# Patent

## Title
Chlamydia trachomatis genomic sequence and polypeptides, fragments thereof and uses thereof, in particular for the diagnosis, prevention and treatment of infection

## Abstract

The subject of the invention is the genomic sequence and the nucleotide sequences encoding polypeptides of Chlamydia trachomatis, such as cellular envelope polypeptides, which are secreted or specific, or which are involved in metabolism, in the replication process or in virulence, polypeptides encoded by such sequences, as well as vectors including the said sequences and cells or animals transformed with these vectors. The invention also relates to transcriptional gene products of the Chlamydia trachomatis genome, such as, for example, antisense and ribozyme molecules, which can be used to control growth of the microorganism. The invention also relates to methods of detecting these nucleic acids or polypeptides and kits for diagnosing Chlamydia trachomatis infection. The invention also relates to a method of selecting compounds capable of modulating bacterial infection and a method for the biosynthesis or biodegradation of molecules of interest using the said nucleotide sequences or the said polypeptides. The invention finally comprises, pharmaceutical, in particular vaccine, compositions for the prevention and/or treatment of bacterial, in particular Chlamydia trachomatis, infections.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional U.S. application Ser. No. 12/491,474, filed on Jun. 25, 2009, now U.S. Pat. No. 7,910,329, which is divisional of U.S. application Ser. No. 11/366,965, filed Mar. 2, 2006, now U.S. Pat. No. 7,575,913, which is a divisional of U.S. application Ser. No. 09/201,228, filed Nov. 30, 1998, now U.S. Pat. No. 7,041,490, which claims priority from U.S. application Ser. No. 60/107,077, filed Nov. 4, 1998, abandoned.


The Sequence Listing for this application is labeled “seq-list.txt”, which was created on Feb. 28, 2006, and is 4,771 KB. The entire contents is incorporated herein by reference in its entirety.
The subject of the invention is the genomic sequence and the nucleotide sequences encoding polypeptides of Chlamydia trachomatis, such as cellular envelope polypeptides, which are secreted or specific, or which are involved in metabolism, in the replication process or in virulence, polypeptides encoded by such sequences as well as vectors including the said sequences and cells or animals transformed with these vectors. The invention also relates to transcriptional gene products of the Chlamydia trachomatis genome, such as, for example, antisense and ribozyme molecules, which can be used to control growth of the microorganism. The invention also relates to methods of detecting these nucleic acids or polypeptides and kits for diagnosing Chlamydia trachomatis infection. The invention also relates to a method of selecting compounds capable of modulating bacterial infection and a method for the biosynthesis or biodegradation of molecules of interest using the said nucleotide sequences or the said polypeptides. The invention finally comprises pharmaceutical, in particular vaccine, compositions for the prevention and/or treatment of bacterial, in particular Chlamydia trachomatis, infections.
The genus Chlamydia is composed of four species: Chlamydia psittaci, Chlamydia pecorum, Chlamydia pneumoniae and Chlamydia trachomatis. 
Chlamydia psittaci comprises numerous species, whose hosts are terrestrial vertebrate animals as well as birds and occasionally humans;
Chlamydia pecorum is a pathogen of ruminants;
Chlamydia pneumoniae is responsible for pneumopathies, for sinusitis and for arterial impairments in humans;
Chlamydia trachomatis (Ct) is responsible for a large number of human diseases:


    
    
        eye diseases: conventional trachoma, nonendemic trachoma, paratrachoma, inclusion conjunctivitis in neonates and in adults;
        genital diseases: nongonococcal uretritis, epididymitis, cervicitis, salpingitis, perihepatitis and bartholinitis as well as pneumopathy in breast-feeding infants;
        systemic diseases: venereal lymphogranulomatosis (LGV).

These diseases affect a very large number of women and men [more than 600 million individuals are trachoma carriers and there are more than 90 million cases of genital Chlamydia infections] worldwide. Accordingly, basic and applied research which makes it possible to understand the physiopathology linked to this bacterium is very important for public health. (Raulston J E., 1995; Hackstadt T. et al., 1996).

    
    


