

Synthetic polycationic agents which are useful include, for example, DEAE-dextran, polybrene. Lipofectin™, and lipofectAMINE™ are monomers that form polycationic complexes when combined with polynucleotides/polypeptides.

Immunodiagnostic Assays

Neisserial antigens of the invention can be used in immunoassays to detect antibody levels (or, conversely, anti-Neisserial antibodies can be used to detect antigen levels). Immunoassays based on well defined, recombinant antigens can be developed to replace invasive diagnostics methods. Antibodies to Neisserial proteins within biological samples, including for example, blood or serum samples, can be detected. Design of the immunoassays is subject to a great deal of variation, and a variety of these are known in the art. Protocols for the immunoassay may be based, for example, upon competition, or direct reaction, or sandwich type assays. Protocols may also, for example, use solid supports, or may be by immunoprecipitation. Most assays involve the use of labeled antibody or polypeptide; the labels may be, for example, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays which amplify the signals from the probe are also known; examples of which are assays which utilize biotin and avidin, and enzyme-labeled and mediated immunoassays, such as ELISA assays.

Kits suitable for immunodiagnosis and containing the appropriate labeled reagents are constructed by packaging the appropriate materials, including the compositions of the invention, in suitable containers, along with the remaining reagents and materials (for example, suitable buffers, salt solutions, etc.) required for the conduct of the assay, as well as suitable set of assay instructions.

Nucleic Acid Hybridisation

“Hybridization” refers to the association of two nucleic acid sequences to one another by hydrogen bonding. Typically, one sequence will be fixed to a solid support and the other will be free in solution. Then, the two sequences will be placed in contact with one another under conditions that favor hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase sequence to the solid support (Denhardt's reagent or BLOTTO); concentration of the sequences; use of compounds to increase the rate of association of sequences (dextran sulfate or polyethylene glycol); and the stringency of the washing conditions following hybridization. See Sambrook et al. [supra] Volume 2, chapter 9, pages 9.47 to 9.57.

“Stringency” refers to conditions in a hybridization reaction that favor association of very similar sequences over sequences that differ. For example, the combination of temperature and salt concentration should be chosen that is approximately 120 to 200° C. below the calculated Tm of the hybrid under study. The temperature and salt conditions can often be determined empirically in preliminary experiments in which samples of genomic DNA immobilized on filters are hybridized to the sequence of interest and then washed under conditions of different stringencies. See Sambrook et al. at page 9.50.

Variables to consider when performing, for example, a Southern blot are (1) the complexity of the DNA being blotted and (2) the homology between the probe and the sequences being detected. The total amount of the fragment(s) to be studied can vary a magnitude of 10, from 0.1 to 1 μg for a plasmid or phage digest to 10⁻⁹ to 10⁻⁸ g for a single copy gene in a highly complex eukaryotic genome. For lower complexity polynucleotides, substantially shorter blotting, hybridization, and exposure times, a smaller amount of starting polynucleotides, and lower specific activity of probes can be used. For example, a single-copy yeast gene can be detected with an exposure time of only 1 hour starting with 1 μg of yeast DNA, blotting for two hours, and hybridizing for 4-8 hours with a probe of 10⁸ cpm/μg. For a single-copy mammalian gene a conservative approach would start with 10 μg of DNA, blot overnight, and hybridize overnight in the presence of 10% dextran sulfate using a probe of greater than 10⁸ cpm/μg, resulting in an exposure time of ˜24 hours.

Several factors can affect the melting temperature (Tm) of a DNA-DNA hybrid between the probe and the fragment of interest, and consequently, the appropriate conditions for hybridization and washing. In many cases the probe is not 100% homologous to the fragment. Other commonly encountered variables include the length and total G+C content of the hybridizing sequences and the ionic strength and formamide content of the hybridization buffer. The effects of all of these factors can be approximated by a single equation:

Tm=81+16.6(log₁₀Ci)+0.4[%(G+C)]−0.6(% formamide)−600/n−1.5(% mismatch).

where Ci is the salt concentration (monovalent ions) and n is the length of the hybrid in base pairs (slightly modified from Meinkoth & Wahl (1984) Anal. Biochem. 138: 267-284).

In designing a hybridization experiment, some factors affecting nucleic acid hybridization can be conveniently altered. The temperature of the hybridization and washes and the salt concentration during the washes are the simplest to adjust. As the temperature of the hybridization increases (ie. stringency), it becomes less likely for hybridization to occur between strands that are nonhomologous, and as a result, background decreases. If the radiolabeled probe is not completely homologous with the immobilized fragment (as is frequently the case in gene family and interspecies hybridization experiments), the hybridization temperature must be reduced, and background will increase. The temperature of the washes affects the intensity of the hybridizing band and the degree of background in a similar manner. The stringency of the washes is also increased with decreasing salt concentrations.

In general, convenient hybridization temperatures in the presence of 50% formamide are 42° C. for a probe with is 95% to 100% homologous to the target fragment, 37° C. for 90% to 95% homology, and 32° C. for 85% to 90% homology. For lower homologies, formamide content should be lowered and temperature adjusted accordingly, using the equation above. If the homology between the probe and the target fragment are not known, the simplest approach is to start with both hybridization and wash conditions which are nonstringent. If non-specific bands or high background are observed after autoradiography, the filter can be washed at high stringency and reexposed. If the time required for exposure makes this approach impractical, several hybridization and/or washing stringencies should be tested in parallel.

Nucleic Acid Probe Assays

Methods such as PCR, branched DNA probe assays, or blotting techniques utilizing nucleic acid probes according to the invention can determine the presence of cDNA or mRNA. A probe is said to “hybridize” with a sequence of the invention if it can form a duplex or double stranded complex, which is stable enough to be detected.

The nucleic acid probes will hybridize to the Neisserial nucleotide sequences of the invention (including both sense and antisense strands). Though many different nucleotide sequences will encode the amino acid sequence, the native Neisserial sequence is preferred because it is the actual sequence present in cells. mRNA represents a coding sequence and so a probe should be complementary to the coding sequence; single-stranded cDNA is complementary to mRNA, and so a cDNA probe should be complementary to the non-coding sequence.

The probe sequence need not be identical to the Neisserial sequence (or its complement)—some variation in the sequence and length can lead to increased assay sensitivity if the nucleic acid probe can form a duplex with target nucleotides, which can be detected. Also, the nucleic acid probe can include additional nucleotides to stabilize the formed duplex. Additional Neisserial sequence may also be helpful as a label to detect the formed duplex. For example, a non-complementary nucleotide sequence may be attached to the 5′ end of the probe, with the remainder of the probe sequence being complementary to a Neisserial sequence. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the probe sequence has sufficient complementarity with the a Neisserial sequence in order to hybridize therewith and thereby form a duplex which can be detected.

The exact length and sequence of the probe will depend on the hybridization conditions, such as temperature, salt condition and the like. For example, for diagnostic applications, depending on the complexity of the analyte sequence, the nucleic acid probe typically contains at least 10-20 nucleotides, preferably 15-25, and more preferably at least 30 nucleotides, although it may be shorter than this. Short primers generally require cooler temperatures to form sufficiently stable hybrid complexes with the template.

Probes may be produced by synthetic procedures, such as the triester method of Matteucci et al. [J. Am. Chem. Soc. (1981) 103:3185], or according to Urdea et al. [Proc. Natl. Acad. Sci. USA (1983) 80: 7461], or using commercially available automated oligonucleotide synthesizers.

The chemical nature of the probe can be selected according to preference. For certain applications, DNA or RNA are appropriate. For other applications, modifications may be incorporated eg. backbone modifications, such as phosphorothioates or methylphosphonates, can be used to increase in vivo half-life, alter RNA affinity, increase nuclease resistance etc. [eg. see Agrawal & Iyer (1995) Curr Opin Biotechnol 6:12-19; Agrawal (1996) TIBTECH 14:376-387]; analogues such as peptide nucleic acids may also be used [eg. see Corey (1997) TIBTECH 15:224-229; Buchardt et al. (1993) TIBTECH 11:384-386].

Alternatively, the polymerase chain reaction (PCR) is another well-known means for detecting small amounts of target nucleic acids. The assay is described in: Mullis et al. [Meth. Enzymol. (1987) 155: 335-350]; U.S. Pat. Nos. 4,683,195 and 4,683,202. Two “primer” nucleotides hybridize with the target nucleic acids and are used to prime the reaction. The primers can comprise sequence that does not hybridize to the sequence of the amplification target (or its complement) to aid with duplex stability or, for example, to incorporate a convenient restriction site. Typically, such sequence will flank the desired Neisserial sequence.

A thermostable polymerase creates copies of target nucleic acids from the primers using the original target nucleic acids as a template. After a threshold amount of target nucleic acids are generated by the polymerase, they can be detected by more traditional methods, such as Southern blots. When using the Southern blot method, the labelled probe will hybridize to the Neisserial sequence (or its complement).

Also, mRNA or cDNA can be detected by traditional blotting techniques described in Sambrook et al [supra]. mRNA, or cDNA generated from mRNA using a polymerase enzyme, can be purified and separated using gel electrophoresis. The nucleic acids on the gel are then blotted onto a solid support, such as nitrocellulose. The solid support is exposed to a labelled probe and then washed to remove any unhybridized probe. Next, the duplexes containing the labeled probe are detected. Typically, the probe is labelled with a radioactive moiety.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-E: For ORF37-1, (A) shows the results of affinity purification of the GST-fusion protein, (B) shows the results of expression of the His-fusion in E. coli. Purified GST-fusion protein was used to immunise mice, whose sera were used for ELISA (positive result), (C) shows FACS analysis, and (D) shows a bactericidal assay (FIG. 1D), and (E) shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF37-1.

FIG. 2A-B: For ORF5-1, (A) shows the results of affinity purification of the GST-fusion protein, and (B) shows the Western blot analysis of sera from mice immunized with purified GST-fusion protein.

FIG. 3A-D: For ORF2-1, (A) shows the results of affinity purification of the GST-fusion protein, (B) shows the results of expression of the His-fusion in E. coli, (C) shows the Western blot analysis of sera from mice immunized with turified GST-fusion protein, (D) shows the ELISA (positive result), and (D) shows the FACS analysis.

FIG. 4A-C: For ORF15-1, (A) shows the results of affinity purification of the GST-fusion protein, (B) shows the results of expression of the His-fusion in E. coli, and (C) shows the Western blot analysis of sera from mice immunized with purified GST-fusion protein.

FIG. 5A-C: For ORF22-1, (A) shows the results of affinity purification of the GST-fusion protein, (B) shows the results of expression of the His-fusion in E. coli, and (C) shows the FACS analysis using sera from mice immunized with the purified GST-fusion protein.

FIG. 6A-B: For ORF28-1, (A) shows the results of affinity purification of the GST-fusion protein, and (B) shows the results of expression of the His-fusion in E. coli.

FIG. 7A-B: For ORF32-1, (A) shows the results of affinity purification of the His-fusion protein, and (B) shows the results of expression of the GST-fusion in E. coli.

FIG. 8A-F: For ORF4-1, (A) shows the results of affinity purification of the His-fusion, (B) shows the results of affinity purification of the GST-fusion proteins, (C) shows the Western blot analysis of sera from mice immunized with the His-fusion protein, (D) shows the FACS analysis, (E) shows a bactericidal assay, and (F) shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF37-1.

FIG. 9 shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF61-1.

FIG. 10A-C: For ORF76-1, (A) shows the results of affinity purification of the His-fusion protein, (B) shows the Western blot analysis of sera from mice immunized with the purified His-fusion protein, and (C) shows the FACS analysis.

FIG. 11 shows the results of affinity purification of the GST-ORF89-1 fusion protein.

FIG. 12A-E: For ORF97-1, (A) show the results of affinity purification of the GST-fusion protein, (B) shows the results of affinity purification of the His-fusion protein, (C) shows the Western blot analysis of sera from mice immunized with purified GST-fusion protein, (D) shows the FACS analysis, and (E) shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF97-1.

FIG. 13A-C: For ORF106-1, (A) shows the results of affinity purification of the His-fusion protein, (B) shows the results of expression of the GST-fusion in E. coli, (C) shows the FACS analysis of sera from mice immunized with the purified His-fusion protein.

FIG. 14A-B: For ORF138-1, (A) shows the results of affinity purification of the GST-fusion protein, and (B) shows the FACS analysis of sera from mice immunized with the purified GST-fusion protein.

FIG. 15A-C: For ORF23-1, (A) shows the results of affinity purification of the His-fusion protein, (B) shows the results of expression of the GST-fusion in E. coli, (C) shows the Western blot analysis of sera from mice immunized with the purified His-fusion protein.

FIG. 16A-E: For ORF25-1, (A) shows the results of affinity purification of the GST-fusion protein, (B) shows the results of expression of the His-fusion in E. coli, (C) shows the Western blot analysis of sera from mice immunized with purified His-fusion protein, (D) shows the FACS analysis, and (E) shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF25-1.

FIG. 17A-B: For ORF27-1, (A) shows the results of affinity purification of the GST-fusion protein, and (B) shows the results of expression of the His-fusion in E. coli.

FIG. 18A-B: For ORF79-1, (A) shows the results of affinity purification of the His-fusion protein, and (B) shows the FACS analysis of sera from mice immunized with purified His-fusion protein.

FIG. 19A-D: For ORF85a, (A) shows the results of affinity purification of the GST-fusion protein, (B) shows Western blot analysis of sera from mice immunized with purified GST-fusion protein, (C) shows FACS analysis, and (D) shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF85a.

FIG. 20A-C: For ORF132-1, (A) shows the results of affinity purification of the His-fusion protein, (B) shows the results of expression of the GST-fusion in E. coli, (C) shows the FACS analysis of sera from mice immunized with purified His-fusion protein.

EXAMPLES

The examples describe nucleic acid sequences which have been identified in N. meningitidis, along with their putative translation products, and also those of N. gonorrhoeae. Not all of the nucleic acid sequences are complete i.e. they encode less than the full-length wild-type protein.

The examples are generally in the following format:

• • a nucleotide sequence which has been identified in N. meningitidis (strain B)
  • the putative translation product of this sequence
  • a computer analysis of the translation product based on database comparisons
  • corresponding gene and protein sequences identified in N. meningitidis (strain A) and in N. gonorrhoeae
  • a description of the characteristics of the proteins which indicates that they might be suitably antigenic
  • results of biochemical analysis (expression, purification, ELISA, FACS etc.)
  • The examples typically include details of sequence identity between species and strains. Proteins that are similar in sequence are generally similar in both structure and function, and the sequence identity often indicates a common evolutionary origin. Comparison with sequences of proteins of known function is widely used as a guide for the assignment of putative protein function to a new sequence and has proved particularly useful in whole-genome analyses.

Sequence comparisons were performed at NCBI (http://www.ncbi.nlm.nih.gov) using the algorithms BLAST, BLAST2, BLASTn, BLASTp, tBLASTn, BLASTx, & tBLASTx [eg. see also Altschul et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:2289-3402]. Searches were performed against the following databases: non-redundant GenBank+EMBL+DDBJ+PDB sequences and non-redundant GenBank CDS translations+PDB+SwissProt+SPupdate+PIR sequences.

To compare Meningococcal and Gonococcal sequences, the tBLASTx algorithm was used, as implemented at http://www.genome.ou.edu/gono_blast.html. The FASTA algorithm was also used to compare the ORFs (from GCG Wisconsin Package, version 9.0).

Dots within nucleotide sequences (eg. position 495 in SEQ ID 11) represent nucleotides which have been arbitrarily introduced in order to maintain a reading frame. In the same way, double-underlined nucleotides were removed. Lower case letters (eg. position 496 in SEQ ID 11) represent ambiguities which arose during alignment of independent sequencing reactions (some of the nucleotide sequences in the examples are derived from combining the results of two or more experiments).

Nucleotide sequences were scanned in all six reading frames to predict the presence of hydrophobic domains using an algorithm based on the statistical studies of Esposti et al. [Critical evaluation of the hydropathy of membrane proteins (1990) Eur J Biochem 190:207-219]. These domains represent potential transmembrane regions or hydrophobic leader sequences.

Open reading frames were predicted from fragmented nucleotide sequences using the program ORFFINDER (NCBI).

Underlined amino acid sequences indicate possible transmembrane domains or leader sequences in the ORFs, as predicted by the PSORT algorithm (http://www.psort.nibb.ac.jp). Functional domains were also predicted using the MOTIFS program (GCG Wisconsin & PROSITE).

Various tests can be used to assess the in vivo immunogencity of the proteins identified in the examples. For example, the proteins can be expressed recombinantly and used to screen patient sera by immunoblot. A positive reaction between the protein and patient serum indicates that the patient has previously mounted an immune response to the protein in question ie. the protein is an immunogen. This method can also be used to identify immunodominant proteins.

The recombinant protein can also be conveniently used to prepare antibodies eg. in a mouse. These can be used for direct confirmation that a protein is located on the cell-surface. Labelled antibody (eg. fluorescent labelling for FACS) can be incubated with intact bacteria and the presence of label on the bacterial surface confirms the location of the protein.

In particular, the following methods (A) to (S) were used to express, purify and biochemically characterise the proteins of the invention:

A) Chromosomal DNA Preparation

N. meningitidis strain 2996 was grown to exponential phase in 100 ml of GC medium, harvested by centrifugation, and resuspended in 5 ml buffer (20% Sucrose, 50 mM Tris-HCl, 50 mM EDTA, pH8). After 10 minutes incubation on ice, the bacteria were lysed by adding 10 ml lysis solution (50 mM NaCl, 1% Na-Sarkosyl, 50 μg/ml Proteinase K), and the suspension was incubated at 37° C. for 2 hours. Two phenol extractions (equilibrated to pH 8) and one ChCl₃/isoamylalcohol (24:1) extraction were performed. DNA was precipitated by addition of 0.3M sodium acetate and 2 volumes ethanol, and was collected by centrifugation. The pellet was washed once with 70% ethanol and redissolved in 4 ml buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). The DNA concentration was measured by reading the OD at 260 nm.

B) Oligonucleotide Design

Synthetic oligonucleotide primers were designed on the basis of the coding sequence of each ORF, using (a) the meningococcus B sequence when available, or (b) the gonococcus/meningococcus A sequence, adapted to the codon preference usage of meningococcus as necessary. Any predicted signal peptides were omitted, by deducing the 5′-end amplification primer sequence immediately downstream from the predicted leader sequence.

For most ORFs, the 5′ primers included two restriction enzyme recognition sites (BamHI-NdeI, BamHI-NheI, or EcoRI-NheI, depending on the gene's own restriction pattern); the 3′ primers included a XhoI restriction site. This procedure was established in order to direct the cloning of each amplification product (corresponding to each ORF) into two different expression systems: pGEX-KG (using either BamHI-XhoI or EcoRI-XhoI), and pET21b+ (using either NdeI-XhoI or NheI-XhoI).

5′-end primer tail:	CGCGGATCCCATATG	(BamHI-NdeI)
	CGCGGATCCGCTAGC	(BamHI-NheI)
	CCGGAATTCTAGCTAGC	(EcoRI-NheI)
3′-end primer tail:	CCCGCTCGAG	(XhoI)

For ORFs 5, 15, 17, 19, 20, 22, 27, 28, 65 & 89, two different amplifications were performed to clone each ORF in the two expression systems. Two different 5′ primers were used for each ORF; the same 3′ XhoI primer was used as before:

5′-end primer tail:	GGAATTCCATATGGCCATGG	(NdeI)
5′-end primer tail:	CGGGATCC	(BamHI)

ORF 76 was cloned in the pTRC expression vector and expressed as an amino-terminus His-tag fusion. In this particular case, the predicted signal peptide was included in the final product. NheI-BamHI restriction sites were incorporated using primers:

5′-end primer tail:	GATCAGCTAGCCATATG	(NheI)
3′-end primer tail:	CGGGATCC	(BamHI)

As well as containing the restriction enzyme recognition sequences, the primers included nucleotides which hybridized to the sequence to be amplified. The number of hybridizing nucleotides depended on the melting temperature of the whole primer, and was determined for each primer using the formulae:

T_m=4(G+C)+2(A+T) (tail excluded)

T_m=64.9+0.41(% GC)−600/N (whole primer)

The average melting temperature of the selected oligos were 65-70° C. for the whole oligo and 50-55° C. for the hybridising region alone.

Table I (page 487) shows the forward and reverse primers used for each amplification. In certain cases, it will be noted that the sequence of the primer does not exactly match the sequence in the ORF. When initial amplifications were performed, the complete 5′ and/or 3′ sequence was not known for some meningococcal ORFs, although the corresponding sequences had been identified in gonococcus. For amplification, the gonococcal sequences could thus be used as the basis for primer design, altered to take account of codon preference. In particular, the following codons were changed: ATA→ATT; TCG→TCT; CAG→CAA; AAG→AAA; GAG→GAA; CGA→CGC; CGG→CGC; GGG→GGC. Italicised nucleotides in Table I indicate such a change. It will be appreciated that, once the complete sequence has been identified, this approach is generally no longer necessary.

Oligos were synthesized by a Perkin Elmer 394 DNA/RNA Synthesizer, eluted from the columns in 2 ml NH₄OH, and deprotected by 5 hours incubation at 56° C. The oligos were precipitated by addition of 0.3M Na-Acetate and 2 volumes ethanol. The samples were then centrifuged and the pellets resuspended in either 100 μl or 1 ml of water. OD₂₆₀ was determined using a Perkin Elmer Lambda Bio spectophotometer and the concentration was determined and adjusted to 2-10 pmol/μl.

C) Amplification

The standard PCR protocol was as follows: 50-200 ng of genomic DNA were used as a template in the presence of 20-40 μM of each oligo, 400-800 μM dNTPs solution, 1×PCR buffer (including 1.5 mM MgCl₂), 2.5 units TaqI DNA polymerase (using Perkin-Elmer AmpliTaQ, GIBCO Platinum, Pwo DNA polymerase, or Tahara Shuzo Taq polymerase).

In some cases, PCR was optimsed by the addition of 10 μl DMSO or 50 μl 2M betaine.

After a hot start (adding the polymerase during a preliminary 3 minute incubation of the whole mix at 95° C.), each sample underwent a double-step amplification: the first 5 cycles were performed using as the hybridization temperature the one of the oligos excluding the restriction enzymes tail, followed by 30 cycles performed according to the hybridization temperature of the whole length oligos. The cycles were followed by a final 10 minute extension step at 72° C.

The standard cycles were as follows:

	Denaturation	Hybridisation	Elongation
First 5 cycles	30 seconds	30 seconds	30-60 seconds
	95° C.	50-55° C.	72° C.
Last 30 cycles	30 seconds	30 seconds	30-60 seconds
	95° C.	65-70° C.	72° C.

The elongation time varied according to the length of the ORF to be amplified.

The amplifications were performed using either a 9600 or a 2400 Perkin Elmer GeneAmp PCR System. To check the results, 1/10 of the amplification volume was loaded onto a 1-1.5% agarose gel and the size of each amplified fragment compared with a DNA molecular weight marker.

The amplified DNA was either loaded directly on a 1% agarose gel or first precipitated with ethanol and resuspended in a suitable volume to be loaded on a 1% agarose gel. The DNA fragment corresponding to the right size band was then eluted and purified from gel, using the Qiagen Gel Extraction Kit, following the instructions of the manufacturer. The final volume of the DNA fragment was 30 μl or 50 μl of either water or 10 mM Tris, pH 8.5.

D) Digestion of PCR Fragments

The purified DNA corresponding to the amplified fragment was split into 2 aliquots and double-digested with:

• • NdeI/XhoI or NheI/XhoI for cloning into pET-21b+ and further expression of the protein as a C-terminus His-tag fusion
  • BamHI/XhoI or EcoRI/XhoI for cloning into pGEX-KG and further expression of the protein as N-terminus GST fusion.
  • For ORF 76, NheI/BamHI for cloning into pTRC-H isA vector and further expression of the protein as N-terminus His-tag fusion.
  • EcoRI/PstI, EcoRI/SalI, SalI/PstI for cloning into pGex-His and further expression of the protein as N-terminus His-tag fusion

Each purified DNA fragment was incubated (37° C. for 3 hours to overnight) with 20 units of each restriction enzyme (New England Biolabs) in a either 30 or 40 μl final volume in the presence of the appropriate buffer. The digestion product was then purified using the QIAquick PCR purification kit, following the manufacturer's instructions, and eluted in a final volume of 30 or 50 μl of either water or 10 mM Tris-HCl, pH 8.5. The final DNA concentration was determined by 1% agarose gel electrophoresis in the presence of titrated molecular weight marker.

E) Digestion of the Cloning Vectors (pET22B, pGEX-KG, pTRC-His A, and pGex-His)

10 μg plasmid was double-digested with 50 units of each restriction enzyme in 200 μl reaction volume in the presence of appropriate buffer by overnight incubation at 37° C. After loading the whole digestion on a 1% agarose gel, the band corresponding to the digested vector was purified from the gel using the Qiagen QIAquick Gel Extraction Kit and the DNA was eluted in 50 μl of 10 mM Tris-HCl, pH 8.5. The DNA concentration was evaluated by measuring OD₂₆₀ of the sample, and adjusted to 50 μg/μl. 1 μl of plasmid was used for each cloning procedure.

The vector pGEX-His is a modified pGEX-2T vector carrying a region encoding six histidine residues upstream to the thrombin cleavage site and containing the multiple cloning site of the vector pTRC99 (Pharmacia).

F) Cloning

The fragments corresponding to each ORF, previously digested and purified, were ligated in both pET22b and pGEX-KG. In a final volume of 20 μl, a molar ratio of 3:1 fragment/vector was ligated using 0.5 μl of NEB T4 DNA ligase (400 units/μl), in the presence of the buffer supplied by the manufacturer. The reaction was incubated at room temperature for 3 hours. In some experiments, ligation was performed using the Boheringer “Rapid Ligation Kit”, following the manufacturer's instructions.

In order to introduce the recombinant plasmid in a suitable strain, 100 μl E. coli DH5 competent cells were incubated with the ligase reaction solution for 40 minutes on ice, then at 37° C. for 3 minutes, then, after adding 800 μl LB broth, again at 37° C. for 20 minutes. The cells were then centrifuged at maximum speed in an Eppendorf microfuge and resuspended in approximately 200 μl of the supernatant. The suspension was then plated on LB ampicillin (100 mg/ml).

The screening of the recombinant clones was performed by growing 5 randomly-chosen colonies overnight at 37° C. in either 2 ml (pGEX or pTC clones) or 5 ml (pET clones) LB broth+100 μg/ml ampicillin. The cells were then pelletted and the DNA extracted using the Qiagen QIAprep Spin Miniprep Kit, following the manufacturer's instructions, to a final volume of 30 μl. 5 μl of each individual miniprep (approximately 1 g) were digested with either NdeI/XhoI or BamHI/XhoI and the whole digestion loaded onto a 1-1.5% agarose gel (depending on the expected insert size), in parallel with the molecular weight marker (1 Kb DNA Ladder, GIBCO). The screening of the positive clones was made on the base of the correct insert size.

For the cloning of ORFs 110, 111, 113, 115, 119, 122, 125 & 130, the double-digested PCR product was ligated into double-digested vector using EcoRI-PstI cloning sites or, for ORFs 115 & 127, EcoRI-SalI or, for ORF 122, SalI-PstI. After cloning, the recombinant plasmids were introduced in the E. coli host W3110. Individual clones were grown overnight at 37° C. in L-broth with 50 μl/ml ampicillin.

G) Expression

Each ORF cloned into the expression vector was transformed into the strain suitable for expression of the recombinant protein product. 1 μl of each construct was used to transform 30 μl of E. coli BL21 (pGEX vector), E. coli TOP 10 (pTRC vector) or E. coli BL21-DE3 (pET vector), as described above. In the case of the pGEX-His vector, the same E. coli strain (W3110) was used for initial cloning and expression. Single recombinant colonies were inoculated into 2 ml LB+Amp (100 μg/ml), incubated at 37° C. overnight, then diluted 1:30 in 20 ml of LB+Amp (100 μg/ml) in 100 ml flasks, making sure that the OD₆₀₀ ranged between 0.1 and 0.15. The flasks were incubated at 30° C. into gyratory water bath shakers until OD indicated exponential growth suitable for induction of expression (0.4-0.8 OD for pET and pTRC vectors; 0.8-1 OD for pGEX and pGEX-His vectors). For the pET, pTRC and pGEX-His vectors, the protein expression was induced by addition of 1 mM IPTG, whereas in the case of pGEX system the final concentration of IPTG was 0.2 mM. After 3 hours incubation at 30° C., the final concentration of the sample was checked by OD. In order to check expression, 1 ml of each sample was removed, centrifuged in a microfuge, the pellet resuspended in PBS, and analysed by 12% SDS-PAGE with Coomassie Blue staining. The whole sample was centrifuged at 6000 g and the pellet resuspended in PBS for further use.

H) GST-Fusion Proteins Large-Scale Purification.

A single colony was grown overnight at 37° C. on LB+Amp agar plate. The bacteria were inoculated into 20 ml of LB+Amp liquid colture in a water bath shaker and grown overnight. Bacteria were diluted 1:30 into 600 ml of fresh medium and allowed to grow at the optimal temperature (20-37° C.) to OD₅₅₀ 0.8-1. Protein expression was induced with 0.2 mM IPTG followed by three hours incubation. The culture was centrifuged at 8000 rpm at 4° C. The supernatant was discarded and the bacterial pellet was resuspended in 7.5 ml cold PBS. The cells were disrupted by sonication on ice for 30 sec at 40 W using a Branson sonifier B-15, frozen and thawed twice and centrifuged again. The supernatant was collected and mixed with 150 μl Glutatione-Sepharose 4B resin (Pharmacia) (previously washed with PBS) and incubated at room temperature for 30 minutes. The sample was centrifuged at 700 g for 5 minutes at 4° C. The resin was washed twice with 10 ml cold PBS for 10 minutes, resuspended in 1 ml cold PBS, and loaded on a disposable column. The resin was washed twice with 2 ml cold PBS until the flow-through reached OD₂₈₀ of 0.02-0.06. The GST-fusion protein was eluted by addition of 700 μl cold Glutathione elution buffer (10 mM reduced glutathione, 50 mM Tris-HCl) and fractions collected until the OD₂₈₀ was 0.1.21 μl of each fraction were loaded on a 12% SDS gel using either Biorad SDS-PAGE Molecular weight standard broad range (M1) (200, 116.25, 97.4, 66.2, 45, 31, 21.5, 14.4, 6.5 kDa) or Amersham Rainbow Marker (M2) (220, 66, 46, 30, 21.5, 14.3 kDa) as standards. As the MW of GST is 26 kDa, this value must be added to the MW of each GST-fusion protein.

I) His-Fusion Solubility Analysis (ORFs 111-129)

To analyse the solubility of the His-fusion expression products, pellets of 3 ml cultures were resuspended in buffer M1 [500 μl PBS pH 7.2]. 25 μl lysozyme (10 mg/ml) was added and the bacteria were incubated for 15 min at 4° C. The pellets were sonicated for 30 sec at 40 W using a Branson sonifier B-15, frozen and thawed twice and then separated again into pellet and supernatant by a centrifugation step. The supernatant was collected and the pellet was resuspended in buffer M2 [8M urea, 0.5M NaCl, 20 mM imidazole and 0.1 M NaH₂ PO₄] and incubated for 3 to 4 hours at 4° C. After centrifugation, the supernatant was collected and the pellet was resuspended in buffer M3 [6M guanidinium-HCl, 0.5M NaCl, 20 mM imidazole and 0.1M NaH₂PO₄] overnight at 4° C. The supernatants from all steps were analysed by SDS-PAGE.

The proteins expressed from ORFs 113, 119 and 120 were found to be soluble in PBS, whereas ORFs 111, 122, 126 and 129 need urea and ORFs 125 and 127 need guanidium-HCl for their solubilization.

J) His-Fusion Large-Scale Purification.

A single colony was grown overnight at 37° C. on a LB+Amp agar plate. The bacteria were inoculated into 20 ml of LB+Amp liquid culture and incubated overnight in a water bath shaker. Bacteria were diluted 1:30 into 600 ml fresh medium and allowed to grow at the optimal temperature (20-37° C.) to OD₅₅₀ 0.6-0.8. Protein expression was induced by addition of 1 mM IPTG and the culture further incubated for three hours. The culture was centrifuged at 8000 rpm at 4° C., the supernatant was discarded and the bacterial pellet was resuspended in 7.5 ml of either (i) cold buffer A (300 mM NaCl, 50 mM phosphate buffer, 10 mM imidazole, pH 8) for soluble proteins or (ii) buffer B (urea 8M, 10 mM Tris-HCl, 100 mM phosphate buffer, pH 8.8) for insoluble proteins. The cells were disrupted by sonication on ice for 30 sec at 40 W using a Branson sonifier B-15, frozen and thawed two times and centrifuged again.

For insoluble proteins, the supernatant was stored at −20° C., while the pellets were resuspended in 2 ml buffer C (6M guanidine hydrochloride, 100 mM phosphate buffer, 10 mM Tris-HCl, pH 7.5) and treated in a homogenizer for 10 cycles. The product was centrifuged at 13000 rpm for 40 minutes.

Supernatants were collected and mixed with 150 μl Ni²⁺-resin (Pharmacia) (previously washed with either buffer A or buffer B, as appropriate) and incubated at room temperature with gentle agitation for 30 minutes. The sample was centrifuged at 700 g for 5 minutes at 4° C. The resin was washed twice with 10 ml buffer A or B for 10 minutes, resuspended in 1 ml buffer A or B and loaded on a disposable column. The resin was washed at either (i) 4° C. with 2 ml cold buffer A or (ii) room temperature with 2 ml buffer B, until the flow-through reached OD₂₈₀ of 0.02-0.06.

The resin was washed with either (i) 2 ml cold 20 mM imidazole buffer (300 mM NaCl, 50 mM phosphate buffer, 20 mM imidazole, pH 8) or (ii) buffer D (urea 8M, 10 mM Tris-HCl, 100 mM phosphate buffer, pH 6.3) until the flow-through reached the OD₂₈₀ of 0.02-0.06. The His-fusion protein was eluted by addition of 700 μl of either (i) cold elution buffer A (300 mM NaCl, 50 mM phosphate buffer, 250 mM imidazole, pH 8) or (ii) elution buffer B (urea 8M, 10 mM Tris-HCl, 100 mM phosphate buffer, pH 4.5) and fractions collected until the OD₂₈₀ was 0.1. 21 μl of each fraction were loaded on a 12% SDS gel.

K) His-Fusion Proteins Renaturation

10% glycerol was added to the denatured proteins. The proteins were then diluted to 20 μg/ml using dialysis buffer I (10% glycerol, 0.5M arginine, 50 mM phosphate buffer, 5 mM reduced glutathione, 0.5 mM oxidised glutathione, 2M urea, pH 8.8) and dialysed against the same buffer at 4° C. for 12-14 hours. The protein was further dialysed against dialysis buffer II (10% glycerol, 0.5M arginine, 50 mM phosphate buffer, 5 mM reduced glutathione, 0.5 mM oxidised glutathione, pH 8.8) for 12-14 hours at 4° C. Protein concentration was evaluated using the formula:

Protein (mg/ml)=(1.55×OD₂₈₀)−(0.76×OD₂₆₀)

L) His-Fusion Large-Scale Purification (ORFs 111-129)

500 ml of bacterial cultures were induced and the fusion proteins were obtained soluble in buffer M1, M2 or M3 using the procedure described above. The crude extract of the bacteria was loaded onto a Ni-NTA superflow column (Quiagen) equilibrated with buffer M1, M2 or M3 depending on the solubilization buffer of the fusion proteins. Unbound material was eluted by washing the column with the same buffer. The specific protein was eluted with the corresponding buffer containing 500 mM imidazole and dialysed against the corresponding buffer without imidazole. After each run the columns were sanitized by washing with at least two column volumes of 0.5 M sodium hydroxide and reequilibrated before the next use.

M) Mice Immunisations

20 μg of each purified protein were used to immunise mice intraperitoneally. In the case of ORFs 2, 4, 15, 22, 27, 28, 37, 76, 89 and 97, Balb-C mice were immunised with Al(OH)₃ as adjuvant on days 1, 21 and 42, and immune response was monitored in samples taken on day 56. For ORFs 44, 106 and 132, CD1 mice were immunised using the same protocol. For ORFs 25 and 40, CD1 mice were immunised using Freund's adjuvant, rather than AL(OH)₃, and the same immunisation protocol was used, except that the immune response was measured on day 42, rather than 56. Similarly, for ORFs 23, 32, 38 and 79, CD1 mice were immunised with Freund's adjuvant, but the immune response was measured on day 49.

N) ELISA Assay (Sera Analysis)

The acapsulated MenB M7 strain was plated on chocolate agar plates and incubated overnight at 37° C. Bacterial colonies were collected from the agar plates using a sterile dracon swab and inoculated into 7 ml of Mueller-Hinton Broth (Difco) containing 0.25% Glucose. Bacterial growth was monitored every 30 minutes by following OD₆₂₀. The bacteria were let to grow until the OD reached the value of 0.3-0.4. The culture was centrifuged for 10 minutes at 10000 rpm. The supernatant was discarded and bacteria were washed once with PBS, resuspended in PBS containing 0.025% formaldehyde, and incubated for 2 hours at room temperature and then overnight at 4° C. with stirring. 100 μl bacterial cells were added to each well of a 96 well Greiner plate and incubated overnight at 4° C. The wells were then washed three times with PBT washing buffer (0.1% Tween-20 in PBS). 200 μl of saturation buffer (2.7% Polyvinylpyrrolidone 10 in water) was added to each well and the plates incubated for 2 hours at 37° C. Wells were washed three times with PBT. 200 μl of diluted sera (Dilution buffer: 1% BSA, 0.1% Tween-20, 0.1% NaN₃ in PBS) were added to each well and the plates incubated for 90 minutes at 37° C. Wells were washed three times with PBT. 100 μl of HRP-conjugated rabbit anti-mouse (Dako) serum diluted 1:2000 in dilution buffer were added to each well and the plates were incubated for 90 minutes at 37° C. Wells were washed three times with PBT buffer. 100 μl of substrate buffer for HRP (25 ml of citrate buffer pH5, 10 mg of O-phenildiamine and 10 μl of H₂O) were added to each well and the plates were left at room temperature for 20 minutes. 100 μl H₂SO₄ was added to each well and OD₄₉₀ was followed. The ELISA was considered positive when OD₄₉₀ was 2.5 times the respective pre-immune sera.

O) FACScan Bacteria Binding Assay Procedure.

The acapsulated MenB M7 strain was plated on chocolate agar plates and incubated overnight at 37° C. Bacterial colonies were collected from the agar plates using a sterile dracon swab and inoculated into 4 tubes containing 8 ml each Mueller-Hinton Broth (Difco) containing 0.25% glucose. Bacterial growth was monitored every 30 minutes by following OD₆₂₀. The bacteria were let to grow until the OD reached the value of 0.35-0.5. The culture was centrifuged for 10 minutes at 4000 rpm. The supernatant was discarded and the pellet was resuspended in blocking buffer (1% BSA, 0.4% NaN₃) and centrifuged for 5 minutes at 4000 rpm. Cells were resuspended in blocking buffer to reach OD₆₂₀ of 0.07. 100 μl bacterial cells were added to each well of a Costar 96 well plate. 100 μl of diluted (1:200) sera (in blocking buffer) were added to each well and plates incubated for 2 hours at 4° C. Cells were centrifuged for 5 minutes at 4000 rpm, the supernatant aspirated and cells washed by addition of 200 μl/well of blocking buffer in each well. 100 μl of R-Phicoerytrin conjugated F(ab)₂ goat anti-mouse, diluted 1:100, was added to each well and plates incubated for 1 hour at 4° C. Cells were spun down by centrifugation at 4000 rpm for 5 minutes and washed by addition of 200 μl/well of blocking buffer. The supernatant was aspirated and cells resuspended in 200 μl/well of PBS, 0.25% formaldehyde. Samples were transferred to FACScan tubes and read. The condition for FACScan setting were: FL1 on, FL2 and FL3 off; FSC-H threshold:92; FSC PMT Voltage: E 02; SSC PMT: 474; Amp. Gains 7.1; FL-2 PMT: 539; compensation values: 0.

P) OMV Preparations

Bacteria were grown overnight on 5 GC plates, harvested with a loop and resuspended in 10 ml 20 mM Tris-HCl. Heat inactivation was performed at 56° C. for 30 minutes and the bacteria disrupted by sonication for 10 minutes on ice (50% duty cycle, 50% output). Unbroken cells were removed by centrifugation at 5000 g for 10 minutes and the total cell envelope fraction recovered by centrifugation at 50000 g at 4° C. for 75 minutes. To extract cytoplasmic membrane proteins from the crude outer membranes, the whole fraction was resuspended in 2% sarkosyl (Sigma) and incubated at room temperature for 20 minutes. The suspension was centrifuged at 10000 g for 10 minutes to remove aggregates, and the supernatant further ultracentrifuged at 50000 g for 75 minutes to pellet the outer membranes. The outer membranes were resuspended in 10 mM Tris-HCl, pH8 and the protein concentration measured by the Bio-Rad Protein assay, using BSA as a standard.

Q) Whole Extracts Preparation

Bacteria were grown overnight on a GC plate, harvested with a loop and resuspended in 1 ml of 20 mM Tris-HCl. Heat inactivation was performed at 56° C. for 30 minutes.

R) Western Blotting

Purified proteins (500 ng/lane), outer membrane vesicles (5 μg) and total cell extracts (25 μg) derived from MenB strain 2996 were loaded on 15% SDS-PAGE and transferred to a nitrocellulose membrane. The transfer was performed for 2 hours at 150 mA at 4° C., in transferring buffer (0.3% Tris base, 1.44% glycine, 20% methanol). The membrane was saturated by overnight incubation at 4° C. in saturation buffer (10% skimmed milk, 0.1% Triton X100 in PBS). The membrane was washed twice with washing buffer (3% skimmed milk, 0.1% Triton X100 in PBS) and incubated for 2 hours at 37° C. with mice sera diluted 1:200 in washing buffer. The membrane was washed twice and incubated for 90 minutes with a 1:2000 dilution of horseradish peroxidase labelled anti-mouse Ig. The membrane was washed twice with 0.1% Triton X100 in PBS and developed with the Opti-4CN Substrate Kit (Bio-Rad). The reaction was stopped by adding water.

S) Bactericidal Assay

MC58 strain was grown overnight at 37° C. on chocolate agar plates. 5-7 colonies were collected and used to inoculate 7 ml Mueller-Hinton broth. The suspension was incubated at 37° C. on a nutator and let to grow until OD₆₂₀ was 0.5-0.8. The culture was aliquoted into sterile 1.5 ml Eppendorf tubes and centrifuged for 20 minutes at maximum speed in a microfuge. The pellet was washed once in Gey's buffer (Gibco) and resuspended in the same buffer to an OD₆₂₀ of 0.5, diluted 1:20000 in Gey's buffer and stored at 25° C.

50 μl of Gey's buffer/]% BSA was added to each well of a 96-well tissue culture plate. 25 μl of diluted mice sera (1:100 in Gey's buffer/0.2% BSA) were added to each well and the plate incubated at 4° C. 25 μl of the previously described bacterial suspension were added to each well. 25 μl of either heat-inactivated (56° C. waterbath for 30 minutes) or normal baby rabbit complement were added to each well. immediately after the addition of the baby rabbit complement, 22 μl of each sample/well were plated on Mueller-Hinton agar plates (time 0). The 96-well plate was incubated for 1 hour at 37° C. with rotation and then 22 μl of each sample/well were plated on Mueller-Hinton agar plates (time 1). After overnight incubation the colonies corresponding to time 0 and time 1 hour were counted.

Table II (page 493) gives a summary of the cloning, expression and prurification results.

Example 1

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 1>:

1	ATGAAACAGA CAGTCAA.AT GCTTGCCGCC GCCCTGATTG
	CCTTGGGCTT
51	GAACCGACCG GTGTGGNCGG ATGACGTATC GGATTTTCGG
	GAAAACTTGC
101	A.GCGGCAGC ACAGGGAAAT GCAGCAGCCC AATACAATTT
	GGGCGCAATG
151	TAT.TACAAA GGACGCGCGT GCGCCGGGAT GATGCTGAAG
	CGGTCAGATG
201	GTATCGGCAG CCGGCGGAAC AGGGGTTAGC CCAAGCCCAA
	TACAATTTGG
251	GCTGGATGTA TGCCAACGGG CGCGC.GTGC GCCAAGATGA
	TACCGAAGCG
301	GTCAGATGGT ATCGGCAGGC GGCAGCGCAG GGGGTTGTCC
	AAGCCCAATA
351	CAATTTGGGC GTGATATATG CCGAAGGACG TGGAGTGCGC
	CAAGACGATG
401	TCGAAGCGGT CAGATGGTTT CGGCAGGCGG CAGCGCAGGG
	GGTAGCCCAA
451	GCCCAAAACA ATTTGGGCGT GATGTATGCC GAAAGANCGC
	GCGTGCGCCA
501	AGACCG...

This corresponds to the amino acid sequence <SEQ ID 2; ORF37>:

1	MKQTVXMLAA ALIALGLNRP VWXDDVSDFR ENLXAAAQGN
	AAAQYNLGAM
51	YXQRTRVRRD DAEAVRWYRQ PAEQGLAQAQ YNLGWMYANG
	RXVRQDDTEA
101	VRWYRQAAAQ GVVQAQYNLG VIYAEGRGVR QDDVEAVRWF
	RQAAAQGVAQ
151	AQNNLGVMYA ERXRVRQD...

Further work revealed the complete nucleotide sequence <SEQ ID 3>:

1	ATGAAACAGA CAGTCAAATG GCTTGCCGCC GCCCTGATTG
	CCTTGGGCTT
51	GAACCGAGCG GTGTGGGCGG ATGACGTATC GGATTTTCGG
	GAAAACTTGC
101	AGGCGGCAGC ACAGGGAAAT GCAGCAGCCC AATACAATTT
	GGGCGCAATG
151	TATTACAAAG GACGCGGCGT GCGCCGGGAT GATGCTGAAG
	CGGTCAGATG
201	GTATCGGCAG GCGGCGGAAC AGGGGTTAGC CCAAGCCCAA
	TACAATTTGG
251	GCTGGATGTA TGCCAACGGG CGCGGCGTGC GCCAAGATGA
	TACCGAAGCG
301	GTCAGATGGT ATCGGCAGGC GGCAGCGCAG GGGGTTGTCC
	AAGCCCAATA
351	CAATTTGGGC GTGATATATG CCGAAGGACG TGGAGTGCGC
	CAAGACGATG
401	TCGAAGCGGT CAGATGGTTT CGGCAGGCGG CAGCGCAGGG
	GGTAGCCCAA
451	GCCCAAAACA ATTTGGGCGT GATGTATGCC GAAAGACGCG
	GCGTGCGCCA
501	AGACCGCGCC CTTGCACAAG AATGGTTTGG CAAGGCTTGT
	CAAAACGGAG
551	ACCAAGACGG CTGCGACAAT GACCAACGCC TGAAGGCGGG
	TTATTGA

This corresponds to the amino acid sequence <SEQ ID 4; ORF37-1>:

1	MKQTVKWLAA ALIALGLNRA VWADDVSDFR ENLQAAAQGN
	AAAQYNLGAM
51	YYKGRGVRRD DAEAVRWYRQ AAEQGLAQAQ YNLGWMYANG
	RGVRQDDTEA
101	VRWYRQAAAQ GVVQAQYNLG VIYAEGRGVR QDDVEAVRWF
	RQAAAQGVAQ
151	AQNNLGVMYA ERRGVRQDRA LAQEWFGKAC QNGDQDGCDN
	DQRLKAGY*

Further work identified the corresponding gene in strain A of N. meningitidis <SEQ ID 5>:

1	ATGAAACAGA CAGTCAAATG GCTTGCCGCC GCCCTGATTG
	CCTTGGGCTT
51	GAACCAAGCG GTGTGGGCGG ATGACGTATC GGATTTTCGG
	GAAAACTTGC
101	AGGCGGCAGC ACAGGGAAAT GCAGCAGCCC AAAACAATTT
	GGGCGTGATG
151	TATGCCGAAA GACGCGGCGT GCGCCAAGAC CGCGCCCTTG
	CACAAGAATG
201	GCTTGGCAAG GCTTGTCAAA ACGGATACCA AGACAGCTGC
	GACAATGACC
251	AACGCCTGAA AGCGGGTTAT TGA

This encodes a protein having amino acid sequence <SEQ ID 6; ORF37a>:

1	MKQTVKWLAA ALIALGLNQA VWADDVSDFR ENLQAAAQGN
	AAAQNNLGVM
51	YAERRGVRQD RALAQEWLGK ACQNGYQDSC DNDQRLKAGY
	*

The originally-identified partial strain B sequence (ORF37) shows 68.0% identity over a 75aa overlap with ORF37a:

Further work identified the corresponding gene in N. gonorrhoeae <SEQ ID 7>:

1	ATGAAACAGA CAGTCAAATG GCTTGCCGCC GCCCTGATTG
	CCTTGGGCTT
51	GAACCAAGCG GTGTGGGCGG GTGACGTATC GGATTTTCGG
	GAAAACTTGC
101	AGgcggcaGA ACaggGAAAT GCAGCAGCCC AATTCAATTT
	GGGCGTGATG
151	TATGAAAATG GACAAGGAGT TCGTCAAGAT TATGTACAGG
	CAGTGCAGTG
201	GTATCGCAAG GCTTCAGAAC AAGGGGATGC CCAAGCCCAA
	TACAATTTGG
251	GCTTGATGTA TTACGATGGA CGCGGCGTGC GCCAAGACCT
	TGCGCTCGCT
301	CAACAATGGC TTGGCAAGGC TTGTCAAAAC GGAGACCAAA
	ACAGCTGCGA
351	CAATGACCAA CGCCTGAAGG CGGGTTATTA A

This encodes a protein having amino acid sequence <SEQ ID 8; ORF37ng>:

1	MKQTVKWLAA ALIALGLNQA VWAGDVSDFR ENLQAAEQGN
	AAAQFNLGVM
51	YENGQGVRQD YVQAVQWYRK ASEQGDAQAQ YNLGLMYYDG
	RGVRQDLALA
101	QQWLGKACQN GDQNSCDNDQ RLKAGY*

The originally-identified partial strain B sequence (ORF37) shows 64.9% identity over a 111aa overlap with ORF37ng:

The complete strain B sequence (ORF37-1) and ORF37ng show 51.5% identity in 198 aa overlap:

Computer analysis of these amino acid sequences indicates a putative leader sequence, and it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF37-1 (11 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 1A shows the results of affinity purification of the GST-fusion protein, and FIG. 1B shows the results of expression of the His-fusion in E. coli. Purified GST-fusion protein was used to immunise mice, whose sera were used for ELISA (positive result), FACS analysis (FIG. 1C), and a bactericidal assay (FIG. 1D). These experiments confirm that ORF37-1 is a surface-exposed protein, and that it is a useful immunogen.

FIG. 1E shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF37-1.

Example 2

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 9>:

	TTCGGCGA CATCGGCGGT TTGAAGGTCA ATGCCCCCGT
	CAAATCCGCA GGCGTATTGG TCGGGCGCGT CGGCGCTATC
	GGACTTGACC CGAAATCCTA TCAGGCGAGG GTGCGCCTCG
	ATTTGGACGG CAAGTATCAG TTCAGCAGCG ACGTTTCCGC
	GCAAATCCTG ACTTCsGGAC TTTTGGGCGA GCAGTACATC
	GGGCTGCAGC AGGGCGGCGA CACGGAAAAC CTTGCTGCCG
	GCGACACCAT CTCCGTAACC AGTTCTGCAA TGGTTCTGGA
	AAACCTTATC GGCAAATTCA TGACGAGTTT TGCCGAGAAA
	AATGCCGACG GCGGCAATGC GGAAAAAGCC GCCGAATAA

This corresponds to the amino acid sequence <SEQ ID 10>:

1 FGDIGGLKVN APVKSAGVLV GRVGAIGLDP KSYQARVRLD LDGKYQFSSD
51 VSAQILTSGL LGEQYIGLQQ GGDTENLAAG DTISVTSSAM VLENLIGKFM
101 TSFAEKNADG GNAEKAAE*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Hypothetical H. influenzae Protein (ybrd.haein; Accession Number p45029)

SEQ ID 9 and ybrd.haein show 48.4% aa identity in 122 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

SEQ ID 9 shows 99.2% identity over a 118aa overlap with a predicted ORF from N. gonorrhoeae:

The complete yrbd H. influenzae sequence has a leader sequence and it is expected that the full-length homologous N. meningitidis protein will also have one. This suggests that it is either a membrane protein, a secreted protein, or a surface protein and that the protein, or one of its epitopes, could be a useful antigen for vaccines or diagnostics.

Example 3

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 11>:

1	..ATTTTGATAT ACCTCATCCG CAAGAATCTA GGTTCGCCCG
	TCTTCTTCTT
51	TCAGGAACGC CCCGGAAAGG ACGGAAAACC TTTTAAAATG
	GTCAAATTCC
101	GTTCCATGCG CGACGGCTTG TATTCAGACG GCATTCCGCT
	GCCCGACGGA
151	GAACGCCTGA CACCGTTCGG CAAAAAACTG CGTGCCGcCA
	GTwTGGACGA
201	ACTGCCTGAA TTATGGAATA TCTTAAAAGG CGAGATGAGC
	CTGGTCGGCC
251	CCCGCCCGCT GCTGATGCAA TATCTGCCGC TGTACGACAA
	CTTCCAAAAC
301	CGCCGCCACG AAATGAAACC CGGCATTACC GGCTGGGCGC
	AGGTCAACGG
351	GCGCAACGCg CTTTCGTGGG ACGAAAAATT CGCCTGCGAT
	GTTTGGTATA
401	TCGACCACTT CAGCCTGTGC CTCGACATCA AAATCCTACT
	GCTGACGGTT
451	AAAAAAGTAT TAATCAAGGA AGGGATTTCC GCACAGGGCG
	AACA.aCCAT
501	GCCCCCTTTC ACAGGAAAAC GCAAACTCGC CGTCGTCGGT
	GCGGGCGGAC
551	ACGGAAAAGT CGTTGCCGAC CTTGCCGCCG CACTCGGCCG
	GTACAGGGAA
601	ATCGTTTTTC TGGACGACCG CGCACAAGGC AGCGTCAACG
	GCTTTTCCGT
651	CATCGGCACG ACGCTGCTGC TTGAAAACAG TTTATCGCCC
	GAACAATACG
701	ACGTCGCCGT CGCCGTCGGC AACAACCGCA TCCGCCGCCA
	AATCGCCGAA
751	AAAGCCGCCG CGCTCGGCTT CGCCCTGCCC GTACTGGTTC
	ATCCGGACGC
801	GACCGTCTCG CCTTCTGCAA CAGTCGGACA AGGCAGCGTC
	GTTATGGCGA
851	AAGCGGTCG..

This corresponds to the amino acid sequence <SEQ ID 12; ORF3>:

1	. . . ILIYLIRKNL GSPVFFFQER PGKDGKPFKM VKFRSMRDGL YSDGIPLPDG
51	ERLTPFGKKL RAASXDELPE LWNILKGEMS LVGPRPLLMQ YLPLYDNFQN
101	RRHEMKPGIT GWAQVNGRNA LSWDEKFACD VWYIDHFSLC LDIKILLLTV
151	KKVLIKEGIS AQGEXTMPPF TGKRKLAVVG AGGHGKVVAD LAAALGRYRE
201	IVFLDDRAQG SVNGFSVIGT TLLLENSLSP EQYDVAVAVG NNRIRRQIAE
251	KAAALGFALP VLVHPDATVS PSATVGQGSV VMAKAV . . .

Further sequence analysis revealed the complete nucleotide sequence <SEQ ID 13>:

1	ATGAGTAAAT TCTTCAAACG CCTGTTTGAC ATTGTTGCCT
	CCGCCTCGGG
51	ACTGATTTTC CTCTCGCCAG TATTTTTGAT TTTGATATAC
	CTCATCCGCA
101	AGAATCTAGG TTCGCCCGTC TTCTTCTTTC AGGAACGCCC
	CGGAAAGGAC
151	GGAAAACCTT TTAAAATGGT CAAATTCCGT TCCATGCGCG
	ACGCGCTTGA
201	TTCAGACGGC ATTCCGCTGC CCGACGGAGA ACGCCTGACA
	CCGTTCGGCA
251	AAAAACTGCG TGCCGCCAGT TTGGACGAAC TGCCTGAATT
	ATGGAATATC
301	TTAAAAGGCG AGATGAGCCT GGTCGGCCCC CGCCCGCTGC
	TGATGCAATA
351	TCTGCCGCTG TACGACAACT TCCAAAACCG CCGCCACGAA
	ATGAAACCCG
401	GCATTACCGG CTGGGCGCAG GTCAACGGGC GCAACGCGCT
	TTCGTGGGAC
451	GAAAAATTCG CCTGCGATGT TTGGTATATC GACCACTTCA
	GCCTGTGCCT
501	CGACATCAAA ATCCTACTGC TGACGGTTAA AAAAGTATTA
	ATCAAGGAAG
551	GGATTTCCGC ACAGGGCGAA GCCACCATGC CCCCTTTCAC
	AGGAAAACGC
601	AAACTCGCCG TCGTCGGTGC GGGCGGACAC GGAAAAGTCG
	TTGCCGACCT
651	TGCCGCCGCA CTCGGCCGGT ACAGGGAAAT CGTTTTTCTG
	GACGACCGCG
701	CACAAGGCAG CGTCAACGGC TTTTCCGTCA TCGGCACGAC
	GCTGCTGCTT
751	GAAAACAGTT TATCGCCCGA ACAATACGAC GTCGCCGTCG
	CCGTCGGCAA
801	CAACCGCATC CGCCGCCAAA TCGCCGAAAA AGCCGCCGCG
	CTCGGCTTCG
851	CCCTGCCCGT TCTGGTTCAT CCGGACGCGA CCGTCTCGCC
	TTCTGCAACA
901	GTCGGACAAG GCAGCGTCGT TATGGCGAAA GCCGTCGTAC
	AGGCAGGCAG
951	CGTATTGAAA GACGGCGTGA TTGTGAACAC TGCCGCCACC
	GTCGATCACG
1001	ACTGCCTGCT TAACGCTTTC GTCCACATCA GCCCAGGCGC
	GCACCTGTCG
1051	GGCAACACGC ATATCGGCGA AGAAAGCTGG ATAGGCACGG
	GCGCGTGCAG
1101	CCGCCAGCAG ATCCGTATCG GCAGCCGCGC AACCATTGGA
	GCGGGCGCAG
1151	TCGTCGTACG CGACGTTTCA GACGGCATGA CCGTCGCGGG
	CAATCCGGCA
1201	AAGCCGCTGC CGCGCAAAAA CCCCGAGACC TCGACAGCAT
	AA

This corresponds to the amino acid sequence <SEQ ID 14; ORF3-1>:

1	MSKFFKRLFD IVASASGLIF LSPVFLILIY LIRKNLGSPV
	FFFQERPGKD
51	GKPFKMVKFR SMRDALDSDG IPLPDGERLT PFGKKLRAAS
	LDELPELWNI
101	LKGEMSLVGP RPLLMQYLPL YDNFQNRRHE MKPGITGWAQ
	VNGRNALSWD
151	EKFACDVWYI DHFSLCLDIK ILLLTVKKVL IKEGISAQGE
	ATMPPFTGKR
201	KLAVVGAGGH GKVVADLAAA LGRYREIVFL DDRAQGSVNG
	FSVIGTTLLL
251	ENSLSPEQYD VAVAVGNNRI RRQIAEKAAA LGFALPVLVH
	PDATVSPSAT
301	VGQGSVVMAK AVVQAGSVLK DGVIVNTAAT VDHDCLLNAF
	VHISPGAHLS
351	GNTHIGEESW IGTGACSRQQ IRIGSRATIG AGAVVVRDVS
	DGMTVAGNPA
401	KPLPRKNPET STA*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF3 shows 93.0% identity over a 286aa overlap with an ORF (ORF3a) from strain A of N. meningitidis:

The complete length ORF3a nucleotide sequence <SEQ ID 15> is:

1	ATGAGTAAAT TCTTCAAACG CCTGTTTGAC ATTGTTGCCT
	CCGCCTCGGG
51	ACTGATTTTC CTCTCGCCAG TATTTTTGAT TTTGATATAC
	CTCATCCGCA
101	AGAATCTGGG TTCGCCCGTC TTCTTCTTTC AGGAACGCCC
	CGGAAAGGAC
151	GGAAAACCTT TTAAAATGGT CAAATTCCGT TCCATGCACG
	ACGCGCTTGA
201	TTCAGACGGC ATTCTGCTGC CCGACGGAGA ACGCCTGACA
	CCGTTCGGCA
251	AAAAACTGCG TGCCGCCAGT TTGGACGAAC TGCCCGAACT
	GTGGAACGTC
301	CTCAAAGGCG ACATGAGCCT GGTCGGCCCC CGCCCGCTGC
	TGATGCAATA
351	TCTGCCGCTG TACGACAACT TCCAAAACCG CCGCCACGAA
	ATGAAACCGG
401	GCATTACCGG CTGGGCGCAG GTCAACGGGC GCAACGCGCT
	TTCGTGGGAC
451	GAACGCTTCG CATGCGACAT CTGGTATATC GACCACTTCA
	GCCTGTGCCT
501	CGAGATCAAA ATCCTACTGC TGACGGTTAA AAAAGTATTA
	ATCAAAGAAG
551	GGATTTCCGC ACAGGGCGAA GCCACCATGC CCCCTTTCAC
	AGGAAAACGC
601	AAACTTGCCG TCGTCGGTGC GGGCGGACAC GGCAAAGTCG
	TTGCCGAGCT
651	TGCCGCCGCA CTCGGCACAT ACGGCGAAAT CGTTTTTCTG
	GACGACCGCG
701	TCCAAGGCAG CGTCAACGGC TTCCCCGTCA TCGGCACGAC
	GCTGCTGCTT
751	GAAAACAGTT TATCGCCCGA ACAATTCGAC ATCGCCGTCG
	CCGTCGGCAA
801	CAACCGCATC CGCCGCCAAA TCGCCGAAAA AGCCGCCGCG
	CTCGGCTTCG
851	CCCTGCCCGT CCTGATTCAT CCGGACTCGA CCGTCTCGCC
	TTCTGCAACA
901	GTCGGACAAG GCGGCGTCGT TATGGCGAAA GCCGTCGTAC
	AGGCTGACAG
951	CGTATTGAAA GACGGCGTAA TTGTGAACAC TGCCGCCACC
	GTCGATCACG
1001	ATTGCCTGCT TGATGCTTTC GTCCACATCA GCCCGGGCGC
	GCACCTGTCG
1051	GGCAACACGC GTATCGGCGA AGAAAGCTGG ATAGGCACAG
	GCGCGTGCAG
1101	CCGCCAGCAG ATCCGTATCG GCAGCCGCGC AACCATTGGA
	GCGGGCGCAG
1151	TCGTCGTGCG CGACGTTTCA GACGGCATGA CCGTCGCGGG
	CAACCCGGCA
1201	AAACCATTGG CAGGCAAAAA TACCGAGACC CTGCGGTCGT
	AA

This is predicted to encode a protein having amino acid sequence <SEQ ID 16>:

1	MSKFFKRLFD IVASASGLIF LSPVFLILIY LIRKNLGSPV
	FFFQERPGKD
51	GKPFKMVKFR SMHDALDSDG ILLPDGERLT PFGKKLRAAS
	LDELPELWNV
101	LKGDMSLVGP RPLLMQYLPL YDNFQNRRHE MKPGITGWAQ
	VNGRNALSWD
151	ERFACDIWYI DHFSLCLDIK ILLLTVKKVL IKEGISAQGE
	ATMPPFTGKR
201	KLAVVGAGGH GKVVAELAAA LGTYGEIVFL DDRVQGSVNG
	FPVIGTTLLL
251	ENSLSPEQFD IAVAVGNNRI RRQIAEKAAA LGFALPVLIH
	PDSTVSPSAT
301	VGQGGVVMAK AVVQADSVLK DGVIVNTAAT VDHDCLLDAF
	VHISPGAHLS
351	GNTRIGEESW IGTGACSRQQ IRIGSRATIG AGAVVVRDVS
	DGMTVAGNPA
401	KPLAGKNTET LRS*

Two transmembrane domains are underlined.

ORF3-1 shows 94.6% identity in 410 aa overlap with ORF3a:

Homology with Hypothetical Protein Encoded by yvfc Gene (Accession Z71928) of B. subtilis

ORF3 and YVFC proteins show 55% aa identity in 170 aa overlap (BLASTp):

ORF3	3	IYLIRKNLGSPVFFFQERPGKDGKPFKMVKFRSMRDGLYSDGIPLPDGERLTPFGKKLRA	62
		I ++R  +GSPVFF Q RPG  GKPF + KFR+M D   S G  LPD  RLT  G+ +R
yvfc	27	IAVVRLKIGSPVFFKQVRPGLHGKPFTLYKFRTMTDERDSKGNLLPDEVRLTKTGRLIRK	86
ORF3	63	ASXDELPELWNILKGEMSLVGPRPLLMQYLPLYDNFQNRRHEMKPGITGWAQVNGRNALS	122
		S DELP+L N+LKG++SLVGPRPLLM YLPLY   Q RRHE+KPGITGWAQ+NGRNA+S
yvfc	87	LSIDELPQLLNVLKGDLSLVGPRPLLMDYLPLYTEKQARRHEVKPGITGWAQINGRNAIS	146
ORF3	123	WDEKFACDVWYIDHFSLCLDXXXXXXXXXXXXXXEGISAQGEXTMPPFTG	172
		W++KF  DVWY+D++S  LD              EGI      T   FTG
yvfc	147	WEKKFELDVWYVDNWSFFLDLKILCLTVRKVLVSEGIQQTNHVTAERFTG	196

Homology with a Predicted ORF from N. gonorrhoeae

ORF3 shows 86.3% identity over a 286aa overlap with a predicted ORF (ORF3.ng) from N. gonorrhoeae:

The complete length ORF3ng nucleotide sequence <SEQ ID 17> is:

1	ATGAGTAAAG CCGTCAAACG CCTGTTCGAC ATCATCGCAT
	CCGCATCGGG
51	GCTGATTGTC CTGTCGCCCG TGTTTTTGGT TTTAATATAC
	CTCATCCGCA
101	AAAACTTAGG TTCGCCCGTC TTCTTCattC GGGAACGCCc
	cgGAAAGGAc
151	ggaaaacCTT TTAAAATGGT CAAATTCCGT TCCAtgcgcg
	acgcgcttGA
201	TTCAGACGGC ATTCCGCTGC CCGATAGCGA ACGCCTGACC
	GATTTCGGCA
251	AAAAATTACG CGCCACCAGT TTGGACGAAC TTCCTGAATT
	ATGGAATGTC
301	CTCAAAGGCG AGATGAGCCT GGTCGGCCCC CGCCCGCTTT
	TGATGCAGTA
351	TCTGCCGCTT TACAACAAAT TTCAAAACCG CCGCCACGAA
	ATGAAACCGG
401	GCATTACCGG CTGGGCGCAG GTCAACGGGC GCAACGCGCT
	TTCGTGGGAC
451	GAAAAGTTCT CCTGCGATGT TTGGTACACC GACAATTTCA
	GCTTTTGGCT
501	GGATATGAAA ATCCTGTTTC TGACAGTCAA AAAAGTCTTG
	ATTAAAGAAG
551	GCATTTCGGC GCAAGGGGAA GCCACCATGC CCCCTTTCGC
	GGGGAATCGC
601	AAACTCGCCG TTATCGGCGC GGGCGGACAC GGCAAAGTCG
	TTGCCGAGCT
651	TGCCGCCGCA CTCGGCACAT ACGGCGAAAT CGTTTTTCTG
	GACGACCGCA
701	CCCAAGGCAG CGTCAACGGC TTCCCCGTCA TCGGCACGAC
	GCTGCTGCTT
751	GAAAACAGTT TATCGCCCGA ACAATTCGAC ATCACCGTCG
	CCGTCGGCAA
801	CAACCGCATC CGCCGCCAAA TCACCGAAAA CGCCGCCGCG
	CTCGGCTTCA
851	AACTGCCCGT TCTGATTCAT CCCGACGCGA CCGTCTCGCC
	TTCTGCAATA
901	ATCGGACAAG GCAGCGTCGT AATGGCGAAA GCCGTCGTAC
	AGGCCGGCAG
951	CGTATTGAAA GACGGCGTGA TTGTGAACAC TGCCGCCACC
	GTCGATCACG
1001	ACTGCCTGCT TGACGCTTTC GtccaCATCA GCCCGGGCGC
	GCACCTGTCG
1051	GGCAACACGC GTATCGGCGA AGAAAGCCGG ATAGGCACGG
	GCGCGTGCAG
1101	CCGCCAGCAG ACAACCGTCG GCAGCGGGGT TACCgccgGT
	GCAGGGgcGG
1151	TTATCGTATG CGACATCCCG GACGGCATGA CCGTCGCGGG
	CAACCCGGCA
1201	AAGCCCCTTA CGGGCAAAAA CCCCAAGACC GGGACGGCAT
	AA

This encodes a protein having amino acid sequence <SEQ ID 18>:

1	MSKAVKRLFD IIASASGLIV LSPVFLVLIY LIRKNLGSPV
	FFIRERPGKD
51	GKPFKMVKFR SMRDALDSDG IPLPDSERLT DFGKKLRATS
	LDELPELWNV
101	LKGEMSLVGP RPLLMQYLPL YNKFQNRRHE MKPGITGWAQ
	VNGRNALSWD
151	EKFSCDVWYT DNFSFWLDMK ILFLTVKKVL IKEGISAQGE
	ATMPPFAGNR
201	KLAVIGAGGH GKVVAELAAA LGTYGEIVFL DDRTQGSVNG
	FPVIGTTLLL
251	ENSLSPEQFD ITVAVGNNRI RRQITENAAA LGFKLPVLIH
	PDATVSPSAI
301	IGQGSVVMAK AVVQAGSVLK DGVIVNTAAT VDHDCLLDAF
	VHISPGAHLS
351	GNTRIGEESR IGTGACSRQQ TTVGSGVTAG AGAVIVCDIP
	DGMTVAGNPA
401	KPLTGKNPKT GTA*

This protein shows 86.9% identity in 413 aa overlap with ORF3-1:

In addition, ORF3ng shows significant homology with a hypothetical protein from B. subtilis:

gnl|PID|e238668 (Z71928) hypothetical protein [Bacillus subtilis]
>gi|1945702|gnl|PID|e313004 (Z94043) hypothetical protein
[Bacillus subtilis]
>gi|2635938|gnl|PID|e1186113 (Z99121) similar to capsular polysaccharide
biosynthesis [Bacillus subtilis] Length = 202
Score = 235 bits (594), Expect = 3e−61
Identities = 114/195 (58%), Positives = 142/195 (72%)

Query:	5	VKRLFDIIASASGLIVLSPVFLVLIYLIRKNLGSPVFFIRERPGKDGKPFKMVKFRSMRD	64
		+KRLFD+ A+   L  S + L  I ++R  +GSPVFF + RPG  GKPF + KFR+M D
Sbjct:	3	LKRLFDLTAAIFLLCCTSVIILFTIAVVRLKIGSPVFFKQVRPGLHGKPFTLYKFRTMTD	62
Query:	65	ALDSDGIPLPDSERLTDFGKKLRATSLDELPELWNVLKGEMSLVGPRPLLMQYLPLYNKF	124
		DS G  LPD  RLT  G+ +R  S+DELP+L NVLKG++SLVGPRPLLM YLPLY +
Sbjct:	63	ERDSKGNLLPDEVRLTKTGRLIRKLSIDELPQLLNVLKGDLSLVGPRPLLMDYLPLYTEK	122
Query:	125	QNRRHEMKPGITGWAQVNGRNALSWDEKFSCDVWYTDNFSFWLDMKILFLTVKKVLIKEG	184
		Q RRHE+KPGITGWAQ+NGRNA+SW++KF  DVWY DN+SF+LD+KIL LTV+KVL+ EG
Sbjct:	123	QARRHEVKPGITGWAQINGRNAISWEKKFELDVWYVDNWSFFLDLKILCLTVRKVLVSEG	182
Query:	185	ISAQGEATMPPFAGN	199
		I      T   F G+
Sbjct:	183	IQQTNHVTAERFTGS	197

The hypothetical product of yvfc gene shows similarity to EXOY of R. meliloti, an exopolysaccharide production protein. Based on this and on the two predicted transmembrane regions in the homologous N. gonorrhoeae sequence, it is predicted that these proteins, or their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 4

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 19>:

1	..AACCATATGG CGATTGTCAT CGACGAATAC GGCGGCACAT
	CCGGCTTGGT
51	CACCTTTGAA GACATCATCG AGCAAATCGT CGGCGAAATC
	GAAGACGAGT
101	TTGACGAAGA CGATAGCGCC GACAATATCC ATGCCGTTTC
	TTCAGACACG
151	TGGCGCATCC ATGCAGCTAC CGAAATCGAA GACATCAACA
	CCTTCTTCGG
201	CACGGAATAC AGCATCGAAG AAGCCGACAC CATT.GGCGG
	CCTGGTCATT
251	CAAGAGTTGG GACATCTGCC CGTGCGCGGC GAAAAAGTCC
	TTATCGGCGG
301	TTTGCAGTTC ACCGTCGCAC GCGCCGACAA CCGCCGCCTG
	CATACGCTGA
351	TGGCGACCCG CGTGAAGTAA GC........ .....ACCGC
	CGTTTCTGCA
401	CAGTTTAG

This corresponds to amino acid sequence <SEQ ID 20; ORF5>:

1	..NHMAIVIDEY GGTSGLVTFE DIIEQIVGEI EDEFDEDDSA
	DNIHAVSSDT
51	WRIHAATEIE DINTFFGTEY SIEEADTIXR PGHSRVGTSA
	RARRKSPYRR
101	FAVHRRTRRQ PPPAYADGDP REVS....XR RFCTV*

Further sequence analysis revealed the complete DNA sequence to be <SEQ ID 21>:

1	ATGGACGGCG CACAACCGAA AACGAATTTT TTTGAACGCC
	TGATTGCCCG
51	ACTCGCCCGC GAACCCGATT CCGCCGAAGA CGTATTAAAC
	CTGCTTCGGC
101	AGGCGCACGA GCAGGAAGTT TTTGATGCGG ATACGCTTTT
	AAGATTGGAA
151	AAAGTCCTCG ATTTTTCCGA TTTGGAAGTG CGCGACGCGA
	TGATTACGCG
201	CAGCCGTATG AACGTTTTAA AAGAAAACGA CAGCATCGAG
	CGCATCACCG
251	CCTACGTTAT CGATACCGCC CATTCGCGCT TCCCCGTCAT
	CGGCGAAGAC
301	AAAGACGAAG TTTTGGGCAT TTTGCACGCC AAAGACCTGC
	TCAAATATAT
351	GTTTAACCCC GAGCAGTTCC ACCTCAAATC CATTCTCCGC
	CCCGCCGTCT
401	TCGTCCCCGA AGGCAAATCG CTGACCGCCC TTTTAAAAGA
	GTTCCGCGAA
451	CAGCGCAACC ATATGGCGAT TGTCATCGAC GAATACGGCG
	GCACATCCGG
501	CTTGGTCACC TTTGAAGACA TCATCGAGCA AATCGTCGGC
	GAAATCGAAG
551	ACGAGTTTGA CGAAGACGAT AGCGCCGACA ATATCCATGC
	CGTTTCTTCC
601	GAACGCTGGC GCATCCATGC AGCTACCGAA ATCGAAGACA
	TCAACACCTT
651	CTTCGGCACG GAATACAGCA GCGAAGAAGC CGACACCATT
	CGGCCTGGTC
701	ATTCAAGAGT TGGGACATCT GCCCGTGCGC GGCGAAAAAG
	TCCTTATCGG
751	CGGTTTGCAG TTCACCGTCG CACGCGCCGA CAACCGCCGC
	CTGCATACGC
801	TGATGGCGAC CCGCGTGAAG TAAGCACCGC CGTTTCTGCA
	CAGTTTAGGA
851	TGACGGTACG GGCGTTTTCT GTTTCAATCC GCCCCATCCG
	CCAAACATAA

This corresponds to amino acid sequence <SEQ ID 22; ORF5-1>:

1	MDGAQPKTNF FERLIARLAR EPDSAEDVLN LLRQAHEQEV
	FDADTLLRLE
51	KVLDFSDLEV RDAMITRSRM NVLKENDSIE RITAYVIDTA
	HSRFPVIGED
101	KDEVLGILHA KDLLKYMFNP EQFHLKSILR PAVFVPEGKS
	LTALLKEFRE
151	QRNHMAIVID EYGGTSGLVT FEDIIEQIVG EIEDEFDEDD
	SADNIHAVSS
201	ERWRIHAATE IEDINTFFGT EYSSEEADTI RPGHSRVGTS
	ARARRKSPYR
251	RFAVHRRTRR QPPPAYADGD PREVSTAVSA QFRMTVRAFS
	VSIRPIRQT*

Further work identified the corresponding gene in strain A of N. meningitidis <SEQ ID 23>:

1	ATGGACGGCG CACAACCGAA AACAAATTTT TTNNAACGCC
	TGATTGCCCG
51	ACTCGCCCGC GAACCCGATT CCGCCGAAGA CGTATTGACC
	CTGTTGCGCC
101	AAGCGCACGA ACAGGAAGTA TTTGATGCGG ATACGCTTTT
	AAGATTGGAA
151	AAAGTCCTCG ATTTTTCTGA TTTGGAAGTG CGCGACGCGA
	TGATTACGCG
201	CAGCCGTATG AACGTTTTAA AAGAAAACGA CAGCATCGAA
	CGCATCACCG
251	CCTACGTTAT CGATACCGCC CATTCGCGCT TCCCCGTCAT
	CGGTGAAGAC
301	AAAGACGAAG TTTTGGGTAT TTTGCACGCC AAAGACCTGC
	TCAAATATAT
351	GTTCAACCCC GAGCAGTTCC ACCTCAAATC GATATTGCGC
	CCTGCCGTCT
401	TCGTCCCCGA AGGCAAATCG CTGACCGCCC TTTTAAAAGA
	GTTCCGCGAA
451	CAGCGCAACC ATATGGCAAT CGTCATCGAC GAATACGGCG
	GCACGTCGGG
501	TTTGGTAACT TTTGAAGACA TCATCGAGCA AATCGTCGGC
	GACATCGAAG
551	ATGAGTTTGA CGAAGACGAA AGCGCGGACA ACATCCACGC
	CGTTTCCGCC
601	GAACGCTGGC GCATCCACGC GGCTACCGAA ATCGAAGACA
	TCAACGCCTT
651	TTTCGGCACG GAATACAGCA GCGAAGAAGC CGACACCATC
	GGCGGCCNTG
701	GTCATTCAGG AATTGGNACA CCTGCCCGTG CGCGGCGAAA
	AAGTCNTTAT
751	CGGCGNNTTG CANTTCACNG TCGCCNGCGC NGACAACCGC
	CGCCTGCATA
801	CGCTGATGGC GACCCGCGTG AAGTAAGCTC CGCCGTTTCT
	GTACAGTTTA
851	GGATGACGGT ACGGGCGTTT TCTGTTTCAA TCCGCCCCAT
	CCGCCANACA
901	TAA

This encodes a protein having amino acid sequence <SEQ ID 24; ORF5a>:

1	MDGAQPKTNF XXRLIARLAR EPDSAEDVLT LLRQAHEQEV
	FDADTLLRLE
51	KVLDFSDLEV RDAMITRSRM NVLKENDSIE RITAYVIDTA
	HSRFPVIGED
101	KDEVLGILHA KDLLKYMFNP EQFHLKSILR PAVFVPEGKS
	LTALLKEFRE
151	QRNHMAIVID EYGGTSGLVT FEDIIEQIVG DIEDEFDEDE
	SADNIHAVSA
201	ERWRIHAATE IEDINAFFGT EYSSEEADTI GGXGHSGIGT
	PARARRKSXY
251	RRXAXHXRXR XQPPPAYADG DPREVSSAVS VQFRMTVRAF
	SVSIRPIRXT
301	*

The originally-identified partial strain B sequence (ORF5) shows 54.7% identity over a 124aa overlap with ORF5a:

The complete strain B sequence (ORF5-1) and ORF5a show 92.7% identity in 300 aa overlap:

Further work identified the a partial DNA sequence in N. gonorrhoeae <SEQ ID 25> which encodes a protein having amino acid sequence <SEQ ID 26; ORF5ng>:

1	MDGAQPKTNF FERLIARLAR EPDSAEDVLN LLRQAHEQEV
	FDADTLTRLE
51	KVLDFAELEV RDAMITRSRM NVLKENDSIE RITAYVIDTA
	HSRFPVIGED
101	KDEVLGILHA KDLLKYMFNP EQFHLKSVLR PAVFVPEGKS
	LTALLKEFRE
151	QRNHMAIVID EYGGTSGLVT FEDIIEQIVG DIEDEFDEDE
	SADDIHSVSA
201	ERWRIHAATE IEDINAFFGT EYGSEEADTI RRLGHSGIGT
	PARARRKSPY
251	RRFAVHRRPR RQPPPAHADG DPREVSRACP HRRFCTV*

Further analysis revealed the complete gonococcal nucleotide sequence <SEQ ID 27> to be:

1	ATGGACGGCG CACAACCGAA AACAAATTTT TTTGAACGCC
	TGATTGCCCG
51	ACTCGCCCGC GAACCCGATT CCGCCGAAGA CGTATTAAAC
	CTGCTTCGGC
101	AGGCGCACGA ACAGGAAGTT TTTGATGCCG ACACACTGAC
	CCGGCTGGAA
151	AAAGTATTGG ACTTTGCCGA GCTGGAAGTG CGCGATGCGA
	TGATTACGCG
201	CAGCCGCATG AACGTATTGA AAGAAAACGA CAGCATCGAA
	CGCATCACCG
251	CCTACGTCAT CGATACCGCC CATTCGCGCT TCCCCGTCAT
	CGGCGAAGAC
301	AAAGACGAAG TTTTGGGCAT TTTGCACGCC AAAGACCTGC
	TCAAATATAT
351	GTTCAACCCC GAGCAGTTCC ACCTGAAATC CGTCTTGCGC
	CCTGCCGTTT
401	TCGTGCCCGA AGGCAAATCT TTGACCGCCC TTTTAAAAGA
	GTTCCGCGAA
451	CAGCGCAACC ATATGGCAAT CGTCATCGAC GAATACGGCG
	GCACGTCGGG
501	TTTGGTCACC TTTGAAGACA TCATCGAGCA AATCGTCGGT
	GACATCGAAG
551	ACGAGTTTGA CGAAGACGAA AGCGccgacg acatCCACTC
	cgTTTccgCC
601	GAACGCTGGC GCATCCacgc ggctaCCGAA ATCGAAGaca
	TCAACGCCTT
651	TTTCGGTACG GAatacggca gcgaagaagc cgacaccatc
	cggcggctTG
701	GTCATTCAGG AATTGGGACA CCTGCCCGTG CGCGGCGAAA
	AAGTCCTTAt
751	cggcgGTTTG Cagttcaccg tCGCCCGCGC CGACAACCGC
	CGCCTGCACA
801	CGCTGATGGC GACCCGCGTG AAGTAAGCAG AGCCTGCCcg
	AccgccgttT
851	CTGCacAGTT TAGGatgACG gtaCGGTCGT TTTCTGTTTC
	AATCCGCCCC
901	ATCCGCCAAA CATAA

This encodes a protein having amino acid sequence <SEQ ID 28; ORF5ng-1>:

1	MDGAQPKTNF FERLIARLAR EPDSAEDVLN LLRQAHEQEV
	FDADTLTRLE
51	KVLDFAELEV RDAMITRSRM NVLKENDSIE RITAYVIDTA
	HSRFPVIGED
101	KDEVLGILHA KDLLKYMFNP EQFHLKSVLR PAVFVPEGKS
	LTALLKEFRE
151	QRNHMAIVID EYGGTSGLVT FEDIIEQIVG DIEDEFDEDE
	SADDIHSVSA
201	ERWRIHAATE IEDINAFFGT EYGSEEADTI RRLGHSGIGT
	PARARRKSPY
251	RRFAVHRRPR RQPPPAHADG DPREVSRACP TAVSAQFRMT
	VRSFSVSIRP
301	IRQT*

The originally-identified partial strain B sequence (ORFS) shows 83.1% identity over a 135aa overlap with the partial gonococcal sequence (ORF5ng):

The complete strain B and gonococcal sequences (ORFS-1 & ORF5ng-1) show 92.4% identity in 304 aa overlap:

Computer analysis of these amino acid sequences indicates a putative leader sequence, and identified the following homologies:

Homology with Hemolysin Homolog TlyC (Accession U32716) of H. influenzae

ORF5 and TlyC proteins show 58% aa identity in 77 aa overlap (BLASTp).

ORF5	2	HMAIVIDEYGGTSGLVTFEDIIEQIVGEIEDEFDEDDSADNIHAVSSDTWRIHAATEIED	61
		HMAIV+DE+G  SGLVT EDI+EQIVG+IEDEFDE++ AD I  +S  T+ + A T+I+D
TlyC	166	HMAIVVDEFGAVSGLVTIEDILEQIVGDIEDEFDEEEIAD-IRQLSRHTYAVRALTDIDD	224
ORF5	62	INTFFGTEYSIEEADTI	78
		N  F T++  EE DTI
TlyC	225	FNAQFNTDFDDEEVDTI	241

ORF5ng-1 also shows significant homology with TlyC:

• • SCORES Init1: 301 Initn: 419 Opt: 668
  • Smith-Waterman score: 668; 45.9% identity in 242 aa overlap

Homology with a Hypothetical Secreted Protein from E. coli:

ORF5a shows homology to a hypothetical secreted protein from E. coli:

sp|P77392|YBEX_ECOLI HYPOTHETICAL 33.3 KD PROTEIN IN CUTE-ASNB INTERGENIC
REGION
>gi|1778577 (U82598) similar to H. influenzae [Escherichia coli]
>gi|1786879 (AE000170) f292; This 292 aa ORF is 23% identical (9 gaps)
to 272 residues of an approx. 440 aa protein YTFL_HAEIN SW: P44717
[Escherichia coli] Length = 292
Score = 212 bits (533), Expect = 3e−54
Identities = 112/230 (48%), Positives = 149/230 (64%), Gaps = 3/230 (1%)

Query:	2	DGAQPKTNFXXRLIARLAR-EPDSAEDVLTLLRQAHEQEVFDADTLLRLEKVLDFSDLEV	60
		D    K  F   L+++L   EP + +++L L+R + + ++ D DT   LE V+D +D  V
Sbjct:	10	DTISNKKGFFSLLLSQLFHGEPKNRDELLALIRDSGQNDLIDEDTRDMLEGVMDIADQRV	69
Query:	61	RDAMITRSRMNVLKENDSIERITAYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYM-FN	119
		RD MI RS+M  LK N +++     +I++AHSRFPVI EDKD + GIL AKDLL +M  +
Sbjct:	70	RDIMIPRSQMITLKRNQTLDECLDVIIESAHSRFPVISEDKDHIEGILMAKDLLPFMRSD	129
Query:	120	PEQFHLKSILRPAVFVPEGKSLTALLKEFREQRNHMAIVIDEYGGTSGLVTFEDIIEQIV	179
		E F +  +LR AV VPE K +  +LKEFR QR HMAIVIDE+GG SGLVT EDI+E IV
Sbjct:	130	AEAFSMDKVLRQAVVVPESKRVDRMLKEFRSQRYHMAIVIDEFGGVSGLVTIEDILELIV	189
Query:	180	GDIEDEFDEDESADNIHAVSAERWRIHAATEIEDINAFFGTEYSSEEADT	229
		G+IEDE+DE++  D    +S   W + A   IED N  FGT +S EE DT
Sbjct:	190	GEIEDEYDEEDDID-FRQLSRHTWTVRALASIEDFNEAFGTHFSDEEVDT	238

Based on this analysis, including the amino acid homology to the TlyC hemolysin-homologue from H. influenzae (hemolysins are secreted proteins), it was predicted that the proteins from N. meningitidis and N. gonorrhoeae are secreted and could thus be useful antigens for vaccines or diagnostics.

ORF5-1 (30.7 kDa) was cloned in the pGex vector and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 2A shows the results of affinity purification of the GST-fusion protein. Purified GST-fusion protein was used to immunise mice, whose sera were used for Western blot analysis (FIG. 1B). These experiments confirm that ORFS-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 5

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 29>:

1	ATGCGCGGCG GCAGGCCGGA TTCCGTTACC GTGCAGATTA
	TCGAAGGTTC
51	GCGTTTTTCG CATATGAGGA AAGTCATCGA CGCAACGCCC
	GACATCGGAC
101	ACGACACCAA AGGCTGGAGC AATGAAAAAC TGATGGCGGA
	AGTTGCGCCC
151	GATGCCTTCA GCGGCAATCC TGAAgGGCAG TTTTTCCCCG
	ACAGCTACGA
201	AATCGATGCG GGCGGCAGTG ATTTGCAGAT TTACCAAACC
	GCCTACAAgG
251	GCGATGCAAC GCCGCCTGAA TGAgGGCATG GGAAAGCAGG
	CAGGACGGGC
301	TGCCTTATAA AAACCCTTAT GAAATGCTGA TTATGGCGAr
	CCTGGTCGAA
351	AAGGAAACAG GGCATGAAGC CGAsCsCGAC CATGTcGCTT
	CCGTCTTCGT
401	CAACCGCCTG AAAATCGGTA TGCGCCTGCA AACCgAssCG
	TCCGTGATTT
451	ACGGCATGGG TGCGGCATAC AAGGGCAAAA TCCGTAAAGC
	CGACCTGCGC
501	CGCGACACGC CGTACAACAC CTACACGCGC GGCGGTCTGC
	CGCCAACCCC
551	GATTGCGCTG CCC..

This corresponds to the amino acid sequence <SEQ ID 30; ORF7>:

1	MRGGRPDSVT VQIIEGSRFS HMRKVIDATP DIGHDTKGWS
	NEKLMAEVAP
51	DAFSGNPEGQ FFPDSYEIDA GGSDLQIYQT AYKAMQRRLN
	EAWESRQDGL
101	PYKNPYEMLI MAXLVEKETG HEAXXDHVAS VFVNRLKIGM
	RLQTXXSVIY
151	GMGAAYKGKI RKADLRRDTP YNTYTRGGLP PTPIALP..

Further sequence analysis revealed the complete DNA sequence <SEQ ID 31>:

1	ATGTTGAGAA AATTGTTGAA ATGGTCTGCC GTTTTTTTGA
	CCGTGTCGGC
51	AGCCGTTTTC GCCGCGCTGC TTTTTGTTCC TAAGGATAAC
	GGCAGGGCAT
101	ACCGAATCAA AATTGCCAAA AACCAGGGTA TTTCGTCGGT
	CGGCAGGAAA
151	CTTGCCGAAG ACCGCATCGT GTTCAGCAGG CATGTTTTGA
	CGGCGGCGGC
201	CTACGTTTTG GGTGTGCACA ACAGGCTGCA TACGGGGACG
	TACAGATTGC
251	CTTCGGAAGT GTCTGCTTGG GATATCTTGC AGAAAATGCG
	CGGCGGCAGG
301	CCGGATTCCG TTACCGTGCA GATTATCGAA GGTTCGCGTT
	TTTCGCATAT
351	GAGGAAAGTC ATCGACGCAA CGCCCGACAT CGGACACGAC
	ACCAAAGGCT
401	GGAGCAATGA AAAACTGATG GCGGAAGTTG CGCCCGATGC
	CTTCAGCGGC
451	AATCCTGAAG GGCAGTTTTT CCCCGACAGC TACGAAATCG
	ATGCGGGCGG
501	CAGTGATTTG CAGATTTACC AAACCGCCTA CAAGGCGATG
	CAACGCCGCC
551	TGAATGAGGC ATGGGAAAGC AGGCAGGACG GGCTGCCTTA
	TAAAAACCCT
601	TATGAAATGC TGATTATGGC GAGCCTGGTC GAAAAGGAAA
	CAGGGCATGA
651	AGCCGACCGC GACCATGTCG CTTCCGTCTT CGTCAACCGC
	CTGAAAATCG
701	GTATGCGCCT GCAAACCGAC CCGTCCGTGA TTTACGGCAT
	GGGTGCGGCA
751	TACAAGGGCA AAATCCGTAA AGCCGACCTG CGCCGCGACA
	CGCCGTACAA
801	CACCTACACG CGCGGCGGTC TGCCGCCAAC CCCGATTGCG
	CTGCCCGGCA
851	AGGCGGCACT CGATGCCGCC GCCCATCCGT CCGGCGAAAA
	ATACCTGTAT
901	TTCGTGTCCA AAATGGACGG CACGGGCTTG AGCCAGTTCA
	GCCATGATTT
951	GACCGAACAC AATGCCGCCG TCCGCAAATA TATTTTGAAA
	AAATAA

This corresponds to the amino acid sequence <SEQ ID 32; ORF7-1>:

1	MLRKLLKWSA VFLTVSAAVF AALLFVPKDN GRAYRIKIAK
	NQGISSVGRK
51	LAEDRIVFSR HVLTAAAYVL GVHNRLHTGT YRLPSEVSAW
	DILQKMRGGR
101	PDSVTVQIIE GSRFSHMRKV IDATPDIGHD TKGWSNEKLM
	AEVAPDAFSG
151	NPEGQFFPDS YEIDAGGSDL QIYQTAYKAM QRRLNEAWES
	RQDGLPYKNP
201	YEMLIMASLV EKETGHEADR DHVASVFVNR LKIGMRLQTD
	PSVIYGMGAA
251	YKGKIRKADL RRDTPYNTYT RGGLPPTPIA LPGKAALDAA
	AHPSGEKYLY
301	FVSKMDGTGL SQFSHDLTEH NAAVRKYILK K*

Computer analysis of this amino acid sequence gave the following results:

Homology with Hypothetical Protein Encoded by yceg Gene (Accession P44270) of H. influenzae

ORF7 and yceg proteins show 44% aa identity in 192 aa overlap:

ORF7   1 MRGGRPDSVTVQIIEGSRFSHMRKVIDATPDIGHDTKGWSNEKLMA-----EVAPDAFSG  55
+  G+     V+ IEG  F   RK ++  P +    K  SNE++ A      ++  +
yceg 102 LNSGKEVQFNVKWIEGKTFKDWRKDLENAPHLVQTLKDKSNEEIFALLDLPDIGQNLELK 161
ORF7  56 NPEGQFFPDSYEIDAGGSDLQIYQTAYKAMQRRLNEAWESRQDGLPYKNPYEMLIMAXLV 115
N EG  +PD+Y      +DL++ + + + M++ LN+AW  R + LP   NPYEMLI+A +V
yceg 162 NVEGWLYPDTYNYTPKSTDLELLKRSAERMKKALNKAWNERDEDLPLANPYEMLILASIV 221
ORF7 116 EKETGHEAXXDHVASVFVNRLKIGMRLQTXXSVIYGMGAAYKGKIRKADLRRDTPYNTYT 175
EKETG       VASVF+NRLK  M+LQT  +VIYGMG  Y G IRK DL   TPYNTY
yceg 222 EKETGIANERAKVASVFINRLKAKMKLQTDPTVIYGMGENYNGNIRKKDLETKTPYNTYV 281
ORF7 176 RGGLPPTPIALP                                                 187
GLPPTPIA+P
yceg 282 IDGLPPTPIAMP                                                 293

The complete length YCEG protein has sequence:

1	MKKFLIAILL LILILAGVAS FSYYKMTEFV KTPVNVQADE
	LLTIERGTTS
51	SKLATLFEQE KLIADGKLLP YLLKLKPELN KIKAGTYSLE
	NVKTVQDLLD
101	LLNSGKEVQF NVKWIEGKTF KDWRKDLENA PHLVQTLKDK
	SNEEIFALLD
151	LPDIGQNLEL KNVEGWLYPD TYNYTPKSTD LELLKRSAER
	MKKALNKAWN
201	ERDEDLPLAN PYEMLILASI VEKETGIANE RAKVASVFIN
	RLKAKMKLQT
251	DPTVIYGMGE NYNGNIRKKD LETKTPYNTY VIDGLPPTPI
	AMPSESSLQA
301	VANPEKTDFY YFVADGSGGH KFTRNLNEHN KAVQEYLRWY
	RSQKNAK

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF7 shows 95.2% identity over a 187aa overlap with an ORF (ORF7a) from strain A of N. meningitidis:

The complete length ORF7a nucleotide sequence <SEQ ID 33> is:

1	ATGTTGAGAA AATTGTTGAA ATGGTCTGCC GTTTTTTTGA
	CCGTATCGGC
51	AGCCGTTTTC GCCGCGCTGC TTTTCGTCCC TAAAGACAAC
	GGCAGGGCAT
101	ACAGGATTAA AATTGCCAAA AACCAGGGTA TTTCGTCGGT
	CGGCAGGAAA
151	CTTGCCGAAG ACCGCATCGT GTTCAGCAGG CATGTTTTGA
	CGGCGGCGGC
201	CTACGTTTTG GGTGTGCACA ACAGGCTGCA TACGGGGACG
	TACAGACTGC
251	CTTCGGAAGT GTCTGCTTGG GATATCTTGC AGAAAATGCG
	CGGCGGCAGG
301	CCGGATTCCG TTACCGTGCA GATTATCGAA GGTTCGCGTT
	TTTCGCATAT
351	GAGGAAAGTC ATCGACGCAA CGCCCGACAT CGAACACGAC
	ACCAAAGGCT
401	GGAGCAATGA AAAACTGATG GCGGAAGTTG CCCCTGATGC
	CTTCAGCGGC
451	AATCCTGAAG GGCAGTTTTT CCCCGACAGC TACGAAATCG
	ATGCGGGCGG
501	CAGCGATTTA CGGATTTACC AAATCGCCTA CAAGGCGATG
	CAACGCCGAC
551	TGAATGAGGC ATGGGAAAGC AGGCAGGACG GGCTGCCTTA
	TAAAAACCCT
601	TATGAAATGC TGATTATGGC GAGCCTGATC GAAAAGGAAA
	CAGGGCATGA
651	AGCCGACCGC GACCATGTCG CTTCCGTCTT CGTCAACCGC
	CTGAAAATCG
701	GTATGCGCCT GCAAACCGAC CCGTCCGTGA TTTACGGCAT
	GGGTGCGGCA
751	TACAAGGGCA AAATCCGTAA AGCCGACCTG CGCCGCGACA
	CGCCGTACAA
801	CACCTACACG CGCGGCGGTC TGCCGCCAAC CCCGATCGCG
	CTGCCCGGCA
851	AGGCGGCACT CGATGCCGCC GCCCATCCGT CCGGTGAAAA
	ATACCTGTAT
901	TTCGTGTCCA AAATGGACGG TACGGGCTTG AGCCAGTTCA
	GCCATGATTT
951	GACCGAACAC AACGCCGCCG TTCGCAAATA TATTTTGAAA
	AAATAA

This is predicted to encode a protein having amino acid sequence <SEQ ID 34>:

1	MLRKLLKWSA VFLTVSAAVF AALLFVPKDN GRAYRIKIAK
	NQGISSVGRK
51	LAEDRIVFSR HVLTAAAYVL GVHNRLHTGT YRLPSEVSAW
	DILQKMRGGR
101	PDSVTVQIIE GSRFSHMRKV IDATPDIEHD TKGWSNEKLM
	AEVAPDAFSG
151	NPEGQFFPDS YEIDAGGSDL RIYQIAYKAM QRRLNEAWES
	RQDGLPYKNP
201	YEMLIMASLI EKETGHEADR DHVASVFVNR LKIGMRLQTD
	PSVIYGMGAA
251	YKGKIRKADL RRDTPYNTYT RGGLPPTPIA LPGKAALDAA
	AHPSGEKYLY
301	FVSKMDGTGL SQFSHDLTEH NAAVRKYILK K*

A leader peptide is underlined.

ORF7a and ORF7-1 show 98.8% identity in 331 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF7 shows 94.7% identity over a 187aa overlap with a predicted ORF (ORF7.ng) from N. gonorrhoeae:

An ORF7ng nucleotide sequence <SEQ ID 35> is predicted to encode a protein having amino acid sequence <SEQ ID 36>:

1	MRGGRPDSVT VQIIEGSRFS HMRKVIDATP DIGHDTKGWS
	NEKLMAEVAP
51	DAFSGNPEGQ FFPDSYEIDA GGSDLQIYQT AYKAMQRRLN
	EAWAGRQDGL
101	PYKNPYEMLI MASLIEKETG HEADRDHVAS VFVNRLKIGM
	RLQTDPSVIY
151	GMGAAYKGKI RKADLRRDTP YNTYTGGGLP PTRIALPGKA
	AMDAAAHPSG
201	EKYLYFVSKM DGTGLSQFSH DLTEHNAAVR KYILKK*

Further sequence analysis revealed a partial DNA sequence of ORF7ng <SEQ ID 37>:

1	..taccgaatca AGATTGCCAA AAATCAGGGT ATTTCGTCGG
	TCGGCAGGAA
51	ACTTGCcgaA GACCGCATCG TGTTCAGCAG GCATGTTTTG
	ACAGCGGCGG
101	CCTACGTTTT GGGTGTGCAC AACAGGCTGC ATACGGGGAC
	gTACAGATTG
151	CCTTCGGAAG TGTCTGCTTG GGATATCTTG CAGAAAATGC
	GCGGCGGCAG
201	GCCGGATTCC GTTACCGTGC AGATTATCGA AGGTTCGCGT
	TTTTCGCATA
251	TGAGGAAAGT CATCGACGCA ACGCCCGACA TCGGACACGA
	CACCAAAGGC
301	TGGAGCAATG AAAAACTGAT GGCGGAAGTT GCGCCCGATG
	CCTTCAGCGG
351	CAATCCTGAA GGGCAGTTTT TTCCCGACAG CTACGAAATC
	GATGCGGGCG
401	GCAGCGATTT GCAGATTTAC CAAACCGCCT ACAAGGCGAT
	GCAACGCCGC
451	CTGAACGAGG CATGGGCAGG CAGGCAGGAC GGGCTGCCTT
	ATAAAAACCC
501	TTATGAAATG CTGATTATGG CGAGCCTGAT CGAAAAGGAA
	ACGGGGCATG
551	AGGCCGACCG CGACCATGTC GCTTCCGTCT TCGTCAACCG
	CCTGAAAATC
601	GGTATGCGCC TGCAAACCGA CCCGTCCGTG ATTTACGGCA
	TGGGTGCGGC
651	ATACAAGGGC AAAATCCGTA AAGCCGACCT GCGCCGCGAC
	ACGCCGTACA
701	aCAccTAtac gggcgggggc ttgccgccaa cccggattgc
	gctgcccggC
751	Aaggcggcaa tggatgccgc cgcccacccg tccggcgaAa
	aatacctgTa
801	tttcgtgtcC AAAATGGACG GCACGGGCTT GAGCCAGTTC
	AGCCATGATT
851	TGACCGAACA CAACGCCGCc gTcCGCAAAT ATATTTTGAA
	AAAATAA

This corresponds to the amino acid sequence <SEQ ID 38; ORF7ng-1>:

1	..YRIKIAKNQG ISSVGRKLAE DRIVFSRHVL TAAAYVLGVH
	NRLHTGTYRL
51	PSEVSAWDIL QKMRGGRPDS VTVQIIEGSR FSHMRKVIDA
	TPDIGHDTKG
101	WSNEKLMAEV APDAFSGNPE GQFFPDSYEI DAGGSDLQIY
	QTAYKAMQRR
151	LNEAWAGRQD GLPYKNPYEM LIMASLIEKE TGHEADRDHV
	ASVFVNALKI
201	GMRLQTDPSV IYGMGAAYKG KIRKADLRRD TPYNTYTGGG
	LPPTRIALPG
251	KAAMDAAAHP SGEKYLYFVS KMDGTGLSQF SHDLTEHNAA
	VRKYILKK*

ORF7ng-1 and ORF7-1 show 98.0% identity in 298 aa overlap:

In addition, ORF7ng-1 shows significant homology with a hypothetical E. coli protein:

sp|P28306|YCEG_ECOLI HYPOTHETICAL 38.2 KD PROTEIN IN PABC-HOLB
INTERGENIC REGION gi|1787339 (AE000210) o340; 100% identical to fragment
YCEG_ECOLI SW: P28306 but has 97 additional C-terminal residues
[Escherichia coli] Length = 340
Score = 79 (36.2 bits), Expect = 5.0e−57, Sum P(2) = 5.0e−57
Identities = 20/87 (22%), Positives = 40/87 (45%)

Query:	10	GISSVGRKLAEDRIVFSRHVLTAAAYVLGVHNRLHTGTYRLPSEVSAWDILQKMRGGRPD	69
		G  ++G +L  D+I+    V      +    +    GTYR   +++  ++L+ +  G+
Sbjct:	49	GRLALGEQLYADKIINRPRVFQWLLRIEPDLSHFKAGTYRFTPQMTVREMLKLLESGKEA	108
Query:	70	SVTVQIIEGSRFSHMRKVIDATPDIGH	96
		++++EG R S   K +   P I H
Sbjct:	109	QFPLRLVEGMRLSDYLKQLREAPYIKH	135

Score = 438 (200.7 bits), Expect = 5.0e−57, Sum P(2) = 5.0e−57
Identities = 84/155 (54%), Positives = 111/155 (71%)

Query:	120	EGQFFPDSYEIDAGGSDLQIYQTAYKAMQRRLNEAWAGRQDGLPYKNPYEMLIMASLIEK	179
		EG F+PD++   A  +D+ + + A+K M + ++ AW GR DGLPYK+  +++ MAS+IEK
Sbjct:	158	EGWFWPDTWMYTANTTDVALLKRAHKKMVKAVDSAWEGRADGLPYKDKNQLVTMASIIEK	217
Query:	180	ETGHEADRDHVASVFVNRLKIGMRLQTDPSVIYGMGAAYKGKIRKADLRRDTPYNTYTGG	239
		ET   ++RD VASVF+NRL+IGMRLQTDP+VIYGMG  Y GK+ +ADL   T YNTYT
Sbjct:	218	ETAVASERDKVASVFINRLRIGMRLQTDPTVIYGMGERYNGKLSRADLETPTAYNTYTIT	277
Query:	240	GLPPTRIALPGKAAMDAAAHPSGEKYLYFVSKMDG	274
		GLPP  IA PG  ++ AAAHP+   YLYFV+   G
Sbjct:	278	GLPPGAIATPGADSLKAAAHPAKTPYLYFVADGKG	312

Based on this analysis, including the fact that the H. influenzae YCEG protein possesses a possible leader sequence, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 6

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 39>:

1	CGTTTCAAAA TGTTAACTGT GTTGACGGCA ACCTTGATTG
	CCGGACAGGT
51	ATCTGCCGCC GGAGGCGGTG CGGGGGATAT GAAACAGCCG
	AAGGAAGTCG
101	GAAAGGTTTT CAGAAAGCAG CAGCGTTACA GCGAGGAAGA
	AATCAAAAAC
151	GAACGCGCAC GGCTTGCGGC AGTGGGCGAG CGGGTTAATC
	AGATATTTAC
201	GTTGCTGGGA GGGGAAACCG CCTTGCAAAA GGGGCAGGCG
	GGAACGGCTC
251	TGGCAACCTA TATGCTGATG TTGGAACGCA CAAAATCCCC
	CGAAGTCGCC
301	GAACGCGCCT TGGAAATGGC CGTGTCGCTG AACGCGTTTG
	AACAGGCGGA
351	AATGATTTAT CAGAAATGGC GGCAGATTGA GCCTATACCG
	GGTAAGGCGC
401	AAAAACGGGC GGGGTGGCTG CGGAACGTGC TGAGGGAAAG
	AGGAAATCAG
451	CATCTGGACG GACGGGAAGA AGTGCTGGCT CAGGCGGACG
	AAGGACAG

This corresponds to the amino acid sequence <SEQ ID 40; ORF9>:

1	..RFKMLTVLTA TLIAGQVSAA GGGAGDMKQP KEVGKVFRKQ
	QRYSEEEIKN
51	ERARLAAVGE RVNQIFTLLG GETALQKGQA GTALATYMLM
	LERTKSPEVA
101	ERALEMAVSL NAFEQAEMIY QKWRQIEPIP GKAQKRAGWL
	RNVLRERGNQ
151	HLDGREEVLA QADEGQ

Further sequence analysis revealed the complete DNA sequence <SEQ ID 41>:

1	ATGTTACCTA ACCGTTTCAA AATGTTAACT GTGTTGACGG
	CAACCTTGAT
51	TGCCGGACAG GTATCTGCCG CCGGAGGCGG TGCGGGGGAT
	ATGAAACAGC
101	CGAAGGAAGT CGGAAAGGTT TTCAGAAAGC AGCAGCGTTA
	CAGCGAGGAA
151	GAAATCAAAA ACGAACGCGC ACGGCTTGCG GCAGTGGGCG
	AGCGGGTTAA
201	TCAGATATTT ACGTTGCTGG GAGGGGAAAC CGCCTTGCAA
	AAGGGGCAGG
251	CGGGAACGGC TCTGGCAACC TATATGCTGA TGTTGGAACG
	CACAAAATCC
301	CCCGAAGTCG CCGAACGCGC CTTGGAAATG GCCGTGTCGC
	TGAACGCGTT
351	TGAACAGGCG GAAATGATTT ATCAGAAATG GCGGCAGATT
	GAGCCTATAC
101	CGGGTAAGGC GCAAAAACGG GCGGGGTGGC TGCGGAACGT
	GCTGAGGGAA
451	AGAGGAAATC AGCATCTGGA CGGACTGGAA GAAGTGCTGG
	CTCAGGCGGA
501	CGAAGGACAG AACCGCAGGG TGTTTTTATT GTTGGCACAA
	GCCGCCGTGC
551	AACAGGACGG GTTGGCGCAA AAAGCATCGA AAGCGGTTCG
	CCGCGCGGCG
601	TTGAAATATG AACATCTGCC CGAAGCGGCG GTTGCCGATG
	TGGTGTTCAG
651	CGTACAGGGA CGCGAAAAGG AAAAGGCAAT CGGAGCTTTG
	CAGCGTTTGG
701	CGAAGCTCGA TACGGAAATA TTGCCCCCCA CTTTAATGAC
	GTTGCGTCTG
751	ACTGCACGCA AATATCCCGA AATACTCGAC GGCTTTTTCG
	AGCAGACAGA
801	CACCCAAAAC CTTTCGGCCG TCTGGCAGGA AATGGAAATT
	ATGAATCTGG
851	TTTCCCTGCA CAGGCTGGAT GATGCCTATG CGCGTTTGAA
	CGTGCTGTTG
901	GAACGCAATC CGAATGCAGA CCTGTATATT CAGGCAGCGA
	TATTGGCGGC
951	AAACCGAAAA GAAGGTGCTT CCGTTATCGA CGGCTACGCC
	GAAAAGGCAT
1001	ACGGCAGGGG GACGGAGGAA CAGCGGAGCA GGGCGGCGCT
	AACGGCGGCG
1051	ATGATGTATG CCGACCGCAG GGATTACGCC AAAGTCAGGC
	AGTGGCTGAA
1101	AAAAGTATCC GCGCCGGAAT ACCTGTTCGA CAAAGGTGTG
	CTGGCGGCTG
1151	CGGCGGCTGT CGAGTTGGAC GGCGGCAGGG CGGCTTTGCG
	GCAGATCGGC
1201	AGGGTGCGGA AACTTCCCGA ACAGCAGGGG CGGTATTTTA
	CGGCAGACAA
1251	TTTGTCCAAA ATACAGATGC TCGCCCTGTC GAAGCTGCCC
	GATAAACGGG
1301	AGGCTTTGAG GGGGTTGGAC AAGATTATCG AAAAACCGCC
	TGCCGGCAGT
1351	AATACAGAGT TACAGGCAGA GGCATTGGTA CAGCGGTCAG
	TTGTTTACGA
1401	TCGGCTTGGC AAGCGGAAAA AAATGATTTC AGATCTTGAA
	AGGGCGTTCA
1451	GGCTTGCACC CGATAACGCT CAGATTATGA ATAATCTGGG
	CTACAGCCTG
1501	CTGACCGATT CCAAACGTTT GGACGAAGGT TTCGCCCTGC
	TTCAGACGGC
1551	ATACCAAATC AACCCGGACG ATACCGCTGT CAACGACAGC
	ATAGGCTGGG
1601	CGTATTACCT GAAAGGCGAC GCGGAAAGCG CGCTGCCGTA
	TCTGCGGTAT
1651	TCGTTTGAAA ACGACCCCGA GCCCGAAGTT GCCGCCCATT
	TGGGCGAAGT
1701	GTTGTGGGCA TTGGGCGAAC GCGATCAGGC GGTTGACGTA
	TGGACGCAGG
1751	CGGCACACCT TACGGGAGAC AAGAAAATAT GGCGGGAAAC
	GCTCAAACGT
1801	CACGGCATCG CATTGCCCCA ACCTTCCCGA AAACCTCGGA
	AATAA

This corresponds to the amino acid sequence <SEQ ID 42; ORF9-1>:

1	MLPNRFKMLT VLTATLIAGQ VSAAGGGAGD MKQPKEVGKV
	FRKQQRYSEE
51	EIKNERARLA AVGERVNQIF TLLGGETALQ KGQAGTALAT
	YMLMLERTKS
101	PEVAERALEM AVSLNAFEQA EMIYQKWRQI EPIPGKAQKR
	AGWLRNVLRE
151	RGNQHLDGLE EVLAQADEGQ NRRVFLLLAQ AAVQQDGLAQ
	KASKAVRRAA
201	LKYEHLPEAA VADVVFSVQG REKEKAIGAL QRLAKLDTEI
	LPPTLMTLRL
251	TARKYPEILD GFFEQTDTQN LSAVWQEMEI MNLVSLHRLD
	DAYARLNVLL
301	ERNPNADLYI QAAILAANRK EGASVIDGYA EKAYGRGTEE
	QRSRAALTAA
351	MMYADRRDYA KVRQWLKKVS APEYLFDKGV LAAAAAVELD
	GGRAALRQIG
401	RVRKLPEQQG RYFTADNLSK IQMLALSKLP DKREALRGLD
	KIIEKPPAGS
451	NTELQAEALV QRSVVYDRLG KRKKMISDLE RAFRLAPDNA
	QIMNNLGYSL
501	LTDSKRLDEG FALLQTAYQI NPDDTAVNDS IGWAYYLKGD
	AESALPYLRY
551	SFENDPEPEV AAHLGEVLWA LGERDQAVDV WTQAAHLTGD
	KKIWRETLKR
601	HGIALPQPSR KPRK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF9 shows 89.8% identity over a 166aa overlap with an ORF (ORF9a) from strain A of N. meningitidis:

The complete length ORF9a nucleotide sequence <SEQ ID 43> is:

1	ATGTTACCCG CCCGTTTCAC CATTTTATCT GTGCTCGCGG
	CAGCCCTGCT
51	TGCCGGGCAG GCGTATGCCG CCGGCGCGGC GGATGCGAAG
	CCGCCGAAGG
101	AAGTCGGAAA GGTTTTCAGA AAGCAGCAGC GTTACAGCGA
	GGAAGAAATC
151	AAAAACGAAC GCGCACGGCT TGCGGCAGTG GGCGAGCGGG
	TTAATCAGAT
201	ATTTACGTTG CTGGGANGGG AAACCGCCTT GCAAAAGGGG
	CAGGCGGGAA
251	CGGCTCTGGC AACCTATATG CTGATGTTGG AACGCACAAA
	ATCCCCCGAA
301	GTCGCCGAAC GCGCCTTGGA AATGGCCGTG TCNCTGAACG
	CGTTTGAACA
351	GGCGGAAATG ATTTATCAGA AATGGCGGCA GATTGAGCCT
	ATACCGGGTA
401	AGGCGCAAAA ACGGGCGGGG TGGCTGCGGA ACGTGCTGAG
	GGAAAGAGGA
451	AATCAGCATC TAGACGGACT GGAAGAANTG CTGGCTCAGG
	CGGACGAANG
501	ACAGAACCGC AGGGTGTTTT TATTGTTGGC ACAAGCCGCC
	GTGCAACAGG
551	ACGGGTTGGC GCAAAAAGCA TCGAAAGCGG TTCGCCGCGC
	GGCGTTGAGA
601	TATGAACATC TGCCCGAAGC GGCGGTTGCC GATGTGGTGT
	TCAGCGTACA
651	GGNACGCGAA AAGGAAAAGG CAATCGGAGC TTTGCAGCGT
	TTGGCGAAGC
701	TCGATACGGA AATATTGCCC CCCACTTTAA TGACGTTGCG
	TCTGACTGCA
751	CGCAAATATC CCGAAATACT CGACGGCTTT TTCGAGCAGA
	CAGACACCCA
801	AAACCTTTCG GCCGTCTGGC AGGAAATGGA AATTATGAAT
	CTGGTTTCCC
851	TGCACAGGCT GGATGATGCC TATGCGCGTT TGAACGTGCT
	GTTGGAACGC
901	AATCCGAATG CAGACCTGTA TATTCAGGCA GCGATATTGG
	CGGCAAACCG
951	AAAAGAANGT GCTTCCGTTA TCGACGGCTA CGCCGAAAAG
	GCATACGGCA
1001	GGGGGACGGG GGAACAGCGG GGCAGGGCGG CAATGACGGC
	GGCGATGATA
1051	TATGCCGACC GAAGGGATTA CACCAAAGTC AGGCAGTGGT
	TGAAAAAAGT
1101	GTCCGCGCCG GAATACCTGT TCGACAAAGG TGTGCTGGCG
	GCTGCGGCGG
1151	CTGTCGAGTT GGACNGCGGC AGGGCGGCTT TGCGGCAGAT
	CGGCAGGGTG
1201	CGGAAACTTC CCGAACAGCA GGGGCGGTAT TTTACGGCAG
	ACAATTTGTC
1251	CAAAATACAG ATGTTCGCCC TGTCGAAGCT GCCCGACAAA
	CGGGAGGCTT
1301	TGAGGGGGTT GGACAAGATT ATCGAAAAAC CGCCTGCCGG
	CAGTAATACA
1351	GAGTTACAGG CAGAGGCATT GGTACAGCGG TCAGTTGTTT
	ACGATCGGCT
1401	TGGCAAGCGG AAAAAAATGA TTTCAGATCT TGAAAGGGCG
	TTCAGGCTTG
1451	CACCCGATAA CGCTCAGATT ATGAATAATC TGGGCTACAG
	CCTGCTTTCC
1501	GATTCCAAAC GTTTGGACGA AGGCTTCGCC CTGCTTCAGA
	CGGCATACCA
1551	AATCAACCCG GACGATACCG CTGTCAACGA CAGCATAGGC
	TGGGCGTATT
1601	ACCTGAAANG CGACGCGGAA AGCGCGCTGC CGTATCTGCG
	GTATTCGTTT
1651	GAAAACGACC CCGAGCCCGA AGTTGCCGCC CATTTGGGCG
	AAGTGTTGTG
1701	GGCATTGGGC GAACGCGATC AGGCGGTTGA CGTATGGACG
	CAGGCGGCAC
1751	ACCTTACGGG AGACAAGAAA ATATGGCGGG AAACGCTCAA
	ACGTCACGGC
1801	ATCGCATTGC CCCAACCTTC CCGAAAACCT CGGAAATAA

This encodes a protein having amino acid sequence <SEQ ID 44>:

1	MLPARFTILS VLAAALLAGQ AYAAGAADAK PPKEVGKVFR
	KQQRYSEEEI
51	KNERARLAAV GERVNQIFTL LGXETALQKG QAGTALATYM
	LMLERTKSPE
101	VAERALEMAV SLNAFEQAEM IYQKWRQIEP IPGKAQKRAG
	WLRNVLRERG
151	NQHLDGLEEX LAQADEXQNR RVFLLLAQAA VQQDGLAQKA
	SKAVRRAALR
201	YEHLPEAAVA DVVFSVQXRE KEKAIGALQR LAKLDTEILP
	PTLMTLRLTA
251	RKYPEILDGF FEQTDTQNLS AVWQEMEIMN LVSLHRLDDA
	YARLNVLLER
301	NPNADLYIQA AILAANRKEX ASVIDGYAEK AYGRGTGEQR
	GRAAMTAAMI
351	YADRRDYTKV RQWLKKVSAP EYLFDKGVLA AAAAVELDXG
	RAALRQIGRV
401	RKLPEQQGRY FTADNLSKIQ MFALSKLPDK REALRGLDKI
	IEKPPAGSNT
451	ELQAEALVQR SVVYDRLGKR KKMISDLERA FRLAPDNAQI
	MNNLGYSLLS
501	DSKRLDEGFA LLQTAYQINP DDTAVNDSIG WAYYLKXDAE
	SALPYLRYSF
551	ENDPEPEVAA HLGEVLWALG ERDQAVDVWT QAAHLTGDKK
	IWRETLKRHG
601	IALPQPSRKP RK*

ORF9a and ORF9-1 show 95.3% identity in 614 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF9 shows 82.8% identity over a 163aa overlap with a predicted ORF (ORF9.ng) from N. gonorrhoeae:

The ORF9ng nucleotide sequence <SEQ ID 45> was predicted to encode a protein having including acid sequence <SEQ ID 46>:

1	MIMLPARFTI LSVLAAALLA GQAYAAGAAD VELPKEVGKV
	LRKHRRYSEE
51	EIKNERARLA AVGERVNRVF TLLGGETALQ KGQAGTALAT
	YMLMLERTKS
101	PEVAERALEM AVSLNAFEQA EMIYQKWRQI EPIPGEAQKP
	AGWLRNVLKE
151	GGNPHLDRLE EVPAQSDYVH QPMIFLLLVQ AAVQHGGVAQ
	KPSKAVRPAA
201	YNYEVLPETA GADAVFCVQG PQYEKAIQSF PPCGRNPQTE
	NIAPPFNELF
251	RPTARPISPK LLQRFFRTEP NLAKPFRPPG PEMETYQTGF
	PRPLTRNNPT

Amino acids 1-28 are a putative leader sequence, and 173-189 are predicted to be a transmembrane domain.

Further sequence analysis revealed the complete length ORF9ng DNA sequence <SEQ ID 47>:

1	ATGTTACCCG CCCGTTTCAC TATTTTATCT GTCCTCGCAG
	CAGCCCTGCT
51	TGCCGGACAG GCGTATGCTG CCGGCGCGGC GGATGTGGAG
	CTGCCGAAGG
101	AAGTCGGAAA GGTTTTAAGG AAACATCGGC GTTACAGCGA
	GGAAGAAATC
151	AAAAACGAAC GCGCACGGCT TGCGGCAGTG GGCGAACGGG
	TCAACAGGGT
201	GTTTACGCTG TTGGGCGGTG AAACGGCTTT GCAGAAAGGG
	CAGGCGGGAA
251	CGGCTCTGGC AACCTATATG CTGATGTTGG AACGCACAAA
	ATCCCCCGAA
301	GTCGCCGAAC GCGCCTTGGA AATGGCCGTG TCGCTGAACG
	CGTTTGAACA
351	GGCGGAAATG ATTTATCAGA AATGgcggca gatcgagcct
	ataCcgggtg
401	aggcgcaaaa accgGcgggG tggctgcgga acgtattgaa
	ggaagggGGa
451	aaTCAGCATC TGGAcgggtt gaaagaggTG CtggcgcaAT
	cggacgatGT
501	GCAAAAAcgc aggaTATTTT TGCTGCTGGT GCAAGCCGCC
	GTGCagcagg
551	gTGGGGTGGC TCAAAAAGCA TCGAAAGCGG TTCGCcgtgc
	GGcgttgaAG
601	TATGAACATC TGCCcgaagc ggcggTTGCC GATGcggTGT
	TCGGCGTACA
651	GGGACGCGAA AAGGAAAagg caaTCGAAGC TTTGCAGCGT
	TTGGCGAAGC
701	TCGATACGGA AATATTGCCC CCCACTTTAA TGACGTTGCG
	TCTGACTGCA
751	CGCAAATATC CCGAAATACT CGACGGCTTT TTCGAGCAGA
	CAGACACCCA
801	AAACCTTTCG GCCGTCTGGC AGGAAATGGA AATTATGAAT
	CTGGTTTCCC
851	TGCGTAAGCC GGATGATGCC TATGCGCGTT TGAACGTGCT
	GTTGGAACAC
901	AACCCGAATG CAAACCTGTA TATTCAGGCG GCGATATTGG
	CGGCAAACCG
951	AAAAGAAGGT GCGTCCGTTA TCGACGGCTA CGCCGAAAAG
	GCATACGGCA
1001	GGGGGACGGG GGAACAGCGG GGCagggcgg cAATgacggc
	GGCGATGATA
1051	TATGCCGACC GCAGGGATTA CGCCAAAGTC AGGCAGTGGT
	TGAAAAAAGT
1101	GTCCGCGCCG GAATACCTGT TCGACAAAGG CGTGCTGGCG
	GCTGCGGCGG
1151	CTGCCGAATT GGACGGAGGC CGGGCGGCTT TGCGGCAGAT
	CGGCAGGGTG
1201	CGGAAACTTC CCGAACAGCA GGGGCGGTAT TTTACGGCAG
	ACAATTTGTC
1251	CAAAATACAG ATGCTCGCCC TGTCGAAGCT GCCCGACAAA
	CGGGAAGCCC
1301	TGATCGGGCT GAACAACATC ATCGCCAAAC TTTCGGCGGC
	GGGAAGCACG
1351	GAACCTTTGG CGGAAGCATT GGCACAGCGT TCCATTATTT
	ACGaacAGTT
1401	cggCAAACGG GGAAAAATGA TTGCCGACCT tgaAACcgcg
	CTCAAACTTA
1451	CGCCCGATAA TGCACAAATT ATGAATAATC TGGGCTACAG
	CCTGCTTTCC
1501	GATTCCAAAC GTTTGGACGA GGGTTTCGCC CTGCTTCAGA
	CGGCATACCA
1551	AATCAACCCG GACGATACCG CCGTTAACGA CAGCATAGGC
	TGGGCGTATT
1601	ACCTGAAAGG CGACgcggaA AGCGCGCTGC CGTATCTGcg
	gtattcgttt
1651	gAAAACGACC CCGAGCCCGA AGTTGCCGCC CATTTGGGCG
	AAGTGTTGTG
1701	GGCATTGGGC GAACGCGATC AGGCGGTTGA CGTATGGACG
	CAGGCGGCAC
1751	ACCTTAGGGG AGACAAGAAA ATATGGCGGG AGACGCTCAA
	ACGCTACGGA
1801	ATCGCCTTGC CCGAGCCTTC CCGAAAACCC CGGAAATAA

This encodes a protein having amino acid sequence <SEQ ID 48>:

1	MLPARFTILS VLAAALLAGQ AYAAGAADVE LPKEVGKVLR
	KHRRYSEEEI
51	KNERARLAAV GERVNRVFTL LGGETALQKG QAGTALATYM
	LMLERTKSPE
101	VAERALEMAV SLNAFEQAEM IYQKWRQIEP IPGEAQKPAG
	WLRNVLKEGG
151	NQHLDGLKEV LAQSDDVQKR RIFLLLVQAA VQQGGVAQKA
	SKAVRRAALK
201	YEHLPEAAVA DAVFGVQGRE KEKAIEALQR LAKLDTEILP
	PTLMTLRLTA
251	RKYPEILDGF FEQTDTQNLS AVWQEMEIMN LVSLRKPDDA
	YARLNVLLEH
301	NPNANLYIQA AILAANRKEG ASVIDGYAEK AYGRGTGEQR
	GRAAMTAAMI
351	YADRRDYAKV RQWLKKVSAP EYLFDKGVLA AAAAAELDGG
	RAALRQIGRV
401	RKLPEQQGRY FTADNLSKIQ MLALSKLPDK REALIGLNNI
	IAKLSAAGST
451	EPLAEALAQR SIIYEQFGKR GKMIADLETA LKLTPDNAQI
	MNNLGYSLLS
501	DSKRLDEGFA LLQTAYQINP DDTAVNDSIG WAYYLKGDAE
	SALPYLRYSF
551	ENDPEPEVAA HLGEVLWALG ERDQAVDVWT QAAHLRGDKK
	IWRETLKRYG
601	IALPEPSRKP RK*

ORF9ng and ORF9-1 show 88.1% identity in 614 aa overlap:

In addition, ORF9ng shows significant homology with a hypothetical protein from P. aeruginosa:

sp|P42810|YHE3_PSEAE HYPOTHETICAL 64.8 KD PROTEIN IN HEMM-HEMA INTERGENIC
REGION (ORF3)
>gi|1072999|pir||S49376 hypothetical protein 3 - Pseudomonas aeruginosa
>gi|557259 (X82071) orf3 [Pseudomonas aeruginosa] Length = 576
Score = 128 bits (318), Expect = 1e−28
Identities = 138/587 (23%), Positives = 228/587 (38%), Gaps = 125/587 (21%)

Query:	67	VFTLLGGETALQKGQAGTALATYMLMLERTKSPEVAERALEMAVSLNAFEQAEMIYQKWR	126
		+++LL  E A Q+ +   AL+ Y++  ++T+ P V+ERA  +A  L A ++A      W
Sbjct:	53	LYSLLVAELAGQRNRFDIALSNYVVQAQKTRDPGVSERAFRIAEYLGADQEALDTSLLWA	112
Query:	127	QIEPIPGEAQKPAG--------------WLRNVLKEGGNQHLDGLKEVLAQSDDVQKRRI	172
		+  P   +AQ+ A               ++  VL   G+ H D L    A++D   +  +
Sbjct:	113	RSAPDNLDAQRAAAIQLARAGRYEESMVYMEKVLNGQGDTHFDFLALSAAETDPDTRAGL	172
Query:	173	FXXXXXXXXXXXXXXXKASKAVRRAALKYEHLPEAAVADAVFGVQGREKEKAIEALQRLA	232
		++      KY +  +     A+   Q    ++A+  L+  +
Sbjct:	173	L------------------QSFDHLLKKYPNNGQLLFGKALLLQQDGRPDEALTLLEDNS	214
Query:	233	KLDTEILPPTLMTLRLTARK-----YPEILDGFFEQTDTQNLSAVWQEMEIMNLVSLRKP	287
		E+ P  L +  L + K      P +  G  E  D + +   +  +    LV   +
Sbjct:	215	ASRHEVAPLLLRSRLLQSMKRSDEALPLLKAGIKEHPDDKRVRLAYARL----LVEQNRL	270
Query:	288	DDAYARLNVLLEHNPN---------------------ANLYIQAAI--------------	312
		DDA A    L++  P+                     A +Y++  +
Sbjct:	271	DDAKAEFAGLVQQFPDDDDDLRFSLALVCLEAQAWDEARIYLEELVERDSHVDAAHFNLG	330
Query:	313	-LAANRKEGASVIDGYAEKAYGRGTGEQRGRAAMTAAMIYADRRDYAKVRQWLKKVSAPE	371
		LA  +K+ A  +D YA+   G G      +   T  ++ A R D A  R    +   P+
Sbjct:	331	RLAEEQKDTARALDEYAQ--VGPGNDFLPAQLRQTDVLLKAGRVDEAAQRLDKARSEQPD	388
Query:	372	YLFDKXXXXXXXXXXXXXXXXXXRQIGRVRKLPEQQGRYFTADNLSKIQMLALSKLPDKR	431
		Y                                        A  L  I+  ALS    +
Sbjct:	389	Y----------------------------------------AIQLYLIEAEALSNNDQQE	408
Query:	432	EALIGLNNIIAKLSAAGSTEPLAEALAQRSIIYEQFGKRGKMIADLETALKLTPDNAQIM	491
		+A   +   + +       E L   L  RS++ E+     +M  DL   +   PDNA  +
Sbjct:	409	KAWQAIQEGLKQYP-----EDL-NLLYTRSMLAEKRNDLAQMEKDLRFVIAREPDNAMAL	462
Query:	492	NNLGYSLLSDSKRLDEGFALLQTAYQINPDDTAVNDSIGWAYYLKGDAESALPYLRYSFE	551
		N LGY+L   + R  E   L+  A+++NPDD A+ DS+GW  Y +G    A  YLR + +
Sbjct:	463	NALGYTLADRTTRYGEARELILKAHKLNPDDPAILDSMGWINYRQGKLADAERYLRQALQ	522
Query:	552	NDPEPEVAAHLGEVLWALGERDQAVDVWTQAAHLRGDKKIWRETLKR	598
		P+ EVAAHLGEVLWA G +  A  +W +    + D  + R T+KR
Sbjct:	523	RYPDHEVAAHLGEVLWAQGRQGDARAIWREYLDKQPDSDVLRRTIKR	569

gi|2983399 (AE000710) hypothetical protein [Aquifex aeolicus] Length = 545
Score = 81.5 bits (198), Expect = 1e−14
Identities = 61/198 (30%), Positives = 98/198 (48%), Gaps = 19/198 (9%)

Query:	408	GRYFTADNL-SKIQMLALSKLPDKREALIGLNNIIAKLSAAGSTEPLAEALAQ-------	459
		G Y  A  L  K ++LA    PDK+E L    +  +K         + + L +
Sbjct:	335	GNYEDAKRLIEKAKVLA----PDKKEILFLEADYYSKTKQYDKALEILKKLEKDYPNDSR	390
Query:	460	----RSIIYEQFGKRGKMIADLETALKLTPDNAQIMNNLGYSLLS--DSKRLDEGFALLQ	513
		+I+Y+  G        L  A++L P+N    N LGYSLL     +R++E   L++
Sbjct:	391	VYFMEAIVYDNLGDIKNAEKALRKAIELDPENPDYYNYLGYSLLLWYGKERVEEAEELIK	450
Query:	514	TAYQINPDDTAVNDSIGWAYYLKGDAESALPYLRYSF-ENDPEPEVAAHLGEVLWALGER	572
		A + +P++ A  DS+GW YYLKGD E A+ YL  +  E   +P V  H+G+VL  +G +
Sbjct:	451	KALEKDPENPAYIDSMGWVYYLKGDYERAMQYLLKALREAYDDPVVNEHVGDVLLKMGYK	510
Query:	573	DQAVDVWTQAAHLRGDKK	590
		++A + + +A  L  + K
Sbjct:	511	EEARNYYERALKLLEEGK	528

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 7

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 49>:

1	AACCTCTACG CCGGCCCGCA GACCACATCC GTCATCGCAA
	ACATCGCCGA
51	CAACCTGCAA CTGGCCAAAG ACTACGGCAA AGTACACTGG
	TTCGCCTCCC
101	CGCTCTTCTG GCTCCTGAAC CAACTGCACA ACATCATCGG
	CAACTGGGGC
151	TGGGCGATTA TCGTTTTAAC CATCATCGTC AAAGCCGTAC
	TGTATCCATT
201	GACCAACGCC TCTTACCGCT CTATGGCGAA AATGCGTGCC
	GCCGCACCCA
251	AACTGCAAGC CATCAAAGAG AAATACGGCG ACGACCGTAT
	GGCGCAACAA
301	CAGGCGATGA TGCAGCTTTA CACAGACGAG AAAATCAACC
	CGaCTGGGCG
351	GCTGCCTGCC TATGCTGTTG CAAATCCCCG TCTTCATCGG
	ATTGTATTGG
401	GCATTGTTCG CCTCCGTAGA ATTGCGCCAG GCACCTTGGC
	TGGGTTGGAT
451	TACCGACCTC AGCCGCGCCG ACCCCTACTA CATCCTGCCC
	ATCATTATGG
501	CGGCAACGAT GTTCGCCCAA ACTTATCTGA ACCCGCCGCC
	GAcCGACCCG
551	ATGCagGCGA AAATGATGAA AATCATGCCG TTGGTTTTCT
	CsGwCrTGTT
601	CTTCTTCTTC CCTGCCGGks TGGTATTGTA CTGGGTAGTC
	AACAACCTCC
651	TGACCATCGC CCAGCAATGG CACATCAACC GCAGCATCGA
	AAAACAACGC
701	GCCCAAGGCG AAGTCGTTTC CTAA

This corresponds to the amino acid sequence <SEQ ID 50; ORF11>:

1	..NLYAGPQTTS VIANIADNLQ LAKDYGKVHW FASPLFWLLN
	QLHNIIGNWG
51	WAIIVLTIIV KAVLYPLTNA SYRSMAKMRA AAPKLQAIKE
	KYGDDRMAQQ
101	QAMMQLYTDE KINPLGGCLP MLLQIPVFIG LYWALFASVE
	LRQAPWLGWI
151	TDLSRADPYY ILPIIMAATM FAQTYLNPPP TDPMQAKMMK
	IMPLVFSXXF
201	FFFPAGXVLY WVVNNLLTIA QQWHINRSIE KQRAQGEVVS *

Further sequence analysis revealed the complete DNA sequence <SEQ ID 51>:

1	ATGGATTTTA AAAGACTCAC GGCGTTTTTC GCCATCGCGC
	TGGTGATTAT
51	GATCGGCTGG GAAAAGATGT TCCCCACTCC GAAGCCAGTC
	CCCGCGCCCC
101	AACAGGCAGC ACAACAACAG GCCGTAACCG CTTCCGCCGA
	AGCCGCGCTC
151	GCGCCCGCAA CGCCGATTAC CGTAACGACC GACACGGTTC
	AAGCCGTCAT
201	TGATGAAAAA AGCGGCGACC TGCGCCGGCT GACCCTGCTC
	AAATACAAAG
251	CAACCGGCGA CGAAAATAAA CCGTTCATCC TGTTTGGCGA
	CGGCAAAGAA
301	TACACCTACG TCGCCCAATC CGAACTTTTG GACGCGCAGG
	GCAACAACAT
351	TCTAAAAGGC ATCGGCTTTA GCGCACCGAA AAAACAGTAC
	AGCTTGGAAG
401	GCGACAAAGT TGAAGTCCGC CTGAGCGCGC CTGAAACACG
	CGGTCTGAAA
451	ATCGACAAAG TTTATACTTT CACCAAAGGC AGCTATCTGG
	TCAACGTCCG
501	CTTCGACATC GCCAACGGCA GCGGTCAAAC CGCCAACCTG
	AGCGCGGACT
551	ACCGCATCGT CCGCGACCAC AGCGAACCCG AGGGTCAAGG
	TTACTTTACC
601	CACTCTTACG TCGGCCCTGT TGTTTATACC CCTGAAGGCA
	ACTTCCAAAA
651	AGTCAGCTTT TCCGACTTGG ACGACGATGC CAAATCCGGC
	AAATCCGAGG
701	CCGAATACAT CCGCAAAACC CCGACCGGCT GGCTCGGCAT
	GATTGAACAC
751	CACTTCATGT CCACCTGGAT TCTCCAACCT AAAGGCAGAC
	AAAGCGTTTG
801	CGCCGCAGGC GAGTGCAACA TCGACATCAA ACGCCGCAAC
	GACAAGCTGT
851	ACAGCACCAG CGTCAGCGTG CCTTTAGCCG CCATCCAAAA
	CGGCGCGAAA
901	GCCGAAGCCT CCATCAACCT CTACGCCGGC CCGCAGACCA
	CATCCGTCAT
951	CGCAAACATC GCCGACAACC TGCAACTGGC CAAAGACTAC
	GGCAAAGTAC
1001	ACTGGTTCGC CTCCCCGCTC TTCTGGCTCC TGAACCAACT
	GCACAACATC
1051	ATCGGCAACT GGGGCTGGGC GATTATCGTT TTAACCATCA
	TCGTCAAAGC
1101	CGTACTGTAT CCATTGACCA ACGCCTCTTA CCGCTCTATG
	GCGAAAATGC
1151	GTGCCGCCGC ACCCAAACTG CAAGCCATCA AAGAGAAATA
	CGGCGACGAC
1201	CGTATGGCGC AACAACAGGC GATGATGCAG CTTTACACAG
	ACGAGAAAAT
1251	CAACCCGCTG GGCGGCTGCC TGCCTATGCT GTTGCAAATC
	CCCGTCTTCA
1301	TCGGATTGTA TTGGGCATTG TTCGCCTCCG TAGAATTGCG
	CCAGGCACCT
1351	TGGCTGGGTT GGATTACCGA CCTCAGCCGC GCCGACCCCT
	ACTACATCCT
1401	GCCCATCATT ATGGCGGCAA CGATGTTCGC CCAAACTTAT
	CTGAACCCGC
1451	CGCCGACCGA CCCGATGCAG GCGAAAATGA TGAAAATCAT
	GCCGTTGGTT
1501	TTCTCCGTCA TGTTCTTCTT CTTCCCTGCC GGTCTGGTAT
	TGTACTGGGT
1551	AGTCAACAAC CTCCTGACCA TCGCCCAGCA ATGGCACATC
	AACCGCAGCA
1601	TCGAAAAACA ACGCGCCCAA GGCGAAGTCG TTTCCTAA

This corresponds to the amino acid sequence <SEQ ID 52; ORF11-1>:

1	MDFKRLTAFF AIALVIMIGW EKMFPTPKPV PAPQQAAQQQ
	AVTASAEAAL
51	APATPITVTT DTVQAVIDEK SGDLRRLTLL KYKATGDENK
	PFILFGDGKE
101	YTYVAQSELL DAQGNNILKG IGFSAPKKQY SLEGDKVEVR
	LSAPETRGLK
151	IDKVYTFTKG SYLVNVRFDI ANGSGQTANL SADYRIVRDH
	SEPEGQGYFT
201	HSYVGPVVYT PEGNFQKVSF SDLDDDAKSG KSEAEYIRKT
	PTGWLGMIEH
251	HFMSTWILQP KGRQSVCAAG ECNIDIKRRN DKLYSTSVSV
	PLAAIQNGAK
301	AEASINLYAG PQTTSVIANI ADNLQLAKDY GKVHWFASPL
	FWLLNQLHNI
351	IGNWGWAIIV LTIIVKAVLY PLTNASYRSM AKMRAAAPKL
	QAIKEKYGDD
401	RMAQQQAMMQ LYTDEKINPL GGCLPMLLQI PVFIGLYWAL
	FASVELRQAP
451	WLGWITDLSR ADPYYILPII MAATMFAQTY LNPPPTDPMQ
	AKMMKIMPLV
501	FSVMFFFFPA GLVLYWVVNN LLTIAQQWHI NRSIEKQRAQ
	GEVVS*

Computer analysis of this amino acid sequence gave the following results:

Homology with a 60 kDa Inner-Membrane Protein (Accession P25754) of Pseudomonas putida

ORF11 and the 60 kDa protein show 58% aa identity in 229 aa overlap (BLASTp).

ORF11	2	LYAGPQTTSVIANIADNLQLAKDYGKVHWFASPLFWLLNQLHNIIGNWGWAIIVLTIIVK	61
		LYAGP+  S +  ++  L+L  DYG + + A P+FWLL  +H+++GNWGW+IIVLT+++K
60K	324	LYAGPKIQSKLKELSPGLELTVDYGFLWFIAQPIFWLLQHIHSLLGNWGWSIIVLTMLIK	383
ORF11	62	AVLYPLTNASYRSMAKMRAAAPKLQAIKEKYGDDRXXXXXXXXXLYTDEKINPLGGCLPM	121
		+ +PL+ ASYRSMA+MRA APKL A+KE++GDDR         LY  EKINPLGGCLP+
60K	384	GLFFPLSAASYRSMARMRAVAPKLAALKERFGDDRQKMSQAMMELYKKEKINPLGGCLPI	443
ORF11	122	LLQIPVFIGLYWALFASVELRQAPWLGWITDLSRADPYYILPIIMAATMFAQTYLNPPPT	181
		L+Q+PVF+ LYW L  SVE+RQAPW+ WITDLS  DP++ILPIIM ATMF Q  LNP P
60K	444	LVQMPVFLALYWVLLESVEMRQAPWILWITDLSIKDPFFILPIIMGATMFIQQRLNPTPP	503
ORF11	182	DPMQAKMMKIMPLVXXXXXXXXPAGXVLYWVVNNLLTIAQQWHINRSIE	230
		DPMQAK+MK+MP++        PAG VLYWVVNN L+I+QQW+I R IE
60K	504	DPMQAKVMKMMPIIFTFFFLWFPAGLVLYWVVNNCLSISQQWYITRRIE	552

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF 11 shows 97.9% identity over a 240aa overlap with an ORF (ORF11a) from strain A of N. meningitidis:

The complete length ORF11a nucleotide sequence <SEQ ID 53> is:

	ANGGATTTTA AAAGACTCAC NGNGTTTTTC GCCATCGCAC
	TGGTGATTAT
51	GATCGGATNG NAAANGATGT TCCCCACTCC GAAGCCCGTC
	CCCGCGCCCC
101	AACAGACGGC ACAACAACAG GCCGTAANCG CTTCCGCCGA
	AGCCGCGCTC
151	GCGCCCGNAN CGCCGATTAC CGTAACGACC GACACGGTTC
	AAGCCGTCAT
201	TGATGAAAAA AGCGGCGACC TGCGCCGGCT GACCCTGCTC
	AAATACAAAG
251	CAACCGGCGA CNAAAATAAA CCGTTCATCC TGTTTGGCGA
	CGGCAAANAA
301	TACACCTACN TCGCCCANTC CGAACTTTTG GACGCGCAGG
	GCAACAACAT
351	TCTAAAAGGC ATCGGCTTTA GCGCACCGAA AAAACAGTAC
	AGCTTGGAAG
401	GCGACAAAGT TGAAGTCCGC CTGAGCGCAC CTGAAACACG
	CGGTCTGAAA
451	ATCGACAAAG TTTATACTTT CACCAAAGGC AGCTATCTGG
	TCAACGTCCG
501	CTTCGACATC GCCAACGGCA GCGGTCAAAC CGCCAACCTG
	AGCGCGGACT
551	ACCGCATCGT CCGCGACCAC AGCGAACCCG AGGGTCAAGG
	CTACTTTACC
601	CACTCTTACG TCGGCCCTGT TGTTTATACC CCTGAAGGCA
	ACTTCCAAAA
651	AGTCAGCTTC TCCGACTTGG ACGACGATGC CAANTCCGGN
	AAATCCGAGG
701	CCGAATACAT CCGCAAAACC CNGACCGGCT GGCTCGGCAT
	GATTGAACAC
751	CACTTCATGT CCACCTGGAT CCTCCAACCC AAAGGCGGAC
	AAAGCGTTTG
801	CGCCGCTGGC GACTGCNGTA TNGACATCAA ACGCCGCAAC
	GACAAGCTGT
851	ACAGCACCAG CGTCAGCGTG CCTTTAGCCG CTATCCAAAA
	CGGTGCGAAA
901	TCCNAAGCCT CCATCAACCT CTACGCCGGC CCACAGACCA
	CATCNGTTAT
951	CGCAAACATC GCCGACAACC TGCAACTGGN CAAAGACTAC
	GGCAAAGTAC
1001	ACTGGTTCGC CTCCCCCCTC TTTTGGCTTT TGAACCAACT
	GCACAACATC
1051	ATCGGCAACT GGGGCTGGGC GATTATCGTT TTAACCATCA
	TCGTCAAAGC
1101	CGTACTGTAT CCATTGACCA ACGCCTCTTA CCGTTCGATG
	GCGAAAATGC
1151	GTGCCGCCGC GCCCAAACTG CAAGCCATCA AAGAGAAATA
	CGGCGACGAC
1201	CGTATGGCGC AGCAACAAGC CATGATGCAG CTTTACACAG
	ACGAGAAAAT
1251	CAACCCGCTG GGCGGCTGCC TGCCTATGCT GTTGCAAATC
	CCCGTCTTCA
1301	TCGGATTGTA TTGGGCATTG TTCGCCTCCG TAGAATTGCG
	CCAGGCACCT
1351	TGGCTGGGTT GGATTACCGA CCTCAGCCGC GCCGACCCNT
	ACTACATCCT
1401	GCCCATCATT ATGGCGGCAA CGATGTTCGC CCAAACCTAT
	CTGAACCCGC
1451	CGCCGACCGA CCCGATGCAG GCGAAAATGA TGAAAATCAT
	GCCTTTGGTT
1501	NTNTCNNNNA NGTTCTTCNN CTTCCCTGCC GGTCTGGTAT
	TGTACTGGGT
1551	GATCAACAAC CTCCTGACCA TCGCCCAGCA ATGGCACATC
	AACCGCAGCA
1601	TCGAAAAACA ACGCGCCCAA GGCGAAGTCG TTTCCTAA

This encodes a protein having amino acid sequence <SEQ ID 54>:

1	XDFKRLTXFF AIALVIMIGX XXMFPTPKPV PAPQQTAQQQ
	AVXASAEAAL
51	APXXPITVTT DTVQAVIDEK SGDLRRLTLL KYKATGDXNK
	PFILFGDGKX
101	YTYXAXSELL DAQGNNILKG IGFSAPKKQY SLEGDKVEVR
	LSAPETRGLK
151	IDKVYTFTKG SYLVNVRFDI ANGSGQTANL SADYRIVRDH
	SEPEGQGYFT
201	HSYVGPVVYT PEGNFQKVSF SDLDDDAXSG KSEAEYIRKT
	XTGWLGMIEH
251	HFMSTWILQP KGGQSVCAAG DCXXDIKRRN DKLYSTSVSV
	PLAAIQNGAK
301	SXASINLYAG PQTTSVIANI ADNLQLXKDY GKVHWFASPL
	FWLLNQLHNI
351	IGNWGWAIIV LTIIVKAVLY PLTNASYRSM AKMRAAAPKL
	QAIKEKYGDD
401	RMAQQQAMMQ LYTDEKINPL GGCLPMLLQI PVFIGLYWAL
	FASVELRQAP
451	WLGWITDLSR ADPYYILPII MAATMFAQTY LNPPPTDPMQ
	AKMMKIMPLV
501	XSXXFFXFPA GLVLYWVINN LLTIAQQWHI NRSIEKQRAQ
	GEVVS*

ORF11a and ORF11-1 show 95.2% identity in 544 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF11 shows 96.3% identity over a 240aa overlap with a predicted ORF (ORF11.ng) from N. gonorrhoeae:

An ORF11ng nucleotide sequence <SEQ ID 55> was predicted to encode a protein having amino acid sequence <SEQ ID 56>:

1	MAVNLYAGPQ TTSVIANIAD NLQLAKDYGK VHWFASPLFW
	LLNQLHNIIG
51	NWGWAIVVLT IIVKAVLYPL TNASYRSMAK MRAAAPELQT
	IKEKYGDDRM
101	AQQQAMMQLF EDEEINPLGG CLPMLLQIPV FIGLYWALFA
	SVELRQAPWL
151	GWITDLSRAD PYYILPIIMA ATMFAQTYLN PPPTDPMQAK
	MMKIMPLVFS
201	VMFFFFPAGL VLYWVVNNLL TIAQQWHINR SIEKQRAQGE
	VVS*

Further sequence analysis revealed the complete gonococcal DNA sequence <SEQ ID 57> to be:

1	ATGGATTTTA AAAGACTCAC GGCGTTTTTC GCCATCGCGC
	TGGTGATTAT
51	GATCGGCTGG GAAAAAATGT TCCCCACCCC GAAACCCGTC
	CCCGCGCCCC
101	AACAGGCGGC ACAAAAACAG GCAGCAACCG CTTCCGCCGA
	AGCCGCGCTC
151	GCGCCCGCAA CGCCGATTAC CGTAACGACC GACACGGTTC
	AAGCCGTTAT
201	TGATGAAAAA AGTGGCGACC TGCGCCGGCT GACCCTGCTC
	AAATACAAAG
251	CAACCGGCGA CGAAAACAAA CCGTTCGTCC TGTTTGGCGA
	CGGCAAAGAA
301	TACACCTACG TCGCCCAATC CGAACTTTTG GACGCGCAGG
	GCAACAACAT
351	TCTGAAAGGC ATCGGCTTTA GCGCACCGAA AAAACAGTAC
	ACCCTCAACG
401	GCGACACAGT CGAAGTCCGC CTGAGCGCGC CCGAAACCAA
	CGGACTGAAA
451	ATCGACAAAG TCTATACCTT TACCAAAGAC AGCTATCTGG
	TCAACGTCCG
501	CTTCGACATC GCCAACGGCA GCGGTCAAAC CGCCAACCTG
	AGCGCGGACT
551	ACCGCATCGT CCGCGACCAC AGCGAACCCG AGGGTCAAGG
	CTACTTTACC
601	CACTCTTACG TCGGCCCTGT TGTTTATACC CCTGAAGGCA
	ACTTCCAAAA
651	AGTCAGCTTC TCCgacTTgg acgACGATGC gaaaTccggc
	aaATccgagg
701	ccgaatacaT CCGCAAAACC ccgaccggtt ggctcggcat
	gattgaacac
751	cacttcatgt ccacctggat cctccAAcct aaaggcggcc
	aaaacgtttg
801	cgcccaggga gactgccgta tcgacattaa aCgccgcaac
	gacaagctgt
851	acagcgcaag cgtcagcgtg cctttaaccg ctatcccaac
	ccgggggcca
901	aaaccgaaaa tggcggTCAA CCTGTATGCC GGTCCGCAAA
	CCACATCCGT
951	TATCGCAAAC ATCGCcgacA ACCTGCAACT GGCAAAAGAC
	TACGGTAAAG
1001	TACACTGGTT CGCATCGCCG CTCTTCTGGC TCCTGAACCA
	ACTGCACAAC
1051	ATTATCGGCA ACTGGGGCTG GGCAATCGTC GTTTTGACCA
	TCATCGTCAA
1101	AGCCGTACTG TATCCATTGA CCAACGcctc ctACCGTTCG
	ATGGCGAAAA
1151	TGCGTGccgc cgcacCcaaA CTGCAGACCA TCAAAGAAAA
	ATAcgGCGAC
1201	GACCGTATGG CGCAACAGCA AGCGATGATG CAGCTTTACA
	AAgacgAGAA
1251	AATCAACCCG CTGGGCGGCT GTctgcctat gctgttgCAA
	ATCCCCGTCT
1301	TCATCGGCTT GTACTGGGCA TTGTTCGCCT CCGTAGAATT
	GCGCCAGGCA
1351	CCTTGGCTGG GCTGGATTAC CGACCTCAGC CGCGCCGACC
	CCTACTACAT
1401	CCTGCCCATC ATTATGGCGG CAACGATGTT CGCCCAAACC
	TATCTGAACC
1451	CGCCGCCGAC CGACCCGATG CAGGCGAAAA TGATGAAAAT
	CATGCCGTTG
1501	GTTTTCTCCG TCATGTTCTT CTTCTTCCCT GCCGGTTTGG
	TTCTCTACTG
1551	GGTGGTCAAC AACCTCCTGA CCATCGCCCA GCAGTGGCAC
	ATCAACCGCA
1601	GCATCGAAAA ACAACGCGCC CAAGGCGAAG TCGTTTCCTA
	A

This encodes a protein having amino acid sequence <SEQ ID 58; ORF11ng-1>:

1	MDFKRLTAFF AIALVIMIGW EKMFPTPKPV PAPQQAAQKQ
	AATASAEAAL
51	APATPITVTT DTVQAVIDEK SGDLRRLTLL KYKATGDENK
	PFVLFGDGKE
101	YTYVAQSELL DAQGNNILKG IGFSAPKKQY TLNGDTVEVR
	LSAPETNGLK
151	IDKVYTFTKD SYLVNVRFDI ANGSGQTANL SADYRIVRDH
	SEPEGQGYFT
201	HSYVGPVVYT PEGNFQKVSF SDLDDDAKSG KSEAEYIRKT
	PTGWLGMIEH
251	HFMSTWILQP KGGQNVCAQG DCRIDIKRRN DKLYSASVSV
	PLTAIPTRGP
301	KPKMAVNLYA GPQTTSVIAN IADNLQLAKD YGKVHWFASP
	LFWLLNQLHN
351	IIGNWGWAIV VLTIIVKAVL YPLTNASYRS MAKMRAAAPK
	LQTIKEKYGD
401	DRMAQQQAMM QLYKDEKINP LGGCLPMLLQ IPVFIGLYWA
	LFASVELRQA
451	PWLGWITDLS RADPYYILPI IMAATMFAQT YLNPPPTDPM
	QAKMMKIMPL
501	VFSVMFFFFP AGLVLYWVVN NLLTIAQQWH INRSIEKQRA
	QGEVVS*

ORF11ng-1 and ORF11-1 shown 95.1% identity in 546 aa overlap:

In addition, ORF11ng-1 shows significant homology with an inner-membrane protein from the database (accession number p25754):

Based on this analysis, including the homology to an inner-membrane protein from P. putida and the predicted transmembrane domains (seen in both the meningococcal and gonoccal proteins), it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 8

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 59>:

1	..GCCGTCTTAA TCATCGAATT ATTGACGGGA ACGGTTTATC
	TTTTGGTTGT
51	NAGCGCGGCT TTGGCGGGTT CGGGCATTGC TTACGGGCTG
	ACCGGCAGTA
101	CGCCTGCCGC CGTCTTGACC GNCGCTCTGC TTTCCGCGCT
	GGGTATTTNG
151	TTCGTACACG CCAAAACCGC CGTTAGAAAA GTTGAAACGG
	ATTCATATCA
201	GGATTTGGAT GCCGGACAAT ATGTCGAAAT CCTCCGNCAC
	ACAGGCGGCA
251	ACCGTTACGA AGTT.TTTAT CGCGGTACG. ACTGGCAGGC
	TCAAAATACG
301	GGGCAAGAAG AGCTTGAACC AGGAACTCGC GCCCTCATTG
	TCCGCAAGGA
351	AGGCAACCTT CTTATTATCA CACACCCTTA A

This corresponds to the amino acid sequence <SEQ ID 60; ORF13>:

1	..AVLIIELLTG TVYLLVVSAA LAGSGIAYGL TGSTPAAVLT
	XALLSALGIX
51	FVHAKTAVRK VETDSYQDLD AGQYVEILRH TGGNRYEVXY
	RGTXWQAQNT
101	GQEELEPGTR ALIVRKEGNL LIITHP*

Further sequence analysis elaborated the DNA sequence slightly <SEQ ID 61>:

1	..GCCGTCTTAA TCATCGAATT ATTGACGGGA ACGGTTTATC
	TTTTGGTTGT
51	nAGCGCGGCT TTGGCGGGTT CGGGCATTGC TTACGGGCTG
	ACCGGCAGTA
101	CGCCTGCCGC CGTCTTGACC GnCGCTCTGC TTTCCGCGCT
	GGGTATTTnG
151	TTCGTACACG CCAAAACCGC CGTTAGAAAA GTTGAAACGG
	ATTCATATCA
201	GGATTTGGAT GCCGGACAAT ATGTCGAAAT CCTCCGACAC
	ACAGGCGGCA
251	ACCGTTACGA AGTTTTtTAT CGCGGTACGc ACTGGCAGGC
	TCAAAATACG
301	GGGCAAGAAG AGCTTGAACC AGGAACTCGC GCCCTCATTG
	TCCGCAAGGA
351	AGGCAACCTT CTTATTATCA CACACCCTTA A

This corresponds to the amino acid sequence <SEQ ID 62; ORF13-1>:

1	..AVLIIELLTG TVYLLVVSAA LAGSGIAYGL TGSTPAAVLT
	XALLSALGIX
51	FVHAKTAVRK VETDSYQDLD AGQYVEILRH TGGNRYEVFY
	RGTHWQAQNT
101	GQEELEPGTR ALIVRKEGNL LIITHP*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF13 shows 92.9% identity over a 126aa overlap with an ORF (ORF13a) from strain A of N. meningitidis:

The complete length ORF13a nucleotide sequence <SEQ ID 63> is:

1	ATGACTGTAT GGTTTGTTGC CGCTGTTGCC GTCTTAATCA
	TCGAATTATT
51	GACGGGAACG GTTTATCTTT TGGTTGTCAG CGCGGCTTTG
	GCGGGTTCGG
101	GCATTGCTTA CGGGCTGACC GGCAGCACGC CTGCCGCCGT
	CTTGACCGCC
151	GCTCTGCTTT CCGCGCTGGG TATTTGGTTC GTACACGCCA
	AAACCGCCGT
201	GGGAAAAGTT GAAACGGATT CATATCAGGA TTTGGATGCC
	GGGCAATATG
251	CCGAAATCCT CCGGCACGCA GGCGGCAACC GTTACGAAGT
	TTTTTATCGC
301	GGTACGCACT GGCAGGCTCA AAATACGGGG CAAGAAGAGC
	TTGAACCAGG
351	AACGCGCGCC CTAATCGTCC GCAAGGAAGG CAACCTTCTT
	ATCATCGCAA
401	AACCTTAA

This encodes a protein having amino acid sequence <SEQ ID 64>:

1	MTVWFVAAVA VLIIELLTGT VYLLVVSAAL AGSGIAYGLT
	GSTPAAVLTA
51	ALLSALGIWF VHAKTAVGKV ETDSYQDLDA GQYAEILRHA
	GGNRYEVFYR
101	GTHWQAQNTG QEELEPGTRA LIVRKEGNLL IIAKP*

ORF13a and ORF13-1 show 94.4% identity in 126 aa overlap

Homology with a Predicted ORF from N. gonorrhoeae

ORF13 shows 89.7% identity over a 126aa overlap with a predicted ORF (ORF13.ng) from N. gonorrhoeae:

The complete length ORF13ng nucleotide sequence <SEQ ID 65> is:

1	ATGACTGTAT GGTTTGTTGC CGCTGTTGCC GTCTTAATCA
	TCGAATTATT
51	GACGGGAACG GTTTATCTTT TGGTTGTCAG CGCGGCTTTG
	GCGGGTTCGG
101	GCATTGCCTA CGGGCTGACT GGCAGCACGC CTGCCGCCGT
	CTTGACCGCC
151	GCACTGCTTT CCGCGCTGGG CATTTGGTTC GTACATGCCA
	AAACCGCCGT
201	GGGAAAAGTT GAAACGGATT CATATCAGGA TTTGGATACC
	GGAAAATATG
251	CCGAAATCCT CCGATACACA GGCGGCAACC GTTACGAAGT
	TTTTTATCGC
301	GGTACGCACT GGCAGGCGCA AAATACGGGG CAGGAAGTGT
	TTGAACCGGG
351	AACGCGCGCC CTCATCGTCC GCAAAGAAGG TAACCTTCTT
	ATCATCGCAA
401	ACCCTTAA

This encodes a protein having amino acid sequence <SEQ ID 66>:

1	MTVWFVAAVA VLIIELLTGT VYLLVVSAAL AGSGIAYGLT
	GSTPAAVLTA
51	ALLSALGIWF VHAKTAVGKV ETDSYQDLDT GKYAEILRYT
	GGNRYEVFYR
101	GTHWQAQNTG QEVFEPGTRA LIVRKEGNLL IIANP*

ORF13ng shows 91.3% identity in 126 aa overlap with ORF13-1:

Based on this analysis, including the extensive leader sequence in this protein, it is predicted that ORF13 and ORF13ng are likely to be outer membrane proteins. It is thus predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 9

The following DNA sequence was identified in N. meningitidis <SEQ ID 67>:

1	ATGTwTGATT TCGGTTTrGG CGArCTGGTT TTTGTCGGCA
	TTATCGCCCT
51	GATwGtCCTC GGCCCCGAAC GCsTGCCCGA GGCCGCCCGC
	AyCGCCGGAC
101	GGcTCATCGG CAGGCTGCAA CGCTTTGTCG GcAGCGTCAA
	ACAGGAATTT
151	GACACTCAAA TCGAACTGGA AGAACTGAGG AAGGCAAAGC
	AGGAATTTGA
201	AGCTGCCGcC GCTCAGGTTC GAGACAGCCT CAAAGAAACC
	GGTACGGATA
251	TGGAAGGCAA TCTGCACGAC ATTTCCGACG GTCTGAAGCC
	TTGGGAAAAA
301	CTGCCCGAAC AGCGGACACC TGCCGATTTC GGTGTCGATG
	AAAACGGCAA
351	TCCGCT.TCC CGATGCGGCA AACACCCTAT CAGACGGCAT
	TTCCGACGTT
401	ATGCCGTC..

This corresponds to the amino acid sequence <SEQ ID 68; ORF2>:

1	MXDFGLGELV FVGIIALIVL GPERXPEAAR XAGRLIGRLQ
	RFVGSVKQEF
51	DTQIELEELR KAKQEFEAAA AQVRDSLKET GTDMEGNLHD
	ISDGLKPWEK
101	LPEQRTPADF GVDENGNPXS RCGKHPIRRH FRRYAV..

Further work revealed the complete nucleotide sequence <SEQ ID 69>:

1	ATGTTTGATT TCGGTTTGGG CGAGCTGGTT TTTGTCGGCA
	TTATCGCCCT
51	GATTGTCCTC GGCCCCGAAC GCCTGCCCGA GGCCGCCCGC
	ACCGCCGGAC
101	GGCTCATCGG CAGGCTGCAA CGCTTTGTCG GCAGCGTCAA
	ACAGGAATTT
151	GACACTCAAA TCGAACTGGA AGAACTGAGG AAGGCAAAGC
	AGGAATTTGA
201	AGCTGCCGCC GCTCAGGTTC GAGACAGCCT CAAAGAAACC
	GGTACGGATA
251	TGGAAGGCAA TCTGCACGAC ATTTCCGACG GTCTGAAGCC
	TTGGGAAAAA
301	CTGCCCGAAC AGCGGACACC TGCCGATTTC GGTGTCGATG
	AAAACGGCAA
351	TCCGCTTCCC GATGCGGCAA ACACCCTATC AGACGGCATT
	TCCGACGTTA
401	TGCCGTCCGA ACGTTCCTAC GCTTCCGCCG AAACCCTTGG
	GGACAGCGGG
451	CAAACCGGCA GTACAGCCGA ACCCGCGGAA ACCGACCAAG
	ACCGCGCATG
501	GCGGGAATAC CTGACTGCTT CTGCCGCCGC ACCCGTCGTA
	CAGACCGTCG
551	AAGTCAGCTA TATCGATACT GCTGTTGAAA CGCCTGTTCC
	GCACACCACT
601	TCCCTGCGCA AACAGGCAAT AAGCCGCAAA CGCGATTTTC
	GTCCGAAACA
651	CCGCGCCAAA CCTAAATTGC GCGTCCGTAA ATCATAA

This corresponds to the amino acid sequence <SEQ ID 70; ORF2-1>:

1	MFDFGLGELV FVGIIALIVL GPERLPEAAR TAGRLIGRLQ
	RFVGSVKQEF
51	DTQIELEELR KAKQEFEAAA AQVRDSLKET GTDMEGNLHD
	ISDGLKPWEK
101	LPEQRTPADF GVDENGNPLP DAANTLSDGI SDVMPSERSY
	ASAETLGDSG
151	QTGSTAEPAE TDQDRAWREY LTASAAAPVV QTVEVSYIDT
	AVETPVPHTT
201	SLRKQAISRK RDFRPKHRAK PKLRVRKS*

Further work identified the corresponding gene in strain A of N. meningitidis <SEQ ID 71>:

1	ATGTTTGATT TCGGTTTGGG CGAGCTGGTT TTTGTCGGCA
	TTATCGCCCT
51	GATTGTCCTC GGCCCCGAAC GCCTGCCCGA GGCCGCCCGC
	ACCGCCGGAC
101	GGCTCATCGG CAGGCTGCAA CGCTTTGTCG GCAGCGTCAA
	ACAGGAATTT
151	GACACGCAAA TCGAACTGGA AGAACTAAGG AAGGCAAAGC
	AGGAATTTGA
201	AGCTGCCGCT GCTCAGGTTC GAGACAGCCT CAAAGAAACC
	GGTACGGATA
251	TGGAGGGTAA TCTGCACGAC ATTTCCGACG GTCTGAAGCC
	TTGGGAAAAA
301	CTGCCCGAAC AGCGCACGCC TGCTGATTTC GGTGTCGATG
	AAAACGGCAA
351	TCCCTTTCCC GATGCGGCAA ACACCCTATT AGACGGCATT
	TCCGACGTTA
401	TGCCGTCCGA ACGTTCCTAC GCTTCCGCCG AAACCCTTGG
	GGACAGCGGG
451	CAAACCGGCA GTACAGCCGA ACCCGCGGAA ACCGACCAAG
	ACCGTGCATG
501	GCGGGAATAC CTGACTGCTT CTGCCGCCGC ACCCGTCGTA
	CAGACCGTCG
551	AAGTCAGCTA TATCGATACC GCTGTTGAAA CCCCTGTTCC
	GCATACCACT
601	TCGCTGCGTA AACAGGCAAT AAGCCGCAAA CGCGATTTGC
	GTCCTAAATC
651	CCGCGCCAAA CCTAAATTGC GCGTCCGTAA ATCATAA

This encodes a protein having amino acid sequence <SEQ ID 72; ORF2a>:

1	MFDFGLGELV FVGIIALIVL GPERLPEAAR TAGRLIGRLQ
	RFVGSVKQEF
51	DTQIELEELR KAKQEFEAAA AQVRDSLKET GTDMEGNLHD
	ISDGLKPWEK
101	LPEQRTPADF GVDENGNPFP DAANTLLDGI SDVMPSERSY
	ASAETLGDSG
151	QTGSTAEPAE TDQDRAWREY LTASAAAPVV QTVEVSYIDT
	AVETPVPHTT
201	SLRKQAISRK RDLRPKSRAK PKLRVRKS*

The originally-identified partial strain B sequence (ORF2) shows 97.5% identity over a 118aa overlap with ORF2a:

The complete strain B sequence (ORF2-1) and ORF2a show 98.2% identity in 228 aa overlap:

Further work identified a partial DNA sequence <SEQ ID 73> in N. gonorrhoeae encoding the following amino acid sequence <SEQ ID 74; ORF2ng>:

1	MFDFGLGELI FVGIIALIVL GPERLPEAAR TAGRLIGRLQ
	RFVGSVKQEL
51	DTQIELEELR KVKQAFEAAA AQVRDSLKET DTDMQNSLHD
	ISDGLKPWEK
101	LPEQRTPADF GVDEKGNSLS RYGKHRIRRH FRRYAV*

Further work identified the complete gonococcal gene sequence <SEQ ID 75>:

1	ATGTTTGATT TCGGTTTGGG CGAGCTGATT TTTGTCGGCA
	TTATCGCCCT
51	GATTGTCCTT GGTCCAGAAC GCCTGCCCGA AGCCGCCCGC
	ACTGCCGGAC
101	GGCTTATCGG CAGGCTGCAA CGCTTTGTAG GAAGCGTCAA
	ACAAGAACTT
151	GACACTCAAA TCGAACTGGA AGAGCTGAGG AAGGTCAAGC
	AGGCATTCGA
201	AGCTGCCGCC GCTCAGGTTC GAGACAGCCT CAAAGAAACC
	GATACGGATA
251	TGCAGAACAG TCTGCACGAC ATTTCCGACG GTCTGAAGCC
	TTGGGAAAAA
301	CTGCCCGAAC AGCGCACGCc tgccgatttc gGTGTCGATg
	AAAacggcaa
351	tccccttccc gATACGGCAA ACACCGTATC AGACGGCATT
	TCCGACGTTA
401	TGCCGTCTGA ACGTTCCGAT ACTtccgcCG AAACCCTTGG
	GGACGACAGG
451	CAAACCGGCA GTACAGCCGA ACCTGCGGAA ACCGACAAAG
	ACCGCGCATG
501	GCGGGAATAC CTGactgctt ctgccgccgc acctgtcgta
	Cagagggccg
551	tcgaagtcag ctaTATCGAT ACTGCTGTTG AAacgcctgT
	tccgcaCacc
601	acttccctgc gcaAACAGGC AATAAACCGC AAACGCGATT
	TttgtccgaA
651	ACACCGCGCc aAACCGAAat tgcgcgtcCG TAAATCATAA

This encodes a protein having the amino acid sequence <SEQ ID 76; ORF2ng-1>:

1	MFDFGLGELI FVGIIALIVL GPERLPEAAR TAGRLIGRLQ
	RFVGSVKQEL
51	DTQIELEELR KVKQAFEAAA AQVRDSLKET DTDMQNSLHD
	ISDGLKPWEK
101	LPEQRTPADF GVDENGNPLP DTANTVSDGI SDVMPSERSD
	TSAETLGDDR
151	QTGSTAEPAE TDKDRAWREY LTASAAAPVV QRAVEVSYID
	TAVETPVPHT
201	TSLRKQAINR KRDFCPKHRA KPKLRVRKS*

The originally-identified partial strain B sequence (ORF2) shows 87.5% identity over a 136aa overlap with ORF2ng:

The complete strain B and gonococcal sequences (ORF2-1 & ORF2ng-1) show 91.7% identity in 229 aa overlap:

Computer analysis of these amino acid sequences indicates a transmembrane region (underlined), and also revealed homology (59% identity) between the gonococcal sequence and the TatB protein of E. coli:

gnl|PID|e1292181 (AJ005830) TatB protein [Escherichia coli] Length = 171
Score = 56.6 bits (134), Expect = 1e−07
Identities = 30/88 (34%), Positives = 52/88 (59%), Gaps = 1/88 (1%)
Query:  1 MFDFGLGELIFVGIIALIVLGPERLPEAARTAGRLIGRLQRFVGSVKQELDTQIELEELR 60
MFD G  EL+ V II L+VLGP+RLP A +T    I  L+     +V+ EL +++L+E  +
Sbjct:  1 MFDIGFSELLLVFIIGLVVLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQELKLQEFQ 60
Query: 61 -KVKQAFEAAAAQVRDSLKETDTDMQNS 87
+K+  +A+   +   LK +  +++ +
Sbjct: 61 DSLKKVEKASLTNLTPELKASMDELRQA 88

Based on this analysis, it was predicted that ORF2, ORF2a and ORF2ng are likely to be membrane proteins and so the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF2-1 (16 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 3A shows the results of affinity purification of the GST-fusion protein, and FIG. 3B shows the results of expression of the His-fusion in E. coli. Purified GST-fusion protein was used to immunise mice, whose sera were used for Western blots (FIG. 3C), ELISA (positive result), and FACS analysis (FIG. 3D). These experiments confirm that ORF37-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 10

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 77>:

1	ATGCAAGCAC GGCTGCTGAT ACCTATTCTT TTTTCAGTTT
	TTATTTTATC
51	CGC.TGCGGG ACACTGACAG GTATTCCATC GCATGGCGgA
	GkTAAACgCT
101	TTgCGGTCGA ACAAGAACTT GTGGCCGCTT CTGCCAGAGC
	TGCCGTTAAA
151	GACATGGATT TACAGGCATT ACACGGACGA AAAGTTGCAT
	TGTACATTGC
201	CACTATGGGC GACCAAGGTT CAGGcAGTTT GACAGGGGGG
	TCGCTACTCC
251	ATTGATGCAC kGrTwCsTGG CGAATACATA AACAGCCCTG
	CCGTCCGTAC
301	CGATTACACC TATCCACGTT ACGAAACCAC CGCTGAAACA
	ACATCAGGCG
351	GTTTGACAGG TTTAACCACT TCTTTATCTA CACTTAATGC
	CCCTGCACTC
401	TCTCGCACCC AATCAGACGG TAGCGGAAGT AAAAGCAGTC
	TGGGCTTAAA
451	TATTGGCGGG ATGGGGGATT ATCGAAATGA AACCTTGACG
	ACTAACCCGC
501	GCGACACTGC CTTTCTTTCC CACTTGGTAC AGACCGTATT
	TTTCCTGCGC
551	GGCATAGACG TTGTTTCTCC TGCCAATGCC GATACAGATG
	TGTTTATTAA
601	CATCGACGTA TTCGGAACGA TACGCAACAG AACCGAAATG..

This corresponds to the amino acid sequence <SEQ ID 78; ORF15>:

1	MQARLLIPIL FSVFILSACG TLTGIPSHGG XKRFAVEQEL
	VAASARAAVK
51	DMDLQALHGR KVALYIATMG DQGSGSLTGG RYSIDAXXXG
	EYINSPAVRT
101	DYTYPRYETT AETTSGGLTG LTTSLSTLNA PALSRTQSDG
	SGSKSSLGLN
151	IGGMGDYRNE TLTTNPRDTA FLSHLVQTVF FLRGIDVVSP
	ANADTDVFIN
201	IDVFGTIRNR TEM..

Further work revealed the complete nucleotide sequence <SEQ ID 79>:

1	ATGCAAGCAC GGCTGCTGAT ACCTATTCTT TTTTCAGTTT
	TTATTTTATC
51	CGCCTGCGGG ACACTGACAG GTATTCCATC GCATGGCGGA
	GGTAAACGCT
101	TTGCGGTCGA ACAAGAACTT GTGGCCGCTT CTGCCAGAGC
	TGCCGTTAAA
151	GACATGGATT TACAGGCATT ACACGGACGA AAAGTTGCAT
	TGTACATTGC
201	CACTATGGGC GACCAAGGTT CAGGCAGTTT GACAGGGGGT
	CGCTACTCCA
251	TTGATGCACT GATTCGTGGC GAATACATAA ACAGCCCTGC
	CGTCCGTACC
301	GATTACACCT ATCCACGTTA CGAAACCACC GCTGAAACAA
	CATCAGGCGG
351	TTTGACAGGT TTAACCACTT CTTTATCTAC ACTTAATGCC
	CCTGCACTCT
401	CTCGCACCCA ATCAGACGGT AGCGGAAGTA AAAGCAGTCT
	GGGCTTAAAT
451	ATTGGCGGGA TGGGGGATTA TCGAAATGAA ACCTTGACGA
	CTAACCCGCG
501	CGACACTGCC TTTCTTTCCC ACTTGGTACA GACCGTATTT
	TTCCTGCGCG
551	GCATAGACGT TGTTTCTCCT GCCAATGCCG ATACAGATGT
	GTTTATTAAC
601	ATCGACGTAT TCGGAACGAT ACGCAACAGA ACCGAAATGC
	ACCTATACAA
651	TGCCGAAACA CTGAAAGCCC AAACAAAACT GGAATATTTC
	GCAGTAGACA
701	GAACCAATAA AAAATTGCTC ATCAAACCAA AAACCAATGC
	GTTTGAAGCT
751	GCCTATAAAG AAAATTACGC ATTGTGGATG GGGCCGTATA
	AAGTAAGCAA
801	AGGAATTAAA CCGACGGAAG GATTAATGGT CGATTTCTCC
	GATATCCGAC
851	CATACGGCAA TCATACGGGT AACTCCGCCC CATCCGTAGA
	GGCTGATAAC
901	AGTCATGAGG GGTATGGATA CAGCGATGAA GTAGTGCGAC
	AACATAGACA
951	AGGACAACCT TGA

This corresponds to the amino acid sequence <SEQ ID 80; ORF15-1>:

1	MQARLLIPIL FSVFILSACG TLTGIPSHGG GKRFAVEQEL
	VAASARAAVK
51	DMDLQALHGR KVALYIATMG DQGSGSLTGG RYSIDALIRG
	EYINSPAVRT
101	DYTYPRYETT AETTSGGLTG LTTSLSTLNA PALSRTQSDG
	SGSKSSLGLN
151	IGGMGDYRNE TLTTNPRDTA FLSHLVQTVF FLRGIDVVSP
	ANADTDVFIN
201	IDVFGTIRNR TEMHLYNAET LKAQTKLEYF AVDRTNKKLL
	IKPKTNAFEA
251	AYKENYALWM GPYKVSKGIK PTEGLMVDFS DIRPYGNHTG
	NSAPSVEADN
301	SHEGYGYSDE VVRQHRQGQP *

Further work identified the corresponding gene in strain A of N. meningitidis <SEQ ID 81>:

1	ATGCAAGCAC GGCTGCTGAT ACCTATTCTT TTTTCAGTTT
	TTATTTTATC
51	CGCCTGCGGG ACACTGACAG GTATTCCATC GCATGGCGGA
	GGTAAACGCT
101	TTGCGGTCGA ACAAGAACTT GTGGCCGCTT CTGCCAGAGC
	TGCCGTTAAA
151	GACATGGATT TACAGGCATT ACACGGACGA AAAGTTGCAT
	TGTACATTGC
201	AACTATGGGC GACCAAGGTT CAGGCAGTTT GACAGGGGGT
	CGCTACTCCA
251	TTGATGCACT GATTCGTGGC GAATACATAA ACAGCCCTGC
	CGTCCGTACC
301	GATTACACCT ATCCACGTTA CGAAACCACC GCTGAAACAA
	CATCAGGCGG
351	TTTGACAGGT TTAACCACTT CTTTATCTAC ACTTAATGCC
	CCTGCACTCT
401	CGCGCACCCA ATCAGACGGT AGCGGAAGTA AAAGCAGTCT
	GGGCTTAAAT
451	ATTGGCGGGA TGGGGGATTA TCGAAATGAA ACCTTGACGA
	CTAACCCGCG
501	CGACACTGCC TTTCTTTCCC ACTTGGTACA GACCGTATTT
	TTCCTGCGCG
551	GCATAGACGT TGTTTCTCCT GCCAATGCCG ATACGGATGT
	GTTTATTAAC
601	ATCGACGTAT TCGGAACGAT ACGCAACAGA ACCGAAATGC
	ACCTATACAA
651	TGCCGAAACA CTGAAAGCCC AAACAAAACT GGAATATTTC
	GCAGTAGACA
701	GAACCAATAA AAAATTGCTC ATCAAACCAA AAACCAATGC
	GTTTGAAGCT
751	GCCTATAAAG AAAATTACGC ATTGTGGATG GGACCGTATA
	AAGTAAGCAA
801	AGGAATTAAA CCGACAGAAG GATTAATGGT CGATTTCTCC
	GATATCCAAC
851	CATACGGCAA TCATATGGGT AACTCTGCCC CATCCGTAGA
	GGCTGATAAC
901	AGTCATGAGG GGTATGGATA CAGCGATGAA GCAGTGCGAC
	GACATAGACA
951	AGGGCAACCT TGA

This encodes a protein having amino acid sequence <SEQ ID 82; ORF15a>:

1	MQARLLIPIL FSVFILSACG TLTGIPSHGG GKRFAVEQEL
	VAASARAAVK
51	DMDLQALHGR KVALYIATMG DQGSGSLTGG RYSIDALIRG
	EYINSPAVRT
101	DYTYPRYETT AETTSGGLTG LTTSLSTLNA PALSRTQSDG
	SGSKSSLGLN
151	IGGMGDYRNE TLTTNPRDTA FLSHLVQTVF FLRGIDVVSP
	ANADTDVFIN
201	IDVFGTIRNR TEMHLYNAET LKAQTKLEYF AVDRTNKKLL
	IKPKTNAFEA
251	AYKENYALWM GPYKVSKGIK PTEGLMVDFS DIQPYGNHMG
	NSAPSVEADN
301	SHEGYGYSDE AVRRHRQGQP *

The originally-identified partial strain B sequence (ORF15) shows 98.1% identity over a 213aa overlap with ORF15a:

The complete strain B sequence (ORF15-1) and ORF15a show 98.8% identity in 320 aa overlap:

Further work identified the corresponding gene in N. gonorrhoeae <SEQ ID 83>:

1	ATGCGGGCAC GGCTGCTGAT ACCTATTCTT TTTTCAGTTT
	TTATTTTATC
51	CGCCTGCGGG ACACTGACAG GTATTCCATC GCATGGCGGA
	GGCAAACGCT
101	TCGCGGTCGA ACAAGAACTT GTGGCCGCTT CTGCCAGAGC
	TGCCGTTAAA
151	GACATGGATT TACAGGCATT ACACGGACGA AAAGTTGCAT
	TGTACATTGC
201	AACTATGGGC GACCAAGGTT CAGGCAGTTT GACAGGGGGT
	CGCTACTCCA
251	TTGATGCACT GATTCGCGGC GAATACATAA ACAGCCCTGC
	CGTCCGCACC
301	GATTACACCT ATCCGCGTTA CGAAACCACC GCTGAAACAA
	CATCAGGCGG
351	TTTGACGGGT TTAACCACTT CTTTATCTAC ACTTAATGCC
	CCTGCACTCT
401	CGCGCACCCA ATCAGACGGT AGCGGAAGTA GGAGCAGTCT
	GGGCTTAAAT
451	ATTGGCGGGA TGGGGGATTA TCGAAATGAA ACCTTGACGA
	CCAACCCGCG
501	CGACACTGCC TTTCTTTCCC ACTTGGTGCA GACCGTATTT
	TTCCTGCGCG
551	GCATAGACGT TGTTTCTCCT GCCAATGCCG ATACAGATGT
	GTTTATTAAC
601	ATCGACGTAT TCGGAACGAT ACGCAACAGA ACCGAAATGC
	ACCTATACAA
651	TGCCGAAACA CTGAAAGCCC AAACAAAACT GGAATATTTC
	GCAGTAGACA
701	GAACCAATAA AAAATTGCTC ATCAAACCCA AAACCAATGC
	GTTTGAAGCT
751	GCCTATAAAG AAAATTACGC ATTGTGGATG GGGCCGTATA
	AAGTAAGCAA
801	AGGAATCAAA CCGACGGAAG GATTGATGGT CGATTTCTCC
	GATATCCAAC
851	CATACGGCAA TCATACGGGT AACTCCGCCC CATCCGTAGA
	GGCTGATAAC
901	AGTCATGAGG GGTATGGATA CAGCGATGAA GCAGTGCGAC
	AACATAGACA
951	AGGGCAACCT TGA

This encodes a protein having amino acid sequence <SEQ ID 84; ORF15ng>:

1	MRARLLIPIL FSVFILSACG TLTGIPSHGG GKRFAVEQEL
	VAASARAAVK
51	DMDLQALHGR KVALYIATMG DQGSGSLTGG RYSIDALIRG
	EYINSPAVRT
101	DYTYPRYETT AETTSGGLTG LTTSLSTLNA PALSRTQSDG
	SGSRSSLGLN
151	IGGMGDYRNE TLTTNPRDTA FLSHLVQTVF FLRGIDVVSP
	ANADTDVFIN
201	IDVFGTIRNR TEMHLYNAET LKAQTKLEYF AVDRTNKKLL
	IKPKTNAFEA
251	AYKENYALWM GPYKVSKGIK PTEGLMVDFS DIQPYGNHTG
	NSAPSVEADN
301	SHEGYGYSDE AVRQHRQGQP *

The originally-identified partial strain B sequence (ORF15) shows 97.2% identity over a 213aa overlap with ORF15ng:

The complete strain B sequence (ORF15-1) and ORF15ng show 98.8% identity in 320 aa overlap:

Computer analysis of these amino acid sequences reveals an ILSAC motif (putative membrane lipoprotein lipid attachment site, as predicted by the MOTIFS program).

Indicates a putative leader sequence, and it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF15-1 (31.7 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 4A shows the results of affinity purification of the GST-fusion protein, and FIG. 4B shows the results of expression of the His-fusion in E. coli. Purified GST-fusion protein was used to immunise mice, whose sera were used for Western blot (FIG. 4C) and ELISA (positive result). These experiments confirm that ORFX-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 11

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 85>:

1	..GG.CAGCACA AAAAACAGGC GGTTGAACGG AAAAACCGTA
	TTTACGATGA
51	TGCCGGGTAT GATATTCGGC GTATTCACGG GCGCATTCTC
	CGCAAAATAT
101	ATCCCCGCGT TCGGGCTTCA AATTTTCTTC ATCCTGTTTT
	TAACCGCCGT
151	CGCATTCAAA ACACTGCATA CCGACCCTCA GACGGCATCC
	CGCCCGCTGC
201	CCGGACTGCC CrGACTGACT GCGGTTTCCA CACTGTTCGG
	CACAATGTCG
251	AGCTGGGTCG GCATAGGCGG CGGTTCACTT TCCGTCCCCT
	TCTTAATCCA
301	CTGCGGCTTC CCCGCCCATA AAGCCATCGG CACATCATCC
	GGCCTTGCCT
351	GGCCGATTGC ACTCTCCGGC GCAATATCGT ATCTGCTCAA
	CGGCCTGAAT
401	ATTGCAGGAT TGCCCGAAGG GTCACTGGGC TTCCTTTACC
	TGCCCGCCGT
451	CGCCGTCCTC AGCGCGGCAA CCATTGCCTT TGCCCCGCTC
	GGTGTCAAAA
501	CCGCCCACAA ACTTTCTTCT GCCAAACTCA AAAAATC.TT
	CGGCATTATG
551	TTGCTTTTGA TTGCCGGAAA AATGCTGTAC AACCTGCTTT
	AA

This corresponds to the amino acid sequence <SEQ ID 86; ORF17>:

1	..GQHKKQAVNG KTVFTMMPGM IFGVFTGAFS AKYIPAFGLQ
	IFFILFLTAV
51	AFKTLHTDPQ TASRPLPGLP XLTAVSTLFG TMSSWVGIGG
	GSLSVPFLIH
101	CGFPAHKAIG TSSGLAWPIA LSGAISYLLN GLNIAGLPEG
	SLGFLYLPAV
151	AVLSAATIAF APLGVKTAHK LSSAKLKKSF GIMLLLIAGK
	MLYNLL*

Further work revealed the complete nucleotide sequence <SEQ ID 87>:

1	ATGTGGCATT GGGACATTAT CTTAATCCTG CTTGCCGTAG
	GCAGTGCGGC
51	AGGTTTTATT GCCGGCCTGT TCGGCGTAGG CGGCGGCACG
	CTGATTGTCC
101	CTGTCGTTTT ATGGGTGCTT GATTTGCAGG GTTTGGCACA
	ACATCCTTAC
151	GCGCAACACC TCGCCGTCGG CACATCCTTC GCCGTCATGG
	TCTTCACCGC
201	CTTTTCCAGT ATGCTGGGGC AGCACAAAAA ACAGGCGGTC
	GACTGGAAAA
251	CCGTATTTAC GATGATGCCG GGTATGATAT TCGGCGTATT
	CACGGGCGCA
301	CTCTCCGCAA AATATATCCC CGCGTTCGGG CTTCAAATTT
	TCTTCATCCT
351	GTTTTTAACC GCCGTCGCAT TCAAAACACT GCATACCGAC
	CCTCAGACGG
401	CATCCCGCCC GCTGCCCGGA CTGCCCGGAC TGACTGCGGT
	TTCCACACTG
451	TTCGGCACAA TGTCGAGCTG GGTCGGCATA GGCGGCGGTT
	CACTTTCCGT
501	CCCCTTCTTA ATCCACTGCG GCTTCCCCGC CCATAAAGCC
	ATCGGCACAT
551	CATCCGGCCT TGCCTGGCCG ATTGCACTCT CCGGCGCAAT
	ATCGTATCTG
601	CTCAACGGCC TGAATATTGC AGGATTGCCC GAAGGGTCAC
	TGGGCTTCCT
651	TTACCTGCCC GCCGTCGCCG TCCTCAGCGC GGCAACCATT
	GCCTTTGCCC
701	CGCTCGGTGT CAAAACCGCC CACAAACTTT CTTCTGCCAA
	ACTCAAAAAA
751	Tc.TTCGGCA TTATGTTGCT TTTGATTGCC GGAAAAATGC
	TGTACAACCT
801	GCTTTAA

This corresponds to the amino acid sequence <SEQ ID 88; ORF17-1>:

1	MWHWDIILIL LAVGSAAGFI AGLFGVGGGT LIVPVVLWVL
	DLQGLAQHPY
51	AQHLAVGTSF AVMVFTAFSS MLGQHKKQAV DWKTVFTMMP
	GMIFGVFTGA
101	LSAKYIPAFG LQIFFILFLT AVAFKTLHTD PQTASRPLPG
	LPGLTAVSTL
151	FGTMSSWVGI GGGSLSVPFL IHCGFPAHKA IGTSSGLAWP
	IALSGAISYL
201	LNGLNIAGLP EGSLGFLYLP AVAVLSAATI AFAPLGVKTA
	HKLSSAKLKK
251	XFGIMLLLIA GKMLYNLL*

Computer analysis of this amino acid sequence gave the following results:

Homology with Hypothetical H. influenzae Transmembrane Protein H10902 (Accession number P44070)

ORF17 and HI0902 proteins show 28% aa identity in 192 aa overlap:

ORF17	3	HKKQAVNGKTVFTMMPGMIFGVFT-GAFSAKYIPAFGLQIF--FILFLTAVAFKTLHTDP	59
		HK   +  + V  + P ++  VF  G F  +       +IF   +++L      ++  D
HI0902	72	HKLGNIVWQAVRILAPVIMLSVFICGLFIGRLDREISAKIFACLVVYLATKMVLSIKKD-	130
ORF17	60	QTASRPLPGLPXLTAVSTLFGTMSSWVGIGGGSLSVPFLIHCGFPAHKAIGTSSGLAWPI	119
		Q  ++ L  L  +     L G  SS  GIGGG   VPFL   G    +AIG+S+     +
HI0902	131	QVTTKSLTPLSSVIG-GILIGMASSAAGIGGGGFIVPFLTARGINIKQAIGSSAFCGMLL	189
ORF17	120	ALSGAISYLLNGLNIAGLPEGSLGFLYLPAVAVLSAATIAFAPLGVXXXXXXXXXXXXXX	179
		+SG  S++++G     +PE SLG++YLPAV  ++A +   + LG
HI0902	190	GISGMFSFIVSGWGNPLMPEYSLGYIYLPAVLGITATSFFTSKLGASATAKLPVSTLKKG	249
ORF17	180	FGIMLLLIAGKM	191
		F + L+++A  M
HI0902	250	FALFLIVVAINM	261

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF17 shows 96.9% identity over a 196aa overlap with an ORF (ORF17a) from strain A of N. meningitidis:

The complete length ORF17a nucleotide sequence <SEQ ID 89> is:

1	ATGTGGCATT GGGACATTAT CTTAATCCTG CTTGCCGTAG
	GCAGTGCGGC
51	AGGTTTTATT GCCGGCCTGT TCGGCGTAGG CGGCGGCACG
	CTGATTGTCC
101	CTGTCGTTTT ATGGGTGCTT GATTTGCAGG GTTTGGCACA
	ACATCCTTAC
151	GCGCAACACC TCGCCGTCGG CACATCCTTC GCCGTCATGG
	TCTTCACCGC
201	CTTTTCCAGT ATGCTGGGGC AGCACAAAAA ACAGGCGGTC
	GACTGGAAAA
251	CCGTATTTAC GATGATGCCG GGTATGGTAT TCGGCGTATT
	CGCTGGCGCA
301	CTCTCCGCAA AATATATCCC AGCGTTCGGG CTTCAAATTT
	TCTTCATCCT
351	GTTTTTAACC GCCGTCGCAT TCAAAACACT GCATACCGAC
	CCTCAGACGG
401	CATCCCGCCC GCTGCCCGGA CTGCCCGGAC TGACTGCGGT
	TTCCACACTG
451	TTCGGCACAA TGTCGAGCTG GGTCGGCATA GGCGGCGGTT
	CACTTTCCGT
501	CCCCTTCTTA ATCCACTGCG GCTTCCCCGC CCATAAAGCC
	ATCGGCACAT
551	CATCCGGCCT TGCCTGGCCG ATTGCACTCT CCGGCGCAAT
	ATCGTATCTG
601	CTCAACGGCC TGAATATTGC AGGATTGCCC GAAGGGTCAC
	TGGGCTTCCT
651	TTACCTGCCC GCCGTCGCCG TCCTCAGCGC GGCAACCATT
	GCCTTTGCCC
701	CGCTCGGTGT CAAAACCGCC CACAAACTTT CTTCTGCCAA
	ACTCAAAAAA
751	TCCTTCGGCA TTATGTTGCT TTTGATTGCC GGAAAAATGC
	TGTACAACCT
801	GCTTTAA

This encodes a protein having amino acid sequence <SEQ ID 90>:

1	MWHWDIILIL LAVGSAAGFI AGLFGVGGGT LIVPVVLWVL
	DLQGLAQHPY
51	AQHLAVGTSF AVMVFTAFSS MLGQHKKQAV DWKTVFTMMP
	GMVFGVFAGA
101	LSAKYIPAFG LQIFFILFLT AVAFKTLHTD PQTASRPLPG
	LPGLTAVSTL
151	FGTMSSWVGI GGGSLSVPFL IHCGFPAHKA IGTSSGLAWP
	IALSGAISYL
201	LNGLNIAGLP EGSLGFLYLP AVAVLSAATI AFAPLGVKTA
	HKLSSAKLKK
251	SFGIMLLLIA GKMLYNLL*

ORF17a and ORF17-1 show 98.9% identity in 268 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF17 shows 93.9% identity over a 196aa overlap with a predicted ORF (ORF17.ng) from N. gonorrhoeae:

An ORF17ng nucleotide sequence <SEQ ID 91> is predicted to encode a protein having amino acid sequence <SEQ ID 92>:

1	MWHWDIILIL LAVGSAAGFI AGLFGVGGGT LIVPVVLWVL
	DLQGLAQHPY
51	AQHLAVGTSF AVMVFTAFSS MLGQHKKQAV DWKTIFAMMP
	GMIFGVFAGA
101	LSAKYIPAFG LQIFFILFLT AVAFKTLHTG RQTASRPLPG
	LPGLTAVSTL
151	FGAMSSWVGI GGGSLSVPFL IHCGFPAHKA IGTSSGLAWP
	IALSGAISYL
201	VNGLNIAGLP EGSLGFLYLP AVAVLSAATI AFAPLGVKTA
	HKLSSAKLKE
251	SFGIMLLLIA GKMLYNLL*

Further work revealed the complete gonococcal DNA sequence <SEQ ID 93>:

1	ATGTGGCATT GGGACATTAT CTTAATCCTG CTTGCcgtag
	gcAGTGCGGC
51	AGGTTTTATT GCCGGCCTGT Tcggtgtagg cggcgGTACG
	CTGATTGTCC
101	CTGTCGTTTT ATGGGTGCTT GATTTGCAGG GTTTGGCACA
	ACATCCTTAC
151	GCGCAACACC TCGCCGTCGG CAcaTccttc gcCGTCATGG
	TCTTCACCGC
201	CTTTTCCAGT ATGTTGGGGC AGCACAAAAA ACAGGCGGTC
	GACTGGAAAA
251	CCATATTTGC GATGATGCCG GGTATGATAT TCGGCGTATT
	CGCTGGCGCA
301	CTCTCCGCAA AATATATCCC CGCGTTCGGG CTTCAAATTT
	TCTTCATCCT
351	GTTTTTAACC GCCGTCGCAT TCAAAACACT GCATACCGGT
	CGTCAGACGG
401	CATCCCGCCC GCTGCCCGGG CTGCCCGGAC TGACTGCGGT
	TTCCACACTG
451	TTCGGCGCAA TGTCGAGCTG GGTCGGCATA GGCGGCGGTT
	CACTTTCCGT
501	CCCCTTCTTA ATCCACTGCG GCTTCCCCGC CCATAAAGCC
	ATCGGCACAT
551	CATCCGGCCT TGCCTGGCCG ATTGCACTCT CCGGCGCAAT
	ATCGTATCTG
601	GTCAACGGTC TGAATATTGC AGGATTGCCC GAAGGGTCGC
	TGGGCTTCCT
651	TTACCTGCCC GCCGTCGCCG TCCTCAGCGC GGCAACCATT
	GCCTTTGCCC
701	CGCTCGGTGT CAAAACCGCC CACAAACTTT CTTCTGCCAA
	ACTCAAAGAA
751	TCCTTCGGCA TTATGTTGCT TTTGATTGCC GGAAAAATGC
	TGTACAACCT
801	GCTTTAA

This corresponds to the amino acid sequence <SEQ ID 94; ORF17ng-1>:

1	MWHWDIILIL LAVGSAAGFI AGLFGVGGGT LIVPVVLWVL
	DLQGLAQHPY
51	AQHLAVGTSF AVMVFTAFSS MLGQHKKQAV DWKTIFAMMP
	GMIFGVFAGA
101	LSAKYIPAFG LQIFFILFLT AVAFKTLHTG RQTASRPLPG
	LPGLTAVSTL
151	FGAMSSWVGI GGGSLSVPFL IHCGFPAHKA IGTSSGLAWP
	IALSGAISYL
201	VNGLNIAGLP EGSLGFLYLP AVAVLSAATI AFAPLGVKTA
	HKLSSAKLKE
251	SFGIMLLLIA GKMLYNLL*

ORF17ng-1 and ORF17-1 show 96.6% identity in 268 aa overlap:

In addition, ORF17ng-1 shows significant homology with a hypothetical H. influenzae protein:

sp|P44070|Y902_HAEIN HYPOTHETICAL PROTEIN HI0902 pir||G64015
hypothetical protein HI0902 - Haemophilus influenzae (strain Rd KW20)
gi|1573922 (U32772) H. influenzae
predicted coding region HI0902 [Haemophilus influenzae]Length = 264
Score = 74 (34.9 bits), Expect = 1.6e−23, Sum P(2) = 1.6e−23
Identities = 15/43 (34%), Positives = 23/43 (53%)

Query:	55	AVGTSFAVMVFTAFSSMLGQHKKQAVDWKTIFAMMPGMIFGVF	97
		A+GTSFA +V T   S    HK   + W+ +  + P ++  VF
Sbjct:	52	ALGTSFATIVITGIGSAQRHHKLGNIVWQAVRILAPVIMLSVF	94

Score = 195 (91.9 bits), Expect = 1.6e−23, Sum P(2) = 1.6e−23
Identities = 44/114 (38%), Positives = 65/114 (57%)

Query:	150	LFGAMSSWVGIGGGSLSVPFLIHCGFPAHKAIGTSSGLAWPIALSGAISYLVNGLNIAGL	209
		L G  SS  GIGGG   VPFL   G    +AIG+S+     + +SG  S++V+G     +
Sbjct:	148	LIGMASSAAGIGGGGFIVPFLTARGINIKQAIGSSAFCGMLLGISGMFSFIVSGWGNPLM	207
Query:	210	PEGSLGFLYLPAVAVLSAATIAFAPLGVKTAFIKLSSAKLKESFGIMLLLIAGKM	263
		PE SLG++YLPAV  ++A +   + LG     KL  + LK+ F + L+++A  M
Sbjct:	208	PEYSLGYIYLPAVLGITATSFFTSKLGASATAKLPVSTLKKGFALFLIVVAINM	261

This analysis, including the homology with the hypothetical H. influenzae transmembrane protein, suggests that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 12

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 95>:

1	..GGAAACGGAT GGCAGGCAGA CCCCGAACAT CCGCTGCTCG
	GGCTTTTTGC
51	CGTCAGTAAT GTATCGATGA CGCTTGCTTT TGTCGGAATA
	TGTGCGTTGG
101	TGCATTATTG CTTTTCGGGA ACGGTTCAAG TGTTTGTGTT
	TGCGGCACTG
151	CTCAAACTTT ATGCGCTGAA GCCGGTTTAT TGGTTCGTGT
	TGCAGTTTGT
201	GCTGATGGCG GTTGCCTATG TCCACCGCTG CGGTATAGAC
	CGGCAGCCGC
251	CGTCAACGTT CGGCGGCTCG CAGCTGCGAC TCGGCGGGTT
	GACGGCAGCG
301	TTGATGCAGG TCTCGGTACT GGTGCTGCTG CTTTCAGAAA
	TTGGAAGATA
351	A

This corresponds to the amino acid sequence <SEQ ID 96; ORF18>:

1	..GNGWQADPEH PLLGLFAVSN VSMTLAFVGI CALVHYCFSG
	TVQVFVFAAL
51	LKLYALKPVY WFVLQFVLMA VAYVHRCGID RQPPSTFGGS
	QLRLGGLTAA
101	LMQVSVLVLL LSEIGR*

Further work revealed the complete nucleotide sequence <SEQ ID 97>:

1	ATGATTTTGC TGCATTTGGA TTTTTTGTCT GCCTTACTGT
	ATGCGGCGGT
51	TTTTCTGTTT CTGATATTCC GCGCAGGAAT GTTGCAATGG
	TTTTGGGCGA
101	GTATTATGCT GTGGCTGGGC ATATCGGTTT TGGGGGCAAA
	GCTGATGCCC
151	GGCATATGGG GAATGACCCG CGCCGCGCCC TTGTTCATCC
	CCCATTTTTA
201	CCTGACTTTG GGCAGCATAT TTTTTTTCAT CGGGCATTGG
	AACCGGAAAA
251	CAGATGGAAA CGGATGGCAG GCAGACCCCG AACATCCGCT
	GCTCGGGCTT
301	TTTGCCGTCA GTAATGTATC GATGACGCTT GCTTTTGTCG
	GAATATGTGC
351	GTTGGTGCAT TATTGCTTTT CGGGAACGGT TCAAGTGTTT
	GTGTTTGCGG
401	CACTGCTCAA ACTTTATGCG CTGAAGCCGG TTTATTGGTT
	CGTGTTGCAG
451	TTTGTGCTGA TGGCGGTTGC CTATGTCCAC CGCTGCGGTA
	TAGACCGGCA
501	GCCGCCGTCA ACGTTCGGCG GCTCGCAGCT GCGACTCGGC
	GGGTTGACGG
551	CAGCGTTGAT GCAGGTCTCG GTACTGGTGC TGCTGCTTTC
	AGAAATTGGA
601	AGATAA

This corresponds to the amino acid sequence <SEQ ID 98; ORF18-1>:

1	MILLHLDFLS ALLYAAVFLF LIFRAGMLQW FWASIMLWLG
	ISVLGAKLMP
51	GIWGMTRAAP LFIPHFYLTL GSIFFFIGHW NRKTDGNGWQ
	ADPEHPLLGL
101	FAVSNVSMTL AFVGICALVH YCFSGTVQVF VFAALLKLYA
	LKPVYWFVLQ
151	FVLMAVAYVH RCGIDRQPPS TFGGSQLRLG GLTAALMQVS
	VLVLLLSEIG
201	R*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF18 shows 98.3% identity over a 116aa overlap with an ORF (ORF18a) from strain A of N. meningitidis:

The complete length ORF18a nucleotide sequence <SEQ ID 99> is:

1	ATGATTTTGC TGCATTTGGA TTTTTTGTCT GCCTTACTGT
	ATGCGGCGGT
51	TTTTCTGTTT CTGATATTCC GCGCAGGAAT GTTGCAATGG
	TTTTGGGCGA
101	GTATTATGCT GTGGCTGGGC ATATCGGTTT TGGGGGCAAA
	GCTGATGCCC
151	GGCATATGGG GAATGACCCG CGCCGCGCCC TTGTTCATCC
	CCCATTTTTA
201	CCTGACTTTG GGCAGCATAT TTTTTTTCAT CGGGCATTGG
	AACCGGAAAA
251	CGGATGGAAA CGGATGGCAG GCAGACCCCG AACATCCTCT
	GCTCGGGCTG
301	TTTGCCGTCA GTAATGTATC GATGACGCTT GCTTTTGTCG
	GAATATGTGC
351	GTTGGTGCAT TATTGCTTTT CGNGAACGGT TCAAGTGTTT
	GTGTTTGCGG
401	CACTGCTCAA ACTTTATGCG CTGAAGCCGG TTTATTGGTT
	CGTGTTGCAG
451	TTTGTGCTGA TGGCGGTTGC CTATGTCCAC CGCTGCGGTA
	TAGACCGGCA
501	GCCGCCGTCA ACGTTCGGCG GNTCGCAGCT GCGACTCGGC
	GGGTTGACGG
551	CAGCGTTGAT GCAGNTCTCG GTACTGGTGC TGCTGCTTTC
	AGAAATTGGA
601	AGATAA

This encodes a protein having amino acid sequence <SEQ ID 100>:

1	MILLHLDFLS ALLYAAVFLF LIFRAGMLQW FWASIMLWLG
	ISVLGAKLMP
51	GIWGMTRAAP LFIPHFYLTL GSIFFFIGHW NRKTDGNGWQ
	ADPEHPLLGL
101	FAVSNVSMTL AFVGICALVH YCFSXTVQVF VFAALLKLYA
	LKPVYWFVLQ
151	FVLMAVAYVH RCGIDRQPPS TFGGSQLRLG GLTAALMQXS
	VLVLLLSEIG
201	R*

ORF18a and ORF18-1 show 99.0% identity in 201 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF18 shows 93.1% identity over a 116aa overlap with a predicted ORF (ORF18.ng) from N. gonorrhoeae:

The complete length ORF18ng nucleotide sequence is <SEQ ID 101>:

1	ATGATTTTGC TGCATTTGGA TTTTTTGTCT GCCTTACTGt
	aTGCGGcggt
51	tttTctgTTT CTGATATTCC GCGCAGGAAT GTTGCAATGG
	TTTTGGGCGA
101	GTATTGCGTT GTGGCTCGGC ATCTCGGTTT TAGGGGTAAA
	GCTGATGCCG
151	GGGATGTGGG GAATGACCCG CGCCGCGCCT TTGTTCATCC
	CCCATTTTTA
201	CCTGACTTTG GGCAGCATAT TTTTTTTCAT CGGGTATTGG
	AACCGGAAAA
251	CAGATGGAAA CGGATGGCAG GCAGACCCCG AACATCCGCT
	GCTCGGGCTT
301	TTTGCCGTCA GTAATGTATC GATGACGCTT GCTTTTGTCG
	GAATATGTGC
351	GTTGGTGCAT TATTGCTTTT CGGGAACGGT TCAAGTGTTT
	GTGTTTGCGG
401	CATTGCTCAA ACTTTATGCG CTGAAGCCGG TTTATTGGTT
	CGTGTTGCAG
451	TTTGTATTGA TGGCGGttgC CTATGTCCAC CGCTGCGGTA
	TAGACCGGCA
501	GCCGCCGTCA ACGTTCGGCG GTTCGCAGCT GCGACTCGGC
	GTGTTGGCGG
551	CGATGTTGAT GCAGGTTGCG GTAACGGCGA TGCTGCTTGC
	CGAAATCGGC
601	AGATGA

This encodes a protein having amino acid sequence <SEQ ID 102>:

1	MILLHLDFLS ALLYAAVFLF LIFRAGMLQW FWASIALWLG
	ISVLGVKLMP
51	GMWGMTRAAP LFIPHFYLTL GSIFFFIGYW NRKTDGNGWQ
	ADPEHPLLGL
101	FAVSNVSMTL AFVGICALVH YCFSGTVQVF VFAALLKLYA
	LKPVYWFVLQ
151	FVLMAVAYVH RCGIDRQPPS TFGGSQLRLG VLAAMLMQVA
	VTAMLLAEIG
201	R*

This ORF18ng protein sequence shows 94.0% identity in 201 aa overlap with ORF18-1:

Based on this analysis, including the presence of several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 13

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 103>:

1	ATGAAAACCC CACTCCTCAA GCCTCTGCTN ATTACCTCGC
	TTCCCGTTTT
51	CGCCAGTGTT TTTACCGCCG CCTCCATCGT CTGGCAGCTA
	GGCGAACCCA
101	AGCTCGCCAT GCCCTTCGTA CTCGGCATCA TCGCCGGCGG
	CCTTGTCGAT
151	TTGGACAACC NCNTGACCGG ACGGCTNAAA AACATCATCA
	CCACCGTCGC
201	CCTGTTCACC CTCTCCTCGC TCACGGCACA AAGCACCCTC
	GGCACAGGGC
251	TGCCCTTCAT CCTCGCCATG ACCCTGATGA CTT.CG.CTT
	CACCATTTTA
301	GGCGCGGNCG ...