Eye impairments due to Chlamydia trachomatis cause trachoma and inclusion conjunctivitis. Trachoma is a chronic conjunctivitis. It is the major cause of curable eye diseases leading to blindness. It is estimated that 20 million cases of loss of sight are due to it worldwide. Moreover, inclusion conjunctivitis is an eye inflammation which is caused by Chlamydia trachomatis and is transmitted by the venereal route. Inclusion conjunctivitis affects adults and neonates exposed to genital secretions.
Two types of eye disease caused by agents of the species Chlamydia trachomatis can be distinguished. The conventional trachomatous disease is found in endemic regions; transmission occurs from eye to eye and through the hands, or it can be passed on by flies. In nonendemic regions, transmission occurs through the genital apparatus; it usually only causes conjunctivitis, most often without associated keratitis; it is rare for a pannus or for scars similar to those in trachoma to develop. This conjunctival impairment is called paratrachoma to differentiate it from the conventional endemic trachoma which is transmitted by the ocular route. The seriousness and the number of cases of trachoma have decreased over the last forty years. This is related to the improvement in hygiene and living conditions. However, trachoma remains the principal cause of avoidable blindness in Africa, in the Middle East and in some regions of Asia. The transmission of the endemic disease occurs in particular through close personal contact, in regions where a secondary exposure exists in a repeated form. Often, the infection is also latent. In some industrialized countries, such as the United States, a mild form of trachoma still exists in some ethnic groups. Sometimes, a tardive trachoma may be found following an immunosuppressive treatment. The eye impairments caused by Chlamydia trachomatis, such as inclusion conjunctivitis and paratrachoma, are also a complication due to a common venereal infection. These infections are not very frequent; they occur most often in young adults. The eye impairments in neonates are produced during the passage through the maternal genital routes during childbirth. Theoretically, endemic trachoma and inclusion conjunctivitis in adults appear in the form of conjunctivitis, the latter being characterized by the presence of lymphoid follicles. In regions where the endemic disease is serious, the disease often starts before the age of 2 years and reinfection is frequent. Superficial neovascularization is added, in this case, to leukocytic infiltration. The conjunctival scars will then cause trichiasis and entropion. The eroded cornea will become a carrier of a corneal ulcer of bacterial origin. The scar on the cornea causes blindness. Impairment of the lachrymal glands gives a picture of dryness of the cornea. Xerosis becomes complicated with secondary bacterial ulcer. In regions where trachoma is endemic, the infectious process disappears towards the age of fifteen. The scars then progress to blindness, which affects almost exclusively adults. In regions where exposure is lower, the infectious process is, in this case, less rapid and adults are carriers of a chronic disease.
Positive diagnosis of trachoma can be most often established by clinical observation: lymphoid follicles are visible on the upper tarsal conjuctiva; conjunctival scar is typical. Vascular pannus exists. In endemic regions, clinical diagnosis is often sufficient. However, isolated cases of inclusion conjunctivitis must be the subject of a differential diagnosis, in particular to distinguish viral conjunctivitis.
Public health measures against the endemic form of the disease provide for mass treatments with tetracycline or erythromycin collyria of all children. The treatment may also provide for surgical correction of the lesions. The other conjunctival impairments respond well to general treatments with tetracyclines or erythromycin. The prevention of trachomatous disease by health measures and by improving living standards is sufficient. Furthermore, to avoid the spread of trachoma, antibiotic collyria may be used.
The role of Chlamydia trachomatis in a number of genital impairments has been demonstrated over the last three decades. Chlamydia trachomatis is responsible in this case for a pathology which may be superposed on the impairments observed with Neisseria gonorrhoeae. The pathologies for which Chlamydia trachomatis may be responsible at the genital level are acquired by the venereal route and are a major source of sexually transmitted diseases.
The epidemiology of Chlamydia trachomatis genital infections shows each year more than 4 million new cases in the United States, and more than 3 million new cases in Europe. Like the other venereal infections, Chlamydia trachomatis affects young subjects. There is a direct relationship between the number of sexual partners and the frequency of the disease. For example, the frequency of Chlamydia trachomatis appears to be five to ten times higher than that of Neisseria gonorrhoea in pregnant women. The Chlamydia trachomatis infection is probably more discreet than its Neisseria gonorrhoea homologue. This relative clinical silence, estimated in women at 50% or even 70% of infections, explains why the total morbidity of Chlamydia trachomatis conditions is high. Diagnosis must therefore be requested in patients who are sometimes asymptomatic carriers of infection.
Chlamydia trachomatis is responsible for nearly 30% of nongonococcal urethritis, or NGU. Chlamydia trachomatis urethritis may be discreet, the disease then progresses to a certain form of chronicity. The diagnosis will, like for the other clinical forms of the disease, be called into play later.
Chlamydia trachomatis is a cause of epididymitis in humans during a period of sexual activity. The bacterium may be found in the urethra, urine, sperm or even a sample collected by aspiration from the epididymis. It is in particular found in humans under 35 years of age. A discharge from the urethra which is associated with the disease suggests the diagnosis of a Chlamydia condition or sometimes a gonococcal condition.
Untreated Reiter's syndrome, if accompanied by urethritis, evokes a Chlamydia trachomatis condition.
Chlamydia trachomatis affects 30% to 40% of women who are clinically carriers of a gonorrhoea (or have had contact), 10% to 20% of women having a venereal origin, and 5% of women consulting having no particular origin.
The cervix is often normal during a Chlamydia trachomatis infection. However, a hypertrophic cervical erythema will cause such an infection to be suspected. Chlamydia trachomatis is responsible for an endocervicitis whereas viral impairments result in exocervicitis. A nongonococcal endocervicitis requires treating the patient and partners with tetracyclines.
Chlamydia trachomatis is responsible for a large number of acute salpingites. The picture is often complicated by an acute peritonitis or even a perihepatitis.
In case of pregnancy, the risk is first that of infection of the neonate at birth. However, the risk of postpartum complications exists (endometritis or salpingitis).
The reference method for the diagnosis of Chlamydia trachomatis is the isolation of the bacterium on cell culture. For all infections, the sample collection should make it possible to obtain a suitable sample with the aid of a swab. This sample should be transported to a laboratory under excellent conditions; in particular, the cold chain must absolutely be maintained. The placing in cell culture on mouse fibroblasts will be carried out by people having specific skills. The distinction of Chlamydia trachomatis with labelled antibodies and the observation of cell cultures under a microscope will take place two days after placing in culture. Provided these imperatives are observed, cell culture is a reliable technique. However, the constraints linked to this technique are many: not only must the laboratory be equipped for the cell culture, but, furthermore, highly competent staff must take care of this type of diagnosis.
Techniques for identifying genetic material can obviously be used for the detection of Chlamydia trachomatis. Among these techniques, enzymatic gene amplification or PCR is favoured by those skilled in the art. The technique indeed makes it possible to identify Chlamydia trachomatis with a very high sensitivity and complete specificity. Initially used in specialist laboratories, PCR is now performed in numerous medical laboratories. This diagnostic approach is important because it allows detection of the bacteria even in samples which have been transported under poor conditions.
The treatment of Chlamydia urethritis with antibiotics such as tetracycline or quinolones is very effective. The duration of treatment varies between 7 and 14 days. The treatment of pregnant women poses the problem of contraindications to tetracycline.
Neonatal infections caused by Chlamydia trachomatis are explained by the frequency of these bacteria in the cervix. In some studies, 5% to 13% of impairments are observed in the cervix in asymptomatic pregnant women. The neonates risk, in this case, developing an inclusion conjunctivitis. Not only can Chlamydia trachomatis be isolated from the children's eyes, but also persistently from the rhinopharynx and also from the rectum. Pneumopathies and otitis media are also found, a result of contamination at childbirth.
Differential diagnosis of inclusion conjunctivitis in neonates is required with gonococcal ophthalmia; while the duration of incubation is from one to three days in the case of a gonococcal ophthalmia, neonatal inclusion conjunctivitis has an acute beginning with discharge and formation of membranes or even of conjunctival scars.
Treatment consists of oral erythromycin at the dose of 40 to 50 mg per kg of weight, for two to three weeks. In a nonendemic trachoma region, this disease never progresses to chronicity.
Finally, mention should be made of infantile pneumopathy. The syndrome is well defined; it is found in children affected by Chlamydia trachomatis. Less than ten children are affected by Chlamydia trachomatis pneumopathies per thousand births. The syndrome is, in this case, always found at an early age (less than four months).
Venereal lymphogranulomatosis is an infection which is transmitted through sexual contact and is due to Chlamydia trachomatis strains L1, L2 and L3. In humans, a passing primary genital lesion is followed by an often suppurative and multiple regional lymphadenopathy. This disease is a general disease which is accompanied by fever and a rise in the number of white blood cells. If it progresses to chronicity, the disease then becomes complicated with genital elephantiasis, stricture or even fistula of the genital apparatus, of the penis, of the urethra and of the rectum.
The three Chlamydia trachomatis strains L1, L2 and L3 are responsible for venereal lymphogranulomatosis. These Chlamydia strains are more virulent than the strains responsible for trachoma and STD. It is very important to note that venereal lymphogranulomatosis is a systemic disease which affects primarily the lymphatic tissue. Generally transmitted by the sexual route, Chlamydia trachomatis L may also cause contamination through direct contact or even during poor laboratory handling. In spite of these variable modes of transmission, the age for the highest incidence of these diseases corresponds to that for greater sexual activity. Venereal lymphogranulomatosis is still endemic in South America, in Africa and sometimes in Asia. For a long time, the prevalence of venereal lymphogranulomatosis was difficult to establish because of the difficulty of performing diagnosis with certitude. It should also be noted that men are affected more often than women. In low endemic regions, it is difficult to recognize the reservoir of microbes. This situation is explained by the fact that the isolation of the strains causing venereal lymphogranulomatoses from asymptomatic subjects is rarely successful.
Clinical impairment by venereal lymphogranulomatosis manifests itself by the appearance of a small ulcer 3 to 21 days after the exposure of small nonpainful vesicles. In both men and women, the lesion is most often silent. Since this impairment disappears within a few days and causes no functional discomfort and leaves no visible scar, the disease is often recognized late. The venereal lymphogranulomatosis strains may be found in the urethra or the endocervix in patients with inguinal adenopathies; these regions are then considered as the initial site of infection. The characteristic feature of the venereal lymphogranulomatosis strains is that from the initial site of infection, Chlamydia exhibits a diffusion drained by the lymphatic ducts. The disease is then complicated by a ganglionic impairment of the region draining the site of inoculation. By way of example, anorectal infection causes deep adenopathies. These adenopathies are marked by the appearance of a periadenitis which forms a fluctuating and suppurative ganglionic mass. Fistulae will appear during the decline of the disease. As general signs are present at this stage of the disease, it is often confused with a malignant lymphoma. The other general complications are rarely observed. Clinical examinations have been able to lead biologists to isolate Chlamydia from the cerebrospinal fluid or from the blood. It should also be noted that in a number of cases (5%), venereal lymphogranulomatosis is complicated by a chronic oedema: this is genital elephantiasis.
The diagnosis of venereal lymphogranulomatosis requires the isolation of the Chlamydia strains involved in the disease. However, isolation on cell cultures is rarely used, but immunological reactions may be used.
The treatment of venereal lymphogranulomatosis in its initial phase is identical to the treatment of other Chlamydia infections. In the chronic phases, antibiotics have little effect on the progress of the disease, but they are however useful in case of superinfection. Although the recommended therapeutic arsenal is identical, it is advisable to prolong the treatment for a period of at least four weeks. In addition to this treatment, reconstructive surgery may be useful in cases of urethral, penile or rectal strictures, as well as for the treatment of fistulae.
In conclusion, a short and effective treatment, without recurrences, and a well-tolerated treatment of Chlamydia trachomatis infections therefore remains desirable.
An even greater need up until now relates to a diagnosis which is specific to each of the strains, which is sensitive, which can be carried out conveniently and rapidly, and which allows early detection of the infection.
No vaccine is currently available against Chlamydia trachomatis. The role of the immune defense in the physiology and pathology of the disease should probably be understood in order to develop satisfactory vaccines.
More detailed information relating to the biology of these strains, their interactions with their hosts, the associated phenomena of infectivity and those of escaping the immune defenses of the host in particular, and finally their involvement in the development of the these associated pathologies, will allow a better understanding of these mechanisms. In the light of the preceding text which shows in particular the limitations of the means of controlling Chlamydia trachomatis infection, it is therefore at present essential, on the one hand, to develop molecular tools, in particular from a better genetic knowledge of Chlamydia trachomatis, but also to develop new preventive and therapeutic treatments, new diagnostic methods and new vaccine strategies which are specific, effective and tolerated. This is precisely the object of the present invention.
The subject of the present invention is the nucleotide sequence having the sequence SEQ ID No. 1 of the Chlamydia trachomatis LGV2 genome. However, the invention is not limited to SEQ ID No. 1, but encompasses genomes and nucleotides encoding polypeptides of strain variants, polymorphisms, allelic variants, and mutants.
Thus, the subject of the present invention encompasses nucleotide sequences characterized in that they are chosen from:
a) the nucleotide sequence of SEQ ID No. 1, a nucleotide sequence exhibiting at least 99.9% identity with the sequence SEQ ID No. 1, the nucleotide sequence of the genomic DNA contained within ECACC Deposit No. 98112618, the nucleotide sequence of a clone insert within ECACC Deposit No. 98112617 (these being provisional deposit numbers);
b) a nucleotide sequence homologous to the sequence SEQ ID No. 1;
c) a polynucleotide sequence that hybridizes to the nucleotide sequence of a) under conditions of high or intermediate stringency as described below:
(i) By way of example and not limitation, procedures using conditions of high stringency are as follows: Prehybridization of filters containing DNA is carried out for 8 h to overnight at 65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65° C., the preferred hybridization temperature, in prehybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5-20×106 cpm of 32P-labeled probe. Alternatively, the hybridization step can be performed at 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na citrate. Subsequently, filter washes can be done at 37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by a wash in 0.1×SSC at 50° C. for 45 min. Alternatively, filter washes can be performed in a solution containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS, or 0.1×SSC and 0.1% SDS at 68° C. for 15 minute intervals. Following the wash steps, the hybridized probes are detectable by autoradiography. Other conditions of high stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety.
(ii) By way of example and not limitation, procedures using conditions of intermediate stringency are as follows: Filters containing DNA are prehybridized, and then hybridized at a temperature of 60° C. in the presence of a 5×SSC buffer and labeled probe. Subsequently, filter washes are performed in a solution containing 2×SSC at 50° C. and the hybridized probes are detectable by autoradiography. Other conditions of intermediate stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety.
d) a nucleotide sequence complementary to the sequence SEQ ID No. 1 or complementary to a nucleotide sequence as defined in a), b) or c), and a nucleotide sequence of their corresponding RNA;
e) a nucleotide sequence of a representative fragment of the sequence SEQ ID No. 1, or of a representative fragment of the nucleotide sequence as defined in a), b), c) or d);
f) a nucleotide sequence comprising a sequence as defined in a), b), c), d) or e);
g) a nucleotide sequence capable of being obtained from a nucleotide sequence as defined in a), b), c), d), e) or f); and
h) a modified nucleotide sequence of a nucleotide sequence as defined in a), b), c), d), e), f) or g).
Sequence of the genome, or genomic sequence of Chlamydia trachomatis is understood to mean the sequence of the chromosome of Chlamydia trachomatis, in contrast with the plasmid sequence of Chlamydia trachomatis. 
Nucleotide sequence, polynucleotide or nucleic acid are understood to mean, according to the present invention, either a double-stranded DNA, a single-stranded DNA or products of transcription of the said DNAs.
It should be understood that the present invention does not relate to the genomic nucleotide sequences of Chlamydia trachomatis taken in their natural environment, that is to say in the natural state. They are sequences which may have been isolated, purified or partially purified, by separation methods such as, for example, ion-exchange chromatography, molecular size exclusion chromatography or affinity chromatography, or alternatively fractionation techniques based on solubility in various solvents, or by genetic engineering methods such as amplification, cloning or subcloning, it being possible for the sequences of the invention to be carried by vectors.
The nucleotide sequence SEQ ID No. 1 was obtained by sequencing the Chlamydia trachomatis LGV2 genome by the method of directed sequencing after fluorescent automated sequencing of the inserts of clones and assembling of these sequences of nucleotide fragments (inserts) by means of softwares (cf. Examples). In spite of the high precision of the sequence SEQ ID No. 1, it is possible that it does not perfectly, 100% represent the nucleotide sequence of the Chlamydia trachomatis LGV2 genome and that a few rare sequencing errors or uncertainties still remain in the sequence SEQ ID No. 1. In the present invention, the presence of an uncertainty for an amino acid is designated by “Xaa” and that for a nucleotide is designated by “N” in the sequence listing below. These few rare errors or uncertainties could be easily detected and corrected by persons skilled in the art using the entire chromosome and/or its representative fragments according to the invention and standard amplification, cloning and sequencing methods, it being possible for the sequences obtained to be easily compared, in particular by means of a computer software and using computer-readable media for recording the sequences according to the invention as described, for example, below. After correcting these possible rare errors or uncertainties, the corrected nucleotide sequence obtained would still exhibit at least 99.9% identity with the sequence SEQ ID No. 1. Such rare sequencing uncertainties are not present within the DNA contained within ECACC Deposit No. 98112617 or 98112618 (provisional numbers), and whatever rare sequence uncertainties that exist within SEQ ID No. 1 can routinely be corrected utilizing the DNA of the ECACC Deposits.
Homologous nucleotide sequence for the purposes of the present invention is understood to mean a nucleotide sequence having a percentage identity with the bases of the nucleotide sequence SEQ ID No. 1 of at least 80%, preferably 90% and 95%, this percentage being purely statistical and it being possible for the differences between the two nucleotide sequences to be distributed randomly and over their entire length. The said homologous sequences exhibiting a percentage identity with the bases of the nucleotide sequence SEQ ID No. 1 of at least 80%, preferably 90% and 95%, may comprise, for example, the sequences corresponding to the genomic sequence or to the sequences of its representative fragments of a bacterium belonging to the Chlamydia family, including the species Chlamydia pneumoniae, Chlamydia psittaci and Chlamydia pecorum mentioned above, as well as the sequences corresponding to the genomic sequence or to the sequences of its representative fragments of a bacterium belonging to the variants of the species Chlamydia trachomatis. In the present invention, the terms family and genus are mutually interchangeable, the terms variant, serotype, strain and subspecies are also mutually interchangeable. These homologous sequences may thus correspond to variations linked to mutations within the same species or between species and may correspond in particular to truncations, substitutions, deletions and/or additions of at least one nucleotide. The said homologous sequences may also correspond to variations linked to the degeneracy of the genetic code or to a bias in the genetic code which is specific to the family, to the species or to the variant and which are likely to be present in Chlamydia. 
Protein and/or nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85(8):2444-2448; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410; Thompson et al., 1994, Nucleic Acids Res. 22(2):4673-4680; Higgins et al., 1996, Methods Enzymol. 266:383-402; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410; Altschul et al., 1993, Nature Genetics 3:266-272).
In a particularly preferred embodiment, protein and nucleic acid sequence homologies are evaluated using the Basic Local Alignment Search Tool (“BLAST”) which is well known in the art (see, e.g., Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267-2268; Altschul et al., 1990, J. Mol. Biol. 2/5:403-410; Altschul et al., 1993, Nature Genetics 3:266-272; Altschul et al., 1997, Nuc. Acids Res. 25:3389-3402). In particular, five specific BLAST programs are used to perform the following task:
(1) BLASTP and BLAST3 compare an amino acid query sequence against a protein sequence database;
(2) BLASTN compares a nucleotide query sequence against a nucleotide sequence database;
(3) BLASTX compares the six-frame conceptual translation products of a query nucleotide sequence (both strands) against a protein sequence database;
(4) TBLASTN compares a query protein sequence against a nucleotide sequence database translated in all six reading frames (both strands); and
(5) TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
The BLAST programs identify homologous sequences by identifying similar segments, which are referred to herein as “high-scoring segment pairs,” between a query amino or nucleic acid sequence and a test sequence which is preferably obtained from a protein or nucleic acid sequence database. High-scoring segment pairs are preferably identified (i.e., aligned) by means of a scoring matrix, many of which are known in the art. Preferably, the scoring matrix used is the BLOSUM62 matrix (Gonnet et al., 1992, Science 256:1443-1445; Henikoff and Henikoff, 1993, Proteins 17:49-61). Less preferably, the PAM or PAM250 matrices may also be used (see, e.g., Schwartz and Dayhoff, eds., 1978, Matrices for Detecting Distance Relationships: Atlas of Protein Sequence and Structure, Washington: National Biomedical Research Foundation)