This corresponds to the amino acid sequence <SEQ ID 104; ORF 19>:

1	MKTPLLKPLL ITSLPVFASV FTAASIVWQL GEPKLAMPFV
	LGIIAGGLVD
51	LDNXXTGRLK NIITTVALFT LSSLTAQSTL GTGLPFILAM
	TLMTXXFTIL
101	GAX...

Further work revealed the complete nucleotide sequence <SEQ ID 105>:

1	ATGAAAACCC CACTCCTCAA GCCTCTGCTC ATTACCTCGC
	TTCCCGTTTT
51	CGCCAGTGTT TTTACCGCCG CCTCCATCGT CTGGCAGCTA
	GGCGAACCCA
101	AGCTCGCCAT GCCCTTCGTA CTCGGCATCA TCGCCGGCGG
	CCTTGTCGAT
151	TTGGACAACC GCCTGACCGG ACGGCTGAAA AACATCATCA
	CCACCGTCGC
201	CCTGTTCACC CTCTCCTCGC TCACGGCACA AAGCACCCTC
	GGCACAGGGC
251	TGCCCTTCAT CCTCGCCATG ACCCTGATGA CCTTCGGCTT
	CACCATTTTA
301	GGCGCGGTCG GGCTCAAATA CCGCACCTTC GCCTTCGGTG
	CACTCGCCGT
351	CGCCACCTAC ACCACACTTA CCTACACCCC CGAAACCTAC
	TGGCTGACCA
401	ACCCCTTCAT GATTTTATGC GGCACCGTAC TGTACAGCAC
	CGCCATCCTC
451	CTGTTCCAAA TCGTCCTGCC CCACCGCCCC GTCCAAGAAA
	GCGTCGCCAA
501	CGCCTACGAC GCACTCGGCG GCTACCTCGA AGCCAAAGCC
	GACTTCTTCG
551	ACCCCGATGA GGCAGCCTGG ATAGGCAACC GCCACATCGA
	CCTCGCCATG
601	AGCAACACCG GCGTCATCAC CGCCTTCAAC CAATGCCGTT
	CCGCCCTGTT
651	TTACCGCCTT CGCGGCAAAC ACCGCCACCC GCGCACCGCC
	AAAATGCTGC
701	GTTACTACTT TGCCGCCCAA GACATACACG AACGCATCAG
	CTCCGCCCAC
751	GTCGATTATC AGGAAATGTC CGAAAAATTC AAAAACACCG
	ACATCATCTT
801	CCGCATCCAC CGCCTGCTCG AAATGCAGGG ACAAGCCTGC
	CGCAACACCG
851	CCCAAGCCCT GCGCGCAAGC AAAGACTACG TTTACAGCAA
	ACGCCTCGGC
901	CGCGCCATCG AAGGCTGCCG CCAATCGCTG CGCCTCCTTT
	CAGACAGCAA
951	CGACAGTCCC GACATCCGCC ACCTGCGCCG CCTTCTCGAC
	AACCTCGGCA
1001	GCGTCGACCA GCAGTTCCGC CAACTCCAGC ACAACGGCCT
	GCAGGCAGAA
1051	AACGACCGCA TGGGCGACAC CCGCATCGCC GCCCTCGAAA
	CCAGCAGCCT
1101	CAAAAACACC TGGCAGGCAA TCCGTCCGCA GCTAAACCTC
	GAATCAGGCG
1151	TATTCCGCCA TGCCGTCCGC CTGTCCCTCG TCGTTGCCGC
	CGCCTGCACC
1201	ATCGTCGAAG CCCTCAACCT CAACCTCGGC TACTGGATAC
	TACTGACCGC
1251	CCTTTTCGTC TGCCAACCCA ACTACACCGC CACCAAAAGC
	CGCGTCCGCC
1301	AGCGCATCGC CGGCACCGTA CTCGGCGTAA TCGTCGGCTC
	GCTCGTCCCC
1351	TACTTCACCC CGTCTGTCGA AACCAAACTC TGGATTGTCA
	TCGCCAGTAC
1401	CACCCTCTTT TTCATGACCC GCACCTACAA ATACAGTTTC
	TCCACCTTCT
1451	TCATTACCAT TCAAGCCCTG ACCAGCCTCT CCCTCGCAGG
	TTTGGACGTA
1501	TACGCCGCCA TGCCCGTACG CATCATCGAC ACCATTATCG
	GCGCATCCCT
1551	TGCCTGGGCG GCAGTCAGCT ACCTGTGGCC AGACTGGAAA
	TACCTCACGC
1601	TCGAACGCAC CGCCGCCCTT GCCGTATGCA GCAACGGTGC
	CTATCTCGAA
1651	AAAATCACCG AACGCCTCAA AAGCGGCGAA ACCGGCGACG
	ACGTCGAATA
1701	CCGCGCCACC CGCCGCCGCG CCCACGAACA CACCGCCGCC
	CTCAGCAGCA
1751	CCCTTTCCGA CATGAGCAGC GAACCCGCAA AATTCGCCGA
	CAGCCTGCAA
1801	CCCGGCTTTA CCCTGCTCAA AACCGGCTAC GCCCTGACCG
	GCTACATCTC
1851	CGCCCTCGGC GCATACCGCA GCGAAATGCA CGAAGAATGC
	AGCCCCGACT
1901	TTACCGCACA GTTCCACCTC GCCGCCGAAC ACACCGCCCA
	CATCTTCCAA
1951	CACCTGCCCG AAACCGAACC CGACGACTTT CAGACAGCAC
	TGGATACACT
2001	GCGCGGCGAA CTCGACACCC TCCGCACCCA CAGCAGCGGA
	ACACAAAGCC
2051	ACATCCTCCT CCAACAGCTC CAACTCATCG CCCGACAGCT
	CGAACCCTAC
2101	TACCGCGCCT ACCGCCAAAT TCCGCACAGG CAGCCCCAAA
	ATGCAGCCTG
2151	A

This corresponds to the amino acid sequence <SEQ ID 106; ORF19-1>:

1	MKTPLLKPLL ITSLPVFASV FTAASIVWQL GEPKLAMPFV
	LGIIAGGLVD
51	LDNRLTGRLK NIITTVALFT LSSLTAQSTL GTGLPFILAM
	TLMTFGFTIL
101	GAVGLKYRTF AFGALAVATY TTLTYTPETY WLTNPFMILC
	GTVLYSTAIL
151	LFQIVLPHRP VQESVANAYD ALGGYLEAKA DFFDPDEAAW
	IGNRHIDLAM
201	SNTGVITAFN QCRSALFYRL RGKHRHPRTA KMLRYYFAAQ
	DIHERISSAH
251	VDYQEMSEKF KNTDIIFRIH RLLEMQGQAC RNTAQALRAS
	KDYVYSKRLG
301	RAIEGCRQSL RLLSDSNDSP DIRHLRRLLD NLGSVDQQFR
	QLQHNGLQAE
351	NDRMGDTRIA ALETSSLKNT WQAIRPQLNL ESGVFRHAVR
	LSLVVAAACT
401	IVEALNLNLG YWILLTALFV CQPNYTATKS RVRQRIAGTV
	LGVIVGSLVP
451	YFTPSVETKL WIVIASTTLF FMTRTYKYSF STFFITIQAL
	TSLSLAGLDV
501	YAAMPVRIID TIIGASLAWA AVSYLWPDWK YLTLERTAAL
	AVCSNGAYLE
551	KITERLKSGE TGDDVEYRAT RRRAHEHTAA LSSTLSDMSS
	EPAKFADSLQ
601	PGFTLLKTGY ALTGYISALG AYRSEMHEEC SPDFTAQFHL
	AAEHTAHIFQ
651	HLPETEPDDF QTALDTLRGE LDTLRTHSSG TQSHILLQQL
	QLIARQLEPY
701	YRAYRQIPHR QPQNAA*

Computer analysis of this amino acid sequence gave the following results:

Homology with Predicted Transmenbrane protein YHFK of H. influenzae (Accession Number P44289)

ORF19 and YHFK proteins show 45% aa identity in 97 aa overlap:

orf19	6	LKPLLITSLPVFASVFTAASIVWQLGEPKLAMPFVLGIIAGGLVDLDNXXTGRLKNIITT	65
		L   +I+++PVF +V  AA  +W       +MP +LGIIAGGLVDLDN  TGRLKN+  T
YHFK	5	LNAKVISTIPVFIAVNIAAVGIWFFDISSQSMPLILGIIAGGLVDLDNRLTGRLKNVFFT	64
orf19	66	VALFTLSSLTAQSTLGTGLPFILAMTLMTXXFTILGA	102
		+  F++SS   Q  +G  + +I+ MT++T  FT++GA
YHFK	65	LIAFSISSFIVQLHIGKPIQYIVLMTVLTFIFTMIGA	101

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF19 shows 92.2% identity over a 102aa overlap with an ORF (ORF19a) from strain A of N. meningitidis:

The complete length ORF19a nucleotide sequence <SEQ ID 107> is:

1	ATGAAAACCC CACCCCTCAA GCCTCTGCTC ATTACCTCGC
	TTCCCGTTTT
51	CGCCAGTGTC TTTACCGCCG CCTCCATCGT CTGGCAGCTG
	GGCGAACCCA
101	AGCTCGCCAT GCCCTTCGTA CTCGGCATCA TCGCTGGCGG
	CCTGGTCGAT
151	TTGGACAACC GCCTGACCGG ACGGCTGAAA AACATCATCG
	CCACCGTCGC
201	CCTGTTCACC CTCTCCTCAC TTGTCGCGCA AAGCACCCTC
	GGCACAGGTT
251	TGCCATTCAT CCTCGCCATG ACCCTGATGA CTTTCGGCTT
	TACCATCATG
301	GGCGCGGTCG GGCTGAAATA CCGCACCTTC GCCTTCGGCG
	CACTCGCCGT
351	CGCCACCTAC ACCACACTTA CCTACACCCC CGAAACCTAC
	TGGCTGACCA
401	ACCCCTTTAT GATTCTGTGC GGAACCGTAC TGTACAGCAC
	CGCCATCATC
451	CTGTTCCAAA TCATCCTGCC CCACCGCCCC GTTCAAGAAA
	ACGTCGCCAA
501	CGCCTACGAA GCACTCGGCA GCTACCTCGA AGCCAAAGCC
	GACTTTTTCG
551	ATCCCGACGA AGCCGAATGG ATAGGCAACC GCCACATCGA
	CCTCGCCATG
601	AGCAACACCG GCGTCATCAC CGCCTTCAAC CAATGCCGTT
	CCGCCCTGTT
651	TTACCGCCTT CGCGGCAAAC ACCGCCACCC GCGCACCGCC
	AAAATGCTGC
701	GCTACTACTT CGCCGCCCAA GACATACACG AACGCATCAG
	CTCCGCCCAC
751	GTCGACTACC AAGAGATGTC CGAAAAATTC AAAAACACCG
	ACATCATCTT
801	CCGCATCCAC CGCCTGCTCG AAATGCAGGG ACAAGCCTGC
	CGCAACACCG
851	CCCAAGCCCT GCGCGCAAGC AAAGACTACG TTTACAGCAA
	ACGCCTCGGC
901	CGCGCCATCG AAGGCTGCCG CCAATCGCTG CGCCTCCTTT
	CAGACAGCAA
951	CGACAATCCC GACATCCGCC ACCTGCGCCG CCTTCTCGAC
	AACCTCGGCA
1001	GCGTCGACCA GCAGTTCCGC CAACTCCAGC ACAACGGCCT
	GCAGGCAGAA
1051	AACGACCGCA TGGGCGACAC CCGCATCGCC GCCCTCGAAA
	CCGGCAGCCT
1101	CAAAAACACC TGGCAGGCAA TCCGTCCGCA GCTAAACCTC
	GAATCAGGCG
1151	TATTCCGCCA TGCCGTCCGC CTGTCCCTTG TCGTTGCCGC
	CGCCTGCACC
1201	ATCGTCGAAG CCCTCAACCT CAACCTCGGC TACTGGATAC
	TACTGACCGC
1251	CCTTTTCGTC TGCCAACCCA ACTACACCGC CACCAAAAGC
	CGCGTCCGCC
1301	AGCGCATCGC CGGCACCGTA CTCGGCGTAA TCGTCGGCTC
	GCTCGTCCCC
1351	TACTTTACCC CCTCCGTCGA AACCAAACTC TGGATCGTCA
	TCGCCAGTAC
1401	CACCCTCTTT TTCATGACCC GCACCTACAA ATACAGCTTC
	TCGACATTTT
1451	TCATCACCAT TCAAGCCCTG ACCAGCCTCT CCCTCGCAGG
	GTTGGACGTA
1501	TACGCCGCCA TGCCCGTACG CATCATCGAC ACCATTATCG
	GCGCATCCCT
1551	TGCCTGGGCG GCAGTCAGCT ACCTGTGGCC AGACTGGAAA
	TACCTCACGC
1601	TCGAACGCAC CGCCGCCCTT GCCGTATGCA GCAACGGCGC
	CTATCTCGAA
1651	AAAATCACCG AACGCCTCAA AAGCGGCGAA ACCGGCGACG
	ACGTCGAATA
1701	CCGCGCCACC CGCCGCCGCG CCCACGAACA CACCGCCGCC
	CTCAGCAGCA
1751	CCCTTTCCGA CATGAGCAGC GAACCCGCAA AATTCGCCGA
	CAGCCTGCAA
1801	CCCGGCTTTA CCCTGCTCAA AACCGGCTAC GCCCTGACCG
	GCTACATCTC
1851	CGCCCTCGGC GCATACCGCA GCGAAATGCA CGAAGAATGC
	AGCCCCGACT
1901	TTACCGCACA GTTCCACCTC GCCGCCGAAC ACACCGCCCA
	CATCTTCCAA
1951	CACCTGCCCG AAACCGAACC CGACGACTTT CAGACAGCAC
	TGGATACACT
2001	GCGCGGCGAA CTCGACACCC TCCGCACCCA CAGCAGCGGA
	ACACAAAGCC
2051	ACATCCTCCT CCAACAGCTC CAACTCATCG CCCGGCAGCT
	CGAACCCTAC
2101	TACCGCGCCT ACCGACAAAT TCCGCACAGG CAGCCCCAAA
	ACGCAGCCTG
2151	A

This encodes a protein having amino acid sequence <SEQ ID 108>:

1	MKTPPLKPLL ITSLPVFASV FTAASIVWQL GEPKLAMPFV
	LGIIAGGLVD
51	LDNRLTGRLK NIIATVALFT LSSLVAQSTL GTGLPFILAM
	TLMTFGFTIM
101	GAVGLKYRTF AFGALAVATY TTLTYTPETY WLTNPFMILC
	GTVLYSTAII
151	LFQIILPHRP VQENVANAYE ALGSYLEAKA DFFDPDEAEW
	IGNRHIDLAM
201	SNTGVITAFN QCRSALFYRL RGKHRHPRTA KMLRYYFAAQ
	DIHERISSAH
251	VDYQEMSEKF KNTDIIFRIH RLLEMQGQAC RNTAQALRAS
	KDYVYSKRLG
301	RAIEGCRQSL RLLSDSNDNP DIRHLRRLLD NLGSVDQQFR
	QLQHNGLQAE
351	NDRMGDTRIA ALETGSLKNT WQAIRPQLNL ESGVFRHAVR
	LSLVVAAACT
401	IVEALNLNLG YWILLTALFV CQPNYTATKS RVRQRIAGTV
	LGVIVGSLVP
451	YFTPSVETKL WIVIASTTLF FMTRTYKYSF STFFITIQAL
	TSLSLAGLDV
501	YAAMPVRIID TIIGASLAWA AVSYLWPDWK YLTLERTAAL
	AVCSNGAYLE
551	KITERLKSGE TGDDVEYRAT RRRAHEHTAA LSSTLSDMSS
	EPAKFADSLQ
601	PGFTLLKTGY ALTGYISALG AYRSEMHEEC SPDFTAQFHL
	AAEHTAHIFQ
651	HLPETEPDDF QTALDTLRGE LDTLRTHSSG TQSHILLQQL
	QLIARQLEPY
701	YRAYRQIPHR QPQNAA*

ORF19a and ORF19-1 show 98.3% identity in 716 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF19 shows 95.1% identity over a 102aa overlap with a predicted ORF (ORF19.ng) from N. gonorrhoeae:

An ORF19ng nucleotide sequence <SEQ ID 109> is predicted to encode a protein having amino acid sequence <SEQ ID 110>:

1	MKTPLLKPLL ITSLPVFASV FTAASIVWQL GEPKLAMPFV
	LGIIAGGLVD
51	LDNRLTGRLK NIIATVALFT LSSLTAQSTL GTGLPFILAM
	TLMTFGFTIL
101	GAVGLKYRTF AFGALAVATY TTLTYTPETY WLTNPFMILC
	GTVLYSTAII
151	LFQIILPHRP VQESVANAYE ALGGYLEAKA DFFDPDEAAW
	IGNRHIDLAM
201	SNTGVITAFN QCRSALFYRL RGKHRHPRTA KMLRYYFAAQ
	DIHERISSAH
251	VDYQEMSEKF KNTDIIFRIR RLLEMQGQAC RNTAQAIRSG
	KDYVYSKRLG
301	RAIEGCRQSL RLLSDGNDSP DIRHLSRLLD NLGSVDQQFR
	QLRHSDSPAE
351	NDRMGDTRIA ALETGSFKNT *

Further work revealed the complete nucleotide sequence <SEQ ID 111>:

1	ATGAAAACCC CACTCCTCAA GCCTCTGCTC ATTACCTCGC
	TTCCCGTTTT
51	CGCCAGTGTC TTTACCGCCG CCTCCATCGT CTGGCAGCTA
	GGCGAACCCA
101	AGCTCGCCAT GCCCTTCGTA CTCGGCATCA TCGCCGGCGG
	CCTGGTCGAT
151	TTGGACAACC GCCTGACCGG ACGGCTGAAA AACATCATCG
	CCACCGTCGC
201	CCTGTTTACC CTCTCCTCGC TCACGGCGCA AAGCACCCTC
	GGCACAGGGC
251	TGCCCTTCAT CCTCGCCATG ACCCTGATGA CCTTCGGCTT
	TACCATTTTA
301	GGCGCGGTCG GGCTGAAATA CCGCACCTTC GCCTTCGGCG
	CACTCGCCGT
351	CGCCACCTAC ACCACGCTTA CCTACACCCC CGAAACCTAC
	TGGCTGACCA
401	ACCCCTTCAT GATTTTATGC GGCACCGTAC TGTACAGCAC
	CGCCATCATC
451	CTGTTCCAAA TCATCCTGCC CCACCGCCCC GTCCAAGAAA
	GCGTCGCCAA
501	TGCCTACGAA GCACTCGGCG GCTACCTCGA AGCCAAAGCC
	GACTTCTTCG
551	ACCCCGATGA GGCAGCCTGG ATAGGCAACC GCCACATCGA
	CCTCGCCATG
601	AGCAACACCG GCGTCATCAC CGCCTTCAAC CAATGCCGTT
	CCGCCCTGTT
651	TTACCGTTTG CGCGGCAAAC ACCGCCACCC GCGCACCGCC
	AAAATGCTGC
701	GCTACTACTT CGCCGCCCAA GACATCCACG AACGCATCAG
	CTCCGCCCAC
751	GTCGACTACC AAGAGATGTC CGAAAAATTC AAAAACACCG
	ACATCATCTT
801	CCGCATCCGC CGCCTGCTCG AAATGCAGGG GCAGGCGTGC
	CGCAACACCG
851	CCCAAGCCAT CCGGTCGGGC AAAGACTAcg tTTACAGCAA
	ACGCCTCGGA
901	CGCGCCATcg aaggctgCCG CCAGTCGCtg cgcctCCTTt
	cagacggcaA
951	CGACAGTCCC GACATCCGCC ACCTGAGccg CCTTCTCGAC
	AACCTCGgca
1001	GCGTcgacca gcagtTCcgc caactCCGAC ACAgcgactC
	CCCCGCcgaa
1051	Aacgaccgca tgggcgacaC CCGCATCGCC GCCCtcgaaa
	ccggcagctT
1101	caaaaaCAcc tggcaggCAA TCCGTCCGCa gctgaaCCTC
	GAATCatgCG
1151	TATTCCGCCA TGCCGTCCGC CTGTCCCTCG TCGTTGCCGC
	CGCCTGCACC
1201	ATCGTCgaag cCCTCAACCT CAACCTCGGC TACTGGATAC
	TGCTGACCGC
1251	CCTTTTCGTC TGCCAACCCA ACTACACCGC CACCAAAAGC
	CGCGTGTACC
1301	AACGCATCGC CGGCACCGTA CTCGGCGTAA TCGTCGGCTC
	GCTCGTCCCC
1351	TACTTCACCC CCTCCGTCGA AACCAAACTC TGGATTGTCA
	TCGCCGGTAC
1401	CACCCTGTTC TTCATGACCC GCACCTACAA ATACAGTTTC
	TCCACCTTCT
1451	TCATCACCAT TCAGGCACTG ACCAGCCTCT CCCTCGCAGG
	TTTGGACGTA
1501	TACGCCGCCA TGCCCGTGCG CATCATcgaC ACCATTATCG
	GCGCATCCCT
1551	TGCCTGGGCG GCGGTCAGCT ACCTGTGGCC AGACTGGAAA
	TACCTCACGC
1601	TCGAACGCAC CGCCGCCCTT GCCGTATGCA GCAGCGGCAC
	ATACCTCCAA
1651	AAAATTGCCG AACGCCTCAA AACCGGCGAA ACCGGCGACG
	ACATAGAATA
1701	CCGCATCACC CGCCGCCGCG CCCACGAACA CACCGCCGCC
	CTCAGCAGCA
1751	CCCTTTCCGA CATGAGCAGC GAACCCGCAA AATTCGCCGA
	CAGCCTGCAA
1801	CCCGGCTTTA CCCTGCTCAA AACCGGCTAC GCCCTGACCG
	GCTACATCTC
1851	CGCCCTCGGC GCATACCGCA GCGAAATGCA CGAAGAATGC
	AGCCCCGACT
1901	TTACCGCACA GTTCCACCTT GCCGCCGAAC ACACCGCCCA
	CATCTTCCAA
1951	CACCTGCCCG ACATGGGACC CGACGACTTT CAGACGGCAT
	TGGATACACT
2001	GCGCGGCGAA CTCGGCACCC TCCGCACCCG CAGCAGCGGA
	ACACAAAGCC
2051	ACATCCTCCT CCAACAGCTC CAACTCATCG CccgGCAACT
	CGAACCCTAC
2101	TACCGCGCCT ACCGACAAAT TCCGCACAGG CAGCCCCAAA
	ACGCAGCCTG
2151	A

This corresponds to the amino acid sequence <SEQ ID 112; ORF19ng-1>:

1	MKTPLLKPLL ITSLPVFASV FTAASIVWQL GEPKLAMPFV
	LGIIAGGLVD
51	LDNRLTGRLK NIIATVALFT LSSLTAQSTL GTGLPFILAM
	TLMTFGFTIL
101	GAVGLKYRTF AFGALAVATY TTLTYTPETY WLTNPFMILC
	GTVLYSTAII
151	LFQIILPHRP VQESVANAYE ALGGYLEAKA DFFDPDEAAW
	IGNRHIDLAM
201	SNTGVITAFN QCRSALFYRL RGKHRHPRTA KMLRYYFAAQ
	DIHERISSAH
251	VDYQEMSEKF KNTDIIFRIR RLLEMQGQAC RNTAQAIRSG
	KDYVYSKRLG
301	RAIEGCRQSL RLLSDGNDSP DIRHLSRLLD NLGSVDQQFR
	QLRHSDSPAE
351	NDRMGDTRIA ALETGSFKNT WQAIRPQLNL ESCVFRHAVR
	LSLVVAAACT
401	IVEALNLNLG YWILLTALFV CQPNYTATKS RVYQRIAGTV
	LGVIVGSLVP
451	YFTPSVETKL WIVIAGTTLF FMTRTYKYSF STFFITIQAL
	TSLSLAGLDV
501	YAAMPVRIID TIIGASLAWA AVSYLWPDWK YLTLERTAAL
	AVCSSGTYLQ
551	KIAERLKTGE TGDDIEYRIT RRRAHEHTAA LSSTLSDMSS
	EPAKFADSLQ
601	PGFTLLKTGY ALTGYISALG AYRSEMHEEC SPDFTAQFHL
	AAEHTAHIFQ
651	HLPDMGPDDF QTALDTLRGE LGTLRTRSSG TQSHILLQQL
	QLIARQLEPY
701	YRAYRQIPHR QPQNAA*

ORF19ng-1 and ORF19-1 show 95.5% identity in 716 aa overlap:

In addition, ORF19ng-1 shows significant homology to a hypothetical gonococcal protein previously entered in the databases:

sp|O33369|YOR2_NEIGO HYPOTHETICAL 45.5 KD PROTEIN (ORF2) gnl|PID|e1154438
(AJ002423) hypothetical protein [Neisseria gonorrh] Length = 417
Score = 1512 (705.6 bits), Expect = 5.3e−203, P = 5.3e−203
Identities = 301/326 (92%), Positives = 306/326 (93%)

Query:	307	RQSLRLLSDGNDSPDIRHLSRLLDNLGSVDQQFRQLRHSDSPAENDRMGDTRIAALETGS	366
		RQSLRLLSDGNDS DIRHLSRLLDNLGSVDQQFRQLRHSDSPAENDRMGDTRIAALETGS
Sbjct:	1	RQSLRLLSDGNDSXDIRHLSRLLDNLGSVDQQFRQLRHSDSPAENDRMGDTRIAALETGS	60
Query:	367	FKNTWQAIRPQLNLESCVFRHAVRLSLVVAAACTIVEALNLNLGYWILLTALFVCQPNYT	426
		FKNTWQAIRPQLNLES VFRHAVRLSLVVAAACTIVEALNLNLGYWILLT LFVCQPNYT
Sbjct:	61	FKNTWQAIRPQLNLESGVFRHAVRLSLVVAAACTIVEALNLNLGYWILLTRLFVCQPNYT	120
Query:	427	ATKSRVYQRIAGTVLGVIVGSLVPYFTPSVETKLWIVIAGTTLFFMTRTYKYSFSTFFIT	486
		ATKSRVYQRIAGTVLGVIVGSLVPYFTPSVETKLWIVIAGTTLFFMTRTYKYSFSTFFIT
Sbjct:	121	ATKSRVYQRIAGTVLGVIVGSLVPYFTPSVETKLWIVIAGTTLFFMTRTYKYSFSTFFIT	180
Query:	487	IQALTSLSLAGLDVYAAMPVRIIDTIIGASLAWAAVSYLWPDWKYLTLERTAALAVCSSG	546
		IQALTSLSLAGLDVYAAMPVRIIDTIIGASLAWAAVSYLWPDWKYLTLERTAALAVCSSG
Sbjct:	181	IQALTSLSLAGLDVYAAMPVRIIDTIIGASLAWAAVSYLWPDWKYLTLERTAALAVCSSG	240
Query:	547	TYLQKIAERLKTGETGDDIEYRITRRRAHEHTAALSSTLSDMSSEPAKFADSLQPGFTLL	606
		TYLQKIAERLKTGETGDDIEYRITRRRAHEHTAALSSTLSDMSSEPAKFAD+  P
Sbjct:	241	TYLQKIAERLKTGETGDDIEYRITRRRAHEHTAALSSTLSDMSSEPAKFADTCNPALPCS	300
Query:	607	KTGYALTGYISALGAYRSEMHEECSP	632
		K   ALTGYISALG   ++  +  +P
Sbjct:	301	KPATALTGYISALGHTAAKCTKNAAP	326

Based on this analysis, including the presence of several putative transmembrane domains in the gonococcal protein (the first of which is also seen in the meningococcal protein), and on homology with the YHFK protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 14

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 113>:

1	ATGAATATGC TGGGAGCTTT GGCAAAAGTC GGCAGCCTGA
	CGATGGTGTC
51	GCGCGTTTTG GGATTTGTGC GCGATACGGT CATTGCGCGG
	GCATTCGGCG
101	CGGGTATGGC GACGGATGCG TTTTTTGTCG CGTTCAAACT
	GCCCAACCTG
151	CTTCGCCGCG TGTTTGCGGA GGGGGCGTTT GCCCAAGCGT
	TTGTGCCGAT
201	TTTGGCGGAA TACAAGGAAA CGCGTTCAAA AGAGGCGG.C
	GAAGCCTTTA
251	TCCGCCATGT GGCGGGGATG CTGTCGTTTG TACTGGTTAT
	CGTTACCGCG
301	CTGGGCATAC TTGCCGCGCC TTGGGTGATT TATGTTTCCG
	CACCCGAGTT
351	TTGCCCAAGA TGCCGACAAA TTTCAGCTCT CCATCGATTT
	GCTGCGGATT
401	ACGTTTCCTT ATATATTATT GATTTCCCTG TCTTCATTTG
	TCGGCTCGGT
451	ACTCAATTCT TATCATAAGT TCGGCATTCC GGCGTTTACG
	CCAC.GTTTC
501	TGAACGTGTC GTTTATCGTA TTCGCGCTGT TTTTCGTGCC
	GTATTTCGAT
551	CCGCCCGTTA CCGCGCyGGC GTGGGCGGTC TTTGTCGGCG
	GCATTTTGCA
601	ACTCGrmTTC CAACTGCCCT GGCTGGCGAA ACTGGGCTTT
	TTGAAACTGC
651	CCAAACtGAG TTTCAAAGAT GCGGCGGTCA ACCGCGTGAT
	GAAACAGATG
701	GCGCCTGCgA TTTTgGGCGT GAgCGTGGCG CAGGTTTCTT
	TGGTGATCAA
751	CACGATTTTc GCGTCTTATC TGCAATCGGG CAGCGTTTCA
	TGGATGTATT
801	ACGCCGACCG CATGATGGAG CTGCCCAGCG GCGTGCTGGG
	GGCGGCACTC
851	GGTACGATTT TGCTGCCGAC TTTGTCCAAA CACTCGGCAA
	ACCaAGATAC
901	GGaACAGTTT TCCGCCCTGC TCGACTGGGG TTTGCGCCTG
	TGCATGCtgc
951	TGACGCTGCC GGCGgcGGTC GGACTGGCGG TGTTGTCGTT
	cCCgCtGGTG
1001	GCGACGCTGT TTATGTACCG CGwATTTACG CTGTTTGACG
	CGCAGATGAC
1051	GCAACACGCG CTGATTGCCT ATTCTTTCGG TTTAATCGGC
	TTAATCATGA
1101	TTAAAGTGTT GGCACCCGGC TTCTATGCGC GGCAAAACAT
	CAAwAmGCCC
1151	GTCAAAATCG CCATCTTCAC GCTCATCTGC mCGCAGTTGA
	TGAACCTTGs
1201	CTTTAyCGGC CCACTrrAAC rCasTCGGAC TTTCGCTTGC
	CATCGGTCTG
1251	GGCGCGTGTA TCAATGCCGG ATTGTTGTTT TACCTGTTGC
	GCAGACACGG
1301	TATTTACCAA CCTGG.CAAG GGTTGGGCAG CGTTCTT.AG
	CAAAAATGCT
1351	GcTCTCGCTC GCCGTGA

This corresponds to the amino acid sequence <SEQ ID 114; ORF20>:

1	MNMLGALAKV GSLTMVSRVL GFVRDTVIAR AFGAGMATDA
	FFVAFKLPNL
51	LRRVFAEGAF AQAFVPILAE YKETRSKEAX EAFIRHVAGM
	LSFVLVIVTA
101	LGILAAPWVI YVSAPSFAQD ADKFQLSIDL LRITFPYILL
	ISLSSFVGSV
151	LNSYHKFGIP AFTPXFLNVS FIVFALFFVP YFDPPVTAXA
	WAVFVGGILQ
201	LXFQLPWLAK LGFLKLPKLS FKDAAVNRVM KQMAPAILGV
	SVAQVSLVIN
251	TIFASYLQSG SVSWMYYADR MMELPSGVLG AALGTILLPT
	LSKHSANQDT
301	EQFSALLDWG LRLCMLLTLP AAVGLAVLSF PLVATLFMYR
	XFTLFDAQMT
351	QHALIAYSFG LIGLIMIKVL APGFYARQNI XXPVKIAIFT
	LICXQLMNLX
401	FXGPLXXIGL SLAIGLGACI NAGLLFYLLR RHGIYQPXQG
	LGSVLXQKCC
451	SRSP*

These sequences were elaborated, and the complete DNA sequence <SEQ ID 115> is:

1	ATGAATATGC TGGGAGCTTT GGCAAAAGTC GGCAGCCTGA
	CGATGGTGTC
51	GCGCGTTTTG GGATTTGTGC GCGATACGGT CATTGCGCGG
	GCATTCGGCG
101	CGGGTATGGC GACGGATGCG TTTTTTGTCG CGTTCAAACT
	GCCCAACCTG
151	CTTCGCCGCG TGTTTGCGGA GGGGGCGTTT GCCCAAGCGT
	TTGTGCCGAT
201	TTTGGCGGAA TACAAGGAAA CGCGTTCAAA AGAGGCGGCG
	GAGGCTTTTA
251	TCCGCCATGT GGCGGGGATG CTGTCGTTTG TACTGGTTAT
	CGTTACCGCG
301	CTGGGCATAC TTGCCGCGCC TTGGGTGATT TATGTTTCCG
	CACCCGGTTT
351	TGCCCAAGAT GCCGACAAAT TTCAGCTCTC CATCGATTTG
	CTGCGGATTA
401	CGTTTCCTTA TATATTATTG ATTTCCCTGT CTTCATTTGT
	CGGCTCGGTA
451	CTCAATTCTT ATCATAAGTT CGGCATTCCG GCGTTTACGC
	CCACGTTTCT
501	GAACGTGTCG TTTATCGTAT TCGCGCTGTT TTTCGTGCCG
	TATTTCGATC
551	CGCCCGTTAC CGCGCTGGCG TGGGCGGTCT TTGTCGGCGG
	CATTTTGCAA
601	CTCGGCTTCC AACTGCCCTG GCTGGCGAAA CTGGGCTTTT
	TGAAACTGCC
651	CAAACTGAGT TTCAAAGATG CGGCGGTCAA CCGCGTGATG
	AAACAGATGG
701	CGCCTGCGAT TTTGGGCGTG AGCGTGGCGC AGGTTTCTTT
	GGTGATCAAC
751	ACGATTTTCG CGTCTTATCT GCAATCGGGC AGCGTTTCAT
	GGATGTATTA
801	CGCCGACCGC ATGATGGAGC TGCCCAGCGG CGTGCTGGGG
	GCGGCACTCG
851	GTACGATTTT GCTGCCGACT TTGTCCAAAC ACTCGGCAAA
	CCAAGATACG
901	GAACAGTTTT CCGCCCTGCT CGACTGGGGT TTGCGCCTGT
	GCATGCTGCT
951	GACGCTGCCG GCGGCGGTCG GACTGGCGGT GTTGTCGTTC
	CCGCTGGTGG
1001	CGACGCTGTT TATGTACCGC GAATTTACGC TGTTTGACGC
	GCAGATGACG
1051	CAACACGCGC TGATTGCCTA TTCTTTCGGT TTAATCGGCT
	TAATCATGAT
1101	TAAAGTGTTG GCACCCGGCT TCTATGCGCG GCAAAACATC
	AAAACGCCCG
1151	TCAAAATCGC CATCTTCACG CTCATCTGCA CGCAGTTGAT
	GAACCTTGCC
1201	TTTATCGGCC CACTGAAACA CGTCGGACTT TCGCTTGCCA
	TCGGTCTGGG
1251	CGCGTGTATC AATGCCGGAT TGTTGTTTTA CCTGTTGCGC
	AGACACGGTA
1301	TTTACCAACC TGGCAAGGGT TGGGCAGCGT TCTTAGCAAA
	AATGCTGCTC
1351	TCGCTCGCCG TGATGTGCGG CGGACTGTGG GCAGCGCAGG
	CTTACCTGCC
1401	GTTTGAATGG GCGCACGCCG GCGGAATGCG GAAAGCGGGG
	CAGCTCTGCA
1451	TCCTGATTGC CGTCGGCGGC GGACTGTATT TCGCATCACT
	GGCGGCTTTG
1501	GGCTTCCGTC CGCGCCATTT CAAACGCGTG GAAAACTGA

This corresponds to the amino acid sequence <SEQ ID 116; ORF20-1>:

1	MNMLGALAKV GSLTMVSRVL GFVRDTVIAR AFGAGMATDA
	FFVAFKLPNL
51	LRRVFAEGAF AQAFVPILAE YKETRSKEAA EAFIRHVAGM
	LSFVLVIVTA
101	LGILAAPWVI YVSAPGFAQD ADKFQLSIDL LRITFPYILL
	ISLSSFVGSV
151	LNSYHKFGIP AFTPTFLNVS FIVFALFFVP YFDPPVTALA
	WAVFVGGILQ
201	LGFQLPWLAK LGFLKLPKLS FKDAAVNRVM KQMAPAILGV
	SVAQVSLVIN
251	TIFASYLQSG SVSWMYYADR MMELPSGVLG AALGTILLPT
	LSKHSANQDT
301	EQFSALLDWG LRLCMLLTLP AAVGLAVLSF PLVATLFMYR
	EFTLFDAQMT
351	QHALIAYSFG LIGLIMIKVL APGFYARQNI KTPVKIAIFT
	LICTQLMNLA
401	FIGPLKHVGL SLAIGLGACI NAGLLFYLLR RHGIYQPGKG
	WAAFLAKMLL
451	SLAVMCGGLW AAQAYLPFEW AHAGGMRKAG QLCILIAVGG
	GLYFASLAAL
501	GFRPRHFKRV EN*

Computer analysis of this amino acid sequence gave the following results:

Homology with the MviN Virulence Factor of S. typhimurium (Accession Number P37169)

ORF20 and MviN proteins show 63% aa identity in 440aa overlap:

Orf20	1	MNMLGALAKVGSLTMVSRVLGFVRDTVIARAFGAGMATDAFFVAFKLPNLLRRVFAEGAF	60
		MN+L +LA V S+TM SRVLGF RD ++AR FGAGMATDAFFVAFKLPNLLRR+FAEGAF
MviN	14	MNLLKSLAAVSSMTMFSRVLGFARDAIVARIFGAGMATDAFFVAFKLPNLLRRIFAEGAF	73
Orf20	61	AQAFVPILAEYKETRSKEAXEAFIRHVAGMLSFVLVIVTALGILAAPWVIYVSAPSFAQD	120
		+QAFVPILAEYK  + +EA   F+ +V+G+L+  L +VT  G+LAAPWVI V+AP FA
MviN	74	SQAFVPILAEYKSKQGEEATRIFVAYVSGLLTLALAVVTVAGMLAAPWVIMVTAPGFADT	133
Orf20	121	ADKFQLSIDLLRITFPYILLISLSSFVGSVLNSYHKFGIPAFTPXFLNVSFIVFALFFVP	180
		ADKF L+  LLRITFPYILLISL+S VG++LN++++F IPAF P FLN+S I FALF  P
MviN	134	ADKFALTTQLLRITFPYILLISLASLVGAILNTWNRFSIPAFAPTFLNISMIGFALFAAP	193
Orf20	181	YFDPPVTAXAWAVFVGGILQLXFQLPWLAKLGFLKLPKLSFKDAAVNRVMKQMAPAILGV	240
		YF+PPV A AWAV VGG+LQL +QLP+L K+G L LP+++F+D    RV+KQM PAILGV
MviN	194	YFNPPVLALAWAVTVGGVLQLVYQLPYLKKIGMLVLPRINFRDTGAMRVVKQMGPAILGV	253
Orf20	241	SVAQVSLVINTIFASYLQSGSVSWMYYADRMMELPSGVLGAALGTILLPTLSKHSANQDT	300
		SV+Q+SL+INTIFAS+L SGSVSWMYYADR+ME PSGVLG ALGTILLP+LSK  A+ +
MviN	254	SVSQISLIINTIFASFLASGSVSWMYYADRLMEFPSGVLGVALGTILLPSLSKSFASGNH	313
Orf20	301	EQFSALLDWGLRLCMLLTLPAAVGLAVLSFPLVATLFMYRXFTLFDAQMTQHALIAYSFG	360
		+++  L+DWGLRLC LL LP+AV L +L+ PL  +LF Y  FT FDA MTQ ALIAYS G
MviN	314	DEYCRLMDWGLRLCFLLALPSAVALGILAKPLTVSLFQYGKFTAFDAAMTQRALIAYSVG	373
Orf20	361	LIGLIMIKVLAPGFYARQNIXXPVKIAIFTLICXQLMNLXFXXXXXXXXXXXXXXXXXCI	420
		LIGLI++KVLAPGFY+RQ+I  PVKIAI TLI  QLMNL F                 C+
MviN	374	LIGLIVVKVLAPGFYSRQDIKTPVKIAIVTLIMTQLMNLAFIGPLKHAGLSLSIGLAACL	433
Orf20	421	NAGLLFYLLRRHGIYQPXQG	440
		NA LL++ LR+  I+ P  G
MviN	434	NASLLYWQLRKQNIFTPQPG	453

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF20 shows 93.5% identity over a 447aa overlap with an ORF (ORF20a) from strain A of N. meningitidis:

The complete length ORF20a nucleotide sequence <SEQ ID 117> is:

1	ATGAATATGC TGGGAGCTTT GGTAAAAGTC GGCAGCCTGA
	CGATGGTGTC
51	GCGCGTTTTG GGATTTGTGC GCGATACGGT CATTGCGCGC
	GCATTCGGCG
101	CAGGCATGGC GACGGATGCG TTCTTTGTCG CGTTCAAACT
	GCCCAACCTG
151	CTTCGCCGCG TGTTTGCGGA GGGGGCGTTT GCCCAAGCGT
	TTGTGCCGAT
201	TTTGGCGGAA TATAAGGAAA CGCGTTCTAA AGAGGCGACG
	GAGGCTTTTA
251	TCCGCCATGT GGCGGGGATG CTGTCGTTTG TACTGGTCAT
	CGTTACCGCG
301	CTGGGCATAC TTGCCGCGCC TTGGGTGATT TATGTTTCCG
	CACCCGGTTT
351	TGCCAAAGAT GCCGACAAAT TTCAGCTCTC TATCGATTTG
	CTGCGGATTA
401	CGTTTCCTTA TATCTTATTG ATTTCACTTT CCTCTTTTGT
	CGGCTCGGTA
451	CTCAATTCCT ATCATAAATT CAGCATTCCT GCGTTTACGC
	CCACGTTCCT
501	GAACGTGTCG TTTATCGTAT TCGCGCTGTT TTTCGTGCCG
	TATTTCGATC
551	CTCCCGTTAC CGCGCTGGCT TGGGCGGTTT TTGTCGGCGG
	CATTTTGCAA
601	CTCGGCTTCC AACTGCCCTG GCTGGCGAAA CTGGGTTTTT
	TGAAACTGCC
651	CAAACTGAGT TTCAAAGATG CGGCGGTCAA CCGCGTGATG
	AAACAGATGG
701	CGCCTGCGAT TTTGGGCGTG AGCGTGGCGC AGATTTCTTT
	GGTGATCAAC
751	ACGATTTTCG CGTCTTATCT GCAATCGGGC AGCGTTTCAT
	GGATGTATTA
801	CGCCGACCGC ATGATGGAAC TGCCCGGCGG CGTGCTGGGG
	GCGGCACTCG
851	GTACGATTTT GCTGCCGACT TTGTCCAAAC ACTCGGCAAA
	CCAAGATACG
901	GAACAGTTTT CCGCCCTGCT CGACTGGGGT TTGCGCNTGT
	GCATGCTGCT
951	GACGCTGCCG GCGGCGGTCG GAATGGCGGT GTTGTCGTTC
	CCGCTGGTGG
1001	CAACCTTGTT TATGTACCGA GAATTCACGC TGTTTGACGC
	GCAGATGACG
1051	CAACACGCGC TGATTGCCTA TTCTTTCGGT TTAATCGGTT
	TAATCATGAT
1101	TAAAGTGTTG GCGCCCGGCT TTTATGCGCG GCAAAACATC
	AAAACGCCCG
1151	TCAAAATCGC CATCTTCACG CTCATTTGCA CGCAGTTGAT
	GAACCTTGCC
1201	TTTATCGGCC CACTGAAACA CGTCGGACTT TCGCTTGCCA
	TCGGTCTGGG
1251	CGCGTGTATC AATGCCGGAT TGTTGTTTTA CCTGTTGCGC
	AGACACGGTA
1301	TTTACCAACC TGGCAAGGGT TGGGCAGCGT TCTTGGCAAA
	AATGCTGCTC
1351	TCGCTCGCCG TGATGGGAGG CGGCCTGTAT GCCGCCCAAA
	TCTGGCTGCC
1401	GTTCGACTGG GCACACGCCG GCGGAATGCA AAAGGCCGCC
	CGGCTCTTCA
1451	TCCTGATTGC CGTCGGCGGC GGACTGTATT TCGCATCACT
	GGCGGCTTTG
1501	GGCTTCCGTC CGCGCCATTT CAAACGCGTG GAAAGCTGA

This encodes a protein having amino acid sequence <SEQ ID 118>:

1	MNMLGALVKV GSLTMVSRVL GFVRDTVIAR AFGAGMATDA
	FFVAFKLPNL
51	LRRVFAEGAF AQAFVPILAE YKETRSKEAT EAFIRHVAGM
	LSFVLVIVTA
101	LGILAAPWVI YVSAPGFAKD ADKFQLSIDL LRITFPYILL
	ISLSSFVGSV
151	LNSYHKFSIP AFTPTFLNVS FIVFALFFVP YFDPPVTALA
	WAVFVGGILQ
201	LGFQLPWLAK LGFLKLPKLS FKDAAVNRVM KQMAPAILGV
	SVAQISLVIN
251	TIFASYLQSG SVSWMYYADR MMELPGGVLG AALGTILLPT
	LSKHSANQDT
301	EQFSALLDWG LRXCMLLTLP AAVGMAVLSF PLVATLFMYR
	EFTLFDAQMT
351	QHALIAYSFG LIGLIMIKVL APGFYARQNI KTPVKIAIFT
	LICTQLMNLA
401	FIGPLKHVGL SLAIGLGACI NAGLLFYLLR RHGIYQPGKG
	WAAFLAKMLL
451	SLAVMGGGLY AAQIWLPFDW AHAGGMQKAA RLFILIAVGG
	GLYFASLAAL
501	GFRPRHFKRV ES*

ORF20a and ORF20-1 show 96.5% identity in 512 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF20 shows 92.1% identity over a 454aa overlap with a predicted ORF (ORF20ng) from N. gonorrhoeae:

An ORF20ng nucleotide sequence <SEQ ID 119> was predicted to encode a protein having amino acid sequence <SEQ ID 120>:

1	MNMLGALAKV GSLTMVSRVL GFVRDTVIAR AFGAGMATDA
	FFVAFKLPNL
51	LRRVFAEGAF AQAFVPILAE YKETRSKEAT EAFIRHVAGM
	LSFVLIVVTA
101	LGILAAPWVI YVSAPGFTKD ADKFQLSISL LRITFPYILL
	ISLSSFVGSI
151	LNSYHKFGIP AFTPTFLNIS FIVFALFFVP YFDPPVTALA
	WAVFVGGILQ
201	LGFQLPWLAK LGFLKLPKLN FKDAAVNRVM KQMAPAILGV
	SVAQISLVIN
251	TIFASYLQSG SVSWMYYADR MMELPGGVLG AALGTILLPT
	LSKHSANQDT
301	EQFSALLDWG LRLCMLLTLP AAAGLAVLSF PLVATLFMYR
	EFTLFDAQMT
351	QHALIAYSFG LIGLIMIKVL ASGFYARQNI KTPVKIAIFT
	LICTQLMNLA
401	FIGPLKHAGL SLAIGLGACI NAGLLFFLFR KHGIYRPGQG
	LGQPSWRKCC
451	SRSP*

Further DNA sequence analysis revealed the following DNA sequence <SEQ ID 121>:

1	ATGAATATGC TTGGAGCTTT GGCAAAAGTC GGCAGCCTGA
	CGATGGTGTC
51	GCGCGTTTTG GGATTTGTGC GCGATACGGT CATTGCGCGG
	GCATTCGGCG
101	CGGGTATGGC GACGGATGCG TTTTTTGTCG CGTTCAAACT
	GCCCAACCTG
151	CTTCGCCGCG TGTTTGCGGA GGGGGCGTTT GCCCAAGCGT
	TTGTGCCGAT
201	TTTGGCGGAA TATAAGGAAA CGCGTTCTAA AGAGGCGAcg
	gAGGCTTTTA
251	TCCGCCACGt tgcgggAatg CTGTCGTTTG TGCTGATcgt
	cGttacCGCG
301	CTGGGCATAC TTGCCGCgcc tTGGGTGATT TATGTTtccg
	CgcccGGCTT
351	TACCAAAGAC GCGGACAAGT TCCAACTTTC CATCAGCCTG
	CTGCGGATTA
401	CGTTTCCTTA TATATTATTG ATTTCTTTGT CTTCTTTTGT
	CGGCTCGATA
451	CTCAATTCCT ACCATAAGTT CGGCATTCCC GCGTTTACGC
	CCACGTTTTT
501	AAACATCTCT TTTATCGTAT TCGCACTGTT TTTCGTGCCG
	TATTTCGATC
551	CGCCCGTTAC CGCGCTGGCG TGGGCGGTTT TTGTCGGCGG
	TATTTTGCAG
601	CTCGGTTTCC AACTGCCGTG GCTGGCGAAA CTGGGCTTTT
	TGAAACTGCC
651	CAAACTGAAT TTCAAAGATG CGGCGGTCAA CCGCGTCATG
	AAACAGATGG
701	CGCCTGCGAT TTTGGGCGTG agcgTGGCGC AAATTTCTTT
	GgttATCAAC
751	ACGATTTTCG CGTCTTATCT GCAATCGGGC AGCGTTTCAT
	GGATGTatta
801	cgCCGACCGC ATGATGGAGc tgcgccGGGG CGTGCTGGGG
	GCTGCACTCG
851	GTACAATTTT GCTGCCGACT TTGTCCAAAC ACTCGGCAAA
	CCAAGATACG
901	GAACAGTTTT CCGCCCTGCT CGACTGGGGT TTGCGCCTGT
	GCATGCTGCT
951	GACGCTGCCG GCGGCGGccg GACTGGCGGT ATTGTCGTTC
	CCGCTGGTGG
1001	CGACGCTGTT TATGTACCGA GAATTCACGC TGTTTGACGC
	ACAAATGACG
1051	CAACACGCGC TGATTGCCTA TTCTTTCGGT TTAATCGGTT
	TAATTATGAT
1101	TAAAGTGTTG GCATCCGGCT TTTATGCGCG GCAAAACATC
	AAAACGCCCG
1151	TCAAAATCGC CATCTTCACG CTCATCTGCA CGCAGTTGAT
	GAACCTCGCC
1201	TTTATCGGTC CGTTGAAACA CGCCGGGCTT TCGCTCGCCA
	TCGGCCTGGG
1251	CGCGTGCATC AACGCCGGAT TGTTGTTCTT CCTGTTGCGC
	AAACACGGTA
1301	TTTACCGGCC cggcaggggt tgggcggcgt TCTTGGCGAA
	AATGCTGCTC
1351	GCGCTCGCCG TGATGTGCGG CGGACTGTGG GCGGCGCAGG
	CTTGCCTGCC
1401	GTTCGAATGG GCGCACGCCG GCGGAATGCG GAAAGCGGGG
	CAGCTCTGCA
1451	TCCTGATTGC CGTCGGCGGC GGACTGTATT TCGCATCTCT
	GGCGGCTTTG
1501	GGCTTCCGTC CGCGCCATTT CAAACGCGTG GAAAGCTGA

This encodes the following amino acid sequence <SEQ ID 122; ORF20ng-1>:

1	MNMLGALAKV GSLTMVSRVL GFVRDTVIAR AFGAGMATDA
	FFVAFKLPNL
51	LRRVFAEGAF AQAFVPILAE YKETRSKEAT EAFIRHVAGM
	LSFVLIVVTA
101	LGILAAPWVI YVSAPGFTKD ADKFQLSISL LRITFPYILL
	ISLSSFVGSI
151	LNSYHKFGIP AFTPTFLNIS FIVFALFFVP YFDPPVTALA
	WAVFVGGILQ
201	LGFQLPWLAK LGFLKLPKLN FKDAAVNRVM KQMAPAILGV
	SVAQISLVIN
251	TIFASYLQSG SVSWMYYADR MMELRRGVLG AALGTILLPT
	LSKHSANQDT
301	EQFSALLDWG LRLCMLLTLP AAAGLAVLSF PLVATLFMYR
	EFTLFDAQMT
351	QHALIAYSFG LIGLIMIKVL ASGFYARQNI KTPVKIAIFT
	LICTQLMNLA
401	FIGPLKHAGL SLAIGLGACI NAGLLFFLLR KHGIYRPGRG
	WAAFLAKMLL
451	ALAVMCGGLW AAQACLPFEW AHAGGMRKAG QLCILIAVGG
	GLYFASLAAL
501	GFRPRHFKRV ES*

ORF20ng-1 and ORF20-1 show 95.7% identity in 512 aa overlap:

In addition, ORF20ng-1 shows significant homology with a virulence factor of S. typhimurium:

sp|P37169|MVIN_SALTY VIRULENCE FACTOR MVIN pir||S40271 mviN protein -
Salmonella typhimurium gi|438252 (Z26133) mviB gene product
[Salmonella typhimurium] gnl|PID|d1005521 (D25292) ORF2
[Salmonella typhimurium] Length = 524
Score = 1573 (750.1 bits), Expect = 1.1e−220, Sum P(2) = 1.1e−220
Identities = 309/467 (66%), Positives = 368/467 (78%)

Query:	1	MNMLGALAKVGSLTMVSRVLGFVRDTVIARAFGAGMATDAFFVAFKLPNLLRRVFAEGAF	60
		MN+L +LA V S+TM SRVLGF RD ++AR FGAGMATDAFFVAFKLPNLLRR+FAEGAF
Sbjct:	14	MNLLKSLAAVSSMTMFSRVLGFARDAIVARIFGAGMATDAFFVAFKLPNLLRRIFAEGAF	73
Query:	61	AQAFVPILAEYKETRSKEATEAFIRHVAGMLSFVLIVVTALGILAAPWVIYVSAPGFTKD	120
		+QAFVPILAEYK  + +EAT  F+ +V+G+L+  L VVT  G+LAAPWVI V+APGF
Sbjct:	74	SQAFVPILAEYKSKQGEEATRIFVAYVSGLLTLALAVVTVAGMLAAPWVIMVTAPGFADT	133
Query:	121	ADKFQLSISLLRITFPYILLISLSSFVGSILNSYHKFGIPAFTPTFLNISFIVFALFFVP	180
		ADKF L+  LLRITFPYILLISL+S VG+ILN++++F IPAF PTFLNIS I FALF  P
Sbjct:	134	ADKFALTTQLLRITFPYILLISLASLVGAILNTWNRFSIPAFAPTFLNISMIGFALFAAP	193
Query:	181	YFDPPVTALAWAVFVGGILQLGFQLPWLAKLGFLKLPKLNFKDAAVNRVMKQMAPAILGV	240
		YF+PPV ALAWAV VGG+LQL +QLP+L K+G L LP++NF+D    RV+KQM PAILGV
Sbjct:	194	YFNPPVLALAWAVTVGGVLQLVYQLPYLKKIGMLVLPRINFRDTGAMRVVKQMGPAILGV	253
Query:	241	SVAQISLVINTIFASYLQSGSVSWMYYADRMMELRRGVLGAALGTILLPTLSKHSANQDT	300
		SV+QISL+INTIFAS+L SGSVSWMYYADR+ME   GVLG ALGTILLP+LSK  A+ +
Sbjct:	254	SVSQISLIINTIFASFLASGSVSWMYYADRLMEFFSGVLGVALGTILLPSLSKSFASGNH	313
Query:	301	EQFSALLDWGLRLCMLLTLPAAAGLAVLSFPLVATLFMYREFTLFDAQMTQHALIAYSFG	360
		+++  L+DWGLRLC LL LP+A  L +L+ PL  +LF Y +FT FDA MTQ ALIAYS G
Sbjct:	314	DEYCRLMDWGLRLCFLLALPSAVALGILAKPLTVSLFQYGKFTAFDAAMTQRALIAYSVG	373
Query:	361	LIGLIMIKVLASGFYARQNIKTPVKIAIFTLICTQLMNLAFIGPLKHAGLSLAIGLGACI	420
		LIGLI++KVLA GFY+RQ+IKTPVKIAI TLI TQLMNLAFIGPLKHAGLSL+IGL AC+
Sbjct:	374	LIGLIVVKVLAPGFYSRQDIKTPVKIAIVTLIMTQLMNLAFIGPLKHAGLSLSIGLAACL	433
Query:	421	NAGLLFFLLRKHGIYRPGRGWXXXXXXXXXXXXVMCGGLWAAQACLP	467
		NA LL++ LRK  I+ P  GW            VM   L+     +P
Sbjct:	434	NASLLYWQLRKQNIFTPQPGWMWFLMRLIISVLVMAAVLFGVLHIMP	480

Score = 70 (33.4 bits), Expect = 1.1e−220, Sum P(2) = 1.1e−220
Identities = 14/41 (34%), Positives = 23/41 (56%)

Query:	469	EWAHAGGMRKAGQLCILIAVGGGLYFASLAALGFRPRHFKR	509
		EW+    + +  +L  ++  G   YFA+LA LGF+ + F R
Sbjct:	481	EWSQGSMLWRLLRLMAVVIAGIAAYFAALAVLGFKVKEFVR	521

Based on this analysis, including the homology with a virulence factor from S. typhimurium, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 15

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 123>:

1	atGATTAAAA TCAAAAAAGG TCTAAACCTG CCCATCGCGG
	GCAGACCGGA
51	GCAAGCCGTT tACGACGGCC CGGCCaTTAC CGAAGtCGCG
	TTGCTTGGCG
101	AAGAATATGC CGGTATGCGC CCCTCGATGA AAGTCAAGGA
	AGGCGATGCC
151	GTcAAAAAAG GCCAAGTGCT GTTTGAAGAC AAAAAGAATC
	CGGGCGTGGT
201	GTTTACTGCG CCGGCTTCAG GcAAAATCGC CGCGATTCAC
	CGTGGCGAAA
251	AGCGCGTACT TCAGTCAGTC GTGATTGCCG TTGAArGCAA
	CGACGAAATC
301	GAGTTTGAAC GCTACGCACC TGAAGCGCTG GCAAACTTAA
	GCGGCGAAGA
351	AGTGCGCCGC AACCTGATCC AATCCGGTTT GTGGACTGCG
	CTGCGCACCC
401	GTCCGTTCAG CAAAATTCCT GCCGTCGATG CCGAGCCGTT
	CGCCATCTTC
451	GTCAATGCGA tGGACACCAA TCCG..

This corresponds to the amino acid sequence <SEQ ID 124; ORF22>:

1	MIKIKKGLNL PIAGRPEQAV YDGPAITEVA LLGEEYAGMR
	PSMKVKEGDA
51	VKKGQVLFED KKNPGVVFTA PASGKIAAIH RGEKRVLQSV
	VIAVEXNDEI
101	EFERYAPEAL ANLSGEEVRR NLIQSGLWTA LRTRPFSKIP
	AVDAEPFAIF
151	VNAMDTNP..

Further work revealed the complete nucleotide sequence <SEQ ID 125>:

1	ATGATTAAAA TCAAAAAAGG TCTAAACCTG CCCATCGCGG
	GCAGACCGGA
51	GCAAGCCGTT TACGACGGCC CGGCCATTAC CGAAGTCGCG
	TTGCTTGGCG
101	AAGAATATGC CGGTATGCGC CCCTCGATGA AAGTCAAGGA
	AGGCGATGCC
151	GTCAAAAAAG GCCAAGTGCT GTTTGAAGAC AAAAAGAATC
	CGGGCGTGGT
201	GTTTACTGCG CCGGCTTCAG GCAAAATCGC CGCGATTCAC
	CGTGGCGAAA
251	AGCGCGTACT TCAGTCAGTC GTGATTGCCG TTGAAGGCAA
	CGACGAAATC
301	GAGTTTGAAC GCTACGCACC TGAAGCGCTG GCAAACTTAA
	GCGGCGAAGA
351	AGTGCGCCGC AACCTGATCC AATCCGGTTT GTGGACTGCG
	CTGCGCACCC
401	GTCCGTTCAG CAAAATTCCT GCCGTCGATG CCGAGCCGTT
	CGCCATCTTC
451	GTCAATGCGA TGGACACCAA TCCGCTGGCT GCCGACCCTA
	CGGTCATTAT
501	CAAAGAAGCC GCCGAGGATT TCAAACGCGG CCTGTTGGTA
	TTGAGCCGTT
551	TGACCGAACG CAAAATCCAT GTTTGTAAGG CAGCTGGCGC
	AGACGTGCCG
601	TCTGAAAATG CTGCCAACAT CGAAACACAT GAATTCGGCG
	GCCCGCATCC
651	TGCCGGTTTG AGTGGCACGC ACATTCATTT CATCGAGCCG
	GTCGGCGCGA
701	ATAAAACCGT GTGGACCATC AATTATCAAG ATGTAATTAC
	CATTGGCCGT
751	TTGTTTGCAA CAGGCCGTCT GAACACCGAG CGCGTGATTG
	CCCTAGGTGG
801	TTCTCAAGTC AACAAACCGC GCCTCTTGCG TACCGTTTTG
	GGTGCGAAAG
851	TATCGCAAAT TACTGCGGGC GAATTGGTTG ACACAGACAA
	CCGCGTGATT
901	TCCGGTTCGG TATTGAACGG CGCGATTACA CAAGGCGCGC
	ACGATTATTT
951	GGGACGCTAC CACAATCAGA TTTCCGTTAT CGAAGAAGGC
	CGCAGCAAAG
1001	AGCTGTTCGG CTGGGTTGCG CCGCAGCCGG ACAAATACTC
	CATCACGCGT
1051	ACAACCCTCG GCCATTTCCT GAAAAACAAA CTCTTCAAGT
	TCAACACAGC
1101	CGTCAACGGC GGCGACCGCG CCATGGTGCC GATTGGTACT
	TACGAGCGCG
1151	TGATGCCCTT GGATATCCTG CCCACCCTGC TTTTGCGCGA
	TTTAATCGTC
1201	GGCGATACCG ACAGCGCGCA GGCATTGGGT TGCTTGGAAT
	TGGACGAAGA
1251	AGACCTCGCT TTGTGCAGCT TCGTCTGCCC GGGCAAATAC
	GAATACGGCC
1301	CGCTGTTGCG CAAAGTGCTG GAAACCATTG AGAAGGAAGG
	CTGA

This corresponds to the amino acid sequence <SEQ ID 126; ORF22-1>:

1	MIKIKKGLNL PIAGRPEQAV YDGPAITEVA LLGEEYAGMR
	PSMKVKEGDA
51	VKKGQVLFED KKNPGVVFTA PASGKIAAIH RGEKRVLQSV
	VIAVEGNDEI
101	EFERYAPEAL ANLSGEEVRR NLIQSGLWTA LRTRPFSKIP
	AVDAEPFAIF
151	VNAMDTNPLA ADPTVIIKEA AEDFKRGLLV LSRLTERKIH
	VCKAAGADVP
201	SENAANIETH EFGGPHPAGL SGTHIHFIEP VGANKTVWTI
	NYQDVITIGR
251	LFATGRLNTE RVIALGGSQV NKPRLLRTVL GAKVSQITAG
	ELVDTDNRVI
301	SGSVLNGAIT QGAHDYLGRY HNQISVIEEG RSKELFGWVA
	PQPDKYSITR
351	TTLGHFLKNK LFKFNTAVNG GDRAMVPIGT YERVMPLDIL
	PTLLLRDLIV
401	GDTDSAQALG CLELDEEDLA LCSFVCPGKY EYGPLLRKVL
	ETIEKEG*

Further work identified the corresponding gene in strain A of N. meningitidis <SEQ ID 127>:

1	ATGATTAAAA TCAAAAAAGG TCTAAACCTG CCCATCGCGG
	GCAGACCGGA
51	GCAAGTCATT TATGACGGGC CCGTCATTAC CGAAGTCGCG
	TTGCTTGGCG
101	AAGAATATGC CGGTATGCGC CCCTNGATGA AAGTCAAGGA
	AGGCGATGCC
151	GTCAAAAAAG GCCAAGTGCT GTTTGAAGAC AAAAAGNATC
	CGGGCGTGGT
201	GTTTACCGCG CCNGTTTCAG GCAAAATCGC CGCCATCCAT
	CGCGGCGAAA
251	AGCGCGTACT TCAGTCGGTC GTGATTGCCG TTGAAGGCAA
	CGACGAAATC
301	GAGTTCGAAC GCTACGCGCC CGAAGCGTTG GCAAACTTAA
	GCGGCGANGA
351	ANTNNGNNGC AATCTGATCC AATCCGGTTT GTGGACTGCG
	CTGCGTANCC
401	GTCCGTTCAG CAAAATCCCT GCCGTCGATG CCGAGCCGTT
	CGCCATCTTC
451	GTCAATGCGA TGGACACCAA TCCGCTNGCG GCAGACCCTG
	TGGTTGTGAT
501	CAAAGAAGCC GNCGANGATT TCAGACGANG TNTGCTGGTA
	TTGAGCCGTT
551	TGACCGAGCG TAAAATCCAT GTGTGTAAGG CAGCTGGCGC
	AGACGTGCCG
601	TCTGAAAATG CTGCCAACAT CGAAACACAT GAATTCGGCG
	GCCCGCATCC
651	GGCCGGTTTG AGTGGCACGC ACATTCATTT CATTGAGCCG
	GTCGGTGCAA
701	ACAAAACCGT TTGGACCATC AATTATCAAG ATGTAATTGC
	CATCGGACGT
751	TTGTTTGCAA CAGGCCGTCT GAACACCGAG CGCGTGATTG
	CTTTGGGTGG
801	TTCTCAAGTC AACAAACCAC GCCTCTTGCG TACCGTTTTG
	GGTGCGAAAG
851	TATCGCAAAT TACTGCGGGC GAATTGGTTG ACGCAGACAA
	CCGCGTGATT
901	TCCGGTTCGG TATTGAACGG CGCGATTACA CAAGGCGCGC
	ACGATTATTT
951	GGGACGCTAC CACAATCAGA TTTCCGTTAT CGAAGAAGGC
	CGCAGCAAAG
1001	AGCTGTTCGG CTGGGTTGCG CCGCAGCCGG ACAAATACTC
	CATCACGCGT
1051	ACGACCCTCG GCCATTTCCT GAAAAACAAA CTCTTCAAGT
	TCACGACAGC
1101	CGTCAACGGT GGCGACCGCG CCATGGTGCC GATTGGTACT
	TACGAGCGCG
1151	TAATGCCGCT AGACATCCTG CCTACCCTGC TTTTGCGCGA
	TTTAATCGTC
1201	GGCGATACCG ACAGCGCGCA AGCATTGGGT TGCTTGGAAT
	TGGACGAAGA
1251	AGACCTCGCT TTGTGCAGCT TCGTCTGCCC GGGCAAATAC
	GAATANGGCC
1301	CGCTGTTGCG TAAGGTGCTG GAAACCNTTG AGAAGGAAGG
	CTGA

This encodes a protein having amino acid sequence <SEQ ID 128; ORF22a>:

1	MIKIKKGLNL PIAGRPEQVI YDGPVITEVA LLGEEYAGMR
	PXMKVKEGDA
51	VKKGQVLFED KKXPGVVFTA PVSGKIAAIH RGEKRVLQSV
	VIAVEGNDEI
101	EFERYAPEAL ANLSGXEXXX NLIQSGLWTA LRXRPFSKIP
	AVDAEPFAIF
151	VNAMDTNPLA ADPVVVIKEA XXDFRRXXLV LSRLTERKIH
	VCKAAGADVP
201	SENAANIETH EFGGPHPAGL SGTHIHFIEP VGANKTVWTI
	NYQDVIAIGR
251	LFATGRLNTE RVIALGGSQV NKPRLLRTVL GAKVSQITAG
	ELVDADNRVI
301	SGSVLNGAIT QGAHDYLGRY HNQISVIEEG RSKELFGWVA
	PQPDKYSITR
351	TTLGHFLKNK LFKFTTAVNG GDRAMVPIGT YERVMPLDIL
	PTLLLRDLIV
401	GDTDSAQALG CLELDEEDLA LCSFVCPGKY EXGPLLRKVL
	ETXEKEG*

The originally-identified partial strain B sequence (ORF22) shows 94.2% identity over a 158aa overlap with ORF22a:

The complete strain B sequence (ORF22-1) and ORF22a show 94.9% identity in 447 aa overlap:

Further work identified a partial gene sequence <SEQ ID 129> from N. gonorrhoeae, which encodes the following amino acid sequence <SEQ ID 130; ORF22ng>:

1	MIKIKKGLNL PIAGRPEQVI YDGPAITEVA LLGEEYVGMR
	PSMKIKEGEA
51	VKKGQVLFED KKNPGVVFTA PASGKIAAIH RGEKRVLQSV
	VIAVEGNDEI
101	EFERYVPEAL AKLSSEKVRR NLIQSGLWTA LRTRPFSKIP
	AVDAEPFAIF
151	VNAMDTNPLA ADPTVIIKEA AEDFKRGLLV LSRLTERKIH
	VCKAAGADVP
201	SENAANIETH EFGGPHPAGL SGTHIHFIEP VGANKTVWTI
	NYQDVIAIGR
251	LFVTGRLNTE RVVALGGLQV NKPRLLRTVL GAKVSQLTAG
	ELVDADNRVI
301	SGSVLNGAIA QGAHDYLGRY HN*

Further work identified complete gonococcal gene <SEQ ID 131>:

1	ATGATTAAAA TCAAAAAAGG TCTAAATCTG CCCATCGCGG
	GCAGACCGGA
51	GCAAGTCATT TATGACGGCC CGGCCATTAC CGAAGTCGCG
	TTGCTTGGCG
101	AAGAATATGT CGGCATGCGC CCCTCGATGA AAATCAAGGA
	AGGTGAAGCC
151	GTCAAAAAAG GCCAAGTGCT GTTTGAAGAC AAAAAGAATC
	CGGGCGTAGT
201	ATTTACTGCG CCGGCTTCAG GCAAAATCGC CGCTATTCAC
	CGTGGCGAAA
251	AGCGCGTACT TCAGTCAGTC GTGATTGCCG TTGAAGGCAA
	CGACGAAATC
301	GAGTTCGAAC GCTACGTACC TGAAGCGCTG GCAAAATTGA
	GCAGCGAAAA
351	AGTGCGCCGC AACCTGATTC AATCAGGCTT ATGGACTGCG
	CTTCGCACCC
401	GTCCGTTCAG CAAAATCCCT GCCGTAGATG CCGAGCCGTT
	CGCCATCTTC
451	GTCAATGCGA TGGACACCAA TCCGCTGGCT GCCGACCCTA
	CGGTCATCAT
501	CAAAGAAGCC GCCGAAGACT TCAAACGCGG CCTGTTGGTA
	TTGAGCCGCC
551	TGACCGAACG TAAAATCCAT GTGTGTAAAG CAGCAGGCGC
	AGACGTGCCG
601	TCTGAAAATG CTGCCAATAT CGAAACACAT GAATTTGGCG
	GCCCGCATCC
651	TGCCGGCTTG AGTGGCACGC ACATTCATTT CATCGAGCCA
	GTCGGCGCGA
701	ATAAAACCGT GTGGACCATC AATTATCAAG ACGTGATTGC
	TATCGGACGT
751	TTGTTCGTAA CAGGCCGTCT GAATACCGAG CGCGTGGTTG
	CCTTGGGCGG
801	CCTGCAAGTC AACAAACCGC GCCTCTTGCG TACCGTTTTG
	GGTGCGAAGG
851	TGTCTCAACT TACCGCCGGC GAATTGGTTG ACGCGGACAA
	CCGCGTGATT
901	TCCGGTTCGG TATTGAACGG TGCGATTGCA CAAGGCGCGC
	ATGATTATTT
951	GGGACGCTAC CACAATCAGA TTTCCGTTAT CGAAGAAGGC
	CGCAGCAAAG
1001	AGCTGTTCGG CTGGGTTGCG CCGCAGCCGG ACAAATACTC
	CATCACGCGC
1051	ACCACTCTCG GCCATTTCCT AAAAAACAAA CTCTTCAAGT
	TCACGACAGC
1101	CGTCAACGGC GGCGACCGCG CCATGGTACC GATCGGCACT
	TATGAGCGCG
1151	TAATGCCGTT GGACATCCTG CCTACCTTGC TTTTGCGCGA
	TTTAATCGTC
1201	GGCGATACCG ACAGCGCGCA GGCTTTGGGT TGCTTGGAAT
	TGGACGAAGA
1251	AGACCTCGCT TTGTGCAGCT TCGTCTGCCC GGGCAAATAC
	GAATACGGCC
1301	CGCTGTTGCG CAAAGTGCTG GAAACCATTG AGAAGGAAGG
	CTGA

This encodes a protein having amino acid sequence <SEQ ID 132; ORF22ng-1>:

1	MIKIKKGLNL PIAGRPEQVI YDGPAITEVA LLGEEYVGMR
	PSMKIKEGEA
51	VKKGQVLFED KKNPGVVFTA PASGKIAAIH RGEKRVLQSV
	VIAVEGNDEI
101	EFERYVPEAL AKLSSEKVRR NLIQSGLWTA LRTRPFSKIP
	AVDAEPFAIF
151	VNAMDTNPLA ADPTVIIKEA AEDFKRGLLV LSRLTERKIH
	VCKAAGADVP
201	SENAANIETH EFGGPHPAGL SGTHIHFIEP VGANKTVWTI
	NYQDVIAIGR
251	LFVTGRLNTE RVVALGGLQV NKPRLLRTVL GAKVSQLTAG
	ELVDADNRVI
301	SGSVLNGAIA QGAHDYLGRY HNQISVIEEG RSKELFGWVA
	PQPDKYSITR
351	TTLGHFLKNK LFKFTTAVNG GDRAMVPIGT YERVMPLDIL
	PTLLLRDLIV
401	GDTDSAQALG CLELDEEDLA LCSFVCPGKY EYGPLLRKVL
	ETIEKEG*

The originally-identified partial strain B sequence (ORF22) shows 93.7% identity over a 158aa overlap with ORF22ng:

The complete sequences from strain B (ORF22-1) and gonococcus (ORF22ng) show 96.2% identity in 447 aa overlap:

Computer analysis of these sequences gave the following results:

Homology with 48 kDa Outer Membrane Protein of Actinobacillus pleuropneumoniae (Accession Number U24492).

ORF22 and this 48 kDa protein show 72% aa identity in 158aa overlap:

Orf22	1	MIKIKKGLNLPIAGRPEQAVYDGPAITEVALLGEEYAGMRPSMKVKEGDAVKKGQVLFED	60
		MI IKKGL+LPIAG P Q +++G  + EVA+LGEEY GMRPSMKV+EGD VKKGQVLFED
48kDa	1	MITIKKGLDLPIAGTPAQVIHNGNTVNEVAMLGEEYVGMRPSMKVREGDVVKKGQVLFED	60
orf22	61	KKNPGVVFTAPASGKIAAIHRGEKRVLQSVVIAVEXNDEIEFERYAPEALANLSGEEVRR	120
		KKNPGVVFTAPASG +  I+RGEKRVLQSVVI VE +++I F RY    LA+LS E+V++
48kDa	61	KKNPGVVFTAPASGTVVTINRGEKRVLQSVVIKVEGDEQITFTRYEAAQLASLSAEQVKQ	120
orf22	121	NLIQSGLWTALRTRPFSKIPAVDAEPFAIFVNAMDTNP	158
		NLI+SGLWTA RTRPFSK+PA+DA P +IFVNAMDTNP
48kDa	121	NLIESGLWTAFRTRPFSKVPALDAIPSSIFVNAMDTNP	158

ORF22a also shows homology to the 48 kDa Actinobacillus pleuropneumoniae protein:

gi|1185395 (U24492) 48 kDa outer membrane protein [Actinobacillus
pleuropneumoniae]
Length = 449
Score = 530 bits (1351), Expect = e−150
Identities = 274/450 (60%), Positives = 323/450 (70%), Gaps = 4/450 (0%)

Query:	1	MIKIKKGLNLPIAGRPEQVIYDGPVITEVALLGEEYAGMRPXMKVKEGDAVKKGQVLFED	60
		MI IKKGL+LPIAG P QVI++G  + EVA+LGEEY GMRP MKV+EGD VKKGQVLFED
Sbjct:	1	MITIKKGLDLPIAGTPAQVIHNGNTVNEVAMLGEEYVGMRPSMKVREGDVVKKGQVLFED	60
Query:	61	KKXPGVVFTAPVSGKIAAIHRGEKRVLQSVVIAVEGNDEIEFERYAPEALANLSGXEXXX	120
		KK PGVVFTAP SG +  I+RGEKRVLQSVVI VEG+++I F RY    LA+LS  +
Sbjct:	61	KKNPGVVFTAPASGTVVTINRGEKRVLQSVVIKVEGDEQITFTRYEAAQLASLSAEQVKQ	120
Query:	121	NLIQSGLWTALRXRPFSKIPAVDAEPFAIFVNAMDTNPLAADPVVVIKEAXXDFRRXXLV	180
		NLI+SGLWTA R RPFSK+PA+DA P +IFVNAMDTNPLAADP VV+KE   DF+    V
Sbjct:	121	NLIESGLWTAFRTRPFSKVPALDAIPSSIFVNAMDTNPLAADPEVVLKEYETDFKDGLTV	180
Query:	181	LSRL--TERKIHVCKAAGADVP-SENAANIETHEFGGPHPAGLSGTHIHFIEPVGANKTV	237
		L+RL   ++ +++CK A +++P S     I    F G HPAGL GTHIHF++PVGA K V
Sbjct:	181	LTRLFNGQKPVYLCKDADSNIPLSPAIEGITIKSFSGVHPAGLVGTHIHFVDPVGATKQV	240
Query:	238	WTINYQDVIAIGRLFATGRLNTERVIALGGSQVNKPRLLRTVLGAKVSQITAGELVDADN	297
		W +NYQDVIAIG+LF TG L T+R+I+L G QV  PRL+RT LGA +SQ+TA EL   +N
Sbjct:	241	WHLNYQDVIAIGKLFTTGELFTDRIISLAGPQVKNPRLVRTRLGANLSQLTANELNAGEN	300
Query:	298	RVISGSVLNGAITQGAHDYLGRYHNQISVIEEGRSKELFGWVAPQPDKYSITRTTLGHFL	357
		RVISGSVL+GA   G  DYLGRY  Q+SV+ EGR KELFGW+ P  DK+SITRT LGHF
Sbjct:	301	RVISGSVLSGATAAGPVDYLGRYALQVSVLAEGREKELFGWIMPGSDKFSITRTVLGHFG	360
Query:	358	KNKLFKFTTAVNGGDRAMVPIGTYERVMXXXXXXXXXXXXXXVGDTDSAQXXXXXXXXXX	417
		K KLF FTTAV+GG+RAMVPIG YERVM               GDTDSAQ
Sbjct:	361	K-KLFNFTTAVHGGERAMVPIGAYERVMPLDIIPTLLLRDLAAGDTDSAQNLGCLELDEE	419
Query:	418	XXXXXSFVCPGKYEXGPLLRKVLETXEKEG	447
		++VCPGK   GP+LR  LE  EKEG

ORF22ng-1 also shows homology with the OMP from A. pleuropneumoniae:

gi|1185395 (U24492) 48 kDa outer membrane protein [Actinobacillus
pleuropneumoniae] Length = 449
Score = 555 bits (1414), Expect = e−157
Identities = 284/450 (63%), Positives = 337/450 (74%), Gaps = 4/450 (0%)

Query:	27	MIKIKKGLNLPIAGRPEQVIYDGPAITEVALLGEEYVGMRPSMKIKEGEAVKKGQVLFED	86
		MI IKKGL+LPIAG P QVI++G  + EVA+LGEEYVGMRPSMK++EG+ VKKGQVLFED
Sbjct:	1	MITIKKGLDLPIAGTPAQVIHNGNTVNEVAMLGEEYVGMRPSMKVREGDVVKKGQVLFED	60
Query:	87	KKNPGVVFTAPASGKIAAIHRGEKRVLQSVVIAVEGNDEIEFERYVPEALAKLSSEKVRR	146
		KKNPGVVFTAPASG +  I+RGEKRVLQSVVI VEG+++I F RY    LA LS+E+V++
Sbjct:	61	KKNPGVVFTAPASGTVVTINRGEKRVLQSVVIKVEGDEQITFTRYEAAQLASLSAEQVKQ	120
Query:	147	NLIQSGLWTALRTRPFSKIPAVDAEPFAIFVNAMDTNPLAADPTVIIKEAAEDFKRGLLV	206
		NLI+SGLWTA RTRPFSK+PA+DA P +IFVNAMDTNPLAADP V++KE   DFK GL V
Sbjct:	121	NLIESGLWTAFRTRPFSKVPALDAIPSSIFVNAMDTNPLAADPEVVLKEYETDFKDGLTV	180
Query:	207	LSRL--TERKIHVCKAAGADVP-SENAANIETHEFGGPHPAGLSGTHIHFIEPVGANKTV	263
		L+RL   ++ +++CK A +++P S     I    F G HPAGL GTHIHF++PVGA K V
Sbjct:	181	LTRLFNGQKPVYLCKDADSNIPLSPAIEGITIKSFSGVHPAGLVGTHIHFVDPVGATKQV	240
Query:	264	WTINYQDVIAIGRLFVTGRLNTERVVALGGLQVNKPRLLRTVLGAKVSQLTAGELVDADN	323
		W +NYQDVIAIG+LF TG L T+R+++L G QV  PRL+RT LGA +SQLTA EL   +N
Sbjct:	241	WHLNYQDVIAIGKLFTTGELFTDRIISLAGPQVKNPRLVRTRLGANLSQLTANELNAGEN	300
Query:	324	RVISGSVLNGAIAQGAHDYLGRYHNQISVIEEGRSKELFGWVAPQPDKYSITRTTLGHFL	383
		RVISGSVL+GA A G  DYLGRY  Q+SV+ EGR KELFGW+ P  DK+SITRT LGHF
Sbjct:	301	RVISGSVLSGATAAGPVDYLGRYALQVSVLAEGREKELFGWIMPGSDKFSITRTVLGHFG	360
Query:	384	KNKLFKFTTAVNGGDRAMVPIGTYERVMXXXXXXXXXXXXXXVGDTDSAQXXXXXXXXXX	443
		K KLF FTTAV+GG+RAMVPIG YERVM               GDTDSAQ
Sbjct:	361	K-KLFNFTTAVHGGERAMVPIGAYERVMPLDIIPTLLLRDLAAGDTDSAQNLGCLELDEE	419
Query:	444	XXXXXSFVCPGKYEYGPLLRKVLETIEKEG	473
		++VCPGK  YGP+LR  LE IEKEG
Sbjct:	420	DLALCTYVCPGKNNYGPMLRAALEKIEKEG	449

Based on this analysis, including the homology with the outer membrane protein of Actinobacillus pleuropneumoniae, it was predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF22-1 (35.4 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 5A shows the results of affinity purification of the GST-fusion protein, and FIG. 5B shows the results of expression of the His-fusion in E. coli. Purified GST-fusion protein was used to immunise mice, whose sera were used for ELISA (positive result) and FACS analysis (FIG. 5C). These experiments confirm that ORF22-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 16

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 133>:

1	..GCGnCGnAAA TCATCCATCC CC..nACGTC GTAGGCCCTG
	AAGCCAACTG
51	GTTTTTTATG GTAGCCAGTA CGTTTGTGAT TGCTTTGATT
	GGTTATTTTG
101	TTACTGAAAA AATCGTCGAA CCGCAATTGG GCCCTTATCA
	ATCAGATTTG
151	TCACAAGAAG AAAAAGACAT TCGGCATTCC AATGAAATCA
	CGCCTTTGGA
201	ATATAAAGGA TTAATTTGGG CTGGCGTGGT GTTTGTTGCC
	TTATCCGCCC
251	TATTGGCTTG GAGCATCGTC CCTGCCGACG GTATTTTGCG
	TCATCCTGAA
301	ACAGGATTGG TTTCCGGTTC GCCGTTTTTA AAATCGATTG
	TTGTTTTTAT
351	TTTCTTGTTG TTTGCACTGC CGGGCATTGT TTATGGCCGG
	GTAACCCGAA
401	GTTTGCGCGG CGAACAGGAA GTCGTTAATG CGmyGGCCGA
	ATCGATGAGT
451	ACTCTGGsGC TTTmTTTGsw CAkcATCTTT TTTGCCGCAC
	AGTTTGTCGC
501	ATTTTTTAAT TGGACGAATA TTGGGCAATA TATTGCCGTT
	AAAGGGGCGA
551	CGTTCTTAAA AGAAGTCGGC TTGGGCGGCA GCGTGTTGTT
	TATCGGTTTT
601	ATTTTAATTT GTGCTTTTAT CAATCTGATG ATAGGCTCCG
	CCTCCGCGCA
651	ATGGGCGGTA ACTGCGCCGA TTTTCGTCCC TATGCTGATG
	TTGGCCGGCT
701	ACGCGCCCGA AGTCATTCAA GCCGCTTACC GCATCGGTGA
	TTCCGTTACC
751	AATATTATTA CGCCGATGAT GAGTTATTTC GGGCTGATTA
	TGGCGACGGT
801	GrkCmmmTAC AAAAAAGATG CGGGCGTGGG TaCGcTGATT
	wCTATGATGT
851	TGCCGTATTC CGCTTTCTTC TTGATTGCgT GGATTGCCTT
	ATTCTGCATT
901	TGGGTATTTg TTTTGGGCCT GCCCGTCGGT CCCGGCGCGC
	CCACATTCTA
951	TCCCGCACCT TAA

This corresponds to the amino acid sequence <SEQ ID 134; ORF12>:

1	..AXXIIHPXXV VGPEANWFFM VASTFVIALI GYFVTEKIVE
	PQLGPYQSDL
51	SQEEKDIRHS NEITPLEYKG LIWAGVVFVA LSALLAWSIV
	PADGILRHPE
101	TGLVSGSPFL KSIVVFIFLL FALPGIVYGR VTRSLRGEQE
	VVNAXAESMS
151	TLXLXLXXIF FAAQFVAFFN WTNIGQYIAV KGATFLKEVG
	LGGSVLFIGF
201	ILICAFINLM IGSASAQWAV TAPIFVPMLM LAGYAPEVIQ
	AAYRIGDSVT
251	NIITPMMSYF GLIMATVXXY KKDAGVGTLI XMMLPYSAFF
	LIAWIALFCI
301	WVFVLGLPVG PGAPTFYPAP *

Further sequence analysis revealed the complete DNA sequence <SEQ ID 135> to be:

1	ATGAGTCAAA CCGATACGCA ACGGGACGGA CGATTTTTAC
	GCACAGTCGA
51	ATGGCTGGGC AATATGTTGC CGCATCCGGT TACGCTTTTT
	ATTATTTTCA
101	TTGTGTTATT GCTGATTGCC TCTGCCGTCG GTGCGTATTT
	CGGACTATCC
151	GTCCCCGATC CGCGCCCTGT TGGTGCGAAA GGACGTGCCG
	ATGACGGTTT
201	GATTTACATT GTCAGCCTGC TCAATGCCGA CGGTTTTATC
	AAAATCCTGA
251	CGCATACCGT TAAAAATTTC ACCGGTTTCG CGCCGTTGGG
	AACGGTGTTG
301	GTTTCTTTAT TGGGCGTGGG GATTGCGGAA AAATCGGGCT
	TGATTTCCGC
351	ATTAATGCGC TTATTGCTCA CAAAATCGCC ACGCAAACTC
	ACTACTTTTA
401	TGGTTGTTTT TACAGGGATT TTATCTAATA CCGCTTCTGA
	ATTGGGCTAT
451	GTCGTCCTAA TCCCTTTGTC CGCCATCATC TTTCATTCCC
	TCGGCCGCCA
501	TCCGCTTGCC GGTCTGGCTG CGGCTTTCGC CGGCGTTTCG
	GGCGGTTATT
551	CGGCCAATCT GTTCTTAGGC ACAATCGATC CGCTCTTGGC
	AGGCATCACC
601	CAACAGGCGG CGCAAATCAT CCATCCCGAC TACGTCGTAG
	GCCCTGAAGC
651	CAACTGGTTT TTTATGGTAG CCAGTACGTT TGTGATTGCT
	TTGATTGGTT
701	ATTTTGTTAC TGAAAAAATC GTCGAACCGC AATTGGGCCC
	TTATCAATCA
751	GATTTGTCAC AAGAAGAAAA AGACATTCGG CATTCCAATG
	AAATCACGCC
801	TTTGGAATAT AAAGGATTAA TTTGGGCTGG CGTGGTGTTT
	GTTGCCTTAT
851	CCGCCCTATT GGCTTGGAGC ATCGTCCCTG CCGACGGTAT
	TTTGCGTCAT
901	CCTGAAACAG GATTGGTTTC CGGTTCGCCG TTTTTAAAAT
	CGATTGTTGT
951	TTTTATTTTC TTGTTGTTTG CACTGCCGGG CATTGTTTAT
	GGCCGGGTAA
1001	CCCGAAGTTT GCGCGGCGAA CAGGAAGTCG TTAATGCGAT
	GGCCGAATCG
1051	ATGAGTACTC TGGGGCTTTA TTTGGTCATC ATCTTTTTTG
	CCGCACAGTT
1101	TGTCGCATTT TTTAATTGGA CGAATATTGG GCAATATATT
	GCCGTTAAAG
1151	GGGCGACGTT CTTAAAAGAA GTCGGCTTGG GCGGCAGCGT
	GTTGTTTATC
1201	GGTTTTATTT TAATTTGTGC TTTTATCAAT CTGATGATAG
	GCTCCGCCTC
1251	CGCGCAATGG GCGGTAACTG CGCCGATTTT CGTCCCTATG
	CTGATGTTGG
1301	CCGGCTACGC GCCCGAAGTC ATTCAAGCCG CTTACCGCAT
	CGGTGATTCC
1351	GTTACCAATA TTATTACGCC GATGATGAGT TATTTCGGGC
	TGATTATGGC
1401	GACGGTGATC AAATACAAAA AAGATGCGGG CGTGGGTACG
	CTGATTTCTA
1451	TGATGTTGCC GTATTCCGCT TTCTTCTTGA TTGCGTGGAT
	TGCCTTATTC
1501	TGCATTTGGG TATTTGTTTT GGGCCTGCCC GTCGGTCCCG
	GCGCGCCCAC
1551	ATTCTATCCC GCACCTTAA

This corresponds to the amino acid sequence <SEQ ID 136; ORF12-1>:

1	MSQTDTQRDG RFLRTVEWLG NMLPHPVTLF IIFIVLLLIA
	SAVGAYFGLS
51	VPDPRPVGAK GRADDGLIYI VSLLNADGFI KILTHTVKNF
	TGFAPLGTVL
101	VSLLGVGIAE KSGLISALMR LLLTKSPRKL TTFMVVFTGI
	LSNTASELGY
151	VVLIPLSAII FHSLGRHPLA GLAAAFAGVS GGYSANLFLG
	TIDPLLAGIT
201	QQAAQIIHPD YVVGPEANWF FMVASTFVIA LIGYFVTEKI
	VEPQLGPYQS
251	DLSQEEKDIR HSNEITPLEY KGLIWAGVVF VALSALLAWS
	IVPADGILRH
301	PETGLVSGSP FLKSIVVFIF LLFALPGIVY GRVTRSLRGE
	QEVVNAMAES
351	MSTLGLYLVI IFFAAQFVAF FNWTNIGQYI AVKGATFLKE
	VGLGGSVLFI
401	GFILICAFIN LMIGSASAQW AVTAPIFVPM LMLAGYAPEV
	IQAAYRIGDS
451	VTNIITPMMS YFGLIMATVI KYKKDAGVGT LISMMLPYSA
	FFLIAWIALF
501	CIWVFVLGLP VGPGAPTFYP AP*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF12 shows 96.3% identity over a 320aa overlap with an ORF (ORF12a) from strain A of N. meningitidis:

The complete length ORF12a nucleotide sequence <SEQ ID 137> is:

1	ATGAGTCAAA CCGATACGCA ACGGGACGGA CGATTTTTAC
	GCACAGTCGA
51	ATGGCTGGGC AATATGTTGC CGCACCCGGT TACGCTTTTT
	ATTATTTTCA
101	TTGTGTTATT GCTGATTGCC TCTGCCGCCG GTGCGTATTT
	CGGACTATCC
151	GTCCCCGATC CGCGCCCTGT TGGTGCGAAA GGACGTGCCG
	ATGACGGTTT
201	GATTCACGTT GTCAGCCTGC TCGATGCTGA CGGTTTGATC
	AAAATCCTGA
251	CGCATACCGT TAAAAATTTC ACCGGTTTCG CGCCGTTGGG
	AACGGTGTTG
301	GTTTCTTTAT TGGGCGTGGG GATTGCGGAA AAATCGGGCT
	TGATTTCCGC
351	ATTAATGCGC TTATTGCTCA CAAAATCTCC ACGCAAACTC
	ACTACTTTTA
401	TGGTTGTTTT TACAGGGATT TTATCTAATA CCGCTTCTGA
	ATTGGGCTAT
451	GTCGTCCTAA TCCCTTTGTC CGCCATCATC TTTCATTCCC
	TCGGCCGCCA
501	TCCGCTTGCC GGTCTGGCTG CGGCTTTCGC CGGCGTTTCG
	GGCGGTTATT
551	CGGCCAATCT GTTCTTAGGC ACAATCGATC CGCTCTTGGC
	AGGCATCACC
601	CAACAGGCGG CGCAAATCAT CCATCCCGAC TACGTCGTAG
	GCCCTGAAGC
651	CAACTGGTTT TTTATGGTAG CCAGTACGTT TGTGATTGCT
	TTGATTGGTT
701	ATTTTGTTAC TGAAAAAATC GTCGAACCGC AATTGGGCCC
	TTATCAATCA
751	GATTTGTCAC AAGAAGAAAA AGACATTCGA CATTCCAATG
	AAATCACGCC
801	TTTGGAATAT AAAGGATTAA TTTGGGCTGG CGTGGTGTTT
	GTTGCCTTAT
851	CCGCCCTATT GGCTTGGAGC ATCGTCCCTG CCGACGGTAT
	TTTGCGTCAT
901	CCTGAAACAG GATTGGTTTC CGGTTCGCCG TTTTTAAAAT
	CAATTGTTGT
951	TTTTATTTTC TTGTTGTTTG CACTGCCGGG CATTGTTTAT
	GGCCGGGTAA
1001	CCCGAAGTTT GCGCGGCGAA CAGGAAGTCG TTAATGCGAT
	GGCCGAATCG
1051	ATGAGTACTC TGGGGCTTTA TTTGGTCATC ATCTTTTTTG
	CCGCACAGTT
1101	TGTCGCATTT TTTAATTGGA CGAATATTGG GCAATATATT
	GCCGTTAAAG
1151	GGGCGACGTT CTTAAAAGAA GTCGGCTTGG GCGGCAGCGT
	GTTGTTTATC
1201	GGTTTTATTT TAATTTGTGC TTTTATCAAT CTGATGATAG
	GCTCCGCCTC
1251	CGCGCAATGG GCGGTAACTG CGCCGATTTT CGTCCCTATG
	CTGATGTTGG
1301	CCGGCTACGC GCCCGAAGTC ATTCAAGCCG CTTACCGCAT
	CGGTGATTCC
1351	GTTACCAATA TTATTACGCC GATGATGAGT TATTTCGGGC
	TGATTATGGC
1401	GACGGTGATC AAATACAAAA AAGATGCGGG CGTGGGTACG
	CTGATTTCTA
1451	TGATGTTGCC GTATTCCGCT TTCTTCTTGA TTGCGTGGAT
	TGCCTTATTC
1501	TGCATTTGGG TATTTGTTTT GGGCCTGCCC GTCGGTCCCG
	GCGCGCCCAC
1551	ATTCTATCCC GCACCTTAA

This encodes a protein having amino acid sequence <SEQ ID 138>:

1	MSQTDTQRDG RFLRTVEWLG NMLPHPVTLF IIFIVLLLIA
	SAAGAYFGLS
51	VPDPRPVGAK GRADDGLIHV VSLLDADGLI KILTHTVKNF
	TGFAPLGTVL
101	VSLLGVGIAE KSGLISALMR LLLTKSPRKL TTFMVVFTGI
	LSNTASELGY
151	VVLIPLSAII FHSLGRHPLA GLAAAFAGVS GGYSANLFLG
	TIDPLLAGIT
201	QQAAQIIHPD YVVGPEANWF FMVASTFVIA LIGYFVTEKI
	VEPQLGPYQS
251	DLSQEEKDIR HSNEITPLEY KGLIWAGVVF VALSALLAWS
	IVPADGILRH
301	PETGLVSGSP FLKSIVVFIF LLFALPGIVY GRVTRSLRGE
	QEVVNAMAES
351	MSTLGLYLVI IFFAAQFVAF FNWTNIGQYI AVKGATFLKE
	VGLGGSVLFI
401	GFILICAFIN LMIGSASAQW AVTAPIFVPM LMLAGYAPEV
	IQAAYRIGDS
451	VTNIITPMMS YFGLIMATVI KYKKDAGVGT LISMMLPYSA
	FFLIAWIALF
501	CIWVFVLGLP VGPGAPTFYP AP*

ORF12a and ORF12-1 show 99.0% identity in 522 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF12 shows 92.5% identity over a 320aa overlap with a predicted ORF (ORF12.ng) from N. gonorrhoeae:

The complete length ORF12ng nucleotide sequence <SEQ ID 139> is:

1	ATGAGTCAAA CCGACGCGCG TCGTAGCGGA CGATTTTTAC
	GCACAGTCGA
51	ATGGCTGGGC AATATGTTGC CGCACCCGGT TACGCTTTTT
	ATTATTTTCA
101	TTGTGTTATT GCTGATTGcc tctgCCGTCG GTGCGTATTT
	CGGACTATCC
151	GTCCCCGATC CGCGTCCTGT TGGGGCGAAA GGACGTGCCG
	ATGACGGTTT
201	GATTCACGTT GTCAGCCTGC TCGATGCCGA CGGTTTGATC
	AAAATCCTGA
251	CGCATACCGT TAAAAATTTC ACCGGTTTCG CGCCGTTGGG
	AACGGTGTTG
301	GTTTCTTTAT TGGGCGTGGG GATTGCGGAA AAATCGGGCT
	TGATTTCCGC
351	ATTAATGCGC TTATTGCTCA CAAAATCCCC ACGCAAACTC
	ACTACTTTTA
401	TGGTTGTTTT TACAGGGATT TTATCCAATA CGGCTTCTGA
	ATTGGGCTAT
451	GTCGTCCTAA TCCCTTTGTC CGCCGTCATC TTTCATTCGC
	TCGGCCGCCA
501	TCCGCTTGCC GGTTTGGCTG CGGCTTTCGC CGGCGTTTCG
	GGCGGTTATT
551	CGGCCAATCT GTTCTTAGGC ACAATCGATC CGCTCTTGGC
	AGGCATCACC
601	CAACAGGCGG CGCAAATCAT CCATCCCGAC TACGTCGTAG
	GCCCTGAAGC
651	CAACTGGTTT TTTATGGCAG CCAGTACGTT TGTGATTGCT
	TTGATTGGTT
701	ATTTTGTTAC TGAAAAAATC GTCGAACCGC AATTGGGCCC
	TTATCAATCA
751	GATTTGTCAC AAGAAGAAAA AGACATTCGG CATTCCAATG
	AAATCACGCC
801	TTTGGAATAT AAAGGATTAA TTTGGGCAGG CGTGGTGTTT
	GTTGCCTTAT
851	CCGCCCTATT GGCTTGGAGC ATCGTCCCTG CCGACGGTAT
	TTTGCGTCAT
901	CCTGAAACAG GATTGGTTGC CGGTTCGCCG TTTTTAAAAT
	CGATTGTTGT
951	TTTTATTTTC TTGTTGTTTG CGCTGCCGGG CATTGTTTAT
	GGCCGGATAA
1001	CCCGAAGTTT GCGCGGCGAA CGGGAAGTCG TTAATGCGAT
	GGCCGAATCG
1051	ATGAGTACTT TGGGACTTTA TTTGGTCATC ATCTTTTTTG
	CCGCACAGTT
1101	TGTCGCATTT TTTAATTGGA CGAATATTGG GCAATATATT
	GCCGTTAAAG
1151	GGGCGGTGTT CTTAAAAGAA GTCGGCTTGG GCGGCAGTGT
	GTTGTTTATC
1201	GGTTTTATTT TAATTTGTGC TTTTATCAAT CTGATGATAG
	GCTCCGCCTC
1251	CGCGCAATGG GCGGTAACTG CGCCGATTTT CGTCCCTATG
	CTGATGTTGG
1301	CCGGCTACGC GCCCGAAGTC ATTCAAGCCG CTTACCGCAT
	CGGTGATTCC
1351	GTTACCAATA TTATTACGCC GATGATGAGT TATTTCGGGC
	TGATTATGGC
1401	GACGGTAATC AAATACAAAA AAGATGCGGG CGTAGGCACG
	CTGATTTCTA
1451	TGATGTTGCC GTATTCCGCT TTCTTCTTAA TTGCATGGAT
	CGCCTTATTC
1501	TGCATTTGGG TATTTGTTTT GGGTCTGCCC GTCGGTCCCG
	GCACACCCAC
1551	ATTCTATCCG GTGCCTTAA

This encodes a protein having amino acid sequence <SEQ ID 140>:

1	MSQTDARRSG RFLRTVEWLG NMLPHPVTLF IIFIVLLLIA
	SAVGAYFGLS
51	VPDPRPVGAK GRADDGLIHV VSLLDADGLI KILTHTVKNF
	TGFAPLGTVL
101	VSLLGVGIAE KSGLISALMR LLLTKSPRKL TTFMVVFTGI
	LSNTASELGY
151	VVLIPLSAVI FHSLGRHPLA GLAAAFAGVS GGYSANLFLG
	TIDPLLAGIT
201	QQAAQIIHPD YVVGPEANWF FMAASTFVIA LIGYFVTEKI
	VEPQLGPYQS
251	DLSQEEKDIR HSNEITPLEY KGLIWAGVVF VALSALLAWS
	IVPADGILRH
301	PETGLVAGSP FLKSIVVFIF LLFALPGIVY GRITRSLRGE
	REVVNAMAES
351	MSTLGLYLVI IFFAAQFVAF FNWTNIGQYI AVKGAVFLKK
	FRLGGSVLFI
401	GFILICAFIN LMIGSASAQW AVTAPIFVPM LMLAGNAPQV
	IQAAYRIGDS
451	VTNIITPMMS YFGLIMATVI KYKKDAGVGT LISMMLPYSA
	FFLIAWIALF
501	CIWVFVLGLP VGPGTPTFYP VP*

ORF12ng shows 97.1% identity in 522 aa overlap with ORF12-1:

In addition, ORF12ng shows significant homology with a hypothetical protein from E. coli:

sp|P46133|YDAH_ECOLI HYPOTHETICAL 55.1 KD PROTEIN IN OGT-DBPA
INTERGENIC REGION
>gi|1787597 (AE000231) hypothetical protein in ogt 5′region
[Escherichia coli]
Length = 510
Score = 329 bits (835), Expect = 2e−89
Identities = 178/507 (35%), Positives = 281/507 (55%), Gaps = 15/507 (2%)

Query:	8	RSGRFLRTVEWLGNMLPHPVTXXXXXXXXXXXASAVGAYFGLSVPDPRPVGAKGRADDGL	67
		+SG+    VE +GN +PHP              +A+ + FG+S  +P         D
Sbjct:	13	QSGKLYGWVERIGNKVPHPFLLFIYLIIVLMVTTAILSAFGVSAKNP--------TDGTP	64
Query:	68	IHVVSLLDADGLIKILTHTVKNFTGFAPXXXXXXXXXXXXIAEKSGLISALMRLLLTKSP	127
		+ V +LL  +GL   L + +KNF+GFAP            +AE+ GL+ ALM  + +
Sbjct:	65	VVVKNLLSVEGLHWFLPNVIKNFSGFAPLGAILALVLGAGLAERVGLLPALMVKMASHVN	124
Query:	128	RKLTTFMVVFTGILSNTASELGYVVLIPLSAVIFHSLGRHPLAGLAAAFAGVSGGYSANL	187
		+  ++MV+F    S+ +S+   V++ P+ A+IF ++GRHP+AGL AA AGV  G++ANL
Sbjct:	125	ARYASYMVLFIAFFSHISSDAALVIMPPMGALIFLAVGRHPVAGLLAAIAGVGCGFTANL	184
Query:	188	FLGTIDPLLAGITQQAAQIIHPDYVVGPEANWFFMAASTFVIALIGYFVTEKIVEPQLGP	247
		+ T D LL+GI+ +AA   +P   V    NW+FMA+S  V+ ++G  +T+KI+EP+LG
Sbjct:	185	LIVTTDVLLSGISTEAAAAFNPQMHVSVIDNWYFMASSVVVLTIVGGLITDKIIEPRLGQ	244
Query:	248	YQSDLSQEEKDIRHSNEITPLEYKGLIWAGVVFVALSALLAWSIVPADGILRHPETGLVA	307
		+Q +  ++ + +  S         GL  AGVV +   A +A  ++P +GILR P    V
Sbjct:	245	WQGNSDEKLQTLTESQRF------GLRIAGVVSLLFIAAIALMVIPQNGILRDPINHTVM	298
Query:	308	GSPFLKSIVVFIFLLFALPGIVYGRITRSLRGEREVVNAMAESMSTLGLYLXXXXXXXXX	367
		SPF+K IV  I L F +  + YG  TR++R + ++ + M E M  +  ++
Sbjct:	299	PSPFIKGIVPLIILFFFVVSLAYGIATRTIRRQADLPHLMIEPMKEMAGFIVMVFPLAQF	358
Query:	368	XXXXNWTNIGQYIAVKGAVFLKEVGLGGSVLFIGFILICAFINLMIGSASAQWAVTAPIF	427
		NW+N+G++IAV     L+  GL G   F+G  L+ +F+ +I S SA W++ APIF
Sbjct:	359	VAMFNWSNMGKFIAVGLTDILESSGLSGIPAFVGLALLSSFLCMFIASGSAIWSILAPIF	418
Query:	428	VPMLMLAGYAPEVIQAAYRIGDSVTNIITPMMSYFGLIMATVIKYKKDAGVGTLISMMLP	487
		VPM ML G+ P   Q  +RI DS    + P+  +  L +  + +YK DA +GT  S++LP
Sbjct:	419	VPMFMLLGFHPAFAQILFRIADSSVLPLAPVSPFVPLFLGFLQRYKPDAKLGTYYSLVLP	478
Query:	488	YSAFFLIAWIALFCIWVFVLGLPVGPG	514
		Y   FL+ W+ +   W +++GLP+GPG
Sbjct:	479	YPLIFLVVWLLMLLAW-YLVGLPIGPG	504

Based on this analysis, including the presence of several putative transmembrane domains and the predicted actinin-type actin-binding domain signature (shown in bold) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 17

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 141>:

1	..ACAGCCGGCG CAGCAGGTTn CnCGGTCTTC GTTTTCGTAA
	CGGACAGTCA
51	GGTGGAGGTG TTCGGGAACA TCCAGACCGC AGTGGAAACA
	GGTTTTTTTC
101	ATGGCATTTC GGTTTCGTCT GTGTTTGGTG CGGCGGCACA
	AGACTCGGCA
151	ATgGCTTCGC GCAGTGCGTC TATACCGGTA TTTTCAGCAA
	CGGAAATGCG
201	GACGGcGgCA ATTTTTCCCG CAGCGTCGCG CCATATGCCC
	GTGTTTTgTT
251	CTTCAGACGG CAGCAGGTCG GTTTTGTTGT ACACCTTgAT
	GCACGGAaTA
301	TCGCCGGCAT GGATTTCTTG CAGTACGTTT TCCACGTCTT
	CAATCTGCTG
351	TCCGCTGTTC GGAGCGGCGG CATCGACGAC GTGCAGCAGC
	ACATCgGcTT
401	gCGCGGTTTC TTCCAGCGTG GCgGAAAAGG CGGAAATCAG
	TTTgTGCGGC
451	agATyGCTnA CGAATCCGAC GGTATCGGTC AGGATAATGC
	TGCATTCGGG
501	ACT..

This corresponds to the amino acid sequence <SEQ ID 142; ORF14>:

1	..TAGAAGXXVF VFVTDSQVEV FGNIQTAVET GFFHGISVSS
	VFGAAAQDSA
51	MASRSASIPV FSATEMRTAA IFPAASRHMP VFCSSDGSRS
	VLLYTLMHGI
101	SPAWISCSTF STSSICCPLF GAAASTTCSS TSACAVSSSV
	AEKAEISLCG
151	RXLTNPTVSV RIMLHSG..

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF From N. meningitidis (Strain A)

ORF14 shows 94.0% identity over a 167aa overlap with an ORF (ORF14a) from strain A of N. meningitidis:

The complete length ORF14a nucleotide sequence <SEQ ID 143> is:

1	ATGGAGGATT TGCAGGAAAT CGGGTTCGAT GTCGCCGCCG
	TAAAGGTAGG
51	TCGGCAGCGC GAACATCATC GTCTGCATCA TCCCCAGCCC
	GGCAACGGCG
101	AGGCGGACGA TGTATTGTTT GCGTTCTTTT TGGTTGGCGG
	CTTCGATTTT
151	TTGCGCGTCA TAGGGTGCGG CGGTGTAGCC TATCTGCCTG
	ATTTTCAACA
201	GAATGTCGGA AAGGCGGATT TTGCCGTCGT CCCAGACGAC
	GCGGCAGCGG
251	TGCGTGCTGT AATTGAGGTC GATGCGGACG ATGCCGTCTG
	TACGCAAAAG
301	CTGCTGTTCG ATCAGCCAGA CGCAGGCGGC GCAGGTGATG
	CCGCCGAGCA
351	TTAAAACCGC CTCGCGCGTG CCGCCGTGGG TTTCCACAAA
	GTCGGACTGG
401	ACTTCGGGCA GGTCGTACAG GCGGATTTGG TCGAGGATTT
	CTTGGGGCGG
451	CAGCTCGGTT TTTTGCGCGT CGGCGGTGCG TTGTTTGTAA
	TAACTGCCCA
501	AGCCCGCGTC AATAATGCTT TGTGCGACTG CCTGACAACC
	GGCGCAGCAG
551	GTTTCGCGGT CTTCGTTTTC GTAACGGACG GTCAGATGCA
	GGTTTTCGGG
601	AACGTCCAGC CCGCAGTGGA AACAGGTTTT TTTCATGGCA
	TTTCGGTTTC
651	GTCTGTGTTT GGTGCGGCGG CACAATACTC GGCAATGGCT
	TCGCGCAGTG
701	CGTCTATACC GGTATTTTCA GCAACGGAAA TGCGGACGGC
	GGCAATTTTT
751	CCCGCAGCGT CGCGCCATAT GCCCGTGTTT TGTTCTTCAG
	ACGGCAGCAG
801	GTCGGTTTTG TTGTACACCT TGATGCACGG AATATCGCCG
	GCATGGATTT
851	CTTGCAGTAC GTTTTCCACG TCTTCAATCT GCTGTCCGCT
	GTTCGGAGCG
901	GCGGCATCGA CGACGTGCAG CAGCACATCG GCTTGCGCGG
	TTTCTTCCAG
951	CGTGGCGGAA AAGGCGGAAA TCAGTTTGTG CGGCAGATCG
	CTGACGAATC
1001	CGACGGTATC GGTCAGGATA ATGCTGCATT CGGGACTGAT
	GTACAGCCGC
1051	CGCGCCGTCG TGTCGAGTGT GGCGAAAAGC TGGTCTTTCG
	CATATATGCC
1101	CGACTTGGTC AGCCGGTTGA ACAGACTGGA TTTGCCGACA
	TTGGTATAG

This encodes a protein having amino acid sequence <SEQ ID 144>:

1	MEDLQEIGFD VAAVKVGRQR EHHRLHHPQP GNGEADDVLF
	AFFLVGGFDF
51	LRVIGCGGVA YLPDFQQNVG KADFAVVPDD AAAVRAVIEV
	DADDAVCTQK
101	LLFDQPDAGG AGDAAEH*NR LARAAVGFHK VGLDFGQVVQ
	ADLVEDFLGR
151	QLGFLRVGGA LFVITAQARV NNALCDCLTT GAAGFAVFVF
	VTDGQMQVFG
201	NVQPAVETGF FHGISVSSVF GAAAQYSAMA SRSASIPVFS
	ATEMRTAAIF
251	PAASRHMPVF CSSDGSRSVL LYTLMHGISP AWISCSTFST
	SSICCPLFGA
301	AASTTCSSTS ACAVSSSVAE KAEISLCGRS LTNPTVSVRI
	MLHSGLMYSR
351	RAVVSSVAKS WSFAYMPDLV SRLNRLDLPT LV*

It should be noted that this sequence includes a stop codon at position 118.

Homology with a Predicted ORF from N. gonorrhoeae

ORF14 shows 89.8% identity over a 167aa overlap with a predicted ORF (ORF14.ng) from N. gonorrhoeae:

The complete length ORF14ng nucleotide sequence <SEQ ID 145> is predicted to encode a protein having amino acid sequence <SEQ ID 146>:

1	MEDLQEIGFD VAAVKVGRQR EHHRLHHTQS GNGKADDVLF
	AFFLVGGFDF
51	LRVIGCGGVA CLPDFQQNVG EADFAVVPDD AAAVRAVIEV
	DADDAVCAQK
101	LLFDQPDAGG AGNAAEHQHC FVRAIMGFHK VGLDFGQVVQ
	ADLVEDFLGR
151	QFGFFRVGGA SFVITAQAGI DDALCDCLTA DAAGFAVFAF
	VADGQMQVFG
201	NVQPAVETGF FHGISVSSVF GAAAQYSAMA SRSASIPVFS
	ATEMRTAAIF
251	PAASRHMPVF CSSDGSRSVL LYTLMHGISW AWISCSTFST
	SSICCPLFRA
301	AASTTCSSTS ACTVSSKVAE KAEISLCGRS LTNPTVSVRI
	MLHAGLMYSR
351	RAVVSRVAKS WSFAYMPDLV SRLNRLDLPT LV*

Based on the putative transmembrane domain in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 18

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 147>:

1	..GGCCATTACT CCGACCGCAC TTGGAAGCCG CGTTTGGNCG
	GCCGCCGTCT
51	GCCGTATCTG CTTTATGGCA CGCTGATTGC GGTTATTGTG
	ATGATTTTGA
101	TGCCGAACTC GGGCAGCTTC GGTTTCGGCT ATGCGTCGCT
	GGCGGCTTTG
151	TCGTTCGGCG CGCTGATGAT TGCGCTGTTA GACGTGTCGT
	CAAATATGGC
201	GATGCAGCCG TTTAAGATGA TGGTCGGCGA CATGGTCAAC
	GAGGAGCAGA
251	AAA.NTACGC CTACGGGATT CAAAGTTTCT TAGCAAATAC
	GGGCGCGGTC
301	GTGGCGGCGA TTCTGCCGTT TGTGTTTGCG TATATCGGTT
	TGGCGAACAC
351	CGCCGANAAA GGCGTTGTGC CGCAGACCGT GGTCGTGGCG
	TTTTATGTGG
401	GTGCGGCGTT GCTGGTGATT ACCAGCGCGT TCACGATTTT
	CAAAGTGAAG
451	GAATACGANC CGGAAACCTA CGCCCGTTAC CACGGCATCG
	ATGTCGCCGC
501	GAATCAGGAA AAAGCCAACT GGATCGCACT CTTAAAA.CC
	GCGC..

This corresponds to the amino acid sequence <SEQ ID 148; ORF16>:

1	..GHYSDRTWKP RLXGRRLPYL LYGTLIAVIV MILMPNSGSF
	GFGYASLAAL
51	SFGALMIALL DVSSNMAMQP FKMMVGDMVN EEQKXYAYGI
	QSFLANTGAV
101	VAAILPFVFA YIGLANTAXK GVVPQTVVVA FYVGAALLVI
	TSAFTIFKVK
151	EYXPETYARY HGIDVAANQE KANWIALLKX A..

Further work revealed the complete nucleotide sequence <SEQ ID 149>:

1	ATGTCGGAAT ATACGCCTCA AACAGCAAAA CAAGGTTTGC
	CCGCGCTGGC
51	AAAAAGCACG ATTTGGATGC TCAGTTTCGG CTTTCTCGGC
	GTTCAGACGG
101	CCTTTACCCT GCAAAGCTCG CAAATGAGCC GCATTTTTCA
	AACGCTAGGC
151	GCAGACCCGC ACAATTTGGG CTGGTTTTTC ATCCTGCCGC
	CGCTGGCGGG
201	GATGCTGGTG CAGCCGATTG TCGGCCATTA CTCCGACCGC
	ACTTGGAAGC
251	CGCGTTTGGG CGGCCGCCGT CTGCCGTATC TGCTTTATGG
	CACGCTGATT
301	GCGGTTATTG TGATGATTTT GATGCCGAAC TCGGGCAGCT
	TCGGTTTCGG
351	CTATGCGTCG CTGGCGGCTT TGTCGTTCGG CGCGCTGATG
	ATTGCGCTGT
401	TAGACGTGTC GTCAAATATG GCGATGCAGC CGTTTAAGAT
	GATGGTCGGC
451	GACATGGTCA ACGAGGAGCA GAAAGGCTAC GCCTACGGGA
	TTCAAAGTTT
501	CTTAGCAAAT ACGGGCGCGG TCGTGGCGGC GATTCTGCCG
	TTTGTGTTTG
551	CGTATATCGG TTTGGCGAAC ACCGCCGAGA AAGGCGTTGT
	GCCGCAGACC
601	GTGGTCGTGG CGTTTTATGT GGGTGCGGCG TTGCTGGTGA
	TTACCAGCGC
651	GTTCACGATT TTCAAAGTGA AGGAATACGA TCCGGAAACC
	TACGCCCGTT
701	ACCACGGCAT CGATGTCGCC GCGAATCAGG AAAAAGCCAA
	CTGGATCGAA
751	CTCTTGAAAA CCGCGCCTAA GGCGTTTTGG ACGGTTACTT
	TGGTGCAATT
801	CTTCTGCTGG TTCGCCTTCC AATATATGTG GACTTACTCG
	GCAGGCGCGA
851	TTGCGGAAAA CGTCTGGCAC ACCACCGATG CGTCTTCCGT
	AGGTTATCAG
901	GAGGCGGGTA ACTGGTACGG CGTTTTGGCG GCGGTGCAGT
	CGGTTGCGGC
951	GGTGATTTGT TCGTTTGTAT TGGCGAAAGT GCCGAATAAA
	TACCATAAGG
1001	CGGGTTATTT CGGCTGTTTG GCTTTGGGCG CGCTCGGCTT
	TTTCTCCGTT
1051	TTCTTCATCG GCAACCAATA CGCGCTGGTG TTGTCTTATA
	CCTTAATCGG
1101	CATCGCTTGG GCGGGCATTA TCACTTATCC GCTGACGATT
	GTGACCAACG
1151	CCTTGTCGGG CAAGCATATG GGCACTTACT TGGGCTTGTT
	TAACGGCTCT
1201	ATCTGTATGC CTCAAATCGT CGCTTCGCTG TTGAGTTTCG
	TGCTTTTCCC
1251	TATGCTGGGC GGCTTGCAGG CCACTATGTT CTTGGTAGGG
	GGCGTCGTCC
1301	TGCTGCTGGG CGCGTTTTCC GTGTTCCTGA TTAAAGAAAC
	ACACGGCGGG
1351	GTTTGA

This corresponds to the amino acid sequence <SEQ ID 150; ORF16-1>:

1	MSEYTPQTAK QGLPALAKST IWMLSFGFLG VQTAFTLQSS
	QMSRIFQTLG
51	ADPHNLGWFF ILPPLAGMLV QPIVGHYSDR TWKPRLGGRR
	LPYLLYGTLI
101	AVIVMILMPN SGSFGFGYAS LAALSFGALM IALLDVSSNM
	AMQPFKMMVG
151	DMVNEEQKGY AYGIQSFLAN TGAVVAAILP FVFAYIGLAN
	TAEKGVVPQT
201	VVVAFYVGAA LLVITSAFTI FKVKEYDPET YARYHGIDVA
	ANQEKANWIE
251	LLKTAPKAFW TVTLVQFFCW FAFQYMWTYS AGAIAENVWH
	TTDASSVGYQ
301	EAGNWYGVLA AVQSVAAVIC SFVLAKVPNK YHKAGYFGCL
	ALGALGFFSV
351	FFIGNQYALV LSYTLIGIAW AGIITYPLTI VTNALSGKHM
	GTYLGLFNGS
401	ICMPQIVASL LSFVLFPMLG GLQATMFLVG GVVLLLGAFS
	VFLIKETHGG
451	V*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. Meningitidis (Strain A)

ORF16 shows 96.7% identity over a 181 as overlap with an ORF (ORF16a) from strain A of N. meningitidis:

The complete length ORF16a nucleotide sequence <SEQ ID 151> is:

1	ATGTCGGAAT ATACGCCTCA AACAGCAAAA CAAGGTTTGC
	CCGCGCTGGC
51	AAAAAGCACG ATTTGGATGC TCAGTTTCGG CTTTCTCGGC
	GTTCAGACGG
101	CCTTTACCCT GCAAAGCTCG CAGATGAGCC GCATCTTCCA
	GACGCTCGGT
151	GCCGATCCGC ACAGCCTCGG CTGGTTCTTT ATCCTGCCGC
	CGCTGGCGGG
201	GATGCTGGTG CAGCCGATTG TCGGCCATTA CTCCGACCGC
	ACTTGGAAGC
251	CGCGTTTGGG CGGCCGCCGT CTGCCGTATC TGCTTTATGG
	CACGCTGATT
301	GCGGTTATTG TGATGATTTT GATGCCGAAC TCGGGCAGCT
	TCGGTTTCGG
351	CTATGCGTCG CTGGCGGCTT TGTCGTTCGG CGCGCTGATG
	ATTGCGCTGT
401	TAGACGTGTC GTCAAATATG GCGATGCAGC CGTTTAAGAT
	GATGGTCGGC
451	GACATGGTCA ACGAGGAGCA GAAAGGCTAC GCCTACGGGA
	TTCAAAGTTT
501	CTTAGCGAAT ACGGGCGCGG TCGTGGCGGC GATTCTGCCG
	TTTGTGTTTG
551	CGTATATCGG TTTGGCGAAC ACCGCCGAGA AAGGCGTTGT
	GCCGCAGACC
601	GTGGTCGTGG CGTTTTATGT GGGTGCGGCG TTGCTGGTGA
	TTACCAGCGC
651	GTTCACGATT TTCAAAGTGA AGGAATACAA TCCGGAAACC
	TACGCCCGTT
701	ACCACGGCAT CGATGTCGCC GCGAATCAGG AAAAAGCCAA
	CTGGATCGAA
751	CTCTTGAAAA CCGCGCCTAA GGCGTTTTGG ACGGTTACTT
	TGGTGCAATT
801	CTTCTGCTGG TTCGCCTTCC AATATATGTG GACTTACTCG
	GCAGGCGCGA
851	TTGCGGAAAA CGTCTGGCAC ACCACCGATG CGTCTTCCGT
	AGGTTATCAG
901	GAGGCGGGTA ACTGGTACGG CGTTTTGGCG GCGGTGCAGT
	CGGTTGCGGC
951	GGTGATTTGT TCGTTTGTAT TGGCGAAAGT GCCGAATAAA
	TACCATAAGG
1001	CGGGTTATTT CGGCTGTTTG GCTTTGGGCG CGCTCGGCTT
	TTTCTCCGTT
1051	TTCTTCATCG GCAACCAATA CGCGCTGGTG TTGTCTTATA
	CCTTAATCGG
1101	CATCGCTTGG GCGGGCATTA TCACTTATCC GCTGACGATT
	GTGACCAACG
1151	CCTTGTCGGG CAAGCATATG GGCACTTACT TGGGCCTGTT
	TAACGGCTCT
1201	ATCTGTATGC CGCAAATCGT CGCTTCGCTG TTGAGTTTCG
	TGCTTTTCCC
1251	TATGCTGGGC GGCTTGCAGG CCACTATGTT CTTGGTAGGG
	GGCGTCGTCC
1301	TGCTGCTGGG CGCGTTTTCC GTGTTCCTGA TTAAAGAAAC
	ACACGGCGGG
1351	GTTTGA

This encodes a protein having amino acid sequence <SEQ ID 152>:

1	MSEYTPQTAK QGLPALAKST IWMLSFGFLG VQTAFTLQSS
	QMSRIFQTLG
51	ADPHSLGWFF ILPPLAGMLV QPIVGHYSDR TWKPRLGGRR
	LPYLLYGTLI
101	AVIVMILMPN SGSFGFGYAS LAALSFGALM IALLDVSSNM
	AMQPFKMMVG
151	DMVNEEQKGY AYGIQSFLAN TGAVVAAILP FVFAYIGLAN
	TAEKGVVPQT
201	VVVAFYVGAA LLVITSAFTI FKVKEYNPET YARYHGIDVA
	ANQEKANWIE
251	LLKTAPKAFW TVTLVQFFCW FAFQYMWTYS AGAIAENVWH
	TTDASSVGYQ
301	EAGNWYGVLA AVQSVAAVIC SFVLAKVPNK YHKAGYFGCL
	ALGALGFFSV
351	FFIGNQYALV LSYTLIGIAW AGIITYPLTI VTNALSGKHM
	GTYLGLFNGS
401	ICMPQIVASL LSFVLFPMLG GLQATMFLVG GVVLLLGAFS
	VFLIKETHGG
451	V*

ORF16a and ORF16-1 show 99.6% identity in 451 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF16 shows 93.9% identity over a 181aa overlap with a predicted ORF (ORF16.ng) from N. gonorrhoeae:

The complete length ORF16ng nucleotide sequence <SEQ ID 153> is:

1	ATGATAGGGG ATCGCCGCGC CGGCAACCAT TTCGGATTTT
	CCAAAGCAAA
51	TACTTTTCAA ATCAAAAAAA AGGATTTACT TTATGTCGGA
	ATATACGCCT
101	CAAACAGCAA AACAAGGTTT GCCCGCGCCG GCAAAAAGCA
	CGATTTGGAT
151	GTTGAGCTTC GGCTATCTCG GCGTTCAGAC GGCCTTTACC
	CTGCAAAGCT
201	CGCAGATGAG CCGCATTTTT CAAACGCTAG GCGCAGACCC
	GCACAATTTG
251	GGCTGGTTTT TCATCCTGCC GCCGCTGGCG GGGATGCTGG
	TTCAGCCGAT
301	AGTGGCTACT ACTCAGACCG CACTTGGAAG CCGCGCTTGG
	GCGGCCGCCG
351	CCTGCCGTAT CTGCTTTACG GCACGCTGAT TGCGGTCATC
	GTGATGATTT
401	TGATGCCGAA CTCGGGCAGC TTCGGTTTCG GCTATGCGTC
	GCTGGCGGCC
451	TTGTCGTTCG GCGCGCTGAT GATTGCGCTG TTGGACGTGT
	CGTCGAATAT
501	GGCGATGCAG CCGTTTAAGA TGATGGTCGG CGATATGGTC
	AACGAGGAGC
551	AGAAAAGCTA CGCCTACGGG ATTCAAAGTT TCTTAGCGAA
	TACGGACGCG
601	GTTGTGGCAG CGATTCTGCC GTTTGTGTTC GCGTATATCG
	GTTTGGCGAA
651	CACTGCCGAG AAAGGCGTTG TGCCACAAAC CGTGGTCGTA
	GCATTCTATG
701	TGGGTGCGGC GTTACTGATT ATTACCAGTG CGTTCACAAT
	CTCCAAAGTC
751	AAAGAATACG ACCCGGAAAC CTACGCCCGT TACCACGGCA
	TCGATGTCGC
801	CGCGAATCAG GAAAAAGCCA ACTGGTTCGA ACTCTTAAAA
	ACCGCGCCTA
851	AAGTGTTTTG GACGGTTACT CCGGTACAGT TTTTCTGCTG
	GTTCGCCTTC
901	CGGTATATGT GGACTTACTC GGCAGGCGCG ATTGCAGAAA
	ACGTCTGGCA
951	CACTACCGAT GCGTCTTCCG TAGGCCATCA GGAGGCGGGC
	AACCGGTACG
1001	GCGTTTTGGC GGCGGTGTAG

This encodes a protein having amino acid sequence <SEQ ID 154>:

1	MIGDRRAGNH FGFSKANTFQ IKKKDLLYVG IYASNSKTRF
	ARAGKKHDLD
51	VELRLSRRSD GLYPAKLADE PHFSNARRRP AQFGLVFHPA
	AAGGDAGSAD
101	SGYYSDRTWK PRLGGRRLPY LLYGTLIAVI VMILMPNSGS
	FGFGYASLAA
151	LSFGALMIAL LDVSSNMAMQ PFKMMVGDMV NEEQKSYAYG
	IQSFLANTDA
201	VVAAILPFVF AYIGLANTAE KGVVPQTVVV AFYVGAALLI
	ITSAFTISKV
251	KEYDPETYAR YHGIDVAANQ EKANWFELLK TAPKVFWTVT
	PVQFFCWFAF
301	RYMWTYSAGA IAENVWHTTD ASSVGHQEAG NRYGVLAAV*

ORF16ng and ORF16-1 show 89.3% identity in 261 aa overlap:

Based on this analysis, including the presence of several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 19

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 155>:

1	ATGTTGTTCC GTAAAACGAC CGCCGCCGTT TTGGCGCATA
	CCTTGATGCT
51	GAACGGCTGT ACGTTGATGT TGTGGGGAAT GAACAACCCG
	GTCAGCGAAA
101	CAATCACCCG NAAACACGTT GNCAAAGACC AAATCCGNGN
	CTTCGGTGTG
151	GTTGCCGAAG ACAATGCCCA ATTGGAAAAG GGCAGCCTGG
	TGATGATGGG
201	CGGAAAATAC TGGTTCGTCG TCAATCCCGA AGATTCGGCG
	AA.NTGACGG
251	GNATTTTGAN GGCAGGGCTG GACAAACCCT TCCAAATAGT
	TNAGGATACC
301	CCGAGCTATG C.TGCCACCA AGCCCTGCCG GTCAAACTCG
	GATCGNCTGG
351	CAGCCAGAAT...

This corresponds to the amino acid sequence <SEQ ID 156; ORF28>:

1	MLFRKTTAAV LAHTLMLNGC TLMLWGMNNP VSETITRKHV
	XKDQIRXFGV
51	VAEDNAQLEK GSLVMMGGKY WFVVNPEDSA XXTGILXAGL
	DKPFQIVXDT
101	PSYXCHQALP VKLGSXGSQN...

Further work revealed the complete nucleotide sequence <SEQ ID 157>:

1	ATGTTGTTCC GTAAAACGAC CGCCGCCGTT TTGGCGGCAA
	CCTTGATGCT
51	GAACGGCTGT ACGTTGATGT TGTGGGGAAT GAACAACCCG
	GTCAGCGAAA
101	CAATCACCCG CAAACACGTT GACAAAGACC AAATCCGCGC
	CTTCGGTGTG
151	GTTGCCGAAG ACAATGCCCA ATTGGAAAAG GGCAGCCTGG
	TGATGATGGG
201	CGGAAAATAC TGGTTCGTCG TCAATCCCGA AGATTCGGCG
	AAGCTGACGG
251	GCATTTTGAA GGCAGGGCTG GACAAACCCT TCCAAATAGT
	TGAGGATACC
301	CCGAGCTATG CTCGCCACCA AGCCCTGCCG GTCAAACTCG
	AATCGCCTGG
351	CAGCCAGAAT TTCAGTACCG AAGGCCTTTG CCTGCGCTAC
	GATACCGACA
401	AGCCTGCCGA CATCGCCAAG CTGAAACAGC TCGGGTTTGA
	AGCGGTCAAA
451	CTCGACAATC GGACCATTTA CACGCGCTGC GTATCCGCCA
	AAGGCAAATA
501	CTACGCCACA CCGCAAAAAC TGAACGCCGA TTACCATTTT
	GAGCAAAGTG
551	TGCCTGCCGA TATTTATTAC ACGGTTACTG AAGAACATAC
	CGACAAATCC
601	AAGCTGTTTG CAAATATCTT ATATACGCCC CCCTTTTTGA
	TACTGGATGC
651	GGCGGGCGCG GTACTGGCCT TGCCTGCGGC GGCTCTGGGT
	GCGGTCGTGG
701	ATGCCGCCCG CAAATGA

This corresponds to the amino acid sequence <SEQ ID 158; ORF28-1>:

1	MLFRKTTAAV LAATLMLNGC TLMLWGMNNP VSETITRKHV
	DKDQIRAFGV
51	VAEDNAQLEK GSLVMMGGKY WFVVNPEDSA KLTGILKAGL
	DKPFQIVEDT
101	PSYARHQALP VKLESPGSQN FSTEGLCLRY DTDKPADIAK
	LKQLGFEAVK
151	LDNRTIYTRC VSAKGKYYAT PQKLNADYHF EQSVPADIYY
	TVTEEHTDKS
201	KLFANILYTP PFLILDAAGA VLALPAAALG AVVDAARK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF28 shows 79.2% identity over a 120aa overlap with an ORF (ORF28a) from strain A of N. meningitidis:

The complete length ORF28a nucleotide sequence <SEQ ID 159> is:

1	ATGTTGTTCC GTAAAACGAC CGCCGCCGTT TTGGCGGCAA
	CCTTGATGTT
51	GAACGGCTGT ACGGTAATGA TGTGGGGTAT GAACAGCCCG
	TTCAGCGAAA
101	CGACCGCCCG CAAACACGTT GACAAGGACC AAATCCGCGC
	CTTCGGTGTG
151	GTTGCCGAAG ACAATGCCCA ATTGGAAAAG GGCAGCCTGG
	TGATGATGGG
201	CGGGAAATAC TGGTTCGTCG TCAATCCTGA AGATTCGGCG
	AAGCTGACGG
251	GCATTTTGAA GGCCGGGTTG GACAAGCAGT TTCAAATGGT
	TGAGCCCAAC
301	CCGCGCTTTG CCTACCAAGC CCTGCCGGTC AAACTCGAAT
	CGCCCGCCAG
351	CCAGAATTTC AGTACCGAAG GCCTTTGCCT GCGCTACGAT
	ACCGACAGAC
401	CTGCCGACAT CGCCAAGCTG AAACAGCTTG AGTTTGAAGC
	GGTCGAACTC
451	GACAATCGGA CCATTTACAC GCGCTGCGTC TCCGCCAAAG
	GCAAATACTA
501	CGCCACACCG CAAAAACTGA ACGCCGATTA TCATTTTGAG
	CAAAGTGTGC
551	CTGCCGATAT TTATTACACG GTTACGAAAA AACATACCGA
	CAAATCCAAG
601	TTGTTTGAAA ATATTGCATA TACGCCCACC ACGTTGATAC
	TGGATGCGGT
651	GGGCGCGGTG CTGGCCTTGC CTGTCGCGGC GTTGATTGCA
	GCCACGAATT
701	CCTCAGACAA ATGA

This encodes a protein having amino acid sequence <SEQ ID 160>:

1	MLFRKTTAAV LAATLMLNGC TVMMWGMNSP FSETTARKHV
	DKDQIRAFGV
51	VAEDNAQLEK GSLVMMGGKY WFVVNPEDSA KLTGILKAGL
	DKQFQMVEPN
101	PRFAYQALPV KLESPASQNF STEGLCLRYD TDRPADIAKL
	KQLEFEAVEL
151	DNRTIYTRCV SAKGKYYATP QKLNADYHFE QSVPADIYYT
	VTKKHTDKSK
201	LFENIAYTPT TLILDAVGAV LALPVAALIA ATNSSDK*

ORF28a and ORF28-1 show 86.1% identity in 238 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF28 shows 84.2% identity over a 120aa overlap with a predicted ORF (ORF28.ng) from N. gonorrhoeae:

The complete length ORF28ng nucleotide sequence <SEQ ID 161> is

1	ATGTTGTTCC GTAAAACGAC CGCCGCCGTT TTGGCGGCAA
	CCTTGATACT
51	GAACGGCTGT ACGATGATGT TGCGGGGGAT GAACAACCCG
	GTCAGCCAAA
101	CAATCACCCG CAAACACGTT GACAAAGACC AAATCCGCGC
	CTTCGGTGTG
151	GTTGCCGAAG ACAATGCCCA ATTGGAAAAG GGCAGCCTGG
	TGATGATGGG
201	CGGGAAATAC TGGTTCGCCG TCAATCCCGA AGATTCGGCG
	AAGCTGACGG
251	GCCTTTTGAA GGCCGGGTTG GACAAGCCCT TCCAAATAGT
	TGAGGATACC
301	CCGAGCTATG CCCGCCACCA AGCCCTGCCG GTCAAATTCG
	AAGCGCCCGG
351	CAGCCAGAAT TTCAGTACCG GAGGTCTTTG CCTGCGCTAT
	GATACCGGCA
401	GACCTGACGA CATCGCCAAG CTGAAACAGC TTGAGTTTAA
	AGCGGTCAAA
451	CTCGACAATC GGACCATTTA CACGCGCTGC GTATCCGCCA
	AAGGCAAATA
501	CTACGCCACG CCGCAAAAAC TGAACGCCGA TTATCATTTT
	GAGCAAAGTG
551	TGCCCGCCGA TATTTATTAT ACGGTTACTG AAAAACATAC
	CGACAAATCC
601	AAGCTGTTTG GAAATATCTT ATATACGCCC CCCTTGTTGA
	TATTGGATGC
651	GGCGGCCGCG GTGCTGGTCT TGCCTATGGC TCTGATTGCA
	GCCGCGAATT
701	CCTCAGACAA ATGA

This encodes a protein having amino acid sequence <SEQ ID 162>:

1	MLFRKTTAAV LAATLILNGC TMMLRGMNNP VSQTITRKHV
	DKDQIRAFGV
51	VAEDNAQLEK GSLVMMGGKY WFAVNPEDSA KLTGLLKAGL
	DKPFQIVEDT
101	PSYARHQALP VKFEAPGSQN FSTGGLCLRY DTGRPDDIAK
	LKQLEFKAVK
151	LDNRTIYTRC VSAKGKYYAT PQKLNADYHF EQSVPADIYY
	TVTEKHTDKS
201	KLFGNILYTP PLLILDAAAA VLVLPMALIA AANSSDK*

ORF28ng and ORF28-1 share 90.0% identity in 231 aa overlap:

Based on this analysis, including the presence of a putative transmembrane domain in the gonococcal protein, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF28-1 (24 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 6A shows the results of affinity purification of the GST-fusion protein, and FIG. 6B shows the results of expression of the His-fusion in E. coli. Purified GST-fusion protein was used to immunise mice, whose sera were used for ELISA, which gave a positive result. These experiments confirm that ORF28-1 is a surface-exposed protein, and that it may be a useful immunogen.

Example 20

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 163>:

1	..GTCAGTCCTG TACTGCCTAT TACACACGAA CGGACAGGGT
	TTGAAGGTGT
51	TATCGGTTAT GAAACCCATT TTTCAGGGCA CGGACATGAA
	GTACACAGTC
101	CGTTCGATCA TCATGATTCA AAAAGCACTT CTGATTTCAG
	CGGCGGTGTA
151	GACGGCGGTT TTACTGTTTA CCAACTTCAT CGAACATGGT
	CGGAAATCCA
201	TCCGGAGGAT GAATATGACG GGCCGCAAGC AGCG.ATTAT
	CCGCCCCCCG
251	GAGGAGCAAG GGATATATAC AGCTATTATG TCAAAGGAAC
	TTCAACAAAA
301	ACAAAGACTA GTATTGTCCC TCAAGCCCCA TTTTCAGACC
	GTTGGCTAGA
351	AGAAAATGCC GGTGCCGCCT CTGGT..

This corresponds to the amino acid sequence <SEQ ID 164; ORF29>:

1	..VSPVLPITHE RTGFEGVIGY ETHFSGHGHE VHSPFDHHDS
	KSTSDFSGGV
51	DGGFTVYQLH RTWSEIHPED EYDGPQAAXY PPPGGARDIY
	SYYVKGTSTK
101	TKTSIVPQAP FSDRWLEENA GAASG..

Further work revealed the complete nucleotide sequence <SEQ ID 165>:

1	ATGAATTTGC CTATTCAAAA ATTCATGATG CTGTTTGCAG
	CAGCAATATC
51	GTTGCTGCAA ATCCCCATTA GTCATGCGAA CGGTTTGGAT
	GCCCGTTTGC
101	GCGATGATAT GCAGGCAAAA CACTACGAAC CGGGTGGTAA
	ATACCATCTG
151	TTTGGTAATG CTCGCGGCAG TGTTAAAAAG CGGGTTTACG
	CCGTCCAGAC
201	ATTTGATGCA ACTGCGGTCA GTCCTGTACT GCCTATTACA
	CACGAACGGA
251	CAGGGTTTGA AGGTGTTATC GGTTATGAAA CCCATTTTTC
	AGGGCACGGA
301	CATGAAGTAC ACAGTCCGTT CGATCATCAT GATTCAAAAA
	GCACTTCTGA
351	TTTCAGCGGC GGTGTAGACG GCGGTTTTAC TGTTTACCAA
	CTTCATCGAA
401	CAGGGTCGGA AATCCATCCG GAGGATGGAT ATGACGGGCC
	GCAAGGCAGC
451	GATTATCCGC CCCCCGGAGG AGCAAGGGAT ATATACAGCT
	ATTATGTCAA
501	AGGAACTTCA ACAAAAACAA AGACTAATAT TGTCCCTCAA
	GCCCCATTTT
551	CAGACCGTTG GCTAAAAGAA AATGCCGGTG CCGCCTCTGG
	TTTTTTCAGC
601	CGTGCGGATG AAGCAGGAAA ACTGATATGG GAAAGCGACC
	CCAATAAAAA
651	TTGGTGGGCT AACCGTATGG ATGATGTTCG CGGCATCGTC
	CAAGGTGCGG
701	TTAATCCTTT TTTAATGGGT TTTCAAGGAG TAGGGATTGG
	GGCAATTACA
751	GACAGTGCAG TAAGCCCGGT CACAGATACA GCCGCGCAGC
	AGACTCTACA
801	AGGTATTAAT GATTTAGGAA AATTAAGTCC GGAAGCACAA
	CTTGCTGCCG
851	CGAGCCTATT ACAGGACAGT GCTTTTGCGG TAAAAGACGG
	TATCAACTCT
901	GCCAAACAAT GGGCTGATGC CCATCCAAAT ATAACAGCTA
	CTGCCCAAAC
951	TGCCCTTTCC GCAGCAGAGG CCGCAGGTAC GGTTTGGAGA
	GGTAAAAAAG
1001	TAGAACTTAA CCCGACTAAA TGGGATTGGG TTAAAAATAC
	CGGTTATAAA
1051	AAACCTGCTG CCCGCCATAT GCAGACTTTA GATGGGGAGA
	TGGCAGGTGG
1101	GAATAAACCT ATTAAATCTT TACCAAACAG TGCCGCTGAA
	AAAAGAAAAC
1151	AAAATTTTGA GAAGTTTAAT AGTAACTGGA GTTCAGCAAG
	TTTTGATTCA
1201	GTGCACAAAA CACTAACTCC CAATGCACCT GGTATTTTAA
	GTCCTGATAA
1251	AGTTAAAACT CGATACACTA GTTTAGATGG AAAAATTACA
	ATTATAAAAG
1301	ATAACGAAAA CAACTATTTT AGAATCCATG ATAATTCACG
	AAAACAGTAT
1351	CTTGATTCAA ATGGTAATGC TGTGAAAACC GGTAATTTAC
	AAGGTAAGCA
1401	AGCAAAAGAT TATTTACAAC AACAAACTCA TATCAGGAAC
	TTAGACAAAT
1451	GA

This corresponds to the amino acid sequence <SEQ ID 166; ORF29-1>:

1	MNLPIQKFMM LFAAAISLLQ IPISHANGLD ARLRDDMQAK
	HYEPGGKYHL
51	FGNARGSVKK RVYAVQTFDA TAVSPVLPIT HERTGFEGVI
	GYETHFSGHG
101	HEVHSPFDHH DSKSTSDFSG GVDGGFTVYQ LHRTGSEIHP
	EDGYDGPQGS
151	DYPPPGGARD IYSYYVKGTS TKTKTNIVPQ APFSDRWLKE
	NAGAASGFFS
201	RADEAGKLIW ESDPNKNWWA NRMDDVRGIV QGAVNPFLMG
	FQGVGIGAIT
251	DSAVSPVTDT AAQQTLQGIN DLGKLSPEAQ LAAASLLQDS
	AFAVKDGINS
301	AKQWADAHPN ITATAQTALS AAEAAGTVWR GKKVELNPTK
	WDWVKNTGYK
351	KPAARHMQTL DGEMAGGNKP IKSLPNSAAE KRKQNFEKFN
	SNWSSASFDS
401	VHKTLTPNAP GILSPDKVKT RYTSLDGKIT IIKDNENNYF
	RIHDNSRKQY
451	LDSNGNAVKT GNLQGKQAKD YLQQQTHIRN LDK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF29 shows 88.0% identity over a 125aa overlap with an ORF (ORF29a) from strain A of N. meningitidis:

The complete length ORF29a nucleotide sequence <SEQ ID 167> is:

1	ATGAATTNGC CTATTCAAAA ATTCATGATG CTGTTTGCAG
	CAGCAATATC
51	GTNGCTGCAA ATCCCNATTA GTCATGCGAA CGGTTTGGAT
	GCCCGTTTGC
101	GCGATGATAT GCAGGCAAAA CACTACGAAC CGGGTGGTAA
	ATACCATCTG
151	TTTGGTAATG CTCGCGGCAG TGTTAAAAAT CGGGTTTACG
	CCGTCCAAAC
201	ATTTGATGCA ACTGCGGTCG GCCCCATACT GCCTATTACA
	CACGAACGGA
251	CAGGATTTGA AGGCATTATC GGTTATGAAA CCCATTTTTC
	AGGACATGGA
301	CATGAAGTAC ACAGTCCGTT CGATAATCAT GATTCAAAAA
	GCACTTCTGA
351	TTTCAGCGGC GGCGTAGACG GTGGTTTTAC CGTTTACCAA
	CTTCATCGGA
401	CAGGGTCGGA AATCCATCCG GAGGATGGAT ATGACGGGCC
	GCAAGGCAGC
451	GATTATCCGC CCCCCGGAGG AGCAAGGGAT ATATACANNT
	ANTATGTCAA
501	AGGAACTTCA ACAAAAACAA AGAGTAATAT TGTTCCCCGA
	GCCCCATTTT
551	CAGACCGCTG GCTAAAAGAA AATGCCGGTG CCGCCTCTGG
	TTTTTTCAGC
601	CGTGCTGATG AAGCAGGAAA ACTGATATGG GAAAGCGACC
	CCAATAAAAA
651	TTGGTGGGCT AACCGTATGG ATGATATTCG CGGCATCGTC
	CAAGGTGCGG
701	TTAATCCTTT TTTAATGGGT TTTCAAGGAG TAGGGATTGG
	GGCAATTACA
751	GACAGTGCAG TAAGCCCGGT CACAGATACA GCCGCGCAGC
	AGACTCTACA
801	AGGTATNAAT CATTTAGGAA ANTTAAGTCC CGAAGCACAA
	CTTGCGGCTG
851	CAACCGCATT ACAAGACAGT GCTTTTGCGG TAAAAGACGG
	TATCAATTCC
901	GCCAGACAAT GGGCTGATGC CCATCCGAAT ATAACTGCAA
	CAGCCCAAAC
951	TGCCCTTGCC GTAGCAGANG CCGCAACTAC GGTTTGGGGC
	GGTAAAAAAG
1001	TAGAACTTAA CCCGACCAAA TGGGATTGGG TTAAAAATAC
	NGGCTATAAN
1051	ACACCTGCTG TTCGCACCAT GCATACTTTG GATGGGGAAA
	TGGCCGGTGG
1101	GAATAGACCG CCTAAATCTA TAACGTCCAA CAGCAAAGCA
	GATGCTTCCA
1151	CACAACCGTC TTTACAAGCG CAACTAATTG GAGAACAAAT
	TANNNNNGGG
1201	CATGCTTATA ACAAGCATGT CATAAGACAA CAAGAATTTA
	CGGATTTAAA
1251	TATCAATTCA CCAGCAGATT TTGCTCGGCA TATTGAAAAT
	ATTGTTAGCC
1301	ATCCANCAAA TATGAAAGAG TTACCTCGCG GTAGAACTGC
	GTATTGGGAT
1351	NATAAAACAG GGACNATAGT TATCCGAGAT AAAAATTCTG
	ACGATGGAGG
1401	TACAGCATTT AGACCAACAT CAGGTAAAAA ATATTATGAT
	GATTTATAG

This encodes a protein having amino acid sequence <SEQ ID 168>:

1	MNXPIQKFMM LFAAAISXLQ IPISHANGLD ARLRDDMQAK
	HYEPGGKYHL
51	FGNARGSVKN RVYAVQTFDA TAVGPILPIT HERTGFEGII
	GYETHFSGHG
101	HEVHSPFDNH DSKSTSDFSG GVDGGFTVYQ LHRTGSEIHP
	EDGYDGPQGS
151	DYPPPGGARD IYXXYVKGTS TKTKSNIVPR APFSDRWLKE
	NAGAASGFFS
201	RADEAGKLIW ESDPNKNWWA NRMDDIRGIV QGAVNPFLMG
	FQGVGIGAIT
251	DSAVSPVTDT AAQQTLQGXN HLGXLSPEAQ LAAATALQDS
	AFAVKDGINS
301	ARQWADAHPN ITATAQTALA VAXAATTVWG GKKVELNPTK
	WDWVKNTGYX
351	TPAVRTMHTL DGEMAGGNRP PKSITSNSKA DASTQPSLQA
	QLIGEQIXXG
401	HAYNKHVIRQ QEFTDLNINS PADFARHIEN IVSHPXNMKE
	LPRGRTAYWD
451	XKTGTIVIRD KNSDDGGTAF RPTSGKKYYD DL*

ORF29a and ORF29-1 show 90.1% identity in 385 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF29 shows 88.8% identity over a 125aa overlap with a predicted ORF (ORF29.ng) from N. gonorrhoeae:

The complete length ORF29ng nucleotide sequence <SEQ ID 169> is predicted to encode a protein having amino acid sequence <SEQ ID 170>:

1 MNLPIQKFMM LFAAAISLLQ IPISHANGLD ARLRDDMQAK HYEPGGKYHL
51 FGNARGSVKN RVCAVQTFDA TAVGPILPIT HERTGFEGVI GYETHFSGHG
101 HEVHSPFDNH DSKSTSDFSG GVDGGFTVYQ LHRTGSEIHP EDGYDGPQGG
151 GYPPPGGARD IYSYHIKGTS TKTKINTVPQ APFSDRWLKE NAGAASGFLS
201 RADEAGKLIW ENDPDKNWRA NRMDDIRGIV QGAVNPFLTG FQGLGVGAIT
251 DSAVSPVTYA AARKTLQGIH NLGNLSPEAQ LAAATALQDS AFAVKDSINS
301 ARQWADAHPN ITATAQTALA VTEAATTVWG GKKVELNPAK WDWVKNTGYK
351 KPAARHMQTV DGEMAGGNKP LESKNTVTTN NFFENTGYTE KVLRQASNGD
401 YHGFPQSVDA FSENGTVIQI VGGDNIVRHK LYIPGSYKGK DGNFEYIREA
451 DGKINHRLFV PNQQLPEK*

In a second experiment, the following DNA sequence <SEQ ID 171> was identified:

1 atgAATTTGC CTATTCAAAA ATTCATGATG ctgttggcAg cggcaatatc
51 gatgctGCat ATCCCCATTA GTCATGCGAA CGGTTTGGAT GCCCGTTTGC
101 GCGATGATAT GCAGGCAAAA CACTACGAAC CGGGTGGCAA ATACCATCTG
151 TTTGGTAATG CTCGCGGCAG TGTTAAAAAT CGGGTTTGCG CCGTCCAAAC
201 ATTTGATGCA ACTGCGGTCG GCCCCATACT GCCTATTACA CACGAACGGA
251 CAGGATTTGA AGGTGTTATC GGCTATGAAA CCCATTTTTC AGGACACGGA
301 CACGAAGTAC ACAGTCCGTT CGATAATCAT GATTCAAAAA GCACTTCTGA
351 TTTCAGCGGC GGCGTAGACG GCGGTTTTAC CGTTTACCAA CTTCATCGGA
401 CAGGGTCGGA AATACATCCC GCAGACGGAT ATGACGGGCC TCAAGGCGGC
451 GGTTATCCGG AACCACAAGG GGCAAGGGAT ATATACAGCT ACCATATCAA
501 AGGAACTTCA ACCAAAACAA AGATAAACAC TGTTCCGCAA GCCCCTTTTT
551 CAGACCGCTG GCTAAAAGAA AATGCCGGTG CCGCTTCCGG TTTTCTCAGC
601 CGTGCGGATG AAGCAGGAAA ACTGATATGG GAAAACGACC CCGATAAAAA
651 TTGGCGGGCT AACCGTATGG ATGATATTCG CGGCATCGTC CAAGGTGCGG
701 TTAATCCTTT TTTAACGGGT TTTCAAGGGG TAGGGATTGG GGCAATTACA
751 GACAGTGCGG TAAGCCCGGT CACAGATACA GCCGCTCAGC AGACTCTACA
801 AGGTATTAAT GATTTAGGAA ATTTAAGTCC GGAAGCACAA CTTGCCGCCG
851 CGAGCCTATT ACAGGACAGT GCCTTTGCGG TAAAAGACGG CATCAATTCC
901 GCCAGACAAT GGGCTGATGC CCATCCGAAT ATAACAGCAA CAGCCCAAAC
951 TGCCCTTGCC GTAGCAGAGG CCGCAGGTAC GGTTTGGCGC GGTAAAAAAG
1001 TAGAACTTAA CCCGACCAAA TGGGATTGGG TTAAAAATAC CGGCTATAAA
1051 AAACCTGCTG CCCGCCATAT GCAGACTGTA GATGGGGAGA TGGCAGGGGG
1101 GAATAGACCG CCTAAATCTA TAACGTCGGA AGGAAAAGCT AATGCTGCAA
1151 CCTATCCTAA GTTGGTTAAT CAGCTAAATG AGCAAAACTT AAATAACATT
1201 GCGGCTCAAG ATCCAAGATT GAGTCTAGCT ATTCATGAGG GTAAAAAAAA
1251 TTTTCCAATA GGAACTGCAA CTTATGAAGA GGCAGATAGA CTAGGTAAAA
1301 TTTGGGTTGG TGAGGGTGCA AGACAAACTA GTGGAGGCGG ATGGTTAAGT
1351 AGAGATGGCA CTCGACAATA TCGGCCACCA ACAGAAAAAA AATCACAATT
1401 TGCAACTACA GGTATTCAAG CAAATTTTGA AACTTATACT ATTGATTCAA
1451 ATGAAAAAAG AAATAAAATT AAAAATGGAC ATTTAAATAT TAGGTAA

This encodes a protein having amino acid sequence <SEQ ID 172; ORF29ng-1>:

1 MNLPIQKFMM LLAAAISMLH IPISHANGLD ARLRDDMQAK HYEPGGKYHL
51 FGNARGSVKN RVCAVQTFDA TAVGPILPIT HERTGFEGVI GYETHFSGHG
101 HEVHSPFDNH DSKSTSDFSG GVDGGFTVYQ LHRTGSEIHP ADGYDGPQGG
151 GYPEPQGARD IYSYHIKGTS TKTKINTVPQ APFSDRWLKE NAGAASGFLS
201 RADEAGKLIW ENDPDKNWRA NRMDDIRGIV QGAVNPFLTG FQGVGIGAIT
251 DSAVSPVTDT AAQQTLQGIN DLGNLSPEAQ LAAASLLQDS AFAVKDGINS
301 ARQWADAHPN ITATAQTALA VAEAAGTVWR GKKVELNPTK WDWVKNTGYK
351 KPAARHMQTV DGEMAGGNRP PKSITSEGKA NAATYPKLVN QLNEQNLNNI
401 AAQDPRLSLA IHEGKKNFPI GTATYEEADR LGKIWVGEGA RQTSGGGWLS
451 RDGTRQYRPP TEKKSQFATT GIQANFETYT IDSNEKRNKI KNGHLNIR*

ORF29ng-1 and ORF29-1 show 86.0% identity in 401 aa overlap:

Based on this analysis, including the presence of a putative leader sequence in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 21

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 173>:

1 ATGAAAAAAC AAATCACCGC AGCCGTAATG ATGCTGTCTA TGATTGCCCC
51 CGCAATGGCA AACGGCTTGG ACAATCAGGC ATTTGAAGAC CAAATGTTCC
101 ACACGCGGGC AGATGCACCG ATGCAG...

This corresponds to the amino acid sequence <SEQ ID 174; ORF30>:

1 MKKQITAAVM MLSMIAPAMA NGLDNQAFED QMFHTRADAP MQ..

Further work revealed the complete nucleotide sequence <SEQ ID 175>:

1 ATGAAAAAAC AAATCACCGC AGCCGTAATG ATGCTGTCTA TGATTGCCCC
51 CGCAATGGCA AACGGCTTGG ACAATCAGGC ATTTGAAGAC CAAGTGTTCC
101 ACACGCGGGC AGATGCACCG ATGCAGTTGG CGGAGCTTTC TCAAAAGGAG
151 ATGAAGGAGA CAGAGGGGGC GTTTCTTCCA TTGGCTATCT TGGGTGGTGC
201 TGCCATTGGT ATGTGGACAC AGCATGGTTT TAGTTATGCA ACGACAGGCA
251 GACCAGCTTC TGTTAGAGAT GTTGCTATTG CTGGCGGATT AGGCGCAATT
301 CCTGGTGGTG TAGGCGCCGC AGGAAAGGTT GTTTCCTTTG CTAAATATGG
351 ACGTGAGATT AAAATCGGCA ATAATATGCG GATAGCCCCT TTCGGTAATA
401 GAACAGGTCA TCCTATTGGA AAATTTCCCC ATTATCATCG TCGAGTTACG
451 GATAATACGG GCAAGACTTT GCCTGGACAG GGAATTGGTC GTCATCGCCC
501 TTGGGAATCA AAATCTACGG ACAGATCATG GAAAAACCGC TTCTAA

This corresponds to the amino acid sequence <SEQ ID 176; ORF30-1>:

1 MKKQITAAVM MLSMIAPAMA NGLDNQAFED QVFHTRADAP MQLAELSQKE
51 MKETEGAFLP LAILGGAAIG MWTQHGFSYA TTGRPASVRD VAIAGGLGAI
101 PGGVGAAGKV VSFAKYGREI KIGNNMRIAP FGNRTGHPIG KFPHYHRRVT
151 DNTGKTLPGQ GIGRHRPWES KSTDRSWKNR F*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF30 shows 97.6% identity over a 42aa overlap with an ORF (ORF30a) from strain A of N. meningitidis:

The complete length ORF30a nucleotide sequence <SEQ ID 177> is:

1 ATGAAAAAAC AAATCACCGC AGCCGTAATG ATGCTGTCTA TGATTGCCCC
51 CGCAATGGCA AACGGCTTGG ACAATCAGGC ATTTGAAGAC CAAGTGTTCC
101 ACACGCGGGC AGATGCACCG ATGCAGTTGG CGGAGCTTTC TCAAAAGGAG
151 ATGAAGGANA CAGNGGGGGC GTTTCTTCCA TTGGNTATCT TGGGTGGTGC
201 TGCCATTGGT ATGTGGACAC AGCATGGTTT TAGTTATGCA ACGACAGGCA
251 GACCAGCTTC TGTTAGAGAT GTTGCTATTG CTGGCGGATT AGGCGCAATT
301 CCTGGTGNTG TAGGCGCCGC AGGAAAGGTT GTTTCCTTTG CTAAATATGG
351 ACGTGAGATT AAAATCGGCA ATAATATGCG GATAGCCCCT TTCGGTAATA
401 GAACAGGTCA TCCTATTGGN AAATTTCCCC ATTATCATCG TCGAGTTACG
451 GATAATACGG GCAAGACTTT GCCTGGACAG GGAATTGGTC GTCATCGCCC
501 TTGGGAATCA AAATCTACGG ACAGATCATG GAAAAACCGC TTCTAA

This encodes a protein having amino acid sequence <SEQ ID 178>:

1 MKKQITAAVM MLSMIAPAMA NGLDNQAFED QVFHTRADAP MQLAELSQKE
51 MKXTXGAFLP LXILGGAAIG MWTQHGFSYA TTGRPASVRD VAIAGGLGAI
101 PGXVGAAGKV VSFAKYGREI KIGNNMRIAP FGNRTGHPIG KFPHYHRRVT
151 DNTGKTLPGQ GIGRHRPWES KSTDRSWKNR F*

ORF30a and ORF30-1 show 97.8% identity in 181 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF30 shows 97.6% identity over a 42aa overlap with a predicted ORF (ORF30.ng) from N. gonorrhoeae:

The complete length ORF30ng nucleotide sequence <SEQ ID 179> is

1 ATGAAAAAAC AAATCACCGC AGCCGTAATG ATGCTGTCTA TGATCGCCCC
51 CGCAATGGCA AACGGATTGG ACAATCAGGC ATTTGAAGAC CAAGTGTTCC
101 ACACGCGGGC AGATGCGCCG ATGCAGTTGG CGGAGCTTTC TCAGAAGGAG
151 ATGAAGGAGA CTGAAGGGGC TTTTCTTCCA TTGGCTATCT TGGGTGGTGC
201 TGCCATTGGT ATGTGGACAC AGCATGGTTT TAGTTATGCA ACGACAGGCA
251 GACCAGCTTC TGTTAGAGAT GTTGCTGGCG GATTAGGCGC AATTCCTGGT
301 GATGTAGGTG CTGCAGGAAA GGTTGTTTCC TTTGCTAAAT ATGGACGTGA
351 GATTAAAATC GGCAATAATA TGCGGATAGC CCCTTTCGGT AATAGAACAG
401 GTCATCCTAT TGGAAAATTT CCCCATTATC ATCGTCGAGT TACGGATAAT
451 ACGGGCAAGA CTTTGCCTGG ACAGGGAATT GGTCGTCATC GCCCTTGGGA
501 ATCAAAATCT ACGGACAGAT CATGGAAAAA CCGCTTCTAA

This encodes a protein having amino acid sequence <SEQ ID 180>:

1 MKKQITAAVM MLSMIAPAMA NGLDNQAFED QVFHTRADAP MQLAELSQKE
51 MKETEGAFLP LAILGGAAIG MWTQHGFSYA TTGRPASVRD VAGGLGAIPG
101 DVGAAGKVVS FAKYGREIKI GNNMRIAPFG NRTGHPIGKF PHYHRRVTDN
151 TGKTLPGQGI GRHRPWESKS TDRSWKNRF*

ORF30ng and ORF30-1 show 98.3% identity in 181 aa overlap:

Based on this analysis, including the presence of a putative leader sequence in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 22

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 181>:

1 ATGAATAAAA CTCTCTATCG TGTAATTTTC AACCGCAAAC GTGGGGCTGT
51 GrTAGCCGTT GCTGAAACTA CCAAGCGCGA AGGTAAAAGC TGTGCCGATA
101 GTGATTCAGG CAGCGCTCAT GTGAAATCTG TTCCTTTTGG TACTACTCAT
151 GCACCTGTTT GTg.CGTTaC AAATATCTTT TCTTTTTCTT TATTGGGCTT
201 TTCTTTATGT TTGGCTGTAG GtacGGyCAA TATTGCTTTT GCTGATGGCA
251 TT..

This corresponds to the amino acid sequence <SEQ ID 182; ORF31>:

1 MNKTLYRVIF NRKRGAVXAV AETTKREGKS CADSDSGSAH VKSVPFGTTH
51 APVCXVTNIF SFSLLGFSLC LAVGTXNIAF ADGI..

Further work revealed a further partial nucleotide sequence <SEQ ID 183>:

1 ATGAATAAAA CTCTCTATCG TGTAATTTTC AACCGCAAAC GTGGGGCTGT
51 GGTAGCCGTT GCTGAAACTA CCAAGCGCGA AGGTAAAAGC TGTGCCGATA
101 GTGATTCAGG CAGCGCTCAT GTGAAATCTG TTCCTTTTGG TACTACTCAT
151 GCACCTGTTT GTCGTTCAAA TATCTTTTCT TTTTCTTTAT TGGGCTTTTC
201 TTTATGTTTG GCTGTAGGTA CGGCCAATAT TGCTTTTGCT GATGGCATT..

This corresponds to the amino acid sequence <SEQ ID 184; ORF31-1>:

• • 1 MNKTLYRVIF NRKRGAVVAV AETTKREGKS CADSDSGSAH VKSVPFGTTH
  • 51 APVCRSNIFS FSLLGFSLCL AVGTANIAFA DGI . . . .

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. gonorrhoeae

ORF31 shows 76.2% identity over a 84aa overlap with a predicted ORF (ORF31.ng) from N. gonorrhoeae:

The complete length ORF31ng nucleotide sequence <SEQ ID 185> is:

1 ATGAACAAAA CCCTCTATCG TGTGATTTTC AACCGCAAAC GCGGTGCTGT
51 GGTAGCTGTT GCCGAAACCA CCAAGCGCGA AGGTAAAAGC TGTGCCGATA
101 GTGGTTCGGG CAGCGTTTAT GTGAAATCCG TTTCTTTCAT TCCTACTCAT
151 TCCAAAGCCT TTTGTTTTTC TGCATTAGGC TTTTCTTTAT GTTTGGCTTT
201 GGGTACGGTC AATATTGCTT TTGCTGACGG CATTATTACT GATAAAGCTG
251 CTCCTAAAAC CCAACAAGCC ACGATTCTGC AAACAGGTaa cGGCATACCG
301 CAAGTCAATA TTCAAACCCC TACTTCGGCA GGGGTTTCTG TTAATCAATA
351 TGCCCAGTTT GATGTGGGTA ATCGCGGGGC GATTTTAAAC AACAGTCGCA
401 GCAACACCCA AACACAGCTA GGCGGTTGGA TTCAAGGCAA TCCTTGGTTG
451 ACAAGGGGCG AAGCACGTGT GGTTGTAAAC CAAATCAACA GCAGCCATCC
501 TTCACAACTG AATGGCTATA TTGAAGTGGG TGGACGACGT GCAGAAGTCG
551 TTATTGCCAA TCCGGCAGGG ATTGCAGTCA ATGGTGGTGG TTTTATCAAT
601 GCTTCCCGTG CCACTTTGAC GACAGGCCAA CCGCAATATC AAGCAGGAGA
651 CTTTAGCGGC TTTAAGATAA GGCAAGGCAA TGCTGTAATC GCCGGACACG
701 GTTTGGATGC CCGTGATACC GATTTCACAC GTATTCTTGT ATGCCAACAA
751 AATCACCTTG ATCAGTACGG CCGAACAAGC AGGCATTCGT AA

This encodes a protein having amino acid sequence <SEQ ID 186>:

1	MNKTLYRVIF NRKRGAVVAV AETTKREGKS CADSGSGSVY
	VKSVSFIPTH
51	SKAFCFSALG FSLCLALGTV NIAFADGIIT DKAAPKTQQA
	TILQTGNGIP
101	QVNIQTPTSA GVSVNQYAQF DVGNRGAILN NSRSNTQTQL
	GGWIQGNPWL
151	TRGEARVVVN QINSSHPSQL NGYIEVGGRR AEVVIANPAG
	IAVNGGGFIN
201	ASRATLTTGQ PQYQAGDFSG FKIRQGNAVI AGHGLDARDT
	DFTRILVCQQ
251	NHLDQYGRTS RHS*

This gonococcal protein shares 50% identity over a 149aa overlap with the pore-forming hemolysins-like HecA protein from Erwinia chrysanthemi (accession number L39897):

orf31ng	96	GNGIPQVNIQTPTSAGVSVNQYAQFDVGNRGAILNNSRSN-TQTQLGGWIQGNPWLTRGE	154
		GNG+P VNI TP ++G+S N+Y  F+V NRG ILNN  +  T +QLGG IQ NP L
HecA	45	GNGVPVVNIATPDASGLSHNRYHDFNVDNRGLILNNGTARLTPSQLGGLIQNNPNLNGRA	104
Orf31ng	155	ARVVVNQINSSHPSQLNGYIEVGGRRAEVVIANPAGIAVNGGGFINASRATLTTGQPQYQ	214
		A  ++N++ S + S+L GY+EV G+ A VV+ANP GI  +G GF+N  R TLTTG PQ+
HecA	105	AAAILNEVVSPNRSRLAGYLEVAGQAANVVVANPYGITCSGCGFLNTPRLTLTTGTPQFD	164
Orf31ng	215	-AGDFSGFKIRQGNAVIAGHGLDARDTDF	242
		AG  SG  +R G+ +I G GLDA  +D+
HecA	165	AAGGLSGLDVRGGDILIDGAGLDASRSDY	193

Furthermore, ORF31ng and ORF31-1 show 79.5% identity in 83 aa overlap:

On this basis, including the homology with hemolysins, and also with adhesins, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 23

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 187>:

1	ATGAATACTC CTCCTTTTGT CTGTTGGATT TTTTGCAAGG
	TCATCGACAA
51	TTTCGGCGAC ATCGGCGTTT CGTGGCGGCT CGCCCGTGTT
	TTGCACCGCG
101	AACTCGGTTG GCAGGTGCAT TTGTGGACGG ACGATGTGTC
	CGCCTTGCGT
151	GCGCTTTGCC CTGATTTGCC CGATGTTCCC TGCGTTCATC
	AGGATATTCA
201	TGTCCGCACT TGGCATTCCG ATGCGGCAGA TATTGATACC
	GCG..

This corresponds to the amino acid sequence <SEQ ID 188; ORF32>:

1	MNTPPFVCWI FCKVIDNFGD IGVSWRLARV LHRELGWQVH
	LWTDDVSALR
51	ALCPDLPDVP CVHQDIHVRT WHSDAADIDT A..

Further work revealed the complete nucleotide sequence <SEQ ID 189>:

1	ATGAATACTC CTCCTTTTGT CTGTTGGATT TTTTGCAAGG
	TCATCGACAA
51	TTTCGGCGAC ATCGGCGTTT CGTGGCGGCT CGCCCGTGTT
	TTGCACCGCG
101	AACTCGGTTG GCAGGTGCAT TTGTGGACGG ACGATGTGTC
	CGCCTTGCGT
151	GCGCTTTGCC CTGATTTGCC CGATGTTCCC TGCGTTCATC
	AGGATATTCA
201	TGTCCGCACT TGGCATTCCG ATGCGGCAGA TATTGATACC
	GCGCCTGTTC
251	CCGATGTCGT CATCGAAACT TTTGCCTGCG ACCTGCCCGA
	AAATGTGCTG
301	CACATTATCC GCCGACACAA GCCGCTTTGG CTGAATTGGG
	AATATTTGAG
351	CGCGGAGGAA AGCAATGAAA GGCTGCATCT GATGCCTTCG
	CCGCAGGAGG
401	GTGTTCAAAA ATATTTTTGG TTTATGGGTT TCAGCGAAAA
	AAGCGGCGGG
451	TTGATACGCG AACGTGATTA CTGCGAAGCC GTCCGTTTCG
	ATACTGAAGC
501	CCTGCGAGAG CGGCTGATGC TGCCCGAAAA AAACGCCTCC
	GAATGGCTGC
551	TTTTCGGCTA TCGGAGCGAT GTTTGGGCAA AGTGGCTGGA
	AATGTGGCGA
601	CAGGCAGGCA GCCCGATGAC ACTGTTGCTG GCGGGGACGC
	AAATCATCGA
651	CAGCCTCAAA CAAAGCGGCG TTATTCCGCA AGATGCCCTG
	CAAAACGACG
701	GCGATGTTTT TCAGACGGCA TCCGTCCGCC TCGTCAAAAT
	CCCTTTCGTG
751	CCGCAACAGG ACTTCGACCA ACTGCTGCAC CTTGCCGACT
	GCGCCGTCAT
801	CCGCGGCGAA GACAGTTTCG TGCGCGCCCA GCTTGCGGGC
	AAACCCTTCT
851	TTTGGCACAT CTACCCGCAA GACGAGAATG TCCATCTCGA
	CAAACTCCAC
901	GCCTTTTGGG ATAAGGCACA CGGTTTCTAC ACGCCCGAAA
	CCGTGTCGGC
951	ACACCGCCGT CTTTCGGACG ACCTCAACGG CGGAGAGGCT
	TTATCCGCAA
1001	CACAACGCCT CGAATGTTGG CAAACCCTGC AACAACATCA
	AAACGGCTGG
1051	CGGCAAGGCG CGGAGGATTG GAGCCGTTAT CTTTTCGGGC
	AGCCGTCAGC
1101	TCCTGAAAAA CTCGCTGCCT TTGTTTCAAA GCATCAAAAA
	ATACGCTAG

This corresponds to the amino acid sequence <SEQ ID 190; ORF32-1>:

1	MNTPPFVCWI FCKVIDNFGD IGVSWRLARV LHRELGWQVH
	LWTDDVSALR
51	ALCPDLPDVP CVHQDIHVRT WHSDAADIDT APVPDVVIET
	FACDLPENVL
101	HIIRRHKPLW LNWEYLSAEE SNERLHLMPS PQEGVQKYFW
	FMGFSEKSGG
151	LIRERDYCEA VRFDTEALRE RLMLPEKNAS EWLLFGYRSD
	VWAKWLEMWR
201	QAGSPMTLLL AGTQIIDSLK QSGVIPQDAL QNDGDVFQTA
	SVRLVKIPFV
251	PQQDFDQLLH LADCAVIRGE DSFVRAQLAG KPFFWHIYPQ
	DENVHLDKLH
301	AFWDKAHGFY TPETVSAHRR LSDDLNGGEA LSATQRLECW
	QTLQQHQNGW
351	RQGAEDWSRY LFGQPSAPEK LAAFVSKHQK IR*w

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF32 shows 93.8% identity over a 81 as overlap with an ORF (ORF32a) from strain A of N. meningitidis:

The complete length ORF32a nucleotide sequence <SEQ ID 191> is:

1	ATGAATACTC CTCCTTTTTC TGCTGGANTT TTTTGCAAGG
	TCATCGACAA
51	TTTCGGCGAC ATCGGCGTTT CGTGGCGGCT TGCCCGTGTT
	TTGCACCGCG
101	AACTCGGTTG GCAGGTGCAT TTGTGGACGG ACGATGTGTC
	CGCCTTGCGT
151	GCGCTTTGCC CTGATTTGCC CGATGTTCNC TGCGTTCATC
	AGGATATTCA
201	TGTCCGCACT TGGCATTCCG ATGCGGCAGA TATTGATACC
	GCGCCTGTTC
251	NCGATGTCGT CATCGAAACT TTTGCCTGCG ACCTGCCCGA
	AAATGTGCTG
301	CACATCATCC GCCGACACAA GCCGCTTTGG CTGAANTGGG
	AATATTTGAG
351	CGCGGAGGAN AGCAATGAAA GGCTGCACNT GATGCCTTCG
	CCGCAGGAGA
401	GTGTTCNAAA ATANTTTTGG TTTATGGGTT TCAGCGAANN
	NAGCGGCGGA
451	CTGATACGCG AACGCGATTA CTGCGAAGCC GTCCGTTTCG
	ATAGCGGAGC
501	CTTGCGCAAG AGGCTGATGC TTCCCGAAAA AAACGNCCCC
	GAATGGCTGC
551	TTTTCGGCTA TCGGAGCGAT GTTTGGGCAA AGTGGCTGGA
	AATGTGGCGA
601	CAGGCAGGCA GTCCGTTGAC ACTTTTGCTG GCNGGGGCGC
	ANATTATCGA
651	CAGCCTCAAA CAAAACGGCG TTATTCCGCA AGATGCCCTG
	CAAAACGACG
701	GCGATGTTTT TCAGACGGCA TCCGTCCGCC TCGTCAAAAT
	CCCTTTCGTG
751	CCGCAACAGG ACTTCGACAA ACTGCTGCAC CTTGCCGACT
	GCGCCGTCAT
801	CCGCGGCGAA GACAGTTTCG TGCGCGCCCA GCTTGCGGGC
	AAACCCTTCT
851	TTTGGCACAT CTACCCGCAA GATGAGAATG TCCATCTCGA
	CAAACTCCAC
901	GCCTTTTGGG ATAAGGCACA CGGTTTCTAC ACGCCCGAAA
	CCGCATCGGC
951	ACACCGCCGC CTTTCAGACG ACCTCAACGG CGGAGAGGCT
	TTATCCGCAA
1001	CACAACGCCT CGAATGTTGG CAAATCCTGC AACAACATCA
	AAACGGCTGG
1051	CGGCAAGGCG CGGAGGATTG GAGCCGTTAT CTTTTTGGGC
	AGCCTTCCGC
1101	ATCCGAAAAA CTCGCCGCCT TTGTTTCAAA GCATCAAAAA
	ATACGCTAG

This encodes a protein having amino acid sequence <SEQ ID 192>:

1	MNTPPFSAGX FCKVIDNFGD IGVSWRLARV LHRELGWQVH
	LWTDDVSALR
51	ALCPDLPDVX CVHQDIHVRT WHSDAADIDT APVXDVVIET
	FACDLPENVL
101	HIIRRHKPLW LXWEYLSAEX SNERLHXMPS PQESVXKXFW
	FMGFSEXSGG
151	LIRERDYCEA VRFDSGALRK RLMLPEKNXP EWLLFGYRSD
	VWAKWLEMWR
201	QAGSPLTLLL AGAXIIDSLK QNGVIPQDAL QNDGDVFQTA
	SVRLVKIPFV
251	PQQDFDKLLH LADCAVIRGE DSFVRAQLAG KPFFWHIYPQ
	DENVHLDKLH
301	AFWDKAHGFY TPETASAHRR LSDDLNGGEA LSATQRLECW
	QILQQHQNGW
351	RQGAEDWSRY LFGQPSASEK LAAFVSKHQK IR*

ORF32a and ORF32-1 show 93.2% identity in 382 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF32 shows 95.1% identity over a 82aa overlap with a predicted ORF (ORF32.ng) from N. gonorrhoeae:

An ORF32ng nucleotide sequence <SEQ ID 193> was predicted to encode a protein having amino acid sequence <SEQ ID 194>:

1	MVMNTYAFPV CWIFCKVIDN FGDIGVSWRL ARVLHRELGW
	QVHLWTDDVS
51	ALRALCPDLP DVPFVHQDIH VRTWHSDAAD IDTAPVPDAV
	IETFACDLPE
101	NVLNIIRRHK PLWLNWEYLS AEESNERLHL MPSPQEGVQK
	YFWFMGFSEK
151	SGGLIRERDY REAVRFDTEA LRRRLVLPEK NAPEWLLFGY
	RGDVWAKWLD
201	MWQQAGSLMT LLLAGAQIID SLKQSGVIPQ NALQNEGGVF
	QTASVRLVKI
251	PFVPQQDFDK LLHLADCAVI RGEDSFVRTQ LAGKPFFWHI
	YPQDENVHLD
301	KLHAFWDKAY GFYTPETASV HRLLSDDLNG GEALSATQRL
	ECGVL*

Further sequencing revealed the following DNA sequence <SEQ ID 195>:

1	ATGAATACAT ACGCTTTTCC TGTCTGTTGG ATTTTTTGCA
	AGGTCATCGA
51	CAATTTCGGC GACATCGGCG TTTCGTGGCG GCTCGCCCGT
	GTTTTGCACC
101	GCGAACTCGG TTGGCAGGTG CATTTGTGGA CGGACGACGT
	GTCCGCCTTG
151	CGCGCGCTTT GTCCCGATTT GCCCGATGTT CCCTTCGTTC
	ATCAGGATAT
201	TCATGTCCGC ACTTGGCATT CCGATGCGGC AGACATTGAT
	ACCGCGCCCG
251	TTCCCGATGC CGTTATCGAA ACTTTTGCCT GCGACCTGCC
	CGAAAATGTG
301	CTGAACATCA TCCGCCGACA CAAACCGCTT TGGCTGAATT
	GGGAATATTT
351	GAGCGCGGAG GAAAGCAATG AAAGGCTGCA CCTGATGCCT
	TCGCCGCAGG
401	AGGGCGTTCA AAAATATTTT TGGTTTATGG GTTTCAGCGA
	AAAAAGCGGC
451	GGGTTGATAC GCGAACGCGA TTACCGCGAA GCCGTCCGTT
	TCGATACCGA
501	AGCCCTGCGC CGGCGGCTGG TGCTGCCCGA AAAAAACGCC
	CCCGAATGGC
551	TGCTTTTCGG CTATCGGGGC GATGTTTGGG CAAAGTGGCT
	GGACATGTGG
601	CAACAGGCAG GCAGCCTGAT GACCCTACTG CTGGCGGGGG
	CGCAAATTAT
651	CGACAGCCTC AAACAAAGCG GCGTTATTCC GCAAAACGCC
	CTGCAAAAtg
701	aaggcgGTGT CTTTCagacG gcatccgTcC gccttGTCAA
	AAtcCCGTTC
751	GTGCcGCAAC AGGAcTTCGA CAAATTGCTG CAcctcgcCG
	ACTGCGCCGT
801	GATACGCGGC GAAGACAGTT TCGTGCGTAC CCAGCTTGCC
	GGAAAACCCT
851	TTTTTTGGCA CATCTACCCG CAAGACGAGA ATGTCCATCT
	CGACAAACTC
901	CACGCCTTTT GGGATAAGGC ATACGGCTTC TACACGCCCG
	AAACCGCATC
951	GGTGCACCGC CTCCTTTCGG ACGACCTCAA CGGCGGAGAG
	GCTTTATCCG
1001	CAACACAACG CCTCGAATGT TGGCAAACCC TGCAACAACA
	TCAAAACGGC
1051	TGGCGGCAAG GCGCGGAGGA TTGGAGCCGT TATCTTTTCG
	GGCAGCCTTC
1101	CGCATCCGAA AAACTCGCCG CCTTTGTTTC AAAGCATCAA
	AAAATACGCT
1151	AG

This encodes a protein having amino acid sequence <SEQ ID 196; ORF32ng-1>:

1	MNTYAFPVCW IFCKVIDNFG DIGVSWRLAR VLHRELGWQV
	HLWTDDVSAL
51	RALCPDLPDV PFVHQDIHVR TWHSDAADID TAPVPDAVIE
	TFACDLPENV
101	LNIIRRHKPL WLNWEYLSAE ESNERLHLMP SPQEGVQKYF
	WFMGFSEKSG
151	GLIRERDYRE AVRFDTEALR RRLVLPEKNA PEWLLFGYRG
	DVWAKWLDMW
201	QQAGSLMTLL LAGAQIIDSL KQSGVIPQNA LQNEGGVFQT
	ASVRLVKIPF
251	VPQQDFDKLL HLADCAVIRG EDSFVRTQLA GKPFFWHIYP
	QDENVHLDKL
301	HAFWDKAYGF YTPETASVHR LLSDDLNGGE ALSATQRLEC
	WQTLQQHQNG
351	WRQGAEDWSR YLFGQPSASE KLAAFVSKHQ KIR*

ORF32ng-1 and ORF32-1 show 93.5% identity in 383 aa overlap:

On this basis, including the RGD sequence in the gonococcal protein, characteristic of adhesins, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF32-1 (42 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 7A shows the results of affinity purification of the His-fusion protein, and FIG. 7B shows the results of expression of the GST-fusion in E. coli. Purified His-fusion protein was used to immunise mice, whose sera were used for ELISA, giving a positive result. These experiments confirm that ORF32-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 24

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 197>:

1	..TTGTTCCTGC GTGTNAAAGT GGGGCGTTTT TTCAGCAGTC
	CGGCGACGTG
51	GTTTCGGGNC AAAGACCCTG TAAATCAGGC GGTGTTGCGG
	CTGTATNCGG
101	ACGAGTGGCG GCA.ACTTCG GTACGTTGGA AAATAGNCGC
	AACGTCGCAC
151	AGCCTGTGGC TCTGCACGCT GCTCGGAATG CTGGTGTCGG
	TATTGTTGCT
201	GCTTTTGGTG CGGCAATATA CGTTCAACTG GGAAAGCACG
	CTGTTGAGCA
251	ATGCCGCTTC GGTACGCGCG GTGGAAATGT TGGCATGGCT
	GCCGTCGAAA
301	CTCGGTTTCC CTGTCCCCGA TGCGCGGTCG GTCATCGAAG
	GCCGTCTGAA
351	CGGCAATATT GCCGATGCGC GGGCTTGGTC GGGGCTGCTG
	GTCGNCAGTA
401	TCGCCTGCTA NGGCATCCTG CCGCGCCTG..

This corresponds to the amino acid sequence <SEQ ID 198; ORF33>:

1	..LFLRVKVGRF FSSPATWFRX KDPVNQAVLR LYXDEWRXTS
	VRWKIXATSH
51	SLWLCTLLGM LVSVLLLLLV RQYTFNWEST LLSNAASVRA
	VEMLAWLPSK
101	LGFPVPDARS VIEGRLNGNI ADARAWSGLL VXSIACXGIL
	PRL..

Further work revealed the complete nucleotide sequence <SEQ ID 199>:

1	ATGTTGAATC CATCCCGAAA ACTGGTTGAG CTGGTCCGTA
	TTTTGGACGA
51	AGGCGGTTTT ATTTTCAGCG GCGATCCCGT ACAGGCGACG
	GAGGCTTTGC
101	GCCGCGTGGA CGGCAGTACG GAGGAAAAAA TCATCCGTCG
	GGCGGAGATG
151	ATTGACAGGA ACCGTATGCT GCGGGAGACG TTGGAACGTG
	TGCGTGCGGG
201	GTCGTTCTGG TTGTGGGTGG TGGCGGCGAC GTTTGCATTT
	TTTACCGGTT
251	TTTCAGTCAC TTATCTTCTA ATGGACAATC AGGGTCTGAA
	TTTCTTTTTG
301	GTTTTGGCGG GCGTGTTGGG CATGAATACG CTGATGCTGG
	CAGTATGGTT
351	GGCAATGTTG TTCCTGCGTG TGAAAGTGGG GCGTTTTTTC
	AGCAGTCCGG
401	CGACGTGGTT TCGGGGCAAA GACCCTGTAA ATCAGGCGGT
	GTTGCGGCTG
451	TATGCGGACG AGTGGCGGCA ACCTTCGGTA CGTTGGAAAA
	TAGGCGCAAC
501	GTCGCACAGC CTGTGGCTCT GCACGCTGCT CGGAATGCTG
	GTGTCGGTAT
551	TGTTGCTGCT TTTGGTGCGG CAATATACGT TCAACTGGGA
	AAGCACGCTG
601	TTGAGCAATG CCGCTTCGGT ACGCGCGGTG GAAATGTTGG
	CATGGCTGCC
651	GTCGAAACTC GGTTTCCCTG TCCCCGATGC GCGGGCGGTC
	ATCGAAGGCC
701	GTCTGAACGG CAATATTGCC GATGCGCGGG CTTGGTCGGG
	GCTGCTGGTC
751	GGCAGTATCG CCTGCTACGG CATCCTGCCG CGCCTGCTGG
	CTTGGGTAGT
801	GTGTAAAATC CTTTTGAAAA CAAGCGAAAA CGGATTGGAT
	TTGGAAAAGC
851	CCTATTATCA GGCGGTCATC CGCCGCTGGC AGAACAAAAT
	CACCGATGCG
901	GATACGCGTC GGGAAACCGT GTCCGCCGTT TCACCGAAAA
	TCATCTTGAA
951	CGATGCGCCG AAATGGGCGG TCATGCTGGA GACCGAGTGG
	CAGGACGGCG
1001	AATGGTTCGA GGGCAGGCTG GCGCAGGAAT GGCTGGATAA
	GGGCGTTGCC
1051	ACCAATCGGG AACAGGTTGC CGCGCTGGAG ACAGAGCTGA
	AGCAGAAACC
1101	GGCGCAACTG CTTATCGGCG TGCGCGCCCA AACTGTGCCG
	GACCGCGGCG
1151	TGTTGCGGCA GATTGTCCGA CTCTCGGAAG CGGCGCAGGG
	CGGCGCGGTG
1201	GTGCAGCTTT TGGCGGAACA GGGGCTTTCA GACGACCTTT
	CGGAAAAGCT
1251	GGAACATTGG CGTAACGCGC TGGCCGAATG CGGCGCGGCG
	TGGCTTGAGC
1301	CTGACAGGGC GGCGCAGGAA GGGCGTTTGA AAGACCAATA
	A

This corresponds to the amino acid sequence <SEQ ID 200; ORF33-1>:

1	MLNPSRKLVE LVRILDEGGF IFSGDPVQAT EALRRVDGST
	EEKIIRRAEM
51	IDRNRMLRET LERVRAGSFW LWVVAATFAF FTGFSVTYLL
	MDNQGLNFFL
101	VLAGVLGMNT LMLAVWLAML FLRVKVGRFF SSPATWFRGK
	DPVNQAVLRL
151	YADEWRQPSV RWKIGATSHS LWLCTLLGML VSVLLLLLVR
	QYTFNWESTL
201	LSNAASVRAV EMLAWLPSKL GFPVPDARAV IEGRLNGNIA
	DARAWSGLLV
251	GSIACYGILP RLLAWVVCKI LLKTSENGLD LEKPYYQAVI
	RRWQNKITDA
301	DTRRETVSAV SPKIILNDAP KWAVMLETEW QDGEWFEGRL
	AQEWLDKGVA
351	TNREQVAALE TELKQKPAQL LIGVRAQTVP DRGVLRQIVR
	LSEAAQGGAV
401	VQLLAEQGLS DDLSEKLEHW RNALAECGAA WLEPDRAAQE
	GRLKDQ*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF33 shows 90.9% identity over a 143aa overlap with an ORF (ORF33a) from strain A of N. meningitidis:

The complete length ORF33a nucleotide sequence <SEQ ID 201> is:

1	ATGTTGAATC CATCCCGAAA ACTGGTTGAG CTGGTCCGTA
	TTTTGGAAGA
51	AGGCGGCTTT ATTTTCAGCG GCGATCCCGT GCAGGCGACG
	GAGGCTTTGC
101	GCCGCGTGGA CGGCAGTACG GAGGAAAAAA TCATCCGTCG
	GGCGAAGATG
151	ATCGACAGGA ACCGTATGCT GCGGGAGACG TTGGAACGTG
	TGCGTGCGGG
201	GTCGTTCTGG TTGTGGGTGG CGGCGGCGAC GTTTGCGTTT
	NTTACCGNTT
251	TTTCAGTTAC TTATCTTCTA ATGGACAATC AGGGTCTGAA
	TTTCTTTTTG
301	GTTTTGGCGG GCGTGNTGGG CATGAATACG CTGATGCTGG
	CAGTATGGTT
351	GGCAATGTTG TTCCTGCGCG TGAAAGTGGG GCGTTTTTTC
	AGCAGTCCGG
401	CGACGTGGTT TCGGGGCAAA GACCCTGTCA ATCAGGCGGT
	GTTGCGGCTG
451	TATGCGGACG AGTGGCGGCN ACCTTCGGTA CGTTGGAAAA
	TAGGCGCAAC
501	GTCGCACAGC CTGTGGCTCT GCACGCTGCT CGGAATGCTG
	GTGTCGGTAT
551	TGTTGCTGCT TTTGGTGCGG CAATATACGT TCAACTGGGA
	AAGCACGCTG
601	TTGGGCGATT CGTCTTCGGT ACGGCTGGTG GAAATGTTGG
	CATGGCTGCC
651	TGCGAAACTG GGTTTTCCCG TGCCTGATGC GCGGGCGGTC
	ATCGAAGGTC
701	GTCTGAACGG CAATATTGCC GATGCGCGGG CTTGGTCGGG
	GCTGCTGGTC
751	GGCAGTATCG CCTGCTACGG CATCCTGCCG CGCCTCTTGG
	CTTGGGCGGT
801	ATGCAAAATC CTTNTGNAAA CAAGCGAAAA CGGCTTGGAT
	TTGGAAAAGC
851	NCNNNNNTCN NNCGNTCATC CGCCGCTGGC AGAACAAAAT
	CACCGATGCG
901	GATACGCGTC GGGAAACCGT GTCCGCCGTT TCGCCGAAAA
	TCGTCTTGAA
951	CGATGCGCCG AAATGGGCGG TCATGCTGGA GACCGAATGG
	CAGGACGGCG
1001	AATGGTTCGA GGGCAGGCTG GCGCAGGAAT GGCTGGATAA
	GGGCGTTGCC
1051	GCCAATCGGG AACAGGTTGC CGCGCTGGAG ACAGAGCTGA
	AGCAGAAACC
1101	GGCGCAACTG CTTATCGGCG TGCGCGCCCA AACTGTGCCC
	GACCGCGGCG
1151	TGTTGCGGCA GATCGTCCGA CTTTCGGAAG CGGCGCAGGG
	CGGCGCGGTG
1201	GTGCANCTTT TGGCGGAACA GGGGCTTTCA GACGACCTTT
	CGGAAAAGCT
1251	GGAACATTGG CGTAACGCGC TGACCGAATG CGGCGCGGCG
	TGGCTGGAAC
1301	CCGACAGAGC GGCGCAGGAA GGCCGTCTGA AAACCAACGA
	CCGCACTTGA

This encodes a protein having amino acid sequence <SEQ ID 202>:

1	MLNPSRKLVE LVRILEEGGF IFSGDPVQAT EALRRVDGST
	EEKIIRRAKM
51	IDRNRMLRET LERVRAGSFW LWVAAATFAF XTXFSVTYLL
	MDNQGLNFFL
101	VLAGVXGMNT LMLAVWLAML FLRVKVGRFF SSPATWFRGK
	DPVNQAVLRL
151	YADEWRXPSV RWKIGATSHS LWLCTLLGML VSVLLLLLVR
	QYTFNWESTL
201	LGDSSSVRLV EMLAWLPAKL GFPVPDARAV IEGRLNGNIA
	DARAWSGLLV
251	GSIACYGILP RLLAWAVCKI LXXTSENGLD LEKXXXXXXI
	RRWQNKITDA
301	DTRRETVSAV SPKIVLNDAP KWAVMLETEW QDGEWFEGRL
	AQEWLDKGVA
351	ANREQVAALE TELKQKPAQL LIGVRAQTVP DRGVLRQIVR
	LSEAAQGGAV
401	VXLLAEQGLS DDLSEKLEHW RNALTECGAA WLEPDRAAQE
	GRLKTNDRT*

ORF33a and ORF33-1 show 94.1% identity in 444 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF33 shows 91.6% identity over a 143aa overlap with a predicted ORF (ORF33.ng) from N. gonorrhoeae:

An ORF33ng nucleotide sequence <SEQ ID 203> was predicted to encode a protein having amino acid sequence <SEQ ID 204>:

1	MIDRDRMLRD TLERVRAGSF WLWVVVASMM FTAGFSGTYL
	LMDNQGLNFF
51	LVLAGVLGMN TLMLAVWLAT LFLRVKVGRF FSSPATWFRG
	KGPVNQAVLR
101	LYADQWRQPS VRWKIGATAH SLWLCTLLGM LVSVLLLLLV
	RQYTFNWEST
151	LLSNAASVRA VEMLAWLPSK LGFPVPDARA VIEGRLNGNI
	ADARAWSGLL
201	VGSIVCYGIL PRLLAWVVCK ILLKTSENGL DLEKTYYQAV
	IRRWQNKITD
251	ADTRRETVSA VSPKIVLNDA PKWALMLETE WQDGQWFEGR
	LAQEWLDKGV
301	AANREQVAAL ETELKQKPAQ LLIGVRAQTV PDRGVLRQIV
	RLSEAAQGGA
351	VVQLLAEQGL SDDLSEKLEH WRNALTECGA AWLEPDRVAQ
	EGRLKDQ*

Further sequence analysis revealed the following DNA sequence <SEQ ID 205>:

1	ATGTTGaatC CATCCCgaAA ACTGgttgag ctGgTCCgtA
	Ttttgaataa
51	agggggtTTT attttcagcg gcgatcctgt gcaggcgacg
	gaggctttgc
101	gccgcgtgga cggcAGTACG GAggAaaaaa tcttccgtcg
	GGCGGAGAtg
151	atcgACAGGg accgtatgtt gcgggACaCg TtggaacGTG
	TGCGTGCggg
201	gtcgtTctgG TTATGGGTGG TggtggCAtC gATGATGTtt
	aCCGCCGGAT
251	TTTCAGgcac ttatCttCTG ATGGACaatC AGGGGCtGAA
	TtTCTTTTTA
301	GTTTTggcgG GAGTGTtggG CATGaatacG ctgATGCTGG
	CAGTATGGtt
351	gGCAACGTTG TTCCTGCGCG TGAAAGTGGG ACGGTTTTTC
	AGCAGTCCGG
401	CGACGTGGTT TCGGGGCAAA GGCCCTGTAA ATCAGGCGGT
	GTTGCGGCTG
451	TATGCGGACC AGTGGCGGCA ACCTTCGGTA CGATGGAAAA
	TAGGCGCAAC
501	GGCGCACAGC TTGTGGCTCT GCACGCTGCT CGGAATGCTG
	GTGTCGGTAT
551	TGCTGCTGCT TTTGGTGCGG CAATATACGT TCAACTGGGA
	AAGCACGCTG
601	TTGAGCAATG CCGCTTCGGT ACGCGCGGTG GAAATGTTGG
	CATGGCTGCC
651	GTCGAAACTC GGTTTCCCTG TCCCCGATGC GCGGGCGGTC
	ATCGAAGGTC
701	GTCTGAACGG CAATATTGCC GATGCGCGGG CTTGGTCGGG
	GCTGCTGGTC
751	GGCAGTATCG TCTGCTACGG CATCCTGCCG CGCCTCTTGG
	CTTGGGTAGT
801	GTGTAAAATC CTTTTGAAAA CAAGCGAAAA CGGattgGAT
	TTGGAAAAAA
851	CCTATTATCA GGCGGTCATC CGCCGCTGGC AGAACAAAAT
	CACCGATGCG
901	GATACGCGTC GGGAAACCGT GTCCGCCGTT TCGCcgaAAA
	TCGTCTTGAA
951	CGATGCGCCG AAATGGGCGC TCATGCTGGA GACCGAGTGG
	CAGGACGGCC
1001	AATGGTTCGA GGGCAGGCTG GCGCAGGAAT GGCTGGATAA
	GGGCGTTGCC
1051	GCCAATCGGG AACAGGTTGC CGCGCTGGAG ACAGAGCTGA
	AGCAGAAACC
1101	GGCGCAACTG CTTATCGGCG TACGCGCCCA AACTGTGCCG
	GACCGGGGCG
1151	TGCTGCGGCA GATTGTGCGG CTTTCGGAAG CGGCGCAGGG
	CGGCGCGGTG
1201	GTGCAGCTTT TGGCGGAACA GGGGCTTTCA GACGACCTTT
	CGGAAAAGCT
1251	GGAACATTGG CGTAACGCGC TGACCGAATG CGGCGCGGCG
	TGGCTTGAGC
1301	CTGACAGGGT GGCGCAGGAA GGCCGTTTGA AAGACCAATA
	A

This encodes a protein having amino acid sequence <SEQ ID 206; ORF33ng-1>:

1	MLNPSRKLVE LVRILNKGGF IFSGDPVQAT EALRRVDGST
	EEKIFRRAEM
51	IDRDRMLRDT LERVRAGSFW LWVVVASMMF TAGFSGTYLL
	MDNQGLNFFL
101	VLAGVLGMNT LMLAVWLATL FLRVKVGRFF SSPATWFRGK
	GPVNQAVLRL
151	YADQWRQPSV RWKIGATAHS LWLCTLLGML VSVLLLLLVR
	QYTFNWESTL
201	LSNAASVRAV EMLAWLPSKL GFPVPDARAV IEGRLNGNIA
	DARAWSGLLV
251	GSIVCYGILP RLLAWVVCKI LLKTSENGLD LEKTYYQAVI
	RRWQNKITDA
301	DTRRETVSAV SPKIVLNDAP KWALMLETEW QDGQWFEGRL
	AQEWLDKGVA
351	ANREQVAALE TELKQKPAQL LIGVRAQTVP DRGVLRQIVR
	LSEAAQGGAV
401	VQLLAEQGLS DDLSEKLEHW RNALTECGAA WLEPDRVAQE
	GRLKDQ*

ORF33ng-1 and ORF33-1 show 94.6% identity in 446 aa overlap:

Based on the presence of several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 25

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 207>:

1	..CAGAAGAGTT TGTCGAGAAT TTCTTTATGG GGTTTGGGCG
	GCGTGTTTTT
51	CGGGGTGTCC GGTCTGGTAT GGTTTTCTTT GGGCGTTTCT
	TT.GAGTGCG
101	CCTGTTTTTC GGGTGTTTCT TTTCGGGGTT CGGGACGGGG
	GACGTTTGTG
151	GGCAGTACGG GGGTTTCTTT GAGTGTGTTT TCAGCTTGTG
	TTCC.GGCGT
201	CGTCCGGCTG CCTGTCGGTT TGAGCTGTGT CGGCAGGTTG
	CG..GTTTGA
251	CCCGGTTTTT CTTGGGTGCG GCAGGGGACG TCATTCTCCT
	GCCGCTTTCG
301	TCTGTGCCGT CCGGCTGTGC GGGTTCGGAT GAGGCGGCGT
	GGTGGTGTTC
351	GGGTTGGGCG GCATCTTGTT CCGACTACGC CGTTTGGCAG
	CCAGAATTCG
401	GTTTCGCGGG GGCTGTCGGT GTGTTGCGGT TCGGCTTGAA
	GGGTTTTGTC
451	GTCC..

This corresponds to the amino acid sequence <SEQ ID 208; ORF34>:

1	..QKSLSRISLW GLGGVFFGVS GLVWFSLGVS XECACFSGVS
	FRGSGRGTFV
51	GSTGVSLSVF SACVXGVVRL PVGLSCVGRL XXLTRFFLGA
	AGDVILLPLS
101	SVPSGCAGSD EAAWWCSGWA ASCPTTPFGS QNSVSRGLSV
	CCGSA*RVLS
151	S..