The BLAST programs evaluate the statistical significance of all high-scoring segment pairs identified, and preferably selects those segments which satisfy a user-specified threshold of significance, such as a user-specified percent homology. Preferably, the statistical significance of a high-scoring segment pair is evaluated using the statistical significance formula of Karlin (see, e.g., Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267-2268).
Nucleotide sequence complementary to a sequence of the invention is understood to mean any DNA whose nucleotides are complementary to those of the sequence of the invention, and whose orientation is reversed (antiparallel sequence).
The present invention further comprises fragments of the sequences of a) through h) above. Representative fragments of the sequences according to the invention will be understood to mean any nucleotide fragment having at least 8 successive nucleotides, preferably at least 12 successive nucleotides, and still more preferably at least 15 or at least 20 successive nucleotides of the sequence from which it is derived. It is understood that such fragments refer only to portions of SEQ ID No. 1 that are not currently listed in a publicly available database.
Among these representative fragments, those capable of hybridizing under stringent conditions with a nucleotide sequence according to the invention are preferred. Hybridization under stringent conditions means that the temperature and ionic strength conditions are chosen such that they allow hybridization to be maintained between two complementary DNA fragments.
By way of illustration, high stringency conditions for the hybridization step for the purposes of defining the nucleotide fragments described above, are advantageously the following.
The hybridization is carried out at a preferred temperature of 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15 M NaCl and 0.05 M Na citrate. The washing steps may be, for example, the following: 2×SSC, 0.1% SDS at room temperature followed by three washes with 1×SSC, 0.1% SDS; 0.5×SSC, 0.1% SDS; 0.1×SSC, 0.1% SDS at 68° C. for 15 minutes.
Intermediate stringency conditions, using, for example, a temperature of 60° C. in the presence of a 5×SSC buffer, or of low stringency, for example a temperature of 50° C. in the presence of a 5×SSC buffer, respectively require a lower overall complementarity for the hybridization between the two sequences.
The stringent hybridization conditions described above for a polynucleotide of about 300 bases in size will be adapted by persons skilled in the art for larger- or smaller-sized oligonucleotides, according to the teaching of Sambrook et al., 1989.
Among the representative fragments according to the invention, those which can be used as primer or probe in methods which make it possible to obtain homologous sequences or their representative fragments according to the invention, or to reconstitute a genomic fragment found to be incomplete in the sequence SEQ ID No. 1 or carrying an error or an uncertainty, are also preferred, these methods, such as the polymerase chain reaction (PCR), cloning and sequencing of nucleic acid being well known to persons skilled in the art. These homologous nucleotide sequences corresponding to mutations or to inter- or intra-species variations, as well as the complete genomic sequence or one of its representative fragments capable of being reconstituted, of course form part of the invention.
Among the said representative fragments, those which can be used as primer or probe in methods allowing diagnosis of the presence of Chlamydia trachomatis or one of its associated microorganisms as defined below are also preferred.
The representative fragments capable of modulating, regulating, inhibiting or inducing the expression of a gene of Chlamydia trachomatis or one of its associated microorganisms, and/or capable of modulating the replication cycle of Chlamydia trachomatis or one of its associated microorganisms in the host cell and/or organism, are also preferred. Replication cycle is intended to designate invasion, multiplication, intracellular localization, in particular retention in the vacuole and inhibition of the process of fusion to the lysosome, and propagation of Chlamydia trachomatis or one of its associated microorganisms from host cells to host cells.
Among the said representative fragments, those corresponding to nucleotide sequences corresponding to open reading frames, called ORF sequences (ORF for open reading frame), and encoding polypeptides, such as for example, but without being limited thereto, the ORF sequences which will be later described, are finally preferred.
The representative fragments according to the invention may be obtained, for example, by specific amplification, such as PCR, or after digestion, with appropriate restriction enzymes, of nucleotide sequences according to the invention; these methods are in particular described in the manual by Sambrook et al., 1989. The said representative fragments may also be obtained by chemical synthesis when they are not too large in size and according to methods well known to persons skilled in the art. For example, such fragments can be obtained by isolating fragments of the genomic DNA of ECACC Deposit No. 98112618 or a clone insert present at this ECACC Deposit No. 98112617 (provisional numbers).
The representative fragments according to the invention may be used, for example, as primer, to reconstitute some of the said representative fragments, in particular those in which a portion of the sequence is likely to be missing or imperfect, by methods well known to persons skilled in the art such as amplification, cloning or sequencing techniques.
Modified nucleotide sequence will be understood to mean any nucleotide sequence obtained by mutagenesis according to techniques well known to persons skilled in the art, and exhibiting modifications in relation to the normal sequences, for example mutations in the regulatory and/or promoter sequences for the expression of a polypeptide, in particular leading to a modification of the level of expression of the said polypeptide or to a modulation of the replicative cycle.
Modified nucleotide sequence will also be understood to mean any nucleotide sequence encoding a modified polypeptide as defined below.
The subject of the present invention also includes Chlamydia trachomatis nucleotide sequences characterized in that they are chosen from a nucleotide sequence of an open reading frame (ORF), that is, the ORF2 to ORF1197 sequences.
The ORF2 to ORF1197 nucleotide sequences are defined in Tables 1 and 2, infra, represented below by their position on the sequence SEQ ID No. 1. For example, the ORF10 sequence is defined by the nucleotide sequence between the nucleotides at position 9828 and 10430 on the sequence SEQ ID No. 1, ends included. ORF2 to ORF1197 have been identified via homology analyses as well as via analyses of potential ORF start sites, as discussed in the examples below. It is to be understood that each identified ORF of the invention comprises a nucleotide sequence that spans the contiguous nucleotide sequence from the codon immediately 3′ to the stop codon of the preceding ORF and through the 5′ codon to the next stop codon of SEQ ID No.:1 in-frame to the ORF nucleotide sequence. Table 2, infra, lists the beginning, end and potential start site of each of ORFs 2-1197. In one embodiment, the ORF comprises the contiguous nucleotide sequence spanning from the potential OR start site downstream (that is, 3′) to the ORF stop codon (or the ORF codon immediately adjacent to and upstream of the ORF stop codon). ORF2 to ORF1197 encode the polypeptides of SEQ ID No. 2 to SEQ ID No. 1197.
Upon introduction of minor frameshifts, certain individual ORFs can comprise larger “combined” ORFs. A list of such putative “combined” ORFs is shown in Table 3, below. For example, a combined ORF can comprise ORF 1076 and ORF 1073, including intervening in-frame, nucleotide sequences. The order of ORFs (5′ to 3′), within each “combined” ORF is as listed. It is to be understood that when ORF2 to ORF 1197 are referred to herein, such reference is also meant to include “combined” ORFs. Polypeptide sequences encoded by such “combined” ORFs are also part of the present invention.