Further work revealed the complete nucleotide sequence <SEQ ID 209>:

1	ATGATGATGC CGTTCATAAT GCTTCCTTGG ATTGCkGGTG
	TGCCTGCCGT
51	GCCGGGTCAG AATAGGTTGT CCAGAATTTC TTTATGGGGT
	TTGGGCGGCG
101	TGTTTTTCGG GGTGTCCGGT TTGGTATGGT TTTCTTTGGG
	CGTTTCTTTG
151	GGCTGCGCCT GTTTTTCGGG TGTTTCTTTT CGGGGTTCGG
	GACGGGGGAC
201	GTTTGTGGGC AGTACGGGGG TTTCTTTGAG TGTGTTTTCA
	GCTTGTGTTC
251	CGGCGTCGTC CGGCTGCCTG TCGGTTTGAG CTGTGTCGGC
	AGGTTGCGGT
301	TTGACCCGGT TTTTCTTGGG TGCGGCAGGG GACGGCAGTC
	CGCTGCCGCT
351	TTCGTCTGTG CCGTCCGGCT GTGCGGGTTC GGATGAGGCG
	GCGTGGTGGT
401	GTTCGGGTTG GGCGGCATCT TGTCCGACTA CGCCGTTTGG
	CAGCCAGAAT
451	TCGGTTTCGC GGGGGCTGTC GGTGTGTTGC GGTTCGGCTT
	GAAGGGTTTT
501	GTCGCCGTTC GGGTTGAATG TGCTGACGAT GCCTATTGCC
	AATGCGCCGA
551	TGGCGGCGAT ACAGATGAGC AATACGGCGC GTATCAGGAG
	TTTGGGGGTC
601	AGCCTGAAGG GTTTGTTCGG TTTTTTTGCC ATTTTGATTG
	TGCTTTTGGG
651	GTGTCGGGCA ATGCCGTCTG AAGGCGGTTC AGACGGCATT
	GCCGAGTCAG
701	CGTTGGACGT AGTTTTGGTA GAGGGTGATG ACTTTTTGTA
	CGCCGACGGT
751	GGTGCTGACT TTTTGGGTAA TCTGCGCCTG TTCTTCGGGG
	GTGAGGATGC
801	CCATAACGTA GGTTACGTTG CCGTAGGTAA CGATTTTGAC
	GCGCGCCTGT
851	GTGGCGGGGC TGATGCCCAA CAGCGTGGCG CGGACTTTGG
	ATGTGTTCCA
901	AGTGTCGCCG GCGATGTCGC CGGCAGTGCG CGGCAGGGAG
	GCGACGGTAA
951	TATAGTTGTA CACGCCTTCG GCGGCCTGTT CGGAACGTGC
	AATCTGACCG
1001	ACGAACTGTT TTTCGCCTTC GGTGGCGACT TGTCCGAGCA
	GCAGCAGGTG
1051	GCGGTTGTAG CCGACGACGG AGATTTGGGG CGTGTAGCCT
	TTGGTTTGGT
1101	TGTTTTGGCG CAGATAGGAA CGGGCGGTGG TTTCGATACG
	CAACGCCATA
1151	ACGTTGTCGT CGGTTTGCGC GCCGGTGGTT CGGCGGTCGA
	CGGCGGATTT
1201	CGCGCCGACG GCGGCGCTTC CGATTACTGC GCTGACGCAG
	CCGCTAAGGG
1251	CAAGGCTGAA AATGGCGGCA ATCAGGGTGC GGACGGTGTG
	CGGTTTGGGT
1301	TTCATCGGGT GCTTCCTTTC TTGGGCGTTT CAGACGGCAT
	TGCTTTGCGC
1351	CATGCCGTCT GA

This corresponds to the amino acid sequence <SEQ ID 210; ORF34-1>:

1	MMMPFIMLPW IAGVPAVPGQ NRLSRISLWG LGGVFFGVSG
	LVWFSLGVSL
51	GCACFSGVSF RGSGRGTFVG STGVSLSVFS ACVPASSGCL
	SV*AVSAGCG
101	LTRFFLGAAG DGSPLPLSSV PSGCAGSDEA AWWCSGWAAS
	CPTTPFGSQN
151	SVSRGLSVCC GSA*RVLSPF GLNVLTMPIA NAPMAAIQMS
	NTARIRSLGV
201	SLKGLFGFFA ILIVLLGCRA MPSEGGSDGI AESALDVVLV
	EGDDFLYADG
251	GADFLGNLRL FFGGEDAHNV GYVAVGNDFD ARLCGGADAQ
	QRGADFGCVP
301	SVAGDVAGSA RQGGDGNIVV HAFGGLFGTC NLTDELFFAF
	GGDLSEQQQV
351	AVVADDGDLG RVAFGLVVLA QIGTGGGFDT QRHNVVVGLR
	AGGSAVDGGF
401	RADGGASDYC ADAAAKGKAE NGGNQGADGV RFGFHRVLPF
	LGVSDGIALR
451	HAV*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF34 shows 73.3% identity over a 161aa overlap with an ORF (ORF34a) from strain A of N. meningitidis:

The complete length ORF34a nucleotide sequence <SEQ ID 211> is:

1	ATGATGATNC CGTTNATAAT GCTTCCTTGG ATTGCGGGTG
	TGCCTGCCGT
51	GCCGGGTCAG AAGAGGTTGT CGAGAANTTC TTTATGGGGT
	TTAGGCGGCN
101	TGTTTTTCGG GGTGTCCGGT TTGGTATGGT TTTCTTTGGG
	CGTTTCTNTT
151	TCTTTGGGTG TTTCTNTGGG CTGTGCCTGT TTTTCGGGTG
	TTTCTTTTCG
201	GGGTTCGGGA CGGGGGACGT TTGTGGGCAG TACNGGGGTT
	TCTTTGAGTG
251	TGTTTTCAGC TTGTGCTCCG GCGTCGTCCG GCTGCCTGTC
	GGTTTNAGCT
301	GTGTCGGCAG GTTGCGGTTT GACCCGGNTT TTCTTNGGTG
	CGGCAGGGGA
351	CGGCAGTCCG CTGCCGCTTT CGTCTGTGCC GTCCGGCTGT
	GCGGGTGCGG
401	ATGAGGAGGC GTNGTNGTGT TCGGGTTGGG CGGCATCTTG
	TCCGACTACG
451	CCGTTTGGCA GCCAGAATTC GGTTTCGCGG GGGCTGTCGG
	TGTGTTGCGG
501	TTCGGTNTGG AGGGTTTTGT CNCCGTTCGG GTNGAATGTG
	CTGACGATGC
551	CTATTGCCAA TGCGCCGATG GCGGTGATAC AGATGAGCAA
	TACGGCGCGT
601	ATCAGGAGTT TGGGGGTCAG CCTGAAGGGT TTGTTCNGTT
	TTTTTGCCAT
651	TTTGATTGTG CTTTTGGGGT GTCGGGCAAT GCCGTCTGAA
	GGCGGTTCAG
701	ACGGCATTGC CGAGTCAGCG TTGGACGTAG TTTNGGTAGA
	GGGTGATGAC
751	TTTTTGTACG CCGACGGTGG TGCTGACTTT TTGGGTAATC
	TGCGCCTGTT
801	CTTCGGGGGT GAGGATGCCC ATAACGTAGG TTACGTTGCC
	GTAGGTAACG
851	ATTTTGACGC GCGCCTGTGT GGCGGGGCTG ATGCCCAACA
	GCGTGGCGCG
901	GACTTTGGAT GTGTTCCAAG TGTCGCCGGC GATGTCGCCG
	GCAGTGCGCG
951	GCAGGGAGGC GACGGTAATG TANTTGTACA CGCCTTCGGC
	GGCCTGTTCG
1001	GAACGTGCAA TCTGACCGAC GAACTGTTTC TCGCCTTCGG
	TGGCGACTTG
1051	TCCGAGCAGC AGCAGGTGGC GGTTGTAGCC GACAACGGAG
	ATTTGGGGCG
1101	TGTANCCTTT GGTTTGGTTG TTTTGGCGCA GATAGGAGCG
	GGCGGTGGTT
1151	TCGATACGCA GCGCCATTAC GTTGTCGTCG GTTNGCGCGC
	CGGTGGTTCG
1201	GCGGTCGACG GCGGATTTCG CGCCGACCGC CGCGCCGCCG
	ACGACTGCGC
1251	TGACGCAGCC GCCGAGGGCA AGGCTGAGGA CGGCGGCAGT
	CAGGGTGCGG
1301	ACGGTGTGCG GTTTGGGTTT CATCGGGTGC TTCCTTTCTT
	GGGCGTTTCA
1351	GACGGCATTG CTTTGCGCCA TGCCGTCTGA

This encodes a protein having amino acid sequence <SEQ ID 212>:

1	MMXPXIMLPW IAGVPAVPGQ KRLSRXSLWG LGGXFFGVSG
	LVWFSLGVSX
51	SLGVSXGCAC FSGVSFRGSG RGTFVGSTGV SLSVFSACAP
	ASSGCLSVXA
101	VSAGCGLTRX FXGAAGDGSP LPLSSVPSGC AGADEEAXXC
	SGWAASCPTT
151	PFGSQNSVSR GLSVCCGSVW RVLSPFGXNV LTMPIANAPM
	AVIQMSNTAR
201	IRSLGVSLKG LFXFFAILIV LLGCRAMPSE GGSDGIAESA
	LDVVXVEGDD
251	FLYADGGADF LGNLRLFFGG EDAHNVGYVA VGNDFDARLC
	GGADAQQRGA
301	DFGCVPSVAG DVAGSARQGG DGNVXVHAFG GLFGTCNLTD
	ELFLAFGGDL
351	SEQQQVAVVA DNGDLGRVXF GLVVLAQIGA GGGFDTQRHY
	VVVGXRAGGS
401	AVDGGFRADR RAADDCADAA AEGKAEDGGS QGADGVRFGF
	HRVLPFLGVS
451	DGIALRHAV*

ORF34a and ORF34-1 show 91.3% identity in 459 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF34 shows 77.6% identity over a 161 as overlap with a predicted ORF (ORF34.ng) from N. gonorrhoeae:

The complete length ORF34ng nucleotide sequence <SEQ ID 213> is:

1	ATGATGATGC CGTTCATAAT GCTTCCTTGG ATTGCGGGTG
	TGCCTGCCGT
51	GCCGGGTCAA AAGAGGTTGT CGAGAATCTC TTTATGGGGT
	TTGGCCGGCG
101	TGTTTTTCGG GGTGTCCGGT TTGGTATGGT TTTCTTTGGG
	CGTTTCTTTT
151	TCTTTGGGTG TTTCTTTGGG CTGCGCCTGT TTTTCGGGTG
	TTTCTTTTCG
201	GGGTTCGGGA TGGGGGGCGT TTGTGGGCAG TACGGGGGTT
	TCTTTGAGTG
251	TGTTTTCAGC TTGTGTTCCG GTGCCGGTTA ACGAATCGGC
	TGCCCGGGCC
301	GCATCCGAAG GGCGCGGTTT gACCCGGTTT TTCTTGGGTG
	CGGCAGGGGA
351	CGGCAGTCCG CTGCCGCTTT CTTCTGTGCC GTCCGGCTGT
	GCGGGTTCGG
401	ATGAGGCGGC GTGGTGGTGT TCGGGTTGGG CGGCATCTTG
	TCCGACGGCG
451	CCGTTTGGCA GCCAGAATTC GGTTTCGCGG GGGCTGTCGG
	TGTGTTGCGG
501	TTCGGTTTGG AGGGTTTTGT CGCCGTTCGG GTTGAATGTG
	CTGACGATGC
551	CTACTGCCAA TGCGCCGATG GCGGTGATAC AGATGAGCAA
	TACGGCGCGT
601	ATCAGGAGTT TGGGGGTCAG CCTGAAGGGT TTGTTCGGTT
	TTTTTGCCAT
651	TTTGATTGTG CTTTTGGGGT GTCGGGCAAT GCCGTCTGAA
	GGCGGTTCAG
701	ACGGCATTGC CGAGTCAGCG TTGGACGTAG TTTTGGTAGA
	GGGTAATGAC
751	TTTTTGTACG CCGAcggTGG TGCTGACTTT TTGGGTAATC
	TGCGCCTGTT
801	CTTCGGGGGT GAGGATGCCC ATAACGTAGG TTACATTGCC
	GTAGGTAATG
851	ATTTTGACGC GCGCCTGTGT AGCGGGGCTG ATGCCCAGCA
	GcgtgGCGCG
901	GACTTTGGAC GTGTTCCAAG TGTCGCCGGC GATGTCGCCC
	GCAGTGCGCG
951	GCAGGGAGGC GACGGTAATG TAGTTGTATA CGCCTTCGGC
	GGCCTGTTCG
1001	GAACGTGCAA TCTGACCGAC GAACTGTTTT TCGCCTTCGG
	TGGCGACTTG
1051	TCCGAGCAGC AGCAGGTGGC GGTTGTAGCC GACGACGGAG
	ATTTGGGGCG
1101	TGTAGCCTTT GGTTTGGTTG TTTTGGCGCA GGTAGGAACG
	GGCGGTGGTT
1151	TCGATACGCA ACGCCATAAC GTtgtCATCG GTTtgcgcgc
	CGGTGGTTcg
1201	gCGGTCGATG ACGGATTTTG CGCCGACGGC GGCCCCGCCG
	ACGACTGCGC
1251	TGAAGCAGCC GCCGAGGGCA AGGCTGAGGA CGGCGGCAAT
	CAGGGTGCGG
1301	ACGGTGTGTG GTTTGGGTTT CATCGGGGAC TTCCTTTCTT
	GGGCGTTTCA
1351	GACGGCATTG CTTTGCGCCA TGCCGTCTGA

This encodes a protein having amino acid sequence <SEQ ID 214>:

1	MMMPFIMLPW IAGVPAVPGQ KRLSRISLWG LAGVFFGVSG
	LVWFSLGVSF
51	SLGVSLGCAC FSGVSFRGSG WGAFVGSTGV SLSVFSACVP
	VPVNESAARA
101	ASEGRGLTRF FLGAAGDGSP LPLSSVPSGC AGSDEAAWWC
	SGWAASCPTA
151	PFGSQNSVSR GLSVCCGSVW RVLSPFGLNV LTMPTANAPM
	AVIQMSNTAR
201	IRSLGVSLKG LFGFFAILIV LLGCRAMPSE GGSDGIAESA
	LDVVLVEGND
251	FLYADGGADF LGNLRLFFGG EDAHNVGYIA VGNDFDARLC
	SGADAQQRGA
301	DFGRVPSVAG DVARSARQGG DGNVVVYAFG GLFGTCNLTD
	ELFFAFGGDL
351	SEQQQVAVVA DDGDLGRVAF GLVVLAQVGT GGGFDTQRHN
	VVIGLRAGGS
401	AVDDGFCADG GPADDCAEAA AEGKAEDGGN QGADGVWFGF
	HRGLPFLGVS
451	DGIALRHAV*

ORF34ng and ORF34-1 show 90.0% identity in 459 aa overlap:

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 26

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 215>:

1	ATGAAAACCT TCTTCAAAAC CCTTTCCGCC GCCGCACTCG
	CGCTCATCCT
51	CGCCGCCTGC GGATT.CAAA AAGACAGCGC GCCCGCCGCA
	TCCGCTTCTG
101	CCGCCGCCGA CAACGGCGCG GCGTAAAAAA GAAATCGTCT
	TCGGCACGAC
151	CGTCGGCGAC TTCGGCGATA TGGTCAAAGA ACAAATCCAA
	GCCGAGCTGG
201	AGAAAAAAGG CTACACCGTC AAACTGGTCG AGTTTACCGA
	CTATGTACGC
251	CCGAATCTGG CATTGGCTGA GGGCGAGTTG

This corresponds to the amino acid sequence <SEQ ID 216; ORF4>:

1	MKTFFKTLSA AALALILAAC G.QKDSAPAA SASAAADNGA
	AKKEIVFGTT
51	VGDFGDMVKE QIQAELEKKG YTVKLVEFTD YVRPNLALAE
	GEL

Further sequence analysis revealed the complete nucleotide sequence <SEQ ID 217>:

1	ATGAAAACCT TCTTCAAAAC CCTTTCCGCC GCCGCACTCG
	CGCTCATCCT
51	CGCCGCCTGC GGCGGTCAAA AAGACAGCGC GCCCGCCGCA
	TCCGCTTCTG
101	CCGCCGCCGA CAACGGCGCG GCGAAAAAAG AAATCGTCTT
	CGGCACGACC
151	GTCGGCGACT TCGGCGATAT GGTCAAAGAA CAAATCCAAG
	CCGAGCTGGA
201	GAAAAAAGGC TACACCGTCA AACTGGTCGA GTTTACCGAC
	TATGTACGCC
251	CGAATCTGGC ATTGGCTGAG GGCGAGTTGG ACATCAACGT
	CTTCCAACAC
301	AAACCCTATC TTGACGACTT CAAAAAAGAA CACAATCTGG
	ACATCACCGA
351	AGTCTTCCAA GTGCCGACCG CGCCTTTGGG ACTGTACCCG
	GGCAAGCTGA
401	AATCGCTGGA AGAAGTCAAA GACGGCAGCA CCGTATCCGC
	GCCCAACGAC
451	CCGTCCAACT TCGCCCGCGT CTTGGTGATG CTCGACGAAC
	TGGGTTGGAT
501	CAAACTCAAA GACGGCATCA ATCCGTTGAC CGCATCCAAA
	GCGGACATCG
551	CCGAGAACCT GAAAAACATC AAAATCGTCG AGCTTGAAGC
	CGCGCAACTG
601	CCGCGTAGCC GCGCCGACGT GGATTTTGCC GTCGTCAACG
	GCAACTACGC
651	CATAAGCAGC GGCATGAAGC TGACCGAAGC CCTGTTCCAA
	GAACCGAGCT
701	TTGCCTATGT CAACTGGTCT GCCGTCAAAA CCGCCGACAA
	AGACAGCCAA
751	TGGCTTAAAG ACGTAACCGA GGCCTATAAC TCCGACGCGT
	TCAAAGCCTA
801	CGCGCACAAA CGCTTCGAGG GCTACAAATC CCCTGCCGCA
	TGGAATGAAG
851	GCGCAGCCAA ATAA

This corresponds to the amino acid sequence <SEQ ID 218; ORF4-1>:

1	MKTFFKTLSA AALALILAAC GGQKDSAPAA SASAAADNGA
	AKKEIVFGTT
51	VGDFGDMVKE QIQAELEKKG YTVKLVEFTD YVRPNLALAE
	GELDINVFQH
101	KPYLDDFKKE HNLDITEVFQ VPTAPLGLYP GKLKSLEEVK
	DGSTVSAPND
151	PSNFARVLVM LDELGWIKLK DGINPLTASK ADIAENLKNI
	KIVELEAAQL
201	PRSRADVDFA VVNGNYAISS GMKLTEALFQ EPSFAYVNWS
	AVKTADKDSQ
251	WLKDVTEAYN SDAFKAYAHK RFEGYKSPAA WNEGAAK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF4 shows 93.5% identity over a 93aa overlap with an ORF (ORF4a) from strain A of N. meningitidis:

The complete length ORF4a nucleotide sequence <SEQ ID 219> is:

1	ATGAAAACCT TCTTCAAAAC CCTTTCCGCC GCCGCACTCG
	CGCTCATCCT
51	CGCCGCCTGC GGCGGTCAAA AAGATAGCGC GCCCGCCGCA
	TCCGCTTCTG
101	CCGCCGCCGA CAACGGCGCG GCGAANAAAG AAATCGTCTT
	CGGCACGACC
151	GTCGGCGACT TCGGCGATAT GGTCAAAGAA CANATCCAAC
	CCGAGCTGGA
201	GAAAAAAGGC TACACCGTCA AACTGGTCGA GTNTACCGAC
	TATGTGCGCN
251	CGAATCTGGC ATTGGCTGAG GGCGAGTTGG ACATCAACGT
	CTTNCAACAC
301	ANACNCTATC TTGACGACTN CAAAAAANAA CACAATCTGG
	ACATCACCNN
351	AGTCTTNCAA GTGCCGACCG CGCCTTTGGG ACTGTACCCG
	GGCAAGCTGA
401	AATCGCTGGA NNAAGTCAAA GANGGCAGCA CCGTATCCGC
	GCCCAACGAC
451	CCGTNNNACT TCGNCCGCGT CTTGGTGATG CTCGACGAAC
	TGGGTTNGAT
501	CAAACTCAAA GACNGCATCA NNNNGNNGNN NNNANCNANA
	NNNGANANNN
551	NNNNANNNNT NNNNNNNNNN NNNNNCNNCG NNNNNNNANN
	NNNNNNNNNN
601	NCGNNTNNNN NNGCNNNNNT NNANNNTNNN NNCNNCNNNN
	NNNNNTNNNN
651	NANNANNAGC GGCATGAAGC TGACCGAAGC CCTGTTCCAA
	GAACCGAGCT
701	TTGCCTATGT CAACTGGTCT GCCGTCAAAA CCGCCGACAA
	AGACAGCCAA
751	TGGCTTAAAG ACGTAACCGA GGCCTATAAC TCCGACGCGT
	TCAAAGCCTA
801	CGCGCACAAA CGCTTCGAGG GCTACAAATC CCCTGCCGCA
	TGGAATGAAG
851	GCGCAGCCAA ATAA

This is predicted to encode a protein having amino acid sequence <SEQ ID 220>:

1	MKTFFKTLSA AALALILAAC GGQKDSAPAA SASAAADNGA
	AXKEIVFGTT
51	VGDFGDMVKE XIQPELEKKG YTVKLVEXTD YVRXNLALAE
	GELDINVXQH
101	XXYLDDXKKX HNLDITXVXQ VPTAPLGLYP GKLKSLXXVK
	XGSTVSAPND
151	PXXFXRVLVM LDELGXIKLK DXIXXXXXXX XXXXXXXXXX
	XXXXXXXXXX
201	XXXXAXXXXX XXXXXXXXXS GMKLTEALFQ EPSFAYVNWS
	AVKTADKDSQ
251	WLKDVTEAYN SDAFKAYAHK RFEGYKSPAA WNEGAAK*

A leader peptide is underlined.

Further analysis of these strain A sequences revealed the complete DNA sequence <SEQ ID 221>:

1	ATGAAAACCT TCTTCAAAAC CCTTTCCGCC GCCGCACTCG
	CGCTCATCCT
51	CGCCGCCTGC GGCGGTCAAA AAGATAGCGC GCCCGCCGCA
	TCCGCTTCTG
101	CCGCCGCCGA CAACGGCGCG GCGAAAAAAG AAATCGTCTT
	CGGCACGACC
151	GTCGGCGACT TCGGCGATAT GGTCAAAGAA CAAATCCAAC
	CCGAGCTGGA
201	GAAAAAAGGC TACACCGTCA AACTGGTCGA GTTTACCGAC
	TATGTGCGCC
251	CGAATCTGGC ATTGGCTGAG GGCGAGTTGG ACATCAACGT
	CTTCCAACAC
301	AAACCCTATC TTGACGACTT CAAAAAAGAA CACAATCTGG
	ACATCACCGA
351	AGTCTTCCAA GTGCCGACCG CGCCTTTGGG ACTGTACCCG
	GGCAAGCTGA
401	AATCGCTGGA AGAAGTCAAA GACGGCAGCA CCGTATCCGC
	GCCCAACGAC
451	CCGTCCAACT TCGCCCGCGT CTTGGTGATG CTCGACGAAC
	TGGGTTGGAT
501	CAAACTCAAA GACGGCATCA ATCCGCTGAC CGCATCCAAA
	GCGGACATTG
551	CCGAAAACCT GAAAAACATC AAAATCGTCG AGCTTGAAGC
	CGCGCAACTG
601	CCGCGTAGCC GCGCCGACGT GGATTTTGCC GTCGTCAACG
	GCAACTACGC
651	CATAAGCAGC GGCATGAAGC TGACCGAAGC CCTGTTCCAA
	GAACCGAGCT
701	TTGCCTATGT CAACTGGTCT GCCGTCAAAA CCGCCGACAA
	AGACAGCCAA
751	TGGCTTAAAG ACGTAACCGA GGCCTATAAC TCCGACGCGT
	TCAAAGCCTA
801	CGCGCACAAA CGCTTCGAGG GCTACAAATC CCCTGCCGCA
	TGGAATGAAG
851	GCGCAGCCAA ATAA

This encodes a protein having amino acid sequence <SEQ ID 222; ORF4a-1>:

1	MKTFFKTLSA AALALILAAC GGQKDSAPAA SASAAADNGA
	AKKEIVFGTT
51	VGDFGDMVKE QIQPELEKKG YTVKLVEFTD YVRPNLALAE
	GELDINVFQH
101	KPYLDDFKKE HNLDITEVFQ VPTAPLGLYP GKLKSLEEVK
	DGSTVSAPND
151	PSNFARVLVM LDELGWIKLK DGINPLTASK ADIAENLKNI
	KIVELEAAQL
201	PRSRADVDFA VVNGNYAISS GMKLTEALFQ EPSFAYVNWS
	AVKTADKDSQ
251	WLKDVTEAYN SDAFKAYAHK RFEGYKSPAA WNEGAAK*

ORF4a-1 and ORF4-1 show 99.7% identity in 287 aa overlap:

Homology with an Outer Membrane Protein of Pasteurella haemolitica (Accession q08869).

ORF4 and this outer membrane protein show 33% aa identity in 91aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF4 shows 93.6% identity over a 94aa overlap with a predicted ORF (ORF4.ng) from N. gonorrhoeae:

The complete length ORF4ng nucleotide sequence <SEQ ID 223> was predicted to encode a protein having amino acid sequence <SEQ ID 224>:

1	MKTFFKTLST ASLALILAAC GGQKDSAPAA SAAAPSADNG
	AAKKEIVFGT
51	TVGDFGDMVK EQIQAELEKK GYTVKLVEFT DYVRPNLALA
	EGELDINVFQ
101	HKPYLDDFKK EHNLDITEAF QVPTAPLGLY PGKLKSLEEV
	KDGSTVSAPN
151	DPSNFARALV MLNELGWIKL KDGINPLTAS KADIAENLKN
	IKIVELEAAQ
201	LPRSRADVDF AVVNGNYAIS SGMKLTEALF QEPSFAYVNW
	SAVKTADKDS
251	QWLKDVTEAY NSDAFKAYAH KRFEGYKYPA AWNEGAAK*

Further analysis revealed the complete length ORF4ng DNA sequence <SEQ ID 225> to be:

1	atgAAAACCT TCTTCAAAAC cctttccgcc gccgcaCTCG
	CGCTCATCCT
51	CGCAGCCTGc ggCggtcaAA AAGACAGCGC GCCCgcagcc
	tctgcCGCCG
101	CCCCTTCTGC CGATAACGgc gCgGCGAAAA AAGAAAtcgt
	ctTCGGCACG
151	Accgtgggcg acttcggcgA TAtggTCAAA GAACAAATCC
	AagcCGAgct
201	gGAGAAAAAA GgctACACcg tcAAattggt cgaatttacc
	gactatgtGC
251	gCCCGAATCT GGCATTGGCG GAGGGCGAGT TGGACATCAA
	CGTCTTCCAA
301	CACAAACCCT ATCTTGACGA TTTCAAAAAA GAACACAACC
	TGGACATCAC
351	CGAAGCCTTC CAAGTGCCGA CCGCGCCTTT GGGACTGTAT
	CCGGGCAAAC
401	TGAAATCGCT GGAAGAAGTC AAAGACGGCA GCACCGTATC
	CGCGCCCAac
451	gACccgTCCA ACTTCGCACG CGCCTTGGTG ATGCTGAACG
	AACTGGGTTG
501	GATCAAACTC AAAGACGGCA TCAATCCGCT GACCGCATCC
	AAAGCCGACA
551	TCGCGGAAAA CCTGAAAAAC ATCAAAATCG TCGAGCTTGA
	AGCCGCACAA
601	CTGCCGCGCA GCCGCGCCGA CGTGGATTTT GCCGTCGTCA
	ACGGCAACTA
651	CGCCATAAGC AGCGGCATGA AGCTGACCGA AGCCCTGTTC
	CAAGAGCCGA
701	GCTTTGCCTA TGTCAACTGG TCTGCCgtcA AAACCGCCGA
	CAAAGACAGC
751	CAATGGCTTA AAGACGTAAC CGAGGCCTAT AACTCCGACG
	CGTTCAAAGC
801	CTACGCGCAC AAACGCTTCG AGGGCTACAA ATACCCTGCC
	GCATGGAATG
851	AAGGCGCAGC CAAATAA

This encodes a protein having amino acid sequence <SEQ ID 226; ORF4ng-1>:

1	MKTFFKTLSA AALALILAAC GGQKDSAPAA SAAAPSADNG
	AAKKEIVFGT
51	TVGDFGDMVK EQIQAELEKK GYTVKLVEFT DYVRPNLALA
	EGELDINVFQ
101	HKPYLDDFKK EHNLDITEAF QVPTAPLGLY PGKLKSLEEV
	KDGSTVSAPN
151	DPSNFARALV MLNELGWIKL KDGINPLTAS KADIAENLKN
	IKIVELEAAQ
201	LPRSRADVDF AVVNGNYAIS SGMKLTEALF QEPSFAYVNW
	SAVKTADKDS
251	QWLKDVTEAY NSDAFKAYAH KRFEGYKYPA AWNEGAAK*

This shows 97.6% identity in 288 aa overlap with ORF4-1:

In addition, ORF4ng-1 shows significant homology with an outer membrane protein from the database:

Based on this analysis, including the homology with the outer membrane protein of Pasteurella haemolitica, and on the presence of a putative prokaryotic membrane lipoprotein lipid attachment site in the gonococcal protein, it was predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF4-1 (30 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIGS. 8A and 8B show, respectively, the results of affinity purification of the His-fusion and GST-fusion proteins. Purified His-fusion protein was used to immunise mice, whose sera were used for ELISA (positive result), Western blot (FIG. 8C), FACS analysis (FIG. 8D), and a bactericidal assay (FIG. 8E). These experiments confirm that ORF4-1 is a surface-exposed protein, and that it is a useful immunogen.

FIG. 8F shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF4-1.

Example 27

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 227>:

1	CCTCGTCGTC CTCGGCATGC TCCAGTTTCA AGGGGCGATT
	TACTCCAAGG
51	CGGTGGAACG TATGCTCGGC ACGGTCATCG GGCTGGGCGC
	GGGTTTGGGC
101	GTTTTATGGC TGAACCAGCA TTATTTCCAC GGCAACCTCC
	TCTTCTACCT
151	CACCGTCGGC ACGGCAAGCG CACTGGCCGG CTGGGCGGCG
	GTCGGCAAAA
201	ACGGCTACGT CCCTmTGCTG GCAGGGCTGA CGATGTGTAT
	GCTCATCGGC
251	GACAACGGCA GCGAATGGCT CGACAGCGGA CTCATGCGCG
	CCATGAACGT
301	CCTCATCGGC GyGGCCATCG CCATCGCCGC CGCCAAACTG
	CTGCCGCTGA
351	AATCCACACT GATGTGGCGT TTCATGCTTG CCGACAACCT
	GGCCGACTGC
401	AGCAAAATGA TTGCCGAAAT CAGCAACGGC AGGCGCATGA
	CCCGCGAACG
451	CCTCGAGGAG AACATGGCGA AAATGCGCCA AATCAACGCA
	CGCATGGTCA
501	AAAGCCGCAG CCATCTCGCC GCCACATCGG GCGAAAGCTG
	CATCAGCCCC
551	GCCATGATGG AAGCCATGCA GCACGCCCAC CGTAAAATCG
	TCAACACCAC
601	CGAGCTGCTC CTGACCACCG CCGCCAAGCT GCAATCTCCC
	AAACTCAACG
651	GCAGCGAAAT CCGGCTGCTT GACCGCCACT TCACACTGCT
	CCAAAC....
701	............................. GC AGACACGCCC
	GCCGCATCCG
751	CATCGACACC GCCATCAACC CCGAACTGGA AGCCCTCGCC
	GAACACCTCC
801	ACTACCAATG GCAGGGCTTC CTCTGGCTCA GCACCGATAT
	GCGTCAGGAA
851	ATTTCCGCCC TCGTCATCCT GCTGCAACGC ACCCGCCGCA
	AATGGCTGGA
901	TGCCCACGAA CGCCAACACC TGCGCCAAAG CCTGCTTGA

This corresponds to the amino acid sequence <SEQ ID 228; ORF8>:

1	......PRRP RHAPVSRGDL LQGGGTYARH GHRAGRGFGR
	FMAEPALFPR
51	QPPLLPHRRH GKRTGRLGGG RQKRLRPXAG RADDVYAHRR
	QRQRMARQRT
101	HARHERPHRR GHRHRRRQTA AAEIHTDVAF HACRQPGRLQ
	QNDCRNQQRQ
151	AHDPRTPRGE HGENAPNQRT HGQKPQPSRR HIGRKLHQPR
	HDGSHAARPP
201	XNRQHHRAAP DHRRQAAISQ TQRQRNPAAX PPLHTAPN..
	.........Q
251	TRPPHPHRHR HQPRTGSPRR TPPLPMAGLP LAQHRYASGN
	FRPRHPAATH
301	PPQMAGCPRT PTPAPKPA*

Computer analysis of this amino acid sequence gave the following results:

Sequence Motifs

ORF8 is proline-rich and has a distribution of proline residues consistent with a surface localization. Furthermore the presence of an RGD motif may indicate a possible role in bacterial adhesion events.

Homology with a Predicted ORF from N. gonorrhoeae

ORF8 shows 86.5% identity over a 312aa overlap with a predicted ORF (ORF8.ng) from N. gonorrhoeae:

The complete length ORF8ng nucleotide sequence <SEQ ID 229> is predicted to encode a protein having amino acid sequence <SEQ ID 230>:

1	MDRDDRLRRP RHAPVPRRDL LQRGGTYARY GHRAGRGFGR
	FMAEPALFPR
51	QPPLLPDHRH GKRTGRLGGG RQKRLRPYVG GADDVHAHRR
	QRQRMARQRP
101	DARDERPHRR RHRHCRRQTA AAEIHTDVAF HACRQPGRLQ
	QNDCRNQQRQ
151	AYDARTFGAE YGQNAPNQRT HGQKPQPPRR HIGRKPHQPL
	HDGSHAARPP
201	QNRQHHRAAP DHRRQAAISQ TQRQRNPAAR PPLHTAPNRP
	ATNRRPHQRQ
251	TRPPHPHRHR HQPRTGSPRR TPPLPMAGFP LAQHQYASGN
	FRPRHPPATH
301	PPQMAGCPRT PTPAPKPA*

Based on the sequence motifs in these proteins, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 28

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 231>:

1	..GAAATCAGCC TGCGGTCCGA CNACAGGCCG GTTTCCGTGN
	CGAAGCGGCG
51	GGATTCGGAA CGTTTTCTGC TGTTGGACGG CGGCAACAGC
	CGGCTCAAGT
101	GGGCGTGGGT GGAAAACGGC ACGTTCGCAA CCGTCGGTAG
	CGCGCCGTAC
151	CGCGATTTGT CGCCTTTGGG CGCGGAGTGG GCGGAAAAGG
	CGGATGGAAA
201	TGTCCGCATC GTCGGTTGCG CTGTGTGCGG AGAATTCAAA
	AAGGCACAAG
251	TGCAGGAACA GCTCGCCCGA AAAATCGAGT GGCTGCCGTC
	TTCCGCACAG
301	GCTTT.GGCA TACGCAACCA CTACCGCCAC CCCGAAGAAC
	ACGGTTCCGA
351	CCGCTGGTTC AACGCCTTGG GCAGCCGCCG CTTCAGCCGC
	AACGCCTGCG
401	TCGTCGTCAG TTGCGGCACG GCGGTAACGG TTGACGCGCT
	CACCGATGAC
451	GGACATTATC TCGGAGA.GG AACCATCATG CCCGGTTTCC
	ACCTGATGAA
501	AGAATCGCTC GCCGTCCGAA CCGCCAACCT CAACCGGCAC
	GCCGGTAAGC
551	GTTATCCTTT CCCGACCGG..

This corresponds to the amino acid sequence <SEQ ID 232; ORF61>:

1	..EISLRSDXRP VSVXKRRDSE RFLLLDGGNS RLKWAWVENG
	TFATVGSAPY
51	RDLSPLGAEW AEKADGNVRI VGCAVCGEFK KAQVQEQLAR
	KIEWLPSSAQ
101	AXGIRNHYRH PEEHGSDRWF NALGSRRFSR NACVVVSCGT
	AVTVDALTDD
151	GHYLGXGTIM PGFHLMKESL AVRTANLNRH AGKRYPFPT..

Further work revealed the complete nucleotide sequence <SEQ ID 233>:

1	ATGACGGTTT TGAAGCTTTC GCACTGGCGG GTGTTGGCGG
	AGCTTGCCGA
51	CGGTTTGCCG CAACACGTCT CGCAACTGGC GCGTATGGCG
	GATATGAAGC
101	CGCAGCAGCT CAACGGTTTT TGGCAGCAGA TGCCGGCGCA
	CATACGCGGG
151	CTGTTGCGCC AACACGACGG CTATTGGCGG CTGGTGCGCC
	CATTGGCGGT
201	TTTCGATGCC GAAGGTTTGC GCGAGCTGGG GGAAAGGTCG
	GGTTTTCAGA
251	CGGCATTGAA GCACGAGTGC GCGTCCAGCA ACGACGAGAT
	ACTGGAATTG
301	GCGCGGATTG CGCCGGACAA GGCGCACAAA ACCATATGCG
	TGACCCACCT
351	GCAAAGTAAG GGCAGGGGGC GGCAGGGGCG GAAGTGGTCG
	CACCGTTTGG
401	GCGAGTGTCT GATGTTCAGT TTTGGCTGGG TGTTTGACCG
	GCCGCAGTAT
451	GAGTTGGGTT CGCTGTCGCC TGTTGCGGCA GTGGCGTGTC
	GGCGCGCCTT
501	GTCGCGTTTA GGTTTGGATG TGCAGATTAA GTGGCCCAAT
	GATTTGGTTG
551	TCGGACGCGA CAAATTGGGC GGCATTCTGA TTGAAACGGT
	CAGGACGGGC
601	GGCAAAACGG TTGCCGTGGT CGGTATCGGC ATCAATTTTG
	TCCTGCCCAA
651	GGAAGTAGAA AATGCCGCTT CCGTGCAATC GCTGTTTCAG
	ACGGCATCGC
701	GGCGGGGCAA TGCCGATGCC GCCGTGCTGC TGGAAACGCT
	GTTGGTGGAA
751	CTGGACGCGG TGTTGTTGCA ATATGCGCGG GACGGATTTG
	CGCCTTTTGT
801	GGCGGAATAT CAGGCTGCCA ACCGCGACCA CGGCAAGGCG
	GTATTGCTGT
851	TGCGCGACGG CGAAACCGTG TTCGAAGGCA CGGTTAAAGG
	CGTGGACGGA
901	CAAGGCGTTT TGCACTTGGA AACGGCAGAG GGCAAACAGA
	CGGTCGTCAG
951	CGGCGAAATC AGCCTGCGGT CCGACGACAG GCCGGTTTCC
	GTGCCGAAGC
1001	GGCGGGATTC GGAACGTTTT CTGCTGTTGG ACGGCGGCAA
	CAGCCGGCTC
1051	AAGTGGGCGT GGGTGGAAAA CGGCACGTTC GCAACCGTCG
	GTAGCGCGCC
1101	GTACCGCGAT TTGTCGCCTT TGGGCGCGGA GTGGGCGGAA
	AAGGCGGATG
1151	GAAATGTCCG CATCGTCGGT TGCGCTGTGT GCGGAGAATT
	CAAAAAGGCA
1201	CAAGTGCAGG AACAGCTCGC CCGAAAAATC GAGTGGCTGC
	CGTCTTCCGC
1251	ACAGGCTTTG GGCATACGCA ACCACTACCG CCACCCCGAA
	GAACACGGTT
1301	CCGACCGCTG GTTCAACGCC TTGGGCAGCC GCCGCTTCAG
	CCGCAACGCC
1351	TGCGTCGTCG TCAGTTGCGG CACGGCGGTA ACGGTTGACG
	CGCTCACCGA
1401	TGACGGACAT TATCTCGGGG GAACCATCAT GCCCGGTTTC
	CACCTGATGA
1451	AAGAATCGCT CGCCGTCCGA ACCGCCAACC TCAACCGGCA
	CGCCGGTAAG
1501	CGTTATCCTT TCCCGACCAC AACGGGCAAT GCCGTCGCCA
	GCGGCATGAT
1551	GGATGCGGTT TGCGGCTCGG TTATGATGAT GCACGGGCGT
	TTGAAAGAAA
1601	AAACCGGGGC GGGCAAGCCT GTCGATGTCA TCATTACCGG
	CGGCGGCGCG
1651	GCAAAAGTTG CCGAAGCCCT GCCGCCTGCA TTTTTGGCGG
	AAAATACCGT
1701	GCGCGTGGCG GACAACCTCG TCATTTACGG GTTGTTGAAC
	ATGATTGCCG
1751	CCGAAGGCAG GGAATATGAA CATATTTAA

This corresponds to the amino acid sequence <SEQ ID 234; ORF61-1>:

1	MTVLKLSHWR VLAELADGLP QHVSQLARMA DMKPQQLNGF
	WQQMPAHIRG
51	LLRQHDGYWR LVRPLAVFDA EGLRELGERS GFQTALKHEC
	ASSNDEILEL
101	ARIAPDKAHK TICVTHLQSK GRGRQGRKWS HRLGECLMFS
	FGWVFDRPQY
151	ELGSLSPVAA VACRRALSRL GLDVQIKWPN DLVVGRDKLG
	GILIETVRTG
201	GKTVAVVGIG INFVLPKEVE NAASVQSLFQ TASRRGNADA
	AVLLETLLVE
251	LDAVLLQYAR DGFAPFVAEY QAANRDHGKA VLLLRDGETV
	FEGTVKGVDG
301	QGVLHLETAE GKQTVVSGEI SLRSDDRPVS VPKRRDSERF
	LLLDGGNSRL
351	KWAWVENGTF ATVGSAPYRD LSPLGAEWAE KADGNVRIVG
	CAVCGEFKKA
401	QVQEQLARKI EWLPSSAQAL GIRNHYRHPE EHGSDRWFNA
	LGSRRFSRNA
451	CVVVSCGTAV TVDALTDDGH YLGGTIMPGF HLMKESLAVR
	TANLNRHAGK
501	RYPFPTTTGN AVASGMMDAV CGSVMMMHGR LKEKTGAGKP
	VDVIITGGGA
551	AKVAEALPPA FLAENTVRVA DNLVIYGLLN MIAAEGREYE
	HI*

FIG. 9 shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF61-1. Further computer analysis of this amino acid sequence gave the following results:

Homology with the Baf Protein of B. pertussis (Accession Number U12020).

ORF61 and baf protein show 33% aa identity in 166aa overlap:

orf61  23 LLLDGGNSRLKWAWVE-NGTFATVGSAPYR----DLSPLGAEWAEKADGNVRIVGCAVCG  77
+L+D GNSRLK  W + +   A    AP      DL  LG   A      R +G V   G
baf     3 ILIDSGNSRLKVGWFDPDAPQAAREPAPVAFDNLDLDALGRWLATLPRRPQRALGVNVAG  62
orf61  78 EFKKAQVQEQLAR---KIEWLPSSAQAXGIRNHYRHPEEHGSDRW---FNALGSRRFSRN 131
+   +   L      I WL +   A G+RN YR+P++ G+DRW      L  +
baf    63 LARGEAIAATLRAGGCDIRWLRAQPLAMGLRNGYRNPDQLGADRWACMVGVLARQPSVHP 122
orf61 132 ACVVVSCGTAVTVDALTDDGHYLGXGTIMPGFHLMKESLAVRTANL               177
+V S GTA T+D + D   + G G I+PG  +M+ +LA  TA+L
baf   123 PLLVASFGTATTLDTIGPDNVFPG-GLILPGPAMMRGALAYGTAHL               167

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF61 shows 97.4% identity over a 189aa overlap with an ORF (ORF61a) from strain A of N. meningitidis:

The complete length ORF61a nucleotide sequence <SEQ ID 235> is:

1	ATGACGGTTT TGAAGCCTTC GCACTGGCGG GTGTTGGCGG
	AGCTTGCCGA
51	CGGTTTGCCG CAACACGTCT CGCAACTGGC GCGTATGGCG
	GATATGAAGC
101	CGCAGCAGCT CAACGGTTTT TGGCAGCAGA TGCCGGCGCA
	CATACGCGGG
151	CTGTTGCGCC AACACGACGG CTATTGGCGG CTGGTGCGCC
	CATTGGCGGT
201	TTTCGATGCC GAAGGTTTGC GCGAGCTGGG GGAAAGGTCG
	GGTTTTCAGA
251	CGGCATTGAA GCACGAGTGC GCGTCCAGCA ACGACGAGAT
	ACTGGAATTG
301	GCGCGGATTG CGCCGGACAA GGCGCACAAA ACCATATGTG
	TGACCCACCT
351	GCAAAGTAAG GGCAGGGGGC GGCAGGGGCG GAAGTGGTCG
	CACCGTTTGG
401	GCGAGTGTCT GATGTTCAGT TTTGGCTGGG TGTTTGACCG
	GCCGCAGTAT
451	GAGTTGGGTT CGCTGTCGCC TGTTGCGGCA GTGGCGTGCC
	GGCGCGCCTT
501	GTCGCGTTTG GGTTTGAAAA CGCAAATCAA GTGGCCAAAC
	GATTTGGTCG
551	TCGGACGCGA CAAATTGGGC GGCATTCTGA TTGAAACGGT
	CAGGACGGGC
601	GGCAAAACGG TTGCCGTGGT CGGTATCGGC ATCAATTTCG
	TGCTGCCCAA
651	GGAAGTGGAA AACGCCGCTT CCGTGCAATC GCTGTTTCAG
	ACGGCATCGC
701	GGCGGGGAAA TGCCGATGCC GCCGTGTTGC TGGAAACGCT
	GTTGGCGGAA
751	CTTGATGCGG TGTTGTTGCA ATATGCGCGG GACGGATTTG
	CGCCTTTTGT
801	GGCGGAATAT CAGGCTGCCA ACCGCGACCA CGGCAAGGCG
	GTATTGCTGT
851	TGCGCGACGG CGAAACCGTG TTCGAAGGCA CGGTTAAAGG
	CGTGGACGGA
901	CAAGGCGTTC TGCACTTGGA AACGGCAGAG GGCAAACAGA
	CGGTCGTCAG
951	CGGCGAAATC AGCCTGCGGT CCGACGACAG GCCGGTTTCC
	GTGCCGAAGC
1001	GGCGGGATTC GGAACGTTTT CTGCTGTTGG ACGGCGGCAA
	CAGCCGGCTC
1051	AAGTGGGCGT GGGTGGAAAA CGGCACGTTC GCAACCGTCG
	GTAGCGCGCC
1101	GTACCGCGAT TTGTCGCCTT TGGGCGCGGA GTGGGCGGAA
	AAGGTGGATG
1151	GAAATGTCCG CATCGTCGGT TGCGCCGTGT GCGGAGAATT
	CAAAAAGGCA
1201	CAAGTGCAGG AACAGCTCGC CCGAAAAATC GAGTGGCTGC
	CGTCTTCCGC
1251	ACAGGCTTTG GGCATACGCA ACCACTACCG CCACCCCGAA
	GAACACGGTT
1301	CCGACCGCTG GTTCAACGCC TTGGGCAGCC GCCGCTTCAG
	CCGCAACGCC
1351	TGCGTCGTCG TCAGTTGCGG CACGGCGGTA ACGGTTGACG
	CGCTCACCGA
1401	TGACGGACAT TATCTCGGGG GAACCATCAT GCCCGGTTTC
	CACCTGATGA
1451	AAGAATCGCT CGCCGTCCGA ACCGCCAACC TCAACCGGCA
	CGCCGGTAAG
1501	CGTTATCCTT TCCCGACCAC AACGGGCAAT GCCGTCGCCA
	GCGGCATGAT
1551	GGATGCGGTT TGCGGCTCGG TTATGATGAT GCACGGGCGT
	TTGAAAGAAA
1601	AAACCGGGGC GGGCAAGCCT GTCGATGTCA TCATTACCGG
	CGGCGGCGCG
1651	GCAAAAGTTG CCGAAGCCCT GCCGCCTGCA TTTTTGGCGG
	AAAATACCGT
1701	GCGCGTGGCG GACAACCTCG TCATTCACGG GCTGCTGAAC
	CTGATTGCCG
1751	CCGAAGGCGG GGAATCGGAA CATACTTAA

This encodes a protein having amino acid sequence <SEQ ID 236>:

1	MTVLKPSHWR VLAELADGLP QHVSQLARMA DMKPQQLNGF
	WQQMPAHIRG
51	LLRQHDGYWR LVRPLAVFDA EGLRELGERS GFQTALKHEC
	ASSNDEILEL
101	ARIAPDKAHK TICVTHLQSK GRGRQGRKWS HRLGECLMFS
	FGWVFDRPQY
151	ELGSLSPVAA VACRRALSRL GLKTQIKWPN DLVVGRDKLG
	GILIETVRTG
201	GKTVAVVGIG INFVLPKEVE NAASVQSLFQ TASRRGNADA
	AVLLETLLAE
251	LDAVLLQYAR DGFAPFVAEY QAANRDHGKA VLLLRDGETV
	FEGTVKGVDG
301	QGVLHLETAE GKQTVVSGEI SLRSDDRPVS VPKRRDSERF
	LLLDGGNSRL
351	KWAWVENGTF ATVGSAPYRD LSPLGAEWAE KVDGNVRIVG
	CAVCGEFKKA
401	QVQEQLARKI EWLPSSAQAL GIRNHYRHPE EHGSDRWFNA
	LGSRRFSRNA
451	CVVVSCGTAV TVDALTDDGH YLGGTIMPGF HLMKESLAVR
	TANLNRHAGK
501	RYPFPTTTGN AVASGMMDAV CGSVMMMHGR LKEKTGAGKP
	VDVIITGGGA
551	AKVAEALPPA FLAENTVRVA DNLVIHGLLN LIAAEGGESE
	HT*

ORF61a and ORF61-1 show 98.5% identity in 591 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF61 shows 94.2% identity over a 189aa overlap with a predicted ORF (ORF61.ng) from N. gonorrhoeae:

An ORF61ng nucleotide sequence <SEQ ID 237> was predicted to encode a protein having amino acid sequence <SEQ ID 238>:

1	MFSFGWAFDR PQYELGSLSP VAALACRRAL GCLGLETQIK
	WPNDLVVGRD
51	KLGGILIETV RAGGKTVAVV GIGINFVLPK EVENAASVQS
	LFQTASRRGN
101	ADAAVLLETL LAELGAVLEQ YAEEGFAPFL NEYETANRDH
	GKAVLLLRDG
151	ETVCEGTVKG VDGRGVLHLE TAEGEQTVVS GEISLRPDNR
	SVSVPKRPDS
201	ERFLLLEGGN SRLKWAWVEN GTFATVGSAP YRDLSPLGAE
	WAEKADGNVR
251	IVGCAVCGES KKAQVKEQLA RKIEWLPSSA QALGIRNHYR
	HPEEHGSDRW
301	FNALGSRRFS RNACVVVSCG TAVTVDALTD DGHYLGGTIM
	PGFHLMKESL
351	AVRTANLNRP AGKRYPFPTT TGNAVASGMM DAVCGSIMMM
	HGRLKEKNGA
401	GKPVDVIITG GGAAKVAEAL PPAFLAENTV RVADNLVIHG
	LLNLIAAEGG
451	ESEHA*

Further analysis revealed the complete gonococcal DNA sequence <SEQ ID 239> to be:

1	ATGACGGTTT TGAAGCCTTC GCATTGGCGG GTGTTGGCGG
	AGCTTGCCGA
51	CGGTTTGCCG CAACACGTAT CGCAATTGGC GCGTGAGGCG
	GACATGAAGC
101	CGCAGCAGCT CAACGGTTTT TGGCAGCAGA TGCCGGCGCA
	TATACGCGGG
151	CTGTTGCGCC AACACGACGG CTATTGGCGG CTGGTGCGCC
	CCTTGGCGGT
201	TTTCGATGCC GAAGGTTTGC GCGATCTGGG GGAAAGGTCG
	GGTTTTCAGA
251	CGGCATTGAA GCACGAGTGC GCGTCCAGCA ACGACGAGAT
	ACTGGAATTG
301	GCGCGGATTG CGCCGGACAA GGCGCACAAA ACCATATGCG
	TGACCCACCT
351	GCAAAGTAAG GGCAGGGGGC GGCAGGGGCG GAAGTGGTCG
	CACCGTTTGG
401	GCGAGTGCCT GATGTTCAGT TTCGGCTGGG CGTTTGACCG
	GCCGCAGTAT
451	GAGTTGGGTT CGCTGTCGCC TGTTGCGGCA CTTGCGTGCC
	GGCGCGCTTT
501	GGGGTGTTTG GGTTTGGAAA CGCAAATCAA GTGGCCAAAC
	GATTTGGTCG
551	TCGGACGCGA CAAATTGGGC GGCATTCTGA TTGAAACAGT
	CAGGGCGGGC
601	GGTAAAACGG TTGCCGTGGT CGGTATCGGC ATCAATTTCG
	TGCTGCCCAA
651	GGAAGTGGAA AACGCCGCTT CCGTGCAGTC GCTGTTTCAG
	ACGGCATCGC
701	GGCGGGGCAA TGCCGATGCC GCCGTATTGC TGGAAACATT
	GCTTGCGGAA
751	CTGGGCGCGG TGTTGGAACA ATATGCGGAA GAAGGGTTCG
	CGCCATTTTT
801	AAATGAGTAT GAAACGGCCA ACCGCGACCA CGGCAAGGCG
	GTATTGCTGT
851	TGCGCGACGG CGAAACCGTG TGCGAAGGCA CGGTTAAAGG
	CGTGGACGGA
901	CGAGGCGTTC TGCACTTGGA AACGGCAgaa ggcgaACAGa
	cggtcgtcag
951	cggcgaaaTC AGcctGCggc ccgacaacaG GTCGGtttcc
	gtgccgaagc
1001	ggccggatTC GgaacgtTTT tTGCtgttgg aaggcgggaa
	cagccgGCTC
1051	AAGTGGGCGT GggtggAAAa cggcacgttc gcaaccgtgg
	gcagcgcgCc
1101	gtaCCGCGAT TTGTCGCCTT TGGGCGCGGA GTGGGCGGAA
	AAGGCGGATG
1151	GAAATGTCCG CATCGTCGGT TGCGCCGTGT GCGGAGAATC
	CAAAAAGGCA
1201	CAAGTGAAGG AACAGCTCGC CCGAAAAATC GAGTGGCTGC
	CGTCTTCCGC
1251	ACAGGCTTTG GGCATACGCA ACCACTACCG CCACCCCGAA
	GAACACGGTT
1301	CCGACCGTTG GTTCAACGCC TTGGGCAGCC GCCGCTTCAG
	CCGCAACGCC
1351	TGCGTCGTCG TCAGTTGCGG CACGGCGGTA ACGGTTGACG
	CGCTCACCGA
1401	TGACGGACAT TATCTCGGCG GAACCATCAT GCCCGGCTTC
	CACCTGATGA
1451	AAGAATCGCT CGCCGTCCGA ACCGCCAACC TCAACCGCCC
	CGCCGGCAAA
1501	CGTTACCCTT TCCCGACCAC AACGGGCAAC GCCGTCGCAA
	GCGGCATGAT
1551	GGACGCGGTT TGCGGCTCGA TAATGATGAT GCACGGCCGT
	TTGAAAGAAA
1601	AAAACGGCGC GGGCAAGCCT GTCGATGTCA TCATTACCGG
	CGGCGGCGCG
1651	GCGAAAGTCG CCGAAGCCCT GCCGCCTGCA TTTTTGGCGG
	AAAATACCGT
1701	GCGCGTGGCG GACAACCTCG TCATCCACGG GCTGCTGAAC
	CTGATTGCCG
1751	CCGAAGGCGG GGAATCGGAA CACGCTTAA

This corresponds to the amino acid sequence <SEQ ID 240; ORF61ng-1>:

1	MTVLKPSHWR VLAELADGLP QHVSQLAREA DMKPQQLNGF
	WQQMPAHIRG
51	LLRQHDGYWR LVRPLAVFDA EGLRDLGERS GFQTALKHEC
	ASSNDEILEL
101	ARIAPDKAHK TICVTHLQSK GRGRQGRKWS HRLGECLMFS
	FGWAFDRPQY
151	ELGSLSPVAA LACRRALGCL GLETQIKWPN DLVVGRDKLG
	GILIETVRAG
201	GKTVAVVGIG INFVLPKEVE NAASVQSLFQ TASRRGNADA
	AVLLETLLAE
251	LGAVLEQYAE EGFAPFLNEY ETANRDHGKA VLLLRDGETV
	CEGTVKGVDG
301	RGVLHLETAE GEQTVVSGEI SLRPDNRSVS VPKRPDSERF
	LLLEGGNSRL
351	KWAWVENGTF ATVGSAPYRD LSPLGAEWAE KADGNVRIVG
	CAVCGESKKA
401	QVKEQLARKI EWLPSSAQAL GIRNHYRHPE EHGSDRWFNA
	LGSRRFSRNA
451	CVVVSCGTAV TVDALTDDGH YLGGTIMPGF HLMKESLAVR
	TANLNRPAGK
501	RYPFPTTTGN AVASGMMDAV CGSIMMMHGR LKEKNGAGKP
	VDVIITGGGA
551	AKVAEALPPA FLAENTVRVA DNLVIHGLLN LIAAEGGESE
	HA*

ORF61ng-1 and ORF61-1 show 93.9% identity in 591 aa overlap:

Based on this analysis, including the homology with the baf protein of B. pertussis and the presence of a putative prokaryotic membrane lipoprotein lipid attachment site, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 29

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 241>:

1	ATGTTTTACC AAATCCTTGC CCTGATTATC TGGAGCAGCT
	CGTTTATTGC
51	CGCCAAATAT GTCTATGGCG GCATCGATCC CGCATTGATG
	GTCGGCGTGC
101	GCCTGCTAAT TGCCGCGCTG CCTGCACTGC CCGCCTGCCG
	CCGTCATGTC
151	GGCAAGATTC CGCGTGAGGA ATGGAAGCCG TTGCTGATTG
	TGTCGTTCGT
201	CAACTATGTG CTGACCCTGC TGCTTCAGTT TGTCGGGTTG
	AAATACACTT
251	CCGCCGCCAG CGCATCGGTC ATTGTCGGAC TCGAGCCGCT
	GCTGATGGTG
301	TTTGTCGGAC ACTTTTTCTT CAACGACAAA GCGCGTGCCT
	ACCACTGGAT
351	ATGCGGCGCG GCGGCATTTG CCGGTGTCGC GCTGCTGATG
	GCGGGCGGTG
401	CGGaAGAGGG CGGCGaAGTC GGCTGGTTCG GCTGCCTGCT
	GGTGTTGTTG
451	GCGGGCGCGG GCTTTTGTGC CGCTATGCGT CCGACGCAAA
	GGCTGATTGC
501	ACGCATCGGC GCACCGGCAT TCACATCTGT TTCCATTGCC
	GCCGCATCGT
551	TGATGTGCCT GCCGTTTTCG CTTGCTTTGG CGCAAAGTTA
	TACCGTGGAC
601	TGGAGCGTCG GGATGGTATT GTCGCTGCTG TATTTGGGTT
	TGGGGTGC..

This corresponds to the amino acid sequence <SEQ ID 242; ORF62>:

1	MFYQILALII WSSSFIAAKY VYGGIDPALM VGVRLLIAAL
	PALPACRRHV
51	GKIPREEWKP LLIVSFVNYV LTLLLQFVGL KYTSAASASV
	IVGLEPLLMV
101	FVGHFFFNDK ARAYHWICGA AAFAGVALLM AGGAEEGGEV
	GWFGCLLVLL
151	AGAGFCAAMR PTQRLIARIG APAFTSVSIA AASLMCLPFS
	LALAQSYTVD
201	WSVGMVLSLL YLGLGC..

Further work revealed the complete nucleotide sequence <SEQ ID 243>:

1	ATGTTTTACC AAATCCTTGC CCTGATTATC TGGAGCAGCT
	CGTTTATTGC
51	CGCCAAATAT GTCTATGGCG GCATCGATCC CGCATTGATG
	GTCGGCGTGC
101	GCCTGCTAAT TGCCGCGCTG CCTGCACTGC CCGCCTGCCG
	CCGTCATGTC
151	GGCAAGATTC CGCGTGAGGA ATGGAAGCCG TTGCTGATTG
	TGTCGTTCGT
201	CAACTATGTG CTGACCCTGC TGCTTCAGTT TGTCGGGTTG
	AAATACACTT
251	CCGCCGCCAG CGCATCGGTC ATTGTCGGAC TCGAGCCGCT
	GCTGATGGTG
301	TTTGTCGGAC ACTTTTTCTT CAACGACAAA GCGCGTGCCT
	ACCACTGGAT
351	ATGCGGCGCG GCGGCATTTG CCGGTGTCGC GCTGCTGATG
	GCGGGCGGTG
401	CGGAAGAGGG CGGCGAAGTC GGCTGGTTCG GCTGCCTGCT
	GGTGTTGTTG
451	GCGGGCGCGG GCTTTTGTGC CGCTATGCGT CCGACGCAAA
	GGCTGATTGC
501	ACGCATCGGC GCACCGGCAT TCACATCTGT TTCCATTGCC
	GCCGCATCGT
551	TGATGTGCCT GCCGTTTTCG CTTGCTTTGG CGCAAAGTTA
	TACCGTGGAC
601	TGGAGCGTCG GGATGGTATT GTCGCTGCTG TATTTGGGTT
	TGGGGTGCGG
651	CTGGTACGCC TATTGGCTGT GGAACAAGGG GATGAGCCGT
	GTTCCTGCCA
701	ATGTTTCGGG ACTGTTGATT TCGCTCGAAC CCGTCGTCGG
	CGTGCTGCTG
751	GCGGTTTTGA TTTTGGGCGA ACACCTGTCG CCCGTGTCCG
	CCTTGGGCGT
801	GTTTGTCGTC ATCGCCGCCA CCTTGGTTGC CGGCCGGCTG
	TCGCATCAAA
851	AATAA

This corresponds to the amino acid sequence <SEQ ID 244; ORF62-1>:

1	MFYQILALII WSSSFIAAKY VYGGIDPALM VGVRLLIAAL
	PALPACRRHV
51	GKIPREEWKP LLIVSFVNYV LTLLLQFVGL KYTSAASASV
	IVGLEPLLMV
101	FVGHFFFNDK ARAYHWICGA AAFAGVALLM AGGAEEGGEV
	GWFGCLLVLL
151	AGAGFCAAMR PTQRLIARIG APAFTSVSIA AASLMCLPFS
	LALAQSYTVD
201	WSVGMVLSLL YLGLGCGWYA YWLWNKGMSR VPANVSGLLI
	SLEPVVGVLL
251	AVLILGEHLS PVSALGVFVV IAATLVAGRL SHQK*

Computer analysis of this amino acid sequence gave the following results:

Homology with Hypothetical Transmembrane Protein H10976 of H. influenzae (Accession Number Q57147)

ORF62 and HI0976 show 50% aa identity in 114aa overlap:

Orf62	1	MFYQILALIIWSSSFIAAKYVYGGIDPALMVGVRXXXXXXXXXXXCRRHVGKIPREEWKP	60
		M YQILAL+IWSSS I  K  Y  +DP L+V VR             R   KI +   K
HI0976	1	MLYQILALLIWSSSLIVGKLTYSMMDPVLVVQVRLIIAMIIVMPLFLRRWKKIDKPMRKQ	60
Orf62	61	LLIVSFVNYVLTLLLQFVGLKYTSAASASVIVGLEPLLMVFVGHFFFNDKARAY	114
		L  ++F NY    LLQF+GLKYTSA+SA  ++GLEPLL+VFVGHFFF  K   +
HI0976	61	LWWLAFFNYTAVFLLQFIGLKYTSASSAVTMIGLEPLLVVFVGHFFFKTKQNGF	114

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF62 shows 99.5% identity over a 216aa overlap with an ORF (ORF62a) from strain A of N. meningitidis:

The complete length ORF62a nucleotide sequence <SEQ ID 245> is:

1	ATGTTTTACC AAATCCTTGC CCTGATTATC TGGAGCAGCT
	CGTTTATTGC
51	CGCCAAATAT GTCTATGGCG GCATCGATCC CGCATTGATG
	GTCGGCGTGC
101	GCCTGCTGAT TGCTGCGCTG CCTGCACTGC CCGCCTGCCG
	CCGTCATGTC
151	GGCAAGATTC CGCGTGAGGA ATGGAAGCCG TTGCTGATTG
	TGTCGTTCGT
201	CAACTATGTG CTGACCCTGC TACTTCAGTT TGTCGGGTTG
	AAATACACTT
251	CCGCCGCCAG CGCATCGGTC ATTGTCGGAC TCGAGCCACT
	GCTGATGGTG
301	TTTGTCGGAC ACTTTTTCTT CAACGACAAA GCGCGTGCCT
	ACCACTGGAT
351	ATGCGGCGCG GCGGCATTTG CCGGTGTCGC GCTGCTGATG
	GCGGGCGGTG
401	CGGAAGAGGG CGGCGAAGTC GGCTGGTTCG GCTGCCTGCT
	GGTGTTGTTG
451	GCGGGCGCGG GCTTTTGTGC CGCTATGCGT CCGACGCAAA
	GGCTGATTGC
501	ACGCATCGGC GCACCGGCAT TCACATCTGT TTCCATTGCC
	GCCGCATCGT
551	TGATGTGCCT GCCGTTTTCG CTTGCTTTGG CGCAAAGTTA
	TACCGTGGAC
601	TGGAGCGTCG GAATGGTATT GTCGCTGCTG TATTTGGGCG
	TGGGGTGCAG
651	CTGGTACGCC TATTGGCTGT GGAACAAGGG GATGAGCCGT
	GTTCCTGCCA
701	ACGTTTCGGG ACTGTTGATT TCGCTCGAAC CCGTCGTCGG
	CGTGCTGCTG
751	GCGGTTTTGA TTTTGGGCGA ACACCTGTCG CCCGTGTCCG
	TCTTGGGCGT
801	GTTTGTCGTC ATCGCCGCCA CCTTGGTTGC CGGCCGGCTG
	TCGCATCAAA
851	AATAA

This encodes a protein having amino acid sequence <SEQ ID 246>:

1	MFYQILALII WSSSFIAAKY VYGGIDPALM VGVRLLIAAL
	PALPACRRHV
51	GKIPREEWKP LLIVSFVNYV LTLLLQFVGL KYTSAASASV
	IVGLEPLLMV
101	FVGHFFFNDK ARAYHWICGA AAFAGVALLM AGGAEEGGEV
	GWFGCLLVLL
151	AGAGFCAAMR PTQRLIARIG APAFTSVSIA AASLMCLPFS
	LALAQSYTVD
201	WSVGMVLSLL YLGVGCSWYA YWLWNKGMSR VPANVSGLLI
	SLEPVVGVLL
251	AVLILGEHLS PVSVLGVFVV IAATLVAGRL SHQK*

ORF62a and ORF62-1 show 98.9% identity in 284 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF62 shows 99.5% identity over a 216aa overlap with a predicted ORF (ORF62.ng) from N. gonorrhoeae:

The complete length ORF62ng nucleotide sequence <SEQ ID 247> is:

1	ATGTTTTACC AAATCCTTGC CCTGATTATC TGGGGCAGCT
	CGTTTATTGC
51	CGCCAAATAT GTCTATGGCG GCATCGATCC CGCATTGATG
	GTCGGCGTGC
101	GCCTGCTGAT TGCCGCGCTG CCTGCACTGC CCGCCTGCCG
	CCGTCATGTC
151	GGCAAGATTC CGCGTGAGGA ATGGAAGCCG TTGCTGATTG
	TGTCGTTCGT
201	CAACTATGTG CTGACCCTGC TGCTTCAGTT TGTCGGGTTG
	AAATACACTT
251	CCGCCGCCAG CGCATCGGTC ATTGTCGGAC TCGAGCCGCT
	GCTGATGGTG
301	TTTGTCGGAC ACTTTTTCTT CAACGACAAA GCGCGTGCCT
	ACCACTGGAT
351	ATGCGGCGCG GCGGCATTTG CCGGTGTCGC GCTGCTGATG
	GCGGGCGGTG
401	CGGAAGAGGG CGGCGAAGTC GGCTGGTTCG GCTGCCTGCT
	GGTGTTGTTG
451	GCGGGCGCGG GCTTTTGTGC CGCTATGCGT CCGACGCAAA
	GGCTGATTGC
501	CCGCATCGGC GCACCGGCAT TCACATCTGT TTCCATTGCC
	GCCGCATCGT
551	TGATGTGCCT GCCGTTTTCG CTTGCTTTGG CGCAAAGTTA
	TACCGTGGAC
601	TGGAGCGTCG GGATGGTATT GTCGCTGTTG TATTTGGGTT
	TGGGGTGCGG
651	CTGGTACGCC TATTGGCTGT GGAACAAGGG GATGAGCCGT
	GTTCCTGCCA
701	ACGCGTCGGG ACTGTTGATT TCGCTCGAAC CCGTCGTCGG
	CGTGCTGTTG
751	GCGGTTTTGA TTTTGGGCGA ACATTTATCG CCCGTGTCCG
	CCTTGGGCGT
801	GTTTGTCGTC ATCGCCGCCA CTTTCGCCGC CGGCCGGCTG
	TCGCGCAGGG
851	ACGCGCAAAA CGGCAATGCC GTCTGA

This encodes a protein having amino acid sequence <SEQ ID 248>:

1	MFYQILALII WGSSFIAAKY VYGGIDPALM VGVRLLIAAL
	PALPACRRHV
51	GKIPREEWKP LLIVSFVNYV LTLLLQFVGL KYTSAASASV
	IVGLEPLLMV
101	FVGHFFFNDK ARAYHWICGA AAFAGVALLM AGGAEEGGEV
	GWFGCLLVLL
151	AGAGFCAAMR PTQRLIARIG APAFTSVSIA AASLMCLPFS
	LALAQSYTVD
201	WSVGMVLSLL YLGLGCGWYA YWLWNKGMSR VPANASGLLI
	SLEPVVGVLL
251	AVLILGEHLS PVSALGVFVV IAATFAAGRL SRRDAQNGNA
	V*

ORF62ng and ORF62-1 show 97.9% identity in 283 aa overlap:

Furthermore, ORF62ng shows significant homology to a hypothetical H. influenzae protein:

sp|Q57147|Y976_HAEIN HYPOTHETICAL PROTEIN HI0976 >gi|1074589|pir||B64163
hypothetical protein HI0976 - Haemophilus influenzae (strain Rd KW20)
>gi|1574004 (U32778) hypothetical [Haemophilus influenzae] Length = 128
Score = 106 bits (262), Expect = 2e−22
Identities = 56/114 (49%), Positives = 68/114 (59%)

Query:	1	MFYQILALIIWGSSFIAAKYVYGGIDPALMVGVRXXXXXXXXXXXCRRHVGKIPREEWKP	60
		M YQILAL+IW SS I  K  Y  +DP L+V VR             R   KI +   K
Sbjct:	1	MLYQILALLIWSSSLIVGKLTYSMMDPVLVVQVRLIIAMIIVMPLFLRRWKKIDKPMRKQ	60
Query:	61	LLIVSFVNYVLTLLLQFVGLKYTSAASASVIVGLEPLLMVFVGHFFFNDKARAY	114
		L  ++F NY    LLQF+GLKYTSA+SA  ++GLEPLL+VFVGHFFF  K   +
Sbjct:	61	LWWLAFFNYTAVFLLQFIGLKYTSASSAVTMIGLEPLLVVFVGHFFFKTKQNGF	114

Based on this analysis, including the homology with the transmembrane protein of H. influenzae and the putative leader sequence and several transmembrane domains in the gonococcal protein, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 30

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 249>:

1	ATGCGCCGTT TTCTACCGAT CGCAGCCATA TGCGCmGwms
	TCCTGkkGTA
51	sGGACTGACG GCGGCAACCG GCAGCACCAG TTCGCTGGCG
	GATTATTTCT
101	GGTGGATTGT TGCGTTCAGC GCAATGCTGC TGCTGGTGTT
	GTCCGCCGTT
151	TTGGCACGTT ATGTCATATT GCTGTTGAAA GACAGGCGCG
	ACGGCGTATT
201	CGGTTCGCtA srTyGCCAAA gsGCCTgkks TGGG.ATGTT
	TACGCTGGTT
251	GCCGkACTGC CCGGCGTGTT TCTGTTCGGC TTTCCCGCAC
	AGTTCATCAA
301	CGGCACGATT AATTCGTGGT TCGGCAACGA TACCCACGAG
	GCGCTTGAAC
351	GCAGCCTCAA TTTGAGCAAG TCCGCATTGA ATTTGGCGGC
	AGACAACGCC
401	CTCGGCAACG CCGTCCCCGT GCAGATAGAC CTCATCGGCG
	CGGCTTCCCT
451	GCCCGGGGAT ATGGGCAGGG TGCTGGAACA TTACGCCGGC
	AGCGGTTTTG
501	CCCAGCTTGC CCTGTACAAy ksCGCAAGCG GCAAAATCGA
	AAAAAGCATC
551	AACCCGCACA AGCTCGATCA GCCGTTTCCA GGTAAGGCGC
	GTTGGGAaAa
601	AATCCaACGG GCGGGTTCGG TCAGGGATTT GGAAAGCATA
	GGCGGCGTAT
651	TGTaCGCGCA GGGCTGGCTG TCGGCGGGTA CGCACwACGG
	GCGCGATTAC
701	GCCTTGTTTT TCCGTCAGCC GGTTCCCAAA GGCGTGGCAG
	AGGATGCCGT
751	yTTAATCGAA AAGGCAAGGG CGAAATATGC TGAGTTGAGT
	TACAGCAAAA
801	AAGGTTTGCA GACCTTTTTC CTGGCAACCC TGCTGATTGC
	CTCGCTGCTG
851	TCGATTTTTC TTGCACTGGT CATGGCACTG TATTTCGCCC
	GCCGTTTCGT
901	CGAACCCGTC CTATCGCTTG CCGAGGGGGC GAAGGCGGTG
	GCGCAAGGCG
951	ATTTCAGCCA GACGCGCCCC GTGTTGCGCA ACGACGAGTT
	CGGACGCTTG
1001	ACCArGTTGT TCAACCACAT GACCGAGCAG CTTTCCATCG
	CCAAAGATGC
1051	AGACGAGCGC AACCGCCGGC GCGAGGAAGC CGCCAGGCAT
	TATCTTGAAT
1101	GCGTGTTGGA GGGGCTGACC ACGGGCGTGG TGGTGTTTGA
	CGAACAAGGC
1151	TGTCTGAAAA CCTTCAACAA AGCGGCGGGT ACC..

This corresponds to the amino acid sequence <SEQ ID 250; ORF64>:

1	MRRFLPIAAI CAXXLXXGLT AATGSTSSLA DYFWWIVAFS
	AMLLLVLSAV
51	LARYVILLLK DRRDGVFGSX XAKXPXXXMF TLVAXLPGVF
	LFGFPAQFIN
101	GTINSWFGND THEALERSLN LSKSALNLAA DNALGNAVPV
	QIDLIGAASL
151	PGDMGRVLEH YAGSGFAQLA LYNXASGKIE KSINPHKLDQ
	PFPGKARWEK
201	IQRAGSVRDL ESIGGVLYAQ GWLSAGTHXG RDYALFFRQP
	VPKGVAEDAV
251	LIEKARAKYA ELSYSKKGLQ TFFLATLLIA SLLSIFLALV
	MALYFARRFV
301	EPVLSLAEGA KAVAQGDFSQ TRPVLRNDEF GRLTXLFNHM
	TEQLSIAKDA
351	DERNRRREEA ARHYLECVLE GLTTGVVVFD EQGCLKTFNK
	AAGT..

Further work revealed the complete nucleotide sequence <SEQ ID 251>:

1	ATGCGCCGTT TTCTACCGAT CGCAGCCATA TGCGCCGTCG
	TCCTGTTGTA
51	CGGACTGACG GCGGCAACCG GCAGCACCAG TTCGCTGGCG
	GATTATTTCT
101	GGTGGATTGT TGCGTTCAGC GCAATGCTGC TGCTGGTGTT
	GTCCGCCGTT
151	TTGGCACGTT ATGTCATATT GCTGTTGAAA GACAGGCGCG
	ACGGCGTATT
201	CGGTTCGCAG ATTGCCAAAC GCCTTTCTGG GATGTTTACG
	CTGGTTGCCG
251	TACTGCCCGG CGTGTTTCTG TTCGGCGTTT CCGCACAGTT
	CATCAACGGC
301	ACGATTAATT CGTGGTTCGG CAACGATACC CACGAGGCGC
	TTGAACGCAG
351	CCTCAATTTG AGCAAGTCCG CATTGAATTT GGCGGCAGAC
	AACGCCCTCG
401	GCAACGCCGT CCCCGTGCAG ATAGACCTCA TCGGCGCGGC
	TTCCCTGCCC
451	GGGGATATGG GCAGGGTGCT GGAACATTAC GCCGGCAGCG
	GTTTTGCCCA
501	GCTTGCCCTG TACAATGCCG CAAGCGGCAA AATCGAAAAA
	AGCATCAACC
551	CGCACAAGCT CGATCAGCCG TTTCCAGGTA AGGCGCGTTG
	GGAAAAAATC
601	CAACGGGCGG GTTCGGTCAG GGATTTGGAA AGCATAGGCG
	GCGTATTGTA
651	CGCGCAGGGC TGGCTGTCGG CGGGTACGCA CAACGGGCGC
	GATTACGCCT
701	TGTTTTTCCG TCAGCCGGTT CCCAAAGGCG TGGCAGAGGA
	TGCCGTCTTA
751	ATCGAAAAGG CAAGGGCGAA ATATGCTGAG TTGAGTTACA
	GCAAAAAAGG
801	TTTGCAGACC TTTTTCCTGG CAACCCTGCT GATTGCCTCG
	CTGCTGTCGA
851	TTTTTCTTGC ACTGGTCATG GCACTGTATT TCGCCCGCCG
	TTTCGTCGAA
901	CCCGTCCTAT CGCTTGCCGA GGGGGCGAAG GCGGTGGCGC
	AAGGCGATTT
951	CAGCCAGACG CGCCCCGTGT TGCGCAACGA CGAGTTCGGA
	CGCTTGACCA
1001	AGTTGTTCAA CCACATGACC GAGCAGCTTT CCATCGCCAA
	AGAAGCAGAC
1051	GAGCGCAACC GCCGGCGCGA GGAAGCCGCC AGGCATTATC
	TTGAATGCGT
1101	GTTGGAGGGG CTGACCACGG GCGTGGTGGT GTTTGACGAA
	CAAGGCTGTC
1151	TGAAAACCTT CAACAAAGCG GCGGAACAGA TTTTGGGGAT
	GCCGCTTACC
1201	CCCCTGTGGG GCAGCAGCCG GCACGGTTGG CACGGCGTTT
	CGGCGCAGCA
1251	GTCCCTGCTT GCCGAAGTGT TTGCCGCCAT CGGCGCGGCG
	GCAGGTACGG
1301	ACAAACCGGT CCATGTGAAA TATGCCGCGC CGGACGATGC
	CAAAATCCTG
1351	CTGGGCAAGG CAACCGTCCT GCCCGAAGAC AACGGCAACG
	GCGTGGTAAT
1401	GGTGATTGAC GACATCACCG TTTTGATACA CGCGCAAAAA
	GAAGCCGCGT
1451	GGGGCGAAGT GGCGAAGCGG CTGGCACACG AAATCCGCAA
	TCCGCTCACG
1501	CCCATCCAGC TTTCCGCCGA ACGGCTGGCG TGGAAATTGG
	GCGGGAAGCT
1551	GGATGAGCAG GATGCGCAAA TCCTGACGCG TTCGACCGAC
	ACCATCGTCA
1601	AACAGGTGGC GGCATTGAAG GAAATGGTCG AAGCATTCCG
	CAATTATGCG
1651	CGTTCCCCTT CGCTCAAATT GGAAAATCAG GATTTGAACG
	CCTTAATCGG
1701	CGATGTGTTG GCATTGTATG AAGCCGGTCC GTGCCGGTTT
	GCGGCGGAGC
1751	TTGCCGGCGA ACCGCTGACG GTGGCGGCGG ATACGACCGC
	CATGCGGCAG
1801	GTGCTGCACA ATATTTTCAA AAATGCCGCC GAAGCGGCGG
	AAGAAGCCGA
1851	TGTGCCCGAA GTCAGGGTAA AATCGGAAAC AGGGCAGGAC
	GGTCGGATTG
1901	TCCTGACGGT TTGCGACAAC GGCAAAGGGT TCGGCAGGGA
	AATGCTGCAC
1951	AACGCCTTCG AGCCGTATGT AACGGACAAA CCGGCGGGAA
	CGGGATTGGG
2001	TCTGCCTGTG GTGAAAAAAA TCATTGAAGA ACACGGCGGC
	CGCATCAGCC
2051	TGAGCAATCA GGATGCGGGT GGCGCGTGTG TCAGAATCAT
	CTTGCCAAAA
2101	ACGGTAAAAA CTTATGCGTA G

This corresponds to the amino acid sequence <SEQ ID 252; ORF64-1>:

1	MRRFLPIAAI CAVVLLYGLT AATGSTSSLA DYFWWIVAFS
	AMLLLVLSAV
51	LARYVILLLK DRRDGVFGSQ IAKRLSGMFT LVAVLPGVFL
	FGVSAQFING
101	TINSWFGNDT HEALERSLNL SKSALNLAAD NALGNAVPVQ
	IDLIGAASLP
151	GDMGRVLEHY AGSGFAQLAL YNAASGKIEK SINPHKLDQP
	FPGKARWEKI
201	QRAGSVRDLE SIGGVLYAQG WLSAGTHNGR DYALFFRQPV
	PKGVAEDAVL
251	IEKARAKYAE LSYSKKGLQT FFLATLLIAS LLSIFLALVM
	ALYFARRFVE
301	PVLSLAEGAK AVAQGDFSQT RPVLRNDEFG RLTKLFNHMT
	EQLSIAKEAD
351	ERNRRREEAA RHYLECVLEG LTTGVVVFDE QGCLKTFNKA
	AEQILGMPLT
401	PLWGSSRHGW HGVSAQQSLL AEVFAAIGAA AGTDKPVHVK
	YAAPDDAKIL
451	LGKATVLPED NGNGVVMVID DITVLIHAQK EAAWGEVAKR
	LAHEIRNPLT
501	PIQLSAERLA WKLGGKLDEQ DAQILTRSTD TIVKQVAALK
	EMVEAFRNYA
551	RSPSLKLENQ DLNALIGDVL ALYEAGPCRF AAELAGEPLT
	VAADTTAMRQ
601	VLHNIFKNAA EAAEEADVPE VRVKSETGQD GRIVLTVCDN
	GKGFGREMLH
651	NAFEPYVTDK PAGTGLGLPV VKKIIEEHGG RISLSNQDAG
	GACVRIILPK
701	TVKTYA*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF64 shows 92.6% identity over a 392aa overlap with an ORF (ORF64a) from strain A of N. meningitidis:

The complete length ORF64a nucleotide sequence <SEQ ID 253> is:

1	ATGCGCCGTT TTCTACCGAT CGCAGCCATA TGCGCCGTCG
	TCCTGTTGTA
51	CGGACTGACG GCGGCAACCG GCAGCACCAG TTCGCTGGCG
	GATTATTTCT
101	GGTGGATTGT TGCGTTCAGC GCAATGCTGC TGCTGGTGTT
	GTCCGCCGTT
151	TTGGCACGTT ATGTCATATT GCTGTTGAAA GACAGGCGCG
	ACGGCGTATT
201	CGGTTCGCAG ATTGCCAAAC GCCTTTCCGG GATGTTTACG
	CTGGTTGCCG
251	TACTGCCCGG CGTGTTTCTG TTCGGCGTTT CCGCACAGTT
	TATCAACGGC
301	ACGATTAATT CGTGGTTCGG CAACGATACC CACGAGGCGC
	TTGAACGCAG
351	CCTCAATTTG AGCAAGTCCG CATTGAATCT GGCGGCAGAC
	AACGCCCTTG
401	GCAACGCCAT CCCCGTGCAG ATAGACNTCA TCGGCGCGGC
	TTCCCTGCCC
451	NGGGATATGG GCAGGGTGCT GGAACATTAC GCCGGCAGCG
	GTTTTGCCCA
501	GCTTGCCCTG TACAATGCCG CAAGCGGCAA AATCGAAAAA
	AGCATCAACC
551	CGCACAAGCT CGATCAGCCG TTTCCAGGTA AGGCGCGTTG
	GGAAAAAATC
601	CAACAGGCGG GTTCGGTCAG GGATNNGGAA AGCATAGGCG
	GCGTATTGTA
651	CGCGCANGGC TGGCTGTCGG CAGNNACGCA CAACGGGCGC
	GATTACGCCT
701	TGTTTTTCCG TCAGCCGGTT CCCAAAGGCG TGGCAGAGGA
	TGCCGTCTTA
751	ATCGAAAAGG CAAGGGCGNA ANANNNTNAG TTGAGTTACA
	GCAAAAAAGG
801	TTTGCAGACC TTTTTCCTNG CAACCCTGCT GATTGCCTCN
	CTGCTGTCGA
851	TTTTTCTTGC ACTGGTCATG GCACTGTATT TCGCCCGCCG
	TTTCGTCGAA
901	CCCGTCCTAT CGCTTGCCGA GGGGGCGAAG GCGGTGGCGC
	AAGGCGATTT
951	CAGCCAGACG CGCCCCGTGT TGCGCAACGA CGAGTTCGGA
	CGCTTGACCA
1001	AGTTGTTCAA CCACATGACC GAGCAGCTTT CCATCGCCAA
	AGAAGCAGAC
1051	GAGCGCAACC GCCGGCGCGA GGAAGCCGCC AGACATTATC
	TCGAATGCGT
1101	GTTGGAGGGG CTGACCACGG GCGTGGTGGT GTTTGACGAA
	CAAGGCTGTC
1151	TGAAAACCTT CAACAAAGCG GCGGAACAGA TTTTGGGGAT
	GCCGCTTACC
1201	CCCCTGTGGG GCAGCAGCCG GCACGGTTGG CACGGCGTTT
	CGGCGCAGCA
1251	GTCCCTGCTT GCCGAAGTGT TTGCCGCCAT CGGCGCGGCG
	GCAGGTACGG
1301	ACAAACCGGT CCATGTGAAA TATGCCGCGC CGGACGATGC
	CAAAATCCTG
1351	CTGGGCAAGG CAACCGTCCT GCCCGAAGAC AACNGCAACG
	GCGTGGTAAT
1401	GGTGATTGAC GACATCACCG TTTTGATACA CGCGCAAAAA
	GAAGCCGCGT
1451	GGGGCGAAGT GGCAAAACGG CTGGCACACG AAATCCGCAA
	TCCGCTCACG
1501	CCCATCCAGC TTTCTGCCGA ACGGCTGGCG TGGAAATTGG
	GCGGGAAGCT
1551	GGACGAGCAN GACGCGCAAA TCCTGACACG TTCGACCGAC
	ACCATCATCA
1601	AACAAGTGGC GGCATTAAAA GAAATGGTCG AGGCATTCCG
	CAATTACNCG
1651	CGTTCCCCTT CGNCTCAATT GGAAAATCAG GATTTGAACG
	CCTTAATCGG
1701	CGATGTGTTG GCATTGTACG AAGCTGGTCC GTGCCGGTTT
	GCGGCGGAAC
1751	TTGCCGGCGA ACCGCTGATG ATGGCGGCGG ATACGACCGC
	CATGCGGCAG
1801	GTGCTGCACA ATATTTTCAA AAATGCCGCC GAAGCGGCGG
	AAGAAGCCGA
1851	TGTGCCCGAA GTCAGGGTAA AATCGGAAGC GGGGCAGGAC
	GGACGGATTG
1901	TCCTGACAGT TTGCGACAAC GGCAAGGGGT TCGGCAGGGA
	AATGCTGCAC
1951	AATGCCTTCG AGCCGTATGT AACGGACAAA CCGGCTGGAA
	CGGGATTGNG
2001	ACTGCCCGTG GTGAAAAAAA TCATTGAAGA ACACGGCGGC
	CNCATCAGCC
2051	TGAGCAATCA GGATGCGGGC GGCGCGTNTG TCAGAATCAT
	CTTGCCAAAA
2101	ACGGTAGAAA CTTATGCGTA G

This encodes a protein having amino acid sequence <SEQ ID 254>:

1	MRRFLPIAAI CAVVLLYGLT AATGSTSSLA DYFWWIVAFS
	AMLLLVLSAV
51	LARYVILLLK DRRDGVFGSQ IAKRLSGMFT LVAVLPGVFL
	FGVSAQFING
101	TINSWFGNDT HEALERSLNL SKSALNLAAD NALGNAIPVQ
	IDXIGAASLP
151	XDMGRVLEHY AGSGFAQLAL YNAASGKIEK SINPHKLDQP
	FPGKARWEKI
201	QQAGSVRDXE SIGGVLYAXG WLSAXTHNGR DYALFFRQPV
	PKGVAEDAVL
251	IEKARAXXXX LSYSKKGLQT FFLATLLIAS LLSIFLALVM
	ALYFARRFVE
301	PVLSLAEGAK AVAQGDFSQT RPVLRNDEFG RLTKLFNHMT
	EQLSIAKEAD
351	ERNRRREEAA RHYLECVLEG LTTGVVVFDE QGCLKTFNKA
	AEQILGMPLT
401	PLWGSSRHGW HGVSAQQSLL AEVFAAIGAA AGTDKPVHVK
	YAAPDDAKIL
451	LGKATVLPED NXNGVVMVID DITVLIHAQK EAAWGEVAKR
	LAHEIRNPLT
501	PIQLSAERLA WKLGGKLDEX DAQILTRSTD TIIKQVAALK
	EMVEAFRNYX
551	RSPSXQLENQ DLNALIGDVL ALYEAGPCRF AAELAGEPLM
	MAADTTAMRQ
601	VLHNIFKNAA EAAEEADVPE VRVKSEAGQD GRIVLTVCDN
	GKGFGREMLH
651	NAFEPYVTDK PAGTGLXLPV VKKIIEEHGG XISLSNQDAG
	GAXVRIILPK
701	TVETYA*

ORF64a and ORF64-1 show 96.6% identity in 706 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF64 shows 86.6% identity over a 387aa overlap with a predicted ORF (ORF64.ng) from N. gonorrhoeae:

An ORF64ng nucleotide sequence <SEQ ID 255> was predicted to encode a protein having amino acid sequence <SEQ ID 256>:

1	MRRFLPIAAI CAVVLLYGLT AATGSTSSLA DYFWWIVSFS
	AMLLLVLSAV
51	LARYVILLLK DRRNGVFGSQ IAKRLSGMFT LVAVLPGLFL
	FGISAQFING
101	TINSWFGNDT HEALERSLNL SKSALDLAAD NAVSNAVPVQ
	IDLIGTASLS
151	GNMGSVLEHY AGSGFAQLAL YNAASGKIEK SINPHQFDQP
	LPDKEHWEQI
201	QQTGSVRSLE SIGGVLYAQG WLSAGTHNGR DYALFFRQPI
	PENVAQDAVL
251	IEKARAKYAE LSYSKKGLQT FFLVTLLIAS LLSIFLALVM
	ALYFARRFVE
301	PILSLAEGAK AVAQGDFSQT RPVLRNDEFG RLTKLFNHMT
	EQLSIAKEAD
351	ERNRRREEAA RHYLECVLDG LTTGVVVSYP LSCCRTAVFS
	TCHSSPLSYF*

Further work revealed the complete gonococcal DNA sequence <SEQ ID 257>:

1	ATGCGCCGCT TCCTACCGAT CGCAGCCATA TGCGCCGTCG
	TCCTGCTGTA
51	CGGATTGACG GCGGCGACCG GCAGCACCAG TTCGCTGGCG
	GATTATTTCT
101	GGTGGATAGT CTCGTTCAGC GCAATGCTGC TGCTGGTGTT
	GTCCGCCGTT
151	TTGGCACGTT ATGTCATATT GCTGTTGAAA GACAGGCGCA
	ACGGCGTGTT
201	CGGTTCGCAG ATTGCCAAAC GCCTTTCCGG GATGTTCACG
	CTGGTCGCCG
251	TACTGCCCGG CTTGTTCCTG TTCGGCATTT CCGCGCAGTT
	TATCAACGGC
301	ACGATTAATT CGTGGTTCGG CAACGACACC CACGAAGCCC
	TCGAACGCAG
351	CCTTAATTTG AGCAAGTCCG CACTGGATTT GGCGGCAGAC
	AATGCCGTCA
401	GCAACGCCGT TCCCGTACAG ATAGACCTCA TCGGCACCGC
	CTCCCTGTCG
451	GGCAATATGG GCAGTGTGCT GGAACACTAC GCCGGCAGCG
	GTTTTGCCCA
501	GCTTGCCCTG TACAATGCCG CAAGCGGGAA AATCGAAAAA
	AGCATCAATC
551	CGCACCAATT CGACCAGCCG CTTCCCGACA AAGAACATTG
	GGAACAGATT
601	CAGCAGACCG GTTCGGTTCG GAGTTTGGAA AGCATAGGCG
	GCGTATTGTA
651	CGCGCAGGGA TGGTTGTCGG CAGGTACGCA CAACGGGCGC
	GATTACGCGC
701	TGTTCTTCCG CCAGCCGATT CCCGAAAATG TGGCACAGGA
	TGCCGTTCTG
751	ATTGAAAAGG CGCGGGCGAA ATATGCCGAA TTGAGTTACA
	GCAAAAAAGG
801	TTTGCAGACC TTTTTTCTGG TAACCCTGCT GATTGCCTCG
	CTGCTGTCGA
851	TTTTTCTTGC GCTGGTAATG GCACTGTATT TTGCCCGCCG
	TTTCGTCGAA
901	CCCATTCTGT CGCTTGCCGA GGGCGCAAAG GCGGTGGCGC
	AGGGTGATTT
951	CAGCCAGACG CGCCCCGTAT TGCGCAACGA CGAGTTCGGA
	CGTTTGACCA
1001	AGCTGTTCAA CCATATGACC GAGCAGCTTT CCATCGCCAA
	AGAAGCAGAC
1051	GAACGCAACC GCCGGCGCGA GGAAGCCGCC CGTCACTACC
	TCGAGTGCGT
1101	GTTGGATGGG TTGACTACCG GTGTGGTGGT GTTTGACGAA
	AAAGGCCGTT
1151	TGAAAACCTT CAACAAGGCG GCGGAACAGA TTTTGGGGAT
	GCCGCTCGCC
1201	CCCCTGTGGG GCAGCAGCCG GCACGGTTGG CACGGCGTTT
	CGGCGCAGCA
1251	GTCCCTGCTT GCCGAAGTGT TtgccgccAT CGGTGCGGCG
	GCAGGTACGG
1301	ACAAACCGGT CCAGGTGGAA TATGCCGCGC CGGACGATGC
	CAAAATCCTG
1351	CTGGGCAAGG CGACGGTATT GCCCGAAGAC AACGGCAACG
	GCGTGGTGAT
1401	GGTGATTGAC GACATCACCG TGCTGATACG CGCGCAAAAA
	GAAGCCGCGT
1451	GGGGTGAAGT GGCGAAGCGG CTGGCACACG AAATCCGCAA
	TCCGCTCACG
1501	CCCATCCAGC TTTCCGCCGA ACGGCTGGCG TGGAAATTGG
	GCGGGAAGCT
1551	GGACGATCAG GACGCGCAAA TCCTGACGCG TtcgACCGAC
	ACCATCATCA
1601	AACAGgtggc gGCGTTAAAA GAAATGGTCG AGGCATTCCG
	CAATTACGCG
1651	CGCGCCCCTT CGCTCAAACT GGAAAATCAG GATTTGAACG
	CCTTAATCGG
1701	CGATGTTTTG GCCCTGTACG AAGCCGGCCC GTGCCGGTTT
	GAGGCGGAAC
1751	TTGCCGGCGA ACCGCTGATG ATGGCGGCGG ATACGACCGC
	CATGCGGCAG
1801	GTGCTGCACA ATATTTTCAA AAATGCCGCC GAAGCGGCGG
	AAGAAGCCGA
1851	TATGCCCGAA GTCAGGGTAA AATCGGAAAC GGGGCAGGAC
	GGACGGATTG
1901	TCCTGACGGT TTGCGACAAC GGCAAGGGAT TCGGCAAGGA
	AATGCTGCAC
1951	AATGCTTTCG AGCCGTATGT GACGGATAAG CCGGCGGGAA
	CGGGACTGGG
2001	TCTGCCTGTA GTGAAAAAAA TCATTGGAGA ACACGGCGGC
	CGCATCAGCC
2051	TGAGCAATCA GGATGCGGGT GGGGCGTGTG TCAGAATCAT
	CTTGCCAAAA
2101	ACGGTAGAAA CTTATGCGTA G

This corresponds to the amino acid sequence <SEQ ID 258; ORF64ng-1>:

1	MRRFLPIAAI CAVVLLYGLT AATGSTSSLA DYFWWIVSFS
	AMLLLVLSAV
51	LARYVILLLK DRRNGVFGSQ IAKRLSGMFT LVAVLPGLFL
	FGISAQFING
101	TINSWFGNDT HEALERSLNL SKSALDLAAD NAVSNAVPVQ
	IDLIGTASLS
151	GNMGSVLEHY AGSGFAQLAL YNAASGKIEK SINPHQFDQP
	LPDKEHWEQI
201	QQTGSVRSLE SIGGVLYAQG WLSAGTHNGR DYALFFRQPI
	PENVAQDAVL
251	IEKARAKYAE LSYSKKGLQT FFLVTLLIAS LLSIFLALVM
	ALYFARRFVE
301	PILSLAEGAK AVAQGDFSQT RPVLRNDEFG RLTKLFNHMT
	EQLSIAKEAD
351	ERNRRREEAA RHYLECVLDG LTTGVVVFDE KGRLKTFNKA
	AEQILGMPLA
401	PLWGSSRHGW HGVSAQQSLL AEVFAAIGAA AGTDKPVQVE
	YAAPDDAKIL
451	LGKATVLPED NGNGVVMVID DITVLIRAQK EAAWGEVAKR
	LAHEIRNPLT
501	PIQLSAERLA WKLGGKLDDQ DAQILTRSTD TIIKQVAALK
	EMVEAFRNYA
551	RAPSLKLENQ DLNALIGDVL ALYEAGPCRF EAELAGEPLM
	MAADTTAMRQ
601	VLHNIFKNAA EAAEEADMPE VRVKSETGQD GRIVLTVCDN
	GKGFGKEMLH
651	NAFEPYVTDK PAGTGLGLPV VKKIIGEHGG RISLSNQDAG
	GACVRIILPK
701	TVETYA*

ORF64ng-1 and ORF64-1 show 93.8% identity in 706 aa overlap:

Furthermore, ORF64ng-1 shows significant homology to a protein from A. caulinodans:

sp|Q04850|NTRY_AZOCA NITROGEN REGULATION PROTEIN NTRY
>gi|77479|pir||S18624 ntrY protein - Azorhizobium caulinodans >gi|38737
(X63841) NtrY gene product [Azorhizobium caulinodans] Length = 771
Score = 218 bits (550), Expect = 7e−56
Identities = 195/720 (27%), Positives = 320/720 (44%), Gaps = 58/720 (8%)

Query:	7	IAAICAVVLLYGLTAATGSTSSLADYFWWIXXXXXXXXXXXXXXXXRYVILLLKDRRNGV	66
		I+A+   ++L GLT    +   +      +                R +  + K R  G
Sbjct:	35	ISALATFLILMGLTPVVPTHQVVIS----VLLVNAAAVLILSAMVGREIWRIAKARARGR	90
Query:	67	FGSQIAKRLSGMFTLVAVLPGLFLFGISAQFINGTINSWFGNDTHEALERSLNLSKSALD	126
		+++  R+ G+F +V+V+P + +  +++  ++  ++ WF   T E +  S++++++ +
Sbjct:	91	AAARLHIRIVGLFAVVSVVPAILVAVVASLTLDRGLDRWFSMRTQEIVASSVSVAQTYVR	150
Query:	127	LAADNAVSNAVPVQIDLIGTASLSGNMGSVLEHYAG--SGFAQLALYNAASGKIEKSINP	184
		A N   + + +  DL    S+          Y G  S F Q+    AA   +  ++
Sbjct:	151	EHALNIRGDILAMSADLTRLKSV----------YEGDRSRFNQILTAQAALRNLPGAMLI	200
Query:	185	HQFDQPLPDKEHWEQIQQTGSVRSLESIGGVLYAQGWLSAGTHNGRDYA-----------	233
		+ D  + ++ +   I +   V +  +IG     Q  +     N  DY
Sbjct:	201	RR-DLSVVERAN-VNIGREFIVPANLAIGDATPDQPVIYLP--NDADYVAAVVPLKDYDD	256
Query:	234	--LFFRQPIPENVAQDAVLIEKARAKYAELSYSKKGLQTFFLVTXXXXXXXXXXXXXVMA	291
		L+  + I   V       ++  A Y  L   + G+Q  F +               +
Sbjct:	257	LYLYVARLIDPRVIGYLKTTQETLADYRSLEERRFGVQVAFALMYAVITLIVLLSAVWLG	316
Query:	292	LYFARRFVEPILSLAEGAKAVAQGDFSQTRPVLRND-EFGRLTKLFNHMTEQLSIXXXXX	350
		L F++  V PI  L   A  VA+G+     P+ R + +   L + FN MT +L
Sbjct:	317	LNFSKWLVAPIRRLMSAADHVAEGNLDVRVPIYRAEGDLASLAETFNKMTHELRSQREAI	376
Query:	351	XXXXXXXXXXXHYLECVLDGLTTGVVVFDEKGRLKTFNKAAEQILGMPLAPLWGSSRHGW	410
		+ E VL G+  GV+  D + R+   N++AE++LG  L+ +    RH
Sbjct:	377	LTARDQIDSRRRFTEAVLSGVGAGVIGLDSQERITILNRSAERLLG--LSEVEALHRHLA	434
Query:	411	HGVSAQQSLLAEVFXXXXXXXXTDKPVQVEYAAPDDAKILLGKATVLPEDNG---NGVVM	467
		V     LL E            + VQ       D +  +    V  E +    +G V+
Sbjct:	435	EVVPETAGLLEEA------EHARQRSVQGNITLTRDGRERVFAVRVTTEQSPEAEHGWVV	488
Query:	468	VIDDITVLIRAQKEAAWGEVAKRLAHEIRNPLTPIQLSAERLAWKLGGKLDDQDAQILTR	527
		+DDIT LI AQ+ +AW +VA+R+AHEI+NPLTPIQLSAERL  K G  +  QD +I  +
Sbjct:	489	TLDDITELISAQRTSAWADVARRIAHEIKNPLTPIQLSAERLKRKFGRHV-TQDREIFDQ	547
Query:	528	STDTIIKQVAALKEMVEAFRNYARAPSLKLENQDLNALIGDVLALYEAGPCRFEAELAGE	587
		TDTII+QV  +  MV+ F ++AR P   +++QD++ +I   + L   G      +
Sbjct:	548	CTDTIIRQVGDIGRMVDEFSSFARMPKPVVDSQDMSEIIRQTVFLMRVGHPEVVFDSEVP	607
Query:	588	PLMMAA-DTTAMRQVLHNIFKNXXXXXXXXDMPEVRVK-------SETGQDGRIVLTVCD	639
		P M A  D   + Q L NI KN          P+VR +       +  G+D  +V+ + D
Sbjct:	608	PAMPARFDRRLVSQALTNILKNAAEAIEAVP-PDVRGQGRIRVSANRVGED--LVIDIID	664
Query:	640	NGKGFGKEMLHNAFEPYVTDKPAGTGLGLPVVKKIIGEHGGRISLSNQDAG-GACVRIIL	698
		NG G  +E  +   EPYVT +  GTGLGL +V KI+ EHGG I L++   G GA +R+ L
Sbjct:	665	NGTGLPQESRNRLLEPYVTTREKGTGLGLAIVGKIMEEHGGGIELNDAPEGRGAWIRLTL	724

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 31

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 259>:

1	ATGTACGCAT TTACCGCCGC ACAGCAACAG AAGGCACTCT
	TCCGGCTGGT
51	GCTTTTTCAT ATCCTCATCA TCGCCGCCAG CAACTATCTG
	GTGCAGTTCC
101	CTTTCCAAAT TTTCGGCATC CACACCACTT GGGGCGCATT
	TTCCTTTCCC
151	TTCATCTTCC TTGCCACCGA CCTGACCGTC CGCATTTTCG
	GTTCTCACTT
201	GGCACGGCGG ATTATCTTTT GGGTGATGTT CCCCGCCCTT
	TTGCTTTCCT
251	ACGTCTTTTC CGTTTTGTTC CACAACGGCA GTTGGACAGG
	CTTGGGCGCG
301	CTGTCCGAAT TCAACACCTT TGTCGGACGC ATCGCCTTAG
	CCAGCTTTGC
351	CGCCTACGCG ATCGGACAAA TCCTTGATAT TTTTGTATTC
	AACAAATTAC
401	GCCGTCTGAA AGCGTGGTGG ATTGCACCGA ACGCATCAAC
	CGTCATCGGG
451	CACGCGTTGG ATACG...

This corresponds to the amino acid sequence <SEQ ID 260; ORF66>:

1	MYAFTAAQQQ KALFRLVLFH ILIIAASNYL VQFPFQIFGI
	HTTWGAFSFP
51	FIFLATDLTV RIFGSHLARR IIFWVMFPAL LLSYVFSVLF
	HNGSWTGLGA
101	LSEFNTFVGR IALASFAAYA IGQILDIFVF NKLRRLKAWW
	IAPNASTVIG
151	HALDT...

Further work revealed the complete nucleotide sequence <SEQ ID 261>:

1	ATGTACGCAT TTACCGCCGC ACAGCAACAG AAGGCACTCT
	TCCGGCTGGT
51	GCTTTTTCAT ATCCTCATCA TCGCCGCCAG CAACTATCTG
	GTGCAGTTCC
101	CTTTCCAAAT TTTCGGCATC CACACCACTT GGGGCGCATT
	TTCCTTTCCC
151	TTCATCTTCC TTGCCACCGA CCTGACCGTC CGCATTTTCG
	GTTCTCACTT
201	GGCACGGCGG ATTATCTTTT GGGTGATGTT CCCCGCCCTT
	TTGCTTTCCT
251	ACGTCTTTTC CGTTTTGTTC CACAACGGCA GTTGGACAGG
	CTTGGGCGCG
301	CTGTCCGAAT TCAACACCTT TGTCGGACGC ATCGCCTTAG
	CCAGCTTTGC
351	CGCCTACGCG ATCGGACAAA TCCTTGATAT TTTTGTATTC
	AACAAATTAC
401	GCCGTCTGAA AGCGTGGTGG ATTGCACCGA CCGCATCAAC
	CGTCATCGGC
451	AACGCCTTGG ATACGCTGGT ATTTTTCGCC GTTGCCTTCT
	ACGCAAGCAG
501	CGATGGATTT ATGGCGGCAA ACTGGCAGGG CATCGCTTTT
	GTCGATTACC
551	TGTTCAAACT TACCGTCTGC ACCCTCTTCT TCCTGCCCGC
	CTACGGCGTG
601	ATACTGAATC TGCTGACGAA AAAACTGACA ACCCTGCAAA
	CCAAACAGGC
651	GCAAGACCGC CCCGCGCCCT CGCTGCAAAA TCCGTAA

This corresponds to the amino acid sequence <SEQ ID 262; ORF66-1>:

1	MYAFTAAQQQ KALFRLVLFH ILIIAASNYL VQFPFQIFGI
	HTTWGAFSFP
51	FIFLATDLTV RIFGSHLARR IIFWVMFPAL LLSYVFSVLF
	HNGSWTGLGA
101	LSEFNTFVGR IALASFAAYA IGQILDIFVF NKLRRLKAWW
	IAPTASTVIG
151	NALDTLVFFA VAFYASSDGF MAANWQGIAF VDYLFKLTVC
	TLFFLPAYGV
201	ILNLLTKKLT TLQTKQAQDR PAPSLQNP*

Computer analysis of this amino acid sequence gave the following results:

Homology with the Hypothetical Protein o221 of E. coli (Accession Number P37619)

ORF66 and o221 protein show 67% aa identity in 155aa overlap:

orf66	1	MYAFTAAQQQKALFRLVLFHILIIAASNYLVQFPFQIFGIHTTWGAFSFPFIFLATDLTV	60
		M  F+  Q+ KALF L LFH+L+I +SNYLVQ P  I G HTTWGAFSFPFIFLATDLTV
o221	1	MNVFSQTQRYKALFWLSLFHLLVITSSNYLVQLPVSILGFHTTWGAFSFPFIFLATDLTV	60
orf66	61	RIFGSHLARRIIFWVMFPALLLSYVFSVLFHNGSWTGLGALSEFNTFVGRIALASFAAYA	120
		RIFG+ LARRIIF VM PALL+SYV S LF+ GSW G GAL+ FN FV RIA ASF AYA
o221	61	RIFGAPLARRIIFAVMIPALLISYVISSLFYMGSWQGFGALAHFNLFVARIATASFMAYA	120
orf66	121	IGQILDIFVFNKLRRLKAWWIAPNASTVIGHALDT	155
		+GQILD+ VFN+LR+ + WW+AP AST+ G+  DT
o221	121	LGQILDVHVFNRLRQSRRWWLAPTASTLFGNVSDT	155

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF66 shows 96.1% identity over a 155aa overlap with an ORF (ORF66a) from strain A of N. meningitidis:

The complete length ORF66a nucleotide sequence <SEQ ID 263> is:

1	ATGTACGCAT TTACCGCCGC ACAGCAACAG AAGGCACTCT
	TCTGGCTGGT
51	GCTTTTTCAT ATCCTCATCA TCGCCGCCAG CAACTATCTG
	GTGCAGTTCC
101	CCTTCCAAAT TTCCGGCATC CACACCACTT GGGGCGCGTT
	TTCCTTTCCC
151	TTCATCTTCC TCGCCACCGA CCTGACCGTC CGCATTTTCG
	GTTCGCACTT
201	GGCACGGCGG ATTATCTTTT GGGTCATGTT CCCCGCCCTT
	TTGCTTTCCT
251	ACGTCTTTTC CGTTTTGTTC CACAACGGCA GTTGGACGGG
	CTTGGGCGCG
301	CTGTCCGAAT TCAACACCTT TGTCGGACGC ATCGCGCTGG
	CAAGTTTTGC
351	CGCCTACGCG CTCGGACAAA TCCTTGATAT TTTTGTGTTC
	AACAAATTAC
401	GCCGTCTGAA AGCGTGGTGG GTTGCCCCGA CTGCATCAAC
	CGTCATCGGC
451	AACGCCTTAG ATACGTTGGT ATTTTTCGCC GTTGCCTTCT
	ACGCAAGCAG
501	CGATGGATTT ATGGCGGCAA ACTGGCAGGG CATCGCTTTT
	GTCGATTACC
551	TGTTCAAACT CACCGTCTGC GGTCTGTTTT TCCTGCCCGC
	CTACGGCGTG
601	ATTCTGAATC TGCTGACGAA AAAACTGACG ACCCTGCAAA
	CCAAACAGGC
651	GCAAGACCGC CCCGCGCCCT CGCTGCAAAA TCCGTAA

This encodes a protein having amino acid sequence <SEQ ID 264>:

1	MYAFTAAQQQ KALFWLVLFH ILIIAASNYL VQFPFQISGI
	HTTWGAFSFP
51	FIFLATDLTV RIFGSHLARR IIFWVMFPAL LLSYVFSVLF
	HNGSWTGLGA
101	LSEFNTFVGR IALASFAAYA LGQILDIFVF NKLRRLKAWW
	VAPTASTVIG
151	NALDTLVFFA VAFYASSDGF MAANWQGIAF VDYLFKLTVC
	GLFFLPAYGV
201	ILNLLTKKLT TLQTKQAQDR PAPSLQNP*

ORF66a and ORF66-1 show 97.8% identity in 228 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF66 shows 94.2% identity over a 155aa overlap with a predicted ORF (ORF66.ng) from N. gonorrhoeae:

The complete length ORF66ng nucleotide sequence <SEQ ID 265> is:

1	ATGTACGCAT TGACCGCCGC ACAGCAACAG AAGGCACTCT
	TCCGGCTGGT
51	GCTTTTCCAT ATCCTCATCA TCGCCGCCAG CAACTATCTG
	GTGCAGTTCC
101	CCTTCCGGAT TTTCGGCATC CACACCACTT GGGGCGCGTT
	TTCCTTTCCC
151	TTCATCTTCC TCGCCACCGA CCTGACCGTC CGCATTTTCG
	GTTCGCACTT
201	GGCGCGGCGG ATTATCTTTT GGGTGATGTT CCCCGCCCTT
	ttgCTTTcat
251	aCGTCTTTTC CGTTTTGTTC CACAACGGCA GTTGGACGGG
	CTTGGGCGCG
301	ctgTCCCAAT TCAACACCTT TGTCGGACGC ATCGCGCTGG
	CAAGTTTTGC
351	CGCCTACGCG CTCGGACAAA TCCTTGATAT TTTCGTATTC
	GACAAATTAC
401	GCCGTCTGAA AGCGTGGTGG ATTGCCCCGG CCGCATCAAC
	CGTCATCGGC
451	AATGCACTGG ACACGTTAGT ATTTTTTGCC GTTGCCTTTT
	ACGCAAGCAG
501	CGATGAATTT ATGGCGGCAA ACTGGCAGGG CATCGCTTTT
	GTCGATTACC
551	TGTTCAAACT TACCGTCTGC ACCCTCTTCT TCCTGCCCGC
	CTACGGCGTG
601	ATACTGAATC TGCTGACGAA AAAACTGACG GCCCTGCAAA
	CCAAACAGGC
651	GCAAGACCGC CCCGTGCCCT CGCTGCAAAA TCCGTAA

This encodes a protein having amino acid sequence <SEQ ID 266>:

1	MYALTAAQQQ KALFRLVLFH ILIIAASNYL VQFPFRIFGI
	HTTWGAFSFP
51	FIFLATDLTV RIFGSHLARR IIFWVMFPAL SLSYVFSVLF
	HNGSWTGLGA
101	PSQFNTFVGR IALASFAAYA LGQILDIFVF DKLRRLKAWW
	IAPAASTVIG
151	NALDTLVFFA VAFYASSDEF MAANWQGIAF VDYLFKLTVC
	TLFFLPAYGV
201	ILNLLTKKLT ALQTKQAQDR PVPSLQNP*

An alternative annotated sequence is:

1	MYALTAAQQQ KALFRLVLFH ILIIAASNYL VQFPFRIFGI
	HTTWGAFSFP
51	FIFLATDLTV RIFGSHLARR IIFWVMFPAL LLSYVFSVLF
	HNGSWTGLGA
101	LSQFNTFVGR IALASFAAYA LGQILDIFVF DKLRRLKAWW
	IAPAASTVIG
151	NALDTLVFFA VAFYASSDEF MAANWQGIAF VDYLFKLTVC
	TLFFLPAYGV
201	ILNLLTKKLT ALQTKQAQDR PVPSLQNP*

ORF66ng and ORF66-1 show 96.1% identity in 228 aa overlap:

Furthermore, ORF66ng shows significant homology with an E. coli ORF:

sp|P37619|YHHQ_ECOLI HYPOTHETICAL 25.3 KD PROTEIN IN FTSY-NIKA INTERGENIC
REGION (O221)
>gi|1073495|pir||S47690 hypothetical protein o221 - Escherichia coli
>gi|466607 (U00039) No definition line found [Escherichia coli]
>gi|1789882 (AE000423) hypothetical 25.3 kD protein in ftsY-nikA
intergenic region [Escherichia coli]
Length = 221
Score = 273 bits (692), Expect = 5e−73
Identities = 132/203 (65%), Positives = 155/203 (76%)

Query:	1	MYALTAAQQQKALFRLVLFHILIIAASNYLVQFPFRIFGIHTTWGAFSFPFIFLATDLTV	60
		M   +  Q+ KALF L LFH+L+I +SNYLVQ P  I G HTTWGAFSFPFIFLATDLTV
Sbjct:	1	MNVFSQTQRYKALFWLSLFHLLVITSSNYLVQLPVSILGFHTTWGAFSFPFIFLATDLTV	60
Query:	61	RIFGSHLARRIIFWVMFPALLLSYVFSVLFHNGSWTGLGALSQFNTFVGRIALASFAAYA	120
		RIFG+ LARRIIF VM PALL+SYV S LF+ GSW G GAL+ FN FV RIA ASF AYA
Sbjct:	61	RIFGAPLARRIIFAVMIPALLISYVISSLFYMGSWQGFGALAHFNLFVARIATASFMAYA	120
Query:	121	LGQILDIFVFDKLRRLKAWWIAPAASTVIGNALDTLVFFAVAFYASSDEFMAANWQGIAF	180
		LGQILD+ VF++LR+ + WW+AP AST+ GN  DTL FF +AF+ S D FMA +W  IA
Sbjct:	121	LGQILDVHVFNRLRQSRRWWLAPTASTLFGNVSDTLAFFFIAFWRSPDAFMAEHWMEIAL	180
Query:	181	VDYLFKLTVCTLFFLPAYGVILN	203
		VDY FK+ +  +FFLP YGV+LN
Sbjct:	181	VDYCFKVLISIVFFLPMYGVLLN	203

Based on this analysis, including the homology with the E. coli protein and the presence of several putative transmembrane domains in the gonococcal protein, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 32

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 267>:

1	ATGGTCATAA AATATACAAA TTTGAATTTT GCGAAATTGT
	CGATAATTGC
51	AATTTTGATG ATGTATTCGT TTGAAGCGAA TGCAAAyGCA
	GTmwrAATAT
101	CTGAAACTGT TTCAGTTGAT ACCGGACAAG GTGCGAAAAT
	TCATAAGTTT
151	GTACCTAAAA ATAGTAAAAC TTATTCATCT GATTTAATAA
	AAACGGTAGA
201	TTTAACACAC AyyCCTACGG GCGCAAAAGC CCGAATCAAC
	GCCAAAATAA
251	CCGCCAGCGT ATCCCGCGCC GGCGTATTGG CGGGGGTCGG
	CAAACTTGCC
301	CGCTTAGgCG CGAAATTCAG CACAAGGGCG GTtCCCTATG
	TCGGAACAGC
351	CcTTTTAGCC CACGACGTAT ACGAAAcTTT CAAAGAAGAC
	ATACAGGCAC
401	GAGGCTACCA ATACGACCCC GAAACCGACA AATTTGTAAA
	AGGCTACGAA
451	TATAGTAATT GCCTTTGGTA CGAAGACAAA AGACGTATTA
	ATAGAACCTA
501	TGGCTGCTAC GGCGTTGAT..

This corresponds to the amino acid sequence <SEQ ID 268; ORF72>:

1	MVIKYTNLNF AKLSIIAILM MYSFEANANA VXISETVSVD
	TGQGAKIHKF
51	VPKNSKTYSS DLIKTVDLTH XPTGAKARIN AKITASVSRA
	GVLAGVGKLA
101	RLGAKFSTRA VPYVGTALLA HDVYETFKED IQARGYQYDP
	ETDKFVKGYE
151	YSNCLWYEDK RRINRTYGCY GVD..

Further work revealed the complete nucleotide sequence <SEQ ID 269>:

1	ATGGTCATAA AATATACAAA TTTGAATTTT GCGAAATTGT
	CGATAATTGC
51	AATTTTGATG ATGTATTCGT TTGAAGCGAA TGCAAATGCA
	GTAAAAATAT
101	CTGAAACTGT TTCAGTTGAT ACCGGACAAG GTGCGAAAAT
	TCATAAGTTT
151	GTACCTAAAA ATAGTAAAAC TTATTCATCT GATTTAATAA
	AAACGGTAGA
201	TTTAACACAC ATCCCTACGG GCGCAAAAGC CCGAATCAAC
	GCCAAAATAA
251	CCGCCAGCGT ATCCCGCGCC GGCGTATTGG CGGGGGTCGG
	CAAACTTGCC
301	CGCTTAGGCG CGAAATTCAG CACAAGGGCG GTTCCCTATG
	TCGGAACAGC
351	CCTTTTAGCC CACGACGTAT ACGAAACTTT CAAAGAAGAC
	ATACAGGCAC
401	GAGGCTACCA ATACGACCCC GAAACCGACA AATTTGCAAA
	GGTCTCAGGC
451	TAA

This corresponds to the amino acid sequence <SEQ ID 270; ORF72-1>:

1	MVIKYTNLNF AKLSIIAILM MYSFEANANA VKISETVSVD
	TGQGAKIHKF
51	VPKNSKTYSS DLIKTVDLTH IPTGAKARIN AKITASVSRA
	GVLAGVGKLA
101	RLGAKFSTRA VPYVGTALLA HDVYETFKED IQARGYQYDP
	ETDKFAKVSG
151	*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF72 shows 98.0% identity over a 147aa overlap with an ORF (ORF72a) from strain A of N. meningitidis:

The complete length ORF72a nucleotide sequence <SEQ ID 271> is:

1	ATGGTCATAA AATATACAAA TTTGAATTTT GCGAAATTGT
	CGATAATTGC
51	AATTTTGATG ATGTATTCGT TTGAAGCGAA TGCAAATGCA
	GTAAAAATAT
101	CTGAAACTGT TTCAGTTGAT ACCGGACAAG GTGCGAAAAT
	TCATAAGTTT
151	GTACCTAAAA ATAGTAAAAC TTATTCATCT GATTTAATAA
	AAACGGTAGA
201	TTTAACACAC ATCCCTACGG GCGCAAAAGC CCGAATCAAC
	GCCAAAATAA
251	CCGCCAGCGT ATCCCGCGCC GGCGTATTGG CGGGGGTCGG
	CAAACTTGCC
301	CGCTTAGGCG CGAAATTCAG CACAAGGGCG GTTCCCTATG
	TCGGAACAGC
351	CCTTTTAGCC CACGACGTAT ACGAAACTTT CAAAGAAGAC
	ATACAGGCAC
401	GAGGCTACCA ATACGACCCC GAAACCGACA AATTTGCAAA
	GGTCTCAGGC
451	TAA

This encodes a protein having amino acid sequence <SEQ ID 272>:

1	MVIKYTNLNF AKLSIIAILM MYSFEANANA VKISETVSVD
	TGQGAKIHKF
51	VPKNSKTYSS DLIKTVDLTH IPTGAKARIN AKITASVSRA
	GVLAGVGKLA
101	RLGAKFSTRA VPYVGTALLA HDVYETFKED IQARGYQYDP
	ETDKFAKVSG
151	*

ORF72a and ORF72-1 show 100.0% identity in 150 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF72 shows 89% identity over a 173aa overlap with a predicted ORF (ORF72.ng) from N. gonorrhoeae:

An ORF72ng nucleotide sequence <SEQ ID 273> was predicted to encode a protein having amino acid sequence <SEQ ID 274>:

1	MVTKHTNLNF AKLSIIAILM MYSFEANANA VKISETLSVD
	TGQGAKVHKF
51	VPKSSNIYSS DLTKAVDLTH IPTGAKARIN AKITASVSRA
	GVLSGVGKLV
101	RQGAKFGTRA VPYVGTALLA HDVYETFKED IQARGCRYDP
	ETDKFVKGYE
151	YANCLWYEDE RRINRTYGCY GVDSSIMRLM PDRSRFPEVK
	QLMESQMYRL
201	ARPFWNWRKE ELNKLSSLDW NNFVLNRCTF DWNGGGCAVN
	KGDDFRAGAS
251	FSLGRNPKYK EEMDAKKPEE ILSLKVDADP DKYIEATGYP
	GYSEKVEVAP
301	GTKVNMGPVT DRNGNPVQVA ATFGRDAQGN TTADVQVIPR
	PDLTPASAEA
351	PHAQPLPEVS PAENPANNPD PDENPGTRPN PEPDPDLNPD
	ANPDTDGQPG
401	TSPDSPAVPD RPNGRHRKER KEGEDGGLSC DYFPEILACQ
	EMGKPSDRMF
451	HDISIPQVTD DKTWSSHNFL PSNGVCPQPK TFHVFGRQYR
	ASYEPLCVFA
501	EKIRFAVLLA FIIMSAFVVF GSLGGE*

After further analysis, the following gonococcal DNA sequence <SEQ ID 275> was identified:

1	ATGGTCACAA AACATACAAA TTTGAATTTT GCGAAATTGT
	CGATAATTGC
51	AATTTTGATG ATGTATTCGT TTGAAGCGAA TGCAAATGCA
	GTAAAAATAT
101	CTGAAACTCT TTCGGTTGAT ACCGGACAAG GCGCGAAAGT
	TCATAAGTTC
151	GTTCCTAAAT CAAGTAATAT TTATTCATCT GATTTAACAA
	AAGCGGTAGA
201	TTTAACGCAT ATCCCCACGG GCGCAAAAGC CCGAATCAAC
	GCCAAAATAA
251	CCGCCAGCGT ATCCCGCGCC GGCGTATTGT CGGGGGTCGG
	CAAACTTGTC
301	CGCCAAGGCG CGAAATTCGG CACAAGGGCG GTTCCCTATG
	TCGGAACAGC
351	CCTTTTAGCC CACGACGTAT ACGAAACTTT CAAAGAAGAC
	ATACAGGCAC
401	GAGGCTGCCG ATACGATCCC GAAACCGACA AATTT

This corresponds to the amino acid sequence <SEQ ID 276; ORF72ng-1>:

1	MVTKHTNLNF AKLSIIAILM MYSFEANANA VKISETLSVD
	TGQGAKVHKF
51	VPKSSNIYSS DLTKAVDLTH IPTGAKARIN AKITASVSRA
	GVLSGVGKLV
101	RQGAKFGTRA VPYVGTALLA HDVYETFKED IQARGCRYDP
	ETDKF

ORF72ng-1 and ORF721-1 show 89.7% identity in 145 aa overlap:

Based on this analysis, including the presence of a putative leader sequence and transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 33

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 277>:

1	ATGAGATTTT TCGGTATCGG TTTTTTGGTG CTGCTGTTTT
	TGGAGATTAT
51	GTCGATTGTG TGGGTTGCCG ATTGGCTGGG CGGCGGCTGG
	ACGTTGTTTT
101	TGATGGCGGC AGGTTTTGCC GCCGGCGTGC TGATGCTCAG
	GCAAACCGGG
151	GCTGACCGGT CTTTTATTGG CGGGCGCGGC AATGAGAAGC
	GGCGGGAAGG
201	TATCCGTTTA TCAGATGTTG TGGCCTATC..

This corresponds to the amino acid sequence <SEQ ID 278; ORF73>:

1	MRFFGIGFLV LLFLEIMSIV WVADWLGGGW TLFLMAAGFA
	AGVLMLRQTG
51	LTGLLLAGAA MRSGGKVSVY QMLWPI..

Further work revealed the complete nucleotide sequence <SEQ ID 279>:

1	ATGAGATTTT TCGGTATCGG TTTTTTGGTG CTGCTGTTTT
	TGGAGATTAT
51	GTCGATTGTG TGGGTTGCCG ATTGGCTGGG CGGCGGCTGG
	ACGTTGTTTT
101	TGATGGCGGC AGGTTTTGCC GCCGGCGTGC TGATGCTCAG
	GCATACGGGG
151	CTGTCCGGTC TTTTATTGGC GGGCGCGGCA ATGAGAAGCG
	GCGGGAGGGT
201	ATCCGTTTAT CAGATGTTGT GGCCTATCCG TTATACGGTG
	GCGGCTGTGT
251	GTCTGATGAG TCCGGGATTC GTATCCTCGG TGTTGGCGGT
	ATTGCTGCTG
301	CTGCCGTTTA AGGGAGGGGC AGTGTTGCAG GCAGGAGGTG
	CGGAAAATTT
351	TTTCAACATG AACCAATCGG GCAGAAAAGA GGGCTTTTCC
	CGCGATGACG
401	ATATTATCGA GGGAGAATAT ACGGTTGAAG AGCCTTACGG
	CGGCAATCGT
451	TCCCGAAACG CCATCGAACA CAAAAAAGAC GAATAA

This corresponds to the amino acid sequence <SEQ ID 280; ORF73-1>:

1	MRFFGIGFLV LLFLEIMSIV WVADWLGGGW TLFLMAAGFA
	AGVLMLRHTG
51	LSGLLLAGAA MRSGGRVSVY QMLWPIRYTV AAVCLMSPGF
	VSSVLAVLLL
101	LPFKGGAVLQ AGGAENFFNM NQSGRKEGFS RDDDIIEGEY
	TVEEPYGGNR
151	SRNAIEHKKD E*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF73 shows 90.8% identity over a 76aa overlap with an ORF (ORF73a) from strain A of N. meningitidis:

The complete length ORF73a nucleotide sequence <SEQ ID 281> is:

1	ATGAGATTTT TCGGTATCGG TTTTTTGGTG CTGCTGTTTT
	TGGAGATTAT
51	GTCGATTGTG TGGGTTGCCG ATTGGTTGGG CGGCGGTTGG
	ACGCTGTTTC
101	TAATGGCGGC AACCTTTGCC GCCGGCGTGG TGATGCTCAG
	GCATACGGGG
151	CTGTCCGGTC TTTTATTGGC GGGCGCGGCA ATGAGAAGCG
	GCGGGAGGGT
201	ATCCGTTTAT CANATGTTGT GGCNTATCCG TTATACGGTG
	GCGGCGGTGT
251	GTCNGATGAG TCCGGGATTC GTATCCTCGG TGTNGGCGGT
	ATTGCTGNTG
301	CTNCCGTTTA AGGGAGGTGC AGTGTTGCAG GCAGGAGGTG
	CGGAAAATTT
351	TTTCAACATG AACCANTCGG GCAGAAAAGA NGGCNTTTCC
	CGCGATGACG
401	ATATTATCGA GGGGGAATAT ACGGTTGAAG ANCCTTACGG
	CGGCANTCGT
451	TTCCGAAACG CCNTNGAACA CAAAAAAGAC GAATAA

This encodes a protein having amino acid sequence <SEQ ID 282>:

1	MRFFGIGFLV LLFLEIMSIV WVADWLGGGW TLFLMAATFA
	AGVVMLRHTG
51	LSGLLLAGAA MRSGGRVSVY XMLWXIRYTV AAVCXMSPGF
	VSSVXAVLLX
101	LPFKGGAVLQ AGGAENFFNM NXSGRKXGXS RDDDIIEGEY
	TVEXPYGGXR
151	FRNAXEHKKD E*

ORF73a and ORF73-1 show 91.3% identity in 161 aa overlap

Homology with a Predicted ORF from N. gonorrhoeae

ORF73 shows 92.1% identity over a 76aa overlap with a predicted ORF (ORF73.ng) from N. gonorrhoeae:

The complete length ORF73ng nucleotide sequence <SEQ ID 283> is:

1	ATGAGATTTT TCGGTATCGG TTTTTTGGTG CTGCTGTTTT
	TGGAAATTAT
51	GTCGATTGTG TGGGTTGCCG ATTGGCTGGG CGGCGGTTGG
	AcgcTGTTTC
101	TAATGGCGGC AACCTTTGCC GCCGGTGTGC TGATGCTCAG
	GCATAcggGG
151	CTGTCCGGTC TTTTATTGGC TGGCGCGGCG GTAAAAagta
	gtgGGAAGGT
201	ATCTGTTTAT CagatgtTGT GGCCTATCCG TTATAcggtg
	gcggcggtgT
251	GTCTGatgag tCcggGATTC GTATCCTccg tgttggCGGT
	ATTGCTGCTG
301	CTGCcgttta aggGaggGgc agtgttgcag gcaggaggtg
	cggaaaATTT
351	TTTCAACATg aaCcaatcgg gcagaaAaga gggatttttc
	cacgatgacg
401	atattatcga gggagaatat acggttgaaa aacctgacgg
	cggcaatcgt
451	tcccgaAAcg ccatcgaaca cgaaaAagac gaataA

This encodes a protein having amino acid sequence <SEQ ID 284>:

1	MRFFGIGFLV LLFLEIMSIV WVADWLGGGW TLFLMAATFA
	AGVLMLRHTG
51	LSGLLLAGAA VKSSGKVSVY QMLWPIRYTV AAVCLMSPGF
	VSSVLAVLLL
101	LPFKGGAVLQ AGGAENFFNM NQSGRKEGFF HDDDIIEGEY
	TVEKPDGGNR
151	SRNAIEHEKD E*

ORF73ng and ORG73-1 show 93.8% identity in 161 aa overlap

Based on this analysis, including the presence of a putative leader sequence and putative transmembrane domain in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 34

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 285>:

1	ATGTTTGTTT TTCAGACGGC ATTCTT.ATG TTTCAGAAAC
	ATTTGCAGAA
51	AGCCTCCGAC AGCGTCGTCG GAGGGACATT ATACGTGGTT
	GCCACGCCCA
101	TCGGCAATTT GGCGGACATT ACCCTGCGCG CTTTGGCGGT
	ATTGCAAAAG
151	GCG....... .....GCCGA AGACACGCGC GTTACCGCAC
	AGCTTTTGAG
201	CGCGTACGGC ATTCAGGGCA AACTCGTCAG TGTGCGCGAA
	CACAACGAAC
251	GGCAGATGGC GGACAAGATT GTCGGCTATC TTTCAGACGG
	CATGGTTGTG
301	GCACAGGTTT CCGATGCGGG TACGCCGGCC GTGTGCGACC
	CGGGCGCGAA
351	ACTCGCCCGC CGCGTGCGTG AGGCCGGGTT TAAAGTCGTT
	CCCGTCGTGG
401	GCGCAAC.GC GGTGATGGCG GCTTTGAGCG TGGCCGGTGT
	GGAAGGATCC
451	GATTTTTATT TCAACGGTTT TGTACCGCCG AAATCGGGAG
	AACGCAGGAA
501	ACTGTTTGCC AAATGGGTGC GGGCGGCGTT TCCTATCGTC
	ATGTTTGAAA
551	CGCCGCACCG CATCGGTGCA GCGCTTGCCG ATATGGCGGA
	ACTGTTCCCC
601	GAACGCCGAT TAATGCTGGC GCGCGAAATT ACGAAAACGT
	TTGAAACGTT
651	CTTAAGCGGC ACGGTTGGGG AAATTCAGAC GGCATTGTCT
	GCCGACGGCG
701	ACCAATCGCG CGGCGAGATG GTGTTGGTGC TTTATCCGGC
	GCAGGATGAA
751	AAACACGAAG GCTTGTCCGA GTCCGCGCAA AACATCATGA
	AAATCCTCAC
801	AGCCGAGCTG CCGACCAAAC AGGCGGCGGA GCTTGCTGCC
	AAAATCACGG
851	GCGAGGGAAA GAAAGCTTTG TACGAT..

This corresponds to the amino acid sequence <SEQ ID 286; ORF75>:

1	MFVFQTAFXM FQKHLQKASD SVVGGTLYVV ATPIGNLADI
	TLRALAVLQK
51	A....AEDTR VTAQLLSAYG IQGKLVSVRE HNERQMADKI
	VGYLSDGMVV
101	AQVSDAGTPA VCDPGAKLAR RVREAGFKVV PVVGAXAVMA
	ALSVAGVEGS
151	DFYFNGFVPP KSGERRKLFA KWVRAAFPIV MFETPHRIGA
	ALADMAELFP
201	ERRLMLAREI TKTFETFLSG TVGEIQTALS ADGDQSRGEM
	VLVLYPAQDE
251	KHEGLSESAQ NIMKILTAEL PTKQAAELAA KITGEGKKAL
	YD..

Further work revealed the complete nucleotide sequence <SEQ ID 287>:

1	ATGTTTCAGA AACATTTGCA GAAAGCCTCC GACAGCGTCG
	TCGGAGGGAC
51	ATTATACGTG GTTGCCACGC CCATCGGCAA TTTGGCGGAC
	ATTACCCTGC
101	GCGCTTTGGC GGTATTGCAA AAGGCGGACA TCATCTGTGC
	CGAAGACACG
151	CGCGTTACCG CACAGCTTTT GAGCGCGTAC GGCATTCAGG
	GCAAACTCGT
201	CAGTGTGCGC GAACACAACG AACGGCAGAT GGCGGACAAG
	ATTGTCGGCT
251	ATCTTTCAGA CGGCATGGTT GTGGCACAGG TTTCCGATGC
	GGGTACGCCG
301	GCCGTGTGCG ACCCGGGCGC GAAACTCGCC CGCCGCGTGC
	GTGAGGCCGG
351	GTTTAAAGTC GTTCCCGTCG TGGGCGCAAG CGCGGTGATG
	GCGGCTTTGA
401	GCGTGGCCGG TGTGGAAGGA TCCGATTTTT ATTTCAACGG
	TTTTGTACCG
451	CCGAAATCGG GAGAACGCAG GAAACTGTTT GCCAAATGGG
	TGCGGGCGGC
501	GTTTCCTATC GTCATGTTTG AAACGCCGCA CCGCATCGGT
	GCGACGCTTG
551	CCGATATGGC GGAACTGTTC CCCGAACGCC GATTAATGCT
	GGCGCGCGAA
601	ATTACGAAAA CGTTTGAAAC GTTCTTAAGC GGCACGGTTG
	GGGAAATTCA
651	GACGGCATTG TCTGCCGACG GCAACCAATC GCGCGGCGAG
	ATGGTGTTGG
701	TGCTTTATCC GGCGCAGGAT GAAAAACACG AAGGCTTGTC
	CGAGTCCGCG
751	CAAAACATCA TGAAAATCCT CACAGCCGAG CTGCCGACCA
	AACAGGCGGC
801	GGAGCTTGCT GCCAAAATCA CGGGCGAGGG AAAGAAAGCT
	TTGTACGATC
851	TGGCTCTGTC TTGGAAAAAC AAATAG

This corresponds to the amino acid sequence <SEQ ID 288; ORF75-1>:

1	MFQKHLQKAS DSVVGGTLYV VATPIGNLAD ITLRALAVLQ
	KADIICAEDT
51	RVTAQLLSAY GIQGKLVSVR EHNERQMADK IVGYLSDGMV
	VAQVSDAGTP
101	AVCDPGAKLA RRVREAGFKV VPVVGASAVM AALSVAGVEG
	SDFYFNGFVP
151	PKSGERRKLF AKWVRAAFPI VMFETPHRIG ATLADMAELF
	PERRLMLARE
201	ITKTFETFLS GTVGEIQTAL SADGNQSRGE MVLVLYPAQD
	EKHEGLSESA
251	QNIMKILTAE LPTKQAAELA AKITGEGKKA LYDLALSWKN
	K*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF75 shows 95.8% identity over a 283aa overlap with an ORF (ORF75a) from strain A of N. meningitidis:

The complete length ORF75a nucleotide sequence <SEQ ID 289> is:

1	ATGTTTCAGA AACATTTGCA GAAAGCCTCC GACAGCGTCG
	TCGGAGGGAC
51	ATTATACGTG GTTGCCACGC CCATCGGCAA TTTGGCGGAC
	ATTACCCTGC
101	GCGCTTTGGC GGTATTGCAA AAGGCGGACA TCATCTGTGC
	CGAAGACACG
151	CGCGTTACCG CGCAGCTTTT GAGCGCGTAC GGCATTCAGG
	GCAAACTCGT
201	CAGCGTGCGC GAACACAACG AACGGCAGAT GGCGGACAAG
	ATTGTCGGCT
251	ATCTTTCAGA CGGCATGGTT GTGGCACAGG TTTCCGATGC
	GGGTACGCCG
301	GCCGTGTGCG ACCCGGGCGC GAAACTCGCC CGCCGCGTGC
	GTGAGGTCGG
351	GTTTAAAGTT GTCCCTGTTG TCGGCGCAAG CGCGGTGATG
	GCGGCTTTGA
401	GTGTGGCTGG TGTGGCGGGA TCCGATTTTT ATTTCAACGG
	TTTTGTACCG
451	CCGAAATCGG GCGAACGTAG GAAATTGTTT GCCAAATGGG
	TGCGGGTGGC
501	GTTTCCCGTC GTGATGTTTG AAACGCCGCA CCGCATCGGG
	GCGACGCTTG
551	CCGATATGGC GGAACTGTTC CCCGAACGCC GATTAATGCT
	GGCGCGCGAA
601	ATCACGAAAA CGTTTGAAAC GTTCTTAAGC GGCACGGTTG
	GGGAAATTCA
651	GACGGCATTG GCGGCGGACG GCAACCAATC GCGCGGCGAG
	ATGGTGTTGG
701	TGCTTTATCC GGCGCAGGAT GAAAAACACG AAGGCTTGTC
	CGAGTCCGCG
751	CAAAACATCA TGAAAATCCT CACAGCCGAG CTGCCGACCA
	AACAGGCGGC
801	GGAGCTTGCC GCCAAAATCA CGGGCGAGGG AAAAAAAGCT
	TTGTACGATC
851	TGGCACTGTC TTGGAAAAAC AAATGA

This encodes a protein having amino acid sequence <SEQ ID 290>:

1	MFQKHLQKAS DSVVGGTLYV VATPIGNLAD ITLRALAVLQ
	KADIICAEDT
51	RVTAQLLSAY GIQGKLVSVR EHNERQMADK IVGYLSDGMV
	VAQVSDAGTP
101	AVCDPGAKLA RRVREVGFKV VPVVGASAVM AALSVAGVAG
	SDFYFNGFVP
151	PKSGERRKLF AKWVRVAFPV VMFETPHRIG ATLADMAELF
	PERRLMLARE
201	ITKTFETFLS GTVGEIQTAL AADGNQSRGE MVLVLYPAQD
	EKHEGLSESA
251	QNIMKILTAE LPTKQAAELA AKITGEGKKA LYDLALSWKN
	K*

ORF75a and ORF75-1 show 98.3% identity in 291 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF75 shows 93.2% identity over a 292aa overlap with a predicted ORF (ORF75.ng) from N. gonorrhoeae:

An ORF75ng nucleotide sequence <SEQ ID 291> was predicted to encode a protein having amino acid sequence <SEQ ID 292>:

1	MSVFQTAFFM FQKHLQKASD SVVGGTLYVV ATPIGNLADI
	TLRALAVLQK
51	ADIICAEDTR VTAQLLSAYG IQGRLVSVRE HNERQMADKV
	IGFLSDGLVV
101	AQVSDAGTPA VCDPGAKLAR RVREAGFKVV PVVGASAVMA
	ALSVAGVAES
151	DFYFNGFVPP KSGERRKLFA KWVRAAFPVV MFETPHRIGA
	TLADMAELFP
201	ERRLMLAREI TKTFETFLSG TVGEIQTALA ADGNQSRGEM
	VLVLYPAQDE
251	KHEGLSESAQ NAMKILAAEL PTKQAAELAA KITGEGKKAL
	YDLALSWKNK
301	*

After further analysis, the following gonococcal DNA sequence <SEQ ID 293> was identified:

1	ATGTTTCAGA AACACTTGCA GAAAGCCTCC GACAGCGTCG
	TCGGAGGGAC
51	ATTATACGTG GTTGCCACGC CCATCGGCAA TTTGGCAGAC
	ATTACCCTGC
101	GCGCTTTGGC GGTATTGCAA AAGGCGGACA TCATTTGTGC
	CGAAGACACG
151	CGCGTTACTG CGCAGCTTTT GAGCGCGTAC GGCATTCAGG
	GCAGGTTGGT
201	CAGTGTGCGC GAACACAACG AGCGGCAGAT GGCGGACAAG
	GTAATCGGTT
251	TCCTTTCAGA CGGCCTGGTT GTGGCGCAGG TTTCCGATGC
	GGGTACGCCG
301	GCCGTGTGCG ACCCGGGCGC GAAACTCGCC CGCCGCGTGC
	GCGAAGCAGG
351	GTTCAAAGTC GTTCCCGTCG TGGGCGCAAG CGCGGTAATG
	GCGGCGTTGA
401	GTGTGGCCGG TGTGGCGGAA TCCGATTTTT ATTTCAACGG
	TTTTGTACCG
451	CCGAAATCGG GCGAACGTAG GAAATTGTTT GCCAAATGGG
	TGCGGGCGGC
501	ATTTCCTGTC GTCATGTTTG AAACGCCGCA CCGAATCGGG
	GCAACGCTTG
551	CCGATATGGC GGAATTGTTC CCCGAACGCC GTCTGATGCT
	GGCGCGCGAA
601	ATCACGAAAA CGTTTGAAAC GTTCTTAAGC GGCACGGTTG
	GGGAAATTCA
651	GACGGCATTG GCGGCGGACG GCAACCAATC GCGCGGCGAG
	ATGGTGTTGG
701	TGCTTTATCC GGCGCAGGAT GAAAAACACG AAGGCTTGTC
	CGAGTCTGCG
751	CAAAATGCGA TGAAAATCCT TGCGGCCGAG CTGCCGACCA
	AGCAGGCGGC
801	GGAGCTTGCC GCCAAGATTA CAGGTGAGGG CAAAAAGGCT
	TTGTACGATT
851	TGGCACTGTC GTGGAAAAAC AAATGA

This corresponds to the amino acid sequence <SEQ ID 294; ORF75ng-1>:

1	MFQKHLQKAS DSVVGGTLYV VATPIGNLAD ITLRALAVLQ
	KADIICAEDT
51	RVTAQLLSAY GIQGRLVSVR EHNERQMADK VIGFLSDGLV
	VAQVSDAGTP
101	AVCDPGAKLA RRVREAGFKV VPVVGASAVM AALSVAGVAE
	SDFYFNGFVP
151	PKSGERRKLF AKWVRAAFPV VMFETPHRIG ATLADMAELF
	PERRLMLARE
201	ITKTFETFLS GTVGEIQTAL AADGNQSRGE MVLVLYPAQD
	EKHEGLSESA
251	QNAMKILAAE LPTKQAAELA AKITGEGKKA LYDLALSWKN
	K*

ORF75ng-1 and ORF75-1 show 96.2% identity in 291 aa overlap:

Furthermore, ORG75ng-1 shows significant homology to a hypothetical E. coli protein:

sp|P45528|YRAL_ECOLI HYPOTHETICAL 31.3 KD PROTEIN IN AGAI-MTR INTERGENIC
REGION (F286)
>gi|606086 (U18997) ORF_f286 [Escherichia coli]
>gi|1789535 (AE000395) hypothetical 31.3 kD protein in agai-mtr
intergenic region [Escherichia coli] Length = 286
Score = 218 bits (550), Expect = 3e−56
Identities = 128/284 (45%), Positives = 171/284 (60%), Gaps = 4/284 (1%)

Query:	4	KHLQKASDSVVGGTLYVVATPIGNLADITLRALAVLQKADIICAEDTRVTAQLLSAYGIQ	63
		K  Q A +S   G LY+V TPIGNLADIT RAL VLQ  D+I AEDTR T  LL  +GI
Sbjct:	2	KQHQSADNSQ--GQLYIVPTPIGNLADITQRALEVLQAVDLIAAEDTRHTGLLLQHFGIN	59
Query:	64	GRLVSVREHNERQMADKVIGFLSDGLVVAQVSDAGTPAVCDPGAKLARRVREAGFKVVPV	123
		RL ++ +HNE+Q A+ ++  L +G  +A VSDAGTP + DPG  L R  REAG +VVP+
Sbjct:	60	ARLFALHDHNEQQKAETLLAKLQEGQNIALVSDAGTPLINDPGYHLVRTCREAGIRVVPL	119
Query:	124	VGASAVMAALSVAGVAESDFYFNGFVPPKSGERRKLFAKWVRAAFPVVMFETPHRIGATL	183
		G  A + ALS AG+    F + GF+P KS  RR            ++ +E+ HR+  +L
Sbjct:	120	PGPCAAITALSAAGLPSDRFCYEGFLPAKSKGRRDALKAIEAEPRTLIFYESTHRLLDSL	179
Query:	184	ADMAELFPERR-LMLAREITKTFETFLSGTVGEIQTALAADGNQSRGEMVLVLYPAQDEK	242
		D+  +  E R ++LARE+TKT+ET     VGE+   +  D N+ +GEMVL++      +
Sbjct:	180	EDIVAVLGESRYVVLARELTKTWETIHGAPVGELLAWVKEDENRRKGEMVLIV-EGHKAQ	238
Query:	243	HEGLSESAQNAMKILAAELPTKQAAELAAKITGEGKKALYDLAL	286
		E L   A   + +L AELP K+AA LAA+I G  K ALY  AL
Sbjct:	239	EEDLPADALRTLALLQAELPLKKAAALAAEIHGVKKNALYKYAL	282

Based on this analysis, including the presence of a putative transmembrane domain in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 35

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 295>:

This corresponds to the amino acid sequence <SEQ ID 296; ORF76>:

Further work revealed the complete nucleotide sequence <SEQ ID 297>:

1	ATGAAACAGA AAAAAACCGC TGCCGCAGTT ATTGCTGCAA
	TGTTGGCAGG
51	TTTTGCGGCA GCCAAAGCAC CCGAAATCGA CCCGGCTTTG
	GTGGATACGC
101	TGGTGGCGCA GATCATGCAG CAGGCAGACC GGCATGCGGA
	GCAGTCCCAA
151	AAACCGGACG GGCAGGCAAT CCGAAACGAT GCCGTCCGCC
	GGCTACAAAC
201	TTTGGAAGTT TTGAAAAACA GGGCATTGAA GGAAGGTTTG
	GATAAGGATA
251	AGGATGTCCA AAACCGCTTT AAAATCGCCG AAGCGTCTTT
	TTATGCCGAG
301	GAGTACGTCC GTTTTCTGGA ACGTTCGGAA ACGGTTTCCG
	AAGACGAGCT
351	GCACAAGTTT TACGAACAGC AAATCCGCAT GATCAAATTG
	CAGCAGGTCA
401	GCTTCGCAAC CGAAGAGGAG GCGCGTCAGG CGCAGCAGCT
	CCTGCTCAAA
451	GGGCTGTCTT TTGAAGGGCT GATGAAGCGT TATCCGAACG
	ACGAGCAGGC
501	TTTTGACGGT TTCATTATGG CGCAGCAGCT TCCCGAGCCG
	CTGGCTTCGC
551	AGTTTGCCGC GATGAATCGG GGCGACGTTA CCCGCGATCC
	GGTCAAATTG
601	GGCGAACGCT ATTATCTGTT CAAACTCAGC GAGGTCGGGA
	AAAACCCCGA
651	CGCGCAGCCT TTCGAGTTGG TCAGAAACCA GTTGGAGCAG
	GGTTTGAGAC
701	AGGAAAAAGC CCGCTTGAAA ATCGATGCCC TTTTGGAAGA
	AAACGGTGTC
751	AAACCGTAA

This corresponds to the amino acid sequence <SEQ ID 298; ORF76-1>:

1	MKQKKTAAAV IAAMLAGFAA AKAPEIDPAL VDTLVAQIMQ
	QADRHAEQSQ
51	KPDGQAIRND AVRRLQTLEV LKNRALKEGL DKDKDVQNRF
	KIAEASFYAE
101	EYVRFLERSE TVSEDELHKF YEQQIRMIKL QQVSFATEEE
	ARQAQQLLLK
151	GLSFEGLMKR YPNDEQAFDG FIMAQQLPEP LASQFAAMNR
	GDVTRDPVKL
201	GERYYLFKLS EVGKNPDAQP FELVRNQLEQ GLRQEKARLK
	IDALLEENGV
251	KP*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF76 shows 96.7% identity over a 30aa overlap and 96.8% identity over a 31aa overlap with an ORF (ORF76a) from strain A of N. meningitidis:

The complete length ORF76a nucleotide sequence <SEQ ID 299> is:

1	ATGAAACAGA AAAAAACCGC TGCCGCAGTT ATTGCTGCAA
	TGTTGGCAGG
51	TTTTGCGGCA GCCAAAGCAC CCGAAATCGA CCCGGCTTTG
	GTGGATACGC
101	TGGTGGCGCA GATCATGCAG CAGGCAGACC GGCATGCGGA
	GCAGTCCCAA
151	AAACCGGACG GGCAGGCAAT CCGAAACGAT GCCGTCCGTC
	GGCTGCAAAC
201	TTTGGAAGTT TTGAAAAACA GGGCATTGAA GGAAGGTTTG
	GATAAGGATA
251	AGGATGTCCA AAACCGCTTT AAAATCGCCG AAGCGTCTTT
	TTATGCCGAG
301	GAGTACGTCC GTTTTCTGGA ACGTTCGGAA ACGGTTTCCG
	AAAGCGCACT
351	GCGTCAGTTT TATGAGCGGC AAATCCGCAT GATCAAATTG
	CAGCAGGTCA
401	GCTTCGCAAC CGAAGAGGAG GCGCGTCAGG CGCAGCAGCT
	CCTGCTCAAA
451	GGGCTGTCTT TTGAAGGGCT GATGAAGCGT TATCCGAACG
	ACGAGCAGGC
501	TTTTGACGGT TTCATTATGG CGCAGCAGCT TCCCGAGCCG
	CTGGCTTCGC
551	AGTTTGCAGC GATGAATCGG GGCGACGTTA CCCGCGATCC
	GGTCAAATTG
601	GGCGAACGCT ATTATCTGTT CAAACTCAGC GAGGTCGGGA
	AAAACCCCGA
651	CGCGCAGCCT TTCGAGTTGG TCAGAAACCA GTTGGAACAA
	GGTTTGAGAC
701	AGGAAAAAGC CCGCTTGAAA ATCGATGCCA TTTTGGAAGA
	AAACGGTGTC
751	AAACCGTAA

This encodes a protein having amino acid sequence <SEQ ID 300>:

1	MKQKKTAAAV IAAMLAGFAA AKAPEIDPAL VDTLVAQIMQ
	QADRHAEQSQ
51	KPDGQAIRND AVRRLQTLEV LKNRALKEGL DKDKDVQNRF
	KIAEASFYAE
101	EYVRFLERSE TVSESALRQF YERQIRMIKL QQVSFATEEE
	ARQAQQLLLK
151	GLSFEGLMKR YPNDEQAFDG FIMAQQLPEP LASQFAAMNR
	GDVTRDPVKL
201	GERYYLFKLS EVGKNPDAQP FELVRNQLEQ GLRQEKARLK
	IDAILEENGV
251	KP*

ORF76a and ORF76-1 show 97.6% identity in 252 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

The aligned aa sequences of ORF76 and a predicted ORF (ORF76.ng) from N. gonorrhoeae of the N- and C-termini show 96.7% and 100% identity in 30 and 31 overlap, respectively:

The complete length ORF76ng nucleotide sequence <SEQ ID 301> is:

1	ATGAAACAGA AAAAGACCGC TGCCGCAGTT ATTGCTGCAA
	TGTTGGCAGG
51	TTTTGCGGCA GCCAAAGCAC CCGAAATCGA CCCGGCTTTG
	GTGGATACGC
101	TGGTGGCGCA GATCATGCAG CAGGCAGACC GGCATGCGGA
	GCAGTCCCAA
151	AGACCGGACG GGCAGGCAAT CCGAAACGAT GCCGTCCGCC
	GGCTGCAAAC
201	TTTGGAAGTT TTGAAAAACA GGGCATTGAA GGAAGGTTTG
	GATAAGGATA
251	AGGATGTCCA AAACCGCTTT AAAATCGCCG AAGCGTCTTT
	TTATGCCGAG
301	GAGTACGTCC GTTTTCTGGA ACGTTCGGAA ACGGTTTCCG
	AAAGCGCACT
351	GCGTCAGTTT TATGAGCGGC AAATCCGCAT GATCAAATTG
	CAGCAGGTCA
401	GCTTCGCAAC CGAAGAGGAG GCGCGTCAGG CGCAGCAGCT
	CCTGCTCAAA
451	GGGCTGTCTT TTGAAGGGCT GATGAAGCGT TATCCGAACG
	ACGAGCAGGC
501	GTTCGACGGT TTCATTATGG CGCAGCAGCT TCCCGAGCCG
	CTGGCTTcgc
551	agtttgCCGG TATGAACCGT GGCGACGTTA CCCGCAATCC
	GGTCAAATTG
601	GGCGAACGCT ATTACCTGTT CAAACTCGGC GCGGTCGGGA
	AAAACCCCGA
651	CGCGCAGCCT TTCGAGTTGG TCAGAAACCA GTTGGAACAA
	GGTTTGAGGC
701	AGGAAAAAGC CCGCTTGAAA ATCGATGCCC TTTTGGAaga
	Aaacggtgtc
751	AaacCGTAA

This encodes a protein having amino acid sequence <SEQ ID 302>:

1	MKQKKTAAAV IAAMLAGFAA AKAPEIDPAL VDTLVAQIMQ
	QADRHAEQSQ
51	RPDGQAIRND AVRRLQTLEV LKNRALKEGL DKDKDVQNRF
	KIAEASFYAE
101	EYVRFLERSE TVSESALRQF YERQIRMIKL QQVSFATEEE
	ARQAQQLLLK
151	GLSFEGLMKR YPNDEQAFDG FIMAQQLPEP LASQFAGMNR
	GDVTRNPVKL
201	GERYYLFKLG AVGKNPDAQP FELVRNQLEQ GLRQEKARLK
	IDALLEENGV
251	KP*

ORF76ng and ORF76-1 show 96.0% identity in 252 aa overlap

Furthermore, ORF76ng shows significant homology to a B. subtilis export protein precursor:

sp|P24327|PRSA_BACSU PROTEIN EXPORT PROTEIN PRSA
PRECURSOR >gi|98227|pir||S15269 33K lipoprotein - Bacillus subtilis
>gi|39782 (X57271) 33 kDa lipoprotein [Bacillus subtilis]
>gi|2226124|gnl|PID|e325181 (Y14077) 33 kDa lipoprotein
[Bacillus subtilis]
>gi|2633331|gnl|PID|e1182997 (Z99109) molecular chaperonin
[Bacillus subtilis]
Length = 292
Score = 50.4 bits (118), Expect = 1e−05
Identities = 48/199 (24%), Positives = 82/199 (41%), Gaps = 32/199 (16%)

Query:	70	VLKNRALKEGLDK-----DKDVQNRFKIAEASF----------YAEEYVRFLERSETVSE	114
		VL     ++ LDK     DK++ N+ K  +             Y ++Y++   + E +++
Sbjct:	53	VLTQLVQEKVLDKKYKVSDKEIDNKLKEYKTQLGDQYTALEKQYGKDYLKEQVKYELLTQ	112
Query:	115	SA-----------LRQFYERQIRMIKLQQVSFATEEEARQAQQLLLKGLSFEGLMKRYPN	163
		A           +++++E     I+   +  A ++ A + ++ L KG  FE L K Y
Sbjct:	113	KAAKDNIKVTDADIKEYWEGLKGKIRASHILVADKKTAEEVEKKLKKGEKFEDLAKEYST	172
Query:	164	DEQAFDG-----FIMAQQLPEPLASQFAAMNRGDVTRDPVKLGERYYLFKLSEVGKNPDA	218
		D  A  G     F    Q+ E  +     +  G+V+ DPVK    Y++ K +E     D
Sbjct:	173	DSSASKGGDLGWFAKEGQMDETFSKAAFKLKTGEVS-DPVKTQYGYHIIKKTEERGKYDD	231
Query:	219	QPFELVRNQLEQGLRQEKA	237
		EL    LEQ L    A
Sbjct:	232	MKKELKSEVLEQKLNDNAA	250

Based on this analysis, including the presence of a putative leader sequence and a RGD motif in the gonococcal protein, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF76-1 (27.8 kDa) was cloned in the pET vector and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 10A shows the results of affinity purification of the His-fusion protein, Purified His-fusion protein was used to immunise mice, whose sera were used for Western blot (FIG. 10B), ELISA (positive result), and FACS analysis (FIG. 10C). These experiments confirm that ORF76-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 36

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 303>:

This corresponds to the amino acid sequence <SEQ ID 304; ORF81>:

Further work revealed the complete nucleotide sequence <SEQ ID 305>:

1	ATGAAAAAAT CTTTCCTTAC GCTTGTTCTG TATTCGTCTT
	TACTTACCGC
51	CAGCGAAATT GCCTATCGCT TTGTATTTGG GATTGAAACC
	TTACCGGCGG
101	CAAAAATTGC GGAAACGTTT GCGCTGACAT TTGTGATTGC
	TGCGCTGTAT
151	CTGTTTGCGC GTTATAAGGT GACGCGTTTG TTGATTGCGG
	TGTTTTTTGC
201	GTTCAGCATT ATTGCCAACA ATGTGCATTA CGCGGTTTAT
	CAAAGCTGGA
251	TGACGGGCAT CAATTATTGG CTGATGCTGA AAGAGGTTAC
	CGAAGTCGGC
301	AGCGCGGGTG CGTCGATGTT GGATAAGTTG TGGCTGCCTG
	TGTTGTGGGG
351	CGTGTTGGAA GTCATGTTGT TTTGCAGCCT TGCCAAGTTC
	CGCCGTAAGA
401	CGCATTTTTC TGCCGATATA CTGTTTGCCT TCCTAATGCT
	GATGATTTTC
451	GTGCGTTCGT TCGACACGAA ACAAGAGCAC GGTATTTCGC
	CCAAACCGAC
501	ATACAGCCGC ATCAAAGCCA ATTATTTCAG CTTCGGTTAT
	TTTGTCGGAC
551	GCGTGTTGCC GTATCAGTTG TTTGATTTAA GCAGGATTCC
	CGCCTTTAAG
601	CAGCCTGCTC CAAGCAAAAT CGGGCAGGGC AGTGTTCAAA
	ATATCGTCCT
651	GATTATGGGC GAAAGCGAAA GCGCGGCGCA TTTGAAGCTG
	TTTGGCTACG
701	GACGCGAAAC TTCGCCGTTT TTAACCCGGC TGTCGCAAGC
	CGATTTTAAG
751	CCGATTGTGA AACAAAGTTA TTCCGCAGGC TTTATGACTG
	CAGTGTCCCT
801	GCCCAGTTTT TTCAATGCGA TACCGCACGC CAACGGCTTG
	GAACAAATCA
851	GCGGCGGCGA TACCAATATG TTCCGCCTCG CCAAAGAGCA
	GGGCTATGAA
901	ACGTATTTTT ACAGCGCGCA GGCGGAAAAC GAGATGGCGA
	TTTTGAACTT
951	AATCGGTAAG AAATGGATAG ACCATCTGAT TCAGCCGACG
	CAACTTGGCT
1001	ACGGCAACGG CGACAATATG CCCGATGAGA AGCTGCTGCC
	GTTGTTCGAC
1051	AAAATCAATT TGCAGCAGGG CAAGCATTTT ATCGTGTTGC
	ACCAACGCGG
1101	TTCGCACGCC CCATACGGCG CATTGTTGCA GCCTCAAGAT
	AAAGTATTCG
1151	GCGAAGCCGA TATTGTGGAT AAGTACGACA ACACCATCCA
	CAAAACCGAC
1201	CAAATGATTC AAACCGTATT CGAGCAGCTG CAAAAGCAGC
	CTGACGGCAA
1251	CTGGCTGTTT GCCTATACCT CCGATCATGG CCAGTATGTT
	CGCCAAGATA
1301	TCTACAATCA AGGCACGGTG CAGCCCGACA GCTATCTCGT
	GCCGCTAGTG
1351	TTGTACAGCC CGGATAAGGC CGTGCAACAG GCTGCCAACC
	AGGCTTTTGC
1401	GCCTTGCGAG ATTGCCTTCC ATCAGCAGCT TTCAACGTTC
	CTGATTCACA
1451	CGTTGGGCTA CGATATGCCG GTTTCAGGTT GTCGCGAAGG
	CTCGGTAACG
1501	GGCAACCTGA TTACGGGTGA TGCAGGCAGC TTGAACATTC
	GCGACGGCAA
1551	GGCGGAATAT GTTTATCCGC AATGA

This corresponds to the amino acid sequence <SEQ ID 306; ORF81-1>:

1	MKKSFLTLVL YSSLLTASEI AYRFVFGIET LPAAKIAETF
	ALTFVIAALY
51	LFARYKVTRL LIAVFFAFSI IANNVHYAVY QSWMTGINYW
	LMLKEVTEVG
101	SAGASMLDKL WLPVLWGVLE VMLFCSLAKF RRKTHFSADI
	LFAFLMLMIF
151	VRSFDTKQEH GISPKPTYSR IKANYFSFGY FVGRVLPYQL
	FDLSRIPAFK
201	QPAPSKIGQG SVQNIVLIMG ESESAAHLKL FGYGRETSPF
	LTRLSQADFK
251	PIVKQSYSAG FMTAVSLPSF FNAIPHANGL EQISGGDTNM
	FRLAKEQGYE
301	TYFYSAQAEN EMAILNLIGK KWIDHLIQPT QLGYGNGDNM
	PDEKLLPLFD
351	KINLQQGKHF IVLHQRGSHA PYGALLQPQD KVFGEADIVD
	KYDNTIHKTD
401	QMIQTVFEQL QKQPDGNWLF AYTSDHGQYV RQDIYNQGTV
	QPDSYLVPLV
451	LYSPDKAVQQ AANQAFAPCE IAFHQQLSTF LIHTLGYDMP
	VSGCREGSVT
501	GNLITGDAGS LNIRDGKAEY VYPQ*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF81 shows 84.7% identity over a 85aa overlap and 99.2% identity over a 121aa overlap with an ORF (ORF81a) from strain A of N. meningitidis:

The complete length ORF81a nucleotide sequence <SEQ ID 307> is:

1	ATGAAAAAAT CCCTTTTCGT TCTCTTTCTG TATTCGTCCC
	TACTTACTGC
51	CAGCGAAATT GCTTATCGCT TTGTATTCGG AATTGAAACC
	TTACCGGCTG
101	CAAAAATGGC AGAAACGTTT GCGCTGACAT TTGTGATTGC
	TGCGCTGTAT
151	CTGTTTGCGC GTTATAAGGC AACGCGTTTG TTGATTGCGG
	TGTTTTTCGC
201	GTTCAGCATT ATTGCCAACA ATGTGCATTA CGCGGTTTAT
	CAAAGCTGGA
251	TAACGGGCAT TAATTATTGG CTGATGCTGA AAGAGATTAC
	CGAAGTTGGC
301	GGCGCAGGGG CGTCGATGTT GGATAAGTTG TGGCTGCCTG
	CGTTGTGGGG
351	CGTGTTGGAA GTCATGTTGT TTTGCAGCCT TGCCAAGTTC
	CGCCGTAAGA
401	CGCATTTTTC TGCCGATATA CTGTTTGCCT TCCTAATGCT
	GATGATTTTC
451	GTGCGTTCGT TCGACACGAA ACAAGAACAC GGTATTTCGC
	CCAAACCGAC
501	ATACAGCCGC ATCAAAGCCA ATTATTTCAG CTTCGGTTAT
	TTTGTCGGAC
551	GCGTGTTGCC GTATCAGTTG TTTGATTTAA GCAAGATTCC
	TGTGTTCAAA
601	CAGCCTGCTC CAAGCAGAAT CGGGCAAGGC AGTATTCAAA
	ATATCGTCCT
651	GATTATGGGC GAAAGCGAAA GCGCGGCGCA TTTGAAATTG
	TTTGGCTACG
701	GGCGCGAAAC TTCGCCGTTT TTGACCCAGC TTTCGCAAGC
	CGATTTTAAG
751	CCGATTGTGA AACAAAGTTA TTCCGCAGGC TTTATGACGG
	CAGTATCCCT
801	GCCCAGTTTC TTTAACGTCA TACCGCATGC CAACGGCTTG
	GAACAAATCA
851	GCGGCGGCGA TATTGTGGAT AAGTACGACA ACACCATCCA
	CAAAACCGAC
901	CAAATGATTC AAACCGTATT CGAGCAGCTG CAAAAGCAGC
	CTGACGGCAA
951	CTGGCTGTTT GCCTATACCT CCGATCATGG CCAGTATGTT
	CGCCAAGATA
1001	TCTACAATCA AGGCACGGTG CAGCCCGACA GCTATCTCGT
	GCCGCTGGTG
1051	TTGTACAGCC CGGATAAGGC CGTGCAACAG GCTGCCAACC
	AGGCTTTTGC
1101	GCCTTGCGAG ATTGCCTTCC ATCAGCAGCT TTCAACGTTC
	CTGATTCACA
1151	CGTTGGGCTA CGATATGCCG GTTTCAGGTT GTCGCGAAGG
	CTCGGTAACG
1201	GGCAACCTGA TTACGGGTGA TGCAGGCAGC TTGAACATTC
	GCGACGGCAA
1251	GGCGGAATAT GTTTATCCGC AATGA

This encodes a protein having amino acid sequence <SEQ ID 308>:

1	MKKSLFVLFL YSSLLTASEI AYRFVFGIET LPAAKMAETF
	ALTFVIAALY
51	LFARYKATRL LIAVFFAFSI IANNVHYAVY QSWITGINYW
	LMLKEITEVG
101	GAGASMLDKL WLPALWGVLE VMLFCSLAKF RRKTHFSADI
	LFAFLMLMIF
151	VRSFDTKQEH GISPKPTYSR IKANYFSFGY FVGRVLPYQL
	FDLSKIPVFK
201	QPAPSRIGQG SIQNIVLIMG ESESAAHLKL FGYGRETSPF
	LTQLSQADFK
251	PIVKQSYSAG FMTAVSLPSF FNVIPHANGL EQISGGDIVD
	KYDNTIHKTD
301	QMIQTVFEQL QKQPDGNWLF AYTSDHGQYV RQDIYNQGTV
	QPDSYLVPLV
351	LYSPDKAVQQ AANQAFAPCE IAFHQQLSTF LIHTLGYDMP
	VSGCREGSVT
401	GNLITGDAGS LNIRDGKAEY VYPQ*

ORF81a and ORF81-1 show 77.9% identity in 524 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

The aligned aa sequences of ORF81 and a predicted ORF (ORF81.ng) from N. gonorrhoeae of the N- and C-termini show 82.4% and 97.5% identity in 85 and 121 overlap, respectively:

The complete length ORF81ng nucleotide sequence <SEQ ID 309> is:

1	ATGAAAAAAT CCCTTTTCGT TCTCTTTCTG TATTCATCCC
	TACTTACCGC
51	CAGCGAAATC GCCTATCGCT TTGTATTCGG AATTGAAACC
	TTACCGGCTG
101	CAAAAATGGC GGAAACGTTT GCGCTGACAT TTATGATTGC
	TGCGCTGTAT
151	CTGTTTGCGC GTTATAAGGC TTCGCGGCTG CTGATTGCGG
	TGTTTTTCGC
201	GTTCAGCATG ATTGCCAACA ATGTGCATTA CGCGGTTTAT
	CAAAGCTGGA
251	TGACGGGTAT TAACTATTGG CTGATGCTGA AAGAGGTTAC
	CGAAGTCGGC
301	AGCGCGGGCG CGTCGATGTT GGATAAGTTG TGGCTGCCTG
	CTTTGTGGGG
351	CGTGGCGGAA GTCATGTTGT TTTGCAGCCT TGCCAAGTTC
	CGCCGTAAGA
401	CGCATTTTTC TGCCGATATA CTGTTTGCCT TCCTAATGCT
	GATGATTTTC
451	GTGCGTTCGT TCGACACGAA ACAAGAGCAC GGTATTTCGC
	CCAAACCGAC
501	ATACAGCCGC ATCAAAGCCA ATTATTTCAG CTTCGGTTAT
	TTTGTCGGGC
551	GCGTGTTGCC GTATCAGTTG TTTGATTTAA GCAAGATCCC
	TGTGTTCAAA
601	CAGCCTGCTC CAAGCAAAAT CGGGCAAGGC AGTATTCAAA
	ATATCGTCCT
651	GATTATGGGC GAAAGCGAAA GCGCGGCGCA TTTGAAATTG
	TTTGGTTACG
701	GGCGCGAAAC TTCGCCGTTT TTAACCCGGC TGTCGCAAGC
	CGATTTTAAG
751	CCGATTGTGA AACAAAGTTA TTCCGCAGGC TTTATGACGG
	CAGTATCCCT
801	GCCCAGTTTC TTTAACGTCA TACCGCACGC CAACGGCTTG
	GAACAAATCA
851	GCGGCGGCGA TACCAATATG TTCCGCCTCG CCAAAGAGCA
	GGGCTATGAA
901	ACGTATTTTT ACAGTGCCCA GGCTGAAAAC CAAATGGCAA
	TTTTGAACTT
951	AATCGGTAAG AAATGGATAG ACCATCTGAT TCAGCCGACG
	CAACTTGGCT
1001	ACGGCAACGG CGACAATATG CCCGATGAGA AGCTGCTGCC
	GTTGTTCGAC
1051	AAAATCAATT TGCAGCAGGG CAGGCATTTT ATCGTGTTGC
	ACCAACGCGG
1101	TTCGCACGCC CCATACGGCG CATTGTTGCA GCCTCAAGAT
	AAAGTATTCG
1151	GCGAAGCCGA TATTGTGGAT AAGTACGACA ACACCATCCA
	CAAAACCGAC
1201	CAAATGATTC AAACCGTATT CGAGCAGCTG CAAAAGCAGC
	CTGACGGCAA
1251	CTGGCTGTTT GCCTATACCT CCGATCATGG CCAGTATGTG
	CGCCAAGATA
1301	TCTACAATCA AGGCACGGTG CAGCCCGACA GCTATATTGT
	GCCTCTGGTT
1351	TTGTACAGCC CGGATAAGGC CGTGCAACAG GCTGCCAACC
	AGGCTTTTGC
1401	GCCTTGCGAG ATTGCCTTCC ATCAGCAGCT TTCAACGTTC
	CTGATTCACA
1451	CGTTGGGCTA CGATATGCCG GTTTCAGGTT GTCGCGAAGG
	CTCGGTAACA
1501	GGCAACCTGA TTACGGGCGA TGCAGGCAGC TTGAACATTC
	GCAACGGCAA
1551	GGCGGAATAT GTTTATCCGC AATAA

This encodes a protein having amino acid sequence <SEQ ID 310>:

1	MKKSLFVLFL YSSLLTASEI AYRFVFGIET LPAAKMAETF
	ALTFMIAALY
51	LFARYKASRL LIAVFFAFSM IANNVHYAVY QSWMTGINYW
	LMLKEVTEVG
101	SAGASMLDKL WLPALWGVAE VMLFCSLAKF RRKTHFSADI
	LFAFLMLMIF
151	VRSFDTKQEH GISPKPTYSR IKANYFSFGY FVGRVLPYQL
	FDLSKIPVFK
201	QPAPSKIGQG SIQNIVLIMG ESESAAHLKL FGYGRETSPF
	LTRLSQADFK
251	PIVKQSYSAG FMTAVSLPSF FNVIPHANGL EQISGGDTNM
	FRLAKEQGYE
301	TYFYSAQAEN QMAILNLIGK KWIDHLIQPT QLGYGNGDNM
	PDEKLLPLFD
351	KINLQQGRHF IVLHQRGSHA PYGALLQPQD KVFGEADIVD
	KYDNTIHKTD
401	QMIQTVFEQL QKQPDGNWLF AYTSDHGQYV RQDIYNQGTV
	QPDSYIVPLV
451	LYSPDKAVQQ AANQAFAPCE IAFHQQLSTF LIHTLGYDMP
	VSGCREGSVT
501	GNLITGDAGS LNIRNGKAEY VYPQ*

ORF81ng and ORF81-1 show 96.4% identity in 524 aa overlap:

Furthermore, ORF81ng shows significant homology to an E. coli OMP:

gi|1256380 (U50906) outer membrane adherence protein-associated
protein [E. coli] Length = 547
Score = 87.4 bits (213), Expect = 2e−16
Identities = 122/468 (26%), Positives = 198/468 (42%),
Gaps = 70/468 (14%)

Query:	25	VFGIETLPAAKMAETFA-LTFMIAALYLFARYKAS--RLLIAVFFAFSMIANNVHYAVYQ	81
		VFGI  L A+  A     L F +  + +  R  +   RLL+A  F   + A ++  ++Y
Sbjct:	29	VFGITNLVASSGAHMVQRLLFFVLTILVVKRISSLPLRLLVAAPFVL-LTAADMSISLY-	86
Query:	82	SWMT-------GINYWLMLKEVTEVGSAGASMLDKLWLPALWGVAEVMLFCSLAKFRRKT	134
		SW T       G    ++  +  EV    A ML  ++ P L   A + L       +
Sbjct:	87	SWCTFGTTFNDGFAISVLQSDPDEV----AKMLG-MYSPYLCAFAFLSLLFLAVIIKYDV	141
Query:	135	HFSADILFAFLMLMIFVRSF---------DTKQEHGISPKPTYSRIKAN--YFSFGYFVG	183
		+   L+L++   S          D K ++  SP    SR      +F+  YF
Sbjct:	142	SLPTKKVTGILLLIVISGSLFSACQFAYKDAKNKNAFSPYILASRFATYTPFFNLNYFAL	201
Query:	184	RVLPYQ--LFDLSKIPVFKQPAPSKIGQGSIQNIVLIMGESESAAHLKLFGYGRETSPFL	241
		+Q  L   + +P F+      +    I   VLI+GES    ++ L+GY R T+P +
Sbjct:	202	AAKEHQRLLSIANTVPYFQL----SVRDTGIDTYVLIVGESVRVDNMSLYGYTRSTTPQV	257
Query:	242	TRLSQADFKPIVKQSYSAGFMTAVSLP---SFFNVIPHANGLEQISGGDTNMFRLAKEQG	298
		+Q     +  Q+ S    TA+S+P   +  +V+ H      I     N+  +A + G
Sbjct:	258	E--AQRKQIKLFNQAISGAPYTALSVPLSLTADSVLSH-----DIHNYPDNIINMANQAG	310
Query:	299	YETYFYSAQA---ENQMAILNLIGKKWIDHLIQPTQLGYGNGDNMPDEKLLPLFDKINLQ	355
		++T++ S+Q+   +N  A+ ++         ++  +  Y  G    DE LLP   +   Q
Sbjct:	311	FQTFWLSSQSAFRQNGTAVTSI--------AMRAMETVYVRGF---DELLLPHLSQALQQ	359
Query:	356	--QGRHFIVLHQRGSHAPYGALLQPQDKVFGEADIVDK-YDNTIHKTDQMIQTVFEQLQK	412
		Q +  IVLH  GSH P  +       VF   D  D  YDN+IH TD ++  VFE L+
Sbjct:	360	NTQQKKLIVLHLNGSHEPACSAYPQSSAVFQPQDDQDACYDNSIHYTDSLLGQVFELLK-	418
Query:	413	QPDGNWLFAYTSDHG---QYVRQDIYNQG--TVQPDSYIVPL-VLYSP	454
		D      Y +DHG      ++++Y  G       +Y VP+ + YSP
Sbjct:	419	--DRRASVMYFADHGLERDPTKKNVYFHGGREASQQAYHVPMFIWYSP	464

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 37

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 311>:

1	...ACCCTGCTCC TCTTCATCCC CCTCGTCCTC ACAC.GTGCG
	GCACACTGAC
51	CGGCATACTC GCCCaCGGCG GCGGCAAACG CTTTGCCGTC
	GAACAAGAAC
101	TCGTCGCCGC ATCGTCCCGC GCCGCCGTCA AAGAAATGGA
	TTTGTCCGCC
151	yTAAAAGGAC GCAAAGCCGC CyTTTACGTC TCCGTTATGG
	GCGACCAAGG
201	TTCGGGCAAC ATAAGCGGCG GACGCTACTC TATCGACGCA
	CTGATACGCG
251	GCGGCTACCA CAACAACCCC GAAAGTGCCA CCCAATACAG
	CTACCCCGCC
301	TACGACACTA CCGCCACCAC CAAATCCGAC GCGCTCTCCA
	GCGTAACCAC
351	TTCCACATCG CTTTTGAACG CCCCCGCCGC CGyCyTGACG
	AAAAACAGCG
401	GACGCAAAGG CGAACGcTCC GCCGGACTGT CCGTCAACGG
	CACGGGCGAC
451	TACCGCAACG AAACCCTGCT CGCCAACCCC CGCGACGTTT
	CCTTCCTGAC
501	CAACCTCATC CAAACCGTCT TCTACCTGCG CGGCATCGAA
	GTCgTACCGC
551	CCGrATACGC CGACACCGAC GTATTCGTAA CCGTCGACGT
	A...

This corresponds to the amino acid sequence <SEQ ID 312; ORF83>:

1	..TLLLFIPLVL TXCGTLTGIL AHGGGKRFAV EQELVAASSR
	AAVKEMDLSA
51	LKGRKAAXYV SVMGDQGSGN ISGGRYSIDA LIRGGYHNNP
	ESATQYSYPA
101	YDTTATTKSD ALSSVTTSTS LLNAPAAXLT KNSGRKGERS
	AGLSVNGTGD
151	YRNETLLANP RDVSFLTNLI QTVFYLRGIE VVPPXYADTD
	VFVTVDV..

Further work revealed the complete nucleotide sequence <SEQ ID 313>:

1	ATGAAAACCC TGCTCCTCCT CATCCCCCTC GTCCTCACAG
	CCTGCGGCAC
51	ACTGACCGGC ATACCCGCCC ACGGCGGCGG CAAACGCTTT
	GCCGTCGAAC
101	AAGAACTCGT CGCCGCATCG TCCCGCGCCG CCGTCAAAGA
	AATGGATTTG
151	TCCGCCCTAA AAGGACGCAA AGCCGCCCTT TACGTCTCCG
	TTATGGGCGA
201	CCAAGGTTCG GGCAACATAA GCGGCGGACG CTACTCTATC
	GACGCACTGA
251	TACGCGGCGG CTACCACAAC AACCCCGAAA GTGCCACCCA
	ATACAGCTAC
301	CCCGCCTACG ACACTACCGC CACCACCAAA TCCGACGCGC
	TCTCCAGCGT
351	AACCACTTCC ACATCGCTTT TGAACGCCCC CGCCGCCGCC
	CTGACGAAAA
401	ACAGCGGACG CAAAGGCGAA CGCTCCGCCG GACTGTCCGT
	CAACGGCACG
451	GGCGACTACC GCAACGAAAC CCTGCTCGCC AACCCCCGCG
	ACGTTTCCTT
501	CCTGACCAAC CTCATCCAAA CCGTCTTCTA CCTGCGCGGC
	ATCGAAGTCG
551	TACCGCCCGA ATACGCCGAC ACCGACGTAT TCGTAACCGT
	CGACGTATTC
601	GGCACCGTCC GCAGCCGTAC CGAACTGCAC CTCTACAACG
	CCGAAACCCT
651	TAAAGCCCAA ACCAAGCTCG AATATTTCGC CGTTGACCGC
	GACAGCCGGA
701	AACTGCTGAT TACCCCTAAA ACCGCCGCCT ACGAATCCCA
	ATACCAAGAA
751	CAATACGCCC TTTGGACCGG CCCTTACAAA GTCAGCAAAA
	CCGTCAAAGC
801	CTCAGACCGC CTGATGGTCG ATTTCTCCGA CATTACCCCC
	TACGGCGACA
851	CAACCGCCCA AAACCGTCCC GACTTCAAAC AAAACAACGG
	TAAAAAACCC
901	GATGTCGGCA ACGAAGTCAT CCGCCGCCGC AAAGGAGGAT
	AA

This corresponds to the amino acid sequence <SEQ ID 314; ORF83-1>:

1	MKTLLLLIPL VLTACGTLTG IPAHGGGKRF AVEQELVAAS
	SRAAVKEMDL
51	SALKGRKAAL YVSVMGDQGS GNISGGRYSI DALIRGGYHN
	NPESATQYSY
101	PAYDTTATTK SDALSSVTTS TSLLNAPAAA LTKNSGRKGE
	RSAGLSVNGT
151	GDYRNETLLA NPRDVSFLTN LIQTVFYLRG IEVVPPEYAD
	TDVFVTVDVF
201	GTVRSRTELH LYNAETLKAQ TKLEYFAVDR DSRKLLITPK
	TAAYESQYQE
251	QYALWTGPYK VSKTVKASDR LMVDFSDITP YGDTTAQNRP
	DFKQNNGKKP
301	DVGNEVIRRR KGG*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF83 shows 96.4% identity over a 197aa overlap with an ORF (ORF83a) from strain A of N. meningitidis:

The complete length ORF83a nucleotide sequence <SEQ ID 315> is:

1	ATGAAAACCC TGCTCNTCCT CATCCCCCTC GTCCTCACAG
	CCTGCGGCAC
51	ACTGACCGGC ATACCCGCCC ACGGCGGCGG CAAACGCTTT
	GCCGTCGAAC
101	AAGAACTCGT CGCCGCATCG TCCCGCGCCG CCGTCAAAGA
	AATGGACTTG
151	TCCGCCCTGA AAGGACGCAA AGCCGCCCTT TACGTCTCCG
	TTATGGGCGA
201	CCAAGGTTCG GGCAACATAA GCGGCGGACG CTACTCTATC
	GACGCACTGA
251	TACGCGGCGG CTACCACAAC AACCCCGAAA GTGCCACCCA
	ATACAGCTAC
301	CCCGCCTACG ACACTACCGC CACCACCAAA TCCGACGCGC
	TCTCCAGCGT
351	AACCACTTCC ACATCGCTTT TGAACGCCCC CGCCGCCGCC
	CTGACGAAAA
401	ACAGCGGACG CAAAGGCGAA CGCTCCGCCG GACTGTCCGT
	CAACGGCACG
451	GGCGACTACC GCAACGAAAC CCTGCTCGCC AACCCCCGCG
	ACGTTTCCTT
501	CCTGACCAAC CTCATCCAAA CCGTCTTCTA CCTGCGCGGC
	ATCGAAGTCG
551	TACCGCCCGA ATACGCCGAC ACCGACGTAT TCGTAACCGT
	CGACGTATTC
601	GGCACCGTCC GCAGCCGCAC CGAACTGCAC CTCTACAACG
	CCGAAACCCT
651	TAAAGCCCAA ACCAAGCTCG AATATTTCGC CGTTGACCGC
	GACAGCCGGA
701	AACTGCTGAT TGCCCCTAAA ACCGCCGCCT ACGAATCCCA
	ATACCAAGAA
751	CAATACGCCC TCTGGATGGG ACCTTACAGC GTCGGCAAAA
	CCGTCAAAGC
801	CTCAGACCGC CTGATGGTCG ATTTCTCCGA CATCACCCCC
	TACGGCGACA
851	CAACCGCCCA AAACCGTCCC GACTTCAAAC AAAACAACGG
	TAAAAAACCC
901	GATGTCGGCA ACGAAGTCAT CCGCCGCCGC AAAGGAGGAT
	AA

This encodes a protein having amino acid sequence <SEQ ID 316>:

1	MKTLLXLIPL VLTACGTLTG IPAHGGGKRF AVEQELVAAS
	SRAAVKEMDL
51	SALKGRKAAL YVSVMGDQGS GNISGGRYSI DALIRGGYHN
	NPESATQYSY
101	PAYDTTATTK SDALSSVTTS TSLLNAPAAA LTKNSGRKGE
	RSAGLSVNGT
151	GDYRNETLLA NPRDVSFLTN LIQTVFYLRG IEVVPPEYAD
	TDVFVTVDVF
201	GTVRSRTELH LYNAETLKAQ TKLEYFAVDR DSRKLLIAPK
	TAAYESQYQE
251	QYALWMGPYS VGKTVKASDR LMVDFSDITP YGDTTAQNRP
	DFKQNNGKKP
301	DVGNEVIRRR KGG*

ORF83a and ORF83-1 show 98.4% identity in 313 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF83 shows 94.9% identity over a 197aa overlap with a predicted ORF (ORF83.ng) from N. gonorrhoeae:

The complete length ORF83ng nucleotide sequence <SEQ ID 317> is:

1	ATGAAAACCC TGCTCCTCCT CATCCCCCTC GTACTCACCG
	CCTGCGGCAC
51	ACTGACCGGC ATACCCGCCC ACGGCGGCGG CAAACGCTTT
	GCCGTCGAAC
101	AGGAACTCGT CGCCGCATCG TCCCGCGCCG CCGTCAAAGA
	AATGGACTTG
151	TCCGCCCTGA AAGGACGCAA AGCCGCCCTT TACGTCTCCG
	TTATGGGCGA
201	CCAAGGTTCG GGCAACATAA GCGGCGGACG CTACTCCATC
	GACGCACTGA
251	TACGCGGCGG CTACCACAAC AACCCCGACA GCGCCACCCG
	ATACAGCTAC
301	CCCGCCTATG ACACTACCGC CACCACCAAA TCCGACGCGC
	TCTCCGGCGT
351	AACCACTTCC ACATCGCTTT TGAACGCCCC CGCCGCCGCC
	CTGACGAAAA
401	ACAACGGACG CAAAGGCGAA CGCTCCGCCG GACTGTCCGT
	CAACGGCACG
451	GGCGACTACC GCAACGAAAC CCTGCTCGCC AACCCCCGCG
	ACGTTTCCTT
501	CCTGACCAAC CTCATCCAAA CCGTCTTCTA CCTGCGCGGC
	ATCGAAGTCG
551	TACCGCCCGA ATACGCCGAC ACCGACGTAT TCGTAACCGT
	CGACGTATTC
601	GGCACCGTCC GCAGCCGTAC CGAACTGCAC CTCTACAACG
	CCGAAACCCT
651	TAAAGCCCAA ACCAAGCTCG AATATTTCGC CGTCGACCGC
	GACAGCCGGA
701	AACTGCTGAT TGCCCCTAAA ACCGCCGCCT ACGAATCCCA
	ATACCAAGAA
751	CAATACGCCC TCTGGATGGG ACCTTACAGC GTCGGCAAAA
	CCGTCAAAGC
801	CTCAGACCGC CTGATGGTCG ATTTCTCCGA CATCACCCCC
	TACGGCGACA
851	CAACCGCCCA AAACCGTCCC GACTTCAAAC AAAACAACGG
	TAAAAACCCC
901	GATGTCGGCA ACGAAGTCAT CCGCCGCCGC AAAGGAGGAT
	AA

This encodes a protein having amino acid sequence <SEQ ID 318>:

1	MKTLLLLIPL VLTACGTLTG IPAHGGGKRF AVEQELVAAS
	SRAAVKEMDL
51	SALKGRKAAL YVSVMGDQGS GNISGGRYSI DALIRGGYHN
	NPDSATRYSY
101	PAYDTTATTK SDALSGVTTS TSLLNAPAAA LTKNNGRKGE
	RSAGLSVNGT
151	GDYRNETLLA NPRDVSFLTN LIQTVFYLRG IEVVPPEYAD
	TDVFVTVDVF
201	GTVRSRTELH LYNAETLKAQ TKLEYFAVDR DSRKLLIAPK
	TAAYESQYQE
251	QYALWMGPYS VGKTVKASDR LMVDFSDITP YGDTTAQNRP
	DFKQNNGKNP
301	DVGNEVIRRR KGG*

ORF83ng and ORF83-1 show 97.1% identity in 313 aa overlap

Based on this analysis, including the presence of a putative ATP/GTP-binding site motif A (P-loop) in the gonococcal protein (double-underlined) and a putative prokaryotic membrane lipoprotein lipid attachment site (single-underlined), it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 38

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 319>:

1	ATGGCAGAGA TCTGTTTGAT AACCGGCACG CCCGGTTCAG
	GGAAAACATT
51	AAAAATGGTT TCCATGATGG CGAATGATGA AATGTTTAAG
	CCTGATGAAA
101	AAGCCATACG CCGTAAAGTA TTTACGAACA TAAAAGGCTT
	GAAAATACCG
151	CACACCTACA TAGAAACGGA CGCAAAAAAG CTGCCGAAAT
	CGACAGATGA
201	GCAGCTTTCG GCGCATGATA TGTACGAATG GATAAAGAAG
	CCCGAAAATA
251	TCGGGTCTAT TGTCATTGTA GATGAAGCTC AAGACGTATG
	GCCGGCACGC
301	TCGGCAGGTT CAAAAATCCC TGAAAATGTC CAATGGCTGA
	ATACGCACAG
351	ACATCAGGGC ATTGATATAT TTGTTTTGAC TCAAGGTCCT
	AAGCTTCTAG
401	ATCAAAATCT TAGAACGCTT GTACGGAAAC ATTACCACAT
	CGCTTCAAAC
451	AAGATGGGTA TGCGTACGCT TTTAGAATGG AAAATATGCG
	CGGACGATCC
501	CGTAAAAATG GCATCAAGCG CATTCTCCAG TATCTATACA
	CTGGATAAAA
551	AAGTTTATGA CTTGTAysrr TmmGCGGAAG TTCATACCGT
	AAATAAGGTC
601	AAGCGGTCAA AGTGGTTTTA CACTCTGCCa GTAATAGTAT
	TGCTGATTCC
651	CGTGTTTGTC GGCCTGTCCT ATAAAATGTT GagCaGTTAC
	GGAAAAAAAC
701	aGGAAGAACC CGCAGCACAA GAATCGGCGG CAACAGAACA
	GCAGGCAGTA
751	CTTCCGGATA AAACAGAAGG CGAGCCGGTA AATAACGGCA
	ACCTTACCGC
801	AGATATGTTT GTTCCGACAT TGTCCGAaAA ACCCGrAAGC
	AAGCcgaTTT
851	ATAACGGTGT AAGGCAGGTA AGAACCTTTG AATATATAGC
	AGGCTGTATA
901	GAAGGCGGAA GAACCGGATG CGCCTGCTAT TCGCaTCAAG
	GGACGGCATt
951	gaAAGAAGTG ACGGaGTTGA TGTGccaAgG aCTATGTaAA
	AAacGGCTTG
1001	CCGTTTAACC CaTACAAAGA AGAAAGCCAA GGGCAGGAAG
	TTCAGCAAAG
1051	CGCGCAgCAA CATTCGGACA GGGCGcCAAG TTGCCACATT
	GGGCGGAAAA
1101	CCGTAGCAGA ACCTAATGTA CGATAATTGG GAAGAACGCG
	GGAAACCGTT
1151	TGAAGGAATC GGaCGQGGGC GTGGTCGGAT CGGCAAACTG
	A

This corresponds to the amino acid sequence <SEQ ID 320; ORF84>:

1	MAEICLITGT PGSGKTLKMV SMMANDEMFK PDEKAIRRKV
	FTNIKGLKIP
51	HTYIETDAKK LPKSTDEQLS AHDMYEWIKK PENIGSIVIV
	DEAQDVWPAR
101	SAGSKIPENV QWLNTHRHQG IDIFVLTQGP KLLDQNLRTL
	VRKHYHIASN
151	KMGMRTLLEW KICADDPVKM ASSAFSSIYT LDKKVYDLYX
	XAEVHTVNKV
201	KRSKWFYTLP VIVLLIPVFV GLSYKMLSSY GKKQEEPAAQ
	ESAATEQQAV
251	LPDKTEGEPV NNGNLTADMF VPTLSEKPXS KPIYNGVRQV
	RTFEYIAGCI
301	EGGRTGCACY SHQGTALKEV TELMCKDYVK NGLPFNPYKE
	ESQGQEVQQS
351	AQQHSDRAQV ATLGGKPXQN LMYDNWEERG KPFEGIGGGV
	VGSAN*

Further work revealed the complete nucleotide sequence <SEQ ID 321>:

1	ATGGCAGAGA TCTGTTTGAT AACCGGCACG CCCGGTTCAG
	GGAAAACATT
51	AAAAATGGTT TCCATGATGG CGAATGATGA AATGTTTAAG
	CCTGATGAAA
101	ACGGCATACG CCGTAAAGTA TTTACGAACA TAAAAGGCTT
	GAAAATACCG
151	CACACCTACA TAGAAACGGA CGCAAAAAAG CTGCCGAAAT
	CGACAGATGA
201	GCAGCTTTCG GCGCATGATA TGTACGAATG GATAAAGAAG
	CCCGAAAATA
251	TCGGGTCTAT TGTCATTGTA GATGAAGCTC AAGACGTATG
	GCCGGCACGC
301	TCGGCAGGTT CAAAAATCCC TGAAAATGTC CAATGGCTGA
	ATACGCACAG
351	ACATCAGGGC ATTGATATAT TTGTTTTGAC TCAAGGTCCT
	AAGCTTCTAG
401	ATCAAAATCT TAGAACGCTT GTACGGAAAC ATTACCACAT
	CGCTTCAAAC
451	AAGATGGGTA TGCGTACGCT TTTAGAATGG AAAATATGCG
	CGGACGATCC
501	CGTAAAAATG GCATCAAGCG CATTCTCCAG TATCTATACA
	CTGGATAAAA
551	AAGTTTATGA CTTGTACGAA TCAGCGGAAG TTCATACCGT
	AAATAAGGTC
601	AAGCGGTCAA AGTGGTTTTA CACTCTGCCA GTAATAGTAT
	TGCTGATTCC
651	CGTGTTTGTC GGCCTGTCCT ATAAAATGTT GAGCAGTTAC
	GGAAAAAAAC
701	AGGAAGAACC CGCAGCACAA GAATCGGCGG CAACAGAACA
	GCAGGCAGTA
751	CTTCCGGATA AAACAGAAGG CGAGCCGGTA AATAACGGCA
	ACCTTACCGC
801	AGATATGTTT GTTCCGACAT TGTCCGAAAA ACCCGAAAGC
	AAGCCGATTT
851	ATAACGGTGT AAGGCAGGTA AGAACCTTTG AATATATAGC
	AGGCTGTATA
901	GAAGGCGGAA GAACCGGATG CGCCTGCTAT TCGCATCAAG
	GGACGGCATT
951	GAAAGAAGTG ACGGAGTTGA TGTGCAAGGA CTATGTAAAA
	AACGGCTTGC
1001	CGTTTAACCC ATACAAAGAA GAAAGCCAAG GGCAGGAAGT
	TCAGCAAAGC
1051	GCGCAGCAAC ATTCGGACAG GGCGCAAGTT GCCACATTGG
	GCGGAAAACC
1101	GTAGCAGAAC CTAATGTACG ATAATTGGGA AGAACGCGGG
	AAACCGTTTG
1151	AAGGAATCGG CGGGGGCGTG GTCGGATCGG CAAACTGA

This corresponds to the amino acid sequence <SEQ ID 322; ORF84-1>:

1	MAEICLITGT PGSGKTLKMV SMMANDEMFK PDENGIRRKV
	FTNIKGLKIP
51	HTYIETDAKK LPKSTDEQLS AHDMYEWIKK PENIGSIVIV
	DEAQDVWPAR
101	SAGSKIPENV QWLNTHRHQG IDIFVLTQGP KLLDQNLRTL
	VRKHYHIASN
151	KMGMRTLLEW KICADDPVKM ASSAFSSIYT LDKKVYDLYE
	SAEVHTVNKV
201	KRSKWFYTLP VIVLLIPVFV GLSYKMLSSY GKKQEEPAAQ
	ESAATEQQAV
251	LPDKTEGEPV NNGNLTADMF VPTLSEKPES KPIYNGVRQV
	RTFEYIAGCI
301	EGGRTGCACY SHQGTALKEV TELMCKDYVK NGLPFNPYKE
	ESQGQEVQQS
351	AQQHSDRAQV ATLGGKP*QN LMYDNWEERG KPFEGIGGGV
	VGSAN*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF84 shows 93.9% identity over a 395aa overlap with an ORF (ORF84a) from strain A of N. meningitidis:

The complete length ORF84a nucleotide sequence <SEQ ID 323> is:

1	ATGGCAGAGA TCTGTTTGAT AACCGGCACG CCCGGTTCAG
	GGAAAACATT
51	AAAAATGGTT TCCATGATGG CAAACGATGA AATGTTTAAG
	CCGGATGAAA
101	ACGGCATACG CCGTAAAGTA TTTACGAACA TCAAAGGCTT
	GAAGATACCG
151	CACACCTACA TAGAAACGGA CGCGAAAAAG CTGCCGAAAT
	CGACAGATGA
201	GCAGCTTTCG GCGCATGATA TGTACGAATG GATAAAGAAG
	CCCGAAAATA
251	TCGGGTCTAT TGTCATTGTA GATGAAGCTC AAGACGTATG
	GCCGGCACGC
301	TCGGCAGGTT CAAAAATCCC TGAAAATGTC CAATGGCTGA
	ATACGCACAG
351	ACATCAGGGC ATTGATATAT TTGTTTTGAC TCAAGGCTCT
	AAGCTTCTAG
401	ATCAAAATCT TAGAACGCTT GTACGGAAAC ATTACCACAT
	CGCTTCAAAC
451	AAGATGGGTA TGCGTACGCT TTTAGAATGG AAAATATGCG
	CGGACGATCC
501	CGTAAAAATG GCATCAAGCG CATTCTCCAG TATCTATACA
	CTGGATAAAA
551	AAGTTTATGA CTTGTACGAA TCAGCGGAAG TTCATACCGT
	AAATAAGGTC
601	AAGCGGTCAA AATGGTTTTA TACTCTGCCA GTAATAATAT
	TGCTGATTCC
651	CGTTTTTGTC GGCCTGTCCT ATAAAATGTT AAGTAGTTAT
	GGAAAAAAAC
701	AGGAAGAACC CGCAGCACAA GAATCGGCGG CAACAGAACA
	TCAGGCAGTA
751	TTTCAGGATA AAACAGAAGG CGAGCCGGTA AACAACGGTA
	ACCTTACCGC
801	AGATATGTTT GTTCCGACAT TGTCCGAAAA ACCCGAAAGC
	AAGCCGATTT
851	ATAACGGTGT AAGGCAGGTA AGAACCTTTG AATATATAGC
	AGGCTGTGTA
901	GAAGGCGGAA GAACCGGATG CACATGCTAT TCGCATCAAG
	GGACGGCATT
951	GAAAGAAATT ACAAAGGAAA TGTGCAAGGA TTACGCAAGA
	AACGGATTGC
1001	CGTTTAACCC ATATAAAGAA GAAAGCCAAG GGCGGGATGT
	CCAGCAAAGT
1051	GAGCAGCACC ATTCGGACAG ACCGCAAGTT GCCACGTTGG
	GCGGAAAGCC
1101	GTGGCAAAAT CTTATGTATG ATAATTGGCA GGAGCGCGGA
	AAACCGTTTG
1151	AAGGAATCGG CGGGGGCGTG GTCGGATCGG CAAACTGA

This encodes a protein having amino acid sequence <SEQ ID 324>:

1	MAEICLITGT PGSGKTLKMV SMMANDEMFK PDENGIRRKV
	FTNIKGLKIP
51	HTYIETDAKK LPKSTDEQLS AHDMYEWIKK PENIGSIVIV
	DEAQDVWPAR
101	SAGSKIPENV QWLNTHRHQG IDIFVLTQGS KLLDQNLRTL
	VRKHYHIASN
151	KMGMRTLLEW KICADDPVKM ASSAFSSIYT LDKKVYDLYE
	SAEVHTVNKV
201	KRSKWFYTLP VIILLIPVFV GLSYKMLSSY GKKQEEPAAQ
	ESAATEHQAV
251	FQDKTEGEPV NNGNLTADMF VPTLSEKPES KPIYNGVRQV
	RTFEYIAGCV
301	EGGRTGCTCY SHQGTALKEI TKEMCKDYAR NGLPFNPYKE
	ESQGRDVQQS
351	EQHHSDRPQV ATLGGKPWQN LMYDNWQERG KPFEGIGGGV
	VGSAN*

ORF84a and ORF84-1 show 95.2% identity in 395 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF84 shows 94.2% identity over a 395aa overlap with a predicted ORF (ORF84.ng) from N. gonorrhoeae:

The complete length ORF84ng nucleotide sequence <SEQ ID 325> is:

1	ATGGCAGAAA TCTGTTTGAT AACCGGCACG CCCGGTTCAG
	GGAAAACATT
51	AAAAATGGTT TCCATGATGG CAAACGATGA AATGTTTAAG
	CCAGATGAAA
101	ACGGCGTACG CCGTAAAGTA TTTACGAACA TCAAAGGTTT
	GAAGATACCG
151	CACACCCACA TAGAAACAGA CGCAAAGAAG CTGCCGAAAT
	CAACCGATGA
201	ACAGCTTTCG GCGCATGATA TGTATGAATG GATCAAGAAG
	CCTGAAAacg
251	tcggcgCAAT CGTTATTGTC GATGAGGCGC AAGACGTATG
	GCCCGCACGC
301	TccgCAGGTT CGAAAATCCC CGAAAACGTC CAATGGCTGA
	ACACACACAG
351	GCATCAGGGC ATAGATATAT TTGTATTGAC ACAAGGTCCT
	AAACTCTTAG
401	ATCAGAACTT GCGAACATTG GTTAAAAGAC ATTACCACAT
	TGCGGCCAAC
451	AAAATGGGTT TGCGTACCCT GCTTGAATGG AAAGTATGCG
	CGGATGACCC
501	GGTAAAAATG GCATCAAGTG CATTTTCCAG TATCTACACA
	CTGGATAAAA
551	AAGTTTATGA CTTGTACGAA TCCGCAGAAA TTCACACGGT
	AAACAAAGTC
601	AAGCGTTCAA AATGGTTTTA TGCATTGCCC GTCATCATAT
	TATTGATTCC
651	GCTATTTGTC GGTTTGTCTT ACAAAATGTT GGGCAGTTAC
	GGAAAAAAAC
701	AGGAAGAACC CGCAGCACAA GAATCGGCGG CAACAGAACA
	GCAGGCAGTA
751	CTTCCGGATA AAACAGAAGG AGAATCGGTG AATAACGGAA
	ACCTTACGGC
801	AGATATGTTT GTTCCGACAT TGCCCGAAAA ACCCGAAAGC
	AAGCCGATTT
851	ATAACGGTGT AAGGCAGGTA AGGACCTTTG AATATATAGC
	AGGCTGTATA
901	GAAGGCGGAA GAACCGGATG CACCTGCTAT TCGCATCAAG
	GGACGGCATT
951	GAAAGAAGTG ACGGAGTTGA TGTGCAAGGA CTATGTAAAA
	AACGGCTTGC
1001	CGTTTAACCC ATACAAAGAA GAAAGCCAAG GGCAGGAAGT
	TCAGCAAAGC
1051	GCGCAGCAAC ATTCGGACAG GGCGCAAGTT GCCACCTTGG
	GCGGAAAACC
1101	GCAGCAGAAC CTAATGTACG ACAATTGGGA AGAACGCGGG
	AAACCGTTTG
1151	AAGGAATCGG CGGGGGCGTG GTCGGATCGG CAAACTGA

This encodes a protein having amino acid sequence <SEQ ID 326>:

1	MAEICLITGT PGSGKTLKMV SMMANDEMFK PDENGVRRKV
	FTNIKGLKIP
51	HTHIETDAKK LPKSTDEQLS AHDMYEWIKK PENVGAIVIV
	DEAQDVWPAR
101	SAGSKIPENV QWLNTHRHQG IDIFVLTQGP KLLDQNLRTL
	VKRHYHIAAN
151	KMGLRTLLEW KVCADDPVKM ASSAFSSIYT LDKKVYDLYE
	SAEIHTVNKV
201	KRSKWFYALP VIILLIPLFV GLSYKMLGSY GKKQEEPAAQ
	ESAATEQQAV
251	LPDKTEGESV NNGNLTADMF VPTLPEKPES KPIYNGVRQV
	RTFEYIAGCI
301	EGGRTGCTCY SHQGTALKEV TELMCKDYVK NGLPFNPYKE
	ESQGQEVQQS
351	AQQHSDRAQV ATLGGKPQQN LMYDNWEERG KPFEGIGGGV
	VGSAN*

ORF84ng and ORF84-1 show 95.4% identity in 395 aa overlap:

Based on this analysis, includng the presence of a putative transmembrane domain (single-underlined) in the gonococcal protein, and a putative ATP/GTP-binding site motif A (P-loop, double-underlined), it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 39

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 327>:

1	GTGGTTTTCC TGAATGCCGA CAACGGGATA TTGGTTCAGG
	ACTTGCCTTT
51	TGAAGTCAAA CTGAAAAAAT TCCATATCGA TTTTTACAAT
	ACGGGTATGC
101	CGCGTGATTT CGCCAGCGAT ATTGAAGTGA CGGACAAGGC
	AACCGGTGAG
151	AAACTCGAGC GCACCATCCG CGTGAACCAT CCTTTGACCT
	TGCACGGCAT
201	CACGATTTAT CAGGCGAGTT TTGCCGACGG CGGTTCGGAT
	TTGACATTCA
251	AGGCGTGGAA TTTGGGTGAT GCTTCGCGCG AGCCTGTCGT
	GTTGAAGGCA
301	ACATCCATAC ACCAGTTTCC GTTGGAAATT GGCAAACACA
	AATATCGTCT
351	TGAGTTCGAT CAGTTCACTT CTATGAATGT GGAGGACATG
	AGCGAGGGCG
401	CGGAACGGGA AAAAAGCCTG AAATCCACGC TGCCCGATGT
	CCGCGCCGTT
451	ACTCAGGAAG GTCACAAATA CACCAAT... ..........
	.....TACCG
501	TATCCGTGAT GCGCCAGGCC AGGCGGTCGA ATATAAAAAC
	TATATGCTGC
551	CGGTTTTGCA GGAACAGGAT TATTTTTGGA TTACCGGCAC
	GCGCAGCGC.
601	TTGCAGCAGC AATACCGCTG GCTGCGTATC CCCTTGGACA
	AGCAGTTGAA
651	AGCGGACACC TTTATGGCAT TGCGTGAGTT TTTGAAAGAT
	GGGGAAGGGC
701	GCAAACGTCT .GTTGCCGAC GCAACCAAAG GCGCACCTGC
	CGAAATCCGC
751	GAACAATTCA TGCTGGCTGC GGAAAACACG CTGAACATCT
	TTGCACAAAA
801	AGGCTATTTG GGATTGGACG AATTTATTAC GTCCAATATC
	CCGAAAGAGC
851	AGCAGGATAA GATGCAGGGC TATTTCTACG AAATGCTTTA
	CGGCGTGATG
901	AACGCTGCTT TGGATGAAAC CAT.ACCCGG TACGGCTTGC
	CCGAATGGCA
951	GCAGGATGAA GCGCGGAATC GTTTCCTGCT GCACAGTATG
	GATGCGTACA
1001	CGGGTTTGAC CGAATATCCC GCGCCTATGC TGCTGCAACT
	TGATGGGTTT
1051	TCCGAGGTGC GTTCGTCGGG TTTGCAGATG ACCCGTTCCC
	C.GGTCCGCT
1101	TTTGGTCTAT CTC...

This corresponds to the amino acid sequence <SEQ ID 328; ORF88>:

1	MVFLNADNGI LVQDLPFEVK LKKFHIDFYN TGMPRDFASD
	IEVTDKATGE
51	KLERTIRVNH PLTLHGITIY QASFADGGSD LTFKAWNLGD
	ASREPVVLKA
101	TSIHQFPLEI GKHKYRLEFD QFTSMNVEDM SEGAEREKSL
	KSTLPDVRAV
151	TQEGHKYTNX XXXXXYRIRD APGQAVEYKN YMLPVLQEQD
	YFWITGTRSX
201	LQQQYRWLRI PLDKQLKADT FMALREFLKD GEGRKRXVAD
	ATKGAPAEIR
251	EQFMLAAENT LNIFAQKGYL GLDEFITSNI PKEQQDKMQG
	YFYEMLYGVM
301	NAALDETXTR YGLPEWQQDE ARNRFLLHSM DAYTGLTEYP
	APMLLQLDGF
351	SEVRSSGLQM TRSXGPLLVY L...

Further work revealed the complete nucleotide sequence <SEQ ID 329>:

1	ATGAGTAAAT CCCGTAGATC TCCCCCACTT CTTTCCCGTC
	CGTGGTTCGC
51	TTTTTTCAGC TCCATGCGCT TTGCAGTCGC TTTGCTCAGT
	CTGCTGGGTA
101	TTGCATCGGT TATCGGTACG GTGTTGCAGC AAAACCAGCC
	GCAGACGGAT
151	TATTTGGTCA AATTCGGATC GTTTTGGGCG CAGATTTTTG
	GTTTTCTGGG
201	ACTGTATGAC GTCTATGCTT CGGCATGGTT TGTCGTTATC
	ATGATGTTTT
251	TGGTGGTTTC TACCAGTTTG TGCCTGATTC GCAATGTGCC
	GCCGTTCTGG
301	CGCGAAATGA AGTCTTTTCG GGAAAAGGTT AAAGAAAAAT
	CTCTGGCGGC
351	GATGCGCCAT TCTTCGCTGT TGGATGTAAA AATTGCGCCC
	GAGGTTGCCA
401	AACGTTATCT GGAAGTACAA GGTTTTCAGG GAAAAACCAT
	TAACCGTGAA
451	GACGGGTCGG TTCTGATTGC CGCCAAAAAA GGCACAATGA
	ACAAATGGGG
501	CTATATCTTT GCCCATGTTG CTTTGATTGT CATTTGCCTG
	GGCGGGTTGA
551	TAGACAGTAA CCTGCTGTTG AAACTGGGTA TGCTGACCGG
	TCGGATTGTT
601	CCGGACAATC AGGCGGTTTA TGCCAAGGAT TTCAAGCCCG
	AAAGTATTTT
651	GGGTGCGTCC AATCTCTCAT TTAGGGGCAA CGTCAATATT
	TCCGAGGGGC
701	AGAGTGCGGA TGTGGTTTTC CTGAATGCCG ACAACGGGAT
	ATTGGTTCAG
751	GACTTGCCTT TTGAAGTCAA ACTGAAAAAA TTCCATATCG
	ATTTTTACAA
801	TACGGGTATG CCGCGTGATT TCGCCAGCGA TATTGAAGTG
	ACGGACAAGG
851	CAACCGGTGA GAAACTCGAG CGCACCATCC GCGTGAACCA
	TCCTTTGACC
901	TTGCACGGCA TCACGATTTA TCAGGCGAGT TTTGCCGACG
	GCGGTTCGGA
951	TTTGACATTC AAGGCGTGGA ATTTGGGTGA TGCTTCGCGC
	GAGCCTGTCG
1001	TGTTGAAGGC AACATCCATA CACCAGTTTC CGTTGGAAAT
	TGGCAAACAC
1051	AAATATCGTC TTGAGTTCGA TCAGTTCACT TCTATGAATG
	TGGAGGACAT
1101	GAGCGAGGGC GCGGAACGGG AAAAAAGCCT GAAATCCACG
	CTGAACGATG
1151	TCCGCGCCGT TACTCAGGAA GGTAAAAAAT ACACCAATAT
	CGGCCCTTCC
1201	ATTGTTTACC GTATCCGTGA TGCGGCAGGG CAGGCGGTCG
	AATATAAAAA
1251	CTATATGCTG CCGGTTTTGC AGGAACAGGA TTATTTTTGG
	ATTACCGGCA
1301	CGCGCAGCGG CTTGCAGCAG CAATACCGCT GGCTGCGTAT
	CCCCTTGGAC
1351	AAGCAGTTGA AAGCGGACAC CTTTATGGCA TTGCGTGAGT
	TTTTGAAAGA
1401	TGGGGAAGGG CGCAAACGTC TGGTTGCCGA CGCAACCAAA
	GGCGCACCTG
1451	CCGAAATCCG CGAACAATTC ATGCTGGCTG CGGAAAACAC
	GCTGAACATC
1501	TTTGCACAAA AAGGCTATTT GGGATTGGAC GAATTTATTA
	CGTCCAATAT
1551	CCCGAAAGAG CAGCAGGATA AGATGCAGGG CTATTTCTAC
	GAAATGCTTT
1601	ACGGCGTGAT GAACGCTGCT TTGGATGAAA CCATACGCCG
	GTACGGCTTG
1651	CCCGAATGGC AGCAGGATGA AGCGCGGAAT CGTTTCCTGC
	TGCACAGTAT
1701	GGATGCGTAC ACGGGTTTGA CCGAATATCC CGCGCCTATG
	CTGCTGCAAC
1751	TTGATGGGTT TTCCGAGGTG CGTTCGTCGG GTTTGCAGAT
	GACCCGTTCC
1801	CCGGGTGCGC TTTTGGTCTA TCTCGGCTCG GTGCTGTTGG
	TATTGGGTAC
1851	GGTATTGATG TTTTATGTGC GCGAAAAACG GGCGTGGGTA
	TTGTTTTCAG
1901	ACGGCAAAAT CCGTTTTGCC ATGTCTTCGG CCCGCAGCGA
	ACGGGATTTG
1951	CAGAAGGAAT TTCCAAAACA CGTCGAGAGT CTGCAACGGC
	TCGGCAAGGA
2001	CTTGAATCAT GACTGA

This corresponds to the amino acid sequence <SEQ ID 330; ORF88-1>:

1	MSKSRRSPPL LSRPWFAFFS SMRFAVALLS LLGIASVIGT
	VLQQNQPQTD
51	YLVKFGSFWA QIFGFLGLYD VYASAWFVVI MMFLVVSTSL
	CLIRNVPPFW
101	REMKSFREKV KEKSLAAMRH SSLLDVKIAP EVAKRYLEVQ
	GFQGKTINRE
151	DGSVLIAAKK GTMNKWGYIF AHVALIVICL GGLIDSNLLL
	KLGMLTGRIV
201	PDNQAVYAKD FKPESILGAS NLSFRGNVNI SEGQSADVVF
	LNADNGILVQ
251	DLPFEVKLKK FHIDFYNTGM PRDFASDIEV TDKATGEKLE
	RTIRVNHPLT
301	LHGITIYQAS FADGGSDLTF KAWNLGDASR EPVVLKATSI
	HQFPLEIGKH
351	KYRLEFDQFT SMNVEDMSEG AEREKSLKST LNDVRAVTQE
	GKKYTNIGPS
401	IVYRIRDAAG QAVEYKNYML PVLQEQDYFW ITGTRSGLQQ
	QYRWLRIPLD
451	KQLKADTFMA LREFLKDGEG RKRLVADATK GAPAEIREQF
	MLAAENTLNI
501	FAQKGYLGLD EFITSNIPKE QQDKMQGYFY EMLYGVMNAA
	LDETIRRYGL
551	PEWQQDEARN RFLLHSMDAY TGLTEYPAPM LLQLDGFSEV
	RSSGLQMTRS
601	PGALLVYLGS VLLVLGTVLM FYVREKRAWV LFSDGKIRFA
	MSSARSERDL
651	QKEFPKHVES LQRLGKDLNH D*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF88 shows 95.7% identity over a 371aa overlap with an ORF (ORF88a) from strain A of N. meningitidis:

The complete length ORF88a nucleotide sequence <SEQ ID 331> is:

1	ATGAGTAAAT CCCGTAGATC TCCCCCACTT CTTTCCCGTC
	CGTGGTTCGC
51	TTTTTTCAGC TCCATGCGCT TTGCGGTCGC TTTGCTCAGT
	CTGCTGGGTA
101	TTGCATCGGT TATCGGTACG GTGTTGCAGC AAAACCAGCC
	GCAGACGGAT
151	TATTTGGTCA AATTCGGATC GTTTTGGGCG CAGATTTTTG
	GTTTTCTGGG
201	ACTGTATGAC GTCTATGCTT CGGCATGGTT TGTCGTTATC
	ATGATGTTTT
251	TGGTGGTTTC TACCAGTTTG TGCCTGATTC GCAATGTGCC
	GCCGTTCTGG
301	CGCGAAATGA AGTCTTTTCG GGAAAAGGTT AAAGAAAAAT
	CTCTGGCGGC
351	GATGCGCCAT TCTTCGCTGT TGGATGTAAA AATTGCGCCC
	GAGGTTGCCA
401	AACGTTATCT GGAAGTACAA GGTTTTCAGG GAAAAACCAT
	TAACCGTGAA
451	GACGGGTCGG TTCTGATTGC CGCCAAAAAA GGCACAATGA
	ACAAATGGGG
501	CTATATCTTT GCCCATGTTG CTTTGATTGT CATTTGCCTG
	GGCGGGTTGA
551	TAGACAGTAA CCTGCTGTTG AAACTGGGTA TGCTGACCGG
	TCGGATTGTT
601	CCGGACAATC AGGCGGTTTA TGCCAAGGAT TTCAAGCCCG
	AAAGTATTTT
651	GGGTGCGTCC AATCTCTCAT TTAGGGGCAA CGTCAATATT
	TCCGAGGGGC
701	AGAGTGCGGA TGTGGTTTTC CTGAATGCCG ACAACGGGAT
	ATTGGTTCAG
751	GACTTGCCTT TTGAAGTCAA ACTGAAAAAA TTCCATATCG
	ATTTTTACAA
801	TACGGGTATG CCGCGCGATT TTGCCAGTGA TATTGAAGTA
	ACGGATAAGG
851	CAACCGGTGA GAAACTCGAG CGCACCATCC GCGTGAACCA
	TCCTTTGACC
901	TTGCACGGCA TCACGATTTA TCAGGCGAGT TTTGCCGACG
	GCGGTTCGGA
951	TTTGACATTC AAGGCGTGGA ATTTGGGTGA TGCTTCGCGC
	GAGCCTGTCG
1001	TGTTGAAGGC AACATCCATA CACCAGTTTC CGTTGGAAAT
	TGGCAAACAC
1051	AAATATCGTC TTGAGTTCGA TCAGTTTACT TCTATGAATG
	TGGAGGACAT
1101	GAGCGAGGGC GCGGAACGGG AAAAAAGCCT GAAATCCACG
	CTGAACGATG
1151	TCCGCGCCGT TACTCAGGAA GGTAAAAAAT ACACCAATAT
	CGGCCCTTCC
1201	ATTGTTTACC GTATCCGTGA TGCGGCAGGG CAGGCGGTCG
	AATATAAAAA
1251	CTATATGCTG CCGGTTTTGC AGGAACAGGA TTATTTTTGG
	ATTACCGGCA
1301	CGCGCAGCGG CTTGCAGCAG CAATACCGCT GGCTGCGTAT
	CCCCTTGGAC
1351	AAGCAGTTGA AAGCGGACAC CTTTATGGCA TTGCGTGAGT
	TTTTGAAAGA
1401	TGGGGAAGGG CGCAAACGTC TGGTTGCCGA CGCAACCAAA
	GGCGCACCTG
1451	CCGAAATCCG CGAACAATTC ATGCTGGCTG CGGAAAACAC
	GCTGAACATC
1501	TTTGCACAAA AAGGCTATTT GGGATTGGAC GAATTTATTA
	CGTCCAATAT
1551	CCCGAAAGAG CAGCAGGATA AGATGCAGGG CTATTTCTAC
	GAAATGCTTT
1601	ACGGCGTGAT GAACGCTGCT TTGGATGAAA CCATACGCCG
	GTACGGCTTG
1651	CCCGAATGGC AGCAGGATGA AGCGCGGAAT CGTTTCCTGC
	TGCACAGTAT
1701	GGATGCGTAC ACGGGTTTGA CCGAATATCC CGCGCCTATG
	CTGCTGCAAC
1751	TTGATGGGTT TTCCGAGGTG CGTTCGTCGG GTTTGCAGAT
	GACCCGTTCC
1801	CCGGGTGCGC TTTTGGTCTA TCTCGGCTCG GTGCTGTTGG
	TATTGGGTAC
1851	GGTATTGATG TTTTATGTGC GCGAAAAACG GGCGTGGGTA
	TTGTTTTCAG
1901	ACGGCAAAAT CCGTTTTGCC ATGTCTTCGG CCCGCAGCGA
	ACGGGATTTG
1951	CAGAAGGAAT TTCCAAAACA CGTCGAGAGT CTGCAACGGC
	TCGGCAAGGA
2001	CTTGAATCAT GACTGA

This encodes a protein having amino acid sequence <SEQ ID 332>:

1	MSKSRRSPPL LSRPWFAFFS SMRFAVALLS LLGIASVIGT
	VLQQNQPQTD
51	YLVKFGSFWA QIFGFLGLYD VYASAWFVVI MMFLVVSTSL
	CLIRNVPPFW
101	REMKSFREKV KEKSLAAMRH SSLLDVKIAP EVAKRYLEVQ
	GFQGKTINRE
151	DGSVLIAAKK GTMNKWGYIF AHVALIVICL GGLIDSNLLL
	KLGMLTGRIV
201	PDNQAVYAKD FKPESILGAS NLSFRGNVNI SEGQSADVVF
	LNADNGILVQ
251	DLPFEVKLKK FHIDFYNTGM PRDFASDIEV TDKATGEKLE
	RTIRVNHPLT
301	LHGITIYQAS FADGGSDLTF KAWNLGDASR EPVVLKATSI
	HQFPLEIGKH
351	KYRLEFDQFT SMNVEDMSEG AEREKSLKST LNDVRAVTQE
	GKKYTNIGPS
401	IVYRIRDAAG QAVEYKNYML PVLQEQDYFW ITGTRSGLQQ
	QYRWLRIPLD
451	KQLKADTFMA LREFLKDGEG RKRLVADATK GAPAEIREQF
	MLAAENTLNI
501	FAQKGYLGLD EFITSNIPKE QQDKMQGYFY EMLYGVMNAA
	LDETIRRYGL
551	PEWQQDEARN RFLLHSMDAY TGLTEYPAPM LLQLDGFSEV
	RSSGLQMTRS
601	PGALLVYLGS VLLVLGTVLM FYVREKRAWV LFSDGKIRFA
	MSSARSERDL
651	QKEFPKHVES LQRLGKDLNH D*

ORF88a and ORF88-1 100.0% identity in 671 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF88 shows 93.8% identity over a 371aa overlap with a predicted ORF (ORF88.ng) from N. gonorrhoeae:

An ORF88ng nucleotide sequence <SEQ ID 333> was predicted to encode a protein having amino acid sequence <SEQ ID 334>:

1	MVFLNADNGM LVQDLPFEVK LKKFHIDFYN TGMPRDFASD
	IEVTDKATGE
51	KLERTIRVNH PLTLHGITIY QASFADGGSD LTFKAWNLRD
	ASREPVVLKA
101	TSIHQFPLEI GKHKYRLEFD QFTSMNVEDM SEGAEREKSL
	KSTLNDVRAV
151	TQEGKKYTNI GPSIVYRIRD AAGQAVEYKN YMLPILQDKD
	YFWLTGTRSG
201	LQQQYRWLRI PLDKQLKADT FMALREFLKD GEGRKRLVAD
	ATKDAPAEIR
251	EQFMLAAENT LNIFAQKGYL GLDEFITSNI PKGQQDKMQG
	YFYEMLYGVM
301	NAALDETIRR YGLPEWQQDE ARNRFLLHSM DAYTGLTEYP
	APMLLQLDGF
351	SEVRSSGLQM TRSPGALLVY LGSVLLVLGT VFMFYVPKKR
	AWVLFSNXKI
401	RFAMSSARSE RDLQKEFPKH VESLQRLGKD LNHD*

Further work revealed the complete gonococcal DNA sequence <SEQ ID 335>:

1	ATGAGTAAAT CCCGTATATC TCCCACACTT CTTTCCCGTC
	CGTGGTTCGC
51	TTTTTTCAGC TCCATGCGCT TTGCGGTCGC TTTGCTCAGT
	CTGCTGGGTA
101	TTGCATCGGT TATCGGCACG GTGTTACAGC AAAACCAGCC
	GCAGACGGAT
151	TATTTGGTCA AATTCGGACC GTTTTGGACT CGGATTTTTG
	ATTTTTTGGG
201	TTTGTATGAT GTCTATGCTT CGGCATGGTT TGTCGTTATC
	ATGATGTTTC
251	TGGTGGTTTC TACCAGTTTG TGTTTAATCC GTAACGTTCC
	GCCGTTTTGG
301	CGCGAAATGA AGTCTTTCCG GGAAAAGGTT AAAGAAAAAT
	CTCTGGCGGC
351	GATGCGCCAT TCTTCGCTGT TGGATGTAAA AATTGCCCCC
	GAAGTTGCCA
401	AACGTTATCT GGAGGTGCGG GGTTTTCAGG GAAAAACCGT
	CAGCCGTGAG
451	GACGGGTCGG TTCTGATTGC CGCCAAAAAA GGCAcaatga
	acaaATGGGG
501	CTATATCTTT GCccaagtag ctTTGATTGT CATTTGCCTG
	GGCGGGTTGA
551	TAGACAGTAA CCTGCTGCTG AAGCTGGGTA TGCTGGCCGG
	TCGGATTGTT
601	CCGGACAATC AGGCGGTTTA TGCCAAGGAT TTCAAGCCCG
	AAAGTATTTT
651	GGGTGCGTCC AATCTCTCAT TTAGGGGCAA CGTCAATATT
	TCCGAGGGGC
701	AAAGTGCGGA TGTGGTTTTC CTGAATGCCG ACAACGGGAT
	GTTGGTTCAG
751	GACTTGCCTT TTGAAGTCAA ACTGAAAAAA TTCCATATCG
	ATTTTTACAA
801	TACGGGTATG CCGCGCGATT TTGCCAGCGA TATTGAAGTA
	ACGGACAAGG
851	CAACCGGTGA GAAACTCGAG CGCACCATCC GCGTGAACCA
	TCCTTTGACC
901	TTGCACGGCA TCACGATTTA TCAGGCGAGT TTTGCCGACG
	GCGGTTCGGA
951	TTTGACATTC AAGGCGTGGA ATTTGAGGGA TGCTTCGCGC
	GAACCTGTCG
1001	TGTTGAAGGC AACCTCCATA CACCAGTTTC CGTTGGAAAT
	CGGCAAACAC
1051	AAATATCGTC TTGAGTTCGA TCAGTTCACT TCTATGAATG
	TGGAGGACAT
1101	GAGCGAGGGT GCGGAACGGG AAAAAAGCCT GAAATCCACT
	CTGAACGATG
1151	TCCGCGCCGT TACTCAGGAA GGTAAAAAAT ACACCAATAT
	CGGCCCTTCC
1201	ATCGTGTACC GCATCCGTGA TGcggCAGGG CAGGCGGTCG
	AATATAAAAA
1251	CTATATGCTG CCGATTTTGC AGGACAAAGA TTATTTTTGG
	CTGACCGGCA
1301	CGCGCAGCGG CTTGCAGCAG CAATACCGCT GGCTGCGTAT
	CCCCTTGGAC
1351	AAGCAGTTGA AAGCGGACAC CTTTATGGCA TTGCGTGAGT
	TTTTGAAAGA
1401	TGGGGAAGGG CGCAAACGTC TGGTTGCCGA CGCAACCAAA
	GACGCACCTG
1451	CCGAAATCCG CGAACAATTC ATGCTGGCTG CGGAAAACAC
	GCTGAATATC
1501	TTTGCGCAAA AAGGCTATTT GGGATTGGAC GAATTTATTA
	CGTCCAATAT
1551	CCCGAAAGGG CAGCAGGATA AGATGCAGGG CTATTTCTAC
	GAAATGCTTT
1601	ACGGCGTGAT GAACGCTGCT TTGGATGAAA CCATACGCCG
	GTACGGCTTG
1651	CCCGAATGGC AGCAGGATGA AGCGCGGAAC CGTTTCCTGC
	TGCACAGTAT
1701	GGATGCCTAT ACGGGGCTGA CGGAATATCC CGCGCCTATG
	CTGCTCCAGC
1751	TTGACGGGTT TTCCGAGGTG CGTTCCTCAG GTTTGCAGAT
	GACCCGTTCG
1801	CCGGGTGCGC TTTTGGTCTA TCtcggctcg gtattgttgg
	TTTTGGgtac
1851	ggtaTttatg tTTTATGTGC GCGAAAAACG GGCGTGGgta
	tTGTTTTCag
1901	aCGGCAAAAT CCGTTTTGCT ATGtCTTcgg CCcgcagcga
	ACGGGATTTG
1951	cAGAaggaaT TTCCAAAACA CGtcgAGAGC CTGCAACggc
	tcggcaaggA
2001	CttgaaTCAT GACTga

This corresponds to the amino acid sequence <SEQ ID 336; ORF88ng-1>:

1	MSKSRISPTL LSRPWFAFFS SMRFAVALLS LLGIASVIGT
	VLQQNQPQTD
51	YLVKFGPFWT RIFDFLGLYD VYASAWFVVI MMFLVVSTSL
	CLIRNVPPFW
101	REMKSFREKV KEKSLAAMRH SSLLDVKIAP EVAKRYLEVR
	GFQGKTVSRE
151	DGSVLIAAKK GTMNKWGYIF AQVALIVICL GGLIDSNLLL
	KLGMLAGRIV
201	PDNQAVYAKD FKPESILGAS NLSFRGNVNI SEGQSADVVF
	LNADNGMLVQ
251	DLPFEVKLKK FHIDFYNTGM PRDFASDIEV TDKATGEKLE
	RTIRVNHPLT
301	LHGITIYQAS FADGGSDLTF KAWNLRDASR EPVVLKATSI
	HQFPLEIGKH
351	KYRLEFDQFT SMNVEDMSEG AEREKSLKST LNDVRAVTQE
	GKKYTNIGPS
401	IVYRIRDAAG QAVEYKNYML PILQDKDYFW LTGTRSGLQQ
	QYRWLRIPLD
451	KQLKADTFMA LREFLKDGEG RKRLVADATK DAPAEIREQF
	MLAAENTLNI
501	FAQKGYLGLD EFITSNIPKG QQDKMQGYFY EMLYGVMNAA
	LDETIRRYGL
551	PEWQQDEARN RFLLHSMDAY TGLTEYPAPM LLQLDGFSEV
	RSSGLQMTRS
601	PGALLVYLGS VLLVLGTVFM FYVREKRAWV LFSDGKIRFA
	MSSARSERDL
651	QKEFPKHVES LQRLGKDLNH D*

ORF88ng-1 and ORF88-1 show 97.0% identity in 671 aa overlap:

Furthermore, ORG88ng-1 shows homology with a hypothetical protein from Aquifex aeolicus:

gi|2984296 (AE000771) hypothetical protein [Aquifex aeolicus]
Length = 537 Score = 94.4 bits (231), Expect = 2e−18.
Identities = 91/334 (27%), Positives = 159/334 (47%), Gaps = 59/334 (17%)

Query:	16	FAFFSSMRFAVALLSLLGIASVIG-TVLQQNQPQTDYLVKFGPFWTRIFDFLGLYDVYAS	74
		+ F +S++ A+ ++ +LGI S++G T ++QNQ    YL +FG         L L DV+ S
Sbjct:	80	YDFLASLKLAIFIMLVLGILSMLGSTYIKQNQSFEWYLDQFGYDVGIWIWKLWLNDVFHS	139
Query:	75	AWFVVIMMFLVVSTSLCLIRNVPPFWREMKSFREKVKEKSLAAMRHSSLLDVKIAPEVAK	134
		++++ ++ L V+   C I+ +P  W++  S +E++ +    A +H   + VKI P+  K
Sbjct:	140	WYYILFIVLLAVNLIFCSIKRLPRVWKQAFS-KERILKLDEHAEKHLKPITVKI-PDKDK	197
Query:	135	--RYLEVRGFQGKTVSREDGSVLIAAKKGTMNKWGYIFAQVALIVICLGGLIDSNLLLKL	192
		++L  +GF+   V  E   + + A+KG  ++ G     +AL+VI  G LID
Sbjct:	198	VLKFLLKKGFK-VFVEEEGNKLYVFAEKGRFSRLGVYITHIALLVIMAGALID-------	249
Query:	193	GMLAGRIVPDNQAVYAKDFKPESILGASNLSFRGNVNISEGQSADVVFLNADNGMLVQDL	252
		+I+G      RG++ ++EG + DV+ + A+       L
Sbjct:	250	----------------------AIVGV-----RGSLIVAEGDTNDVMLVGAE--QKPYKL	280
Query:	253	PFEVKLKKFHIDFY---NTGMPRDFA-------SDIEVTDKATGEKLER--TIRVNHPLT	300
		PF V L  F I  Y   N  + + FA       SDIE+ +   G K+E   T++VN P
Sbjct:	281	PFAVHLIDFRIKTYAEENPNVDKRFAQAVSSYESDIEIIN---GGKVEAKGTVKVNEPFD	337
Query:	301	LHGITIYQASFA--DGGSDLTFKAWNLRDASREP	332
		++QA++   DG S +     + + A  +P
Sbjct:	338	FGRYRLFQATYGILDGTSGMGVIVVDRKKAHEDP	371

Based on this analysis, including the putative transmembrane domain in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 40

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 337>:

1	ATGATGAGTA ATAmAATGGm ACAAAAAGGG TTTACATTGA
	TTGmGmTGAT
51	GATAGTCGTC GCGATACTCG GCATTATCAG CGTCATTGCC
	ATACCTTCTT
101	ATCmAAGTTA TATTGAAAAA GGCTATCAGT CCCAGCTTTA
	TACGGAGATG
151	GyCGGTATCA ACAATATTTC CAAACAGTTT ATTTTGAAAA
	ATCCCCTGGA
201	CGATAATCAG ACCATCGAGA ACAAACTGGA AATATTTGTC
	TCAGGCTATA
251	AGATGAATCC GAAAATTGCC AAAAAaTATA GTGTTTCGGT
	AAAGTTTGTC
301	GATAAGGAAA AATCAAGGGC ATACAGGTTG GTCGGCGTTC
	CGAAGGCGGG
351	GACGGGTTAT ACTTTGTCGG TATGGATGAA CAGCGTGGGC
	GACGGATACA
401	AATGCCGTGA TGCCGCTTCT GCCCAAGCCC ATTTGGAGAC
	CTTGTCCTCA
451	GATGTCGGCT GTGAAGCCTT CTCTAATCGT AAAAAATAA

This corresponds to the amino acid sequence <SEQ ID 338; ORF89>:

1	MMSNXMXQKG FTLIXXMIVV AILGIISVIA IPSYXSYIEK
	GYQSQLYTEM
51	XGINNISKQF ILKNPLDDNQ TIENKLEIFV SGYKMNPKIA
	KKYSVSVKFV
101	DKEKSRAYRL VGVPKAGTGY TLSVWMNSVG DGYKCRDAAS
	AQAHLETLSS
151	DVGCEAFSNR KK*

Further work revealed the complete nucleotide sequence <SEQ ID 339>:

1	ATGATGAGTA ATAAAATGGA ACAAAAAGGG TTTACATTGA
	TTGAGATGAT
51	GATAGTCGTC GCGATACTCG GCATTATCAG CGTCATTGCC
	ATACCTTCTT
101	ATCAAAGTTA TATTGAAAAA GGCTATCAGT CCCAGCTTTA
	TACGGAGATG
151	GTCGGTATCA ACAATATTTC CAAACAGTTT ATTTTGAAAA
	ATCCCCTGGA
201	CGATAATCAG ACCATCGAGA ACAAACTGGA AATATTTGTC
	TCAGGCTATA
251	AGATGAATCC GAAAATTGCC AAAAAATATA GTGTTTCGGT
	AAAGTTTGTC
301	GATAAGGAAA AATCAAGGGC ATACAGGTTG GTCGGCGTTC
	CGAAGGCGGG
351	GACGGGTTAT ACTTTGTCGG TATGGATGAA CAGCGTGGGC
	GACGGATACA
401	AATGCCGTGA TGCCGCTTCT GCCCAAGCCC ATTTGGAGAC
	CTTGTCCTCA
451	GATGTCGGCT GTGAAGCCTT CTCTAATCGT AAAAAATAA

This corresponds to the amino acid sequence <SEQ ID 340; ORF89-1>:

1	MMSNKMEQKG FTLIEMMIVV AILGIISVIA IPSYQSYIEK
	GYQSQLYTEM
51	VGINNISKQF ILKNPLDDNQ TIENKLEIFV SGYKMNPKIA
	KKYSVSVKFV
101	DKEKSRAYRL VGVPKAGTGY TLSVWMNSVG DGYKCRDAAS
	AQAHLETLSS
151	DVGCEAFSNR KK*

Computer analysis of this amino acid sequence gave the following results:

Homology with PilE of N. gonorrhoeae (Accession Number Z69260).

ORF89 and PilE protein show 30% aa identity in 120a overlap:

orf89	8	QKGFTLIXXMIVVAILGIISVIAIPSYXSYIEKGYQSQLYTEMXGINNISKQFILKNPL-	66
		QKGFTLI  MIV+AI+GI++ +A+P+Y  Y  +   S+      G  +   ++ L + +
PilE	5	QKGFTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGIW	64
orf89	67	-DDNQTIENKLEIFVSGYKMNPKIAKKYSVSVKFVDKEKSRAYRLVGVPKAGTGYTLSVW	125
		DN +         +G   + KI  KY  SV       +      GV K   G  LS+W
PilE	65	PKDNTS---------AGVASSDKIKGKYVQSVTVAKGVVTAEMASTGVNKEIQGKKLSLW	115

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF89 shows 83.3% identity over a 162aa overlap with an ORF (ORF89a) from strain A of N. meningitidis:

The complete length ORF89a nucleotide sequence <SEQ ID 341> is:

1	ATGATGAGTA ATAAAATGGA ACAAAAAGGG TTTACATTGA
	TTGNGANGNT
51	NATNGNCNTC GCGATACNCN GCNTTANCAG CGTCATTNCN
	ATNNNTNCNT
101	ATCNNAGTTA TATTGAAAAA GGCTATCAGT CCCAGCTTTA
	TACGGAGATG
151	GTCGGTATCA ACAATATTTC CAAACAGTNT ATTTTGAAAA
	ATCCCCTGGA
201	CGATAATCAG ACCATCAAGA GCAAACTGGA AATATTTGTC
	TCAGGCTATA
251	AGATGAATCC GAAAATTGCC GAAAAATATA ATGTTTCGGT
	GCATTTTGTC
301	AATGAGGAAA AACCNAGGGC ATACAGCTTG GTCGGCGTTC
	CAAAGACGGG
351	GACGGGTTAT ACTTTGTCGG TATGGATGAA CAGCGTGGGC
	GACGGATACA
401	AATGCCGTGA TGCCGCTTCT GCCCGAGCCC ATTTGGAGAC
	CTTGTCCTCA
451	GATGTCGGCT GTGAAGCCTT CTCTAATCGT AAAAAATAG

This encodes a protein having amino acid sequence <SEQ ID 342>:

1	MMSNKMEQKG FTLIXXXXXX AIXXXXSVIX XXXYXSYIEK
	GYQSQLYTEM
51	VGINNISKQX ILKNPLDDNQ TIKSKLEIFV SGYKMNPKIA
	EKYNVSVHFV
101	NEEKPRAYSL VGVPKTGTGY TLSVWMNSVG DGYKCRDAAS
	ARAHLETLSS
151	DVGCEAFSNR KK*

ORF89a and ORF89-1 show 83.3% identity in 162 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF89 shows 84.6% identity over a 162aa overlap with a predicted ORF (ORF89.ng) from N. gonorrhoeae:

The complete length ORF89ng nucleotide sequence <SEQ ID 343> is:

1	aTGATGAGCA ATAAAATGGA ACAAAAAGGG TTTACATTGA
	TTGAGATGAT
51	GATAGTTGTC ACGATACTCG GCATCATCAG CGTCATTGCC
	ATACCTTCTT
101	ATCAGAGTTA TATTGAAAAA GGCTATCAGT CCCAGCTTTA
	TACGGAGATG
151	GTCGGTATCA ACAATGTTCT CAAACAGTTT ATTTTGAAAA
	ATCCCCAGGA
201	CGATAATGAT ACCCTCAAGA GCAAACTGAA AATATTTGTC
	TCAGGCTATA
251	AGATGAATCC GAAAAttgCC AAAAAATATA GTGTTTCGGt
	aaggtttGTC
301	gatGCGGAAA AACCAAGGGC ATACAGGTTG GTCGGCGTTC
	CGAACGCGGG
351	GACGGGTTAT ACTTTGTCGG TATGGATGAA CAGCGTGGGC
	GACGGATACA
401	AATGCCGTGA TGCCACTTCT GCCCAGGCCT ATTCGGACAC
	CTTGTCCGCA
451	GATAGCGGCT GTGAAGCTTT CTCTAATCGT AAAAAATAG

This encodes a protein having amino acid sequence <SEQ ID 344>:

1	MMSNKMEQKG FTLIEMMIVV TILGIISVIA IPSYQSYIEK
	GYQSQLYTEM
51	VGINNVLKQF ILKNPQDDND TLKSKLKIFV SGYKMNPKIA
	KKYSVSVRFV
101	DAEKPRAYRL VGVPNAGTGY TLSVWMNSVG DGYKCRDATS
	AQAYSDTLSA
151	DSGCEAFSNR KK*

This gonococcal protein has a putative leader peptide (underlined) and N-terminal methylation site (NMePhe or type-4 pili, double-underlined). In addition, ORF89ng and ORF89-1 show 88.3% identity in 162 aa overlap:

Based on this analysis, including the gonococcal motifs and the homology with the known PilE protein, it was predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF89-1 (13.6 kDa) was cloned in the pGex vector and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 11A shows the results of affinity purification of the GST-fusion protein. Purified GST-fusion protein was used to immunise mice, whose sera gave a positive result in the ELISA test, confirming that ORF89-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 41

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 345>:

1	ATGAAAAAAT CCTCCCTCAT CAGCGCATTG GGCATCGGTA
	TTTTGAGCAT
51	CGGCATGGCA TTTGCCGCCC CTGCCGACGC GGTAAGCCAA
	ATCCGTCAAA
101	ACGCCACTCA AGTATTGAGC ATCTTAAAAA ACGGCGATGC
	CAACACCGCT
151	CGCCAAAAAG CCGAAGCCTA TGCGATTCCC TATTTCGATT
	TCCAACGTAT
201	GACCGCATTG GCGGTCGGCA ACCCTTGGsG CACCG.GTCC
	GACG.GCAAA
251	AACAAGCGTT GGCCn.AGAA TTTCAACCC...

This corresponds to the amino acid sequence <SEQ ID 346; ORF91>:

1	MKKSSLISAL GIGILSIGMA FAAPADAVSQ IRQNATQVLS
	ILKNGDANTA
51	RQKAEAYAIP YFDFQRMTAL AVGNPWXTXS DXQKQALAXE
	FQP...

Further work revealed the complete nucleotide sequence <SEQ ID 347>:

1	ATGAAAAAAT CCTCCCTCAT CAGCGCATTG GGCATCGGTA
	TTTTGAGCAT
51	CGGCATGGCA TTTGCCGCCC CTGCCGACGC GGTAAGCCAA
	ATCCGTCAAA
101	ACGCCACTCA AGTATTGAGC ATCTTAAAAA ACGGCGATGC
	CAACACCGCT
151	CGCCAAAAAG CCGAAGCCTA TGCGATTCCC TATTTCGATT
	TCCAACGTAT
201	GACCGCATTG GCGGTCGGCA ACCCTTGGCG CACCGCGTCC
	GACGCGCAAA
251	AACAAGCGTT GGCCAAAGAA TTTCAAACCC TGCTGATCCG
	CACCTATTCC
301	GGCACGATGC TGAAATTAAA AAACGCCAAC GTCAACGTCA
	AAGACAATCC
351	CATCGTCAAT AAAGGCGGCA AAGAAATCAT CGTCCGCGCC
	GAAGTCGGCG
401	TACCCGGGCA AAAACCCGTC AACATGGACT TCACCACCTA
	CCAAAGCGGC
451	GGTAAATACC GTACCTACAA CGTCGCCATC GAAGGCGCGA
	GCCTGGTTAC
501	CGTGTACCGC AACCAATTCG GCGAAATTAT CAAAGCGAAA
	GGCGTGGACG
551	GACTGATTGC CGAGTTGAAA GCCAAAAACG GCGGCAAATA
	A

This corresponds to the amino acid sequence <SEQ ID 348; ORF91-1>:

1	MKKSSLISAL GIGILSIGMA FAAPADAVSQ IRQNATQVLS
	ILKNGDANTA
51	RQKAEAYAIP YFDFQRMTAL AVGNPWRTAS DAQKQALAKE
	FQTLLIRTYS
101	GTMLKLKNAN VNVKDNPIVN KGGKEIIVRA EVGVPGQKPV
	NMDFTTYQSG
151	GKYRTYNVAI EGASLVTVYR NQFGEIIKAK GVDGLIAELK
	AKNGGK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF91 shows 92.4% identity over a 92aa overlap with an ORF (ORF91a) from strain A of N. meningitidis:

The complete length ORF91a nucleotide sequence <SEQ ID 349> is:

1	ATGAAAAAAT CCTCCTTCAT CAGCGCATTG GGCATCGGTA
	TTTTGAGCAT
51	CGGCATGGCA TTTGCCGCCC CTGCCGACGC GGTAAACCAA
	ATCCGTCAAA
101	ACGCCACTCA AGTATTGAGC ATCTTAAAAA GCGGTGATGC
	CAACACCGCC
151	CGCCAAAAAG CCGAAGCCTA TGCGATTCCC TATTTCGATT
	TCCAACGTAT
201	GACCGCATTG GCGGTCGGCA ACCCTTGGCG CACCGCGTCC
	GACGCGCAAA
251	AACAAGCGTT GGCCAAAGAA TTTCAAACCC TGCTGATCCG
	CACCTATTCC
301	GGCACGATGC TGAAATTAAA AAACGCCAAC GTCAACGTCA
	AAGACAATCC
351	CATCGTCAAT AAAGGCGGCA AAGAAATCAT CGTCCGCGCC
	GAAGTCGGCG
401	TACCCGGGCA AAAACCCGTC AACATGGACT TCACCACCTA
	CCAAAGCGGC
451	GGTAAATACC GTACCTACAA CGTCGCCATC GAAGGCGCGA
	GCCTGGTTAC
501	CGTGTACCGC AACCAATTCG GCGAAATTAT CAAAGCGAAA
	GGCGTGGACG
551	GACTGATTGC CGAGTTGAAG GCTAAAAACG GCAGCAAGTA
	A

This encodes a protein having amino acid sequence <SEQ ID 350>:

1	MKKSSFISAL GIGILSIGMA FAAPADAVNQ IRQNATQVLS
	ILKSGDANTA
51	RQKAEAYAIP YFDFQRMTAL AVGNPWRTAS DAQKQALAKE
	FQTLLIRTYS
101	GTMLKLKNAN VNVKDNPIVN KGGKEIIVRA EVGVPGQKPV
	NMDFTTYQSG
151	GKYRTYNVAI EGASLVTVYR NQFGEIIKAK GVDGLIAELK
	AKNGSK*

ORF91a and ORF91-1 show 98.0% identity in 196 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF91 shows 84.8% identity over a 92aa overlap with a predicted ORF (ORF91.ng) from N. gonorrhoeae:

The complete length ORF91ng nucleotide sequence <SEQ ID 351> is predicted to encode a protein having amino acid sequence <SEQ ID 352>:

1	VKKSSFISAL GIGILSIGMA FASPADAVGQ IRQNATQVLT
	ILKSGDAASA
51	RPKAEAYAVP YFDFQRMTAL AVGNPWRTAS DAQKQALAKE
	FQTLLIRTYS
101	GTMLKFKNAT VNVKDNPIVN KGGKEIVVRA EVGIPGQKPV
	NMDFTTYQSG
151	GKYRTYNVAI EGTSLVTVYR NQFGEIIKAK GIDGLIAELK
	AKNGGK*

Further work revealed the complete nucleotide sequence <SEQ ID 353>:

1	ATGAAAAAAT CCTCCTTCAT CAGCGCATTG GGCATCGGTA
	TTTTGAGCAT
51	CGGCATGGCA TTTGCCTCCC CGGCCGACGC AGTGGGACAA
	ATCCGCCAAA
101	ACGCCACACA GGTTTTGACC ATCCTCAAAA GCGGCGACGC
	GGCTTCTGCA
151	CGCCCAAAAG CCGAAGCCTA TGCGGTTCCC TATTTCGATT
	TCCAACGTAT
201	GACCGCATTG GCGGTCGGCA ACCCTTGGCG TACCGCGTCC
	GACGCGCAAA
251	AACAAGCGTT GGCCAAAGAA TTTCAAACCC TGCTGATCCG
	CACCTATTCC
301	GGCACGATGC TGAAATTCAA AAACGCGACC GTCAACGTCA
	AAGACAATCC
351	CATCGTCAAT AAGGGCGGCA AGGAAATCGT CGTCCGTGCC
	GAAGTCGGCA
401	TCCCCGGTCA GAAGCCCGTC AATATGGACT TTACCACCTA
	CCAAAGCGGC
451	GGCAAATACC GTACCTACAA CGTCGCCATC GAAGGCACGA
	GCCTGGTTAC
501	CGTGTACCGC AACCAATTCG GCGAAATCAT CAAAGCCAAA
	GGCATCGACG
551	GGCTGATTGC CGAGTTGAAA GCCAAAAACG GCGGCAAATA
	A

This corresponds to the amino acid sequence <SEQ ID 354; ORF91ng-1>:

1	MKKSSFISAL GIGILSIGMA FASPADAVGQ IRQNATQVLT
	ILKSGDAASA
51	RPKAEAYAVP YFDFQRMTAL AVGNPWRTAS DAQKQALAKE
	FQTLLIRTYS
101	GTMLKFKNAT VNVKDNPIVN KGGKEIVVRA EVGIPGQKPV
	NMDFTTYQSG
151	GKYRTYNVAI EGTSLVTVYR NQFGEIIKAK GIDGLIAELK
	AKNGGK*

ORF91ng-1 and ORF91-1 show 92.3% identity in 196 aa overlap:

In addition, ORF91ng-1 shows homology to a hypothetical E. coli protein:

sp|P45390|YRBC_ECOLI HYPOTHETICAL 24.0 KD PROTEIN IN MURA-RPON
INTERGENIC
REGION PRECURSOR (F211) >gi|606130 (U18997) ORF_f211 [Escherichia coli]
>gi|1789583 (AE000399) hypothetical 24.0 kD protein in murZ-rpoN
intergenic region [Escherichia coli]Length = 211
Score = 70.6 bits (170), Expect = 6e−12
Identities = 42/137 (30%), Positives = 76/137 (54%), Gaps = 6/137 (4%)

Query:	59	VPYFDFQRMTALAVGNPWRTASDAQKQALAKEFQTLLIRTYSGTMLKFKNATVNVKDNPI	118
		+PY   +   AL +G  +++A+ AQ++A    F+  L + Y   +  +   T  +   P
Sbjct:	65	LPYVQVKYAGALVLGQYYKSATPAQREAYFAAFREYLKQAYGQALAMYHGQTYQIA--PE	122
Query:	119	VNKGGKEIV-VRAEVGIP-GQKPVNMDFTTYQSG--GKYRTYNVAIEGTSLVTVYRNQFG	174
		G K IV +R  +  P G+ PV +DF   ++   G ++ Y++  EG S++T  +N++G
Sbjct:	123	QPLGDKTIVPIRVTIIDPNGRPPVRLDFQWRKNSQTGNWQAYDMIAEGVSMITTKQNEWG	182
Query:	175	EIIKAKGIDGLIAELKA	191
		+++ KGIDGL A+LK+
Sbjct:	183	TLLRTKGIDGLTAQLKS	199

Based on this analysis, including the presence of a putative leader sequence in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 42

The following DNA sequence was identified in N. meningitidis <SEQ ID 355>:

1	ATGAAACACA TACTCCCCCT GATTGCCGCA TCCGCACTCT
	GCATTTCAAC
51	CGCTTCGGCA CATCCTGCCA GCGAACCGTC CACTCAAAAC
	GAAACCGCTA
101	TGATCACGCA TACCCTCATC TCAAAATACA GTTTTGGnnn
	nnnnnnnnnn
151	nnnnnnnnnn nnGCCATAAA AAGCAAAGGG ATGGACATTT
	TTGCCGTCAT
201	CGACCATCAG GAAGCCGCAC GCCGAAACGG CTTAACGATG
	CAGCCGGCAA
251	AAGTCATCGT CTTCGGCACG CCCAAAGCCG GCACGCCGCT
	GATGGTCAAA
301	GACCCCGCCT TCGCCCTGCA ACTGCCCCTA CGCGTCCTCG
	TTACCGAAAC
351	GGACGGCAAA GTACGCGCCG CCTATACCGA TACGCGCGCC
	CTCATCGCCG
401	GCAGCCGCAT CGGTTTCGAC GAAGTGGCAA ACACTTTGGC
	AAACGCCGAA
451	AAACTGATAC AAAAAACCGT AGGCGAATAA

This corresponds to the amino acid sequence <SEQ ID 356; ORF97>:

1	MKHILPLIAA SALCISTASA HPASEPSTQN ETAMITHTLI
	SKYSFGXXXX
51	XXXXAIKSKG MDIFAVIDHQ EAARRNGLTM QPAKVIVFGT
	PKAGTPLMVK
101	DPAFALQLPL RVLVTETDGK VRAAYTDTRA LIAGSRIGFD
	EVANTLANAE
151	KLIQKTVGE*

Further work revealed the complete nucleotide sequence <SEQ ID 357>:

1	ATGAAACACA TACTCCCCCT GATTGCCGCA TCCGCACTCT
	GCATTTCAAC
51	CGCTTCGGCA CATCCTGCCA GCGAACCGTC CACCCAAAAC
	GAAACCGCTA
101	TGACCACGCA TACCCTCACC TCAAAATACA GTTTTGACGA
	AACCGTCAGC
151	CGCCTTGAAA CCGCCATAAA AAGCAAAGGG ATGGACATTT
	TTGCCGTCAT
201	CGACCATCAG GAAGCCGCCC GCCGAAACGG CTTAACGATG
	CAGCCGGCAA
251	AAGTCATCGT CTTCGGCACG CCCAAAGCCG GCACGCCGCT
	GATGGTCAAA
301	GACCCCGCCT TCGCCCTGCA ACTGCCCCTA CGCGTCCTCG
	TTACCGAAAC
351	GGACGGCAAA GTACGCGCCG CCTATACCGA TACGCGCGCC
	CTCATCGCCG
401	GCAGCCGCAT CGGTTTCGAC GAAGTGGCAA ACACTTTGGC
	AAACGCCGAA
451	AAACTGATAC AAAAAACCGT AGGCGAATAA

This corresponds to the amino acid sequence <SEQ ID 358; ORF97-1>:

1	MKHILPLIAA SALCISTASA HPASEPSTQN ETAMTTHTLT
	SKYSFDETVS
51	RLETAIKSKG MDIFAVIDHQ EAARRNGLTM QPAKVIVFGT
	PKAGTPLMVK
101	DPAFALQLPL RVLVTETDGK VRAAYTDTRA LIAGSRIGFD
	EVANTLANAE
151	KLIQKTVGE*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF97 shows 88.7% identity over a 159aa overlap with an ORF (ORF97a) from strain A of N. meningitidis:

The complete length ORF97a nucleotide sequence <SEQ ID 359> is:

1	ATGANACACA TACTCCCCCT GANTGNCGCA TCCGCACTCT
	GCATTTCAAC
51	CGCTTCGGNN CATCCTGCCA GCGAACCGCA AACCCAAAAC
	GAAACCGCTA
101	TGACCACGCA TACCCTCACC TCAAAATACA GTTTTGACGA
	AACCGTCAGC
151	CGCCTTGAAA CCGCCATAAA AAGCAAAGGG ATGGACATTT
	TTGCCGTCAT
201	CGACCATCAG GAAGCCGCCC GCCGAAACGG CTTAACGATG
	CAGCCGGCAA
251	AAGTCATCGT CTTCGGCACG CCCAAAGCCG GTACGCCGCT
	GATGGTCAAA
301	GACCCCGCCT TCGCCCTGCA ACTGCCCCTG CGCGTCNTCG
	TTACCGAAAC
351	GGACGGCAAA GTACGCGCCG CCTATACCGA TACGCGCGCC
	CTCATCGCCG
401	GCAGCCGCAT CGGTTTCGAC GAAGTGGCAA ACACTTTGGC
	AAACGCCGAA
451	AAACTGATAC AAAAAACCAT AGGCGAATAA

This encodes a protein having amino acid sequence <SEQ ID 360>:

1	MXHILPLXXA SALCISTASX HPASEPQTQN ETAMTTHTLT
	SKYSFDETVS
51	RLETAIKSKG MDIFAVIDHQ EAARRNGLTM QPAKVIVFGT
	PKAGTPLMVK
101	DPAFALQLPL RVXVTETDGK VRAAYTDTRA LIAGSRIGFD
	EVANTLANAE
151	KLIQKTIGE*

ORF97a and ORF97-1 show 95.6% identity in 159 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF97 shows 88.1% identity over a 159aa overlap with a predicted ORF (ORF97.ng) from N. gonorrhoeae:

The complete length ORF97ng nucleotide sequence <SEQ ID 361> is predicted to encode a protein having amino acid sequence <SEQ ID 362>:

1	MKHILPPIAA SAFCISTASA HPAGKPPTQN ETAMTTHTLT
	SKYSFDETVS
51	RLETAIKSKG MDIFAVIDHQ EAARRNGLTM QPAKVIVFGT
	PKAGTPLMVK
101	DPAFALQLPL RVLVTETDGK VRTAYTDTRA LIVGSRISFD
	EVANTLANAE
151	KLIQKTVGE*

Further work revealed the complete nucleotide sequence <SEQ ID 363>:

1	ATGAAACACA TACTCCCcct gatcgccgca TccgcactCT
	GCATTTCAAC
51	CGCTTCGGCA CACCCTGCCG GCAAACCGCC CACCCAAAAC
	GAAACCGCTA
101	TGACCACGCA CACCCTCACC TCGAAATACA GTTTTGACGA
	AACCGTCAGC
151	CGCCTTGAAA CCGCCATAAA AAGCAAAGGG ATGGACATTT
	TTGCCGTCAT
201	CGACCATCAG GAAGCGGCAC GCCGAAACGG CCTGACCATG
	CAGCCGGCAA
251	AAGTCATCGT CTTCGGCACG CCCAAGGCCG GTACGCCgct
	GATGGTCAAA
301	GACCCCGCCT TCGCCCTGCA ACTGCCCCTG CGCGTCCTCG
	TTACCGAAAC
351	GGACGGCAAA GTACGCACCG CCTATACCGA TACGCGCGCC
	CTCATCGTCG
401	GCAGCCGCAT CAGTTTCGAC GAAGTGGCAA ACACTTTGGC
	AAACGCCGAA
451	AAACTGATAC AAAAAACCGT AGGCGAATAA

This corresponds to the amino acid sequence <SEQ ID 364; ORF97ng-1>:

1	MKHILPLIAA SALCISTASA HPAGKPPTQN ETAMTTHTLT
	SKYSFDETVS
51	RLETAIKSKG MDIFAVIDHQ EAARRNGLTM QPAKVIVFGT
	PKAGTPLMVK
101	DPAFALQLPL RVLVTETDGK VRTAYTDTRA LIVGSRISFD
	EVANTLANAE
151	KLIQKTVGE*

ORF97ng-1 and ORF97-1 show 96.2% identity in 159 aa overlap:

Based on this analysis, including the presence of a putative leader sequence in the gonococcal protein, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF97-1 (15.3 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIGS. 12A & 12B show, respectively, the results of affinity purification of the GST-fusion and His-fusion proteins. Purified GST-fusion protein was used to immunise mice, whose sera were used for Western Blot (FIG. 12C), ELISA (positive result), and FACS analysis (FIG. 12D). These experiments confirm that ORF97-1 is a surface-exposed protein, and that it is a useful immunogen. FIG. 12E shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF97-1.

Example 43

The following DNA, believed to be complete, sequence was identified in N. meningitidis <SEQ ID 365>:

1	ATGGCTTTTA TTACGCGCTT ATTCAAAAGC AGTAAATGGC
	TGATTGTGCC
51	GCTGATGCTC CCCGCCTTTC AGAATGTGGC GGCGGAGGGG
	ATAGATGTGA
101	GCCGTGCCGA AGCGAGGATA ACCGACGGCG GGCAGCTTTC
	CATCAGCAGC
151	CGCTTCCAAA CCGAGCTGCC CGACCAGCTC CAACAGGCGT
	TGCGCCGGGg
201	CGTGCCGCTC AACTTTACCT TAAGCTGGCA GCTTTCCGCC
	CCGATAATCG
251	CTTCTTATCG GTTTAAATTG GGGCAACTGA TTGGCGATGA
	CGACaATATT
301	GACTACAAAC TGAGTTTCCA TCCGCTGACc AaACGCTACC
	GCGTTACCgT
351	CGgCGCGTTT TCGACAGACT ACGACACCTT GGATGCGGCA
	TTGCGCGCGA
401	CCGGCGCGGT TGCCAACTGG AAAGTCCTGA ACAAAGGCGC
	GCTGTCCGGT
451	GCGGAAGCAG GGGAAACCAA GGCGGAAATC CGCCTGACGC
	TGTCCACTTC
501	AAAACTGCCC AAGCCTTTTC AAATCAATGC ATTGACTTCT
	CAAAACTGGC
551	ATTTGGATTC GGGTTGGAAA CCTCTAAACA TCATCGGGAA
	CAAATAA

This corresponds to the amino acid sequence <SEQ ID 366; ORF106>:

1	MAFITRLFKS SKWLIVPLML PAFQNVAAEG IDVSRAEARI
	TDGGQLSISS
51	RFQTELPDQL QQALRRGVPL NFTLSWQLSA PIIASYRFKL
	GQLIGDDDNI
101	DYKLSFHPLT KRYRVTVGAF STDYDTLDAA LRATGAVANW
	KVLNKGALSG
151	AEAGETKAEI RLTLSTSKLP KPFQINALTS QNWHLDSGWK
	PLNIIGNK*

Further work revealed the following DNA sequence <SEQ ID 367>:

1	ATGGCTTTTA TTACGCGCTT ATTCAAAAGC AGTAAATGGC
	TGATTGTGCC
51	GCTGATGCTC CCCGCCTTTC AGAATGTGGC GGCGGAGGGG
	ATAGATGTGA
101	GCCGTGCCGA AGCGAGGATA ACCGACGGCG GGCAGCTTTC
	CATCAGCAGC
151	CGCTTCCAAA CCGAGCTGCC CGACCAGCTC CAACAGGCGT
	TGCGCCGGGG
201	CGTGCCGCTC AACTTTACCT TAAGCTGGCA GCTTTCCGCC
	CCGATAATCG
251	CTTCTTATCG GTTTAAATTG GGGCAACTGA TTGGCGATGA
	CGACAATATT
301	GACTACAAAC TGAGTTTCCA TCCGCTGACC AACCGCTACC
	GCGTTACCGT
351	CGGCGCGTTT TCGACAGACT ACGACACCTT GGATGCGGCA
	TTGCGCGCGA
401	CCGGCGCGGT TGCCAACTGG AAAGTCCTGA ACAAAGGCGC
	GCTGTCCGGT
451	GCGGAAGCAG GGGAAACCAA GGCGGAAATC CGCCTGACGC
	TGTCCACTTC
501	AAAACTGCCC AAGCCTTTTC AAATCAATGC ATTGACTTCT
	CAAAACTGGC
551	ATTTGGATTC GGGTTGGAAA CCTCTAAACA TCATCGGGAA
	CAAATAA

This corresponds to the amino acid sequence <SEQ ID 368; ORF106-1>:

1	MAFITRLFKS SKWLIVPLML PAFQNVAAEG IDVSRAEARI
	TDGGQLSISS
51	RFQTELPDQL QQALRRGVPL NFTLSWQLSA PIIASYRFKL
	GQLIGDDDNI
101	DYKLSFHPLT NRYRVTVGAF STDYDTLDAA LRATGAVANW
	KVLNKGALSG
151	AEAGETKAEI RLTLSTSKLP KPFQINALTS QNWHLDSGWK
	PLNIIGNK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF106 shows 87.4% identity over a 199aa overlap with an ORF (ORF106a) from strain A of N. meningitidis:

Due to the K→N substitution at residue 111, the homology between ORF106a and ORF106-1 is 87.9% over the same 199 aa overlap.

The complete length ORF106a nucleotide sequence <SEQ ID 369> is:

1	ATGGCTTTTA TTACGCGCTT ATTCAAAAGC ATTAAACAAT
	GGCTTGTGCT
51	GCTGCCGATG CTTTCCGTTT TGCCGGACGC GGCGGCGGAG
	GGGATAGATG
101	TGAGCCGCGC CGAAGCGAGG ATAANCGACG GCGGGCAGCT
	TTCCATNAGN
151	AGCCGCTTCC AAACCGAGCT GCCCGACCAG CTCCAANNNG
	CGNNGNGCCG
201	GGGCGTGNCG CTCAACTNTA CCTTAAGNTG GCAGCTTTCC
	GCCCCGATAA
251	TCGCTTCTTA TCGGTTTNAA TTGGGGCAAC TGATTGGCGA
	TGACGACNAT
301	ATTGACTACA AACTGAGTTT CCATCCGCTG ACCAACCGCT
	ACCGCGTTAC
351	CGTCGGCGCG TTTTCGACAG ANTACGACAC CTTGGATGCG
	GCATTGCGCG
401	CGACCGGCGC GGTTGCCAAC TGGAAAGTCC TGAACAAAGG
	CGCGCTGTCC
451	GGTGCGGAAG CAGGGGAAAC CAAGGCGGAA ATCCGCCTGA
	CGCTGTCCAC
501	TTCAAAACTG CCCAAGCCTT TTCAAATCAA TGCATTGACT
	TCTCAAAACT
551	GGCATTTGGA TTCGGGTTGG AAACCTCTAA ACATCATCGG
	GAACAAATAA

This encodes a protein having amino acid sequence <SEQ ID 370>:

1	MAFITRLFKS IKQWLVLLPM LSVLPDAAAE GIDVSRAEAR
	IXDGGQLSXX
51	SRFQTELPDQ LQXAXXRGVX LNXTLXWQLS APIIASYRFX
	LGQLIGDDDX
101	IDYKLSFHPL TNRYRVTVGA FSTXYDTLDA ALRATGAVAN
	WKVLNKGALS
151	GAEAGETKAE IRLTLSTSKL PKPFQINALT SQNWHLDSGW
	KPLNIIGNK*

Homology with a Predicted ORF from N. gonorrhoeae

ORF106 shows 90.5% identity over a 199aa overlap with a predicted ORF (ORF106.ng) from N. gonorrhoeae:

Due to the K→N substitution at residue 111, the homology between ORF106ng and ORF106-1 is 91.0% over the same 199 aa overlap.

The complete length ORF106ng nucleotide sequence <SEQ ID 371> is:

1	ATGGCTTTTA TTACGCGCTT ATTCAAAAGC ATTAAACAAT
	GGCTTGTGCT
51	GTTGCCGATA CTCTCCGTTT TGCCGGACGC GGCGGCGGAG
	GGCATTGCCG
101	CGACCCGCGC CGAAGCGAGG ATAACCGACG GCGGGCGGCT
	TTCCATCAGC
151	AGCCGCTTCC AAACCGAGCT GCCCGACCAG CTCCAACAGG
	CGTTGCGCCG
201	GGGCGTACCG CTCAACTTTA CCTTAAGCTG GCAGCTTTCC
	GCCCCGACAA
251	TCGCTTCTTA TCGGTTTAAA TTGGGGCAAC TGATTGGCGA
	TGACGACAAT
301	ATTGACTACA AACTAAGTTT CCATCCGCTG ACCAACCGCT
	ACCGCGTTAC
351	CGTCGGCGCA TTTTCCACCG ATTACGACAC TTTGGATGCG
	GCATTGCGCG
401	CGACCGGCGC GGTTGCCAAC TGGAAAGTCC TGAACAAAGG
	CGCGTTGTCC
451	GGTGCGGAAG CAGGGGAAAC CAAGGCGGAA ATCCGCCTGA
	CGCTGTCCAC
501	TTCAAAACTG CCCAAGCCTT TCCAAATCAA CGCATTGACT
	TCTCAAAACT
551	GGCATTTGGA TTCGGGTTGG AAACCTCTAA ACATCATCGG
	GAACAAATAA

This encodes a protein having amino acid sequence <SEQ ID 372>:

1	MAFITRLFKS IKQWLVLLPI LSVLPDAAAE GIAATRAEAR
	ITDGGRLSIS
51	SRFQTELPDQ LQQALRRGVP LNFTLSWQLS APTIASYRFK
	LGQLIGDDDN
101	IDYKLSFHPL TNRYRVTVGA FSTDYDTLDA ALRATGAVAN
	WKVLNKGALS
151	GAEAGETKAE IRLTLSTSKL PKPFQINALT SQNWHLDSGW
	KPLNIIGNK*

Based on this analysis, including the presence of a putative leader sequence in the gonococcal protein, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF106-1 (18 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 13A shows the results of affinity purification of the His-fusion protein, and FIG. 13B shows the results of expression of the GST-fusion in E. coli. Purified His-fusion protein was used to immunise mice, whose sera were used for FACS analysis (FIG. 13C) These experiments confirm that ORF106-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 44

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 373>:

1	ATGGACACAA AAGAAATCCT CGG.TACGCG GcAGGcTCGA
	TCGGCAGCGC
51	GGTTTTAGCC GTCATCATCc TGCCGCTGCT GTCGTGGTAT
	TTCCCCGCCG
101	ACGACATCGG GCGCATCGTG CTGATGCAGA CGGCGGCGGG
	GCTgACGGTG
151	TCGGTGTTGT GCCTCGGGCT GGATCAGGCA TACGTCCGCG
	AATACTATGC
201	CACCGCCGAC AAAGACAcCT TGTTCAAAAC CCTGTTCCTG
	CCGCCGCTGC
251	TGTCTGCCGC CGCGATAGCC GCCCTGCTGC TTTCCCGCCC
	GTCCCTGCCG
301	TCTGAAATCC TGTTTTCACT CGACGATGCC gCCGCCGGCa
	TCGGGCTGGT
351	GCTGTTTGAA CtGAGCTTCC TGCCCATCCG cTTTCTCTTA
	CTGGTTTTGC
401	GTATGGAAGG ACGCGCCcTT GCCTTTTCGT CCGCGCAACT
	CGTGCcCAAG
451	CTCGCCATCC TGCTGCTG.T GCCGCTGACG GTCGGGCTGC
	TGCACTTTCC
501	AGCGAACACC GCCGTCCTGA CCGCCGTTTA CGCGCTGGCA
	AACCTTGCCG
551	CCGCCGCCTT TTTGCTGTTT CAAAACCGAT GCCGTCTGAA
	GGCCGTCCGG
601	CACGCACCGT TTTCGCCCGC CGTCCTGCAC CGGGGG.TGC
	GCTACGGCAT
651	ACCGATCGCA CTGAGCAGCA TCGCCTATTG GGGGCTGGCA
	TCCGCCGACC
701	GTTTGTTCCT GAAAAAATAT GCCGGCCTGG AACAGCTCGG
	CGTTTATTCG
751	ATGGGTATTT CGTTCGGCGG GGCGGCATTA TTGTTCCAAA
	GCATCTTTTC
801	AACGGTCTGG ACACCGTATA TTTTCCGCGC AATCGAAGAA
	AACGCCCCGC
851	CCGCTCGCCT CTCGGCAACG GCAGAATCCG CCGCCGCCCT
	GCTTGCCTCC
901	GCCCTCTGC. TGACCGGCAT TTTCTCGCCC CTTGCCTCCC
	TCCTGCTGCC
951	GGAAAACTAC GCCGCCGTCC GGTTTATCGT CGTATCGTGT
	ATG.TGCCGC
1001	CGCTGTTTTG CACGCTGGCG GAAATCAGCG GCATCGGTTT
	GAACGTCGTT
1051	CGCAAAACGC GCCCGATCGC GCTCGCCACC TTGGGCGCGC
	TGGCGGCAAA
1101	CCTGCTGCTG CTGGGGCTTG ACCGTGCCGT ACCGGCGAGG
	CCGCC.GGCG
1151	CGGCGGTTGC CTGTGCCGCC TCATTCTGGC TGTTTTTTGC
	CTTCAAGACC
1201	GAAAGCTCyT GCCGCCTGTG GCAGCCGCTC AAACGCCTGC
	CGCTTTATCT
1251	GCACACATTG TTCTGCCTGA CCTCCTCGGC GGCCTACACC
	TGCTTCGGCA
1301	CGCCGGCAAA CTATCCCCTG TTTGCCGGCG TATGGGCGGC
	ATATCTGGCA
1351	GGCTGCATCC TGCGCCACCG GAAAGATTTG CACAAACTGT
	TTCATTATTT
1401	GAAAAAACAA GGTTTCCCAT TATGA

This corresponds to the amino acid sequence <SEQ ID 374; ORF10>:

1	MDTKEILXYA AGSIGSAVLA VIILPLLSWY FPADDIGRIV
	LMQTAAGLTV
51	SVLCLGLDQA YVREYYATAD KDTLFKTLFL PPLLSAAAIA
	ALLLSRPSLP
101	SEILFSLDDA AAGIGLVLFE LSFLPIRFLL LVLRMEGRAL
	AFSSAQLVPK
151	LAILLLXPLT VGLLHFPANT AVLTAVYALA NLAAAAFLLF
	QNRCRLKAVR
201	HAPFSPAVLH RGXRYGIPIA LSSIAYWGLA SADRLFLKKY
	AGLEQLGVYS
251	MGISFGGAAL LFQSIFSTVW TPYIFRAIEE NAPPARLSAT
	AESAAALLAS
301	ALCXTGIFSP LASLLLPENY AAVRFIVVSC MXPPLFCTLA
	EISGIGLNVV
351	RKTRPIALAT LGALAANLLL LGLDRAVPAR PXGAAVACAA
	SFWLFFAFKT
401	ESSCRLWQPL KRLPLYLHTL FCLTSSAAYT CFGTPANYPL
	FAGVWAAYLA
451	GCILRHRKDL HKLFHYLKKQ GFPL*

Further sequence analysis revealed the complete DNA sequence <SEQ ID 375> to be:

1	ATGGACACAA AAGAAATCCT CGGCTACGCG GCAGGCTCGA
	TCGGCAGCGC
51	GGTTTTAGCC GTCATCATCC TGCCGCTGCT GTCGTGGTAT
	TTCCCCGCCG
101	ACGACATCGG GCGCATCGTG CTGATGCAGA CGGCGGCGGG
	GCTGACGGTG
151	TCGGTGTTGT GCCTCGGGCT GGATCAGGCA TACGTCCGCG
	AATACTATGC
201	CACCGCCGAC AAAGACACCT TGTTCAAAAC CCTGTTCCTG
	CCGCCGCTGC
251	TGTCTGCCGC CGCGATAGCC GCCCTGCTGC TTTCCCGCCC
	GTCCCTGCCG
301	TCTGAAATCC TGTTTTCACT CGACGATGCC GCCGCCGGCA
	TCGGGCTGGT
351	GCTGTTTGAA CTGAGCTTCC TGCCCATCCG CTTTCTCTTA
	CTGGTTTTGC
401	GTATGGAAGG ACGCGCCCTT GCCTTTTCGT CCGCGCAACT
	CGTGCCCAAG
451	CTCGCCATCC TGCTGCTGCT GCCGCTGACG GTCGGGCTGC
	TGCACTTTCC
501	AGCGAACACC GCCGTCCTGA CCGCCGTTTA CGCGCTGGCA
	AACCTTGCCG
551	CCGCCGCCTT TTTGCTGTTT CAAAACCGAT GCCGTCTGAA
	GGCCGTCCGG
601	CACGCACCGT TTTCGCCCGC CGTCCTGCAC CGGGGGCTGC
	GCTACGGCAT
651	ACCGATCGCA CTGAGCAGCA TCGCCTATTG GGGGCTGGCA
	TCCGCCGACC
701	GTTTGTTCCT GAAAAAATAT GCCGGCCTGG AACAGCTCGG
	CGTTTATTCG
751	ATGGGTATTT CGTTCGGCGG GGCGGCATTA TTGTTCCAAA
	GCATCTTTTC
801	AACGGTCTGG ACACCGTATA TTTTCCGCGC AATCGAAGAA
	AACGCCCCGC
851	CCGCCCGCCT CTCGGCAACG GCAGAATCCG CCGCCGCCCT
	GCTTGCCTCC
901	GCCCTCTGCC TGACCGGCAT TTTCTCGCCC CTTGCCTCCC
	TCCTGCTGCC
951	GGAAAACTAC GCCGCCGTCC GGTTTATCGT CGTATCGTGT
	ATGCTGCCGC
1001	CGCTGTTTTG CACGCTGGCG GAAATCAGCG GCATCGGTTT
	GAACGTCGTC
1051	CGCAAAACGC GCCCGATCGC GCTCGCCACC TTGGGCGCGC
	TGGCGGCAAA
1101	CCTGCTGCTG CTGGGGCTTG CCGTGCCGTC CGGCGGCGCG
	CGCGGCGCGG
1151	CGGTTGCCTG TGCCGCCTCA TTCTGGCTGT TTTTTGCCTT
	CAAGACCGAA
1201	AGCTCCTGCC GCCTGTGGCA GCCGCTCAAA CGCCTGCCGC
	TTTATCTGCA
1251	CACATTGTTC TGCCTGACCT CCTCGGCGGC CTACACCTGC
	TTCGGCACGC
1301	CGGCAAACTA TCCCCTGTTT GCCGGCGTAT GGGCGGCATA
	TCTGGCAGGC
1351	TGCATCCTGC GCCACCGGAA AGATTTGCAC AAACTGTTTC
	ATTATTTGAA
1401	AAAACAAGGT TTCCCATTAT GA

This corresponds to the amino acid sequence <SEQ ID 376; ORF10-1>:

1	MDTKEILGYA AGSIGSAVLA VIILPLLSWY FPADDIGRIV
	LMQTAAGLTV
51	SVLCLGLDQA YVREYYATAD KDTLFKTLFL PPLLSAAAIA
	ALLLSRPSLP
101	SEILFSLDDA AAGIGLVLFE LSFLPIRFLL LVLRMEGRAL
	AFSSAQLVPK
151	LAILLLLPLT VGLLHFPANT AVLTAVYALA NLAAAAFLLF
	QNRCRLKAVR
201	HAPFSPAVLH RGLRYGIPIA LSSIAYWGLA SADRLFLKKY
	AGLEQLGVYS
251	MGISFGGAAL LFQSIFSTVW TPYIFRAIEE NAPPARLSAT
	AESAAALLAS
301	ALCLTGIFSP LASLLLPENY AAVRFIVVSC MLPPLFCTLA
	EISGIGLNVV
351	RKTRPIALAT LGALAANLLL LGLAVPSGGA RGAAVACAAS
	FWLFFAFKTE
401	SSCRLWQPLK RLPLYLHTLF CLTSSAAYTC FGTPANYPLF
	AGVWAAYLAG
451	CILRHRKDLH KLFHYLKKQG FPL*

Computer analysis of this amino acid sequence gave the following results:

Prediction

ORF10-1 is predicted to be the precursor of an integral membrane protein, since it comprises several (12-13) potential transmembrane segments, and a probable cleavable signal peptide

Homology with EpsM from Streptococcus thermophilus (Accession Number U40830).

ORF10 shows homology with the epsM gene of S. thermophilus, which encodes a protein of a size similar to ORF10 and is involved in expolysaccharide synthesis. Other homologies are with prokaryotic membrane proteins:

Identities = (25%)

Query:	213	LRYGIPLALSSLAYWGLASADRLFLKKYAGLEQLGVYSMGISFGGAALLLQSIFSTVW	270
		L Y +PL  SS+ +W L ++ R F+  + G    G+ ++         +  +IF+  W
Sbjct:	210	LYYALPLIPSSILWWLLNASSRYFVLFFLGAGANGLLAVATKIPSIISIFNTIFTQAW	267

Identities = 15/57 (26%), Positives = 31/57 (54%)

Query:	7	LGYAAGSIGSAVLAVIILPLLSWYFPADDIGRIVLMQTAAGLTVSVLCLGLDQAYVR	63
		L +  G++GS +L  +++PL ++     + G   L QT A L + ++ + +  A +R
Sbjct:	12	LVFTIGNLGSKLLVFLLVPLYTYAMTPQEYGMADLYQTTANLLLPLITMNVFDATLR	68

Identities = 16/96 (16%), Positives = 36/96 (37%)

Query:	307	IFSPLASLLLPENYAAVRFTVVSCMLPPLFYTLTEISGIGLNVVRKTRPIXXXXXXXXXX	366
		+  P+   ++  +YA+    V   ML  LF + ++  G      ++T+ +
Sbjct:	305	VLKPIVEKVVSSDYASSWQYVPFFMLSMLFSSFSDFFGTNYIAAKQTKGVFMTSIYGTIV	364

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF10 shows 95.4% identity over a 475aa overlap with an ORF (ORF10a) from strain A of N. meningitidis:

The complete length ORF10a nucleotide sequence <SEQ ID 377> is:

1	ATGGACACAA AAGAAATCCT CGGCTACGCG GCAGGCTCGA
	TCGGCAGCGC
51	GGTTTTAGCC GTCATCATCC TGCCGCTGCT GTCGTGGTAT
	TTCCCTGCCG
101	ACGACATCGG ACGCATCGTG CTGATGCAGA CGGCGGCGGG
	GCTGACGGTG
151	TCGGTGTTGT GCCTCGGGCT GGATCAGGCA TACGTCCGCG
	AATACTATGC
201	CGCCGCCGAC AAAGACACTT TGTTCAAAAC CCTGTTCCTG
	CCGCCGCTGC
251	TGTCTGCCGC CGCGATAGCC GCCCTGCTGC TTTCCCGCCC
	ATCCCTGCCG
301	TCTGAAATCC TGTTTTCGCT CGACGATGCC GCCGCCGGCA
	TCGGGCTGGT
351	GCTGTTTGAA CTGAGCTTCC TGCCCATCCG CTTTCTCTTA
	CTGGTTTTGC
401	GTATGGAAGG ACGCGCCCTT GCCTTTTCGT CCGCGCAACT
	CGTGTCCAAG
451	CTCGCCATCC TGCTGCTGCT GCCGCTGACG GTCGGGCTGC
	TGCACTTTCC
501	GGCGAACACC GCCGTCCTGA CCGCCGTTTA CGCGCTGGCA
	AACCTTGCCG
551	CCGCCGCCTT TTTGCTGTTT CAAAACCGAT GCCGTCTGAA
	GGCCGTCCGG
601	CGCGCACCGT TTTCATCCGC CGTCCTGCAT CGCGGCCTGC
	GCTACGGCAT
651	ACCGATCGCA CTAAGCAGCA TCGCCTATTG GGGGCTGGCA
	TCCGCCGACC
701	GTTTGTTCCT GAAAAAATAT GCCGGCCTAG AACAGCTCGG
	CGTTTATTCG
751	ATGGGTATTT CGTTCGGCGG AGCGGCATTA TTGTTCCAAA
	GCATCTTTTC
801	AACGGTCTGG ACACCGTATA TTTTCCGCGC AATCGAAGCA
	AACGCCCCGC
851	CCGCCCGCCT CTCGGCAACG GCAGAATCCG CCGCCGCCCT
	GCTTGCCTCC
901	GCCCTCTGCC TGACCGGCAT TTTCTCGCCC CTCGCCTCCC
	TCCTGCTGCC
951	GGAAAACTAC GCCGCCGTCC GGTTTATCGT CGTATCGTGT
	ATGCTGCCTC
1001	CGCTGTTTTG CACGCTGGTA GAAATCAGCG GCATCGGTTT
	GAACGTCGTC
1051	CGAAAAACAC GCCCGATCGC GCTCGCCACC TTGGGCGCGC
	TGGCGGCAAA
1101	CCTGCTGCTG CTGGGGCTTG CCGTACCGTC CGGCGGCGCG
	CGCGGCGCGG
1151	CGGTTGCCTG TGCCGCCTCA TTTTGGCTGT TTTTTGTTTT
	CAAGACCGAA
1201	AGCTCCTGCC GCCTGTGGCA GCCGCTCAAA CGCCTGCCGC
	TTTATATGCA
1251	CACATTGTTC TGCCTGGCCT CCTCGGCGGC CTACACCTGC
	TTCGGCACTC
1301	CGGCAAACTA CCCCCTGTTT GCCGGCGTAT GGGCGGTATA
	TCTGGCAGGC
1351	TGCATCCTGC GCCACCGGAA AGATTTGCAC AAACTGTTTC
	ATTATTTGAA
1401	AAAACAAGGT TTCCCATTAT GA

This encodes a protein having amino acid sequence <SEQ ID 378>:

1	MDTKEILGYA AGSIGSAVLA VIILPLLSWY FPADDIGRIV
	LMQTAAGLTV
51	SVLCLGLDQA YVREYYAAAD KDTLFKTLFL PPLLSAAAIA
	ALLLSRPSLP
101	SEILFSLDDA AAGIGLVLFE LSFLPIRFLL LVLRMEGRAL
	AFSSAQLVSK
151	LAILLLLPLT VGLLHFPANT AVLTAVYALA NLAAAAFLLF
	QNRCRLKAVR
201	RAPFSSAVLH RGLRYGIPIA LSSIAYWGLA SADRLFLKKY
	AGLEQLGVYS
251	MGISFGGAAL LFQSIFSTVW TPYIFRAIEA NAPPARLSAT
	AESAAALLAS
301	ALCLTGIFSP LASLLLPENY AAVRFIVVSC MLPPLFCTLV
	EISGIGLNVV
351	RKTRPIALAT LGALAANLLL LGLAVPSGGA RGAAVACAAS
	FWLFFVFKTE
401	SSCRLWQPLK RLPLYMHTLF CLASSAAYTC FGTPANYPLF
	AGVWAVYLAG
451	CILRHRKDLH KLFHYLKKQG FPL*

ORF10a and ORF10-1 show 95.4% identity in 475 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF10 shows 94.1% identity over a 475aa overlap with a predicted ORF (ORF10.ng) from N. gonorrhoeae:

The complete length ORF10ng nucleotide sequence <SEQ ID 379> is:

1	ATGGACACAA AAGAAATCCT CGGCTACGCG GCAGGCTCGA
	TCGGCAGCGC
51	GGTTTTAGCC GTCATCATCC TGCCGCTGCT GTCGTGGTAT
	TTCcccgCCG
101	ACGACATCGG GCGCATCGTG CTGATGCAGA CGGCGGCGGG
	ACTGACGGTG
151	TCGGTATTGT GCCTCGGGCT GGATCAGGCA TACGTCCGCG
	AATACTATGC
201	CGCCGCCGAC AAAGACACTT TGTTCAAAAC CCTGTTCCTG
	CCGCCGCTGC
251	TGTTTTCCGC CGCGATAGCC GCCCTGCTGC TTTCCCGCCC
	GTCCCTGCCG
301	TCTGAAATCC TGTTTTCGCT CGACGATGCC GCCGCCGGCA
	TCGGGCTGGT
351	GCTGTTTGAA CTGAGCTTCC TGCCCATCCG CTTTCTCTTA
	CTGGTTTTGC
401	GTATGGAAGG GCGCGCCCTT GCCTTTTCGT CCGCGCAACT
	CGTGCCCAAA
451	CTCGCCATTC TGCTGCTGTT GCCGCTGACG GTCGGGCTGC
	TGCACTTTCC
501	GGCGAACACC TCCGTCCTGA CCGCCGTTTA CGCGCTGGCA
	AACCTTGCCG
551	CCGCCGCCTT TTTGCTGTTT CAAAACCGAT GCCGTCTGAA
	GGCCGTCCGG
601	CGCGCGCCGT TTTCGCCCGC CGTCCTGCAC CGGGGGCTGC
	GCTACGGCAT
651	ACCGCTCGCA CTGAGCAGCC TTGCCTATTG GGGGCTGGCA
	TCCGCCGACC
701	GTTTGTTCCT GAAAAAATAT GCGGGCCTGG AACAGCTCGG
	CGTTTATTCG
751	ATGGGTATTT CGTTCGGCGG GGCGGCATTA TTGCTCCAAA
	GCATCTTTTC
801	AACGGTCTGG ACACCGTATA TTTTCCGTGC AATCGAAGAA
	AACGCCACGC
851	CCGCCCGCCT CTCGGCAACG GCAGAATCCG CCGCCGCCCT
	GCTTGCCTCC
901	GCCCTCTGCC TGACCGGAAT TTTCTCGCCC CTCGCCTCCC
	TCCTGCTGCC
951	GGAAAACTAC GCCGCCGTCC GGTTTACCGT CGTATCGTGT
	ATGCTGccgc
1001	cgctGTTTTA CACGCTGACC GAAATCAGCG GCATCGGTTT
	GAACGTCGTC
1051	CGCAAAACGC GTCCGATCGC GCTTGCCACC TTGGGCGCGC
	TGGCGGCAAA
1101	CCTGCTGCTG CTGGGGCTTG CCGTACCGTC CGGCGGCACG
	CGCGGCGCGG
1151	CGGTTGCCTG TGCCGCCTCA TTCTGGTTGT TTTTTGTTTT
	CAAGACAGAA
1201	AGCTCCTGCC GCCTGTGGCA GCCGCTCAAA CGCCTGCCGC
	TTTATATGCA
1251	CACATTGTTC TGCCTgGCCT CCTCGGCGGC CTACACCTGC
	TTCGGCACAC
1301	CGGCAAACTA CCCcctgttt gccggcgtAT GGGCGGCATA
	TCTGGCAGGC
1351	TGCATCCTGC GCCACCGGAA AAATTTGCAC AAACTGTTTC
	ATTATTTGAA
1401	AAAACAAGGT TTCCCATTAT GA

This encodes a protein having amino acid sequence <SEQ ID 380>:

1	MDTKEILGYA AGSIGSAVLA VIILPLLSWY FPADDIGRIV
	LMQTAAGLTV
51	SVLCLGLDQA YVREYYAAAD KDTLFKTLFL PPLLFSAAIA
	ALLLSRPSLP
101	SEILFSLDDA AAGIGLVLFE LSFLPIRFLL LVLRMEGRAL
	AFSSAQLVPK
151	LAILLLLPLT VGLLHFPANT SVLTAVYALA NLAAAAFLLF
	QNRCRLKAVR
201	RAPFSPAVLH RGLRYGIPLA LSSLAYWGLA SADRLFLKKY
	AGLEQLGVYS
251	MGISFGGAAL LLQSIFSTVW TPYIFRAIEE NATPARLSAT
	AESAAALLAS
301	ALCLTGIFSP LASLLLPENY AAVRFTVVSC MLPPLFYTLT
	EISGIGLNVV
351	RKTRPIALAT LGALAANLLL LGLAVPSGGT RGAAVACAAS
	FWLFFVFKTE
401	SSCRLWQPLK RLPLYMHTLF CLASSAAYTC FGTPANYPLF
	AGVWAAYLAG
451	CILRHRKNLH KLFHYLKKQG FPL*

ORF10ng and ORF10-1 show 96.4% identity in 473 aa overlap:

Based on this analysis, including the presence of a putative leader peptide and several transmembrane segments and the presence of a leucine-zipper motif(4 Leu residues spaced by 6 aa, shown in bold), it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 45

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 381>:

1	..ATCCTGAAAC CGCATAACCA GCTTAAGGAA GACATCCAAC
	CTGATCCGGC
51	CGATCAAAAC GCCTTGTCCG AACCGGATGC TGCGACAGAG
	GCAGAGCAGT
101	CGGATGCGGA AAATGCTGCC GACAAGCAGC CCGTTGCCGA
	TAAAGCCGAC
151	GAGGTTGAAG AAAAGGCGGG CGAGCCGGAA CGGGAAGAGC
	CGGACGGACA
201	GGCAGTGCGT AAGAAAGCGC TGACGGAAGA GCGTGAACAA
	ACCGTCAGGG
251	AAAAAGCGCA GAAGAAAGAT GCCGAAACGG TTAAAATACA
	AGCGGTAAAA
301	CCGTCTAAAG AAACAGAGAA AAAAGCTTCA AAAGAAGAGA
	AAAAGGCGGC
351	GAAGGAAAAA GTTGCACCCA AACCAACCCC GGAACAAATC
	CTCAACAGCG
401	GCAgCATCGA AAAmGCGCGC AgTGCCGCCG CCAAAGAAGT
	GCAGAAAATG
451	AA.AACGTCC GACAAGGCGG AAGC.AACGC ATTATCTGCA
	AATGGGCGCG
501	TATGCCGACC GTCAGAGCGC GGAAGGGCAG CGTGCCAAAC
	TGGCAATCTT
551	GGGCATATCT TCCAAGGTGG TCGGTTATCA GGCGGGACAT
	AAAACGCTTT
601	ACCGGGTGCA AAGCGGCAAT ATGTCTGCCG ATGCGGTGA

This corresponds to the amino acid sequence <SEQ ID 382; ORF65>:

1	..ILKPHNQLKE DIQPDPADQN ALSEPDAATE AEQSDAENAA
	DKQPVADKAD
51	EVEEKAGEPE REEPDGQAVR KKALTEEREQ TVREKAQKKD
	AETVKIQAVK
101	PSKETEKKAS KEEKKAAKEK VAPKPTPEQI LNSGSIEXAR
	SAAAKEVQKM
151	XNVRQGGSXR IICKWARMPT VRARKGSVPN WQSWAYLPRW
	SVIRRDIKRF
201	TGCKAAICLP MR*

Further work revealed the complete nucleotide sequence <SEQ ID 383>:

1	ATGTTTATGA ACAAATTTTC CCAATCCGGA AAAGGTCTGT
	CCGGTTTTTT
51	CTTCGGTTTG ATACTGGCGA CGGTCATTAT TGCCGGTATT
	TTGTTTTATC
101	TGAACCAGAG CGGTCAAAAT GCGTTCAAAA TCCCGGCTTC
	GTCGAAGCAG
151	CCTGCAGAAA CGGAAATCCT GAAACCGAAA AACCAGCCTA
	AGGAAGACAT
201	CCAACCTGAA CCGGCCGATC AAAACGCCTT GTCCGAACCG
	GATGCTGCGA
251	CAGAGGCAGA GCAGTCGGAT GCGGAAAAAG CTGCCGACAA
	GCAGCCCGTT
301	GCCGATAAAG CCGACGAGGT TGAAGAAAAG GCGGGCGAGC
	CGGAACGGGA
351	AGAGCCGGAC GGACAGGCAG TGCGTAAGAA AGCGCTGACG
	GAAGAGCGTG
401	AACAAACCGT CAGGGAAAAA GCGCAGAAGA AAGATGCCGA
	AACGGTTAAA
451	AAACAAGCGG TAAAACCGTC TAAAGAAACA GAGAAAAAAG
	CTTCAAAAGA
501	AGAGAAAAAG GCGGCGAAGG AAAAAGTTGC ACCCAAACCA
	ACCCCGGAAC
551	AAATCCTCAA CAGCGGCAGC ATCGAAAAAG CGCGCAGTGC
	CGCCGCCAAA
601	GAAGTGCAGA AAATGAAAAC GTCCGACAAG GCGGAAGCAA
	CGCATTATCT
651	GCAAATGGGC GCGTATGCCG ACCGTCAGAG CGCGGAAGGG
	CAGCGTGCCA
701	AACTGGCAAT CTTGGGCATA TCTTCCAAGG TGGTCGGTTA
	TCAGGCGGGA
751	CATAAAACGC TTTACCGGGT GCAAAGCGGC AATATGTCTG
	CCGATGCGGT
801	GAAAAAAATG CAGGACGAGT TGAAAAAACA TGAAGTCGCC
	AGCCTGATCC
851	GTTCTATCGA AAGCAAATAA

This corresponds to the amino acid sequence <SEQ ID 384; ORF65-1>:

1	MFMNKFSQSG KGLSGFFFGL ILATVIIAGI LFYLNQSGQN
	AFKIPASSKQ
51	PAETEILKPK NQPKEDIQPE PADQNALSEP DAATEAEQSD
	AEKAADKQPV
101	ADKADEVEEK AGEPEREEPD GQAVRKKALT EEREQTVREK
	AQKKDAETVK
151	KQAVKPSKET EKKASKEEKK AAKEKVAPKP TPEQILNSGS
	IEKARSAAAK
201	EVQKMKTSDK AEATHYLQMG AYADRQSAEG QRAKLAILGI
	SSKVVGYQAG
251	HKTLYRVQSG NMSADAVKKM QDELKKHEVA SLIRSIESK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF65 shows 92.0% identity over a 150aa overlap with an ORF (ORF65a) from strain A of N. meningitidis:

The complete length ORF65a nucleotide sequence <SEQ ID 385> is:

1	ATGTTTATGA ACAAATTTTC CCAATCCGGA AAAGGTCTGT
	CCGGTTTTTT
51	CTTCGGTTTG ATACTGGCGA CGGTCATTAT TGCCGGTATT
	TTGTTTTATC
101	TGAACCAGAG CGGTCAAAAT GCGTTCAAAA TCCCGGTTCC
	GTCGAAGCAG
151	CCTGCAGAAA CGGAAATCCT GAAACCGAAA AACCAGCCTA
	AGGAAGACAT
201	CCAACCTGAA CCGGCCGATC AAAACGCCTT GTCCGAACCG
	GATGCTGCGA
251	AAGAGGCAGA GCAGTCGGAT GCGGAAAAAG CTGCCGACAA
	GCAGCCCGTT
301	GCCGACAAAG CCGACGAGGT TGAGGAAAAG GCGGACGAGC
	CGGAGCGGGA
351	AAAGTCGGAC GGACAGGCAG TGCGCAAGAA AGCACTGACG
	GAAGAGCGTG
401	AACAAACCGT CGGGGAAAAA GCGCAGAAGA AAGATGCCGA
	AACGGTTAAA
451	AAACAAGCGG TAAAACCATC TAAAGAAACA GAGAAAAAAG
	CTTCAAAAGA
501	AGAGAAAAAG GCGGAGAAGG AAAAAGTTGC ACCCAAACCG
	ACCCCGGAAC
551	AAATCCTCAA CAGCGGCAGC ATCGAAAAAG CGCGCAGTGC
	CGCTGCCAAA
601	GAAGTGCAGA AAATGAAAAC GCCCGACAAG GCGGAAGCAA
	CGCATTATCT
651	GCAAATGGGC GCGTATGCCG ACCGCCGGAG CGCGGAAGGG
	CAGCGTGCCA
701	AACTGGCAAT CTTGGGCATA TCTTCCAAGG TGGTCGGTTA
	TCAGGCGGGA
751	CATAAAACGC TTTACCGGGT GCAAAGCGGC AATATGTCTG
	CCGATGCGGT
801	GAAAAAAATG CAGGACGAGT TGAAAAAACA TGAAGTCGCC
	AGCCTGATCC
851	GTTCTATCGA AAGCAAATAA

This encodes a protein having amino acid sequence <SEQ ID 386>:

1	MFMNKFSQSG KGLSGFFFGL ILATVIIAGI LFYLNQSGQN
	AFKIPVPSKQ
51	PAETEILKPK NQPKEDIQPE PADQNALSEP DAAKEAEQSD
	AEKAADKQPV
101	ADKADEVEEK ADEPEREKSD GQAVRKKALT EEREQTVGEK
	AQKKDAETVK
151	KQAVKPSKET EKKASKEEKK AEKEKVAPKP TPEQILNSGS
	IEKARSAAAK
201	EVQKMKTPDK AEATHYLQMG AYADRRSAEG QRAKLAILGI
	SSKVVGYQAG
251	HKTLYRVQSG NMSADAVKKM QDELKKHEVA SLIRSIESK*

ORF65a and ORF65-1 show 96.5% identity in 289 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF65 shows 89.6% identity over a 212aa overlap with a predicted ORF (ORF65.ng) from N. gonorrhoeae:

An ORF65ng nucleotide sequence <SEQ ID 387> was predicted to encode a protein having amino acid sequence <SEQ ID 388>:

1	MFMNKFSQSG KGLSGFFFGL ILATVIIAGI LLYLNQGGQN
	AFKIPAPSKQ
51	PAETEILKLK NQPKEDIQPE PADQNALSEP DVAKEAEQSD
	AEKAADKQPV
101	ADKADEVEEK AGEPEREEPD GQAVRKKALT EEREQTVREK
	AQKKDAETVK
151	KKAVKPSKET EKKASKEEKK AAKEKVAPKP TPEQILNSRS
	IEKARSAAAK
201	EVQKMKNFGQ GGSQRIICKW ARMPNPGARK GSVPNWQSWA
	YLPKWSAIRR
251	DIKRFTACKA AICPPMR*

After further analysis, the complete gonococcal DNA sequence <SEQ ID 389> was found to be:

1	ATGTTTATGA ACAAATTTTC CCAATCCGGA AAAGGTCTGT
	CCGGTTTCTT
51	CTTCGGTTTG ATACTGGCAA CGGTCATTAT TGCCGGTATT
	TTGCTTTATC
101	TGAACCAGGG CGGTCAAAAT GCGTTCAAAA TCCCGGCTCC
	GTCGAAGCAG
151	CCTGCAGAAA CGGAAATCCT GAAACTGAAA AACCAGCCTA
	AGGAAGACAT
201	CCAACCTGAA CCGGCCGATC AAAACGCCTT GTCCGAACCG
	GATGTTGCGA
251	AAGAGGCAGA GCAGTCGGAT GCGGAAAAAG CTGCCGACAA
	GCAGCCCGTT
301	GCCGACAAag ccgacgAGGT TGAAGAAAag GcGGgcgAgc
	cggaACGGga
351	aGAGCCGGAC ggACAGGCAG TGCGCAAGAA AGCACTGAcg
	gAAGAgcGTG
401	AACAAACcgt cagggAAAAA GCGCagaaga AAGATGCCGA
	AACGgTTAAA
451	AAacaaGCgg tAaaaccgtc tAAAGAAACa gagaaaaaag
	cTtcaaaaga
501	agagaaaaag gcggcgaaag aaaAAGttgc acccaaaccg
	accccggaaC
551	aaatcctcaa cagccgCagc atcgaaaaag cgcgtagtgc
	cgctgccaaa
601	gaAgtgcaGA AAatgaaaaa ctTtgggcaa ggcgGaagcc
	aacgcattaT
651	CTGcaaatgg gcgcgtatgc cgaccgtccg gagcgcggaA
	gggcagcgtg
701	ccaaACtggc aAtcttgGgc atatctTccg aagtggtcgG
	CTATCAGGCG
751	GGACATAAAA CGCTTTACCG CGTGCAAagc GGCAatatgt
	ccgccgatgc
801	gGTGAAAAAA ATGCAGGACG AGTTGAAAAA GCATGGGGtt
	gcCAGCCTGA
851	TCCGTGcgAT TGAAGGCAAA TAA

This encodes the following amino acid sequence <SEQ ID 390>:

1	MFMNKFSQSG KGLSGFFFGL ILATVIIAGI LLYLNQGGQN
	AFKIPAPSKQ
51	PAETEILKLK NQPKEDIQPE PADQNALSEP DVAKEAEQSD
	AEKAADKQPV
101	ADKADEVEEK AGEPEREEPD GQAVRKKALT EEREQTVREK
	AQKKDAETVK
151	KQAVKPSKET EKKASKEEKK AAKEKVAPKP TPEQILNSRS
	IEKARSAAAK
201	EVQKMKNFGQ GGSQRIICKW ARMPTVRSAE GQRAKLAILG
	ISSEVVGYQA
251	GHKTLYRVQS GNMSADAVKK MQDELKKHGV ASLIRAIEGK
	*

ORF65ng-1 and ORF65-1 show 89.0% identity in 290 aa overlap:

On this basis, including the presence of a putative transmembrane domain in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 46

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 391>:

1	ATGAACCACG ACATCACTTT CCTCACCCTG TTCCTACTCG
	GTkTCTTCGG
51	CGGAAcGCAC TGCATCGGTA TGTGCGGCGG ATTAAGCAGC
	GcGTTTGs.s
101	TCCAACTCCC CCCGCATATC AACCGCTTTT GGCTGATCCT
	GCTGCTTAAC
151	ACAGGACGGG TAAGCAGCTA TACGGCAAtC GGCCTGATAC
	TCGGATTAAT
201	CGGACAGGTC GGCGTTTCAC TCGAcCAaAC CCGCGTCCTG
	CAGAATATTT
251	TATACACGGC CGCCAACCTC CTGCTGCTCT TTTTAGGCTT
	ATACTTGAGC
301	GGTATTTCTT CCTTGGCGGC AAAAATCGAG AAaATCGGCA
	AACCGATATG
351	GCGGAACCTG AACCCGATAC TCAACCGGCT GTTACCCATA
	AAATCCATAC
401	CCGCCTGCCT tGCGgTCGGA ATATTATGGG GCTGGCTGCC
	GTGCGGACTG
451	GTTTACAGCG CGTCGCTTTA CGCGCTGGGA AgCGGTAGTG
	CGGCAACGGG
501	CGGGTTATAT ATGCTTGCCT TTGCACTGGG TACGCTGCCC
	AATCTTtTAG
551	CAATCGGCAT TTTtTCCCTG CAACTGAAwA AAATCATGCA
	AAACCGATAT
601	ATCCGCCTGT GTACGGGATT ATCCGTATCA TTATGGGCAT
	TATGGAAACT
651	TGCCGTCCTG TGGCTGTAA

This corresponds to the amino acid sequence <SEQ ID 392; ORF103>:

1	MNHDITFLTL FLLGXFGGTH CIGMCGGLSS AFXXQLPPHI
	NRFWLILLLN
51	TGRVSSYTAI GLILGLIGQV GVSLDQTRVL QNILYTAANL
	LLLFLGLYLS
101	GISSLAAKIE KIGKPIWRNL NPILNRLLPI KSIPACLAVG
	ILWGWLPCGL
151	VYSASLYALG SGSAATGGLY MLAFALGTLP NLLAIGIFSL
	QLXKIMQNRY
201	IRLCTGLSVS LWALWKLAVL WL*

Further work elaborated the DNA sequence <SEQ ID 393> as:

1	ATGAACCACG ACATCACTTT CCTCACCCTG TTCCTACTCG
	GTTTCTTCGG
51	CGGAACGCAC TGCATCGGTA TGTGCGGCGG ATTAAGCAGC
	GCGTTTGCGC
101	TCCAACTCCC CCCGCATATC AACCGCTTTT GGCTGATCCT
	GCTGCTTAAC
151	ACAGGACGGG TAAGCAGCTA TACGGCAATC GGCCTGATAC
	TCGGATTAAT
201	CGGACAGGTC GGCGTTTCAC TCGACCAAAC CCGCGTCCTG
	CAGAATATTT
251	TATACACGGC CGCCAACCTC CTGCTGCTCT TTTTAGGCTT
	ATACTTGAGC
301	GGTATTTCTT CCTTGGCGGC AAAAATCGAG AAAATCGGCA
	AACCGATATG
351	GCGGAACCTG AACCCGATAC TCAACCGGCT GTTACCCATA
	AAATCCATAC
401	CCGCCTGCCT TGCGGTCGGA ATATTATGGG GCTGGCTGCC
	GTGCGGACTG
451	GTTTACAGCG CGTCGCTTTA CGCGCTGGGA AGCGGTAGTG
	CGGCAACGGG
501	CGGGTTATAT ATGCTTGCCT TTGCACTGGG TACGCTGCCC
	AATCTTTTAG
551	CAATCGGCAT TTTTTCCCTG CAACTGAAAA AAATCATGCA
	AAACCGATAT
601	ATCCGCCTGT GTACGGGATT ATCCGTATCA TTATGGGCAT
	TATGGAAACT
651	TGCCGTCCTG TGGCTGTAA

This corresponds to the amino acid sequence <SEQ ID 394; ORF103-1>:

1	MNHDITFLTL FLLGFFGGTH CIGMCGGLSS AFALQLPPHI
	NRFWLILLLN
51	TGRVSSYTAI GLILGLIGQV GVSLDQTRVL QNILYTAANL
	LLLFLGLYLS
101	GISSLAAKIE KIGKPIWRNL NPILNRLLPI KSIPACLAVG
	ILWGWLPCGL
151	VYSASLYALG SGSAATGGLY MLAFALGTLP NLLAIGIFSL
	QLKKIMQNRY
201	IRLCTGLSVS LWALWKLAVL WL*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF103 shows 93.8% identity over. a 222aa overlap with an ORF (ORF103a) from strain A of N. meningitidis:

The complete length ORF103a nucleotide sequence <SEQ ID 395> is:

1	ATGAACCANG ACATCACTTT CCTCACCCTG TTCCTACTCG
	GTTTCTTCGG
51	CGGAACGCAC TGCATCGGTA TGTGCGGCGG ATTAAGCAGC
	GCGTTTGCGC
101	TCCAACTCCC CCCGCATATC AACCGCTTNT GGCTGATCCT
	GCTGCTTAAC
151	ACAGGACGGG TAAGCAGCTA TACGGCAATC GGCCTGATAC
	TCGGATTAAT
201	CGGACAGGTC GGCGTTTCAC TCGACCAAAC CCGCGTCNTG
	CAGAATATTT
251	TATACACGGC CGCCAACCTC CTGCTGCTCT TTTTAGGCTT
	ATACTTGAGC
301	GGTATTTCTT CCTTGGCGGC AAAAATCGAG AAAATCGGCA
	AACCGATATG
351	GCGGAACCTG AACCCGATAC TCAACCGGCT GTTACCCATA
	AAATCCATAC
401	CCGCCTGCCT TGCGGTCGGA ATATTATGGG GCTGGCTGCC
	GTGCGGACTA
451	GTTTACAGCG CGTCGCTTTA CGCGCTGGGA AGCGGTAGTG
	CGGCAACGGG
501	CGGGTTATAT ATGCTTGCCT TTGCACTGGG TACGCTGCCC
	AATCTTTNGG
551	CAATCGGCAT TTTTTCCCTG CAACTGNAAA AAATCATGCA
	AAACCGATAT
601	ATCCGCCTGT GTACGGGATT ATCCGTATCA TTATGGGCAT
	TATGGAAACT
651	TGCCGTCCTG TGGCTGTAA

This encodes a protein having amino acid sequence <SEQ ID 396>:

1	MNXDITFLTL FLLGFFGGTH CIGMCGGLSS AFALQLPPHI
	NRXWLILLLN
51	TGRVSSYTAI GLILGLIGQV GVSLDQTRVX QNILYTAANL
	LLLFLGLYLS
101	GISSLAAKIE KIGKPIWRNL NPILNRLLPI KSIPACLAVG
	ILWGWLPCGL
151	VYSASLYALG SGSAATGGLY MLAFALGTLP NLXAIGIFSL
	QLXKIMQNRY
201	IRLCTGLSVS LWALWKLAVL WL*

ORF103a and ORF103-1 show 97.7% identity in 222 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF103 shows 95.5% identity over a 222aa overlap with a predicted ORF (ORF103.ng) from N. gonorrhoeae:

The complete length ORF103ng nucleotide sequence <SEQ ID 397> is:

1	ATGAACCACG ACATCACTTT CCTCACCCTG TTCCTGCTCG
	GTTTCTTCGG
51	CGGAACTCAC TGCATCGGTA TGTGCGGCGG ATTAAGCAGC
	GCGTTTGCGC
101	TCCAACTCCC CCCGCATATC AACCGCTTTT GGCTGATTCT
	GCTGCTTAAC
151	ACAGGACGGA TAAGCAGCTA TACGGCAATC GGCCTGATGC
	TCGGATTAAT
201	CGGACAACTC GGCATTTCAC TCGACCAAAc ccgcgTCCTG
	CAAAATATTT
251	tatacacagc ctccaaCCTC CTGCTGCTCT TTTTAGGCTT
	ATACTTGAGC
301	GGTATTTCTT CCTTGGCGGC AAAAATCGAG AAAATCGGCA
	AACCGATATG
351	GCGCAACCTG AACCCGATAC TCAACCGGCT GCTGCCCATA
	AAATCCATAC
401	CCGCCTGCCT TGCTGTCGGA ATATTATGGG GCTGGCTGCC
	GTGCGGACTG
451	GTTTACAGCG CATCACTTTA CGCGCTGGGA AGCGGTAGTG
	CGACAACCGG
501	CGGACTGTAT ATGCTTGCCT TTGCACTGGG TACGCTGCCC
	AATCTTTTGG
551	CAATCGGCAT TTTTTCCCTG CAACTGAAAA AAATCATGCA
	AAACCGATAT
601	ATCCGCCTGT GTACAGGATT ATCCGTATCA TTATGGGCAT
	TATGGAAGCT
651	TGCCGTCCTG TGGCTGTAA

This encodes a protein having amino acid sequence <SEQ ID 398>:

1	MNHDITFLTL FLLGFFGGTH CIGMCGGLSS AFALQLPPHI
	NRFWLILLLN
51	TGRISSYTAI GLMLGLIGQL GISLDQTRVL QNILYTASNL
	LLLFLGLYLS
101	GISSLAAKIE KIGKPIWRNL NPILNRLLPI KSIPACLAVG
	ILWGWLPCGL
151	VYSASLYALG SGSATTGGLY MLAFALGTLP NLLAIGIFSL
	QLKKIMQNRY
201	IRLCTGLSVS LWALWKLAVL WL*

In addition, ORF103ng and ORF103-1 show 97.3% identity in 222 aa overlap:

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 47

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 399>:

1	ATGGAAAACC AAAGGCCGCT CCTAGGCTTT CGCTTGGCAC
	TTTTGGCGGC
51	GATGACGTGG GGAACGCTGC CGAT.TCCGT GCGGCAGGTA
	TTGAAGTTTG
101	TCGATGCGCC GACGCTGGTG TGGGTGCGTT TTACCGTGGC
	GGCGGCGGTA
151	TTGTTTGTTT TGCTGGCACT GGGCGGGCGG CTGCcGAAGC
	GGCGaGGATT
201	TTTCTTGGTG CTCATTCAGG CTGCTGCTGC TCGGCGTGGC
	GGGCATTTCG
251	GCAAACTTTG TGCTGATTGC CCAAGGGCTG CATTATATTT
	CGCCGACCAC
301	GACGCAGGTT TTGTGGCAGA TTTCGCCGTT TACGATGATT
	GTwGTCGGTG
351	TGTTGGTGTT TAAAGACCGG ATGACTGCCG CTCAGAAAAT
	CGGCTTGGTT
401	TTGCTGCTTG CCGGTTTGCT TATGTATTTT AACGATAAAT
	TCGGCGAGTT
451	GTCGGGTTTG GGCGCGTATG C.AAGGGCGT GTTGCTGTGT
	GCGGCAGGCA
501	GTATGGCATG GGTGTGTAAT GCCGTGGCGC AAAAGCTGCT
	GTCGGCGCAA
551	TTCGGGCCGC AACAGATTCT GCTGTTGATT TATGCGGCAA
	GTGCCGCCGT
601	GTTCCTGCCG TTTGCCGAAC CGGCACACAT CGGAAGTATG
	GACGGTACGT
651	TGGCGTGGGT ATGTATTGCG TATTGCTGCT TGAATACGTT
	AATCGGTTAC
701	GGCTCGTTCG GCGAGGCGTT GAAACATTGG GAGGCTTCCA
	AAGTCAGCGC
751	GGTAACAACC TTGCTCCCCG TGTTTACCGT AATAAATACT
	TTGCTCGGGC
801	ATTATGTGAT GCCTGAAACT TTTGCCGCGC CGGA..

This corresponds to the amino acid sequence <SEQ ID 400; ORF104>:

1	MENQRPLLGF RLALLAAMTW GTLPXSVRQV LKFVDAPTLV
	WVRFTVAAAV
51	LFVLLALGGR LPKRRDFSWC SFRLLLLGVA GISANFVLIA
	QGLHYISPTT
101	TQVLWQISPF TMIVVGVLVF KDRMTAAQKI GLVLLLAGLL
	MYFNDKFGEL
151	SGLGAYXKGV LLCAAGSMAW VCNAVAQKLL SAQFGPQQIL
	LLIYAASAAV
201	FLPFAEPAHI GSMDGTLAWV CIAYCCLNTL IGYGSFGEAL
	KHWEASKVSA
251	VTTLLPVFTV INTLLGHYVM PETFAAP...

Further work revealed further, partial DNA sequence <SEQ ID 401>:

1	ATGGAAAACC AAAGGCCGCT CCTAGGCTTC GCGTTGGCAC
	TTTTGGCGGC
51	GATGACGTGG GGAACGCTGC CGATTGCCGT GCGGCAGGTA
	TTGAAGTTTG
101	TCGATGCGCC GACGCTGGTG TGGGTGCGTT TTACCGTGGC
	GGCGGCGGTA
151	TTGTTTGTTT TGCTGGCACT GGGCGGGCGG CTGCCGAAGC
	GGCGGGATTT
201	TTCTTGGTGC TCATTCAGGC TGCTGCTGCT CGGCGTGGCG
	GGCATTTCGG
251	CAAACTTTGT GCTGATTGCC CAAGGGCTGC ATTATATTTC
	GCCGACCACG
301	ACGCAGGTTT TGTGGCAGAT TTCGCCGTTT ACGATGATTG
	TTGTCGGTGT
351	GTTGGTGTTT AAAGACCGGA TGACTGCCGC TCAGAAAATC
	GGCTTGGTTT
401	TGCTGCTTGC CGGTTTGCTT ATGTTTTTTA ACGATAAATT
	CGGCGAGTTG
451	TCGGGTTTGG GCGCGTATGC GAAGGGCGTG TTGCTGTGTG
	CGGCAGGCAG
501	TATGGCATGG GTGTGTTATG CCGTGGCGCA AAAGCTGCTG
	TCGGCGCAAT
551	TCGGGCCGCA ACAGATTCTG CTGTTGATTT ATGCGGCAAG
	TGCCGCCGTG
601	TTCCTGCCGT TTGCCGAACC GGCACACATC GGAAGTTTGG
	ACGGTACGTT
651	GGCGTGGGTT TGTTTTGCGT ATTGCTGCTT GAATACGTTA
	ATCGGTTACG
701	GCTCGTTCGG CGAGGCGTTG AAACATTGGG AGGCTTCCAA
	AGTCAGCGCG
751	GTAACAACCT TGCTCCCCGT GTTTACCGTA ATAwTwwCTT
	TGCTCGGGCA
801	TTATGTGATG CCTGAAACTT TTGCCGCGCC GGA...

This corresponds to the amino acid sequence <SEQ ID 402; ORF104-1>:

1	MENQRPLLGF ALALLAAMTW GTLPIAVRQV LKFVDAPTLV
	WVRFTVAAAV
51	LFVLLALGGR LPKRRDFSWC SFRLLLLGVA GISANFVLIA
	QGLHYISPTT
101	TQVLWQISPF TMIVVGVLVF KDRMTAAQKI GLVLLLAGLL
	MFFNDKFGEL
151	SGLGAYAKGV LLCAAGSMAW VCYAVAQKLL SAQFGPQQIL
	LLIYAASAAV
201	FLPFAEPAHI GSLDGTLAWV CFAYCCLNTL IGYGSFGEAL
	KHWEASKVSA
251	VTTLLPVFTV IXXLLGHYVM PETFAAP...

Computer analysis of this amino acid sequence gave the following results:

Homology with Hypothetical HI0878 Protein of H. influenzae (Accession Number U32769)

ORF104 and HI0878 show 40% aa identity in 277aa overlap:

orf104	4	QRPLLGFRLALLAAMTWGTLPXSVRQVLKFVDAPTLVWXXXXXXXXXXXXXXXXXXXXP-	62
		Q+PLLGF  AL+ AM WG+LP +++QVL  ++A T+VW                    P
HI0878	3	QQPLLGFTFALITAMAWGSLPIALKQVLSVMNAQTIVWYRFIIAAVSLLALLAYKKQLPE	62
orf104	63	--KRRDFSWCSFRLLLLGVAGISANFVLIAQGLHYISPTTTQVLWQISPFTMIVVGVLVF	120
		K R ++W    ++L+GV G+++NF+L +  L+YI P+  Q+   +S F M++ GVL+F
HI0878	63	LMKVRQYAW----IMLIGVIGLTSNFLLFSSSLNYIEPSVAQIFIHLSSFGMLICGVLIF	118
orf104	121	KDRMTAAQKIXXXXXXXXXXMYFNDKFGELSGLGAYXKGVLLCAAGSMAWVCNAVAQKLL	180
		K+++   QKI          ++FND+F   +GL  Y  GV+L   G++ WV   +AQKL+
HI0878	119	KEKLGLHQKIGLFLLLIGLGLFFNDRFDAFAGLNQYSTGVILGVGGALIWVAYGMAQKLM	178
orf104	181	SAQFGPQQILLLIYAASAAVFLPFAEPAHIGSMDGTLAWVCIAYCCLNTLIGYGSFGEAL	240
		+F  QQILL++Y   A  F+P A+ + +  +   LA +C  YCCLNTLIGYGS+ EAL
HI0878	179	LRKFNSQQILLMMYLGCAIAFMPMADFSQVQELT-PLALICFIYCCLNTLIGYGSYAEAL	237
orf104	241	KHWEASKVSAVTTLLPVFTVINTLLGHYVMPETFAAP	277
		W+ SKVS V TL+P+FT++ + + HY  P  FAAP
HI0878	238	NRWDVSKVSVVITLVPLFTILFSHIAHYFSPADFAAP	274

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF104 shows 95.3% identity over a 277aa overlap with an ORF (ORF104a) from strain A of N. meningitidis:

The complete length ORF104a nucleotide sequence <SEQ ID 403> is:

1	ATGGAAAACC AAAGGCCGCT CCTAGGCTTC GCGTTGGCAC
	TTTTGGCGGC
51	GATGACGTGG GGAACGCTGC CGATTGCCGT GCGGCAGGTA
	TTGAAGTTTG
101	TCGATGCGCC GACGCTGGTG TGGGTGCGTT TTACCGTGGC
	GGCGGCGGTA
151	TTGTTTGTTT TGCTGGCATT GGGCGGGCGG CTGCCGAAGT
	GGCGGGATTT
201	TTCTTGGTGC TCATTCAGGC TGCTGCTGCT CGGCGTGGCG
	GGCATTTCGG
251	CAAACTTTGT GCTGATTGCC CAAGGGCTGC ATTATATTTC
	GCCGACCACG
301	ACGCAGGTTT TGTGGCAGAT TTCGCCGTTT ACGATGATTG
	TTGTCGGTGT
351	GTTGGTGTTT AAAGACCGGA TGACTGCCGC TCAGAAAATC
	GGCTTGGTTT
401	TGCTGCTTGC CGGTTTGCTT ATGTTTTTTA ACGATAAATT
	CGGCGAGTTG
451	TCGGGTTTGG GCGCGTATGC GAAGGGCGTG TTGCTGTGTG
	CGGCAGGCAG
501	TATGGCATGG GTGTGTTATG CCGTGGCGCA AAAGCTGCTG
	TCGGCGCAAT
551	TCGGGCCGCA ACAGATTCTG CTGTTGATTT ATGCGGCAAG
	TGCCGCCGTG
601	TTCCTGCCGT TTGCCGAACT GGCACACATC GGAAGTTTGG
	ACGGTACGTT
651	GGCGTGGGTT TGTTTTGCGT ATTGCTGCTT GAATACGTTA
	ATCGGTTACG
701	GCTCGTTCGG CGAGGCGTTG AAACATTGGG AGGCTTCCAA
	AGTCAGCGCG
751	GTAACAACCT TGCTCCCCGT GTTTACCGTA ATATTTTCTT
	TGCTCGGGCA
801	TTATGTGATG CCTGATACTT TTGCCGCGCC GGATATGAAC
	GGTTTGGGTT
851	ATGCCGGCGC ACTGGTCGTG GTCGGGGGTG CGGTTACGGC
	GGCGGTGGGG
901	GACAGGCTGT TCAAACGCCG CTAG

This encodes a protein having amino acid sequence <SEQ ID 404>:

1	MENQRPLLGF ALALLAAMTW GTLPIAVRQV LKFVDAPTLV
	WVRFTVAAAV
51	LFVLLALGGR LPKWRDFSWC SFRLLLLGVA GISANFVLIA
	QGLHYISPTT
101	TQVLWQISPF TMIVVGVLVF KDRMTAAQKI GLVLLLAGLL
	MFFNDKFGEL
151	SGLGAYAKGV LLCAAGSMAW VCYAVAQKLL SAQFGPQQIL
	LLIYAASAAV
201	FLPFAELAHI GSLDGTLAWV CFAYCCLNTL IGYGSFGEAL
	KHWEASKVSA
251	VTTLLPVFTV IFSLLGHYVM PDTFAAPDMN GLGYAGALVV
	VGGAVTAAVG
301	DRLFKRR*

ORF104a and ORF104-1 show 98.2% identity in 277 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF104 shows 93.9% identity over a 277aa overlap with a predicted ORF (ORF104.ng) from N. gonorrhoeae:

The complete length ORF104ng nucleotide sequence <SEQ ID 405> is predicted to encode a protein having amino acid sequence <SEQ ID 406>:

1	MENQRPLLGF ALALLAAMTW GTLPIAVRQV LKFVDAPTLV
	WVRFTVAAAV
51	LFVLLALGGR LPKRRDFSWH SFRLLLLGVT GISANFVLIA
	QGLHYISPTT
101	TQVLWQISPF TMIVVGVLVF KDRMTAAQKI GLVLLLVGLL
	MFFNDKFGEL
151	SGLGAYAKGV LLCAAGSMAW VCYAVAQKLL SAQFGPQQIL
	LLIYAASAAV
201	FLLXAEPAHI GSLDGTLAWV CFVYCCLNTL IGYGSFGEAL
	KHWEASKVSA
251	VTTLLPVFTV IFSLLGHYVM PDTFAAPDMN GLGYVGALVV
	VGGAVTAAVG
301	DRPFKRR*

Further work revealed the complete gonococcal nucleotide sequence <SEQ ID 407>:

1	ATGGAAAACC AAAGGCCGCT CCTAGGCTTC GCGTTGGCAC
	TTTTGGCGGC
51	GATGACGTGG GGGACGCTGC CGATTGCCGT GCGGCAGGTA
	TTGAAGTTTG
101	TCGATGCGCC GACGCTGGTG TGGGTGCGTT TTACCGTGGC
	GGCGGCGGTA
151	TTGTTTGTTT TGCTGGCATT GGGCGGGCGG CTGCCGAAGC
	GGCGGGATTT
201	TTCTTGGCAT TCATTCAGGC TGCTGCTGCT CGGCGTGACG
	GGCATTTCGG
251	CAAACTTTGT GCTGATTGCC CAAGGGCTGC ATTATATTTC
	GCCGACCACG
301	ACGCAGGTTT TGTGGCAGAT TTCGCCGTTT ACGATGATTG
	TTGTCGGCGT
351	GTTGGTGTTT AAAGACCGGA tgaCTGCCGC GCAGAAAATC
	GGTTTGGTTT
401	TGCTGCttgT CGGTttgCTT ATGTTTTtta ACGACAAATT
	CGGCGAGTTG
451	TCGGGTTTGG GCGCGTATGC GAAGGGCGTG TTGCTGTGTG
	CGGCAGGCAG
501	TATGGCCTGG GTGTGTTATG CCGTGGCGCA AAAGCTGCTG
	TCGGCGCAAT
551	TCGGGCCGCA ACAGATTCTG CTGTTGATTT ATGCGGcaag
	tgccgccGTG
601	TTCCtgccgT TTGccgaaCC GGCACACATC GGAAGTTTgg
	aCGGTACGtt
651	GGCGTGGGTT TGTTTTGTGT ATTGCTGCTT GAATACGTTA
	ATCGGTTACG
701	GCTCGTTCGG CGAGGCGTTG AAACATTGGG AGGCTTCCAA
	AGTCAGCGCG
751	GTAACAACCT TGCTCCCCGT GTTTACCGTA ATATTTTCTT
	TGCTCGGGCA
801	TTATGTGATG CCTGATACTT TTGCCGCGCC GGATATGAAC
	GGTTTGGGTT
851	ATGTCGGCGC ACTGGTCGTG GTCGGGGGTG CGGTTACGGC
	GGCGGTGGGG
901	GACAGGCCGT TCAAACGCCG CTAG

This corresponds to the amino acid sequence <SEQ ID 408; ORF104ng-1>:

1	MENQRPLLGF ALALLAAMTW GTLPIAVRQV LKFVDAPTLV
	WVRFTVAAAV
51	LFVLLALGGR LPKRRDFSWH SFRLLLLGVT GISANFVLIA
	QGLHYISPTT
101	TQVLWQISPF TMIVVGVLVF KDRMTAAQKI GLVLLLVGLL
	MFFNDKFGEL
151	SGLGAYAKGV LLCAAGSMAW VCYAVAQKLL SAQFGPQQIL
	LLIYAASAAV
201	FLPFAEPAHI GSLDGTLAWV CFVYCCLNTL IGYGSFGEAL
	KHWEASKVSA
251	VTTLLPVFTV IFSLLGHYVM PDTFAAPDMN GLGYVGALVV
	VGGAVTAAVG
301	DRPFKRR*

ORF104ng-1 and ORF104-1 show 97.5% identity in 277 aa overlap:

In addition, ORF104ng-1 shows significant homology with a hypothetical H. influenzae protein:

gi|1573895 (U32769) hypothetical [Haemophilus influenzae] Length = 306
Score = 237 bits (598), Expect = 8e−62
Identities = 114/280 (40%), Positives = 168/280 (59%), Gaps = 8/280 (2%)

Query:	30	QRPXXXXXXXXXXXMTWGTLPIAVRQVLKFVDAPTLVWXXXXXXXXXXXXXXXXXXXXP-	88
		Q+P           M WG+LPIA++QVL  ++A T+VW                    P
Sbjct:	3	QQPLLGFTFALITAMAWGSLPIALKQVLSVMNAQTIVWYRFIIAAVSLLALLAYKKQLPE	62
Query:	89	--KRRDFSWHSFRLLLLGVTGISANFVLIAQGLHYISPTTTQVLWQISPFTMIVVGVLVF	146
		K R ++W    ++L+GV G+++NF+L +  L+YI P+  Q+   +S F M++ GVL+F
Sbjct:	63	LMKVRQYAW----IMLIGVIGLTSNFLLFSSSLNYIEPSVAQIFIHLSSFGMLICGVLIF	118
Query:	147	KDRMTAAQKIXXXXXXXXXXMFFNDKFGELSGLGAYAKGVLLCAAGSMAWVCYAVAQKLL	206
		K+++   QKI          +FFND+F   +GL  Y+ GV+L   G++ WV Y +AQKL+
Sbjct:	119	KEKLGLHQKIGLFLLLIGLGLFFNDRFDAFAGLNQYSTGVILGVGGALIWVAYGMAQKLM	178
Query:	207	SAQFGPQQILLLIYAASAAVFLPFAEPAHIGSLDGTLAWVCFVYCCLNTLIGYGSFGEAL	266
		+F  QQILL++Y   A  F+P A+ + +  L   LA +CF+YCCLNTLIGYGS+ EAL
Sbjct:	179	LRKFNSQQILLMMYLGCAIAFMPMADFSQVQELT-PLALICFIYCCLNTLIGYGSYAEAL	237
Query:	267	KHWEASKVSAVTTLLPVFTVIFSLLGHYVMPDTFAAPDMN	306
		W+ SKVS V TL+P+FT++FS + HY  P  FAAP++N
Sbjct:	238	NRWDVSKVSVVITLVPLFTILFSHIAHYFSPADFAAPELN	277

Based on this analysis, including the presence of a putative leader sequence and several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 48

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 409>:

1	ATGGTAGCTC GTCGGGCTCA TAACCCGAAG GTCGTAGGTT
	CGAATCCTGT
51	.CCCGCAACC TAATTTCAAA CCCCTCGGTT CAATGCCGAG
	GG.GTTTTGT
101	T.TTGCCTGT TTCCTGTTTC CTGTTTCCTG CCGCCTCCGT
	TTTTTGCCGG
151	ATTTTCCTTC CGGCCGCAAT ATCGGAACGG CAGACCGCCG
	TCTGTTTGCG
201	GTTGCAAATT CAGGCAGTTT GGCTACAATC TTCCGCATTG
	TCTTCAAGAA
251	AGCCAACCAT GCCGACCGTC CGTTTTACCG AATCCGTCAG
	CAAACAAGAC
301	CTTGATGCTC TGTTCGAGTG GGCAAAAGCA AGTTACGGTG
	CAGAAAGTTG
351	CTGGAAAACG CTGTATCTGA ACGGTCysCC TTTGGGCAAC
	CTGTCGCCGG
401	AATGGGTGGA ACGCGTsmmA AAAGACTGGG AGGCAGGCTG
	CyCGGAGTCT
451	TCAGACGGCA TTTTTCTGAA TgCGGACGGc TGgCctGATA
	TGGgCGGAcg
501	cTTACAGCAC CTCGCCCTCG GTTGGCACTG TGCGGGGCTG
	TTGGACGgsT
551	GGCGCAACGA GTGTTTCGAC CTGACCGACG GCGGCGGCAA
	CCCCTTGTTC
601	ACGCTCGaAc GCGCCGyTTT mCGTCCTkTC GGACTGCTCA
	GCCGCGCCGT
651	CCATCTCAAC GGTCTGACCG AATCGGACGG CCGATGGCAT
	TTCTGGATAG
701	GCAGGCGCAG TCCGCACAAA GCAGTCGATC CCAACAAACT
	CGACAATACT
751	rCCGCCGGCG GTGTTTCCGG CGGCGAAATG CCGTCTGAAG
	CCGTGTGTCG
801	CGAAAGCAGC GAAGAAGCCG GTTTGGATAA AACGCTGcTT
	CCGCTCATCC
851	GCCCGGTATC GCAGCTGCAC AGCCTGCGCT CCGTCAGCCG
	GGGTGTACAC
901	AATGAAATCC TGTATGTATT CGATGCCGTC CTGCCG...

This corresponds to the amino acid sequence <SEQ ID 410; ORF105>:

1	MVARRAHNPK VVGSNPXPAT XFQTPRFNAE XVLXLPVSCF
	LFPAASVFCR
51	IFLPAAISER QTAVCLRLQI QAVWLQSSAL SSRKPTMPTV
	RFTESVSKQD
101	LDALFEWAKA SYGAESCWKT LYLNGXPLGN LSPEWVERVX
	KDWEAGCXES
151	SDGIFLNADG WPDMGGRLQH LALGWHCAGL LDGWRNECFD
	LTDGGGNPLF
201	TLERAXXRPX GLLSRAVHLN GLTESDGRWH FWIGRRSPHK
	AVDPNKLDNT
251	XAGGVSGGEM PSEAVCRESS EEAGLDKTLL PLIRPVSQLH
	SLRSVSRGVH
301	NEILYVFDAV LP...

Further work revealed the complete nucleotide sequence <SEQ ID 411>:

1	ATGCCGACCG TCCGTTTTAC CGAATCCGTC AGCAAACAAG
	ACCTTGATGC
51	TCTGTTCGAG TGGGCAAAAG CAAGTTACGG TGCAGAAAGT
	TGCTGGAAAA
101	CGCTGTATCT GAACGGTCTG CCTTTGGGCA ACCTGTCGCC
	GGAATGGGTG
151	GAACGCGTCA AAAAAGACTG GGAGGCAGGC TGCTCGGAGT
	CTTCAGACGG
201	CATTTTTCTG AATGCGGACG GCTGGCCTGA TATGGGCGGA
	CGCTTACAGC
251	ACCTCGCCCT CGGTTGGCAC TGTGCGGGGC TGTTGGACGG
	CTGGCGCAAC
301	GAGTGTTTCG ACCTGACCGA CGGCGGCGGC AACCCCTTGT
	TCACGCTCGA
351	ACGCGCCGCT TTCCGTCCTT TCGGACTGCT CAGCCGCGCC
	GTCCATCTCA
401	ACGGTCTGAC CGAATCGGAC GGCCGATGGC ATTTCTGGAT
	AGGCAGGCGC
451	AGTCCGCACA AAGCAGTCGA TCCCAACAAA CTCGACAATA
	CTGCCGCCGG
501	CGGTGTTTCC GGCGGCGAAA TGCCGTCTGA AGCCGTGTGT
	CGCGAAAGCA
551	GCGAAGAAGC CGGTTTGGAT AAAACGCTGC TTCCGCTCAT
	CCGCCCGGTA
601	TCGCAGCTGC ACAGCCTGCG CTCCGTCAGC CGGGGTGTAC
	ACAATGAAAT
651	CCTGTATGTA TTCGATGCCG TCCTGCCCGA AACCTTCCTG
	CCTGAAAATC
701	AGGATGGCGA AGTGGCGGGT TTTGAGAAAA TGGACATCGG
	CGGTCTGTTG
751	GATGCCATGT TGTCGGGAAA CATGATGCAC GACGCGCAAC
	TGGTTACGCT
801	GGACGCGTTT TGCCGTTACG GTCTGATTGA TGCCGCCCAT
	CCGCTGTCCG
851	AGTGGCTGGA CGGCATACGT TTATAG

This corresponds to the amino acid sequence <SEQ ID 412; ORF105-1>:

1	MPTVRFTESV SKQDLDALFE WAKASYGAES CWKTLYLNGL
	PLGNLSPEWV
51	ERVKKDWEAG CSESSDGIFL NADGWPDMGG RLQHLALGWH
	CAGLLDGWRN
101	ECFDLTDGGG NPLFTLERAA FRPFGLLSRA VHLNGLTESD
	GRWHFWIGRR
151	SPHKAVDPNK LDNTAAGGVS GGEMPSEAVC RESSEEAGLD
	KTLLPLIRPV
201	SQLHSLRSVS RGVHNEILYV FDAVLPETFL PENQDGEVAG
	FEKMDIGGLL
251	DAMLSGNMMH DAQLVTLDAF CRYGLIDAAH PLSEWLDGIR
	L*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF105 shows 89.4% identity over a 226aa overlap with an ORF (ORF105a) from strain A of N. meningitidis:

The complete length ORF105a nucleotide sequence <SEQ ID 413> is:

1	ATGCCGACCG TCCGTTTTAC CGAATCCGTC AGCAAACACG
	ACCTTGATGC
51	CCTATTCGAG TGGGCAAAGG CAAGTTACGG TGCGGAAAGT
	TGCTGGAAAA
101	CGCTGTATCT GAACGGTCTG CCTTTGGGCA ATCTGTCGCC
	GGAATGGGCG
151	GAGCGCGTCA AAAAAGACTG GGAGGCAGGC TGCTCGGAGT
	CTTCAGACGG
201	CATTTTCCTG AATGCGGACG GCTGGCCAGA TATGGGCAGA
	CGCTTGCAGC
251	ACCTCGCCCG AATATGGAAA GAAGCGGGAC TGCTTCACGG
	CTGGCGCGAC
301	GAGTGTTTCG ACCTGACCGA CGGCGGCAGC AATCCCTTGT
	TCGCGCTCGA
351	ACGCGCCGCT TTCCGTCCGT TCGGACTGCT CAGCCGCGCC
	GTCCATCTCA
401	ACGGTTTGGT CGAATCGGAC GGCCGATGGC ATTTCTGGAT
	AGGCAGGCGC
451	AGTCCGCACA AAGCAGTCGA TCCCGACAAA CTCGACAATA
	CTGCCGCCGG
501	CGGTGTTTCC AGCGGTGAAT TGCCGTCTGA AACCGTGTGT
	CGCGAAAGCA
551	GCGAAGAAGC CGGTTTGGAT AAAACGCTGC TTCCGCTCAT
	CCGCCCGGTA
601	TCGCAGCTGC ACAGCCTGCG CCCCGTCAGC CGGGGTGTGC
	ACAATGAAAT
651	CCTGTATGTA TTCGATGCCG TCCTGCCCGA AACCTTCCTG
	CCTGAAAATC
701	AGGATGGCGA AGTGGCGGGT TTTGAGAAAA TGGACATCGG
	CGGTCTGTTG
751	GCTGCCATGT TGTCGGGAAA CATGATGCAC GACGCGCAAC
	TGGTTACGCT
801	GGACGCGTTT TGCCGTTACG GTCTGATTGA TGCCGCCCAT
	CCGCTGTCCG
851	AGTGGCTGGA CGGCATACGT TTATAG

This encodes a protein having amino acid sequence <SEQ ID 414>:

1	MPTVRFTESV SKHDLDALFE WAKASYGAES CWKTLYLNGL
	PLGNLSPEWA
51	ERVKKDWEAG CSESSDGIFL NADGWPDMGR RLQHLARIWK
	EAGLLHGWRD
101	ECFDLTDGGS NPLFALERAA FRPFGLLSRA VHLNGLVESD
	GRWHFWIGRR
151	SPHKAVDPDK LDNTAAGGVS SGELPSETVC RESSEEAGLD
	KTLLPLIRPV
201	SQLHSLRPVS RGVHNEILYV FDAVLPETFL PENQDGEVAG
	FEKMDIGGLL
251	AAMLSGNMMH DAQLVTLDAF CRYGLIDAAH PLSEWLDGIR
	L*

ORF105a and ORF105-1 show 93.8% identity in 291 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF105 shows 87.5% identity over a 312aa overlap with a predicted ORF (ORF105.ng) from N. gonorrhoeae:

A complete length ORF105ng nucleotide sequence <SEQ ID 415> was predicted to encode a protein having amino acid sequence <SEQ ID 416>:

1	MVARRAHNPK VVGSNPAPAT KYQTPRFNAE GVLFFLFPAA
	SVFCRIFLPA
51	AISERQAAVC LRLQIQAVWL QSSALCSRKP AMPTVRFTES
	VSKQDLDALF
101	ERAKASYGAE SCWKTLYLNR LPLGNLSPEW AERIKKDWEA
	GCSESSNGIF
151	LNADGWPDMG GRLQHLARTW NKAGLLHGWR NECFDLTDGG
	GNPLFTLERA
201	AFRPFGLLIR AVHLNGLVES NGRWHFWIGR RSPHKAVDPG
	KLDNIAGGGV
251	SGGEMPSEAV CRESSEEAGL DKTLFPLIRP VSRLHSLRPV
	SRGVHNEILY
301	VFDAVLPETF LPENQDGEVA GFEKMDIGGL LDAMLSKNMM
	HDAQLVTLDA
351	FYRYGLIDAA HPLSEWLDGI RL*

Further work revealed the complete nucleotide sequence <SEQ ID 417>:

1	ATGCCGACCG TCCGTTTTAC CGAATCCGTC AGCAAACAAG
	ACCTTGATGC
51	CCTGTTCGAG CGGGCAAAAG CAAGTTACGG TGCCGAAAGT
	TGCTGGAAAA
101	CGCTGTATCT GAACCGTCTT CCTTTGGGCA ATCTGTCGCC
	GGAATGGGCT
151	GAGCGCATCA AAAAAGACTG GGAGGCAGGC TGCTCCGAGT
	CTTCAGACGG
201	CATTTTTCTG AATGCGGACG GCTGGCCGGA TATGGGCGGA
	CGCTTGCAGC
251	ACCTCGCCCG CACATGGAAC AAGGCGGGGC TGCTTCACGG
	ATGGCGCAAC
301	GAGTGTTTCG ACCTGACCGA CGGCGGCGGC AACCCCTTGT
	TCACGCTCGA
351	ACGCGCCGCT TTCCGTCCGT TCGGACTACT CAGCCGCGCC
	GTCCATCTCA
401	ACGGTTTGGT CGAATCGAAC GGCAGATGGC ATTTTTGGAT
	AGGCAGGCGC
451	AGTCCGCACA AAGCAGTCGa tcCCGGCAAG CTCGACAATA
	TTGCCGGCGG
501	CGGTGTTTCC GGCGGCGAAA TGCCGTCTGA AGCCGTGTGC
	CGCGAAAGCA
551	GCGAAGAAGC CGGTTTGGAT AAAACGCTGT TTCCGCTCAT
	CCGCCCAGTA
601	TCGCGGCTGC ACAGCCTTCG CCCCGTCAGC CGAGGTGTGC
	ACAATGAAAT
651	CCTGTATGTG TTCGATGCCG TCCTGCCCGA AACCTTCCTG
	CCTGAAAATC
701	AGGATGGCGA GGTAGCGGGT TTTGAAAAGA TGGACATTGG
	CGGCCTATTG
751	GATGCCATGT TGTCGAAAAA CATGATGCAC GACGCGCAAC
	TGGTTACGCT
801	GGACGCGTTT TACCGTTACG GTCTGATTGA TGCCGCCCAT
	CCGCTGTCCG
851	AGTGGCTGGA CGGCATACGT TTATAG

This corresponds to the amino acid sequence <SEQ ID 418; ORF105ng-1>:

1	MPTVRFTESV SKQDLDALFE RAKASYGAES CWKTLYLNRL
	PLGNLSPEWA
51	ERIKKDWEAG CSESSDGIFL NADGWPDMGG RLQHLARTWN
	KAGLLHGWRN
101	ECFDLTDGGG NPLFTLERAA FRPFGLLSRA VHLNGLVESN
	GRWHFWIGRR
151	SPHKAVDPGK LDNIAGGGVS GGEMPSEAVC RESSEEAGLD
	KTLFPLIRPV
201	SRLHSLRPVS RGVHNEILYV FDAVLPETFL PENQDGEVAG
	FEKMDIGGLL
251	DAMLSKNMMH DAQLVTLDAF YRYGLIDAAH PLSEWLDGIR
	L*

ORG105ng-1 and ORF105-1 show 93.5% identity in 291 aa overlap:

Furthermore, ORF105ng-1 shows homology with a yeast enzyme:

sp|P41888|TNR3_SCHPO THIAMIN PYROPHOSPHOKINASE (TPK) (THIAMIN KINASE)
>gi|1076928|pir||S52350 thiamin pyrophosphokinase (EC 2.7.6.2) - fission
yeast (Schizosaccharomyces pombe) >gi|666111 (X84417) thiamin
pyrophosphokinase [Schizosaccharomyces pombe]
>gi|2330852|gnl|PID|e334056 (Z98533) thiamin
pyrophosphokinase [Schizosaccharomyces pombe] Length = 569
Score = 105 bits (259), Expect = 4e−22
Identities = 64/192 (33%), Positives = 94/192 (48%), Gaps = 3/192 (1%)

Query:	268	NKAGLLHGWRNECFDLTDGGGNPLFTLERAAFRPFGLLSRAVHLNGLVESNGRW--HFWI	441
		N  G+   WRNE + +      P+  +ER  F  FG LS  VH    + +        W+
Sbjct:	96	NTFGIADQWRNELYTVYGKSKKPVLAVERGGFWLFGFLSTGVHCTMYIPATKEHPLRIWV	155
Query:	442	GRRSPHKAVDPGKLDNIAGGGVSGGEMPSEAVCRESSEEAGLDKTLFPLIRPVSRLHSLR	621
		RRSP K   P  LDN   GG++ G+     + +E SEEA LD +   LI P   +  ++
Sbjct:	156	PRRSPTKQTWPNYLDNSVAGGIAHGDSVIGTMIKEFSEEANLDVSSMNLI-PCGTVSYIK	214
Query:	622	PVSRG-VHNEILYVFDAVLPETFLPENQDGEVAGFEKMDIGGLLDAMLSKNMMHDAQLVT	798
		R  +  E+ YVFD  + +  +P   DGEVAGF  + +  +L  +  K+   +  LV
Sbjct:	215	MEKRHWIQPELQYVFDLPVDDLVIPRINDGEVAGFSLLPLNQVLHELELKSFKPNCALVL	274
Query:	799	LDAFYRYGLIDAAHP	843
		LD   R+G+I   HP
Sbjct:	275	LDFLIRHGIITPQHP	289

Based on this analysis, including the presence of a putative transmembrane domain in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 49

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 419>:

1	ATGAATAGAC CCAAGCAACC CTTCTTCCGT CCCGAAGTCG
	CCGTTGCCCG
51	CCAAACCAGC CTGACGGGTA AAGTGATTCT GACACGACCG
	TTGTCATTTT
101	CCCTATGGAC GACATTTGCA TCGATATCTG CGTTATTGAT
	TATCCTGTTT
151	TTGATATTTG GTAACTATAC GCGAAAGACA ACAGTGGAGG
	GACAAATTTT
201	ACCTGCATCG GGCGTAATCA GGGTGTATGC ACCGgATACG
	rGkACAATTA
251	CAGCGAAATT CGTGGAAGAT GGmsAAAAGG TTAAGGCTGG
	CGACAAGCTA
301	TTTGCGCTTT CGACCTCACG TTTCGGCGCA GGAGGTAGCG
	TGCAGCAGCA
351	GTTGAAAACG GAGGCAGTTT TGAAGAAAAC GTTGGCAGAA
	CAGGAACTGG
401	GTCGTCTGAA GCTGATACAC GGGAATGAAA CGCGCAgCcT
	TAAAGCAACT
451	GTCGAACGTT TGGAAAACCA GGAACTCCAT ATTTCGCAAC
	AGATAGACGG
501	TCAGAAAAGG CGCATTAGAC TTGCGGAAGA AATGTTGCAG
	AAATATCGTT
551	TCCTATCCGC .CAATGA

This corresponds to the amino acid sequence <SEQ ID 420; ORF107>:

1	MNRPKQPFFR PEVAVARQTS LTGKVILTRP LSFSLWTTFA
	SISALLIILF
51	LIFGNYTRKT TVEGQILPAS GVIRVYAPDT XTITAKFVED
	GXKVKAGDKL
101	FALSTSRFGA GGSVQQQLKT EAVLKKTLAE QELGRLKLIH
	GNETRSLKAT
151	VERLENQELH ISQQIDGQKR RIRLAEEMLQ KYRFLSXQ*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF107 shows 97.8% identity over a 186aa overlap with an ORF (ORF107a) from strain A of N. meningitidis:

The complete length ORF107a nucleotide sequence <SEQ ID 421> is:

1	ATGAATAGAC CCAAGCAACC NTTCTTCCGT CCCGAAGTCG
	CCGTTGCCCG
51	CCAAACCAGC CTGACGGGTA AAGTGATTCT GACACGACCG
	TTGTCATTTT
101	CCCTATGGAC GACATTTGCA TCGATATCTG CGTTATTGAT
	TATCCTGTTT
151	TTGATATTTG GTAACTATAC GCGAAAGACA ACAGTGGAGG
	GACAAATTTT
201	ACCTGCATCG GGCGTAATCA GGGTGTATGC ACCGGATACG
	GGGACAATTA
251	CNGCGAAATT CNTGGAAGAT GGAGAAAAGG TTAAGGCTGG
	CGACAAGCTA
301	TTTGCGCTTT CGACCTCACG TTTCGGCGCA GGAGATAGCG
	TGCAGCAGCA
351	GTTGAAAACG GAGGCAGTTT TGAAGAAAAC GTTGGCAGAA
	CAGGAACTGG
401	GTCGTCTGAA GCTGATACAC GGGAATGAAA CGCGCAGCCT
	TAAAGCAACT
451	GTCGAACGTT TGGAAAACCA GGAACTCCAT ATTTCGCAAC
	AGATAGACGG
501	TCAGAAAAGG CGCATTAGAC TTGCGGAAGA AATGTTGCAG
	AAATATCGTT
551	TCCTATCCGC CAATGATGCA GTGCCAAAAC AAGAAATGAT
	GAATGTCAAG
601	GCAGAGCTTT TAGAGCAGAA AGCCAAACTT GATGCCTACC
	GCCGAGAAGA
651	AGTCGGGCTG CTTCAGGAAA TCCGCACGCA GAATCTGACA
	TTGGNNAGCC
701	TCCCCCAAGC GGCATGA

This encodes a protein having amino acid sequence <SEQ ID 422>:

1	MNRPKQPFFR PEVAVARQTS LTGKVILTRP LSFSLWTTFA
	SISALLIILF
51	LIFGNYTRKT TVEGQILPAS GVIRVYAPDT GTITAKFXED
	GEKVKAGDKL
101	FALSTSRFGA GDSVQQQLKT EAVLKKTLAE QELGRLKLIH
	GNETRSLKAT
151	VERLENQELH ISQQIDGQKR RIRLAEEMLQ KYRFLSANDA
	VPKQEMMNVK
201	AELLEQKAKL DAYRREEVGL LQEIRTQNLT LXSLPQAA*

Homology with a Predicted ORF from N. gonorrhoeae

ORF107 shows 95.7% identity over a 188aa overlap with a predicted ORF (ORF107.ng) from N. gonorrhoeae:

The complete length ORF107ng nucleotide sequence <SEQ ID 423> is predicted to encode a protein having amino acid sequence <SEQ ID 424>:

1	MNRPKQPFFR PEVAIARQTS LTGKVILTRP LSFSLWTTFA
	SISALLIILF
51	LIFGNYTRKT TMEGQILPAS GVIRVYAPDT GTITAKFVED
	GEKVKAGDKL
101	FALSTSRFGA GGSVQQQLKT EAVLKKTLAE QELGRLKLIH
	ENETRSLKAT
151	VERLENQKLH ISQQIDGQKR RIRLAEEMLR KYRFLSAQ*

Based on the presence of a putative transmembrane domain in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 50

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 425>:

1	ATGCTGAATA CTTTTTTTGC CGTATTGGGC GGCTGCCTGC
	TGCT.TTGCC
51	GTGCGGCAAA TCCGTAAATA CGGCGGTACA GCCGCAAAAC
	GCGGTACAAA
101	GCGCGCCGAA ACCGGTTTTC AAAGTCATAT ATATCGACAA
	TACGGCGATT
151	GCCGGTTTGG ATTTGGGACA AAGCAGCGAA GGCAAAACCA
	ACGACGGCAA
201	AAAACAAATC AGTTATCCGA TTAAAGGCTT GCCGGAACAA
	AATGTTATCC
251	GACTGATCGG CAAGCATCCC GGCGACTTGG AAGCCGTCAG
	CGGCAAATGT
301	ATGGAAACCG ATGATAAGGA CAGTCCGGCA GGTTGGGCAG
	AAAACGGCGT
351	GTGCCATACC TTGTTTGCCA AACTGGTGGG CAATATCGCC
	GAAGACGGCG
401	GCAAACTGAC GGATTACCTA GTTTCGCATG CCGCCCTGCA
	ACCCTATCAG
451	GCAGGCAAAA GCGGCTATGC CGCCGTGCAG AACGGACGCT
	ATGTGCTGGA
501	AATCGACAGC GAAGGGGCGT TTTATTTCCG CCGCCGCCAT
	TATTGA

This corresponds to the amino acid sequence <SEQ ID 426; ORF108>:

1	MLNTFFAVLG GCLLXLPCGK SVNTAVQPQN AVQSAPKPVF
	KVIYIDNTAI
51	AGLDLGQSSE GKTNDGKKQI SYPIKGLPEQ NVIRLIGKHP
	GDLEAVSGKC
101	METDDKDSPA GWAENGVCHT LFAKLVGNIA EDGGKLTDYL
	VSHAALQPYQ
151	AGKSGYAAVQ NGRYVLEIDS EGAFYFRRRH Y*

Further work revealed the following DNA sequence <SEQ ID 427>:

1	ATGCTGAAAA CATCTTTTGC CGTATTGGGC GGCTGCCTGC
	TGCTTGCCGC
51	CTGCGGCAAA TCCGAAAATA CGGCGGAACA GCCGCAAAAC
	GCGGTACAAA
101	GCGCGCCGAA ACCGGTTTTC AAAGTCAAAT ATATCGACAA
	TACGGCGATT
151	GCCGGTTTGG ATTTGGGACA AAGCAGCGAA GGCAAAACCA
	ACGACGGCAA
201	AAAACAAATC AGTTATCCGA TTAAAGGCTT GCCGGAACAA
	AATGTTATCC
251	GACTGATCGG CAAGCATCCC GGCGACTTGG AAGCCGTCAG
	CGGCAAATGT
301	ATGGAAACCG ATGATAAGGA CAGTCCGGCA GGTTGGGCAG
	AAAACGGCGT
351	GTGCCATACC TTGTTTGCCA AACTGGTGGG CAATATCGCC
	GAAGACGGCG
401	GCAAACTGAC GGATTACCTA GTTTCGCATG CCGCCCTGCA
	ACCCTATCAG
451	GCAGGCAAAA GCGGCTATGC CGCCGTGCAG AACGGACGCT
	ATGTGCTGGA
501	AATCGACAGC GAAGGGGCGT TTTATTTCCG CCGCCGCCAT
	TATTGA

This corresponds to the amino acid sequence <SEQ ID 428; ORF108-1>:

1	MLKTSFAVLG GCLLLAACGK SENTAEQPQN AVQSAPKPVF
	KVKYIDNTAI
51	AGLDLGQSSE GKTNDGKKQI SYPIKGLPEQ NVIRLIGKHP
	GDLEAVSGKC
101	METDDKDSPA GWAENGVCHT LFAKLVGNIA EDGGKLTDYL
	VSHAALQPYQ
151	AGKSGYAAVQ NGRYVLEIDS EGAFYFRRRH Y*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. gonorrhoeae

ORF108 shows 88.4% identity over a 181 aa overlap with a predicted ORF (ORF 108.ng) from N. gonorrhoeae:

ORF108-1 shows 92.3% identity with ORF108ng over the same 181 aa overlap:

The complete length ORF108ng nucleotide sequence <SEQ ID 429> is:

1	ATGCTGAAAa tacctTTTGC CGTGTtgggc ggCtgcctGC
	TGCTTGCCGC
51	CTGCGGCAAA TCCGAAAATa cggcggaACA GCCGCAAAAT
	gcggCACAAA
101	GCGCGCCGAA ACCGGTTTTC AAAGTCAAAT ACATCGACAA
	TACGGCGATT
151	GCCGGTTTGG CTTTGGGACA AAGTAGCGAA GGCAAAACCA
	acgacgGCAA
201	AAAACAAATC AGTTATccgA TTAAAGGCTT GCCGGAACAA
	Aacgccgtcc
251	gGCTGACCGG AAAGCATCCC AACGACTTGG AagccgtcgT
	CGGCAAATGT
301	ATGGAAACCG ACGGAAAGGA CGCGCCTTCG GGCTGGGCGG
	AAAACGGCGT
351	GTGCCATACC TTGTTTGCCA AACTGGTGGG CAATATCGCC
	GAAGACGGCG
401	GCAAACTGAC TGATTACCTG ATTTCGCATT CCGCCCTGCA
	ACCCTATCAG
451	GCAGGCAAAA GCGGCTATGC CGCCGTGCAG AACGGACGCT
	ATGTGCTGGA
501	AATCGACAGC GagggGGCGT TTTATttccg ccgccgccat
	tattgA

This encodes a protein having amino acid sequence <SEQ ID 430>:

1	MLKIPFAVLG GCLLLAACGK SENTAEQPQN AAQSAPKPVF
	KVKYIDNTAI
51	AGLALGQSSE GKTNDGKKQI SYPIKGLPEQ NAVRLTGKHP
	NDLEAVVGKC
101	METDGKDAPS GWAENGVCHT LFAKLVGNIA EDGGKLTDYL
	ISHSALQPYQ
151	AGKSGYAAVQ NGRYVLEIDS EGAFYFRRRH Y*

Based on this analysis, including the presence of a predicted prokaryotic membrane lipoprotein lipid attachment site (underlined) and a putative ATP/GTP-binding site motif A (P-loop, double-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 51

The following DNA sequence was identified in N. meningitidis <SEQ ID 431>:

1	ATGGAAGATT TATATATAAT ACTCGCTTTG GGTTTGGTTG
	CGATGATTGC
51	CGgATTTATC GATgcgatTg cGggCGGGGG TGGTTTGATT
	ACGCTGCCCG
101	CACTCTTGTT GGCAGGTATT CCTCCCGTGT CGGCAATTGC
	CACCAACAAG
151	CTGCAAgCAG CCGCTGCTAC GTTTTCAGCT ACGGTTTCTT
	TTGCACGCAA
201	AGGTTTGATT GATTGGAAGA AAGGTCTCCC GATTGCCGCA
	GCATCGTTTG
251	TAGGCGGCGT GGcCGGTGCA TTATCGGTCA GCTTGGTTTC
	CAAAGATATT
301	CTgCTgGCGG TCGTGCCGGT TTTGTTGATA TTTGTCGCAC
	TGTATTTTGT
351	GTTTTCGCCC AAGCTCGACG GCAGTAAGGA AGGCAAAGCC
	AGAATGTCTT
401	TTTTTCTGTT cGGGCTGACG GTCGC.ACCG CTTTTGGGTT
	TTTACGACGG
451	TGTGTTCGGA CCGGGTGTCG GCTCGTTTTT TCTGATTGCC
	TTTATTGTTT
501	TGCTCGGCTG CAAgCTGTTG AACGCGATGT CTTACACCAA
	ATTGGCGAAC
551	GTTGCCTGCA ATCTTGGTTC GCTATCGGTA TTCCTGCTGC
	ACGGTTCGAT
601	TATTTTCCCG ATTGCGGCAA CGaTGGCGGT CGGTGCGTTT
	GTCGGtGCGA
651	ATTTAgGTGC GAGATTTGCC GTaCgctTCG GTTCGAAGCT
	GATTAA

This corresponds to the amino acid sequence <SEQ ID 432; ORF109>:

1	MEDLYIILAL GLVAMIAGFI DAIAGGGGLI TLPALLLAGI
	PPVSAIATNK
51	LQAAAATFSA TVSFARKGLI DWKKGLPIAA ASFVGGVAGA
	LSVSLVSKDI
101	LLAVVPVLLI FVALYFVFSP KLDGSKEGKA RMSFFLFGLT
	VXTAFGFLRR
151	CVRTGCRLVF SDCLYCFARL QAVERDVLHQ IGERCLQSWF
	AIGIPAARFD
201	YFPDCGNDGG RCVCRCEFRC EICRTLRFEA D*

Further work revealed the following DNA sequence <SEQ ID 433>:

1	ATGGAAGATT TATATATAAT ACTCGCTTTG GGTTTGGTTG
	CGATGATTGC
51	CGGATTTATC GATGCGATTG CGGGCGGGGG TGGTTTGATT
	ACGCTGCCCG
101	CACTCTTGTT GGCAGGTATT CCTCCCGTGT CGGCAATTGC
	CACCAACAAG
151	CTGCAAGCAG CCGCTGCTAC GTTTTCAGCT ACGGTTTCTT
	TTGCACGCAA
201	AGGTTTGATT GATTGGAAGA AAGGTCTCCC GATTGCCGCA
	GCATCGTTTG
251	TAGGCGGCGT GGCCGGTGCA TTATCGGTCA GCTTGGTTTC
	CAAAGATATT
301	CTGCTGGCGG TCGTGCCGGT TTTGTTGATA TTTGTCGCAC
	TGTATTTTGT
351	GTTTTCGCCC AAGCTCGACG GCAGTAAGGA AGGCAAAGCC
	AGAATGTCTT
401	TTTTTCTGTT CGGGCTGACG GTCGCACCGC TTTTGGGTTT
	TTACGACGGT
451	GTGTTCGGAC CGGGTGTCGG CTCGTTTTTT CTGATTGCCT
	TTATTGTTTT
501	GCTCGGCTGC AAGCTGTTGA ACGCGATGTC TTACACCAAA
	TTGGCGAACG
551	TTGCCTGCAA TCTTGGTTCG CTATCGGTAT TCCTGCTGCA
	CGGTTCGATT
601	ATTTTCCCGA TTGCGGCAAC GATGGCGGTC GGTGCGTTTG
	TCGGTGCGAA
651	TTTAGGTGCG AGATTTGCCG TCCGCTTCGG TTCGAAGCTG
	ATTAAGCCGC
701	TGCTGATTGT CATCAGCATT TCGATGGCTG TGAAATTGTT
	GATAGACGAG
751	AGAAATCCGC TGTATCAGAT GATTGTTTCG ATGTTTTAA

This corresponds to the amino acid sequence <SEQ ID 434; ORF109-1>:

1	MEDLYIILAL GLVAMIAGFI DAIAGGGGLI TLPALLLAGI
	PPVSAIATNK
51	LQAAAATFSA TVSFARKGLI DWKKGLPIAA ASFVGGVAGA
	LSVSLVSKDI
101	LLAVVPVLLI FVALYFVFSP KLDGSKEGKA RMSFFLFGLT
	VAPLLGFYDG
151	VFGPGVGSFF LIAFIVLLGC KLLNAMSYTK LANVACNLGS
	LSVFLLHGSI
201	IFPIAATMAV GAFVGANLGA RFAVRFGSKL IKPLLIVISI
	SMAVKLLIDE
251	RNPLYQMIVS MF*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF109 shows 95.9% identity over a 147aa overlap with an ORF (ORF109a) from strain A of N. meningitidis:

The complete length ORF109a nucleotide sequence <SEQ ID 435> is:

1	ATGGAAGATT TATACATAAT ACTCGCTTTG GGTTTGGTTG
	CGATGATTGC
51	CGGATTTATC GATGCGATTG CGGGTGGGGG TGGTTTGATT
	ACGCTGCCTG
101	CACTCTTGTT GGCAGGTATT CCTCCCGTGT CGGCAATTGC
	CACCAACAAG
151	CTGCAAGCAG CCGCTGCTAC GTTTTCGGCT ACGGTTTCTT
	TTGCACGCAA
201	AGGTTTGATT GATTGGAAGA AAGGTCTCCC GATTGCGGCA
	GCATCGTTTG
251	CAGGCGGCGT GGTCGGTGCA TTATCGGTCA GCTTGGTTTC
	CAAAGATATT
301	CTGCTGGCGG TCGTGCCGGT TTTGTTGATA TTTGTCGCGC
	TGTATTTTGT
351	GTTTTCGCCC AAGCTCGACG GCAGTAAGGA AGGCAAAGCC
	AGAATGTCTT
401	TTTTTCTGTT CGGTCTGACG GTTGCACCAC TTTTGGGTTT
	TTACGACGGT
451	GTGTTCGGAC CGGGTGTCGG CTCGTTTTTT CTGATTGCCT
	TTATTGTTTT
501	GCTCGGCTGC AAGCTGTTGA ACGCGATGTC TTACACCAAA
	TTGGCGAACG
551	TTGCCTGCAA TCTTGGTTCG CTATCGGTAT TCCTGCTGCA
	CGGTTCGATT
601	ATTTTCCCGA TTGCGGCAAC GATGGCGGTC GGTGCGTTTG
	TCGGTGCGAA
651	TTTAGGTGCG AGATTTGCCG TCCGCTTCGG TTCGAAGCTG
	ATTAAGCCGC
701	TGCTGATTGT CATCAGCATT TCGATGGCTG TGAAATTGTT
	GATAGACGAG
751	AGAAATCCGC TGTATCAGAT GATTGTTTCG ATGTTTTAA

This encodes a protein having amino acid sequence <SEQ ID 436>:

1	MEDLYIILAL GLVAMIAGFI DAIAGGGGLI TLPALLLAGI
	PPVSAIATNK
51	LQAAAATFSA TVSFARKGLI DWKKGLPIAA ASFAGGVVGA
	LSVSLVSKDI
101	LLAVVPVLLI FVALYFVFSP KLDGSKEGKA RMSFFLFGLT
	VAPLLGFYDG
151	VFGPGVGSFF LIAFIVLLGC KLNAMSYTK LANVACNLGS
	LSVFLLHGSI
201	IFPIAATMAV GAFVGANLGA RFAVRFGSKL IKPLLIVISI
	SMAVKLLIDE
251	RNPLYQMIVS MF*

ORF109a and ORF109-1 show 99.2% identity in 262 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF109 shows 98.3% identity over a 231aa overlap with a predicted ORF (ORF109.ng) from N. gonorrhoeae:

An ORF109ng nucleotide sequence <SEQ ID 437> was predicted to encode a protein having amino acid sequence <SEQ ID 438>:

1	MEDLYIILAL GLVAMIAGFI DAIAGGGGLI TLPALLLAGI
	PPVSAIATNK
51	LQAAAATFSA TVSFARKGLI DWKKGLPIAA ASFAGGVVGA
	LSVSLVSKDI
101	LLAVVPVLLI FVALYFVFSP KLDGSKEGKA RMSFFLFGLT
	VATAFGFLRR
151	CVRTGCRLVF SDCLYCFARL QAVERDVLHQ IGERCLQSWF
	AIGIPAARFD
201	YFPDCGNDGG RCVCRCEFRC EICRPLRFEA D*

Further work revealed the following gonococcal DNA sequence <SEQ ID 439>:

1	ATGGAAGATT TATACATAAT ACTCGCTTTG GGTTTGGTTG
	CGATGATCGC
51	CGGATTTATC GATGCGATTG CGGGCGGGGG TGGTTTGATT
	ACGCTGCCTG
101	CACTCTTGTT GGCAGGTATT CCTCCCGTGT CGGCAATTGC
	CACCAACAAG
151	CTGCAAGCAG CCGCTGCTAC GTTTTCGGCT ACGGTTTCTT
	TTGCACGCAA
201	AGGTTTGATT GATTGGAAGA AAGGTCTCCC GATTGCCGCA
	GCATCGTTTG
251	CAGGCGGCGT GGTCGGTGCA TTATCGGTCA GCTTGGTTTC
	CAAAGATATT
301	TTGCTGGCGG TCGTGCCGGT TTTGTTGATA TTTGTCGCGC
	TGTATTTTGT
351	GTTTTCGCCC AAGCTCGACG GCAGTAAGGA AGGCAAAGCC
	AGAATGTCTT
401	TTTTTCTATT CGGGCTGACG GTTGCACCGC TTTTGGGTTT
	TTACGACGGT
451	GTGTTCGGAC CGGGTGTCGG CTCGTTTTTT CTGATTGCCT
	TTATTGTTTT
501	GCTCGGCTGC AAGCTGTTGA ACGCGATGTC TTACACCAAA
	TTGGCGAACG
551	TTGCTTGCAA TCTTGGTTCG CTATCGGTAT TCCTGCTGCA
	CGGTTCGATT
601	ATTTTCCCGA TTGTGGCAAC GATGGCGGTC GGTGCGTTTG
	TCGGTGCGAA
651	TTTAGGTGCG AGATTTGCCG TCCGCTTCGG TTCGAAGCTG
	ATTAAGCCGC
701	TGCTGATTGT CATCAGCATT TCGATGGCTG TGAAATTGTT
	GATAGACGAG
751	AGAAATCCGC TGTATCAGAT GATTGTTTCG ATGTTTTAA

This corresponds to the amino acid sequence <SEQ ID 440; ORF109ng-1>:

1	MEDLYIILAL GLVAMIAGFI DAIAGGGGLI TLPALLLAGI
	PPVSAIATNK
51	LQAAAATFSA TVSFARKGLI DWKKGLPIAA ASFAGGVVGA
	LSVSLVSKDI
101	LLAVVPVLLI FVALYFVFSP KLDGSKEGKA RMSFFLFGLT
	VAPLLGFYDG
151	VFGPGVGSFF LIAFIVLLGC KLLNAMSYTK LANVACNLGS
	LSVFLLHGSI
201	IFPIVATMAV GAFVGANLGA RFAVRFGSKL IKPLLIVISI
	SMAVKLLIDE
251	RNPLYQMIVS MF*

ORF109ng-1 and ORF109-1 show 98.9% identity in 262 aa overlap:

In addition, ORF109ng-1 shows homology to a hypothetical Pseudomonas protein:

sp|P29942|YCB9_PSEDE HYPOTHETICAL 27.4 KD PROTEIN IN COBO 3′REGION (ORF9)
>gi|94984|pir||I38164 hypothetical protein 9 - Pseudomonas sp >gi|551929
(M62866) ORF9 [Pseudomonas denitrificans] Length = 261
Score = 175 bits (439), Expect = 3e−43
Identities = 83/214 (38%), Positives = 131/214 (60%), Gaps = 1/214 (0%)

Query:	41	PPVSAIATNKLQXXXXXXXXXXXXXRKGLIDWKKGLPIXXXXXXXXXXXXXXXXXXXKDI	100
		PP+  + TNKLQ             R+G ++ K+ LP+                    D+
Sbjct:	43	PPLQTLGTNKLQGLFGSGSATLSYARRGHVNLKEQLPMALMSAAGAVLGALLATIVPGDV	102
Query:	101	LLAVVPVLLIFVALYFVFSPKLDGSKEGKARMSFFLFGLTVAPLLGFYDGVFGPGVGSFF	160
		L A++P LLI +ALYF   P + G  +  +R++ F+F LT+ PL+GFYDGVFGPG GSFF
Sbjct:	103	LKAILPFLLIAIALYFGLKPNM-GDVDQHSRVTPFVFTLTLVPLIGFYDGVFGPGTGSFF	161
Query:	161	LIAFIVLLGCKLLNAMSYTKLANVACNLGSLSVFLLHGSIIFPIVATMAVGAFVGANLGA	220
		++ F+ L G  +L A ++TK  N   N+G+  VFL  G++++ +   M +G F+GA +G+
Sbjct:	162	MLGFVTLAGFGVLKATAHTKFLNFGSNVGAFGVFLFFGAVLWKVGLLMGLGQFLGAQVGS	221
Query:	221	RFAVRFGSKLIKPLLIVISISMAVKLLIDERNPL	254
		R+A+  G+K+IKPLL+++SI++A++LL D  +PL
Sbjct:	222	RYAMAKGAKIIKPLLVIVSIALAIRLLADPTHPL	255

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 52

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 441>:

1	..CTGCTAGGGT ATTGCATCGG TTATCGGTAC GGCTGTTGCA
	GCAAAACCAG
51	CCGCAGACGG ATTATTTGGT CAAATTCGGA TCGTTTTGGG
	CGAG.ATTTT
101	TGGTTTTCTG GGACTGTATG ACGTCTATGC TTCGGCATGG
	TTTGTCGTTA
151	TCATGATGTT TTTGGTGGTT TCTACCAGTT TGTGCCTGAT
	TCGCAATGTG
201	CCGCCGTTCT GGCGCGAAAT GAAGTCTTTT CGGGAAAAGG
	TTAAAGAAAA
251	ATCTCTGGCG GCGATGCGCC ATTCTTCGCT GTTGGATGTA
	AAAATTGCGC
301	CCGAGGTTGC CAAACGTTAT CTGGAAGTAC AAGGTTTTCA
	GGGGAAAACC
351	ATTAACCGTG AAGACGGGTC GGTTCTGATT GCCGCCAAAA
	AAGGCACAAT
401	GAACAAATGG GGCTATATCT TTGCCCATGT TGCTTTGATT
	GTCATTTGCC
451	TGGGCGGGTT GATAGACAGT AACCTGCTGT TGAAACTGGG
	TATGCTGACC
501	GGTCGGATTG TTCCGGACAA TCAGGCGGTT TATGCCAAGG
	ATTTC.AAGC
551	CCGAAAGTAT .TTTGGGTGC gTCCAATCTC TCATTTAGGG
	GCAACGTCAA
601	TATTTCCG.A GGGGCAGAgT GCGGATGTGG TTTTCCTGA

This corresponds to the amino acid sequence <SEQ ID 442; ORF110>:

1	..LLGIASVIGT LLQQNQPQTD YLVKFGSFWA XIFGFLGLYD
	VYASAWFVVI
51	MMFLVVSTSL CLIRNVPPFW REMKSFREKV KEKSLAAMRH
	SSLLDVKIAP
101	EVAKRYLEVQ GFQGKTINRE DGSVLIAAKK GTMNKWGYIF
	AHVALIVICL
151	GGLIDSNLLL KLGMLTGRIF RTIRRFMPRI XKPESXFGCV
	QSLI*GQRQY
201	FXRGRVRMWF S*

Computer analysis of this amino acid sequence gave the following results:

Homology with ORF88a from N. meningitidis (Strain A)

ORF110 shows 91.5% identity over a 188aa overlap with ORF88a from strain A of N. meningitidis:

However, ORF88 and ORF110 do not align, because they represent two different fragments of the same protein.

Homology with a Predicted ORF from N. gonorrhoeae

ORF110 shows 88.6% identity over a 211 as overlap with a predicted ORF (ORF110.ng) from N. gonorrhoeae:

The complete length ORF110ng nucleotide sequence <SEQ ID 443> is predicted to encode a protein having amino acid sequence <SEQ ID 444>:

1	MSKSRISPTL LSRPWFAFFS SMRFAVALLS LLGIASVIGT
	VLQQNQPQTD
51	YLVKFGPFWT RIFDFLGLYD VYASAWFVVI MMFLVVSTSL
	CLIRNVPPFW
101	REMKSFREKV KEKSLAAMRH SSLLDVKIAP EVAKRYLEVR
	GFQGKTVSRE
151	DGSVLIAAKK GTMNKWGYIX AHVALIVICL GRLINXNLLL
	KLGMLAGSIF
201	RNNRRVMPRI SKPESIWGGV QSLIKGQRQY FQRGKVRMWF
	S*

Based on the putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 53

The following DNA sequence was identified in N. meningitidis <SEQ ID 445>:

1	ATGCCGTCTG AAACACGCCT GCCGAACTTT ATCCGCGTCT
	TGATATTTGC
51	CCTGGGTTTC ATCTTCCTGA ACGCCTGTTC GGAACAAACC
	GCGCAAACCG
101	TTACCCTGCA AGGCGAAACG ATGGGCACGA CCTATACCGT
	CAAATACCTT
151	TCAAATAATC GGGACAAACT CCCCTCACCT GCCGAAATAC
	AAAAACGCAT
201	CGATGACGCG CTTAAAGAAG TCAACCGGCA GATGTCCACC
	TATCAGCCCG
251	ACTCCGAAAT CAGCCGGTTC AACCAACACA CAGCCGGCAA
	GCCCCTCCGC
301	ATTTCAAGCG ACTTCGCACA CGTTACTGCC GAAGCCGTCC
	GCCTGAACCG
351	CCTGACACAC GGCGCGCTGG ACGTAACCGT CGGCCCCTTG
	GTCAACCTTT
401	GGGGATTCGG CCCCGACAAA TCCGTTACCC GTGAACCGTC
	GCCGGAACAA
451	ATCAAACAGG CGGCATCTTA TACGGGCATA GACAAAATCA
	TTTTGAAACA
501	AGGCAAAGAT TACGCTTCCT TGAGCAAAAC CCACCCCAAG
	GCCTATTTGG
551	ATTTATCTTC GATTGCCAAA GGCTTCGGCG TTGATAAAGT
	TGCGGGCGAA
601	CTGGAAAAAT ACGGCATTCA AAATTATCTG GTCGAAATCG
	GCGGCGAGTT
651	GCACGGCAAA GGCAAAAACG CGCGCGGCGA ACCGTGGCGC
	ATCGGTATCG
701	AGCAGCCCAA TATCGTCCAA GGCGGCAATA CGCAGATTAT
	CGTCCCGCTG
751	AACAACCGTT CGCTTGCCAC TTCCGGCGAT TACCGTATTT
	TCCACGTCGA
801	TAAAAACGGC AAACGCCTCT CCCATATCAT CAACCCGAAC
	AACAAACGAC
851	CCATCAGCCA CAACCTCGCC TCCATCAGCG TGGTCGCAGA
	CAGTGCGATG
901	ACGGCGGACG GCTTGTCCAC AGGATTATTC GTATTGGGCG
	AAACCGAAGC
951	CTTAAAGCTG GCAGAGCGCG AAAAACTCGC TGTTTTCCTG
	ATTGTCAGGG
1001	ATAAAGGCGG CTACCGCACC GCCATGTCTT CCGAATTTGA
	AAAACTGCTC
1051	CGCTAA

This corresponds to the amino acid sequence <SEQ ID 446; ORF111>:

1	MPSETRLPNF IRVLIFALGF IFLNACSEQT AQTVTLQGET
	MGTTYTVKYL
51	SNNRDKLPSP AEIQKRIDDA LKEVNRQMST YQPDSEISRF
	NQHTAGKPLR
101	ISSDFAHVTA EAVRLNRLTH GALDVTVGPL VNLWGFGPDK
	SVTREPSPEQ
151	IKQAASYTGI DKIILKQGKD YASLSKTHPK AYLDLSSIAK
	GFGVDKVAGE
201	LEKYGIQNYL VEIGGELHGK GKNARGEPWR IGIEQPNIVQ
	GGNTQIIVPL
251	NNRSLATSGD YRIFHVDKNG KRLSHIINPN NKRPISHNLA
	SISVVADSAM
301	TADGLSTGLF VLGETEALKL AEREKLAVFL IVRDKGGYRT
	AMSSEFEKLL
351	R*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF111 shows 96.9% identity over a 351aa overlap with an ORF (ORF111a) from strain A of N. meningitidis:

The complete length ORF111a nucleotide sequence <SEQ ID 447> is:

1	ATGCCGTCTG AAACACGCCT GCCGAACTTT ATCCGCACCT
	TGATATTTGC
51	CCTGAGTTTT ATCTTCCTGA ACGCCTGTTC GGAACAAACC
	GCGCAAACCG
101	TTACCCTGCA AGGTGAAACG ATGGGCACGA CCTATACCGT
	CAAATACCTT
151	TCAAATAATC GGGACNAACT CCCNTCACCT GCCGAAATAC
	AAAANCGCAT
201	CGATGACGCG CTTAAAGAAG TCAACCGGCA GATGTCCACC
	TATCAGCCCG
251	ACTCCGAAAT CAGCCGGTTC AACCAACACA CAGCCGGCAA
	GCCCCTCCGC
301	ATTTCAAGCG ACTTCGCACA CGTTACTGCC GAAGCCGTCC
	ACCTGAACCG
351	CCTGACACAC GGCGCGCTGG ACGTAACCGT CGGCCCCTTG
	GTCAACCTTT
401	GGGGATTCGG CCCCGACAAA TCCGTTACCC GTGAACCGTC
	GCCGGAACAA
451	ATCAAACAAG CAGCATCTTA TACGGGCATA GACAAAATCA
	TTTTGAAACA
501	AGGCAAAGAT TACGCTTCCT TGAGCAAAAC CCACCCCAAG
	GCCTATTTGG
551	ATTTATCTTC GATTGCCAAA GGCTTCGGCG TTGATNANGT
	TGCGGGCGAA
601	CTGGAAAAAT ACGGCATTCA AAATTATCTG GTCGAAATCG
	GCGGNGAGTT
651	GCACGGCAAA GNCAAAAACG CGCGCGGCGA ACCTTGGCGC
	ATCGGCATCG
701	AACAGCCCAA CATCGTCCAA GGCGGCAATA CGCAGATTAT
	CGTCCCGCTG
751	AACAACCGTT CGNTTGCCAC TTCCGGCGAT TACCGTATTT
	TCCACGTCGA
801	TAAAAGCGGC AAACGCCTCT CCCATATCAT TAATCCGAAC
	AACAAACGAC
851	CCATCAGCCA CAACCTCGCC TCCATCAGCG TGNTCGCAGA
	CAGTGCGATG
901	ACGGCGGACG GCTTNTCCAC AGGATTATTC GTATTGGGCG
	AAACCGAAGC
951	CTTAAAGCTG GCAGAGCGCG AAAAACTCGC TGTTTTCCTG
	ATTGTCAGGG
1001	ATAAAGGCGG CTACCGCACC GCCATGTCTT CCGAATTTGA
	AAAACTGCTC
1051	CGCTAA

This encodes a protein having amino acid sequence <SEQ ID 448>:

1	MPSETRLPNF IRTLIFALSF IFLNACSEQT AQTVTLQGET
	MGTTYTVKYL
51	SNNRDXLPSP AEIQXRIDDA LKEVNRQMST YQPDSEISRF
	NQHTAGKPLR
101	ISSDFAHVTA EAVHLNRLTH GALDVTVGPL VNLWGFGPDK
	SVTREPSPEQ
151	IKQAASYTGI DKIILKQGKD YASLSKTHPK AYLDLSSIAK
	GFGVDXVAGE
201	LEKYGIQNYL VEIGGELHGK XKNARGEPWR IGIEQPNIVQ
	GGNTQIIVPL
251	NNRSXATSGD YRIFHVDKSG KRLSHIINPN NKRPISHNLA
	SISVXADSAM
301	TADGXSTGLF VLGETEALKL AEREKLAVFL IVRDKGGYRT
	AMSSEFEKLL
351	R*

Homology with a Predicted ORF from N. gonorrhoeae

ORF111 shows 96.6% identity over a 351aa overlap with a predicted ORF (ORF111.ng) from N. gonorrhoeae:

The complete length ORF111ng nucleotide sequence <SEQ ID 449> is:

1	ATGCCGTCTG AAACACGCCT GCCGAACCTT ATCCGCGCCT
	TGATATTTGC
51	CCTGGGTTTC ATCTTCCTGA ACGCCTGTTC GGaacaaacC
	GCGCAaaccg
101	TTACCCTGCA AGGCGAAAcg aTGGGTACGA CCTATACCGT
	CAAATACCTT
151	TCAAATAATC GGGACAAACT CCCCTCCCCT GCCAAAATAC
	AAAAGCGCAT
201	TGATGATGCG CTTAAAGAAG TCAACCGGCA GATGTCCACC
	TACCAGACCG
251	ATTCCGAAAT CAGCCGGTTC AACCAACACA CAGCCGGCAA
	GCCCCTCCGC
301	ATTTCAAGCG ATTTCGCACA CGTTACCGCC GAAGCCGTCC
	GCCTGAACCG
351	CCTGACTCAC GGCGCACTGG ACGTAACCGT CGGCCCTTTG
	GTCAACCTTT
401	GGGGGTTCGG CCCCGACAAA TCCGTTACCC GTGAACCGTC
	GCCGGAACAA
451	ATCAAACAGG CGGCATCTTA TACGGGCATA GACAAAATCA
	TTTTGCAACA
501	AGGCAAAGAT TACGCTTCCT TGAGCAAAAC CCACCCCAAA
	GCCTATTTGG
551	ATTTATCTTC GATTGCCAAA GGCTTCGGCG TTGATAAAGT
	TGCGGGCGAA
601	CTGGAAAAAT ACGGCATTCA AAATTATCTG GTCGAAAtcg
	gcggcGAGTT
651	GCACGGCAAA GGCAAAAATG CGCACGGCGA ACCGTGGCGC
	ATCGGTATAG
701	AGCAACCCAA TATCATCCAA GgcgGCAata CGCAGATTAt
	cgtcccgctg
751	aaCaaccgtt cgctTGCCAC TTCCGGCGAT TAccgtaTTT
	tccacgtcgA
801	TAAAAAcggc aaacgccttt cccacaTCAT CAATCCCaAC
	aacAAACgac
851	ccATCAGcca caacctcgcc tccatcagcg tggtctcAGA
	CAGTGCAATG
901	ACGGCGGACG GTTtatCCAC AGGATTATTT GTTTTAGGCG
	AAACCGAAGC
951	CTTAAGGCTG GCAGAACAAG AAAAACTCGC TGTTTTCCTA
	ATTGTCCGGG
1001	ATAAGGACGG CTACCGCACC GCCATGTCTT CCGAATTTGC
	CAAGCTGCTC
1051	CGCTAA

This encodes a protein having amino acid sequence <SEQ ID 450>:

1	MPSETRLPNL IRALIFALGF IFLNACSEQT AQTVTLQGET
	MGTTYTVKYL
51	SNNRDKLPSP AKIQKRIDDA LKEVNRQMST YQTDSEISRF
	NQHTAGKPLR
101	ISSDFAHVTA EAVRLNRLTH GALDVTVGPL VNLWGFGPDK
	SVTREPSPEQ
151	IKQAASYTGI DKIILQQGKD YASLSKTHPK AYLDLSSIAK
	GFGVDKVAGE
201	LEKYGIQNYL VEIGGELHGK GKNAHGEPWR IGIEQPNIIQ
	GGNTQIIVPL
251	NNRSLATSGD YRIFHVDKNG KRLSHIINPN NKRPISHNLA
	SISVVSDSAM
301	TADGLSTGLF VLGETEALRL AEQEKLAVFL IVRDKDGYRT
	AMSSEFAKLL
351	R*

This protein shows homology with a hypothetical lipoprotein precursor from H. influenzae:

sp|P44550|YOJL_HAEIN HYPOTHETICAL LIPOPROTEIN HI0172 PRECURSOR >gi|1074292|pir|4
hypothetical protein HI0172 - Haemophilus influenzae (strain Rd KW20)
>gi|1573128 (U32702) hypothetical [Haemophilus influenzae] Length = 346
Score = 353 bits (896), Expect = 9e−97
Identities = 181/344 (52%), Positives = 247/344 (71%), Gaps = 4/344 (1%)

Query:	7	LPNLIRALIFALGFIFLNACSEQTAQTVTLQGETMGTTYTVKYLSNNRDKLPSPAKIQKR	66
		+  LI  +I     + L AC ++T + ++L G+TMGTTY VKYL +      S  K  +
Sbjct:	1	MKKLISGIIAVAMALSLAACQKET-KVISLSGKTMGTTYHVKYLDDGSITATSE-KTHEE	58
Query:	67	IDDALKEVNRQMSTYQTDSEISRFNQHT-AGKPLRISSDFAHVTAEAVRLNRLTHGALDV	125
		I+  LK+VN +MSTY+ DSE+SRFNQ+T    P+ IS+DFA V AEA+RLN++T GALDV
Sbjct:	59	IEAILKDVNAKMSTYKKDSELSRFNQNTQVNTPIEISADFAKVLAEAIRLNKVTEGALDV	118
Query:	126	TVGPLVNLWGFGPDKSVTREPSPEQIKQAASYTGIDKIILQQGKDYASLSKTHPKAYLDL	185
		TVGP+VNLWGFGP+K   ++P+PEQ+ +  ++ GIDKI L   K+ A+LSK  P+ Y+DL
Sbjct:	119	TVGPVVNLWGFGPEKRPEKQPTPEQLAERQAWVGIDKITLDTNKEKATLSKALPQVYVDL	178
Query:	186	SSIAKGFGVDKVAGELEKYGIQNYLVEIGGELHGKGKNAHGEPWRIGIEQPNIIQGGNTQ	245
		SSIAKGFGVD+VA +LE+   QNY+VEIGGE+  KGKN  G+PW+I IE+P        +
Sbjct:	179	SSIAKGFGVDQVAEKLEQLNAQNYMVEIGGEIRAKGKNIEGKPWQIAIEKPTTTGERAVE	238
Query:	246	IIVPLNNRSLATSGDYRIFHVDKNGKRLSHIINPNNKRPISHNLASISVVSDSAMTADGL	305
		++ LNN  +A+SGDYRI+  ++NGKR +H I+P    PI H+LASI+V++ ++MTADGL
Sbjct:	239	AVIGLNNMGMASSGDYRIY-FEENGKRFAHEIDPKTGYPIQHHLASITVLAPTSMTADGL	297
Query:	306	STGLFVLGETEALRLAEQEKLAVFLIVRDKDGYRTAMSSEFAKL	349
		STGLFVLGE +AL +AE+  LAV+LI+R  +G+ T  SS F KL
Sbjct:	298	STGLFVLGEDKALEVAEKNNLAVYLIIRTDNGFVTKSSSAFKKL	341

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 54

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 451>:

1	..CCGTGCCGCC GACAGGGCGA CGACGTGTAT GCGGCGCACG
	CGTCCCGTCA
51	AAAATTGTGG CTGCGCTTCA TCGGCGGCCG GTCGCATCAA
	AATATACGGG
101	GCGGCGCGGC TGCGGACGGG TGGCGCAAAG GCGTGCAAAT
	CGGCGGCGAG
151	GTGTTTGTAC GGCAAAATGA AGGCAGCCkA yTGGCAATCG
	GCGTGATGGG
201	CGGCAGGGCC GGCCAGCACG CwTCAGTCAA CGGCAAAGGC
	GGTGCGGCAG
251	gCAGTGATTT GTATGGTTAT GgCGGGGgTG TTTATGCTgC
	GTGGCATCAG
301	TTGCGCGATA AACAAACGGG TgCGTATTTG GACGGCTGGT
	TGCAATACCA
351	ACGTTTCAAA CACCGCATCA ATGATGAAAA CCGTGCGGAA
	CgCTACAAAA
401	CCAAAGGTTG GACGGCTTCT GTCGAAGGCG GCTACAACGC
	GCTTGTGGCG
451	GAAGGCATTG TCGGAAAAGG CAATAATGTG CGGTTTTACC
	TACAACCGCA
501	GgCGCAGTTT ACCTACTTGG GCGTAAACGG CGGCTTTACC
	GACAGCGAGG
551	GGACGGCGGT CGGACTGCTC GGCAGCGGTC AGTGGCAAAG
	CCGCGCCGGC
601	AtTCGGGCAA AAACCCGTTT TGCTTTGCGT AACGGTGTCA
	ATCTTCAGCC
651	TTTTGCCGCT TTTAATGTtt TGCACAGGTC AAAATCTTTC
	GGCGTGGAAA
701	TGGACGGCGA AAAACAGACG CTGGCAGGCA GGACGGCACT
	CGAAGGGCGG
751	TTCGGTATTG AAGCCGGTTG GAAAGGCCAT ATGTCCGCA..

This corresponds to the amino acid sequence <SEQ ID 452; ORF35>:

1	..PCRRQGDDVY AAHASRQKLW LRFIGGRSHQ NIRGGAAADG
	WRKGVQIGGE
51	VFVRQNEGSX LAIGVMGGRA GQHASVNGKG GAAGSDLYGY
	GGGVYAAWHQ
101	LRDKQTGAYL DGWLQYQRFK HRINDENRAE RYKTKGWTAS
	VEGGYNALVA
151	EGIVGKGNNV RFYLQPQAQF TYLGVNGGFT DSEGTAVGLL
	GSGQWQSRAG
201	IRAKTRFALR NGVNLQPFAA FNVLHRSKSF GVEMDGEKQT
	LAGRTALEGR
251	FGIEAGWKGH MSA..

Computer analysis of this amino acid sequence gave the following results:

Homology with Putative Secreted VirG-Homolgue of N. meningitidis (Accession Number A32247)

ORF and virg-h protein show 51% aa identity in 261aa overlap:

Orf35	5	QGDDVYAAHASRQKLWLRFIGGRSHQNIRGGAA-ADGWRKGVQIGGEVFVRQNEGSXLAI	63
		+  D++     R+ LWLR I G S+Q ++G  A  +G+RKGVQ+GGEVF  QNE + L+I
virg-h	396	KNSDIFDRTLPRKGLWLRVIDGHSNQWVQGKTAPVEGYRKGVQLGGEVFTWQNESNQLSI	455
Orf35	64	GVMGGRAGQHASVNGKG--GAAGSDLYGYGGGVYAAWHQLRDKQTGAYLDGWLQYQRFKH	121
		G+MGG+A Q ++ +          ++ G+G GVYA WHQL+DKQTGAY D W+QYQRF+H
virg-h	456	GLMGGQAEQRSTFHNPDTDNLTTGNVKGFGAGVYATWHQLQDKQTGAYADSWMQYQRFRH	515
Orf35	122	RINDENRAERYKTKGWTASVEGGYNALVAEGIVGKGNNVRFYLQPQAQFTYLGVNGGFTD	181
		RIN E+  ER+ +KG TAS+E GYNAL+AE    KGN++R YLQPQAQ TYLGVNG F+D
virg-h	516	RINTEDGTERFTSKGITASIEAGYNALLAEHFTKKGNSLRVYLQPQAQLTYLGVNGKFSD	575
Orf35	182	SEGTAVGLLGSGQWQSRAGIRAKTRFALRNGVNLQPFAAFNVLHRSKSFGVEMDGEKQTL	241
		SE   V LLGS Q Q+R G++AK +F+L   + ++PFAA N L+ +K FGVEMDGE++ +
virg-h	576	SENAHVNLLGSRQLQTRVGVQAKAQFSLYKNIAIEPFAAVNALYHNKPFGVEMDGERRVI	635
Orf35	242	AGRTALEGRFGIEAGWKGHMS	262
		+TA+E + G+    K H++
virg-h	636	NNKTAIESQLGVAVKIKSHLT	656

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF35 shows 96.9% identity over a 259aa overlap with an ORF (ORF35a) from strain A of N. meningitidis:

The complete length ORF35a nucleotide sequence <SEQ ID 453> is:

1	ATGTTCAGAG CTCAGCTTGG TTCAAATACT CGTTCTACCA
	AAATCGGCGA
51	CGATGCCGAT TTTTCATTTT CAGACAAGCC GAAACCCGGC
	ACTTCCCATT
101	ATTTTTCCAG CGGTAAAACC GATCAAAATT CATCCGAATA
	TGGGTATGAC
151	GAAATCAATA TCCAAGGTAA AAACTACAAT AGCGGCATAC
	TCGCCGTCGA
201	TAATATGCCC GTTGTTAAGA AATATATTAC AGATACTTAC
	GGGGATAATT
251	TAAAGGATGC GGTTAAGAAG CAATTACAGG ATTTATACAA
	AACAAGACCC
301	GAAGCTTGGG AAGAAAATAA AAAACGGACT GAGGAGGCGT
	ATATAGAACA
351	GCTTGGACCA AAATTTAGTA TACTCAAACA GAAAAACCCC
	GATTTAATTA
401	ATAAATTGGT AGAAGATTCC GTACTCACTC CTCATAGTAA
	TACATCACAG
451	ACTAGTCTCA ACAACATCTT CAATAAAAAA TTACACGTCA
	AAATCGAAAA
501	CAAATCCCAC GTCGCCGGAC AGGTGTTGGA ACTGACCAAG
	ATGACGCTGA
551	AAGATTCCCT TTGGGAACCG CGCCGCCATT CCGACATCCA
	TATGCTGGAA
601	ACTTCCGATA ATGCCCGCAT CCGCCTGAAC ACGAAAGATG
	AAAAACTGAC
651	CGTCCATAAA GCGTATCAGG GCGGTGCGGA TTTCCTGTTC
	GGCTACGACG
701	TGCGGGAGTC GGACAAACCC GCCCTGACCT TTGAAGAAAA
	AGTCAGCGGA
751	CAATCCGGCG TGGTTTTGGA ACGCCGGCCG GAAAATCTGA
	AAACGCTCGA
801	CGGGCGCAAA CTGATTGCGG CGGAAAAGGC AGACTCTAAT
	TCGTTTGCGT
851	TTAAACAAAA TTACCGGCAG GGACTGTACG AATTATTGCT
	CAAGCAATGC
901	GAAGGCGGAT TTTGCTTGGG CGTGCAGCGT TTGGCTATCC
	CCGAGGCGGA
951	AGCGGTTTTA TATGCCCAAC AGGCTTATGC GGCAAATACT
	TTGTTCGGGC
1001	TGCGTGCCGC CGACAGGGGC GACGACGTGT ATGCCGCCGA
	TCCGTCCCGT
1051	CAAAAATTGT GGCTGCGCTT CATCGGCGGC CGGTCGCATC
	AAAATATACG
1101	GGGCGGCGCG GCTGCGGACG GGCGGCGCAA AGGCGTGCAA
	ATCGGCGGCG
1151	AGGTGTTTGT ACGGCAAAAT GAAGGCAGCC GGCTGGCAAT
	CGGCGTGATG
1201	GGCGGCAGGG CTGGCCAGCA CGCATCAGTC AACGGCAAAG
	GCGGTGCGGC
1251	AGGCAGTTAT TTGCATGGTT ATGGCGGGGG TGTTTATGCT
	GCGTGGCATC
1301	AGTTGCGCGA TAAACAAACG GGTGCGTATT TGGACGGCTG
	GTTGCAATAC
1351	CAACGTTTCA AACACCGCAT CAATGATGAA AACCGTGCGG
	AACGCTACAA
1401	AACCAAAGGT TGGACGGCTT CTGTCGAAGG CGGCTACAAC
	GCGCTTGTGG
1451	CGGAAGGCGT TGTCGGAAAA GGCAATAATG TGCGGTTTTA
	CCTGCAACCG
1501	CAGGCGCAGT TTACCTACTT GGGCGTAAAC GGCGGCTTTA
	CCGACAGCGA
1551	GGGGACGGCG GTCGGACTGC TCGGCAGCGG TCAGTGGCAA
	AGCCGCGCCG
1601	GCATTCGGGC AAAAACCCGT TTTGCTTTGC GTAACGGTGT
	CAATCTTCAG
1651	CCTTTTGCCG CTTTTAATGT TTTGCACAGG TCAAAATCTT
	TCGGCGTGGA
1701	AATGGACGGC GAAAAACAGA CGCTGGCAGG CAGGACGGCG
	CTCGAAGGGC
1751	GGTTCGGCAT TGAAGCCGGT TGGAAAGGCC ATATGTCCGC
	ACGCATCGGA
1801	TACGGCAAAA GGACGGACGG CGACAAAGAA GCCGCATTGT
	CGCTCAAATG
1851	GCTGTTTTGA

This encodes a protein having amino acid sequence <SEQ ID 454>:

1	MFRAQLGSNT RSTKIGDDAD FSFSDKPKPG TSHYFSSGKT
	DQNSSEYGYD
51	EINIQGKNYN SGILAVDNMP VVKKYITDTY GDNLKDAVKK
	QLQDLYKTRP
101	EAWEENKKRT EEAYIEQLGP KFSILKQKNP DLINKLVEDS
	VLTPHSNTSQ
151	TSLNNIFNKK LHVKIENKSH VAGQVLELTK MTLKDSLWEP
	RRHSDIHMLE
201	TSDNARIRLN TKDEKLTVHK AYQGGADFLF GYDVRESDKP
	ALTFEEKVSG
251	QSGVVLERRP ENLKTLDGRK LIAAEKADSN SFAFKQNYRQ
	GLYELLLKQC
301	EGGFCLGVQR LAIPEAEAVL YAQQAYAANT LFGLRAADRG
	DDVYAADPSR
351	QKLWLRFIGG RSHQNIRGGA AADGRRKGVQ IGGEVFVRQN
	EGSRLAIGVM
401	GGRAGQHASV NGKGGAAGSY LHGYGGGVYA AWHQLRDKQT
	GAYLDGWLQY
451	QRFKHRINDE NRAERYKTKG WTASVEGGYN ALVAEGVVGK
	GNNVRFYLQP
501	QAQFTYLGVN GGFTDSEGTA VGLLGSGQWQ SRAGIRAKTR
	FALRNGVNLQ
551	PFAAFNVLHR SKSFGVEMDG EKQTLAGRTA LEGRFGIEAG
	WKGHMSARIG
601	YGKRTDGDKE AALSLKWLF*

Homology with a Predicted ORF from N. gonorrhoeae

ORF35 shows 51.7% identity over a 261aa overlap with a predicted ORF (ORF35ngh) from N. gonorrhoeae:

A partial ORF35ngh nucleotide sequence <SEQ ID 455> is predicted to encode a protein having partial amino acid sequence <SEQ ID 456>:

1	..KKLRDRNSEY WKEETYHIKS NGRTYPNIPA LFPKHPFDPF
	ENINNSKKIS
51	FYDKEYTEDY LVGFARGFGV EKRNGEEEKP LRQYFKDCVN
	TENSNNDNCK
101	ISSFGNYGPI LIKSDIFALA SQIKNSHINS EILSVGNYIE
	WLRPTLNKLT
151	GWQEHLYAGL DPFHYIEVTD NSHVIGQTID LGALELTNSL
	WKPRWNSNID
201	YLITKNAEIR FNTKNESLLV KEDYAGGARF RFAYDLKDKV
	PEIPVLTFEK
251	NITGTSDIIF EGKALDNLKH LDGHQIVKVN DTADKDAFRL
	SSKYRKGIYT
301	LSLQQRPEGF FTKVQERDDI AIYAQQAQAA NTLFALRLND
	KNSDIFDRTL
351	PRKGLWLRVI DGHSNQWVQG KTAPVEGYRK GVQLGGEVFT
	WQNESNQLSI
401	GLMGGQAEQR STFRNPDTDN LTTGNVKGFG AGVYATWHQL
	QDKQTGAYVD
451	SWMQYQRFRH RINTEYATER FTSKGITASI EAGYNALLAE
	HFTKKGNSLR
501	VYLQPQAQLT YLGVNGKFSD SENAQVNLLG SRQLQSRVGV
	QAKAQFAFTN
551	GVTFQPFVAV NSIYQQKPFG VEIDGDRRVI NNKTVIETQL
	GVAAKIKSHL
601	TLQASFNRQT SKHHHAKQGA LNLQWTF*

Based on this prediction, these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 55

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 457>:

1	..GCGGAATATG TTCAGTTCTC TATAGATTTG TTCAGTGTGG
	GTAAATCGGG
51	GGGCGGTATA CCTAAGGCTA AGCCTGTGTT TGATGCGAAA
	CCGAGATGGG
101	AGGTTGATAG GAAGCTTAAT AAATTGACAA CTCGTGAGCA
	GGTGGAGAAA
151	AATGTTCAGG AAACGAGAAG AAGGAGTCAG AGTAGTCAGT
	TTAAAGCCCA
201	TGCGCAACGA GAATGGGAAA ATAAAACAGG GTTAGATTTT
	AATCATTTTA
251	TAGGTGGTGA TATCAATAAA AAAGGCACAG TAACAGGAGG
	GCATAGTCTA
301	ACCCGTGGTG ATGTACGGGT GATACAACAA ACCTCGGCAC
	CTGATAAACA
351	TGGGGT.TTA TCAAGCGACA GTGGAAATTN A

This corresponds to the amino acid sequence <SEQ ID 458; ORF46>:

1	..AEYVQFSIDL FSVGKSGGGI PKAKPVFDAK PRWEVDRKLN
	KLTTREQVEK
51	NVQETRRRSQ SSQFKAHAQR EWENKTGLDF NHFIGGDINK
	KGTVTGGHSL
101	TRGDVRVIQQ TSAPDKHGXL SSDSGNX

Further work revealed further partial nucleotide sequence <SEQ ID 459>:

1	..GCAGTGTGCC TnCCGATGCA TGCACACGCC TCAnATTTGG
	CAAACGATTC
51	TTTTATCCGG CAGGTTCTCG ACCGTCAGCA TTTCGAACCC
	GACGGGAAAT
101	ACCACCTATT CGGCAGCAGG GGGGAACTTG CCGAGCGCCA
	GTCTCATATC
151	GGATTGGGAA AAATACAAAG CCATCAGTTG GGCAACCTGA
	TGATTCAACA
201	GGCGGCCATT AAAGGAAATA TCGGCTACAT TGTCCGCTTT
	TCCGATCACG
251	GGCACGAAGT CCATTCCCCs TTCGACAACC ATGCCTCACA
	TTCCGATTCT
301	GATGAAGCCG GTAGTCCCGT TGACGGATTT AGCCTTTACC
	GCATCCATTG
351	GGACGGATAC GAACACCATC CCGCCGACGG CTATGACGGG
	CCACAGGGCG
401	GCGGCTATCC CGCTCCCAAA GGCGCGAGGG ATATATACAG
	TTACGACATA
451	AAAGGCGTTG CCCAAAATAT CCGCCTCAAC CTGACCGACA
	ACCGCAGCAC
501	CGGACAACGG CTTGCCGACC GTTTCCACAA TGCCGGTAGT
	ATGCTGACGC
551	AAGGAGTAGG CGACGGATTC AAACGCGCCA CCCGATACAG
	CCCCGAGCTG
601	GACAGATCGG GCAATGCCGC CGAAGCCTTC AACGGCACTG
	CAGATATCGT
651	TAAAAACATC ATCGGCGCTG CAGGAGAAAT TGT

This corresponds to the amino acid sequence <SEQ ID 460; ORF46-1>:

1	..AVCLPMHAHA SXLANDSFIR QVLDRQHFEP DGKYHLFGSR
	GELAERQSHI
51	GLGKIQSHQL GNLMIQQAAI KGNIGYIVRF SDHGHEVHSP
	FDNHASHSDS
101	DEAGSPVDGF SLYRIHWDGY EHHPADGYDG PQGGGYPAPK
	GARDIYSYDI
151	KGVAQNIRLN LTDNRSTGQR LADRFHNAGS MLTQGVGDGF
	KRATRYSPEL
201	DRSGNAAEAF NGTADIVKNI IGAAGEI

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. gonorrhoeae

ORF46 shows 98.2% identity over, a 111 aa overlap with a predicted ORF (ORF46ng) from N. gonorrhoeae:

A partial ORF46ng nucleotide sequence <SEQ ID 461> is predicted to encode a protein having partial amino acid sequence <SEQ ID 462>:

1	..RRLKHCCHAR LGSAFHRKQD GAHQRFGRYG ATQRLCRSSH
	PRLGSPKPQC
51	RTRHRSRQQY LYGSHPHQRD WSCPGKIQLG RHHGTSCRAV
	ADXRDRICER
101	EIRRQRQXCR CRLGKIPSLS IPKYPLKLEQ RYGKENITSS
	TVPPSNGKNV
151	KLADQRHPKT GVPFDGKGFP NFEKHVKYDT KLDIQELSGG
	GIPKAKPVFD
201	AKPRWEVDRK LNKLTTREQV EKNVQETRRR SQSSQFKAHA
	QREWENKTGL
251	DFNHFIGGDI NKKGAVTGGH SLTRGDVRVI QQTSAPDKHG
	VLSSDSGN*

Further work revealed the complete gonococcal DNA sequence <SEQ ID 463>:

1	TTGGGCATTT CCCGCAAAAT ATCCCTTATT CTGTCCATAC
	TGGCAGTGTG
51	CCTGCCGATG CATGCACACG CCTCAGATTT GGcaAACGAT
	CCCTTTATCC
101	GgCaggttcT CGaccGTCAG CATTTCGaac ccgacggGAa
	ATACCaCCTA
151	TTcggCaGCA GGGGGGAGCT TgccnagcGC aacggccATa
	tcggattggG
201	aaacaTAcaa Agccatcagt tGggccacct gatgattcaa
	caggcggccg
251	ttgaaggaaA TAtcgGctac attgtccgct tttccgatca
	cgggcacaaa
301	ttccattcgc ccttcGAcaa ccaTGCCTCA CATTCCGATT
	CTGACGAAGC
351	CGGTAGTCCC GTTGACGGAT TCAGCCTTTA CCGCATCCAT
	TGGGACGGAT
401	ACGAACACCA TCCCGCCGAC GGCTATGACG GGCCACAGGG
	CGGCGGCTAT
451	CCCGCTCCCA AAGGCGCGAG GGATATATAC AGCTACGACA
	TAAAAGGCGT
501	TGCCCAAAAT ATCCGCCTCA ACCTGACCGA CAACCGCAGC
	ACCGGACAAC
551	GGCTTGCCGA CCGTTTCCAC AATGCCGGCG CTATGCTGAC
	GCAAGGAGTA
601	GGCGACGGAT TCAAACGCGC CACCCGATAC AGCCCCGAGC
	TGGACAGATC
651	GGGCAATGCc gccGAAGCCT TCAACGGCAC TGCAGATATC
	GTCAAAAACA
701	TCATCGGCGC GGCAGGAGAA ATTGTCGGCG CAGGCGATGC
	CGTGCagGGT
751	ATAAGCGAAG GCTCAAACAT TGCTGTCATG CACGGCTTGG
	GTCTGCTTTC
801	CACCGAAAAC AAGATGGCGC GCATCAACGA TTTGGCAGAT
	ATGGCGCAAC
851	TCAAAGACTA TGCCGCAGCA GCCATCCGCG ATTGGGCAGT
	CCAAAACCCC
901	AATGCCGCAC AAGGCATAGA AGCCGTCAGC AATATCTTTA
	TGGCAGCCAT
951	CCCCATCAAA GGGATTGGAG CTGTCCGGGG AAAATACGGC
	TTGGGCGGCA
1001	TCACGGCACA TCCTGTCAAG CGGTCGCAGA TGGGCGCGAT
	CGCATTGCCG
1051	AAAGGGAAAT CCGCCGTCAG CGACAATTTT GCCGATGCGG
	CATACGCCAA
1101	ATACCCGTCC CCTTACCATT CCCGAAATAT CCGTTCAAAC
	TTGGAGCAGC
1151	GTTACGGCAA AGAAAACATC ACCTCCTCAA CCGTGCCGCC
	GTCAAACGGC
1201	AAAAATGTCA AACTGGCAGA CCAACGCCAC CCGAAGACAG
	GCGTACCGTT
1251	TGACGGTAAA GGGTTTCCGA ATTTTGAGAA GCACGTGAAA
	TATGATACGA
1301	AGCTCGATAT TCAAGAATTA TCGGGGGGCG GTATACCTAA
	GGCTAAGCCT
1351	GTGTTTGATG CGAAACCGAG ATGGGAGGTT GATAGGAAGC
	TTAATAAATT
1401	GACAACTCGT GAGCAGGTGG AGAAAAATGT TCAGGAAACG
	AGAAGAAGGA
1451	GTCAGAGTAG TCAGTTTAAA GCCCATGCGC AACGAGAATG
	GGAAAATAAA
1501	ACAGGGTTAG ATTTTAATCA TTTTATAGGT GGTGATATCA
	ATAAGAAAGG
1551	CACAGTAACA GGAGGGCATA GTCTAACCCG TGGTGATGTA
	CGGGTGATAC
1601	AACAAACCTC GGCACCTGAT AAACATGGGG TTTATCAAGC
	GACAGTGGAA
1651	ATTAAAAAGC CTGATGGAAG TTGGGAGGTG AAAACGAAAA
	AAGGTGGGAA
1701	AGTGATGACC AAGCACACCA TGTTCCCAAA AGATTGGGAT
	GAGGCTAGAA
1751	TTAGGGCTGA AGTTACTTCG GCTTGGGAAA GTAGAATAAT
	GCTTAAGGAT
1801	AATAAATGGC AGGGTACAAG TAAATCGGGT ATTAAAATAG
	AAGGATTTAC
1851	CGAACCTAAT AGAACAGCAT ATCCCATTTA TGAATAG

This corresponds to the amino acid sequence <SEQ ID 464; ORF46ng-1>:

1	LGISRKISLI LSILAVCLPM HAHASDLAND PFIRQVLDRQ
	HFEPDGKYHL
51	FGSRGELAXR NGHIGLGNIQ SHQLGHLMIQ QAAVEGNIGY
	IVRFSDHGHK
101	FHSPFDNHAS HSDSDEAGSP VDGFSLYRIH WDGYEHHPAD
	GYDGPQGGGY
151	PAPKGARDIY SYDIKGVAQN IRLNLTDNRS TGQRLADRFH
	NAGAMLTQGV
201	GDGFKRATRY SPELDRSGNA AEAFNGTADI VKNIIGAAGE
	IVGAGDAVQG
251	ISEGSNIAVM HGLGLLSTEN KMARINDLAD MAQLKDYAAA
	AIRDWAVQNP
301	NAAQGIEAVS NIFMAAIPIK GIGAVRGKYG LGGITAHPVK
	RSQMGAIALP
351	KGKSAVSDNF ADAAYAKYPS PYHSRNIRSN LEQRYGKENI
	TSSTVPPSNG
401	KNVKLADQRH PKTGVPFDGK GFPNFEKHVK YDTKLDIQEL
	SGGGIPKAKP
451	VFDAKPRWEV DRKLNKLTTR EQVEKNVQET RRRSQSSQFK
	AHAQREWENK
501	TGLDFNHFIG GDINKKGTVT GGHSLTRGDV RVIQQTSAPD
	KHGVYQATVE
551	IKKPDGSWEV KTKKGGKVMT KHTMFPKDWD EARIRAEVTS
	AWESRIMLKD
601	NKWQGTSKSG IKIEGFTEPN RTAYPIYE*

ORF46ng-1 and ORF46-1 show 94.7% identity in 227 aa overlap:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF46ng-1 shows 87.4% identity over a 486aa overlap with an ORF (ORF46a) from strain A of N. meningitidis:

The complete length ORF46a DNA sequence <SEQ ID 465> is:

1	TTGGGCATTT CCCGCAAAAT ATCCCTTATT CTGTCCATAC
	TGGCAGTGTG
51	CCTGCCGATG CATGCACACG CCTCAGATTT GGCAAACGAT
	TCTTTTATCC
101	GGCAGGTTCT CGACCGTCAG CATTTCGAAC CCGACGGGAA
	ATACCACCTA
151	TTCGGCAGCA GGGGGGAACT TGCCGAGCGC AGCGGTCATA
	TCGGATTGGG
201	AAACATACAA AGCCATCAGT TGGGCAACCT GTTCATCCAG
	CAGGCGGCCA
251	TTAAAGGAAA TATCGGCTAC ATTGTCCGCT TTTCCGATCA
	CGGGCACGAA
301	GTCCATTCCC CCTTCGACAA CCATGCCTCA CATTCCGATT
	CTGATGAAGC
351	CGGTAGTCCC GTTGACGGAT TCAGCCTTTA CCGCATCCAT
	TGGGACGGAT
401	ACGAACACCA TCCCGCCGAC GGCTATGACG GGCCACAGGG
	CGGCGGCTAT
451	CCCGCTCCCA AAGGCGCGAG GGATATATAC AGCTACGACA
	TAAAAGGCGT
501	TGCCCAAAAT ATCCGCCTCA ACCTGACCGA CAACCGCAGC
	ACCGGACAAC
551	GGCTTGTCGA CCGTTTCCAC AATACCGGTA GTATGCTGAC
	GCAAGGAGTA
601	GGCGACGGAT TCAAACGCGC CACCCGATAC AGCCCCGAGC
	TGGACAGATC
651	GGGCAATGCC GCCGAAGCTT TCAACGGCAC TGCAGATATC
	GTCAAAAACA
701	TCATCGGCGC GGCAGGAGAA ATTGTCGGCG CAGGCGATGC
	CGTGCAGGGT
751	ATAAGCGAAG GCTCAAACAT TGCTGTTATG CACGGCTTGG
	GTCTGCTTTC
801	CACCGAAAAC AAGATGGCGC GCATCAACGA TTTGGCAGAT
	ATGGCGCAAC
851	TCAAAGACTA TGCCGCAGCA GCCATCCGCG ATTGGGCAGT
	CCAAAACCCC
901	AATGCCGCAC AAGGCATAGA AGCCGTCAGC AATATCTTTA
	CGGCAGTCAT
951	CCCCGTCAAA GGGATTGGAG CTGTTCGGGG AAAATACGGC
	TTGGGCGGCA
1001	TCACGGCACA TCCTGTCAAG CGGTCGCAGA TGGGCGAGAT
	CGCATTGCCG
1051	AAAGGGAAAT CCGCCGTCAG CGACAATTTT GCCGATGCGG
	CATACGCCAA
1101	ATACCCGTCC CCTTACCATT CCCGAAATAT CCGTTCAAAC
	TTGGAGCAGC
1151	GTTACGGCAA AGAAAACATC ACCTCCTCAA CCGTGCCGCC
	GTCAAACGGA
1201	AAGAATGTGA AACTGGCAAA CAAACGCCAC CCGAAGACCA
	AAGTGCCGTT
1251	TGACGGTAAA GGGTTTCCGA ATTTTGAAAA AGACGTAAAA
	TACGATACGA
1301	GAATTAATAC CGCTGTACCA CAAGTGAATC CTATAGATGA
	ACCCGTCTTT
1351	AATCCTAAAG GTTCTGTCGG ATCGGCTCAT TCTTGGTCTA
	TAACTGCCAG
1401	AATTCAATAC GCAAAATTAC CAAGGCAAGG TAGAATCAGA
	TATATCCCAC
1451	CTAAAAATTA CTCTCCTTCA GCACCGCTAC CAAAAGGACC
	TAATAATGGA
1501	TATTTGGATA AATTTGGTAA TGAATGGACT AAAGGTCCAT
	CAAGAACTAA
1551	AGGTCAAGAA TTTGAATGGG ATGTTCAATT GTCTAAAACA
	GGAAGAGAGC
1601	AACTTGGATG GGCTAGTAGG GATGGTAAGC ATTTAAATAT
	ATCAATTGAT
1651	GGAAAGATTA CACACAAATG A

This corresponds to the amino acid sequence <SEQ ID 466>:

1	LGISRKISLI LSILAVCLPM HAHASDLAND SFIRQVLDRQ
	HFEPDGKYHL
51	FGSRGELAER SGHIGLGNIQ SHQLGNLFIQ QAAIKGNIGY
	IVRFSDHGHE
101	VHSPFDNHAS HSDSDEAGSP VDGFSLYRIH WDGYEHHPAD
	GYDGPQGGGY
151	PAPKGARDIY SYDIKGVAQN IRLNLTDNRS TGQRLVDRFH
	NTGSMLTQGV
201	GDGFKRATRY SPELDRSGNA AEAFNGTADI VKNIIGAAGE
	IVGAGDAVQG
251	ISEGSNIAVM HGLGLLSTEN KMARINDLAD MAQLKDYAAA
	AIRDWAVQNP
301	NAAQGIEAVS NIFTAVIPVK GIGAVRGKYG LGGITAHPVK
	RSQMGEIALP
351	KGKSAVSDNF ADAAYAKYPS PYHSRNIRSN LEQRYGKENI
	TSSTVPPSNG
401	KNVKLANKRH PKTKVPFDGK GFPNFEKDVK YDTRINTAVP
	QVNPIDEPVF
451	NPKGSVGSAH SWSITARIQY AKLPRQGRIR YIPPKNYSPS
	APLPKGPNNG
501	YLDKFGNEWT KGPSRTKGQE FEWDVQLSKT GREQLGWASR
	DGKHLNISID
551	GKITHK*

Based on this analysis, including the presence of a RGD sequence in the gonococcal protein, typical of adhesins, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 56

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 467>:

1	ATGAATATTC ACACCCTGCT CTCCAAACAA TGGACGCTGC
	CGCCATTCCT
51	GCCGAAACGG CTGCTGCTGT CCCTGCTGAT ACTGCTTGCC
	CCCAATGCGG
101	TGTTTTGGGT TTTGGCACTG CTGACCGCCA CCGCCCGCCC
	GATTGTCAAT
151	TTGGACTATC TTCCCGCCGC GCTGCTGATC GCCCTGCCTT
	GGCGTTTCGT
201	CAAAATTGCC GGCGTATTGG CGTTTTGGCT GGCGGTTTTG
	TTTGACGGGC
251	TGATGATGGT GATCCAACTC TTCCCTTTTA TGGATCTCAT
	CGGCGCCATC
301	AACCTCGTCC CCTTCATCCT GACCGCCCCC GCCCCTTATC
	AGATAATGAC
351	CGGGCTG...