TABLE 3







ORF 1076, ORF 1073;


ORF 3, ORF 2;


ORF 23, ORF 22, ORF 21;


ORF 1141, ORF 477, ORF 478, ORF 479;


ORF 487, ORF 486, ORF 485, ORF 484, ORF 483, ORF 482, ORF 481;


ORF 488, ORF 489;


ORF 573, ORF 572, ORF 571;


ORF 817, ORF 818;


ORF 819, ORF 820;


ORF 1037, ORF 1038;


ORF 1071, ORF 1070;


ORF 17, ORF 1077;


ORF 1185, ORF 933, ORF 934;


ORF 1060, ORF 1059;


ORF 155, ORF 156;


ORF 679, ORF 680;


ORF 879, ORF 878;


ORF 1028; ORF 1029,


and representative fragments.









Table 1 also depicts the results of homology searches that compared the sequences of the polypeptides encoded by each of the ORFs to sequences present in public published databases. It is understood that in one embodiment, those polypeptides listed in Table 1 as exhibiting greater than about 95% identity to a polypeptide present in a publicly disclosed database are not considered part of the present invention; likewise in this embodiment, those nucleotide sequences encoding such polypeptides are not considered part of the invention. In another embodiment, it is understood that those polypeptides listed in Table 1 as exhibiting greater than about 99% identity to a polypeptide present in a publicly disclosed database are not considered part of the invention; likewise, in this embodiment, those nucleotide sequences encoding such polypeptides are not considered part of the invention.
The invention also relates to the nucleotide sequences characterized in that they comprise a nucleotide sequence chosen from:
a) an ORF2 to ORF1197, a “combined” ORF nucleotide sequence, the nucleotide sequence of the genomic DNA contained within ECACC Deposit No. 98112618 or the nucleotide sequence of a clone insert in ECACC Deposit No. 98112617 according to the invention;
b) a homologous nucleotide sequence exhibiting at least 80% identity across an entire ORF2 to ORF1197 nucleotide sequence according to the invention or as defined in a);
c) a polynucleotide sequence that hybridizes to ORF2 to ORF1197 under conditions of high or intermediate stringency as described below:

    
    
        (i) By way of example and not limitation, procedures using conditions of high stringency are as follows: Prehybridization of filters containing DNA is carried out for 8 h to overnight at 65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65° C., the preferred hybridization temperature, in prehybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5−20×106 cpm of 32P-labeled probe. Alternatively, the hybridization step can be performed at 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na citrate. Subsequently, filter washes can be done at 37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by a wash in 0.1×SSC at 50° C. for 45 min. Alternatively, filter washes can be performed in a solution containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS, or 0.1×SSC and 0.1% SDS at 68° C. for 15 minute intervals. Following the wash steps, the hybridized probes are detectable by autoradiography. Other conditions of high stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety. Preferably, such sequences encode a homolog of a polypeptide encoded by one of ORF2 to ORF1197. In one embodiment, such sequences encode a Chlamydia trachomatis polypeptide.
        (ii) By way of example and not limitation, procedures using conditions of intermediate stringency are as follows: Filters containing DNA are prehybridized, and then hybridized at a temperature of 60° C. in the presence of a 5×SSC buffer and labeled probe. Subsequently, filter washes are performed in a solution containing 2×SSC at 50° C. and the hybridized probes are detectable by autoradiography. Other conditions of intermediate stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety. Preferably, such sequences encode a homolog of a polypeptide encoded by one of ORF2 to ORF1197. In one embodiment, such sequences encode a Chlamydia trachomatis polypeptide.
    
    


d) a complementary or RNA nucleotide sequence corresponding to an ORF2 to ORF1197 sequence according to the invention or as defined in a), b) or c);
e) a nucleotide sequence of a representative fragment of an ORF2 to ORF1197 sequence according to the invention or of a sequence as defined in a), b), c) or d);
f) a nucleotide sequence capable of being obtained from an ORF2 to ORF1197 sequence according to the invention or as defined in a), b), c), d) or e); and
g) a modified nucleotide sequence of an ORF2 to ORF1197 sequence according to the invention or as defined in a), b), c), d), e) or f).
As regards the homology with the ORF2 to ORF1197 nucleotide sequences, the homologous sequences exhibiting a percentage identity with the bases of one of the ORF2 to ORF1197 nucleotide sequences of at least 80%, preferably 90% and 95%, are preferred. Such homologous sequences are identified routinely via, for example, the algorithms described above and in the examples below. The said homologous sequences correspond to the homologous sequences as defined above and may comprise, for example, the sequences corresponding to the ORF sequences of a bacterium belonging to the Chlamydia family, including the species Chlamydia pneumoniae, Chlamydia psittaci and Chlamydia pecorum mentioned above, as well as the sequences corresponding to the ORF sequences of a bacterium belonging to the variants of the species Chlamydia trachomatis. These homologous sequences may likewise correspond to variations linked to mutations within the same species or between species and may correspond in particular to truncations, substitutions, deletions and/or additions of at least one nucleotide. The said homologous sequences may also correspond to variations linked to the degeneracy of the genetic code or to a bias in the genetic code which is specific to the family, to the species or to the variant and which are likely to be present in Chlamydia. 
The invention comprises the polypeptides encoded by a nucleotide sequence according to the invention, preferably by a representative fragment of the sequence SEQ ID No. 1 and corresponding to an ORF sequence, in particular the Chlamydia trachomatis polypeptides, characterized in that they are chosen from the sequences SEQ ID No. 2 to SEQ ID No. 1197, and representative fragments thereof. However, the invention is not limited to polypeptides encoded by ORFs in SEQ ID No. 1 and its corresponding ORF sequences, but encompasses polypeptides of strain variants, polymorphisms, allelic variants, and mutants.
Thus, the invention also comprises the polypeptides characterized in that they comprise a polypeptide chosen from:
a) a polypeptide encoded by a polynucleotide sequence in SEQ ID No. 1 (e.g., any polypeptide encoded by a polynucleotide sequence corresponding to ORF2 to ORF1197) and/or representative fragments thereof according to the invention;
b) a polypeptide homologous to a polypeptide according to the invention, or as defined in a);
c) a polypeptide encoded by a polynucleotide sequence that hybridizes to SEQ ID No. 1 or ORF2 to ORF1197 under high or intermediate stringency as described below:

    
    