This corresponds to the amino acid sequence <SEQ ID 468; ORF48>:

1	MNIHTLLSKQ WTLPPFLPKR LLLSLLILLA PNAVFWVLAL
	LTATARPIVN
51	LDYLPAALLI ALPWRFVKIA GVLAFWLAVL FDGLMMVIQL
	FPFMDLIGAI
101	NLVPFILTAP APYQIMTGL...

Further work revealed the complete nucleotide sequence <SEQ ID 469>:

1	ATGAATATTC ACACCCTGCT CTCCAAACAA TGGACGCTGC
	CGCCATTCCT
51	GCCGAAACGG CTGCTGCTGT CCCTGCTGAT ACTGCTTGCC
	CCCAATGCGG
101	TGTTTTGGGT TTTGGCACTG CTGACCGCCA CCGCCCGCCC
	GATTGTCAAT
151	TTGGACTATC TTCCCGCCGC GCTGCTGATC GCCCTGCCTT
	GGCGTTTCGT
201	CAAAATTGCC GGCGTATTGG CGTTTTGGCT GGCGGTTTTG
	TTTGACGGGC
251	TGATGATGGT GATCCAACTC TTCCCTTTTA TGGATCTCAT
	CGGCGCCATC
301	AACCTCGTCC CCTTCATCCT GACCGCCCCC GCCCCTTATC
	AGATAATGAC
351	CGGGCTGTTG CTGCTGTATA TGCTGGCGAT GCCGTTTGTG
	TTGCAGAAAG
401	CCGCCGCCAA AACCGACTTC CGGCACATTG CCGTCTGCGC
	CGCCGTTGTG
451	GCGGCAGCCG GCTATTTCAC CGGCCATTTG AGTTACTACG
	ACCGGGGTCG
501	GATGGCCAAT ATCTTCGGCG CAAACAACTT CTACTACGCC
	AAAAGTCAGG
551	CGATGCTCTA CACCGTCAGC CAGAATGCCG ACTTTATTAC
	CGCCGGCCTG
601	GTCGATCCCG TCTTCCTCCC CTTGGGCAAT CAACAGCGTG
	CCGCCACGCA
651	TCTGAACGAG CCGAAATCTC AAAAAATCCT CTTTATCGTC
	GCCGAATCTT
701	GGGGGCTGCC GGCCAATCCC GAACTTCAAA ACGCCACTTT
	TGCCAAACTG
751	CTGGCGCAAA AAGACCGTTT TTCGGTTTGG GAAAGCGGCA
	GTTTTCCCTT
801	CATCGGCGCG ACGGTCGAAG GCGAAATGCG CGAACTGTGT
	GCCTACGGCG
851	GTTTGCGCGG GTTCGCACTG CGCCGCGCGC CCGACGAAAA
	ATTTGCCCGC
901	TGCCTCCCCA ACCGTTTGAA ACAAGAAGGT TACGCCACCT
	TTGCGATGCA
951	CGGCGCGGGC AGTTCGCTTT ACGACCGCTT CAGCTGGTAT
	CCGAGGGCGG
1001	GCTTTCAAGA AATCAAAACC GCCGAAAACC TGATCGGTAA
	AAAAACCTGC
1051	GCCATTTTCG GCGGCGTGTG CGACAGCGAG CTGTTCGGCG
	AAGTGTCGGC
1101	ATTTTTCAAA AAACACGACA AGGGACTGTT TTACTGGATG
	ACGCTGACCA
1151	GCCACGCCGA CTATCCCGAA TCCGACATTT TCAACCACAG
	GCTCAAATGC
1201	ACCGAATATG GCCTGCCCGC CGAAACCGAC CTCTGCCGCA
	ATTTCAGCCT
1251	GCACACCCAA TTCTTCGACC AACTGGCGGA TTTGATCCAA
	CGCCCCGAAA
1301	TGAAAGGCAC GGAAGTCATC ATCGTCGGCG ACCATCCGCC
	GCCCGTCGGC
1351	AACCTCAATG AAACCTTCCG CTACCTCAAA CAGGGGCACG
	TCGCCTGGCT
1401	GAACTTCAAA ATCAAATAA

This corresponds to the amino acid sequence <SEQ ID 470; ORF48-1>:

1	MNIHTLLSKQ WTLPPFLPKR LLLSLLILLA PNAVFWVLAL
	LTATARPIVN
51	LDYLPAALLI ALPWRFVKIA GVLAFWLAVL FDGLMMVIQL
	FPFMDLIGAI
101	NLVPFILTAP APYQIMTGLL LLYMLAMPFV LQKAAAKTDF
	RHIAVCAAVV
151	AAAGYFTGHL SYYDRGRMAN IFGANNFYYA KSQAMLYTVS
	QNADFITAGL
201	VDPVFLPLGN QQRAATHLNE PKSQKILFIV AESWGLPANP
	ELQNATFAKL
251	LAQKDRFSVW ESGSFPFIGA TVEGEMRELC AYGGLRGFAL
	RRAPDEKFAR
301	CLPNRLKQEG YATFAMHGAG SSLYDRFSWY PRAGFQEIKT
	AENLIGKKTC
351	AIFGGVCDSE LFGEVSAFFK KHDKGLFYWM TLTSHADYPE
	SDIFNHRLKC
401	TEYGLPAETD LCRNFSLHTQ FFDQLADLIQ RPEMKGTEVI
	IVGDHPPPVG
451	NLNETFRYLK QGHVAWLNFK IK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF48 shows 94.1% identity over a 119aa overlap with an ORF (ORF48a) from strain A of N. meningitidis:

The complete length ORF48a nucleotide sequence <SEQ ID 471> is:

1	ATGAATATTC ACACCCTGCT CTCCAAACAA TGGACGCTGC
	CGCCATTCCT
51	GCCGAAACGG CTGCTGCTGT CCCTGCTGAT ACTGCTNNCC
	CCCAATGCGG
101	TGTTTTGGGT TTTGGCACTG CTGACCGCCA CCGCCCGCCC
	GATTGTCAAT
151	TTGGANTACC TTCCCGCCGC GCTGCTGATC GCCCTGCCTT
	GGCGTNTCGT
201	CAAAATTGNC GGCGTATTGG CGTNTTGGCT GGCGGTTTTG
	TTTGACGGGC
251	TGATGATGGT GATCCAACTC TTCCCTTTTA TGGATCTCAT
	CGGCGCCATC
301	AACCTCGTCC CCTTCATCNT GACCGCCCCC GCCCTTTATC
	AGATAATGAC
351	CGGGCTGTTA CTGCTGTATA TGCTGGCGAT GCCGTTTGTG
	TTGCAGAAAG
401	CCGCCGCCAA AACCGACTTC CGACACATTG CCGCCTGTGC
	CGCCGTTGTG
451	GTGGCAGCCG GCTATTTTAC CGGCCATTTG AGTTANTACG
	ACCGGGGGCG
501	GATGGCCAAT ATCTTCGGCG CAAACAACTT CTATTACGCC
	AAAAGTCAGG
551	CGATGCTCTA CACCGTCAGC CAGAATGCCG ACTTTATTAC
	CGCCGGCCTG
601	GTCGATCCCG TCTTCCTCCC CTTGGGCAAT CAACAGCGTG
	CCGCCACGCA
651	TCTGAACGAG CCGAAATCTC AAAAAATCCT CTTTATCGTC
	GCCGAATCTT
701	GGGGGCTGCC GGCCAATCCC GAACTTCAAA ACGCCACTTT
	TGCCAAACTG
751	CTGGCGCAAA AAGANCGTTT TTCGGTTTGG GAAAGCGGCA
	GTTTTCCCTT
801	CATCGGCGCG ACGATCGAAG GCGAAATGCG CGAACTGTGT
	GCCTACGGCG
851	GTTTGCGCGG GTTCGCACTG CGCCGCGCGC CCGACGAAAA
	ATTTGCCCGC
901	TGCCTCCCCA ACCGTTTGAA ACAAGAAGGT TACGCCACCT
	TTGCGATGCA
951	CGGCGCGGGC AGTTCGCTTT ACGACCGCTT CAGCTGGTAT
	CCGAGGGCGG
1001	GCTTTCAAGA AATCAAAACC GCCGAAAACC TGATCGGTAA
	AAAAACCTGC
1051	GCCATTTTCG GCGGCGTGTG CGACAGCGAG CTGTTCGGCG
	AAGTGTCGGC
1101	ANTTTTCAAA AAACACGACA AGGGACTGTT TTACTGGATG
	ACGCTGACCA
1151	GCCACGCCGA CTATCCCGAA TCNGACATTT TCAACCACAG
	GCTCAAATGC
1201	ACCGAATATG GCCTGCCCGC CGAAACCGAC NTCTGCCGCA
	ATTTCAGCCT
1251	GCACACCCAA TTCTTCGACC AACTGGCGGA TTTGATCCAA
	CGCCCCGAAA
1301	TGAAAGGCAC GGAAGTCATC ATCGTCGGCG ACCATCCGCC
	GCCCGTCGGC
1351	AACCTCAATG AAACCTTCCG CTACCTCAAA CAGGGGCACG
	TCGNCTGGCT
1401	GAACTTCAAA ATCAAATAA

This encodes a protein having amino acid sequence <SEQ ID 472>:

1	MNIHTLLSKQ WTLPPFLPKR LLLSLLILLX PNAVFWVLAL
	LTATARPIVN
51	LXYLPAALLI ALPWRXVKIX GVLAXWLAVL FDGLMMVIQL
	FPFMDLIGAI
101	NLVPFIXTAP ALYQIMTGLL LLYMLAMPFV LQKAAAKTDF
	RHIAACAAVV
151	VAAGYFTGHL SXYDRGRMAN IFGANNFYYA KSQAMLYTVS
	QNADFITAGL
201	VDPVFLPLGN QQRAATHLNE PKSQKILFIV AESWGLPANP
	ELQNATFAKL
251	LAQKXRFSVW ESGSFPFIGA TIEGEMRELC AYGGLRGFAL
	RRAPDEKFAR
301	CLPNRLKQEG YATFAMHGAG SSLYDRFSWY PRAGFQEIKT
	AENLIGKKTC
351	AIFGGVCDSE LFGEVSAXFK KHDKGLFYWM TLTSHADYPE
	SDIFNHRLKC
401	TEYGLPAETD XCRNFSLHTQ FFDQLADLIQ RPEMKGTEVI
	IVGDHPPPVG
451	NLNETFRYLK QGHVXWLNFK IK*

ORF48a and ORF48-1 show 96.8% identity in 472 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF48 shows 97.5% identity over a 119aa overlap with a predicted ORF (ORF48ng) from N. gonorrhoeae:

The ORF48ng nucleotide sequence <SEQ ID 473> was predicted to encode a protein having amino acid sequence <SEQ ID 474>:

1	MNIHALLSEQ WTLPPFLPKR LLLSLLILLA PNAVFWVLAL
	LTATARPIVN
51	LDYLPAALLI ALPWRFVKIA GVLAFWPAVL FDGLMMVIQL
	FPFMDLIGAI
101	NLVPFILTAP APYQIMTGLL LLYMLAMPFV LQKAAVKTDF
	RHIAVCAAVV
151	AAARYFTGPF ELLRTGGRWQ YVQHRRLLLS GSRASFRRRQ
	KADVLRRLGN
201	PYASMGNGG..

Further work identified the complete gonococcal DNA sequence <SEQ ID 475>:

1	ATGAATATTC ACGCCCTGCT CTCCGAACAA TGGACGCTGC
	CGCCATTCCT
51	GCCGAAACGG CTGCTGCTGT CCCTGCTGAT ACTGCTGGCC
	CCCAATGCGG
101	TGTTTTGGGT TTTGGCACTG CTGACCGCCA CCGCCCGCCC
	GATTGTCAAT
151	TTGGACTACC TTCCCGCCGC GCTGCTGATC GCCCTGCCTT
	GGCGTTTCGT
201	CAAAATTGCC GGCGTATTGG CGTTTTGGCC GGCGGTTTTG
	TTTGACGGGC
251	TGATGATGGT GATCCAACTC TTCCCTTTTA TGGACCTCAT
	CGGCGCCATC
301	AACCTCGTCC CCTTCATCCT GACCGCCCCC GCCCCTTATC
	AGATAATGAC
351	CGGGCTGTTG CTGCTGTATA TGCTGGCGAT GCCGTTTGTG
	TTGCAAAAAG
401	CCGCCGTCAA AACCGACTTC CGACACATTG CCGTCTGTGC
	CGCCGTTGTG
451	GCGGCAGCCG GCTATTTCAC CGGCCATTTG AGTTACTACG
	ACCGGGGGCG
501	GATGGCCAAT ATCTTCGGCG CAAACAACTT CTATTACGCc
	aAAAGTCAGG
551	CGATGCTCTA CACCGTCAGC CAGAATGCCG ACTTTATTAC
	CGCCGgcctG
601	GTCGACCCCG TCTTCCTCCC CTTGGGCAAT CAGCAGCGTG
	CCGCCACGCG
651	GCTGAGTGAG CCGAAATCTC AAAAAATCCT CTTTATCGTC
	GCCGAATCTT
701	GGGGGCTGCC GGGCAATCCC GAGCTTCAAA ACGCCACTTT
	TGCCAAACTG
751	CTGGCGCAAA AAGACCGTTT TTCGGTTTGG GAAAGCGGCA
	GTTTTCCCTT
801	CATCGGCGCG ACGGTCGAAG GCGAAATGCG CGAATTGTGC
	GCCTACGGCG
851	GTTTGCGCGG GTTCGCACTG CGCCGCGCGC CCGACGAAAA
	ATTTGCCCGC
901	TGCCTCCCCA ACCGTTTGAA ACAAGAAGGT TACGCCACCT
	TTGCGATGCA
951	CGGCGCGGGT AGTTCGCTTT ACGACCGCTT CAGCTGGTAT
	CCGAGGGCGG
1001	GCTTTCAAAA AATCAAAACC GCCGAAAACC TGATCGGTAA
	AAAAACCTGC
1051	GCCATTTTCG GCGGCGTGTG CGACAGCGAG CTGTTCGGCG
	AAGTGTCGGC
1101	ATTTTTCAAA AAACACGACA AGGGACTGTT TTACTGGATG
	ACGCTGACCA
1151	GCCACGCCGA CTATCCCGAA TCCGACATTT TCAACCACAG
	GCTCAAATGC
1201	ACCGAATACG GCCTGCCCGC CGAAACCGAC CTCTGCCGCA
	ATTTCAGCCT
1251	GCACACCCAA TtcttcgACC AACTGGCGGA TTTGATCCGA
	CGCCCCGAAA
1301	TGAAAGGCAC GGAAGTCATC ATCGTCGGCG ACCATCCGCC
	GCCCGTCGGC
1351	AACCTCAATG AAACCTTCCG CTACCTCAAA CAGGGACACG
	TCGCCTGGCT
1401	GCACTTCAAA ATCAAATAA

This encodes a protein having amino acid sequence <SEQ ID 476; ORF48ng-1>:

1	MNIHALLSEQ WTLPPFLPKR LLLSLLILLA PNAVFWVLAL
	LTATARPIVN
51	LDYLPAALLI ALPWRFVKIA GVLAFWPAVL FDGLMMVIQL
	FPFMDLIGAI
101	NLVPFILTAP APYQIMTGLL LLYMLAMPFV LQKAAVKTDF
	RHIAVCAAVV
151	AAAGYFTGHL SYYDRGRMAN IFGANNFYYA KSQAMLYTVS
	QNADFITAGL
201	VDPVFLPLGN QQRAATRLSE PKSQKILFIV AESWGLPGNP
	ELQNATFAKL
251	LAQKDRFSVW ESGSFPFIGA TVEGEMRELC AYGGLRGFAL
	RRAPDEKFAR
301	CLPNRLKQEG YATFAMHGAG SSLYDRFSWY PRAGFQKIKT
	AENLIGKKTC
351	AIFGGVCDSE LFGEVSAFFK KHDKGLFYWM TLTSHADYPE
	SDIFNHRLKC
401	TEYGLPAETD LCRNFSLHTQ FFDQLADLIR RPEMKGTEVI
	IVGDHPPPVG
451	NLNETFRYLK QGHVAWLHFK IK*

ORG48ng-1 and ORF48-1 show 97.9% identity in 472 aa overlap:

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and two putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 57

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 477>:

1	..GTGAGCGGAC GTTACCGCGC TTTGGATCGC GTTTCCAAAA
	TCATCATCGT
51	TACTTTGAGT ATCGCCACGC TTGCCGCCGC CGGCATCGCT
	ATGTCGCGCG
101	GTATGCAGAT GCAGTCCGAT TTTATCGAGC CGACACCGTG
	GACGCTTGCC
151	GGTTTGGGCT TCCTGATCGC GCTGATGGGC TGGATGCCCG
	CGCCGATTGA
201	AATTTCCGCC ATCAATTCTT TGTGGGTAAC CGAAAAACAA
	CGCATCAATC
251	CTTCCGAATA CCGCGACGGG ATTTTTGAAT TCAACGTCGG
	TTATATCGCC
301	AGTGCGGTTT TGGCTTTGGT TTTCCTTGCA CTGGGCGC.G
	TAGCGCCGAA
351	CGGCAACGGC GA.ACAGTGC AGATGGCGGG CGGCAAATAT
	AACGGGCAAT
401	TGATCAATAT GTACGCC..

This corresponds to the amino acid sequence <SEQ ID 478; ORF53>:

1	..VSGRYRALDR VSKIIIVTLS IATLAAAGIA MSRGMQMQSD
	FIEPTPWTLA
51	GLGFLIALMG WMPAPIEISA INSLWVTEKQ RINPSEYRDG
	IFEFNVGYIA
101	SAVLALVFLA LGXVAPNGNG XTVQMAGGKY NGQLINMYA..

Further work revealed the complete nucleotide sequence <SEQ ID 479>:

1	ATGTCCGAAC AACATATTTC GACTTGGAAA AGTAAAATCA
	ACGCATTGGG
51	TCCGGGGATC ATGATGGCTT CGGCGGCGGT CGGCGGTTCG
	CACCTGATTG
101	CCTCGACGCA GGCGGGCGCG CTTTACGGCT GGCAGATCGC
	GCTCATCATC
151	ATCCTGACCA ACCTCTTCAA ATACCCGTTT TTCCGCTTCA
	GCGCGCATTA
201	CACGCTGGAC ACGGGCAAGA GCCTGATTGA AGGTTATGCC
	GAGAAAAGCC
251	GCGTTTATTT GTGGGTATTC CTGATTTTGT GCATCCTCTC
	CGCCACGATT
301	AACGCGGGCG CGGTCGCCAT TGTAACCGCC GCCATCGTCA
	AAATGGCGAT
351	TCCCTCGCTG ATGTTTGATG CCGGCACGGT TGCCGCCTTG
	ATTATGGCAT
401	CCTGCCTGAT TATTTTGGTG AGCGGACGTT ACCGCGCTTT
	GGATCGCGTT
451	TCCAAAATCA TCATCGTTAC TTTGAGTATC GCCACGCTTG
	CCGCCGCCGG
501	CATCGCTATG TCGCGCGGTA TGCAGATGCA GTCCGATTTT
	ATCGAGCCGA
551	CACCGTGGAC GCTTGCCGGT TTGGGCTTCC TGATCGCGCT
	GATGGGCTGG
601	ATGCCCGCGC CGATTGAAAT TTCCGCCATC AATTCTTTGT
	GGGTAACCGA
651	AAAACAACGC ATCAATCCTT CCGAATACCG CGACGGGATT
	TTTGATTTCA
701	ACGTCGGTTA TATCGCCAGT GCGGTTTTGG CTTTGGTTTT
	CCTTGCACTG
751	GGCGCGTTTG TGCAATACGG CAACGGCGAA GCAGTGCAGA
	TGGCGGGCGG
801	CAAATATATC GGGCAATTGA TCAATATGTA CGCCGTTACC
	ATCGGCGGCT
851	GGTCGCGCCC GCTGGTGGCG TTTATCGCGT TTGCCTGTAT
	GTACGGCACG
901	ACGATTACCG TCGTGGACGG CTATGCCCGT GCCATTGCCG
	AACCCGTGCG
951	CCTGCTGCGC GGAAAAGACA AAACGGGCAA CGCCGAATTC
	TTTGCCTGGA
1001	ATATTTGGGT GGCGGGCAGC GGTTTGGCGG TGATTTTCTG
	GTTTGACGGC
1051	GTAATGGCGA ATCTGCTCAA ATTTGCGATG ATTGCCGCTT
	TTGTGTCCGC
1101	CCCTGTGTTT GCCTGGCTGA ATTACCGTTT GGTTAAAGGT
	GATGAAAAAC
1151	ACAAACTCAC ATCAGGTATG AATGCCCTTG CATTGGCAGG
	CTTGATTTAT
1201	CTGACCGGTT TTACCGTTTT GTTCTTATTG AATTTGGCGG
	GAATGTTCAA
1251	ATGA

This corresponds to the amino acid sequence <SEQ ID 480; ORF53-1>:

1	MSEQHISTWK SKINALGPGI MMASAAVGGS HLIASTQAGA
	LYGWQIALII
51	ILTNLFKYPF FRFSAHYTLD TGKSLIEGYA EKSRVYLWVF
	LILCILSATI
101	NAGAVAIVTA AIVKMAIPSL MFDAGTVAAL IMASCLIILV
	SGRYRALDRV
151	SKIIIVTLSI ATLAAAGIAM SRGMQMQSDF IEPTPWTLAG
	LGFLIALMGW
201	MPAPIEISAI NSLWVTEKQR INPSEYRDGI FDFNVGYIAS
	AVLALVFLAL
251	GAFVQYGNGE AVQMAGGKYI GQLINMYAVT IGGWSRPLVA
	FIAFACMYGT
301	TITVVDGYAR AIAEPVRLLR GKDKTGNAEF FAWNIWVAGS
	GLAVIFWFDG
351	VMANLLKFAM IAAFVSAPVF AWLNYRLVKG DEKHKLTSGM
	NALALAGLIY
401	LTGFTVLFLL NLAGMFK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF53 shows 93.5% identity over a 139aa overlap with an ORF (ORF53a) from strain A of N. meningitidis:

The complete length ORF53a nucleotide sequence <SEQ ID 481> is:

1	ATGTCCGAAC AACATATTTC GACTTGGAAA AGTAAAATCA
	ACGCATTGGG
51	ACCGGGGATT ATGATGGCTT CGGCGGCGGT CGGCGGTTCG
	CACCTGATTG
101	CCTCGACGCA GGCGGGCGCG CTTTACGGCT GGCAGATCGC
	GCTCATCATC
151	ATCCTGACCA ACCTCTTCAA ATACCCGTTT TTCCGCTTCA
	GCGCGCATTA
201	CACGCTGGAC ACGGGCAAGA GCCTGATTGA AGGTTATGCC
	GAGAAAAGCC
251	GCGTTTATTT GTGGGTATTC CTGATTTTGT GCATCCTCTC
	CGCCACGATT
301	AACGCGGGCG CGGTCGCCAT TGTAACCGCC GCCATCGTCA
	AAATGGCGAT
351	TCCCTCGCTG ATGTTTGATG CCGGCACGGT TGCCGCCTTG
	ATTATGGCAT
401	CCTGCCTGAT TATTTTGGTG AGCGGACGTT ACCGCGCTTT
	GGATCGCGTT
451	TCCAAAATCA TCATCGTTAC TTTGAGTATC GCCACGCTTG
	CCGCCGCCGG
501	CATCGCTATG TCGCGCGGTA TGCAGATGCA GTCCGATTTT
	ATCGAGCCGA
551	CACCGTGGAC GCTTGCCGGT TTGGGCTTCC TGATCGCGCT
	GATGGGCTGG
601	ATGCCCGCGC CGATTGAAAT TTCCGCCATC AATTCTTTGT
	GGGTAACCGA
651	AAAACAACGC ATCAATCCTT CCGAATACCG CGACGGGATT
	TTTGATTTCA
701	ACGTCGGTTA TATCGCCAGT GCGGTTTTGG CTTTGGTTTT
	CCTTGCACTG
751	GGCGCGTTTG TGCAATACGG CAACGGCGAA GCAGTGCAGA
	TGGCGGGCGG
801	CAAATATATC GGGCAATTGA TCAATATGTA CGCCGTTACC
	ATCGGCGGCT
851	GGTCGCGCCC GCTGGTGGCG TTTATCGCGT TTGCCTGTAT
	GTACGGCACG
901	ACGATTACCG TTGTGGACGG CTATGCCCGT GCCATTGCCG
	AACCCGTGCG
951	CCTGCTGCGC GGAAAAGACA AAACGGGCAA CGCCGAATTC
	TTTGCCTGGA
1001	ATATTTGGGT GGCGGGCAGC GGTTTGGCGG TGATTTTCTG
	GTTTGACGGC
1051	GTAATGGCGA ATCTGCTCAA ATTTGCGATG ATTGCCGCTT
	TTGTGTCCGC
1101	CCCTGTGTTT GCCTGGCTGA ATTACCGTTT GGTCAAAGGT
	GATGAAAAAC
1151	ACAAACTCAC ATCAGGTATG AATGCCCTTG CATTGGCAGG
	CTTGATTTAT
1201	CTGACCGGTT TTACCGTTTT GTTCTTATTG AATTTGGCGG
	GAATGTTCAA
1251	ATGA

This encodes a protein having amino acid sequence <SEQ ID 482>:

1	MSEQHISTWK SKINALGPGI MMASAAVGGS HLIASTQAGA
	LYGWQIALII
51	ILTNLFKYPF FRFSAHYTLD TGKSLIEGYA EKSRVYLWVF
	LILCILSATI
101	NAGAVAIVTA AIVKMAIPSL MFDAGTVAAL IMASCLIILV
	SGRYRALDRV
151	SKIIIVTLSI ATLAAAGIAM SRGMQMQSDF IEPTPWTLAG
	LGFLIALMGW
201	MPAPIEISAI NSLWVTEKQR INPSEYRDGI FDFNVGYIAS
	AVLALVFLAL
251	GAFVQYGNGE AVQMAGGKYI GQLINMYAVT IGGWSRPLVA
	FIAFACMYGT
301	TITVVDGYAR AIAEPVRLLR GKDKTGNAEF FAWNIWVAGS
	GLAVIFWFDG
351	VMANLLKFAM IAAFVSAPVF AWLNYRLVKG DEKHKLTSGM
	NALALAGLIY
401	LTGFTVLFLL NLAGMFK*

ORF 53a shows 100.0% identity in 417 aa overlap with ORF53-1:

Homology with a Predicted ORF from N. gonorrhoeae

ORF53 shows 92.1% identity over a 139aa overlap with a predicted ORF (ORF53ng) from N. gonorrhoeae:

An ORF53ng nucleotide sequence <SEQ ID 483> was predicted to encode a protein having amino acid sequence <SEQ ID 484>:

1	MPKKSCVYLW VFLILCIASA TINAGAVAIV TAAIVKMAIP
	SLMFDAGTVA
51	ALIMASCLII LVSGRYRALD RVSKIIIVTL SIATLAAAGI
	AMSRGMQMQP
101	DFIEPTPWTL AGLGFLIALM GWMPAPIEIS AINSLWVTEK
	QRINPSEYRD
151	GIFDFNVGYI ASAVLALVFL ALGAFVQYGN GEAVQMGGGK
	YIGQLINMYA
201	VTIGGGSRPL VAFIAFACMY GAASTVVDGY ARAIAEPVRL
	LRGKDKTARP
251	IVLLEKLGGR HRFGRDFLV*

Further analysis revealed further partial DNA gonococcal sequence <SEQ ID 485>:

1	..aagaAAAGCT GCGTTTATTT GTGGGTTTTT TTGATTTTGT
	GTATCGCCTC
51	CGCCACGATT AACGCGGGCG CGGTCGCCAT TGTAACCGCC
	GCCATCGTCA
101	AAATGGCGAT TCCCTCGCTG ATGTTTGATG CCGGCACGGT
	TGCCGCCTTG
151	ATTATGGCAT CCTGCCTGAT TATTTTGGTG AGCGGACGTT
	ACCGCGCTTT
201	GGATCGTGTT TCCAAAATCA TCATTGTTAC TTTGAGCATC
	GCCACGCTTG
251	CCGCCGCCGG CATCGCTATG TCGCGCGGTA TGCAGATGCA
	GCCCGATTTT
301	ATCGAGCCGA CACCGTGGAC GCTTGCCGGT TTGGGCTTCC
	TGATCGCGCT
351	GATGGGCTGG ATGCCCGCGC CGATCGAAAT TTCCGCCATC
	AATTCTTTGT
401	GGGTAACCGA AAAACAACGC ATCAATCCTT CTGAATACCG
	CGACGGGATT
451	TTCGATTTCA ACGTCGGTTA TATCGCcagT GCGGTTTTGG
	CTTTGGTTTT
501	CCTTGCACTG GGCGCGTTTG TGCAATACGG CAACGGCGAA
	GCAGTGCAGA
551	TGGCGGGCGG CAAATATATC GGGCAATTGA TTAATATGTA
	TGCCGTAACC
601	ATCGGCGGCT GGTCTCGTCC GCTGGTGGCG TTTATCGCGT
	TTGCCTGTAT
651	GTACGGCACG ACGATTACCG TTGTGGACGG TTATGCGCGT
	GCCATTGCCG
701	AACCCGTGCG CCTGCTGCGC GGCAGGGATA AAACCGGCAA
	CGCCGAGTTG
751	TTtgccTGGA ATATTTGGGT GGCGGGCAGC GGTTTGGCGG
	TGATTTTCTG
801	GTTTGACggc gcaaTGGCgG AACtgcTCAA ATTTGCGATG
	ATtgccgcCT
851	TTGTGTCCGC CCCTGTGTTC GCCTGGCTCA ACTACCGCCT
	CGTCAAAGGG
901	GACAAACGCC ACAGGCTTAC CGCCGGTATG AACGCCCTTG
	CCATTGTCGG
951	CCTGCTCTAC CTGGCCGGGT TTGCCGTTTT GTTCCTGTTG
	AACCTTACCG
1001	GACTTTTGGC ATAG

This corresponds to the amino acid sequence <SEQ ID 486; ORF53ng-1>:

1	..KKSCVYLWVF LILCIASATI NAGAVAIVTA AIVKMAIPSL
	MFDAGTVAAL
51	IMASCLIILV SGRYRALDRV SKIIIVTLSI ATLAAAGIAM
	SRGMQMQPDF
101	IEPTPWTLAG LGFLIALMGW MPAPIEISAI NSLWVTEKQR
	INPSEYRDGI
151	FDFNVGYIAS AVLALVFLAL GAFVQYGNGE AVQMAGGKYI
	GQLINMYAVT
201	IGGWSRPLVA FIAFACMYGT TITVVDGYAR AIAEPVRLLR
	GRDKTGNAEL
251	FAWNIWVAGS GLAVIFWFDG AMAELLKFAM IAAFVSAPVF
	AWLNYRLVKG
301	DKRHRLTAGM NALAIVGLLY LAGFAVLFLL NLTGLLA*

ORF53ng-1 and ORF53-1 show 94.0% identity in 336 aa overlap:

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 58

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 487>:

1	..TTGCGGGAAA CGGCATATGT TTTGGATAGT TTTGATCGTT
	ATTTTGTTGT
51	TGCGCTTGCC GGCTTGTTTT TTGTCCGCGC ACAATCCGAA
	CGCGAGTGGA
101	TGCGCGAGGT TTCTGCGTGG CAGGAAAAGA AAGGGGAAAA
	ACAGGCGGAG
151	CTGCCTGAAA TCAAAGACGG TATGCCCGAT TTTCCCGAAC
	TTGCCCTGAT
201	GCTTTTCCAC GCCGTCAAAA CGGCAGTGTA TTGGCTGTTT
	GTCGGTGTCG
251	TCCGTTTCTG CCGAAACTAT CTGGCGCACG AATCCGAACC
	GGACAGGCCC
301	GTTCCGCCT..

This corresponds to the amino acid sequence <SEQ ID 488; ORF58>:

1	..LRETAYVLDS FDRYFVVALA GLFFVRAQSE REWMREVSAW
	QEKKGEKQAE
51	LPEIKDGMPD FPELALMLFH AVKTAVYWLF VGVVRFCRNY
	LAHESEPDRP
101	VPP..

Further work revealed the complete nucleotide sequence <SEQ ID 489>:

1	ATGTTTTGGA TAGTTTTGAT CGTTATTTTG TTGCTTGCGC
	TTGCCGGCTT
51	GTTTTTTGTC CGCGCACAAT CCGAACGCGA GTGGATGCGC
	GAGGTTTCTG
101	CGTGGCAGGA AAAGAAAGGG GAAAAACAGG CGGAGCTGCC
	TGAAATCAAA
151	GACGGTATGC CCGATTTTCC CGAACTTGCC CTGATGCTTT
	TCCATGCCGT
201	CAAAACGGCA GTGTATTGGC TGTTTGTCGG TGTCGTCCGT
	TTCTGCCGAA
251	ACTATCTGGC GCACGAATCC GAACCGGACA GGCCCGTTCC
	GCCTGCTTCT
301	GCAAACCGTG CGGATGTTCC GACCGCATCC GACGGATATT
	CAGACAGTGG
351	AAACGGGACG GAAGAAGCGG AAACGGAAGA AGCAGAAGCT
	GCGGAGGAAG
401	AGGCTGCCGA TACGGAAGAC ATTGCAACTG CCGTAATCGA
	CAACCGCCGC
451	ATCCCATTCG ACCGGAGTAT TGCTGAAGGG TTGATGCCGT
	CTGAAAGCGA
501	AATTTCGCCC GTCCGTCCGG TTTTTAAAGA AATCACTTTG
	GAAGAAGCAA
551	CGCGTGCTTT AAACAGCGCG GCTTTAAGGG AAACGAAAAA
	ACGCTATATC
601	GATGCATTTG AGAAAAACGA AACAGCGGTC CCCAAAGTCC
	GCGTGTCCGA
651	TACCCCGATG GAAGGGCTGC AGATTATCGG TTTGGACGAC
	CCTGTGCTTC
701	AACGCACGTA TTCCCATATG TTCGATGCGG ACAAAGAAGC
	GTTTTCCGAG
751	TCTGCGGATT ACGGATTTGA GCCGTATTTT GAGAAGCAGC
	ATCCGTCTGC
801	CTTTTCTGCA GTCAAAGCCG AAAATGCACG GAATGCGCCG
	TTCCACCGTC
851	ATGCAGGGCA GGGGAAAGGG CAGGCGGAGG CAAAATCCCC
	GGATGTTTCC
901	CAAGGGCAGT CCGTTTCAGA CGGCACGGCC GTCCGCGATG
	CCCGCCGCCG
951	CGTTTCCGTC AATTTGAAAG AACCGAACAA GGCAACGGTT
	TCTGCGGAGG
1001	CGCGAATTTC TCGCCTGATT CCGGAAAGTC AGACGGTTGT
	CGGGAAACGG
1051	GATGTCGAAA TGCCGTCTGA AACCGAAAAT GTTTTCACGG
	AAACCGTTTC
1101	GTCTGTGGGA TACGGCGGTC CGGTTTATGA TGAAACTGCC
	GATATCCATA
1151	TTGAAGAACC TGCCGCGCCC GATGCTTGGG TGGTCGAACC
	ACCCGAAGTG
1201	CCGAAAGTTC CCATGACCGC AATCGATATT CAGCCGCCGC
	CTCCCGTATC
1251	GGAAATCTAC AACCGTACCT ATGAACCGCC GTCAGGATTC
	GAGCAGGTGC
1301	AACGCAGCCG CATTGCCGAG ACCGACCATC TTGCCGATGA
	TGTTTTGAAT
1351	GGAGGTTGGC AGGAGGAAAC CGCCGCTATT GCGGATGACG
	GCAGTGAAGG
1401	TGCGGCAGAG CGGTCAAGCG GGCAATATCT GTCGGAAACC
	GAAGCGTTCG
1451	GGCATGACAG TCAGGCGGTT TGTCCGTTTG AAAATGTGCC
	GTCTGAACGC
1501	CCGTCCTGCC GGGTATCGGA TACGGAAGCG GATGAAGGGG
	CGTTCCCATC
1551	TGAAGAAACC GGTGCGGTAT CCGAACACCT GCCGACAACC
	GACCTGCTTC
1601	TGCCTCCGCT GTTCAATCCC GAGGCGACGC AAACCGAAGA
	AGAACTGTTG
1651	GAAAACAGCA TCACCATCGA AGAAAAATTG GCGGAGTTCA
	AAGTCAAGGT
1701	CAAGGTTGTC GATTCTTATT CCGGCCCCGT AATTACGCGT
	TATGAAATCG
1751	AACCCGATGT CGGCGTGCGC GGCAATTCCG TTCTGAATCT
	GGAAAAAGAT
1801	TTGGCGCGTT CGCTCGGCGT GGCTTCCATC CGCGTTGTCG
	AAACCATCCC
1851	CGGCAAAACC TGCATGGGTT TGGAACTTCC GAACCCGAAA
	CGCCAAATGA
1901	TACGCCTGAG CGAAATCTTC AATTCGCCCG AGTTTGCCGA
	ATCCAAATCC
1951	AAGCTGACGC TCGCGCTCGG TCAGGACATC ACCGGACAGC
	CCGTCGTAAC
2001	CGACTTGGGA AAAGCACCGC ATTTGTTGGT TGCCGGCACG
	ACCGGTTCGG
2051	GCAAATCGGT GGGTGTCAAC GCGATGATTC TGTCTATGCT
	TTTCAAAGCC
2101	GCGCCGGAAG ACGTGCGTAT GATTATGATC GATCCGAAAA
	TGCTGGAATT
2151	GAGCATTTAC GAAGGCATCC CGCACCTGCT CGCCCCTGTC
	GTTACCGATA
2201	TGAAGCTGGC GGCAAACGCG CTGAACTGGT GTGTTAACGA
	AATGGAAAAA
2251	CGCTACCGCC TGATGAGCTT TATGGGCGTG CGTAATCTTG
	CGGGCTTCAA
2301	TCAAAAAATC GCCGAAGCCG CAGCAAGGGG AGAAAAAATC
	GGCAATCCGT
2351	TCAGCCTCAC GCCCGACGAT CCCGAACCTT TGGAAAAACT
	GCCGTTTATC
2401	GTGGTCGTGG TCGATGAGTT TGCCGACCTG ATGATGACGG
	CAGGCAAGAA
2451	AATCGAAGAA CTGATTGCCC GCCTCGCCCA AAAAGCCCGC
	GCGGCAGGCA
2501	TCCATTTGAT TCTTGCCACA CAACGCCCCA GCGTCGATGT
	CATCACGGGT
2551	CTGATTAAGG CGAACATCCC GACGCGTATC GCGTTCCAAG
	TGTCCAGCAA
2601	AATCGACAGC CGCACGATTC TCGACCAAAT GGGCGCGGAA
	AACCTGCTCG
2651	GTCAGGGCGA TATGCTGTTC CTGCTGCCGG GTACTGCCTA
	TCCGCAGCGC
2701	GTTCACGGCG CGTTTGCCTC GGATGAAGAG GTGCACCGCG
	TGGTCGAATA
2751	TTTGAAACAG TTTGGCGAAC CGGACTATGT TGACGATATT
	TTGAGCGGCG
2801	GCGGCAGCGA AGAGCTGCCC GGCATCGGGC GCAGCGGCGA
	CGACGAAACC
2851	GATCCGATGT ACGACGAGGC CGTATCCGTT GTCCTGAAAA
	CGCGCAAAGC
2901	CAGCATTTCG GGCGTACAGC GCGCCTTGCG TATCGGCTAC
	AACCGCGCCG
2951	CGCGTCTGAT TGACCAGATG GAGGCGGAAG GCATTGTGTC
	CGCACCGGAA
3001	CACAACGGCA ACCGTACGAT TCTCGTCCCC TTGGACAATG
	CTTGA

This corresponds to the amino acid sequence <SEQ ID 490; ORF58-1>:

1	MFWIVLIVIL LLALAGLFFV RAQSEREWMR EVSAWQEKKG
	EKQAELPEIK
51	DGMPDFPELA LMLFHAVKTA VYWLFVGVVR FCRNYLAHES
	EPDRPVPPAS
101	ANRADVPTAS DGYSDSGNGT EEAETEEAEA AEEEAADTED
	IATAVIDNRR
151	IPFDRSIAEG LMPSESEISP VRPVFKEITL EEATRALNSA
	ALRETKKRYI
201	DAFEKNETAV PKVRVSDTPM EGLQIIGLDD PVLQRTYSHM
	FDADKEAFSE
251	SADYGFEPYF EKQHPSAFSA VKAENARNAP FHRHAGQGKG
	QAEAKSPDVS
301	QGQSVSDGTA VRDARRRVSV NLKEPNKATV SAEARISRLI
	PESQTVVGKR
351	DVEMPSETEN VFTETVSSVG YGGPVYDETA DIHIEEPAAP
	DAWVVEPPEV
401	PKVPMTAIDI QPPPPVSEIY NRTYEPPSGF EQVQRSRIAE
	TDHLADDVLN
451	GGWQEETAAI ADDGSEGAAE RSSGQYLSET EAFGHDSQAV
	CPFENVPSER
501	PSCRVSDTEA DEGAFPSEET GAVSEHLPTT DLLLPPLFNP
	EATQTEEELL
551	ENSITIEEKL AEFKVKVKVV DSYSGPVITR YEIEPDVGVR
	GNSVLNLEKD
601	LARSLGVASI RVVETIPGKT CMGLELPNPK RQMIRLSEIF
	NSPEFAESKS
651	KLTLALGQDI TGQPVVTDLG KAPHLLVAGT TGSGKSVGVN
	AMILSMLFKA
701	APEDVRMIMI DPKMLELSIY EGIPHLLAPV VTDMKLAANA
	LNWCVNEMEK
751	RYRLMSFMGV RNLAGFNQKI AEAAARGEKI GNPFSLTPDD
	PEPLEKLPFI
801	VVVVDEFADL MMTAGKKIEE LIARLAQKAR AAGIHLILAT
	QRPSVDVITG
851	LIKANIPTRI AFQVSSKIDS RTILDQMGAE NLLGQGDMLF
	LLPGTAYPQR
901	VHGAFASDEE VHRVVEYLKQ FGEPDYVDDI LSGGGSEELP
	GIGRSGDDET
951	DPMYDEAVSV VLKTRKASIS GVQRALRIGY NRAARLIDQM
	EAEGIVSAPE
1001	HNGNRTILVP LDNA*

Computer analysis of this amino acid sequence predicts the indicated transmembrane region, and also gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF58 shows 96.6% identity over a 89aa overlap with an ORF (ORF58a) from strain A of N. meningitidis:

The complete length ORF58a nucleotide sequence <SEQ ID 491> is:

1	ATGTTTTGGA TAGTTTTGAT CGTTATTTTG TTGCTTGCGC
	TTGCCGGCTT
51	GTTTTTTGTC CGCGCACAAT CCGAACGCGA GTGGATGCGC
	GAGGTTTCTG
101	CGTGGCAGGA AAAGAAAGGG GAAAAACAGG CGGAGCTGCC
	TGAAATCAAA
151	GACGGTATGC CCGATTTTCC CGAACTTGCC CTGATGCTTT
	TCCATGCCGT
201	CAAAACGGCA GTGTATTGGC TGTTTGTCGG TGTCGTCCGT
	TTCTGCCGAA
251	ACTATCTGGC GCACGAATCC GAACCGGACA GGCCCGTTCC
	GCCTGCTTCT
301	GCAAATCGTG CGGATGTTCC GACCGCATCC GACGGATATT
	CAGACAGTGG
351	AAACGGGACG GAAGAAGCGG AAACGGAAGA AGCAGAAGCT
	GCGGAGGAAG
401	AGGCTGCCGA TACGGAAGAC ATTGCAACTG CCGTAATCGA
	CAACCGCCGC
451	ATCCCATTCG ACCGGAGTAT TGCTGAAGGG TTGATGCCGT
	CTGAAAGCGA
501	AATTTCGCCC GTCCGTCCGG TTTTTAAGGA AATCACTTTG
	GAAGAAGCAA
551	CGCGTGCTTT AAACAGCGCG GCTTTAAGGG AAACGAAAAA
	ACGCTATATC
601	GATGCATTTG AGAAAAACGA AACAGCGGTC CCCAAAGTCC
	GCGTGTCCGA
651	TACCCCGATG GAAGGGCTGC AGATTATCGG TTTGGACGAC
	CCTGTGCTTC
701	AACGCACGTA TTCCCGTATG TTCGATGCGG ACAAAGAAGC
	GTTTTCCGAG
751	TCTGCGGATT ACGGATTTGA GCCGTATTTT GAGAAGCAGC
	ATCCGTCTGC
801	CTTTTCTGCA GTCAAAGCCG AAAATGCACG GAATGCGCCG
	TTCCGCCGTC
851	ATGCAGGGCA GGGNAAAGGG CAGGCGGAGG CNAAATCCCC
	GGATGTTTCC
901	CAAGGGCAGT CCGTTTCAGA CGGCACAGCC GTCCGCGATG
	CCNGCCGCCG
951	CGTTTCCGTC AATTTGAAAG AACCGAACAA GGCAACGGTT
	TCTGCGGAGG
1001	CGCGGATTTC GCGCCTGATT CCGGAAAGTC GGACGGTTGT
	CGGGAAACGG
1051	GATGTCGAAA TGCCGTCTGA AACCGAAAAT GTTTTCACGG
	AAANTGTTTC
1101	GTCTGTGGGA TACGGCGNTC CGGTTTATGA TGAAACTGCC
	GATATCCATA
1151	TTGAAGAACC TGCCGCGCCC GATGCTTGGG TGGTCGAACC
	ACCCGAAGTG
1201	CCGAAAGTTC CCATGCCCGC AATNGATATT CCGCCGCCGC
	CTCCCGTATC
1251	GGAAATCTAC AACCGTACCT ATGAACCGCC GGCAGGATTC
	GAGCAGGTGC
1301	AACGCAGCCG CATTGCCGAA ACCGATCATC TTGCCGATGA
	TGTTTTGAAT
1351	GGAGGTTGGC AGGAGGAAAC CGCCGCTATT GCGAATGACG
	GCAGTGAGGG
1401	TGTGGCAGAG CGGTCAAGCG GGCAATATTT GTCGGAAACC
	GAAGCGTTCG
1451	GGCATGACAG TCAGGCGGTT TGTCCGTTTG AAAATGTGCC
	GTCTGAACGC
1501	CCGTCCCGCC GGGCATNGGA TACGGAAGCG GATGAAGGGG
	CGTTCCAATC
1551	TGAAGAAACC GGTGCGGTAT CCGAACACCT GCCGACAACC
	GACCTGCTTC
1601	TGCCGCCGCT GTTCAATCCC GGGGCGACGC AAACCGAAGA
	AGANCTGTTG
1651	GANAACAGCA TCACCATCGA AGAAAAATNG GCGGAGTTCA
	AAGTCAAGGT
1701	CAAGGTTGTC GATTCTTATT CCGGCCCCGT GATTACGCGT
	TATGAAATCG
1751	AACCCGATGT CGGCGTGCGC GGCAATTCCG TTCTAAATCT
	GGAAAAAGAN
1801	TTGGCGCGTT CGCTCGGCGT GGCTTCCATC CGCGTTGTCG
	AAACCATCCT
1851	CGGCAAAACC TGTATGGGTT TGGAACTTCC GAACCCGAAA
	CGCCAAATGA
1901	TACGCCTGAG CGAAATCTTC AATTCGCCCG AGTTTGCCGA
	ATCCAAATCC
1951	AAGCTGACGC TCGCGCTCGG TCAGGACATC ACCGGACAGC
	CCGTCGTAAC
2001	CGACTTGGGC AAAGCACCGC ATTTGTTGGT TGCCGGCACG
	ACCGGTTCGG
2051	GCAAATCGGT GGGTGTCAAC GCGATGATTC TGTCTATGCT
	TTTCAAAGCC
2101	GCGCCGGAAG ACGTGCGTAT GATTATGATC GATCCGAAAA
	TGCTGGAATT
2151	GAGCATTTAC GAAGGCATCC CGCACCTGCT CGCCCCTGTC
	GTTACCGATA
2201	TGAAGCTGGC GGCAAACGCG CTGAACTGGT GTGTTAACGA
	AATGGAAAAA
2251	CGCTACCGCC TGATGAGCTT TATGGGCGTG CGCAATCTTG
	CGGGTNTCAA
2301	TCAAAAAATC GCCGAAGCCG CAGCAAGGGG GGAGAAAATC
	GGCAACCCGT
2351	TCAGCCTCAC GCCCGACAAT CCCGAACCTT TGGANAAATT
	GCCGTTTATC
2401	GTGGTCGTGG TTGATGAGTT TGCCGACCTG ATGATGACGG
	CAGGCAAGAA
2451	AATCGAAGAA CTGATTGCCC GCCTCGCCCA AAAAGCCCGC
	GCGGCAGGCA
2501	TCCATCTTAT CCTTGCCACA CAACGCCCCA GTGTCGATGT
	CATCACGGGT
2551	CTGATTAAGG CGAACATCCC GACGCGTATC GCGTTCCAAG
	TGTCCAGCAA
2601	AATCGACAGC CGCACGATTC TTGACCAAAT GGGTGCGGAA
	AACCTGCTCG
2651	GGCAGGGCGA TATGCTGTTC CTGCCGCCGG GTACGGCCTA
	TCCGCAGCGC
2701	GTTCACGGCG CGTTTGCCTC GGATGAAGAG GTGCACCGCG
	TGGTCGAATA
2751	TCTGAAACAG TTTGGCGAAC CGGACTATGT TGACGATATN
	TTGAGCGGCG
2801	GTATGTCCGA CGATTTGCTG GGAATCAGCC GGAGCGGCGA
	CGGCGAAACC
2851	GATCCGATGT ACGACGAGGC CGTGTCNGTT GTTTTGAAAA
	CGCGCAAAGC
2901	CAGCATTTCT GGCGTGCAGC GCGCATTGCG TATCGGCTAT
	AATCGCGCCG
2951	CGCGTCTGAT TGACCAGATG GAGGCGGAAG GCATTGTGTC
	CGCACCGGAA
3001	CACAACGGCA ACCGTACGAT TCTCGTCCCC TTNGACAATG
	CTTGA

This encodes a protein having amino acid sequence <SEQ ID 492>:

1	MFWIVLIVIL LLALAGLFFV RAQSEREWMR EVSAWQEKKG
	EKQAELPEIK
51	DGMPDFPELA LMLFHAVKTA VYWLFVGVVR FCRNYLAHES
	EPDRPVPPAS
101	ANRADVPTAS DGYSDSGNGT EEAETEEAEA AEEEAADTED
	IATAVIDNRR
151	IPFDRSIAEG LMPSESEISP VRPVFKEITL EEATRALNSA
	ALRETKKRYI
201	DAFEKNETAV PKVRVSDTPM EGLQIIGLDD PVLQRTYSRM
	FDADKEAFSE
251	SADYGFEPYF EKQHPSAFSA VKAENARNAP FRRHAGQGKG
	QAEAKSPDVS
301	QGQSVSDGTA VRDAXRRVSV NLKEPNKATV SAEARISRLI
	PESRTVVGKR
351	DVEMPSETEN VFTEXVSSVG YGXPVYDETA DIHIEEPAAP
	wDAWVVEPPEV
401	PKVPMPAXDI PPPPPVSEIY NRTYEPPAGF EQVQRSRIAE
	TDHLADDVLN
451	GGWQEETAAI ANDGSEGVAE RSSGQYLSET EAFGHDSQAV
	CPFENVPSER
501	PSRRAXDTEA DEGAFQSEET GAVSEHLPTT DLLLPPLFNP
	GATQTEEXLL
551	XNSITIEEKX AEFKVKVKVV DSYSGPVITR YEIEPDVGVR
	GNSVLNLEKX
601	LARSLGVASI RVVETILGKT CMGLELPNPK RQMIRLSEIF
	NSPEFAESKS
651	KLTLALGQDI TGQPVVTDLG KAPHLLVAGT TGSGKSVGVN
	AMILSMLFKA
701	APEDVRMIMI DPKMLELSIY EGIPHLLAPV VTDMKLAANA
	LNWCVNEMEK
751	RYRLMSFMGV RNLAGXNQKI AEAAARGEKI GNPFSLTPDN
	PEPLXKLPFI
801	VVVVDEFADL MMTAGKKIEE LIARLAQKAR AAGIHLILAT
	QRPSVDVITG
851	LIKANIPTRI AFQVSSKIDS RTILDQMGAE NLLGQGDMLF
	LPPGTAYPQR
901	VHGAFASDEE VHRVVEYLKQ FGEPDYVDDX LSGGMSDDLL
	GISRSGDGET
951	DPMYDEAVSV VLKTRKASIS GVQRALRIGY NRAARLIDQM
	EAEGIVSAPE
1001	HNGNRTILVP XDNA*

ORF58a and ORF58-1 show 96.6% identity in 1014 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF58 shows complete identity over a 9aa overlap with a predicted ORF (ORF58ng) from N. gonorrhoeae:

The ORF58ng nucleotide sequence <SEQ ID 493> is predicted to encode a protein having partial amino acid sequence <SEQ ID 494>:

1	..SEPDRPVPPA SANRADVPTA SDGYSDSGNG TEEAETEAAE
	AAEEEAADTE
51	DIATAVIDNR RIPFDRSIAE GLMQSESKTS PVRPVFKEIT
	LEEATRALSS
101	AALRETKKRY IDAFEKNGTA VPKVRVSDTP MEGLQIIGLD
	DPVLQRTYSR
151	MFDADKEAFS ESADYGFEPY FEKQHPSAFS AVKAENARNA
	PFRRHAGQEK
201	GQAEAKSPDV SQGQSVSDGT AVRDARRRVS VNLKEPNKAT
	VSAEARISRL
251	IPESRTVVGK RDVEMPSETE NVFTETVSSV GYGGPVYDEA
	ADIHIEEPAA
301	PDAWVVEPPE VPEVAVPEID ILPPPPVSEI YNRTYEPPAG
	FEQAQRSRIA
351	ETDHLAADVL NGGWQEETAA IADDGSEGAA ERSSGQYLSE
	TEAFGHDSQA
401	VCPFEDVPSE RPSCRVSDTE ADEGAFQSEE TGAVSEHLPT
	TDLLLPPLFN
451	PEATQTEEEL LENSITIEEK LAEFKVKVKV VDSYSGPVIT
	RYEIEPDVGV
501	RGNSVLNLEK DLARSLGVAS IRVVETIPGK TCMGLELPNP
	KRQMIRLSEI
551	FNSPEFAESK SKLTLALGQD ITGQPVVTDL GKAPHLLVAG
	TTGSGKSVGV
601	NAMILSMLFK AAPEDVRMIM IDPKMLELSI YEGITHLLAP
	VVTDMKLAAN
651	ALNWCVNEME KRYRLMSFMG VRNLAGFNQK IAEAAARGEK
	IGNPFSLTPD
701	DPEPLEKLPF IVVVVDEFAD LMMTAGKKIE ELIARLAQKA
	RAAGIHLILA
751	TQRPSVDVIT GLIKANIPTR IAFQVSSKID SRTILDQMGA
	ENLLGQGDML
801	FLPPGTAYPQ RVHGAFASDE EVHRVVEYLK QFGEPDYVDD
	ILSGGGSEEL
851	PGIGRSGDGE TDPMYDEAVS VVLKTRKASI SGVQRALRIG
	YNRAARLIDQ
901	MEAEGIVSAP EHNGNRTILV PLDNA*

This partial gonococcal sequence contains a predicted transmembrane region and a predicted ATP/GTP-binding site motif A (P-loop; double underlined). Furthermore, it has a domain homologous to the FTSK cell division protein of E. coli. Alignment of ORF58ng and FtsK (accession number p46889) show a 65% amino acid identity in 459 overlap:

ORF58ng:  467 IEEKLAEFKVKVKVVDSYSGPVITRYEIEPDVGVRGNSVLNLEKDLARSLGVASIRVVET  526
+E +LA+F++K  VV+   GPVITR+E+    GV+   + NL +DLARSL    ++RVVE
FtsK:     868 VEARLADFRIKADVVNYSPGPVITRFELNLAPGVKAARISNLSRDLARSLSTVAVRVVEV  927
ORF58ng:  527 IPGKTCMGLELPNPKRQMIRLSEIFNSPEFAESKSKLTLALGQDITGQPVVTDLGKAPHL  586
IPGK  +GLELPN KRQ + L E+ ++ +F ++ S LT+ LG+DI G+PVV DL K  PHL
FtSK:     928 IPGKPYVGLELPNKKRQTVYLREVLDNAKFRDNPSPLTVVLGKDIAGEPVVADLAKMPHL  987
ORF58ng:  587 LVAGTTGSGKSVGVNAMILSMLFKAAPEDVRMIMIDPKMLELSIYEGITHLLAPVVTDMK  646
LVAGTTGSGKSVGVNAMILSML+KA PEDVR IMIDPKMLELS+YEGI HLL  VVTDMK
FtsK:     988 LVAGTTGSGKSVGVNAMILSMLYKAQPEDVRFIMIDPKMLELSVYEGIPHLLTEVVTDMK 1047
ORF58ng:  647 LAANALNWCVNEMEKRYRLMSFMGVANLAGFNQKIAEAAARGEKIGNPFSLTPDDPEP--  704
AANAL WCVNEME+RY+LMS +GVRNLAG+N+KIAEA      I +P+     D  +
FtsK:    1048 DAANALRWCVNEMERRYKLMSALGVRNLAGYNEKIAEADRMMRPIPDPYWKPGDSMDAQH 1107
ORF58ng:  705 --LEKLPFIVVVVDEFADLMMTAGKKIEELIARLAQKARAAGIHLILATQRPSVDVITGL  762
L+K P+IVV+VDEFADLMMT GKK+EELIARLAQKARAAGIHL+LATQRPSVDVITGL
FtsK:    1108 PVLKKEPYIVVLVDEFADLMMTVGKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGL 1167
ORF58ng:  763 IKANIPTRIAFQVSSKIDSRTILDQMGAENLLGQGDMLFLPPGTAYPQRVHGAFASDEEV  822
IKANIPTRIAF VSSKIDSRTILDQ GAE+LLG GDML+  P +  P RVHGAF  D+EV
FtsK:    1168 IKANIPTRIAFTVSSKIDSRTILDQAGAESLLGMGDMLYSGPNSTLPVRVHGAFVRDQEV 1227
ORF58ng:  823 HRVVEYLKQFGEPDYVDDILSGGGSEELPGIGRSGDGETDPMYDEAVSVVLKTRKASISG   882
H VV+  K  G P YVD I S   SE   G G  G  E DP++D+AV  V + RKASISG
FtsK:    1228 HAVVQDWKARGRPQYVDGITSDSESEGGAG-GFDGAEELDPLFDQAVQFVTEKRKASISG  1286
ORF58ng:  883 VQRALRIGYNRAARLIDQMEAEGIVSAPEHNGNRTILVP                       921
VQR  RIGYNRAAR+I+QMEA+GIVS   HNGNR +L P
FtsK:    1287 VQRQFRIGYNRAARIIEQMEAQGIVSEQGHNGNREVLAP                      1325

Further work on ORF58ng revealed the complete gonococcal DNA sequence to be <SEQ ID 495>:

1	ATGTTTTGGA TAGTTTTGAT CGTTATtgtg TTGCTTGCGC
	TTGCCGGCCT
51	GTTTTTTGTC CGCGCACAAT CCGAACGCGA GTGGATGCGC
	GAGGTTTCTG
101	CGTGGCAGGA AAAGAAAGGG GAAAAACAGG CGGAGCTGCC
	TGAAATCAAA
151	GACGGTATGC CCGATTTTCC CGAGTTTTCC CTGATGCTTT
	TCCATGCCGT
201	CAAAACGGCA GTGTATTGGC TGTTTGTCGG TGTCGTCCGT
	TTCTGCCGAA
251	ACTATCTGGC GCACGAATCC GAACCGGACA GGCCCGTTCC
	GCCTGCTTCT
301	GCAAACCGTG CGGATGTTCC GACCGCATCC GACGGGTATT
	CAGACAGTGG
351	AAACGGGACG GAAGAAGCGG AAACGGAAGC AGCAGAAGCT
	GCGGAGGAAG
401	AGGCTGCCgA TACgGAAGAC ATTGCAACTG CCGTAATCGA
	CAACCGCCGC
451	ATCCcatTCG ACCGGAGTAT TGCTGAAGGG TTGATGCAGT
	CTGAAAGCAA
501	AACTTCGCCC GTCCGTCCGG TTTTTAAGGA AATCACTTTG
	GAAGAAGCAA
551	CGCGTGCTTT AAGCAGCGCG GCTTTAAGGG AAACGAAAAA
	ACGCTATATC
601	GATGCATTTG AGAAAAACGG AACAGCCGTC CCCAAAGTAC
	GCGTGTCCGA
651	TACCCCGATG GAAGGGCTGC AGATTATCGG TTTGGACGAC
	CCTGTGCTTC
701	AACGCACGTA TTCCCGTATG TTTGATGCGG ACAAAGAAGC
	GTTTTCCGAG
751	TCTGCGGATT ACGGATTTGA GCCGTATTTT GAGAAGCAGC
	ATCCGTCTGC
801	CTTTTCTGCA GTCAAAGCCG AAAATGCACG GAATGCGCCG
	TTCCGCCGTC
851	ATGCAGGGCA GGAGAAAGGG CAGGCGGAGG CAAAATCCCC
	GGATGTTTCC
901	CAAGGGCAGT CCGTTTCAGA CGGCACAGCC GTCCGCGATG
	CCCGCCGCCG
951	CGTTTCCGTC AATTTGAAAG AACCGAACAA GGCAACGGTT
	TCTGCGGAGG
1001	CGCGGATTTC GCGCCTGATT CCGGAAAGTC GGACGGTTGT
	CGGGAAACGG
1051	GATGTCGAAA TGCCGTCTGA AACCGAAAAT GTTTTCACGG
	AAACCGTTTC
1101	GTCTGTGGGA TACGGCGGTC CGGTTTATGA TGAAGCTGCC
	GATATCCATA
1151	TTGAAGAGCC TGCCGCGCCC GATGCTTGGG TGGTCGAACC
	ACCCGAAGTG
1201	CCGGAGGTAG CCGTACCCGA AATCGATATT CTGCCGCCGC
	CTCCCGTATC
1251	GGAAATCTAC AACCGTACCT ATGAGCCGCC GGCAGGATTC
	GAGCAGGCGC
1301	AACGCAGCCG CATTGCCGAA ACCGACCATC TTGCCGCTGA
	TGTTTTGAAT
1351	GGAGGTTGGC AGGAGGAAAC CGCCGCTATT GCAGATGACG
	GCAGTGAGGG
1401	TGCGGCAGAG CGGTCAAGCG GGCAATATCT GTCGGAAACC
	GAAGCGTTCG
1451	GGCATGACAG TCAGGCGGTT TGTCCGTTTG AAGATGTGCC
	GTCTGAACGC
1501	CCGTCCTGCC GGGTATCGGA TACGGAAGCG GATGAAGGGG
	CGTTCCAATC
1551	GGAAGAGACC GGTGCGGTAT CCGAACACCT GCCGACAACC
	GACCTGCTTC
1601	TGCCTCCGCT GTTCAATCCC GAGGCGACGC AAACCGAAGA
	AGAACTGTTG
1651	GAAAACAGCA TCACCATCGA AGAAAAATTG GCGGAGTTCA
	AAGTCAAGGT
1701	CAAGGTTGTC GATTCTTATT CCGGCCCCGT GATTACGCGT
	TATGAAATCG
1751	AACCCGATGT CGGCGTGCGC GGCAATTCCG TTCTGAATTT
	GGAAAAAGAC
1801	TTGGCGCGTT CGCTCGGCGT GGCTTCCATC CGCGTTGTCG
	AAACCATCCC
1851	CGGCAAAACC TGCATGGGTT TGGAACTTCC GAACCCGAAA
	CGCCAAATGA
1901	TACGCCTGAG CGAAATTTTC AATTCGCCCG AGTTTGCCGA
	ATCCAAATCC
1951	AAGCTGACGC TCGCGCTCGG TCAGGACATT ACCGGACAGC
	CCGTCGTAAC
2001	CGACTTGGGC AAAGCACCGC ATTTGCTGGT TGCCGGCACG
	ACCGGTTCGG
2051	GCAAATCGGT GGGTGTCAAC GCGATGATTC TGTCTATGCT
	TTTCAAAGCC
2101	GCGCCGGAAG ACGTGCGTAT GATTATGATC GATCCGAAAA
	TGCTGGAATT
2151	GAGCATTTAC GAAGGCATCA CGCACCTGCT CGCCCCTGTC
	GTTACCGATA
2201	TGAAGCTGGC GGCAAACGCG CTGAACTGGT GTGTTAACGA
	AATGGAAAAA
2251	CGCTACCGCC TGATGAGCTT TATGGGCGTG CGCAATCTTG
	CGGGCTTCAA
2301	CCAAAAAATC GCCGAAGCCG CAGCAAGGGG AGAAAAAATC
	GGCAATCCGT
2351	TCAGCCTCAC GCCCGACGAT CCCGAACCTT TGGAAAAACT
	GCCGTTTATC
2401	GTGGTCGTGG TCGATGAGTT TGCCGATTTG ATGATGACGG
	CAGGCAAGAA
2451	AATCGAAGAA CTGATTGCGC GCCTCGCCCA AAAAGCCCGC
	GCGGCAGGCA
2501	TCCACCTTAT CCTTGCCACA CAACGCCCCA GCGTCGATGT
	CATCACGGGT
2551	CTGATTAAGG CGAACATCCC GACGCGTATC GCGTTCCAAG
	TGTCCAGCAA
2601	AATCGACAGC CGCACGATTC TCGACCAAAT GGGCGCGGAA
	AACCTGCTCG
2651	GTCAGGGCGA TATGCTGTTC CTGCCGCCGG GTACTGCCTA
	TCCGCAGCGC
2701	GTTCACGGCG CGTTTGCCTC GGATGAAGAG GTGCACCGCG
	TGGTCGAATA
2751	TCTGAAGCAG TTTGGCGAGC CGGACTATGT TGACGATATT
	TTGAGCGGCG
2801	GCGGCAGCGA AGAGCTGCCC GGCATCGGGC GCAGCGGCGA
	CGGCGAAACC
2851	GATCCGATGT ACGACGAGGC CGTATCCGTT GTCCTGAAAA
	CGCGCAAAGC
2901	CAGCATTTCG GGCGTACAGC GCGCCTTGCG CATCGGCTAC
	AACCGCGCCG
2951	CGCGTCTGAT TGACCAAATG GAAGCGGAAG GCATTGTGTC
	CGCACCGGAA
3001	CACAACGGCA ACCGTACGAT TCTCGTCCCC TTGGACAATG
	CTTGA

This corresponds to the amino acid sequence <SEQ ID 496; ORF58ng-1>:

1	MFWIVLIVIV LLALAGLFFV RAQSEREWMR EVSAWQEKKG
	EKQAELPEIK
51	DGMPDFPEFS LMLFHAVKTA VYWLFVGVVR FCRNYLAHES
	EPDRPVPPAS
101	ANRADVPTAS DGYSDSGNGT EEAETEAAEA AEEEAADTED
	IATAVIDNRR
151	IPFDRSIAEG LMQSESKTSP VRPVFKEITL EEATRALSSA
	ALRETKKRYI
201	DAFEKNGTAV PKVRVSDTPM EGLQIIGLDD PVLQRTYSRM
	FDADKEAFSE
251	SADYGFEPYF EKQHPSAFSA VKAENARNAP FRRHAGQEKG
	QAEAKSPDVS
301	QGQSVSDGTA VRDARRRVSV NLKEPNKATV SAEARISRLI
	PESRTVVGKR
351	DVEMPSETEN VFTETVSSVG YGGPVYDEAA DIHIEEPAAP
	DAWVVEPPEV
401	PEVAVPEIDI LPPPPVSEIY NRTYEPPAGF EQAQRSRIAE
	TDHLAADVLN
451	GGWQEETAAI ADDGSEGAAE RSSGQYLSET EAFGHDSQAV
	CPFEDVPSER
501	PSCRVSDTEA DEGAFQSEET GAVSEHLPTT DLLLPPLFNP
	EATQTEEELL
551	ENSITIEEKL AEFKVKVKVV DSYSGPVITR YEIEPDVGVR
	GNSVLNLEKD
601	LARSLGVASI RVVETIPGKT CMGLELPNPK RQMIRLSEIF
	NSPEFAESKS
651	KLTLALGQDI TGQPVVTDLG KAPHLLVAGT TGSGKSVGVN
	AMILSMLFKA
701	APEDVRMIMI DPKMLELSIY EGITHLLAPV VTDMKLAANA
	LNWCVNEMEK
751	RYRLMSFMGV RNLAGFNQKI AEAAARGEKI GNPFSLTPDD
	PEPLEKLPFI
801	VVVVDEFADL MMTAGKKIEE LIARLAQKAR AAGIHLILAT
	QRPSVDVITG
851	LIKANIPTRI AFQVSSKIDS RTILDQMGAE NLLGQGDMLF
	LPPGTAYPQR
901	VHGAFASDEE VHRVVEYLKQ FGEPDYVDDI LSGGGSEELP
	GIGRSGDGET
951	DPMYDEAVSV VLKTRKASIS GVQRALRIGY NRAARLIDQM
	EAEGIVSAPE
1001	HNGNRTILVP LDNA*

ORF58ng-1 and ORF58-1 show 97.2% identity in 1014 aa overlap:

Furthermore, ORF58ng-1 shows significant homology to the E. coli protein FtsK:

sp|P46889|FTSK_ECOLI CELL DIVISION PROTEIN FTSK >gi|1651412|gnl|PID|d1015290
(Dl division protein FtsK [Escherichia coli] >gi|1651418|gnl|PID|d1015296
(D90727) Cell division protein FtsK [Escherichia coli] >gi|1787117 (AE000191)
cell division protein FtsK [Escherichia coli] Length = 1329
Score = 576 bits (1469), Expect = e−163
Identities = 301/459 (65%), Positives = 353/459 (76%), Gaps = 5/459 (1%)

Query:	556	IEEKLAEFKVKVKVVDSYSGPVITRYEIEPDVGVRGNSVLNLEKDLARSLGVASIRVVET	615
		+E +LA+F++K  VV+   GPVITR+E+    GV+   + NL +DLARSL   ++RVVE
Sbjct:	868	VEARLADFRIKADVVNYSPGPVITRFELNLAPGVKAARISNLSRDLARSLSTVAVRVVEV	927
Query:	616	IPGKTCMGLELPNPKRQMIRLSEIFNSPEFAESKSKLTLALGQDITGQPVVTDLGKAPHL	675
		IPGK  +GLELPN KRQ + L E+ ++ +F ++ S LT+ LG+DI G+PVV DL K PHL
Sbjct:	928	IPGKPYVGLELPNKKRQTVYLREVLDNAKFRDNPSPLTVVLGKDIAGEPVVADLAKMPHL	987
Query:	676	LVAGTTGSGKSVGVNAMILSMLFKAAPEDVRMIMIDPKMLELSIYEGITHLLAPVVTDMK	735
		LVAGTTGSGKSVGVNAMILSML+KA  PEDVR IMIDPKMLELS+YEGI HLL  VVTDMK
Sbjct:	988	LVAGTTGSGKSVGVNAMILSMLYKAQPEDVRFIMIDPKMLELSVYEGIPHLLTEVVTDMK	1047
Query:	736	LAANALNWCVNEMEKRYRLMSFMGVRNLAGFNQKIAEAAARGEKIGNPFSLTPDDPEP--	793
		AANAL WCVNEME+RY+LMS +GVRNLAG+N+KIAEA      I +P+    D  +
Sbjct:	1048	DAANALRWCVNEMERRYKLMSALGVRNLAGYNEKIAEADRMMRPIPDPYWKPGDSMDAQH	1107
Query:	794	--LEKLPFIVVVVDEFADLMMTAGKKIEELIARLAQKARAAGIHLILATQRPSVDVITGL	851
		L+K P+IVV+VDEFADLMMT GKK+EELIARLAQKARAAGIHL+LATQRPSVDVITGL
Sbjct:	1108	PVLKKEPYIVVLVDEFADLMMTVGKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGL	1167
Query:	852	IKANIPTRIAFQVSSKIDSRTILDQMGAENLLGQGDMLFLPPGTAYPQRVHGAFASDEEV	911
		IKANIPTRIAF VSSKIDSRTILDQ GAE+LLG GDML+  P +  P RVHGAF  D+EV
Sbjct:	1168	IKANIPTRIAFTVSSKIDSRTILDQAGAESLLGMGDMLYSGPNSTLPVRVHGAFVRDQEV	1227
Query:	912	HRVVEYLKQFGEPDYVDDILSGGGSEELPGIGRSGDGETDPMYDEAVSVVLKTRKASISG	971
		H VV+  K  G P YVD I S   SE   G G  G  E DP++D+AV  V + RKASISG
Sbjct:	1228	HAVVQDWKARGRPQYVDGITSDSESEGGAG-GFDGAEELDPLFDQAVQFVTEKRKASISG	1286
Query:	972	VQRALRIGYNRAARLIDQMEAEGIVSAPEHNGNRTILVP	1010
		VQR  RIGYNRAAR+I+QMEA+GIVS   HNGNR +L P
Sbjct:	1287	VQRQFRIGYNRAARIIEQMEAQGIVSEQGHNGNREVLAP	1325

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 59

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 497>:

This corresponds to the amino acid sequence <SEQ ID 498; ORF101>:

Further work revealed the complete nucleotide sequence <SEQ ID 499>:

1	ATGATTTATC AAAGAAACCT CATCAAAGAA CTCTCTTTTA
	CCGCCGTCGG
51	CATTTTCGTC GTCCTCTTGG CGGTATTGGT CTCCACGCAG
	GCAATCAACC
101	TGCTCGGCCG TGCCGCCGAC GGGCGTGTCG CCATCGATGC
	CGTGTTGGCA
151	TTGGTCGGCT TCTGGGTCAT CGGTATGACG CCGCTTTTGC
	TGGTGTTGAC
201	CGCATTTATC AGTACGTTGA CCGTGTTGAC CCGCTACTGG
	CGCGACAGCG
251	AAATGTCGGT CTGGCTATCC TGCGGATTGG CATTGAAACA
	ATGGATACGC
301	CCGGTGATGC AGTTTGCCGT GCCGTTTGCC GTTTTGGTTG
	CCGTCATGCA
351	GCTTTGGGTG ATACCGTGGG CAGAGCTACG CAGCCGCGAA
	TACGCTGAAA
401	TCCTGAAGCA GAAGCAGGAA TTGTCTTTGG TGGAGGCAGG
	CGAGTTCAAC
451	AGTTTGGGCA AGCGCAACGG CAGGGTTTAT TTTGTCGAAA
	CCTTCGATAC
501	CGAATCCGGC ATCATGAAAA ACCTGTTCCT GCGCGAACAG
	GACAAAAACG
551	GCGGCGACAA CATCATCTTC GCCAAAGAAG GTAACTTCTC
	GCTGAACGAC
601	AACAAACGCA CGCTCGAATT GCGCCACGGC TACCGTTACA
	GCGGCACGCC
651	CGGACGCGCC GACTACAATC AGGTTTCCTT CCAAAAACTC
	AACCTGATTA
701	TCAGCACCAC GCCCAAACTC ATCGACCCCG TTTCCCACCG
	CCGTACCATT
751	CCGACCGCCC AACTGATTGG CAGCAGCAAC CCGCAACATC
	AGGCGGAATT
801	GATGTGGCGC ATCTCGCTGA CCGTCAGCGT CCTCCTACTC
	TGCCTGCTTG
851	CCGTGCCGCT TTCCTATTTC AACCCGCGCA GCGGACATAC
	CTACAATATC
901	TTGATTGCCA TCGGTTTGTT TTTAATTTAC CAAAACGGGC
	TGACCCTGCT
951	TTTTGAAGCC GTGGAAGACG GCAAAATCCA TTTTTGGCTC
	GGACTGCTGC
1001	CTATGCACAT TATCATGTTT GCCGTTGCAC TCATCCTGTT
	GCGCGTCCGC
1051	AGTATGCCCA GCCAGCCCTT CTGGCAGGCG GTTGGCAAAA
	GTCTGACATT
1101	GAAAGGCGGA AAATGA

This corresponds to the amino acid sequence <SEQ ID 500; ORF101-1>:

1	MIYQRNLIKE LSFTAVGIFV VLLAVLVSTQ AINLLGRAAD
	GRVAIDAVLA
51	LVGFWVIGMT PLLLVLTAFI STLTVLTRYW RDSEMSVWLS
	CGLALKQWIR
101	PVMQFAVPFA VLVAVMQLWV IPWAELRSRE YAEILKQKQE
	LSLVEAGEFN
151	SLGKRNGRVY FVETFDTESG IMKNLFLREQ DKNGGDNIIF
	AKEGNFSLND
201	NKRTLELRHG YRYSGTPGRA DYNQVSFQKL NLIISTTPKL
	IDPVSHRRTI
251	PTAQLIGSSN PQHQAELMWR ISLTVSVLLL CLLAVPLSYF
	NPRSGHTYNI
301	LIAIGLFLIY QNGLTLLFEA VEDGKIHFWL GLLPMHIIMF
	AVALILLRVR
351	SMPSQPFWQA VGKSLTLKGG K*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF101 shows 91.2% identity over a 57aa overlap and 95.7% identity over a 69aa overlap with an ORF (ORF101a) from strain A of N. meningitidis:

The complete length ORF101a nucleotide sequence <SEQ ID 501> is:

1	ATGATTTATC AAAGAAACCT CATCAAAGAA CTCTCTTTTA
	CCGCCGTCGG
51	CATTTTCGTC GTCCTCTTGG CGGTATTGGT CTCCACGCAG
	GCAATCAACC
101	TGCTCGGCCN TGCCGCCGAC NGGCGTNTCG CCATCGATGC
	CGTGTTGGCA
151	TTGGTCGGCT TCTGGGTCNN NNGNATGACG CCGCTTTTGC
	TNGTGTTGAC
201	CGCATTTATC AGTACGTTGA CCGTGTTGAC CCGCTACTGG
	CGNGACAGCG
251	AAATGTCGGT CTGGNTATCC TGCGGATTGG CATTGAAACA
	ATGGATACGC
301	CCGGTGATGC AGTTTGCCGT GCCGTTTGCC GTTTTGGTTG
	CCGTCATGCA
351	GCTTTGGGTG ATACCGTGGG CAGAGCTACG CAGCCGCGAA
	TACGCTGAAA
401	TCCTGAAGCA GAAGCAGGAA TTGTCTTTGG TGGAGGCAGG
	CGGGTTCAAC
451	AGTTTGGGCA AGCGCAACGG CAGGGTTTAT TTTGTCGAAA
	CCTTCGATAC
501	CGAATCCGGC ATCATGAAAA ACCTGTTCCT GCGCGAACAG
	GACAAAAACG
551	GCGGCGACAA CATCATCTTC NCCAAAGAAA GTAACTTCTC
	GCTGAACGAC
601	AACAAACGCA CGCTCGAATT GCGCCACGGC TACCGTTACA
	GCGGCACGCC
651	CGGACGCGCC GACTACAATC AGGTTTCCTT CCNAAAACTC
	AACCTGATTA
701	TCAGCACCAC GCCCAAACTC ATCGACCCCG TTTCCCACCG
	CCGTACNATN
751	CCNACNGCCC AACTGATTGG CAGCAGCAAC CCGCAACATC
	ANGCGGAATT
801	GATGTGGCGC ATCTCGCTGA CCGTCAGCGT CCTCCTACTC
	TGCCTGCTTG
851	CCGTGCCGCT TTCCTATTTC AACCCGCGCA GCGGACATAC
	CTACAATATC
901	TTGANTGCCA TCGGTTTGTT TTTAATTTAC CAAAACGGGC
	TGACCCTGCT
951	TTTTGAAGCC GTGGAAGACG GCAAAATCCA TTTTTGGCTC
	GGACTGCTGC
1001	CTATGCACAT CATCATGTTC GTCATCGCAA TCGTACTTCT
	GCGCGTCCGC
1051	AGCATGCCCA GCCAGCCCTT CTGGCAGGCG GTTGGCAAAA
	GTCTGACATT
1101	GAAAGGCGGA AAATGA

This encodes a protein having amino acid sequence <SEQ ID 502>:

	1	MIYQRNLIKE LSFTAVGIFV VLLAVLVSTQ AINLLGXAAD
		XRXAIDAVLA
	51	LVGFWVXXMT PLLLVLTAFI STLTVLTRYW RDSEMSVWXS
		CGLALKQWIR
	101	PVMQFAVPFA VLVAVMQLWV IPWAELRSRE YAEILKQKQE
		LSLVEAGGFN
	151	SLGKRNGRVY FVETFDTESG IMKNLFLREQ DKNGGDNIIF
		XKESNFSLND
	201	NKRTLELRHG YRYSGTPGRA DYNQVSFXKL NLIISTTPKL
		IDPVSHRRTX
	251	PTAQLIGSSN PQHXAELMWR ISLTVSVLLL CLLAVPLSYF
		NPRSGHTYNI
	301	LXAIGLFLIY QNGLTLLFEA VEDGKIHFWL GLLPMHIIMF
		VIAIVLLRVR
	351	SMPSQPFWQA VGKSLTLKGG K*

ORF101a and ORF101-1 show 95.4% identity in 371 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF101 shows 96.5% identity in 57aa overlap at the N-terminal domain and 95.1% identity in 61 as overlap at the C-terminal domain, respectively, with a predicted ORF (ORF101ng) from N. gonorrhoeae:

The ORF101ng nucleotide sequence <SEQ ID 503> is predicted to encode a protein having partial amino acid sequence <SEQ ID 504>:

1	MIYQRNLIKE LSFTAVGIFV VLLAVLVSTQ AINLLGRAAD
	GRVAIDAVLA
51	LVGFWVIGMT PLLLVLTAFI STLTVLTRYW RDSEMSVWLS
	CGLALKQWIR
101	PVMQFAVPFA ILIAVMQLWV IPWAELRSRE YAEILKQKQE
	LSLVEAGEFN
151	NLGKRNGRVY FVETFDTESG IMKNLFLREQ DKNGGDNIIF
	AKEGNFSLKD
201	NKRTLELRHG YRYSGTPGRA DYNQVSFQKL NLIISTTPKL
	IDPVSHRRTI
251	STAQLIGSSN PQHQAELMWR ISLTVSVLLL CLLAVPLSYF
	NPRSGHTYNI
301	LIAIGLFLIY QNGLTLLFEA VEDGKIHFWL GLLPMHIIMF
	VIAIVLLRVR
351	SMPSQPFWQA VG...

Further work revealed the complete nucleotide sequence <SEQ ID 505>:

1	ATGATTTATC AAAGAAACCT CATCAAAGAA CTCTCTTTTA
	CCGCCGTCGG
51	CATTTTCGTC GTCCTCTTGG CGGTGTTGGT GTCCACGCAG
	GCGATCAACC
101	TGCTTGGCCG CGCAGCTGAC GGGCGTGTCG CCATCGATGC
	CGTGTTGGCC
151	TTAGTCGGCT TCTGGGTCAT CGGTATGACC CCGCTTTTGC
	TGGTGTTGAC
201	CGCATTCATC AGCACGCTGA CCGTATTGAC CCGCTACTGG
	CGCGACAGCG
251	AAATGTCGGT CTGGCTATCC TGCGGATTGG CGTTGAAACA
	GTGGATACGC
301	CCCGTCATGC AGTTTGCCGT GCCGTTTGCC ATCCTGATTG
	CCGTCATGCA
351	GCTTTGGGTG ATACCGTGGG CAGAGCTGCG CAGCCGCGAA
	TATGCCGAAA
401	TTTTGAAGCA GAAGCAGGAA TTGTCTTTGG TGGAAGCCGG
	CGAGTTCAAT
451	AACTTGGGCA AGCGCAACGG CAgggtttaT TtcgtcgaaA
	CCTTTGACAC
501	CGaatccgGC ATCATGAAAA ACCTGTtcct GcGCGAACAG
	GACAAAAACG
551	gcggcgacaA CATCATCTTC GCcaaaGAag gtaactTctc
	gctgaaggaC
601	AACAAAcgca cgctcgaATT GCGCCACGGC TACCGTTACA
	GCGGcacgcC
651	CGGacGCGCc gactaCAATC AGGTTtcctt cCAAAAacTc
	aacctgATta
701	TCAGCACCAC GCCCAAacTT ATCGaccCCG TTTCCCACCG
	CCGCACCATT
751	tcgacCGCCC AAcTGATTGG CAGCAGCAAT CCGCAACATC
	AGGCAGAATT
801	GATGTGGCGC ATCTCGCTGA CCGTCAGCGT CCTCCTGCTC
	TGCCTACTCG
851	CCGTGCCGCT TTCCTATTTC AACCCGCGCA GCGGACATAC
	CTACAATATC
901	TTGATTGCCA TCGGTTTGTT TTTAATTTAC CAAAACGGGC
	TGACCCTGCT
951	TTTTGAAGCC GTGGAAGACG GCAAAATCCA TTTTTGGCTC
	GGACTGCTGC
1001	CTATGCACAT CATCATGTTC GTCATCGCAA TCGTACTTCT
	GCGCGTCCGC
1051	AGTATGCCCA GCCAGCCCTT CTGGCAGGCG GTTGGCAAAA
	GTCTGACATT
1101	GAAAGgcgGA AAATGA

This corresponds to the amino acid sequence <SEQ ID 506; ORF101ng-1>:

	1	MIYQRNLIKE LSFTAVGIFV VLLAVLVSTQ AINLLGRAAD
		GRVAIDAVLA
	51	LVGFWVIGMT PLLLVLTAFI STLTVLTRYW RDSEMSVWLS
		CGLALKQWIR
	101	PVMQFAVPFA ILIAVMQLWV IPWAELRSRE YAEILKQKQE
		LSLVEAGEFN
	151	NLGKRNGRVY FVETFDTESG IMKNLFLREQ DKNGGDNIIF
		AKEGNFSLKD
	201	NKRTLELRHG YRYSGTPGRA DYNQVSFQKL NLIISTTPKL
		IDPVSHRRTI
	251	STAQLIGSSN PQHQAELMWR ISLTVSVLLL CLLAVPLSYF
		NPRSGHTYNI
	301	LIAIGLFLIY QNGLTLLFEA VEDGKIHFWL GLLPMHIIMF
		VIAIVLLRVR
	351	SMPSQPFWQA VGKSLTLKGG K*

ORF101ng-1 and ORF101-1 show 97.6% identity in 371 aa overlap:

Based on this analysis, including the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 60

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 507>:

1	..GGTGGTGGTT TTATCAATGC TTCCTGTGCC ACTTTGACGA
	CAGCCAAACC
51	GCAATATCAA GCAGGAGACC TTAGCGCTTT TAAGATAAGG
	CAAGGCAATG
101	TTGTAATCGC CGGACACGGT TTGGATGCAC GTGATACCGA
	TTACACACGT
151	ATTCTCAGTT ATCATTCCAA AATCGATGCA CCCGTATGGG
	GACAAGATGT
201	TCGTGTCGTC GCGGGACAAA ACGATGTGGC CGCAACAGGT
	GATGCACATT
251	CGCCTATTCT CAATAATGCT GCTGCCAATA CGTCAAACAA
	TACAGCCAAC
301	AACGGCACAC ATATCCCTTT ATTTGCGATT GATACAGGCA
	AATTAGGAGG
351	TAT.GTATGC CAACAAAATC ACCTTGATCA GTACGGTCGA
	GCAAGCAGGC
401	ATTCGTAA

This corresponds to the amino acid sequence <SEQ ID 508; ORF113>:

1	..GGGFINASCA TLTTAKPQYQ AGDLSAFKIR QGNVVIAGHG
	LDARDTDYTR
51	ILSYHSKIDA PVWGQDVRVV AGQNDVAATG DAHSPILNNA
	AANTSNNTAN
101	NGTHIPLFAI DTGKLGGXVC QQNHLDQYGR ASRHS*

Computer analysis of this amino acid sequence gave the following results:

Homology with pspA Putative Secreted Protein of N. meningitidis (Accession AF030941)

ORF and pspA show 44% aa identity in 179aa overlap:

orf113	GGGFINASCATLTTAKPQYQAGDLSAFKIRQGNVVIAGHGLDARDTDYTRILSYHSKIDA	60
	GGG INA+  TLT+  P    G+L+ F +  G VVI G GLD  D DYTRILS  ++I+A
pspa	GGGLINAASVTLTSGVPVLNNGNLTGFDVSSGKVVIGGKGLDTSDADYTRILSRAAEINA	256
orf113	PVWGQDVRVVAGQNDVAATGDAHSPILXXXXXXXXXXXXXXGTHIPLFAIDTGKLGGMYA	120
	VWG+DV+VV+G+N +   G                      +  P  AIDT  LGGMYA
pspa	GVWGKDVKVVSGKNKLDFDG---------SLAKTASAPSSSDSVTPTVAIDTATLGGMYA	307
orf113	NKITLISTVEQAGIRNQGQWFASAGNVAVNAEGKLVNTGMIAATGENHAVSLHARNVHN	179
	+KITLIST   A IRN+G+ FA+ G V ++A+GKL N+G I A      +++ A+ V N
pspa	DKITLISTDNGAVIRNKGRIFAATGGVTLSADGKLSNSGSIDAA----EITISAQTVDN	362

Homology with a Predicted ORF from N. gonorrhoeae

ORF113 shows 86.5% identity in 52aa overlap at the N-terminal part and 94.1% identity in 17aa overlap at the C-terminal part with a predicted ORF (ORF113ng) from N. gonorrhoeae:

The complete length ORF113ng nucleotide sequence <SEQ ID 509> is predicted to encode a protein having amino acid sequence <SEQ ID 510>:

1	MNKTLYRVIF NRKRGAVVAV AETTKREGKS CADSGSGSVY
	VKSVSFIPTH
51	SKAFCFSALG FSLCLALGTV NIAFADGIIT DKAAPKTQQA
	TILQTGNGIP
101	QVNIQTPTSA GVSVNQYAQF DVGNRGAILN NSRSNTQTQL
	GGWIQGNPWL
151	TRGEARVVVN QINSSHPSQL NGYIEVGGRR AEVVIANPAG
	IAVNGGGFIN
201	ASRATLTTGQ PQYQAGDFSG FKIRQGNAVI AGHGLDARDT
	DFTRILVCQQ
251	NHLDQYGRTS RHS*

Based on this analysis, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 61

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 511>:

1	..TCAACGGGAC ATAGCGAACA AAATTACACT TTGCCGCGAG
	AAATCACACG
51	CAACATTTCA CTGGGTTCAT TTGCCTATGA ATCGCATCGC
	AAAGCATTAA
101	GCCATCATGC GCCCAGCCAA GGCACTGAGT TGCCGCAAAG
	CAACGGTATT
151	TCGCTACCCT ATACGTCCAA TTCTTTTACC CCATTACCCA
	GCAGCAGCTT
201	ATACATTATC AATCCTGTCA ATAAAGGCTA TCTTGTTGAA
	ACCGATCCAC
251	GCTTTGCCAA CTACCGTCAA TGGTTGGGTA GTGACTATAT
	GCtGGACAGC
301	CTCAAACTAG ACCCAAACAA TTTACATAAA CGTTTGGGTG
	ATGGTTATTA
351	CGAGCAACGT TTAATCAATG AACAAATCGC AGAGCTGACA
	GGGCATCGTC
401	GTTTAGAcGG TTATCAAAAC GACGAAGAAC AATTTAAAGC
	CTTAATGGAT
451	AATGGCGCGA CTGCGGCACG TTcGATGAAT CTCAGCGTTG
	GCATTGCATT
501	AAGTGCCGAG CAAGTAGCGC AACTGACCAG CGATATTGTT
	TGGTTGGTAC
551	AAAAAGAAGT TAAGCTTCCT GATGGCGGCA CACAAACCGT
	ATTGGTGCCA
601	CAGGTTTATG TACGCGTTAA AAATGGCGAC ATAGACGGTA
	AAGGTGCATT
651	GTTGTCAGGC AGCAATACAC AAATCAATGT TTCAGGCAGC
	CTGAAAAACT
701	CAGGCACGAT TGCAGGgCGC AATGCGCTTA TTATCAATAC
	CGATACGCTA
751	GACAATATCG GTGGGCGTAT TCATGCGCAA AAATCAGCGG
	TTACGGCCAC
801	ACAAGACATC AATAATATTG GCGGCATGCT TTCTGCCGAA
	CAGACATTAT
851	TGCTCAACGC AGGCAACAAC ATCAACAGCC AAAGCACCAC
	CGCCAGCAGT
901	CAAAATACAC AAGGCAGCAG CACCTACCTA GACCGAATGG
	CAGGTATTTA
951	TATCACAGGC AAAGAAAAAG GTGTTT..

This corresponds to the amino acid sequence <SEQ ID 512; ORF115>:

1	..STGHSEQNYT LPREITRNIS LGSFAYESHR KALSHHAPSQ
	GTELPQSNGI
51	SLPYTSNSFT PLPSSSLYII NPVNKGYLVE TDPRFANYRQ
	WLGSDYMLDS
101	LKLDPNNLHK RLGDGYYEQR LINEQIAELT GHRRLDGYQN
	DEEQFKALMD
151	NGATAARSMN LSVGIALSAE QVAQLTSDIV WLVQKEVKLP
	DGGTQTVLVP
201	QVYVRVKNGD IDGKGALLSG SNTQINVSGS LKNSGTIAGR
	NALIINTDTL
251	DNIGGRIHAQ KSAVTATQDI NNIGGMLSAE QTLLLNAGNN
	INSQSTTASS
301	QNTQGSSTYL DRMAGIYITG KEKGV..

Computer analysis of this amino acid sequence gave the following results:

Homology with the pspA Putative Secreted Protein of N. meningitidis (Accession Number AF030941)

ORF115 and pspA protein show 50% aa identity in 325aa overlap:

Orf115:	1	STGHSEQNYTLPREITRNISLGSFAYESHRKALSHHAPSQGTELPQSNGISLPYTSNSFT	60
		STG+S   Y    E++ +I +G  AY+ +    +   P     +   NGI   +T
pspA:	778	STGYSRSPYEPAPEVS-SIRMGISAYKGYAPQQASDIPGTVVPVVAENGIHPTFT-----	831
Orf115:	61	PLPSSSLYIINPVNKGYLVETDPRFANYRQWLGSDYMLDSLKLDPNNLHKRLGDGYYEQR	120
		LP+SSL+ I P NKGYL+ETDP F +YR+WLGS YML +L+ DPN++HKRLGDGYYEQ+
pspA:	832	-LPNSSLFAIAPNNKGYLIETDPAFTDYRKWLGSGYMLAALQQDPNHIHKRLGDGYYEQK	890
Orf115:	121	LINEQIAELTGHRRLDGYQNDEEQFKALMDNGATAARSMNLSVGIALSAEQVAQLTSDIV	180
		L+NEQIA+LTG+RRLDGY NDEEQFKALMDNG T A+ + L+ GIALSAEQVA+LTSDIV
pspA:	891	LVNEQIAKLTGYRRLDGYTNDEEQFKALMDNGITIAKELQLTPGIALSAEQVARLTSDIV	950
Orf115:	181	WLVQKEVKLPDGGTQTVLVPQVYVRVKNGDIDGKGALLSGSNTQINVSGSLKN-SGTIAG	239
		WL  + V LPDG TQTVL P+VYVR +  D++G+GALLSGS   I  SG+++N  G IAG
pspA:	951	WLENETVTLPDGTTQTVLKPKVYVRARPKDMNGQGALLSGSVVDIG-SGAIENRGGLIAG	1009
Orf115:	240	RNALIINTDTLDNIGGRIHAQKSAVTATQDINNIGGMLSAEQTLLLNAGXXXXXXXXXXX	299
		R ALI+N   + N+ G +  +     A  DI N G  + AE  LLL A
pspA:	1010	REALILNAQNIKNLQGDLQGKNIFAAAGSDITNTGS-IGAENALLLKASNNIESRSETRS	1068
Orf115:	300	XXXXXXXXXYLDRMAGIYITGKEKG	324
		+ R+AGIY+TG++ G
pspA:	1069	NQNEQGSVRNIGRVAGIYLTGRQNG	1093

Homology with a Predicted ORF from N. gonorrhoeae

ORF115 shows 91.9% identity over a 334aa overlap with a predicted ORF (ORF115ng) from N. gonorrhoeae:

An ORF115ng nucleotide sequence <SEQ ID 513> was predicted to encode a protein having amino acid sequence <SEQ ID 514>:

1	MLVQTEKDGL HNEQTFGEKK VFSENGKLHN YWRARRKGHD
	ETGHREQNYT
51	LPEEITRDIS LGSFAYESHS KALSRHAPSQ GTELPQSNRD
	NIRTAKSNGI
101	SLPYTPNSFT PLPGSSLYII NPANKGYLVE TDPRFANYRQ
	WLGSDYMLGS
151	LKLDPNNLHK RLGDGYYEQR LINEQIAELT GHRRLDGYQN
	DEEQFKALMD
201	NGATAARSMN LSVGIALSAE QAAQLTSDIV WLVQKEVKLP
	DGGTQTVLMP
251	QVYVRVKNGG IDGKGALLSG SNTQINVSGS LKNSGTIAGR
	NALIINTDTL
301	DNIGGRIHAQ KSAVTATQDI NNIGGILSAE QTLLLNAGNN
	INNQSTAKSS
351	QNAQGSSTYL DRMAGIYITG KEKGVLAAQA GKDINIIAGQ
	ISNQSDQGQT
401	RLQAGRDINL DTVQTGKYQE IHFDADNHTI RGSTNEVGSS
	IQTKGDVTLL
451	SGNNLNAKAA EVGSAKGTLA VYAKNDITIS SGIHAGQVDD
	ASKHTGRSGG
501	GNKLVITDKA QSHHETAQSS TFEGKQVVLQ AGNDANILGS
	NVISDNGTRI
551	QAGNHVRIGT TQTQSQSETY HQTQKSGLMS AGIGFTIGSK
	TNTQENQSQS
601	NEHTGSTVGS LKGDTTIVAS KHYEQTGSNV SSPEGNNLIS
	TQSMDIGAAQ
651	NQLNSKTTQT YEQKGLTVAF SSPVTDLAQQ AIAVAHKAAK
	QFDKAKTTAL
701	MPWRLPMQVG RLFKQAKAPK K*

Further work revealed the following partial gonococcal DNA sequence <SEQ ID 515>:

1	TTGCTTGTGC AAACAGAAAA AGACGGTTTG CATAACGAGC
	AAACCTTTGG
51	CGAGAAGAAA GTCTTCAGCG AAAATGGTAA GTTGCACAAC
	TACTGGCGTG
101	CGCGTCGTAA AGGACATGAT GAAACAGGGC ATCGTGAACA
	AAATTATACT
151	TTGCCGGAGG AAATCACACG CGACATTTCA CTGGGTTCAT
	TTGCCTATGA
201	ATCGCATAGC AAAGCATTAA GCCGTCATGC GCCCAGCCAA
	GGCACTGAGT
251	TGCCACAAAG TAACCGGGAT AATATCCGTA CTGCGAAAAG
	CAACGGTATT
301	TCGCTACCCT ATACGCCCAA TTCTTTTACC CCATTACCCG
	GCAGCAGCTT
351	ATACATTATC AATCCTGCCA ATAAAGGCTA TCTTGTTGAA
	ACCGATCCAC
401	GCTTTGCCAA CTACCGTCAA TGGTTGGGTA GTGACTATAT
	GCTGGGCAGC
451	CTCAAACTAG ACCCAAACAA TTTACATAAA CGTTTGGGTG
	ATGGTTATTA
501	CGAGCAACGT TTAATCAATG AACAAATCGC AGAGCTGACA
	GGGCATCGTC
551	GTTTAGACGG TTATCAAAAC GACGAAGAAC AATTTAAAGC
	CTTAATGGAT
601	AATGGCGCGA CTGCGGCACG TTCGATGAAT CTCAGCGTTG
	GCATTGCATT
651	AAGTGCCGAG CAAGCAGCGC AACTGACCAG CGATATTGTT
	TGGTTGGTAC
701	AAAAAGAAGT TAAACTTCCT GATGGCGGCA CACAAACCGT
	ATTGATGCCA
751	CAGGTTTATG TACGCGTTAA AAATGGCGGC ATAGACGGTA
	AAGGTGCATT
801	GTTGTCAGGC AGCAATACAC AAATCAATGT TTCAGGCAGC
	CTGAAAAACT
851	CAGGCACGAT TGCAGGGCGC AATGCGCTTA TTATCAATAC
	CGATACGCTA
901	GACAATATCG GTGGGCGTAT TCATGCGCAA AAATCAGCGG
	TTACGGCCAC
951	ACAAGACATC AATAATATTG GCGGCATTCT TTCTGCCGAA
	CAGACATTAT
1001	TGCTCAATGC GGGTAACAAC ATCAACAACC AAAGCACGGC
	CAAGAGCAGT
1051	CAAAATGCAC AAGGTAGCAG CACCTACCTA GACCGAATGG
	CAGGTATTTA
1101	TATCACAGGC AAAGAAAAAG GTGTTTTAGC AGCGCAGGCA
	GGCAAAGACA
1151	TCAACATCAT TGCCGGTCAA ATCAGCAATC AATCAGATCA
	AGGGCAAACC
1201	CGGCTGCAGG CAGGACGCGA CATTAACCTG GATACGGTAC
	AAACCGGCAA
1251	ATATCAAGAA ATCCATTTTG ATGCCGATAA CCATACCATC
	CGAGGTTCAA
1301	CGAACGAAGT CGGCAGCAGC ATTCAAACAA AAGGCGATGT
	TACCCtatTG
1351	TCAGGGAATA ATCTCAATGC CAAAGCTGCC GAAGTCGGCA
	GCGCAAAAGG
1401	CACACTTGCC GTGTATGCTA AAAATGACAT TACTATCAGC
	TCAGGCATCC
1451	ATGCCGGCCA AGTTGATGAT GCGTCCAAAC ATACAGGCAG
	AAGCGGCGGC
1501	GGTAATAAAT TAGTCATTAC CGATAAAGCC CAAAGTCATC
	ACGAAACTGC
1551	TCAAAGCAGC ACCTTTGAAG GCAAGCAAGT TGTATTGCAG
	GCAGGAAACG
1601	ATGCCAACAT CCTTGGCAGT AATGTTATTT CCGATAATGG
	CACCCGGATT
1651	CAAGCAGGCA ATCATGTTCG CATTGGTACA ACCCAAACTC
	AAAGCCAAAG
1701	CGAAACCTAT CATCAAACCC AAAAATCAGG ATTGATGAGT
	GCAGGTATCG
1751	GCTTCACTAT TGGCAGCAAG ACAAACACAC AAGAAAACCA
	ATCCCAAAGC
1801	AACGAACATA CAGGCAGTAC CGTAGGCAGC CTGAAAGGCG
	ATACCACCAT
1851	TGTTGCAAGC AAACACTACG AACAAACCGG CAGCAACGTT
	TCCAGCCCTG
1901	AGGGCAACAA CCTTATCAGC ACGCAAAGTA TGGATATTGG
	CGCAGCACAA
1951	AACCAATTAA ACAGCAAAAC CACCCAAACC TACGAACAAA
	AAGGCTTAAC
2001	GGTGGCATTC AGTTCGCCCG TTACCGATTT GGCACAACAA
	GCGATTGCCG
2051	TAGCACACAA AGCAGCAAAC AAGTCGGACA AAGCAAAAAC
	GACCGCGTTA
2101	ATGCCATGGC GGCTGCCAAT GCAGGTTGGC AGGCCTATCA
	AACAGGCAAA
2151	GGCGCACAAA ACTTAG

This corresponds to the amino acid sequence <SEQ ID 516; ORF115ng-1>:

1	LLVQTEKDGL HNEQTFGEKK VFSENGKLHN YWRARRKGHD
	ETGHREQNYT
51	LPEEITRDIS LGSFAYESHS KALSRHAPSQ GTELPQSNRD
	NIRTAKSNGI
101	SLPYTPNSFT PLPGSSLYII NPANKGYLVE TDPRFANYRQ
	WLGSDYMLGS
151	LKLDPNNLHK RLGDGYYEQR LINEQIAELT GHRRLDGYQN
	DEEQFKALMD
201	NGATAARSMN LSVGIALSAE QAAQLTSDIV WLVQKEVKLP
	DGGTQTVLMP
251	QVYVRVKNGG IDGKGALLSG SNTQINVSGS LKNSGTIAGR
	NALIINTDTL
301	DNIGGRIHAQ KSAVTATQDI NNIGGILSAE QTLLLNAGNN
	INNQSTAKSS
351	QNAQGSSTYL DRMAGIYITG KEKGVLAAQA GKDINIIAGQ
	ISNQSDQGQT
401	RLQAGRDINL DTVQTGKYQE IHFDADNHTI RGSTNEVGSS
	IQTKGDVTLL
451	SGNNLNAKAA EVGSAKGTLA VYAKNDITIS SGIHAGQVDD
	ASKHTGRSGG
501	GNKLVITDKA QSHHETAQSS TFEGKQVVLQ AGNDANILGS
	NVISDNGTRI
551	QAGNHVRIGT TQTQSQSETY HQTQKSGLMS AGIGFTIGSK
	TNTQENQSQS
601	NEHTGSTVGS LKGDTTIVAS KHYEQTGSNV SSPEGNNLIS
	TQSMDIGAAQ
651	NQLNSKTTQT YEQKGLTVAF SSPVTDLAQQ AIAVAHKAAN
	KSDKAKTTAL
701	MPWRLPMQVG RPIKQAKAHK T*

This gonococcal protein (ORF115ng-1) shows 91.9% identity with ORF115 over 334aa:

In addition, it shows homology with a secreted N. meningitidis protein in the database:

gi|2623258 (AF030941) putative secreted protein [Neisseria meningitidis]
Length = 2273
Score = 604 bits (1541), Expect = e−172
Identities = 325/678 (47%), Positives = 449/678 (65%), Gaps = 22/678 (3%)

Query:	1	LLVQTEKDGLHNEQTFGEKKVFSENGKLHNYWRARRKGHDETGHREQNYTLPEEITRDIS	60
		L+V T +  L N++T G K + ++ G LH Y R  +KG D TG+    Y    E++  I
Sbjct:	739	LIVGTPESALDNDETLGTKTI-TDKGDLHRYHRHHKKGRDSTGYSRSPYEPAPEVS-SIR	796
Query:	61	LGSFAYESHSKALSRHAPSQGTELPQSNRDNIRTAKSNGISLPYTPNSFTPLPGSSLYII	120
		+G  AY+ +       AP Q +++P +    +     NGI   +T      LP SSL+ I
Sbjct:	797	MGISAYKGY-------APQQASDIPGTV---VPVVAENGIHPTFT------LPNSSLFAI	840
Query:	121	NPANKGYLVETDPRFANYRQWLGSDYMLGSLKLDPNNLHKRLGDGYYEQRLINEQIAELT	180
		P NKGYL+ETDP F +YR+WLGS YML +L+ DPN++HKRLGDGYYEQ+L+NEQIA+LT
Sbjct:	841	APNNKGYLIETDPAFTDYRKWLGSGYMLAALQQDPNHIHKRLGDGYYEQKLVNEQIAKLT	900
Query:	181	GHRRLDGYQNDEEQFKALMDNGATAARSMNLSVGIALSAEQAAQLTSDIVWLVQKEVKLP	240
		G+RRLDGY NDEEQFKALMDNG T A+ + L+ GIALSAEQ A+LTSDIVWL  + V LP
Sbjct:	901	GYRRLDGYTNDEEQFKALMDNGITIAKELQLTPGIALSAEQVARLTSDIVWLENETVTLP	960
Query:	241	DGGTQTVLMPQVYVRVKNGGIDGKGALLSGSNTQINVSGSLKN-SGTIAGRNALIINTDT	299
		DG TQTVL P+VYVR +   ++G+GALLSGS   I  SG+++N  G IAGR ALI+N
Sbjct:	961	DGTTQTVLKPKVYVRARPKDMNGQGALLSGSVVDIG-SGAIENRGGLIAGREALILNAQN	1019
Query:	300	LDNIGGRIHAQKSAVTATQDINNIGGILSAEQTLLLNAGNNINNQSTAKSSQNAQGSSTY	359
		+ N+ G +  +     A  DI N G I  AE  LLL A NNI ++S  +S+QN QGS
Sbjct:	1020	IKNLQGDLQGKNIFAAAGSDITNTGSI-GAENALLLKASNNIESRSETRSNQNEQGSVRN	1078
Query:	360	LDRMAGIYITGKEKGVLAAQAGKDINIIAGQISNQSDQGQTRLQAGRDINLDTVQTGKYQ	419
		+ R+AGIY+TG++ G +   AG +I + A +++NQS+ GQT L AG DI  DT    + Q
Sbjct:	1079	IGRVAGIYLTGRQNGSVLLDAGNNIVLTASELTNQSEDGQTVLNAGGDIRSDTTGISRNQ	1138
Query:	420	EIHFDADNHTIRGSTNEVGSSIQTKGDVTLLSGNNLNAKAAEVGSAKGTLAVYAKNDITI	479
		FD+DN+ IR   NEVGS+I+T+G+++L +  ++  +AAEVGS + G L + A  DI +
Sbjct:	1139	NTIFDSDNYVIRKEQNEVGSTIRTRGNLSLNAKGDIRIRAAEVGSEQGRLKLAAGRDIKV	1198
Query:	480	SSGIHAGQVDDASKHTGRSGGGNKLVITDKAQSHHETAQSSTFEGKQVVLQAGNDANILG	539
		+G    + +DA K+TGRSGGG K  +T   ++ +  A S T +GK+++L +G D  + G
Sbjct:	1199	EAGKAHTETEDALKYTGRSGGGIKQKMTRHLKNQNGQAVSGTLDGKEIILVSGRDITVTG	1258
Query:	540	SNVISDNGTRIQAGNHVRIGTTQTQSQSETYHQTQKSGLM-SAGIGFTIGSKTNTQENQS	598
		SN+I+DN T + A N++ +   +T+S+S   ++ +KSGLM S GIGFT GSK +TQ N+S
Sbjct:	1259	SNIIADNHTILSAKNNIVLKAAETRSRSAEMNKKEKSGLMGSGGIGFTAGSKKDTQTNRS	1318
Query:	599	QSNEHTGSTVGSLKGDTTIVASKHYEQTGSNVSSPEGNNLISTQSMDIGAAQNQLNSKTT	658
		++  HT S VGSL G+T I A KHY QTGS +SSP+G+  IS+  + I AAQN+ + ++
Sbjct:	1319	ETVSHTESVVGSLNGNTLISAGKHYTQTGSTISSPQGDVGISSGKISIDAAQNRYSQESK	1378
Query:	659	QTYEQKGLTVAFSSPVTD	676
		Q YEQKG+TVA S PV +
Sbjct:	1379	QVYEQKGVTVAISVPVVN	1396

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 62

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 517>:

1	..TCAGGGAATA ACCTCAATGC CAAAGCTGCC GAAGTCAGCA
	GCGCAAACGG
51	TACACTCGCT GTGTCTGCCA ATAATGACAT CAACATCAGC
	GCAGGCATCA
101	ACACGACCCA TGTTGATGAT GCGTCCAAAC ACACAGGCAG
	AAGCGGTGGT
151	GGCAATAAAT TAGTCATTAC CGATAAAGCC CAAAGTCATC
	ACGAAACCGC
201	CCAAAGCAGC ACCTTTGAAG GCAAGCAAGT TGTATTGCAG
	GCAGGAAACG
251	ATGCCAACAT CCTTGGCAGC AATGTTATTT CCGATAATGG
	CACCCAGATT
301	CAAGCAGGCA ATCATGTTCG CATTGGTACA ACCCAAACTC
	AAAGCCAAAG
351	CGAAACCTAT CATCAAACCC AGAAATCAGG ATTGATGAGT
	GCAGGTATCG
401	GCTTCACTAT TGGCAGCAAG ACAAACACAC AAGAAAACCA
	ATCCCAAAGC
451	AACGAACATA CAGGCAGTAC CGTAGGCAGC TTGAAAGGCG
	ATACCACCAT
501	TGTTGCAGGC AAACACTACG AACAAATCGG CAGTACCGTT
	TCCAGCCCGG
551	AAGGCAACAA TACCATCTAT GCCCAAAGCA TAGACATTCA
	AGCGGCACAC
601	AACAAATTAA ACAGTAATAC CACCCAAACC TATGAACAAA
	AAGG.CTAAC
651	GGTGGCATTC AGTTCGCCCG TTACCGATTT GGCACAACAA
	...

This corresponds to the amino acid sequence <SEQ ID 518; ORF117>:

1	..SGNNLNAKAA EVSSANGTLA VSANNDINIS AGINTTHVDD
	ASKHTGRSGG
51	GNKLVITDKA QSHHETAQSS TFEGKQVVLQ AGNDANILGS
	NVISDNGTQI
101	QAGNHVRIGT TQTQSQSETY HQTQKSGLMS AGIGFTIGSK
	TNTQENQSQS
151	NEHTGSTVGS LKGDTTIVAG KHYEQIGSTV SSPEGNNTIY
	AQSIDIQAAH
201	NKLNSNTTQT YEQKXLTVAF SSPVTDLAQQ ...

Computer analysis of this amino acid sequence gave the following results:

Homology with the pspA Putative Secreted Protein of N. meningitidis (Accession Number AF030941)

ORF117 and pspA protein show 45% aa identity in 224aa overlap:

Orf117:	4	NLNAKAAEVSSANGTLAVSANNDINISAGINTTHVDDASKHTGRSGGGNKLVITDKAQSH	63
		++  +AAEV S  G L ++A  DI + AG   T  +DA K+TGRSGGG K  +T   ++
pspA:	1173	DIRIRAAEVGSEQGRLKLAAGRDIKVEAGKAHTETEDALKYTGRSGGGIKQKMTRHLKNQ	1232
Orf117:	64	HETAQSSTFEGKQVVLQAGNDANILGSNVISDNGTQIQAGNHVRIGTTQTQSQSETYHQT	123
		+  A S T +GK+++L +G D  + GSN+I+DN T + A N++ +   +T+S+S   ++
pspA:	1233	NGQAVSGTLDGKEIILVSGRDITVTGSNIIADNHTILSAKNNIVLKAAETRSRSAEMNKK	1292
Orf117:	124	QKSGLM-SAGIGFTIGSKTNTQENQSQSNEHTGSTVGSLKGDTTIVAGKHYEQIGSTVSS	182
		+KSGLM S GIGFT GSK +TQ N+S++  HT S VGSL G+T I AGKHY Q GST+SS
pspA:	1293	EKSGLMGSGGIGFTAGSKKDTQTNRSETVSHTESVVGSLNGNTLISAGKHYTQTGSTISS	1352
Orf117:	183	PEGNNTIYAQSIDIQAAHNKLNSNTTQTYEQKXLTVAFSSPVTD	226
		P+G+  I +  I I AA N+ +  + Q YEQK +TVA S PV +
pspA:	1353	PQGDVGISSGKISIDAAQNRYSQESKQVYEQKGVTVAISVPVVN	1396

Homology with a Predicted ORF from N. gonorrhoeae

ORF117 shows 90% identity over a 230aa overlap with a predicted ORF (ORF117ng) from N. gonorrhoeae:

An ORF117ng nucleotide sequence <SEQ ID 519> was predicted to encode a protein having amino acid sequence <SEQ ID 520>:

1	..LLVQTEKDGL HNEQTFGEKK VFSENGKLHN YWRARRKGHD
	ETGHREQNYT
51	LPEEITRDIS LGSFAYESHS KALSRHAPSQ GTELPQSNRD
	NIRTAKSNGI
101	SLPYTPNSFT PLPGSSLYII NPANKGYLVE TDPRFANYRQ
	WLGSDYMLGS
151	LKLDPNNLHK RLGDGYYEQR LINEQIAELT GHRRLDGYQN
	DEEQFKALMD
201	NGATAARSMN LSVGIALSAE QAAQLTSDIV WLVQKEVKLP
	DGGTQTVLMP
251	QVYVRVKNGG IDGKGALLSG SNTQINVSGS LKNSGTIAGR
	NALIINTDTL
301	DNIGGRIHAQ KSAVTATQDI NNIGGILSAE QTLLLNAGNN
	INNQSTAKSS
351	QNAQGSSTYL DRMAGIYITG KEKGVLAAQA GKDINIIAGQ
	ISNQSDQGQT
401	RLQAGRDINL DTVQTGKYQE IHFDADNHTI RGSTNEVGSS
	IQTKGDVTLL
451	SGNNLNAKAA EVGSAKGTLA VYAKNDITIS SGIHAGQVDD
	ASKHTGRSGG
501	GNKLVITDKA QSHHETAQSS TFEGKQVVLQ AGNDANILGS
	NVISDNGTRI
551	QAGNHVRIGT TQTQSQSETY HQTQKSGLMS AGIGFTIGSK
	TNTQENQSQS
601	NEHTGSTVGS LKGDTTIVAS KHYEQTGSNV SSPEGNNLIS
	TQSMDIGAAQ
651	NQLNSKTTQT YEQKGLTVAF SSPVTDLAQQ AIAVAHKAAK
	QFDKAKTTAL
701	MPWRLPMQVG RLFKQAKAPK K*

Further work revealed the following gonococcal partial DNA sequence <SEQ ID 521>:

1	TTGCTTGTGC AAACAGAAAA AGACGGTTTG CATAACGAGC
	AAACCTTTGG
51	CGAGAAGAAA GTCTTCAGCG AAAATGGTAA GTTGCACAAC
	TACTGGCGTG
101	CGCGTCGTAA AGGACATGAT GAAACAGGGC ATCGTGAACA
	AAATTATACT
151	TTGCCGGAGG AAATCACACG CGACATTTCA CTGGGTTCAT
	TTGCCTATGA
201	ATCGCATAGC AAAGCATTAA GCCGTCATGC GCCCAGCCAA
	GGCACTGAGT
251	TGCCACAAAG TAACCGGGAT AATATCCGTA CTGCGAAAAG
	CAACGGTATT
301	TCGCTACCCT ATACGCCCAA TTCTTTTACC CCATTACCCG
	GCAGCAGCTT
351	ATACATTATC AATCCTGCCA ATAAAGGCTA TCTTGTTGAA
	ACCGATCCAC
401	GCTTTGCCAA CTACCGTCAA TGGTTGGGTA GTGACTATAT
	GCTGGGCAGC
451	CTCAAACTAG ACCCAAACAA TTTACATAAA CGTTTGGGTG
	ATGGTTATTA
501	CGAGCAACGT TTAATCAATG AACAAATCGC AGAGCTGACA
	GGGCATCGTC
551	GTTTAGACGG TTATCAAAAC GACGAAGAAC AATTTAAAGC
	CTTAATGGAT
601	AATGGCGCGA CTGCGGCACG TTCGATGAAT CTCAGCGTTG
	GCATTGCATT
651	AAGTGCCGAG CAAGCAGCGC AACTGACCAG CGATATTGTT
	TGGTTGGTAC
701	AAAAAGAAGT TAAACTTCCT GATGGCGGCA CACAAACCGT
	ATTGATGCCA
751	CAGGTTTATG TACGCGTTAA AAATGGCGGC ATAGACGGTA
	AAGGTGCATT
801	GTTGTCAGGC AGCAATACAC AAATCAATGT TTCAGGCAGC
	CTGAAAAACT
851	CAGGCACGAT TGCAGGGCGC AATGCGCTTA TTATCAATAC
	CGATACGCTA
901	GACAATATCG GTGGGCGTAT TCATGCGCAA AAATCAGCGG
	TTACGGCCAC
951	ACAAGACATC AATAATATTG GCGGCATTCT TTCTGCCGAA
	CAGACATTAT
1001	TGCTCAATGC GGGTAACAAC ATCAACAACC AAAGCACGGC
	CAAGAGCAGT
1051	CAAAATGCAC AAGGTAGCAG CACCTACCTA GACCGAATGG
	CAGGTATTTA
1101	TATCACAGGC AAAGAAAAAG GTGTTTTAGC AGCGCAGGCA
	GGCAAAGACA
1151	TCAACATCAT TGCCGGTCAA ATCAGCAATC AATCAGATCA
	AGGGCAAACC
1201	CGGCTGCAGG CAGGACGCGA CATTAACCTG GATACGGTAC
	AAACCGGCAA
1251	ATATCAAGAA ATCCATTTTG ATGCCGATAA CCATACCATC
	CGAGGTTCAA
1301	CGAACGAAGT CGGCAGCAGC ATTCAAACAA AAGGCGATGT
	TACCCtatTG
1351	TCAGGGAATA ATCTCAATGC CAAAGCTGCC GAAGTCGGCA
	GCGCAAAAGG
1401	CACACTTGCC GTGTATGCTA AAAATGACAT TACTATCAGC
	TCAGGCATCC
1451	ATGCCGGCCA AGTTGATGAT GCGTCCAAAC ATACAGGCAG
	AAGCGGCGGC
1501	GGTAATAAAT TAGTCATTAC CGATAAAGCC CAAAGTCATC
	ACGAAACTGC
1551	TCAAAGCAGC ACCTTTGAAG GCAAGCAAGT TGTATTGCAG
	GCAGGAAACG
1601	ATGCCAACAT CCTTGGCAGT AATGTTATTT CCGATAATGG
	CACCCGGATT
1651	CAAGCAGGCA ATCATGTTCG CATTGGTACA ACCCAAACTC
	AAAGCCAAAG
1701	CGAAACCTAT CATCAAACCC AAAAATCAGG ATTGATGAGT
	GCAGGTATCG
1751	GCTTCACTAT TGGCAGCAAG ACAAACACAC AAGAAAACCA
	ATCCCAAAGC
1801	AACGAACATA CAGGCAGTAC CGTAGGCAGC CTGAAAGGCG
	ATACCACCAT
1851	TGTTGCAAGC AAACACTACG AACAAACCGG CAGCAACGTT
	TCCAGCCCTG
1901	AGGGCAACAA CCTTATCAGC ACGCAAAGTA TGGATATTGG
	CGCAGCACAA
1951	AACCAATTAA ACAGCAAAAC CACCCAAACC TACGAACAAA
	AAGGCTTAAC
2001	GGTGGCATTC AGTTCGCCCG TTACCGATTT GGCACAACAA
	GCGATTGCCG
2051	TAGCACACAA AGCAGCAAAC AAGTCGGACA AAGCAAAAAC
	GACCGCGTTA
2101	ATGCCATGGC GGCTGCCAAT GCAGGTTGGC AGGCCTATCA
	AACAGGCAAA
2151	GGCGCACAAA ACTTAG

This corresponds to the amino acid sequence <SEQ ID 522; ORF117ng-1>:

1	LLVQTEKDGL HNEQTFGEKK VFSENGKLHN YWRARRKGHD
	ETGHREQNYT
51	LPEEITRDIS LGSFAYESHS KALSRHAPSQ GTELPQSNRD
	NIRTAKSNGI
101	SLPYTPNSFT PLPGSSLYII NPANKGYLVE TDPRFANYRQ
	WLGSDYMLGS
151	LKLDPNNLHK RLGDGYYEQR LINEQIAELT GHRRLDGYQN
	DEEQFKALMD
201	NGATAARSMN LSVGIALSAE QAAQLTSDIV WLVQKEVKLP
	DGGTQTVLMP
251	QVYVRVKNGG IDGKGALLSG SNTQINVSGS LKNSGTIAGR
	NALIINTDTL
301	DNIGGRIHAQ KSAVTATQDI NNIGGILSAE QTLLLNAGNN
	INNQSTAKSS
351	QNAQGSSTYL DRMAGIYITG KEKGVLAAQA GKDINIIAGQ
	ISNQSDQGQT
401	RLQAGRDINL DTVQTGKYQE IHFDADNHTI RGSTNEVGSS
	IQTKGDVTLL
451	SGNNLNAKAA EVGSAKGTLA VYAKNDITIS SGIHAGQVDD
	ASKHTGRSGG
501	GNKLVITDKA QSHHETAQSS TFEGKQVVLQ AGNDANILGS
	NVISDNGTRI
551	QAGNHVRIGT TQTQSQSETY HQTQKSGLMS AGIGFTIGSK
	TNTQENQSQS
601	NEHTGSTVGS LKGDTTIVAS KHYEQTGSNV SSPEGNNLIS
	TQSMDIGAAQ
651	NQLNSKTTQT YEQKGLTVAF SSPVTDLAQQ AIAVAHKAAN
	KSDKAKTTAL
701	MPWRLPMQVG RPIKQAKAHK T*

ORF117ng-1 shows the same 90% identity over a 230aa overlap with ORF117. In addition, it shows homology with a secreted N. meningitidis protein in the database:

gi|2623258 (AF030941) putative secreted protein [Neisseria meningitidis]
Length = 2273
Score = 604 bits (1541), Expect = e−172
Identities = 325/678 (47%), Positives = 449/678 (65%), Gaps = 22/678 (3%)

Query:	1	LLVQTEKDGLHNEQTFGEKKVFSENGKLHNYWRARRKGHDETGHREQNYTLPEEITRDIS	60
		L+V T +  L N++T G K + ++ G LH Y R  +KG D TG+    Y    E++  I
Sbjct:	739	LIVGTPESALDNDETLGTKTI-TDKGDLHRYHRHHKKGRDSTGYSRSPYEPAPEVS-SIR	796
Query:	61	LGSFAYESHSKALSRHAPSQGTELPQSNRDNIRTAKSNGISLPYTPNSFTPLPGSSLYII	120
		+G  AY+ +       AP Q +++P +    +     NGI   +T      LP SSL+ I
Sbjct:	797	MGISAYKGY-------APQQASDIPGTV---VPVVAENGIHPTFT------LPNSSLFAI	840
Query:	121	NPANKGYLVETDPRFANYRQWLGSDYMLGSLKLDPNNLHKRLGDGYYEQRLINEQIAELT	180
		P NKGYL+ETDP F +YR+WLGS YML +L+ DPN++HKRLGDGYYEQ+L+NEQIA+LT
Sbjct:	841	APNNKGYLIETDPAFTDYRKWLGSGYMLAALQQDPNHIHKRLGDGYYEQKLVNEQIAKLT	900
Query:	181	GHRRLDGYQNDEEQFKALMDNGATAARSMNLSVGIALSAEQAAQLTSDIVWLVQKEVKLP	240
		G+RRLDGY NDEEQFKALMDNG T A+ + L+ GIALSAEQ A+LTSDIVWL  + V LP
Sbjct:	901	GYRRLDGYTNDEEQFKALMDNGITIAKELQLTPGIALSAEQVARLTSDIVWLENETVTLP	960
Query:	241	DGGTQTVLMPQVYVRVKNGGIDGKGALLSGSNTQINVSGSLKN-SGTIAGRNALIINTDT	299
		DG TQTVL P+VYVR +   ++G+GALLSGS   I  SG+++N  G IAGR ALI+N
Sbjct:	961	DGTTQTVLKPKVYVRARPKDMNGQGALLSGSVVDIG-SGAIENRGGLIAGREALILNAQN	1019
Query:	300	LDNIGGRIHAQKSAVTATQDINNIGGILSAEQTLLLNAGNNINNQSTAKSSQNAQGSSTY	359
		+ N+ G +  +     A  DI N G I  AE  LLL A NNI ++S  +S+QN QGS
Sbjct:	1020	IKNLQGDLQGKNIFAAAGSDITNTGSI-GAENALLLKASNNIESRSETRSNQNEQGSVRN	1078
Query:	360	LDRMAGIYITGKEKGVLAAQAGKDINIIAGQISNQSDQGQTRLQAGRDINLDTVQTGKYQ	419
		+ R+AGIY+TG++ G +   AG +I + A +++NQS+ GQT L AG DI  DT    + Q
Sbjct:	1079	IGRVAGIYLTGRQNGSVLLDAGNNIVLTASELTNQSEDGQTVLNAGGDIRSDTTGISRNQ	1138
Query:	420	EIHFDADNHTIRGSTNEVGSSIQTKGDVTLLSGNNLNAKAAEVGSAKGTLAVYAKNDITI	479
		FD+DN+ IR   NEVGS+I+T+G+++L +  ++  +AAEVGS +G L + A  DI +
Sbjct:	1139	NTIFDSDNYVIRKEQNEVGSTIRTRGNLSLNAKGDIRIRAAEVGSEQGRLKLAAGRDIKV	1198
Query:	480	SSGIHAGQVDDASKHTGRSGGGNKLVITDKAQSHHETAQSSTFEGKQVVLQAGNDANILG	539
		+G    + +DA K+TGRSGGG K  +T   ++ +  A S T +GK+++L +G D  + G
Sbjct:	1199	EAGKAHTETEDALKYTGRSGGGIKQKMTRHLKNQNGQAVSGTLDGKEIILVSGRDITVTG	1258
Query:	540	SNVISDNGTRIQAGNHVRIGTTQTQSQSETYHQTQKSGLM-SAGIGFTIGSKTNTQENQS	598
		SN+I+DN T + A N++ +   +T+S+S   ++ +KSGLM S GIGFT GSK +TQ N+S
Sbjct:	1259	SNIIADNHTILSAKNNIVLKAAETRSRSAEMNKKEKSGLMGSGGIGFTAGSKKDTQTNRS	1318
Query:	599	QSNEHTGSTVGSLKGDTTIVASKHYEQTGSNVSSPEGNNLISTQSMDIGAAQNQLNSKTT	658
		++  HT S VGSL G+T I A KHY QTGS +SSP+G+  IS+  + I AAQN+ + ++
Sbjct:	1319	ETVSHTESVVGSLNGNTLISAGKHYTQTGSTISSPQGDVGISSGKISIDAAQNRYSQESK	1378
Query:	659	QTYEQKGLTVAFSSPVTD	676
		Q YEQKG+TVA S PV +
Sbjct:	1379	QVYEQKGVTVAISVPVVN	1396

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 63

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 523>:

1	ATGATTTACA TCGTACTGTT TCTAGCTGTC GTCCTCGCCG
	TTGTCGCCTA
51	CAACATGTAT CAGGAAAACC AATACCGCAA AAAAGTGCGC
	GACCAGTTCG
101	GACACTCCGA CAAAGATGCC CTGCTCAACA GCAwAACCAG
	CCATGTCCGC
151	GACGGCAAAC CGTCCGGCGG GTCAGTCATG ATGCCGAAAC
	CCCAACCGGC
201	GGTCAAAAAA ACGGCAAAAC CCCAAGACCC CGyCATGCGC
	AACCTGCAAG
251	AACAGGATGC CGTCTACATC GCCAAGCAGA AACAGGCAAA
	AGCCTCCCCG
301	TTCAAAACCG AAATCGAAAC CGCCTTGGAA GAAAGCGGCA
	TTATCGGCAA
351	CTCCGCCCAC ACCGTTTCCG AACCCCAAAC CGGACATTCC
	GCAACGAAAC
401	CTGCCGACGC GTCGGCAAAA CCTGCACCCG TTCCGCAAAC
	ACCTGCAAAA
451	CCGCTGATTA CGCTCAAAGA ACTGTCAAAA GTCGAATTAT
	CCTGGTTTGA
501	CGTGCGCATC GACTTCATCT CCTAT...

This corresponds to the amino acid sequence <SEQ ID 524; ORF119>:

1	MIYIVLFLAV VLAVVAYNMY QENQYRKKVR DQFGHSDKDA
	LLNSXTSHVR
51	DGKPSGGSVM MPKPQPAVKK TAKPQDPXMR NLQEQDAVYI
	AKQKQAKASP
101	FKTEIETALE ESGIIGNSAH TVSEPQTGHS ATKPADASAK
	PAPVPQTPAK
151	PLITLKELSK VELSWFDVRI DFISY...

Further work revealed the complete nucleotide sequence <SEQ ID 525>:

1	ATGATTTACA TCGTACTGTT TCTAGCTGTC GTCCTCGCCG
	TTGTCGCCTA
51	CAACATGTAT CAGGAAAACC AATACCGCAA AAAAGTGCGC
	GACCAGTTCG
101	GACACTCCGA CAAAGATGCC CTGCTCAACA GCAAAACCAG
	CCATGTCCGC
151	GACGGCAAAC CGTCCGGCGG GTCAGTCATG ATGCCGAAAC
	CCCAACCGGC
201	GGTCAAAAAA ACGGCAAAAC CCCAAGACCC CGCCATGCGC
	AACCTGCAAG
251	AACAGGATGC CGTCTACATC GCCAAGCAGA AACAGGCAAA
	AGCCTCCCCG
301	TTCAAAACCG AAATCGAAAC CGCCTTGGAA GAAAGCGGCA
	TTATCGGCAA
351	CTCCGCCCAC ACCGTTTCCG AACCCCAAAC CGGACATTCC
	GCACCGAAAC
401	CTGCCGACGC GCCGGCAAAA CCTGCACCCG TTCCGCAAAC
	ACCTGCAAAA
451	CCGCTGATTA CGCTCAAAGA ACTGTCAAAA GTCGAATTAC
	CCTGGTTTGA
501	CGTGCGCTTC GACTTCATCT CCTATATCGC GCTGACCGAA
	GCCAAAGAAC
551	TGCACGCACT GCCGCGCCTT TCCAACCGCT GCCGCTACCA
	GATTGTCGGC
601	TGCACCATGG ACGACCATTT CCAGATTGCC GAACCCATCC
	CGGGCATCCG
651	CTATCAGGCA TTTATCGTGG GTATTCAGGC AGTCAGCCGC
	AACGGACTTG
701	CCTCGCAGGA AGAACTCTCC GCATTCAACC GCCAGGTGGA
	CGCATTCGCA
751	CAAAGCATGG GCGGTCAGAC GCTGCACACC GACCTTGCCG
	CCTTTATCGA
801	AGTGGCTTCC GCACTGGACG CATTCTGCGC GCGCGTCGAC
	CAGACCATCG
851	CCATCCATTT GGTTTCCCCG ACCAGCATCA GCGGCGTAGA
	ACTGCGTTCC
901	GCCGTAACGG GCGTGGGTTT CGTTTTGGAA GACGACGGCG
	CGTTCCACTA
951	TACCGACACG TCGGGCTCGA CCATGTTCTC CATCTGCTCG
	CTCAACAACG
1001	AGCCGTTTAC CAACGCCCTT TTGGACAACC AGTCCTACAA
	AGGCTTCAGT
1051	ATGCTGCTCG ACATCCCGCA CTCTCCGGCA GGCGAAAAAA
	CCTTCGACGA
1101	TTTGTTTATG GATTTGGCGG TACGCCTGTC CGGCCAGTTG
	AACCTGAATC
1151	TGGTCAACGA CAAAATGGAA GAAGTTTCGA CCCAATGGCT
	CAAAGACGTG
1201	CGCACTTATG TATTGGCGCG TCAGTCCGAG ATGCTCAAAG
	TCGGTATCGA
1251	ACCGGGCGGC AAAACCGCAT TGCGCCTGTT CTCCTAA

This corresponds to the amino acid sequence <SEQ ID 526; ORF119-1>:

1	MIYIVLFLAV VLAVVAYNMY QENQYRKKVR DQFGHSDKDA
	LLNSKTSHVR
51	DGKPSGGSVM MPKPQPAVKK TAKPQDPAMR NLQEQDAVYI
	AKQKQAKASP
101	FKTEIETALE ESGIIGNSAH TVSEPQTGHS APKPADAPAK
	PAPVPQTPAK
151	PLITLKELSK VELPWFDVRF DFISYIALTE AKELHALPRL
	SNRCRYQIVG
201	CTMDDHFQIA EPIPGIRYQA FIVGIQAVSR NGLASQEELS
	AFNRQVDAFA
251	QSMGGQTLHT DLAAFIEVAS ALDAFCARVD QTIAIHLVSP
	TSISGVELRS
301	AVTGVGFVLE DDGAFHYTDT SGSTMFSICS LNNEPFTNAL
	LDNQSYKGFS
351	MLLDIPHSPA GEKTFDDLFM DLAVRLSGQL NLNLVNDKME
	EVSTQWLKDV
401	RTYVLARQSE MLKVGIEPGG KTALRLFS*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF119 shows 93.7% identity over. a 175aa overlap with an ORF (ORF119a) from strain A of N. meningitidis:

The complete length ORF119a nucleotide sequence <SEQ ID 527> is:

1	ATGATTTACA TCGTACTGTT CCTCGCCGCC GTCCTCGCCG
	TTGTCGCCTA
51	CAATATGTAT CAGGAAAACC AATACCGCAA AAAAGTGCGC
	GACCAGTTCG
101	GGCACTCCGA CAAAGATGCC CTGCTCAACA GCAAAACCAG
	CCATGTCCGC
151	GACGGCAAAC CGTCCGGCGG GCCAGTCATG ATGCCGAAAC
	CCCAACCGGC
201	GGTCAAAAAA ACGGCAAAAT CCCAAGACCC CGCCATGCGC
	AACCTGCAAG
251	AGCAGGATGC CGTCTACATC GCCAAGCAGA AACAGGCAAA
	AGCCTCCCCG
301	TTCAAAACCG AAATCGAAAC CGCCTTGGAA GAAAGCGGCA
	TTATCGGCAA
351	CTCCGCCCAC ACCGTTCCCG AACCCCAAAC CGGACATTCC
	GCACCAAAAC
401	CTGCCGACGC GCCGGCAAAA CCTGTTCCCG TTCCGCAAAC
	GCCGGCAAAA
451	CCGCTGATTA CGCTCAAAGA GCTGTCGAAG GTCGAGCTGC
	CCTGGTTTGA
501	CGTGCGCTTC GACTTCATCT CTTATATCGC GCTGACCGAA
	GCCAAAGAAC
551	TGCACGCACT GCCGCGCCTT TCCAACCGCT GCCGCTACCA
	GATTGTCGGC
601	TGCACCATGG ACGACCATTT CCAGATTGCC GAACCCATCC
	CGGGCATCCG
651	CTATCAGGCA TTTATCGTGG GTATTCAGGC AGTCAGCCGC
	AACGGACTTG
701	CCTCGCAGGA AGAACTCTCC GCATTCAACC GCCAGGTGGA
	TGCATTCGCA
751	CACAGCATGG GCGGTCAGAC GCTGCACACC GACCTTGCCG
	CCTTTATCGA
801	AGTGGCTTCC GCACTGGACG CATTCTGCGC GCGCGTCGAC
	CAGACTATCG
851	CCATCCATTT GGTTTCCCCG ACCAGCATCA GCGGCGTAGA
	ACTGCGTTCC
901	GCCGTAACGG GCGTGGGTTT CGTTTTGGAA GACGACGGCG
	CGTTCCACTA
951	TACCGACACG TCGGGCTCGA CCATGTTCTC CATCTGCTCG
	CTCAACAACG
1001	AGCCGTTTAC CAATGCCCTT TTGGACAACC AGTCCTATAA
	AGGCTTCAGT
1051	ATGCTGCTCG ACATCCCGCA CTCTCCGGCA GGCGAAAAAA
	CCTTCGACGA
1101	TTTGTTTATG GATTTGGCGG TACGCCTGTC CGGCCAGTTG
	AACCTGAATC
1151	TGGTCAACGA CAAAATGGAA GAAGTTTCGA CCCAATGGCT
	CAAAGACGTG
1201	CGCACTTATG TATTGGCTCG TCAGTCCGAG ATGCTCAAAG
	TCGGTATCGA
1251	ACCGGGCGGC AAAACCGCAT TGCGCCTGTT CTCCTAA

This encodes a protein having amino acid sequence <SEQ ID 528>:

1	MIYIVLFLAA VLAVVAYNMY QENQYRKKVR DQFGHSDKDA
	LLNSKTSHVR
51	DGKPSGGPVM MPKPQPAVKK TAKSQDPAMR NLQEQDAVYI
	AKQKQAKASP
101	FKTEIETALE ESGIIGNSAH TVPEPQTGHS APKPADAPAK
	PVPVPQTPAK
151	PLITLKELSK VELPWFDVRF DFISYIALTE AKELHALPRL
	SNRCRYQIVG
201	CTMDDHFQIA EPIPGIRYQA FIVGIQAVSR NGLASQEELS
	AFNRQVDAFA
251	HSMGGQTLHT DLAAFIEVAS ALDAFCARVD QTIAIHLVSP
	TSISGVELRS
301	AVTGVGFVLE DDGAFHYTDT SGSTMFSICS LNNEPFTNAL
	LDNQSYKGFS
351	MLLDIPHSPA GEKTFDDLFM DLAVRLSGQL NLNLVNDKME
	EVSTQWLKDV
401	RTYVLARQSE MLKVGIEPGG KTALRLFS*

ORF119a and ORF119-1 show 98.6% identity in 428 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF119 shows 93.1% identity over a 175aa overlap with a predicted ORF (ORF119ng) from N. gonorrhoeae:

The complete length ORF119ng nucleotide sequence <SEQ ID 529> is:

1	ATGATTTACA TCGTACTGTT CCTCGCCGCC GTCCTCGCCG
	TTGTCGCCTA
51	CAATATGTAT CAGGAAAACC AATACCGCAA AAAAGTGCGC
	GACCAGTTCG
101	GACACTCCGA CAAAGATGCC CTGCTCAACA GCAAAACCAG
	CCATGTCCGC
151	GACGGCAAAC CGTCCGGCGG GCCAGTCATG ATGCCGAAAC
	CCCAACCGGC
201	GGTCAAAAAA CCGGCCAAAC CCCAAGACTC CGCCATGCGC
	AACCTGCAAG
251	AACAGGATGC CGTCTACATC GCCAAGCAGA AACAGGCAAA
	AGCCTCCCCG
301	TTCAAAACCG AAATCGAAAC CGCCTTGGAA GAAATCGGCA
	TTATCGGCAA
351	CTCCGCCCAC ACCGTTTCCG AACCCCAAAC CGGACATTCC
	GCACCGAAAC
401	CTGCCGACGC GCCGGCAAAA CCCGTTCCCG TTCCGCAAAC
	GCCGGCAAAA
451	CCGCTGATTA CGCTCAAAGA GCTGTCGAAG GTCGAGCTGC
	CCTGGTTTGA
501	CGTGCGCTtc gACTTCATCT CCTATATCGC GCTGACCGAA
	GCCAAAGAAC
551	TGCACGCACT GCCGCGCCTT tccAACCGCT GCCGCTACCA
	GATTGTCGGC
601	TGCACCATGG ACGACCATTT CCAGATTGCC GAACCCATCC
	CGGGCATCCG
651	CTATCAGGCA TTTATCGTGG GTATCCAGGC AGTCAGCCGC
	AACGGACTTG
701	CCTCGCAGGA AGAACTCTCC GCATTCAACC GCCAGGCGGA
	CGCATTCGCA
751	CAAAGCATGG GCGGTCAGAC GCTGCACACC GACCTTGCCG
	CCTTTATCGA
801	AGTGGCTTCC GCACTGGACG CATTCTGCGC GCGCGTCGAC
	CAGACCATCG
851	CCATCCATTT GGTTTCGCCG ACCAGCATCA GCGGCGTAGA
	ACTGCGTTCC
901	GCCGTAACGG GCGTGGGTTT CGTTTTGGAA GACGACGGCG
	CGTTCCACTA
951	TACCGACACG TCGGGCTCGA CCATGTTCTC CATCTGCTCG
	CTCAACAACG
1001	AGCCGTTTAC CAATGCCCTT TTGGACAACC AGTCCTACAA
	AGGCTTCAGT
1051	ATGCTGCTCG ACATCCCGCA CTCTCCGGCA GGCGAAAAAA
	CCTTCGACGA
1101	TTTGTTTATG GATTTGGCGG TACGCCTGTC CGGTCAGTTG
	AACCTGAATC
1151	TGGTCAACGA CAAAATGGAA GAAGTTTCGA CCCAATGGCT
	CAAAGACGTA
1201	CGCACTTATG TATTGGCGCG TCAGTCCGAG ATGCTCAAAG
	TCGGTATCGA
1251	ACCGGGCGGC AAAACCGCCC TGCGCCTGTT TTCATAA

This encodes a protein having amino acid sequence <SEQ ID 530>:

1	MIYIVLFLAA VLAVVAYNMY QENQYRKKVR DQFGHSDKDA
	LLNSKTSHVR
51	DGKPSGGPVM MPKPQPAVKK PAKPQDSAMR NLQEQDAVYI
	AKQKQAKASP
101	FKTEIETALE EIGIIGNSAH TVSEPQTGHS APKPADAPAK
	PVPVPQTPAK
151	PLITLKELSK VELPWFDVRF DFISYIALTE AKELHALPRL
	SNRCRYQIVG
201	CTMDDHFQIA EPIPGIRYQA FIVGIQAVSR NGLASQEELS
	AFNRQADAFA
251	QSMGGQTLHT DLAAFIEVAS ALDAFCARVD QTIAIHLVSP
	TSISGVELRS
301	AVTGVGFVLE DDGAFHYTDT SGSTMFSICS LNNEPFTNAL
	LDNQSYKGFS
351	MLLDIPHSPA GEKTFDDLFM DLAVRLSGQL NLNLVNDKME
	EVSTQWLKDV
401	RTYVLARQSE MLKVGIEPGG KTALRLFS*

ORF119ng and ORF119-1 show 98.4% identity over 428 aa overlap:

Based on this analysis, including the presence of a putative leader sequence in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 64

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 531>

1	..GCGCGGCACG GCACGGAAGA TTTCTTCATG AACAACAGCG
	ACAC.ATCAG
51	GCAGATAGTC GAAAGCACCA CCGGTACGAT GAAGCTGCTG
	ATTTCCTCCA
101	TCGCCCTGAT TTCATTGGTA GTCGGCGGCA TCGGCGTGAT
	GAACATCATG
151	CTGGTGTCCG TTACCGAGCG CACCAAAGAA ATCGGCATAC
	GGATGGCAAT
201	CGGCGCGCGG CGCGGCAATA TTTyGCAGCA GTTTTTGATT
	GAGGCGGTGT
251	TAATCTGCGT CATCGGCGGT TTGGTCGGCG TGGGTTTGTC
	CGCCGCCGTC
301	AGCCTCGTGT TCAATCATTT TGTAACCGAC TTCCCGATGG
	ACATTTCCGC
351	CATGTCCGTC ATCGGCGCGG TCGCCTGTTC GACCGGAATC
	GGCATCGCGT
401	TCGGCTTTAT GCCTGCCAAT AAAGCAGCCA AACTCAATCC
	GATAGACGCA
451	TTGGCACAGG ATTGA

This corresponds to the amino acid sequence <SEQ ID 532; ORF134>:

1	..ARHGTEDFFM NNSDXIRQIV ESTTGTMKLL ISSIALISLV
	VGGIGVMNIM
51	LVSVTERTKE IGIRMAIGAR RGNIXQQFLI EAVLICVIGG
	LVGVGLSAAV
101	SLVFNHFVTD FPMDISAMSV IGAVACSTGI GIAFGFMPAN
	KAAKLNPIDA
151	LAQD*

Further work revealed the complete nucleotide sequence <SEQ ID 533>:

1	ATGTCGGTGC AAGCAGTATT GGCGCACAAA ATGCGTTCGC
	TTCTGACGAT
51	GCTCGGCATC ATCATCGGTA TCGCGTCGGT GGTTTCCGTC
	GTCGCATTGG
101	GCAATGGTTC GCAGAAAAAA ATCCTTGAAG ACATCAGTTC
	GATAGGGACG
151	AACACCATCA GCATCTTCCC GGGGCGCGGC TTCGGCGACA
	GGCGCAGCGG
201	CAGGATTAAA ACCCTGACCA TAGACGACGC AAAAATCATC
	GCCAAACAAA
251	GCTACGTTGC TTCCGCCACG CCCATGACTT CGAGCGGCGG
	CACGCTGACT
301	TACCGCAACA CCGACCTGAC CGCCTCGCTT TACGGCGTGG
	GCGAACAATA
351	TTTCGACGTG CGCGGACTGA AGCTGGAAAC GGGGCGGCTG
	TTTGACGAAA
401	ACGATGTGAA AGAAGACGCG CAGGTCGTCG TCATCGACCA
	AAATGTCAAA
451	GACAAACTCT TTGCGGACTC GGATCCGTTG GGTAAAACCA
	TTTTGTTCAG
501	GAAACGCCCC TTGACCGTCA TCGGCGTGAT GAAAAAAGAC
	GAAAACGCTT
551	TCGGCAATTC CGACGTGCTG ATGCTTTGGT CGCCCTATAC
	GACGGTGATG
601	CACCAAATCA CAGGCGAGAG CCACACCAAC TCCATCACCG
	TCAAAATCAA
651	AGACAATGCC AATACCCAGG TTGCCGAAAA AGGGCTGACC
	GATCTGCTCA
701	AAGCGCGGCA CGGCACGGAA GATTTCTTCA TGAACAACAG
	CGACAGCATC
751	AGGCAGATAG TCGAAAGCAC CACCGGTACG ATGAAGCTGC
	TGATTTCCTC
801	CATCGCCCTG ATTTCATTGG TAGTCGGCGG CATCGGCGTG
	ATGAACATCA
851	TGCTGGTGTC CGTTACCGAG CGCACCAAAG AAATCGGCAT
	ACGGATGGCA
901	ATCGGCGCGC GGCGCGGCAA TATTTTGCAG CAGTTTTTGA
	TTGAGGCGGT
951	GTTAATCTGC GTCATCGGCG GTTTGGTCGG CGTGGGTTTG
	TCCGCCGCCG
1001	TCAGCCTCGT GTTCAATCAT TTTGTAACCG ACTTCCCGAT
	GGACATTTCC
1051	GCCATGTCCG TCATCGGCGC GGTCGCCTGT TCGACCGGAA
	TCGGCATCGC
1101	GTTCGGCTTT ATGCCTGCCA ATAAAGCAGC CAAACTCAAT
	CCGATAGACG
1151	CATTGGCACA GGATTGA

This corresponds to the amino acid sequence <SEQ ID 534; ORF134-1>:

1	MSVQAVLAHK MRSLLTMLGI IIGIASVVSV VALGNGSQKK
	ILEDISSIGT
51	NTISIFPGRG FGDRRSGRIK TLTIDDAKII AKQSYVASAT
	PMTSSGGTLT
101	YRNTDLTASL YGVGEQYFDV RGLKLETGRL FDENDVKEDA
	QVVVIDQNVK
151	DKLFADSDPL GKTILFRKRP LTVIGVMKKD ENAFGNSDVL
	MLWSPYTTVM
201	HQITGESHTN SITVKIKDNA NTQVAEKGLT DLLKARHGTE
	DFFMNNSDSI
251	RQIVESTTGT MKLLISSIAL ISLVVGGIGV MNIMLVSVTE
	RTKEIGIRMA
301	IGARRGNILQ QFLIEAVLIC VIGGLVGVGL SAAVSLVFNH
	FVTDFPMDIS
351	AMSVIGAVAC STGIGIAFGF MPANKAAKLN PIDALAQD*

Computer analysis of this amino acid sequence gave the following results:

Homology with the Hypothetical Protein o648 of E. coli (Accession Number AE000189)

ORF134 and o648 protein show 45% aa identity in 153aa overlap:

Orf134:   2 RHGTEDFFMNNSDXIRQIVESTTGTMKXXXXXXXXXXXVVGGIGVMNIMLVSVTERTKEI  61
RHG +DFFN   D + + VE TT T++            VVGGIGVMNIMLVSVTERT+EI
o648:   496 RHGKKDFFTWNMDGVLKTVEKTTRTLQLFLTLVAVISLVVGGIGVMNIMLVSVTERTREI 555
Orf134:  62 GIRMAIGARRGNIXQQFLIEAXXXXXXXXXXXXXXXXXXXXXFNHFVTDFPMDISAMSVI 121
GIRMA+GAR  ++ QQFLIEA                        F+ + +   S ++++
o648:   556 GIRMAVGARASDVLQQFLIEAVLVCLVGGALGITLSLLIAFTLQLFLPGWEIGFSPLALL 615
Orf134: 122 GAVACSTGIGIAFGFMPANKAAKLNPIDALAQD                            154
A  CST  GI FG++PA  AA+L+P+DALA++
o648:   616 LAFLCSTVTGILFGWLPARNAARLDPVDALARE                            648

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF134 shows 98.7% identity over a 154aa overlap with an ORF (ORF134a) from strain A of N. meningitidis:

The complete length ORF134a nucleotide sequence <SEQ ID 535> is:

1	ATGTCGGTGC AAGCAGTATT GGCGCACAAA ATGCGTTCGC
	TTCTGACGAT
51	GCTCGGCATC ATCATCGGTA TCGCTTCGGT TGTCTCCGTC
	GTCGCATTGG
101	GCAACGGTTC GCAGAAAAAA ATCCTTGAAG ACATCAGTTC
	GATAGGGACG
151	AACACCATCA GCATCTTCCC AGGGCGCGGC TTCGGCGACA
	GGCGCAGCGG
201	CAGGATTAAA ACCCTGACCA TAGACGACGC AAAAATCATC
	GCCAAACAAA
251	GCTACGTTGC TTCCGCCACG CCCATGACTT CGAGCGGCGG
	CACGCTGACT
301	TACCGCAATA CCGACCTGAC CGCTTCTTTG TACGGTGTGG
	GCGAACAATA
351	TTTCGACGTG CGCGGGCTGA AGCTGGAAAC GGGGCGGCTG
	TTTGACGAAA
401	ACGATGTGAA AGAAGACGCG CAGGTCGTCG TCATCGACCA
	AAATGTCAAA
451	GACAAACTCT TTGCGGACTC GGATCCGTTG GGTAAAACCA
	TTTTGTTCAG
501	GAAACGCCCC TTGACCGTCA TCGGCGTGAT GAAAAAAGAC
	GAAAACGCTT
551	TCGGCAATTC CGACGTGCTG ATGCTTTGGT CGCCCTATAC
	GACGGTGATG
601	CACCAAATCA CAGGCGAGAG CCACACCAAC TCCATCACCG
	TCAAAATCAA
651	AGACAATGCC AATACCCAGG TTGCCGAAAA AGGGCTGACC
	GATCTGCTCA
701	AAGCGCGGCA CGGCACGGAA GATTTCTTCA TGAACAACAG
	CGACAGCATC
751	AGGCAGATAG TCGAAAGCAC CACCGGTACG ATGAAGCTGC
	TGATTTCCTC
801	CATCGCCCTG ATTTCATTGG TAGTCGGCGG CATCGGCGTG
	ATGAACATCA
851	TGCTGGTGTC CGTTACCGAG CGCACCAAAG AAATCGGCAT
	ACGGATGGCA
901	ATCGGCGCGC GGCGCGGCAA TATTTTGCAG CAGTTTTTGA
	TTGAGGCGGT
951	GTTAATCTGC GTCATCGGCG GTTTGGTCGG CGTGGGTTTG
	TCCGCCGCCG
1001	TCAGCCTCGT GTTCAATCAT TTTGTAACCG ACTTCCCGAT
	GGACATTTCC
1051	GCCATGTCCG TCATCGGCGC GGTCGCCTGT TCGACCGGAA
	TCGGCATCGC
1101	GTTCGGCTTT ATGCCTGCCA ATAAAGCAGC CAAACTCAAT
	CCGATAGATG
1151	CATTGGCGCA GGATTGA

This encodes a protein having amino acid sequence <SEQ ID 536>:

1	MSVQAVLAHK MRSLLTMLGI IIGIASVVSV VALGNGSQKK
	ILEDISSIGT
51	NTISIFPGRG FGDRRSGRIK TLTIDDAKII AKQSYVASAT
	PMTSSGGTLT
101	YRNTDLTASL YGVGEQYFDV RGLKLETGRL FDENDVKEDA
	QVVVIDQNVK
151	DKLFADSDPL GKTILFRKRP LTVIGVMKKD ENAFGNSDVL
	MLWSPYTTVM
201	HQITGESHTN SITVKIKDNA NTQVAEKGLT DLLKARHGTE
	DFFMNNSDSI
251	RQIVESTTGT MKLLISSIAL ISLVVGGIGV MNIMLVSVTE
	RTKEIGIRMA
301	IGARRGNILQ QFLIEAVLIC VIGGLVGVGL SAAVSLVFNH
	FVTDFPMDIS
351	AMSVIGAVAC STGIGIAFGF MPANKAAKLN PIDALAQD*

ORF134a and ORF134-1 show 100.0% identity in 388 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF134 shows 96.8% identity over a 154aa overlap with a predicted ORF (ORF 134.ng) from N. gonorrhoeae:

The complete length ORF134ng nucleotide sequence <SEQ ID 537> is:

1	ATGTCGGTGC AAGCAGTATT GGCGCACAAA ATGCGTTCGC
	TTCTGACCAT
51	GCTCGGCATC ATCATCGGTA TCGCTTCGGT TGTCTCCGTC
	GTCGCGCTGG
101	GCAACGGTTC GCAGAAAAAA ATCCTCGAAG ACATCAGTTC
	GATGGGGACG
151	AACACCATCA GCATCTTCCC CGGGCGCGGC TTCGGCGACA
	GGCGCAGCGG
201	CAAAATCAAA ACCCTGACCA TAGACGACGC AAAAATCATC
	GCCAAACAAA
251	GCTACGTTGC CTCCGCCACG CCCATGACTT CGAGCGGCGG
	CACGCTGACC
301	TACCGCAATA CCGACCTGAC CGCTTCTTTG TACGGTGTGG
	GCGAACAATA
351	TTTCGACGTG CGCGGGCTGA AGCTGGAAAC GGGGCGGCTG
	TTTGATGAGA
401	ACGATGTGAA AGAAGACGCG CAAGTCGTCG TCATCGACCA
	AAATGTCAAA
451	GACAAACTCT TTGCGGACTC GGATCCGTTG GGTAAAACCA
	TTTTGTTCAG
501	GAAACGCCCC TTGACCGTCA TCGGCGTGAT GAAAAAAGAC
	GAAAACGCTT
551	TCGGCAATTC CGACGTGCTG ATGCTTTGGT CGCCCTATAC
	GACGGTGATG
601	CACCAAATCA CAGGCGAGAG CCACACCAAC TCCATCACCG
	TCAAAATCAA
651	AGACAATGCC AATACCCGGG TTGCCGAAAA AGGGCTGGCC
	GAGCTGCTCA
701	AAGCACGGCA CGGCACGGAA GACTTCTTTA TGAACAACAG
	CGACAGCATC
751	AGGCAGATGG TCGAAAGCAC CACCGGTACG ATGAAGCTGC
	TGATTTCCTC
801	CATCGCCCTG ATTTCATTGG TAGTCGGCGG CATCGGTGTG
	ATGAACATTA
851	TGCTGGTGTC CGTTACCGAG CGCACCAAAG AAATCGGCAT
	ACGGATGGCA
901	ATCGGCGCGC GGCGCGGCAA TATTTTGCAG CAGTTTTTGA
	TTGAGGCGGT
951	GTTAATCTGC ATCATCGGAG GCTTGGTCGG CGTAGGTTTG
	TCCGCCGCCG
1001	TCAGCCTCGT GTTCAATCAT TTTGTAACCG ATTTCCCGAT
	GGACATTTCG
1051	GCGGCATCCG TTATCGGGGC GGTCGCCTGT TCGACCGGAA
	TCGGCATCGC
1101	GTTCGGCTTT ATGCCTGCCA ATAAGGCAGC CAAACTCAAT
	CCGATAGATG
1151	CATTGGCGCA GGATTGA

This encodes a protein having amino acid sequence <SEQ ID 538>:

1	MSVQAVLAHK MRSLLTMLGI IIGIASVVSV VALGNGSQKK
	ILEDISSMGT
51	NTISIFPGRG FGDRRSGKIK TLTIDDAKII AKQSYVASAT
	PMTSSGGTLT
101	YRNTDLTASL YGVGEQYFDV RGLKLETGRL FDENDVKEDA
	QVVVIDQNVK
151	DKLFADSDPL GKTILFRKRP LTVIGVMKKD ENAFGNSDVL
	MLWSPYTTVM
201	HQITGESHTN SITVKIKDNA NTRVAEKGLA ELLKARHGTE
	DFFMNNSDSI
251	RQMVESTTGT MKLLISSIAL ISLVVGGIGV MNIMLVSVTE
	RTKEIGIRMA
301	IGARRGNILQ QFLIEAVLIC IIGGLVGVGL SAAVSLVFNH
	FVTDFPMDIS
351	AASVIGAVAC STGIGIAFGF MPANKAAKLN PIDALAQD*

ORF134ng and ORF134-1 show 97.9% identity in 388 aa overlap:

ORF134ng also shows homology to an E. coli ABC transporter:

sp|P75831|YBJZ_ECOLI HYPOTHETICAL ABC TRANSPORTER ATP-BINDING
PROTEIN YBJZ >gi5 (AE000189) o648; similar to YBBA_HAEIN SW: P45247
[Escherichia coli] Length = 648
Score = 297 bits (753), Expect = 6e−80
Identities = 162/389 (41%), Positives = 230/389 (58%), Gaps = 1/389 (0%)

Query:	1	MSVQAVLAHKMRSLLTMLXXXXXXXXXXXXXXLGNGSQKKILEDISSMGTNTISIFPGRG	60
		M+ +A+ A+KMR+LLTML              +G+ +++ +L DI S+GTNTI ++PG+
Sbjct:	260	MAWRALAANKMRTLLTMLGIIIGIASVVSIVVVGDAAKQMVLADIRSIGTNTIDVYPGKD	319
Query:	61	FGDRRSGKIKTLTIDDAKIIAKQSYVASATPMTSSGGTLTYRNTDLTASLYGVGEQYFDV	120
		FGD      + L  DD   I KQ +VASATP  S    L Y N D+ AS  GV   YF+V
Sbjct:	320	FGDDDPQYQQALKYDDLIAIQKQPWVASATPAVSQNLRLRYNNVDVAASANGVSGDYFNV	379
Query:	121	RGLKLETGRLFDENDVKEDAQVVVIDQNVKDKLFAD-SDPLGKTILFRKRPLTVIGVMKK	179
		G+    G  F++  +   AQVVV+D N + +LF   +D +G+ IL    P  VIGV ++
Sbjct:	380	YGMTFSEGNTFNQEQLNGRAQVVVLDSNTRRQLFPHKADVVGEVILVGNMPARVIGVAEE	439
Query:	180	DENAFGNSDVLMLWSPYTTVMHQITGESHTNSITVKIKDNANTRVAEKGLAELLKARHGT	239
		++ FG+S VL +W PY+T+  ++ G+S  NSITV++K+  ++  AE+ L  LL  REG
Sbjct:	440	KQSMFGSSKVLRVWLPYSTMSGRVMGQSWLNSITVRVKEGFDSAEAEQQLTRLLSLRHGK	499
Query:	240	EDFFMNNSDSIRQMVESTTGTMKXXXXXXXXXXXVVGGIGVMNIMLVSVTERTKEIGIRM	299
		+DFF  N D + + VE TT T++           VVGGIGVMNIMLVSVTERT+EIGIRM
Sbjct:	500	KDFFTWNMDGVLKTVEKTTRTLQLFLTLVAVISLVVGGIGVMNIMLVSVTERTREIGIRM	559
Query:	300	AIGARRGNILQQFLIEXXXXXXXXXXXXXXXXXXXXXXFNHFVTDFPMDISAASVIGAVA	359
		A+GAR  ++LQQFLIE                         F+  + +  S  +++ A
Sbjct:	560	AVGARASDVLQQFLIEAVLVCLVGGALGITLSLLIAFTLQLFLPGWEIGFSPLALLLAFL	619
Query:	360	CSTGIGIAFGFMPANKAAKLNPIDALAQD	388
		CST  GI FG++PA  AA+L+P+DALA++
Sbjct:	620	CSTVTGILFGWLPARNAARLDPVDALARE	648

Based on this analysis, including the presence of the leader peptide and transmembrane regions in the gonococcal protein, it is prediceted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 65

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 539>:

1	..GGGACGGGAG CGATGCTGCT GCTGTTTTAC GCGGTAACGA
	T.CTGCCTTT
51	GGCCACTGGC GTTACCCTGA GTTACACCTC GTCGATTTTT
	TTGGCGGTAT
101	TTTCCTTCCT GATTTTGAAA GAACGGATTT CCGTTTACAC
	GCAGGCGGTG
151	CTGCTCCTTG GTTTTGCCGG CGTGGTATTG CTGCTTAATC
	CCTCGTTCCG
201	CAGCGGTCAG GAAACGGCGG CACTCGCCGG GCTGGCGGGC
	GGCGCGATGT
251	CCGGCTGGGC GTATTTGAAA GTGCGCGAAC TGTCTTTGGC
	GGGCGAACCC
301	GGCTGGCGCG TCGTGTTTTA CCTTTCCGTG ACAGGTGTGG
	CGATGTCGTC
351	GGTTTGGGCG ACGCTGACCG GCTGGCACAC CCTGTCCTTT
	CCATCGGCAG
401	TTTATCTGTC GTGCATCGGC GTGTCCGCGC TGATTGCCCA
	ACTGTCGATG
451	ACGCGCGCCT ACAAAGTCGG CGACAAATTC ACGGTTGCCT
	CGCTTTCCTA
501	TATGACCGTC GTTTTTTCCG CTCTGTCTGC CGCATTTTTT
	CTGGGCGAAG
551	AGCTTTTCTG GCAGGAAATA CTCGGTATGT GCATCATCAT
	CCTCAGCGGT
601	ATTTTGA

This corresponds to the amino acid sequence <SEQ ID 540; ORF135>:

1	..GTGAMLLLFY AVTILPLATG VTLSYTSSIF LAVFSFLILK
	ERISVYTQAV
51	LLLGFAGVVL LLNPSFRSGQ ETAALAGLAG GAMSGWAYLK
	VRELSLAGEP
101	GWRVVFYLSV TGVAMSSVWA TLTGWHTLSF PSAVYLSCIG
	VSALIAQLSM
151	TRAYKVGDKF TVASLSYMTV VFSALSAAFF LGEELFWQEI
	LGMCIIISAV
201	F*

Further work revealed the complete nucleotide sequence <SEQ ID 541>:

1	ATGGATACCG CAAAAAAAGA CATTTTAGGA TCGGGCTGGA
	TGCTGGTGGC
51	GGCGGCCTGC TTTACCATTA TGAACGTATT GATTAAAGAG
	GCATCGGCAA
101	AATTTGCCCT CGGCAGCGGC GAATTGGTCT TTTGGCGCAT
	GCTGTTTTCA
151	ACCGTTGCGC TCGGGGCTGC CGCCGTATTG CGTCGGGACA
	mCTTCCGCAC
201	GCCCCATTGG AAAAACCACT TAAACCGCAG TATGGTCGGG
	ACGGGGGCGA
251	TGCTGCTGCT GTTTTACGCG GTAACGCATC TGCCTTTGGC
	CACTGGCGTT
301	ACCCTGAGTT ACACCTCGTC GATTTTTTTG GCGGTATTTT
	CCTTCCTGAT
351	TTTGAAAGAA CGGATTTCCG TTTACACGCA GGCGGTGCTG
	CTCCTTGGTT
401	TTGCCGGCGT GGTATTGCTG CTTAATCCCT CGTTCCGCAG
	CGGTCAGGAA
451	ACGGCGGCAC TCGCCGGGCT GGCGGGCGGC GCGATGTCCG
	GCTGGGCGTA
501	TTTGAAAGTG CGCGAACTGT CTTTGGCGGG CGAACCCGGC
	TGGCGCGTCG
551	TGTTTTACCT TTCCGTGACA GGTGTGGCGA TGTCGTCGGT
	TTGGGCGACG
601	CTGACCGGCT GGCACACCCT GTCCTTTCCA TCGGCAGTTT
	ATCTGTCGTG
651	CATCGGCGTG TCCGCGCTGA TTGCCCAACT GTCGATGACG
	CGCGCCTACA
701	AAGTCGGCGA CAAATTCACG GTTGCCTCGC TTTCCTATAT
	GACCGTCGTT
751	TTTTCCGCTC TGTCTGCCGC ATTTTTTCTG GGCGAAGAGC
	TTTTCTGGCA
801	GGAAATACTC GGTATGTGCA TCATCATCCT CAGCGGTATT
	TTGAGCAGCA
851	TCCGCCCCAC TGCCTTCAAA CAGCGGCTGC AATCCCTGTT
	CCGCCAAAGA
901	TAA

This corresponds to the amino acid sequence <SEQ ID 542; ORF135-1>:

1	MDTAKKDILG SGWMLVAAAC FTIMNVLIKE ASAKFALGSG
	ELVFWRMLFS
51	TVALGAAAVL RRDXFRTPHW KNHLNRSMVG TGAMLLLFYA
	VTHLPLATGV
101	TLSYTSSIFL AVFSFLILKE RISVYTQAVL LLGFAGVVLL
	LNPSFRSGQE
151	TAALAGLAGG AMSGWAYLKV RELSLAGEPG WRVVFYLSVT
	GVAMSSVWAT
201	LTGWHTLSFP SAVYLSCIGV SALIAQLSMT RAYKVGDKFT
	VASLSYMTVV
251	FSALSAAFFL GEELFWQEIL GMCIIILSGI LSSIRPTAFK
	QRLQSLFRQR
301	*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF135 shows 99.0% identity over a 197aa overlap with an ORF (ORF135a) from strain A of N. meningitidis:

The complete length ORF135a nucleotide sequence <SEQ ID 543> is:

1	ATGGATACCG CAAAAAAAGA CATTTTAGGA TCGGGCTGGA
	TGCTGGTGGC
51	GGCGGCCTGC TTTACCATTA TGAACGTATT GATTAAAGAG
	GCATCGGCAA
101	AATTTGCCCT CGGCAGCGGC GAATTGGTCT TTTGGCGCAT
	GCTGTTTTCA
151	ACCGTTGCGC TCGGGGCTGC CGCCGTATTG CGTCGGGACA
	CCTTCCGCAC
201	GCCCCATTGG AAAAACCACT TAAACCGCAG TATGGTCGGG
	ACGGGGGCGA
251	TGCTGCTGCT GTTTTACGCG GTAACGCATC TGCCTTTGGC
	CACCGGCGTT
301	ACCCTGAGTT ACACCTCGTC GATTTTTTTG GCGGTATTTT
	CCTTCCTGAT
351	TTTGAAAGAA CGGATTTCCG TTTACACGCA GGCGGTGCTG
	CTCCTTGGTT
401	TTGCCGGCGT GGTATTGCTG CTTAATCCCT CGTTCCGCAG
	CGGTCAGGAA
451	ACGGCGGCAC TCGCCGGGCT GGCGGGCGGC GCGATGTCCG
	GCTGGGCGTA
501	TTTGAAAGTG CGCGAACTGT CTTTGGCGGG CGAACCCGGC
	TGGCGCGTCG
551	TGTTTTACCT TTCCGTGACA GGTGTGGCGA TGTCATCGGT
	TTGGGCGACG
601	CTGACCGGCT GGCACACCCT GTCCTTTCCA TCGGCAGTTT
	ATCTGTCGTG
651	CATCGGCGTG TCCGCGCTGA TTGCCCAACT GTCGATGACG
	CGCGCCTACA
701	AAGTCGGCGA CAAATTCACG GTTGCCTCGC TTTCCTATAT
	GACCGTCGTT
751	TTTTCCGCTC TGTCTGCCGC ATTTTTTCTG GCCGAAGAGC
	TTTTCTGGCA
801	GGAAATACTC GGTATGTGCA TCATCATCCT CAGCGGTATT
	TTGAGCAGCA
851	TCCGCCCCAC TGCCTTCAAA CAGCGGCTGC AATCCCTGTT
	CCGCCAAAGA
901	TAA

This encodes a protein having amino acid sequence <SEQ ID 544>:

1	MDTAKKDILG SGWMLVAAAC FTIMNVLIKE ASAKFALGSG
	ELVFWRMLFS
51	TVALGAAAVL RRDTFRTPHW KNHLNRSMVG TGAMLLLFYA
	VTHLPLATGV
101	TLSYTSSIFL AVFSFLILKE RISVYTQAVL LLGFAGVVLL
	LNPSFRSGQE
151	TAALAGLAGG AMSGWAYLKV RELSLAGEPG WRVVFYLSVT
	GVAMSSVWAT
201	LTGWHTLSFP SAVYLSCIGV SALIAQLSMT RAYKVGDKFT
	VASLSYMTVV
251	FSALSAAFFL AEELFWQEIL GMCIIILSGI LSSIRPTAFK
	QRLQSLFRQR
301	*

ORF135a and ORF135-1 show 99.3% identity in 300 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF135 shows 97% identity over a 201aa overlap with a predicted ORF (ORF135ng) from N. gonorrhoeae:

An ORF135ng nucleotide sequence <SEQ ID 545> was predicted to encode a protein having amino acid sequence <SEQ ID 546>:

1	MPSEKAFRRH LRTASFQGLH LHHFHQKVGK CGIIGFGIHI
	FPTLLPAAQG
51	ILDIQLGLFR IDFAALAVYR RTQVDFIHTV IDGIASDQAF
	SEVVQILRRL
101	NLGHFTDTHL IAQARRFIAD FGNIRPMRRG EAKTFCRCFR
	FDGIDGIHGD
151	FRQCGHINRL APGKDCRNGK RDKVFFHTRH YNQVCLEKTN
	CSARKIKFRH
201	QKQAKTHSTS LAARFTIRPS LSQRPFMDTA KKDILGSGWM
	LVAAACFTVM
251	NVLIKEASAK FALGSGELVF WRMLFSTVTL GAAAVLRRDT
	FRTPHWKNHL
301	NRSMVGTGAM LLLFYAVTHL PLTTGVTLSY TSSIFLAVFS
	FLILKERISV
351	YTQAVLLLGF AGVVLLLNPS FRSGQEPAAL AGLAGGAMSG
	WAYLKVRELS
401	LAGEPGWRVV FYLSATGVAM SSVWATLTGW HTLSFPSAVY
	LSGIGVSALI
451	AQLSMTRAYK VGDKFTVASL SYMTVVFSAL SAAFFLGEEL
	FWQEILGMCI
501	IISAAF*

Further work revealed the following gonococcal sequence <SEQ ID 547>:

1	ATGGATACCG CAAAAAAAGA CATTTTAGGA TCGGGCTGGA
	TGCTGGTGGC
51	GGCGGCCTGC TTCACCGTTA TGAACGTATT GATTAAAGAG
	GCATCGGCAA
101	AATTTGCCCT CGGCAGCGGC GAATTGGTCT TTTGGCGCAT
	GCTGTTTTCA
151	ACCGTTACGC TCGGTGCTGC CGCCGTATTG CGGCGCGACA
	CCTTCCGCAC
201	GCCCCATTGG AAAAACCACT TAAACCGCAG TATGGTCGGG
	ACGGGGGCGA
251	TGCTGCTGCT GTTTTACGCG GTAACGCATC TGCCTTTGAC
	AACCGGCGTT
301	ACCCTGAGTT ACACCTCGTC GATTTTTttg GCGGTATTTT
	CCTTCCTCAT
351	TTTGAAAGAA CGGATTTCCG TTTACACGCA GGCGGTGCTG
	CTCCTTGGTT
401	TTGCCGGCGT GGTATTGCTG CTTAATCCCT CGTTCCGCAG
	CGGTCAGGAA
451	CCGGCGGCAC TCGCCGGGCT GGCGGGCGGC GCGATGTCCG
	GCTGGGCGTA
501	TTTGAAAGTG CGCGAACTGT CTTTGGCGGG CGAACCCGGC
	TGGCGCGTCG
551	TGTTTTACCT TTCCGCAACC GGCGTGGCGA TGTCGTCggt
	ttgggcgacg
601	Ctgaccggct ggCACAcccT GTCCTTTcca tcggcagttt
	ATCtgtCGGG
651	CATCGGCGTG tccgcgCtgA TTGCCCAaCT GtcgatgAcg
	cGCGcctaca
701	aaGTCGGCGA CAAATTCACG GTTGCCTCGC tttcctaTAt
	gaccgtcGTC
751	TTTTCCGCCC TGTCTGCCGC ATTTTTTCTg ggcgaagagc
	tttTCtggCA
801	GGAAATACTC GGTATGTGCA TCATTAtccT CAGCGGCATT
	TTGAGCAGCA
851	TCCGCCCCAT TGCCTTCAAA CAGCGGCTGC AAGCCCTCTT
	CCGCCAAAGA
901	TAA

This corresponds to the amino acid sequence <SEQ ID 548; ORF135ng-1>:

1	MDTAKKDILG SGWMLVAAAC FTVMNVLIKE ASAKFALGSG
	ELVFWRMLFS
51	TVTLGAAAVL RRDTFRTPHW KNHLNRSMVG TGAMLLLFYA
	VTHLPLTTGV
101	TLSYTSSIFL AVFSFLILKE RISVYTQAVL LLGFAGVVLL
	LNPSFRSGQE
151	PAALAGLAGG AMSGWAYLKV RELSLAGEPG WRVVFYLSAT
	GVAMSSVWAT
201	LTGWHTLSFP SAVYLSGIGV SALIAQLSMT RAYKVGDKFT
	VASLSYMTVV
251	FSALSAAFFL GEELFWQEIL GMCIIILSGI LSSIRPIAFK
	QRLQALFRQR
301	*

ORF135ng-1 and ORF135-1 show 97.0% identity in 300 aa overlap:

Based on this analysis, including the presence of several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 66

The following DNA sequence was identified in N. meningitidis <SEQ ID 549>:

1	ATGAAGCGGC GTATAGCCGT CTTCGTCCTG TTCCCGCAGA
	TAATCCGAGT
51	TTTGGGACAA CTGTTGCCGA AAATCGTCAA TACAGTTCCG
	GCACATCGGA
101	TGCTCTTCCA GATTTTCGGG ATGTTCTTTT TCTTCATACA
	CCAGCAATAT
151	CTGCCCGGGA TCGCCGAAAT CGATTCCCCA TGCGGCATCG
	TGTTCGGTGC
201	GCTCCTCTTC CGTCATCTGC CCGCGCATTG CCTGTATGGT
	AAAGCCGCCG
251	TAGGGGATGC CgTTGCACAC GAACATCCAG TCGCTGATGT
	CGTCAACCGG
301	AACGCAAACG cTTTCGCCTT GTTCGACATT GGTCAGTTCG
	CCsGGTTCAT
351	TGTTCAGCAC ACCGTAAATA TAAAGACCGT CAAAATAAAT
	ATCGTCGATC
401	CACATATGTT CGCAAATTTC GCCGTCTTCG CCGTCTTGGA
	AAAAAGGGAC
451	TTTGACCATG GCAAAATCCA AGGCGGAAAT AATGCGGCGG
	CGTTCCCAAA
501	AAAGcTCGCG CCAAAAATAT TTGAATGTTT TACGGGCGCG
	TTCGTCGGCA
551	CGGTTTACCG GTTCGTCTGC CTGTTCTACA TAATAAATGA
	CGGAATCGCC
601	CATCATATCT GCTCCTCAAC GTGTACGGTA TCTGTTTGCA
	CCTTACTGCG
651	GCTTTCTgcC kTCGGCATCC GATTCGGATT TGAAAAGTTC
	mmrwyATTCG
701	GAATAG

This corresponds to the amino acid sequence <SEQ ID 550; ORF136>:

1	MKRRIAVFVL FPQIIRVLGQ LLPKIVNTVP AHRMLFQIFG
	MFFFFIHQQY
51	LPGIAEIDSP CGIVFGALLF RHLPAHCLYG KAAVGDAVAH
	EHPVADVVNR
101	NANAFALFDI GQFAXFIVQH TVNIKTVKIN IVDPHMFANF
	AVFAVLEKRD
151	FDHGKIQGGN NAAAFPKKLA PKIFECFTGA FVGTVYRFVC
	LFYIINDGIA
201	HHSAPQRVRY LFAPYCGFLP SASDSDLKSS XXSE*

Further work revealed the complete nucleotide sequence <SEQ ID 551>:

1	ATGATGAAGC GGCGTATAGC CGTCTTCGTC CTGTTCCCGC
	AGATAATCCG
51	AGTTTTGGGA CAACTGTTGC CGAAAATCGT CAATACAGTT
	CCGGCACATC
101	GGATGCTCTT CCAGATTTTC GGGATGTTCT TTTTCTTCAT
	ACACCAGCAA
151	TATCTGCCCG GGATCGCCGA AATCGATTCC CCATGCGGCA
	TCGTGTTCGG
201	TGCGCTCCTC TTCCGTCATC TGCCCGCGCA TTGCCTGTAT
	GGTAAAGCCG
251	CCGTAGGGGA TGCCGTTGCA CACGAACATC CAGTCGCTGA
	TGTCGTCAAC
301	CGGAACGCAA ACGCTTTCGC CTTGTTCGAC ATTGGTCAGT
	TCGCCGGGTT
351	CATTGTTCAG CACACCGTAA ATATAAAGAC CGTCAAAATA
	AATATCGTCG
401	ATCCACATAT GTTCGCAAAT TTCGCCGTCT TCGCCGTCTT
	GGAAAAAAGG
451	GACTTTGACC ATGGCAAAAT CCAAGGCGGA AATAATGCGG
	CGGCGTTCCC
501	AAAAAAGCTC GCGCCAAAAA TATTTGAATG TTTTACGGGC
	GCGTTCGTCG
551	GCACGGTTTA CCGGTTCGTC TGCCTGTTCT ACATAATAAA
	TGACGGAATC
601	GCCCATCATT CTGCTCCTCA ACGTGTACGG TATCTGTTTG
	CACCTTACTG
651	CGGCTTTCTG CCTTCGGCAT CCGATTCGGA TTTGAAAAGT
	TCCAAATATT
701	CGGAATAG

This corresponds to the amino acid sequence <SEQ ID 552; ORF136-1>:

1	MMKRRIAVFV LFPQIIRVLG QLLPKIVNTV PAHRMLFQIF
	GMFFFFIHQQ
51	YLPGIAEIDS PCGIVFGALL FRHLPAHCLY GKAAVGDAVA
	HEHPVADVVN
101	RNANAFALFD IGQFAGFIVQ HTVNIKTVKI NIVDPHMFAN
	FAVFAVLEKR
151	DFDHGKIQGG NNAAAFPKKL APKIFECFTG AFVGTVYRFV
	CLFYIINDGI
201	AHHSAPQRVR YLFAPYCGFL PSASDSDLKS SKYSE*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF136 shows 71.7% identity over. a 237aa overlap with an ORF (ORF136a) from strain A of N. meningitidis:

The complete length ORF136a nucleotide sequence <SEQ ID 553> is:

1	ATGATGAAGC GGCGTATAGC CGTCTTCGTC CTGCTCATGC
	AGAAAATCCG
51	GATTTTGGGA CAACTGTTGC CGAAAATCGT CAATACAGTT
	CCGGCACATC
101	GGATGCTCTT CCAGATNTTC GGGATGTTCT TTTTCTTCAT
	ACACCAGCAA
151	TACCTGCCCG GGATCGCCGA AATCGATTCC CCATGCGGCA
	TCGTGTTCGG
201	TACGCTCCTC TTCCGTCATC NGTCCACGCA TTGCCTGTAT
	GGTAAAGCCG
251	CCGTAGGGAA TGCCGTTGCA CACGAACATC CAGTCGCTGA
	TGTCGTCAAC
301	CGGAACGCAA ACGCTTTCGC CTTGTTCGAC ATTGGTCAGT
	TCGCCGGGTT
351	CATTGTTCAG CACGCCATAA ATGTAAAGAC CGTCAAAATA
	AATATCGTCG
401	ATCCACATAT GTTCGCAAAT TTCGCCNTCT TCGCCGTCTT
	GGAAAAAAGG
451	GCTTTGACCA TGGCAAAATC TAAGGNGNNA NNGATGCGGC
	GGCGTTCCCA
501	AAAAAGCTCG CGCCAAAAAT ATTTGAATGT TTTGCGGGCG
	CGTTCGCCGG
551	CACGGTTTAC CGGTTTGTCT GCCTGTTCTA CATAATAAAT
	GACGGAATCG
601	CCCATCATAT CTGCTCCTCA ACGTGTACGG TATCTGTTTG
	CACCTTACTG
651	CGGCTTTCTG CCTTCGGCAT CCGATTCGGA TTTGAAAAGT
	TCCAAATATT
701	CGGAATAG

This encodes a protein having amino acid sequence <SEQ ID 554>:

1	MMKRRIAVFV LLMQKIRILG QLLPKIVNTV PAHRMLFQXF
	GMFFFFIHQQ
51	YLPGIAEIDS PCGIVFGTLL FRHXSTHCLY GKAAVGNAVA
	HEHPVADVVN
101	RNANAFALFD IGQFAGFIVQ HAINVKTVKI NIVDPHMFAN
	FAXFAVLEKR
151	ALTMAKSKXX XMRRRSQKSS RQKYLNVLRA RSPARFTGLS
	ACST**MTES
201	PIISAPQRVR YLFAPYCGFL PSASDSDLKS SKYSE*

ORF136a and ORF136-1 show 73.1% identity in 238 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF136 shows 92.3% identity over a 234aa overlap with a predicted ORF (ORF136ng) from N. gonorrhoeae:

The complete length ORF136ng nucleotide sequence <SEQ ID 555> is:

1	ATGATGAAGC GGCGTATAGC CGTCTTCGTC CTGCTCATGC
	AGAAAATCCG
51	GATTTTGGGA CAACTGTTGC CGAAAATCGT CAATACAGTT
	CCGGCACATC
101	GGATGCTCTT CCAAATTTTC GGGATGTTCT TTTTCTTCAT
	ACACCGGCAA
151	TACCTGCCCG GGATCGCCGA AATCGATTCC CCAGGCGGTA
	TCGTGTTCGG
201	TACGCTCCTC TTCCGTCATC TGTCCGCGCA TTGCCTGTAC
	GGTAAAGCCG
251	CCGTAGGGGA TGCCGTTGCA CACGAACATC CAGTCGCTGA
	TGTCGCCAAC
301	CGGAACGCAA ACGCTTTCGC CTTGTTCGAC ATTGGTCAGT
	CCGCCGGGTT
351	CATTGTTCAG CACACCGTAA ATATAAAGAC CGTCAAAATA
	AATATCGTCG
401	ATCCACATAT GTTCGCAAAT TTCGCCGTCT TCGCCGTCTT
	GGAAAAAAGG
451	GACTTTGACC ATGGCAAAAT CCAAGGCGGA AATAATGCGG
	CGGCGTTCCC
501	AAAAAAGCTC GCGCCAAAAG TATTTGAATG TTTTACGGGC
	GCGTTCGCCG
551	GCACGGTTTA CCGGTTCGTC TGCCTGTTCT ACATAATAAA
	TGACGGAATC
601	GCCCATCATA CTGCTCCTCA ACGTGTACGG TATCTGTTTG
	CACCTTACCG
651	CGGTTTTCTA CCTCCGGCAT CCGATTCGGA TTTGAAAAGT
	TCCAAATATT
701	CGGAATAG

This encodes a protein having amino acid sequence <SEQ ID 556>:

1	MMKRRIAVFV LLMQKIRILG QLLPKIVNTV PAHRMLFQIF
	GMFFFFIHRQ
51	YLPGIAEIDS PGGIVFGTLL FRHLSAHCLY GKAAVGDAVA
	HEHPVADVAN
101	RNANAFALFD IGQSAGFIVQ HTVNIKTVKI NIVDPHMFAN
	FAVFAVLEKR
151	DFDHGKIQGG NNAAAFPKKL APKVFECFTG AFAGTVYRFV
	CLFYIINDGI
201	AHHTAPQRVR YLFAPYRGFL PPASDSDLKS SKYSE*

ORF136ng and ORF136-1 show 93.6% identity in 235 aa overlap:

Based on the presence of the putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 67

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 557>:

1	ATGGAAAATA TGGTAACGTT TTCAAAAATC AGACCGCTTT
	TGGCAATCGC
51	CGCCGCCGCG TTGCTTGCCG CC.TGCGGAC GGCGGGAAAT
	AATGCTGTCC
101	GCAAGCCGGT GCAAACCGCC AAACCCGCCG CAGTGGTCGG
	TTTGGCACTC
151	GGTGGCGGCG CATCTAAAGG ATTTGCCCAT GTAGGTATTA
	TTAAGGTTTT
201	GAAAGAAAAC GGTATTCCTG TGAAGGTGGT TACCGGCACC
	TCCGCAGGTT
251	CGATTGTCGG CAACCTTTTT GCATCGGGTA TGTCGCCCGA
	CCGCCTCGAA
301	TTGGAAGCCG AAATTTTAGG CAAAACCGAT TTGGTCGATT
	TAACCTTGTC
351	CACCAATGGG TTTATCAAAG GCGCAAAGCT GCAAAATTAC
	ATCAACCGAA
401	AACTCCGCGG CATGCAGATT CAGCAGTTTC CCATCAAATT
	TGCCGCC..

This corresponds to the amino acid sequence <SEQ ID 558; ORF137>:

1	MENMVTFSKI RPLLAIAAAA LLAAXRTAGN NAVRKPVQTA
	KPAAVVGLAL
51	GGGASKGFAH VGIIKVLKEN GIPVKVVTGT SAGSIVGNLF
	ASGMSPDRLE
101	LEAEILGKTD LVDLTLSTNG FIKGAKLQNY INRKLRGMQI
	QQFPIKFAA..

Further work revealed the complete nucleotide sequence <SEQ ID 559>:

1	ATGGAAAATA TGGTAACGTT TTCAAAAATC AGACCGCTTT
	TGGCAATCGC
51	CGCCGCCGCG TTGCTTGCCG CCTGCGGCAC GGCGGGAAAT
	AATGCTGTCC
101	GCAAGCCGGT GCAAACCGCC AAACCCGCCG CAGTGGTCGG
	TTTGGCACTC
151	GGTGGCGGCG CATCTAAAGG ATTTGCCCAT GTAGGTATTA
	TTAAGGTTTT
201	GAAAGAAAAC GGTATTCCTG TGAAGGTGGT TACCGGCACA
	TCGGCAGGTT
251	CGATTGTCGG CAGCCTTTTT GCATCGGGTA TGTCGCCCGA
	CCGCCTCGAA
301	TTGGAAGCCG AAATTTTAGG CAAAACCGAT TTGGTCGATT
	TAACCTTGTC
351	CACCAGTGGT TTTATCAAAG GCGAAAAGCT GCAAAATTAC
	ATCAACCGAA
401	AAGTCGGCGG CAGGCAGATT CAGCAGTTTC CCATCAAATT
	TGCCGCCGTT
451	GCTACTGATT TTGAAACCGG CAAGGCCGTC GCTTTCAATC
	AGGGGAATGC
501	CGGGCAGGCT GTGCGCGCTT CCGCCGCCAT TCCCAATGTG
	TTCCAACCCG
551	TTATCATCGG CAGGCATACA TATGTTGACG GCGGTCTGTC
	GCAGCCCGTG
601	CCCGTCAGTG CCGCCCGGCG GCAGGGGGCG AATTTCGTGA
	TTGCCGTCGA
651	TATTTCCGCC CGTCCGGGCA AAAACATCAG CCAAGGTTTC
	TTCTCTTATC
701	TCGATCAGAC GCTGAACGTA ATGAGCGTTT CTGCGTTGCA
	AAATGAGTTG
751	GGGCAGGCGG ATGTGGTTAT CAAACCGCAG GTTTTGGATT
	TGGGTGCAGT
801	CGGCGGATTC GATCAGAAAA AACGCGCCAT CCGGTTGGGT
	GAGGAGGCAG
851	CACGTGCCGC ATTGCCTGAA ATCAAACGCA AACTGGCGGC
	ATACCGTTAT
901	TGA

This corresponds to the amino acid sequence <SEQ ID 560; ORF137-1>:

1	MENMVTFSKI RPLLAIAAAA LLAACGTAGN NAVRKPVQTA
	KPAAVVGLAL
51	GGGASKGFAH VGIIKVLKEN GIPVKVVTGT SAGSIVGSLF
	ASGMSPDRLE
101	LEAEILGKTD LVDLTLSTSG FIKGEKLQNY INRKVGGRQI
	QQFPIKFAAV
151	ATDFETGKAV AFNQGNAGQA VRASAAIPNV FQPVIIGRHT
	YVDGGLSQPV
201	PVSAARRQGA NFVIAVDISA RPGKNISQGF FSYLDQTLNV
	MSVSALQNEL
251	GQADVVIKPQ VLDLGAVGGF DQKKRAIRLG EEAARAALPE
	IKRKLAAYRY
301	*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF137 shows 93.3% identity over a 149aa overlap with an ORF (ORF137a) from strain A of N. meningitidis:

The complete length ORF137a nucleotide sequence <SEQ ID 561> is:

1	ATGGAAAATA TGGTAACGTT TTCAAAAATC AGACCGCTTT
	TGGCAATCGC
51	CGCCGCCGCG TTGCTTGCCG CCTGCGGCAC GGCGGGAAAT
	AATGCTGCCC
101	GCAAGCCGGT GCAAACCGCC AAACCCGCCG CAGTGGTCGG
	TTTGGCACTC
151	GGTGGCGGCG CATCTAAAGG ATTTGCCCAT GTAGGTATTA
	TTAAGGTTTT
201	GAAAGAAAAC GGTATTCCTG TGAAGGTGGT TACCGGCACA
	TCGGCAGGTT
251	CGATAGTCGG CAGCCTTTTT GCATCGGGTA TGTCGCCCGA
	CCGCCTCGAA
301	TTGGAAGCCG AAATTTTAGG TAAAACCGAT TTGGTCGATT
	TAACCTTGTC
351	CACCAGTGGT TTTATCAAAG GCGAAAAGCT GCAAAATTAC
	ATCAACCGAA
401	AAGTCGGCGG CAGGCGGATT CAGCAGTTTC CCATCAAATT
	TGCCGCCGTT
451	GCTACTGATT TTGAAACCGG CAAGGCCGTC GCTTTCAATC
	AAGGGAATGC
501	CGGGCAGGCT GTGCGCGCTT CCGCCGCCAT TCCCAATGTG
	TTCCAACCCG
551	TTATCATCGG CAGGCATACA TATGTTGACG GCGGTCTGTC
	GCAGCCCGTG
601	CCCGTCAGTG CCGCCCGGCG GCANGNNNNG NATNTCGTGA
	TTGCCGTCGA
651	TATTTCCGCC CGTCCGAGCA AAAACATCAG CCAAGGCTTC
	TTCTCTTATC
701	TCGATCAGAC GCTGAACGTA ATGAGCGTTT CCGCGTTGCA
	AAATGAGTTG
751	GGGCAGGCGG ATGTGGTTAT CAAACCGCAG GTTTTGGATT
	TGGGTGCAGT
801	CGGCGGATTC GATCAGAAAA AACGCGCCAT CCGGTTGGGT
	GAGGAGGCAG
851	CACGTGCCGC ATTGCCTGAA ATCAAACGCA AACTGGCGGC
	ATACCGTTAT
901	TGA

This encodes a protein having amino acid sequence <SEQ ID 562>:

1	MENMVTFSKI RPLLAIAAAA LLAACGTAGN NAARKPVQTA
	KPAAVVGLAL
51	GGGASKGFAH VGIIKVLKEN GIPVKVVTGT SAGSIVGSLF
	ASGMSPDRLE
101	LEAEILGKTD LVDLTLSTSG FIKGEKLQNY INRKVGGRRI
	QQFPIKFAAV
151	ATDFETGKAV AFNQGNAGQA VRASAAIPNV FQPVIIGRHT
	YVDGGLSQPV
201	PVSAARRXXX XXVIAVDISA RPSKNISQGF FSYLDQTLNV
	MSVSALQNEL
251	GQADVVIKPQ VLDLGAVGGF DQKKRAIRLG EEAARAALPE
	IKRKLAAYRY
301	*

ORF137a and ORF137-1 show 97.3% identity in 300 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF137 shows 89.9% identity over a 149aa overlap with a predicted ORF (ORF137ng) from N. gonorrhoeae:

The complete length ORF137ng nucleotide sequence <SEQ ID 563> is:

1	ATGGAAAATA TGGTAACGTT TTCAAAAATC AGATCATTTT
	TGGCAATCGC
51	CGCCGCCGCG TTGCTTGCCG CCTGCGGTAC GGCGGGAAAC
	AATGCCGCCC
101	GCAAGCCGGT GCAAACCGCC AAACCCGCCG CAGTGGTCGC
	TTTGGCACTC
151	GGTGGCGGCG CATCTAAAGG ATTTGCCCAT ATAGGAATTG
	TTAAGGTTTT
201	GAAAGAAAAC GGTATTCCTG TGAAGGTGGT TACCGGCACA
	TCGGCAGGTT
251	CGATAGTCGG CAGCCTTTTG GCATCGGGTA TGTCGCCCGA
	CCGCCTCGAA
301	TTGGAAGCCG AGATTTTAGG TAAAACCGAT TTAGTCGATT
	TAACCTTGTC
351	CACCAGTGGT TTTATCAAAG GCGAAAAGCT GCAAAATTAC
	ATCAACCGAA
401	AAGTCGGCGG CAGGCAGATT CAGCAGTTTC CCATCAAATT
	TGCCGCCGTT
451	GCCACTGATT TTGAAACCGG CAAGGCCGTC GCTTTCAATC
	AAGGGAATGC
501	CGGGCAGGCG GTTCGTGCTT CCGCCGCCAT TCCCAATGTG
	TTCCAGCCAG
551	TCATCATCGG CAGGCACAAA TATGTTGACG GCGGTCTGTC
	GCAGCCCGTG
601	CCCGTCAGTG CCGCTCGGCG GCAGGGGGCG AATTTCGTGA
	TTGCCGTCGA
651	TATTTCCGCA CGTCCGAGCA AAAATGTCGG TCAAGGTTTC
	TTCTCTTATC
701	TCGATCAGAC GCTGAACGTG ATGAGCGTTT CCGTGTTGCA
	AAACGAGTTG
751	gggcAGGCGG ATGTGGTTAT CAAACCGCag gtTTTGGATT
	TGGGTGCAGT
801	CGGCGGATTC GATCAGAAAA AGCGCGCCAT CCGGTTGGGC
	GAGGAGGCAG
851	CACGTGCCGC ATTGCCTGAA ATCAAACGCA AACTGGCGGC
	ATACCGTTAT
901	TGA

This encodes a protein having amino acid sequence <SEQ ID 564>:

1	MENMVTFSKI RSFLAIAAAA LLAACGTAGN NAARKPVQTA
	KPAAVVALAL
51	GGGASKGFAH IGIVKVLKEN GIPVKVVTGT SAGSIVGSLL
	ASGMSPDRLE
101	LEAEILGKTD LVDLTLSTSG FIKGEKLQNY INRKVGGRQI
	QQFPIKFAAV
151	ATDFETGKAV AFNQGNAGQA VRASAAIPNV FQPVIIGRHK
	YVDGGLSQPV
201	PVSAARRQGA NFVIAVDISA RPSKNVGQGF FSYLDQTLNV
	MSVSVLQNEL
251	GQADVVIKPQ VLDLGAVGGF DQKKRAIRLG EEAARAALPE
	IKRKLAAYRY
301	*

ORF137ng and ORF137-1 show 96.0% identity in 300 aa overlap:

Based on the presence of a predicted prokaryotic membrane lipoprotein lipid attachment site (underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 68

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 565>:

1	ATGTTTCGTT TACAATTCAG GCTGTTTCCC CCTTTGCGAA
	CCGCCATGCA
51	CATCCTGTTG ACCGCCCTGC TCAAATGCCT CTCCCTGcTG
	CCGCTTTCCT
101	GTCTGCACAC GCTGGGAAAC CGGCTCGGAC ATCTGGCGTT
	TTACCTTTTA
151	AAGGAAGACC GCGCGCGCAT CGTCGCCmAT ATGCGGCAGG
	CGGGTTTGAA
201	CCCCGACCCC AAAACGGTCA AAGCCGTTTT TGCGGAAACG
	GCAAAAGGCG
251	GTTTGGAACT TGCCCCCGCG TTTTTCAGAA AACCGGAAGA
	CATAGAAACA
301	ATGTTCAAAG CGGTACACGG CTGGGAACAT GTGCAGCAGG
	CTTTGGACAA
351	ACACGAAGGG CTGCTATTC..

This corresponds to the amino acid sequence <SEQ ID 566; ORF138>:

1	MFRLQFRLFP PLRTAMHILL TALLKCLSLL PLSCLHTLGN
	RLGHLAFYLL
51	KEDRARIVAX MRQAGLNPDP KTVKAVFAET AKGGLELAPA
	FFRKPEDIET
101	MFKAVHGWEH VQQALDKHEG LLF

Further work revealed the complete nucleotide sequence <SEQ ID 567>:

1	ATGTTTCGTT TACAATTCAG GCTGTTTCCC CCTTTGCGAA
	CCGCCATGCA
51	CATCCTGTTG ACCGCCCTGC TCAAATGCCT CTCCCTGCTG
	CCGCTTTCCT
101	GTCTGCACAC GCTGGGAAAC CGGCTCGGAC ATCTGGCGTT
	TTACCTTTTA
151	AAGGAAGACC GCGCGCGCAT CGTCGCCAAT ATGCGGCAGG
	CGGGTTTGAA
201	CCCCGACCCC AAAACGGTCA AAGCCGTTTT TGCGGAAACG
	GCAAAAGGCG
251	GTTTGGAACT TGCCCCCGCG TTTTTCAGAA AACCGGAAGA
	CATAGAAACA
301	ATGTTCAAAG CGGTACACGG CTGGGAACAT GTGCAGCAGG
	CTTTGGACAA
351	ACACGAAGGG CTGCTATTCA TCACGCCGCA CATCGGCAGC
	TACGATTTGG
401	GCGGACGCTA CATCAGCCAG CAGCTTCCGT TCCCGCTGAC
	CGCCATGTAC
451	AAACCGCCGA AAATCAAAGC GATAGACAAA ATCATGCAGG
	CGGGCAGGGT
501	TCGCGGCAAA GGAAAAACCG CGCCTACCAG CATACAAGGG
	GTCAAACAAA
551	TCATCAAAGC CCTGCGTTCG GGCGAAGCAA CCATCGTCCT
	GCCCGACCAC
601	GTCCCCTCCC CTCAAGAAGG CGGGGAAGGC GTATGGGTGG
	ATTTCTTCGG
651	CAAACCTGCC TATACCATGA CGCTGGCGGC AAAATTGGCA
	CACGTCAAAG
701	GCGTGAAAAC CCTGTTTTTC TGCTGCGAAC GCCTGCCTGG
	CGGACAAGGT
751	TTCGATTTGC ACATCCGCCC CGTCCAAGGG GAATTGAACG
	GCGACAAAGC
801	CCATGATGCC GCCGTGTTCA ACCGCAATGC CGAATATTGG
	ATACGCCGTT
851	TTCCGACGCA GTATCTGTTT ATGTACAACC GCTACAAAAT
	GCCGTAA

This corresponds to the amino acid sequence <SEQ ID 568; ORF138-1>:

1	MFRLQFRLFP PLRTAMHILL TALLKCLSLL PLSCLHTLGN
	RLGHLAFYLL
51	KEDRARIVAN MRQAGLNPDP KTVKAVFAET AKGGLELAPA
	FFRKPEDIET
101	MFKAVHGWEH VQQALDKHEG LLFITPHIGS YDLGGRYISQ
	QLPFPLTAMY
151	KPPKIKAIDK IMQAGRVRGK GKTAPTSIQG VKQIIKALRS
	GEATIVLPDH
201	VPSPQEGGEG VWVDFFGKPA YTMTLAAKLA HVKGVKTLFF
	CCERLPGGQG
251	FDLHIRPVQG ELNGDKAHDA AVFNRNAEYW IRRFPTQYLF
	MYNRYKMP*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF138 shows 99.2% identity over a 123aa overlap with an ORF (ORF138a) from strain A of N. meningitidis:

The complete length ORF138a nucleotide sequence <SEQ ID 569> is:

1	ATGTTTCGTT TACAATTCAG GCTGTTTCCC CCTTTGCGAA
	CCGCCATGCA
51	CATCCTGTTG ACCGCCCTGC TCAAATGCCT CTCCCTGCTG
	CCGCTTTCCT
101	GTCTGCACAC GCTGGGAAAC CGGCTCGGAC ATCTGGCGTT
	TTACCTTTTA
151	AAGGAAGACC GCGCGCGCAT CGTCGCCAAT ATGCGTCAGG
	CAGGCATGAA
201	TCCCGACCCC AAAACGGTCA AAGCCGTTTT TGCGGAAACG
	GCAAAAGGCG
251	GTTTGGAACT TGCCCCCGCG TTTTTCAGAA AACCGGAAGA
	CATAGAAACA
301	ATGTTCAAAG CGGTACACGG CTGGGAACAT GTGCAGCAGG
	CTTTGGACAA
351	ACACGAAGGG CTGCTATTCA TCACGCCGCA CATCGGCAGC
	TACGATTTGG
401	GCGGACGCTA CATCAGCCAG CAGCTTCCGT TCCCGCTGAC
	CGCCATGTAC
451	AAACCGCCGA AAATCAAAGC GATAGACAAA ATCATGCAGG
	CGGGCAGGGT
501	TCGCGGCAAA GGAAAAACCG CGCCTACCAG CATACAAGGG
	GTCAAACAAA
551	TCATCAAAGC CCTGCGTTCG GGCGAAGCAA CCATCGTCCT
	GCCCGACCAC
601	GTCCCCTCCC CTCAAGAAGG CGGGGAAGGC GTATGGGTGG
	ATTTCTTCGG
651	CAAACCTGCC TATACCATGA CGCTGGCGGC AAAATTGGCA
	CACGTCAAAG
701	GCGTGAAAAC CCTGTTTTTC TGCTGCGAAC GCCTGCCTGG
	CGGACAAGGT
751	TTCGATTTGC ACATCCGCCC CGTCCAAGGG GAATTGAACG
	GCGACAAAGC
801	CCATGATGCC GCCGTGTTCA ACCGCAATGC CGAATATTGG
	ATACGCCGTT
851	TTCCGACGCA GTATCTGTTT ATGTACAACC GCTACAAAAT
	GCCGTAA

This encodes a protein having amino acid sequence <SEQ ID 570>:

1 MFRLQFRLFP PLRTAMHILL TALLKCLSLL PLSCLHTLGN RLGHLAFYLL
51 KEDRARIVAN MRQAGLNPDP KTVKAVFAET AKGGLELAPA FFRKPEDIET
101 MFKAVHGWEH VQQALDKHEG LLFITPHIGS YDLGGRYISQ QLPFPLTAMY
151 KPPKIKAIDK IMQAGRVRGK GKTAPTSIQG VKQIIKALRS GEATIVLPDH
201 VPSPQEGGEG VWVDFFGKPA YTMTLAAKLA HVKGVKTLFF CCERLPGGQG
251 FDLHIRPVQG ELNGDKAHDA AVFNRNAEYW IRRFPTQYLF MYNRYKMP*

ORF138a and ORF138-1 show 99.7% identity over a 298aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF138 shows 94.3% identity over a 123aa overlap with a predicted ORF (ORF138ng) from N. gonorrhoeae:

The complete length ORF138ng nucleotide sequence <SEQ ID 571> is:

1	ATGTTTCGTT TACAATTCAG GCTGTTTCCC CCTTTGCGAA
	CCGCCATGCA
51	CATCCTGTTG ACCGCCCTGC TCAAATGCCT CTCCCTGCTG
	TCGCTTTCCT
101	GTCTGCACAC GCTGGGAAAC CGGCTCGGAC ATCTGGCGTT
	TTACCTTTTA
151	AAGGAAGACC GCGCGCGCAT CGTCGCCAAT ATGCGGCAGG
	CGGGTTTGAA
201	CCCCGACACG CAGACGGTCA AAGCCGTTTT TGCGGAAACG
	GCAAAATGCG
251	GTTTGGAACT TGCCCCCGCG TTTTTCAAAA AACCGGAAGA
	CATCGAAACA
301	ATGTTCAAAG CGGTACACGG CTGGGAACAC GTGCAGCAGG
	CTTTGGACAA
351	GGGCGAAGGG CTGCTGTTCA TCACGCCGCA CATCGGCAGC
	TACGATTTGG
401	GCGGACGCTA CATCAGCCAG CAGCTTCCGT TCCACCTGAC
	CGCCATGTAC
451	AAGCCGCCGA AAATCAAAGC GATAGACAAA ATCATGCAGG
	CGGGCAGGGT
501	GCGCGGCAAA GGCAAAACcg cgcccaccgg catACAAGGG
	GTCAAACAAA
551	tcatcaAGGC CCTGCGCGCG GGCGAGGCAA CCAtcATCCT
	GCCCGACCAC
601	GTCCCTTCTC CGCAGGAagg cggCGGCGTG TGGGCGGATT
	TTTTCGGCAA
651	ACCTGCATAC acCATGACAC TGGCGGCAAA ATTGGCACAC
	GTCAAAGGCG
701	TGAAAACCCT GTTTTTCTGC TGCGAACGCC TGCCCGACGG
	ACAAGGCTTC
751	GTGTTGCACA TCCGCCCCGT CCAAGGGGAA TTGAACGGCA
	ACAAAGCCCA
801	CGATGCCGCC GTGTTCAACC GCAATACCGA ATATTGGATA
	CGCCGTTTTC
851	CGACGCAGTA TCTGTTTATG TACAACCGCT ATAAAACGCC
	GTAA

This encodes a protein having amino acid sequence <SEQ ID 572>:

1	MFRLQFRLFP PLRTAMHILL TALLKCLSLL SLSCLHTLGN
	RLGHLAFYLL
51	KEDRARIVAN MRQAGLNPDT QTVKAVFAET AKCGLELAPA
	FFKKPEDIET
101	MFKAVHGWEH VQQALDKGEG LLFITPHIGS YDLGGRYISQ
	QLPFHLTAMY
151	KPPKIKAIDK IMQAGRVRGK GKTAPTGIQG VKQIIKALRA
	GEATIILPDH
201	VPSPQEGGGV WADFFGKPAY TMTLAAKLAH VKGVKTLFFC
	CERLPDGQGF
251	VLHIRPVQGE LNGNKAHDAA VFNRNTEYWI RRFPTQYLFM
	YNRYKTP*

ORF138ng and ORF138-1 show 94.3% identity over 299aa overlap:

In addition, ORF138ng is homologous to htrB protein from Pseudomonas fluorescens:

gnl|PID|e334283 (Y14568) htrB [Pseudomonas fluorescens] Length = 253
Score = 80.8 bits (196), Expect = 9e−15
Identities = 49/151 (32%), Positives = 79/151 (51%), Gaps = 6/151 (3%)

Query:	101	MFKAVHGWEHVQQALDKGEGLLFITPHIGSYD-LGGRYISQQLPFHLTAMYKPPKIKAID	159
		+ + V G E +++AL  G+G++ IT H+G+++ L   Y SQ  P      Y+PPK+KA+D
Sbjct:	94	LVREVEGLEVLKEALASGKGVVGITSHLGNWEVLNHFYCSQCKPI---IFYRPPKLKAVD	150
Query:	160	KIMQAGRVRGKGKTAPTGIQGVKQIIKALRAGEATIILPDHVPSPQEGGGVWADFFGKPA	219
		++++  RV+   K A +  +G+  +IK +R G    I  D  P P E  G++  FF   A
Sbjct:	151	ELLRKQRVQLGNKVAASTKEGILSVIKEVRKGGQVGIPAD--PEPAESAGIFVPFFATQA	208
Query:	220	YTMTLAAKLAHVKGVKTLFFCCERLPDGQGF	250
		T      +        +F    RLPDG G+
Sbjct:	209	LTSKFVPNMLAGGKAVGVFLHALRLPDGSGY	239

Based on this analysis, including the presence of a putative transmembrane domain in the gonococcal protein, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF138-1 (57 kDa) was cloned in the pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 14A shows the results of affinity purification of the GST-fusion protein. Purified GST-fusion protein was used to immunise mice, whose sera were used for ELISA (positive result) and FACS analysis (FIG. 14B). These experiments confirm that ORF138-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 69

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 573>:

1	..GCGTGGTCGG CCGGCGAATC GTGGCGTGTG TTAATGGAAA
	GTGAAACGTG
51	GCATGCGGTG TGGAATACTT TGCGCTTCTC GGCGGCGGCG
	GTGTATGCGG
101	CAGCGGTTTT GGGTGTGGTG TATGCGGCGC CGGCGCGGCG
	GTCGGCGTGG
151	ATGCGCGGGC TGATGTTTTA GCCGTTTATG GTGTCGCCGG
	TTTGTGTTTC
201	GGCGGGCGTG CTGCTGCTTT ATCCGCAGTG GACGGCTTCG
	TTGCCGTTGC
251	TGCTGGCGAT GTATGCGCTG CTGGCGTATC CGTTTGTGGC
	AAAAGATGTT
301	TTATCAGCCT GGGATGCACT GCCGCCGGAT TACGGCAGGG
	CGGCGGCGGG
351	TTTGGGTGCA AACGGCTTTC AGACGGCATG CCGCATCACG
	TTCCCCCTCT
401	TGAAACCGGC GTTGCGGCGC GGTCTGACTT TGGCGGCGGC
	AACCTGCGTG
451	GGCGAATTTG CGGCGACATT GTTTCTGTCG CGTCCGGAAT
	GGCAGACGCT
501	GACGACTTTG ATTTATGCCT ATTTGGGACG CGCGGGTGAG
	GATAATTACG
551	CGCGGGCGAT GGTGCTG..

This corresponds to the amino acid sequence <SEQ ID 574; ORF139>:

1	..AWSAGESWRV LMESETWHAV WNTLRFSAAA VYAAAVLGVV
	YAAPARRSAW
51	MRGLMFXPFM VSPVCVSAGV LLLYPQWTAS LPLLLAMYAL
	LAYPFVAKDV
101	LSAWDALPPD YGRAAAGLGA NGFQTACRIT FPLLKPALRR
	GLTLAAATCV
151	GEFAATLFLS RPEWQTLTTL IYAYLGRAGE DNYARAMVL..

Further work revealed the complete nucleotide sequence <SEQ ID 575>:

1	ATGGATGGAC GGCGTTGGGT GGTATGGGGT GCTTTTGCCC
	TGCTGCCTTC
51	GGCTTTTTTG GCGGTAATGG TCGTTGCGCC TTTGTGGGCG
	GTGGCGGCGT
101	ATGACGGTTT GGCGTGGCGC GCGGTGCTGT CGGATGCCTA
	TATGCTCAAA
151	CGTTTGGCGT GGACGGTATT TCAGGCAGCG GCAACCTGTG
	TGCTGGTGCT
201	GCCTTTGGGC GTGCCTGTCG CGTGGGTGCT GGCGCGGCTG
	GCGTTTCCGG
251	GGCGGGCTTT GGTGCTGCGC CTGCTGATGC TGCCTTTTGT
	GATGCCCACG
301	TTGGTGGCGG GCGTGGGCGT GCTGGCCCTG TTCGGGGCGG
	ACGGGCTGTT
351	GTGGCGCGGC AGGCAGGATA CGCCGTATCT GTTGTTGTAC
	GGCAATGTGT
401	TTTTCAACCT TCCTGTGTTG GTCAGGGCGG CGTATCAGGG
	GTTTGTGCAA
451	GTGCCTGCGG CACGGCTTCA GACGGCACGG ACGTTGGGCG
	CGGGGGCGTG
501	GCGGCGGTTT TGGGACATTG AAATGCCCGT TTTGCGCCCG
	TGGCTTGCCG
551	GCGGCGTGTG CCTTGTCTTT CTGTATTGTT TTTCCGGGTT
	CGGGCTGGCG
601	CTGCTGCTGG GCGGCAGCCG TTATGCCACG GTCGAAGTGG
	AAATTTACCA
651	GTTGGTCATG TTCGAACTCG ATATGGCGGT TGCTTCGGTG
	CTGGTGTGGC
701	TGGTGTTGGG GGTAACGGCG GCGGCAGGGT TGCTGTATGC
	GTGGTTCGGC
751	AGGCGCGCGG TTTCGGATAA GGCGGTTTCC CCTGTGATGC
	CGTCGCCGCC
801	GCAGTCGGTC GGGGAATATG TGCTGCTGGC GTTTGCGGCG
	GCGGTGTTGT
851	CTGTGTGCTG CCTGTTTCCT TTGTTGGCAA TTGTTGTGAA
	AGCGTGGTCG
901	GCCGGCGAAT CGTGGCGTGT GTTAATGGAA AGTGAAACGT
	GGCAGGCGGT
951	GTGGAATACT TTGCGCTTCT CGGCGGCGGC GGTGTATGCG
	GCGGCGGTTT
1001	TGGGTGTGGT GTATGCGGCG GCGGCGCGGC GGTCGGCGTG
	GATGCGCGGG
1051	CTGATGTTTT TGCCGTTTAT GGTGTCGCCG GTTTGTGTTT
	CGGCGGGCGT
1101	GCTGCTGCTT TATCCGCAGT GGACGGCTTC GTTGCCGTTG
	CTGCTGGCGA
1151	TGTATGCGCT GCTGGCGTAT CCGTTTGTGG CAAAAGATGT
	TTTATCAGCC
1201	TGGGATGCAC TGCCGCCGGA TTACGGCAGG GCGGCGGCGG
	GTTTGGGTGC
1251	AAACGGCTTT CAGACGGCAT GCCGCATCAC GTTCCCCCTC
	TTGAAACCGG
1301	CGTTGCGGCG CGGTCTGACT TTGGCGGCGG CAACCTGCGT
	GGGCGAATTT
1351	GCGGCGACAT TGTTTCTGTC GCGTCCGGAA TGGCAGACGC
	TGACGACTTT
1401	GATTTATGCC TATTTGGGAC GCGCGGGTGA GGATAATTAC
	GCGCGGGCGA
1451	TGGTGCTGAC ATTGCTGTTG GCGGCGTTCG CGCTGGGTAT
	TTTCCTGCTG
1501	TTGGACGGCG GCGAAGGCGG AAAACAGACG GAAACGTTAT
	AA

This corresponds to the amino acid sequence <SEQ ID 576; ORF139-1>:

1	MDGRRWVVWG AFALLPSAFL AVMVVAPLWA VAAYDGLAWR
	AVLSDAYMLK
51	RLAWTVFQAA ATCVLVLPLG VPVAWVLARL AFPGRALVLR
	LLMLPFVMPT
101	LVAGVGVLAL FGADGLLWRG RQDTPYLLLY GNVFFNLPVL
	VRAAYQGFVQ
151	VPAARLQTAR TLGAGAWRRF WDIEMPVLRP WLAGGVCLVF
	LYCFSGFGLA
201	LLLGGSRYAT VEVEIYQLVM FELDMAVASV LVWLVLGVTA
	AAGLLYAWFG
251	RRAVSDKAVS PVMPSPPQSV GEYVLLAFAA AVLSVCCLFP
	LLAIVVKAWS
301	AGESWRVLME SETWQAVWNT LRFSAAAVYA AAVLGVVYAA
	AARRSAWMRG
351	LMFLPFMVSP VCVSAGVLLL YPQWTASLPL LLAMYALLAY
	PFVAKDVLSA
401	WDALPPDYGR AAAGLGANGF QTACRITFPL LKPALRRGLT
	LAAATCVGEF
451	AATLFLSRPE WQTLTTLIYA YLGRAGEDNY ARAMVLTLLL
	AAFALGIFLL
501	LDGGEGGKQT ETL*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF139 shows 94.7% identity over a 189aa overlap with an ORF (ORF139a) from strain A of N. meningitidis:

The complete length ORF139a nucleotide sequence <SEQ ID 577> is:

1	ATGGATGGAC GGCGTTGGGC GGTATGGGGT GCTTTTGCCC
	TGCTGCCTTC
51	GGCTTTTTTG GCGGCAATGG TCGTTGCGCC TTTGTGGGCG
	GTGGCGGCGT
101	ATGACGGTTT GGCGTGGCGC GCGGTGCTGT CGGATGCCTA
	TATGCTCAAA
151	CGTTTGGCGT GGACGGTATT TCAGGCAGCG GCAACCTGTG
	TGCTGGTGCT
201	GCCTTTGGGC GTGCCTGTCG CGTGGGTGCT GGCGCGGCTG
	GCGTTTCCGG
251	GGCGGGCTTT GGTGCTGCGC CTGCTGATGC TGCCTTTTGT
	GATGCCCACG
301	TTGGTGGCGG GCGTGGGCGT GCTGGCTCTG TTCGGGGCGG
	ACGGCCTGTN
351	GTGGCGCGGC TGGCAGGATA CGCCGTATCT GTTGTTGTAC
	GGCAATGTGT
401	TTTTTNACCT TCCTGTGTTG GTCAGGGCGG CATATCAGGG
	GTTTGTGCAA
451	GTGCCTGCGG CACGGCTTCA GACGGCACNG ACATTGGGCG
	CGGGGGCGTG
501	GCGGCGGTTT TGGGACATTG AAATGCCCGT TTTGCGCCCG
	TGGCTTGCCG
551	GCGGCGTGTG CCTTGTCTTC CTGTATTGTT TTTCGGGGTT
	CGGGCTGGCA
601	TTGCTGCTGG GCGGCAGCCG TTATGCCACG GTCGAAGTGG
	AAATTTACCA
651	GTTGGTCATG TTCGAACTCG ATATGGCGGT TGCTTCGGTG
	CTNGTGTGGC
701	TGGTGTNGGG GGTAACNGCG GCGGCAGGGT TGCTGTATGC
	GTGGTTCGGC
751	AGGCGCGCGG TTTCGGATAA GGCNGTTTCC CCTGTGATGC
	CGTCGCCGCC
801	GCAGTCGGTC GGGGAATATG TGCTNCTGGC GTTTGCGGCG
	GCGGTGTNGT
851	CTGTGTGCTG CCTGTTTCNT TTGTTGGCAA TTGTTGTGAA
	AGCGTGGTCG
901	GCCGGCGAAT CGTGGCGTGT GTTAATGGAA AGTGAAACGT
	GGCAGGCGGT
951	GTGGAATACT NTGCGCTTCT CGGCGGCGGC GGTGTATGCG
	GCGGCGGTTT
1001	TGGGTGTGGT GTATGCGGCG GCGGCGCGGC GGTCGGCGTG
	GATGCGCGGG
1051	CTGATGTTTT TGCCGTTTAT GGTGTCGCCG GTTTGTGTTT
	CGGCGGGCGT
1101	GCTGCTGCTT NATCCGCAGT GGACGGCTTC GTTGCCGCTG
	CTGCTGGCGA
1151	TGTATGCGCT GCTGGCGTAT CCGTTTGTGG CAAAAGATGT
	TTTATCAGCC
1201	TGNGATGCAC TGCCGCCGGA TTACGGCAGG GCGGCGGCGG
	GTTTGGGTGC
1251	AAACGGCTTT CAGACGGCAT GCCGCATCAC GTTCCCCCTC
	TTGAAACCGG
1301	CGTTGCGGCG CGGTCTGACT TTGGCGGCGG CAACCTGCGT
	GGGCGAATTT
1351	GCGGCAACCT TGTTCNTGTC GCGTCNCGAG TGGCAGACGC
	TGACGACTTT
1401	GATTTATGCC TATNTGGGAC GCGCGGGTGA NGATAATTAC
	GCGCGGGCGA
1451	TGGTGCTGAC ATTGCTGTTG GCGGCGTTCG CGCTGGGTAT
	NTTCCTGCTG
1501	TTGGACGGCG GCGAAGGCGG AAAACGGACG GAAACGTTAT
	AA

This encodes a protein having amino acid sequence <SEQ ID 578>:

1	MDGRRWAVWG AFALLPSAFL AAMVVAPLWA VAAYDGLAWR
	AVLSDAYMLK
51	RLAWTVFQAA ATCVLVLPLG VPVAWVLARL AFPGRALVLR
	LLMLPFVMPT
101	LVAGVGVLAL FGADGLXWRG WQDTPYLLLY GNVFFXLPVL
	VRAAYQGFVQ
151	VPAARLQTAX TLGAGAWRRF WDIEMPVLRP WLAGGVCLVF
	LYCFSGFGLA
201	LLLGGSRYAT VEVEIYQLVM FELDMAVASV LVWLVXGVTA
	AAGLLYAWFG
251	RRAVSDKAVS PVMPSPPQSV GEYVLLAFAA AVXSVCCLFX
	LLAIVVKAWS
301	AGESWRVLME SETWQAVWNT XRFSAAAVYA AAVLGVVYAA
	AARRSAWMRG
351	LMFLPFMVSP VCVSAGVLLL XPQWTASLPL LLAMYALLAY
	PFVAKDVLSA
401	XDALPPDYGR AAAGLGANGF QTACRITFPL LKPALRRGLT
	LAAATCVGEF
451	AATLFXSRXE WQTLTTLIYA YXGRAGXDNY ARAMVLTLLL
	AAFALGXFLL
501	LDGGEGGKRT ETL*

ORF139a and ORF139-1 show 96.5% homology over a 514aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF139 shows 95.2% identity over a 189aa overlap with a predicted ORF (ORF139ng) from N. gonorrhoeae:

The complete length ORF139ng nucleotide sequence <SEQ ID 579> is predicted to encode a protein having amino acid sequence <SEQ ID 580>:

1	MDGRCWAVRG AFSLLPSAFL AVMVVAPLWA VAAYDGLAWR
	AVLSDAYMLK
51	RLAWTVFQAA ATCVLVLPLG VPVAWVLARL AFPGRALVLR
	LLMLPFVMPT
101	LVAGVGVLAL FGADGLLWRG RQDTPYLLLY GNVFFNLPVL
	VRAAYQGFAQ
151	VPAARLQTAR TLGAGAWRPF WDIEMPVLRP WLAGGVCLVF
	LYCFSGFGLA
201	LLLGGSRYAT VEVEIYQLVM FELDMAGASA LVWLVLGVTA
	AAGLLYAWFG
251	RRAVSDKAVS PVMPSPPQSV GEYVLLAFSV AVLSVCCLFP
	LSAIVVKAWS
301	AGESRRVLME SETWQAVWNT LRFSAAAVFA AAVLGVVYAA
	AARRLVWMRG
351	LVFLPFMVSP VCVSAGVLLL YPGWTASLPL LLAMYALLAY
	PFVAKDVLSA
401	WDALPPDYGR AAAGLGANGF QTACRITFPL LKPALRRGLT
	LAAATCVGEF
451	AATLFLSRPE WQTLTTLIYA YLGRAGEDNY ARAMVLTLLL
	SAFAVCIFLL
501	LDNGEGGKRT ETL*

Further work revealed a variant gonococcal DNA sequence <SEQ ID 581>:

1	ATGGATGGAC GGTGTTGGGC GGTACGGGGT GCTTTTTCCC
	TGCTGCCTTC
51	GGCTTTTTTG GCGGTAATGG TCGTTGCGCC TTTGTGGGCG
	GTGGCGGCGT
101	ATGACGGTTT GGCGTGGCGC GCGGTGCTGT CGGATGCCTA
	TATGCTCAAA
151	CGTTTGGCGT GGACGGTGTT TCAGGCGGCG GCAACCTGTG
	TGCTGGTGCT
201	GCCTTTGGGC GTGCCTGTCG CGTGGGTGCT GGCGCGGCTG
	GCGTTCCCGG
251	GGCGGGCTTT GGTGCTGCGC CTGCTGATGC TGCCGTTTGT
	GATGCCCACG
301	CTGGTGGCGG GCGTGGGCGT GCTGGCTCTG TTCGGGGCGG
	ACGGGCTGTT
351	GTGGCGCGGC CGGCAGGATA CGCCGTATCT GTTGTTGTAC
	GGCAATGTGT
401	TTTTCAACCT GCCCGTGTTG GTCAGGGCGG CGTATCAGGG
	GTTTGCTCAA
451	GTGCCTGCGG CACGGCTTCA GACGGCACGG ACGTTGGGCG
	CGGGGGCGTG
501	GCGGCGGTTT TGGGACATTG AAATGCCCGT TTTGCGCCCG
	TGGCTTGCCG
551	GCGGCGTGTG CCTTGTCTTC CTGTATTGTT TTTCGGGGTT
	CGGGCTGGCA
601	TTGCTGTTGG GCGGCAGCCG TTATGCCACG GTCGAAGTGG
	AAATTTACCA
651	GTTGGTTATG TTCGAACTCG ATATGGCGGG GGCTTCGGCG
	CTGGTGTGGC
701	TGGTGTTGGG GGTAACGGCG GCGGCAGGGT TGCTGTATGC
	GTGGTTCGGC
751	AGGCGCGCGG TTTCGGATAA GGCGGTTTCC CCCGTGATGC
	CGTCGCCGCC
801	GCAATCGGTG GGGGAATATG TATTGCTGGC ATTTTCGGTG
	GCGGTGTTGT
851	CCGTGTGCTG CCTGTTTCCT TTGTCGGCAA TTGTTGTGAA
	AGCGTGGTCG
901	GCCGGCGAAT CGCGGCGTGT GTTAATGGAA AGTGAAACGT
	GGCAGGCAGT
951	GTGGAATACt ttGCGCTTTT CGGCGGCGGC GGTGTTTGCG
	GCGGCGGTTT
1001	TGGGTGTGGT GTATGCGGCG GCGGCGCGGC GGCTGGTGTG
	GATGCGCGGA
1051	CTGGTGTTTT TACCGTTTAT GGTGTCGCCG GTTTGTGTTT
	CGGCGGGCGT
1101	GCTGCTGCTT TATCCGGGGT GGACGGCTTC GTTACCGCTG
	CTGCTGGCGA
1151	TGTATGCGCT GCTGGCGTAT CCGTTTGTGG CAAAAGATGT
	TTTATCGGCC
1201	TGGGATGCAC TGCCGCCGGA TTACGGCAGG GCGGCGGCAG
	GTTTGGGCGC
1251	AAACGGCTTT CAGACGGCAT GCCGTATCAC GTTCCCCCTC
	TTGAAACCGG
1301	CGTTGCGGCG CGGTCTGACT TTGGCGGCGG CGACGTGTGT
	GGGCGAATTT
1351	GCGGCAACCT TGTTCCTGTC GCGTCCGGAA TGGCAGACGT
	TGACGACTTT
1401	GATTTATGCC TATTTGGGGC GTGCGGGTGA GGACAATTAT
	GCGCGGGCAA
1451	TGGTGTTGAC ATTGCTGTTG TCGGCATTTG CGGTGTGCAT
	TTTCCTGCTG
1501	TTGGACAACG GCGAAGGCGg aaaACGGACG GAAACGTTAT
	AA

This corresponds to the amino acid sequence <SEQ ID 582; ORF139ng-1>:

1	MDGRCWAVRG AFSLLPSAFL AVMVVAPLWA VAAYDGLAWR
	AVLSDAYMLK
51	RLAWTVFQAA ATCVLVLPLG VPVAWVLARL AFPGRALVLR
	LLMLPFVMPT
101	LVAGVGVLAL FGADGLLWRG RQDTPYLLLY GNVFFNLPVL
	VRAAYQGFAQ
151	VPAARLQTAR TLGAGAWRRF WDIEMPVLRP WLAGGVCLVF
	LYCFSGFGLA
201	LLLGGSRYAT VEVEIYQLVM FELDMAGASA LVWLVLGVTA
	AAGLLYAWFG
251	RRAVSDKAVS PVMPSPPQSV GEYVLLAFSV AVLSVCCLFP
	LSAIVVKAWS
301	AGESRRVLME SETWQAVWNT LRFSAAAVFA AAVLGVVYAA
	AARRLVWMRG
351	LVFLPFMVSP VCVSAGVLLL YPGWTASLPL LLAMYALLAY
	PFVAKDVLSA
401	WDALPPDYGR AAAGLGANGF QTACRITFPL LKPALRRGLT
	LAAATCVGEF
451	AATLFLSRPE WQTLTTLIYA YLGRAGEDNY ARAMVLTLLL
	SAFAVCIFLL
501	LDNGEGGKRT ETL*

ORF139ng-1 and ORF139-1 show 95.9% identity over 513aa overlap:

Based on the presence of a predicted binding-protein-dependent transport systems inner membrane component signature (underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 70

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 583>:

1	ATGGACGGCT GGACACAGAC GCTGTCCGCG CAAACCCTGT
	TGGGCATTTC
51	GGCGGCGGCA ATCATCCTCA TTCTGATTTT AATCGTCAGA
	TTCCGCATCC
101	ACGCGCTGCT GACACTGGTC ATCGTCAGCC TGCTGACGGC
	TTTGGCAACC
151	GGTTTGCCCA CAGGCAGCAT TGTCAAAGAC ATACTGGTCA
	AAAACTTCGG
201	CGGCACGCTC GGCGGCGTGG CGCTTCTGGT CGGCCTGGGC
	GCGATGCTCG
251	AACGTTTGGT C...

This corresponds to the amino acid sequence <SEQ ID 584; ORF140>:

1	MDGWTQTLSA QTLLGISAAA IILILILIVR FRIHALLTLV
	IVSLLTALAT
51	GLPTGSIVKD ILVKNFGGTL GGVALLVGLG AMLERLV..

Further work revealed the complete nucleotide sequence <SEQ ID 585>:

1	ATGGACGGCT GGACACAGAC GCTGTCCGCG CAAACCCTGT
	TGGGCATTTC
51	GGCGGCGGCA ATCATCCTCA TTCTGATTTT AATCGTCAAA
	TTCCGCATCC
101	ACGCGCTGCT GACACTGGTC ATCGTCAGCC TGCTGACGGC
	TTTGGCAACC
151	GGTTTGCCCA CAGGCAGCAT TGTCAACGAC ATACTGGTCA
	AAAACTTCGG
201	CGGCACGCTC GGCGGCGTGG CGCTTCTGGT CGGCCTGGGC
	GCGATGCTCG
251	GACGTTTGGT CGAAACATCC GGCGGCGCAC AGTCGCTGGC
	GGACGCGCTG
301	ATCCGGATGT TCGGCGAAAA ACGCGCACCG TTCGCGCTGG
	GCGTTGCCTC
351	GCTGATTTTC GGCTTCCCGA TTTTCTTCGA TGCCGGACTA
	ATCGTCATGC
401	TGCCCATCGT GTTCGCCACC GCACGGCGCA TGAAACAGGA
	CGTACTGCCC
451	TTCGCGCTTG CCTCCATCGG CGCATTTTCC GTCATGCACG
	TCTTCCTGCC
501	GCCCCATCCG GGCCCGATTG CCGCTTCCGA ATTTTACGGC
	GCGAACATCG
551	GCCAAGTTTT GATTTTGGGT CTGCCGACCG CCTTCATCAC
	ATGGTATTTC
601	AGCGGCTATA TGCTCGGCAA AGTGTTGGGG CGCACCATCC
	ATGTTCCCGT
651	TCCCGAACTG CTCAGCGGCG GCACGCAAGA CAACGACCTG
	CCGAAAGAAC
701	CTGCCAAAGC AGGAACGGTC GTCGCCATCA TGCTGATTCC
	CATGCTGCTG
751	ATTTTCCTGA ATACCGGCGT ATCGGCCCTC ATCAGCGAAA
	AACTCGTAAG
801	TGCGGACGAA ACCTGGGTTC AGACGGCAAA AATAATCGGT
	TCGACACCGA
851	TCGCCCTTCT GATTTCCGTA TTGGTCGCAC TGTTTGTCTT
	GGGACGCAAA
901	CGCGGCGAAA GCGGCAGCGC GTTGGAAAAA ACCGTGGACG
	GCGCACTCGC
951	CCCCGTCTGT TCCGTGATTC TGATTACCGG CGCGGGCGGT
	ATGTTCGGCG
1001	GCGTTTTGCG CGCTTCCGGC ATCGGCAAGG CACTCGCCGA
	CAGCATGGCG
1051	GATTTGGGCA TTCCCGTCCT TTTGGGCTGT TTCCTTGTCG
	CCTTGGCACT
1101	GCGTATCGCG CAAGGTTCGG CAACCGTCGC CCTGACCACC
	GCCGCCGCGC
1151	TGATGGCTCC TGCCGTTGCC GCCGCCGGCT TTACCGACTG
	GCAGCTCGCC
1201	TGTATCGTAT TGGCAACGGC GGCAGGTTCG GTCGGTTGCA
	GCCACTTCAA
1251	CGACTCCGGC TTCTGGCTGG TCGGCCGTCT CTTGGACATG
	GACGTACCGA
1301	CCACGCTGAA AACCTGGACG GTCAACCAAA CCCTCATCGC
	ACTCATCGGC
1351	TTTGCCTTGT CCGCACTGCT GTTCGCCATC GTCTGA

This corresponds to the amino acid sequence <SEQ ID 586; ORF140-1>:

1	MDGWTQTLSA QTLLGISAAA IILILILIVK FRIHALLTLV
	IVSLLTALAT
51	GLPTGSIVND ILVKNFGGTL GGVALLVGLG AMLGRLVETS
	GGAQSLADAL
101	IRMFGEKRAP FALGVASLIF GFPIFFDAGL IVMLPIVFAT
	ARRMKQDVLP
151	FALASIGAFS VMHVFLPPHP GPIAASEFYG ANIGQVLILG
	LPTAFITWYF
201	SGYMLGKVLG RTIHVPVPEL LSGGTQDNDL PKEPAKAGTV
	VAIMLIPMLL
251	IFLNTGVSAL ISEKLVSADE TWVQTAKIIG STPIALLISV
	LVALFVLGRK
301	RGESGSALEK TVDGALAPVC SVILITGAGG MFGGVLRASG
	IGKALADSMA
351	DLGIPVLLGC FLVALALRIA QGSATVALTT AAALMAPAVA
	AAGFTDWQLA
401	CIVLATAAGS VGCSHFNDSG FWLVGRLLDM DVPTTLKTWT
	VNQTLIALIG
451	FALSALLFAI V*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF140 shows 95.4% identity over a 87aa overlap with an ORF (ORF140a) from strain A of N. meningitidis:

The complete length ORF140a nucleotide sequence <SEQ ID 587> is:

1	ATGGACGGCT GGACACAGAC GCTGTCCGCG CAAACCCTGT
	TGGGCATTTC
51	GGCGGCGGCA ATCATCCTCA TTCTGATTTT AATCGTCAAA
	TTCCGCATCC
101	ACGCGCTGCT GACACTGGTC ATCGTCAGCC TGCTGACGGC
	TTTGGCAACC
151	GGTTTGCCCA CAGGCAGCAT TGTCAACGAC GTACTGGTCA
	AAAACTTCGG
201	CGGCACGCTC GGCGGCGTGG CGCTTCTGGT CGGCCTGGGC
	GCGATGCTCG
251	GACGTTTGGT CGAAACATCC GGCGGCGCAC AGTCGCTGGC
	GGACGCGCTG
301	ATCCGGATGT TCGGCGAAAA ACGCGCACCG TTCGCGCTGG
	GCGTTGCCTC
351	GCTGATTTTC GGCTTCCCGA TTTTCTTCGA TGCCGGACTA
	ATCGTCATGC
401	TGCCCATCGT GTTCGCCACC GCACGGCGCA TGAAACAGGA
	CGTACTGCCC
451	TTCGCGCTTG CCTCCATCGG CGCATTTTCC GTCATGCACG
	TCTTCCTGCC
501	GCCCCATCCG GGCCCGATTG CCGCTTCCGA ATTTTACGGC
	GCGAACATCG
551	GCCAAGTTTT GATTTTGGGT CTGCCGACCG CCTTCATCAC
	ATGGTATTTC
601	AGCGGCTATA TGCTCGGCAA AGTGTTGGGG CGCACCATCC
	ATGTTCCCGT
651	TCCCGAACTG CTCAGCGGCG GCACGCAAGA CAACGACCTG
	CCGAAAGAAC
701	CTGCCAAAGC AGGAACGGTC GTCGCCATCA TGCTGATTCC
	CATGCTGCTG
751	ATTTTCCTGA ATACCGGCGT ATCGGCCCTC ATCAGCGAAA
	AACTCGTAAG
801	TGCGGACGAA ACCTGGGTTC AGACGGCAAA AATAATCGGT
	TCGACACCGA
851	TCGCCCTTCT GATTTCCGTA TTGGTCGCAC TGTTTGTCTT
	GGGACGCAAA
901	CGCGGCGAAA GCGGCAGCGC GTTGGAAAAA ACCGTGGACG
	GCGCACTCGC
951	CCCCGTCTGT TCCGTGATTC TGATTACCGG CGCGGGCGGT
	ATGTTCGGCG
1001	GCGTTTTGCG CGCTTCCGGC ATCGGCAAGG CACTCGCCGA
	CAGCATGGCG
1051	GATTTGGGCA TTCCCGTCCT TTTGGGCTGT TTCCTTGTCG
	CCTTGGCACT
1101	GCGTATCGCG CAAGGTTCGG CAACCGTCGC CCTGACCACC
	GCCGCCGCGC
1151	TGATGGCTCC TGCCGTTGCC GCCGCCGGCT TTACCGACTG
	GCAGCTCGCC
1201	TGTATCGTAT TGGCAACGGC GGCAGGTTCG GTCGGTTGCA
	GCCACTTCAA
1251	CGACTCCGGC TTCTGGCTGG TCGGCCGCCT CTTGGACATG
	GACGTACCGA
1301	CCACGCTGAA AACCTGGACG GTCAACCAAA CCCTCATCGC
	ACTCATCGGC
1351	TTTGCCTTGT CCGCACTGCT GTTCGCCATC GTCTGA

This encodes a protein having amino acid sequence <SEQ ID 588>:

1	MDGWTQTLSA QTLLGISAAA IILILILIVK FRIHALLTLV
	IVSLLTALAT
51	GLPTGSIVND VLVKNFGGTL GGVALLVGLG AMLGRLVETS
	GGAQSLADAL
101	IRMFGEKRAP FALGVASLIF GFPIFFDAGL IVMLPIVFAT
	ARRMKQDVLP
151	FALASIGAFS VMHVFLPPHP GPIAASEFYG ANIGQVLILG
	LPTAFITWYF
201	SGYMLGKVLG RTIHVPVPEL LSGGTQDNDL PKEPAKAGTV
	VAIMLIPMLL
251	IFLPNTGVSAL ISEKLVSADE TWVQTAKIIG STPIALLISV
	LVALFVLGRK
301	RGESGSALEK TVDGALAPVC SVILITGAGG MFGGVLRASG
	IGKALADSMA
351	DLGIPVLLGC FLVALALRIA QGSATVALTT AAALMAPAVA
	AAGFTDWQLA
401	CIVLATAAGS VGCSHFNDSG FWLVGRLLDM DVPTTLKTWT
	VNQTLIALIG
451	FALSALLFAI V*

ORF140a and ORF140-1 show 99.8% identity over a 461aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF140 shows 92% identity over a 87aa overlap with a predicted ORF (ORF140ng) from N. gonorrhoeae:

The complete length ORF140ng nucleotide sequence <SEQ ID 589> was predicted to encode a protein having amino acid sequence <SEQ ID 590>:

	1	MDGRTQTLSA QTLLGISAAA IILILILIVK FRIRALLTLV
		IASLLTALAT
	51	GLPTGSIVND VLVKNFGGTL GGVALLVGLG AMLGRLVETS
		GGAQSLADAL
	101	IRMFGEKRAP FAPGVASLIF GFPIFFDAGL IVMLPIVFAT
		ARRMKQDVLP
	151	FALASVGAFS VMHVFLPPHP GPIAASEFYG ANIGQVLILG
		LPTAFITWYF
	201	SGYMLGKVLG RAIHVPVPEL LSGGTQDSDP PKEPAKAGTV
		VAVMLIPMLL
	251	IFLNTGVSAL ISEKLVSADE TWVQTAKMIG STPVALLISV
		LAALLVLGRK
	301	RGESGSTLEK TVDGALAPAC SVILITGAGG MFGGVLRASG
		IGKALADSMA
	351	DLGIPVLLGC FLVALALRIA QGSATVALTT AAALMAPAVA
		AAGFTDWQLA
	401	CIVLATAAGS VGCSHFNDSG FWLVGRLSDM DVPTTLKTWT
		VNQTLIAFIG
	451	FALSALLFAI V*

Further work revealed a variant gonococcal DNA sequence <SEQ ID 591>:

1	ATGGACGGCC GGACACAGAC GCTGTCCGCG CAAACCTTGT
	TGGGCATTTC
51	GGCGGCGGCA ATCATCCTCA TTCTGATTTT AATCGTCAAA
	TTCCGCATCC
101	GCGCGCTGCT GACACTGGTC ATCGCCAGCC TGCTGACGGC
	TTTGGCAACC
151	GGTTTGCCCA CAGGCAGCAT CGTCAACGAC GTACTGGTCA
	AAAACTTCGG
201	CGGCACGCTC GGCGGCGTGG CGCTTCTGGT CGGTCTGGGC
	GCAATGCTCG
251	GACGTTTGGT AGAAACATCC GGCGGCGCAC AGTCGCTGGC
	GGACGCGCTG
301	ATCCGGATGT TCGGCGAAAA ACGCGCACCG TTCGCTCCGG
	GCGTTGCCTC
351	GCTGATTTTC GGCTTCCCGA TTTTCTTCGA TGCCGGACTA
	ATCGTCATGC
401	TGCCCATCGT ATTCGCCACC GCACGGCGCA TGAAACAGGA
	CGTACTGCCC
451	TTCGCGCTTG CCTCCGTCGG CGCATTTTCC GTCATGCACG
	TCTTCCTGCC
501	GCCCCATCCG GGCCCGATTG CCGCTTCCGA ATTTTACGGC
	GCGAACATCG
551	GCCAGGTTTT GATTTTGGGT CTGCCGACCG CCTTCATCAC
	ATGGTATTTC
601	AGCGGCTATA TGCTCGGCAA AGTGTTGGGG CGCGCCATCC
	ATGTTCCCGT
651	TCCCGAACTG CTCAGCGGCG GCACGCAAGA CAGCGACCCG
	CCGAAAGAAC
701	CTGCCAAAGC AGGAACGGTC GTCGCCGTCA TGCTGATTCC
	CATGCTGCTG
751	ATTTTCCTGA ATACCGGCGT ATCAGCCCTC ATCAGCGAAA
	AACTCGTAAG
801	TGCGGACGAA ACTTGGGTTC AGACGGCAAA AATGATCGGT
	TCGACACCTG
851	TCGCCCTTCT GATTTCCGTA TTGGCCGCAC TGTTGGTCTT
	GGGACGCAAA
901	CGCGGCGAAA GCGGCAGCAC GTTGGAAAAA ACCGTGGACG
	GCGCACTCGC
951	CCCCGCCTGT TCCGTGATTC TGATTACCGG CGCGGGCGGT
	ATGTTCGGCG
1001	GCGTTTTGCG CGCTTCCGGC ATCGGCAAGG CACTCGCCGA
	CAGCATGGCG
1051	GATTTGGGCA TTCCCGTCCT TTTGGGCTGC TTCCTTGTCG
	CCTTGGCACT
1101	GCGTATCGCG CAAGGTTCGG CAACCGTCGC CCTGACCACA
	GCCGCCGCGC
1151	TGATGGCTCC TGCCGTTGCC GCCGCCGGCT TTACCGACTG
	GCAGCTCGCC
1201	TGTATCGTAT TGGCAACGGC GGCAGGTTCG GTCGGTTGCA
	GCCACTTCAA
1251	CGACTCCGGC TTCTGGCTGG TCGGCCGCCT CTTGGATATG
	GACGTACCGA
1301	CCACGCTGAA AACCTGGACG GTCAACCAAA CCCTCATCGC
	ATTCATCGGC
1351	TTTGCCTTGT CCGCACTGCT GTTTGCCATC GTCTGA

This corresponds to the amino acid sequence <SEQ ID 592; ORF140ng-1>:

1	MDGRTQTLSA QTLLGISAAA IILILILIVK FRIRALLTLV
	IASLLTALAT
51	GLPTGSIVND VLVKNFGGTL GGVALLVGLG AMLGRLVETS
	GGAQSLADAL
101	IRMFGEKRAP FAPGVASLIF GFPIFFDAGL IVMLPIVFAT
	ARRMKQDVLP
151	FALASVGAFS VMHVFLPPHP GPIAASEFYG ANIGQVLILG
	LPTAFITWYF
201	SGYMLGKVLG RAIHVPVPEL LSGGTQDSDP PKEPAKAGTV
	VAVMLIPMLL
251	IFLTGVSAL ISEKLVSADE TWVQTAKMIG STPVALLISV
	LAALLVLGRK
301	RGESGSTLEK TVDGALAPAC SVILITGAGG MFGGVLRASG
	IGKALADSMA
351	DLGIPVLLGC FLVALALRIA QGSATVALTT AAALMAPAVA
	AAGFTDWQLA
401	CIVLATAAGS VGCSHFNDSG FWLVGRLLDM DVPTTLKTWT
	VNQTLIAFIG
451	FALSALLFAI V*

ORF140ng-1 and ORF140-1 show 96.3% identity over 461aa overlap:

Furthermore, ORF140ng-1 is homologous to an E. coli protein:

gi|882633 (U29579) ORF_o454 [Escherichia coli] >gi|1789097 (AE000358) o454;
This 454 aa ORF is 34% identical (9 gaps) to 444 residues of an approx.
456 aa protein GNTP_BACLI SW: P46832 [Escherichia coli] Length = 454
Score = 210 bits (529), Expect = 1e−53
Identities = 130/384 (33%), Positives = 194/384 (49%), Gaps = 19/384 (4%)

Query:	88	ETSGGAQSLADALIRMFGEKRAPFAPGVASLIFGFPIFFDAGLIVMLPIVFATARRMKQD	147
		E SGGA+SLA+   R  G+KR   A  +A+   G P+FFD G I++ PI++  A+  K
Sbjct:	80	EHSGGAESLANYFSRKLGDKRTIAALTLAAFFLGIPVFFDVGFIILAPIIYGFAKVAKIS	139
Query:	148	VLPFALASVGAFSVMHVFLPPHPGPIAASEFYGANIGQVLILGLPTAFITWYFSGYMLGK	207
		L F L   G    +HV +PPHPGP+AA+    A+IG + I+G+  + I    GY   K
Sbjct:	140	PLKFGLPVAGIMLTVHVAVPPHPGPVAAAGLLHADIGWLTIIGIAIS-IPVGVVGYFAAK	198
Query:	208	VLGRAIHVPVPELL----------SGGTQDSDPPKEPAKAGTVVAVMLIPMLLIFLNTGV	257
		++ +  +    E+L           G T+ SD    P  A  V ++++IP+ +I   T
Sbjct:	199	IINKRQYAMSVEVLEQMQLAPASEEGATKLSDKINPPGVA-LVTSLIVIPIAIIMAGT--	255
Query:	258	SALISEKLVSADETWVQTAKMIGSTPXXXXXXXXXXXXXXGRKRGESGSTLEKTVDGALA	317
		+S  L+      + T ++IGS                  +RG S       +  AL
Sbjct:	256	---VSATLMPPSHPLLGTLQLIGSPMVALMIALVLAFWLLALRRGWSLQHTSDIMGSALP	312
Query:	318	PACSVILITGAGGMFGGVLRASGIGKALADSMADLGIPVLLGCFLVALALRIAQGSXXXX	377
		A  VIL+TGAGG+FG VL  SG+GKALA+ +  + +P+L   F+++LALR +QGS
Sbjct:	313	TAAVVILVTGAGGVFGKVLVESGVGKALANMLQMIDLPLLPAAFIISLALRASQGS--AT	370
Query:	378	XXXXXXXXXXXXXXXGFTDWQLACIVLATAAGSVGCSHFNDSGFWLVGRLLDMDVPTTLK	437
		G   Q   + LA   G +G SH NDSGFW+V + L + V   LK
Sbjct:	371	VAILTTGGLLSEAVMGLNPIQCVLVTLAACFGGLGASHINDSGFWIVTKYLGLSVADGLK	430
Query:	438	TWTVNQTLIAFIGFALSALLFAIV	461
		TWTV  T++ F GF ++  ++A++
Sbjct:	431	TWTVLTTILGFTGFLITWCVWAVI	454

Based on this analysis, including the identification of the presence of a putative leader sequence (double-underlined) and several putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 71

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 593>:

1	..GATTTCGGCA TATCGCCCGT GTATCTTTGG GTTGCCGCCG
	CGTTCAAACA
51	TTTGCTGTCG CCGTGGGCTG CCGACTCATA CGATGTCGCA
	CGCTTTGCAG
101	GCGTATTTTT TGCCGTTATC GGACTGACTT CCTGCGGCTT
	TGCCGGTTTC
151	AACTTTTTGG GCAGACACCA CGGGCGCAC. GTCGTCCTGA
	TTCTCATCGG
201	CTGTATCGGG CTGATTCCAG TTGCCCATTT CCTCAACCCC
	GCTGCCGCCG
251	CCTTTGCCGC CGCCGGACTG GTGCTGCACG GTTATTCTTT
	GGCTCGCCGG
301	CGCGTGATTG CCGCCTCTTT TCTGCTCGGT ACGGGCTGGA
	CGCTGATGTC
351	GTTGGCAGCA GCTTATCCGG CAGCATTTGC CCTGATGCTG
	CCCTTGCCCG
401	TACTGATGTT TTTCCGTCCG ..

This corresponds to the amino acid sequence <SEQ ID 594; ORF141>:

1	..DFGISPVYLW VAAAFKHLLS PWAADSYDVA RFAGVFFAVI
	GLTSCGFAGF
51	NFLGRHHGRX VVLILIGCIG LIPVAHFLNP AAAAFAAAGL
	VLHGYSLARR
101	RVIAASFLLG TGWTLMSLAA AYPAAFALML PLPVLMFFRP
	..

Further work revealed the complete nucleotide sequence <SEQ ID 595>:

1	ATGCTGACCT ATACCCCGCC CGATGCCCGC CCGCCCGCCA
	AAACCCACGA
51	AAAGCCGTGG CTGCTGCTGT TGATGGCGTT TGCCTGGTTG
	TGGCCCGGCG
101	TGTTTTCCCA CGATTTGTGG AATCCTGACG AACCTGCCGT
	CTATACCGCC
151	GTCGAAGCAC TGGCAGGCAG CCCCACCCCC TTGGTTGCCC
	ATCTGTTCGG
201	TCAAACCGAT TTCGGCATAC CGCCCGTGTA TCTTTGGGTT
	GCCGCCGCGT
251	TCAAACATTT GCTGTCGCCG TGGGCTGCCG ACTCATACGA
	TGCCGCACGC
301	TTTGCAGGCG TATTTTTTGC CGTTATCGGA CTGACTTCCT
	GCGGCTTTGC
351	CGGTTTCAAC TTTTTGGGCA GACACCACGG GCGCAgCGTC
	GTCCTGATTC
401	TCATCGGCTG TATCGGGCTG ATTCCAGTTG CCCATTTCCT
	CAACCCCGCT
451	GCCGCCGCCT TTGCCGCCGC CGGACTGGTG CTGCACGGTT
	ATTCTTTGGC
501	TCGCCGGCGC GTGATTGCCG CCTCTTTTCT GCTCGGTACG
	GGCTGGACGC
551	TGATGTCGTT GGCAGCAGCT TATCCGGCAG CATTTGCCCT
	GATGCTGCCC
601	TTGCCCGTAC TGATGTTTTT CCGTCCGTGG CAAAGCAGGC
	GTTTGATGTT
651	GACGGCAGTC GCCTCACTTG CCTTTGCCCT GCCGCTTATG
	ACCGTTTACC
701	CGCTGCTCTT GGCAAAAACG CAGCCCGCGC TGTTCGCGCA
	ATGGCTCGAC
751	TATCACGTTT TCGGTACGTT CGGCGGCGTG CGGCACGTTC
	AGACGGCATT
801	CAGTTTGTTT TACTATCTGA AAAACCTGCT TTGGTTTGCA
	TTGCCCGCGC
851	TGCCGCTGGC GGTTTGGACG GTTTGCCGCA CGCGCCTGTT
	TTCGACCGAC
901	TGGGGGATTT TGGGCGTCGT CTGGATGCTT GCCGTTTTGG
	TGCTGCTTGC
951	CGTCAATCCG CAGCGTTTTC AGGATAACCT CGTCTGGCTG
	CTTCCGCCGC
1001	TTGCCCTGTT CGGCGCGGCG CAACTGGACA GCCTGAGGCG
	CGGCGCGGCG
1051	GCGTTTGTCA ACTGGTTCGG CATTATGGCG TTCGGACTGT
	TTGCCGTGTT
1101	CCTGTGGACG GGCTTTTTCG CCATGAATTA CGGCTGGCCC
	GCCAAGCTTG
1151	CCGAACGCGC CGCCTATTTC AGCCCGTATT ATGTTCCTGA
	TATCGATCCC
1201	ATTCCGATGG CGGTTGCCGT ACTGTTCACA CCCTTGTGGC
	TGTGGGCGAT
1251	TACCCGGAAA AACATACGCG GCAGGCAGGC GGTTACCAAC
	TGGGCGGCAG
1301	GCGTTACCCT GACCTGGGCT TTGCTGATGA CGCTGTTCCT
	GCCGTGGCTG
1351	GACGCGGCGA AAAGCCACGC GCCGGTCGTC CGGAGTATGG
	AGGCATCGCT
1401	TTCCCCGGAA TTGAAACGGG AGCTTTCAGA CGGCATCGAG
	TGTATCGGCA
1451	TAGGCGGCGG CGACCTGCAC ACGCGGATTG TTTGGACGCA
	GTACGGCACA
1501	TTGCCGCACC GCGTCGGCGA TGTACAATGC CGCTACCGCA
	TCGTCCTCCT
1551	GCCCCAAAAT GCGGATGCGC CGCAAGGCTG GCAGACGGTT
	TGGCAGGGTG
1601	CGCGTCCGCG CAACAAAGAC AGTAAGTTCG CACTGATACG
	GAAAATCGGG
1651	GAAAATATAT AA

This corresponds to the amino acid sequence <SEQ ID 596; ORF141-1>:

1	MLTYTPPDAR PPAKTHEKPW LLLLMAFAWL WPGVFSHDLW
	NPDEPAVYTA
51	VEALAGSPTP LVAHLFGQTD FGIPPVYLWV AAAFKHLLSP
	WAADSYDAAR
101	FAGVFFAVIG LTSCGFAGFN FLGRHHGRSV VLILIGCIGL
	IPVAHFLNPA
151	AAAFAAAGLV LHGYSLARRR VIAASFLLGT GWTLMSLAAA
	YPAAFALMLP
201	LPVLMFFRPW QSRRLMLTAV ASLAFALPLM TVYPLLLAKT
	QPALFAQWLD
251	YHVFGTFGGV RHVQTAFSLF YYLKNLLWFA LPALPLAVWT
	VCRTRLFSTD
301	WGILGVVWML AVLVLLAVNP QRFQDNLVWL LPPLALFGAA
	QLDSLRRGAA
351	AFVNWFGIMA FGLFAVFLWT GFFAMNYGWP AKLAERAAYF
	SPYYVPDIDP
401	IPMAVAVLFT PLWLWAITRK NIRGRQAVTN WAAGVTLTWA
	LLMTLFLPWL
451	DAAKSHAPVV RSMEASLSPE LKRELSDGIE CIGIGGGDLH
	TRIVWTQYGT
501	LPHRVGDVQC RYRIVLLPQN ADAPQGWQTV WQGARPRNKD
	SKFALIRKIG
551	ENI*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF141 shows 95.0% identity over a 140aa overlap with an ORF (ORF141a) from strain A of N. meningitidis:

The complete length ORF141a nucleotide sequence <SEQ ID 597> is:

1	ATGCTGACCT ATACCCCGCC CGATGCCCGC CCGCCCGCCA
	AAACCCACGA
51	AAAGCCGTGG CTGTTGCTGT TGATGGCGTT TGCCTGGTTG
	TGGCCCGGCG
101	TGTTTTCCCA CGATTTGTGG AATCCTGACG AACCTGCCGT
	CTATACCGCC
151	GTCGAAGCAC TGGCAGGCAG CCCCACCCCT TTGGTTGCCC
	ATCTGTTCGG
201	TCAAATCGAT TTCGGCATAC CGCCCGTGTA TCTTTGGGTT
	GCCGCCGCGT
251	TCAAACATTT GCTGTCGCCG TGGGCTGCCG ACCCGTATGA
	TGCCGCACGC
301	TTTGCCGGCG TGTTTTTCGC CGTTGTCGGA CTGACTTCCT
	GCGGCTTTGC
351	CGGTTTCAAC TTTTTGGGCA GACACCACGG GCGCAGCGTC
	GTCCTGATTC
401	TCATCGGCTG TATCGGGCTG ATTCCGACCG TACACTTTCT
	CAACCCCGCT
451	GCCGCCGCCT TTGCCGCCGC CGGACTGGTG CTGCACGGTT
	ATTCTTTGGC
501	TCGCCGGCGC GTGATTGCCG CCTCTTTTCT GCTCGGTACG
	GGTTGGACGC
551	TGATGTCGTT GGCAGCAGCT TATCCGGCGG CATTTGCCCT
	GATGCTGCCC
601	CTGCCCGTGC TGATGTTTTT CCGTCCGTGG CAAAGCAGGC
	GTTTGATGTT
651	GACGGCAGTC GCCTCGCTTG CCTTTGCCCT GCCGCTTATG
	ACCGTTTACC
701	CGCTGCTCTT GGCAAAAACG CAGCCCGCGC TGTTCGCGCA
	ATGGCTCGAC
751	GATCACGTTT TCGGTACGTT CGGCGGCGTG CGGCACATTC
	AGACGGCATT
801	CAGTTTGTTT TACTATCTGA AAAACCTGCT TTGGTTTGCA
	TTGCCTGCGC
851	TGCCGCTGGC GGTTTGGACG GTTTGCCGCA CGCGCCTGTT
	TTCGACCGAC
901	TGGGGGATTT TGGGCGTCGT CTGGATGCTT GCCGTTTTGG
	TGCTGCTTGC
951	CGTCAATCCG CAGCGTTTTC AGGATAACCT CGTCTGGCTG
	CTTCCGCCGC
1001	TTGCCCTGTT CGGCGCGGCG CAACTGGACA GCCTGAGACG
	CGGCGCGGCG
1051	GCGTTTGTCA ACTGGTTCGG CATTATGGCG TTCGGACTGT
	TTGCCGTGTT
1101	CCTGTGGACG GGCTTTTTCG CCATGAATTA CGGCTGGCCC
	GCCAAGCTTG
1151	CCGAACGCGC CGCCTATTTC AGCCCGTATT ATGTTCCTGA
	TATCGATCCC
1201	ATTCCGATGG CGGTTGCCGT ACTGTTCACA CCCTTGTGGC
	TGTGGGCGAT
1251	TACCCGCAAA AACATACGCG GCAGGCAGGC GGTTACCAAC
	TGGGCGGCAG
1301	GCGTTACCCT GACCTGGGCT TTGCTGATGA CGCTGTTCCT
	GCCGTGGCTG
1351	GACGCGGCGA AAAGCCACGC GCCCGTCGTC CGGAGTATGG
	AGGCATCGCT
1401	TTCCCCGGAA TTAAAACGGG AGCTTTCAGA CGGCATCGAG
	TGTATCGACA
1451	TAGGCGGCGG CGACCTACAC ACGCGGATTG TTTGGACGCA
	GTACGGCACA
1501	TTGCCGCACC GCGTCGGCGA TGTACAATGC CGCTACCGCA
	TCGTCCGCTT
1551	GCCCCAAAAC GCGGATGCGC CGCAAGGCTG GCAGACGGTC
	TGGCAGGGTG
1601	CGCGCCCGCG CAACAAAGAC AGTAAGTTCG CACTGATACG
	GAAAACCGGG
1651	GAAAATATAT TAAAAACAAC AGATTGA

This encodes a protein having amino acid sequence <SEQ ID 598>:

1	MLTYTPPDAR PPAKTHEKPW LLLLMAFAWL WPGVFSHDLW
	NPDEPAVYTA
51	VEALAGSPTP LVAHLFGQID FGIPPVYLWV AAAFKHLLSP
	WAADPYDAAR
101	FAGVFFAVVG LTSCGFAGFN FLGRHHGRSV VLILIGCIGL
	IPTVHFLNPA
151	AAAFAAAGLV LHGYSLARRR VIAASFLLGT GWTLMSLAAA
	YPAAFALMLP
201	LPVLMFFRPW QSRRLMLTAV ASLAFALPLM TVYPLLLAKT
	QPALFAQWLD
251	DHVFGTFGGV RHIQTAFSLF YYLKNLLWFA LPALPLAVWT
	VCRTRLFSTD
301	WGILGVVWML AVLVLLAVNP QRFQDNLVWL LPPLALFGAA
	QLDSLRRGAA
351	AFVNWFGIMA FGLFAVFLWT GFFAMNYGWP AKLAERAAYF
	SPYYVPDIDP
401	IPMAVAVLFT PLWLWAITRK NIRGRQAVTN WAAGVTLTWA
	LLMTLFLPWL
451	DAAKSHAPVV RSMEASLSPE LKRELSDGIE CIDIGGGDLH
	TRIVWTQYGT
501	LPHRVGDVQC RYRIVRLPQN ADAPQGWQTV WQGARPRNKD
	SKFALIRKTG
551	ENILKTTD*

ORF141a and ORF141-1 show 98.2% identity in 553 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF141 shows 95% identity over a 140aa overlap with a predicted ORF (ORF141ng) from N. gonorrhoeae:

An ORF141ng nucleotide sequence <SEQ ID 599> was predicted to encode a protein having amino acid sequence <SEQ ID 600>:

1	MPSEAVSARP LCEYLLHLAI RPFLLTLMLT YTPPDARPPA
	KTHEKPWLLL
51	LMAFAWLWPG VFSHDLWNPA EPAVYTAVEA LAGSPTPLVA
	HLFGQTDFGI
101	PPVYLWVAAA FKHLLSPWAA HPYDAARFAG VFFAVIGLTS
	CGFAGFNFLG
151	RHHGRSVVLI HIGCIGLIPV AHFFNPAAAA FAAAGLVLHG
	YSLARRRVIA
201	ASFLLGTGWT LMSLAAAYPA AFALMLPLPV LMFFRPWQSR
	RLMLTAVASL
251	AFALPLMTVY PLLLAKTQPA LFAQWLNYHV FGTFGGVRHI
	QRAFSLFHYL
301	KNLLWFAPPG LPLAVWTVCR TRLFSTDWGI LGIVWMLAVL
	VLLAFNPQRF
351	QDNLVWLLPP LALFGAAQLD SLRRGAAAFV NWFGIMAFGL
	FAVFLWTGFF
401	AMNYGWPAKL AERAAYFSPY YVPDIDPIPM AVAVLFTPLW
	LWAITRKNIR
451	GRQAVTNWAA GVTLTWALLM TLFLPWLDAA KSHAPVVRSM
	EASFSPELKR
501	ELSDGIECIG IGGGDLHTRI VWTQYGTLPH RVGDVRCRYR
	IVRLPQNADA
551	PQGWQTVWQG ARPRNKDSKF ALIRKIGENI LKTTD*

Further work revealed the following gonococcal DNA sequence <SEQ ID 601>:

1	ATGCTGACCT ATACCCCGCC CGATGCCCGC CCGCCCGCCA
	AAACCCACGA
51	AAAACCGTGG CTGCTGCTGT TGATGGCGTT TGCCTGGCTG
	TGGCCCGGCG
101	TGTTTTCCCA CGATTTGTGG AATCCTGCCG AACCTGCCGT
	CTATACCGCC
151	GTCGAAGCAC TGGCAGGCAG CCCCACCCCC TTGGTTGCCC
	ATCTGTTCGG
201	TCAAACCGAT TTCGGCATAC CGCCCGTGTA TCTTTGGGTT
	GCCGCCGCAT
251	TCAAACATTT GCTGTCGCCG TGGGCAGCCG ACCCGTATGA
	TGCCGCACGC
301	TTTGCAGGCG TATTTTTTGC CGTTATCGGA CTGACTTCTT
	GCGGCTTTGC
351	CGGTTTCAAC TTTTTGGGCA GACACCACGG GCGCAGCGTT
	GTTTTAATCC
401	ATATCGGCTG TATCGGGCTG ATTCCGGTTG CCCATTTCCT
	CAATCCcgcc
451	gccgccgcct tTGCCGCCGC CGGACTGGTG CTGCacggct
	actcgctgGC
501	ACGCCGGCGC GTGATtgccg cctctTtccT GCTCGGTACG
	GGTTGGACGT
551	TGATGTCGCT GGCGGCAGCT TATCCGGCGG CGTTTGCGCT
	GATGCTGCCC
601	CTGCCCGTGC TGATGTTTTT CCGTCCGTGG CAAAGCAGGC
	GTTTGATGTT
651	GACGGCAGTC GCCTCGCTTG CCTTTGCCCT GCCGCTTATG
	ACCGTTTACC
701	CGCTGCTCtt gGCAAAAACG CAGCCCGCGC TGTTTGCGCA
	ATGGCTCAAC
751	TATCACGTTT TCGGTACGTt cggcgGCGTG CGGCAcaTTC
	AGAggGCatT
801	Cagtttgttt cactatctgA AAaatctgct ttggttcgca
	ccgcccgggC
851	TGCCGCTGGC GGTTTGGACG GTTTGCCGCA CACGCCTGTT
	TTCGACCGAC
901	TGGGGGATTT TGGGCATTGT CTGGATGCTT GCCGTTTTGG
	TGCTGCTCGC
951	CTTTAATCCG CAGCGTTTTC AAGACAACCT CGTCTGGCTG
	CTGCCGCCGC
1001	TTGCCCTGTT CGGCGCGGCG CAACTGGACA GCCTGAGGCG
	CGGCGCGGCG
1051	GCTTTTGTCA ACTGGTTCGG CATTATGGCG TTCGGGCTGT
	TTGCCGTGTT
1101	CCTGTGGACG GGCTTTTTCG CCATGAATTA CGGCTGGCCC
	GCCAAGCTTG
1151	CCGAACGCGC CGCCTACTTC AGCCCGTATT ACGTTCCCGA
	CATCGATCCC
1201	ATTCCGATGG CGGTTGCCGT ACTGTTCACA CCCTTGTGGC
	TGTGGGCGAT
1251	TACCCGGAAA AACATACGCG GCAGGCAGGC GGTTACCAAC
	TGGGCGGCAG
1301	GCGTTACCCT GACCTGGGCT TTGCTGATGA CGCTGTTCCT
	GCCGTGGCTG
1351	GACGCGGCGA AAAGCCACGC GCCCGTCGTC CGGAGTATGG
	AGGCATCGTT
1401	TTCCCCGGAA TTAAAACGGG AGCTTTCAGA CGGCATCGAG
	TGTATCGGCA
1451	TAGGCGGCGG CGACCTGCAC ACGCGGATTG TTTGGACGCA
	GTACGGCACA
1501	TTGCCGCACC GCGTCGGCGA TGTCCGTTGC CGCTACCGTA
	TCGTCCGCCT
1551	GCCCCAAAAC GCGGATGCGC CGCAAGGCTG GCAGACGGTC
	TGGCAGGGTG
1601	CGCGCCCGCG CAACAAAGAC AGTAAGTTTG CACTGATACG
	GAAAATCGGG
1651	GAAAATATAT TAAAAACAAC AGATTGA

This corresponds to the amino acid sequence <SEQ ID 602; ORF141ng-1>:

1	MLTYTPPDAR PPAKTHEKPW LLLLMAFAWL WPGVFSHDLW
	NPAEPAVYTA
51	VEALAGSPTP LVAHLFGQTD FGIPPVYLWV AAAFKHLLSP
	WAADPYDAAR
101	FAGVFFAVIG LTSCGFAGFN FLGRHHGRSV VLIHIGCIGL
	IPVAHFLNPA
151	AAAFAAAGLV LHGYSLARRR VIAASFLLGT GWTLMSLAAA
	YPAAFALMLP
201	LPVLMFFRPW QSRRLMLTAV ASLAFALPLM TVYPLLLAKT
	QPALFAQWLN
251	YHVFGTFGGV RHIQRAFSLF HYLKNLLWFA PPGLPLAVWT
	VCRTRLFSTD
301	WGILGIVWML AVLVLLAFNP QRFQDNLVWL LPPLALFGAA
	QLDSLRRGAA
351	AFVNWFGIMA FGLFAVFLWT GFFAMNYGWP AKLAERAAYF
	SPYYVPDIDP
401	IPMAVAVLFT PLWLWAITRK NIRGRQAVTN WAAGVTLTWA
	LLMTLFLPWL
451	DAAKSHAPVV RSMEASFSPE LKRELSDGIE CIGIGGGDLH
	TRIVWTQYGT
501	LPHRVGDVRC RYRIVRLPQN ADAPQGWQTV WQGARPRNKD
	SKFALIRKIG
551	ENILKTTD*

ORF141ng-1 and ORF141-1 show 97.5% identity in 553 aa overlap:

Based on the presence of several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 72

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 603>:

1	..CAATCCGCCA AATGGTTATC GGGCCAAACT CTAGTCGGCA
	CAGCAATTGG
51	GATACGCGGG CAGATAAAGC TTGGCGGCAA CCTGCATTAC
	GATATATTTA
101	CCGGCCGCGC ATTGAAAAAG CCCGAATTTT TCCAATCAAG
	GAAATGGGCA
151	AGCGGTTTTC AGGTAGGCTA TACGTTTTAA

This corresponds to the amino acid sequence <SEQ ID 604; ORF142>:

1	..QSAKWLSGQT LVGTAIGIRG QIKLGGNLHY DIFTGRALKK
	PEFFQSRKWA
51	SGFQVGYTF*

Further work revealed the complete nucleotide sequence <SEQ ID 605>:

1	ATGGATAATT CGGGTAGTGA GGCGACAGGA AAATACCAAG
	GAAATATCAC
51	TTTCTCTGCC GACAATCCTT TGGGACTGAG TGATATGTTC
	TATGTAAATT
101	ATGGACGTTC GATTGGCGGT ACGCCCGATG AGGAAAGTTT
	TGACGGCCAT
151	CGCAAAGAAG GCGGATCAAA CAATTACGCC GTACATTATT
	CAGCCCCTTT
201	CGGTAAATGG ACATGGGCAT TCAATCACAA TGGCTACCGT
	TACCATCAGG
251	CAGTTTCCGG ATTATCGGAA GTCTATGACT ATAATGGAAA
	AAGTTACAAT
301	ACTGATTTCG GCTTCAACCG CCTGTTGTAT CGTGATGCCA
	AACGCAAAAC
351	CTATCTCGGT GTAAAACTGT GGATGAGGGA AACAAAAAGT
	TACATTGATG
401	ATGCCGAACT GACTGTACAA CGGCGTAAAA CTGCGGGTTG
	GTTGGCAGAA
451	CTTTCCCACA AAGAATATAT CGGTCGCAGT ACGGCAGATT
	TTAAGTTGAA
501	ATATAAACGC GGCACCGGCA TGAAAGATGC TCTGCGCGCG
	CCTGAAGAAG
551	CCTTTGGCGA AGGCACGTCA CGTATGAAAA TTTGGACGGC
	ATCGGCTGAT
601	GTAAATACTC CTTTTCAAAT CGGTAAACAG CTATTTGCCT
	ATGACACATC
651	CGTTCATGCA CAATGGAACA AAACCCCGCT AACATCGCAA
	GACAAACTGG
701	CTATCGGCGG ACACCACACC GTACGTGGCT TCGACGGTGA
	AATGAGTTTG
751	TCTGCCGAGC GGGGATGGTA TTGGCGCAAC GATTTGAGCT
	GGCAATTTAA
801	ACCAGGCCAT CAGCTTTATC TTGGGGCTGA TGTAGGACAT
	GTTTCAGGAC
851	AATCCGCCAA ATGGTTATCG GGCCAAACTC TAGTCGGCAC
	AGCAATTGGG
901	ATACGCGGGC AGATAAAGCT TGGCGGCAAC CTGCATTACG
	ATATATTTAC
951	CGGCCGCGCA TTGAAAAAGC CCGAATTTTT CCAATCAAGG
	AAATGGGCAA
1001	GCGGTTTTCA GGTAGGCTAT ACGTTTTAA

This corresponds to the amino acid sequence <SEQ ID 606; ORF142-1>:

1	MDNSGSEATG KYQGNITFSA DNPLGLSDMF YVNYGRSIGG
	TPDEESFDGH
51	RKEGGSNNYA VHYSAPFGKW TWAFNHNGYR YHQAVSGLSE
	VYDYNGKSYN
101	TDFGFNRLLY RDAKRKTYLG VKLWMRETKS YIDDAELTVQ
	RRKTAGWLAE
151	LSHKEYIGRS TADFKLKYKR GTGMKDALRA PEEAFGEGTS
	RMKIWTASAD
201	VNTPFQIGKQ LFAYDTSVHA QWNKTPLTSQ DKLAIGGHHT
	VRGFDGEMSL
251	SAERGWYWRN DLSWQFKPGH QLYLGADVGH VSGQSAKWLS
	GQTLVGTAIG
301	IRGQIKLGGN LHYDIFTGRA LKKPEFFQSR KWASGFQVGY
	TF*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. gonorrhoeae

ORF142 shows 88.1% identity over a 59aa overlap with a predicted ORF (ORF142ng) from N. gonorrhoeae:

The complete length ORF142ng nucleotide sequence <SEQ ID 607> is:

1	ATGGATAATT CGGGTAGTGA GGCGACAGGA AAATACCAAG
	GAAATATCAC
51	TTTCTCTGCC GACAATCCTT TTGGACTGAG TGATATGTTC
	TATGTAAATT
101	ATGGACGTTC AATTGGCGGT ACGCCCGATG AGGAAAATTT
	TGACGGCCAT
151	CGCAAAGAAG GCGGATCAAA CAATTACGCC GTACATTATT
	CAGCCCCTTT
201	CGGTAAATGG ACATGGGCAT TCAATCACAA TGGCTACCGT
	TACCATCAGG
251	CGGTTTCCGG ATTATCGGAA GTCTATGACT ATAATGGAAA
	AAGTTACAAC
301	ACTGATTTCG GCTTCAACCG CCTGTTGTAT CGTGATGCCA
	AACGCAAAAC
351	CTATCTCAGT GTAAAACTGT GGACGAGGGA AACAAAAAGT
	TACATTGATG
401	ATGCCGAACT GACTGTACAA CGGCGTAAAA CCACAGGTTG
	GTTGGCAGAA
451	CTTTCCCACA AAGGATATAT CGGTCGCAGT ACGGCAGATT
	TTAAGTTGAA
501	ATATAAACAC GGCACCGGCA TGAAAGATGC TCTGCGCGCG
	CCTGAAGAAG
551	CCTTTGGCGA AGGCACGTCA CGTATGAAAA TTTGGACGGC
	ATCGGCTGAT
601	GTAAATACTC CTTTTCAAAT CGGTAAACAG CTATTTGCCT
	ATGACACATC
651	CGTTCATGCA CAATGGAACA AAACCCCGCT AACATCGCAA
	GACAAACTGG
701	CTATCGGCGG ACACCACACC GTACGTGGCT TCGACGGTGA
	AATGAGTTTG
751	CCTGCCGAGC GGGGATGGTA TTGGCGCAAC GATTTGAGCT
	GGCAATTTAA
801	ACCAGGCCAT CAGCTTTATC TTGGGGCTGA TGTAGGACAT
	GTTTCAGGAC
851	AATCCGCCAA ATGGTTATCG GGCCAAACTC TAGCCGGCAC
	AGCAATTGGG
901	ATACGCGGGC AGATAAAGCT TGGCGGCAAC CTGCATTACG
	ATATATTTAC
951	CGGCCGTGCA TTGAAAAAGC CCGAATATTT TCAGACGAAG
	AAATGGGTAA
1001	CGGGGTTTCA GGTGGGTTAT TCGTTTTGA

This encodes a protein having amino acid sequence <SEQ ID 608>:

1	MDNSGSEATG KYQGNITFSA DNPFGLSDMF YVNYGRSIGG
	TPDEENFDGH
51	RKEGGSNNYA VHYSAPFGKW TWAFNHNGYR YHQAVSGLSE
	VYDYNGKSYN
101	TDFGFNRLLY RDAKRKTYLS VKLWTRETKS YIDDAELTVQ
	RRKTTGWLAE
151	LSHKGYIGRS TADFKLKYKH GTGMKDALRA PEEAFGEGTS
	RMKIWTASAD
201	VNTPFQIGKQ LFAYDTSVHA QWNKTPLTSQ DKLAIGGHHT
	VRGFDGEMSL
251	PAERGWYWRN DLSWQFKPGH QLYLGADVGH VSGQSAKWLS
	GQTLAGTAIG
301	IRGQIKLGGN LHYDIFTGRA LKKPEYFQTK KWVTGFQVGY
	SF*

The underlined sequence (aromatic-Xaa-aromatic amino acid motif) is usually found at the C-terminal end of outer membrane proteins.

ORF142ng and ORF142-1 show 95.6% identity over 342aa overlap:

In addition, ORF142ng is homologous to the HecB protein of E. chrysanthemi:

gi|1772622 (L39897) HecB [Erwinia chrysanthemi] Length = 558
Score = 119 bits (295), Expect = 3e−26
Identities = 88/346 (25%), Positives = 151/346 (43%),
Gaps = 22/346 (6%)

Query:	2	DNSGSEATGKYQGNITFSADNPFGLSDMFYVNYGRSIGGTPDEENFDGHRKEGGSNNYAV	61
		DNSG ++TG+ Q N + + DN FGL+D ++++ G S   +    + D    + G
Sbjct:	230	DNSGQKSTGEEQLNGSLALDNVFGLADQWFISAGHS---SRFATSHDAESLQAG------	280
Query:	62	HYSAPFGKWTWAFNHNGYRYHQAVSGLSEVYDYNGKSYNTDFGFNRLLYRDAKRKTYLSV	121
		+S P+G W   +N++  RY          +   G S    F  +R+++RD   KT ++
Sbjct:	281	-FSMPYGYWNLGYNYSQSRYRNTFINRDFPWHSTGDSDTHRFSLSRVVFRDGTMKTAIAG	339
Query:	122	KLWTRETKSYIDDAELTVQRRKTTGWLAELSHKGYIGRSTADFKLKYKHGTGMKDALRAP	181
		R   +Y++ + L    RK +     ++H   +    A F   Y  G     +
Sbjct:	340	TFSQRTGNNYLNGSLLPSSSRKLSSVSLGVNHSQKLWGGLATFNPTYNRGVRWLGSETDT	399
Query:	182	EEAFGEGTSRMKIWTASADVNTPFQIGKQLFAYDTSVHAQWNKTPLTSQDKLAIGGHHTV	241
		+++  E  +    WT SA    P         Y  S++ Q++   L   ++L +GG  ++
Sbjct:	400	DKSADEPRAEFNKWTLSASYYHPV---TDSITYLGSLYGQYSARALYGSEQLTLGGESSI	456
Query:	242	RGFDGEMSLPAERGWYWRNDLSWQFKP----GHQLYLGA-DVGHVSGQSAKWLSGQTLAG	296
		RGF  E      RG YWRN+L+WQ       G+  ++ A D GH+        +  +L G
Sbjct:	457	RGF-REQYTSGNRGAYWRNELNWQAWQLPVLGNVTFMAAVDGGHLYNHKQDNSTAASLWG	515
Query:	297	TAIGIRGQIKLGGNLHYDIFTGRALKKPEYFQTKKWVTGFQVGYSF	342
		A+G+    +    L   +  G  +  P + Q    V G++VG SF
Sbjct:	516	GAVGMTVASRW---LSQQVTVGWPISYPAWLQPDTMVVGYRVGLSF	558

On the basis of this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 73

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 609>:

1	ATGCGGACGA AATGGTCAGC AGTGAGAAGC TGCTTACTTG
	GgCGGACACC
51	GCCGACATCG ATACCGCTTT GAACCTGTTG TACCGTTTGC
	AAAAACTCGA
101	ATTCCTCTAT GGCGATGAAA ACGGTCATTC AGACGGCATC
	AATTTGwCGG
151	ACGAGCAATT GCCGTTGCTG ATGGAACAAT TGTCCGGCAG
	CGGTAAGGCG
201	TTATTGGTCG ATCGGAACGG TCTGTATCTT GCCAACGCCA
	ATTTCCATCA
251	TGAGGCGGCG GAAGAGTTGG GGTTGTTGGC GGCAGAAGTC
	GCACAGATGG
301	AAAAGAAATA CCGGCTGCTG ATTAAGAACA AC..

This corresponds to the amino acid sequence <SEQ ID 610; ORF143>:

1	MRTKWSAVRS CTWADTADID TALNLLYRLQ KLEFLYGDEN
	GHSDGINLXD
51	EQLPLLMEQL SGSGKALLVD RNGLYLANAN FHHEAAEELG
	LLAAEVAQME
101	KKYRLLIKNN ..

Further work revealed the complete nucleotide sequence <SEQ ID 611>:

1	ATGGAATCAA CACTTTCACT ACAAGCAAAT TTATATCCCC
	GCCTGACTCC
51	TGCCGGTGCA TTTTATGCCG TATCCAGCGA TGCCCCCAGT
	GCCGGTAAAA
101	CTTTGTTGCA CAGCCTGTTG AAAGCAGATG CGGACGAAAT
	GGTCAGCAGT
151	GAGAAGCTGC TTACTTGGGC GGACACCGCC GACATCGATA
	CCGCTTTGAA
201	CCTGTTGTAC CGTTTGCAAA AACTCGAATT CCTCTATGGC
	GATGAAAACG
251	GTCATTCAGA CGGCATCAAT TTGTCGGACG AGCAATTGCC
	GTTGCTGATG
301	GAACAATTGT CCGGCAGCGG TAAGGCGTTA TTGGTCGATC
	GGAACGGTCT
351	GTATCTTGCC AACGCCAATT TCCATCATGA GGCGGCGGAA
	GAGTTGGGGT
401	TGTTGGCGGC AGAAGTCGCA CAGATGGAAA AGAAATACCG
	GCTGCTGATT
451	AAGAACAACC TGTATATCAA CAATAACGCT TGGGGCGTTT
	GCGATCCTTC
501	CGGTCAGAGC GAATTGACAT TTTTCCCATT GTATATCGGT
	TCAACCAAAT
551	TTATTTTGGT TATCGGCGGC ATTCCCGATT TGGGCAAAGA
	GGCATTTGTT
601	ACTTTGGTAA GGATTTTATA CCGCCGTTAC AGCAACCGCG
	TGTAA

This corresponds to the amino acid sequence <SEQ ID 612; ORF143-1>:

1	MESTLSLQAN LYPRLTPAGA FYAVSSDAPS AGKTLLHSLL
	KADADEMVSS
51	EKLLTWADTA DIDTALNLLY RLQKLEFLYG DENGHSDGIN
	LSDEQLPLLM
101	EQLSGSGKAL LVDRNGLYLA NANFHHEAAE ELGLLAAEVA
	QMEKKYRLLI
151	KNNLYINNNA WGVCDPSGQS ELTFFPLYIG STKFILVIGG
	IPDLGKEAFV
201	TLVRILYRRY SNRV*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF143 shows 92.4% identity over a 105aa overlap with an ORF (ORF143a) from strain A of N. meningitidis:

The complete length ORF143a nucleotide sequence <SEQ ID 613> is:

1	ATGGAATCAA CANTTTCACT ACAAGCAAAT TTATATCNCC
	GCCTGACTCC
51	TGCCGGTGCA TTTTATGCCG TATCCAGCGA TGNCCCCAGT
	GCCGGTAAAA
101	CTTTGTTGCA CAGCCTGTTG AAAGCGGATG CGGACGAAAT
	GGTNAGCAGT
151	GAGAAGCTGC TTACCTGGGC GGANACCGCC GACATCGATA
	CCGCTTTGAA
201	CCTGTTGTAC CGTTTGCAAA AACTCGAATT CCTCTATGGC
	GATGAAAACG
251	GTCATTCAGA CGGCATCAAT TTGTCGGACG AGCAATTGCC
	GTTGCTGATG
301	GAACAATTGT CCGGCAGCGG TAAGGCGTTA TTGGTCGATC
	GGAACGGTCT
351	GTATCTTGCC AACGCCAATT TCCATCATGA GGCGGCGGAA
	GAGTTGGGGT
401	TGTTGGCGGC AGAAGTCGCA CAGATGGAAA AGAAATACCG
	GCTGCNNATT
451	AAGAACAACC TGTATATCAA CAATAACGCT TGGGGCGTTT
	GCGATCCTTC
501	CGGTCAGAGC GAATTGACAT TTTTCCCATT GTATATCGGT
	TCAACCAAAT
551	TTATTTTGGT TATCGGCGGC ATTCCCGATT TGGGCAAAGA
	GGCATTTGTT
601	ACTTTGGTAA GGATNTTATA CCNCCNGTTA CAGCAACCGC
	GTGTAAAACT
651	TGGGAGAGAG GANGGGTTAT GCAGCAATTA TTGA

This encodes a protein having amino acid sequence <SEQ ID 614>:

1	MESTXSLQAN LYXRLTPAGA FYAVSSDXPS AGKTLLHSLL
	KADADEMVSS
51	EKLLTWAXTA DIDTALNLLY RLQKLEFLYG DENGHSDGIN
	LSDEQLPLLM
101	EQLSGSGKAL LVDRNGLYLA NANFHHEAAE ELGLLAAEVA
	QMEKKYRLXI
151	KNNLYINNNA WGVCDPSGQS ELTFFPLYIG STKFILVIGG
	IPDLGKEAFV
201	TLVRXLYXXL QQPRVKLGRE XGLCSNY*

ORF143a and ORF143-1 show 97.1% identity in 207 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF143 shows 95.5% identity over a 110aa overlap with a predicted ORF (ORF143ng) from N. gonorrhoeae:

An ORF143ng nucleotide sequence <SEQ ID 615> was predicted to encode a protein having amino acid sequence <SEQ ID 616>:

1	MRTKWSAVRS CSRADTADID TALNLLYRLQ KLEFLYGDEN
	GHSDGINLSD
51	EQLPLLMEQL SGSGKALLVD RNGLYLANAN FHHESAEELG
	LLAAEVAQME
101	KKYRLLIRNN LYINNNAWGV CDPSGQSELT FFPLYIGSTK
	FILVIAGIPD
151	LSKGGICYFG KDFIPPLQQP RVKLGTGGIM RQLLISILED
	LNNTSTDIIA
201	SAVISTDGLP MATMLPSHLN SDRVGAISAT LLALGSRSVQ
	ELACGELEQV
251	MIKGKSGYIL LSQAGKDAVL VLVAKETGRL GLILLDAKRA
	ARHIAEAI*

Further work revealed the following gonococcal DNA sequence <SEQ ID 617>:

1	ATGGAATCAA CACTTTCACT ACAAGCGAAT TTATATCCCT
	GCCTGACTCC
51	TGCCGGTGCA TTTTATGCCG TATCCAGCGA TGCCCCCAGT
	GCCGGTAAAA
101	CTTTGTTGCG CAGCCTGTTG AAAGCGGATG CGGACGAAGT
	GGTCAGCAGT
151	GAGAAGCTGC TCGCGGCGGA CACCGCCGAC ATCGATACCG
	CTTTGAACCT
201	GTTGTACCGT TTGCAAAAAC TCGAATTCCT CTATGGCGAT
	GAAAACGGTC
251	ATTCAGACGG CATCAATTTG TCGGACGAGC AATTGCCGTT
	GCTGATGGAA
301	CAATTGTCCG GCAGCGGTAA GGCATTATTG GTCGATCGGA
	ACGGTCTGTA
351	TCTTGCCAAC GCCAATTTCC ATCATGAGTC GGCGGAAGAG
	TTGGGGTTGT
401	TGGCGGCAGA AGTCGCACAG ATGGAAAAGA AATACCGGCT
	GCTGATTAGG
451	AACAACCTGT ATATCAACAA TAACGCTTGG GGCGTTTGCG
	ATCCTTCCGG
501	TCAGAGCGAA TTGACATTTT TCCCATTGTA TATCGGTTCA
	ACCAAATTTA
551	TTTTGGTTAT CGCCGGCATT CCCGATTTGA GCAAAGAGGC
	ATTTGTTACT
601	TTGGTAAGGA TTTTATACCG CCGTTACAGC AACCGCGTGT
	AA

This corresponds to the amino acid sequence <SEQ ID 618; ORF143ng-1>:

1	MESTLSLQAN LYPCLTPAGA FYAVSSDAPS AGKTLLRSLL
	KADADEVVSS
51	EKLLAADTAD IDTALNLLYR LQKLEFLYGD ENGHSDGINL
	SDEQLPLLME
101	QLSGSGKALL VDRNGLYLAN ANFHHESAEE LGLLAAEVAQ
	MEKKYRLLIR
151	NNLYINNNAW GVCDPSGQSE LTFFPLYIGS TKFILVIAGI
	PDLSKEAFVT
201	LVRILYRRYS NRV*

ORF143ng-1 and ORF143-1 show 95.8% identity in 214 aa overlap:

Based on the presence of the putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 74

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 619>:

1	ATGACCTTTT TACAACGTTT GCAAGGTTTG GCAGACAATA
	AAATCTGTGC
51	GTTTGCATGG TTCGTCGTCC GCCGCTTTGA TGAAGAACGC
	GTACCGCAGr
101	CGGCGGCAAG CATGACGTTT ACGACGCTGC TGGCACTCGT
	CCCCGTGCTG
151	ACCGTGATGG TGGCGGTCGC TTCGATTTTC CCCGTGTTCG
	ACCGCTGGTC
201	GGATTCGTTC GTCTCCTTCG TCAACCAAAC CATTGTGCCG
	CA.GGCGCGG
251	ACATGGTGTT CGACTATATC AATGCGTTCC GCGAGCAGGC
	GAACCGGCTG
301	ACGGCAATCG GCAGCGTGAT GCTGGTCGTT ACCTCGCTGA
	TGCTGATTCG
351	GACGATAGAC AATACGTTCA ACCGCATCTG GaCGGGTCAA
	wTyCCAGCGT
401	CCGTGGATG..

This corresponds to the amino acid sequence <SEQ ID 620; ORF144>:

1	MTFLQRLQGL ADNKICAFAW FVVRRFDEER VPQXAASMTF
	TTLLALVPVL
51	TVMVAVASIF PVFDRWSDSF VSFVNQTIVP XGADMVFDYI
	NAFREQANRL
101	TAIGSVMLVV TSLMLIRTID NTFNRIWRVX XQRPWM...

Further work revealed the complete nucleotide sequence <SEQ ID 621>:

1	ATGACCTTTT TACAACGTTT GCAAGGTTTG GCAGACAATA
	AAATCTGTGC
51	GTTTGCATGG TTCGTCGTCC GCCGCTTTGA TGAAGAACGC
	GTACCGCAGG
101	CGGCGGCAAG CATGACGTTT ACGACGCTGC TGGCACTCGT
	CCCCGTGCTG
151	ACCGTGATGG TGGCGGTCGC TTCGATTTTC CCCGTGTTCG
	ACCGCTGGTC
201	GGATTCGTTC GTCTCCTTCG TCAACCAAAC CATTGTGCCG
	CAGGGCGCGG
251	ACATGGTGTT CGACTATATC AATGCGTTCC GCGAGCAGGC
	GAACCGGCTG
301	ACGGCAATCG GCAGCGTGAT GCTGGTCGTT ACCTCGCTGA
	TGCTGATTCG
351	GACGATAGAC AATACGTTCA ACCGCATCTG GCGGGTCAAT
	TCCCAGCGTC
401	CGTGGATGAT GCAGTTTCTC GTCTATTGGG CTTTACTGAC
	GTTCGGGCCG
451	CTGTCTTTGG GCGTGGGCAT TTCCTTTATG GTCGGCTCGG
	TACAGGATGC
501	CGCGCTTGCC TCAGGTGCGC CGCAGTGGTC GGGCGCGTTG
	CGAACGGCGG
551	CGACGCTGAC CTTCATGACG CTTTTGCTGT GGGGGCTGTA
	CCGCTTCGTG
601	CCAAACCGCT TCGTTCCCGC GCGGCAGGCG TTTGTCGGGG
	CTTTGGCAAC
651	AGCGTTTTGT CTGGAAACCG CGCGCTCCCT CTTCACTTGG
	TATATGGGCA
701	ATTTCGACGG CTACCGCTCG ATTTACGGCG CGTTTGCCGC
	CGTGCCGTTT
751	TTTCTGTTGT GGCTGAACCT GTTGTGGACG CTGGTCTTGG
	GCGGCGCGGT
801	GCTGACTTCT TCACTCTCCT ACTGGCAGGG AGAAGCGTTC
	CGCAGGGGCT
851	TCGACTCGCG CGGACGGTTT GACGACGTGT TGAAAATCCT
	GCTGCTTCTG
901	GATGCGGCGC AAAAAGAAGG CAAAGCCTTG CCTGTTCAGG
	AGTTCAGACG
951	GCATATCAAT ATGGGCTACG ACGAGTTGGG CGAGCTTTTG
	GAAAAGCTGG
1001	CGCGGCACGG CTACATCTAT TCCGGCAGAC AGGGTTGGGT
	GTTGAAAACG
1051	GGGGCGGATT CGATTGAGTT GAACGAACTC TTCAAGCTCT
	TCGTTTACCG
1101	TCCGTTGCCT GTGGAAAGGG ATCATGTGAA CCAAGCTGTC
	GATGCGGTAA
1151	TGACACCGTG TTTGCAGACT TTGAACATGA CGCTGGCAGA
	GTTTGACGCT
1201	CAGGCGAAAA AACGGCAGTA G

This corresponds to, the amino acid sequence <SEQ ID 622; ORF144-1>:

1	MTFLQRLQGL ADNKICAFAW FVVRRFDEER VPQAAASMTF
	TTLLALVPVL
51	TVMVAVASIF PVFDRWSDSF VSFVNQTIVP QGADMVFDYI
	NAFREQANRL
101	TAIGSVMLVV TSLMLIRTID NTFNRIWRVN SQRPWMMQFL
	VYWALLTFGP
151	LSLGVGISFM VGSVQDAALA SGAPQWSGAL RTAATLTFMT
	LLLWGLYRFV
201	PNRFVPARQA FVGALATAFC LETARSLFTW YMGNFDGYRS
	IYGAFAAVPF
251	FLLWLNLLWT LVLGGAVLTS SLSYWQGEAF RRGFDSRGRF
	DDVLKILLLL
301	DAAQKEGKAL PVQEFRRHIN MGYDELGELL EKLARHGYIY
	SGRQGWVLKT
351	GADSIELNEL FKLFVYRPLP VERDHVNQAV DAVMTPCLQT
	LNMTLAEFDA
401	QAKKRQ*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF144 shows 96.3% identity over a 136aa overlap with an ORF (ORF144a) from strain A of N. meningitidis:

The complete length ORF144a nucleotide sequence <SEQ ID 623> is:

1	ATGACCTTTT TACAACGTTT GCAAGGTTTG GCAGACAATA
	AAATCTGTGC
51	GTTTGCATGG TTCGTCGTCC GCCGCTTTGA TGAAGAACGC
	GTACCGCAGG
101	CGGCGGCAAG CATGACGTTT ACGACACTGC TGGCACTCGT
	CCCCGTGCTG
151	ACCGTGATGG TGGCGGTCGC TTCGATTTTC CCCGTGTTCG
	ACCGNTGGTC
201	GGATTCGTTC GTCTCCTTCG TCAACCAAAC CATTGTGCCG
	CAGGGCGCGG
251	ACATGGTNTT CGACTATATC AATGCGTTCC GCGAGCAGGC
	GAACCGGCTG
301	ACGGCAATCG GCAGCGTGAT GCTGGTCGTT ACCTCGCNGA
	TGCTGATTCG
351	GACGATAGAC AATACGTTCA ACCGCATCTG GCGGGTCAAT
	TCCCAGCGTC
401	CGTGGATGAT GCAGTTTCTC GTCTATTGGG CTTTACTGAC
	GTTCGGGCCG
451	CTGTCTTTGG GCGTGGGCAT TTCCTTTATN GTCGGCTCGG
	TACAGGATGC
501	CGCGCTTGCC TCAGGTGCGC CGCAGTGGTC GGGCGCGTTG
	CGAACGGCGG
551	CGACGCTGAN CTTCATGACG CTTTTGCTGT GGGGGCTGTA
	CCGCTNCGTG
601	CCAAACCGCT TCGTTCCCGC GCGGCANGCG TTTGTCGGGG
	CTTTGGCAAC
651	AGCGTTCTGT CTGGAAACCG CGCGTTCCCT CTTTACTTGG
	TATATGGGCA
701	ATTTCGACGG CTACCGCTCG ATTTACGGNG CGTTTGCCGC
	CGTGCCGTTT
751	TTTCTGTTGT GGCTGAACCT GTTGTGGACG CTGGTCTTGG
	GCGGCGCGGT
801	GCTGACTTCT TCACTCTCCT ACTGGCAGGG AGAAGCGTTC
	CGCAGGGNCT
851	TCGACTCGCG CGGACGGTTT GACGACGTGT TGAAAATCCT
	GCTGCTTCTG
901	GATGCGGCGC AAAAAGAAGG CNAAGCCTTG CCTGTTCAGG
	AGTTCAGACG
951	GCATATCAAT ATGGGCTACG ACGAGTTGGG CGAGCTTTTG
	GAAAAGCTGG
1001	CGCGGCACGG CTACATCTAT TCCGGCAGAC AGGGTTGGGT
	GTTGAAAACG
1051	GGGGCGGATT CGATTGAGTT GAACGAACTC TTCAAGCTCT
	TCGTTTACCG
1101	TCCGTTGCCT GTGGAAAGGG ATCATGTGAA CCAAGCTGTC
	GATGCGGTAA
1151	TGATGCCGTG TTTGCAGACT TTGAACATGA CGCTGGCAGA
	GTTTGACGCT
1201	CAGGCGAAAA AACAGCAGCA ATCTTGA

This encodes a protein having amino acid sequence <SEQ ID 624>:

1	MTFLQRLQGL ADNKICAFAW FVVRRFDEER VPQAAASMTF
	TTLLALVPVL
51	TVMVAVASIF PVFDRWSDSF VSFVNQTIVP QGADMVFDYI
	NAFREQANRL
101	TAIGSVMLVV TSXMLIRTID NTFNRIWRVN SQRPWMMQFL
	VYWALLTFGP
151	LSLGVGISFX VGSVQDAALA SGAPQWSGAL RTAATLXFMT
	LLLWGLYRXV
201	PNRFVPARXA FVGALATAFC LETARSLFTW YMGNFDGYRS
	IYGAFAAVPF
251	FLLWLNLLWT LVLGGAVLTS SLSYWQGEAF RRXFDSRGRF
	DDVLKILLLL
301	DAAQKEGXAL PVQEFRRHIN MGYDELGELL EKLARHGYIY
	SGRQGWVLKT
351	GADSIELNEL FKLFVYRPLP VERDHVNQAV DAVMMPCLQT
	LNMTLAEFDA
401	QAKKQQQS*

ORF144a and ORF144-1 show 97.8% identity in 406 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF144 shows 91.2% identity over a 136aa overlap with a predicted ORF (ORF144ng) from N. gonorrhoeae:

The complete length ORF144ng nucleotide sequence <SEQ ID 625> is predicted to encode a protein having amino acid sequence <SEQ ID 626>:

1	MTFLQCWQGS ADNKICAFAW FVIRRFSEER VPQAAASMTF
	TTLLALVPVL
51	TVMVAVASIF PVFDRWSDSF VSFVNQTIVP QGADMVFDYI
	DAFRDQANRL
101	TAIGSVMLVV TSLMLIRTID NAFNRIWRVN TQRPWMMQFL
	VYWALLTFGP
151	LSLGVGISFM VGSVQDSVLS SGAQQWADAL KTAARLAFMT
	LLLWGLYRFV
201	PNRFVPARQA FVGALITAFC LETARFLFTW YMGNFDGYRS
	IYGAFAAVPF
251	FLLWLNLLWT LVLGGAVLTS SLSYWQGEAF RRGFDSRGRF
	DDVLKILLLL
301	DAAQKEGRTL SVQEFRRHIN MGYDELGELL EKLARYGYIY
	SGRQGWVLKT
351	GADSIELSEL FKLFVYRPLP VERDHVNQAV DAVMTPCLQT
	LNMTLAEFDA
401	QAKKQQQS*

Further work revealed the following gonococcal DNA sequence <SEQ ID 627>:

1	ATGACCTTTT TACAACGTTG GCAAGGTTTG GCGGACAATA
	AAATCTGTGC
51	ATTTGCATGG TTCGTCATCC GCCGTTTCAG TGAAGAGCGC
	GTACCGCAGG
101	CAGCGGCGAG CATGACGTTT ACGACACTGC TGGCACTCGT
	CCCCGTACTG
151	ACCGTAATGG TCGCGGTCGC TTCGATTTTC CCCGTGTTCG
	ACCGCTGGTC
201	GGATTCGTTC GTCTCCTTCG TCAACCAAAC CATTGTGCCG
	CAGGGCGCGG
251	ATATGGTGTT CGACTATATC GACGCATTCC GCGATCAGGC
	AAACCGGCTG
301	ACCGCCATCG GCAGCGTGAT GCTGGTCGTA ACCTCGCTGA
	TGCTGATTCG
351	GACGATAGAC AATGCGTTCA ACCGCATCTG GCGGGTTAAC
	ACGCAACGCC
401	CCTGGATGAT GCAGTTCCTC GTTTATTGGG CGTTGCTGAC
	TTTCGGGCCT
451	TTGTCTTTGG GTGTGGGCAT TTCCTTTATG GTCGGGTCGG
	TTCAAGACTC
501	CGTACTCTCC TCCGGAGCGC AACAATGGGC GGACGCGTTG
	AAGACGGCGG
551	CAAGGCTGGC TTTCATGACG CTTTTGCTGT GGGGGCTGTA
	CCGCTTCGTG
601	CCCAACCGCT TCGTGCCCGC CCGGCAGGCG TTTGTCGGAG
	CTTTGATTAC
651	GGCATTCTGC CTGGAGACGG CACGTTTCCT GTTCACCTGG
	TATATGGGCA
701	ATTTCGACGG CTACCGCTCG ATTTACGGCG CATTTGCCGC
	CGTGCCGTTT
751	TTCCTGCTGT GGTTAAACCT GCTGTGGACG CTGGTCTTGG
	GCGGGGCGGT
801	GCTGACTTCG TCGCTGTCTT ATTGGCAGGG CGAGGCCTTC
	CGCAGGGGAT
851	TCGACTCGCG CGGACGGTTT GACGACGTGT TGAAAATCCT
	GCTGCTTCTG
901	GATGCGGCGC AAAAAGAAGG CCGAACCCTG TCCGTTCAGG
	AGTTCAGACG
951	GCATATCAAT ATGGGTTACG ATGAATTGGG CGAGCTTTTG
	GAAAAGCTGG
1001	CGCGGTACGG CTATATCTAT TCCGGCAGAC AGGGCTGGGT
	TTTGAAAACG
1051	GGGGCGGATT CGATTGAGTT GAGCGAACTC TTCAAGCTCT
	TCGTGTACCG
1101	CCCGTTGCct gtggaAAGGG ATCATGTGAA CCAAGCTGtc
	gaTGCGGTAA
1151	TGAcgccgtG TTTGCAGACT TTGAACATGA CGCTGGCGGA
	GTTTGACGCT
1201	CAGgcgAAAA AACAGCAGCA GTCTTGA

This encodes a variant of ORF144ng, having the amino acid sequence <SEQ ID 628; ORF144ng-1>:

1	MTFLQCWQGL ADNKICAFAW FVIRRFSEER VPQAAASMTF
	TTLLALVPVL
51	TVMVAVASIF PVFDRWSDSF VSFVNQTIVP QGADMVFDYI
	DAFRDQANRL
101	TAIGSVMLVV TSLMLIRTID NAFNRIWRVN TQRPWMMQFL
	VYWALLTFGP
151	LSLGVGISFM VGSVQDSVLS SGAQQWADAL KTAARLAFMT
	LLLWGLYRFV
201	PNRFVPARQA FVGALITAFC LETARFLFTW YMGNFDGYRS
	IYGAFAAVPF
251	FLLWLNLLWT LVLGGAVLTS SLSYWQGEAF RRGFDSRGRF
	DDVLKILLLL
301	DAAQKEGRTL SVQEFRRHIN MGYDELGELL EKLARYGYIY
	SGRQGWVLKT
351	GADSIELSEL FKLFVYRPLP VERDHVNQAV DAVMTPCLQT
	LNMTLAEFDA
401	QAKKQQQS*

ORF144ng-1 and ORF144-1 show 94.1% identity in 406 aa overlap:

On this basis of this analysis, including the identification of several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 75

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 629>:

1	..AGACACGCCC GCCGCATCCG CATCGACACC GCCATCAACC
	CCGAACTGGA
51	AGCCCTCGCC GAACACCTCC ACTACCAATG GCAGGGCTTC
	CTCTGGCTCA
101	GCACCGATAT GCGTCAGGAA ATTTCCGCCC TCGTCATCCT
	GCTGCAACGC
151	ACCCGCCGCA AATGGCTGGA TGCCCACGAA CGCCAACACC
	TGCGCCAAAG
201	CCTGCTTGAA ACACGGGAAC ACGGCTGA

This corresponds to the amino acid sequence <SEQ ID 630; ORF146>:

1	..RHARRIRIDT AINPELEALA EHLHYQWQGF LWLSTDMRQE
	ISALVILLQR
51	TRRKWLDAHE RQHLRQSLLE TREHG*

Further work revealed the complete nucleotide sequence <SEQ ID 631>:

1	ATGAACACCT CGCAACGCAA CCGCCTCGTC AGCCGCTGGC
	TCAACTCCTA
51	CGAACGCTAC CGCTACCGCC GCCTCATCCA CGCCGTCCGG
	CTCGGCGGGG
101	CCGTCCTGTT CGCCACCGCC TCCGCCCGGC TGCTCCACCT
	CCAACACGGC
151	GAGTGGATAG GGATGACCGT CTTCGTCGTC CTCGGCATGC
	TCCAGTTTCA
201	AGGGGCGATT TACTCCAAGG CGGTGGAACG TATGCTCGGC
	ACGGTCATCG
251	GGCTGGGCGC GGGTTTGGGC GTTTTATGGC TGAACCAGCA
	TTATTTCCAC
301	GGCAACCTCC TCTTCTACCT CACCGTCGGC ACGGCAAGCG
	CACTGGCCGG
351	CTGGGCGGCG GTCGGCAAAA ACGGCTACGT CCCTATGCTG
	GCAGGGCTGA
401	CGATGTGTAT GCTCATCGGC GACAACGGCA GCGAATGGCT
	CGACAGCGGA
451	CTCATGCGCG CCATGAACGT CCTCATCGGC GCGGCCATCG
	CCATCGCCGC
501	CGCCAAACTG CTGCCGCTGA AATCCACACT GATGTGGCGT
	TTCATGCTTG
551	CCGACAACCT GGCCGACTGC AGCAAAATGA TTGCCGAAAT
	CAGCAACGGC
601	AGGCGCATGA CCCGCGAACG CCTCGAGGAG AACATGGCGA
	AAATGCGCCA
651	AATCAACGCA CGCATGGTCA AAAGCCGCAG CCATCTCGCC
	GCCACATCGG
701	GCGAAAGCCG CATCAGCCCC GCCATGATGG AAGCCATGCA
	GCACGCCCAC
751	CGTAAAATCG TCAACACCAC CGAGCTGCTC CTGACCACCG
	CCGCCAAGCT
801	GCAATCTCCC AAACTCAACG GCAGCGAAAT CCGGCTGCTT
	GACCGCCACT
851	TCACACTGCT CCAAACCGAC CTGCAACAAA CCGTCGCCCT
	TATCAACGGC
901	AGACACGCCC GCCGCATCCG CATCGACACC GCCATCAACC
	CCGAACTGGA
951	AGCCCTCGCC GAACACCTCC ACTACCAATG GCAGGGCTTC
	CTCTGGCTCA
1001	GCACCAATAT GCGTCAGGAA ATTTCCGCCC TCGTCATCCT
	GCTGCAACGC
1051	ACCCGCCGCA AATGGCTGGA TGCCCACGAA CGCCAACACC
	TGCGCCAAAG
1101	CCTGCTTGAA ACACGGGAAC ACGGCTGA

This corresponds to the amino acid sequence <SEQ ID 632; ORF146-1>:

1	MNTSQRNRLV SRWLNSYERY RYRRLIHAVR LGGAVLFATA
	SARLLHLQHG
51	EWIGMTVFVV LGMLQFQGAI YSKAVERMLG TVIGLGAGLG
	VLWLNQHYFH
101	GNLLFYLTVG TASALAGWAA VGKNGYVPML AGLTMCMLIG
	DNGSEWLDSG
151	LMRAMNVLIG AAIAIAAAKL LPLKSTLMWR FMLADNLADC
	SKMIAEISNG
201	RRMTRERLEE NMAKMRQINA RMVKSRSHLA ATSGESRISP
	AMMEAMQHAH
251	RKIVNTTELL LTTAAKLQSP KLNGSEIRLL DRHFTLLQTD
	LQQTVALING
301	RHARRIRIDT AINPELEALA EHLHYQWQGF LWLSTNMRQE
	ISALVILLQR
351	TRRKWLDAHE RQHLRQSLLE TREHG*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF146 shows 98.6% identity over a 74aa overlap with an ORF (ORF146a) from strain A of N. meningitidis:

The complete length ORF146a nucleotide sequence <SEQ ID 633> is:

1	ATGAACACCT CGCAACGCAA CCGCCTCGTC AGCCGCTGGC
	TCAACTCCTA
51	CGAACGCTAC CGCTACCGCC GCCTCATCCA CGCCGTCCGG
	CTCGGCGGGG
101	CCGTCCTGTT CGCCACCGCC TCCGCCCGGC TGCTCCACCT
	CCAACACGGC
151	GAGTGGATAG GGATGACCGT CTTCGTCGTC CTCGGCATGC
	TCCAGTTTCA
201	AGGGGCGATT TACTCCAAGG CGGTGGAACG TATGCTCGGC
	ACGGTCATCG
251	GGCTGGGCGC GGGTTTGGGC GTTTTATGGC TGAACCAGCA
	TTATTTCCAC
301	GGCAACCTCC TCTTCTACCT CACCGTCGGC ACGGCAAGCG
	CACTGGCCGG
351	CTGGGCGGCG GTCGGCAAAA ACGGCTACGT CCCTATGCTG
	GCGGGGCTGA
401	CGATGTGCAT GCTCATCGGC GACAACGGCA GCGAATGGTT
	CGACAGCGGC
451	CTGATGCGCG CGATGAACGT CCTCATCGGC GCGGCCATCG
	CCATCGCCGC
501	CGCCAAACTG CTGCCGCTGA AATCCACACT GATGTGGCGT
	TTCATGCTTG
551	CCGACAACCT GACCGACTGC AGCAAAATGA TTGCCGAAAT
	CAGCAACGGC
601	AGGCGCATGA CCCGCGAACG CCTCGAAGAG AACATGGCGA
	AAATGCGCCA
651	AATCAACGCA CGCATGGTCA AAAGCCGCAG CCACCTCGCC
	GCCACATCGG
701	GCGAAAGCCG CATCAGCCCC GCCATGATGG AAGCCATGCA
	GCACGCCCAC
751	CGTAAAATTG TCAACACCAC CGAGCTGCTC CTGACCACCG
	CCGCCAAGCT
801	GCAATCTCCC AAACTCAACG GCAGCGAAAT CCGGCTGCTT
	GACCGCCACT
851	TCACACTGCT CCAAACCGAC CTGCAACAAA CCGTCGCCCT
	TATCAACGGC
901	AGACACGCCC GCCGCATCCG CATCGACACC GCCATCAACC
	CCGAACTGGA
951	AGCCCTCGCC GAACACCTCC ACTACCAATG GCAGGGCTTC
	CTCTGGCTCA
1001	GCACCAATAT GCGTCAGGAA ATTTCCGCCC TCGTCATCCT
	GCTGCAACGC
1051	ACCCGCCGCA AATGGCTGGA TGCCCACGAA CGCCAACACC
	TGCGCCAAAG
1101	CCTGCTTGAA ACACGGGAAC ACAGTTGA

This encodes a protein having amino acid sequence <SEQ ID 634>:

1	MNTSQRNRLV SRWLNSYERY RYRRLIHAVR LGGAVLFATA
	SARLLHLQHG
51	EWIGMTVFVV LGMLQFQGAI YSKAVERMLG TVIGLGAGLG
	VLWLNQHYFH
101	GNLLFYLTVG TASALAGWAA VGKNGYVPML AGLTMCMLIG
	DNGSEWFDSG
151	LMRAMNVLIG AAIAIAAAKL LPLKSTLMWR FMLADNLTDC
	SKMIAEISNG
201	RRMTRERLEE NMAKMRQINA RMVKSRSHLA ATSGESRISP
	AMMEAMQHAH
251	RKIVNTTELL LTTAAKLQSP KLNGSEIRLL DRHFTLLQTD
	LQQTVALING
301	RHARRIRIDT AINPELEALA EHLHYQWQGF LWLSTNMRQE
	ISALVILLQR
351	TRRKWLDAHE RQHLRQSLLE TREHS*

ORF146a and ORF146-1 show 99.5% identity in 374 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF146 shows 97.3% identity over a 75aa overlap with a predicted ORF (ORF146ng) from N. gonorrhoeae:

An ORF146ng nucleotide sequence <SEQ ID 635> was predicted to encode a protein having amino, acid sequence <SEQ ID 636>:

1	MSGVRFPSPA PIPSTDPPSG SLCFFTFPLQ TASDMNSSQR
	KRLSGRWLNS
51	YERYRHRRLI HAVRLGGTVL FATALARLLH LQHGEWIGMT
	VFVVLGMLQF
101	QGAIYSNAVE RMLGTVIGLG AGLGVLWLNQ HYFHGNLLFY
	LTIGTASALA
151	GWAAVGKNGY VPMLAGLTMC MLIGDNGSEW LDSGLMRAMN
	VLIGAAIAIA
201	AAKLLPLKST LMWRFMLADN LADCSKMIAE ISNGRRMTRE
	RLEQNMVKMR
251	QINARMVKSR SHLAATSGES RISPSMMEAM QHAHRKIVNT
	TELLLTTAAK
301	LQSPKLNGSE IRLLDRHFTL LQTDLQQTAA LINGRHARRI
	RIDTAINPEL
351	EALAEHLHYQ WQGFLWLSTN MRQEISALVI PLQRTRRKWL
	DAHERQHLRQ
401	SLLETREHG*

Further work revealed the following gonococcal DNA sequence <SEQ ID 637>:

1	ATGAACTCCT CGCAACGCAA ACGCCTTTCC GgccGCTGGC
	TCAACTCCTA
51	CGAACGCTac cGCCaccGCC GCCTCATACA TGCCGTGCGG
	CTCGGCggaa
101	ccgtCCTGTT CGCCACCGCA CTCGCCCGgc tACTCCACCT
	CCAacacggc
151	gAATGGATAG GGAtgaCCGT CTTCGTCGTC CTCGGCATGC
	TCCAGTTCCA
201	AGGCgcgatt tActccaacg cggtgGAacg taTGctcggt
	acggtcatcg
251	ggctgGGCGC GGGTTTGGgc gTTTTATGGC TGAACCAGCA
	TTAtttccac
301	ggcaacCTcc tcttctacct gaccatcggc acggcaagcg
	cactggccgg
351	ctGGGCGGCG GTCGGCAAAA acggctacgt ccctatgctg
	GCGGGGctgA
401	CGATGTGCAT gctcatcggc gACAACGGCA GCGAATGGCT
	CGACAGCGGC
451	CTGATGCGCG CGATGAACGT CCTCATCGGC GCCGCCATCG
	CCATTGCCGC
501	CGCCAAACTG CTGCCGCTGA AATCCACACT GATGTGGCGT
	TTCATGCTTG
551	CCGACAACCT GGCCGACTGC AGCAAAATGA TTGCCGAAAT
	CAGCAACGGC
601	AGGCGTATGA CGCGCGAACG TTTGGAGCAG AATATGGTCA
	AAATGCGCCA
651	AATCAACGCA CGCATGGTCA AAAGCCGCAG CCACCTCGCC
	GCCACATCGG
701	GCGAAAGCCG CATCAGCCCC TCCATGATGG AAGCCATGCA
	GCACGCCCAC
751	CGCAAAATCG TCAACACCAC CGAGCTGCTC CTGACCACCG
	CCGCCAAGCT
801	GCAATCTCCC AAACTCAACG GCAGCGAAAT CCGGCTGCTC
	GACCGCCACT
851	TCACACTGCT CCAAACCGAC CTGCAACAAA CCGCCGCCCT
	CATCAACGGC
901	AGACACGCCC GCCGCATCCG CATCGACACC GCCATCAACC
	CCGAACTGGA
951	AGCCCTCGCC GAACACCTCC ACTACCAATG GCAGGGCTTC
	CTCTGGCTCA
1001	GCACCAATAT GCGTCAGGAA ATTTCCGCCC TCGTCATCCT
	GCTGCAACGC
1051	ACCCGCCGCA AATGGCTGGA TGCCCACGAA CGCCAACACC
	TGCGCCAAAG
1101	CCTGCTTGAA ACACGGGAAC ACGGCTGA

This corresponds to the amino acid sequence <SEQ ID 638; ORF146ng-1>:

1	MNSSQRKRLS GRWLNSYERY RHRRLIHAVR LGGTVLFATA
	LARLLHLQHG
51	EWIGMTVFVV LGMLQFQGAI YSNAVERMLG TVIGLGAGLG
	VLWLNQHYFH
101	GNLLFYLTIG TASALAGWAA VGKNGYVPML AGLTMCMLIG
	DNGSEWLDSG
151	LMRAMNVLIG AAIAIAAAKL LPLKSTLMWR FMLADNLADC
	SKMIAEISNG
201	RRMTRERLEQ NMVKMRQINA RMVKSRSHLA ATSGESRISP
	SMMEAMQHAH
251	RKIVNTTELL LTTAAKLQSP KLNGSEIRLL DRHFTLLQTD
	LQQTAALING
301	RHARRIRIDT AINPELEALA EHLHYQWQGF LWLSTNMRQE
	ISALVILLQR
351	TRRKWLDAHE RQHLRQSLLE TREHG*

ORF146ng-1 and ORF146-1 show 96.5% identity in 375 aa overlap

Furthermore, ORF146ng-1 shows homology with a hypothetical E. coli protein:

sp|P33011|YEEA_ECOLI HYPOTHETICAL 40.0 KD PROTEIN IN
COBU-SBMC INTERGENIC REGION
>gi|1736674|gnl|PID|d1016553 (D90838) ORF_ID: o348#20;
similar to [SwissProt Accession Number P33011] [Escherichia coli]
>gi|1736682|gnl|PID|d1016560 (D90839) ORF_ID: o348#20;
similar to [SwissProt Accession Number P33011] [Escherichia coli]
>gi|1788318 (AE000292) f352; 100% identical to fragment YEEA_ECOLI
SW: P33011 but has 203 additional C-terminal residues [Escherichia coli]
Length = 352 Score = 109 bits (271), Expect = 2e−23
Identities = 89/347 (25%), Positives = 150/347 (42%), Gaps = 21/347 (6%)

Query:	20	YRHRRLIHAVRLGGTVLFATALARLLHLQHGEWIGMTVFVVLGMLQFQGAIYSNAVERML	79
		YRH R++H  R+    L    + RL  +    W  +T+ V++G + F G +   A ER+
Sbjct:	15	YRHYRIVHGTRVALAFLLTFLIIRLFTIPESTWPLVTMVVIMGPISFWGNVVPRAFERIG	74
Query:	80	GTVIGLGAGLGVLWLNQHYFHGNLLFYLTIGTASALAGWAAVGKNGYVPMLAGLTMCMLI	139
		GTV+G   GL  L L         L  +    A  L GW A+GK  Y  +L G+T+ +++
Sbjct:	75	GTVLGSILGLIALQLE---LISLPLMLVWCAAAMFLCGWLALGKKPYQGLLIGVTLAIVV	131
Query:	140	GDNGSEWLDSGLMRAMNVLIGXXXXXXXXKLLPLKSTLMWRFMLADNLADCSKMIAEISN	199
		G    E +D+ L R+ +V++G         + P ++ + WR  LA +L + +++     +
Sbjct:	132	GSPTGE-IDTALWRSGDVILGSLLAMLFTGIWPQRAFIHWRIQLAKSLTEYNRVYQSAFS	190
Query:	200	GRRMTRERLEQNMVKMRQINARMVKSRSHLAATSGESRISPSMMEAMQHAHRKIVNXXXX	259
		+ R RLE ++ K+       VK R  +A  S E+RI  S+ E +Q  +R +V
Sbjct:	191	PNLLERPRLESHLQKLL---TDAVKMRGLIAPASKETRIPKSIYEGIQTINRNLVCMLEL	247
Query:	260	XXXXXXXXQSPK---LNGSEIRLLDRHFXXXXXXXXXXAALINGRHARRIRIDTAINPEL	316
		+      LN  ++R  D              AL  G           +N  +
Sbjct:	248	QINAYWATRPSHFVLLNAQKLR--DTQHMMQQILLSLVHALYEGNPQPVFANTEKLNDAV	305
Query:	317	EALAEHL--HYQWQ-------GFLWLSTNMRQEISALVILLQRTRRK	354
		E L + L  H+  +       G++WL+     ++  L  L+ R  RK
Sbjct:	306	EELRQLLNNHHDLKVVETPIYGYVWLNMETAHQLELLSNLICRALRK	352

On the basis of this analysis, including the identification of several transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 76

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 639>

1	..GCCGAAGACA CGCGCGTTAC CGCACAGCTT TTGAGCGCGT
	ACGGCATTCA
51	GGGCAAACTC GTCAGTGTGC GCGAACACAA CGAACGGCAG
	ATGGCGGACA
101	AGATTGTCGG CTATCTTTCA GACGGCATGG TTGTGGCACA
	GGTTTCCGAT
151	GCGGGTACGC CGGCCGTGTG CGACCCGGGC GCGAAACTCG
	CCCGCCGCGT
201	GCGTGAGGCC GGGTTTAAAG TCGTTCCCGT CGTGGGCGCA
	AC.GCGGTGA
251	TGGCGGCTTT GAGCGTGGCC GGTGTGGAAG GATCCGATTT
	TTATTTCAAC
301	GGTTTTGTAC CGCCGAAATC GGGAGAACGC AGGAAACTGT
	TTGCCAAATG
351	GGTGCGGGCG GCGTTTCCTA TCGTCATGTT TGAAACGCCG
	CACCGCATCG
401	GTGCAGCGCT TGCCGATATG GCGGAACTGT TCCCCGAACG
	CCGATTAATG
451	CTGGCGCGCG AAATTACGAA AACGTTTGAA ACGTTCTTAA
	GCGGCACGGT
501	TGGGGAAATT CAGACGGCAT TGTCTGCCGA CGGCGACCAA
	TCGCGCGGCG
551	AGATGGTGTT GGTGCTTTAT CCGGCGCAGG ATGAAAAACA
	CGAAGGCTTG
601	TCCGAGTCCG CGCAAAACAT CATGAAAATC CTCACAGCCG
	AGCTGCCGAC
651	CAAACAGGCG GCGGAGCTTG CTGCCAAAAT CACGGGCGAG
	GGAAAGAAAG
701	CTTTGTACGA T..

This corresponds to the amino acid sequence <SEQ ID 640; ORF147>:

1	..AEDTRVTAQL LSAYGIQGKL VSVREHNERQ MADKIVGYLS
	DGMVVAQVSD
51	AGTPAVCDPG AKLARRVREA GFKVVPVVGA XAVMAALSVA
	GVEGSDFYFN
101	GFVPPKSGER RKLFAKWVRA AFPIVMFETP HRIGAALADM
	AELFPERRLM
151	LAREITKTFE TFLSGTVGEI QTALSADGDQ SRGEMVLVLY
	PAQDEKHEGL
201	SESAQNIMKI LTAELPTKQA AELAAKITGE GKKALYD..

Further work revealed the complete nucleotide sequence <SEQ ID 641>:

1	ATGTTTCAGA AACATTTGCA GAAAGCCTCC GACAGCGTCG
	TCGGAGGGAC
51	ATTATACGTG GTTGCCACGC CCATCGGCAA TTTGGCGGAC
	ATTACCCTGC
101	GCGCTTTGGC GGTATTGCAA AAGGCGGACA TCATCTGTGC
	CGAAGACACG
151	CGCGTTACCG CACAGCTTTT GAGCGCGTAC GGCATTCAGG
	GCAAACTCGT
201	CAGTGTGCGC GAACACAACG AACGGCAGAT GGCGGACAAG
	ATTGTCGGCT
251	ATCTTTCAGA CGGCATGGTT GTGGCACAGG TTTCCGATGC
	GGGTACGCCG
301	GCCGTGTGCG ACCCGGGCGC GAAACTCGCC CGCCGCGTGC
	GTGAGGCCGG
351	GTTTAAAGTC GTTCCCGTCG TGGGCGCAAG CGCGGTGATG
	GCGGCTTTGA
401	GCGTGGCCGG TGTGGAAGGA TCCGATTTTT ATTTCAACGG
	TTTTGTACCG
451	CCGAAATCGG GAGAACGCAG GAAACTGTTT GCCAAATGGG
	TGCGGGCGGC
501	GTTTCCTATC GTCATGTTTG AAACGCCGCA CCGCATCGGT
	GCGACGCTTG
551	CCGATATGGC GGAACTGTTC CCCGAACGCC GATTAATGCT
	GGCGCGCGAA
601	ATTACGAAAA CGTTTGAAAC GTTCTTAAGC GGCACGGTTG
	GGGAAATTCA
651	GACGGCATTG TCTGCCGACG GCAACCAATC GCGCGGCGAG
	ATGGTGTTGG
701	TGCTTTATCC GGCGCAGGAT GAAAAACACG AAGGCTTGTC
	CGAGTCCGCG
751	CAAAACATCA TGAAAATCCT CACAGCCGAG CTGCCGACCA
	AACAGGCGGC
801	GGAGCTTGCT GCCAAAATCA CGGGCGAGGG AAAGAAAGCT
	TTGTACGATC
851	TGGCTCTGTC TTGGAAAAAC AAATAG

This corresponds to the amino acid sequence <SEQ ID 642; ORF147-1>:

1	MFQKHLQKAS DSVVGGTLYV VATPIGNLAD ITLRALAVLQ
	KADIICAEDT
51	RVTAQLLSAY GIQGKLVSVR EHNERQMADK IVGYLSDGMV
	VAQVSDAGTP
101	AVCDPGAKLA RRVREAGFKV VPVVGASAVM AALSVAGVEG
	SDFYFNGFVP
151	PKSGERRKLF AKWVRAAFPI VMFETPHRIG ATLADMAELF
	PERRLMLARE
201	ITKTFETFLS GTVGEIQTAL SADGNQSRGE MVLVLYPAQD
	EKHEGLSESA
251	QNIMKILTAE LPTKQAAELA AKITGEGKKA LYDLALSWKN
	K*

Computer analysis of this amino acid sequence gave the following results:

Homology with Hypothetical Protein ORF286 of E. coli (Accession Number U 18997)

ORF147 and E. coli ORF286 protein show 36% aa identity in 237aa overlap:

Orf147:	1	AEDTRVTAQLLSAYGIQGKLVSVREHNERQMADKIVGYLSDGMVVAQVSDAGTPAVCDPG	60
		AEDTR T  LL  +GI  +L ++ +HNE+Q A+ ++  L +G  +A VSDAGTP + DPG
Orf286:	43	AEDTRHTGLLLQHFGINARLFALHDHNEQQKAETLLAKLQEGQNIALVSDAGTPLINDPG	102
Orf147:	61	AKLARRVREXXXXXXXXXXXXXXXXXXXXXXXEGSDFYFNGFVPPKSGERRKLFAKWVRA	120
		L R  RE                           F + GF+P KS  RR
Orf286:	103	YHLVRTCREAGIRVVPLPGPCAAITALSAAGLPSDRFCYEGFLPAKSKGRRDALKAIEAE	162
Orf147:	121	AFPIVMFETPHRIGAALADMAELFPERR-LMLAREITKTFETFLSGTVGEIQTALSADGD	179
		++ +E+ HR+  +L D+  +  E R ++LARE+TKT+ET     VGE+   +  D +
Orf286:	163	PRTLIFYESTHRLLDSLEDIVAVLGESRYVVLARELTKTWETIHGAPVGELLAWVKEDEN	222
Orf147:	180	QSRGEMVLVLYPAQDEKHEGLSESAQNIMKILTAELPTKQAAELAAKITGEGKKALY	236
		+ +GEMVL++      + E L   A   + +L AELP K+AA LAA+I G  K ALY
Orf286:	223	RRKGEMVLIV-EGHKAQEEDLPADALRTLALLQAELPLKKAAALAAEIHGVKKNALY	278

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF147 shows 96.6% identity over a 237aa overlap with ORF75a from strain A of N. meningitidis:

ORF147a is identical to ORF75a, which includes aa 56-292 of ORF75.

Homology with a Predicted ORF from N. gonorrhoeae

ORF147 shows 94.1% identity over a 237aa overlap with a predicted ORF (ORF147ng) from N. gonorrhoeae:

An ORF147ng nucleotide sequence <SEQ ID 643> was predicted to encode a protein having amino acid sequence <SEQ ID 644>:

1	MSVFQTAFFM FQKHLQKASD SVVGGTLYVV ATPIGNLADI
	TLRALAVLQK
51	ADIICAEDTR VTAQLLSAYG IQGRLVSVRE HNERQMADKV
	IGFLSDGLVV
101	AQVSDAGTPA VCDPGAKLAR RVREAGFKVV PVVGASAVMA
	ALSVAGVAES
151	DFYFNGFVPP KSGERRKLFA KWVRAAFPVV MFETPHRIGA
	TLADMAELFP
201	ERRLMLAREI TKTFETFLSG TVGEIQTALA ADGNQSRGEM
	VLVLYPAQDE
251	KHEGLSESAQ NAMKILAAEL PTKQAAELAA KITGEGKKAL
	YDLALSWKNK
301	*

Further work revealed the following gonococcal DNA sequence <SEQ ID 645>:

1	ATGTTTCAGA AACACTTGCA GAAAGCCTCC GACAGCGTCG
	TCGGAGGGAC
51	ATTATACGTG GTTGCCACGC CCATCGGCAA TTTGGCAGAC
	ATTACCCTGC
101	GCGCTTTGGC GGTATTGCAA AAGGCGGACA TCATTTGTGC
	CGAAGACACG
151	CGCGTTACTG CGCAGCTTTT GAGCGCGTAC GGCATTCAGG
	GCAGGTTGGT
201	CAGTGTGCGC GAACACAACG AGCGGCAGAT GGCGGACAAG
	GTAATCGGTT
251	TCCTTTCAGA CGGCCTGGTT GTGGCGCAGG TTTCCGATGC
	GGGTACGCCG
301	GCCGTGTGCG ACCCGGGCGC GAAACTCGCC CGCCGCGTGC
	GCGAAGCAGG
351	GTTCAAAGTC GTTCCCGTCG TGGGCGCAAG CGCGGTAATG
	GCGGCGTTGA
401	GTGTGGCCGG TGTGGCGGAA TCCGATTTTT ATTTCAACGG
	TTTTGTACCG
451	CCGAAATCGG GCGAACGTAG GAAATTGTTT GCCAAATGGG
	TGCGGGCGGC
501	ATTTCCTGTC GTCATGTTTG AAACGCCGCA CCGAATCGGG
	GCAACGCTTG
551	CCGATATGGC GGAATTGTTC CCCGAACGCC GTCTGATGCT
	GGCGCGCGAA
601	ATCACGAAAA CGTTTGAAAC GTTCTTAAGC GGCACGGTTG
	GGGAAATTCA
651	GACGGCATTG GCGGCGGACG GCAACCAATC GCGCGGCGAG
	ATGGTGTTGG
701	TGCTTTATCC GGCGCAGGAT GAAAAACACG AAGGCTTGTC
	CGAGTCTGCG
751	CAAAATGCGA TGAAAATCCT TGCGGCCGAG CTGCCGACCA
	AGCAGGCGGC
801	GGAGCTTGCC GCCAAGATTA CAGGTGAGGG CAAAAAGGCT
	TTGTACGATT
851	TGGCACTGTC GTGGAAAAAC AAATGA

This corresponds to the amino acid sequence <SEQ ID 646; ORF147ng-1>:

1	MFQKHLQKAS DSVVGGTLYV VATPIGNLAD ITLRALAVLQ
	KADIICAEDT
51	RVTAQLLSAY GIQGRLVSVR EHNERQMADK VIGFLSDGLV
	VAQVSDAGTP
101	AVCDPGAKLA RRVREAGFKV VPVVGASAVM AALSVAGVAE
	SDFYFNGFVP
151	PKSGERRKLF AKWVRAAFPV VMFETPHRIG ATLADMAELF
	PERRLMLARE
201	ITKTFETFLS GTVGEIQTAL AADGNQSRGE MVLVLYPAQD
	EKHEGLSESA
251	QNAMKILAAE LPTKQAAELA AKITGEGKKA LYDLALSWKN
	K*

ORF147ng shows homology to a hypothetical E. coli protein:

sp|P45528|YRAL_ECOLI HYPOTHETICAL 31.3 KD PROTEIN IN AGAI-MTR
INTERGENIC REGION (F286)
>gi|606086 (U18997) ORF_f286 [Escherichia coli]
>gi|1789535 (AE000395) hypothetical 31.3 kD protein in agai-mtr intergenic region
[Escherichia coli] Length = 286
Score = 218 bits (550), Expect = 3e−56
Identities = 128/284 (45%), Positives = 171/284 (60%), Gaps = 4/284 (1%)

Query:	4	KHLQKASDSVVGGTLYVVATPIGNLADITLRALAVLQKADIICAEDTRVTAQLLSAYGIQ	63
		K  Q A +S   G LY+V TPIGNLADIT RAL VLQ  D+I AEDTR T  LL  +GI
Sbjct:	2	KQHQSADNSQ--GQLYIVPTPIGNLADITQRALEVLQAVDLIAAEDTRHTGLLLQHFGIN	59
Query:	64	GRLVSVREHNERQMADKVIGFLSDGLVVAQVSDAGTPAVCDPGAKLARRVREAGFKVVPV	123
		RL ++ +HNE+Q A+ ++  L +G  +A VSDAGTP + DPG  L R  REAG +VVP+
Sbjct:	60	ARLFALHDHNEQQKAETLLAKLQEGQNIALVSDAGTPLINDPGYHLVRTCREAGIRVVPL	119
Query:	124	VGASAVMAALSVAGVAESDFYFNGFVPPKSGERRKLFAKWVRAAFPVVMFETPHRIGATL	183
		G  A + ALS AG+    F + GF+P KS  RR            ++ +E+ HR+  +L
Sbjct:	120	PGPCAAITALSAAGLPSDRFCYEGFLPAKSKGRRDALKAIEAEPRTLIFYESTHRLLDSL	179
Query:	184	ADMAELFPERR-LMLAREITKTFETFLSGTVGEIQTALAADGNQSRGEMVLVLYPAQDEK	242
		D+  +  E R ++LARE+TKT+ET     VGE+   +  D N+ +GEMVL++      +
Sbjct:	180	EDIVAVLGESRYVVLARELTKTWETIHGAPVGELLAWVKEDENRRKGEMVLIV-EGHKAQ	238
Query:	243	HEGLSESAQNAMKILAAELPTKQAAELAAKITGEGKKALYDLAL	286
		E L   A   + +L AELP K+AA LAA+I G  K ALY  AL
Sbjct:	239	EEDLPADALRTLALLQAELPLKKAAALAAEIHGVKKNALYKYAL	282

Based on the computer analysis and the presence of a putative transmembrane domain in the gonococcal protein, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 77

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 647>

This corresponds to the amino acid sequence <SEQ ID 648; ORF1>:

Further sequencing analysis revealed the complete nucleotide sequence <SEQ ID 649>:

1	ATGAAAACAA CCGACAAACG GACAACCGAA ACACACCGCA
	AAGCCCCGAA
51	AACCGGCCGC ATCCGCTTCT CGCCTGCTTA CTTAGCCATA
	TGCCTGTCGT
101	TCGGCATTCT TCCCCAAGCC TGGGCGGGAC ACACTTATTT
	CGGCATCAAC
151	TACCAATACT ATCGCGACTT TGCCGAAAAT AAAGGCAAGT
	TTGCAGTCGG
201	GGCGAAAGAT ATTGAGGTTT ACAACAAAAA AGGGGAGTTG
	GTCGGCAAAT
251	CAATGACAAA AGCCCCGATG ATTGATTTTT CTGTGGTGTC
	GCGTAACGGC
301	GTGGCGGCAT TGGTGGGCGA TCAATATATT GTGAGCGTGG
	CACATAACGG
351	CGGCTATAAC AACGTTGATT TTGGTGCGGA AGGAAGAAAT
	CCCGATCAAC
401	ATCGTTTTAC TTATAAAATT GTGAAACGGA ATAATTATAA
	AGCAGGGACT
451	AAAGGCCATC CTTATGGCGG CGATTATCAT ATGCCGCGTT
	TGCATAAATT
501	TGTCACAGAT GCAGAACCTG TTGAAATGAC CAGTTATATG
	GATGGGCGGA
551	AATATATCGA TCAAAATAAT TACCCTGACC GTGTTCGTAT
	TGGGGCAGGC
601	AGGCAATATT GGCGATCTGA TGAAGATGAG CCCAATAACC
	GCGAAAGTTC
651	ATATCATATT GCAAGTGCGT ATTCTTGGCT CGTTGGTGGC
	AATACCTTTG
701	CACAAAATGG ATCAGGTGGT GGCACAGTCA ACTTAGGTAG
	TGAAAAAATT
751	AAACATAGCC CATATGGTTT TTTACCAACA GGAGGCTCAT
	TTGGCGACAG
801	TGGCTCACCA ATGTTTATCT ATGATGCCCA AAAGCAAAAG
	TGGTTAATTA
851	ATGGGGTATT GCAAACGGGC AACCCCTATA TAGGAAAAAG
	CAATGGCTTC
901	CAGCTGGTTC GTAAAGATTG GTTCTATGAT GAAATCTTTG
	CTGGAGATAC
951	CCATTCAGTA TTCTACGAAC CACGTCAAAA TGGGAAATAC
	TCTTTTAACG
1001	ACGATAATAA TGGCACAGGA AAAATCAATG CCAAACATGA
	ACACAATTCT
1051	CTGCCTAATA GATTAAAAAC ACGAACCGTT CAATTGTTTA
	ATGTTTCTTT
1101	ATCCGAGACA GCAAGAGAAC CTGTTTATCA TGCTGCAGGT
	GGTGTCAACA
1151	GTTATCGACC CAGACTGAAT AATGGAGAAA ATATTTCCTT
	TATTGACGAA
1201	GGAAAAGGCG AATTGATACT TACCAGCAAC ATCAATCAAG
	GTGCTGGAGG
1251	ATTATATTTC CAAGGAGATT TTACGGTCTC GCCTGAAAAT
	AACGAAACTT
1301	GGCAAGGCGC GGGCGTTCAT ATCAGTGAAG ACAGTACCGT
	TACTTGGAAA
1351	GTAAACGGCG TGGCAAACGA CCGCCTGTCC AAAATCGGCA
	AAGGCACGCT
1401	GCACGTTCAA GCCAAAGGGG AAAACCAAGG CTCGATCAGC
	GTGGGCGACG
1451	GTACAGTCAT TTTGGATCAG CAGGCAGACG ATAAAGGCAA
	AAAACAAGCC
1501	TTTAGTGAAA TCGGCTTGGT CAGCGGCAGG GGTACGGTGC
	AACTGAATGC
1551	CGATAATCAG TTCAACCCCG ACAAACTCTA TTTCGGCTTT
	CGCGGCGGAC
1601	GTTTGGATTT AAACGGGCAT TCGCTTTCGT TCCACCGTAT
	TCAAAATACC
1651	GATGAAGGGG CGATGATTGT CAACCACAAT CAAGACAAAG
	AATCCACCGT
1701	TACCATTACA GGCAATAAAG ATATTGCTAC AACCGGCAAT
	AACAACAGCT
1751	TGGATAGCAA AAAAGAAATT GCCTACAACG GTTGGTTTGG
	CGAGAAAGAT
1801	ACGACCAAAA CGAACGGGCG GCTCAACCTT GTTTACCAGC
	CCGCCGCAGA
1851	AGACCGCACC CTGCTGCTTT CCGGCGGAAC AAATTTAAAC
	GGCAACATCA
1901	CGCAAACAAA CGGCAAACTG TTTTTCAGCG GCAGACCAAC
	ACCGCACGCC
1951	TACAATCATT TAAACGACCA TTGGTCGCAA AAAGAGGGCA
	TTCCTCGCGG
2001	GGAAATCGTG TGGGACAACG ACTGGATCAA CCGCACATTT
	AAAGCGGAAA
2051	ACTTCCAAAT TAAAGGCGGA CAGGCGGTGG TTTCCCGCAA
	TGTTGCCAAA
2101	GTGAAAGGCG ATTGGCATTT GAGCAATCAC GCCCAAGCAG
	TTTTTGGTGT
2151	CGCACCGCAT CAAAGCCACA CAATCTGTAC ACGTTCGGAC
	TGGACGGGTC
2201	TGACAAATTG TGTCGAAAAA ACCATTACCG ACGATAAAGT
	GATTGCTTCA
2251	TTGACTAAGA CCGACATCAG CGGCAATGTC GATCTTGCCG
	ATCACGCTCA
2301	TTTAAATCTC ACAGGGCTTG CCACACTCAA CGGCAATCTT
	AGTGCAAATG
2351	GCGATACACG TTATACAGTC AGCCACAACG CCACCCAAAA
	CGGCAACCTT
2401	AGCCTCGTGG GCAATGCCCA AGCAACATTT AATCAAGCCA
	CATTAAACGG
2451	CAACACATCG GCTTCGGGCA ATGCTTCATT TAATCTAAGC
	GACCACGCCG
2501	TACAAAACGG CAGTCTGACG CTTTCCGGCA ACGCTAAGGC
	AAACGTAAGC
2551	CATTCCGCAC TCAACGGTAA TGTCTCCCTA GCCGATAAGG
	CAGTATTCCA
2601	TTTTGAAAGC AGCCGCTTTA CCGGACAAAT CAGCGGCGGC
	AAGGATACGG
2651	CATTACACTT AAAAGACAGC GAATGGACGC TGCCGTCAGG
	CACGGAATTA
2701	GGCAATTTAA ACCTTGACAA CGCCACCATT ACACTCAATT
	CCGCCTATCG
2751	CCACGATGCG GCAGGGGCGC AAACCGGCAG TGCGACAGAT
	GCGCCGCGCC
2801	GCCGTTCGCG CCGTTCGCGC CGTTCCCTAT TATCCGTTAC
	ACCGCCAACT
2851	TCGGTAGAAT CCCGTTTCAA CACGCTGACG GTAAACGGCA
	AATTGAACGG
2901	TCAGGGAACA TTCCGCTTTA TGTCGGAACT CTTCGGCTAC
	CGCAGCGACA
2951	AATTGAAGCT GGCGGAAAGT TCCGAAGGCA CTTACACCTT
	GGCGGTCAAC
3001	AATACCGGCA ACGAACCTGC AAGCCTCGAA CAATTGACGG
	TAGTGGAAGG
3051	AAAAGACAAC AAACCGCTGT CCGAAAACCT TAATTTCACC
	CTGCAAAACG
3101	AACACGTCGA TGCCGGCGCG TGGCGTTACC AACTCATCCG
	CAAAGACGGC
3151	GAGTTCCGCC TGCATAATCC GGTCAAAGAA CAAGAGCTTT
	CCGACAAACT
3201	CGGCAAGGCA GAAGCCAAAA AACAGGCGGA AAAAGACAAC
	GCGCAAAGCC
3251	TTGACGCGCT GATTGCGGCC GGGCGCGATG CCGTCGAAAA
	GACAGAAAGC
3301	GTTGCCGAAC CGGCCCGGCA GGCAGGCGGG GAAAATGTCG
	GCATTATGCA
3351	GGCGGAGGAA GAGAAAAAAC GGGTGCAGGC GGATAAAGAC
	ACCGCCTTGG
3401	CGAAACAGCG CGAAGCGGAA ACCCGGCCGG CTACCACCGC
	CTTCCCCCGC
3451	GCCCGCCGCG CCCGCCGGGA TTTGCCGCAA CTGCAACCCC
	AACCGCAGCC
3501	CCAACCGCAG CGCGACCTGA TCAGCCGTTA TGCCAATAGC
	GGTTTGAGTG
3551	AATTTTCCGC CACGCTCAAC AGCGTTTTCG CCGTACAGGA
	CGAATTAGAC
3601	CGCGTATTTG CCGAAGACCG CCGCAACGCC GTTTGGACAA
	GCGGCATCCG
3651	GGACACCAAA CACTACCGTT CGCAAGATTT CCGCGCCTAC
	CGCCAACAAA
3701	CCGACCTGCG CCAAATCGGT ATGCAGAAAA ACCTCGGCAG
	CGGGCGCGTC
3751	GGCATCCTGT TTTCGCACAA CCGGACCGAA AACACCTTCG
	ACGACGGCAT
3801	CGGCAACTCG GCACGGCTTG CCCACGGCGC CGTTTTCGGG
	CAATACGGCA
3851	TCGACAGGTT CTACATCGGC ATCAGCGCGG GCGCGGGTTT
	TAGCAGCGGC
3901	AGCCTTTCAG ACGGCATCGG AGGCAAAATC CGCCGCCGCG
	TGCTGCATTA
3951	CGGCATTCAG GCACGATACC GCGCCGGTTT CGGCGGATTC
	GGCATCGAAC
4001	CGCACATCGG CGCAACGCGC TATTTCGTCC AAAAAGCGGA
	TTACCGCTAC
4051	GAAAACGTCA ATATCGCCAC CCCCGGCCTT GCATTCAACC
	GCTACCGCGC
4101	GGGCATTAAG GCAGATTATT CATTCAAACC GGCGCAACAC
	ATTTCCATCA
4151	CGCCTTATTT GAGCCTGTCC TATACCGATG CCGCTTCGGG
	CAAAGTCCGA
4201	ACACGCGTCA ATACCGCCGT ATTGGCTCAG GATTTCGGCA
	AAACCCGCAG
4251	TGCGGAATGG GGCGTAAACG CCGAAATCAA AGGTTTCACG
	CTGTCCCTCC
4301	ACGCTGCCGC CGCCAAAGGC CCGCAACTGG AAGCGCAACA
	CAGCGCGGGC
4351	ATCAAATTAG GCTACCGCTG GTAA

This corresponds to the amino acid sequence <SEQ ID 650; ORF1-1>:

1	MKTTDKRTTE THRKAPKTGR IRFSPAYLAI CLSFGILPQA
	WAGHTYFGIN
51	YQYYRDFAEN KGKFAVGAKD IEVYNKKGEL VGKSMTKAPM
	IDFSVVSRNG
101	VAALVGDQYI VSVAHNGGYN NVDFGAEGRN PDQHRFTYKI
	VKRNNYKAGT
151	KGHPYGGDYH MPRLHKFVTD AEPVEMTSYM DGRKYIDQNN
	YPDRVRIGAG
201	RQYWRSDEDE PNNRESSYHI ASAYSWLVGG NTFAQNGSGG
	GTVNLGSEKI
251	KHSPYGFLPT GGSFGDSGSP MFIYDAQKQK WLINGVLQTG
	NPYIGKSNGF
301	QLVRKDWFYD EIFAGDTHSV FYEPRQNGKY SFNDDNNGTG
	KINAKHEHNS
351	LPNRLKTRTV QLFNVSLSET AREPVYHAAG GVNSYRPRLN
	NGENISFIDE
401	GKGELILTSN INQGAGGLYF QGDFTVSPEN NETWQGAGVH
	ISEDSTVTWK
451	VNGVANDRLS KIGKGTLHVQ AKGENQGSIS VGDGTVILDQ
	QADDKGKKQA
501	FSEIGLVSGR GTVQLNADNQ FNPDKLYFGF RGGRLDLNGH
	SLSFHRIQNT
551	DEGAMIVNHN QDKESTVTIT GNKDIATTGN NNSLDSKKEI
	AYNGWFGEKD
601	TTKTNGRLNL VYQPAAEDRT LLLSGGTNLN GNITQTNGKL
	FFSGRPTPHA
651	YNHLNDHWSQ KEGIPRGEIV WDNDWINRTF KAENFQIKGG
	QAVVSRNVAK
701	VKGDWHLSNH AQAVFGVAPH QSHTICTRSD WTGLTNCVEK
	TITDDKVIAS
751	LTKTDISGNV DLADHAHLNL TGLATLNGNL SANGDTRYTV
	SHNATQNGNL
801	SLVGNAQATF NQATLNGNTS ASGNASFNLS DHAVQNGSLT
	LSGNAKANVS
851	HSALNGNVSL ADKAVFHFES SRFTGQISGG KDTALHLKDS
	EWTLPSGTEL
901	GNLNLDNATI TLNSAYRHDA AGAQTGSATD APRRRSRRSR
	RSLLSVTPPT
951	SVESRFNTLT VNGKLNGQGT FRFMSELFGY RSDKLKLAES
	SEGTYTLAVN
1001	NTGNEPASLE QLTVVEGKDN KPLSENLNFT LQNEHVDAGA
	WRYQLIRKDG
1051	EFRLHNPVKE QELSDKLGKA EAKKQAEKDN AQSLDALIAA
	GRDAVEKTES
1101	VAEPARQAGG ENVGIMQAEE EKKRVQADKD TALAKQREAE
	TRPATTAFPR
1151	ARRARRDLPQ LQPQPQPQPQ RDLISRYANS GLSEFSATLN
	SVFAVQDELD
1201	RVFAEDRRNA VWTSGIRDTK HYRSQDFRAY RQQTDLRQIG
	MQKNLGSGRV
1251	GILFSHNRTE NTFDDGIGNS ARLAHGAVFG QYGIDRFYIG
	ISAGAGFSSG
1301	SLSDGIGGKI RRRVLHYGIQ ARYRAGFGGF GIEPHIGATR
	YFVQKADYRY
1351	ENVNIATPGL AFNRYRAGIK ADYSFKPAQH ISITPYLSLS
	YTDAASGKVR
1401	TRVNTAVLAQ DFGKTRSAEW GVNAEIKGFT LSLHAAAAKG
	PQLEAQHSAG
1451	IKLGYRW*

Computer analysis of these sequences gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF1 shows 57.8% identity over a 1456aa overlap with an ORF (ORF1a) from strain A of N. meningitidis:

The complete length ORF1a nucleotide sequence <SEQ ID 651> is:

1	ATGAAAACAA CCGACAAACG GACAACCGAA ACACACCGCA
	AAGCCCCGAA
51	AACCGGCCGC ATCCGCTTCT CGCCTGCTTA CTTAGCCATA
	TGCCTGTCGT
101	TCGGCATTCT TCCCCAAGCT TGGGCGGGAC ACACTTATTT
	CGGCATCAAC
151	TACCAATACT ATCGCGACTT TGCCGAAAAT AAAGGCAAGT
	TTGCAGTCGG
201	GGCGAAAGAT ATTGAGGTNT ACAACAAAAA AGGGGAGTTG
	GTCGGCAAAT
251	CAATGACAAA AGCCCCGATG ATTGATTTTT CTGTGGTGTC
	GCGTAACGGC
301	GTGGCGGCAT TGGTGGGCGA TCAATATATT GTGAGCGTGG
	CACATAACGG
351	CGGCTATAAC AACGTTGATT TTGGTGCGGA AGGAAGNAAT
	CCCGATCAGC
401	ACCGTTTTTC TTACCAAATT GTGAAAAGAA ATAATTATAA
	GCCTGACAAT
451	TCACACCCTT ACAACGGCGA TTANCATATG CCGCGTTTGC
	ATAAATTTGT
501	CACAGATGCA GAACCTGTCG AAATGACGAG TGACATGAGG
	GGGAATACCT
551	ATTCCGATAA AGAAAAATAT CCCGAGCGTG TCCGCATCGG
	CTCAGGACAC
601	CACTATTGGC GTTATGATGA TGACAAACAC GGCGATTTAT
	CCTACTCCGG
651	CGCATGGTTA ATTGGCGGCA ATACACATAT GCAGGGTTGG
	GGAAATAATG
701	GCGTANTTAG TTTGAGCGGC GATGTGCGCC ATGCCAACGA
	CTATGGCCCT
751	ATGCCGATTG CAGGTGCGGC AGGCGACAGC GGTTCGCCAA
	TGTTTATTTA
801	TGACAAAACA AACAATAAAT GGCTGCTCAA CGGAGTTTTA
	CAAACCGGCT
851	ACCCTTATTC CGGCAGGGAA AACGGTTTCC AGCTGATACG
	CAAAGATTGG
901	TTCTACGATG ACATTTACAG AGGCGATACA CATACCGTCT
	NTTTTGAACC
951	GCGCAGTAAC GGACATTTTT CCTTTACATC CAACAACAAC
	GGTACGGGTA
1001	CGGTAACAGA AACCAACGAA AAGGTNTCCA ATCCAAAGCT
	TAAAGTACAG
1051	ACAGTCCGAC TGTTTGACGA ATCTTTGAAT GAAACTGATA
	AAGAACCAGT
1101	TTACGCGGCA GGGGGTGTTA ATCAGTACCG TCCAAGGTTA
	AACAACGGTG
1151	AAAACCTTTC TTTTATCGAT TACGGCAACG GCAAACTCAT
	CTTATCAAAC
1201	AACATCAACC AAGGCGCGGG CGGTTTGTAT TTTGAAGGTG
	ATTTTACGGT
1251	CTCGCCTGAA AACAACGAAA CGTGGCAAGG CGCGGGCGTT
	CATATCAGTG
1301	AAGACAGTAC CGTTACTTGG AAAGTAAACG GCGTGGCAAA
	CGACCGCCTG
1351	TCCAAAATCG GCAAAGGCAC GCTGCACGTT CAAGCCAAAG
	GGGAAAACCA
1401	AGGCTCGATC AGCGTGGGCG ACGGTACAGT CATTTTGGAT
	CAGCAGGCAG
1451	ACGATAAAGG CAAAAAACAA GCCTTTAGTG AAATCGGCTT
	GNTCAGCGGC
1501	AGGGGTACGG TGCAACTGAA TGCCGATAAT CAGTTCAACC
	CCGACAAACT
1551	CTATTTCGGC TTTCGCGGCG GACGTTTGGA TTTAAACGGG
	CATTCGCTTT
1601	CGTTCCACCG TATTCAAAAT ACCGATGAAG GGGCGATGAT
	TGNCNATCAT
1651	AATGCCACAA CAACATCCAC CGTTACCATT ACAGGGAATG
	AAAGTATTAC
1701	ACAACCGAGT GGTAAGAATA TCAATAGACT TAATTACAGC
	AAAGAAATTG
1751	CCTACAACGG TTGGTTTGGC GAGAAAGATA CGACCAAAAC
	GAACGGGCGG
1801	CTCAACCTTG TTTACCAGCC CGCCGCAGAA GACCGCACCC
	NGCTGCTTTC
1851	CGGCGGAACA AATTTAAACG GCAACATCAC GCAAACAAAC
	GGCAAACTGT
1901	TTTTCAGCGG CAGACCGACA CCGCACGCCT ACAATCATTT
	AGGAAGCGGG
1951	TGGTCAAAAA TGGAAGGTAT CCCACAAGGA GAAATCGTGT
	GGGACAACGA
2001	CTGGATCNAC CGCACGTTTA AAGCGGAAAA TTTCCATATT
	CAGGGCGGGC
2051	AGGCGGTGAT TTCCCGCAAT GTTGCCAAAG TGGAAGGCGA
	TTGNCATTTG
2101	AGCAATCACG CCCAAGCAGT TTTTGGTGTC GCACCGCATC
	AAAGCCATAC
2151	AATCTGTACA CGTTCGGACT GGACNGGTCT GACAAATTGT
	GTCGAANAAA
2201	NCATTACCGA CGATAAAGTG ATTGCTTCAT TGACTAAGAC
	NGACNTNAGC
2251	GGCANTGTNA GNCTNNCCNA TNACGNTNNT TNAAANCTCN
	CNGGGCNTGC
2301	NNCACTNAAN GGCAATCTTA GTGCAAATGG CGATACACGT
	TATACAGTCA
2351	GCCACAACGC CACCCAAAAC GGCAACCTTA GCCTCGTGGG
	CAATGCCCAA
2401	GCAACATTTA ATCAAGCCAC ATTAAACGGC AACNCATCGG
	NTTCGGGCAA
2451	TGCTTCATTT AATCTAAGCA ACAACGCCGC ACAAAACGGC
	AGTCTGACGC
2501	TTTCCGACAA CGCTAAGGCA AACGTAAGCC ATTCCGCACT
	CAACGGCAAT
2551	GTCTCCCTAG CCGATAAGGC AGTATTCCAT TTTGAAAACA
	GCCGCTTTAC
2601	CGGACAACTC AGCGGCAGCA AGGANACAGC ATTACACTTA
	AAAGACAGCG
2651	AATGGACGCT GCCGTCAGGC ACGGAATTAG GCAATTTAAA
	CCTTGACAAC
2701	GCCACCATTA CACTCAATTC CGCCTATCGC CACGATGCTG
	CAGGCGCGCA
2751	AACCGGCAGN GTGTCAGACA CGCCGCGCCG CCGTTCGCGC
	CGTTCCCTAT
2801	TATCCGTTAC ACCGCCAACT TCGGTAGAAT CCCGTTTCAA
	CACGCTGACG
2851	GTAAACGGCA AATTGAACNG TCAAGGAACA TTCCGCTTTA
	TGTCGGAACT
2901	CTTCGGCTAC CGAAGCGACA AATTGAAGCT GGCGGAAAGT
	TCCGAAGGNA
2951	CTTACACCTT GGCGGTCAAC AATACCGGCA ACGAACCCGT
	AAGCCTCGAT
3001	CAATTGACGG TAGTGGAAGG GAAAGACAAC AAACCGCTGT
	CCGAAAACCT
3051	TAATTTCACC CTGCAAAACG AACACGTCGA TGCCGGCGCG
	TGGCGTTACC
3101	AACTCATCCG CAAAGACGGC GAGTTCCGCC TGCATAATCC
	GGTCAAAGAA
3151	CAAGAGCTTT CCGACAAACT CGGCAAGGCA GAAGCCAAAA
	AACAGGCGGA
3201	AAAAGACAAC GCGCAAAGCC TTGACGCGCT GATTGCGGCC
	GGGCGCGATG
3251	CCGCCGAAAA GACAGAAAGC GTTGCCGAAC CGGCCCGGCN
	GGCAGGCGGG
3301	GAAAATGTCG GCATTATGCA GGCGGAGGAA GAGAAAAAAC
	GGGTGCAGGC
3351	GGATAAAGAC AGCGCNTTGG CGAAACAGCG CGAAGCGGAA
	ACCCGGCCGG
3401	NTACCACCGC CTTCCCCCGC GCCCGCNGCG CCCGCCGGGA
	TTTGCCGCAA
3451	CCGCAGCCCC AACCGCAACC TCAACCCCAA CCGCAGCGCG
	ACCTGATNAG
3501	CCGTTATGCC AATAGCGGTT TGAGTGAATT TTCCGCCACG
	CTCAACAGCG
3551	TTTTCGCCGT ACAGGACGAA TTGGACCGCG TGTTTGCCGA
	AGACCGCCGC
3601	AACGCNGTTT GGACAAGCNG CATCCGGNAC ACCAAACACT
	ACCGTTCGCA
3651	AGATTTCCGC GCCTACCGCC AACAAACCGA CCTGCGCCAA
	ATCGGTATGC
3701	AGAAAAACCT CGGCAGCGGG CGCGTCGGCA TCCTGTTTTC
	GCACAACCGG
3751	ACCGAAAACA NCTTCGACGA CGGCATCGGC AACTCGGCAC
	GGCTTGCCCA
3801	CGGCGCCGTT TTCGGGCAAT ACGGCATCGG CAGGTTCGAC
	ATCGGCATCA
3851	GCACGGGCGC GGGTTTTAGC AGCGGCANTC TNTCAGACGG
	CATCGGAGGC
3901	AAAATCCGCC GCCGCGTGCT GCATTACGGC ATTCAGGCAC
	GATACCGCGC
3951	CGGTTTCGGC GGATTCGGCA TCGAACCGTA CATCGGCGCA
	ACGCGCTATT
4001	TCGTCCAAAA AGCGGATTAC CGCTACGAAA ACGTCAATAT
	CGCCACCCCC
4051	GGTCTTGCGT TCAACCGNTA CCGNGCGGGC ATTAAGGCAG
	ATTATTCATT
4101	CAAACCGGCG CAACACATNT CCATCACNCC TTATTTNAGC
	CTGTCCTATA
4151	CCGATGCCGC TTCGGGCAAA GTCCGAACAC GCGTCAATAC
	CGCNGTATTG
4201	GCTCAGGATT TCGGCAAAAC CCGCAGTGCG GAATGGGGCG
	TAAACGCCGA
4251	AATCAAAGGT TTCACGCTGT CCNTCCACGC TGCCGCCGCC
	AAAGGNCCGC
4301	AACTGGAAGC GCAACACAGC GCGGGCATCA AATTAGGCTA
	CCGCTGGTAA

This encodes a protein having amino acid sequence <SEQ ID 652>:

1	MKTTDKRTTE THRKAPKTGR IRFSPAYLAI CLSFGILPQA
	WAGHTYFGIN
51	YQYYRDFAEN KGKFAVGAKD IEVYNKKGEL VGKSMTKAPM
	IDFSVVSRNG
101	VAALVGDQYI VSVAHNGGYN NVDFGAEGXN PDQHRFSYQI
	VKRNNYKPDN
151	SHPYNGDXHM PRLHKFVTDA EPVEMTSDMR GNTYSDKEKY
	PERVRIGSGH
201	HYWRYDDDKH GDLSYSGAWL IGGNTHMQGW GNNGVXSLSG
	DVRHANDYGP
251	MPIAGAAGDS GSPMFIYDKT NNKWLLNGVL QTGYPYSGRE
	NGFQLIRKDW
301	FYDDIYRGDT HTVXFEPRSN GHFSFTSNNN GTGTVTETNE
	KVSNPKLKVQ
351	TVRLFDESLN ETDKEPVYAA GGVNQYRPRL NNGENLSFID
	YGNGKLILSN
401	NINQGAGGLY FEGDFTVSPE NNETWQGAGV HISEDSTVTW
	KVNGVANDRL
451	SKIGKGTLHV QAKGENQGSI SVGDGTVILD QQADDKGKKQ
	AFSEIGLXSG
501	RGTVQLNADN QFNPDKLYFG FRGGRLDLNG HSLSFHRIQN
	TDEGAMIXXH
551	NATTTSTVTI TGNESITQPS GKNINRLNYS KEIAYNGWFG
	EKDTTKTNGR
601	LNLVYQPAAE DRTXLLSGGT NLNGNITQTN GKLFFSGRPT
	PHAYNHLGSG
651	WSKMEGIPQG EIVWDNDWIX RTFKAENFHI QGGQAVISRN
	VAKVEGDXHL
701	SNHAQAVFGV APHQSHTICT RSDWTGLTNC VEXXITDDKV
	IASLTKTDXS
751	GXVXLXXXXX XXLXGXAXLX GNLSANGDTR YTVSHNATQN
	GNLSLVGNAQ
801	ATFNQATLNG NXSXSGNASF NLSNNAAQNG SLTLSDNAKA
	NVSHSALNGN
851	VSLADKAVFH FENSRFTGQL SGSKXTALHL KDSEWTLPSG
	TELGNLNLDN
901	ATITLNSAYR HDAAGAQTGX VSDTPRRRSR RSLLSVTPPT
	SVESRFNTLT
951	VNGKLNXQGT FRFMSELFGY RSDKLKLAES SEGTYTLAVN
	NTGNEPVSLD
1001	QLTVVEGKDN KPLSENLNFT LQNEHVDAGA WRYQLIRKDG
	EFRLHNPVKE
1051	QELSDKLGKA EAKKQAEKDN AQSLDALIAA GRDAAEKTES
	VAEPARXAGG
1101	ENVGIMQAEE EKKRVQADKD SALAKQREAE TRPXTTAFPR
	ARXARRDLPQ
1151	PQPQPQPQPQ PQRDLXSRYA NSGLSEFSAT LNSVFAVQDE
	LDRVFAEDRR
1201	NAVWTSXIRX TKHYRSQDFR AYRQQTDLRQ IGMQKNLGSG
	RVGILFSHNR
1251	TENXFDDGIG NSARLAHGAV FGQYGIGRFD IGISTGAGFS
	SGXLSDGIGG
1301	KIRRRVLHYG IQARYRAGFG GFGIEPYIGA TRYFVQKADY
	RYENVNIATP
1351	GLAFNRYRAG IKADYSFKPA QHXSITPYXS LSYTDAASGK
	VRTRVNTAVL
1401	AQDFGKTRSA EWGVNAEIKG FTLSXHAAAA KGPQLEAQHS
	AGIKLGYRW*

A transmembrane region is underlined.

ORF1-1 shows 86.3% identity over a 1462aa overlap with ORF1a:

Homology with Adhesion and Penetration Protein Hap Precursor of H. influenzae (Accession Number P45387)

Amino acids 23-423 of ORF1 show 59% aa identity with hap protein in 450aa overlap:

orf1	23	FXAAYLAICLSFGILPQAWAGHTYFGINYQYYRDFAENKGKFAVGAKDIEVYNKKGELVG	82
		F   +L  C+S GI  QAWAGHTYFGI+YQYYRDFAENKGKF VGAK+IEVYNK+G+LVG
hap	6	FRLNFLTACVSLGIASQAWAGHTYFGIDYQYYRDFAENKGKFTVGAKNIEVYNKEGQLVG	65
orf1	83	KSMTKAPMIDFSVVSRNGVAALVGVQYIVSVAHNGGYNNVDFGAEGXNIXDQXRXTYKIV	142
		SMTKAPMIDFSVVSRNGVAALVG QYIVSVAHNGGYN+VDFGAEG N  DQ R TY+IV
hap	66	TSMTKAPMIDFSVVSRNGVAALVGDQYIVSVAHNGGYNDVDFGAEGRN-PDQHRFTYQIV	124
orf1	143	KRNNYKAGTKGHPYGGDYHMPRLHKXVTDAEPVEMTSYMDGRKYIDQNNYPDRVRIGAGR	202
		KRNNY+A  + HPY GDYHMPRLHK VT+AEPV MT+ MDG+ Y D+ NYP+RVRIG+GR
hap	125	KRNNYQAWERKHPYDGDYHMPRLHKFVTEAEPVGMTTNMDGKVYADRENYPERVRIGSGR	184
orf1	203	QYWRSDEDEPNNRESSYHIA----------------------------------------	222
		QYWR+D+DE  N  SSY+++
hap	185	QYWRTDKDEETNVHSSYYVSGAYRYLTAGNTHTQSGNGNGTVNLSGNVVSPNHYGPLPTG	244
orf1	223	-----SGSPMFIYDAQKQKWLINGVLQTGNPYIGKSNGFQLVRKDWFYDEIFAGDTHSVF	277
		SGSPMFIYDA+K++WLIN VLQTG+P+ G+ NGFQL+R++WFY+E+ A DT SVF
hap	245	GSKGDSGSPMFIYDAKKKQWLINAVLQTGHPFFGRGNGFQLIREEWFYNEVLAVDTPSVF	304
orf1	278	--YEPRQNGKYSFNDDNNGTGKIN-AKHEHNSLPNRLKTRTVQLFNVSLSETAREPVYHA	334
		Y P  NG YSF  +N+GTGK+   +   +    + +  TV+LFN SL++TA+E V  A
hap	305	QRYIPPINGHYSFVSNNDGTGKLTLTRPSKDGSKAKSEVGTVKLFNPSLNQTAKEHV-KA	363
orf1	335	AGGVNSYRPRLNNGENISFIDEGKGELILTSNINQGAGGLYFQGDFTV-SPENNETWQGA	393
		A G N Y+PR+  G+NI   D+GKG L + +NINQGAGGLYF+G+F V   +NN TWQGA
hap	364	AAGYNIYQPRMEYGKNIYLGDQGKGTLTIENNINQGAGGLYFEGNFVVKGKQNNITWQGA	423
orf1	394	GVHISEDSTVTWKVNGVANDRLSKIGKGTL	423
		GV I +D+TV WKV+   NDRLSKIG GTL
hap	424	GVSIGQDATVEWKVHNPENDRLSKIGIGTL	453

Amino acids 715-1011 of ORF1 show 50% aa identity with hap protein in 258aa overlap:

Orf1	41	DTRYTVSHNATQ-NGNXSLVXNAQATFNQ-ATLNGNTSASGNASFNLSDHAVQNGSLTLS	98
		DT+   S   TQ NG+ +L  NA    +  A LNGN +   ++ F LS++A Q G++ LS
hap	733	DTKVINSIPITQINGSINLTNNATVNIHGLAKLNGNVTLIDHSQFTLSNNATQTGNIKLS	792
orf1	99	GNAKANVSHSALNGNVSLADKAVFHFESSRFTGQISGGKDTALHLKDSEWTLPSGXELGN	158
		+A A V+++ LNGNV L D A F  ++S F  QI G KDT + L+++ WT+PS   L N
hap	793	NHANATVNNATLNGNVHLTDSAQFSLKNSHFWHQIQGDKDTTVTLENATWTMPSDTTLQN	852
orf1	159	LNLDNATITLNSAYRHDAAGAQTGSATDAPXXXXXXXXXXLLXVTPPTSVESRFNTLTVN	218
		L L+N+T+TLNSAY        + S+ +AP          L   T PTS E RFNTLTVN
hap	853	LTLNNSTVTLNSAY--------SASSNNAPRHRRS-----LETETTPTSAEHRFNTLTVN	899
orf1	219	GKLNGQGTFRFMSELFGYRSDKLKLAESSEGTYTLAVNNTGNEPASLEQLTVVEGKDNKP	278
		GKL+GQGTF+F S LFGY+SDKLKL+  +EG YTL+V NTG EP +LEQLT++E  DNKP
hap	900	GKLSGQGTFQFTSSLFGYKSDKLKLSNDAEGDYTLSVRNTGKEPVTLEQLTLIESLDNKP	959
orf1	279	LSENLNFTLQNEHVDAGA	296
		LS+ L FTL+N+HVDAGA
hap	960	LSDKLKFTLENDHVDAGA	977

Amino acids 1192-1450 of ORF1 show 41% aa identity with hap protein in 259aa overlap:

Orf1	1	LDRVFAEDRRNAVWTSGIRDTKHYRSQDFRAYRQQTDLRQIGMQKNLGSGRVGILFSHNR	60
		LDR+F +  ++AVWT+  +D + Y S  FRAY+Q+T+LRQIG+QK L +GR+G +FSH+R
hap	1135	LDRLFVDQAQSAVWTNIAQDKRRYDSDAFRAYQQKTNLRQIGVQKALANGRIGAVFSHSR	1194
orf1	61	TENTFDDGIGNSARLAHGAVFGQYGIDRFYXXXXXXXXXXXXXXXXXIGXKXRRRVLHYG	120
		++NTFD+ + N A L   + F QY                          K  R+ ++YG
hap	1195	SDNTFDEQVKNHATLTMMSGFAQYQWGDLQFGVNVGTGISASKMAEEQSRKIHRKAINYG	1254
orf1	121	IQARYRAGFGGFGIEPHIGATRYFVQKADYRYENVNIATPGLAFNRYRAGIKADYSFKPA	180
		+ A Y+   G  GI+P+ G  RYF+++ +Y+ E V + TP LAFNRY AGI+ DY+F P
hap	1255	VNASYQFRLGQLGIQPYFGVNRYFIERENYQSEEVRVKTPSLAFNRYNAGIRVDYTFTPT	1314
orf1	181	QHISITPYLSLSYTDAASGKVRTRVNTAVLAQDFGKTRSAEWGVNAEIKGFTLSLHAAAA	240
		+IS+ PY  ++Y D ++  V+T VN  VL Q FG+    E G+ AEI  F +S   + +
hap	1315	DNISVKPYFFVNYVDVSNANVQTTVNLTVLQQPFGRYWQKEVGLKAEILHFQISAFISKS	1374
orf1	241	KGPQLEAQHSAGIKLGYRW	259
		+G QL  Q + G+KLGYRW
hap	1375	QGSQLGKQQNVGVKLGYRW	1393

Homology with a Predicted ORF from N. gonorrhoeae

The blocks of ORF1 show 83.5%, 88.3%, and 97.7% identities in 467, 298, and 259 aa overlap, respectively with a predicted ORF (ORF1ng) from N. gonorrhoeae:

The complete length ORF1ng nucleotide sequence was identified <SEQ ID 653>:

1	ATGAAAACAA CCGACAAACG GACAACCGAA ACACACCGCA
	AAGCCCCTAA
51	AACCGGCCGC ATCCGCTTCT CGCCCGCTTA CTTAGCCATA
	TGCCTGTCGT
101	TCGGCATTCT GCCCCAAGCC CGGGCGGGAC ACACTTATTT
	CGGCATCAAC
151	TACCAATACT ATCGCGACTT TGCCGAAAAT AAAGGCAAGT
	TTGCAGTCGG
201	GGCGAAAGAT ATTGAGGTTT ACAACAAAAA AGGGGAGTTG
	GTCGGCAAAT
251	CGATGACGAA AGCCCCGATG ATTGATTTTT CTGTGGTATC
	GCGTAACGGC
301	GTGGCGGCAT TGGCGGGCGA TCAATATATT GTGAGCGTGG
	CACATAACGG
351	CGGCTATAAC AATGTTGATT TTGGTGCGGA GGGAAGCAAT
	CCCGATCAGC
401	ACCGCTTTTC TTACCAAATT GTGAAAAGAA ATAATTATAA
	AGCAGGGACT
451	AACGGCCATC CTTATGGCGG CGATTATCAT ATGCCGCGTT
	TGCACAAATT
501	TGTCACAGAT GCAGAACCTG TTGAGATGAC CAGTTATATG
	GATGGGTGGA
551	AATACGCTGA TTTAAATAAA TACCCTGATC GTGTTCGAAT
	CGGAGCAGGC
601	AGACAATATT GGCGGTCTGA TGAAGACGAA CCCAATAACC
	GCGAAAGTTC
651	ATATCATATT GCAAGCGCAT ATTCTTGGCT CGTCGGTGGC
	AATACCTTTG
701	CACAAAATGG ATCAGGTGGT GGCACAGTCA ACTTAGGTAG
	CGAAAAAATT
751	AAACATAGCC CATATGGTTT TTTACCAACA GGAGGCTCAT
	TTGGCGACAG
801	TGGCTCACCA ATGTTTATCT ATGATGCCCA AAAGCAAAAG
	TGGTTAATTA
851	ATGGGGTATT GCAAACAGGC AACCCCTATA TAGGAAAAAG
	CAATGGCTTC
901	CAGCTAGTTC GTAAAGATTG GTTCTATGAT GAAATCTTTG
	CTGGAGATAC
951	CCATTCAGTA TTCTACGAAC CACATCAAAA TGGGAAATAC
	TTTTTTAACG
1001	ACAATAATAA TGGCGCAGGA AAAATCGATG CCAAACATAA
	ACACTATTCT
1051	CTACCTTATA GATTAAAAAC ACGAACCGTT CAATTGTTTA
	ATGTTTCTTT
1101	ATCCGAGACA GCAAGAGAAC CTGTTTATCA TGCTGCAGGT
	GGGGTCAACA
1151	GTTATCGACC CAGACTGAAT AATGGAGAAA ATATTTCCTT
	TATTGACAAA
1201	GGAAAAGGTG AATTGATACT TACCAGCAAC ATCAACCAAG
	GCGCGGGCGG
1251	TTTGTATTTT GAGGGTAATT TTACGGTCTC GCCTAAAAAC
	AACGAAACGT
1301	GGCAAGGCGC GGGCGTTCAT ATCAGTGATG GCAGTACCGT
	TACTTGGAAA
1351	GTAAACGGCG TGGCAAACGA CCGCCTGTCC AAAATCGGCA
	AAGGCACGCT
1401	GCTGGTTCAA GCCAAAGGGG AAAACCAAGG CTCGGTCAGC
	GTGGGCGACG
1451	GTAAAGTCAT CTTAGATCAG CAGGCGGACG ATCAAGGCAA
	AAAACAAGCC
1501	TTTAGTGAAA TCGGCTTGGT CAGCGGCAGG GGGACGGTGC
	AACTGAATGC
1551	CGATAATCAG TTCAACCCCG ACAAACTCTA TTTCGGCTTT
	CGCGGCGGAC
1601	GTTTGGATTT GAACGGGCAT TCGCTTTCGT TCCACCGCAT
	TCAAAATACC
1651	GATGAAGGGG CGATGATTGT CAACCACAAT CAAGACAAAG
	AATCCACCGT
1701	TACCATTACA GGCAATAAAG ATATTACTAC AACCGGCAAT
	AACAACAACT
1751	TGGATAGCAA AAAAGAAATT GCCTACAACG GTTGGTTTGG
	CGAGAAAGAT
1801	GCAACCAAAA CGAACGGGCG GCTCAATCTG AATTACCAAC
	CGGAAGAAGC
1851	GGATCGCACT TTACTGCTTT CCGGCGGAAC AAATTTAAAC
	GGCAATATCA
1901	CGCAAACAAA CGGCAAACTG TTTTTCAGCG GCAGACCGAC
	ACCGCACGCC
1951	TACAATCATT TAGGAAGCGG GTGGTCAAAA ATGGAAGGTA
	TCCCACAAGG
2001	AGAAATCGTG TGGGACAACG ATTGGATCGA CCGCACATTT
	AAAGCGGAAA
2051	ACTTCCATAT TCAGGGCGGA CAAGCGGTGG TTTCCCGCAA
	TGTTGCCAAA
2101	GTGGAAGGCG ATTGGCATTT AAGCAATCAC GCCCAAGCAG
	TTTTCGGTGT
2151	CGCACCGCAT CAAAGCCACA CAATCTGTAC ACGTTCGGAC
	TGGACGGGTC
2201	TGACAAGTTG TACCGAAAAA ACCATTACCG ACGATAAAGT
	GATTGCTTCA
2251	TTGAGCAAGA CCGACATCAG AGGCAATGTC AGCCTTGCCG
	ATCACGCTCA
2301	TTTAAATCTC ACAGGACTTG CCACACTCAA CGGCAATCTT
	AGTGCAGGCG
2351	GAGACACGCA CTATACGGTT ACGCGCAACG CCACCCAAAA
	CGGCAACCTC
2401	AGCCTCGTGG GCAATGCCCA AGCAACATTT AATCAAGCCA
	CATTAAACGG
2451	CAACACATCG GCTTCGGACA ATGCTTCATT TAATCTAAGC
	AACAACGCCG
2501	TACAAAACGG CAGTCTGACG CTTTCCGACA ACGCTAAGGC
	AAACGTAAGC
2551	CATTCCGCAC TCAACGGCAA TGTCTCCCTA GCCGATAAGG
	CAGTATTCCA
2601	TTTTGAAAAC AGCCGCTTTA CCGGAAAAAT CAGCGGCGGC
	AAGGATACGG
2651	CATTACACTT AAAAGACAGC GAATGGACGC TGCCGTCGGG
	CACGGAATTA
2701	GGCAATTTAA ACCTTGACAA CGCCACCATT ACACTCAATT
	CCGCCTATCG
2751	ACACGATGCG GCAGGCGCGC AAACCGGCAG TGCGGCAGAT
	GCGCCGCGCC
2801	GCCGTTCGCG CCGTTCCCTA TTATCCGTTA CGCCGCCAAC
	TTCGGCAGAA
2851	TCCCGTTTCA ACACGCTGAC GGTAAACGGC AAATTGAACG
	GTCAGGGAAC
2901	ATTCCGCTTT ATGTCGGAAC TCTTCGGCTA CCGCAGCGGC
	AAATTGAAGC
2951	TGGCGGAAAG TTCCGAAGGC ACTTACACCT TGGCTGTCAA
	CAATACCGGC
3001	AACGAACCCG TAAGTCTCGA GCAATTGACG GTAGTGGAAG
	GAAAAGACAA
3051	CACACCGCTG TCCGAAAATC TTAATTTCAC CCTGCaaaAc
	gaacacgtcg
3101	atgccggcgc atggCGTTAT CAGCTTATCC gcaaagacgG
	CGAGTTCCgc
3151	CTGCATAATC CGGTCAAAGA ACAAGAGCTT TCCGACAAAC
	TCGGCAAGgc
3201	gggagaaACA GAggccgccT TGACGGCAAA ACAGGCacaA
	CTTGCCGCCA
3251	AAcaacaggc ggaaaAAGAC AACgcgcaaa gccttgAcgc
	gctgattgcg
3301	gCcgggcgca atgccaccga AAAGGCAgaa agtgttgccg
	aaccgGCCCG
3351	GCAGGCAGGC GGGGAAAAtg ccgGCATTAT GCAGGCGGAG
	GAAGAGAAAA
3401	AACGGGTGCA GGCGGATAAA GACACCGCCT TGGCGAAACA
	GCGCGAAGCG
3451	GAAACCCGGC CGGCTACCAC CGCCTTCCCC CGCGCCCGCC
	GCGCCCGCCG
3501	GGATTTGCCG CAACCGCAGC CCCAACCGCA ACCCCAACCG
	CAGCGCGACC
3551	TGATCAGCCG TTATGCCAAT AGCGGTTTGA GTGAATTTTC
	CGCCACGCTC
3601	AACAGCGTTT TCGCCGTACA GGACGAATTG GACCGCGTGT
	TTGCCGAAGA
3651	CCGCCGCAAC GCCGTTTGGA CAAGCGGCAT CCGGGACACC
	AAACACTACC
3701	GTTCGCAAGA TTTCCGCGCC TACCGCCAAC AAACCGACCT
	GCGCCAAATC
3751	GGTATGCAGA AAAACCTCGG CAGCGGGCGC GTCGGCATCC
	TGTTTTCGCA
3801	CAACCGGACC GGAAACACCT TCGACGACGG CATCGGCAAC
	TCGGCACGGC
3851	TTGCCCACGG TGCCGTTTTC GGGCAATACG GCATCGGCAG
	GTTCGACATC
3901	GGCATCAGCG CGGGCGCGGG TTTTAGTAGC GGCAGCCTTT
	CAGACGGCAT
3951	CAGAGGCAAA ATCCGCCGCC GCGTGCTGCA TTACGGCATT
	CAGGCAAGAT
4001	ACCGCGCAGG TTTCGGCGGA TTCGGCATCG AACCGCACAT
	CGGCGCAACG
4051	CGCTATTTCG TCCAAAAAGC GGATTACCGA TACGAAAACG
	TCAATATCGC
4101	CACCCCGGGC CTTGCATTCA ACCGCTACCG CGCGGGCATT
	AAGGCAGATT
4151	ATTCATTCAA ACCGGCGCAA CACATTTCCA TCACGCCTTA
	TTTGAGCCTG
4201	TCCTATACCG ATGCCGCTTC CGGCAAAGTC CGAACGCGCG
	TCAATACCGC
4251	CGTATTGGCG CAGGATTTCG GCAAAACCCG CAGTGCGGAA
	TGGGGCGTAA
4301	ACGCCGAAAT CAAAGGTTTC ACGCTGTCCC TCCACGCTGC
	CGCCGCCAAG
4351	GGGCCGCAAT TGGAAGCGCA GCACAGCGCG GGCATCAAAT
	TAGGCTACCG
4401	CTGGTAA

This is predicted to encode a protein having amino acid sequence <SEQ ID 654>:

1	MKTTDKRTTE THRKAPKTGR IRFSPAYLAI CLSFGILPQA
	RAGHTYFGIN
51	YQYYRDFAEN KGKFAVGAKD IEVYNKKGEL VGKSMTKAPM
	IDFSVVSRNG
101	VAALAGDQYI VSVAHNGGYN NVDFGAEGSN PDQHRFSYQI
	VKRNNYKAGT
151	NGHPYGGDYH MPRLHKFVTD AEPVEMTSYM DGWKYADLNK
	YPDRVRIGAG
201	RQYWRSDEDE PNNRESSYHI ASAYSWLVGG NTFAQNGSGG
	GTVNLGSEKI
251	KHSPYGFLPT GGSFGDSGSP MFIYDAQKQK WLINGVLQTG
	NPYIGKSNGF
301	QLVRKDWFYD EIFAGDTHSV FYEPHQNGKY FFNDNNNGAG
	KIDAKHKHYS
351	LPYRLKTRTV QLFNVSLSET AREPVYHAAG GVNSYRPRLN
	NGENISFIDK
401	GKGELILTSN INQGAGGLYF EGNFTVSPKN NETWQGAGVH
	ISDGSTVTWK
451	VNGVANDRLS KIGKGTLLVQ AKGENQGSVS VGDGKVILDQ
	QADDQGKKQA
501	FSEIGLVSGR GTVQLNADNQ FNPDKLYFGF RGGRLDLNGH
	SLSFHRIQNT
551	DEGAMIVNHN QDKESTVTIT GNKDITTTGN NNNLDSKKEI
	AYNGWFGEKD
601	ATKTNGGLNL NYPPEEADRT LLLSGGTNLN GNITQTNGKL
	FFSGRPTPHA
651	YNHLGSGWSK MEGIPQGEIV WDNDWIDRTF KAENFHIQGG
	QAVVSRNVAK
701	VEGDWHLSNH AQAVFGVAPH QSHTICTRSD WTGLTSCTEK
	TITDDKVIAS
751	LSKTDVRGNV SLADHAHLNL TGLATFNGNL VQAETRTIRL
	RANATQNGNL
801	SLVGNAQATF NQATLNGNTS ASDNASFNLS NNAVQNGSLT
	LSDNAKANVS
851	HSALNGNVSL ADKAVFHFEN SRFTGKISGG KDTALHLKDS
	EWTLPSGTEL
901	GNLNLDNATI TLNSAYRHDA AGAQTGSAAD APRRRSRRSL
	LSVTPPTSAE
951	SRFNTLTVNG KLNGQGTFRF MSELFGYRSG KLKLAESSEG
	TYTLAVNNTG
1001	NEPVSLEQLT VVEGKDNTPL SENLNFTLQN EHVDAGAWRY
	QLIRKDGEFR
1051	LHNPVKEQEL SDKLGKAGET EAALTAKQAQ LAAKQQAEKD
	NAQSLDALIA
1101	AGRNATEKAE SVAEPARQAG GENAGIMQAE EEKKRVQADK
	DTALAKQREA
1151	ETRPATTAFP RARRARRDLP QPQPQPQPQP QRDLISRYAN
	SGLSEFSATL
1201	NSVFAVQDEL DRVFAEDRRN AVWTSGIRDT KHYRSQDFRA
	YRQQTDLRQI
1251	GMQKNLGSGR VGILFSHNRT GNTFDDGIGN SARLAHGAVF
	GQYGIGRFDI
1301	GISAGAGFSS GSLSDGIRGK IRRRVLHYGI QARYRAGFGG
	FGIEPHIGAT
1351	RYFVQKADYR YENVNIATPG LAFNRYRAGI KADYSFKPAQ
	HISITPYLSL
1401	SYTDAASGKV RTRVNTAVLA QDFGKTRSAE WGVNAEIKGF
	TLSLHAAAAK
1451	GPQLEAQHSA GIKLGYRW*

Underlined and double-underlined sequences represent the active site of a serine protease (trypsin family) and an ATP/GTP-binding site motif A (P-loop).

ORF1-1 and ORF1ng show 93.7% identity in 1471 aa overlap:

In addition, ORF1ng shows 55.7% identity with hap protein (P45387) over a 1455aa overlap:

Based on this analysis, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 78

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 655>:

1	..AAGGTGTGGC AATTTGTCGA AGA.CCGCTG CGTGCCGTCG
	TGCCTGCCGA
51	CAGTTTTGAA CCGACCGCGC AAAAATTGAA CCTGTTTAAG
	GCGGGTGCGG
101	CAACCATTTT GTTTTATGAA GATCAAAATG TCGTCAAAGG
	TTTGCAGGAG
151	CAGTTCCCTG CTTATGCCGC TAACTTCCCC GTTTGGGCGg
	ATCAGGCAAA
201	CGCGATGGTG CAGTATGCCG TTTGGACGAC ACTTGCCGCG
	GTCGGCGTAG
251	GTGCAAACCT GCAACATTAC AATCCCTTGC CCGATGCGGC
	GATTGCCAAA
301	GCGTGGAATA TCCCCGAAAA CTGGTTGTTG CGCGCACAAA
	TGGTTATCGG
351	CGGTATTGAA GGGGCGGCAG GTGAAAAGAC CTTTGAACCC
	GTTGCAGAAC
401	GTTTGAAAGT GTTCGGCGCA TAA

This corresponds to the amino acid sequence <SEQ ID 656; ORF6>:

1	. . . KVWQFVEXPL RAWPADSFE PTAQKLNLFK AGAATILFYE  DQNVVKGLQE
51	QFPAYAANFP VWADQANAMV QYAVWTTLAA VGVGANLQHY NPLPDAAIAK
101	AWNIPENWLL RAQMVIGGIE GAAGEKTFEP VAERLKVFGA *

Further sequence analysis revealed a further partial DNA sequence <SEQ ID 657>:

1	. . . CTGCGTGCCG TCGTGCCTGC CGACAGTTTT GAACCGACCG CGCAAAAATT
51	GAACCTGTTT AAGGCGGGTG CGGCAACCAT TTTGTTTTAT GAAGATCAAA
101	ATGTCGTCAA AGGTTTGCAG GAGCAGTTCC CTGCTTATGC CGCTAACTTC
151	CCCGTTTGGG CGGATCAGGC AAACGCGATG GTGCAGTATG CCGTTTGGAC
201	GACACTTGCC GCGGTCGGCG TAGGTGCAAA CCTGCAACAT TACAATCCCT
251	TGCCCGATGC GGCGATTGCC AAAGCGTGGA ATATCCCCGA AAACTGGTTG
301	TTGCGCGCAC AAATGGTTAT CGGCGGTATT GAAGGGGCGG CAGGTGAAAA
351	GACCTTTGAA CCCGTTGCAG AACGTTTGAA AGTGTTCGGC GCATAA

This corresponds to the amino acid sequence <SEQ ID 658; ORF6-1>:

1	. . . LRAVVPADSF EPTAQKLNLF KAGAATILFY EDQNVVKGLQ EQFPAYAANF
51	PVWADQANAM VQYAVWTTLA AVGVGANLQH YNPLPDAAIA KAWNIPENWL
101	LRAQMVIGGI EGAAGEKTFE PVAERLKVFG A*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF6 shows 98.6% identity over a 140aa overlap with an ORF (ORF6a) from strain A of N. meningitidis:

The complete length ORF6a nucleotide sequence <SEQ ID 659> is:

1	ATGACCCGTC AATCTCTGCA ACAGGCTGCC GAAAGCCGCC GTTCCATTTA
51	TTCGTTAAAT AAAAATCTGC CCGTCGGCAA AGATGAAATC GTCCAAATCG
101	TCGAACACGC CGTTTTGCAC ACACCTTCTT CGTTCAATTC CCAATCTGCC
151	CGTGTGGTCG TGCTGTTTGG CGAAGAGCAT GATAAGGTGT GGCAATTTGT
201	CGAAGACGCG CTGCGTGCCG TCGTGCCTGC CGACAGTTTT GAACCGACCG
251	CGCAAAAATT GAACCTGTTT AAGGCGGGTG CGGCAACTAT TTTGTTTTAT
301	GAAGATCAAA ATGTCGTCAA AGGTTTGCAG GAGCAGTTCC CTGCTTATGC
351	CGCCAACTTT CCCGTTTGGG CGGACCAGGC GAACGCGATG GTGCAGTATG
401	CCGTTTGGAC GACACTTGCC GCGGTCGGCG TAGGTGCAAA CCTGCAACAT
451	TACAATCCCT TGCCCGATGC GGCGATTGCC AAAGCGTGGA ATATCCCCGA
501	AAACTGGTTG TTGCGCGCAC AAATGGTTAT CGGCGGTATT GAAGGGGCGG
551	CAGGTGAAAA GACCTTTGAA CCAGTTGCAG AACGTTTGAA AGTGTTCGGC
601	GCATAA

This is predicted to encode a protein having amino acid sequence <SEQ ID 660>:

1	MTRQSLQQAA ESRRSIYSLN KNLPVGKDEI VQIVEHAVLH TPSSFNSQSA
51	RVVVLFGEEH DKVWQFVEDA LRAVVPADSF EPTAQKLNLF KAGAATILFY
101	EDQNVVKGLQ EQFPAYAANF PVWADQANAM VQYAVWTTLA AVGVGANLQH
151	YNPLPDAAIA KAWNIPENWL LRAQMVIGGI EGAAGEKTFE PVAERLKVFG
201	A*

ORF6a and ORF6-1 show 100.0% identity in 131 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF6 shows 95.7% identity over a 140aa overlap with a predicted ORF (ORF6ng) from N. gonorrhoeae:

The complete length ORF6ng nucleotide sequence <SEQ ID 661> was identified as:

1	ATGGCCGTTG CGTCAAATGT CAGCTTGGAT ATGTCCAATC CTACGGTGTT
51	ACGCATGGGA TTACCCTTAT ATATTGCGTC CCTAAGAAGG GGCGCAATAT
101	ATAAGGTGTG GCAATTTGTC GAAGACGCGC TGCGTGCCGT CGTGCCTGCC
151	GACAGTTTTG AACCGACCGC GCAAAAATTG AAGCTGTTTA AGGCGGGCGC
201	GGCAACCATT TTGTTTTATG AAGATCAAAA TGTCGTCAAA GGTTTGCAGG
251	AGCAGTTCCC TGCTTATGCC GCCAACTTTC CCGTTTGGGC GGACCAGGCG
301	AACGCTATGG TACAGTATGC CGTCTGGACG ACACTTGCCG CGGTCGGTGC
351	AGGTGCAAAT CTGCAACATT ACAACCCCTT GCCCGATGTG GCGATTGCTA
401	AAGCGTGGAA TATTCCCGAA AACTGGCTGT TGCGCGCGCA AATGGTTATC
451	GGTGGTATTG AAGGGGcggc aggtgaaaaa gtctttgaac CCGTTGCgga
501	acgtttgAAA GTGTTCGGCG CATAA

This encodes a protein having amino acid sequence <SEQ ID 662>:

1	MAVASNVSLD MSNPTVLRMG LPLYIASLRR GAIYKVWQFV EDALRAVVPA
51	DSFEPTAQKL KLFKAGAATI LFYEDQNVVK GLQEQFPAYA ANFPVWADQA
101	NAMVQYAVWT TLAAVGAGAN LQHYNPLPDV AIAKAWNIPE NWLLRAQMVI
151	GGIEGAAGEK VFEPVAERLK VFGA*

ORF6ng and ORF6-1 show 96.9% identity in 131 aa overlap:

It is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 79

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 663>

1	. . . GGCTACAACT ACCTGTTCGC GCGCGGCAGC CGCATCGCCA ACTACCAAAT
51	CAACGGCATC CCCGTTGCCG ACGCGCTGGC CGATACGGGt CAATGCCAAC
101	ACCGCCGCCT ATGAGCGCGT AGAAGTCGTG CGCGGCGTGG CGGGGCTGCT
151	GGACGGCACG GGCGAGCCTT CCGCCACCGT CAATCTGGTG CGCAAACGCC
201	TGACCCGCAA GCCATTGTTT GAAGTCCGCG CCGAAGCgGG CAACCGcAAA
251	CATTTCGGGC TGGACGCGGA CGTATCGGGC AGCCTGAACA CCGAAG.crC
301	rCTGCGCgGC CGCCTGGTTT CCAcCTTCGG ACGCGGCGAC TCGTGGCGGC
351	GGCGCGAACG CAGCCGskAT GCCGAACTCT ACGGCATTTT GGAATACGAC
401	ATCGCACCGC AAACCCGCGT CCACGCArGC ATGGACTACC AGCAGGCGAA
451	AGAAACCGCC GACGCGCCGC TCAGcTACGC CGTGTACGAC AGCCAAGGTT
501	ATGCCACCGC CTTCGGCCCG AAAGACAACC CCGCCACAAA TTGGGCGAAC
551	AGCCACCACC GTGCGCTCAA CCTGTTCGCC GGCATCGAAC ACCGCTTCAA
601	CCAAGACTGG AAACTCAAAG CCGAATACGA CTAC . . .

This corresponds to the amino acid sequence <SEQ ID 664; ORF23>:

1	. . . GYNYLFARGS RIANYQINGI PVADALADTG NANTAAYERV EVVRGVAGLL
51	DGTGEPSATV NLVRKRLTRK PLFEVRAEAG NRKHFGLDAD VSGSLNTEXX
101	LRGRLVSTFG RGDSWRRRER SRXAELYGIL EYDIAPQTRV HAXMDYQQAK
151	ETADAPLSYA VYDSQGYATA FGPKDNPATN WANSHHRALN LFAGIEHRFN
201	QDWKLKAEYD Y . . .