        (i) By way of example and not limitation, procedures using conditions of high stringency are as follows: Prehybridization of filters containing DNA is carried out for 8 h to overnight at 65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65° C., the preferred hybridization temperature, in prehybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5−20×106 cpm of 32P-labeled probe. Alternatively, the hybridization step can be performed at 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na citrate. Subsequently, filter washes can be done at 37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by a wash in 0.1×SSC at 50° C. for 45 min. Alternatively, filter washes can be performed in a solution containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS, or 0.1×SSC and 0.1% SDS at 68° C. for 15 minute intervals. Following the wash steps, the hybridized probes are detectable by autoradiography. Other conditions of high stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety. Preferably, such sequences encode a homolog of a polypeptide encoded by one of ORF2 to ORF1197. In one embodiment, such sequences encode a Chlamydia trachomatis polypeptide.
        (ii) By way of example and not limitation, procedures using conditions of intermediate stringency are as follows: Filters containing DNA are prehybridized, and then hybridized at a temperature of 60° C. in the presence of a 5×SSC buffer and labeled probe. Subsequently, filters washes are performed in a solution containing 2×SSC at 50° C. and the hybridized probes are detectable by autoradiography. Other conditions of intermediate stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety. Preferably, such sequences encode a homolog of a polypeptide encoded by one of ORF2 to ORF1197. In one embodiment, such sequences encode a Chlamydia trachomatis polypeptide.
    
    


d) a fragment of at least 5 amino acids of a polypeptide according to the invention, or as defined in a), b) or c);
e) a biologically active fragment of a polypeptide according to the invention, or as defined in a), b), c) or d); and
f) a modified polypeptide of a polypeptide according to the invention, as defined in a), b), c), d) or e).
In the present description, the terms polypeptide, peptide and protein are interchangeable.
It should be understood that the invention does not relate to the polypeptides in natural form, that is to say that they are not taken in their natural environment but that they may have been isolated or obtained by purification from natural sources, or alternatively obtained by genetic recombination, or else by chemical synthesis and that they may, in this case, comprise normatural amino acids, as will be described below.
Homologous polypeptide will be understood to designate the polypeptides exhibiting, in relation to the natural polypeptide, certain modifications such as in particular a deletion, addition or substitution of at least one amino acid, a truncation, an extension, a chimeric fusion, and/or a mutation, or polypeptides exhibiting post-translational modifications. Among the homologous polypeptides, those whose amino acid sequence exhibits at least 80%, preferably 90%, homology or identity with the amino acid sequences of the polypeptides according to the invention are preferred. In the case of a substitution, one or more consecutive or nonconsecutive amino acids are replaced by “equivalent” amino acids. The expression “equivalent” amino acid is intended here to designate any amino acid capable of being substituted for one of the amino acids in the basic structure without, however, essentially modifying the biological activities of the corresponding peptides and as will be defined later.
Protein and/or nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85(8):2444-2448; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410; Thompson et al., 1994, Nucleic Acids Res. 22(2):4673-4680; Higgins et al., 1996, Methods Enzymol. 266:383-402; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410; Altschul et al., 1993, Nature Genetics 3:266-272).
In a particularly preferred embodiment, protein and nucleic acid sequence homologies are evaluated using the Basic Local Alignment Search Tool (“BLAST”) which is well known in the art (see, e.g., Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267-2268; Altschul et al. 1990, J. Mol. Biol. 215:403-410; Altschul et al., 1993, Nature Genetics 3:266-272; Altschul et al., 1997, Nuc. Acids Res. 25:3389-3402). In particular, five specific BLAST programs are used to perform the following task:
(1) BLASTP and BLAST3 compare an amino acid query sequence against a protein sequence database;
(2) BLASTN compares a nucleotide query sequence against a nucleotide sequence database;
(3) BLASTX compares the six-frame conceptual translation products of a query nucleotide sequence (both strands) against a protein sequence database;
(4) TBLASTN compares a query protein sequence against a nucleotide sequence database translated in all six reading frames (both strands); and
(5) TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
The BLAST programs identify homologous sequences by identifying similar segments, which are referred to herein as “high-scoring segment pairs,” between a query amino or nucleic acid sequence and a test sequence which is preferably obtained from a protein or nucleic acid sequence database. High-scoring segment pairs are preferably identified (i.e., aligned) by means of a scoring matrix, many of which are known in the art. Preferably, the scoring matrix used is the BLOSUM62 matrix (Gonnet et al., 1992, Science 256:1443-1445; Henikoff and Henikoff, 1993, Proteins 17:49-61). Less preferably, the PAM or PAM250 matrices may also be used (see, e.g., Schwartz and Dayhoff, eds., 1978, Matrices, for Detecting Distance Relationships: Atlas of Protein Sequence and Structure, Washington: National Biomedical Research Foundation).
The BLAST programs evaluate the statistical significance of all high-scoring segment pairs identified, and preferably selects those segments which satisfy a user-specified threshold of significance, such as a user-specified percent homology. Preferably, the statistical significance of a high-scoring segment pair is evaluated using the statistical significance formula of Karlin (see, e.g., Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267-2268).
Equivalent amino acids may be determined either based on their structural homology with the amino acids for which they are substituted, or on results of comparative tests of biological activity between the various polypeptides which may be carried out.
By way of example, there may be mentioned the possibilities of substitutions which may be carried out without resulting in a substantial modification of the biological activity of the corresponding modified polypeptides; the replacements, for example, of leucine with valine or isoleucine, of aspartic acid with glutamic acid, of glutamine with asparagine, of arginine with lysine, and the like, the reverse substitutions naturally being feasible under the same conditions.
The homologous polypeptides also correspond to the polypeptides encoded by the homologous nucleotide sequences as defined above and thus comprise in the present definition the mutated polypeptides or polypeptides corresponding to inter- or intra-species variations which may exist in Chlamydia, and which correspond in particular to truncations, substitutions, deletions and/or additions of at least one amino acid residue.
Biologically active fragment of a polypeptide according to the invention will be understood to designate in particular a polypeptide fragment, as defined below, exhibiting at least one of the characteristics of the polypeptides according to the invention, in particular in that it is:

    
    
        capable of eliciting an immune response directed against Chlamydia trachomatis; and/or
        capable of being recognized by an antibody specific for a polypeptide according to the invention; and/or
        capable of binding to a polypeptide or to a nucleotide sequence of Chlamydia trachomatis; and/or
        capable of modulating, regulating, inducing or inhibiting the expression of a gene of Chlamydia trachomatis or one of its associated microorganisms, and/or capable of modulating the replication cycle of Chlamydia trachomatis or one of its associated microorganisms in the host cell and/or organism; and/or
        capable of generally exerting an even partial physiological activity, such as for example a structural activity (cellular envelope, ribosome), an enzymatic (metabolic) activity, a transport activity, an activity in the secretion or in the virulence.
    