Further work revealed the complete nucleotide sequence <SEQ ID 665>:

1	ATGACACGCT TCAAATATTC CCTGCTGTTT GCCGCCCTGT TGCCCGTGTA
51	CGCGCAGGCC GATGTTTCTG TTTCAGACGA CCCCAAACCG CAGGAAAGCA
101	CTGAATTGCC GACCATCACC GTTACCGCCG ACCGCACCGC GAGTTCCAAC
151	GACGGCTACA CTGTTTCCGG CACGCACACC CCGCTCGGGC TGCCCATGAC
201	CCTGCGCGAA ATCCCGCAGA GCGTCAGCGT CATCACATCG CAACAAATGC
251	GCGACCAAAA CATCAAAACG CTCGACCGCG CCCTGTTGCA GGCGACCGGC
301	ACCAGCCGCC AGATTTACGG CTCCGACCGC GCGGGCTACA ACTACCTGTT
351	CGCGCGCGGC AGCCGCATCG CCAACTACCA AATCAACGGC ATCCCCGTTG
401	CCGACGCGCT GGCCGATACG GGCAATGCCA ACACCGCCGC CTATGAGCGC
451	GTAGAAGTCG TGCGCGGCGT GGCGGGGCTG CTGGACGGCA CGGGCGAGCC
501	TTCCGCCACC GTCAATCTGG TGCGCAAACG CCTGACCCGC AAGCCATTGT
551	TTGAAGTCCG CGCCGAAGCG GGCAACCGCA AACATTTCGG GCTGGACGCG
601	GACGTATCGG GCAGCCTGAA CACCGAAGGC ACGCTGCGCG GCCGCCTGGT
651	TTCCACCTTC GGACGCGGCG ACTCGTGGCG GCGGCGCGAA CGCAGCCGCG
701	ATGCCGAACT CTACGGCATT TTGGAATACG ACATCGCACC GCAAACCCGC
751	GTCCACGCAG GCATGGACTA CCAGCAGGCG AAAGAAACCG CCGACGCGCC
801	GCTCAGCTAC GCCGTGTACG ACAGCCAAGG TTATGCCACC GCCTTCGGCC
851	CGAAAGACAA CCCCGCCACA AATTGGGCGA ACAGCCGCCA CCGTGCGCTC
901	AACCTGTTCG CCGGCATCGA ACACCGCTTC AACCAAGACT GGAAACTCAA
951	AGCCGAATAC GACTACACCC GCAGCCGCTT CCGCCAGCCC TACGGCGTAG
1001	CAGGCGTGCT TTCCATCGAC CACAACACCG CCGCCACCGA CCTGATTCCC
1051	GGTTATTGGC ACGCCGACCC GCGCACCCAC AGCGCCAGCG TGTCATTGAT
1101	CGGCAAATAC CGCCTGTTCG GCCGCGAACA CGATTTAATC GCGGGTATCA
1151	ACGGTTACAA ATACGCCAGC AACAAATACG GCGAACGCAG CATCATCCCC
1201	AACGCCATTC CCAACGCCTA CGAATTTTCC CGCACGGGTG CCTACCCGCA
1251	GCCTGCATCG TTTGCCCAAA CCATCCCGCA ATACGGCACC AGGCGGCAAA
1301	TCGGCGGCTA TCTCGCCACC CGTTTCCGCG CCGCCGACAA CCTTTCGCTG
1351	ATTTTGGGCG GACGATACAC CCGTTACCGC ACCGGCAGCT ACGACAGCCG
1401	CACACAAGGC ATGACCTATG TGTCCGCCAA CCGTTTCACC CCCTACACAG
1451	GCATCGTGTT CGACCTGACC GGCAACCTGT CTCTTTACGG CTCGTACAGC
1501	AGCCTGTTCG TCCCGCAATC GCAAAAAGAC GAACACGGCA GCTACCTGAA
1551	ACCCGTAACC GGCAACAATC TGGAAGCCGG CATCAAAGGC GAATGGCTTG
1601	AAGGCCGTCT GAACGCATCC GCCGCCGTGT ACCGCGCCCG TAAAAACAAC
1651	CTCGCCACCG CAGCAGGACG CGACCCGAGC GGCAACACCT ACTACCGCGC
1701	CGCCAACCAA GCCAAAACCC ACGGCTGGGA AATCGAAGTC GGCGGCCGCA
1751	TCACGCCCGA ATGGCAGATA CAGGCAGGTT ACAGCCAAAG CAAAACCCGC
1801	GACCAAGACG GCAGCCGCCT GAACCCCGAC AGCGTACCCG AACGCAGCTT
1851	CAAACTCTTC ACTGCCTACC ACTTTGCCCC CGAAGCCCCC AGCGGCTGGA
1901	CCATCGGCGC AGGCGTGCGC TGGCAGAGCG AAACCCACAC CGACCCTGCC
1951	ACGCTCCGCA TCCCCAACCC CGCCGCCAAA GCCCGCGCCG CCGACAACAG
2001	CCGCCAAAAA GCCTACGCCG TCGCCGACAT CATGGCGCGT TACCGCTTCA
2051	ATCCGCGCGC CGAACTGTCG CTGAACGTGG ACAATCTGTT CAACAAACAC
2101	TACCGCACCC AGCCCGACCG CCACAGCTAC GGCGCACTGC GGACAGTGAA
2151	CGCGGCGTTT ACCTATCGGT TTAAATAA

This corresponds to the amino acid sequence <SEQ ID 666; ORF23-1>:

1	MTRFKYSLLF AALLPVYAQA DVSVSDDPKP QESTELPTIT VTADRTASSN
51	DGYTVSGTHT PLGLPMTLRE IPQSVSVITS QQMRDQNIKT LDRALLQATG
101	TSRQIYGSDR AGYNYLFARG SRIANYQING IPVADALADT GNANTAAYER
151	VEVVRGVAGL LDGTGEPSAT VNLVRKRLTR KPLFEVRAEA GNRKHFGLDA
201	DVSGSLNTEG TLRGRLVSTF GRGDSWRRRE RSRDAELYGI LEYDIAPQTR
251	VHAGMDYQQA KETADAPLSY AVYDSQGYAT AFGPKDNPAT NWANSRHRAL
301	NLFAGIEHRF NQDWKLKAEY DYTRSRFRQP YGVAGVLSID HNTAATDLIP
351	GYWHADPRTH SASVSLIGKY RLFGREHDLI AGINGYKYAS NKYGERSIIP
401	NAIPNAYEFS RTGAYPQPAS FAQTIPQYGT RRQIGGYLAT RFRAADNLSL
451	ILGGRYTRYR TGSYDSRTQG MTYVSANRFT PYTGIVFDLT GNLSLYGSYS
501	SLFVPQSQKD EHGSYLKPVT GNNLEAGIKG EWLEGRLNAS AAVYRARKNN
551	LATAAGRDPS GNTYYRAANQ AKTHGWEIEV GGRITPEWQI QAGYSQSKTR
601	DQDGSRLNPD SVPERSFKLF TAYHFAPEAP SGWTIGAGVR WQSETHTDPA
651	TLRIPNPAAK ARAADNSRQK AYAVADIMAR YRFNPRAELS LNVDNLFNKH
701	YRTQPDRHSY GALRTVNAAF TYRFK*

Computer analysis of this amino acid sequence gave the following results:

Homology with the Ferric-Pseudobactin Receptor PupB of Pseudomonas putida (Accession Number P38047)

ORF23 and PupB protein show 32% aa identity in 205aa overlap:

Orf23	6	FARGSRIANYQINGIPVADALADTGNANTAAYERVEVVRGVAGLLDGTGEPSATVNLVRK	65
		++RG  I NY+++G+P +   L D  + + A ++RVE+VRG  GL+ G G PSAT+NL+RK
PupB	215	WSRGFAIQNYEVDGVPTSTRL-DNYSQSMAMFDRVEIVRGATGLISGMGNPSATINLIRK	273
Orf23	66	RLTRKPLFEVRAEAGNRKHFGLDADVSGSLNTEXXLRGRLVSTFXXXXXXXXXXXXXXAE	125
		R T +    +  EAGN   +G   DVSG L     +RGR V+ +
PupB	274	RPTAEAQASITGEAGNWDRYGTGFDVSGPLTETGNIRGRFVADYKTEKAWIDRYNQQSQL	333
Orf23	126	LYGILEYDIAPQTRVHAXMDYQQAKETADAPLSYAVYD--SQGYATAFGPKDNPATNWAN	183
		+YGI E+D++  T+      Y   +    D+PL   +    S G  T      N A +W+
PupB	334	MYGITEFDLSEDTLLTVGFSY--LRSDIDSPLRSGLPTRFSTGERTNLKRSLNAAPDWSY	391
Orf23	184	SHHRALNLFAGIEHRFNQDWKLKAE	208
		+ H   + F  IE +    W  K E
PupB	392	NDHEQTSFFTSIEQQLGNGWSGKIE	416

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF23 shows 95.7% identity over a 211aa overlap with an ORF (ORF23a) from strain A of N. meningitidis:

The complete length ORF23a nucleotide sequence <SEQ ID 667> is:

1	ATGACACGCT TCAAATATTC CCTGCTGTTT GCCGCCCTGT TGCCCGTGTA
51	CGCGCAGGCC GATGTTTCTG TTTCAGACGA CCCAAAACCG CAGGAAAGCA
101	CTGAATTGCC GACCATCACC GTTACCGCCG ACCGCACCGC GAGTTCCAAC
151	GACGGCTACA CTGTTTCCGG CACGCACACC CCGCTCGGGC TGCCCATGAC
201	CCTGCGCGAA ATCCCGCAGA GCGTCAGCGT CATCACATCG CAACAAATGC
251	GCGACCAAAA CATCAAAGCG CTCGACCGCG CCCTGTTGCA GGCGACCGGC
301	ACCAGCCGCC AGATTTACGG CTCCGACCGC GCGGGCTACA ACTACCTGTT
351	CGCGCGCGGC AGCCGCATCG CCAACTACCA AATCAACGGC ATCCCCGTTG
401	CCGACGCGCT GGCCGATACG GGCAATGCCA ACACCGCCGC CTATGAGCGC
451	GTAGAAGTCG TGCGCGGCGT GGCGGGGCTG CTGGACGGCA CGGGCGAGCC
501	TTCCGCCACC GTCAATCTGG TGCGCAAACG CCCGACCCGC AAGCCATTGT
551	TTGAAGTCCG CGCCGAAGCG GGCAACCGCA AACATTTCGG GCTGGGCGCG
601	GACGTATCGG GCAGCCTGAA TGCCGAAGGC ACGCTGCGCG GCCGCCTGGT
651	TTCCACCTTC GGACGCGGCG ACTCGTGGCG GCAGCGCGAA CGCAGCCGCG
701	ATGCCGAACT CTACGGCATT TTGGAATACG ACATCGCACC GCAAACCCGC
751	GTCCACGCAG GCATGGACTA CCAGCAGGCG AAAGAAACCG CCGACGCGCC
801	GCTCAGCTAC GCCGTGTACG ACAGCCAAGG TTATGCCACC GCCTTCGGCC
851	CGAAAGACAA CCCCGCCACA AATTGGGCGA ACAGCCGCCA CCGTGCGCTC
901	AACCTGTTCG CCGGCATCGA ACACCGCTTC AACCAAGACT GGAAACTCAA
951	AGCCGAATAC GACTACACCC GCAGCCGCTT CCGCCAGCCC TACGGCGTAG
1001	CAGGCGTGCT TTCCATCGAC CACAACACCG CCGCCACCGA CCTGATTCCC
1051	GGTTATTGGC ACGCCGACCC GCGCACCCAC AGCGCCAGCG TGTCATTAAT
1101	CGGCAAATAC CGCCTGTTCG GCCGCGAACA CGATTTAATC GCGGGTATCA
1151	ACGGTTACAA ATACGCCAGC AACAAATACG GCGAACGCAG CATCATCCCC
1201	AACGCCATTC CCAACGCCTA CGAATTTTCC CGCACGGGTG CCTACCCGCA
1251	GCCTGCATCG TTTGCCCAAA CCATCCCGCA ATACGGCACC AGGCGGCAAA
1301	TCGGCGGCTA TCTCGCCACC CGTTTCCGCG CCGCCGACAA CCTTTCGCTG
1351	ATACTCGGCG GCAGATACAG CCGTTACCGC ACCGGCAGCT ACGACAGCCG
1401	CACACAAGGC ATGACCTATG TGTCCGCCAA CCGTTTCACC CCCTACACAG
1451	GCATCGTGTT CGACCTGACC GGCAACCTGT CGCTTTACGG CTCGTACAGC
1501	AGCCTGTTCG TCCCGCAATC GCAAAAAGAC GAACACGGCA GCTACCTGAA
1551	ACCCGTAACC GGCAACAATC TGGAAGCCGG CATCAAAGGC GAATGGCTTG
1601	AAGGCCGTCT GAACGCATCC GCCGCCGTGT ACCGCGCCCG TAAAAACAAC
1651	CTCGCCACCG CAGCAGGACG CGACCCGAGC GGCAACACCT ACTACCGCGC
1701	CGCCAACCAA GCCAAAACCC ACGGCTGGGA AATCGAAGTC GGCGGCCGCA
1751	TCACGCCCGA ATGGCAGATA CAGGCAGGTT ACAGCCAAGG CAAAACCCGC
1801	GACCAAGACG GCAGCCGCCT GAACCCCGAC AGCGTACCCG AACGCAGCTT
1851	CAAACTCTTC ACTGCCTACC ACTTTGCCCC CGAAGCCCCC AGCGGCTGGA
1901	CCATCGGCGC AGGCGTGCGC TGGCAGAGCG AAACCCACAC CGACCCTGCC
1951	ACGCTCCGCA TCCCCAACCC CGCCGCCAAA GCCCGCGCCG CCGACAACAG
2001	CCGCCAAAAA GCCTACGCCG TCGCCGACAT CATGGCGCGT TACCGCTTCA
2051	ATCCGCGCGC CGAACTGTCG CTGAACGTGG ACAATCTGTT CAACAAACAC
2101	TACCGCACCC AGCCCGACCG CCACAGCTAC GGCGCACTGC GGACAGTGAA
2151	CGCGGCGTTT ACCTATCGGT TTAAATAA

This encodes a protein having amino acid sequence <SEQ ID 668>:

1	MTRFKYSLLF AALLPVYAQA DVSVSDDPKP QESTELPTIT VTADRTASSN
51	DGYTVSGTHT PLGLPMTLRE IPQSVSVITS QQMRDQNIKA LDRALLQATG
101	TSRQIYGSDR AGYNYLFARG SRIANYQING IPVADALADT GNANTAAYER
151	VEVVRGVAGL LDGTGEPSAT VNLVRKRPTR KPLFEVRAEA GNRKHFGLGA
201	DVSGSLNAEG TLRGRLVSTF GRGDSWRQRE RSRDAELYGI LEYDIAPQTR
251	VHAGMDYQQA KETADAPLSY AVYDSQGYAT AFGPKDNPAT NWANSRHRAL
301	NLFAGIEHRF NQDWKLKAEY DYTRSRFRQP YGVAGVLSID HNTAATDLIP
351	GYWHADPRTH SASVSLIGKY RLFGREHDLI AGINGYKYAS NKYGERSIIP
401	NAIPNAYEFS RTGAYPQPAS FAQTIPQYGT RRQIGGYLAT RFRAADNLSL
451	ILGGRYSRYR TGSYDSRTQG MTYVSANRFT PYTGIVFDLT GNLSLYGSYS
501	SLFVPQSQKD EHGSYLKPVT GNNLEAGIKG EWLEGRLNAS AAVYRARKNN
551	LATAAGRDPS GNTYYRAANQ AKTHGWEIEV GGRITPEWQI QAGYSQSKTR
601	DQDGSRLNPD SVPERSFKLF TAYHFAPEAP SGWTIGAGVR WQSETHTDPA
651	TLRIPNPAAK ARAADNSRQK AYAVADIMAR YRFNPRAELS LNVDNLFNKH
701	YRTQPDRHSY GALRTVNAAF TYRFK*

ORF23a and ORF23-1 show 99.2% identity in 725 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF23 shows 93.4% identity over a 211 as overlap with a predicted ORF (ORF23.ng) from N. gonorrhoeae:

The ORF23ng nucleotide sequence <SEQ ID 669> is predicted to encode a protein comprising amino acid sequence <SEQ ID 670>:

1	SAVDACRIPG YNYLFARGSR IANYQINGIP VADALADTGN ANTAAYERVE
51	VVRGVAGLPD GTGEPSATVN LVRKHPTRKP LFEVRAEAGN RKHFGLGADV
101	SGSLNAEGTL RGRLVSTFGR GDSWRQLERS RDAELYGILE YDIAPQTRVH
151	AGMDYQQAKE TADAPLSYAV YDSQGYATAF GPKDNPATNW SNSRNRALNL
201	FAGIEHRFNQ DWKLKAEYDY TRSRFRQPYG VAGVLSIDHS TAATDLIPGY
251	WHADPRTHSA SMSLTGKYRL FGREHDLIAG INGYKYASNK YGERSIIPNA
301	IPNAYEFSRT GAYPQPSSFA QTIPQYDTRR QIGGYLATRF RAADNLSLIL
351	GGRYSRYRAG SYNSRTQGMT YVSANRFTPY TGIVFDLTGN LSLYGSYSSL
401	FVPQLQKDEH GSYLKPVTGN NLEADIKGEW LEGRLNASAA VYRARKNNLA
451	TAAGRDQSGN TYYRAANQAK THGWEIEVGG RITPEWQIQA GYSQSKPRDQ
501	DGSRLNPDSV PERSFKLFTA YHLAPEAPSG RTIGAGVRRQ GETHTDPAAL
551	RIPNPAAKAR AVANSRQKAY AVADIMARYR FNPRTELSLN VDNLFNKHYR
601	TQPDRHSYGA LRTVNAAFTY RFK*

Further work revealed the complete nucleotide sequence <SEQ ID 671>:

1	ATGACACGCT TCAAATACTC CCTGCTTTTT GCCGCCCTGC
	TACCCGTGTA
51	CGCGCAGGCC GATGTTTCTG TTTCAGACGA CCCCAAACCG
	CAGGAAAGCA
101	CCGAATTGCC GACCATCACC GTTACCGCCG ACCGCACCGC
	GAGTTCCAAC
151	GACGGCTACA CCGTTTCCGG CACGCACACC CCGTTCGGGC
	TGCCCATGAC
201	CCTGCGCGAA ATCCCGCAGA GCGTCAGCGT CATCACATCG
	CAACAAATGC
251	GCGACCAAAA CATCAAAACG CTCGACCGCG CCCTGTTGCA
	GGCGACCGGC
301	ACCAGCCGCC AGATTTACGG CTCCGACCGC GCGGGCTACA
	ACTACCTGTT
351	CGCGCGCGGC AGCCGCATCG CCAACTACCA AATCAACGGC
	ATCCCCGTTG
401	CCGACGCGCT GGCCGATACG GGCAATGCCA ACACCGCCGC
	CTATGAGCGC
451	GTAGAAGTCG TGCGCGGCGT GGCGGGGCTG CCGGACGGCA
	CGGGCGAGCC
501	TTCTGCCACC GTCAATCTGG TACGCAAACA CCCGACCCGC
	AAGCCATTGT
551	TTGAAGTCCG CGCCGAAGCC GGCAACCGCA AACATTTCGG
	GCTGGGCGCG
601	GACGTATCGG GCAGCCTGAA CGCCGAAGGC ACGCTGCGCG
	GCCGCCTGGT
651	TTCCACCTTC GGACGCGGCG ACTCGTGGCG GCAGCTCGAA
	CGCAGCCGCG
701	ATGCCGAACT CTACGGCATT TTGGAATACG ACATCGCACC
	GCAAACCCGC
751	GTCCACGCAG GCATGGACTA CCAGCAGGCG AAAGAAACCG
	CAGACGCGCC
801	GCTCAGCTAC GCCGTGTACG ACAGCCAAGG TTATGCCACC
	GCCTTCGGCC
851	CAAAAGACAA CCCCGCCACA AATTGGTCGA ACAGCCGCAA
	CCGTGCGCTC
901	AACCTGTTCG CCGGCATAGA ACACCGCTTC AACCAAGACT
	GGAAACTCAA
951	AGCCGAATAC GACTACACCC GTAGCCGCTT CCGCCAGCCC
	TACGGTGTGG
1001	CAGGCGTACT TTCCATCGAC CACAGCACTG CCGCCACCGA
	CCTGATTCCC
1051	GGTTATTGGC ACGCcgatcc GCGCACCCAC AGCGCCAGCA
	TGTCATTGAC
1101	CGGCAAATAC CgcctGTTCG GCCGCGAGCA CGATTTAATC
	GCGGGTATCA
1151	ACGGCTACAA ATACGCCAGC AACAAATACG GCGAACGCAG
	CATCATTCCC
1201	AACGCCATTC CCAACGCCTA CGAATTTTCC CGCACGGGCG
	CCTATCCGCA
1251	GCCATCATCG TTTGCCCAAA CCATCCCGCA ATACGACACC
	AGGCGGCAAA
1301	TCGGCGGCTA TCTCGCCACC CGTTTCCGCG CCGCCGACAA
	CCTTTCGCTG
1351	ATACTCGGCG GCAGATACAG CCGCTACCGC GCAGGCAGCT
	ACAACAGCCG
1401	CACACAAGGC ATGACCTATG TGTCCGCCAA CCGTTTCACC
	CCCTACACAG
1451	GCATCGTGTT CGATCTGACC GGCAACCTGT CGCTTTACGG
	CTCGTACAGC
1501	AGCCTGTTCG TCCCGCAATT GCAAAAAGAC GAACACGGCA
	GCTACCTGAA
1551	ACCCGTAACC GGCAACAATC TGGAAGCCGA CATCAAAGGC
	GAATGGCTTG
1601	AAGGGCGTCT GAACGCATCC GCCGCCGTGT ACCGCGCCCG
	TAAAAACAAC
1651	CTCGCCACCG CAGCAGGACG CGACCAGAGC GGCAACACCT
	ACTATCGCGC
1701	CGCCAACCAA GCCAAAACCC ACGGCTGGGA AATCGAAGTC
	GGCGGCCGCA
1751	TCACGCCCGA ATGGCAGATA CAGGCAGGCT ACAGCCAAAG
	CAAACCCCGC
1801	GACCAAGACG GCAGCCGCCT GAACCCCGAC AGCGTAcCCG
	AACGCAGCTT
1851	CAAACTCTTC ACCGCCTACC ACTTAGCCCC CGAAGCCCCC
	AGCGGCCGGA
1901	CCATcggTGC GGGTGTGCGC CGGCAGGGCG AAACCCACAC
	CGACCCAGCC
1951	GCGCTCCGCA TCCCCAACCC CGCCGCCAAA GCCCGCGCCG
	TCGCCAACAG
2001	CCGCCAGAAA GCCTACGCCG TCGCCGACAT CATGGCGCGT
	TACCGCTTCA
2051	ATCCGCGCAC CGAACTGTCG CTGAACGTGG ACAACCTGTT
	CAACAAACAC
2101	TACCGCACCC AGCCCGACCG CCACAGCTAC GGCGCACTGC
	GGACAGTGAA
2151	CGCGGCGTTT ACCTATCGGT TTAAATAA

This corresponds to the amino acid sequence <SEQ ID 672; ORF23ng-1>:

1	MTRFKYSLLF AALLPVYAQA DVSVSDDPKP QESTELPTIT
	VTADRTASSN
51	DGYTVSGTHT PFGLPMTLRE IPQSVSVITS QQMRDQNIKT
	LDRALLQATG
101	TSRQIYGSDR AGYNYLFARG SRIANYQING IPVADALADT
	GNANTAAYER
151	VEVVRGVAGL PDGTGEPSAT VNLVRKHPTR KPLFEVRAEA
	GNRKHFGLGA
201	DVSGSLNAEG TLRGRLVSTF GRGDSWRQLE RSRDAELYGI
	LEYDIAPQTR
251	VHAGMDYQQA KETADAPLSY AVYDSQGYAT AFGPKDNPAT
	NWSNSRNRAL
301	NLFAGIEHRF NQDWKLKAEY DYTRSRFRQP YGVAGVLSID
	HSTAATDLIP
351	GYWHADPRTH SASMSLTGKY RLFGREHDLI AGINGYKYAS
	NKYGERSIIP
401	NAIPNAYEFS RTGAYPQPSS FAQTIPQYDT RRQIGGYLAT
	RFRAADNLSL
451	ILGGRYSRYR AGSYNSRTQG MTYVSANRFT PYTGIVFDLT
	GNLSLYGSYS
501	SLFVPQLQKD EHGSYLKPVT GNNLEADIKG EWLEGRLNAS
	AAVYRARKNN
551	LATAAGRDQS GNTYYRAANQ AKTHGWEIEV GGRITPEWQI
	QAGYSQSKPR
601	DQDGSRLNPD SVPERSFKLF TAYHLAPEAP SGRTIGAGVR
	RQGETHTDPA
651	ALRIPNPAAK ARAVANSRQK AYAVADIMAR YRFNPRTELS
	LNVDNLFNKH
701	YRTQPDRHSY GALRTVNAAF TYRFK*

ORF23ng-1 and ORF23-1 show 95.9% identity in 725 aa overlap:

In addition, ORF23ng-1 shows significant homology with an OMP from E. coli:

sp|P16869|FHUE_ECOLI OUTER-MEMBRANE RECEPTOR FOR FE(III)-COPROGEN,
FE(III)-FERRIOXAMINE B AND FE(III)-RHODOTRULIC ACID PRECURSOR
>gi|1651542|gnl|PID|d1015403
(D90745) Outer membrane protein FhuE precursor [Escherichia coli]
>gi|1651545|gnl|PID|d1015405 (D90746) Outer membrane protein
FhuE precursor [Escherichia coli] >gi|1787344 (AE000210)
outer-membrane receptor for Fe(III)-
coprogen, Fe(III)-ferrioxamine B and Fe(III)-rhodotrulic acid precursor
[Escherichia coli] Length = 729
Score = 332 bits (843), Expect = 3e−90
Identities = 228/717 (31%), Positives = 350/717 (48%),
Gaps = 60/717 (8%)

Query:	38	TITVTADRTASSN--DGYTVSGTHTPFGLPMTLREIPQSVSVITSQQMRDQNIKTLDRAL	95
		T+ V    TA  +  + Y+V+ T     + MT R+IPQSV++++ Q+M DQ ++TL   +
Sbjct:	43	TVIVEGSATAPDDGENDYSVTSTSAGTKMQMTQRDIPQSVTIVSQQRMEDQQLQTLGEVM	102
Query:	96	LQATGTSRQIYGSDRAGYNYLFARGSRIANYQINGIP--------VADALADTGNANTAA	147
		G S+    SDRA Y   ++RG +I NY ++GIP        + DAL+D      A
Sbjct:	103	ENTLGISKSQADSDRALY---YSRGFQIDNYMVDGIPTYFESRWNLGDALSDM-----AL	154
Query:	148	YERVEVVRGVAGLPDGTGEPSATVNLVRKHPTRKPLF-EVRAEAGNRKHFGLGADVSGSL	206
		+ERVEVVRG  GL  GTG PSA +N+VRKH T +    +V AE G+       AD+   L
Sbjct:	155	FERVEVVRGATGLMTGTGNPSAAINMVRKHATSREFKGDVSAEYGSWNKERYVADLQSPL	214
Query:	207	NAEGTLRGRLVSTFGRGDSWRQLERSRDAELYGILEYDIAPQTRVHAGMDYQQAKETADA	266
		+G +R R+V  +   DSW     S      GI++ D+   T + AG +YQ+    +
Sbjct:	215	TEDGKIRARIVGGYQNNDSWLDRYNSEKTFFSGIVDADLGDLTTLSAGYEYQRIDVNSPT	274
Query:	267	PLSYAVYDSQGYATAFGPKDNPATNWSNSRNRALNLFAGIEHRFNQDWKLKAEYDYTRSR	326
		+++ G + ++    + A +W+ +      +F  ++ +F   W+      ++
Sbjct:	275	WGGLPRWNTDGSSNSYDRARSTAPDWAYNDKEINKVFMTLKQQFADTWQATLNATHSEVE	334
Query:	327	F--RQPYGVAGVLSIDHSTAA--TDLIPGY-------WHADPRTHSA-SMSLTGKYRLFG	374
		F  +  Y  A V   D       ++  PG+       W++  R   A  +   G Y LFG
Sbjct:	335	FDSKMMYVDAYVNKADGMLVGPYSNYGPGFDYVGGTGWNSGKRKVDALDLFADGSYELFG	394
Query:	375	REHDLIAGINGYKYASNKYGER--SIIPNAIPNAYEFSRTGAYPQPSSFAQTIPQYDTRR	432
		R+H+L+ G   Y   +N+Y     +I P+ I + Y F+  G +PQ     Q++ Q DT
Sbjct:	395	RQHNLMFG-GSYSKQNNRYFSSWANIFPDEIGSFYNFN--GNFPQTDWSPQSLAQDDTTH	451
Query:	433	QIGGYLATRFRAADNLSLILGGRYSRYRAGSYNSRTQGMTY-VSANRFTPYTGIVFDXXX	491
		Y ATR   AD L LILG RY+ +R  +       +TY +  N  TPY G+VFD
Sbjct:	452	MKSLYAATRVTLADPLHLILGARYTNWRVDT-------LTYSMEKNHTTPYAGLVFDIND	504
Query:	492	XXXXXXXXXXXFVPQLQKDEHGSYLKPVTGNNLEADIKGEWLEGRLNASAAVYRARKNNL	551
		F PQ  +D  G YL P+TGNN E  +K +W+  RL  + A++R  ++N+
Sbjct:	505	NWSTYASYTSIFQPQNDRDSSGKYLAPITGNNYELGLKSDWMNSRLTTTLAIFRIEQDNV	564
Query:	552	ATAAGR---DQSGNTYYRAANQAKTHGWEIEVGGRITPEWQIQAGYSQSKPRDQDGSRLN	608
		A + G      +G T Y+A +   + G E E+ G IT  WQ+  G ++    D +G+ +N
Sbjct:	565	AQSTGTPIPGSNGETAYKAVDGTVSKGVEFELNGAITDNWQLTFGATRYIAEDNEGNAVN	624
Query:	609	PDSVPERSFKLFTAYHLAPEAPSGRTIGAGVRRQGETHTDPAALRIPNPAAKARAVANSR	668
		P ++P  + K+FT+Y L P  P   T+G GV  Q   +TD        P    RA
Sbjct:	625	P-NLPRTTVKMFTSYRL-PVMPE-LTVGGGVNWQNRVYTDTV-----TPYGTFRA----E	672
Query:	669	QKAYAVADIMARYRFNPRTELSLNVDNLFNKHYRTQPDRH-SYGALRTVNAAFTYRF	724
		Q +YA+ D+  RY+      L  NV+NLF+K Y T  +    YG  R  +   TY+F
Sbjct:	673	QGSYALVDLFTRYQVTKNFSLQGNVNNLFDKTYDTNVEGSIVYGTPRNFSITGTYQF	729

Based on this analysis, it was predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF23-1 (77.5 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 15A shows the results of affinity purification of the His-fusion protein, and FIG. 15B shows the results of expression of the GST-fusion in E. coli. Purified His-fusion protein was used to immunise mice, whose sera were used for Western blot (FIG. 15C) and for ELISA (positive result). These experiments confirm that ORF23-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 80

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 673>:

1	ATGCGCACGG CAGTGGTTTT GCTGTTGATC ATGCCGATGG
	CGGCTTCGTC
51	GGCAATGATG CCGGAAATGG TGTGCGCGGG CGTGTCGCCG
	GGAACGGCAA
101	TCATATCCAA GCCGACCGAA CAAACGGCGG TCATGGCTTC
	GAGTTTGTCC
151	AGCGTCAgcA CGCCTGCTTC GGCGgcGgCa ATCATACCTT
	CGTCTTCGGA
201	AACGGGGATA AACGcGCCAC TCAAACCCCC GACCGCGCTG
	GAAGCCATCA
251	TGCCGCCTTT TTTCACGGCA TCGTTCAGCA ATGCCAAAGC
	TGCTGTTGTG
301	CCGTGCGTAC CGCAGACGCT CAAGCCCATT TnTTCAAGAA
	TGCGTGCCAC
351	TnAGTCGCCG ACGGGG..

This corresponds to the amino acid sequence <SEQ ID 674; ORF24>:

1	MRTAVVLLLI MPMAASSAMM PEMVCAGVSP GTAIISKPTE
	QTAVMASSLS
51	SVSTPASAAA IIPSSSETGI NAPLKPPTAL EAIMPPFFTA
	SFSNAKAAVV
101	PCVPQTLKPI XSRMRATXSP TG..

Further work revealed the complete nucleotide sequence <SEQ ID 675>:

1	ATGCGCACGG CAGTGGTTTT GCTGTTGATC ATGCCGATGG
	CGGCTTCGTC
51	GGCAATGATG CCGGAAATGG TGTGCGCGGG CGTGTCGCCG
	GGAACGGCAA
101	TCATATCCAA GCCGACCGAA CAAACGGCGG TCATGGCTTC
	GAGTTTGTCC
151	AGCGTCAGCA CGCCTGCTTC GGCGGCGGCA ATCATACCTT
	CGTCTTCGGA
201	AACGGGGATA AACGCGCCAC TCAAACCCCC GACCGCGCTG
	GAAGCCATCA
251	TGCCGCCTTT TTTCACGGCA TCGTTCAGCA ATGCCAAAGC
	TGCTGTTGTG
301	CCGTGCGTAC CGCAGACGCT CAAGCCCATT TCTTCAAGAA
	TGCGTGCCAC
351	TGAGTCGCCG ACGGCGGGGG TCGGCGCCAG CGACAAGTCG
	AGAATACCAA
401	ACGGGATATT CAGCATTTTT GAGGCTTCGC GGCCGATGAG
	TTCGCCCACG
451	CGGGTAATTT TGAAAGCAGT TTTCTTCACT ACTTCCGCAA
	CTTCGGTCAA
501	TGTCGTTGCA TCTGAATTTT CCAACGCGGC TTTTACGACA
	CCTGGGCCGG
551	ATACGCCGAC ATTGATAACG GCATCCGCTT CGCCCGAACC
	ATGAAACGCG
601	CCCGCCATAA ACGGGTTGTC TTCCACCGCG TTGCAGAACA
	CGACAATTTT
651	AGCGCAGCCG AAACCTTCGG GCGTGATTTC CGCCGTGCGT
	TTGACGGTTT
701	CGCCCGCCAG CTTGACCGCA TCCATATTGA TACCGGCACG
	CGTACTGCCG
751	ATATTGATGG AGCTGCACAC AATATCGGTA GTCTTCATCG
	CTTCGGGAAT
801	GGAGCGGATT AACACCTCAT CCGAAGGCGA CATCCCTTTT
	TGCACCAACG
851	CGGAAAAACC GCCGATAAAA GACACACCGA TGGCTTTGGC
	AGCTTTATCC
901	AAAGTTTGCG CCACGCTGAC GTAA

This corresponds to the amino acid sequence <SEQ ID 676; ORF24-1>:

1	MRTAVVLLLI MPMAASSAMM PEMVCAGVSP GTAIISKPTE
	QTAVMASSLS
51	SVSTPASAAA IIPSSSETGI NAPLKPPTAL EAIMPPFFTA
	SFSNAKAAVV
101	PCVPQTLKPI SSRMRATESP TAGVGASDKS RIPNGIFSIF
	EASRPMSSPT
151	RVILKAVFFT TSATSVNVVA SEFSNAAFTT PGPDTPTLIT
	ASASPEP*NA
201	PAINGLSSTA LQNTTILAQP KPSGVISAVR LTVSPASLTA
	SILIPARVLP
251	ILMELHTISV VFIASGMERI NTSSEGDIPF CTNAEKPPIK
	DTPMALAALS
301	KVCATLT*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF24 shows 96.4% identity over a 307 aa overlap with an ORF (ORF24a) from strain A of N. meningitidis:

The complete length ORF24a nucleotide sequence <SEQ ID 677> is:

1	ATGCGCACGG CAGTGGTTTT GCTGTTGATC ATGCCGATGG
	CGGCTTCGTC
51	GGCAATGATG CCGGAAATGG TGTGCGCGGG TGTGTCGCCG
	GGAACGGCAA
101	TCATATCCAA NCCGACCGAA CAAACGGCGG TCATCGCTTC
	GAGTTTATCC
151	AACGTCAGCA CGCCTGCTTC GGCGGCGGCA ATCATACCTT
	CGTCTTCGGA
201	NACGGGGATA AACGCGCCAC TCAAACCGCC AACCGCGCTC
	GAAGCCATCA
251	TGCCGCCCTT TTTCACGGCA TCGTTCAGCA ATGCCAAAGC
	TGCTGTTGTG
301	CCGTGCGTAC CGCAGACGCT CAAACCCATT TCTTCAAGAA
	TGCGCGCCAC
351	CGAGTCGCCG ACGGCAGGGG TCGGTGCCAG CGACAAGTCG
	AGAATACCAA
401	ACGGGATATT CAGCATTTTT GAGGCTTCGC GGCCGATGAG
	TTCGCCCACG
451	CGGGTAATTT TGAAGGCGGT TTTCTTCACA ACTTCGGCAA
	CTTCGGTCAA
501	TGTCGTTGCA TCCGAATTTT CCAACGCGGC TTTTACGACA
	CCCGGGCCGG
551	ATACGCCGAC ATTAATCACA GCATCCGCTT CGCCTGAGCC
	GTGAAACGCG
601	CCCGCCATAN ACGGGTTGTC TTCCNCCGCG TTGCAGAACA
	CGACGATTTT
651	GGCGCAGCCG AAACCTTCTA GTGTGATTTC ANCCGTGCGT
	TTGATGGTTT
701	CGCCCGCCAG TCTGACCGCG TCCATATTGA TACCGGCGCG
	CGTACTGCCG
751	ATATTGATGG AGCTGCACAC GATATCAGTA GTCTTCATCG
	CTTCGGGAAT
801	GGAACGGATN AACACCTCGT CAGAAGGCGA CATACCTTTT
	TGCACCAGCG
851	CGGAAAAGCC GCCAATAAAA GACACGCCGA TGGCTTTGGC
	AGCCTTATCC
901	AAAGTTTGCG CCACGCTGAC GTAA

This encodes a protein having amino acid sequence <SEQ ID 678>:

1	MRTAVVLLLI MPMAASSAMM PEMVCAGVSP GTAIISXPTE
	QTAVIASSLS
51	NVSTPASAAA IIPSSSXTGI NAPLKPPTAL EAIMPPFFTA
	SFSNAKAAVV
101	PCVPQTLKPI SSRMRATESP TAGVGASDKS RIPNGIFSIF
	EASRPMSSPT
151	RVILKAVFFT TSATSVNVVA SEFSNAAFTT PGPDTPTLIT
	ASASPEP*NA
201	PAIXGLSSXA LQNTTILAQP KPSSVISXVR LMVSPASLTA
	SILIPARVLP
251	ILMELHTISV VFIASGMERX NTSSEGDIPF CTSAEKPPIK
	DTPMALAALS
301	KVCATLT*

It should be noted that this protein includes a stop codon at position 198.

ORF24a and ORF24-1 show 96.4% identity in 307 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF24 shows 96.7% identity over a 121 aa overlap with a predicted ORF (ORF24ng) from N. gonorrhoeae:

The complete length ORF24ng nucleotide sequence <SEQ ID 679> is:

1	ATGCGCACGG CGGTGGTTTT GCTGTTGATC ATGCCGATGG
	CGGCTTCGTC
51	GGCGATGATG CCGGAAATGG TGTGCGCGGG CGTGTCGCCG
	GGAACGGCAA
101	TCATGTCCAA ACCAACGGAG CAGACGGCGG TCATGGCTTC
	GAGTTTGTCC
151	AGCGTCAACA CGCCTGCCTC GGCGGCGGCA ATCATACCTT
	CGTCTTCGGA
201	AACGGGGATA AACGCGCCGC TCAAACCGCC GACCGCGCTG
	GAAGCCATCA
251	TGCCGCCCTT TTTCACGGCA TCGTTCAGCA ATGCCAAAGC
	TGCTGTTGTG
301	CCGTGCGTAC CGCAGACGCT CAAGCCCATT TCTTCAAGAA
	TGCGCGCCAC
351	CGAGTCGCCG ACGGCGGGGG TCGGTGCCAG CGACAAATCG
	AGAATGCCGA
401	ACGGGATATT CAGCATTTTT GAGGCTTCGC GACCGATGAG
	TTCGCCCACG
451	CGGGTGATTT TGAAAGCGGT TTTCTTCACG ACTTCGGCGA
	CCTCGGTCAG
501	GCTGACCGCG TCCGAATTTT CCAGCGCGGC TTTGACCACG
	CCTGGACCGG
551	ATACGCCGAC ATTAATCACA GCATCCGCTT CGCCCGAGCC
	GTGGAACGCA
601	CCCGCCATAA ACGGATTGTC TTCCACCGCG TTGCAGAACA
	CGACGATTTT
651	GGCGCAGCCG AAACCTTCGG GTGTGATTTC AGCCGTGCGT
	TTGATGGTTT
701	CGCCTGCCAG CTTGACCGCA TCCATATTGA TACCGGCACG
	CGTGCTGCCG
751	ATATTGATGG AGCTGCACAC GATATCGGTA GTTTTCATCG
	CTTCGGGAAC
801	GGAACGGATC AACACCTCAT CCGAAGGCGA CATACCTTTT
	TGCACCAGCG
851	CGGAAAAGCC GCCGATAAAG GACACGCCGA TGGCTTTGGC
	TGCCTTGTCC
901	AAAGTCTGCG CCACGCTGAC ATAA

This encodes a protein having amino acid sequence <SEQ ID 680>:

1	MRTAVVLLLI MPMAASSAMM PEMVCAGVSP GTAIMSKPTE
	QTAVMASSLS
51	SVNTPASAAA IIPSSSETGI NAPLKPPTAL EAIMPPFFTA
	SFSNAKAAVV
101	PCVPQTLKPI SSRMRATESP TAGVGASDKS RMPNGIFSIF
	EASRPMSSPT
151	RVILKAVFFT TSATSVRLTA SEFSSAALTT PGPDTPTLIT
	ASASPEPWNA
201	PAINGLSSTA LQNTTILAQP KPSGVISAVR LMVSPASLTA
	SILIPARVLP
251	ILMELHTISV VFIASGTERI NTSSEGDIPF CTSAEKPPIK
	DTPMALAALS
301	KVCATLT*

ORF24ng and ORF24-1 show 96.1% identity in 307 aa overlap:

Based on this analysis, including the presence of a putative leader sequence (first 18 aa—double-underlined) and putative transmembrane domains (single-underlined) in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 81

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 681>:

1	..ACCGACGTGC AAAAAGAGTT GGTCGGCGAA CAACGCAAGT
	GGGCGCAGGA
51	AAAAATCAGC AACTGCCGAC AAGCCGCCGC GCAGGCAGAC
	CGGCAGGAAT
101	ACGCCGAATA CCTCAAGCTG CAATGCGACA CGCGGATGAC
	GCGCGAACGG
151	ATACAGTATC TTCGCGGCTA TTCCATCGAT TAG

This corresponds to the amino acid sequence <SEQ ID 682; ORF25>:

• • 1 . . . TDVQKELVGE QRKWAQEKIS NCRQAAAQAD RQEYAEYLKL QCDTRMTRER
  • 51 IQYLRGYSID *

Further work revealed the complete nucleotide sequence <SEQ ID 683>:

1	ATGTATCGGA AACTCATTGC GCTGCCGTTT GCCCTGCTGC
	TTGCCGCTTG
51	CGGCAGGGAA GAACCGCCCA AGGCATTGGA ATGCGCCAAC
	CCCGCCGTGT
101	TGCAAGGCAT ACGCGGCAAT ATTCAGGAAA CGCTCACGCA
	GGAAGCGCGT
151	TCTTTCGCGC GCGAAGACGG CAGGCAGTTT GTCGATGCCG
	ACAAAATTAT
201	CGCCGCCGCC TACGGTTTGG CGTTTTCTTT GGAACACGCT
	TCGGAAACGC
251	AGGAAGGCGG GCGCACGTTC TGTATCGCCG ATTTGAACAT
	TACCGTGCCG
301	TCTGAAACGC TTGCCGATGC CAAGGCAAAC AGCCCCCTGT
	TGTACGGGGA
351	AACTGCTTTG TCGGATATTG TGCGGCAGAA GACGGGCGGC
	AATGTCGAGT
401	TTAAAGACGG CGTATTGACG GCAGCCGTCC GCTTCCTGCC
	CGTCAAAGAC
451	GGTCAGACGG CATTTGTCGA CAACACGGTC GGTATGGCGG
	CGCAAACGCT
501	GTCTGCCGCG CTGCTGCCTT ACGGCGTGAA GAGCATCGTG
	ATGATAGACG
551	GCAAGGCGGT GAAAAAAGAA GACGCGGTCA GGATTTTGAG
	CGGAAAAGCC
601	CGTGAAGAAG AACCGTCCAA ACCCACGCCC GAAGACATTT
	TGGAACACAA
651	TGCCGCCGGC GGCGATGCGG GCGTACCCCA AGCCGCAGAA
	GGCGCGCCCG
701	AACCGGAAAT CCTGCATCCT GACGACGGCG AGCGTGCCGA
	TACCGTTACC
751	GTATCACGGG GCGAAGTGGA AGAGGCGCGC GTACAAAACC
	AGCGTGCGGA
801	ATCCGAAATT ACCAAACTTT GGGGAGGACT CGATACCGAC
	GTGCAAAAAG
851	AGTTGGTCGG CGAACAACGC AAGTGGGCGC AGGAAAAAAT
	CAGCAACTGC
901	CGACAAGCCG CCGCGCAGGC AGACCGGCAG GAATACGCCG
	AATACCTCAA
951	GCTGCAATGC GACACGCGGA TGACGCGCGA ACGGATACAG
	TATCTTCGCG
1001	GCTATTCCAT CGATTAG

This corresponds to the amino acid sequence <SEQ ID 684; ORF25-1>:

1	MYRKLIALPF ALLLAACGRE EPPKALECAN PAVLQGIRGN
	IQETLTQEAR
51	SFAREDGRQF VDADKIIAAA YGLAFSLEHA SETQEGGRTF
	CIADLNITVP
101	SETLADAKAN SPLLYGETAL SDIVRQKTGG NVEFKDGVLT
	AAVRFLPVKD
151	GQTAFVDNTV GMAAQTLSAA LLPYGVKSIV MIDGKAVKKE
	DAVRILSGKA
201	REEEPSKPTP EDILEHNAAG GDAGVPQAAE GAPEPEILHP
	DDGERADTVT
251	VSRGEVEEAR VQNQRAESEI TKLWGGLDTD VQKELVGEQR
	KWAQEKISNC
301	RQAAAQADRQ EYAEYLKLQC DTRMTRERIQ YLRGYSID*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF25 shows 98.3% identity over a 60aa overlap with an ORF (ORF25a) from strain A of N. meningitidis:

The complete length ORF25a nucleotide sequence <SEQ ID 685> is:

1	ATGTATCGGA AACTCATTGC GCTGCCGTTT GCCCTGCTGC
	TTGCCGCTTG
51	CGGCAGGGAA GAACCGCCCA AGGCATTGGA ATGCGCCAAC
	CCCGCCGTGT
101	TGCAANGCAT ACGCNGCAAT ATTCAGGAAA CGCTCACGCA
	GGAAGCGCGT
151	TCTTTCGCGC GCGAAGACNG CANGCAGTTT GTCGATGCCG
	ACNAAATTAT
201	CGCCGCCGCC TANGNTNNGN NGNTNTCTTT GGAACACGCT
	TCGGAAACGC
251	AGGAAGGCGG GCGCACGTTC TGTNTCGCCG ATTTGAACAT
	TACCGTGCCG
301	TCTGAAACGC TTGCCGATGC CAAGGCAAAC AGCCCCCTGC
	TGTACGGGGA
351	AACCGCTTTG TCGGATATTG TGCGGCAGAA GACGGGCGGC
	AATGTCGAGT
401	TTAAAGACGG CGTATTGACG GCAGCCGTCC GCTTCCTACC
	CGTCAAAGAC
451	GGTCAGANGG CATTTGTCGA CAACACGGTC GGTATGGCGG
	CGCAAACGCT
501	GTCTGCCGCG TTGCTGCCTT ACGGCGTGAA GAGCATCGTG
	ATGATAGACG
551	GCAAGGCGGT AAAAAAAGAA GACGCGGTCA GGATTNTGAG
	CNGANAAGCC
601	CGTGAANAAG AACCGTCCAA ANCCNNGCCC GAAGACATTT
	TGGAACATAA
651	TGCCGCCGGA GGGGATGCAG ACGTACCCCA AGCCGGAGAA
	GACGCGCCCG
701	AACCGGAAAT CCTGCATCCT GACGACGGCG AGCGTGCCGA
	TACCGTTACC
751	GTATCACGGG GCGAAGTGGA AGAGGCGCGN GTACAAAACC
	AGCGTGCGGA
801	ATCCGAAATT ACCAAACTTT GGGGAGGACT CGATACCGAC
	GTGCAAAAAG
851	AGTTGGTCGG CGAANAACGC AAGTGGGCGC AGGAAAAAAT
	CAGCAACTGC
901	CGACAAGCCG CCGCGCAGGC AGACCGGCAG GAATACGCCG
	AATACCTCAA
951	GCTGCAATGC GACACGCGGA TGACGCGCGA ACGGATACAG
	TATCTTCGCG
1001	GCTATTCCAT CGATTAG

This encodes a protein having amino acid sequence <SEQ ID 686>:

1	MYRKLIALPF ALLLAACGRE EPPKALECAN PAVLQXIRXN
	IQETLTQEAR
51	SFAREDXXQF VDADXIIAAA XXXXXSLEHA SETQEGGRTF
	CXADLNITVP
101	SETLADAKAN SPLLYGETAL SDIVRQKTGG NVEFKDGVLT
	AAVRFLPVKD
151	GQXAFVDNTV GMAAQTLSAA LLPYGVKSIV MIDGKAVKKE
	DAVRIXSXXA
201	REXEPSKXXP EDILEHNAAG GDADVPQAGE DAPEPEILHP
	DDGERADTVT
251	VSRGEVEEAR VQNQRAESEI TKLWGGLDTD VQKELVGEXR
	KWAQEKISNC
301	RQAAAQADRQ EYAEYLKLQC DTRMTRERIQ YLRGYSID*

ORF25a and ORF25-1 show 93.5% identity in 338 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF25 shows 100% identity over a 60aa overlap with a predicted ORF (ORF25ng) from N. gonorrhoeae:

The complete length ORF25ng nucleotide sequence <SEQ ID 687> is:

1	ATGTATCGGA AACTCATTGC GCTGCCGTTT GCCCTGCTGC
	TTGCAGCGTG
51	CGGCAGGGAA GAACCGCCCA AGGCGTTGGA ATGCGCCAAC
	CCCGCCGTGT
101	TGCAGGACAT ACGCGGCAGT ATTCAGGAAA CGCTCACGCA
	GGAAGCGCGT
151	TCTTTCGCGC GCGAAGACGG CAGGCAGTTT GTCGATGCCG
	ACAAAATTAT
201	CGCCGCCGCC TACGGTTTGG CGTTTTCTTT GGAACACGCT
	TCGGAAACGC
251	AGGAAGGCGG GCGCACGTTC TGTATCGCCG ATTTGAACAT
	TACCGTGCCG
301	TCTGAAACGC TTGCCGATGC CGAGGCAAAC AGCCCCCTGC
	TGTATGGGGA
351	AACGTCTTTG GCAGACATCG TGCAGCAGAA GACGGGCGGC
	AATGTCGAGT
401	TTAAAGACGG CGTATTGACG GCAGCCGTCC GCTTCCTGCC
	CGCCAAAGAC
451	GCTCGGACGG CATTTATCGA CAACACGGTC GGTATGGCGA
	CGCAAACGCT
501	GTCTGCCGCG TTGCTGCCTT ACGGCGTGAA GAGCATCGTG
	ATGATAGACG
551	GCAAGGCGGT GACAAAAGAA GACGCGGTCA GGGTTTTGAG
	CGGCAAAGCC
601	CGTGAAGAAG AACCGTCCAA ACCCACCCCC GAAGACATTT
	TGGAACACAA
651	TGCCGCCGGC GGCGATGCGG GCGTACCCCA AGCCGCAGAA
	GGCGCACCCG
701	AACCCGAAAT CCTGCATCCC GACGACGTCG AGCGTGCCGA
	TACCGTTACC
751	GTATCACGGG GCGAAGTGGA AGAGGCGCGC GTACAAAACC
	AACGTGCGGA
801	ATCCGAAATT ACCAAACTTT GGGGAGGACT CGATACCGAC
	GTGCAAAAAG
851	AGTTGGTCGG CGAACAGCGC AAGTGGGCGC AGGAAAAAAT
	CAGcaactgc
901	cgACAAGCCG CCGCGCAGGC AGACCGGCAG GAATACGCCG
	AATACCTCAA
951	GCTCCAATGC GACACGCGGA TGACGCGCGA ACggaTACAG
	TATCTTCGCG
1001	GCTATTCCAT CGATTAG

This encodes a protein having amino acid sequence <SEQ ID 688>:

1	MYRKLIALPF ALLLAACGRE EPPKALECAN PAVLQDIRGS
	IQETLTQEAR
51	SFAREDGRQF VDADKIIAAA YGLAFSLEHA SETQEGGRTF
	CIADLNITVP
101	SETLADAEAN SPLLYGETSL ADIVQQKTGG NVEFKDGVLT
	AAVRFLPAKD
151	ARTAFIDNTV GMATQTLSAA LLPYGVKSIV MIDGKAVTKE
	DAVRVLSGKA
201	REEEPSKPTP EDILEHNAAG GDAGVPQAAE GAPEPEILHP
	DDVERADTVT
251	VSRGEVEEAR VQNQRAESEI TKLWGGLDTD VQKELVGEQR
	KWAQEKISNC
301	RQAAAQADRQ EYAEYLKLQC DTRMTRERIQ YLRGYSID*

ORF25ng and ORF25-1 show 95.9% identity in 338 aa overlap:

Based on this analysis, including the presence of a predicted prokaryotic membrane lipoprotein lipid attchment site (underlined) in the gonococcal protein, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF25-1 (37 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 16A shows the results of affinity purification of the GST-fusion protein, and FIG. 16B shows the results of expression of the His-fusion in E. coli. Purified His-fusion protein was used to immunise mice, whose sera were used for Western blot (FIG. 16C), ELISA (positive result), and FACS analysis (FIG. 16D). These experiments confirm that ORF25-1 is a surface-exposed protein, and that it is a useful immunogen.

FIG. 16E shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF25-1.

Example 82

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 689>

1	ATGCAGCTGA TCGACTATTC ACATTCATTT TTCTCGGTTG
	TGCCACCCTT
51	TTTGGCACTG GCACTTGCCG TCATTACCCG CCGCGTACTG
	CTGTCTTTAG
101	GCATCGGTAT TCTGGwysGC GTTGCCTTTT TGGTCGGCGG
	CAACCCCGTC
151	GACGGTCTGA CACACCTGAA AGACATGGTC GTCGGCTTGG
	CTTGGTCAGA
201	CGsyGATTGG TCGCTGGGCA AACCAAAAAT CTTGGTTTTC
	CkGATACTTT
251	TGGGTATTTT TACTTCCCTG CTGACCTACT CCGGCAGCAA
	T.........
	//
851	.......... .......... .......... ........AC
	TTCGCTGGTA
901	TTCGGCGGCA CTTGCGGCGT CTTTGCCGTC GTTCTCTGCA
	CGCTCGGCAC
951	GATTAAAACC GCCGACTATC CCAAAGCCGT TTGGCAGGGT
	GCGAAATCTA
1001	TGTTCGGCGC AATCGCCATT TTAATCCTCG CTTGGCTCAT
	CAGTACGGTT
1051	GTCGGCGAAA TGCACACCGG CGATTACCTC TCCACACTGG
	TTGCGGGCAA
1101	CATCCATCCC GGCTTCCTGC CCGTCATCCT CTTCCTGCTC
	GCCAGCGTGA
1151	TGGCGTTTGC CACAGGCACA AGCTGGGGGA CGTTCGGCAT
	TATGCTGCCG
1201	ATTGCCGCCG CCATGGCGGT CAAAGTCGAA CCCGCGCTGA
	TTATCCCGTG
1251	TATGTCCGCA GTAATGGCGG GGGCGGTATG CGGCGACCAC
	TGCTCGCCCA
1301	TTTCCGACAC GACCATCCTG TCGTCCACCG GCGCGCGCTG
	CAACCACATC
1351	GACCACGTTA CCTCGCAACT GCCTTACGCC TTAACCGTTG
	CCGCCGCCGC
1401	CGCATCGGGC TACCTCGCAT TGGGTCTGAC AAAATCCGCG
	CTGTTGGGCT
1451	TTGGCACGAC AGGCATTGTA TTGGCGGTGC TGATTTTTCT
	GTTGAAAGAT
1501	AAAAAA..

This corresponds to the amino acid sequence <SEQ ID 690; ORF26>:

1	MQLIDYSHSF FSVVPPFLAL ALAVITRRVL LSLGIGILXX
	VAFLVGGNPV
51	DGLTHLKDMV VGLAWSDXDW SLGKPKILVF XILLGIFTSL
	LTYSGSN...
	//
251	.......... .......... .......... ..........
	......TSLV
301	FGGTCGVFAV VLCTLGTIKT ADYPKAVWQG AKSMFGAIAI
	LILAWLISTV
351	VGEMHTGDYL STLVAGNIHP GFLPVILFLL ASVMAFATGT
	SWGTFGIMLP
401	IAAAMAVKVE PALIIPCMSA VMAGAVCGDH CSPISDTTIL
	SSTGARCNHI
451	DHVTSQLPYA LTVAAAAASG YLALGLTKSA LLGFGTTGIV
	LAVLIFLLKD
501	KK..

Further work revealed the complete nucleotide sequence <SEQ ID 691>:

1	ATGCAGCTGA TCGACTATTC ACATTCATTT TTCTCGGTTG
	TGCCACCCTT
51	TTTGGCACTG GCACTTGCCG TCATTACCCG CCGCGTACTG
	CTGTCTTTAG
101	GCATCGGTAT TCTGGTCGGC GTTGCCTTTT TGGTCGGCGG
	CAACCCCGTC
151	GACGGTCTGA CACACCTGAA AGACATGGTC GTCGGCTTGG
	CTTGGTCAGA
201	CGGCGATTGG TCGCTGGGCA AACCAAAAAT CTTGGTTTTC
	CTGATACTTT
251	TGGGTATTTT TACTTCCCTG CTGACCTACT CCGGCAGCAA
	TCAGGCGTTT
301	GCCGACTGGG CAAAACGGCA CATTAAAAAC CGGCGCGGCG
	CGAAAATGCT
351	GACCGCCTGC CTCGTGTTCG TAACCTTTAT CGACGACTAT
	TTCCACAGTC
401	TCGCCGTCGG TGCGATTGCC CGCCCCGTTA CCGACAAGTT
	TAAAGTTTCC
451	CGCACCAAAC TCGCCTACAT CCTCGACTCC ACTGCCGCTC
	CTATGTGCGT
501	GCTGATGCCC GTTTCAAGCT GGGGCGCGTC GATTATCGCC
	ACGCTTGCCG
551	GACTGCTCGT TACCTACAAA ATCACCGAAT ACACGCCGAT
	GGGGACGTTT
601	GTCGCCATGA GCCTGATGAA CTATTACGCA CTGTTTGCCC
	TGATTATGGT
651	GTTCGTCGTC GCATGGTTTT CCTTCGACAT CGGCTCGATG
	GCACGTTTCG
701	AACAAGCCGC GTTGAACGAA GCCCACGATG AAACTGCCGT
	TTCAGACGCT
751	ACCAAAGGTC GTGTTTACGC ACTGATTATT CCCGTTTTGG
	CCTTAATCGC
801	CTCAACGGTT TCCGCCATGA TCTACACCGG CGCGCAGGCA
	AGCGAAACCT
851	TCAGCATTTT GGGGGCATTT GAAAACACGG ACGTAAACAC
	TTCGCTGGTA
901	TTCGGCGGCA CTTGCGGCGT CCTTGCCGTC GTTCTCTGCA
	CGCTCGGCAC
951	GATTAAAACC GCCGACTATC CCAAAGCCGT TTGGCAGGGT
	GCGAAATCTA
1001	TGTTCGGCGC AATCGCCATT TTAATCCTCG CTTGGCTCAT
	CAGTACGGTT
1051	GTCGGCGAAA TGCACACCGG CGATTACCTC TCCACACTGG
	TTGCGGGCAA
1101	CATCCATCCC GGCTTCCTGC CCGTCATCCT CTTCCTGCTC
	GCCAGCGTGA
1151	TGGCGTTTGC CACAGGCACA AGCTGGGGGA CGTTCGGCAT
	TATGCTGCCG
1201	ATTGCCGCCG CCATGGCGGT CAAAGTCGAA CCCGCGCTGA
	TTATCCCGTG
1251	TATGTCCGCA GTAATGGCGG GGGCGGTATG CGGCGACCAC
	TGCTCGCCCA
1301	TTTCCGACAC GACCATCCTG TCGTCCACCG GCGCGCGCTG
	CAACCACATC
1351	GACCACGTTA CCTCGCAACT GCCTTACGCC TTAACCGTTG
	CCGCCGCCGC
1401	CGCATCGGGC TACCTCGCAT TGGGTCTGAC AAAATCCGCG
	CTGTTGGGCT
1451	TTGGCACGAC AGGCATTGTA TTGGCGGTGC TGATTTTTCT
	GTTGAAAGAT
1501	AAAAAACGCG CCAACGCCTG A

This corresponds to the amino acid sequence <SEQ ID 692; ORF26-1>:

1	MQLIDYSHSF FSVVPPFLAL ALAVITRRVL LSLGIGILVG
	VAFLVGGNPV
51	DGLTHLKDMV VGLAWSDGDW SLGKPKILVF LILLGIFTSL
	LTYSGSNQAF
101	ADWAKRHIKN RRGAKMLTAC LVFVTFIDDY FHSLAVGAIA
	RPVTDKFKVS
151	RTKLAYILDS TAAPMCVLMP VSSWGASIIA TLAGLLVTYK
	ITEYTPMGTF
201	VAMSLMNYYA LFALIMVFVV AWFSFDIGSM ARFEQAALNE
	AHDETAVSDA
251	TKGRVYALII PVLALIASTV SAMIYTGAQA SETFSILGAF
	ENTDVNTSLV
301	FGGTCGVLAV VLCTLGTIKT ADYPKAVWQG AKSMFGAIAI
	LILAWLISTV
351	VGEMHTGDYL STLVAGNIHP GFLPVILFLL ASVMAFATGT
	SWGTFGIMLP
401	IAAAMAVKVE PALIIPCMSA VMAGAVCGDH CSPISDTTIL
	SSTGARCNHI
451	DHVTSQLPYA LTVAAAAASG YLALGLTKSA LLGFGTTGIV
	LAVLIFLLKD
501	KKRANA*

Computer analysis of this amino acid sequence gave the following results:

Homology with the Hypothetical Transmembrane Protein HI1586 of H. influenzae (Accession Number P44263)

ORF26 and HI1586 show 53% and 49% amino acid identity in 97 and 221 aa overlap at the N-terminus and C-terminus, respectively:

Orf26	1	MQLIDYSHSFFSVVPPFLALALAVITRRVXXXXXXXXXXXVAFLVGGNPVDGLTHLKDMV	60
		M+LID+S S +S+VP  LA+ LA+ TRRV              L          +L   V
HI1586	14	MELIDFSSSVWSIVPALLAIILAIATRRVLVSLSAGIIIGSLMLSDWQIGSAFNYLVKNV	73
Orf26	61	VGLAWSDXDWSLGKPKILVFXILLGIFTSLLTYSGSN	97
		V L ++D + +     I++F +LLG+ T+LLT SGSN
HI1586	74	VSLVYADGEIN-SNMNIVLFLLLLGVLTALLTVSGSN	109
		//
Orf26	86	IFTSLLTYSGS--NTSLVFGGTCGVFAVVLCTL--GTIKTADYPKAVWQGAKSMFGXXXX	141
		+F+ L T+  +   TSLV GG C +    L  +    +   +Y ++   G KSM G
HI1586	299	VFSVLGTFENTVVGTSLVVGGFCSIIISTLLIILDRQVSVPEYVRSWIVGIKSMSGAIAI	358
Orf26	142	XXXXXXXSTVVGEMHTGDYLSTLVAGNIHPGFLPVILFLLASVMAFATGTSWGTFGIMLP	201
		+ +VG+M TG YLS+LV+GNI   FLPVILF+L + MAF+TGTSWGTFGIMLP
HI1586	359	LFFAWTINKIVGDMQTGKYLSSLVSGNIPMQFLPVILFVLGAAMAFSTGTSWGTFGIMLP	418
Orf26	202	IAAAMAVKVEPALIIPCMSAVMAGAVCGDHCSPISDTTILSSTGARCNHIDHVTSQXXXX	261
		IAAAMA    P L++PC+SAVMAGAVCGDHCSP+SDTTILSSTGA+CNHIDHVT+Q
HI1586	419	IAAAMAANAAPELLLPCLSAVMAGAVCGDHCSPVSDTTILSSTGAKCNHIDHVTTQLPYA	478
Orf26	262	XXXXXXXXXXXXXXXXXKSALLGFGTTGIVLAVLIFLLKDK	302
		S L GF  T + L V+IF +K +
HI1586	479	ATVATATSIGYIVVGFTYSGLAGFAATAVSLIVIIFAVKKR	519

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF26 shows 58.2% identity over a 502aa overlap with an ORF (ORF26a) from strain A of N. meningitidis:

The complete length ORF26a nucleotide sequence <SEQ ID 693> is:

1	ATGCAGCTGA TCGACTATTC ACATTCATTT TTCTCGGTTG
	TGCCACCCTT
51	TTTGGCACTG GCACTTGCCG TCATTACCCG CCGCGTACTG
	CTGTCTTTAG
101	GCATCGGTAT TCTGGTCGGC GTTGCCTTTT TGGTCGGCGG
	CAACCCCGTC
151	GACGGTCTGA CACACCTGAA AGACATGGTC GTCGGCTTGG
	CTTGGTCAGA
201	CGGCGATTGG TCGCTGGGCA AACCAAAANT CTTGGTTTTC
	CTGATACTTT
251	TGGGTATTTT TACTTCCCTG CTGACCTACT CCGGCAGCAA
	TCAGGCGTTT
301	GCCGACTGGG CAAAACGGCA CATTAAAAAC CGGCGCGGCG
	CGAAAATGCT
351	GACCGCCTGC CTCGTGTTCG TAACCTTTAT CGACGACTAT
	TTCCACAGTC
401	TCGCCGTCGG TGCGNTTGCC CGCCCCGTTA CCGACAAGTT
	TAAAGTTTCC
451	CGCGCCAAAC TCGCCTACAT CCTCGACTCC ACTGCCGCGC
	CTATGTGCGT
501	GCTGATGCCC GTTTCAAGCT GGGGCGCGTC GATTATCGCC
	ACGCTTGCCG
551	GACTGCTCGT TACCTACAAA ATCACCGAAT ACACGCCGAT
	GGGGACGTTT
601	GTCGCCATGA GCCTGATGAA CTATTACGCA CTGTTTGCCC
	TGATTATGGT
651	GTTCGTCGTC GCATGGTTCT CCTTCGACAT CGGCTCGATG
	GCACGTTTCG
701	AACAAGCCGC GTTGAACGAA GCCCACGATG AAACTGCCGT
	TTCAGACGGC
751	AGCTGGGGCA GGGTTTACGC ATTGATTATT CCCGTTTTGG
	CCTTAATCGC
801	CTCAACGGTT TCCGCCATGA TCTACACCGG TGCACAGGCA
	AGCGAAACCT
851	TCAGCATTTT GGGTGCATTT GAAAATACGG ACGTGAACAC
	TTCGCTGGTA
901	TTCGGCGGCA CTTGCGGCGT GCTTGCCGTC GTCCTCTGCA
	CGCTCGGCAC
951	GATTAAAATC GCCGATTATC CCAAAGCCGT TTGGCAGGGT
	GCGAAATCCA
1001	TGTTCGGCGC AATCGCCATT TTAATCCTTG CCTGGCTCAT
	CAGTACGGTT
1051	GTCGGCGAAA TGCACACAGG CGACTACCTC TCCACGCTGG
	TTGCGGGCAA
1101	CATCCATCCC GGCTTCCTGN CCGTCATCCT TTTCCTGCTC
	GCCAGCGTGA
1151	TGGCGTTTGC CACAGGCACA AGCTGGGGGA CGTTCGGCAT
	CATGCTGCCG
1201	ATTGCCGCCG CCATGGCGGT CAAAGTCGAT CCCTCACTGA
	TTATCCCGTG
1251	TATGTCCGCC GTGATGGCGG GGGCGGTATG CGGCGACCAC
	TGCTCGCCCA
1301	TTTCCGACAC GACCATCCTG TCGTCCACCG GCGCGCGCTG
	CAACCACATC
1351	GACCACGTTA CNTCGCAACT GCCTTACGCC TTAACCGTTG
	CCGCCGCCGC
1401	CGCATCGGGN TACCTCGCAT TGGGTCTGAC AAAATCCGCG
	CTGTTGGGTT
1451	TTGGCANGAC AGGCATTGTA TTGGCGGTGC TGATTTTTCT
	GTTGAAAGAT
1501	AAAAAACGCG CCAACGCCTG A

This encodes a protein having amino acid sequence <SEQ ID 694>:

1	MQLIDYSHSF FSVVPPFLAL ALAVITRRVL LSLGIGILVG
	VAFLVGGNPV
51	DGLTHLKDMV VGLAWSDGDW SLGKPKXLVF LILLGIFTSL
	LTYSGSNQAF
101	ADWAKRHIKN RRGAKMLTAC LVFVTFIDDY FHSLAVGAXA
	RPVTDKFKVS
151	RAKLAYILDS TAAPMCVLMP VSSWGASIIA TLAGLLVTYK
	ITEYTPMGTF
201	VAMSLMNYYA LFALIMVFVV AWFSFDIGSM ARFEQAALNE
	AHDETAVSDG
251	SWGRVYALII PVLALIASTV SAMIYTGAQA SETFSILGAF
	ENTDVNTSLV
301	FGGTCGVLAV VLCTLGTIKI ADYPKAVWQG AKSMFGAIAI
	LILAWLISTV
351	VGEMHTGDYL STLVAGNIHP GFLXVILFLL ASVMAFATGT
	SWGTFGIMLP
401	IAAAMAVKVD PSLIIPCMSA VMAGAVCGDH CSPISDTTIL
	SSTGARCNHI
451	DHVTSQLPYA LTVAAAAASG YLALGLTKSA LLGFGXTGIV
	LAVLIFLLKD
501	KKRANA*

ORF26a and ORF26-1 show 97.8% identity in 506 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF26 shows 94.8% and 99% identity in 97 and 206 aa overlap at the N-terminus and C-terminus, respectively, with a predicted ORF (ORF26ng) from N. gonorrhoeae:

The complete length ORF26ng nucleotide sequence <SEQ ID 695> is:

1	ATGCAGCTGA TTGACTATTC ACATTCATTT TTCTCGGTTG
	TGCCACCCTT
51	TTTGGCACTG GCACTTGCCG TCATTACCCG CCGCGTACTG
	CTGTCTTTAG
101	GCATCGGTAT TTTGGTCGGC GTTGCCTTTT TGGTCGGCGG
	CAACCCCGTC
151	GACGGTCTGA CACACCTGAA AGACATGGTC GTCGGCTTGG
	CTTGGGCAGA
201	CGGCGATTGG TCGCTGGGCA AACCAAAAAT CTTGGTTTTC
	CTGATACTTT
251	TGGGCATTTT CACTTCACTG CTGACCTACT CCGGCAGCAA
	TCAGGCGTTT
301	GCCGACTGGG CAAAACGGCA CATTAAAAAC CGGTGCGGCG
	CGAAAATGCT
351	GACCGCCTGC CTCGTGTTCG TAACCTTTAT CGACGACTAT
	TTCCACAGCC
401	TCGCCGTCGG TGCGATTGCC CGCCCCGTTA CCGACAAGTT
	TAAAGTTTCC
451	CGCGCCAAAC TCGCCTACAT CCTCGACTCC ACTGCCTCGC
	CCATGTGCGT
501	GCTGATGCCC GTTTCAAGCT GGGGCGCGTC GATTATCGCC
	ACGCTTGCCG
551	GATTGCTCGT TACCTACAAA ATTACCGAAT ACACGCCGAT
	GGGGACGTTT
601	GTCGCCATGA GCCTGATGAA CTATTACGCG CTGTTTGCCC
	TGATTATGGT
651	ATTCGTCGTC GCATGGTTCT CCTTCGACAT CGGCTCGAtg
	gCGCGTTTCG
701	AACAGGCTGC GTTGAACGAA gcccaggacg aaaccgccgc
	tTCAGACgCT
751	ACCAAAGGTC GTGTTTACGC ATTGATTATT CCCGTTTTGG
	CCTTAATCGC
801	CTCAACGGTT TCCGCCATGA TCTACACCGG CGCGCAGGCA
	AGCGAAACCT
851	TCAGCATTTT GGGGGCATTT GAAAATACCG ACGTAAACAC
	TTCGCTGGTA
901	TTCGGCGGCA CTTGCGGCGT GCTTGCCGTC GTCCTCTGCA
	CGTTCGGCAC
951	GATTAAAACC GCCGATTATC CCAAAGCCGT GTGGCAGGGT
	GCGAAATCCA
1001	TGTTCGGCGC AATCGCCATT TTAATCCTCG CCTGGCTCAT
	CAGTACGGTT
1051	GTCGGCGAAA TGCACACGGG CGACTACCTC TCCACGCTGG
	TTGCGGGCAA
1101	CATCCATCCC GGCTTCCTGC CCGTCATCCT CTTCCTGCTC
	GCCAGCGTGA
1151	TGGCGTTTGC CACAGGCACA AGCTGGGGGA CGTTCGGCAT
	TATGCTGCCG
1201	ATTGCCGCCG CCATGGCGGT CAAAGTCGAA CCCGCGCTGA
	TTAtcccGTG
1251	TATGTCCGCA GTAATGGCGG GGGCGGTATG CGGCGACCAC
	TGTTCGCCCA
1301	TCTCCGACAC GACCATCCTG TCGTCCACCG GCGCGCGCTG
	CAACCACATC
1351	GACCACGTTA CCTCGCAACT GCCTTATGCC CTGACGGTTG
	CCGCCGCCGC
1401	CGCATCGGGC TACCTCGCAT TGGGTCTGAC AAAATCCGCG
	CTGTTGGGCT
1451	TTGGCACGAC CGGTATTGTA TTGGCGGTGC TGATTTTTCT
	GTTGAAAGAT
1501	AAAAAACGCG CCGACGTTTG A

This encodes a protein having amino acid sequence <SEQ ID 696>:

1	MQLIDYSHSF FSVVPPFLAL ALAVITRRVL LSLGIGILVG
	VAFLVGGNPV
51	DGLTHLKDMV VGLAWADGDW SLGKPKILVF LILLGIFTSL
	LTYSGSNQAF
101	ADWAKRHIKN RCGAKMLTAC LVFVTFIDDY FHSLAVGAIA
	RPVTDKFKVS
151	RAKLAYILDS TASPMCVLMP VSSWGASIIA TLAGLLVTYK
	ITEYTPMGTF
201	VAMSLMNYYA LFALIMVFVV AWFSFDIGSM ARFEQAALNE
	AQDETAASDA
251	TKGRVYALII PVLALIASTV SAMIYTGAQA SETFSILGAF
	ENTDVNTSLV
301	FGGTCGVLAV VLCTFGTIKT ADYPKAVWQG AKSMFGAIAI
	LILAWLISTV
351	VGEMHTGDYL STLVAGNIHP GFLPVILFLL ASVMAFATGT
	SWGTFGIMLP
401	IAAAMAVKVE PALIIPCMSA VMAGAVCGDH CSPISDTTIL
	SSTGARCNHI
451	DHVTSQLPYA LTVAAAAASG YLALGLTKSA LLGFGTTGIV
	LAVLIFLLKD
501	KKRADV*

ORF26ng and ORF26-1 show 98.4% identity in 505 aa overlap:

In addition, ORF26 ng shows significant homology to a hypothetical H. influenzae protein:

sp|P44263|YF86_HAEIN HYPOTHETICAL PROTEIN HI1586 >gi|1074850|pir||C64037
hypothetical
protein HI1586 - Haemophilus influenzae (strain Rd KW20) >gi|1574427
(U32832) H. influenzae predicted coding region HI1586 [Haemophilus
influenzae] Length = 519
Score = 538 bits (1370), Expect = e−152
Identities = 280/507 (55%), Positives = 346/507 (68%), Gaps = 7/507 (1%)

Query:	1	MQLIDYSHSFFSVVPPFLALALAVITRRXXXXXXXXXXXXXAFLVGGNPVDGLTHLKDMV	60
		M+LID+S S +S+VP  LA+ LA+ TRR               L          +L   V
Sbjct:	14	MELIDFSSSVWSIVPALLAIILAIATRRVLVSLSAGIIIGSLMLSDWQIGSAFNYLVKNV	73
Query:	61	VGLAWADGDWSLGKPKILVFLILLGIFTSLLTYSGSNQAFADWAKRHIKNRCGAKMLTAC	120
		V L +ADG+ +     I++FL+LLG+ T+LLT SGSN+AFA+WA+  IK R GAK+L A
Sbjct:	74	VSLVYADGEIN-SNMNIVLFLLLLGVLTALLTVSGSNRAFAEWAQSRIKGRRGAKLLAAS	132
Query:	121	LVFVTFIDDYFHSLAVGAIARPVTDKFKVSRAKLAYILDSTASPMCVLMPVSSWGASIIA	180
		LVFVTFIDDYFHSLAVGAIARPVTD+FKVSRAKLAYILDSTA+PMCV+MPVSSWGA II
Sbjct:	133	LVFVTFIDDYFHSLAVGAIARPVTDRFKVSRAKLAYILDSTAAPMCVMMPVSSWGAYIIT	192
Query:	181	TLAGLLVTYKITEYTPMGTFVAMSLMNYYALFALIMVFVVAWFSFDIGSMARFEQAALNE	240
		+ GLL TY ITEYTP+G FVAMS MN+YA+F++IMVF VA+FSFDI SM R E+ AL
Sbjct:	193	LIGGLLATYSITEYTPIGAFVAMSSMNFYAIFSIIMVFFVAYFSFDIASMVRHEKLALKN	252
Query:	241	AQDETAASDATKGRVYALIIPVLALIASTVSAMIYTGAQA----SETFSILGAFENTDVN	296
		+D+      TKG+V  LI+P+L LI +TVS MIYTGA+A     + FS+LG FENT V
Sbjct:	253	TEDQLEEETGTKGQVRNLILPILVLIIATVSMMIYTGAEALAADGKVFSVLGTFENTVVG	312
Query:	297	TSLVFGGTCGVL--AVVLCTFGTIKTADYPKAVWQGAKSMFGXXXXXXXXXXXSTVVGEM	354
		TSLV GG C ++   +++     +   +Y ++   G KSM G           + +VG+M
Sbjct:	313	TSLVVGGFCSIIISTLLIILDRQVSVPEYVRSWIVGIKSMSGAIAILFFAWTINKIVGDM	372
Query:	355	HTGDYLSTLVAGNIHPGFLPVILFLLASVMAFATGTSWGTFGIMLPIAAAMAVKVEPALI	414
		TG YLS+LV+GNI   FLPVILF+L + MAF+TGTSWGTFGIMLPIAAAMA    P L+
Sbjct:	373	QTGKYLSSLVSGNIPMQFLPVILFVLGAAMAFSTGTSWGTFGIMLPIAAAMAANAAPELL	432
Query:	415	IPCMSAVMAGAVCGDHCSPISDTTILSSTGARCNHIDHVTSQXXXXXXXXXXXXXXXXXX	474
		+PC+SAVMAGAVCGDHCSP+SDTTILSSTGA+CNHIDHVT+Q
Sbjct:	433	LPCLSAVMAGAVCGDHCSPVSDTTILSSTGAKCNHIDHVTTQLPYAATVATATSIGYIVV	492
Query:	475	XXXKSALLGFGTTGIVLAVLIFLLKDK	501
		S L GF  T + L V+IF +K +
Sbjct:	493	GFTYSGLAGFAATAVSLIVIIFAVKKR	519

Based on this analysis, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 83

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 697>:

1	..AAGCAATGGT ATGCCGACGN .AGTATCAAG ACGGAAATGG
	TTATGGTCAA
51	CGATGAGCCT GCCAAAATTC TGACTTGGGA TGAAAGCGGC
	CGATTACTCT
101	CGGAACTGTC TATCCGCCAC CATCAACGCA ACGGGGTGGT
	TTTGGAGTGG
151	TATGAAGATG GTTCTAAAAA GAGCGAAGT. GTTTATCAGG
	ATGACAAGTT
201	GGTCAGGAAA ACCCAGTGGG ATAAGGATGG TTATTTAATC
	GAACCCTGA

This corresponds to the amino acid sequence <SEQ ID 698; ORF27>:

1	..KQWYADXSIK TEMVMVNDEP AKILTWDESG RLLSELSIRH
	HQRNGVVLEW
51	YEDGSKKSEX VYQDDKLVRK TQWDKDGYLI EP*

Further work revealed the complete nucleotide sequence <SEQ ID 699>:

1	ATGAAAAAAT TATCTCGGAT TGTATTTTCA ACTGTCCTGT
	TGGGTTTTTC
51	GGCCGCTTTG CCGGCGCAGA CCTATTCTGT TTATTTTAAT
	CAGAACGGAA
101	AGCTGACGGC GACGATGTCT TCTGCCGCTT ATATCAGGCA
	ATATAGTGTG
151	GTGGCGGGTA TTGCGCACGC GCAGGATTTT TATTATCCGT
	CGATGAAGAA
201	ATATTCTGAA CCTTATATCG TTGCTTCAAC GCAAATCAAA
	TCTTTTGTGC
251	CTACCCTGCA AAACGGTATG TTGATTTTGT GGCATTTTAA
	TGGTCAGAAA
301	AAAATGGCGG GGGGCTTCAG CAAGGGTAAG CCGGACGGGG
	AGTGGGTCAA
351	CTGGTATCCG AACGGTAAAA AATCTGCCGT TATGCCTTAT
	AAAAATGGCT
401	TGAGTGAGGG TACGGGATAC CGCTATTACC GTAACGGCGG
	CAAGGAAAGC
451	GAAATCCAGT TTAAGCAAAA TAAGGCAAAC GGCGTATGGA
	AGCAATGGTA
501	TGCCGACGGC AGTATCAAGA CGGAAATGGT TATGGTCAAC
	GATGAGCCTG
551	CCAAAATTCT GACTTGGGAT GAAAGCGGCC GATTACTCTC
	GGAACTGTCT
601	ATCCGCCACC ATCAACGCAA CGGGGTGGTT TTGGAGTGGT
	ATGAAGATGG
651	TTCTAAAAAG AGCGAAGCTG TTTATCAGGA TGACAAGTTG
	GTCAGGAAAA
701	CCCAGTGGGA TAAGGATGGT TATTTAATCG AACCCTGA

This corresponds to the amino acid sequence <SEQ ID 700; ORF27-1>:

1	MKKLSRIVFS TVLLGFSAAL PAQTYSVYFN QNGKLTATMS
	SAAYIRQYSV
51	VAGIAHAQDF YYPSMKKYSE PYIVASTQIK SFVPTLQNGM
	LILWHFNGQK
101	KMAGGFSKGK PDGEWVNWYP NGKKSAVMPY KNGLSEGTGY
	RYYRNGGKES
151	EIQFKQNKAN GVWKQWYADG SIKTEMVMVN DEPAKILTWD
	ESGRLLSELS
201	IRHHQRNGVV LEWYEDGSKK SEAVYQDDKL VRKTQWDKDG
	YLIEP*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF27 shows 91.5% identity over a 82aa overlap with an ORF (ORF27a) from strain A of N. meningitidis:

The complete length ORF27a nucleotide sequence <SEQ ID 701> is:

1	ATGAAAAAAT TATCTCGGAT TGTATTTTCA ACTGTCCTGT
	TGGGTTTTTC
51	GGCCGCTTTG CCGGCGCAGA NCTATTCTGT TTATTTTAAT
	CAGAACGGGA
101	AACTGACGGC GACGNTGTCT TCTGCCGCNT ATATCAGGCA
	ATATAGTGTG
151	GCGGAGGGTA TTGCGCACGC GCAGGANTTT TANTATCCGT
	CGATGAAGAA
201	ATATTCCGAA CCTTATATCG TTGCTTCAAC GCAAATCAAA
	TCTTTTGTGC
251	CTACCCTGCA AAACGGTATG TTGATTTTGT GGCATTTTAA
	NGGTCAGAAA
301	AAAATGGCNG GGGGCTTCAG CAAGGGTAAG CCGGACGGGG
	AGTGGGTCAA
351	CTGGTATCCG AACGGTAAAA AATCTGCCGT TATGCCTTAT
	AAAAATGGTT
401	TGAGTGAAGG TACGGGGTNN CGCTATTACC GTAACGGCGG
	CAAGGAAAGC
451	GAAATCCAGT TTAAACAGAA TAAGGCAAAC GGCGTATGGA
	AGCAATGGTA
501	TGCCGACGGC AATATCAAAA CGGAAATGGT TATGGTCAAT
	GATGAGCCTG
551	CCAAAATTCT GACATGGGAT GAAAGCGGTC GATTACTCTC
	GGAACTGTCT
601	ATCCATCATC ATNAACGTAA TGGAGTAGTC TTAGAGTGGT
	ATGAAGATGG
651	TTCTAAAAAG ANTGAAGCTG TTTATCAGGA TGATAAGTTG
	GTCAGGAAAA
701	CCCAGTGGGA TAANGATGGT TATTTAATCG AACCCTGA

This encodes a protein having amino acid sequence <SEQ ID 702>:

1	MKKLSRIVFS TVLLGFSAAL PAQXYSVYFN QNGKLTATXS
	SAAYIRQYSV
51	AEGIAHAQXF XYPSMKKYSE PYIVASTQIK SFVPTLQNGM
	LILWHFXGQK
101	KMAGGFSKGK PDGEWVNWYP NGKKSAVMPY KNGLSEGTGX
	RYYRNGGKES
151	EIQFKQNKAN GVWKQWYADG NIKTEMVMVN DEPAKILTWD
	ESGRLLSELS
201	IHHHXRNGVV LEWYEDGSKK XEAVYQDDKL VRKTQWDXDG
	YLIEP*

ORF27a and ORF27-1 show 94.7% identity in 245 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF27 shows 96.3% identity over 82 aa overlap with a predicted ORF (ORF27ng) from N. gonorrhoeae:

The complete length ORF27ng nucleotide sequence <SEQ ID 703> is:

1	ATGAAGAAAT TATCTCGGAT TGTATTTTCA ATCGTACTGT
	TGGGTTTTTC
51	GGCCGCTTTG CCGGCGCAGA CCTATTCTGT TTATTTTAAT
	CAGAACGGGA
101	AACTGACGGC GACGATGTCT TCTGCCGCTT ATATCAGGCA
	ATATAGTGTG
151	GCGGCGGGTA TCGCACACGC GCAGGATTTT TATTATCCGT
	CGATGAAGAA
201	ATATTCCGAA CCTTATATCG TTGCTTCAAC GCAAATCAAA
	TCTTTTGTGC
251	CTACCCTGCA AAACGGTATG TTGATTTTGT GGCATTTTAA
	TGGTCAGAAA
301	AAAATGGCGG GGGGCTTCAG CAAGGGTAAG CCGGACGGGG
	AATGGGTCAA
351	CTGGTATCCG AACGGTAAAA AATCTGCGGT TATGCCTTAT
	AAAAATGGCT
401	TGAGTGAGGG TACGGGATAC CGTTATTACC GTAACGGCGG
	CAAGGAAAGC
451	GAAATCCAGT TTAAGCAAAA TAAGGCGAAC GGCGTATGGA
	AGCAATGGTA
501	TGCCGATGGA AGTATCAAGA CGGAAATGGT TATGGTCAAC
	GATGAGCCTG
551	CCAAAATTCT GACTTGGGAT GAAAGCGGCC GATTACTTTC
	GGAACTGTCT
601	ATCCGCCACC ATAAACGCAA CGGGGTGGTT TTGGAGTGGT
	ATGAAGATGG
651	TTCTAAAAAG AGCGAGGCTG TTTATCAGGA TGACAAGTTG
	GTCAGGAAAA
701	CCCAATGGGA TAAGGATGGT TATTTAATCG AACCCTGA

This encodes a protein having amino acid sequence <SEQ ID 704>:

1	MKKLSRIVFS IVLLGFSAAL PAQTYSVYFN QNGKLTATMS
	SAAYIRQYSV
51	AAGIAHAQDF YYPSMKKYSE PYIVASTQIK SFVPTLQNGM
	LILWHFNGQK
101	KMAGGFSKGK PDGEWVNWYP NGKKSAVMPY KNGLSEGTGY
	RYYRNGGKES
151	EIQFKQNKAN GVWKQWYADG SIKTEMVMVN DEPAKILTWD
	ESGRLLSELS
201	IRHHKRNGVV LEWYEDGSKK SEAVYQDDKL VRKTQWDKDG
	YLIEP*

ORF27ng and ORF27-1 show 98.8% identity in 245 aa overlap:

Based on this analysis, including the putative leader sequence in the gonococcal protein, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF27-1 (24.5 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 17A shows the results of affinity purification of the GST-fusion protein, and FIG. 17B shows the results of expression of the His-fusion in E. coli. Purified GST-fusion protein was used to immunise mice, whose sera were used for ELISA, which gave a positive result, confirming that ORF27-1 is a surface-exposed protein and a useful immunogen.

Example 84

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 705>:

1	ATGAAATTTA CCAAGCACCC CGTCTGGGCA ATGGCGTTCC
	GCCCATTTTA
51	TTCGCTGGCG GCTCTGTACG GCGCATTGTC CGTATTGCTG
	TGGGGTTTCG
101	GCTACACGGG AACGCACkAG CTGTCCGGTT TCTATTGGCA
	CGCGCATGAg
151	ATGATTTGGG GTTATGCCGG ACTGGTCGTC ATCGCCTTCC
	TGCTGACCGC
201	CGTCGCCACT TGGACGGGGC AGCCGCCCAC GCGGGGCGGC
	GTaTCTGGTC
251	GGCTTGACTA TCTTTTGGCT GGCTGCGCGG ATTGCCGCCT
	TTATCCCGGG
301	TTGGGGTGCG TCGGCAAGCG GCATACTCGG TACGCTGTTT
	TTCTGGTACG
351	GCGCGGTGTG CATGGCTTTG CCCGTTATCC GTTCGCAGAA
	TCAACGCAAC
401	TATGTTgCCG TGTTCGCGCT GTTCGTCTTG GGCGGCACGC
	ATGCGGCGTT
451	CCACGTCCAG CTGCACAACG GCAACCTAGG CGGACTCTTG
	AGCGGATTGC
501	AGTCGGGCTT GGTGATG

This corresponds to the amino acid sequence <SEQ ID 706; ORF47>:

1	MKFTKHPVWA MAFRPFYSLA ALYGALSVLL WGFGYTGTHX
	LSGFYWHAHE
51	MIWGYAGLVV IAFLLTAVAT WTGQPPTRGG VLVGLTIFWL
	AARIAAFIPG
101	WGASASGILG TLFFWYGAVC MALPVIRSQN QRNYVAVFAL
	FVLGGTHAAF
151	HVQLHNGNLG GLLSGLQSGL VM

Further work revealed the complete nucleotide sequence <SEQ ID 707>:

1	ATGAAATTTA CCAAGCACCC CGTCTGGGCA ATGGCGTTCC
	GCCCATTTTA
51	TTCGCTGGCG GCTCTGTACG GCGCATTGTC CGTATTGCTG
	TGGGGTTTCG
101	GCTACACGGG AACGCACGAG CTGTCCGGTT TCTATTGGCA
	CGCGCATGAG
151	ATGATTTGGG GTTATGCCGG ACTGGTCGTC ATCGCCTTCC
	TGCTGACCGC
201	CGTCGCCACT TGGACGGGGC AGCCGCCCAC GCGGGGCGGC
	GTTCTGGTCG
251	GCTTGACTAT CTTTTGGCTG GCTGCGCGGA TTGCCGCCTT
	TATCCCGGGT
301	TGGGGTGCGT CGGCAAGCGG CATACTCGGT ACGCTGTTTT
	TCTGGTACGG
351	CGCGGTGTGC ATGGCTTTGC CCGTTATCCG TTCGCAGAAT
	CAACGCAACT
401	ATGTTGCCGT GTTCGCGCTG TTCGTCTTGG GCGGCACGCA
	TGCGGCGTTC
451	CACGTCCAGC TGCACAACGG CAACCTAGGC GGACTCTTGA
	GCGGATTGCA
501	GTCGGGCTTG GTGATGGTGT CGGGTTTTAT CGGTCTGATT
	GGTACGCGGA
551	TTATTTCGTT TTTTACGTCC AAACGCTTGA ATGTGCCGCA
	GATTCCCAGT
601	CCGAAATGGG TGGCGCAGGC TTCGCTGTGG CTGCCCATGC
	TGACTGCCAT
651	GCTGATGGCG CACGGTGTGT TGGCTTGGCT GTCTGCCGTT
	TTTGCCTTTG
701	CGGCAGGTGT GATTTTTACC GTGCAGGTGT ACCGCTGGTG
	GTATAAACCC
751	GTGTTGAAAG AGCCGATGCT GTGGATTCTG TTTGCCGGCT
	ATCTGTTTAC
801	CGGATTGGGG CTGATTGCGG TCGGCGCGTC TTATTTCAAA
	CCCGCTTTCC
851	TCAATCTGGG TGTGCATCTG ATCGGGGTCG GCGGTATCGG
	CGTGCTGACT
901	TTGGGCATGA TGGCGCGTAC CGCGCTTGGT CATACGGGCA
	ATCCGATTTA
951	TCCGCCGCCC AAAGCCGTTC CCGTTGCGTT TTGGCTGATG
	ATGGCGGCAA
1001	CCGCCGTCCG TATGGTTGCC GTATTTTCTT CCGGCACTGC
	CTACACGCAC
1051	AGCATCCGCA CCTCTTCGGT TTTGTTTGCA CTCGCGCTTT
	TGGTGTATGC
1101	GTGGAAGTAT ATTCCTTGGC TGATTCGTCC GCGTTCGGAC
	GGCAGGCCCG
1151	GTTGA

This corresponds to the amino acid sequence <SEQ ID 708; ORF47-1>:

1	MKFTKHPVWA MAFRPFYSLA ALYGALSVLL WGFGYTGTHE
	LSGFYWHAHE
51	MIWGYAGLVV IAFLLTAVAT WTGQPPTRGG VLVGLTIFWL
	AARIAAFIPG
101	WGASASGILG TLFFWYGAVC MALPVIRSQN QRNYVAVFAL
	FVLGGTHAAF
151	HVQLHNGNLG GLLSGLQSGL VMVSGFIGLI GTRIISFFTS
	KRLNVPQIPS
201	PKWVAQASLW LPMLTAMLMA HGVLAWLSAV FAFAAGVIFT
	VQVYRWWYKP
251	VLKEPMLWIL FAGYLFTGLG LIAVGASYFK PAFLNLGVHL
	IGVGGIGVLT
301	LGMMARTALG HTGNPIYPPP KAVPVAFWLM MAATAVRMVA
	VFSSGTAYTH
351	SIRTSSVLFA LALLVYAWKY IPWLIRPRSD GRPG*

Computer analysis of this amino acid sequence predicts a leader peptide and also gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF47 shows 99.4% identity over a 172aa overlap with an ORF (ORF47a) from strain A of N. meningitidis:

The complete length ORF47a nucleotide sequence <SEQ ID 709> is:

1	ATGAAATTTA CCAAGCACCC CGTTTGGGCA ATGGCGTTCC
	GCCCGTTTTA
51	TTCACTGGCG GCTCTGTACG GCGCATTGTC CGTATTGCTG
	TGGGGTTTCG
101	GCTACACGGG AACGCACGAG CTGTCCGGTT TCTATTGGCA
	CGCGCATGAG
151	ATGATTTGGG GTTATGCCGG ACTGGTCGTC ATCGCCTTCC
	TGCTGACCGC
201	CGTCGCCACT TGGACGGGGC AGCCGCCCAC GCGGGGCGGC
	GTTCTGGTCG
251	GCTTGACTAT CTTTTGGCTG GCTGCGCGGA TTGCCGCCTT
	TATCCCGGGT
301	TGGGGTGCGT CGGCAAGCGG CATACTCGGT ACGCTGTTTT
	TCTGGTACGG
351	CGCGGTGTGC ATGGCTTTGC CCGTTATCCG TTCGCAGAAT
	CAACGCAATT
401	ATGTTGCCGT GTTCGCGCTG TTCGTCTTGG GCGGTACGCA
	CGCGGCGTTC
451	CACGTCCAGC TGCACAACGG CAACCTAGGC GGACTCTTGA
	GCGGATTGCA
501	GTCGGGCTTG GTGATGGTGT CGGGTTTTAT CGGTCTGATT
	GGTACGCGGA
551	TTATTTCGTT TTTTACGTCC AAACGGTTGA ATGTGCCGCA
	GATTCCCAGT
601	CCGAAATGGG TGGCGCAGGC TTCGCTGTGG CTGCCCATGC
	TGACCGCCAT
651	GCTGATGGCG CACGGCGTGA TGCCTTGGCT GTCGGCGGCT
	TTCGCGTTTG
701	CGGCAGGTGT GATTTTTACC GTGCAGGTGT ACCGCTGGTG
	GTATAAGCCT
751	GTGTTGAAAG AGCCGATGCT GTGGATTCTG TTTGCCGGCT
	ATCTGTTTAC
801	CGGATTGGGG CTGATTGCGG TCGGCGCGTC TTATTTCAAA
	CCCGCTTTCC
851	TCAATCTGGG TGTGCATCTG ATCGGGGTCG GCGGTATCGG
	CGTGCTGACT
901	TTGGGCATGA TGGCGCGTAC CGCGCTCGGT CATACGGGCA
	ATCCGATTTA
951	TCCGCCGCCC AAAGCCGTTC CCGTTGCGTT TTGGCTGATG
	ATGGCGGCAA
1001	CCGCCGTCCG TATGGTTGCC GTATTTTCTT CCGGCACTGC
	CTACACGCAC
1051	AGCATACGCA CCTCTTCGGT TTTGTTTGCA CTCGCGCTTT
	TGGTGTATGC
1101	GTGGAAGTAT ATTCCTTGGC TGATTCGTCC GCGTTCGGAC
	GGCAGGCCCG
1151	GTTGA

This encodes a protein having amino acid sequence <SEQ ID 710>:

1	MKFTKHPVWA MAFRPFYSLA ALYGALSVLL WGFGYTGTHE
	LSGFYWHAHE
51	MIWGYAGLVV IAFLLTAVAT WTGQPPTRGG VLVGLTIFWL
	AARIAAFIPG
101	WGASASGILG TLFFWYGAVC MALPVIRSQN QRNYVAVFAL
	FVLGGTHAAF
151	HVQLHNGNLG GLLSGLQSGL VMVSGFIGLI GTRIISFFTS
	KRLNVPQIPS
201	PKWVAQASLW LPMLTAMLMA HGVMPWLSAA FAFAAGVIFT
	VQVYRWWYKP
251	VLKEPMLWIL FAGYLFTGLG LIAVGASYFK PAFLNLGVHL
	IGVGGIGVLT
301	LGMMARTALG HTGNPIYPPP KAVPVAFWLM MAATAVRMVA
	VFSSGTAYTH
351	SIRTSSVLFA LALLVYAWKY IPWLIRPRSD GRPG*

ORF47a and ORF47-1 show 99.2% identity in 384 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF47 shows 97.1% identity over 172 aa overlap with a predicted ORF (ORF47ng) from N. gonorrhoeae:

The ORF47ng nucleotide sequence <SEQ ID 711> is predicted to encode a protein comprising amino acid sequence <SEQ ID 712>:

1	MKFTKHPVWA MAFRPFYSLA ALYGALSVLL WGFGYTGTHE
	LSGFYWHAHE
51	MIWGYAGLVV IAFLLTAVAT WTGQPPTRGG VLVGLTAFWL
	AARIAAFIPG
101	WGAAASGILG TLFFWYGAVC MALPVIRSQN RRNYVAVFAI
	FVLGGTHAAF
151	HVQLHNGNLG GLLSGLQSGL VMVWGFIGLI GMKIISFFTS
	KRLKLPQIPS
201	PKWVAHASLW LPMLNAILMA HRVMPWLSAA FPFAAGVIFT
	VQVYAGGITP
251	IEETSCGSVA GICYRLGNSS G

The predicted leader peptide and transmembrane domains are identical (except for an Ile/Ala substitution at residue 87 and an Leu/Ile substitution at position 140) to sequences in the meningococcal protein (see also Pseudomonas stutzeri orf396, accession number e246540):

TM segments in ORF47ng

INTEGRAL	Likelihood = −5.63	Transmembrane	52 - 68
INTEGRAL	Likelihood = −3.88	Transmembrane	169 - 185
INTEGRAL	Likelihood = −3.08	Transmembrane	82 - 98
INTEGRAL	Likelihood = −1.91	Transmembrane	134 - 150
INTEGRAL	Likelihood = −1.44	Transmembrane	107 - 123
INTEGRAL	Likelihood = −1.38	Transmembrane	227 - 243

Further work revealed the complete gonococcal DNA sequence <SEQ ID 713>:

1	ATGAAATTTA CCAAACATCC CGTCTGGGCA ATGGCGTTCC
	GCCCGTTTTA
51	TTCACTGGCG GCACTGTACG GCGCATTGTC CGTATTGCTG
	TGGGGTTTCG
101	GCTACACGGG AACGCACGAG CTGTCCGGTT TCTATTGGCA
	CGCGCATGAG
151	ATGATTTGGG GTTATGCCGG TCTCGTCGTC ATCGCCTTCC
	TGCTGACCGC
201	CGTCGCCACT TGGACGGGAC AGCCGCCCAC GAGGGGCGGC
	GTTCTGGTCG
251	GCTTGACCGC CTTTTGGCTG GCTGCGCGGA TTGCCGCCTT
	TATCCCGGGT
301	TGGGGTGCGG CGGCAAGCGG CATACTCGGT ACGCTGTTTT
	TCTGGTACGG
351	CGCGGTGTGC ATGGCTTTGC CCGTTATCCG TtcgCAAAAC
	CGGCGCAACT
401	ATGtcgCCGT ATTCGCAATA TTTGTGCTGG GCGGTACGCA
	TGCGgcgTTC
451	CACGtccAgc tGCACAACGG CAACCTAGGC GGACTCTTGA
	GCGGATTGCA
501	GTCGGGCCTG GTTATGGTGT CGGGCTTTAT CGGCCTGATT
	GGGATGAGGA
551	TTATTTCGTT TTTTACGTCC AAACGGTTGA ACGTGCCGCA
	GATTCCCAGT
601	CCGAAATGGG TGGCGCAGGC TTCGCTGTGG CTACCCATGC
	TGACCGCCAT
651	ACTGATGGCG CACGGCGTGA TGCCTTGGCT GTCGGCGGCT
	TTCGCGTTTG
701	CGGCGGGCGT GATTTTTACC GTACAGGTGT ACCGCTGGTG
	GTATAAACCC
751	GTATTGAAAG AACCGATGCT GTGGATTCTG TTTGCCGGCT
	ATCTGTTTAC
801	CGGATTGGGG CTGATTGCGG TCGGCGCGTC TTATTTCAAA
	CCTGCCTTCC
851	TCAATCTGGG CGTACATCTG ATCGGGGTCG GCGGTATCGG
	CGTGCTGACT
901	TTGGGCATGA TGGCGCGTAC CGCGCTCGGT CATACGGGCA
	ATTCGATTTA
951	TCCGCCGCCC AAAGCCGTTC CCGTTGCGTT TTGGCTGATG
	ATGGCGGCAA
1001	CCGCCGTCCG TATGGTTGCC GTATTTTCTT CCGGCACTGC
	CTACACGCAC
1051	AGCATCCGCA CGTCTTCGGT TTTGTTTGCA CTCGCGCTGC
	TGGTGTATGC
1101	GTGGAAATAC ATTCCGTGGC TGATCCGTCC GCGTTCGGAC
	GGCAGGCCCG
1151	GTTGA

This encodes a protein having amino acid sequence <SEQ ID 714; ORF47ng-1>:

1	MKFTKHPVWA MAFRPFYSLA ALYGALSVLL WGFGYTGTHE
	LSGFYWHAHE
51	MIWGYAGLVV IAFLLTAVAT WTGQPPTRGG VLVGLTAFWL
	AARIAAFIPG
101	WGAAASGILG TLFFWYGAVC MALPVIRSQN RRNYVAVFAI
	FVLGGTHAAF
151	HVQLHNGNLG GLLSGLQSGL VMVSGFIGLI GMRIISFFTS
	KRLNVPQIPS
201	PKWVAQASLW LPMLTAILMA HGVMPWLSAA FAFAAGVIFT
	VQVYRWWYKP
251	VLKEPMLWIL FAGYLFTGLG LIAVGASYFK PAFLNLGVHL
	IGVGGIGVLT
301	LGMMARTALG HTGNSIYPPP KAVPVAFWLM MAATAVRMVA
	VFSSGTAYTH
351	SIRTSSVLFA LALLVYAWKY IPWLIRPRSD GRPG*

ORF47ng-1 and ORF47-1 show 97.4% identity in 384 aa overlap:

Furthermore, ORF47ng-1 shows significant homology to an ORF from Pseudomonas stutzeri:

gnl|PID|e246540 (Z73914) ORF396 protein [Pseudomonas stutzeri]
Length = 396 Score = 155 bits (389), Expect = 5e−37
Identities = 121/391 (30%), Positives = 169/391 (42%), Gaps = 21/391 (5%)

Query:	7	PVWAMAFRPFYSLAALYGALSVLLWGFGYTGTHELSGFY-------WHAHEMIWGYAGLV	59
		P+W +AFRPF+   +LY  L++ LW   +TG     GF        WH HEM++G+A  +
Sbjct:	14	PIWRLAFRPFFLAGSLYALLAIPLWVAAWTGLWP--GFQPTGGWLAWHRHEMLFGFAMAI	71
Query:	60	VIAFLLTAVATWTGQPPTRGGVLVGLTAFWLAARIAAFIPGWGAAASGILGTLFFWYGAV	119
		V  FLLTAV TWTGQ    G  LVGL A WLAAR+  ++ G  AA    L  LF
Sbjct:	72	VAGFLLTAVQTWTGQTAPSGNRLVGLAAVWLAARL-GWLFGLPAAWLAPLDLLFLVALVW	130
Query:	120	CMALPVIRSQNRRNYVAVFAIFVLGGTHAAFXXXXXXXXXXXXXXXXXXXXXMVSGFIGL	179
		MA  +   + +RNY  V  + ++ G                          +V+  + L
Sbjct:	131	MMAQMLWAVRQKRNYPIVVVLSLMLGADVLILTGLLQGNDALQRQGVLAGLWLVAALMAL	190
Query:	180	IGMRIISFFTSKRLNVPQIPSP-KWVAQASLWLPMLTAILMAHGV----MPWLSAAFAFA	234
		IG R+I FFT + L       P  W+  A L    + A+L A GV     P L   F  A
Sbjct:	191	IGGRVIPFFTQRGLGKVDAVKPWVWLDVALLVGTGVIALLHAFGVAMRPQPLLGLLFV-A	249
Query:	235	AGVIFTVQVYRWWYKPVLKEPMLWILFAGYLFTGLGLIAVGASYF-KPAFXXXXXXXXXX	293
		GV   +++ RW+ K + K  +LW L    L+  +    +   +F   A
Sbjct:	250	IGVGHLLRLMRWYDKGIWKVGLLWSLHVAMLWLVVAAFGLALWHFGLLAQSSPSLHALSV	309
Query:	294	XXXXXXXXXMMARTALGHTGNSIYPPPKAVPVAFWLXXXXXXXXXXXXFSSGTAYTHSIR	353
		M+AR  LGHTG  +  P   +  AF L            F S       +
Sbjct:	310	GSMSGLILAMIARVTLGHTGRPLQLPAGIIG-AFVL---FNLGTAARVFLSVAWPVGGLW	365
Query:	354	TSSVLFALALLVYAWKYIPWLIRPRSDGRPG	384
		++V + LA  +Y W+Y P L+  R DG PG
Sbjct:	366	LAAVCWTLAFALYVWRYAPMLVAARVDGHPG	396

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 85

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 715>:

1	..ATGCCGTCTG AAGGTTCAGA CGGCmTCGGT GyCGGGGAAy
	CAGAAGyGGT
51	AGCGCATGCC CAATGAGACT TCGTGGGTTT TGAAGCGGGT
	GTTTTCCAAG
101	CGTCCCCAGT TGTGGTAACG GTATCCGGTG TCyAArGTCA
	GCTTGGGyGT
151	GATGTCGAAa CCGACACCGG CGATGACACC AAGACCyAmG
	CTGCTGATrC
201	TGTkGCTTTC GTGATAGGsA GGTTTGyTGG kmksAsyTTG
	TAyrATwkkG
251	CCTssCwsTG kAGmGCCkTk CkyTGGTkkA swGrwArTAG
	TCGTGGTTTy
301	TkTTyyCACC GAATGAACyT GATGTTTAAC GTGTCCGTAG
	GCGACGCGCG
351	CGCCGATATA GGGTTTGAAT TTATCGTTGA GTTTGAAATC
	GTAAATGGCG
401	GACAAGCCGA GAGAAGAAAC GGCGTGGAAG CTGCCGTTTC
	CCTGATGTTT
451	TGTTTGGGTT TCTTTGTAGT TGTTGTTTAT CTCTTCAGTA
	ACTTTTTTAG
501	TAGAAGAATT ACTTTCTTTC CATTTTCTGT AACTGGCATA
	ATCTGCCGCT
551	ATTCTCCAGC CGCCGAAATC ..

This corresponds to the amino acid sequence <SEQ ID 716; ORF67>:

1	..MPSEGSDGXG XGEXEXVAHA QXDFVGFEAG VFQASPVVVT
	VSGVXXQLGX
51	DVETDTGDDT KTXAADXVAF VIGRFXGXXL YXXAXXXXAX
	XWXXXXSRGF
101	XXHRMNLMFN VSVGDARADI GFEFIVEFEI VNGGQAERRN
	GVEAAVSLMF
151	CLGFFVVVVY LFSNFFSRRI TFFPFSVTGI ICRYSPAAEI
	..

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. gonorrhoeae

ORF67 shows 51.8% identity over 199 aa overlap with a predicted ORF (ORF67ng) from N. gonorrhoeae:

The ORF67ng nucleotide sequence <SEQ ID 717> is predicted to encode a protein comprising amino acid sequence <SEQ ID 718>:

1	MPSETVGSIV NVGVDESVGF SPPFPSIQHF YRFHRIHRIR
	LFRPPGPMQL
51	NRHSHGSGNL GRGVWATVLS DKFPCGQVRI PACAGMTNFE
	IAVLSGMTVR
101	VFYCARPAPV NGGRLKMPSE GSDGIGIGES EAVAHAQRGF
	VGFEAGVFQA
151	SPVVVAVAGV QGQAGRDVYA HARHRAEAQA AAAVAFLIGV
	FLRMSVRINR
201	NCCVSITRVG GKSTCYFFSR IDAVSDVSVG DARTDIGFEF
	VVEFEIVNGG
251	QAERRNGVEC AVFLMFRLLV FYVKLVAAKS FIILSFQLFY
	VHGIFIVVPF
301	PVTGIIRGDA PAAEVVADRH PGVDGMRTDV SEIIAYRAYF
	VFAWSGWFRI
351	IVGNAFGGVG *

Based on the presence of a several putative transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 86

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 719>

1	ATGTTTGCTT TTTTAGAAGC CTTTTTTGTC GAATACGGTT
	ATGCGGCTGT
51	TTTTTTTGTA TTGGTCATCT GCGGTTTCGG CGTGCCGATT
	CCCGAGGATT
101	TGACCTTGGT AACAGGCGGC GTGATTTCGG GTATGGGTTA
	TACCAATCCG
151	CATATTATGT TTGCAGTCGG TATGCTCGGC GTATTGGTCG
	GGGACGGCAT
201	CATGTTCGCC GCCGGACGAA TTTGGGGGCA GArArTCCTA
	rGGTTCArAC
251	CTATTGCGsG CATCATGACG CCGrAACGTT ATGAGCAGGT
	TCAGGAAAAA
301	TTCGACAAAT ACGGTAACTG GGTCTTATTT GTCGCCCGTT
	TCCTGCCCGG
351	TTTGAGAACG GCCGTATTTG TTACAGCCGG TATCAGCCGC
	AAGGTTTCAT
401	ACTTGCGTTT TATCATTATG GATGGACTGG CCGCA...

This corresponds to the amino acid sequence <SEQ ID 720; ORF78>:

1	MFAFLEAFFV EYGYAAVFFV LVICGFGVPI PEDLTLVTGG
	VISGMGYTNP
51	HIMFAVGMLG VLVGDGIMFA AGRIWGQXXL XFXPIAXIMT
	PXRYEQVQEK
101	FDKYGNWVLF VARFLPGLRT AVFVTAGISR KVSYLRFIIM
	DGLAA...

Further work revealed the complete nucleotide sequence <SEQ ID 721>:

1	ATGTTTGCTT TTTTAGAAGC CTTTTTTGTC GAATACGGTT
	ATGCGGCTGT
51	TTTTTTTGTA TTGGTCATCT GCGGTTTCGG CGTGCCGATT
	CCCGAGGATT
101	TGACCTTGGT AACAGGCGGC GTGATTTCGG GTATGGGTTA
	TACCAATCCG
151	CATATTATGT TTGCAGTCGG TATGCTCGGC GTATTGGTCG
	GGGACGGCAT
201	CATGTTCGCC GCCGGACGAA TTTGGGGGCA GAAAATCCTA
	AGGTTCAAAC
251	CTATTGCGCG CATCATGACG CCGAAACGTT ATGAGCAGGT
	TCAGGAAAAA
301	TTCGACAAAT ACGGTAACTG GGTCTTATTT GTCGCCCGTT
	TCCTGCCCGG
351	TTTGAGAACG GCCGTATTTG TTACAGCCGG TATCAGCCGC
	AAGGTTTCAT
401	ACTTGCGTTT TATCATTATG GATGGACTGG CCGCACTGAT
	TTCCGTCCCT
451	ATTTGGATTT ATCTGGGCGA ATACGGTGCG CACAACATCG
	ATTGGCTGAT
501	GGCGAAAATG CACAGCCTGC AATCGGGTAT TTTTGTTATC
	TTGGGTATAG
551	GTGCGACCGT TGTCGCTTGG ATTTGGTGGA AAAAACGCCA
	ACGTATCCAG
601	TTTTACCGCA GCAAATTGAA AGAAAAGCGG GCGCAACGCA
	AAGCCGCCAA
651	GGCAGCCAAA AAAGCCGCGC AAAGCAAACA ATAA

This corresponds to the amino acid sequence <SEQ ID 722; ORF78-1>:

1	MFAFLEAFFV EYGYAAVFFV LVICGFGVPI PEDLTLVTGG
	VISGMGYTNP
51	HIMFAVGMLG VLVGDGIMFA AGRIWGQKIL RFKPIARIMT
	PKRYEQVQEK
101	FDKYGNWVLF VARFLPGLRT AVFVTAGISR KVSYLRFIIM
	DGLAALISVP
151	IWIYLGEYGA HNIDWLMAKM HSLQSGIFVI LGIGATVVAW
	IWWKKRQRIQ
201	FYRSKLKEKR AQRKAAKAAK KAAQSKQ*

Computer analysis of this amino acid sequence predicts several transmembrane domains, and also gave the following results:

Homology with the dedA Homologue of H. influenzae (Accession Number P45280)

ORF78 and the dedA homologue show 58% aa identity in 144aa overlap:

Orf78:	4	FLEAFFVEYGYAAVFFVLVICGFGVPIPEDLTLVTGGVISGM--GYTNPHIMFAVGMLGV	61
		FL  FF EYGY AV FVL+ICGFGVPIPED+TLV+GGVI+G+     N H+M  V M+GV
DedA:	20	FLIGFFTEYGYWAVLFVLIICGFGVPIPEDITLVSGGVIAGLYPENVNSHLMLLVSMIGV	79
Orf78:	62	LVGDGIMFAAGRIWGQXXLXFXPIAXIMTPKRYEQVQEKFDKYGNWVLFVARFLPGLRTA	121
		L GD  M+  GRI+G   L F PI  I+T  R   V+EKF +YGN VLFVARFLPGLR
DedA:	80	LAGDSCMYWLGRIYGTKILRFRPIRRIVTLQRLRMVREKFSQYGNRVLFVARFLPGLRAP	139
Orf78:	122	VFVTAGISRKVSYLRFIIMDGLAA	145
		+++ +GI+R+VSY+RF+++D  AA
DedA:	140	IYMVSGITRRVSYVRFVLIDFCAA	163

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF78 shows 93.8% identity over a 145aa overlap with an ORF (ORF78a) from strain A of N. meningitidis:

The complete length ORF78a nucleotide sequence <SEQ ID 723> is:

1	ATGTTTGCCC TTTTGGAAGC CTTTTTTGTC GAATACGGCT
	ATGCGGCCGT
51	GTTTTTCGTT TTGGTCATCT GCGGTTTCGG CGTGCCGATT
	CCCGAGGATT
101	TGACCTTGGT AACAGGCGGC GTGATTTCGG GTATGGGTTA
	TACCAATCCG
151	CATATTATGT TTGCAGTCGG TATGCTCGGC GTATTGGTCG
	GGGACGGCAT
201	CATGTTCGCC GCCGGACGCA TCTGGGGGCA GAAAATCCTC
	AAGTTCAAAC
251	CGATTGCGCG CATCATGACG CCGAAACGTT ACGCACAGGT
	TCAGGAAAAA
301	TTCGACAAAT ACGGCAACTG GGTGTTATTT GTCGCTCGTT
	TCCTGCCCGG
351	TTTGCGGACT GCCGTTTTCG TTACCGCCGG CATCAGCCGC
	AAAGTATCGT
401	ATCTGCGCTT TCTGATTATG GACGGGCTTG CCGCGCTGAT
	TTCCGTGCCC
451	GTTTGGATTT ACTTGGGCGA GTACGGCGCG CACAACATCG
	ATTGGCTGAT
501	GGCGAAAATG CACAGCCTGC AATCCGGCAT CTTCATCGCA
	TTGGGCGTGC
551	TGGCGGCGGC GCTGGCGTGG TTCTGGTGGC GCAAACGCCG
	ACATTATCAG
601	CTTTACCGCG CACAATTGAG CGAAAAACGC GCCAAACGCA
	AGGCGGAAAA
651	GGCAGCGAAA AAAGCGGCAC AGAAGCAGCA GTAA

This encodes a protein having amino acid sequence <SEQ ID 724>:

1	MFALLEAFFV EYGYAAVFFV LVICGFGVPI PEDLTLVTGG
	VISGMGYTNP
51	HIMFAVGMLG VLVGDGIMFA AGRIWGQKIL KFKPIARIMT
	PKRYAQVQEK
101	FDKYGNWVLF VARFLPGLRT AVFVTAGISR KVSYLRFLIM
	DGLAALISVP
151	VWIYLGEYGA HNIDWLMAKM HSLQSGIFIA LGVLAAALAW
	FWWRKRRHYQ
201	LYRAQLSEKR AKRKAEKAAK KAAQKQQ*

ORF78a and ORF78-1 show 89.0% identity in 227 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF78 shows 97.4% identity over 38 aa overlap with a predicted ORF (ORF78ng) from N. gonorrhoeae:

The ORF78ng nucleotide sequence <SEQ ID 725> is predicted to encode a protein comprising amino acid sequence <SEQ ID 726>:

1	..YPVLFVARFL PGLRTAVFVT AGISRKVSYL RFLIMDGLAA
	LISVPVWIYL
51	GEYGAHNIDW LMAKMHSLQS GIFIALGVLA AALAWFWWRK
	RRHYQLYRAQ
101	LSEKRAKRKA EKAAKKAAQK QQ*

Further work revealed the complete gonococcal nucleotide sequence <SEQ ID 727>:

1	atgtttgccc tttTggaagc CTTTTTTGTC GAAtacggCt
	atgcGGCCGT
51	GTTTTTCGTT TTGGTCATCT GCGGTTTCGG CGTGCCGATT
	CCCGAAGATT
101	TGACCTTGGT AACGGGCGGC GTGATTTCGG GTATGGGTTA
	TACCAATCCG
151	CATATTATGT TTGCGGTCGG TATGCTCGGC GTGTTGGCGG
	GCGACGGCGT
201	GATGTTTGCC GCCGGACGCA TCTGGGGGCA GAAAATCCTC
	AAGTTCAAAC
251	CGATTGCGCG CATCATGACG CCGAAACGTT ACGCGCAGGT
	TCAGGAAAAA
301	TTCGACAAAT ACGGCAACTG GGTTCTGTTT GTCGCCCGTT
	TCCTGCCGGG
351	TTTGCGGACT GCCGTTTTCG TTACCGCCGG CATCAGCCGC
	AAAGTATCGT
401	ATCTGCGCTT TCTGATTATG GACGGGCTGG CCGCGCTGAT
	TTCCGTGCCC
451	GTTTGGATTT ACTTGGGCGA GTACGGCGCG CACAACATCG
	ATTGGCTGAT
501	GGCGAAAATG CACAGCCTGC AATCGGGCAT CTTCATCGCA
	TTGGGCGTGC
551	TGGCGGCGGC GCTGGCGTGG TTCTGGTGGC GCAAACGCCG
	ACATTATCAG
601	CTTTACCGCG CACAATTGAG CGAAAAACGC GCCAAACGCA
	AGGCGGAAAA
651	GGCAGCGAAA AAAGCGGCAC AGAAGCAGCA GTAa

This corresponds to the amino acid sequence <SEQ ID 728; ORF78ng-1>:

1	MFALLEAFFV EYGYAAVFFV LVICGFGVPI PEDLTLVTGG
	VISGMGYTNP
51	HIMFAVGMLG VLAGDGVMFA AGRIWGQKIL KFKPIARIMT
	PKRYAQVQEK
101	FDKYGNWVLF VARFLPGLRT AVFVTAGISR KVSYLRFLIM
	DGLAALISVP
151	VWIYLGEYGA HNIDWLMAKM HSLQSGIFIA LGVLAAALAW
	FWWRKRRHYQ
201	LYRAQLSEKR AKRKAEKAAK KAAQKQQ*

ORF78ng-1 and ORF78-1 show 88.1% identity in 227 aa overlap:

Furthermore, orf78ng-1 shows homology to the dedA protein from H. influenzae:

sp|P45280|YG29_HAEIN HYPOTHETICAL PROTEIN HI1629 >gi|1073983|pir||D64133
dedA protein (dedA) homolog - Haemophilus influenzae (strain Rd KW20)
>gi|1574476 (U32836) dedA protein (dedA) [Haemophilus influenzae]
Length = 212 Score = 223 bits (563), Expect = 7e−58
Identities = 108/182 (59%), Positives = 140/182 (76%), Gaps = 2/182 (1%)

Query:	5	LEAFFVEYGYAAVFFVLVICGFGVPIPEDLTLVTGGVISGM--GYTNPHIMFAVGMLGVL	62
		L  FF EYGY AV FVL+ICGFGVPIPED+TLV+GGVI+G+     N H+M  V M+GVL
Sbjct:	21	LIGFFTEYGYWAVLFVLIICGFGVPIPEDITLVSGGVIAGLYPENVNSHLMLLVSMIGVL	80
Query:	63	AGDGVMFAAGRIWGQKILKFKPIARIMTPKRYAQVQEKFDKYGNWVLFVARFLPGLRTAV	122
		AGD  M+  GRI+G KIL+F+PI RI+T +R   V+EKF +YGN VLFVARFLPGLR  +
Sbjct:	81	AGDSCMYWLGRIYGTKILRFRPIRRIVTLQRLRMVREKFSQYGNRVLFVARFLPGLRAPI	140
Query:	123	FVTAGISRKVSYLRFLIMDGLAALISVPVWIYLGEYGAHNIDWLMAKMHSLQSGIFIALG	182
		++ +GI+R+VSY+RF+++D  AA+ISVP+WIYLGE GA N+DWL  ++   Q  I+I +G
Sbjct:	141	YMVSGITRRVSYVRFVLIDFCAAIISVPIWIYLGELGAKNLDWLHTQIQKGQIVIYIFIG	200
Query:	183	VL	184
		L
Sbjct:	201	YL	202

Based on this analysis, including the presence of putative transmembrane domains, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 87

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 729>:

1	ATGAAAAAAT TATTGGCGGC CGTGATGATG GCAGGTTTGG
	CAGGCGCGGT
51	TTCCGCCGCC GGAGTCCACG TTGAGGACGG CTGGGCGCGC
	ACCACCGTCG
101	AAGGTATGAA AATAGGCGGC GCGTTCATGA AAATCCACAA
	CGACGAAGCC
151	AAACAAGACT TTTTGCTCGG CGGAAGCAGC CCCGTTGCCG
	ACCGCGTCGA
201	AGTGCATACC CACATCAACG ACAACGGCGT GATGCGGATG
	CGCGAAGTCG
251	AAGGCGGCGT GCCTTTGGAA GCGAAATCCG TTACCGAACT
	CAAACCCGGC
301	AGCTATCATG TGATGTTTAT GGGTTTGAAA AAACAATTAA
	AAGAGGGCGA
351	TAAAATTCCC GTTACCCTGA AATTTAAAAA CGCCAAAGCG
	CAAACCGTCC
401	AACTGGAAGT CAAAATCGCG CCGATGCCGG CAATGAACCA
	C...

This corresponds to the amino acid sequence <SEQ ID 730; ORF79>:

1	MKKLLAAVMM AGLAGAVSAA GVHVEDGWAR TTVEGMKIGG
	AFMKIHNDEA
51	KQDFLLGGSS PVADRVEVHT HINDNGVMRM REVEGGVPLE
	AKSVTELKPG
101	SYHVMFMGLK KQLKEGDKIP VTLKFKNAKA QTVQLEVKIA
	PMPAMNH..

Further work revealed the complete nucleotide sequence <SEQ ID 731>:

1	ATGAAAAAAT TATTGGCGGC CGTGATGATG GCAGGTTTGG
	CAGGCGCGGT
51	TTCCGCCGCC GGAGTCCACG TTGAGGACGG CTGGGCGCGC
	ACCACCGTCG
101	AAGGTATGAA AATAGGCGGC GCGTTCATGA AAATCCACAA
	CGACGAAGCC
151	AAACAAGACT TTTTGCTCGG CGGAAGCAGC CCCGTTGCCG
	ACCGCGTCGA
201	AGTGCATACC CACATCAACG ACAACGGCGT GATGCGGATG
	CGCGAAGTCG
251	AAGGCGGCGT GCCTTTGGAA GCGAAATCCG TTACCGAACT
	CAAACCCGGC
301	AGCTATCATG TGATGTTTAT GGGTTTGAAA AAACAATTAA
	AAGAGGGCGA
351	TAAAATTCCC GTTACCCTGA AATTTAAAAA CGCCAAAGCG
	CAAACCGTCC
401	AACTGGAAGT CAAAATCGCG CCGATGCCGG CAATGAACCA
	CGGTCATCAC
451	CACGGCGAAG CGCATCAGCA CTAA

This corresponds to the amino acid sequence <SEQ ID 732; ORF79-1>:

1	MKKLLAAVMM AGLAGAVSAA GVHVEDGWAR TTVEGMKIGG
	AFMKIHNDEA
51	KQDFLLGGSS PVADRVEVHT HINDNGVMRM REVEGGVPLE
	AKSVTELKPG
101	SYHVMFMGLK KQLKEGDKIP VTLKFKNAKA QTVQLEVKIA
	PMPAMNHGHH
151	HGEAHQH*

Computer analysis of this amino acid sequence revealed a putative leader peptide and also gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF79 shows 94.6% identity over a 147aa overlap with an ORF (ORF79a) from strain A of N. meningitidis:

The complete length ORF79a nucleotide sequence <SEQ ID 733> is:

1	ATGAAANAAC TATTGGCAGC CGTGATGATG GCAGGTTTGG
	CAGGCGCGGT
51	TTCCGCCGCC GGAATCCACG TTGAGGACGG CTGGGCGCGC
	ACCACCGTCG
101	AAGGTATGAA AATGGGCGGC GCGTTCATGA AAATCCACAA
	CGACGAAGCC
151	AAACAAGACT TTTTGCTCGG CGGAAGCAGC CCTGTTGCCG
	ACCGCGTCGA
201	AGTGCATACC CATATCAATG ATAACGGTGT GATGCGGATG
	CGCGAAGTCG
251	AAGGCGGCGT GCCTTTGGAG GCGAAATCCG TTACCGAACT
	CAAACCCGGC
301	AGCTATCATG TCATGTTTAT GGGTNTGAAA AAACAATTAA
	AAGANGGCGA
351	CAAGATTCCC GTTACCCTGA AATTTAAAAA CGCCAAAGCA
	CAAACCGTCC
401	AACTGGAAGT CAAAACCGCG CCGATGTCGG CAATGGACCA
	CGGTCATCAC
451	CACGGCGAAG CGCATCAGCA CTAA

This encodes a protein having amino acid sequence <SEQ ID 734>:

1	MKXLLAAVMM AGLAGAVSAA GIHVEDGWAR TTVEGMKMGG
	AFMKIHNDEA
51	KQDFLLGGSS PVADRVEVHT HINDNGVMRM REVEGGVPLE
	AKSVTELKPG
101	SYHVMFMGXK KQLKXGDKIP VTLKFKNAKA QTVQLEVKTA
	PMSAMDHGHH
151	HGEAHQH*

ORF79a and ORF79-1 show 94.9% identity in 157 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF79 shows 96.1% identity over 76 aa overlap with a predicted ORF (ORF79ng) from N. gonorrhoeae:

An ORF79ng nucleotide sequence <SEQ ID 735> was predicted to encode a protein comprising amino acid sequence <SEQ ID 736>:

1	..INDNGVMRMR EVKGGVPLEA KSVTELKPGS YHVMFMGLKK
	QLKEGDKIPV
51	TLKFKNAKAQ TVQLEVKTAP MSAMNHGHHH GEAHQH*

Further work revealed the complete gonococcal DNA sequence <SEQ ID 737>:

1	ATGAAAAAAT TATTGGCAGC CGTGATGATG GCAGGTTTGG
	CAGGCGCGGT
51	TTccgccgCc GGagTccAtG TCGAggACGG CTGGGCGCGc
	accaCTGtcg
101	aaggtATgaa aatggGCGGC GCgttCATga aaATCCACAA
	CGACGaaGcc
151	atacaaGACt ttgtgcTCgg CGGaagcatg cccgttgccg
	accgcGTCGA
201	AGTGCAtaca cacATCAACG ACAACGGCGT GATGCGTATG
	CGCGAAGTCA
251	AAGGCGGCGT GCCTTTGGAG GCGAAATCCG TTACCGAACT
	CAAACCCGGC
301	AGCTATCACG TGATGTTTAT GGGTTTGAAA AAACAACTGA
	AAGAGGGCGA
351	CAAGATTCCC GTTACCCTGA AATTTAAAAA CGCCAAAGCG
	CAAACCGTCC
401	AACTGGAAGT CAAAACCGCG CCGATGTCGG CAATGAACCA
	CGGTCATCAC
451	CACGGCGAAG CGCATCAGCA CTAA

This corresponds to the amino acid sequence <SEQ ID 738; ORF79ng-1>:

1	MKKLLAAVMM AGLAGAVSAA GVHVEDGWAR TTVEGMKMGG
	AFMKIHNDEA
51	IQDFVLGGSM PVADRVEVHT HINDNGVMRM REVKGGVPLE
	AKSVTELKPG
101	SYHVMFMGLK KQLKEGDKIP VTLKFKNAKA QTVQLEVKTA
	PMSAMNHGHH
151	HGEAHQH*

ORF79ng-1 and ORF79-1 show 95.5% identity in 157 aa overlap:

Furthermore, ORF79ng-1 shows significant homology to a protein from Aquifex aeolicus:

gi|2983695 (AE000731) putative protein [Aquifex aeolicus] Length = 151
Score = 63.6 bits (152), Expect = 6e−10
Identities = 38/114 (33%), Positives = 58/114 (50%), Gaps = 1/114 (0%)

Query:	24	VEDGWARTTVEGMKMGGAFMKIHNDEAIQDFVLGGSMPVADRVEVHTHINDNGVMRMREV	83
		V+  W      G       M I N+    D+++G    +A RVE+H  + +N V +M
Sbjct:	27	VKHPWVMEPPPGPNTTMMGMIIVNEGDEPDYLIGAKTDIAQRVELHKTVIENDVAKMVPQ	86
Query:	84	KGGVPLEAKSVTELKPGSYHVMFMGLKKQLKEGDKIPVTLKFKNAKAQTVQLEV	137
		+  + +  K   E K   YHVM +GLKK++KEGDK+ V L F+ +   TV+  V
Sbjct:	87	ER-IEIPPKGKVEFKHHGYHVMIIGLKKRIKEGDKVKVELIFEKSGKITVEAPV	139

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF79-1 (15.6 kDa) was cloned in the pET vector and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 18A shows the results of affinity purification of the His-fusion protein. Purified His-fusion protein was used to immunise mice, whose sera were used for ELISA (positive result) and FACS analysis (FIG. 18B) These experiments confirm that ORF79-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 88

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 739>:

1	ATGACGGTAA CTGCGGCCGA AGGCGGCAAA GCTGCCAAGG
	CGTTAAAAAA
51	ATATCTGATT ACGGGCATTT TGGTCTGGCT GCCGATTGCG
	GTAACGGTTT
101	GGGTGGTTTC CTATATCGTT TCCGCGTCCG ATCAGCTCGT
	CAACCTGCTG
151	CCGAAGCAAT GGCGGCCGCA ATATGTTTTG GGGTTTAATA
	TCCCGGGGCT
201	GGGCGTTATC GTTGCCATTG CCGTATTGTT TGTAACCGGA
	TTGTTTGCCG
251	CCAACGTATT GGGTCGGCAG ATCCTCGCCG CGTGGGACAG
	CCTGTTGGGG
301	CGGATTCCGG TTGTGAAAtC CATCTATTCG AGTGTGAAAA
	AAGTATCCGA
351	ATacgTGCTG TCCGACAGCA GCCGTTCGTT TAAAACGCCG
	GTACTCGTGC
401	CGTTTCCCCA GCCCGGTATT TGGACGATyG CTTTCGTGTC
	AGGGCAGGTG
451	TCGAATGCGG TTAAGGCCGC ATTGCCGAAs GACGGCGATT
	ATCTTTCCGT
501	GTATGTTCCG ACCACGCCGA ATCCGACCGG CGGTTACTAT
	ATTATGGTAA
551	AGAAAAGCGA TGTGCGCGAA CTCGATATGA GCGTGGACGA
	AsCATTGAAA
601	TATGTGATTT CGCTGGGTAT GGTCATCCCT GACGACCTGC
	CCGTCAAAAC
651	ATTGGCAsGA CCTATGCCGT CTGAAAAGGC GGATTTGCCC
	GAACAACAAT
701	AA

This corresponds to the amino acid sequence <SEQ ID 740; ORF98>:

1	MTVTAAEGGK AAKALKKYLI TGILVWLPIA VTVWVVSYIV
	SASDQLVNLL
51	PKQWRPQYVL GFNIPGLGVI VAIAVLFVTG LFAANVLGRQ
	ILAAWDSLLG
101	RIPVVKSIYS SVKKVSEYVL SDSSRSFKTP VLVPFPQPGI
	WTIAFVSGQV
151	SNAVKAALPX DGDYLSVYVP TTPNPTGGYY IMVKKSDVRE
	LDMSVDEXLK
201	YVISLGMVIP DDLPVKTLAX PMPSEKADLP EQQ*

Further work revealed the complete nucleotide sequence <SEQ ID 741>:

1	ATGACGGAAC nTGCGGCCGA AGGCGGCAAA GCTGCCAArG
	CGTTAAAAAA
51	ATATCTGATT ACGGGCATTT TGGTCTGGCT GCCGATTGCG
	GTAACGGTTT
101	GGGTGGTTTC CTATATCGTT TCCGCGTCCG ATCAGCTCGT
	CAACCTGCTG
151	CCGAAGCAAT GGCGGCCGCA ATATGTTTTG GGGTTTAATA
	TCCCGGGGCT
201	GGGCGTTATC GTTGCCATTG CCGTATTGTT TGTAACCGGA
	TTGTTTGCCG
251	CCAACGTATT GGGTCGGCAG ATCCTCGCCG CGTGGGACAG
	CCTGTTGGGG
301	CGGATTCCGG TTGTGAAATC CATCTATTCG AGTGTGAAAA
	AAGTATCCGA
351	ATCGCTGCTG TCCGACAGCA GCCGTTCGTT TAAAACGCCG
	GTACTCGTGC
401	CGTTTCCCCA GCCCGGTATT TGGACGATTG CTTTCGTGTC
	AGGGCAGGTG
451	TCGAATGCGG TTAAGGCCGC ATTGCCGAAG GACGGCGATT
	ATCTTTCCGT
501	GTATGTTCCG ACCACGCCGA ATCCGACCGG CGGTTACTAT
	ATTATGGTAA
551	AGAAAAGCGA TGTGCGCGAA CTCGATATGA GCGTGGACGA
	AGCATTGAAA
601	TATGTGATTT CGCTGGGTAT GGTCATCCCT GACGACCTGC
	CCGTCAAAAC
651	ATTGGCAGGA CCTATGCCGT CTGAAAAGGC GGATTTGCCC
	GAACAACAAT
701	AA

This corresponds to the amino acid sequence <SEQ ID 742; ORF98-1>:

1	MTEXAAEGGK AAKALKKYLI TGILVWLPIA VTVWVVSYIV
	SASDQLVNLL
51	PKQWRPQYVL GFNIPGLGVI VAIAVLFVTG LFAANVLGRQ
	ILAAWDSLLG
101	RIPVVKSIYS SVKKVSESLL SDSSRSFKTP VLVPFPQPGI
	WTIAFVSGQV
151	SNAVKAALPK DGDYLSVYVP TTPNPTGGYY IMVKKSDVRE
	LDMSVDEALK
201	YVISLGMVIP DDLPVKTLAG PMPSEKADLP EQQ*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF98 shows 96.1% identity over a 233aa overlap with an ORF (ORF98a) from strain A of N. meningitidis:

The complete length ORF98a nucleotide sequence <SEQ ID 743> is:

1	ATGACGGAAC CTGCGGCCGA AGGCGGCAAA GCTGCCAAGG
	CGTTAAAAAA
51	ATATCTGATT ACGGGCATTT TGGTCTGGCT GCCGATTGCG
	GTAACGGTTT
101	GGGTGGTTTC CTATATCGTT TCCGCGTCCG ATCAGCTCGT
	CAACCTGCTG
151	CCGAAGCAAT GGCGGCCGCA ATATGTTTTG GGGTTTAATA
	TCCCGGGGCT
201	GGGCGTTATC GTTGCCATTG CCGTATTGTT TGTAACCGGA
	TTATTTGCCG
251	CAAACGTATT GGGCCGGCAG ATTCTTGCCG CGTGGGACAG
	CTTGTTGGGG
301	CGGATTCCGG TTGTGAAGTC CATCTATTCG AGTGTGAAAA
	AAGTATCCGA
351	NTCGTTGCTG TCCGACAGCA GCCGTTCGTT TAAAACACCA
	GTACTCGTGC
401	CGTTTCCCCA ATCGGGTATT TGGACAATCG CATTCGTGTC
	CGGTCAGGTG
451	TCGAATGCGG TTAAGGCCGC ATTGCCGAAG GACGGCGATT
	ATCTTTCCGT
501	GTATGTTCCG ACCACGCCGA ATCCGACCGG CGGTTACTAT
	ATTATGGTAA
551	AGAAAAGCGA TGTGCGCGAA CTCGATATGA GCGTGGACGA
	AGCGTTGAAA
601	TATGTGATTT CGCTGGGTAT GGTCATCCCT GACGACCTGC
	CCGTCAAAAC
651	ATTGGCAGGA CCTATGCCGT CTGAAAAGGC GGATTTGCCC
	GAACAACAAT
701	AA

This encodes a protein having amino acid sequence <SEQ ID 744>:

1	MTEPAAEGGK AAKALKKYLI TGILVWLPIA VTVWVVSYIV
	SASDQLVNLL
51	PKQWRPQYVL GFNIPGLGVI VAIAVLFVTG LFAANVLGRQ
	ILAAWDSLLG
101	RIPVVKSIYS SVKKVSXSLL SDSSRSFKTP VLVPFPQSGI
	WTIAFVSGQV
151	SNAVKAALPK DGDYLSVYVP TTPNPTGGYY IMVKKSDVRE
	LDMSVDEALK
201	YVISLGMVIP DDLPVKTLAG PMPSEKADLP EQQ*

ORF98a and ORF98-1 show 98.7% identity in 233 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF98 shows 95.3% identity over a 233 aa overlap with a predicted ORF (ORF98ng) from N. gonorrhoeae:

The complete length ORF98ng nucleotide sequence <SEQ ID 745> is predicted to encode a protein having amino acid sequence <SEQ ID 746>:

1	MTEPAAEGGK AAKALKKYLI TGILVWLPIA VTVWVVSYIV
	SASDQLVNLL
51	PKQWRPQYVL GFNIPGLGVI VAIAVLFVTG LFAANVLGRQ
	ILAAWDSLLX
101	RIPVVKSIYS SVKKVSESLL SDSSRSFKTP VLVPFPQSGI
	WTIAFVSGQV
151	SNAVKAALPQ DGDYLSVYVP TTPNPTGGYY IMVKKSDVRE
	LDMSVDEALK
201	YVISLGMVIP DDLPVKTLAG PMPPEKAELP EQQ*

Further work revealed the complete nucleotide sequence <SEQ ID 747>:

1	ATGACGGAAC CTGCGGCCGA AGGCGGCAAA GCTGCCAAGG
	CGTTAAAAAA
51	ATATCTGATT ACAGGCATTT TGGTCTGGCT GCCGATTGCG
	GTAACGGTTT
101	GGGTGGTTTC CTATATCGTT TCCGCGTCCG ACCAGCTTGT
	CAACCTGCTG
151	CCGAAGCAAT GGCGGCCGCA ATATGTTTTG GGGTTTAATA
	TCCCCGGGCT
201	CGGCGTTATT GTTGCCATTG CCGTATTGTT TGTAACCGGA
	TTATTTGCCG
251	CAAACGTGTT GGGCCGGCAG ATTCTTGCCG CGTGGGACAG
	CCTGTTgggg
301	cggaTTCCGG TTGTCAAATC CATCTATTCG AGTGTGAAAA
	AAGTATCCGA
351	ATCGCTGCTG TCCGACAGCA GCCGTTCGTT TAAAACGCCG
	GTACTCGTGC
401	CGTTTCCCCA ATCGGGTATT TGGACAATCG CATTCGTGTC
	CGGTCAGGTG
451	TCGAATGCGG TTAAGGCCGC ATTGCCGCAG GATGGCGATT
	ATCTTTCCGT
501	GTATGTCCCG ACCACGCCCA ACCCGACCGG CGGTTACTAT
	ATTATGGTAA
551	AGAAAAGCGA TGTGCGCGAA CTCGATATGA GCGTGGACGA
	AGCGTTGAAA
601	TATGTGATTT CGCTGGGTAT GGTCATCCCT GACGACCTGC
	CCGTCAAAAC
651	ATTGGCAGGA CCTATGCCGC CTGAAAAGGC GGAGTTGCCC
	GAACAACAAT
701	AA

This corresponds to the amino acid sequence <SEQ ID 748; ORF98ng-1>:

1	MTEPAAEGGK AAKALKKYLI TGILVWLPIA VTVWVVSYIV
	SASDQLVNLL
51	PKQWRPQYVL GFNIPGLGVI VAIAVLFVTG LFAANVLGRQ
	ILAAWDSLLG
101	RIPVVKSIYS SVKKVSESLL SDSSRSFKTP VLVPFPQSGI
	WTIAFVSGQV
151	SNAVKAALPQ DGDYLSVYVP TTPNPTGGYY IMVKKSDVRE
	LDMSVDEALK
201	YVISLGMVIP DDLPVKTLAG PMPPEKAELP EQQ*

ORF98ng-1 and ORF98-1 show 97.9% identity in 233 aa overlap:

Based on this analysis, including the fact that the putative transmembrane domains in the gonococcal protein are identical to the sequences in the meningococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 89

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 749>:

1	ATgAAAACGG TAGTCTGGAT TGTCGTCCTG TTTGCCGCCG
	CCGTCGGACT
51	GGCGCTGGCT TCGGGCATTT ACACCGGCGA CGTGTATATC
	GTACTCGGAC
101	AGACCATGCT CAGAATCAAC CTGCACGCCT TTGTGTTAGG
	TTCGCTGATT
151	GCCGTCGTGG TGTGGTATTT CTTGTTTAAA TTCATTATCG
	GsGgTACTCA
201	ATATCCCCGA AAAGATGCAG CGTTTCGGTT CGGCnCGTAA
	AGGCCkCAAG
251	ssCGsGCTTG CCTTGAACAA GGCGGGTTTG GCGTATTTTG
	AAGGGCGTTT
301	TGAAAAGGCG GAACTAGAAG CCTCACGCGT GTTGGTCAAC
	AAAGtAGGCC
351	GaGAGACAAC CGGACTTTGG CATTGATGCT GrGCGCGCAC
	GCCGCCGGAC
401	AGATGGAAAA CATCGAssTG CGCGACCGTT ATCTTGCGGA
	AATCGCCAAA
451	CTGCCGGAAA AACAGCAGCT TTCCCGTTAT CTTTTGTTGG
	CGGAATCGGC
501	GTTGAACCGG CGCGATTACG AAGCGGCGGA AGCCAATCTT
	CATGCGGCGG
551	CGAAGATGAA TGCCAACCTT ACGCGCCTCG TGCGTCTGCA
	.ATTCGTTAC
601	GCTTTCGACA GGGGCGACGC GTTGCAGGTT CTGGCAAAAA
	CCGAAAAACT
651	TTCCAAGGCG GGCGCGTTGG GCAAATCGGA AATGGAACGG
	TATCAAAATT
701	GGGCATATCC GTCGCCAGCT GGCGGATGCT GCCGATGCCG
	CCGCTTTGAA
751	AACCTGCCTG AAGCGGATTC CCGACAGCCT CAAAAACGGG
	GAATTGAGCG
801	TATCGGTTGC GGAAAAGTAC GAACGTTTGG GACTGTATGC
	CGATGCGGTC
851	AAATGGGTCA AACAGCATTA TCCGCAsAAC CGCCGCCCCG
	AGCTTTTGGA
901	AGCCTTTGTC GAAAGCGTGC GCTTTTTGGG CGAGCGCGAA
	CAGCAGAAAG
951	CCATCGATTT TGCCGATGCT TGGCTGAAAG AACAGCCCGA
	TAACGCGCTT
1001	CTGCTGATGT ATCTCGGTCG GCTCGCCTTC GGCCGCAAAC
	TTTGGGGCAA
1051	GGCAAAAGGC TACCTTGAAG CGAGCATTGC ATTAAAGCCG
	AGTATTTCCG
1101	CGCGTTTGGT TCTAACAAAG GTTTTCGACG AAATCGGAGA
	ACCGCAGAAG
1151	GCGGAGGCGC AC...

This corresponds to the amino acid sequence <SEQ ID 750; ORF100>:

1	MKTVVWIVVL FAAAVGLALA SGIYTGDVYI VLGQTMLRIN
	LHAFVLGSLI
51	AVVVWYFLFK FIIGVLNIPE KMQRFGSARK GXKXXLALNK
	AGLAYFEGRF
101	EKAELEASRV LVNKVGRDNR TLALMLXAHA AGQMENIXXR
	DRYLAEIAKL
151	PEKQQLSRYL LLAESALNRR DYEAAEANLH AAAKMNANLT
	RLVRLXIRYA
201	FDRGDALQVL AKTEKLSKAG ALGKSEMERY QNWAYRRQLA
	DAADAAALKT
251	CLKRIPDSLK NGELSVSVAE KYERLGLYAD AVKWVKQHYP
	XNRRPELLEA
301	FVESVRFLGE REQQKAIDFA DAWLKEQPDN ALLLMYLGRL
	AFGRKLWGKA
351	KGYLEASIAL KPSISARLVL TKVFDEIGEP QKAEAH...

Further work revealed the complete nucleotide sequence <SEQ ID 751>:

1	ATGAAAACGG TAGTCTGGAT TGTCGTCCTG TTTGCCGCCG
	CCGTCGGACT
51	GGCGCTGGCT TCGGGCATTT ACACCGGCGA CGTGTATATC
	GTACTCGGAC
101	AGACCATGCT CAGAATCAAC CTGCACGCCT TTGTGTTAGG
	TTCGCTGATT
151	GCCGTCGTGG TGTGGTATTT CTTGTTTAAA TTCATTATCG
	GCGTACTCAA
201	TATCCCCGAA AAGATGCAGC GTTTCGGTTC GGCGCGTAAA
	GGCCGCAAGG
251	CCGCGCTTGC CTTGAACAAG GCGGGTTTGG CGTATTTTGA
	AGGGCGTTTT
301	GAAAAGGCGG AACTAGAAGC CTCACGCGTG TTGGTCAACA
	AAGAGGCCGG
351	AGACAACCGG ACTTTGGCAT TGATGCTGGG CGCGCACGCC
	GCCGGACAGA
401	TGGAAAACAT CGAGCTGCGC GACCGTTATC TTGCGGAAAT
	CGCCAAACTG
451	CCGGAAAAAC AGCAGCTTTC CCGTTATCTT TTGTTGGCGG
	AATCGGCGTT
501	GAACCGGCGC GATTACGAAG CGGCGGAAGC CAATCTTCAT
	GCGGCGGCGA
551	AGATGAATGC CAACCTTACG CGCCTCGTGC GTCTGCAACT
	TCGTTACGCT
601	TTCGACAGGG GCGACGCGTT GCAGGTTCTG GCAAAAACCG
	AAAAACTTTC
651	CAAGGCGGGC GCGTTGGGCA AATCGGAAAT GGAACGGTAT
	CAAAATTGGG
701	CATACCGCCG CCAGCTGGCG GATGCTGCCG ATGCCGCCGC
	TTTGAAAACC
751	TGCCTGAAGC GGATTCCCGA CAGCCTCAAA AACGGGGAAT
	TGAGCGTATC
801	GGTTGCGGAA AAGTACGAAC GTTTGGGACT GTATGCCGAT
	GCGGTCAAAT
851	GGGTCAAACA GCATTATCCG CACAACCGCC GCCCCGAGCT
	TTTGGAAGCC
901	TTTGTCGAAA GCGTGCGCTT TTTGGGCGAG CGCGAACAGC
	AGAAAGCCAT
951	CGATTTTGCC GATGCTTGGC TGAAAGAACA GCCCGATAAC
	GCGCTTCTGC
1001	TGATGTATCT CGGTCGGCTC GCCTACGGCC GCAAACTTTG
	GGGCAAGGCA
1051	AAAGGCTACC TTGAAGCGAG CATTGCATTA AAGCCGAGTA
	TTTCCGCGCG
1101	TTTGGTTCTA GCAAAGGTTT TCGACGAAAT CGGAGAACCG
	CAGAAGGCGG
1151	AGGCGCAGCG CAACTTGGTT TTGGAAGCCG TCTCCGATGA
	CGAACGTCAC
1201	GCAGCGTTAG AGCAGCATAG CTGA

This corresponds to the amino acid sequence <SEQ ID 752; ORF100-1>:

1	MKTVVWIVVL FAAAVGLALA SGIYTGDVYI VLGQTMLRIN
	LHAFVLGSLI
51	AVVVWYFLFK FIIGVLNIPE KMQRFGSARK GRKAALALNK
	AGLAYFEGRF
101	EKAELEASRV LVNKEAGDNR TLALMLGAHA AGQMENIELR
	DRYLAEIAKL
151	PEKQQLSRYL LLAESALNRR DYEAAEANLH AAAKMNANLT
	RLVRLQLRYA
201	FDRGDALQVL AKTEKLSKAG ALGKSEMERY QNWAYRRQLA
	DAADAAALKT
251	CLKRIPDSLK NGELSVSVAE KYERLGLYAD AVKWVKQHYP
	HNRRPELLEA
301	FVESVRFLGE REQQKAIDFA DAWLKEQPDN ALLLMYLGRL
	AYGRKLWGKA
351	KGYLEASIAL KPSISARLVL AKVFDEIGEP QKAEAQRNLV
	LEAVSDDERH
401	AALEQHS*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF100 shows 93.5% identity over a 386aa overlap with an ORF (ORF100a) from strain A of N. meningitidis:

The complete length ORF100a nucleotide sequence <SEQ ID 753> is:

1	ATGAAAACGG TAGTCTGGAT TGTCGTCCTG TTTGCCGCCG
	CNNTCGGGCT
51	GGCATTGGCG TCGGGCATTN ACACCGGCGA CGTGTATATC
	GTACTCGGAC
101	AGACCATGCT CAGAATCAAC CTGCACGCCT TTGTGTTAGG
	TTCGCTGATT
151	GCCGTCGTGG TGTGGTATTT CCTGTTCAAA TTCATCATCG
	GCGTACTCAA
201	TANCCCCGAA AAGATGCAGC GTTTCGGTTC GGCGCGTAAA
	GGCCGCAAGG
251	CCGCGCTTGC TTTGAACAAG GCGGGTTTGG CGTATTTTGA
	AGGGCGTTTT
301	GAAAAGGCGG AACTTGAAGC CTCGCGCGTA TTGGGAAACA
	AAGAGGCGGG
351	GGATAACCGG ACTTTGGCAT TGATGTTGGG CGCACATGCC
	GCCGGGCAGA
401	TGGAAAACAT CGAGCTGCGC GACCGTTATC TTGCGGAAAT
	CGCCAAACTG
451	CCGGAAAAGC AGCAGCTTTC CCGTTATCTT TTGTTGGCGG
	AATCGGCGTT
501	GAACCGGCGC GATTACGAAG CGGCGGAAGC CAATCTTCAT
	GCGGCGGCGA
551	AGATGAATGC CAACCTTACG CGCCTCGTGC GTCTGCAACT
	TCGTTACGCT
601	TTCGACAGGG GCGACGCGTT GCAGGTTCTG GCAAAAACCG
	AAAAANTTTC
651	CAAGGCGGGC GCGTNGGGCA AATCGGAAAT GGAACGGTAT
	CAAAATTGGG
701	CATACCGCCG CCAGCTGNCG GATGCTGCCG ATGCCGCCGC
	TTTGAAAACC
751	TGCCTGAAGC GGATTCCCGA CAGCCTCAAA AACGGGGAAT
	TGAGCGTATC
801	GGTTGCGGAA AAGTACGAAC GTTTGGGACT GTATGCCGAT
	GCGGTCAAAT
851	GGGTCAAACA GCATTATCCG CACAACCGCC GACCCGAACT
	TTTGGAAGCN
901	TTTGTCGAAA GCGTGCGCTT TTTGGGCGAA CGCGATCAGC
	AGAAAGCCAT
951	CGATTTTGCC GATGCTTGGC TGAAAGAACA GCCCGATAAT
	GCGCTTCTGC
1001	TGANGTATCT CGGTCGGCTC GCCTACGGCC GCAAACTTTG
	GGGCAAGGCA
1051	AAAGGCTACC TTGAAGCGAG CATTGCATTA AAGCCGAGTA
	TTTCCGCGCG
1101	TTTGGTTCTG GCAAAGGTTT TTGACGAAAC CGGAGAACCG
	CAGAAGGCGG
1151	AGGCGCAGCG CAACTTGGTT TTGGCAAGCG TTGCCGAGGA
	AAACCGNCCT
1201	TCCGCCGAAA CCCATTGA

This encodes a protein having amino acid sequence <SEQ ID 754>:

	1	MKTVVWIVVL FAAAXGLALA SGIXTGDVYI VLGQTMLRIN
		LHAFVLGSLI
	51	AVVVWYFLFK FIIGVLNXPE KMQRFGSARK GRKAALALNK
		AGLAYFEGRF
	101	EKAELEASRV LGNKEAGDNR TLALMLGAHA AGQMENIELR
		DRYLAEIAKL
	151	PEKQQLSRYL LLAESALNRR DYEAAEANLH AAAKMNANLT
		RLVRLQLRYA
	201	FDRGDALQVL AKTEKXSKAG AXGKSEMERY QNWAYRRQLX
		DAADAAALKT
	251	CLKRIPDSLK NGELSVSVAE KYERLGLYAD AVKWVKQHYP
		HNRRPELLEA
	301	FVESVRFLGE RDQQKAIDFA DAWLKEQPDN ALLLXYLGRL
		AYGRKLWGKA
	351	KGYLEASIAL KPSISARLVL AKVFDETGEP QKAEAQRNLV
		LASVAEENRP
	401	SAETH*

ORF100a and ORF100-1 show 95.1% identity in 406 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF100 shows 93.3% identity over a 386 aa overlap with a predicted ORF (ORF100ng) from N. gonorrhoeae:

The complete length ORF100ng nucleotide sequence <SEQ ID 755> is:

1	ATGAAAACGG TAGTCTGGAT TGTTGTCCTG TTTGCCGCCG
	CCGTCGGACT
51	GGCGCTGGCT TCGGGCATTT ACACCGGCGA CGTGTATATC
	GTACTCGGAC
101	AGACCATGCT CAGAATCAAC CTGCACGCCT TTGTGTTAGG
	TTCGCTGATT
151	GCCGTCGTGG TGTGGTATTT CCTGTTTAAA TTCATCATCG
	GCGTACTCAA
201	TATCCCCGAA AATATGCGGC GTTCCGGTTC GGCGCGGAAA
	GGCCGCAAGG
251	CCGCGCTTGC CTTGAATAAG GCGGGTTTGG CGTATTTCGA
	AGGGCGTTTT
301	GAAAAGGCGG AACTCGAAGC CTCTCGAGTG TTGGGCAACA
	AAGAGGCCGG
351	AGACAACCGG ACTTTGGCAT TGATGCTGGG CGCGCACGCG
	GCAGGACAGA
401	TGGAAAATAT CGAGCTGCGC GACCGTTATC TTGCGGAAAT
	CGCCAAACTG
451	CCGGAAAAAC AGCAGCTTTC CCGCTATCTT CTGCTGGCGG
	AATCGGCGTT
501	AAACCGGCGC GATTACGAAG CGGCGGAAGC CAATCTTCAT
	GCGGCGGCGA
551	AGATGAATGC CAACCTTACG CGCCTCGTGC GTCTGCAACT
	TCGTTACGCC
601	TTCGATCGGG GCGATGCGTT GCAGGTTCTG GCAAAAaccG
	AAAAACTTTC
651	CAAGGCGGGC GCGTTGGGCA AATCGGAAAT GGAACGGTAT
	CAAAATTGGG
701	CATACCGCCG CCAGATGGCG GATGCTGCCG ATGCCGCCGC
	TTTGAAAACC
751	TGCCTGAAGC GGATTCCCGA CAGCCTCAAA AACGGGGAAT
	TGagcGTATC
801	GGTTGCGGAA AAGTACGAAC GTTTGGGACT GTATGCCGAT
	GCGGTCAAAT
851	GGGTCAAACA GCATTATCCG CACAACCGCC GCCCCGAGCT
	TTTGGAAGCC
901	TTTGTCGAAA GCGTGCGCTT TTTGGGCGAG CGCGAACAGC
	AGAAAGCCAT
951	CGATTTTGCC GATTCTTGGC TGAAAGAACA GCCCGATAAC
	GCGCTTCTGC
1001	TGATGTATCT CGGCCGGCTC GCCTACGGCC GCAAACTTTG
	GGGTAAGGCA
1051	AAAGGCTACC TTGAAGCGAG TATTGCACTG AAGCCGAGTA
	TTCCGGCGCG
1101	TTTGGTGTTG GCAAAGGTTT TTGACGAAAC CGCACAGTCG
	CAAAAAGCCG
1151	AAGCACAGCG CAACTTGGTT TTGGCAAGCG TTGCCGGGGA
	AAACCGCCCT
1201	TCCGCCGAAA CCCGTTGA

This encodes a protein having amino acid sequence <SEQ ID 756>:

	1	MKTVVWIVVL FAAAVGLALA SGIYTGDVYI VLGQTMLRIN
		LHAFVLGSLI
	51	AVVVWYFLFK FIIGVLNIPE NMRRSGSARK GRKAALALNK
		AGLAYFEGRF
	101	EKAELEASRV LGNKEAGDNR TLALMLGAHA AGQMENIELR
		DRYLAEIAKL
	151	PEKQQLSRYL LLAESALNRR DYEAAEANLH AAAKMNANLT
		RLVRLQLRYA
	201	FDRGDALQVL AKTEKLSKAG ALGKSEMERY QNWAYRRQMA
		DAADAAALKT
	251	CLKRIPDSLK NGELSVSVAE KYERLGLYAD AVKWVKQHYP
		HNRRPELLEA
	301	FVESVRFLGE REQQKAIDFA DSWLKEQPDN ALLLMYLGRL
		AYGRKLWGKA
	351	KGYLEASIAL KPSIPARLVL AKVFDETAQS QKAEAQRNLV
		LASVAGENRP
	401	SAETR*

ORF100ng and ORF100-1 show 95.3% identity in 402 aa overlap:

Based on this analysis, including the presence of a putative leader sequence, a putative transmembrane domain, and a RGD motif, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 90

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 757>

	1	ATGATGTTTT CTTGGTTCAA GCTGTTTCAC TTGTTTTTTG
		TCATTTCGTG
	51	GTTTGCAGGG CTGTTTTACC TGCCGAGGAT TTTCGTCAAT
		ATGGCGATGA
	101	TTGATGTGCC GCGCGGCAAT CCCGAGTATG TGCGTCTGTC
		GGGCATGGCG
	151	GTGCGGCTGT ACCGTTTTAT GTCGCCGTTG GGCTTCGGCG
		CGGTCGTGTT
	201	CGGCGCGGCG ATACCGTTTG CCGCCGGCTG GTGGGGCAGC
		GGCTGGGTAC
	251	ACGTCAAACT GTGTTTGGGC TTGATGCTCT TGGCTTACCA
		GTTGTATTGC
	301	GGCGTGCTGC TGCGCCGTTT TCAGGATTAC AGCAATGCTT
		TTTCACACCG
	351	CTGGTACCGC GTGTTCAACG AAATCCCCGT GCTGCTGATG
		GTTGCCGCGC
	401	TGTATsTGGT CGTGTTCAAA CCGTTTTGA

This corresponds to the amino acid sequence <SEQ ID 758; ORF102>:

	1	MMFSWFKLFH LFFVISWFAG LFYLPRIFVN MAMIDVPRGN
		PEYVRLSGMA
	51	VRLYRFMSPL GFGAVVFGAA IPFAAGWWGS GWVHVKLCLG
		LMLLAYQLYC
	101	GVLLRRFQDY SNAFSHRWYR VFNEIPVLLM VAALYXVVFK
		PF*

Further work revealed the complete nucleotide sequence <SEQ ID 759>:

	1	ATGATGTTTT CTTGGTTCAA GCTGTTTCAC TTGTTTTTTG
		TCATTTCGTG
	51	GTTTGCAGGG CTGTTTTACC TGCCGAGGAT TTTCGTCAAT
		ATGGCGATGA
	101	TTGATGTGCC GCGCGGCAAT CCCGAGTATG TGCGTCTGTC
		GGGCATGGCG
	151	GTGCGGCTGT ACCGTTTTAT GTCGCCGTTG GGCTTCGGCG
		CGGTCGTGTT
	201	CGGCGCGGCG ATACCGTTTG CCGCCGGCTG GTGGGGCAGC
		GGCTGGGTAC
	251	ACGTCAAACT GTGTTTGGGC TTGATGCTCT TGGCTTACCA
		GTTGTATTGC
	301	GGCGTGCTGC TGCGCCGTTT TCAGGATTAC AGCAATGCTT
		TTTCACACCG
	351	CTGGTACCGC GTGTTCAACG AAATCCCCGT GCTGCTGATG
		GTTGCCGCGC
	401	TGTATCTGGT CGTGTTCAAA CCGTTTTGA

This corresponds to the amino acid sequence <SEQ ID 760; ORF102-1>:

1	MMFSWFKLFH LFFVISWFAG LFYLPRIFVN MAMIDVPRGN
	PEYVRLSGMA
51	VRLYRFMSPL GFGAVVFGAA IPFAAGWWGS GWVHVKLCLG
	LMLLAYQLYC
101	GVLLRRFQDY SNAFSHRWYR VFNEIPVLLM VAALYLVVFK
	PF*

Computer analysis of this amino acid sequence gave the following results:

Homology with HP1484 Hypothetical Integral Membrane Protein of H. pylori (Accession Number AE000647)

ORF102 and HP1484 show 33% aa identity in 143aa overlap:

orf102	3	FSWFKLFHLFFVISWFAGLFYLPRIFVNMAMIDVPRGNPEYVRLSGMAVRLYRFMSPLGF	62
		F W K FH+  VISW A LFYLPR+FV  A     +     V++     +LY F++
HP1484	8	FLWVKAFHVIAVISWMAALFYLPRLFVYHAENAHKKEFVGVVQIQEK--KLYSFIASPAM	65
orf102	63	GAVVFGAAIPFAAG---WWGSGWVHVKLCLGLMLLAYQLYCGVLLRRFQDYSNAFSHRWY	119
		G  +    +        +   GW+H KL L ++LLAY  YC   +R  +      + R+Y
HP1484	66	GFTLITGILMLLIEPTLFKSGGWLHAKLALVVLLLAYHFYCKKCMRELEKDPTRRNARFY	125
orf102	120	RVFNEIPXXXXXXXXXXXXFKPF	142
		RVFNE P             KPF
HP1484	126	RVFNEAPTILMILIVILVVVKPF	148

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF102 shows 99.3% identity over a 142aa overlap with an ORF (ORF102a) from strain A of N. meningitidis:

The complete length ORF102a nucleotide sequence <SEQ ID 761> is:

1	ATGATGTTTT CTTGGTTCAA GCTGTTTCAC TTGTTTTTTG
	TCATTTCGTG
51	GTTTGCAGGG CTGTTTTACC TGCCGAGGAT TTTCGTCAAT
	ATGGCGATGA
101	TTGATGTGCC GCGCGGCAAT CCCGAGTATG TGCGTCTGTC
	GGGCATGGCG
151	GTGCGGCTGT ACCGTTTTAT GTCGCCGTTG GGCTTCGGCG
	CGGTCGTGTT
201	CGGCGCGGCG ATACCGTTTG CCGCCGGCTG GTGGGGCAGC
	GGCTGGGTAC
251	ACGTCAAACT GTGTTTGGGC TTGATGCTCT TGGCTTACCA
	GTTGTATTGC
301	GGCGTGCTGC TGCGCCGTTT TCAGGATTAC AGCAATGCTT
	TTTCACACCG
351	CTGGTACCGC GTGTTCAACG AAATCCCCGT GCTGCTGATG
	GTTGCCGCGC
401	TGTATCTGGT CGTGTTCAAA CCGTTTTGA

This encodes a protein having amino acid sequence <SEQ ID 762>:

1	MMFSWFKLFH LFFVISWFAG LFYLPRIFVN MAMIDVPRGN
	PEYVRLSGMA
51	VRLYRFMSPL GFGAVVFGAA IPFAAGWWGS GWVHVKLCLG
	LMLLAYQLYC
101	GVLLRRFQDY SNAFSHRWYR VFNEIPVLLM VAALYLVVFK
	PF*

ORF102a and ORF102-1 show complete identity in 142 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF102 shows 97.9% identity over a 142 aa overlap with a predicted ORF (ORF102ng) from N. gonorrhoeae:

The complete length ORF102ng nucleotide sequence <SEQ ID 763> is:

1	ATGATGTTTT CTTGGTTCAA GCTGTTTCAC TTGTTTTTTG
	TCATTTCGTG
51	GTTTGCAGGG CTGTTTTACC TGCCGAGGAT TTTCGTCAAT
	ATGGCGATGA
101	TTGATGCGCC GCGCGGCAAT CCCGAGTATG TGCGCCTGTC
	GGGGATGGCG
151	GTGCGGTTGT ACCGTTTTAT GTCGCCTTTG GGTTTCGGCG
	CGGTCGTGTT
201	CGGCGCGGCG ATACCGTTTG CCGCcggccg GTGGGGCagc
	ggctggGTTC
251	ACGTCAAACT GTGTTTGGGC TTGATGCTCT TGGCTTATCA
	GTTGTATTGC
301	GGCGTGCTGC TGCGCCGTTT TCAGGATTAC AGCAATGCTT
	TTTCACACCG
351	CTGGTACCGC GTGTTCAAcg aAATCCCCGT GCTGCTGATG
	GTTGCCGCGC
401	TGTATCTGGT CGTGTTCAAA CCGTTTTGA

This encodes a protein having amino acid sequence <SEQ ID 764>:

1	MMFSWFKLFH LFFVISWFAG LFYLPRIFVN MAMIDAPRGN
	PEYVRLSGMA
51	VRLYRFMSPL GFGAVVFGAA IPFAAGRWGS GWVHVKLCLG
	LMLLAYQLYC
101	GVLLRRFQDY SNAFSHRWYR VFNEIPVLLM VAALYLVVFK
	PF*

ORF102ng and ORF102-1 show 98.6% identity in 142 aa overlap:

In addition, ORF102ng shows significant homology to a membrane protein from H. pylori:

gi|2314656 (AE000647) conserved hypothetical integral membrane protein
[Helicobacter pylori] Length = 148
Score = 79.2 bits (192), Expect = 1e−14
Identities = 50/147 (34%), Positives = 68/147 (46%), Gaps = 13/147 (8%)

Query:	3	FSWFKLFHLFFVISWFAGLFYLPRIFVNMAMIDAPRGNPEYVRLSGMAVRLYRFMSPLGF	62
		F W K FH+  VISW A LFYLPR+FV  A     +     V++     +LY F++
Sbjct:	8	FLWVKAFHVIAVISWMAALFYLPRLFVYHAENAHKKEFVGVVQIQEK--KLYSFIASPAM	65
Query:	63	GAVVFGAAIP-------FAAGRWGSGWVHVKLCLGLMLLAYQLYCGVLLRRFQDYSNAFS	115
		G  +    +        F +G    GW+H KL L ++LLAY  YC   +R  +      +
Sbjct:	66	GFTLITGILMLLIEPTLFKSG----GWLHAKLALVVLLLAYHFYCKKCMRELEKDPTRRN	121
Query:	116	HRWYRVFNEIPXXXXXXXXXXXXFKPF	142
		R+YRVFNE P             KPF
Sbjct:	122	ARFYRVFNEAPTILMILIVILVVVKPF	148

Based on this analysis, it is predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 91

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 765>:

1  ATGGCAAAAA TGATGAAATG GGCGGCTGTT GCGGCGGTCG CGGCGGCAGC
51  GGTTTGGGGC GGATGGTCTT AACTGAAGCC CGAGCCGCAC GTGCTTGATA
101  TTACGGAAAC GGTCAGGCGC GGC // .....
//.. ATTTCGTTTA CGATTTTGTC CGAACCGGAT ACGCCGATTA AGGCGAAGCT
51  CGACAGCGTC GACCCCGGGC TGACCACGAT GTCGTCGGGC GGTTACAACA
101  GCAGTACGGA TACGGCTTCC AATGCGGTCT ACTATTATGC CCGTTCGTTT
151  GTGCCGAATC CGGACGGCAA ACTCGCCACG GGGATGACGA CGCAGAATAC
201  GGTTGAAATC GACGGCGTGA AAAATGTGCT GATTATTCCG TCGCTGACCG
251  TGAAAAATCG CGGCGGCAAG GCGTTTGTGC GCGTGTTGGG TGCGGACGGC
301  AAGGCGGCGG AACGCGAAAT CCGGACCGGT ATGAGAGACA GTATGAATAC
351  CGAAGTAAAA AGCGGGTTGA AAGAGGGGGA CAAAGTGGTC ATCTCCGAAA
401  TAACCGCCGC CGAGCAACAG GAAAGCGGCG AACGCGCCCT AGGCGGCCCG
451  CCGCGCCGAT AA

This corresponds to the amino acid sequence <SEQ ID 766; ORF85>:

1	MAKMMKWAAV AAVAAAAVWG GWS.LKPEPH VLDITETVRR
	G.........
51	.......... .......... .......... ..........
	..........
101	.......... .......... .......... ..........
	..........
151	.......... .......... .......... ..........
	..........
201	.......... .......... .......... .........I
	SFTILSEPDT
251	PIKAKLDSVD PGLTTMSSGG YNSSTDTASN AVYYYARSFV
	PNPDGKLATG
301	MTTQNTVEID GVKNVLIIPS LTVKNRGGKA FVRVLGADGK
	AAEREIRTGM
351	RDSMNTEVKS GLKEGDKVVI SEITAAEQQE SGERALGGPP
	RR*

Further work revealed the further partial nucleotide sequence <SEQ ID 767>:

1	..GTATCGGTCG GCGCGCAGGC ATCGGGGCAG ATTAAGATAC
	TTTATGTCAA
51	ACTCGGGCAA CAGGTTAAAA AGGGCGATTT GATTGCGGAA
	ATCAATTCGA
101	CCTCGCAGAC CAATACGCTC AATACGGAAA AATCCAAGTT
	GGAAACGTAT
151	CAGGCGAAGC TGGTGTCGGC ACAGATTGCA TTGGGCAGCG
	CGGAGAAGAA
201	ATATAAGCGT CAGGCGGCGT TATGGAAGGA AAACGCGACT
	TCCAAAGAGG
251	ATTTGGAAAG CGCGCAGGAT GCGTTTGCCG CCGCCAAAGC
	CAATGTTGCC
301	GAGCTGAAGG CTTTAATCAG ACAGAGCAAA ATTTCCATCA
	ATACCGCCGA
351	GTCGGAATTG GGCTACACGC GCATTACCGC AACGATGGAC
	GGCACGGTGG
401	TGGCGATTCT CGTGGAAGAG GGGCAGACTG TGAACGCGGC
	GCAGTCTACG
451	CCGACGATTG TCCAATTGGC GAATCTGGAT ATGATGTTGA
	ACAAAATGCA
501	GATTGCCGAG GGCGATATTA CCAAGGTGAA GGCGGGGCAG
	GATATTTCGT
551	TTACGATTTT GTCCGAACCG GATACGCCGA TTAAGGCGAA
	GCTCGACAGC
601	GTCGACCCCG GGCTGACCAC GATGTCGTCG GGCGGTTACA
	ACAGCAGTAC
651	GGATACGGCT TCCAATGCGG TCTACTATTA TGCCCGTTCG
	TTTGTGCCGA
701	ATCCGGACGG CAAACTCGCC ACGGGGATGA CGACGCAGAA
	TACGGTTGAA
751	ATCGACGGCG TGAAAAATGT GCTGATTATT CCGTCGCTGA
	CCGTGAAAAA
801	TCGCGGCGGC AAGGCGTTTG TGCGCGTGTT GGGTGCGGAC
	GGCAAGGCGG
851	CGGAACGCGA AATCCGGACC GGTATGAGAG ACAGTATGAA
	TACCGAAGTA
901	AAAAGCGGGT TGAAAGAGGG GGACAAAGTG GTCATCTCCG
	AAATAACCGC
951	CGCCGAGCAA CAGGAAAGCG GCGAACGCGC CCTAGGCGGC
	CCGCCGCGCC
1001	GATAA

This corresponds to the amino acid sequence <SEQ ID 768; ORF85-1>:

1	..VSVGAQASGQ IKILYVKLGQ QVKKGDLIAE INSTSQTNTL
	NTEKSKLETY
51	QAKLVSAQIA LGSAEKKYKR QAALWKENAT SKEDLESAQD
	AFAAAKANVA
101	ELKALIRQSK ISINTAESEL GYTRITATMD GTVVAILVEE
	GQTVNAAQST
151	PTIVQLANLD MMLNKMQIAE GDITKVKAGQ DISFTILSEP
	DTPIKAKLDS
201	VDPGLTTMSS GGYNSSTDTA SNAVYYYARS FVPNPDGKLA
	TGMTTQNTVE
251	IDGVKNVLII PSLTVKNRGG KAFVRVLGAD GKAAEREIRT
	GMRDSMNTEV
301	KSGLKEGDKV VISEITAAEQ QESGERALGG PPRR*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF85 shows 87.8% identity over a 41 aa overlap and 99.3% identity over a 153aa overlap with an ORF (ORF85a) from strain A of N. meningitidis:

The complete length ORF85a nucleotide sequence <SEQ ID 769> is:

1	ATGGCAAAAA TGATGAAATG GGCGGCTGTT GCGGCGGTCG
	CGGCGGCAGC
51	GGTTTGGGGC GGATGGTCTT ATCTGAAGCC CGAGCCGCAG
	GCTGCTTATA
101	TTACGGAAAC GGTCAGGCGC GGCGACATCA GCCGGACGGT
	TTCTGCAACA
151	GGGGAGATTT CGCCGTCCAA CCTGGTATCG GTCGGCGCGC
	AGGCATCGGG
201	GCAGATTAAG AAACTTTATG TCAAACTCGG GCAACAGGTT
	AAAAAGGGCG
251	ATTTGATTGC GGAAATCAAT TCGACCTCGC AGACCAATAC
	GCTCAATACG
301	GAAAAATCCA AATTGGAAAC GTATCAGGCG AAGCTGGTGT
	CGGCACAGAT
351	TGCATTGGGC AGCGCGGAGA AGAAATATAA GCGTCAGGCG
	GCGTTGTGGA
401	AGGATGATGC GACCGCTAAA GAAGATTTGG AAAGCGCACA
	GGATGCGCTT
451	GCCGCCGCCA AAGCCAATGT TGCCGAGCTG AAGGCTCTAA
	TCAGACAGAG
501	CAAAATTTCC ATCAATACCG CCGAGTCGGA ATTGGGCTAC
	ACGCGCATTA
551	CCGCAACGAT GGACGGCACG GTGGTGGCGA TTCTCGTGGA
	AGAGGGGCAG
601	ACTGTGAACG CGGCGCAGTC TACGCCGACG ATTGTCCAAT
	TGGCGAATCT
651	GGATATGATG TTGAACAAAA TGCAGATTGC CGAGGGCGAT
	ATTACCAAGG
701	TGAAGGCGGG GCAGGATATT TCGTTTACGA TTTTGTCCGA
	ACCGGATACG
751	CCGATTAAGG CGAAGCTCGA CAGCGTCGAC CCCGGGCTGA
	CCACGATGTC
801	GTCGGGCGGC TACAACAGCA GTACGGATAC GGCTTCCAAT
	GCGGTCTACT
851	ATTATGCCCG TTCGTTTGTG CCGAATCCGG ACGGCAAACT
	CGCCACGGGG
901	ATGACGACGC AGAATACGGT TGAAATCGAC GGTGTGAAAA
	ATGTGCTGAT
951	TATTCCGTCG CTGACCGTGA AAAATCGCGG CGGCAGGGCG
	TTTGTGCGCG
1001	TGTTGGGTGC AGACGGCAAG GCGGCGGAAC GCGAAATCCG
	GACCGGTATG
1051	AGAGACAGTA TGAATACCGA AGTAAAAAGC GGGTTGAAAG
	AGGGGGACAA
1101	AGTGGTCATC TCCGAAATAA CCGCCGCCGA GCAGCAGGAA
	AGCGGCGAAC
1151	GCGCCCTAGG CGGCCCGCCG CGCCGATAA

This encodes a protein having amino acid sequence <SEQ ID 770>:

1	MAKMMKWAAV AAVAAAAVWG GWSYLKPEPQ AAYITETVRR
	GDISRTVSAT
51	GEISPSNLVS VGAQASGQIK KLYVKLGQQV KKGDLIAEIN
	STSQTNTLNT
101	EKSKLETYQA KLVSAQIALG SAEKKYKRQA ALWKDDATAK
	EDLESAQDAL
151	AAAKANVAEL KALIRQSKIS INTAESELGY TRITATMDGT
	VVAILVEEGQ
201	TVNAAQSTPT IVQLANLDMM LNKMQIAEGD ITKVKAGQDI
	SFTILSEPDT
251	PIKAKLDSVD PGLTTMSSGG YNSSTDTASN AVYYYARSFV
	PNPDGKLATG
301	MTTQNTVEID GVKNVLIIPS LTVKNRGGRA FVRVLGADGK
	AAEREIRTGM
351	RDSMNTEVKS GLKEGDKVVI SEITAAEQQE SGERALGGPP
	RR*

ORF85a and ORF85-1 show 98.2% identity in 334 aa overlap:

FIG. 19D shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF85a.

Homology with a Predicted ORF from N. gonorrhoeae

ORF85 shows a high degree of identity with a predicted ORF (ORF85ng) from N. gonorrhoeae:

The complete length ORF85ng nucleotide sequence <SEQ ID 771> is:

1	ATGGCAAAAA TGATGAAATG GGCGGCTGTT GCGGCGGTCG
	CGGCGGCaac
51	GGTTTGGGGC GGATGGTCTT ATCTGAAGCC CGAACCGCAG
	GCTGCTTATA
101	TTACGGAaac ggTCAGGCGC GGCGATATCA GCCGGACGGT
	TTCCGCGACG
151	GgcgAGATTT CGCCGTCCAA CCTGGTATCG GTCGGCGCGC
	AGGCTTCGGG
201	GCAGATTAAA AAGCTTTATG TCAAACTCGG GCAACAGGTC
	AAAAAGGGCG
251	ATTTGATTGC GGAAATCAAT TCGACCACGC AGACCAACAC
	GATCGATATG
301	GAAAAATCCA AATTGGAAAC GTATCAGGCG AAGCTGGTGT
	CGGCACAGAT
351	TGCATTGGGC AGCGCGGAGA AGAAATATAA GCGTCAGGCG
	GCGTTGTGGA
401	AGGATGATGC GACCTCTAAA GAAGATTTGG AAAGCGCGCA
	GGATGCGCTT
451	GCCGCCGCCA AAGCCAATGT TGCCGAGTTG AAGGCTTTAA
	TCAGACAGAG
501	CAAAATTTCC ATCAATACCG CCGAGTCGGA TTTGGGCTAC
	ACGCGCATTA
551	CCGCGACGAT GGACGGCACG GTGGTGGCGA TTCCCGTGGA
	AGAGGGGCAG
601	ACTGTGAACG CGGCGCAGTC TACGCCGACG ATTGTCCAAT
	TGGCGAATCT
651	GGATATGATG TTGAACAAAA TGCAGATTGC CGAGGGCGAT
	ATTACCAAGG
701	TGAAGGCGGG GCAGGATATT TCGTTTACGA TTTTGTCCGA
	ACCGGATACG
751	CCGATTAAGG CGAAGCTCGA CAGCGTCGAC CCCGGGCTGA
	CCACGATGTC
801	GTCGGGCGGC TACAACAGCA GTACGGATAC GGCTTCCAAT
	GCGGTCTATT
851	ATTATGCCCG TTCGTTTGTG CCGAATCCGG ACGGCAAACT
	CGCCACGGGG
901	ATGACGACGC AGAATACGGT TGAAATCGAC GGTGTGAAAA
	ATGTGTTGCT
951	TATTCCGTCG CTGACCGTGA AAAATCGCGG CGGCAAGGCG
	TTCGTACGCG
1001	TGTTGGGTGC GGACGGCAAG GCAGTGGAAC GCGAAATCCG
	GACCGGTATG
1051	AAAGACAGTA TGAATACCGA AGTGAAAAGC GGGTTGAAAG
	AGGGGGACAA
1101	AGTGGTCATC TCCGAAATAA CCGCCGCCGA GCAGCAGGAA
	AGCGGCGAAC
1151	GCGCCCTAGG CGGCCCGCCG CGCCGATAA

This encodes a protein having amino acid sequence <SEQ ID 772>:

1	MAKMMKWAAV AAVAAAAVWG GWSYLKPEPQ AAYITEAVRR
	GDISRTVSAT
51	GEISPSNLVS VGAQASGQIK KLYVKLGQQV KKGDLIAEIN
	STTQTNTIDM
101	EKSKLETYQA KLVSAQIALG SAEKKYKRQA ALWKDDATSK
	EDLESAQDAL
151	AAAKANVAEL KALIRQSKIS INTAESDLGY TRITATMDGT
	VVAIPVEEGQ
201	TVNAAQSTPT IVQLANLDMM LNKMQIAEGD ITKVKAGQDI
	SFTILSEPDT
251	PIKAKLDSVD PGLTTMSSGG YNSSTDTASN AVYYYARSFV
	PNPDGKLATG
301	MTTQNTVEID GVKNVLLIPS LTVKNRGGKA FVRVLGADGK
	AVEREIRTGM
351	KDSMNTEVKS GLKEGDKVVI SEITAAEQQE SGERALGGPP
	RR*

ORF85ng and ORF85-1 show 96.1% identity in 334 aa overlap:

In addition, ORF85ng shows significant homology to an E. coli membrane fusion protein:

gi|1787104 (AE000189) o380; 27% identical (27 gaps) to 332 residues from
membrane fusion protein precursor, MTRC_NEIGO SW: P43505 (412 aa)
[Escherichia coli] Length = 380
Score = 193 bits (485), Expect = 2e−48
Identities = 120/345 (34%), Positives = 182/345 (51%), Gaps = 13/345 (3%)

Query:	29	PQAAYITETVRRGDISRTVSATGEISPSNLVSVGAQASGQIKKLYVKLGQQVKKGDLIAE	88
		P   Y T  VR GD+ ++V ATG++     V VGAQ SGQ+K L V +G +VKK  L+
Sbjct:	41	PVPTYQTLIVRPGDLQQSVLATGKLDALRKVDVGAQVSGQLKTLSVAIGDKVKKDQLLGV	100
Query:	89	INSTTQTNTIDMEKSKLETYQAKLVSAQIALGSAEKKYKRQAALWKDDATSKEXXXXXXX	148
		I+     N I   ++ L   +A+   A+  L  A   Y RQ  L +  A S++
Sbjct:	101	IDPEQAENQIKEVEATLMELRAQRQQAEAELKLARVTYSRQQRLAQTKAVSQQDLDTAAT	160
Query:	149	XXXXXXXXXXXXXXXIRQSKISINTAESDLGYTRITATMDGTVVAIPVEEGQTVNAAQST	208
		I++++ S++TA+++L YTRI A M G V  I   +GQTV AAQ
Sbjct:	161	EMAVKQAQIGTIDAQIKRNQASLDTAKTNLDYTRIVAPMAGEVTQITTLQGQTVIAAQQA	220
Query:	209	PTIVQLANLDMMLNKMQIAEGDITKVKAGQDISFTILSEPDTPIKAKLDSVDPGLTTMSS	268
		P I+ LA++  ML K Q++E D+  +K GQ   FT+L +P T  + ++  V P
Sbjct:	221	PNILTLADMSAMLVKAQVSEADVIHLKPGQKAWFTVLGDPLTRYEGQIKDVLP-------	273
Query:	269	GGYNSSTDTASNAVYYYARSFVPNPDGKLATGMTTQNTVEIDGVKNVLLIPSLTVKNRGG	328
		+ +  ++A++YYAR  VPNP+G L   MT Q  +++  VKNVL IP   + +  G
Sbjct:	274	-----TPEKVNDAIFYYARFEVPNPNGLLRLDMTAQVHIQLTDVKNVLTIPLSALGDPVG	328
Query:	329	KAFVRV-LGADGKAVEREIRTGMKDSMNTEVKSGLKEGDKVVISE	372
		+V L  +G+  ERE+  G ++  + E+  GL+ GD+VVI E
Sbjct:	329	DNRYKVKLLRNGETREREVTIGARNDTDVEIVKGLEAGDEVVIGE	373

Based on this analysis, it was predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF85-1 (40.4 kDa) was cloned in the pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 19A shows the results of affinity purification of the GST-fusion protein. Purified GST-fusion protein was used to immunise mice, whose sera were used for Western blot (FIG. 19B), FACS analysis (FIG. 19C), and ELISA (positive result). These experiments confirm that ORF85-1 is a surface-exposed protein, and that it is a useful immunogen.

Example 92

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 773>:

1	..ATTCCCGCCA CGATGACATT TGAACGCAGC GGCAATGCTT
	ACAAAATCGT
51	TTCGACGATT AAAGTGCCGC TATACAATAT CCGTTTCGAG
	TCCGGCGGTA
101	CGGTTGTCGG CAATACCCTG CACCCTACCT ACTATAGAGA
	CATACGCAGG
151	GGCAAACTGT ATGCGGAAgc CAAATTCGCC GACgGcAGCG
	TAACTTACGG
201	CAAAGCGGGC GAGAGCAAAA CCGAGCAAAG CCCCAAGGCT
	ATGGATTTGT
251	TCACGCTTGC CTGGCAGTTG GCGGCAAATG ACGCGAAACT
	CCCCCCGGGG
301	CTGAAAATCA CCAACGGCAA AAAACTTTAT TCCGTCGGCG
	GTTTGAATAA
351	GGCGGGTACA GGAAAATACA GCATAGGCGG CGTGGAAACC
	GAAGTCGTCA
401	AATATCGGGT GCGGCGCGGC GACGATGCGG TAATGTATTT
	cTTCGCACCG
451	TCCCTGAACA ATATTCCGGC ACAAATCGGC TATACCGACG
	ACGGCAAAAC
501	CTATACGCTG AAACTCAAAT CGGTGCAGAT CAACGGCCAG
	GCAGCCAAAC
551	CGTAA

This corresponds to the amino acid sequence <SEQ ID 774; ORF120>:

1	..IPATMTFERS GNAYKIVSTI KVPLYNIRFE SGGTVVGNTL
	HPTYYRDIRR
51	GKLYAEAKFA DGSVTYGKAG ESKTEQSPKA MDLFTLAWQL
	AANDAKLPPG
101	LKITNGKKLY SVGGLNKAGT GKYSIGGVET EVVKYRVRRG
	DDAVMYFFAP
151	SLNNIPAQIG YTDDGKTYTL KLKSVQINGQ AAKP*

Further work revealed the complete nucleotide sequence <SEQ ID 775>:

1	ATGATGAAGA CTTTTAAAAA TATATTTTCC GCCGCCATTT
	TGTCCGCCGC
51	CCTGCCGTGC GCGTATGCGG CAGGGCTGCC CCAATCCGCC
	GTGCTGCACT
101	ATTCCGGCAG CTACGGCATT CCCGCCACGA TGACATTTGA
	ACGCAGCGGC
151	AATGCTTACA AAATCGTTTC GACGATTAAA GTGCCGCTAT
	ACAATATCCG
201	TTTCGAGTCC GGCGGTACGG TTGTCGGCAA TACCCTGCAC
	CCTACCTACT
251	ATAGAGACAT ACGCAGGGGC AAACTGTATG CGGAAGCCAA
	ATTCGCCGAC
301	GGCAGCGTAA CTTACGGCAA AGCGGGCGAG AGCAAAACCG
	AGCAAAGCCC
351	CAAGGCTATG GATTTGTTCA CGCTTGCCTG GCAGTTGGCG
	GCAAATGACG
401	CGAAACTCCC CCCGGGGCTG AAAATCACCA ACGGCAAAAA
	ACTTTATTCC
451	GTCGGCGGTT TGAATAAGGC GGGTACAGGA AAATACAGCA
	TAGGCGGCGT
501	GGAAACCGAA GTCGTCAAAT ATCGGGTGCG GCGCGGCGAC
	GATGCGGTAA
551	TGTATTTCTT CGCACCGTCC CTGAACAATA TTCCGGCACA
	AATCGGCTAT
601	ACCGACGACG GCAAAACCTA TACGCTGAAA CTCAAATCGG
	TGCAGATCAA
651	CGGCCAGGCA GCCAAACCGT AA

This corresponds to the amino acid sequence <SEQ ID 776; ORF120-1>:

1	MMKTFKNIFS AAILSAALPC AYAAGLPQSA VLHYSGSYGI
	PATMTFERSG
51	NAYKIVSTIK VPLYNIRFES GGTVVGNTLH PTYYRDIRRG
	KLYAEAKFAD
101	GSVTYGKAGE SKTEQSPKAM DLFTLAWQLA ANDAKLPPGL
	KITNGKKLYS
151	VGGLNKAGTG KYSIGGVETE VVKYRVRRGD DAVMYFFAPS
	LNNIPAQIGY
201	TDDGKTYTLK LKSVQINGQA AKP*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF120 shows 92.4% identity over a 184aa overlap with an ORF (ORF120a) from strain A of N. meningitidis:

The complete length ORF120a nucleotide sequence <SEQ ID 777> is:

1	ATGATGAAGA CTTTTAAAAA TATATTTTCC GCCGCCATTT
	TGTCCGCCGC
51	CCTGCCGTGC GCGTATGCGG CAGGGCTGCC CNAATCCGCC
	GTGCTGCACT
101	ATTCCGGCAG CTACGGCATT CCCGCCACNA NNANNTNNGN
	ACNNNGNGNC
151	AATGCTTNCA AAATCGTTTC GACGATTAAA GTGCCGCTAT
	ACAATATCCG
201	TTTCGAGTCC GGCGGTACGG TTGTCGGCAA TACCCTGCAC
	CCTACCTACT
251	ATAGAGACAT ACGCAGGGGC AAACTGTATG CGGAAGCCAA
	ATTCGCCGAC
301	GGCAGCGTAA CCTACGGCAA AGCGGNNNNN ANCNNNNNNG
	NGCAAAGCCC
351	CAAGGCTATG GATTTGTTCA CGCTTGCNTG GCAGTTGGCG
	GCAAATGACG
401	CGAAACTCCC CCCGGGGCTG AAAATCACCA ACGGCAAAAA
	ACTTTATTCC
451	GTCGGCGGTT TGAATAAGGC GGGTACAGGA AAATACAGCA
	TAGGCGGCGT
501	GGAAACCGAA GTCGTCAAAT ATCGGGTGCG GCGCGGCGAC
	GATGCGGTAA
551	TGTATTTCTT CGCACCGTCC CTGAACAATA TTCCGGCACA
	AATCGGCTAT
601	ACCGACGACG GCAAAACCTA TACGCTGAAA CTCAAATCGG
	TGCAGATCAA
651	CGGCCAGGCA GCCAAACCGT AA

This encodes a protein having amino acid sequence <SEQ ID 778>:

1	MMKTFKNIFS AAILSAALPC AYAAGLPXSA VLHYSGSYGI
	PATXXXXXXX
51	NAXKIVSTIK VPLYNIRFES GGTVVGNTLH PTYYRDIRRG
	KLYAEAKFAD
101	GSVTYGKAXX XXXXQSPKAM DLFTLAWQLA ANDAKLPPGL
	KITNGKKLYS
151	VGGLNKAGTG KYSIGGVETE VVKYRVRRGD DAVMYFFAPS
	LNNIPAQIGY
201	TDDGKTYTLK LKSVQINGQA AKP*

ORF120a and ORF120-1 show 93.3% identity in 223 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF120 shows 97.8% identity over 184 aa overlap with a predicted ORF (ORF120ng) from N. gonorrhoeae:

The complete length ORF120ng nucleotide sequence <SEQ ID 779> is:

1	ATGATGAAGA CTTTTAAAAA TATATTTTCC GCCGCCATTT
	TGTCCGCCGC
51	CCTGCCGTGC GCGTATGCGG CAAGGCTACC CCAATCCGCC
	GTGCTGCACT
101	ATTCCGGCAG CTACGGCATT CCCGCCACGA TGACATTTGA
	ACGCAGCGGC
151	AATGCTTACA AAATCGTTTC GACGATTAAA GTGCCGCTAT
	ACAATATCCG
201	TTTCGAATCC GGCGGTACGG TTGTCGGCAA TACCCTGCAC
	CCTGCCTACT
251	ATAAAGACAT ACGCAGGGGC AAACTGTATG CGGAAGCCAA
	ATTCGCCGAC
301	GGCAGCGTAA CCTACGGCAA AGCGGGCGAG AGCAAAACCG
	AGCAAAGCCC
351	CAAGGCTATG GATTTGTTCA CGCTTGCCTG GCAGTTGGCG
	GCAAATGACG
401	CGAAACTCCC CCCGGGTCTG AAAATCACCA ACGGCAAAAA
	ACTTTATTCC
451	GTCGGCGGCC TGAATAAGGC GGGTACGGGA AAATACAGCA
	TaggCGGCGT
501	GGAAACCGAA GTCGTCAAAT ATCGGGTGCG GCGCGGCGAC
	GATACGGTAA
551	CGTATTTCTT CGCACCGTCC CTGAACAATA TTCCGGCACA
	AATCGGCTAT
601	ACCGACGACG GCAAAACCTA TACGCTGAAG CTCAAATCGG
	TGCAGATCAA
651	CGGACAGGCC GCCAAACCGT AA

This encodes a protein having amino acid sequence <SEQ ID 780>:

1	MMKTFKNIFS AAILSAALPC AYAARLPQSA VLHYSGSYGI
	PATMTFERSG
51	NAYKIVSTIK VPLYNIRFES GGTVVGNTLH PAYYKDIRRG
	KLYAEAKFAD
101	GSVTYGKAGE SKTEQSPKAM DLFTLAWQLA ANDAKLPPGL
	KITNGKKLYS
151	VGGLNKAGTG KYSIGGVETE VVKYRVRRGD DTVTYFFAPS
	LNNIPAQIGY
201	TDDGKTYTLK LKSVQINGQA AKP*

In comparison with ORF120-1, ORF120ng shows 97.8% identity in 223 aa overlap:

This analysis, including the presence of a putative leader sequence in the gonococcal protein suggests that the proteins from N. meningitidis and N. gonorrhoeae, and, their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 93

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 781>:

1	ATGTATCGGA GGAAAGGGCG GGGCATCAAG CCGTGGATGG
	GTGCCGGTGC
51	.GCGTTTGCC GCCTTGGTCT GGCTGGTTTT CGCGCTCGGC
	GATACTTTGA
101	CTCCGTTTGC GGTTGCGGCG GTGCTGGCGT ATGTATTGGA
	CCCTTTGGTC
151	GAATGGTTGC AGAAAAAGGG TTTGAACCGT GCATCCGCTT
	CGATGTCTGT
201	GATGGTGTTT TCCTTGATTT TGTTGTTGGC ATTATTGTTG
	ATTATCGTCC
251	CTATGCTGGT CGGGCAGTTC AACAATTTGG CATCGCGCCT
	GCCCCAATTA
301	ATCGGTTTTA TGCAGAACAC GCTGCTGCCG TGGTTGAAAA
	ATACAATCGG
351	CGGATATGTG GAAATCGATC AGGCATCTAT TATTGCGTGG
	CTTCAGGCGC
401	ATACGGGAGA GTTGAGCAAC GCGCTTAAGG CGTGGTTTCC
	CGTTTTGATG
451	AGGCAGGGCG GCAATATT..

This corresponds to the amino acid sequence <SEQ ID 782; ORF121>:

1	MYRRKGRGIK PWMGAGXAFA ALVWLVFALG DTLTPFAVAA
	VLAYVLDPLV
51	EWLQKKGLNR ASASMSVMVF SLILLLALLL IIVPMLVGQF
	NNLASRLPQL
101	IGFMQNTLLP WLKNTIGGYV EIDQASIIAW LQAHTGELSN
	ALKAWFPVLM
151	RQGGNI..

Further work revealed the complete nucleotide sequence <SEQ ID 783>:

1	ATGTATCGGA GGAAAGGGCG GGGCATCAAG CCGTGGATGG
	GTGCCGGTGC
51	GGCGTTTGCC GCCTTGGTCT GGCTGGTTTT CGCGCTCGGC
	GATACTTTGA
101	CTCCGTTTGC GGTTGCGGCG GTGCTGGCGT ATGTATTGGA
	CCCTTTGGTC
151	GAATGGTTGC AGAAAAAGGG TTTGAACCGT GCATCCGCTT
	CGATGTCTGT
201	GATGGTGTTT TCCTTGATTT TGTTGTTGGC ATTATTGTTG
	ATTATCGTCC
251	CTATGCTGGT CGGGCAGTTC AACAATTTGG CATCGCGCCT
	GCCCCAATTA
301	ATCGGTTTTA TGCAGAACAC GCTGCTGCCG TGGTTGAAAA
	ATACAATCGG
351	CGGATATGTG GAAATCGATC AGGCATCTAT TATTGCGTGG
	CTTCAGGCGC
401	ATACGGGAGA GTTGAGCAAC GCGCTTAAGG CGTGGTTTCC
	CGTTTTGATG
451	AGGCAGGGCG GCAATATTGT CAGCAGTATC GGCAACCTGC
	TGCTGCTTCC
501	CTTGCTGCTT TACTATTTCC TGCTGGATTG GCAGCGGTGG
	TCGTGCGGCA
551	TTGCCAAACT GGTTCCGAgG CGTTTTGCCG GTGCTTATAC
	GCGCATTACA
601	GGCAATTTGA ACGAGGTATT GGGCGAATTT TTGCGCGGGC
	AGCTTCTGGT
651	AATGCTGATT ATGGGCTTGG TTTACGGTTT GGGATTGGTG
	CTGGTCGGGC
701	TGGATTCGGG GTTTGCCATC GGTATGCTTG CCGGTATTTT
	GGTGTTTGTC
751	CCTTATCTCG GGGCGTTTAC GGGATTGCTG CTTGCCACCG
	TCGCCGCCTT
801	GCTCCAGTTC GGTTCGTGGA ACGGCATCCT ATCGGTTTGG
	GCGGTTTTTG
851	CCGTAGGACA GTTTCTCGAA AGTTTTTTCA TTACGCCGAA
	AATCGTGGGA
901	GACCGTATCG GGCTGTCGCC GTTTTGGGTT ATCTTTTCGC
	TGATGGCGTT
951	CGGGCAGCTG ATGGGCTTTG TCGGAATGTT GGCGGGATTG
	CCTTTGGCCG
1001	CCGTAACCTT GGTCTTGCTT CGCGAGGGCG TGCAGAAATA
	TTTTGCCGGC
1051	AGTTTTTACC GGGGCAGGTA G

This corresponds to the amino acid sequence <SEQ ID 784; ORF121-1>:

1	MYRRKGRGIK PWMGAGAAFA ALVWLVFALG DTLTPFAVAA
	VLAYVLDPLV
51	EWLQKKGLNR ASASMSVMVF SLILLLALLL IIVPMLVGQF
	NNLASRLPQL
101	IGFMQNTLLP WLKNTIGGYV EIDQASIIAW LQAHTGELSN
	ALKAWFPVLM
151	RQGGNIVSSI GNLLLLPLLL YYFLLDWQRW SCGIAKLVPR
	RFAGAYTRIT
201	GNLNEVLGEF LRGQLLVMLI MGLVYGLGLV LVGLDSGFAI
	GMLAGILVFV
251	PYLGAFTGLL LATVAALLQF GSWNGILSVW AVFAVGQFLE
	SFFITPKIVG
301	DRIGLSPFWV IFSLMAFGQL MGFVGMLAGL PLAAVTLVLL
	REGVQKYFAG
351	SFYRGR*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF121 shows 98.7% identity over a 156aa overlap with an ORF (ORF121a) from strain A of N. meningitidis:

The complete length ORF121a nucleotide sequence <SEQ ID 785> is:

1	ATGTATCGGA GGAAAGGGCG GGGCATCAAG CCGTGGATGG
	ATGCCGGTGC
51	GGCGTTTGCC GCCTTGGTCT GGCTGGTTTT CGCGCTCGGC
	GATACTTTGA
101	CTCCGTTTGC GGTTGCGGCG GTGCTGGCGT ATGTATTGGA
	CCCTTTGGTC
151	GAATGGTTGC AGAAAAAGGG TTTGAACCGT GCATCCGCTT
	CGATGTCTGT
201	GATGGTGTTT TCCTTGATTT TGTTGTTGGC ATTATTGTTG
	ATTATTGTCC
251	CTATGCTGGT CGGGCAGTTC AACAATTTGG CATCGCGCCT
	GCCCCAATTA
301	ATCGGTTTTA TGCAGAACAC GCTGCTGCCG TGGTTGAAAA
	ATACAATCGG
351	CGGATATGTG GAAATCGATC AGGCATCTAT TATTGCGTGG
	CTTCAGGCGC
401	ATACGGGCGA GTTGAGCAAC GCGCTTAAGG CGTGGTTTCC
	CGTTTTGATG
451	AGGCAGGGCG GCAATATTGT CAGCAGTATC GGCAACCTGC
	TGCTGCTTCC
501	CTTGCTGCTT TACTATTTCC TGCTGGATTG GCAGCGGTGG
	TCGTGCGGCA
551	TTGCCAAACT GGTTCCGAGG CGTTTTGCCG GTGCTTATAC
	GCGCATTACA
601	GGCAATTTGA ACGAGGTATT GGGCGAATTT TTGCGCGGGC
	AGCTTCTGGT
651	GATGCTGATT ATGGGTTTGG TTTACGGCTT GGGGTTGGTG
	CTGGTCGGGC
701	TGGATTCGGG GTTTGCAATC GGTATGGTTG CCGGTATTTT
	GGTTTTTGTT
751	CCCTATTTGG GCGCGTTTAC AGGACTGCTG CTGGCAACCG
	TCGCCGCCTT
801	GCTCCAGTTC GGTTCGTGGA ACGGCATCTT GGCTGTTTGG
	GCGGTTTTTG
851	CCGTAGGACA GTTTCTCGAA AGTTTTTTCA TTACGCCGAA
	AATCGTGGGA
901	GACCGTATCG GCCTGTCGCC GTTTTGGGTT ATCTTTTCGC
	TGATGGCGTT
951	CGGGCAGCTG ATGGGCTTTG TCGGAATGTT GGCCGGATTG
	CCTTTGGCCG
1001	CCGTAACCTT GGTCTTGCTT CGCGAGGGCG TGCAGAAATA
	TTTTGCCGGC
1051	AGTTTTTACC GGGGCAGGTA G

This encodes a protein having amino acid sequence <SEQ ID 786>:

1	MYRRKGRGIK PWMDAGAAFA ALVWLVFALG DTLTPFAVAA
	VLAYVLDPLV
51	EWLQKKGLNR ASASMSVMVF SLILLLALLL IIVPMLVGQF
	NNLASRLPQL
101	IGFMQNTLLP WLKNTIGGYV EIDQASIIAW LQAHTGELSN
	ALKAWFPVLM
151	RQGGNIVSSI GNLLLLPLLL YYFLLDWQRW SCGIAKLVPR
	RFAGAYTRIT
201	GNLNEVLGEF LRGQLLVMLI MGLVYGLGLV LVGLDSGFAI
	GMVAGILVFV
251	PYLGAFTGLL LATVAALLQF GSWNGILAVW AVFAVGQFLE
	SFFITPKIVG
301	DRIGLSPFWV IFSLMAFGQL MGFVGMLAGL PLAAVTLVLL
	REGVQKYFAG
351	SFYRGR*

ORF121a and ORF121-1 show 99.2% identity in 356 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF121 shows 97.4% identity over a 156 aa overlap with a predicted ORF (ORF121ng) from N. gonorrhoeae:

An ORF121ng nucleotide sequence <SEQ ID 787> was predicted to encode a protein having amino acid sequence <SEQ ID 788>:

1	MYRRKGRGIK PWMGAGAAFA ALVWLVYALG DTLTPFAVAA
	VLAYVLDPLV
51	EWLQKKGLNR ASASMSVMVF SLILLLALLL IIVPMLVGQF
	NNLASRLPQL
101	IGFMQNTLLP WLKNTIGGYV EIDQASIIAW FQAHTGELSN
	ALKAWFPVLM
151	KQGGNIVSTI GNLLLPPLLL YYFLLDWHRW SCGIPKLVPR
	RFAGAYTRIT
201	GNLNKVWGKF LRGQLLGETE RGAVVCRVGR ECWEGGGARS
	RPSDDGWPRW
251	GGG*

Further work revealed the following gonoccocal DNA sequence <SEQ ID 789>:

1	ATGTATCGGA GAAAAGGACG GGGCATCAAG CCGTGGATGG
	GTGCCGGCGC
51	GGCGTTTGCC GCCTTGGTCT GGCTGGTTTA CGCGCTCGGC
	GATACTTTGA
101	CTCCGTTTGC GGTTGCGGCG GTGCTGGCGT ATGTGTTGGA
	CCCTTTGGTC
151	GAATGGTTGC AGAAAAAGGG TTTGAACCGT GCATCCGCTT
	CGATGTCTGT
201	GATGGTGTTT TCCTTGATTT TGTTGTTGGC ATTATTGTTG
	ATTATTGTCC
251	CTATGCTGGT CGGGCAGTTC AATAATTTGG CATCTCGCCT
	GCCCCAATTA
301	ATCGGTTTTA TGCAGAACAC GCTGCTGCCG TGGTTGAAAA
	ATACAATCGG
351	CGGATATGTG GAAATCGATC AGGCATCTAT TATTGCGTGG
	TTTCAGGCGC
401	ATACGGGCGA GTTGAGCAAC GCGCTTAAGG CGTGGTTTCC
	CGTTTTGATG
451	AAACAGGGCG GCAATATTGT CAGCAGTATC GGCAACCTGC
	TGCTGCCGCC
501	CTTGCTGCTT TACTATTTCC TGCTGGATTG GCAGCGGTGG
	TCGTGCGGCA
551	TCGCCAAACT GGTTCCGAGG CGTTTTGCCG GTGCTTATAC
	GCGCATTACG
601	GGTAATTTGA ACGAGGTATT GGGCGAATTT TTGCGCGGTC
	AGCTTCTGGT
651	GATGCTGATT ATGGGCTTGG TTTACGGTTT GGGATTGATG
	CTAGTCGGAC
701	TGGATTCGGG ATTTGCCATC GGTATGGTTG CCGGTATTTT
	GGTGTTTGTC
751	CCCTATTTGG GTGCGTTTAC GGGATTGCTG CTTGCCACTG
	TTGCAGCCTT
801	GCTCCAGTTC GGTTCGTGGA ACGGAATCTT GGCTGTTTGG
	GCGGTTTTTG
851	CCGTCGGTCA GTTTCTCGAA AGTTTTTTCA TTACGCCGAA
	AATTGTAGGA
901	GACCGTATCG GCCTGTCGCC GTTTTGGGTT ATCTTTTCGC
	TGATGGCGTT
951	CGGAGAGCTG ATGGGCTTTG TCGGAATGTT GGCCGGATTG
	CCTTTGGCCG
1001	CCGTAACCTT GGTCTTGCTT CGCGAGGGCG CGCAGAAATA
	TTTTGCCGGC
1051	AGTTTTTACC GGGGCAGGTA G

This corresponds to the amino acid sequence <SEQ ID 790; ORF121ng-1>:

1	MYRRKGRGIK PWMGAGAAFA ALVWLVYALG DTLTPFAVAA
	VLAYVLDPLV
51	EWLQKKGLNR ASASMSVMVF SLILLLALLL IIVPMLVGQF
	NNLASRLPQL
101	IGFMQNTLLP WLKNTIGGYV EIDQASIIAW FQAHTGELSN
	ALKAWFPVLM
151	KQGGNIVSSI GNLLLPPLLL YYFLLDWQRW SCGIAKLVPR
	RFAGAYTRIT
201	GNLNEVLGEF LRGQLLVMLI MGLVYGLGLM LVGLDSGFAI
	GMVAGILVFV
251	PYLGAFTGLL LATVAALLQF GSWNGILAVW AVFAVGQFLE
	SFFITPKIVG
301	DRIGLSPFWV IFSLMAFGEL MGFVGMLAGL PLAAVTLVLL
	REGAQKYFAG
351	SFYRGR*

ORF121ng-1 and ORF121-1 show 97.5% identity in 356 aa overlap:

In addition, ORF121ng-1 shows homology to a permease from H. influenzae:

sp|P43969|PERM_HAEIN PUTATIVE PERMEASE PERM HOMOLOG Length = 349
Score = 69.9 bits (168), Expect = 2e−11
Identities = 67/317 (21%), Positives = 120/317 (37%), Gaps = 7/317 (2%)

Query:	26	VYALGDTLTPFAVAAVLAYVLDPLVEWL-QKKGLNRASASMSVMVFSXXXXXXXXXXXVP	84
		+Y  GD + P  +A VL+Y+L+  + +L Q     R  A++ +               VP
Sbjct:	32	IYFFGDLIAPLLIALVLSYLLEIPINFLNQYLKCPRMLATILIFGSFIGLAAVFFLVLVP	91
Query:	85	MLVGQFNNLASRLPQLIGFMQNTLLPWLKNTIGGYVE-IDQASIIAWFQAHTGELSNALK	143
		ML  Q  +L S LP +     N    WL N    Y E ID + + + F +   ++    +
Sbjct:	92	MLWNQTISLLSDLPAMF----NKSNEWLLNLPKNYPELIDYSMVDSIFNSVREKILGFGE	147
Query:	144	AWFPVLMKQGGNIVSSIGNXXXXXXXXXXXXXDWQRWSCGIAKLVPRRFAGAYTRITGNL	203
		+   + +    N+VS                 D      G+++ +P+    A+ R    +
Sbjct:	148	SAVKLSLASIMNLVSLGIYAFLVPLMMFFMLKDKSELLQGVSRFLPKNRNLAFXRWK-EM	206
Query:	204	NEVLGEFLRGQXXXXXXXXXXXXXXXXXXXXDSGFAIGMVAGILVFVPYXXXXXXXXXXX	263
		+ +  ++ G+                    +    +    G+ V VPY
Sbjct:	207	QQQISNYINGKLLEILIVTLITYIIFLIFGLNYPLLLAFAVGLSVLVPYIGAVIVTIPVA	266
Query:	264	XXXXXQFGSWNGILAVWAVFAVGQFLESFFITPKIVGDRIGLSPFWVIFSLMAFGELMGF	323
		QFG       +   FAV Q L+   + P +  + + L P  +I S++ FG L GF
Sbjct:	267	LVALFQFGISPTFWYIIIAFAVSQLLDGNLLVPYLFSEAVNLHPLIIIISVLIFGGLWGF	326
Query:	324	VGMLAGLPLAAVTLVLL	340
		G+   +PLA +   ++
Sbjct:	327	WGVFFAIPLATLVKAVI	343

Based on this analysis, including the presence of a putative leader sequence and transmembrane domains in the two proteins, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 94

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 791>:

1	..ACTGCTTTTT CGGCGGCGCT GCGCTTGAGT CCATCATGAC
	TCGTCATATT
51	TTTGTCCTTT GGGAAACCGT ATCAACAAAC AGCCGCCATC
	TTAACATTTT
101	TTTGCACGTC CTGCCCGCCG CGTTCAAATG CGTACCAGCA
	ATACCGCCGC
151	CTGCGCCTCT ATGCCTTCCA TCCGCCCGAG ATAGCCGAGT
	TTTTCGTTGG
201	TTTTGCCTTT GATGTTGACG CACGAAATGT CTATGCCCAA
	ATCGGCGGCG
251	ATGTTGGCAC GCATTTGCGG AATGTGCGGC GCGAGTGTGG
	GTTTCTGTGC
301	AATCACGGTC GTATCGACAT TGACCGCCTG CCAACCCTGC
	GCCTGAACGC
351	TTTGATACGC CGCACGCAAA AGGACGCGGC TGTCCGCATC
	TTTGAACTCT
401	GCGGCGGTGT CGGGGAAATG GCTGCCGATA TCGCCCAAAC
	CTGCCGCACC
451	GAGCAGCGCG TCGGTAACGG CGTGCAGCAG CGCATCGGCA
	TCGGAGTGTC
501	CGAGCAGCCC TTTTTCAAAT GGGATTTCAA CTCCGCCAAG
	TATCAG..

This corresponds to the amino acid sequence <SEQ ID 792; ORF122>:

1	..TAFSAALRLS PSXLVIFLSF GKPYQQTAAI LTFFCTSCPP
	RSNAYQQYRR
51	LRLYAFHPPE IAEFFVGFAF DVDARNVYAQ IGGDVGTHLR
	NVRRECGFLC
101	NHGRIDIDRL PTLRLNALIR RTQKDAAVRI FELCGGVGEM
	AADIAQTCRT
151	EQRVGNGVQQ RIGIGVSEQP FFKWDFNSAK YQ..

Further work revealed the complete nucleotide sequence <SEQ ID 793>:

1	ATATCGTACT GGGCAAGCAG TTCGCCGGAT TTTTTGGAAG
	TAGATACCGC
51	GCCTTTGATT TTTTTGCCGC TCTTACCCAA GGCTTCGATG
	AAAAAGTTGA
101	TGGTCGAGCC GGTACCGATG CCGATATATT CATTTTCGGG
	TACGAATTCG
151	ACTGCTTTTT CGGCGGCGAT GCGCTTGAGT TCGTCTTGTG
	TCGTCATATT
201	TTTGTCCTTT GGGAAACCGT ATCAACAAAC AGCCGCCATC
	TTAACATTTT
251	TTTGCACGTC CTGCCCGCCG CGTTCAAATG CGTACCAGCA
	ATACCGCCGC
301	CTGCGCCTCT ATGCCTTCCA TCCGCCCGAG ATAGCCGAGT
	TTTTCGTTGG
351	TTTTGCCTTT GATGTTGACG CACGAAATGT CTATGCCCAA
	ATCGGCGGCG
401	ATGTTGGCAC GCATTTGCGG AATGTGCGGC GCGAGTTTGG
	GTTTCTGTGC
451	AATCACGGTC GTATCGACAT TGACCGCCTG CCAACCCTGC
	GCCTGAACGC
501	TTTGATACGC CGCACGCAAA AGGACGCGGC TGTCCGCATC
	TTTGAACTCT
551	GCGGCGGTGT CGGGGAAATG GCTGCCGATA TCGCCCAAAC
	CTGCCGCACC
601	GAGCAGCGCG TCGGTAACGG CGTGCAGCAG CGCATCGGCA
	TCGGAGTGTC
651	CGAGCAGCCC TTTTTCAAAT GGGATTTCAA CTCCGCCAAG
	TATCAGCTTT
701	CTGCCTTCGG TCAGTTGGTG GACATCGTAG CCCTGTCCGA
	TACGGATGTT
751	CGTCATCGTT TGTGTTCCTG A

This corresponds to the amino acid sequence <SEQ ID 794; ORF122-1>:

1	ISYWASSSPD FLEVDTAPLI FLPLLPKASM KKLMVEPVPM
	PIYSFSGTNS
51	TAFSAAMRLS SSCVVIFLSF GKPYQQTAAI LTFFCTSCPP
	RSNAYQQYRR
101	LRLYAFHPPE IAEFFVGFAF DVDARNVYAQ IGGDVGTHLR
	NVRREFGFLC
151	NHGRIDIDRL PTLRLNALIR RTQKDAAVRI FELCGGVGEM
	AADIAQTCRT
201	EQRVGNGVQQ RIGIGVSEQP FFKWDFNSAK YQLSAFGQLV
	DIVALSDTDV
251	RHALCS*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF122 shows 94.0% identity over a 182aa overlap with an ORF (ORF122a) from strain A of N. meningitidis:

The complete length ORF122a nucleotide sequence <SEQ ID 795> is:

1	ATATCATATT GGGCAAGCAG TTCACTGGAT TTTTTGGAAG
	TAGATACCGC
51	GCCTTTGATT TTTTTGCCGC TCTTACCCAA GGCTTCGATG
	AAAAAGTTGA
101	TGGTCGAACC GGTACCGATG CCGATGTATT CGTTTTCGGG
	TACGAATTCG
151	ACTGCNTTTT CGGCGGCGAT GCGCTTGAGT TCGTCTTGTG
	TCGTCATATT
201	TTTGTCCTTT GGGAAACCGT ATCAACAAAC AGCCGCCATC
	TTAACATTTT
251	TTNNNACGTC CTGCCCGCCG CGTTCAAATC CTTACCAGCA
	ATACCGCCGC
301	CTGCGACTCT ATGCCTTCCA TGCGCCCGAG ATAACCGAGT
	TTTTCGTTGG
351	TTTTGCCTTT GANGTTGACG CACGAAATGT CTATGCCCAA
	ATCGGCGGCG
401	ATGTTGGCAC GCATTTGCGG AATATGCGGC GCGAGTTTGG
	GTTTCTGTGC
451	AATCACGGTC GTATCGACAT TGACCGCCTG CCAACCCTGC
	GCCTGAACGC
501	TTTGATACGC CGCACGCAAA AGGACGCGGC TGTCCGCATC
	TTTGAACTCT
551	GCGGCGGTGT CGGGGAAATG GCTGCCGATA TCGCCCAAAC
	CTGCCGCACC
601	GAGCAGCGCG TCGGTAACGG CGTGCAGCAG CGCATCGGCA
	TCGGAGTGTC
651	CGAGCAGCCC TTTTTCAAAT GGGATTTCAA CTCCGCCAAG
	TATCAGCTTT
701	CTGCCTTCGG TCAGTTGGTG GACATCGTAG CCCTGTCCGA
	TACGGATGTT
751	CGTCATCGTT TGTGTTCCTG A

This encodes a protein having amino acid sequence <SEQ ID 796>:

1	ISYWASSSLD FLEVDTAPLI FLPLLPKASM KKLMVEPVPM
	PMYSFSGTNS
51	TAFSAAMRLS SSCVVIFLSF GKPYQQTAAI LTFFXTSCPP
	RSNPYQQYRR
101	LRLYAFHAPE ITEFFVGFAF XVDARNVYAQ IGGDVGTHLR
	NMRREFGFLC
151	NHGRIDIDRL PTLRLNALIR RTQKDAAVRI FELCGGVGEM
	AADIAQTCRT
201	EQRVGNGVQQ RIGIGVSEQP FFKWDFNSAK YQLSAFGQLV
	DIVALSDTDV
251	RHRLCS*

ORF122a and ORF122-1 show 96.9% identity in 256 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF122 shows 89.6% identity over a 182 aa overlap with a predicted ORF (ORF122ng) from N. gonorrhoeae:

The complete length ORF122ng nucleotide sequence <SEQ ID 797> is:

1	ATGTCGTACC GGGCAAGCAG TTCGCCGGAT TTTTTGGAGG
	TTGAAACCGC
51	GCCTTTGATT TTTTTACCGC TTTTGCCCAA GGCTTCGATG
	AAGAAATTGa
101	tgGTCGAACC GgtaCCGATG CCGATGTATT CGTTTTCGGG
	TACGAATTCG
151	ACTGCTTTTT CGGCGGCGAT GCGCttgAgt TCgtcttgcg
	TcgTCATATT
201	TTTAtccttt gGGAAaccct atcaAcaAAc agccgccatC
	TTAACATTTT
251	TTTGCACGtc ctggccgccg cgttcaAATc cgtaccaGca
	ataccgccgc
301	ctgcgcctCT AtgcCTTCCA TCCGCCCGAG ATAGCCGAGT
	TTTTCGTTGG
351	TTTTGCCTTT GATatTGACG CACGAAATAT CGatacCCAa
	atcggcgGCG
401	ATGTTGGCAC GCATTTGCGG AATGTGCGGT GCGAGTTTGG
	GTTTCTGTGC
451	AATCACGGTC GTATCGACAT TGACCACCTG CCAACCCTGC
	GCCTGAACGC
501	TTTGATACGC CGCACGCAAA AGGACGCGGC TGTCCGCATC
	TTTGAACTCT
551	GCGGCGGTGT CGGGAAAATG GCTGCCGATG TCGCCCAAAC
	CTGCCGCACC
601	GAGCAGCgcg tcggtaaCGG CGTGCAGCAG cgcgTcgGCA
	TCCGAATGCC
651	CGAGCAGCCC TTTTTCAAAT GGGATTTCAA CTCCGCCAAG
	TATCAGCTTT
701	CTGCCTTCGG TCAATTGGTG GACATCGTAG CCCTGTCCGA
	TACGGATATT
751	CGTCATCGTT TGTGTTCCTG A

This encodes a protein having amino acid sequence <SEQ ID 798>:

1	MSYRASSSPD FLEVETAPLI FLPLLPKASM KKLMVEPVPM
	PMYSFSGTNS
51	TAFSAAMRLS SSCVVIFLSF GKPYQQTAAI LTFFCTSWPP
	RSNPYQQYRR
101	LRLYAFHPPE IAEFFVGFAF DIDARNIDTQ IGGDVGTHLR
	NVRCEFGFLC
151	NHGRIDIDHL PTLRLNALIR RTQKDAAVRI FELCGGVGKM
	AADVAQTCRT
201	EQRVGNGVQQ RVGIRMPEQP FFKWDFNSAK YQLSAFGQLV
	DIVALSDTDI
251	RHRLCS*

ORF122ng and ORF122-1 show 92.6% identity in 256 aa overlap:

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 95

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 799>:

1	..GCCGGCGCGA GTGCGAACAA CATTTCCGCG CGTTTTGCGG
	AAACACCCGT
51	CGCTGTCAGC GTTACCCTGA TCGGCACGGT ACTTGCCGTC
	ATGCTGCCCG
101	TTACCGAATA TGAAAACTTC CTGCTGCTTA TCGGCTCGGT
	ATTTGCGCCG
151	ATGGGGCGGA TTTTGATTGC CGACTTTTTC GTCTTGAAAC
	GGCGTGA

This corresponds to the amino acid sequence <SEQ ID 800; ORF125>:

1	..AGASANNISA RFAETPVAVS VTLIGTVLAV MLPVTEYENF
	LLLIGSVFAP
51	MGGFDCRLFR LETA*

Further work revealed the complete nucleotide sequence <SEQ ID 801>:

1	ATGTCGGGCA ATGCCTCCTC TCCTTCATCT TCCTCCGCCA
	TCGGGCTGAT
51	TTGGTTCGGC GCGGCGGTAT CGATTGCCGA AATCAGCACG
	GGTACGCTGC
101	TTGCGCCTTT GGGCTGGCAG CGCGGTCTGG CGGCTCTACT
	TTTGGGTCAT
151	GCCGTCGGCG GCGCGCTGTT TTTTGCGGCG GCGTATATCG
	GCGCACTGAC
201	CGGACGCAGC TCGATGGAAA GCGTGCGCCT GTCGTTCGGC
	AAACGCGGTT
251	CAGTGCTGTT TTCCGTGGCG AATATGCTGC AACTGGCCGG
	CTGGACGGCG
301	GTGATGATTT ACGCCGGCGC AACGGTCAGC TCCGCTTTGG
	GCAAAGTGTT
351	GTGGGACGGC GAATCTTTTG TCTGGTGGGC ATTGGCAAAC
	GGCGCGCTGA
401	TTGTGCTGTG GCTGGTTTTC GGCGCACGCA AAACAGGCGG
	GCTGAAAACC
451	GTTTCGATGC TGCTGATGCT GTTGGCGGTT CTGTGGCTGA
	GTGCCGAAGT
501	CTTTTCCACG GCAGGCAGCA CCGCCGCACA GGTTTCAGAC
	GGCATGAGTT
551	TCGGAACGGC AGTCGAGCTG TCCGCCGTGA TGCCGCTTTC
	CTGGCTGCCG
601	CTTGCCGCCG ACTACACGCG CCACGCGCGC CGCCCGTTTG
	CGGCAACCCT
651	GACGGCAACG CTCGCCTACA CGCTGACCGG CTGCTGGATG
	TATGCCTTGG
701	GTTTGGCAGC GGCGTTGTTC ACCGGAGAAA CCGACGTGGC
	AAAAATCCTG
751	CTGGGCGCAG GTTTGGGTGC GGCAGGCATT TTGGCGGTCG
	TCCTCTCCAC
801	CGTTACCACA ACGTTTCTCG ATGCCTATTC CGCCGGCGCG
	AGTGCGAACA
851	ACATTTCCGC GCGTTTTGCG GAAACACCCG TCGCTGTCGG
	CGTTACCCTG
901	ATCGGCACGG TACTTGCCGT CATGCTGCCC GTTACCGAAT
	ATGAAAACTT
951	CCTGCTGCTT ATCGGCTCGG TATTTGCGCC GATGGCGGCG
	GTTTTGATTG
1001	CCGACTTTTT CGTCTTGAAA CGGCGTGAGG AGATTGAAGG
	CTTTGACTTT
1051	GCCGGACTGG TTCTGTGGCT TGCGGGCTTC ATCCTCTACC
	GCTTCCTGCT
1101	CTCGTCCGGC TGGGAAAGCA GCATCGGTCT GACCGCCCCC
	GTAATGTCTG
1151	CCGTTGCCAT TGCCACCGTA TCGGTACGCC TTTTCTTTAA
	AAAAACCCAA
1201	TCTTTACAAA GGAACCCGTC ATGA

This corresponds to the amino acid sequence <SEQ ID 802; ORF125-1>:

1	MSGNASSPSS SSAIGLIWFG AAVSIAEIST GTLLAPLGWQ
	RGLAALLLGH
51	AVGGALFFAA AYIGALTGRS SMESVRLSFG KRGSVLFSVA
	NMLQLAGWTA
101	VMIYAGATVS SALGKVLWDG ESFVWWALAN GALIVLWLVF
	GARKTGGLKT
151	VSMLLMLLAV LWLSAEVFST AGSTAAQVSD GMSFGTAVEL
	SAVMPLSWLP
201	LAADYTRHAR RPFAATLTAT LAYTLTGCWM YALGLAAALF
	TGETDVAKIL
251	LGAGLGAAGI LAVVLSTVTT TFLDAYSAGA SANNISARFA
	ETPVAVGVTL
301	IGTVLAVMLP VTEYENFLLL IGSVFAPMAA VLIADFFVLK
	RREEIEGFDF
351	AGLVLWLAGF ILYRFLLSSG WESSIGLTAP VMSAVAIATV
	SVRLFFKKTQ
401	SLQRNPS*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF125 shows 76.5% identity over a 51 as overlap with an ORF (ORF125a) from strain A of N. meningitidis:

The ORF125a partial nucleotide sequence <SEQ ID 803> is:

1	ATGTCGGGCA ATGCCTCCTC TCNTTCATCT TCCGCCGCCA
	TCGGGCTGAT
51	TTGGTTCGGC GCGGCGGTAT CGATTGCCGA AATCAGCACG
	GGTACACTGC
101	TTGCGCCTTT GGGCTGGCAG CGCGGTCTGG CNGCTCTGCT
	TTTGGGTCAT
151	GCCGTCGGCG GCGCGCTGTT TTTTGCGGCG GCGTATATCG
	GCGCACTGAC
201	CGGACNCANC TCGATGGAAA GCGTGCGCCT GTCGTTCGGC
	AAACGCGGTT
251	CAGTGCTGTT TTCCGTGGCG AATATGCTGC AACTGGCCGG
	CTGGACGGCG
301	GTGATGATTT ACGCCGGCGC AACGGTCAGC TCCGCTTTGG
	GCAAAGTGTT
351	GTGGGACGGC GAATCTTTTG TCTGGTGGGC ATTGGCAAAC
	GGCGCGCTGA
401	TTGTGCTGTG GCTGGTTTTC GGCGCACGCA AAACAGGCGG
	GCTGAAAACC
451	GTTTCGATGC TGCTGATGCT GTTGGCGGTT CTGTGGCTGA
	GTGCCGAANT
501	NTTTTCCACG GCAGGCAGCA CCGCCGCANN GGTNNCAGAC
	GGCATGAGTT
551	TCGGAACGGC AGTCGAGCTG TCCGCCGTNA TGCCGCTTTC
	TTGGCTGCCG
601	CTGGCCGCCG ACTACACGCG CCACGCGCGC CGCCCGTTTG
	CGGCAACCCT
651	GACGGCAACG CTCGCCTACA CGCTGACCGG CTGCTGGATG
	TATGCCTTGG
701	GTTTGGCAGC GGCGTTGTTC ACCGGAGAAA CCGACGTGGC
	AAAAATCCTG
751	CTGGGCGCAG GTTTGGGTGC GGCAGGCATT TTGGCGGTCG
	TCCTGTCGAC
801	CGTTACCACC ACTTTTCTCG ATGCNTACTC CGCCGGCGTA
	AGTGCCAACA
851	ATATTTCCGC CAAACTTTCG GAAATACCNA TCGCCGTTGC
	CGTCGCCGTT
901	GTCGGCACAC TGCTTGCCGT CCTCCTGCCC GTTACCGAAT
	ATGAAAACTT
951	CCTGCTGCTT ATCGGCTCGG TATTTGCGCC GATGGCGGCG
	GTTTTGATTG
1001	CCGACTTTTT CGTCTTGAAA CGGCGTGAGG AGATTGAAGG
	C..

This encodes a protein having the partial amino acid sequence <SEQ ID 804>:

1	MSGNASSXSS SAAIGLIWFG AAVSIAEIST GTLLAPLGWQ
	RGLAALLLGH
51	AVGGALFFAA AYIGALTGXX SMESVRLSFG KRGSVLFSVA
	NMLQLAGWTA
101	VMIYAGATVS SALGKVLWDG ESFVWWALAN GALIVLWLVF
	GARKTGGLKT
151	VSMLLMLLAV LWLSAEXFST AGSTAAXVXD GMSFGTAVEL
	SAVMPLSWLP
201	LAADYTRHAR RPFAATLTAT LAYTLTGCWM YALGLAAALF
	TGETDVAKIL
251	LGAGLGAAGI LAVVLSTVTT TFLDAYSAGV SANNISAKLS
	EIPIAVAVAV
301	VGTLLAVLLP VTEYENFLLL IGSVFAPMAA VLIADFFVLK
	RREEIEG..

ORF125a and ORF125-1 show 94.5% identity in 347 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF125 shows 86.2% identity over a 65aa overlap with a predicted ORF (ORF125ng) from N. gonorrhoeae:

An ORF125ng nucleotide sequence <SEQ ID 805> was predicted to encode a protein having amino acid sequence <SEQ ID 806>:

1	MSGNASSPSS SAAIGLVWFG AAVSIAEIST GTLLAPLGWQ
	RGLAALLLGH
51	AVGGALFFAA AYIGALTGRS SMESVRLSFG KCGSVLFSVA
	NMLQLAGWTA
101	VMIYVGATVS SALGKVLWDG ESFVWWALAN GALIVLWLVF
	GARRTGGLKT
151	VSMLLMLLAV LWLSVEVFAS SGTNAAPAVS DGMTFGTAVE
	LSAVMPLSWL
201	PLAADYTRQA RRPFAATLTA TLAYTLTGCW MYALGLAAAL
	FTGETDVAKI
251	LLGAGLGITG ILAVVLSTVT TTFLDTYSAG ASANNISARF
	AEIPVAVGVT
301	LIRTVLAVML PVTEYKNFLL LIRSVFGPMA GGFDCRLFCL
	KTA*

Further work revealed the following gonococcal DNA sequence <SEQ ID 807>:

1	ATGTCGGGCA ATGCCTCCTC TCCTTCATCT TCCGCCGCCA
	TCGGGCTGGT
51	TTGGTTCGGC GCGGCGGTAT CGATTGCCGA AATCAGCACG
	GGTACGCTGC
101	TCGCCCCCTT GGGCTGGCAG CGCGGTCTGG CGGCCCTGCT
	TTTGGGTCAT
151	GCCGTCGGCG GCGCGCTGTT TTTTGCGGCG GCGTATATCG
	GCGCACTGAC
201	CGGACGCAGC TCGATGGAAA GTGTGCGCCT GTCGTTCGGC
	AAATGCGGTT
251	CAGTGCTGTT TTCCGTGGCG AATATGCTGC AACTGGCCGG
	CTGGACGGCG
301	GTGATGATTT ACGTCGGCGC AACGGTCAGC TCCGCTTTGG
	GCAAAGTGTT
351	GTGGGACGGC GAATCCTTTG TCTGGTGGGC ATTGGCAAAC
	GGCGCACTGA
401	TCGTGCTGTG GCTGGTTTTC GGCGCACGCA GAACGGGCGG
	GCTGAAAACC
451	GTTTCGATGC TGCTGATGCT GCTTGCCGTG TTGTGGTTGA
	GCGTCGAAGT
501	GTTCGCTTCG TCCGGCACAA ACGCCGCGCC CGCCGTTTCA
	GACGGCATGA
551	CCTTCGGAAC GGCAGTCGAA CTGTCCGCCG TCATGCCGCT
	TTCCTGGCTG
601	CCGCTGGCCG CCGACTACAC GCGCCAAGCA CGCCGCCCGT
	TTGCGGCAAC
651	CCTGACGGCA ACGCTCGCCT ATACGCTGAC GGGCTGCTGG
	ATGTATGCCT
701	TGGGTTTGGC GGCGGCTCTG TTTACCGGAG AAACCGACGT
	GGCGAAAATC
751	CTGTTGGGCG CGGGCTTGGG CATAACGGGC ATTCTGGCAG
	TCGTCCTCTC
801	CACCGTTACC ACAACGTTTC TCGATACCTA TTCCGCCGGC
	GCGAGTGCGA
851	ACAACATTTC CGCGCGTTTT GCGGAAATAC CCGTCGCTGT
	CGGCGTTACC
901	CTGATCGGCA CGGTGCTTGC CGTCATGCTG CCCGTTACCG
	AATATAAAAA
951	CTTCCTGCTG CTTATCGGCT CGGTATTTGC GCCGATGGCG
	GCGGTTTTGA
1001	TTGCCGACTT TTTCGTCTTA AAACGGCGTG AGGAGATTGA
	AGGCTTTGAC
1051	TTTGCCGGAC TGGTTCTGTG GCTGGCAGGC TTCATCCTCT
	ACCGCTTCCT
1101	GCTCTCGTCC GGTTGGGAAA GCAGCATCGG TCTGACCGCC
	CCCGTAATGT
1151	CTGCCGTTGC CATTGCCACC GTATCGGTAC GCCTTTTCTT
	TAAAAAAACC
1201	CAATCTTTAC AAAGGAACCC GTCATGA

This corresponds to the amino acid sequence <SEQ ID 808; ORF125ng-1>:

1	MSGNASSPSS SAAIGLVWFG AAVSIAEIST GTLLAPLGWQ
	RGLAALLLGH
51	AVGGALFFAA AYIGALTGRS SMESVRLSFG KCGSVLFSVA
	NMLQLAGWTA
101	VMIYVGATVS SALGKVLWDG ESFVWWALAN GALIVLWLVF
	GARRTGGLKT
151	VSMLLMLLAV LWLSVEVFAS SGTNAAPAVS DGMTFGTAVE
	LSAVMPLSWL
201	PLAADYTRQA RRPFAATLTA TLAYTLTGCW MYALGLAAAL
	FTGETDVAKI
251	LLGAGLGITG ILAVVLSTVT TTFLDTYSAG ASANNISARF
	AEIPVAVGVT
301	LIGTVLAVML PVTEYKNFLL LIGSVFAPMA AVLIADFFVL
	KRREEIEGFD
351	FAGLVLWLAG FILYRFLLSS GWESSIGLTA PVMSAVAIAT
	VSVRLFFKKT
401	QSLQRNPS*

ORF125ng-1 and ORF125-1 show 95.1% identity in 408 aa overlap:

Based on this analysis, including the presence of putative leader sequence and transmembrane domains in the gonococcal protein, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 96

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 809>:

1	ATGACCCGTA TCGCCATCCT CGGCGGCGGC CTCTCGGGAA
	GGCTGACCGC
51	GTTGCAGCTT GCAGAACAAG GTTATCAGAT TGCACTTTTC
	GATAAAAGCT
101	GCCGCCGGGG CGAACACGCC GCCGCCTATG TAGCCGCCGC
	CATGCTCGCG
151	CCTGCAGCGG A.ACGGTCGA AGCCACGCCC GAAGTGGTCA
	GGCTGGGCAG
201	GCAGAGCATC CCGCTTTGGC GCGGCATCCG ATGCCGTCTG
	AACACGCACA
251	CGATGATGCA GGAAAACGGC AGCCTGATTG TATGGCACGG
	GCAGGACAAG
301	CCATTATCCA GCGAGTTCGT CCGCCATCTC AAACGCGGCG
	GCGT.ACGGA
351	TGACGAAATC GTCCGTTGGC GCGCCGACGA CATCGCCGAA
	CGCGAACCGC
401	AACTCGGCGG ACGTTTTTAA GACGGCATCT ACCTGCCGAC
	CGAAGC.CAG
451	CTCGACGGGC GGCAATTATA GTCTGCACTT GCCGACGCTT
	TGGACGAACT
501	GAACGTCCCC TGCCATTGGG AACACGAATG CGTCCCCGAA
	GCCTGCAAG..

This corresponds to the amino acid sequence <SEQ ID 810; ORF126>:

1	MTRIAILGGG LSGRLTALQL AEQGYQIALF DKSCRRGEHA
	AAYVAAAMLA
51	PAAXTVEATP EVVRLGRQSI PLWRGIRCRL NTHTMMQENG
	SLIVWHGQDK
101	PLSSEFVRHL KRGGXTDDEI VRWRADDIAE REPQLGGRFX
	DGIYLPTEXQ
151	LDGRQLXSAL ADALDELNVP CHWEHECVPE ACK...

Further work revealed the complete nucleotide sequence <SEQ ID 811>:

1	ATGACCCGTA TCGCCATCCT CGGCGGCGGC CTCTCGGGAA
	GGCTGACCGC
51	GTTGCAGCTT GCAGAACAAG GTTATCAGAT TGCACTTTTC
	GATAAAGGCT
101	GCCGCCGGGG CGAACACGCC GCCGCCTATG TTGCCGCCGC
	CATGCTCGCG
151	CCTGCGGCGG AAGCGGTCGA AGCCACGCCC GAAGTGGTCA
	GGCTGGGCAG
201	GCAGAGCATC CCGCTTTGGC GCGGCATCCG ATGCCGTCTG
	AACACGCACA
251	CGATGATGCA GGAAAACGGC AGCCTGATTG TGTGGCACGG
	GCAGGACAAG
301	CCATTATCCA GCGAGTTCGT CCGCCATCTC AAACGCGGCG
	GCGTAGCGGA
351	TGACGAAATC GTCCGTTGGC GCGCCGACGA CATCGCCGAA
	CGCGAACCGC
401	AACTCGGCGG ACGTTTTTCA GACGGCATCT ACCTGCCGAC
	CGAAGGCCAG
451	CTCGACGGGC GGCAAATATT GTCTGCACTT GCCGACGCTT
	TGGACGAACT
501	GAACGTCCCC TGCCATTGGG AACACGAATG CGTCCCCGAA
	GGCCTGCAAG
551	CCCAATACGA CTGGCTGATC GACTGCCGCG GCTACGGCGC
	AAAAACCGCG
601	TGGAACCAAT CCCCCGAGCA CACCAGCACC CTGCGCGGCA
	TACGCGGCGA
651	AGTGGCGCGG GTTTACACAC CCGAAATCAC GCTCAACCGC
	CCCGTGCGTC
701	TGCTCCATCC GCGTTATCCG CTCTACATCG CCCCGAAAGA
	AAACCACGTC
751	TTCGTCATCG GCGCGACCCA AATCGAAAGC GAAAGCCAAG
	CCCCCGCCAG
801	CGTGCGTTCA GGGTTGGAAC TCTTGTCCGC ACTCTATGCC
	ATCCACCCCG
851	CCTTCGGCGA AGCCGACATC CTCGAAATCG CCACCGGCCT
	GCGCCCCACG
901	CTCAACCACC ACAACCCCGA AATCCGTTAC AACCGCGCCC
	GACGCCTGAT
951	TGAAATCAAC GGCCTTTTCC GCCACGGTTT CATGATCTCC
	CCCGCCGTAA
1001	CCGCCGCCGC CGCCAGATTG GCAGTGGCAC TGTTTGACGG
	AAAAGACGCG
1051	CCCGAACGCG ATAAAGAAAG CGGTTTGGCG TATATCCGAA
	GACAAGATTA
1101	A

This corresponds to the amino acid sequence <SEQ ID 812; ORF126-1>:

1	MTRIAILGGG LSGRLTALQL AEQGYQIALF DKGCRRGEHA
	AAYVAAAMLA
51	PAAEAVEATP EVVRLGRQSI PLWRGIRCRL NTHTMMQENG
	SLIVWHGQDK
101	PLSSEFVRHL KRGGVADDEI VRWRADDIAE REPQLGGRFS
	DGIYLPTEGQ
151	LDGRQILSAL ADALDELNVP CHWEHECVPE GLQAQYDWLI
	DCRGYGAKTA
201	WNQSPEHTST LRGIRGEVAR VYTPEITLNR PVRLLHPRYP
	LYIAPKENHV
251	FVIGATQIES ESQAPASVRS GLELLSALYA IHPAFGEADI
	LEIATGLRPT
301	LNHHNPEIRY NRARRLIEIN GLFRHGFMIS PAVTAAAARL
	AVALFDGKDA
351	PERDKESGLA YIRRQD*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF126 shows 90.0% identity over a 180aa overlap with an ORF (ORF126a) from strain A of N. meningitidis:

The complete length ORF126a nucleotide sequence <SEQ ID 813> is:

1	ATGACCCGTA TCGCCATCCT CGGCGGCGGC CTCTCNGGAA
	GGCTGACCGC
51	ACTGCAGCTT GCAGAACAAG GTTATCAGAT TGCACTTTTC
	GATAAAGGCT
101	GCCGCCGGGG CGAACACGCC GCCGCCTATG TTGCCGCCGC
	CATGCTCGCG
151	CCTGCGGCGG AAGCGGTCGA AGCCACGCCT GAAGTGGTCA
	GGCTGGGCAG
201	GCAGANCATC CCGCTTTGGC GCGGCATCCG ATGCCATCTG
	AAAACGCCTG
251	CCATGATGCA NGAAAACGGC AGCCTGATTG TGTGGCACGG
	GCAGGACAAA
301	CCTTTATCCA ACGAGTTCGT CCGCCATCTC AAACGCGGCG
	GCGTAGCGGA
351	TGACNAAATC GTCCGTTGGC GCGCCGACGA CATCGCCGAA
	CGCGAACCGC
401	AACTCGGCGG ACGTTTTTCA GACGGCATCT ACCTGCCGAC
	CGAAGGCCAG
451	CTCGACGGGC GGCAAATATT GTCTGCACTT GCCGACGCTT
	TGGACGAACT
501	GAACGTCCCC TGCCATTGGG AACACGAATG TGCCCCCGAA
	GACTTGCAAG
551	CCCAATACGA CTGGCTGATC GACTGCCGCG GCTACGGCGC
	AAAAACCGCG
601	TGGAACCAAT CCCCCGANNA NACCAGCACC CTGCGCGGCA
	TACGCGGCGA
651	AGTGGCGCGG GTTTACACAC CCGAAATCAC GCTCAACCGC
	CCCGTGCGCC
701	TGCTACACCC GCGCTATCCG CTNTACATCG CCCCGAAAGA
	AAACCNCGTC
751	TTCGTCATCG GCGCGACCCA AATCGAAAGC GAAAGCCAAG
	CACCTGCCAG
801	CGTGCGTTCC GGGCTGGAAC TCTTATCCGC ACTCTATGCC
	GTCCACCCCG
851	CCTTCGGCGA AGCCGACATC CTCGAAATCG CCACCGGCCT
	GCGCCCCACG
901	CTCAATCACC ACAACCCCGA AATCCGTTAC AACCGCGCCC
	GACGCCTGAT
951	TGAAATCAAC GGCCTTTTCC GCCACGGTTT CATGATCTCC
	CCCGCCGTAA
1001	CCGCCGCCGC CGTCAGATTG GCAGTGGCAC TGTTTGACGG
	AAAAGANGCG
1051	CCCGAACGCG ATGAAGAAAG CGGTTTGGCG TATATCCGAA
	GACAAGATTA
1101	A

This encodes a protein having amino acid sequence <SEQ ID 814>:

1	MTRIAILGGG LSGRLTALQL AEQGYQIALF DKGCRRGEHA
	AAYVAAAMLA
51	PAAEAVEATP EVVRLGRQXI PLWRGIRCHL KTPAMMXENG
	SLIVWHGQDK
101	PLSNEFVRHL KRGGVADDXI VRWRADDIAE REPQLGGRFS
	DGIYLPTEGQ
151	LDGRQILSAL ADALDELNVP CHWEHECAPE DLQAQYDWLI
	DCRGYGAKTA
201	WNQSPXXTST LRGIRGEVAR VYTPEITLNR PVRLLHPRYP
	LYIAPKENXV
251	FVIGATQIES ESQAPASVRS GLELLSALYA VHPAFGEADI
	LEIATGLRPT
301	LNHHNPEIRY NRARRLIEIN GLFRHGFMIS PAVTAAAVRL
	AVALFDGKXA
351	PERDEESGLA YIRRQD*

ORF126a and ORF126-1 show 95.4% identity in 366 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF126 shows 90% identity over a 180 aa overlap with a predicted ORF (ORF126ng) from N. gonorrhoeae:

An ORF126ng nucleotide sequence <SEQ ID 815> was predicted to encode a protein having amino acid sequence <SEQ ID 816>:

1	MTRIAVLGGG LSGRLTALQL AEQGYQIELF DKGTRQGEHA
	AAYVAAAMLA
51	PAAEAVEATP EVIRLGRQSI PLWRGIRCRL NTLTMMQENG
	SLIVWHGQDK
101	PLSSEFVRHL KRGGVADDEI VRWRADEIAE REPQLGGRFS
	DGIYLPTEGQ
151	LDGRQILSAL ADALDELNVP CHWEHECAPQ DLQAQYDWVI
	DCRGYGAKTA
201	WNQSPEHTST LRGIRGEVRG FTRPKSRSTA PCACCTRAIR
	STSPRKKTTS
251	SSSARPKSKA KAKPPPAYVP GWNSYPRSMP STPPSAKPTS
	SKWRPGLRPT
301	LNHHNPEIRY SRERRLIEIN GLFRHGFMIS PAVTAAAVRL
	AVALFDGKDA
351	PERDEESGLA YIGRQD*

Further work revealed the following gonococcal DNA sequence <SEQ ID 817>:

1	ATGACCCGTA TCGCCGTCCT CGGAGGCGGC CTTTCCGGAA
	GGCTGACCGC
51	ATTGCAGCTT GCAGAACAAG GTTATCAGAT TGAACTTTTC
	GACAAGGGCA
101	CCCGCCAAGG CGAACACGCC GCCGCCTATG TTGCCGCCGC
	GATGCTCGCG
151	CCTGCGGCGG AAGCGGTCGA GGCAACGCCC GAAGTCATCA
	GGCTGGGCAG
201	GCAGAGCATT CCGCTTTGGC GCGGCATCCG ATGCCGTCTG
	AACACGCTCA
251	CGATGATGCA GGAAAACGGC AGCCTGATTG TGTGGCACGG
	GCAGGACAAG
301	CCATTATCCA GCGAGTTCGT CCGCCATCTC AAACGCGGCG
	GCGTAGCGGA
351	TGACGAAATC GTCCGTTGGC GCGCCGATGA AATCGCCGAA
	CGCGAACCGC
401	AACTCGGCGG ACGTTTTTCA GACGGCATCT ACCTGCCGAC
	CGAAGGCCAG
451	CTCGACGGGC GGCAAATATT GTCTGCACTT GCCGACGCTT
	TGGACGAACT
501	GAACGTCCCT TGCCATTGGG AACACGAATG CGCCCCCCAA
	GACCTGCAAG
551	CCCAATACGA CTGGGTAATC GACTGCCGGG GCTACGGCGC
	GAAAACCGCG
601	TGGAACCAAT CCCCCGAGCA CACCAGCACC TTGCGCGGCA
	TACGCGGCGA
651	AGTGGCGCGG GTTTACACGC CCGAAATCAC GCTCAACCGC
	CCCGTGCGCC
701	TGCTGCACCC GCGCTATCCG CTCTACATCG CCCCGAAAGA
	AAACCACGTC
751	TTCGTCATCG GCGCGACCCA AATCGAAAGC GAAAGCCAAG
	CCCCCGCCAG
801	CGTACGTTCC GGGCTGGAAC TCTTATCCGC GCTCTATGCC
	GTCCACCCCG
851	CCTTCGGCGA AGCCGACATC CTCGAAATCG CCGCCGGCCT
	GCGCCCCACG
901	CTCAACCACC ACAACCCCGA AATCCGCTAC AGCCGCGAAC
	GCCGCCTCAT
951	CGAAATCAAC GGCCTTTTCC GGCACGGCTT TATGATTTCC
	CCCGCCGTAA
1001	CCGCCGCCGC CGTCAGATTG GCAGTGGCAC TGTTTGACGG
	AAAAGACGCG
1051	CCCGAACGTG ATGAAGAAAG CGGTTTGGCG TATATCGGAA
	GACAAGATTA
1101	A

This corresponds to the amino acid sequence <SEQ ID 818; ORF126ng-1>:

1	MTRIAVLGGG LSGRLTALQL AEQGYQIELF DKGTRQGEHA
	AAYVAAAMLA
51	PAAEAVEATP EVIRLGRQSI PLWRGIRCRL NTLTMMQENG
	SLIVWHGQDK
101	PLSSEFVRHL KRGGVADDEI VRWRADEIAE REPQLGGRFS
	DGIYLPTEGQ
151	LDGRQILSAL ADALDELNVP CHWEHECAPQ DLQAQYDWVI
	DCRGYGAKTA
201	WNQSPEHTST LRGIRGEVAR VYTPEITLNR PVRLLHPRYP
	LYIAPKENHV
251	FVIGATQIES ESQAPASVRS GLELLSALYA VHPAFGEADI
	LEIAAGLRPT
301	LNHHNPEIRY SRERRLIEIN GLFRHGFMIS PAVTAAAVRL
	AVALFDGKDA
351	PERDEESGLA YIGRQD*

ORF126ng-1 and ORF126-1 show 95.1% identity in 366 aa overlap:

Furthermore, ORF126ng-1 shows homology to a putative Rhizobium oxidase flavoprotein:

gi|2627327 (AF004408) putative amino acid oxidase
flavoprotein [Rhizobium etli]
Length = 327
Score = 169 bits (423), Expect = 3e−41
Identities = 112/329 (34%), Positives = 163/329 (49%), Gaps = 25/329 (7%)

Query:	3	RIAVLGGGLSGRLTALQLAEQGYQIELFDKGTRQGEHXXXXXXXXXXXXXXXXXXXXXXX	62
		RI V G G++G   A QL   G+++ L ++    G
Sbjct:	2	RILVNGAGVAGLTVAWQLYRHGFRVTLAERAGTVGA-GASGFAGGMLAPWCERESAEEPV	60
Query:	63	IRLGRQSIPLWRGIRCRLNTLTMMQENGSLIVWHGQDKPLSSEFVRHLKRGGVADDEIVR	122
		+ LGR +   W            +   G+L+V  G+D      F R    G    DE+
Sbjct:	61	LTLGRLAADWWEAA-----LPGHVHRRGTLVVAGGRDTGELDRFSRRTS-GWEWLDEVA-	113
Query:	123	WRADEIAEREPQLGGRFSDGIYLPTEGQLDGRQILSALADALDELNVPCHWEHECAPQDL	182
		IA  EP L GRF   ++   E  LD RQ L+ALA  L++  +           +
Sbjct:	114	-----IAALEPDLAGRFRRALFFRQEAHLDPRQALAALAAGLEDARMRLTLG---VVGES	165
Query:	183	QAQYDWVIDCRGYGAKTAWNQSPEHTSTLRGIRGEVARVYTPEITLNRPVRLLHPRYPLY	242
		+D V+DC G                LRG+RGE+  V T E++L+RPVRLLHPR+P+Y
Sbjct:	166	DVDHDRVVDCTGAA-------QIGRLPGLRGVRGEMLCVETTEVSLSRPVRLLHPRHPIY	218
Query:	243	IAPKENHVFVIGATQIESESQAPASVRSGLELLSALYAVHPAFGEADILEIAAGLRPTLN	302
		I P++ + F++GAT IES+   P + RS +ELL+A YA+HPAFGEA + E  AG+RP
Sbjct:	219	IVPRDKNRFMVGATMIESDDGGPITARSLMELLNAAYAMHPAFGEARVTETGAGVRPAYP	278
Query:	303	HHNPEIRYSRERRLIEINGLFRHGFMISP	331
		+ P  R ++E R + +NGL+RHGF+++P
Sbjct:	279	DNLP--RVTQEGRTLHVNGLYRHGFLLAP	305

This analysis suggests that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 97

The following DNA sequence, believed to be complete, was identified in N. meningitidis <SEQ ID 819>:

1	ATGACTGATA ATCGGGGGTT TACGCTGGTT GAATTAATAT
	CAGTGGTCTT
51	GATATTGTCT GTACTTGCTT TAATTGTTTA TCCGAGCTAT
	CGCAATTATG
101	TTGAGAAAGC AAAGATAAAT GCAGTGCGGG CAGCCTTGTT
	AGAAAATGCA
151	CATTTTATGG AAAAGTTTTA TCTGCAGAAT GGGAGGTTTA
	AACAAACATC
201	TACCAAGTGG CCAAGTTTGC CGATTAAAGA GGCAGAAGGC
	TTTTGTATCC
251	GTTTGAATGG AATCGtCGCG CGGG..GCTT TAGACAGTAA
	ATTCATGTTG
301	AAGGCGGTAG CCATAGATAA AGATAAAAAT CCTTTTATTA
	TTAAGATGAA
351	TGAAAATCTA GTAACCTTTA aTTTGCAAGA AGTCCGCCAG
	TTCGTGTAGT
401	GACGGGCTGG ATTATTTTAA AGGAAATGAT AAGGACTGCA
	AGTTACTTAA
451	GTAG

This corresponds to the amino acid sequence <SEQ ID 820; ORF127>:

1	MTDNRGFTLV ELISVVLILS VLALIVYPSY RNYVEKAKIN
	AVRAALLENA
51	HFMEKFYLQN GRFKQTSTKW PSLPIKEAEG FCIRLNGIVA
	RXALDSKFML
101	KAVAIDKDKN PFIIKMNENL VTFICKKSAS SCSDGLDYFK
	GNDKDCKLLK
151	*

Further work revealed the following DNA sequence <SEQ ID 821>:

1	ATGACTGATA ATCGGGGGTT TACGCTGGTT GAATTAATAT
	CAGTGGTCTT
51	GATATTGTCT GTACTTGCTT TAATTGTTTA TCCGAGCTAT
	CGCAATTATG
101	TTGAGAAAGC AAAGATAAAT GCAGTGCGGG CAGCCTTGTT
	AGAAAATGCA
151	CATTTTATGG AAAAGTTTTA TCTGCAGAAT GGGAGGTTTA
	AACAAACATC
201	TACCAAGTGG CCAAGTTTGC CGATTAAAGA GGCAGAAGGC
	TTTTGTATCC
251	GTTTGAATGG AATCGCGCGC GGGGCTTTAG ACAGTAAATT
	CATGTTGAAG
301	GCGGTAGCCA TAGATAAAGA TAAAAATCCT TTTATTATTA
	AGATGAATGA
351	AAATCTAGTA ACCTTTATTT GCAAGAAGTC CGCCAGTTCG
	TGTAGTGACG
401	GGCTGGATTA TTTTAAAGGA AATGATAAGG ACTGCAAGTT
	ACTTAAGTAG

This corresponds to the amino acid sequence <SEQ ID 822; ORF127-1>:

1	MTDNRGFTLV ELISVVLILS VLALIVYPSY RNYVEKAKIN
	AVRAALLENA
51	HFMEKFYLQN GRFKQTSTKW PSLPIKEAEG FCIRLNGIAR
	GALDSKFMLK
101	AVAIDKDKNP FIIKMNENLV TFICKKSASS CSDGLDYFKG
	NDKDCKLLK*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF127 shows 98.0% identity over a 150aa overlap with an ORF (ORF127a) from strain A of N. meningitidis:

The complete length ORF127a nucleotide sequence <SEQ ID 823> is:

1	ATGACTGATA ATCGGGGGTT TACGCTGGTT GAATTAATAT
	CAGTGGTCTT
51	GATATTGTCT GTACTTGCTT TAATTGTTTA TCCGAGCTAT
	CGCAATTATG
101	TTGAGAAAGC AAAGATAAAT ACAGTGCGGG CAGCCTTGTT
	AGAAAATGCA
151	CATTTTATGG AAAAGTTTTA TCTGCAGAAT GGGAGATTTA
	AACAAACATC
201	TACCAAATGG CCAAGTTTGC CGATTAAAGA GGCAGAAGGC
	TTTTGTATCC
251	GTTTGAATGG AATCGCGCGC GGGGCCTTAG ACAGTAAATT
	CATGTTGAAG
301	GCGGTAGCCA TAGATAAAGA TAAAAATCCT TTTATTATTA
	AGATGAATGA
351	AAATCTAGTA ACCTTTATTT GCAAGAAGTC CGCCAGTTCG
	TGTAGTGACG
401	GGCTGGATTA TTTTAAAGGA AATGATAAGG ACTGCAAGTT
	ACTTAAGTAG

This encodes a protein having amino acid sequence <SEQ ID 824>:

1	MTDNRGFTLV ELISVVLILS VLALIVYPSY RNYVEKAKIN
	TVRAALLENA
51	HFMEKFYLQN GRFKQTSTKW PSLPIKEAEG FCIRLNGIAR
	GALDSKFMLK
101	AVAIDKDKNP FIIKMNENLV TFICKKSASS CSDGLDYFKG
	NDKDCKLLK*

ORF127a and ORF127-1 show 99.3% identity in 149 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF127 shows 97.3% identity over a 150 aa overlap with a predicted ORF (ORF127ng) from N. gonorrhoeae:

The complete length ORF127ng nucleotide sequence <SEQ ID 825> is:

1	ATGACTGATA ATCGGGGGTT TACACTGGTT GAATTAATAT
	CAGTGGTCTT
51	GATATTGTCT GTACTTGCTT TAATTGTTTA TCCGAGCTAT
	CGCAATTATG
101	TTGAGAAAGC AAAGATAAAT GCAGTGCGGG CAGCCTTGTT
	AGAAAATGCA
151	CATTTTATGG AAAAGTTTTA TCTGCAGAAT GGGAGATTTA
	AACAAACATC
201	TACCAAATGG CCAAGTTTGC CGATTAAAGA GGCAGAAGGC
	TTTTGTATCC
251	GTTTGAATGG AATCGCGCGC GGGGCTTTAG ACAGTAAATT
	CATGTTGAAG
301	GCGGTAGCCA TAGATAAAGA TAAAAATCCT TTTATTATTA
	AGATGAATGA
351	AAATCTAGTA ACCTTTATTT GCAAGAAGTC CGCCAGTTCG
	TGTAGTGACG
401	GGCTGGATTA TTTTAAAGGA AATGATAAGG ACTGCAAGTT
	ACTTAAGTAG

This encodes a protein having amino acid sequence <SEQ ID 826>:

1	MTDNRGFTLV ELISVVLILS VLALIVYPSY RNYVEKAKIN
	AVRAAFLENA
51	HFMEKFYLQN GRFKQTSTKW PSLPIKEAEG FCIRLNGIAR
	GALDSKFMLK
101	AVAIDKDKNP FIIKMNENLV TFICKKSASS CSDRLDYFKG
	NDKDCKLLK*

ORF127ng and ORF127-1 show 100.0% identity in 149 aa overlap:

This analysis, including the fact that the predicted transmembrane domain is shared by the meningococcal and gonococcal proteins, suggests that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 98

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 827>

1	..GTGTCGCTGG CTTCGGTGAT TGCCTCTCAA ATCTTCCTTT
	ACGAAGATTT
51	CAACCAAATG CGGAAAACCC GTGGAGCTAT CTGCGGTTTT
	CTTGTCCAAT
101	ATTTATCTGG GGTTTCAGCA GGGGTATTTC GATTTGAGTG
	CCGACGAGAA
151	CCCCGTACTG CATATCTGGT CTTTGGCAGT AGAGGAACAG
	TATTACCTCC
201	TGTATCCCCT TTTGCTGATA TTTTGCTGCA AAAAAACCAA
	ATCGCTACGG
251	GTGCTGCGTA ACATCAGCAT CATCCTGTTT TTGATTTTGA
	CTGCCTCATC
301	GTTTTTGCCA AGCGGGTTTT ATACCGACAT CCTCAACCAA
	CCCAATACTT
351	ATTACCTTTC GACACTGAGG TTTCCCGAGC TGTTGGCAGG
	TTCGCTGCTG
401	GCGGTTTACG GGCAAACGCA AAACGGCAGA CGGCAAACAG
	CAAATGGAAA
451	ACGGCAGTTG CTTTCATCAC TCTGCTTCGG CGCATTGCTT
	GCCTGCCTGT
501	TCGTGATTGA CAAACACAAT CCGTTTATCC CGGGAATGAC
	CCTGCTCCTT
551	CCCTGCCTGC TGACGGCACT GCTTATCCGG AGTATGCAAT
	ACGGGACACT
601	TCCGACCCGC ATCCTGTCGG CAAGCCCCAT CGTATTTGTC
	GGCAAAATCT
651	CTTATTCCCT ATACCTGTAC CATTGGATTT TTATTGCTTT
	CGCTCCGCTC
701	ATTAGAGGCG GGAAACAGCT CGGACTGCCT GCCG..

This corresponds to the amino acid sequence <SEQ ID 828; ORF128>:

1	..VSLASVIASQ IFLYEDFNQM RKTVELSAVF LSNIYLGFQQ
	GYFDLSADEN
51	PVLHIWSLAV EEQYYLLYPL LLIFCCKKTK SLRVLRNISI
	ILFLILTASS
101	FLPSGFYTDI LNQPNTYYLS TLRFPELLAG SLLAVYGQTQ
	NGRRQTANGK
151	RQLLSSLCFG ALLACLFVID KHNPFIPGMT LLLPCLLTAL
	LIRSMQYGTL
201	PTRILSASPI VFVGKISYSL YLYHWIFIAF APLIRGGKQL
	GLPA..

Further work revealed the complete nucleotide sequence <SEQ ID 829>:

1	ATGCAAGCTG TCCGATACAG ACCGGAAATT GACGGATTGC
	GGGCCGTCGC
51	CGTGCTATCC GTCATGATTT TCCACCTGAA TAACCGCTGG
	CTGCCCGGAG
101	GATTCCTGGG GGTGGACATT TTCTTTGTCA TCTCAGGATT
	CCTCATTACC
151	GGCATCATTC TTTCTGAAAT ACAGAACGGT TCTTTTTCTT
	TCCGGGATTT
201	TTATACCCGC AGGATTAAGC GGATTTATCC TGCCTTTATT
	GCGGCCGTGT
251	CGCTGGCTTC GGTGATTGCC TCTCAAATCT TCCTTTACGA
	AGATTTCAAC
301	CAAATGCGGA AAACCGTGGA GCTTTCTGCG GTTTTCTTGT
	CCAATATTTA
351	TCTGGGGTTT CAGCAGGGGT ATTTCGATTT GAGTGCCGAC
	GAGAACCCCG
401	TACTGCATAT CTGGTCTTTG GCAGTAGAGG AACAGTATTA
	CCTCCTGTAT
451	CCCCTTTTGC TGATATTTTG CTGCAAAAAA ACCAAATCGC
	TACGGGTGCT
501	GCGTAACATC AGCATCATCC TGTTTTTGAT TTTGACTGCC
	TCATCGTTTT
551	TGCCAAGCGG GTTTTATACC GACATCCTCA ACCAACCCAA
	TACTTATTAC
601	CTTTCGACAC TGAGGTTTCC CGAGCTGTTG GCAGGTTCGC
	TGCTGGCGGT
651	TTACGGGCAA ACGCAAAACG GCAGACGGCA AACAGCAAAT
	GGAAAACGGC
701	AGTTGCTTTC ATCACTCTGC TTCGGCGCAT TGCTTGCCTG
	CCTGTTCGTG
751	ATTGACAAAC ACAATCCGTT TATCCCGGGA ATGACCCTGC
	TCCTTCCCTG
801	CCTGCTGACG GCACTGCTTA TCCGGAGTAT GCAATACGGG
	ACACTTCCGA
851	CCCGCATCCT GTCGGCAAGC CCCATCGTAT TTGTCGGCAA
	AATCTCTTAT
901	TCCCTATACC TGTACCATTG GATTTTTATT GCTTTCGCCC
	ATTACATTAC
951	AGGCGACAAA CAGCTCGGAC TGCCTGCCGT ATCGGCGGTT
	GCCGCGTTGA
1001	CGGCCGGATT TTCCCTGTTG AGTTATTATT TGATTGAACA
	GCCGCTTAGA
1051	AAACGGAAGA TGACCTTCAA AAAGGCATTT TTCTGCCTCT
	ATCTCGCCCC
1101	GTCCCTGATA CTTGTCGGTT ACAACCTGTA CGCAAGGGGG
	ATATTGAAAC
1151	AGGAACACCT CCGCCCGTTG CCCGGCGCGC CCCTTGCTGC
	GGAAAATCAT
1201	TTTCCGGAAA CCGTCCTGAC CCTCGGCGAC TCGCACGCCG
	GACACCTGAG
1251	GGGGTTTCTG GATTATGTCG GCAGCCGGGA AGGGTGGAAA
	GCCAAAATCC
1301	TGTCCCTCGA TTCGGAGTGT TTGGTTTGGG TAGATGAGAA
	GCTGGCAGAC
1351	AACCCGTTAT GTCGAAAATA CCGGGATGAA GTTGAAAAAG
	CCGAAGCCGT
1401	TTTCATTGCC CAATTCTATG ATTTGAGGAT GGGCGGCCAG
	CCTGTGCCGA
1451	GATTTGAAGC GCAATCCTTC CTAATACCCG GGTTCCCAGC
	CCGATTCAGG
1501	GAAACCGTCA AAAGGATAGC CGCCGTCAAA CCCGTCTATG
	TTTTTGCAAA
1551	CAACACATCA ATCAGCCGTT CGCCCCTGAG GGAGGAAAAA
	TTGAAAAGAT
1601	TTGCCGCAAA CCAATATCTC CGCCCCATTC AGGCTATGGG
	CGACATCGGC
1651	AAGAGCAATC AGGCGGTCTT TGATTTGATT AAAGATATTC
	CCAATGTGCA
1701	TTGGGTGGAC GCACAAAAAT ACCTGCCCAA AAACACGGTC
	GAAATATACG
1751	GCCGCTATCT TTACGGCGAC CAAGACCACC TGACCTATTT
	CGGTTCTTAT
1801	TATATGGGGC GGGAATTCCA CAAACACGAA CGCCTGCTTA
	AATCTTCCCA
1851	CGGCGGCGCA TTGCAGTAG

This corresponds to the amino acid sequence <SEQ ID 830; ORF128-1>:

1	MQAVRYRPEI DGLRAVAVLS VMIFHLNNRW LPGGFLGVDI
	FFVISGFLIT
51	GIILSEIQNG SFSFRDFYTR RIKRIYPAFI AAVSLASVIA
	SQIFLYEDFN
101	QMRKTVELSA VFLSNIYLGF QQGYFDLSAD ENPVLHIWSL
	AVEEQYYLLY
151	PLLLIFCCKK TKSLRVLRNI SIILFLILTA SSFLPSGFYT
	DILNQPNTYY
201	LSTLRFPELL AGSLLAVYGQ TQNGRRQTAN GKRQLLSSLC
	FGALLACLFV
251	IDKHNPFIPG MTLLLPCLLT ALLIRSMQYG TLPTRILSAS
	PIVFVGKISY
301	SLYLYHWIFI AFAHYITGDK QLGLPAVSAV AALTAGFSLL
	SYYLIEQPLR
351	KRKMTFKKAF FCLYLAPSLI LVGYNLYARG ILKQEHLRPL
	PGAPLAAENH
401	FPETVLTLGD SHAGHLRGFL DYVGSREGWK AKILSLDSEC
	LVWVDEKLAD
451	NPLCRKYRDE VEKAEAVFIA QFYDLRMGGQ PVPRFEAQSF
	LIPGFPARFR
501	ETVKRIAAVK PVYVFANNTS ISRSPLREEK LKRFAANQYL
	RPIQAMGDIG
551	KSNQAVFDLI KDIPNVHWVD AQKYLPKNTV EIYGRYLYGD
	QDHLTYFGSY
601	YMGREFHKHE RLLKSSHGGA LQ*

Computer analysis of this amino acid sequence gave the following results:

Homology with Hypothetical Integral Membrane Protein H10392 of H. influenzae (Accession Number U32723)

ORF128 and HI0392 show 52% aa identity in 180aa overlap:

Orf128:	1	VSLASVIASQIFLYEDFNQMRKTVELSAVFLSNIYLGFQQGYFDLSADENPVLHIWSLAV	60
		++L S IAS IF+Y DFN++RKT+EL+  FLSN YLG  QGYFDLSA+ENPVLHIWSLAV
HI0392:	46	MALVSFIASAIFIYNDFNKLRKTIELAIAFLSNFYLGLTQGYFDLSANENPVLHIWSLAV	105
Orf128:	61	EEQXXXXXXXXXIFCCKKTKSLRVLRNISIILFLILTASSFLPSGFYTDILNQPNTYYLS	120
		E Q         I   KK + ++VL  I++ILF IL A+SF+ + FY ++L+QPN YYLS
HI0392:	106	EGQYYLIFPLILILAYKKFREVKVLFIITLILFFILLATSFVSANFYKEVLHQPNIYYLS	165
Orf128:	121	TLRFPELLAGSLLAVYGQTQNGRRQTANGKRQLLSSLCFGALLACLFVIDKHNPFIPGMT	180
		LRFPELL GSLLA+Y    N + Q +     +L+ L    L +CLF+++ +  FIPG+T
HI0392:	166	NLRFPELLVGSLLAIYHNLSN-KVQLSKQVNNILAILSTLLLFSCLFLMNNNIAFIPGIT	224

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF128 shows 98.0% identity over a 244aa overlap with an ORF (ORF128a) from strain A of N. meningitidis:

The complete length ORF128a nucleotide sequence <SEQ ID 831> is:

1	ATGCAAGCTG TCCGATACAG ACCGGAAATT GACGGATTGC
	GGGCCGTCGC
51	CGTGCTATCC GTCATGATTT TCCACCTGAA TAACCGCTGG
	CTGCCCGGAG
101	GATTCCTGGG GGTGGACATT TTCTTTGTCA TCTCAGGATT
	CCTCATTACC
151	GGCATCATTC TTTCTGAAAT ACAGAACGGT TCTTTTTCTT
	TCCGGGATTT
201	TTATACCCGC AGGATTAAGC GGATTTATCC TGCTTTTATT
	GCGGCCGTGT
251	CGCTGGCTTC GGTGATTGCC TCTCAAATCT TCCTTTACGA
	AGATTTCAAC
301	CAAATGCGGA AAACCGTGGA GCTTTCTGCG GTTTTCTTGT
	CCAATATTTA
351	TCTGGGGTTT CAGCAGGGGT ATTTCGATTT GAGTGCCGAC
	GAGAACCCCG
401	TACTGCATAT CTGGTCTTTG GCAGTAGAGG AACAGTATTA
	CCTCCTGTAT
451	CCTCTTTTGC TGATATTTTG CTGCAAAAAA ACAAAATCGC
	TACGGGTGCT
501	GCGTAACATC AGCATCATCC TATTTCTGAT TTTGACTGCC
	ACATCGTTTT
551	TGCCAAGCGG GTTTTATACC GATATTCTCA ACCAACCCAA
	TACTTATTAC
601	CTTTCGACAC TGAGGTTTCC CGAGCTGTTG GCAGGTTCGC
	TGCTGGCGGT
651	TTACGGGCAA ACGCAAAACG GCAGACGGCA AACAGCAAAT
	GGAAAACGGC
701	AGTTGCTTTC ATCACTCTGC TTCGGCGCAT TGCTTGCCTG
	CCTGTTCGTG
751	ATTGACAAAC ACAATCCGTT TATCCCGGGA ATGACCCTGC
	TCCTTCCCTG
801	CCTGCTGACG GCACTGCTTA TCCGGAGTAT GCAATACGGG
	ACACTTCCGA
851	CCCGCATCCT GTCGGCAAGC CCCATCGTAT TTGTCGGCAA
	AATCTCTTAT
901	TCCCTATACC TGTACCATTG GATTTTTATT GCTTTCGCCC
	ATTACATTAC
951	AGGCGACAAA CAGCTCGGAC TGCCTGCCGT ATCGGCGGTT
	GCCGCGTTGA
1001	CGGCCGGATT TTCCCTGTTG AGTTATTATT TGATTGAACA
	GCCGCTTAGA
1051	AAACGGAAGA TGACCTTCAA AAAGGCATTT TTCTGCCTCT
	ATCTCGCCCC
1101	GTCCCTGATA CTTGTCGGTT ACAACCTGTA CGCAAGGGGG
	ATATTGAAAC
1151	AGGAACACCT CCGCCCGTTG CCCGGCGCGC CCCTTGCTGC
	GGAAAATCAT
1201	TTTCCGGAAA CCGTCCTGAC CCTCGGCGAC TCGCACGCCG
	GACACCTGCG
1251	GGGGTTTCTG GATTATGTCG GCAGCCGGGA AGGGTGGAAA
	GCCAAAATCC
1301	TGTCCCTCGA TTCGGAGTGT TTGGTTTGGG TAGATGAGAA
	GCTGGCAGAC
1351	AACCCGTTAT GTCGAAAATA CCGGGATGAA GTTGAAAAAG
	CCGAAGCCGT
1401	TTTCATTGCC CAATTCTATG ATTTGAGGAT GGGCGGCCAG
	CCCGTGCCGA
1451	GATTTGAAGC GCAATCCTTC CTAATACCCG GGTTCCCAGC
	CCGATTCAGG
1501	GAAACCGTCA AAAGGATAGC CGCCGTCAAA CCCGTCTATG
	TTTTTGCAAA
1551	CAACACATCA ATCAGCCGTT CGCCCCTGAG GGAGGAAAAA
	TTGAAAAGAT
1601	TTGCCGCAAA CCAATATCTC CGCCCCATTC AGGCTATGGG
	CGACATCGGC
1651	AAGAGCAATC AGGCGGTCTT TGATTTGATT AAAGATATTC
	CCAATGTGCA
1701	TTGGGTGGAC GCACAAAAAT ACCTGCCCAA AAACACGGTC
	GAAATATACG
1751	GCCGCTATCT TTACGGCGAC CAAGACCACC TGACCTATTT
	CGGTTCTTAT
1801	TATATGGGGC GGGAATTTCA CAAACACGAA CGCCTGCTTA
	AATCTTCTCG
1851	CGACGGCGCA TTGCAGTAG

This encodes a protein having amino acid sequence <SEQ ID 832>:

1	MQAVRYRPEI DGLRAVAVLS VMIFHLNNRW LPGGFLGVDI
	FFVISGFLIT
51	GIILSEIQNG SFSFRDFYTR RIKRIYPAFI AAVSLASVIA
	SQIFLYEDFN
101	QMRKTVELSA VFLSNIYLGF QQGYFDLSAD ENPVLHIWSL
	AVEEQYYLLY
151	PLLLIFCCKK TKSLRVLRNI SIILFLILTA TSFLPSGFYT
	DILNQPNTYY
201	LSTLRFPELL AGSLLAVYGQ TQNGRRQTAN GKRQLLSSLC
	FGALLACLFV
251	IDKHNPFIPG MTLLLPCLLT ALLIRSMQYG TLPTRILSAS
	PIVFVGKISY
301	SLYLYHWIFI AFAHYITGDK QLGLPAVSAV AALTAGFSLL
	SYYLIEQPLR
351	KRKMTFKKAF FCLYLAPSLI LVGYNLYARG ILKQEHLRPL
	PGAPLAAENH
401	FPETVLTLGD SHAGHLRGFL DYVGSREGWK AKILSLDSEC
	LVWVDEKLAD
451	NPLCRKYRDE VEKAEAVFIA QFYDLRMGGQ PVPRFEAQSF
	LIPGFPARFR
501	ETVKRIAAVK PVYVFANNTS ISRSPLREEK LKRFAANQYL
	RPIQAMGDIG
551	KSNQAVFDLI KDIPNVHWVD AQKYLPKNTV EIYGRYLYGD
	QDHLTYFGSY
601	YMGREFHKHE RLLKSSRDGA LQ*

ORF128a and ORF128-1 show 99.5% identity in 622 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF128 shows 93.4% identity over 244 aa overlap with a predicted ORF (ORF128ng) from N. gonorrhoeae:

The complete length ORF128ng nucleotide sequence <SEQ ID 833> is:

1	ATGCAAGCTG TCCGATACAG GCCTGAAATT GACGGATTGC
	GGGCCGTCGC
51	CGTGCTATCC GTCATTATTT TCCACCTGAA TAACCGCTGG
	CTGCCCGGAG
101	GATTCCTGGG GGTGGACATT TTCTTTGTCA TCTCGGGATT
	CCTCATTACC
151	AACATCATTC TTTCTGAAAT ACAGAACGGT TCTTTTTCTT
	TCCGGGATTT
201	TTATACCCGC AGGATTAAGC GGATTTATCC TGCTTTTATT
	GCGGCCGTGT
251	CCCTGGCTTC GGTGATTGCT TCTCAAATCT TCCTTTACGA
	AGATTTCAAC
301	CAAATGAGGA AAACCATAGA GCTTTCTACG GTTTTTTTGT
	CCAATATTTA
351	TTTGGGGTTC CGATTGGGGT ATTTCGATTT GAGTGCCGAC
	GAGAACCCCG
401	TACTGCATAT CTGGTCTTTG GCGGTAGAGG AACAGTATTA
	CCTCCTGTAT
451	CCTCTTTTGC TGATATTCTG TTACAAAAAA ACCAAATCAC
	TACGGGTGCT
501	GCGTAATATC AGCATCATCC TGTTTCTGAT TTTGACCGCA
	TCATCGTTTT
551	TGCCGGCCGG GTTTTATACC GACATCCTCA ACCAACCcaa
	TACTTATTAC
601	CTTTCGACAC TGAGGTTTCC CGAGCTGTTG GTGGGTTCGC
	TGTTGGCGGT
651	TTACGGGCAA ACGCAAAACG GCAGACGGCA AACAGAAAAT
	GGAAAACGGC
701	AGTTGCTTTC ATTACTCTGT TTCGGCGCat tgCTTGTCTG
	CCTGTTCGTG
751	ATCGACAAAC ACGATCCGTT TATCCCGGGA ATAACCCTGC
	TCCTTCCCTG
801	CCTGCTGACG GCGCTGCTTA TCCGGAGTAT GCAATACGGG
	ACACTTCCGA
851	CCCGCATCCT GTCGGCAAGC CCCATCGTAT TTGTCGGCAA
	AATCTCTTAT
901	TCCCTATACC TGTACCATTG GATTTTTATT GCCTTCGCCC
	ATTACATTAC
951	AGGCGACAAA CAGCTCGGAC TGCCTGCCGT ATCGGCGGTT
	GCCGCGTTGA
1001	CGGCCGGATT TTCCCTGTTG AGCTATTATT TGATTGAACA
	GCCGCTTAGA
1051	AAACGGAAGA TGACCTTCAA AAAGGCATTT TTCTGCCTTT
	ATCTCGCCCC
1101	GTCCCTGATG CTTGTCGGTT ACAACCTGTA TTCAAGAGGG
	ATATTGAAAC
1151	AGGAACACCT CCGCCCGCTG CCCGGCACGC CCGTTGCTGC
	GGAAAATAAT
1201	TTTCCGGAAA CCGTCTTGAC CCTCGGCGAC TCGCACGCCG
	GACACCTGCG
1251	GGGGTTTCTG GATTATGTCG GCGGCAGGGA AGGGTGGAAA
	GCTAAAATCC
1301	TGTCCCTCGA TTCGGAGTGT TTGGTTTGGG TGGATGAGAA
	GCTGGCAGAC
1351	AACCCGTTGT GCCGAAAATA CCGGGATGAA GTTGAAAAAG
	CCGAAGCTGT
1401	TTTCATTGCC CAATTCTATG ATTTGAGGAT GGGCGGCCAG
	CCCGTGCCGA
1451	GATTTGAAGC GCAATCCTTC CTGATACCCG GGTTCAAAGC
	CCGATTCAGG
1501	GAAACCGTCA AGAGGATAGC CGCCGTCAAA CCTGTATATG
	TTTTTGCAAA
1551	CAATACATCA ATCAGCCGTT CTCCCTTGAG GGAGGAAAAA
	TTGAAAAGAT
1601	TTGCTATAAA CCAATACCTC CGGCCTATTC GGGCTATGGG
	CGACATCGGC
1651	AAGAGCAATC AGGCGGTCTT TGATTTGGTT AAAGATATTC
	CCAATGTGCA
1701	TTGGGTGGAC GCACAAAAAT ACCTGCCCAA AAACACGGTC
	GAAATACACG
1751	GACGCTATCT TTACGGCGAC CAAGACCACC TGACCTATTT
	CGGTTCTTAT
1801	TATATGGGGC GGGAATTTCA CAAACACGAA CGCCTGCTCA
	AGCATTCCCG
1851	AGGCGGCGCA TTGCAGTAG

This encodes a protein having amino acid sequence <SEQ ID 834>:

1	MQAVRYRPEI DGLRAVAVLS VIIFHLNNRW LPGGFLGVDI
	FFVISGFLIT
51	NIILSEIQNG SFSFRDFYTR RIKRIYPAFI AAVSLASVIA
	SQIFLYEDFN
101	QMRKTIELST VFLSNIYLGF RLGYFDLSAD ENPVLHIWSL
	AVEEQYYLLY
151	PLLLIFCYKK TKSLRVLRNI SIILFLILTA SSFLPAGFYT
	DILNQPNTYY
201	LSTLRFPELL VGSLLAVYGQ TQNGRRQTEN GKRQLLSLLC
	FGALLVCLFV
251	IDKHDPFIPG ITLLLPCLLT ALLIRSMQYG TLPTRILSAS
	PIVFVGKISY
301	SLYLYHWIFI AFAHYITGDK QLGLPAVSAV AALTAGFSLL
	SYYLIEQPLR
351	KRKMTFKKAF FCLYLAPSLM LVGYNLYSRG ILKQEHLRPL
	PGTPVAAENN
401	FPETVLTLGD SHAGHLRGFL DYVGGREGWK AKILSLDSEC
	LVWVDEKLAD
451	NPLCRKYRDE VEKAEAVFIA QFYDLRMGGQ PVPRFEAQSF
	LIPGFKARFR
501	ETVKRIAAVK PVYVFANNTS ISRSPLREEK LKRFAINQYL
	RPIRAMGDIG
551	KSNQAVFDLV KDIPNVHWVD AQKYLPKNTV EIHGRYLYGD
	QDHLTYFGSY
601	YMGREFHKHE RLLKHSRGGA LQ*

ORF128ng and ORF128-1 show 95.7% identity in 622 aa overlap:

In addition, ORF218ng shows homology to a hypothetical H. influenzae protein:

sp|P43993|Y392_HAEIN HYPOTHETICAL PROTEIN HI0392 >gi|1074385|pir||B64007
hypothetical protein HI0392 - Haemophilus influenzae (strain Rd KW20)
>gi|1573364 (U32723) H. influenzae predicted coding region HI0392
[Haemophilus influenzae] Length = 245
Score = 239 bits (604), Expect = 3e−62
Identities = 124/225 (55%), Positives = 152/225 (67%), Gaps = 1/225 (0%)

Query:	38	VDIFFVISGFLITNIILSEIQNGSFSFRDFYTRRIKRIYPXXXXXXXXXXXXXXXXFLYE	97
		+DIFFVISGFLIT II++EIQ  SFS + FYTRRIKRIYP                F+Y
Sbjct:	1	MDIFFVISGFLITGIIITEIQQNSFSLKQFYTRRIKRIYPAFITVMALVSFIASAIFIYN	60
Query:	98	DFNQMRKTIELSTVFLSNIYLGFRLGYFDLSADENPVLHIWSLAVEEQXXXXXXXXXIFC	157
		DFN++RKTIEL+  FLSN YLG   GYFDLSA+ENPVLHIWSLAVE Q         I
Sbjct:	61	DFNKLRKTIELAIAFLSNFYLGLTQGYFDLSANENPVLHIWSLAVEGQYYLIFPLILILA	120
Query:	158	YKKTKSLRVLRNISIILFLILTASSFLPAGFYTDILNQPNTYYLSTLRFPELLVGSLLAV	217
		YKK + ++VL  I++ILF IL A+SF+ A FY ++L+QPN YYLS LRFPELLVGSLLA+
Sbjct:	121	YKKFREVKVLFIITLILFFILLATSFVSANFYKEVLHQPNIYYLSNLRFPELLVGSLLAI	180
Query:	218	YGQTQNGRRQTENGKRQLLSLLCFGALLVCLFVIDKHDPFIPGIT	262
		Y    N + Q       +L++L    L  CLF+++ +  FIPGIT
Sbjct:	181	YHNLSN-KVQLSKQVNNILAILSTLLLFSCLFLMNNNIAFIPGIT	224

This analysis, including the identification of several putative transmembrane domains, suggests that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 99

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 835>:

1	..ATTATTTACG AATACCGCTG GATGTTTCTT TACGGCGCAC
	TGACGACCTT
51	GGGGCTGACG GTCGTGGCAA C.GCGGGCGG TTCGGTATTG
	GGTCTGTTGT
101	TGGCGTTGGC GCGCCTGATT CACTTGGAAA AAGCCGGTGC
	GCCGATGCGC
151	GTGCTGGCGT GGGCGTTGCG TAAAGTTTCG CTGCTGTATG
	TTACGCTGTT
201	CCGGGGTACG CCGCTGTTTG TGCAGATTGT GATTTGGGCG
	TATGTGTGGT
251	TTCCGTTTTT CGTC..

This corresponds to the amino acid sequence <SEQ ID 836; ORF129>:

1	..IIYEYRWMFL YGALTTLGLT VVAXAGGSVL GLLLALARLI
	HLEKAGAPMR
51	VLAWALRKVS LLYVTLFRGT PLFVQIVIWA YVWFPFFV..

Further work revealed the complete nucleotide sequence <SEQ ID 837>:

1	ATGGATTTTC GTTTTGACAT TATTTACGAA TACCGCTGGA
	TGTTTCTTTA
51	CGGCGCACTG ACGACCTTGG GGCTGACGGT CGTGGCAACG
	GCGGGCGGTT
101	CGGTATTGGG TCTGTTGTTG GCGTTGGCGC GCCTGATTCA
	CTTGGAAAAA
151	GCCGGTGCGC CGATGCGCGT GCTGGCGTGG GCGTTGCGTA
	AAGTTTCGCT
201	GCTGTATGTT ACGCTGTTCC GGGGTACGCC GCTGTTTGTG
	CAGATTGTGA
251	TTTGGGCGTA TGTGTGGTTT CCGTTTTTCG TCCATCCTTC
	AGACGGCATT
301	TTGGTCAGCG GCGAGGCGGC AATCGCGCTG CGTCGCGGAT
	ACGGGCCGCT
351	GATTGCCGGT TCTTTGGCAC TGATCGCCAA CTCGGGGGCG
	TATATCTGTG
401	AGATTTTCCG CGCGGGCATC CAGTCTATAG ACAAAGGACA
	GATGGAGGCG
451	GCGCGTTCTT TGGGGCTGAC CTATCCGCAG GCGATGCGCT
	ATGTGATTCT
501	GCCGCAGGCA TTGCGCCGCA TGCTGCCGCC TTTGGCGAGC
	GAGTTCATCA
551	CGCTCTTGAA AGACAGCTCG CTGCTGTCGG TCATTGCTGT
	GGCGGAGTTG
601	GCGTATGTTC AGAATACGAT TACGGGCCGG TATTCGGTTT
	ATGAAGAACC
651	GCTTTACACC GTCGCCCTGA TTTATCTGTT GATGACGACT
	TTCTTAGGCT
701	GGATATTCCT GCGTTTGGAA AAACGTTACA ATCCGCAACA
	CCGCTGA

This corresponds to the amino acid sequence <SEQ ID 838; ORF129-1>:

1	MDFRFDIIYE YRWMFLYGAL TTLGLTVVAT AGGSVLGLLL
	ALARLIHLEK
51	AGAPMRVLAW ALRKVSLLYV TLFRGTPLFV QIVIWAYVWF
	PFFVHPSDGI
101	LVSGEAAIAL RRGYGPLIAG SLALIANSGA YICEIFRAGI
	QSIDKGQMEA
151	ARSLGLTYPQ AMRYVILPQA LRRMLPPLAS EFITLLKDSS
	LLSVIAVAEL
201	AYVQNTITGR YSVYEEPLYT VALIYLLMTT FLGWIFLRLE
	KRYNPQHR*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF129 shows 98.9% identity over a 88aa overlap with an ORF (ORF129a) from strain A of N. meningitidis:

The complete length ORF129a nucleotide sequence <SEQ ID 839> is:

1	ATGGATTTTC GTTTTGACAT TATTTACGAA TACCGCTGGA
	TGTTTCTTTA
51	CGGCGCACTG ACGACCTTGG GGCTGACGGT CGTGGCGACG
	GCGGGCGGTT
101	CGGTATTGGG TCTGTTGTTG GCGTTGGCGC GCCTGATTCA
	CTTGGAAAAA
151	GCCGGTGCGC CGATGCGCGT GCTGGCGTGG GCGTTGCGTA
	AGGTTTCGCT
201	GCTGTATGTT ACGCTGTTCC GGGGTACGCC GCTGTTTGTG
	CAGATTGTGA
251	TTTGGGCGTA TGTGTGGTTT CCGTTTTTCG TCCATCCTTC
	AGACGGCATT
301	TTGGTTAGCG GCGAGGCGGC AATCGCGCTG CGTCGCGGAT
	ACGGGCCGCT
351	GATTGCCGGT TCTTTGGCAC TGATCGCCAA CTCGGGGGCG
	TATATCTGTG
401	AGATTTTCCG CGCGGGCATC CAGTCTATAG ACAAAGGACA
	GATGGAGGCG
451	GCGCGTTCTT TGGGGCTGAC CTATCCGCAG GCGATGCGCT
	ATGTGATTCT
501	GCCGCAGGCA TTGCGCCGTA TGCTGCCGCC TTTGGCGAGC
	GAGTTCATCA
551	CGCTCTTGAA AGACAGCTCG CTGCTGTCGG TCATTGCTGT
	GGCGGAGTTG
601	GCGTATGTTC AGAATACGAT TACGGGCCGG TATTCGGTTT
	ATGAAGAACC
651	GCTTTACACC GTCGCCCTGA TTTATCTGTT GATGACGACT
	TTCTTAGGCT
701	GGATATTCCT GCGTTTGGAA AAACGTTACA ATCCGCAACA
	CCGCTGA

This encodes a protein having amino acid sequence <SEQ ID 840>:

1	MDFRFDIIYE YRWMFLYGAL TTLGLTVVAT AGGSVLGLLL
	ALARLIHLEK
51	AGAPMRVLAW ALRKVSLLYV TLFRGTPLFV QIVIWAYVWF
	PFFVHPSDGI
101	LVSGEAAIAL RRGYGPLIAG SLALIANSGA YICEIFRAGI
	QSIDKGQMEA
151	ARSLGLTYPQ AMRYVILPQA LRRMLPPLAS EFITLLKDSS
	LLSVIAVAEL
201	AYVQNTITGR YSVYEEPLYT VALIYLLMTT FLGWIFLRLE
	KRYNPQHR*

ORF129a and ORF129-1 show 100.0% identity in 248 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF129 shows 98.9% identity over a 88 aa overlap with a predicted ORF (ORF129ng) from N. gonorrhoeae:

An ORF129ng nucleotide sequence <SEQ ID 841> was predicted to encode a protein having amino acid sequence <SEQ ID 842>:

1	MDFRFDIIYE YRWMFLYGAL TTLGLTVVAT AGGSVLGLLL
	ALARLIHLEK
51	AGAPMRVLAW ALRKVSLLYV TLFRGTPLFV QIVIWAYVWF
	PFFVILHTAF
101	LGNAMRQSRR VPDKGRWIAG SLELNCQPRG RKTRGEFPPG
	ESNLGTEPRN
151	PLSMGQRRFP GCENWYPPQN FIKK*

Further work revealed the following gonococcal sequence <SEQ ID 843>:

1	ATGGATTTTc gtTTTGACAT TATTTAcgaA TACCGCTGGA
	TGTTTCTTTA
51	CGGCGCACTG Acgaccttgg ggctgacggt cgtggcgacg
	gCGGGCGGTT
101	CGGtattggG TCTGTTGTTG GCGTTGGCGC GCCTGATTCA
	CTTGGAAAAA
151	GCCGGTGCGC CGATGCGCGT GCTGGCGTGG GCGTTGCGTA
	AGGTTTCGCT
201	GCTGTACGTT ACCCTGTTCC GGGGTACGCC GCTGTTTGTG
	CAGATTGTGA
251	TTTGGGCGTA TGTGTGGTTT CCGTTTTTCG TCCATCCTTC
	AGACGGCATT
301	TTGGTCAGCG GCGAGGCGGC AATCGCGCTG CGTCGCGGAT
	ACGGGCCGCT
351	GATTGCCGGT TCTTTGGCAC TGATCGCCAA CTCGGGGGCG
	TATATCTGTG
401	AGATTTTCCG CGCGGGCATC CAGTCTATAG ACAAAGGACA
	GATGGAGGCG
451	GCGTGTTCTT TGGGACTGAC CTATCCGCAG GCGATGCGCT
	ATGTGATTCT
501	GCCGCAGGCA TTGCGCCGTA TGCTGCCGCC TTTGGCGAGC
	GAGTTCATCA
551	CGCTCTTGAA AGACAGCTCG CTGCTGTCGG TCATTGCTGT
	GGCGGAGTTG
601	GCGTATGTTC AGAATACGAT TACGGGCCGG TATTCGGTTT
	ATGAAGAACC
651	GCTTTACACC GCCGCCCTGA TTTATCTGTT GATGACGACT
	TTCTTAGGCT
701	GGATATTCCT GCGTTTGGAA AAACGTTACA ATCCGCAACA
	CCGCTGA

This corresponds to the amino acid sequence <SEQ ID 844; ORF129ng-1>:

1	MDFRFDIIYE YRWMFLYGAL TTLGLTVVAT AGGSVLGLLL
	ALARLIHLEK
51	AGAPMRVLAW ALRKVSLLYV TLFRGTPLFV QIVIWAYVWF
	PFFVHPSDGI
101	LVSGEAAIAL RRGYGPLIAG SLALIANSGA YICEIFRAGI
	QSIDKGQMEA
151	ARSLGLTYPQ AMRYVILPQA LRRMLPPLAS EFITLLKDSS
	LLSVIAVAEL
201	AYVQNTITGR YSVYEEPLYT VALIYLLMTT FLGWIFLRLE
	KRYNPQHR*

ORF129ng-1 and ORF129-1 show 99.2% identity in 248 aa overlap:

In addition, ORF129ng-1 is homologous to an ABC transporter from A. fulgidus:

2650409(AE001090) glutamine ABC transporter, permease protein (glnP)
[Archaeoglobus fulgidus] Length = 224
Score = 132 bits (329), Expect = 2e−30
Identities = 86/178 (48%), Positives = 103/178 (57%), Gaps = 18/178 (10%)

Query:	65	VSLLYVTLFRGTPLFVQIVIWAYVWFPFFVHPSDGILVSGEAAIALRRGYGPLIAGSLAL	124
		+S  YV + RGTPL VQI+I       +F  P+ GI +  E A            G +AL
Sbjct:	58	ISTAYVEVIRGTPLLVQILI------VYFGLPAIGINLQPEPA------------GIIAL	99
Query:	125	IANSGAYICEIFRAGIQSIDKGQMEAACSLGLTYPQAMRYVILPQALRRMLPPLASEFIT	184
		SGAYI EI RAGI+SI  GQMEAA SLG+TY QAMRYVI PQA R +LP L +EFI
Sbjct:	100	SICSGAYIAEIVRAGIESIPIGQMEAARSLGMTYLQAMRYVIFPQAFRNILPALGNEFIA	159
Query:	185	LLKDSSLLSVIAVAELAYVQNTITGRYSVYEEPLYTAALIYLLMTTFLGWIFLRLEKR	242
		LLKDSSLLSVI++ EL  V   I         P    AL YL+MT  L  +    +K+
Sbjct:	160	LLKDSSLLSVISIVELTRVGRQIVNTTFNAWTPFLGVALFYLMMTIPLSRLVAYSQKK	217

This analysis, including the identification of transmembrane domains in the two proteins, suggests that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 100

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 845>:

1	..CTGAAAGAAT GCCGTCTGAA AGACCCTGTT TTTATTCCAA
	ATATCGTTTA
51	TAAGAACATC GCCATTACTT TCCTGCTCTT GCACGCCGCC
	GCCGAACTTT
101	GGCTGCCCGC GCAAACCGCC GGTTTTACCG CGCTCGCCGT
	CGGCTTCATC
151	CTGCTCGCCA AGCTGCGTGA gCTTCACCAT CACGAACTCT
	TACGTAAACA
201	cTACGTCCGC ACTTATTACy TGCTCCAACT CTTTGCCGCC
	GCAGgcTAgT
251	TTGTGGACAG GCGCGGCGwA ATTACAAAAC CTGCCCGCyT
	CCGCGCCCCT
301	GCACCTGATT ACCCTCGGCG GCATGATGGG CGGCGTGATG
	ATGGTGTGGc
351	TGACCGCCGG ACTGTGGCAC AGCGGCTTTA CCAAACTCGA
	CTACCCCAAA
401	CTCTGCCGCA TTGCCGTCCC CATCCTTTTC GCCGCCGCCG
	TCTCGCGCGC
451	TTTCTTGrTG AACGTGAACC CGrTATTTTT CATTACCGTT
	CCTGCGATTC
501	TGACCGCCGC CGTATTCGTA CTGTATCTTT TCrCGTTTAT
	ACCGATATTT
551	CGGGCGAATG CGTTTACAGA CGATCCGGAr TAr

This corresponds to the amino acid sequence <SEQ ID 846; ORF130>:

1	..LKECRLKDPV FIPNIVYKNI AITFLLLHAA AELWLPAQTA
	GFTALAVGFI
51	LLAKLRELHH HELLRKHYVR TYYLLQLFAA AGSLWTGAAX
	LQNLPASAPL
101	HLITLGGMMG GVMMVWLTAG LWHSGFTKLD YPKLCRIAVP
	ILFAAAVSRA
151	FLXNVNPXFF ITVPAILTAA VFVLYLFXFI PIFRANAFTD
	DPE*

Further work revealed the complete nucleotide sequence <SEQ ID 847>:

1	ATGCGGCCGT TTTTCGTCGG CGCGGCGGTG CTTGCCATAC
	TCGGTGCGCT
51	GGTGTTTTTC ATCAACCCCG GTGCCATCGT CCTGCACCGC
	CAAATTTTCT
101	TGGAACTTAT GCTGCCGGCG GCATACGGCG GTTTTTTGAC
	TGCGGCTTTG
151	TTGGACTGGA CGGGTTTTTC GGGTAACCTG AAACCTGTCG
	CGACTTTGAT
201	GGCGGCATTA TTGCTCGCCG CATCCGCTAT ACTGCCCTTT
	TCGCCGCAAA
251	CTGCCTCGTT TTTCGTCGCC GCCTATTGGC TGGTGTTGCT
	GCTGTTCTGC
301	GCCCGGCTGA TTTGGCTAGA CCGAAACACC GACAACTTCG
	CCCTGCTAAT
351	GTTACTTGCC GCGTTCACTG TTTTTCAGAC GGCATATGCC
	GTCAGCGGCG
401	ATTTGAACCT GTTGCGCGCG CAAGTGCATC TAAATATGGC
	GGCGGTGATG
451	TTCGTATCCG TGCGCGTCAG TATTCTTTTG GGCGCGGAAG
	CCCTGAAAGA
501	ATGCCGTCTG AAAGACCCTG TTTTTATTCC AAATATCGTT
	TATAAAAACA
551	TCGCCATTAC TTTCCTGCTC TTGCACGCCG CCGCCGAACT
	TTGGCTGCCC
601	GCGCAAACCG CCGGTTTTAC CGCGCTCGCC GTCGGCTTCA
	TCCTGCTCGC
651	CAAGCTGCGT GAGCTTCACC ATCACGAACT CTTACGTAAA
	CACTACGTCC
701	GCACTTATTA CCTGCTCCAA CTCTTTGCCG CCGCAGGCTA
	TTTGTGGACA
751	GGCGCGGCGA AATTACAAAA CCTGCCCGCC TCCGCGCCCC
	TGCACCTGAT
801	TACCCTCGGC GGCATGATGG GCGGCGTGAT GATGGTGTGG
	CTGACCGCCG
851	GACTGTGGCA CAGCGGCTTT ACCAAACTCG ACTACCCCAA
	ACTCTGCCGC
901	ATTGCCGTCC CCATCCTTTT CGCCGCCGCC GTCTCGCGCG
	CTTTCTTGAT
951	GAACGTGAAC CCGATATTTT TCATTACCGT TCCTGCGATT
	CTGACCGCCG
1001	CCGTATTCGT ACTGTATCTT TTCACGTTTA TACCGATATT
	TCGGGCGAAT
1051	GCGTTTACAG ACGATCCGGA ATAA

This corresponds to the amino acid sequence <SEQ ID 848; ORF130-1>:

1	MRPFFVGAAV LAILGALVFF INPGAIVLHR QIFLELMLPA
	AYGGFLTAAL
51	LDWTGFSGNL KPVATLMAAL LLAASAILPF SPQTASFFVA
	AYWLVLLLFC
101	ARLIWLDRNT DNFALLMLLA AFTVFQTAYA VSGDLNLLRA
	QVHLNMAAVM
151	FVSVRVSILL GAEALKECRL KDPVFIPNIV YKNIAITFLL
	LHAAAELWLP
201	AQTAGFTALA VGFILLAKLR ELHHHELLRK HYVRTYYLLQ
	LFAAAGYLWT
251	GAAKLQNLPA SAPLHLITLG GMMGGVMMVW LTAGLWHSGF
	TKLDYPKLCR
301	IAVPILFAAA VSRAFLMNVN PIFFITVPAI LTAAVFVLYL
	FTFIPIFRAN
351	AFTDDPE*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF130 shows 94.3% identity over a 193aa overlap with an ORF (ORF130a) from strain A of N. meningitidis:

The complete length ORF130a nucleotide sequence <SEQ ID 849> is:

1	ATGCGGCCGT TTTTCGTCGG CGCGGCGGTG CTTGCCATAC
	TCGGTGCGCT
51	GGTGTTTTTC ATCAACCCCG GTGCCATCGT CCTGCACCGC
	CAAATTTTCT
101	TGGAACTTAT GCTGCCGGCG GCATACGGCG GTTTTTTGAC
	TGCGGCTTTG
151	TTGGACTGGA CGGGTTTTTC GGGTAACCTG AAACCTGTCG
	CGACTTTGAT
201	GGCGGCATTA TTGCTCGCCG CATCCGCTAT ACTGCCCTTT
	TCGCCGCAAA
251	CTGCCTCGTT TTTCGTCGCC GCCTATTGGC TGGTGTTGCT
	GCTGTTCTGC
301	GCCCGGCTGA TTTGGCTAGA CCGAAACACC GACAACTTCG
	CCCTGCTAAT
351	GTTACTTGCC GCGTTCACTG TTTTTCAGAC GGCATATGCC
	GTCAGCGGCG
401	ATTTGAACCT GTTGCGCGCG CAAGTGCATC TAAATATGGC
	GGCGGTGATG
451	TTCGTATCCG TGCGCGTCAG TATTCTTTTG GGCGCGGAAG
	CCCTGAAAGA
501	ATGCCGTCTG AAAGACCCAG TATTCATCCC CAATGTCGTC
	TATAAAAACA
551	TCGCCATTAC CTTCCTGCTC CTGCACGCCG CCGCCGAACT
	TTGGCTGCCT
601	GCGCAAACCG CCGGTTTTAC CTCGCTCGCC GTCGGCTTTA
	TCCTGCTTGC
651	CAAGCTGCGT GAGCTTCACC ATCACGAACT CCTGCGCAAA
	CACTACGTCC
701	GCACTTATTA CCTGCTCCAA CTCTTTGCCG CCGCAGGCTA
	TTTGTGGACA
751	GGCGCGGCGA AATTACAAAA CCTGCCCGCC TCCGCGCCCC
	TGCACCTGAT
801	TACCCTCGGT GGCATGATGG GCAGCGTGAT GATGGTGTGG
	CTGACTGCCG
851	GACTGTGGCA CAGCGGCTTT ACCAAGCTCG ACTACCCGAA
	ACTCTGCCGC
901	ATCGCCGTCC CCATCCTNTT CGCCGCCGCC GTTTCGCGCG
	CTGTTTTAAT
951	GAACGTAAAC CCGATATTCT TCATCACCGT CCCCGCAATT
	CTGACCGCCG
1001	CCGTGTTCGT GCTTTACCTG CTGACATTCG TACCGATCTT
	TCGGGCGAAC
1051	GCGTTTACAG ACGATCCGGA ATAA

This encodes a protein having amino acid sequence <SEQ ID 850>:

1	MRPFFVGAAV LAILGALVFF INPGAIVLHR QIFLELMLPA
	AYGGFLTAAL
51	LDWTGFSGNL KPVATLMAAL LLAASAILPF SPQTASFFVA
	AYWLVLLLFC
101	ARLIWLDRNT DNFALLMLLA AFTVFQTAYA VSGDLNLLRA
	QVHLNMAAVM
151	FVSVRVSILL GAEALKECRL KDPVFIPNVV YKNIAITFLL
	LHAAAELWLP
201	AQTAGFTSLA VGFILLAKLR ELHHHELLRK HYVRTYYLLQ
	LFAAAGYLWT
251	GAAKLQNLPA SAPLHLITLG GMMGSVMMVW LTAGLWHSGF
	TKLDYPKLCR
301	IAVPILFAAA VSRAVLMNVN PIFFITVPAI LTAAVFVLYL
	LTFVPIFRAN
351	AFTDDPE*

ORF130a and ORF130-1 show 98.3% identity in 357 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF130 shows 91.7% identity over a 193 aa overlap with a predicted ORF (ORF130ng) from N. gonorrhoeae:

An ORF130ng nucleotide sequence <SEQ ID 851> was predicted to encode a protein having amino acid sequence <SEQ ID 852>:

1	MNKFFTHPMR PFFVGAAVLA ILGALVFFHQ PRRYHPAPPN
	FLGTYAAGCI
51	RRFFDYRFVG PDGFFRQPET CRYFDGGVVA CCGCFIAVFT
	ATCRIFRRRL
101	LAGVAAVLRL ADLARRQHRT LRSVDVTAAF TVFQTAYAVS
	GDLNLLRAQV
151	HLNMAAVMFV SVRVSVLLGT ETLKECRLKD PVFIPNVIYK
	NIAITLLLHA
201	AAELWLPAQT AGFTALAVGF ILLAKLRELH HHELLRKHYV
	RTYYLLQLFA
251	AAGYLWTGAA KLQNLPASAP LHLITLGGMT GGVMMVWLTA
	GLWHSGFTKL
301	DYPKLCRIAV SILFASAVSR AVLMNVNPIF FITVPEILTA
	AVFMLYLLTF
351	VPIFRANAFT DDPE*

Further work revealed the following gonococcal DNA sequence <SEQ ID 853>:

1	ATGCGCCCGT TTTTCGTCGG TGCGGCAGTA CTTGCCATAC
	TCGGTGCGTT
51	GGTGTTTTTT ATCAACCCCG GCGCTATCAT CCTGCACCGC
	CAAATTTTCT
101	TGGAACTTAT GCTGCCGGCT GCATACGGCG GTTTTTTGAC
	TACCGCTTTG
151	TTGGACCGGA CGGGTTTTTC AGGCAACCTG AAACCTGCCG
	CTACTTTGAT
201	GGCGGTGTTG TTGCTTGTTG CGGCTGTTTT ATTGCCGTTT
	TTACCGCAAC
251	TTGCCGCATT TTTCGTCGCC GCCTATTGGC TGGTGTTGCT
	GCTGTTCTGC
301	GCCTGGCTGA TTTGGCTCGA CCGCAACACC GACAACTTCG
	CTCTGTTGAT
351	GTTACTTGCC GCATTTACCG TTTTTCAGAC GGCCTATGCC
	GTCAGCGGCG
401	ATTTGAACTT ACTGCGCGCG CAAGTGCATT TGAATATGGC
	GGCGGTCATG
451	TTCGTATCCG TCCGCGTCAG CGTCCTTTTG GGCACGGAAA
	CCCTGAAAGA
501	ATGCCGTCTG AAAGACCCCG TATTCATCCC CAACGTTATC
	TATAAAAACA
551	TCGCCATCAC CCTGCTGCTG CACGCCGCCG CCGAACTTTG
	GCTGCCCGCG
601	CAAACCGCCG GTTTTACTGC GCTTGCCGTC GGCTTCATCC
	TGCTCGCCAA
651	GCTGCGCGAA CTGCACCATC ACGAACTCTT ACGCAAACAC
	TACGTCCGCA
701	CTTATTACCT GCTCCAGCTC TTTGCCGCCG CAGGTTATCT
	GTGGACAGGC
751	GCGGCGAAAC TGCAAAACCT GCCCGCCTCC GCGCCCCTGC
	ACCTGATTAC
801	CCTCGGCGGC ATGACGGGTG GCGTGATGAT GGTGTGGCTG
	ACTGCCGGAC
851	TGTGGCACAG CGGCTTTACC AAACTCGACT ACCCGAAACT
	CTGCCGCATC
901	GCCGTCTCCA TCCTTTTCGC CTCCGCCGTT TCGCGCGCTG
	TTTTAATGAA
951	CGTGAATCCG ATATTCTTCA TCACCGTTCC CGAGATTCTG
	ACCGCCGCCG
1001	TGTTCATGCT TTACCTGCTG ACGTTCGTAC CGATTTTTCG
	AGCGAACGCG
1051	TTTACAGACG ATCCGGAATA A

This corresponds to the amino acid sequence <SEQ ID 854; ORF130ng-1>:

1	MRPFFVGAAV LAILGALVFF INPGAIILHR QIFLELMLPA
	AYGGFLTTAL
51	LDRTGFSGNL KPAATLMAVL LLVAAVLLPF LPQLAAFFVA
	AYWLVLLLFC
101	AWLIWLDRNT DNFALLMLLA AFTVFQTAYA VSGDLNLLRA
	QVHLNMAAVM
151	FVSVRVSVLL GTETLKECRL KDPVFIPNVI YKNIAITLLL
	HAAAELWLPA
201	QTAGFTALAV GFILLAKLRE LHHHELLRKH YVRTYYLLQL
	FAAAGYLWTG
251	AAKLQNLPAS APLHLITLGG MTGGVMMVWL TAGLWHSGFT
	KLDYPKLCRI
301	AVSILFASAV SRAVLMNVNP IFFITVPEIL TAAVFMLYLL
	TFVPIFRANA
351	FTDDPE*

ORF130ng-1 and ORF130-1 show 92.4% identity in 357 aa overlap:

Based on this analysis, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 101

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 855>:

1	ATGGAAATTC GGGCAATAAA ATATACGGCA ATGGCTGCGT
	TGCTTGCATT
51	TACGGTTGCA GGCTGCCGGC TGGCGGGGTG GTATGAGTGT
	TCGTCCCTCA
101	CCGGCTGGTG TAAGCCGAGA AAACCGGCTG CCATCGATTT
	TTGGGATATT
151	GGCGGCGAGA GTCCGCCGTC TTTAGGGGAC TACGAGATAC
	CGCTTTCAGA
201	CGGCAATAGT TCCGTCAGGG CAAACGAATA TGAATCCGCA
	CAACAATCTT
251	ACTTTTACAG GAAAATAGGG AAGTTTGAAG C.TGCGGGCT
	GGATTGGCGT
301	ACGCGTGACG GCAAACCTTT GATTGAGACG TTCAAACAGG
	GAGGATTTGA
351	CTGCTTGGAA AAG..

This corresponds to the amino acid sequence <SEQ ID 856; ORF131>:

1	MEIRAIKYTA MAALLAFTVA GCRLAGWYEC SSLTGWCKPR
	KPAAIDFWDI
51	GGESPPSLGD YEIPLSDGNS SVRANEYESA QQSYFYRKIG
	KFEXCGLDWR
101	TRDGKPLIET FKQGGFDCLE K..

Further work revealed the complete nucleotide sequence <SEQ ID 857>:

1	ATGGAAATTC GGGCAATAAA ATATACGGCA ATGGCTGCGT
	TGCTTGCATT
51	TACGGTTGCA GGCTGCCGGC TGGCGGGGTG GTATGAGTGT
	TCGTCCCTCA
101	CCGGCTGGTG TAAGCCGAGA AAACCGGCTG CCATCGATTT
	TTGGGATATT
151	GGCGGCGAGA GTCCGCCGTC TTTAGGGGAC TACGAGATAC
	CGCTTTCAGA
201	CGGCAATCGT TCCGTCAGGG CAAACGAATA TGAATCCGCA
	CAACAATCTT
251	ACTTTTACAG GAAAATAGGG AAGTTTGAAG CCTGCGGGCT
	GGATTGGCGT
301	ACGCGTGACG GCAAACCTTT GATTGAGACG TTCAAACAGG
	GAGGATTTGA
351	CTGCTTGGAA AAGCAGGGGT TGCGGCGCAA CGGTCTGTCC
	GAGCGCGTCC
401	GATGGTAA

This corresponds to the amino acid sequence <SEQ ID 858; ORF131-1>:

1	MEIRAIKYTA MAALLAFTVA GCRLAGWYEC SSLTGWCKPR
	KPAAIDFWDI
51	GGESPPSLGD YEIPLSDGNR SVRANEYESA QQSYFYRKIG
	KFEACGLDWR
101	TRDGKPLIET FKQGGFDCLE KQGLRRNGLS ERVRW*

Computer analysis of this amino acid sequence gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF131 shows 95.0% identity over a 121 aa overlap with an ORF (ORF131a) from strain A of N. meningitidis:

The complete length ORF131a nucleotide sequence <SEQ ID 859> is:

1	ATGGAAATTC GGGCAATAAA ATATACGGCA ATGGCTGCGT
	TGCTTGCATT
51	TACGGTTGCA GGCTGCCGGT TGGCAGGTTG GTATGAGTGT
	TCGTCCCTGT
101	CCGGCTGGTG TAAGCCGAGA AAACCTGCCG CCATCGATTT
	TTGGGATATT
151	GGCGGCGAGA GTCCTCCGTC TTTAGAGGAC TACGAGATAC
	CGCTTTCAGA
201	CGGCAATCGT TCCGTCAGGG CAAACGAATA TGAATCCGCA
	CAACAATCTT
251	ACTTTTACAG GAAAATAGGG AAGTTTGAAG CCTGCGGGTT
	GGATTGGCGT
301	ACGCGTGACG GCAAACCTTT GATTGAGACG TTCAAACAGG
	AAGGTTTTGA
351	TTGTTTGAAA AAGCAGGGGT TGCGGCGCAA CGGTCTGTCC
	GAGCGCGTCC
401	GATGGTAA

This encodes a protein having amino acid sequence <SEQ ID 860>:

1	MEIRAIKYTA MAALLAFTVA GCRLAGWYEC SSLSGWCKPR
	KPAAIDFWDI
51	GGESPPSLED YEIPLSDGNR SVRANEYESA QQSYFYRKIG
	KFEACGLDWR
101	TRDGKPLIET FKQEGFDCLK KQGLRRNGLS ERVRW*

ORF131a and ORF131-1 show 97.0% identity in 135 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF131 shows 89.3% identity over 121 aa overlap with a predicted ORF (ORF131ng) from N. gonorrhoeae:

A complete length ORF131ng nucleotide sequence <SEQ ID 861> was predicted to encode a protein having amino acid sequence <SEQ ID 862>:

1	MEIRVIKYTA TAALFAFTVA GCRLAGWYEC LSLSGWCKPR
	KPAAIDFWDI
51	GGESPLSLED YEIPLSDGNR SVRANEYESA QKSYFYRKIG
	KFEACGLDWR
101	TRDGKPLVER FKQEGFDCLE KQGLRRNGLS ERVRW*

Further work revealed the following gonococcal DNA sequence <SEQ ID 863>:

1	ATGGAAATTC GGGTAATAAA ATATACGGCA ACGGCTGCGT
	TGTTTGCATT
51	TACGGTTGCA GGCTGCCGGC TGGCGGGGTG GTATGAGTGT
	TCGTCCTTGT
101	CCGGCTGGTG TAAGCCGAGA AAACCTGCCG CCATCGATTT
	TTGGGATATT
151	GGCGGCGAGA GtccgctGTC TTTAGAGGAC TACGAGATAC
	CGCTTTCAGA
201	CGGCAATCGT TCCGTCAGGG CAAACGAATA TGAATCCGCG
	CAAAAATCTT
251	ACTTTTATAG GAAAATAGGG AAGTTTGAAG CCTGCGGGTT
	GGATTGGCGT
301	ACGCGTGACG GCAAACCTTT GGTTGAGAGG TTCAAACAGG
	AAGGTTTCGA
351	CTGTTTGGAA AAGCAGGGGT TGCGGCGCAA CGGCCTGTCC
	GAGCGCGTCC
401	GATGGTAA

This corresponds to the amino acid sequence <SEQ ID 864; ORF131ng-1>:

1	MEIRVIKYTA TAALFAFTVA GCRLAGWYEC SSLSGWCKPR
	KPAAIDFWDI
51	GGESPLSLED YEIPLSDGNR SVRANEYESA QKSYFYRKIG
	KFEACGLDWR
101	TRDGKPLVER FKQEGFDCLE KQGLRRNGLS ERVRW*

ORF131ng-1 and ORF131-1 show 92.6% identity in 135 aa overlap:

Based on the presence of a predicted prokaryotic membrane lipoprotein lipid attachment site, it is predicted that the proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 102

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 865>

1	ATGAAACACA TCCATATTAT CGGTATCGGC GGCACGTTTA
	TGGGCGGGCT
51	TGCCGCCATT GCCAAAGAAG CGGGGTTTGA AGTCAGCGGT
	TGCGACGCGA
101	AGATGTATCC GCCGATGAGC ACCCAGCTCG AAGCCTTGGG
	TATAGACGTG
151	TATGAAGGCT TCGATGCCGC TCAGTTGGAC GAATTTAAAG
	CCGACGTTTA
201	CGTTATCGGC AATGTCGCCA AGCGCGGGAT GGATGTGGTT
	GAAGCGATTT
251	TGAACCTCGG CCTGCCtTAT ATtTcCGGCC CGCAATGGCT
	GTCGGAAAAC
301	GTGCTGCACC ATCATTGGGT ACTCGGTGTG GCGGGGACgC
	ACGGCAAAAC
351	GACCACCGCC TCCATGCTCG CATGGGTCTT GGAATATgCC
	GGCCTCGCGC
401	CGGGCTTCCT TATtGGCGGC GTACC.GGAA AATttCGGCG
	TTTCCGCCCG
451	CCTGCCGCAA ACGCCGCGCC AAGACCCGAA CAGCCAATCG
	CCGTTTTTcG
501	TCATCGAAGC CGACGAATAC GACACCGCCT TTtTCGACAA
	ACGTTCTAAA
551	TtCGTGCATT ACCGTCCGCG TACCGCCGTG TTGAACAATC
	TGGAATTCGA
601	CCACGCCGAC ATCTTTGCCG ACTTGGGCGC GATACAGACc
	CAGTTCCACT
651	ACCTCGTGCG TACCGTGCCG TCTGAAGGCT TAATCGTCTG
	CAACGGACGG
701	CAGCAAAGCC TGCAAGATAC TTTGGACAAA GGCTGCTGGA
	CGCCGGTGGA
751	AAAATTCGGC ACGGAACACG GCTGGCA..

This corresponds to the amino acid sequence <SEQ ID 866; ORF132>:

1	MKHIHIIGIG GTFMGGLAAI AKEAGFEVSG CDAKMYPPMS
	TQLEALGIDV
51	YEGFDAAQLD EFKADVYVIG NVAKRGMDVV EAILNLGLPY
	ISGPQWLSEN
101	VLHHHWVLGV AGTHGKTTTA SMLAWVLEYA GLAPGFLIGG
	VXGKFRRFRP
151	PAANAAPRPE QPIAVFRHRS RRIRHRLFRQ TFXIRALPSA
	YRRVEQSGIR
201	PRRHLCRLGR DTDPVPLPRA YRAVXRLNRL QRTAAKPARY
	FGQRLLDAGG
251	KIRHGTRLA..

Further work revealed the complete nucleotide sequence <SEQ ID 867>:

1	ATGAAACACA TCCATATTAT CGGTATCGGC GGCACGTTTA
	TGGGCGGGCT
51	TGCCGCCATT GCCAAAGAAG CGGGGTTTGA AGTCAGCGGT
	TGCGACGCGA
101	AGATGTATCC GCCGATGAGC ACCCAGCTCG AAGCCTTGGG
	TATAGACGTG
151	TATGAAGGCT TCGATGCCGC TCAGTTGGAC GAATTTAAAG
	CCGACGTTTA
201	CGTTATCGGC AATGTCGCCA AGCGCGGGAT GGATGTGGTT
	GAAGCGATTT
251	TGAACCTCGG CCTGCCTTAT ATTTCCGGCC CGCAATGGCT
	GTCGGAAAAC
301	GTGCTGCACC ATCATTGGGT ACTCGGTGTG GCGGGGACGC
	ACGGCAAAAC
351	GACCACCGCC TCCATGCTCG CATGGGTCTT GGAATATGCC
	GGCCTCGCGC
401	CGGGCTTCCT TATTGGCGGC GTACCGGAAA ATTTCGGCGT
	TTCCGCCCGC
451	CTGCCGCAAA CGCCGCGCCA AGACCCGAAC AGCCAATCGC
	CGTTTTTCGT
501	CATCGAAGCC GACGAATACG ACACCGCCTT TTTCGACAAA
	CGTTCTAAAT
551	TCGTGCATTA CCGTCCGCGT ACCGCCGTGT TGAACAATCT
	GGAATTCGAC
601	CACGCCGACA TCTTTGCCGA CTTGGGCGCG ATACAGACCC
	AGTTCCACTA
651	CCTCGTGCGT ACCGTGCCGT CTGAAGGCTT AATCGTCTGC
	AACGGACGGC
701	AGCAAAGCCT GCAAGATACT TTGGACAAAG GCTGCTGGAC
	GCCGGTGGAA
751	AAATTCGGCA CGGAACACGG CTGGCAGGCC GGCGAAGCCA
	ATGCCGACGG
801	CTCGTTCGAC GTGTTGCTCG ACGGCAAAAC CGCCGGACGC
	GTCAAATGGG
851	ATTTGATGGG CAGGCACAAC CGCATGAACG CGCTCGCCGT
	CATTGCCGCC
901	GCGCGTCATG TCGGTGTCGA TATTCAGACC GCCTGCGAAG
	CCTTGGGCGC
951	GTTTAAAAAC GTCAAACGCC GGATGGAAAT CAAAGGCACG
	GCAAACGGCA
1001	TCACCGTTTA CGACGACTTC GCCCACCACC CGACCGCCAT
	CGAAACCACG
1051	ATTCAAGGTT TGCGCCAACG CGTCGGCGGC GCGCGCATCC
	TCGCCGTCCT
1101	CGAACCGCGT TCCAACACGA TGAAGCTGGG CACGATGAAG
	TCCGCCCTGC
1151	CTGTAAGCCT CAAAGAAGCC GACCAAGTGT TCTGCTACGC
	CGGCGGCGTG
1201	GACTGGGACG TCGCCGAAGC CCTCGCGCCT TTGGGCGGCA
	GGCTGAACGT
1251	CGGCAAAGAC TTCGATGCCT TCGTTGCCGA AATCGTGAAA
	AACGCCGAAG
1301	TAGGCGACCA TATTTTGGTG ATGAGCAACG GCGGTTTCGG
	CGGAATACAC
1351	GGAAAGCTGC TGGAAGCTTT GAGATAG

This corresponds to the amino acid sequence <SEQ ID 868; ORF132-1>:

1	MKHIHIIGIG GTFMGGLAAI AKEAGFEVSG CDAKMYPPMS
	TQLEALGIDV
51	YEGFDAAQLD EFKADVYVIG NVAKRGMDVV EAILNLGLPY
	ISGPQWLSEN
101	VLHHHWVLGV AGTHGKTTTA SMLAWVLEYA GLAPGFLIGG
	VPENFGVSAR
151	LPQTPRQDPN SQSPFFVIEA DEYDTAFFDK RSKFVHYRPR
	TAVLNNLEFD
201	HADIFADLGA IQTQFHYLVR TVPSEGLIVC NGRQQSLQDT
	LDKGCWTPVE
251	KFGTEHGWQA GEANADGSFD VLLDGKTAGR VKWDLMGRHN
	RMNALAVIAA
301	ARHVGVDIQT ACEALGAFKN VKRRMEIKGT ANGITVYDDF
	AHHPTAIETT
351	IQGLRQRVGG ARILAVLEPR SNTMKLGTMK SALPVSLKEA
	DQVFCYAGGV
401	DWDVAEALAP LGGRLNVGKD FDAFVAEIVK NAEVGDHILV
	MSNGGFGGIH
451	GKLLEALR*

Computer analysis of this amino acid sequence gave the following results:

Homology with the Hypothetical o457 Protein of E. coli (Accession Number U14003)

ORF132 and o457 show 58% aa identity in 140 aa overlap:

Orf132:	4	IHIIGIGGTFMGGLAAIAKEAGFEVSGCDAKMYPPMSTQLEALGIDVYEGFDAAQLDEFK	63
		IHI+GI GTFMGGLA +A++ G EV+G DA +YPPMST LE  GI++ +G+DA+QL+  +
o457:	3	IHILGICGTFMGGLAMLARQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLEP-Q	61
Orf132:	64	ADVYVIGNVAKRGMDVVEAILNLGLPYISGPQWLSENVLHHHWVLGVAGTHGKTTTASML	123
		D+ +IGN   RG   VEA+L   +PY+SGPQWL + VL   WVL VAGTHGKTTTA M
o457:	62	PDLVIIGNAMTRGNPCVEAVLEKNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMA	121
Orf132:	124	AWVLEYAGLAPGFLIGGVXG	143
		W+LE  G  PGF+IGGV G
o457:	122	TWILEQCGYKPGFVIGGVPG	141

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF132 shows 74.6% identity over a 189aa overlap with an ORF (ORF132a) from strain A of N. meningitidis:

The complete length ORF132a nucleotide sequence <SEQ ID 869> is:

1 ATGAAACACA TCCACATTAT CGGTATCGGC GGCACGTTTA TGGGTGGGAT
51 TGCCGCCATT GCCAAAGAAG CAGGGTTTGA ANTCAGCGGT TGCGATGCGA
101 AGATGTATCC GCCGATGAGC ACCCAGCTCG AAGCCTTGGG CATAGGCGTG
151 TATGAAGGCT TCGACACCGC GCAGTTGGAC GAATTTAAAG CCGACGTTTA
201 CGTTATCGGC AATGTCGCCA AGCGCGGGAT GGATGTGGTT GAAGCGATTT
251 TGAACCGTGG GCTGCCTTAT ATTTCCGGCC CGCAATGGCT GGCTGAAAAC
301 NTGCTGCACC ATCATTGGNN ACTCGGCGTG GCGGNGACGC ACGGCAAAAC
351 GACCACCGCG TCTATGCTCG CGTGGGTTTT GGAATATGCC GGACTCGCAC
401 CGGGCTTCNT TATCGGCGGC GTACCGGAAA ACTTCAGCGT TTCCGCCCGC
451 CTGCCGCAAA CGCCGCGCCA AGACCCGAAC AGCCAATCGC CGTTTTTCGT
501 CATTGAAGCC GACGAATACG ACACCGCGTT TTTCGACAAA CGCTCCAAAT
551 TCGTGCATTA CCGTCCGCGT ACCGCCGTGT TGAACAATCT GGAATTCGAC
601 CACGCCGACA TCTTCGCCGA TTTGGGCGCG ATACAGACCC AGTTCCACCA
651 CCTCGTGCGT ACCGTGCCGT CTGAAGGCCT CATCGTCTGC AACGGACGGC
701 AGCAAAGCCT GCAAGACACT TTGGACAAAG GCTGCTGGAC GCCGGTGGAA
751 AAATTCGGCA CGGAACACGG CTGGCAGGCC GGCGAAGCCA ATGCCGATGG
801 CTCGTTCGAC GTGTTGCTTG ACGGCAAAAA AGCCGGACAC GTCGCTTGGA
851 GTTTGATGGG CGGACACAAC CGCATGAACG CGCTCGCNGT CATCGCCGCC
901 GCGCGTCATG CCGGAGTNGA CATTCAGACG GCCTGCGAAG CCTTGAGCAC
951 GTTTAAAAAC GTCAAACGCC GCATGGAAAT CAAAGGCACG GCAAACGGTA
1001 TCACCGTTTA CGACGACTTC GCCCACCATC CGACCGCTAT CGAAACCACG
1051 ATTCAAGGTT TGCGCCAGCG CGTCGGCGGC GCGCGCATCC TCGCCGTCCT
1101 CGAACCGCGT TCCAATACGA TGAAGCTGGG TACGATGAAA GCCGCCCTGC
1151 CCGCAAGCCT CAAAGAAGCC GACCAAGTGT TCTGNTACGC CGGCGGCGCG
1201 GACTGGGACG TTGCCGAAGC CCTCGCGCCT TTGGGCGGCA GGCTGCACGT
1251 CGGCAAAGAC TTCGATGCCT TCGTTGCCGA AATCGTGAAA AACGCCGAAG
1301 CAGGCGACCA TATTTTGGTG ATGAGCAACG GCGGTTTCGG CGGAATACAC
1351 ACCAAACTGC TGGACGCTTT GAGATAG

This encodes a protein having-amino acid sequence <SEQ ID 870>:

1 MKHIHIIGIG GTFMGGIAAI AKEAGFEXSG CDAKMYPPMS TQLEALGIGV
51 YEGFDTAQLD EFKADVYVIG NVAKRGMDVV EAILNRGLPY ISGPQWLAEN
101 XLHHHWXLGV AXTHGKTTTA SMLAWVLEYA GLAPGFXIGG VPENFSVSAR
151 LPQTPRQDPN SQSPFFVIEA DEYDTAFFDK RSKFVHYRPR TAVLNNLEFD
201 HADIFADLGA IQTQFHHLVR TVPSEGLIVC NGRQQSLQDT LDKGCWTPVE
251 KFGTEHGWQA GEANADGSFD VLLDGKKAGH VAWSLMGGHN RMNALAVIAA
301 ARHAGVDIQT ACEALSTFKN VKRRMEIKGT ANGITVYDDF AHHPTAIETT
351 IQGLRQRVGG ARILAVLEPR SNTMKLGTMK AALPASLKEA DQVFXYAGGA
401 DWDVAEALAP LGGRLHVGKD FDAFVAEIVK NAEAGDHILV MSNGGFGGIH
451 TKLLDALR*

ORF132a and ORF132-1 show 93.9% identity in 458 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF132 shows 89.6% identity over 259 aa overlap with a predicted ORF (ORF132ng) from N. gonorrhoeae:

An ORF132ng nucleotide sequence <SEQ ID 871> was predicted to encode a protein having amino acid sequence <SEQ ID 872>:

1	MKHIHIIGIG GTFMGGIAAI AKEAGFKVSG CDAKMYPPMS
	TQLEALGIGV
51	HEGFDAAQLE EFQADIYVIG NVARRGMDVV EAILNRGLPY
	ISGPQWLAEN
101	VLHHHWVLGV AGTHGKTTTA SMLAWVLEYA GLAPGFLIGG
	VPGKFRRFRP
151	PTANAASRPE QQIAVFRHRS RRIRHRLFRQ TLQIRALSPA
	YRRVEQSGIR
201	PRRHLRRLGR DTDPVPPPRA HRTIRRPHRL QRTAAKPARY
	FGQRLLDAGG
251	KIRHRTRLAD W*

Further work revealed the following gonococcal DNA sequence <SEQ ID 873>:

1	ATGAAACACA TCCACATTAT CGGTATCGGC GGCACGTTTA
	TGGGCGGGAT
51	TGCCGCCATT GCCAAAGAAG CCGGGTTCAA AGTCAGCGGT
	TGCGACGCGA
101	AGATGTATCC GCCGATGAGC ACCCAGCTCG AAGCCTTGGG
	CATAGGCGTA
151	CACGAAGGCT TCGATGCCGC GCAGTTGGAA GAATTTCAAG
	CCGATATTTA
201	CGTCATCGGC AATGTCGCCA GGCGCGGGAT GGATGTGGTC
	GAGGCGATTT
251	TGAACCGTGG GCTGCCTTAT ATTTCCGGCC CGCAATGGCT
	GGCTGAAAac
301	GTGCtgcacc atcaTTGGgt ACTCGGCGTG GcagggaCGC
	ACGGcaaAac
351	gaccaCcGcg tCCATGCTCG CCTGGGTCTT GGAATATGCC
	GGACTCGCGC
401	CGGGCTTCCT CATCGGCGGt gtaccggaAA ATTTCGGCGT
	TTCCGCCCGC
451	CTACCGCAAA CGCCGCGTCA AGACCCGAAC AGCAAATCGC
	CGTTTTTCGT
501	CATCGAAGCC GACGAATACG ACACCGCCTT TTTCGACAAA
	CGCTCCAAAT
551	TCGTGCATTA TCGCCCGCGT ACCGCCGTGT TGAACAATCT
	GGAATTCGAC
601	CACGCCGACA TCTTCGCCGA CTTGGGCGCG ATACAGACCC
	AGTTCCACCA
651	CCTCGTGCGC ACCGTACCAT CCGAAGGCCT CATCGTCTGC
	AACGGACAGC
701	AGCAAAGCCT GCAAGATACT TTGGACAAAG GCTGCTGGAC
	GCCGGTGGAA
751	AAATTCGGCA CCGGACACGG CTGGCAGATT GGTGAAGTCA
	ATGCCGACGG
801	CTCGTTCGAC GTATTGCTTG ACGGCAAAAA AGCCGGACAC
	GTCGCATGGG
851	ATTTGATGGG CGGACACAAC CGCATGAACG CGCTCGCCGT
	CATCGCTGCC
901	GCACGCCATG CCGGAGTCGA TGTTCAGACG GCCTGCGAAG
	CCTTGGGTGC
951	GTTTAAAAAC GTCAAACGCC GCATGGAAAT CAAAGGCACG
	GCAAACGGCA
1001	TCACCGTTTA CGACGATTTC GCCCACCACC CGACCGCCAT
	CGAAACCACG
1051	ATTCAAGGTT TGCGCCAACG TGTCGGCGGC GCGCGCATCC
	TCGCCGTCCT
1101	CGAGCCGCGT TCCAACACCA TGAAACTCGG CACGATGAAG
	TCCGCCCTGC
1151	CCGCAAGCCT CAAAGAAGCC GACCAAGTGT TCTGCTACGC
	CGGCGGCGCG
1201	GACTGGGACG TTGCCGAAGC CCTCGCGCCT TTGGGCTGCA
	GGCTGCGCGT
1251	CGGTAAAGAT TTCGATACCT TCGTTGCCGA AATTGTGAAA
	AACGCCCGAA
1301	CCGGCGACCA TATTTTGGTG ATGAGCAACG GCGGTTTCGG
	CGGAATACAC
1351	ACCAAACTGC TGGACGCTTT GAGATAG

This corresponds to the amino acid sequence <SEQ ID 874; ORF132ng-1>:

1	MKHIHIIGIG GTFMGGIAAI AKEAGFKVSG CDAKMYPPMS
	TQLEALGIGV
51	HEGFDAAQLE EFQADIYVIG NVARRGMDVV EAILNRGLPY
	ISGPQWLAEN
101	VLHHHWVLGV AGTHGKTTTA SMLAWVLEYA GLAPGFLIGG
	VPENFGVSAR
151	LPQTPRQDPN SKSPFFVIEA DEYDTAFFDK RSKFVHYRPR
	TAVLNNLEFD
201	HADIFADLGA IQTQFHHLVR TVPSEGLIVC NGQQQSLQDT
	LDKGCWTPVE
251	KFGTGHGWQI GEVNADGSFD VLLDGKKAGH VAWDLMGGHN
	RMNALAVIAA
301	ARHAGVDVQT ACEALGAFKN VKRRMEIKGT ANGITVYDDF
	AHHPTAIETT
351	IQGLRQRVGG ARILAVLEPR SNTMKLGTMK SALPASLKEA
	DQVFCYAGGA
401	DWDVAEALAP LGCRLRVGKD FDTFVAEIVK NARTGDHILV
	MSNGGFGGIH
451	TKLLDALR*

ORF132ng-1 and ORF132-1 show 93.2% identity in 458 aa overlap:

In addition, ORF132ng-1 is homologous to a hypothetical E. coli protein:

pir||S556459 hypothetical protein o457 - Escherichia coli >gi|537075 (U14003)
ORF_o457 [Escherichia coli] >gi|1790660 (AE000494). hypothetical 48.5 kD protein
in fbp-pmba intergenic region [Escherichia coli] Length = 457
Score = 474 bits (1207), Expect = e−133
Identities = 249/439 (56%), Positives = 294/439 (66%), Gaps = 13/439 (2%)
Query:  22 KEAGFKVSGCDAKMYPPMSTQLEALGIGVHEGFDAAQLEEFQADIYVIGNVARRGMDVVE  81
++ G +V+G DA +YPPMST LE  GI + +G+DA+QLE  Q D+ +IGN   RG    VE
Sbjct:  21 RQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLEP-OPDLVIIGNAMTRGNPCVE  79
Query:  82 AILNRGLPYISGPQWLAENVLHHHWVLGVAGTHGKTTTASMLAWVLEYAGLAPGFLIGGV 141

A+L  ++PY+SGPQWL  +VL   WVL VAGTHGKTTTA M  W+LE  G   PGF+IGGV

Sbjct:  80 AVLEKNIPYMSGPQWLHDFVLADRWVLAVAGTHGKTTTAGMATWILEQCGYKPGFVIGGV 139
Query: 142 PENFGVSARLPQTPRQDPNSKSPFFVIEADEYDTAFFDKRSKFVHYRPRTAVLNNLEFDH 201

P NF VSA L          +S FFVIEADEYD AFFDKRSKFVHY PRT +LNNLEFDH

Sbjct: 140 PGNFEVSAHL---------GESDFFVIEADEYDCAFFDKRSKFVHYCPRTLILNNLEFDH 190
Query: 202 ADIFADLGAIQTQFHHLVRTVPSEGLIVCNGQQQSLQDTLDKGCWTPVEKFGTGHGWQIG 261
ADIF DL AIQ QFHHLVR VP +G I+      +L+ T+  GCW+  E  G     WQ
Sbjct: 191 ADIFDDLKAIQKQFHHLVRIVPGOGRIIWPENDINLKQTMAMGCWSEQELVGEQGHWQAK 250
Query: 262 EVNADGS-FDVLLDGKKAGHVAWDLMGGHNRMNALAVIAAARHAGVDVQTACEALGAFKN 320
++  D S ++VLLDG+K G V W L+G HN  N L  IAAARH GV    A   ALG+FN
Sbjct: 251 KLTTDASEWEVLLDGEKVGEVKWSLVGEHNMHNGLMAIAAARHVGVAPADAANALGSFIN 310
Query: 321 VKRRMEIKGTANGITVYDDFAHHPTAIETTIQGLRQRVGG-ARILAVLEPRSNTMKLGTM 379
+RR+E++G ANG+TVYDDFAHHPTAI  T+  LR +VGG  ARI+AVLEPRSNTMK+G
Sbjct: 311 ARRRLELRGEANGVTVYDDFAHHPTAILATLAALRGKVGGTARIIAVLEPRSNTMKMGIC 370
Query: 380 KSALPASLKEADQVF-CYAGGADWDVAEALAPLGCRLRVGKDFDTFVAEIVKNARTGDHI 438
K  L  SL  AD+VF        W VAE             D DT    +VK A+ GDHI
Sbjct: 371 KDDLAPSLGRADEVFLLQPAHIPWQVAEVAEACVQPAHWSGDVDTLADMVVKTAQPGDHI 430
Query: 439 LVMSNGGFGGIHTKLLDAL                                          457
LVMSNGGFGGIH KLLD L
Sbjct: 931 LVMSNGGFGGIHQKLLDGL                                          999

Based on this analysis, it was predicted that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

ORF132-1 (26.4 kDa) was cloned in pET and pGex vectors and expressed in E. coli, as described above. The products of protein expression and purification were analyzed by SDS-PAGE. FIG. 20A shows the results of affinity purification of the His-fusion protein, and FIG. 20B shows the results of expression of the GST-fusion in E. coli. Purified His-fusion protein was used to immunise mice, whose sera were used for FACS analysis (FIG. 20C) and ELISA (positive result). These experiments confirm that ORF132 is a surface-exposed protein, and that it is a useful immunogen.

Example 103

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 875>

1 ..CCGGGCTATT ACGGCTCGGA TGACGAATTT AAGCGGGCAT TCGGAGAAAA
51   CTCGCCGACA TmCAAGAAAC ATTGCAACCG GAGCTGCGGG ATTTATGAAC
101   CCGTATTGAA AAAATACGGC AAAAAGCGCG CCAACAACCA TTCGGTCAGC
151   ATTAGTGCGG ACTTCGGCGA TTATTTCATG CCGTTCGCCA GCTATTCGCG
201   CACACACCGT ATGCCCAACA TCCAAGAAAT GTATTTTTCC CAAATCGGCG
251   ACTCCGGCGT TCACACCGCC TTAAAACCAG AGCGCGCAAA CACTTGGCAA
301   TTTGGCTTCr ATACCTATAA AAAAGGATTG TTAAAACAAG ATGATACATT
351   AGGATTAAAA CTGGTCGGCT ACCGCAGCCG CATCGACAAC TACATCCACA
401   ACGTTTACGG GAAATGGTGG GATTTGAACG GGGATATTCC GAGCTGGGTC
451   AGCAGCACCG GGCTTGCCTA CACCATCCAA CATCGCrATT TCAwAGACAA
501   AGTGCATCAA nnnnnnnnnn nnnnnnnnnn nnnnTACGAT TATGGGCGTT
551   TTTTCACCAA CCTTTCTTAC GCCTATCAAA AAAGCACGCA ACCGACCAAC
601   TTCAGCGATG CGAGCGAATC GCCCAACAAT GCGTCCAAAG AAGACCAACT
651   CAAACAAGGT TATGGGTTGA GCAGGGTTTC CGCCCTGCCG CGAGATTACG
701   GACGTTTGGA AGTCGGTACG CGCTGGTTGG GCAACAAACT GACTTTGGGC
751   GGCGCGATGC GCTATTTCGG CAAGAGCATC CGCGCGACGG CTGAAGAACG
801   CTATATCGAC GGCACCAACG GGGGAAATAC CAGCAATTTC CGGCAACTGG
851   GCAAGCGTTC CATCAAACAA ACCGAAACTC TTGCCCGCCA GCCTTTGATT
901   TTwGATTTTa ACGCCGCTTA CGAGCCGAAG AAAAACCTTA TTTTCCGCGC
951   CGAAGTCAAA AATCTGTTCG ACAGGCGTTA TATCGATCCG CTCGATGCGG
1001   GCAATGATGC GGCAAC.GAG CGTTATTACA GCTCGTTCGA CCCGAAAGAC
1051   AAGGACrrAG ACGTAACGTG TAATGCTGAT AAAACGTTGT GCaACGGCAA
1101   ATACGGCGGC ACAAGCAAAA GCGTATTGAC CAATTTTGCA CGCGGACGCA
1151   CCTTTTTgAT GACGATGAGC TACAAGTTTT AA

This corresponds to the amino acid sequence <SEQ ID 876; ORF133>:

1	..PGYYGSDDEF KRAFGENSPT XKKHCNRSCG IYEPVLKKYG
	KKRANNHSVS
51	ISADFGDYFM PFASYSRTHR MPNIQEMYFS QIGDSGVHTA
	LKPERANTWQ
101	FGFXTYKKGL LKQDDTLGLK LVGYRSRIDN YIHNVYGKWW
	DLNGDIPSWV
151	SSTGLAYTIQ HRXFXDKVHQ XXXXXXXXYD YGRFFTNLSY
	AYQKSTQPTN
201	FSDASESPNN ASKEDQLKQG YGLSRVSALP RDYGRLEVGT
	RWLGNKLTLG
251	GAMRYFGKSI RATAEERYID GTNGGNTSNF RQLGKRSIKQ
	TETLARQPLI
301	XDFNAAYEPK KNLIFRAEVK NLFDRRYIDP LDAGNDAAXE
	RYYSSFDPKD
351	KDXDVTCNAD KTLCNGKYGG TSKSVLTNFA RGRTFLMTMS
	YKF*

Further work revealed the further partial DNA sequence <SEQ ID 877>:

1	GAGGCGCAGA TACAGGTTTT GGAAGATGTG CACGTCAAGG
	CGAAGCGCGT
51	ACCGAAAGAC AAAAAAGTGT TTACCGATGC GCGTGCCGTA
	TCGACCCGTC
101	AGGATATATT CAAATCCAGC GAAAACCTCG ACAACATCGT
	ACGCAGCATC
151	CCCGGTGCGT TTACACAGCA AGATAAAAGC TCGGGCATTG
	TGTCTTTGAA
201	TATTCGCGGC GACAGCGGGT TCGGGCGGGT CAATACGATG
	GTGGACGGCA
251	TCACGCAGAC CTTTTATTCG ACTTCTACCG ATGCGGGCAG
	GGCAGGCGGT
301	TCATCTCAAT TCGGTGCATC TGTCGACAGC AATTTTATTG
	CCGGACTGGA
351	TGTCGTCAAA GGCAGCTTCA GCGGCTCGGC AGGCATCAAC
	AGCCTTGCCG
401	GTTCGGCGAA TCTGCGGACT TTAGGCGTGG ATGACGTCGT
	TCAGGGCAAT
451	AATACCTACG GCCTGCTGCT AAAAGGTCTG ACCGGCACCA
	ATTCAACCAA
501	AGGTAATGCG ATGGCGGCGA TAGGTGCGCG CAAATGGCTG
	GAAAGCGGAG
551	CATCTGTCGG TGTGCTTTAC GGGCACAGCA GGCGCAGCGT
	GGCGCAAAAT
601	TACCGCGTGG GCGGCGGCGG GCAGCACATC GGAAATTTTG
	GCGCGGAATA
651	TTTGGAACGG CGCAAGCAGC GATATTTTGT ACAAGAGGGT
	GCTTTGAAAT
701	TCAATTCCGA CAGCGGAAAA TGGGAGCGGG ATTTACAAAG
	GCAACAGTGG
751	AAATACAAGC CGTATAAAAA TTACAACAAC CAAGAACTAC
	AaAAATACAT
801	CGAAGAGCAT GACAAAAGCT GGCGGGAAAA CCTg.CaCCG
	CAATACGACA
851	TTACCCCCAT CGATCCGTCC AGCCTGAAGC AGCAGTCGGC
	AGGCAATCTG
901	TTTAAATTGG AATACGACGG CGTATTCAAT AAATACACGG
	CGCAATTTCG
951	CGATTTAAAC ACCAAAATCG GCAGCCGCAA AATCATCAAC
	CGCAATTATC
1001	AGTTCAATTA CGGTTTGTCT TTGAACCCGT ATACCAACCT
	CAATCTGACC
1051	GCAGCCTACA ATTCGGGCAG GCAGAAATAT CCGAAAGGGT
	CGAAGTTTAC
1101	AGGCTGGGGG CTTTTAAAGG ATTTTGAAAC CTACAACAAC
	GCGAAAATCC
1151	TCGACCTCAA CAACACCGCC ACCTTCCGGC TGCCCCGCGA
	AACCGAGTTG
1201	CAAACCACTT TGGGCTTCAA TTATTTCCAC AACGAATACG
	GCAAAAACCG
1251	CTTTCCTGAA GAATTGGGGC TGTTTTTCGA CGGTCCTGAT
	CAGGACAACG
1301	GGCTTTATTC CTATTTGGGG CGGTTTAAGG GCGATAAAGG
	GCTGCTGCCC
1351	CAAAAATCAA CCATTGTCCA ACCGGCCGGC AGCCAATATT
	TCAACACGTT
1401	CTACTTCGAT GCCGCGCTCA AAAAAGACAT TTACCGCTTA
	AACTACAGCA
1451	CCAATACCGT CGGCTACCGT TTCGGCGGCG AATATACGGG
	CTATTACGGC
1501	TCGGATGACG AATTTAAGCG GGCATTCGGA GAAAACTCGC
	CGACATACAA
1551	GAAACATTGC AACCGGAGCT GCGGGATTTA TGAACCCGTA
	TTGAAAAAAT
1601	ACGGCAAAAA GCGCGCCAAC AACCATTCGG TCAGCATTAG
	TGCGGACTTC
1651	GGCGATTATT TCATGCCGTT CGCCAGCTAT TCGCGCACAC
	ACCGTATGCC
1701	CAACATCCAA GAAATGTATT TTTCCCAAAT CGGCGACTCC
	GGCGTTCACA
1751	CCGCCTTAAA ACCAGAGCGC GCAAACACTT GGCAATTTGG
	CTTCAATACC
1801	TATAAAAAAG GATTGTTAAA ACAAGATGAT ACATTAGGAT
	TAAAACTGGT
1851	CGGCTACCGC AGCCGCATCG ACAACTACAT CCACAACGTT
	TACGGGAAAT
1901	GGTGGGATTT GAACGGGGAT ATTCCGAGCT GGGTCAGCAG
	CACCGGGCTT
1951	GCCTACACCA TCCAACATCG CAATTTCAAA GACAAAGTGC
	ACAAACACGG
2001	TTTTGAGTTG GAGCTGAATT ACGATTATGG GCGTTTTTTC
	ACCAACCTTT
2051	CTTACGCCTA TCAAAAAAGC ACGCAACCGA CCAACTTCAG
	CGATGCGAGC
2101	GAATCGCCCA ACAATGCGTC CAAAGAAGAC CAACTCAAAC
	AAGGTTATGG
2151	GTTGAGCAGG GTTTCCGCCC TGCCGCGAGA TTACGGACGT
	TTGGAAGTCG
2201	GTACGCGCTG GTTGGGCAAC AAACTGACTT TGGGCGGCGC
	GATGCGCTAT
2251	TTCGGCAAGA GCATCCGCGC GACGGCTGAA GAACGCTATA
	TCGACGGCAC
2301	CAACGGGGGA AATACCAGCA ATTTCCGGCA ACTGGGCAAG
	CGTTCCATCA
2351	AACAAACCGA AACTCTTGCC CGCCAGCCTT TGATTTTTGA
	TTTTTACGCC
2401	GCTTACGAGC CGAAGAAAAA CCTTATTTTC CGCGCCGAAG
	TCAAAAATCT
2451	GTTCGACAGG CGTTATATCG ATCCGCTCGA TGCGGGCAAT
	GATGCGGCAA
2501	CGCAGCGTTA TTACAGCTCG TTCGACCCGA AAGACAAGGA
	CGAAGACGTA
2551	ACGTGTAATG CTGATAAAAC GTTGTGCAAC GGCAAATACG
	GCGGCACAAG
2601	CAAAAGCGTA TTGACCAATT TTGCACGCGG ACGCACCTTT
	TTGATGACGA
2651	TGAGCTACAA GTTTTAA

This corresponds to the amino acid sequence <SEQ ID 878; ORF133-1>:

1	EAQIQVLEDV HVKAKRVPKD KKVFTDARAV STRQDIFKSS
	ENLDNIVRSI
51	PGAFTQQDKS SGIVSLNIRG DSGFGRVNTM VDGITQTFYS
	TSTDAGRAGG
101	SSQFGASVDS NFIAGLDVVK GSFSGSAGIN SLAGSANLRT
	LGVDDVVQGN
151	NTYGLLLKGL TGTNSTKGNA MAAIGARKWL ESGASVGVLY
	GHSRRSVAQN
201	YRVGGGGQHI GNFGAEYLER RKQRYFVQEG ALKFNSDSGK
	WERDLQRQQW
251	KYKPYKNYNN QELQKYIEEH DKSWRENLXP QYDITPIDPS
	SLKQQSAGNL
301	FKLEYDGVFN KYTAQFRDLN TKIGSRKIIN RNYQFNYGLS
	LNPYTNLNLT
351	AAYNSGRQKY PKGSKFTGWG LLKDFETYNN AKILDLNNTA
	TFRLPRETEL
401	QTTLGFNYFH NEYGKNRFPE ELGLFFDGPD QDNGLYSYLG
	RFKGDKGLLP
451	QKSTIVQPAG SQYFNTFYFD AALKKDIYRL NYSTNTVGYR
	FGGEYTGYYG
501	SDDEFKRAFG ENSPTYKKHC NRSCGIYEPV LKKYGKKRAN
	NHSVSISADF
551	GDYFMPFASY SRTHRMPNIQ EMYFSQIGDS GVHTALKPER
	ANTWQFGFNT
601	YKKGLLKQDD TLGLKLVGYR SRIDNYIHNV YGKWWDLNGD
	IPSWVSSTGL
651	AYTIQHRNFK DKVHKHGFEL ELNYDYGRFF TNLSYAYQKS
	TQPTNFSDAS
701	ESPNNASKED QLKQGYGLSR VSALPRDYGR LEVGTRWLGN
	KLTLGGAMRY
751	FGKSIRATAE ERYIDGTNGG NTSNFRQLGK RSIKQTETLA
	RQPLIFDFYA
801	AYEPKKNLIF RAEVKNLFDR RYIDPLDAGN DAATQRYYSS
	FDPKDKDEDV
851	TCNADKTLCN GKYGGTSKSV LTNFARGRTF LMTMSYKF*

Computer analysis of this amino acid sequence gave the following results:

Homology with the Probable TonB-Dependent Receptor HI121 of H. influenzae (Accession Number U32801)

ORF133 and HI121 show 57% aa identity in 363aa overlap:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF133 shows 90.8% identity over a 392aa overlap with an ORF (ORF133a) from strain A of N. meningitidis:

A partial ORF133a nucleotide sequence <SEQ ID 879> is:

1	AAAGACAAAA AAGTGTTTAC CGATGCGCGT GCCGTATCGA
	CCCGTCAGGA
51	TATATTCAAA TCCANCGAAA ACCTCGACAA CATCGTACGC
	ANCATCCCCG
101	GTGCGTTTAC ACANCAANAT AAAAGCTCGG GCNTTGTGTC
	TTTGAATATT
151	CGCNGCGACA GCGGGTTCGG GCGGGTCAAT ACNATGGTNG
	ACGGCATCAC
201	NCANACCTTT TATTCGACTT CTACCGATGC GGGCAGGGCA
	GGCGGTTCAT
251	CTCAATTCGG TGCATCTGTC GACAGCAATT TTATNGCCGG
	ACTGGATGTC
301	GTCAAAGGCA GCTTCAGCGG CTCGGCAGGC ATCAACAGCC
	TTGCCGGTTC
351	GGCGAATCTG CGGACTTTAN GCGTGGATGA TGTCGTTCAG
	GGCAATANTA
401	CNTACGGCCT GCTGCTAAAA GGTCTGACCG GCACCAATTC
	AACCAAAGGT
451	AATGCGATGG CGGCGATAGG TGCGCGCAAA TGGCTGGAAA
	GCGGAGCATC
501	TGTCGGTGTG CTTTACGGGC ACAGCAGGCG CAGCGTGGCG
	CAAAATTACC
551	GCGTGGGCGG CGGCGGGCAG CACATCGGAA ATTTTGGCGC
	GGAATATCTG
601	GAACGACGCA AGCAACGATA TTTTGAGCAA GAAGGCGGGT
	TGAAATTCAA
651	TTCCAACAGC GGAAAATGGG AGCGGGATTT CCAAAAGTCG
	TACTGGAAAA
701	CCAAGTGGTA TCAAAAATAC GATGCCCCCC AAGAACTGCA
	AAAATACATC
751	GAAGGTCATG ATAAAAGCTG GCGGGAAAAC CTGGCGCCGC
	AATACGACAT
801	CACCCCCATC GATCCGTCCA GCCTGAAGCN GCAGTCGGCA
	GGCAACCTGT
851	TTAAATTGGA ATACGACGGC GTATTCAATA AATACACGGC
	GCAATTTCGC
901	GATTTAAACA CCAAAATCGG CAGCCGCAAA ATCATCAACC
	GCAATTATCA
951	ATTCAATTAC GGTTTGTCTT TGAACCCGTA TACCAACCTC
	AATCTGACCG
1001	CAGCCTACAA TTCGGGCAGG CAGAAATATC CGAAAGGGTC
	GAAGTTTACA
1051	GGCTGGGGGC TTTTNAAAGA TTTTGAAACC TACAACAACG
	CAAAAATCCT
1101	CGACCTCANC AACACCTCCA CCTTCCGGCT GCCCCGTGAA
	ACCGAGTTGC
1151	AAACCACTTT GGGCTTCAAT TATTTCCACA ACGAATACGG
	CAAAAACCGC
1201	TTTCCTGAAG AATTGGGGCT GTTTTTCGAC GGTCCGGATC
	ANGACAACGG
1251	GCTTTATTCC TATTTGGGGC GGTTTAAGGG CGATAAAGGG
	CTGCTGCCCC
1301	AAAAATCAAC CATTGTCCAA CCGGCCGGCA GCCAATATTT
	CAACACGTTC
1351	TACTTCGATG CCGCGCTCAA AAAAGACATT TACCGCTTAA
	ACTACAGCAC
1401	CAATACCGTC GGCTACCGTT TCGGCGGCNA ATATACGGGC
	TATTACNGCT
1451	CGGATGACGA ATTTAAGCGG GCATTCGGAG AAAACTCGCC
	GACATACANG
1501	AAACATTGCA ACCAGAGCTG CGGAATTTAT GAACCCGTAT
	TGAAAAAATA
1551	CGGCAAAAAG CGCGCCAACA ACCATTCGGT CAGCATTAGT
	GCGGACTTCG
1601	GCGATTATTT CATGCCGTTC GCCAGCTATT CGCGCACACA
	CCGTATGCCC
1651	AACATCCAAG AAATGTATTT TTCCCAAATC GGCGACTCCG
	GCGTTCACAC
1701	CGCCTTAAAA CCAGAGCGCG CAAACACTTG GCAATTTGGC
	TTCAATACCT
1751	ATAAAAAAGG ATTGTTAAAA CAAGATGATA TATTAGGATT
	AAAACTGGTC
1801	GGCTACCGCA GCCGCATCGA CNACTACATC CACAACGTTT
	ACGGGAAATG
1851	GTGGGATTTG AACGGGAATA TTCCGAGCTG GGTCAGCAGC
	ACCGGGCTTG
1901	CCTACACCAT CCAACACCGC AATTTCAAAG ACAAAGTGCA
	CAAACACGGT
1951	TTTGAGTTGG AGCTGAATTA CGATTATNGG CGTTTTTTCA
	CCAACCTTTC
2001	TTACGCCTAT CAAAAAAGCA CGCAACCGAC CAACTTCAGC
	GATGCGAGCG
2051	AATCGCCCAA CAATGCGTCC AAAGAAGACC AACTCAAACA
	AGGTTATGGG
2101	TTGAGCAGGG TTTCCGCCCT GCCGCGAGAT TACGGACGTT
	TGGAAGTCGG
2151	TACGCGCTGG TTGGGCAACA AACTGACTTT GGGCGGCGCG
	ATGCGCTATT
2201	TCGGCAAGAG CATCCGCGCG ACGGCTGAAG AACGCTATAT
	CGACGNCACC
2251	AATGGGGNAN NTACCAGCAA TTTCCGGCAA CTGGGCAAGC
	GTTCCATCAN
2301	ACAAACCGAA ACCCTTGCCC GCCAGCCTTT GATTTTTGAT
	TTNTACGCCG
2351	CTTACGAGCC GAAGAAAAAN CTTATTTTCC GCGCCGAAGT
	CAAAAATCTG
2401	TTCGACAGGC GTTATATCGA TCCGCTCGAT GCGGGCAATG
	ATGCGGCAAC
2451	GCAGCGTTAT TACAGTTCGT TCGACCCGAA AGACAAGGAC
	GAAGAAGTAA
2501	CGTGTAATGA TGATAACACG TTATGCAACG GCAAATACGG
	CGGCACAAGC
2551	AAAAGCGTAT TGACCAATTT TGCACGCGGA CNCACCTTTT
	TGATAACGAT
2601	GAGCTACAAG TTTTAA

This encodes a protein having (partial) amino acid sequence <SEQ ID 880>:

1	KDKKVFTDAR AVSTRQDIFK SXENLDNIVR XIPGAFTXQX
	KSSGXVSLNI
51	RXDSGFGRVN TMVDGITXTF YSTSTDAGRA GGSSQFGASV
	DSNFXAGLDV
101	VKGSFSGSAG INSLAGSANL RTLXVDDVVQ GNXTYGLLLK
	GLTGTNSTKG
151	NAMAAIGARK WLESGASVGV LYGHSRRSVA QNYRVGGGGQ
	HIGNFGAEYL
201	ERRKQRYFEQ EGGLKFNSNS GKWERDFQKS YWKTKWYQKY
	DAPQELQKYI
251	EGHDKSWREN LAPQYDITPI DPSSLKXQSA GNLFKLEYDG
	VFNKYTAQFR
301	DLNTKIGSRK IINRNYQFNY GLSLNPYTNL NLTAAYNSGR
	QKYPKGSKFT
351	GWGLXKDFET YNNAKILDLX NTSTFRLPRE TELQTTLGFN
	YFHNEYGKNR
401	FPEELGLFFD GPDXDNGLYS YLGRFKGDKG LLPQKSTIVQ
	PAGSQYFNTF
451	YFDAALKKDI YRLNYSTNTV GYRFGGXYTG YYXSDDEFKR
	AFGENSPTYX
501	KHCNQSCGIY EPVLKKYGKK RANNHSVSIS ADFGDYFMPF
	ASYSRTHRMP
551	NIQEMYFSQI GDSGVHTALK PERANTWQFG FNTYKKGLLK
	QDDILGLKLV
601	GYRSRIDXYI HNVYGKWWDL NGNIPSWVSS TGLAYTIQHR
	NFKDKVHKHG
651	FELELNYDYX RFFTNLSYAY QKSTQPTNFS DASESPNNAS
	KEDQLKQGYG
701	LSRVSALPRD YGRLEVGTRW LGNKLTLGGA MRYFGKSIRA
	TAEERYIDXT
751	NGXXTSNFRQ LGKRSIXQTE TLARQPLIFD XYAAYEPKKX
	LIFRAEVKNL
801	FDRRYIDPLD AGNDAATQRY YSSFDPKDKD EEVTCNDDNT
	LCNGKYGGTS
851	KSVLTNFARG XTFLITMSYK F*

ORF133a and ORF133-1 show 94.3% identity in 871 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF133 shows 92.3% identity over 392 aa overlap with a predicted ORF (ORF133ng) from N. gonorrhoeae:

The complete length ORF133ng nucleotide sequence <SEQ ID 881> is predicted to encode a protein having amino acid sequence <SEQ ID 882>:

1	MRSSFRLKPI CFYLMGVMLY HHSYAEDAGR AGSEAQIQVL
	EDVHVKAKRV
51	PKDKKVFTDA RAVSTRQDVF KSGENLDNIV RSIPGAFTQQ
	DKSSGIVSLN
101	IRGDSGFGRV NTMVDGITQT FYSTSTDAGR AGGSSQFGAS
	VDSNFIAGLD
151	VVKGSFSGSA GINSLAGSAN LRTLGVDDVV QGNNTYGLLL
	KGLTGTNSTK
201	GNAMAAIGAR KWLESGASVG VLYGHSRRGV AQNYRVGGGG
	QHIGNFGEEY
251	LERRKQQYFV QEGGLKFNAG SGKWERDLQR QYWKTKWYKK
	YEDPQELQKY
301	IEEHDKSWRE NLAPQYDITP IDPSGLKQQS AGNLLNLEYD
	GVFNKYTAQF
351	RDLNTRIGSR KIINRNYQFN YGLSLNPYTN LNLTAAYNSG
	RQKYPKGAKF
401	TGWGLLKDFE TYNNAKILDL NNTATFRLPR ETELQTTLGF
	NYFHNEYGKN
451	RFPEELGLFF DGPDQDNGLY SYLGRFKGDK GLLPQKSTIV
	QPAGSQYFNT
501	FYFDAALKKD IYRLNYSTNA INYRFGGEYT GYYGSENEFK
	RAFGENSPAY
551	KEHCDPSCGL YEPVLKKYGK KRANNHSVSI SADFGDYFMP
	FAGYSRTHRM
601	PNIQEMYFSQ IGDSGVHTAL KPERANTWQF GFNTYKKGLL
	KQDDILGLKL
651	VGYRSRIDNY IHNVYGKWWD LNGDIPSWVG STGLAYTIRH
	RNFKDKVHKH
701	GFELELNYDY GRFFTNLSYA YQKSTQPTNF SDASESPNNA
	SKEDQLKQGY
751	GLSRVSALPR DYGRLEVGTR WLGNKLTLGG AMRYFGKSIR
	ATAEERYIDG
801	TNGGNTSNVR QLGKRSIKQT ETLARQPLIF DFYAAYEPKK
	NLIFRAEVKN
851	LFDRRYIDPL DAGNDAATQR YYSSFDPKDK DEDVTCNADK
	TLCNGKYGGT
901	SKSVLTNFAR GRTFLMTMSY KF*

A variant was also identified, being encoded by the gonococcal DNA sequence <SEQ ID 883>:

1 ATGAGATCTT CTTTCCGGTT GAAGCCGATT TGTTTTTATC TTATGGGTGT
51 TATGCTATAT CATCATAGTT ATGCCGAAGA TGCAGGGCGC GCGGGCAGCG
101 AGGCGCAGAT ACAGGTTTTG GAAGATGTGC ACGTCAAGGC GAAGCGCGTA
151 CCGAAAGACA AAAAAGTGTT TACCGATGCG CGTGCCGTAT CGACCCGTca
201 gGATGTGTTC AAATCCGGCG AAAACCTCGA CAACATCGTA CGCAGCATAC
251 CCGGTGCGTT TACACAGCAA GATAAAAGCT CGGGCATTGT GTCTTTGAAT
301 ATTCCCGGCG ACAGCGGGTT CGGGCGGGTC AATACGATGG TGGACGGCAT
351 CACGCAGACC TTTTATTCGA CTTCTACCGA TGCGGGCAGG GCAGGCGGTT
401 CATCTCAATT CGGTGCATCT GTCGACAGCA ATTTTATTGC CGGACTGGAT
451 GTCGTCAAAG GCAGCTTCAG CGGCTCGGCA GGCATCAACA GCCTTGCCGG
501 TTCGGCGAAT CTGCGGACTT TAGGCGTGGA TGACGTCGTT CAGGGCAATA
551 ATACCTACGG CCTGCTGCTA AAAGGTCTGA CCGGCACCAA TTCAACCAAA
601 GGTAATGCGA TGGCGGCGAT AGGTGCGCGC AAATGGCTGG AAAGCGGAGC
651 GTCTGTCGGT GTGCTTTACG GGCACAGCAG GCGCGGCGTG GCGCAAAATT
701 ACCGCGTGGG CGGCGGCGGG CAGCACATCG GAAATTTTGG TGAAGAATAT
751 CTGGAACGGC GCAAACAGCA ATATTTTGTA CAAGAGGGTG GTTTGAAATT
801 CAATGCCGGC AGCGGAAAAT GGGAACGGGA TTTGCAAAGG CAATACTGGA
851 AAACAAAGTG GTATAAAAAA TACGAAGACC CCCAAGAACT GCAAAAATAC
901 ATCGAAGAGC ATGATAAAAG CTGGCGGGAA AACCTGGCGC CGCAATACGA
951 CATCACCCCC ATCGATCCGT CCGGCCTGAA GCAGCAGTCG GCAGGCAATC
1001 TGTTTAAATT GGAATACGAC GGCGTATTCA ATAAATACAC GGCGCAATTT
1051 CGCGATTTAA ACACCAGAAT CGGCAGCCGC AAAATCATCA ACCGCAATTA
1101 TCAATTCAAT TACGGTTTGT CTTTGAACCC GTATACCAAC CTCAATCTGA
1151 CCGCAGCCTA CAATTCGGGC AGGCAGAAAT ATCCGAAAGG GGCGAAGTTT
1201 ACAGGCTGGG GGCTTTTAAA AGATTTTGAA ACCTACAACA ACGCGAAAAT
1251 CCTCGACCTC AACAACACCG CCACCTTCCG GCTGCCCCGC GAAACCGAGT
1301 TGCAAACCAC TTTGGGCTTC AATTATTTCC ACAACGAATA CGGCAAAAAC
1351 CGCTTTCCTG AAGAATTGGG GCTGTTTTTC GACGGTCCTG ATCAGGACAA
1401 CGGGCTTTAT TCCTATTTGG GGCGGTTTAA GGGCGATAAA GGGCTGTTGC
1451 CTCAAAAATC AACCATTGTC CAACCGGCCG GCAGCCAATA TTTCAACACG
1501 TTCTACTTCG ATGCCGCGCT CAAAAAAGAC ATTTACCGCT TAAACTACAG
1551 CACCAATGCA ATCAACTACC GTTTCGGCGG CGAATATACG GGCTATTACG
1601 GCTCGGAAAA CGAATTTAAG CGGGCATTCG GAGAAAACTC GCCGGCATAC
1651 AAGGAACATT GCGACCCGAG CTGCGGGCTT TATGAACCCG TATTGAAAAA
1701 ATACGGCAAA AAGCGCGCCA ACAACCATTC GGTCAGCATT AGTGCGGACT
1751 TCGGCGATTA TTTCATGCCG TTCGCCGGCT ATTCGCGCAC ACACCGTATG
1801 CCCAACATCC AAGAAATGTA TTTTTCCCAA ATCGGCGACT CCGGCGTTCA
1851 CACCGCCTTA AAACCAGAGC GCGCAAACAC TTGGCAATTT GGCTTCAATA
1901 CCTATAAAAA AGGATTGTTA AAACAAGATG ATATATTAGG ATTGAAACTG
1951 GTCGGCTACC GCAGCCGCAT TGACAACTAC ATCCACAACG TTTACGGGAA
2001 ATGGTGGGAT TTGAACGGGG ATATTCCGAG CTGGGTCGGC AGCACCGGGC
2051 TTGCCTACAC CATCCGACAC CGCAATTTCA AAGACAAAGT GCACAAACAC
2101 GGTTTTGAGC TGGAGCTGAA TTACGATTAT GGGCGTTTTT TCACCAACCT
2151 TTCTTACGCC TATCAAAAAA GCACGCAACC GACCAATTTC AGCGATGCGA
2201 GCGAATCGCC CAACAATGCC tccaaAGAAG ACCAACTCAA ACAAGGTTAT
2251 GGGCTGAGCA GGGTTTCCGC CCTGCCGCGA GATTACGGAC GTTTGGAAGT
2301 CGGTACGCGC TGGTTGGGCA ACAAACTGAC TTTGGGCGGC GCGAtgCGCT
2351 ATTTCGGCAA GAGCATCCGC GCGACGGCTG AAGAACGCTA TATCGACGGC
2401 ACCAACGGGG GAAATACCAG CAATGTCCGG CAACTGGGCA AGCGTTCCAT
2451 CAAACAAACC GAAACCCTTG CCCGACAGCC TTTGATTTTT GATTTTTACG
2501 CCGCTTACGA GCCGAAGAAA AACCTTATTT TCCGCGCCGA AGTCAAAAAC
2551 CTGTTCGACA GGCGTTATAT CGATCCGCTC GATGCGGGCA ATGATGCGGC
2601 AACGCAGCGT TATTACAGCT CGTTCGACCC GAAAGACAAG GACGAAGACG
2651 TAACGTGTAA TGCTGATAAA ACGTTGTGCA ACGGCAAATA CGGCGGCACA
2701 AGCAAAAGCG TATTGACCAA TTTCGCACGC GGACGCACCT TCTTGATGAC
2751 GATGAGCTAC AAGTTTTAA

This corresponds to the amino acid sequence <SEQ ID 884; ORF133ng-1>:

1 MRSSFRLKPI CFYLMGVMLY HHSYAEDAGR AGSEAQIQVL EDVHVKAKRV
51 PKDKKVFTDA RAVSTRQDVF KSGENLDNIV RSIPGAFTQQ DKSSGIVSLN
101 IRGDSGFGRV NTMVDGITQT FYSTSTDAGR AGGSSQFGAS VDSNFIAGLD
151 VVKGSFSGSA GINSLAGSAN LRTLGVDDVV QGNNTYGLLL KGLTGTNSTK
201 GNAMAAIGAR KWLESGASVG VLYGHSRRGV AQNYRVGGGG QHIGNFGEEY
251 LERRKQQYFV QEGGLKFNAG SGKWERDLQR QYWKTKWYKK YEDPQELQKY
301 IEEHDKSWRE NLAPQYDITP IDPSGLKQQS AGNLFKLEYD GVFNKYTAQF
351 RDLNTRIGSR KIINRNYQFN YGLSLNPYTN LNLTAAYNSG RQKYPKGAKF
401 TGWGLLKDFE TYNNAKILDL NNTATFRLPR ETELQTTLGF NYFHNEYGKN
451 RFPEELGLFF DGPDQDNGLY SYLGRFKGDK GLLPQKSTIV QPAGSQYFNT
501 FYFDAALKKD IYRLNYSTNA INYRFGGEYT GYYGSENEFK RAFGENSPAY
551 KEHCDPSCGL YEPVLKKYGK KRANNHSVSI SADFGDYFMP FAGYSRTHRM
601 PNIQEMYFSQ IGDSGVHTAL KPERANTWQF GFNTYKKGLL KQDDILGLKL
651 VGYRSRIDNY IHNVYGKWWD LNGDIPSWVG STGLAYTIRH RNFKDKVHKH
701 GFELELNYDY GRFFTNLSYA YQKSTQPTNF SDASESPNNA SKEDQLKQGY
751 GLSRVSALPR DYGRLEVGTR WLGNKLTLGG AMRYFGKSIR ATAEERYIDG
801 TNGGNTSNVR QLGKRSIKQT ETLARQPLIF DFYAAYEPKK NLIFRAEVKN
851 LFDRRYIDPL DAGNDAATQR YYSSFDPKDK DEDVTCNADK TLCNGKYGGT
901 SKSVLTNFAR GRTFLMTMSY KF*

ORF133ng-1 and ORF133-1 show 96.2% identity in 889 aa overlap:

In addition, ORF133ng-1 is homologous to a TonB-dependent receptor in H. influenzae:

sp|P45114|YC17_HAEIN PROBABLE TONB-DEPENDENT RECEPTOR HI1217 PRECURSOR
>gi|1075372|pir||G64110 transferrin binding protein 1 precursor (tbp1)
homolog - Haemophilus influenzae (strain Rd KW20) >gi|1574147 (U32801)
transferrin binding protein 1 precursor (tbp1) [Haemophilus influenzae]
Length = 913
Score = 930 bits (2377), Expect = 0.0
Identities = 476/921 (51%), Positives = 619/921 (66%), Gaps = 72/921 (7%)

Query:	38	QVLEDVHVKAKRVPKDKKVFTDARAVSTRQDVFKSGENLDNIVRSIPGAFTQQDKSSGIV	97
		+ L  + V  K +  DKK FT+A+A STR++VFK  + +D ++RSIPGAFTQQDK SG+V
Sbjct:	29	ETLGQIDVVEKVISNDKKPFTEAKAKSTRENVFKETQTIDQVIRSIPGAFTQQDKGSGVV	88
Query:	98	SLNIRGDSGFGRVNTMVDGITQTFYSTSTDAGRAGGSSQFGASVDSNFIAGLDVVKGSFS	157
		S+NIRG++G GRVNTMVDG+TQTFYST+ D+G++GGSSQFGA++D NFIAG+DV K +FS
Sbjct:	89	SVNIRGENGLGRVNTMVDGVTQTFYSTALDSGQSGGSSQFGAAIDPNFIAGVDVNKSNFS	148
Query:	158	GSAGINSLAGSANLRTLGVDDVVQXXXXXXXXXXXXXXXXXXXXXAMAAIGARKWLESGA	217
		G++GIN+LAGSAN RTLGV+DV+                       M     RKWL++G
Sbjct:	149	GASGINALAGSANFRTLGVNDVITDDKPFGIILKGMTGSNATKSNFMTMAAGRKWLDNGG	208
Query:	218	SVGVLYGHSRRGVAQNYRVGGGGQHIGNFGEEYLERRKQQYFVQEGGLKFNAGSGKWERD	277
		VGV+YG+S+R V+Q+YR+ GGG+ + + G++ L + K+ YF +  G   N   G+W  D
Sbjct:	209	YVGVVYGYSQREVSQDYRI-GGGERLASLGQDILAKEKEAYF-RNAGYILNP-EGQWTPD	265
Query:	278	LQRQYWK-----------TKWY--------------------KKYEDPQELQK---YIEE	303
		L +++W              +Y                    KK +D ++LQK    IEE
Sbjct:	266	LSKKHWSCNKPDYQKNGDCSYYRIGSAAKTRREILQELLTNGKKPKDIEKLQKGNDGIEE	325
Query:	304	HDKSWRENLAPQYDITPIDPSGLKQQSAGNLFKLEYDGVFNKYTAQFRDLNTRIGSRKII	363
		DKS+  N   QY + PI+P  L+ +S  +L K EY        AQ R L+ +IGSRKI
Sbjct:	326	TDKSFERN-KDQYSVAPIEPGSLQSRSRSHLLKFEYGDDHQNLGAQLRTLDNKIGSRKIE	384
Query:	364	NRNYQFNYGLSLNPYTNLNLTAAYNSGRQKYPKGAKFTGWGLLKDFETYNNAKILDLNNT	423
		NRNYQ NY  + N Y +LNL AA+N G+  YPKG  F GW +     T N A I+D+NN+
Sbjct:	385	NRNYQVNYNFNNNSYLDLNLMAAHNIGKTIYPKGGFFAGWQVADKLITKNVANIVDINNS	444
Query:	424	ATFRLPRETELQTTLGFNYFHNEYGKNRFPEELGLFFDGPDQDNGLYSY--LGRFKGDKG	481
		TF LP+E +L+TTLGFNYF NEY KNRFPEEL LF++    D GLYS+   GR+ G K
Sbjct:	445	HTFLLPKEIDLKTTLGFNYFTNEYSKNRFPEELSLFYNDASHDQGLYSHSKRGRYSGTKS	504
Query:	482	LLPQKSTIVQPAGSQYFNTFYFDAALKKDIYRLNYSTNAINYRFGGEYTGYYGSENEFKR	541
		LLPQ+S I+QP+G Q F T YFD AL K IY LNYS N  +Y F GEY GY
Sbjct:	505	LLPQRSVILQPSGKQKFKTVYFDTALSKGIYHLNYSVNFTHYAFNGEYVGY---------	555
Query:	542	AFGENSPAYKEHCDPSCGLYEPVLKKYGKKRANNHSVSISADFGDYFMPFAGYSRTHRMP	601
		EN+   +        + EP+L K G K+A NHS ++SA+  DYFMPF  YSRTHRMP
Sbjct:	556	---ENTAGQQ--------INEPILHKSGHKKAFNHSATLSAELSDYFMPFFTYSRTHRMP	604
Query:	602	NIQEMYFSQIGDSGVHTALKPERANTWQFGFNTYKKGLLKQDDILGLKLVGYRSRIDNYI	661
		NIQEM+FSQ+ ++GV+TALKPE+++T+Q GFNTYKKGL  QDD+LG+KLVGYRS I NYI
Sbjct:	605	NIQEMFFSQVSNAGVNTALKPEQSDTYQLGFNTYKKGLFTQDDVLGVKLVGYRSFIKNYI	664
Query:	662	HNVYGKWWDLNGDIPSWVGSTGLAYTIRHRNFKDKVHKHGFELELNYDYGRFFTNLSYAY	721
		HNVYG WW     +P+W  S G  YTI H+N+K  V K G ELE+NYD GRFF N+SYAY
Sbjct:	665	HNVYGVWW--RDGMPTWAESNGFKYTIAHQNYKPIVKKSGVELEINYDMGRFFANVSYAY	722
Query:	722	QKSTQPTNFSDASESPNNASKEDQLKQGYGLSRVSALPRDYGRLEVGTRWLGNKLTLGGA	781
		Q++ QPTN++DAS  PNNAS+ED LKQGYGLSRVS LP+DYGRLE+GTRW   KLTLG A
Sbjct:	723	QRTNQPTNYADASPRPNNASQEDILKQGYGLSRVSMLPKDYGRLELGTRWFDQKLTLGLA	782
Query:	782	MRYFGKSIRATAEERYIDGTNGGNTSNVRQLGKRSIKQTETLARQPLIFDFYAAYEPKKN	841
		RY+GKS RAT EE YI+G+     + +R+    ++K+TE + +QP+I D + +YEP K+
Sbjct:	783	ARYYGKSKRATIEEEYINGSR-FKKNTLRRENYYAVKKTEDIKKQPIILDLHVSYEPIKD	841
Query:	842	LIFRAEVKNLFDRRYIDPLDAGNDAATQRYYSSFDPKDKDEDVTCNADKTLCNGKYGGTS	901
		LI +AEV+NL D+RY+DPLDAGNDAA+QRYYSS      +  + C  D + C    GG+
Sbjct:	842	LIIKAEVQNLLDKRYVDPLDAGNDAASQRYYSSL-----NNSIECAQDSSAC----GGSD	892
Query:	902	KSVLTNFARGRTFLMTMSYKF	922
		K+VL NFARGRT++++++YKF
Sbjct:	893	KTVLYNFARGRTYILSLNYKF	913

The underlined motif in the gonococcal protein (also present in the meningococcal protein) is predicted to be an ATP/GTP-binding site motif A (P-loop), and the analysis suggests that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

Example 104

The following partial DNA sequence was identified in N. meningitidis <SEQ ID 885>

1	ATGAACCTGA TTTCACGTTA CATCATCCGT CAAATGGCGG
	TTATGGCGGT
51	TTACGCGCTC CTTGCCTTCC TCGCTTTGTA CAGCTTTTTT
	GAAATCCTGT
101	ACGAAACCGG CAACCTCGGC AAAGGCAGTT ACGGCATATG
	GGAAATGCTG
151	GGCTACACCG CCCTCAAAAT GCCCGCCCGC GCCTACGAAC
	TGATTCCCCT
201	CGCCGTCCTT ATCGGCGGAC TGGTCTCCCT CAGCCAGCTT
	GCCGCCGGCA
251	GCGAACTGAC CGTCATCAAA GCCAGCGGCA TGAGCACCAA
	AAAGCTGCTG
301	TTGATTCTGT CGCAGTTCGG TTTTATTTTT GCTATTGCCA
	CCGTCGCGCT
351	CGGCGAATGG GTTGCGCCCA CACTGAGCCA AAAAGCCGAA
	AACATCAAAG
401	CCGCCGCCAT CAACGGCAAA ATCAGCACCG GCAATACCGG
	CCTTTGGCTG
451	AAAGAAAAAA ACAGCGTGAT CAATGTGCGC GAAATGTTGC
	CCGACCAT..

This corresponds to the amino acid sequence <SEQ ID 886; ORF112>:

1	MNLISRYIIR QMAVMAVYAL LAFLALYSFF EILYETGNLG
	KGSYGIWEML
51	GYTALKMPAR AYELIPLAVL IGGLVSLSQL AAGSELTVIK
	ASGMSTKKLL
101	LILSQFGFIF AIATVALGEW VAPTLSQKAE NIKAAAINGK
	ISTGNTGLWL
151	KEKNSVINVR EMLPDH...

Further work revealed further partial nucleotide sequence <SEQ ID 887>:

1	ATGAACCTGA TTTCACGTTA CATCATCCGT CAAATGGCGG
	TTATGGCGGT
51	TTACGCGCTC CTTGCCTTCC TCGCTTTGTA CAGCTTTTTT
	GAAATCCTGT
101	ACGAAACCGG CAACCTCGGC AAAGGCAGTT ACGGCATATG
	GGAAATGCTG
151	gGCTACACCG CCCTCAAAAT GCCCGCCCGC GCCTACGAAC
	TGATTCCCCT
201	CGCCGTCCTT ATCGGCGGAC TGGTCTCCCT CAGCCAGCTT
	GCCGCCGGCA
251	GCGAACTGAC CGTCATCAAA GCCAGCGGCA TGAGCACCAA
	AAAGCTGCTG
301	TTGATTCTGT CGCAGTTCGG TTTTATTTTT GCTATTGCCA
	CCGTCGCGCT
351	CGGCGAATGG GTTGCGCCCA CACTGAGCCA AAAAGCCGAA
	AACATCAAAG
401	CCGCCGCCAT CAACGGCAAA ATCAGCACCG GCAATACCGG
	CCTTTGGCTG
451	AAAGAAAAAA ACAGCrTkAT CAATGTGCGC GAAATGTTGC
	CCGACCATAC
501	GCTTTTGGGC ATCAAAATTT GGGCGCGCAA CGATAAAAAC
	GAATTGGCAG
551	AGGCAGTGGA AGCCGATTCC GCCGTTTTGA ACAGCGACGG
	CAGTTGGCAG
601	TTGAAAAACA TCCGCCGCAG CACGCTTGGC GAAGACAAAG
	TCGAGGTCTC
651	TATTGCGGCT GAAGAAAACT GGCCGATTTC CGTCAAACGC
	AACCTGATGG
701	ACGTATTGCT CGTCAAACCC GACCAAATGT CCGTCGGCGA
	ACTGACCACC
751	TACATCCGCC ACCTCCAAAA CAACAGCCAA AACACCCGAA
	TCTACGCCAT
801	CGCATGGTGG CGCAAATTGG TTTACCCCGC CGCAGCCTGG
	GTGATGGCGC
851	TCGTCGCCTT TGCCTTTACC CCGCAAACCA CCCGCCACGG
	CAATATGGGC
901	TTAAAACTCT TCGGCGGCAT CTGTsTCGGA TTGCTGTTCC
	ACCTTGCCGG
951	ACGGCTCTTT GGGTTTACCA GCCAACTCGG...

This corresponds to the amino acid sequence <SEQ ID 888; ORF112-1>:

1	MNLISRYIIR QMAVMAVYAL LAFLALYSFF EILYETGNLG
	KGSYGIWEML
51	GYTALKMPAR AYELIPLAVL IGGLVSLSQL AAGSELTVIK
	ASGMSTKKLL
101	LILSQFGFIF AIATVALGEW VAPTLSQKAE NIKAAAINGK
	ISTGNTGLWL
151	KEKNSXINVR EMLPDHTLLG IKIWARNDKN ELAEAVEADS
	AVLNSDGSWQ
201	LKNIRRSTLG EDKVEVSIAA EENWPISVKR NLMDVLLVKP
	DQMSVGELTT
251	YIRHLQNNSQ NTRIYAIAWW RKLVYPAAAW VMALVAFAFT
	PQTTRHGNMG
301	LKLFGGICXG LLFHLAGRLF GFTSQL...

Computer analysis of this amino acid sequence predicts two transmembrane domains and gave the following results:

Homology with a Predicted ORF from N. meningitidis (Strain A)

ORF112 shows 96.4% identity over a 166aa overlap with an ORF (ORF112a) from strain A of N. meningitidis:

The ORF112a nucleotide sequence <SEQ ID 889> is:

1	ATGAACCTGA TTTCACGTTA CATCATCCGT CAAATGGCGG
	TTATGGCGGT
51	TTACGCGCTC CTTGCCTTCC TCGCTTTGTA CAGCTTTTTT
	GAAATCCTGT
101	ACGAAACCGG CAACCTCGGC AAAGGCAGTT ACGGCATATG
	GGAAATGNTG
151	GGNTACACCG CCCTCAAAAT GNCCGCCCGC GCCTACGAAC
	TGATGCCCCT
201	CGCCGTCCTT ATCGGCGGAC TGGTCTCTNT CAGCCAGCTT
	GCCGCCGGCA
251	GCGAACTGAN CGTCATCAAA GCCAGCGGCA TGAGCACCAA
	AAAGCTGCTG
301	TTGATTCTGT CGCAGTTCGG TTTTATTTTT GCTATTGCCA
	CCGTCGCGCT
351	CGGCGAATGG GTTGCGCCCA CACTGAGCCA AAAAGCCGAA
	AACATCAAAG
401	CCGCGGCCAT CAACGGCAAA ATCAGTACCG GCAATACCGG
	CCTTTGGCTG
451	AAAGAAAAAA ACAGCATTAT CAATGTGCGC GAAATGTTGC
	CCGACCATAC
501	CCTGCTGGGC ATTAAAATCT GGGCCCGCAA CGATAAAAAC
	GAACTGGCAG
551	AGGCAGTGGA AGCCGATTCC GCCGTTTTGA ACAGCGACGG
	CAGTTGGCAG
601	TTGAAAAACA TCCGCCGCAG CACGCTTGGC GAAGACAAAG
	TCGAGGTCTC
651	TATTGCGGCT GAAGAAAANT GGCCGATTTC CGTCAAACGC
	AACCTGATGG
701	ACGTATTGCT CGTCAAACCC GACCAAATGT CCGTCGGCGA
	ACTGACCACC
751	TACATCCGCC ACCTCCAAAN NNACAGCCAA AACACCCGAA
	TCTACGCCAT
801	CGCATGGTGG CGCAAATTGG TTTACCCCGC CGCAGCCTGG
	GTGATGGCGC
851	TCGTCGCCTT TGCCTTTACC CCGCAAACCA CCCGCCACGG
	CAATATGGGC
901	TTAAAANTCT TCGGCGGCAT CTGTCTCGGA TTGCTGTTCC
	ACCTTGCCGG
951	NCGGCTCTTC NGGTTTACCA GCCAACTCTA CGGCATCCCG
	CCCTTCCTCG
1001	NCGGCGCACT ACCTACCATA GCCTTCGCCT TGCTCGCCGT
	TTGGCTGATA
1051	CGCAAACAGG AAAAACGCTA A

This encodes a protein having the amino acid sequence <SEQ ID 890>:

1	MNLISRYIIR QMAVMAVYAL LAFLALYSFF EILYETGNLG
	KGSYGIWEMX
51	GYTALKMXAR AYELMPLAVL IGGLVSXSQL AAGSELXVIK
	ASGMSTKKLL
101	LILSQFGFIF AIATVALGEW VAPTLSQKAE NIKAAAINGK
	ISTGNTGLWL
151	KEKNSIINVR EMLPDHTLLG IKIWARNDKN ELAEAVEADS
	AVLNSDGSWQ
201	LKNIRRSTLG EDKVEVSIAA EEXWPISVKR NLMDVLLVKP
	DQMSVGELTT
251	YIRHLQXXSQ NTRIYAIAWW RKLVYPAAAW VMALVAFAFT
	PQTTRHGNMG
301	LKXFGGICLG LLFHLAGRLF XFTSQLYGIP PFLXGALPTI
	AFALLAVWLI
351	RKQEKR*

ORF112a and ORF112-1 show 96.3% identity in 326 aa overlap:

Homology with a Predicted ORF from N. gonorrhoeae

ORF112 shows 95.8% identity over 166aa overlap with a predicted ORF (ORF112ng) from N. gonorrhoeae:

The complete length ORF112ng nucleotide sequence <SEQ ID 891> is:

1	ATGAACCTGA TTTCACGTTA CATCATCCGC CAAATGGCGG
	TTATGGCGGT
51	TTACGCGCTC CTTGCCTTCC TCGCTTTGTA CAGCTTTTTT
	GAAATCCTGT
101	ACGAAACCGG CAACCTCGGC AAAGGCAGTT ACGGCATATG
	GGAAATGCTG
151	GGCTACACCG CCCTCAAAAT GCCCGCCCGC GCCTACGAAC
	TCATGCCCCT
201	CGCCGTCCTC ATCGGCGGAC TGGCCTCTCT CAGCCAGCTT
	GCCGCCGGCA
251	GCGAACTGGC CGTCATCAAA GCCAGCGGCA TGAGCACCAA
	AAAGCTGCTG
301	TTGATTCTGT CTCAGTTCGG TTTTATTTTT GCTATTGCCG
	CCGTCGCGCT
351	CGGCGAATGG GTTGCGCCCA CGCTGAGCCA AAAAGCCGAA
	AACATCAAag
401	cCGCCGCCAt taacggCAAA ATCAGCAccg gcAATACCGG
	CCTTTggcTG
451	AAAGAAAAAa ccAGCATTAT CAATGTGcGc GGAATGTTGC
	CCGACCATAC
501	GCTTTTGGGC ATCAAAATTT GGGCGCGCAA CGATAAAAAC
	GAATTGGCAG
551	AGGCAGTGGA AGCCGATTCC GCCGTTTTGA ACAGCGACGG
	CAGCTGGCAG
601	TTGAAAAACA TCCGCCGCAG CATCATGGGT ACAGACAAAA
	TCGAAACATC
651	cgCCGCCGCC GAAGAAACTT gGCCGATTGC CGTCAGACGC
	AACCTGATGG
701	ACGTATTGCT CGTCAAGCCC GACCAAATGT CCGTCGGCGA
	GCTGACCACC
751	TACATCCGCC ACCTCCAAAA CAACAGCCAA AACACCCAAA
	TCTACGCCAT
801	CGCATGGTGG CGTAAACTCG TTTACCCCGT CGCCGCATGG
	GTCATGGCGC
851	TCGTTGCCTT CGCCTTTACG CCGCAAACCA CGCGCCACGG
	CAATATGGGC
901	TTAAAACTCT TCGGCGGCAT CTGTCTCGGA TTGCTGTTCC
	ACCTTGCCGG
951	CAGGCTCTTC GGGTTTACCA GCCAACTCTA CGGCACCCCA
	CCCTTCCTCG
1001	CCGGCGCACT GCCTACCATA GCCTTCGCCT TGCTCGCTGT
	TTGGCTGATA
1051	CGCAAACAGG AAAAACGTTG A

This encodes a protein having amino acid sequence <SEQ ID 892>:

1	MNLISRYIIR QMAVMAVYAL LAFLALYSFF EILYETGNLG
	KGSYGIWEML
51	GYTALKMPAR AYELMPLAVL IGGLASLSQL AAGSELAVIK
	ASGMSTKKLL
101	LILSQFGFIF AIAAVALGEW VAPTLSQKAE NIKAAAINGK
	ISTGNTGLWL
151	KEKTSIINVR GMLPDHTLLG IKIWARNDKN ELAEAVEADS
	AVLNSDGSWQ
201	LKNIRRSIMG TDKIETSAAA EETWPIAVRR NLMDVLLVKP
	DQMSVGELTT
251	YIRHLQNNSQ NTQIYAIAWW RKLVYPVAAW VMALVAFAFT
	PQTTRHGNMG
301	LKLFGGICLG LLFHLAGRLF GFTSQLYGTP PFLAGALPTI
	AFALLAVWLI

• • 351 RKQEKR*

ORF112ng and ORF112-1 show 94.2% identity in 326 aa overlap:

This analysis suggests that these proteins from N. meningitidis and N. gonorrhoeae, and their epitopes, could be useful antigens for vaccines or diagnostics, or for raising antibodies.

It will be appreciated that the invention has been described by means of example only, and that modifications may be made whilst remaining within the spirit and scope of the invention.

TABLE I
PCR primers

ORF	Primer	Sequence	Restriction sites
ORF 1	Forward	CGCGGATCCGCTAGC-GGACACACTTATTTCGG	BamHI-NheI
	Reverse	CCCGCTCGAG-CCAGCGGTAGCCTAATT	XhoI
ORF 2	Forward	GCGGATCCCATATG-TTTGATTTCGGTTTGGG	BamHI-NdeI
	Reverse	CCCGCTCGAG-GACGGCATAACGGCG	XhoI
ORF 2-1	Forward	GCGGATCCCATATG-TTTGATTTCGGTTTGGG	BamHI-NdeI
	Reverse	CCCGCTCGAG-TGATTTACGGACGCGCA	XhoI
ORF 4	Forward	GCGGATCCCATATG-TGCGGAGGTCAAAAAGAC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTTGGCTGCGCCTTC	XhoI
ORF 5	Forward	GGAATTCCATATGGCCATGG-TGGAAGGCGCACAACC	NdeI-NcoI
	Forward	CGGGATCC-ATGGAAGGCGCACAAC	BamHI
	Reverse	CCCGCTCGAG-GACTGTGCAAAAACGG	XhoI
ORF 6	Forward	CGCGGATCCCATATG-ACCCGTCAATCTCTGCA	BamHI-NdeI
	Reverse	CCCGCTCGAG-TGCGCCGAACACTTTC	XhoI
ORF 7	Forward	CGCGGATCCGCTAGC-GCGCTGCTTTTTGTTCC	BamHI-NheI
	Reverse	CCCGCTCGAG-TTTCAAAATATATTTGCGGA	XhoI
ORF 8	Forward	GCGGATCCCATATG-GCTCAACTGCTTCGTAC	BamHI-NdeI
	Reverse	CCCGCTCGAG-AGCAGGCTTTGGCGC	XhoI
ORF 9	Forward	CGCGGATCCCATATG-CCGAAGGAAGTCGGAAA	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTTCCGAGGTTTTCGGG	XhoI
ORF 10	Forward	GCGGATCCCATATG-GACACAAAAGAAATCCTC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TAATGGGAAACCTTGTTTT	XhoI
ORF 11	Forward	GCGGATCCCATATG-GCGGTCAACCTCTACG	BamHI-NdeI
	Reverse	CCCGCTCGAG-GGAAACGACTTCGCC	XhoI
ORF 13	Forward	CGCGGATCCCATATG-GCTCTGCTTTCCGCGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-AGGGTGTGTGATAATAAG	XhoI
ORF 15	Forward	GGAATTCCATATGGCCATGG-GCGGGACACTGACAG	NdeI-NcoI
	Forward	CGGGATCC-TGCGGGACACTGACAGG	BamHI
	Reverse	CCCGCTCGAG-AGGTTGGCCTTGTCTATG	XhoI
ORF 17	Forward	GGAATTCCATATGGCCATGG-TTGCCGGCCTGTTCG	NdeI-NcoI
	Forward	CGGGATCC-ATTGCCGGCCTGTTCG	BamHI
	Reverse	CCCGCTCGAG-AAGCAGGTTGTACAGC	XhoI
ORF 18	Forward	GCGGATCCCATATG-ATTTTGCTGCATTTGGAT	BamHI-NdeI
	Reverse	CCCGCTCGAG-TCTTCCAATTTCTGAAAGC	XhoI
ORF 19	Forward	GGAATTCCATATGGCCATGG -TCGCCAGTGTTTTTACC	NdeI-NcoI
	Forward	CGGGATCC-TTCGCCAGTGTTTTTACCG	BamHI
	Reverse	CCCGCTCGAG-GGTGTTTTTGAAGCTGCC	XhoI
ORF 20	Forward	GGAATTCCATATGGCCATGG -TCGGCGCGGGTATG	NdeI-NcoI
	Forward	CGGGATCC-TTCGGCGCGGGTATG	BamHI
	Reverse	CCCGCTCGAG-CGGCGAGCGAGAGCA	XhoI
ORF 22	Forward	GGAATTCCATATGGCCATGG-TGATTAAAATCAAAAAAGGTCT	NdeI-NcoI
	Forward	CGGGATCC-ATGATTAAAATCAAAAAAGGTCTAAACC	BamHI
	Reverse	CCCGCTCGAG-ATTATGATAGCGGCCC	XhoI
ORF 23	Forward	CGCGGATCCCATATG-GATGTTTCTGTTTCAGAC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTTAAACCGATAGGTAAACG	XhoI
ORF 24	Forward	GGAATTCCATATGGCCATGG- TGATGCCGGAAATGGTG	NdeI-NcoI
	Forward	CGGGATCC-ATGATGCCGGAAATGGTG	BamHI
	Reverse	CCCGCTCGAG-TGTCAGCGTGGCGCA	XhoI
ORF 25	Forward	GCGGATCCCATATG-TATCGCAAACTGATTGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-ATCGATGGAATAGCCG	XhoI
ORF 26	Forward	GCGGATCCCATATG -CAGCTGATCGACTATTC	BamHI-NdeI
	Reverse	CCCGCTCGAG-GACATCGGCGCGTTTT	XhoI
ORF 27	Forward	GGAATTCCATATGGCCATGG-AGACCTATTCTGTTTA	NdeI-NcoI
	Forward	CGGGATCC- CAGACCTATTCTGTTTATTTTAATC	BamHI
	Reverse	CCCGCTCGAG-GGGTTCGATTAAATAACCAT	XhoI
ORF 28	Forward	GGAATTCCATATGGCCATGG-ACGGCTGTACGTTGATGT	NdeI-NcoI
	Forward	CGGGATCC-AACGGCTGTACGTTGATG	BamHI
	Reverse	CCCGCTCGAG-TTTGTCAGAGGAATTCGCG	XhoI
ORF 29	Forward	GCGGATCCCATATG -AACGGTTTGGATGCCCG	BamHI-NdeI
	Forward	CGCGGATCCGCTAGC-AACGGTTTGGATGCCCG	BamHI-NheI
	Reverse	CCCGCTCGAG-TTTGTCTAAGTTCCTGATATG	XhoI
ORF 32	Forward	CGCGGATCCCATATG-AATACTCCTCCTTTTG	BamHI-NdeI
	Reverse	CCCGCTCGAG-GCGTATTTTTTGATGCTTTG	XhoI
ORF 33	Forward	GCGGATCCCATATG -ATTGATAGGGATCGTATG	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTGATCTTTCAAACGGCC	XhoI
ORF 35	Forward	GCGGATCCCATATG-TTCAGAGCTCAGCTT	BamHI-NdeI
	Forward	CGCGGATCCGCTAGC-TTCAGAGCTCAGCTT	BamHI-NheI
	Reverse	CCCGCTCGAG-AAACAGCCATTTGAGCGA	XhoI
ORF 37	Forward	GCGGATCCCATATG-GATGACGTATCGGATTTT	BamHI-NdeI
	Reverse	CCCGCTCGAG-ATAGCCCGCTTTCAGG	XhoI
ORF 58	Forward	CGCGGATCCGCTAGC-TCCGAACGCGAGTGGAT	BamHI-NheI
	Reverse	CCCGCTCGAG-AGCATTGTCCAAGGGGAC	XhoI
ORF 65	Forward	GGAATTCCATATGGCCATGG -TGCTGTATCTGAATCAAG	NdeI-NcoI
	Forward	CGGGATCC-TTGCTGTATCTGAATCAAGG	BamHI
	Reverse	CCCGCTCGAG-CCGCATCGGCAGACA	XhoI
ORF 66	Forward	GCGGATCCCATATG-TACGCATTTACCGCCG	BamHI-NdeI
	Reverse	CCCGCTCGAG-TGGATTTTGCAGAGATGG	XhoI
ORF 72	Forward	CGCGGATCCCATATG- AATGCAGTAAAAATATCTGA	BamHI-NdeI
	Reverse	CCCGCTCGAG-GCCTGAGACCTTTGCAA	XhoI
ORF 73	Forward	GCGGATCCCATATG-AGATTTTTCGGTATCGG	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTCATCTTTTTCATGTTCG	XhoI
ORF 75	Forward	GCGGATCCCATATG- TCTGTCTTTCAAACGGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTTGTTTTTGCAAGACAG	XhoI
ORF 76	Forward	GATCAGCTAGCCATATG-AAACAGAAAAAAACCGC	NheI-NdeI
	Reverse	CGGGATCC-TTACGGTTTGACACCGTT	BamHI
ORF 79	Forward	CGCGGATCCCATATG-GTTTCCGCCGCCG	BamHI-NdeI
	Reverse	CCCGCTCGAG-GTGCTGATGCGCTTCG	XhoI
ORF 83	Forward	GCGGATCCCATATG-AAAACCCTGCTGCTGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-GCCGCCTTTGCGGC	XhoI
ORF 84	Forward	GCGGATCCCATATG-GCAGAGATCTGTTTG	BamHI-NdeI
	Reverse	CCCGCTCGAG-GTTTGCCGATCCGACCA	XhoI
ORF 85	Forward	CGCGGATCCCATATG- GCGGTTTGGGGCGGA	BamHI-NdeI
	Reverse	CCCGCTCGAG-TCGGCGCGGCGGGC	XhoI
ORF 89	Forward	GGAATTCCATATGGCCATGG-CCATACCTTCTTATCA	NdeI-NcoI
	Forward	CGGGATCC-GCCATACCTTCTTATCAGAG	BamHI
	Reverse	CCCGCTCGAG-TTTTTTGCGATTAGAAAAAGC	XhoI
ORF 97	Forward	GCGGATCCCATATG-CATCCTGCCAGCGAAC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTCGCCTACGGTTTTTTG	XhoI
ORF 98	Forward	GCGGATCCCATATG-ACGGTAACTGCGG	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTGTTGTTCGGGCAAATC	XhoI
ORF 100	Forward	GCGGATCCCATATG-TCGGGCATTTACACCG	BamHI-NdeI
	Reverse	CCCGCTCGAG-ACGGGTTTCGGCGGAA	XhoI
ORF 101	Forward	GCGGATCCCATATG-ATTTATCAAAGAAACCTC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTTTCCGCCTTTCAATGT	XhoI
ORF 102	Forward	GCGGATCCCATATG-GCAGGGCTGTTTTACC	BamHI-NdeI
	Reverse	CCCGCTCGAG-AAACGGTTTGAACACGAC	XhoI
ORF 103	Forward	GCGGATCCCATATG-AACCACGACATCAC	BamHI-NdeI
	Reverse	CCCGCTCGAG-CAGCCACAGGACGGC	XhoI
ORF 104	Forward	GCGGATCCCATATG-ACGTGGGGAACGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-GCGGCGTTTGAACGGC	XhoI
ORF 105	Forward	GCGGATCCCATATG-ACCAAATTTCAAACCCCTC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TAAACGAATGCCGTCCAG	XhoI
ORF 106	Forward	GCGGATCCCATATG-AGGATAACCGACGGCG	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTTGTTCCCGATGATGTT	XhoI
ORF 109	Forward	GCGGATCCCATATG-GAAGATTTATATATAATACTCG	BamHI-NdeI
	Reverse	CCCGCTCGAG-ATCAGCTTCGAACCGAAG	XhoI
ORF 110	Forward	AAAGAATTC-ATGAGTAAATCCCGTAGATCTCCC	EcoRI
	Reverse	AAACTGCAG-GGAAAACCACATCCGCACTCTGCC	PstI
ORF 111	Forward	AAAGAATTC-GCACCGCAAAAGGCAAAAACCGCA	EcoRI
	Reverse	AAACTGCAG-TCTGCGCGTTTTCGGGCAGGGTGG	PstI
ORF 113	Forward	AAAGAATTC-ATGAACAAAACCCTCTATCGTGTGATTTTCAACCG	EcoRI
	Reverse	AAACTGCAG-TTACGAATGCCTGCTTGCTCGACCGTACTG	PstI
ORF 115	Forward	AAAGAATTC-TTGCTTGTGCAAACAGAAAAAGACGG	EcoRI
	Reverse	AAAAAAGTCGAC-CTATTTTTTAGGGGCTTTTGCTTGTTTGAAAAGCCTGCC	SalI
ORF 119	Forward	AAAGAATTC-TACAACATGTATCAGGAAAACCAATACCG	EcoRI
	Reverse	AAACTGCAG-TTATGAAAACAGGCGCAGGGCGGTTTTGCC	PstI
ORF 120	Forward	AAAGAATTC-GCAAGGCTACCCCAATCCGCCGTG	EcoRI
	Reverse	AAACTGCAG-CGGTTTGGCTGCCTGGCCGTTGAT	PstI
ORF 121	Forward	AAAGAATTC-GCCTTGGTCTGGCTGGTTTTCGC	EcoRI
	Reverse	AAACTGCAG-TCATCCGCCACCCCACCTCGGCCATCCATC	PstI
ORF 122	Forward	AAAAAAGTCGAC-ATGTCTTACCGCGCAAGCAGTTCTCC	SalI
	Reverse	AAACTGCAG-TCAGGAACACAAACGATGACGAATATCCGTATC	PstI
ORF 125	Forward	AAAGAATTC-GCGCTGTTTTTTGCGGCGGCGTAT	EcoRI
	Reverse	AAACTGCAG-CGCCGTTTCAAGACGAAAAAGTCG	PstI
ORF 126	Forward	AAAGAATTC-GCGGAAACGGTCGAAG	EcoRI
	Reverse	AAACTGCAG-TTAATCTTGTCTTCCGATATAC	PstI
ORF 127	Forward	AAAGAATTC-ATGACTGATAATCGGGGGTTTACG	EcoRI
	Reverse	AAAAAAGTCGAC-CTTAAGTAACTTGCAGTCCTTATC	SalI
ORF 128	Forward	AAAGAATTC-ATGCAAGCTGTCCGCTACAGGCC	EcoRI
	Reverse	AAACTGCAG-CTATTGCAATGCGCCGCCGCGGGAATGTTTGAGCAGGCG	PstI
ORF 129	Forward	AAAGAATTC-ATGGATTTTCGTTTTGACATTATTTACGAATACCG	EcoRI
	Reverse	AAACTGCAG-TTATTTTTTGATGAAATTTTGGGGCGG	PstI
ORF 130	Forward	AAAGAATTC-GCAGTACTTGCCATTCTCGGTGCG	EcoRI
	Reverse	AAACTGCAG-CTCCGGATCGTCTGTAAACGCATT	PstI
ORF 131	Forward	GCGGATCCCATATG-GAAATTCGGGCAATAAAAT	BamHI-NdeI
	Reverse	CCCGCTCGAG-CCAGCGGACGCGTTC	XhoI
ORF 132	Forward	GCGGATCCCATATG-AAAGAAGCGGGGTTTG	BamHI-NdeI
	Reverse	CCCGCTCGAG-CCAATCTGCCAGCCGT	XhoI
ORF 133	Forward	CGCGGATCCCATATG-GAAGATGCAGGGCGCG	BamHI-NdeI
	Reverse	CCCGCTCGAG-AAACTTGTAGCTCATCGT	XhoI
ORF 134	Forward	GCGGATCCCATATG-TCTGTGCAAGCAGTATTG	BamHI-NdeI
	Reverse	CCCGCTCGAG-ATCCTGTGCCAATGCG	XhoI
ORF 135	Forward	GCGGATCCCATATG-CCGTCTGAAAAAGCTTT	BamHI-NdeI
	Reverse	CCCGCTCGAG-AAATACCGCTGAGGATG	XhoI
ORF 136	Forward	CGCGGATCCGCTAGC-ATGAAGCGGCGTATAGCC	BamHI-NheI
	Reverse	CCCGCTCGAG-TTCCGAATATTTGGAACTTTT	XhoI
ORF 137	Forward	CGCGGATCCCATATG-GGCACGGCGGGAAATA	BamHI-NdeI
	Reverse	CCCGCTCGAG-ATAACGGTATGCCGCC	XhoI
ORF 138	Forward	GCGGATCCCATATG-TTTCGTTTACAATTCAGGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-CGGCGTTTTATAGCGG	XhoI
ORF 139	Forward	GCGGATCCCATATG-GCTTTTTTGGCGGTAATG	BamHI-NdeI
	Reverse	CCCGCTCGAG-TAACGTTTCCGTGCGTTT	XhoI
ORF 140	Forward	GCGGATCCCATATG-TTGCCCACAGGCAGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-GACGATGGCAAACAGC	XhoI
ORF 141	Forward	GCGGATCCCATATG-CCGTCTGAAGCAGTCT	BamHI-NdeI
	Reverse	CCCGCTCGAG-ATCTGTTGTTTTTAAAATATT	XhoI
ORF 142	Forward	GCGGATCCCATATG-GATAATTCTGGTAGTGAAG	BamHI-NdeI
	Reverse	CCCGCTCGAG-AAACGTATAGCCTACCT	XhoI
ORF 143	Forward	GCGGATCCCATATG-GATACCGCTTTGAACCT	BamHI-NdeI
	Reverse	CCCGCTCGAG-AATGGCTTCCGCAATATG	XhoI
ORF 144	Forward	GCGGATCCCATATG-ACCTTTTTACAACGTTTGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-AGATTGTTGTTGTTTTTTCG	XhoI
ORF 147	Forward	GCGGATCCCATATG-TCTGTCTTTCAAACGGC	BamHI-NdeI
	Reverse	CCCGCTCGAG-TTTGTTTTTGCAAGACAG	XhoI
NB:
restriction sites are underlined
for ORFs 110-130, where the ORF itself carries an EcoRI site (eg. ORF 122), a SalI site was used in the forward primer instead. Similarly, where the ORF carries a PstI site (eg. ORFs 115 and 127), a SalI site was used in the reverse primer.

TABLE II
Summary of cloning, expression and purification

		PCR/	His-fusion	GST-fusion
	ORF	cloning	expression	expression	Purification
	orf 1	+	+	+	His-fusion
	orf 2	+	+	+	GST-fusion
	orf 2.1	+	n.d.	+	GST-fusion
	orf 4	+	+	+	His-fusion
	orf 5	+	n.d.	+	GST-fusion
	orf 6	+	+	+	GST-fusion
	orf 7	+	+	+	GST-fusion
	orf 8	+	n.d.	n.d.
	orf 9	+	+	+	GST-fusion
	orf 10	+	n.d.	n.d.
	orf 11	+	n.d.	n.d.
	orf 13	+	n.d.	+	GST-fusion
	orf 15	+	+	+	GST-fusion
	orf 17	+	n.d.	n.d.
	orf 18	+	n.d.	n.d.
	orf 19	+	n.d.	n.d.
	orf 20	+	n.d.	n.d.
	orf 22	+	+	+	GST-fusion
	orf 23	+	+	+	His-fusion
	orf 24	+	n.d.	n.d.
	orf 25	+	+	+	His-fusion
	orf 26	+	n.d.	n.d.
	orf 27	+	+	+	GST-fusion
	orf 28	+	+	+	GST-fusion
	orf 29	+	n.d.	n.d.
	orf 32	+	+	+	His-fusion
	orf 33	+	n.d.	n.d.
	orf 35	+	n.d.	n.d.
	orf 37	+	+	+	GST-fusion
	orf 58	+	n.d.	n.d.
	orf 65	+	n.d.	n.d.
	orf 66	+	n.d.	n.d.
	orf 72	+	+	n.d.	His-fusion
	orf 73	+	n.d.	+	n.d.
	orf 75	+	n.d.	n.d.
	orf 76	+	+	n.d.	His-fusion
	orf 79	+	+	n.d.	His-fusion
	orf 83	+	n.d.	+	n.d.
	orf 84	+	n.d.	n.d.
	orf 85	+	n.d.	+	GST-fusion
	orf 89	+	n.d.	+	GST-fusion
	orf 97	+	+	+	GST-fusion
	orf 98	+	n.d.	n.d.
	orf 100	+	n.d.	n.d.
	orf 101	+	n.d.	n.d.
	orf 102	+	n.d.	n.d.
	orf 103	+	n.d.	n.d.
	orf 104	+	n.d.	n.d.
	orf 105	+	n.d.	n.d.
	orf 106	+	+	+	His-fusion
	orf 109	+	n.d.	n.d.
	orf 110	+	n.d.	n.d.
	orf 111	+	+	n.d.	His-fusion
	orf 113	+	+	n.d.	His-fusion
	orf 115	n.d.	n.d.	n.d.
	orf 119	+	+	n.d.	His-fusion
	orf 120	+	+	n.d.	His-fusion
	orf 121	+	n.d.	n.d.
	orf 122	+	+	n.d.	His-fusion
	orf 125	+	+	n.d.	His-fusion
	orf 126	+	+	n.d.	His-fusion
	orf 127	+	+	n.d.	His-fusion
	orf 128	+	n.d.	n.d.
	orf 129	+	+	n.d.	His-fusion
	orf 130	+	n.d.	n.d.
	orf 131	+	+	+	n.d.
	orf 132	+	+	+	His-fusion
	orf 133	+	n.d.	+	GST-fusion
	orf 134	+	n.d.	n.d.
	orf 135	+	n.d.	n.d.
	orf 136	+	n.d.	n.d.
	orf 137	+	n.d.	+	GST-fusion
	orf 138	+	n.d.	+	GST-fusion
	orf 139	+	n.d.	n.d.
	orf 140	+	n.d.	n.d.
	orf 141	+	n.d.	n.d.
	orf 142	+	n.d.	n.d.
	orf 143	+	n.d.	n.d.
	orf 144	+	n.d.	+	n.d.
	orf 147	+	n.d.	n.d.