    


A representative polypeptide fragment according to the invention is understood to designate a polypeptide comprising a minimum of 5 amino acids, preferably 10 amino acids or preferably 15 amino acids. It is to be understood that such fragments refer only to portions of polypeptides encoded by ORF2 or ORF1197 that are not currently listed in a publicly available database.
The polypeptide fragments according to the invention may correspond to isolated or purified fragments which are naturally present in Chlamydia trachomatis or which are secreted by Chlamydia trachomatis, or may correspond to fragments capable of being obtained by cleaving the said polypeptide with a proteolytic enzyme, such as trypsin or chymotrypsin or collagenase, or with a chemical reagent, such as cyanogen bromide (CNBr) or alternatively by placing the said polypeptide in a highly acidic environment, for example at pH 2.5. Such polypeptide fragments may be equally well prepared by chemical synthesis, using hosts transformed with an expression vector according to the invention containing a nucleic acid allowing the expression of the said fragments, placed under the control of appropriate elements for regulation and/or expression.
“Modified polypeptide” of a polypeptide according to the invention is understood to designate a polypeptide obtained by genetic recombination or by chemical synthesis as will be described below, exhibiting at least one modification in relation to the normal sequence. These modifications may in particular affect amino acids responsible for a specificity or for the efficiency of the activity, or responsible for the structural conformation, for the charge or for the hydrophobicity, and for the capacity for multimerization and for membrane insertion of the polypeptide according to the invention. It is thus possible to create polypeptides with an equivalent, an increased or a reduced activity, and with an equivalent, a narrower or a broader specificity. Among the modified polypeptides, there may be mentioned the polypeptides in which up to 5 amino acids may be modified, truncated at the N- or C-terminal end, or alternatively deleted, or else added.
As is indicated, the modifications of the polypeptide may have in particular the objective:

    
    
        of making it capable of modulating, regulating, inhibiting or inducing the expression of a gene of Chlamydia, in particular of Chlamydia trachomatis and its variants, or one of its associated micro-organisms, and/or capable of modulating the replication cycle of Chlamydia, in particular of Chlamydia trachomatis and its variants, or one of its associated microorganisms, in the host cell and/or organism,
        of allowing its use in methods of biosynthesis or of biodegradation, or its incorporation into vaccine compositions,
        of modifying its bioavailability as a compound for therapeutic use.
    
    


The said modified polypeptides may also be used on any cell or microorganism for which the said modified polypeptides will be capable of modulating, regulating, inhibiting or inducing gene expression, or of modulating the growth or the replication cycle of the said cell or of the said microorganism. The methods allowing demonstration of the said modulations on eukaryotic or prokaryotic cells are well known to persons skilled in the art. The said cells or microorganisms will be chosen, in particular, from tumour cells or infectious microorganisms and the said modified polypeptides may be used for the prevention or treatment of pathologies linked to the presence of the said cells or of the said microorganisms. It is also clearly understood that the nucleotide sequences encoding the said modified polypeptides may be used for the said modulations, for example by the intermediacy of vectors according to the invention and which are described below, so as to prevent or to treat the said pathologies.
The above modified polypeptides may be obtained using combinatory chemistry, in which it is possible to systematically vary portions of the polypeptide before testing them on models, cell cultures or microorganisms for example, so as to select the compounds which are the most active or which exhibit the desired properties.
Chemical synthesis also has the advantage of being able to use:

    
    
        normatural amino acids, or
        nonpeptide bonds.
    
    


Accordingly, in order to extend the life of the polypeptides according to the invention, it may be advantageous to use normatural amino acids, for example in the D form, or alternatively amino acid analogues, in particular sulphur-containing forms for example.
Finally, the structure of the polypeptides according to the invention, its homologous or modified forms, as well as the corresponding fragments may be integrated into chemical structures of the polypeptide type and the like. Accordingly, it may be advantageous to provide at the N- and C-terminal ends compounds which are not recognized by proteases.
Also forming part of the invention are the nucleotide sequences encoding a polypeptide according to the invention. Described below are ORF nucleotide sequences encoding polypeptides exhibiting particularly preferable characteristics. For each group of preferred ORFs described below, it is to be understood that in addition to the individual ORFs listed, in instances wherein such ORFs are present as part of “combined” ORFs, the “combined” ORFs are also to be included within the preferred group.
More particularly, the subject of the invention is nucleotide sequences, characterized in that they encode a polypeptide of the cellular envelope, preferably of the outer cellular envelope of Chlamydia trachomatis or one of its representative fragments, such as for example the predominant proteins of the outer membrane, the adhesion proteins or the proteins entering into the composition of the Chlamydia wall. Among these sequences, the sequences comprising a nucleotide sequence chosen from the following sequences are most preferred:
ORF3; ORF19; ORF51; ORF189; ORF212; ORF213; ORF324; ORF477; ORF478; ORF479; ORF481; ORF482; ORF483; ORF484; ORF486; ORF488; ORF489; ORF490; ORF572; ORF573; ORF742; ORF817; ORF818; ORF820; ORF1035; ORF1036; ORF1037; ORF1038; ORF1070; ORF1071; ORF1073 and one of their representative fragments.
The structure of the cytoplasmic membranes and of the wall of bacteria is dependent on the associated proteins. The structure of the cytoplasmic membrane makes it impermeable to water, to water-soluble substances and to small-sized molecules (ions, small inorganic molecules, peptides or proteins). To enter into or to interfere with a cell or a bacterium, a ligand must establish a special relationship with a protein anchored in the cytoplasmic membrane (the receptor). These proteins which are anchored on the membrane play an important role in metabolism since they control the exchanges in the bacterium. These exchanges apply to molecules of interest for the bacterium (small molecules such as sugars and small peptides) as well as undesirable molecules for the bacterium such as antibiotics or heavy metals.
The double lipid layer structure of the membrane requires the proteins which are inserted therein to have hydrophobic domains of about twenty amino acids forming an alpha helix. Predominantly hydrophobic and potentially transmembrane regions may be predicted from the primary sequence of the proteins, itself deduced from the nucleotide sequence. The presence of one or more putative transmembrane domains raises the possibility for a protein to be associated with the cytoplasmic membrane and to be able to play an important metabolic role therein or alternatively for the protein thus exposed to be able to exhibit potentially protective epitopes.
If the proteins inserted into the membrane exhibit several transmembrane domains capable of interacting with one another via electrostatic bonds, it then becomes possible for these proteins to form pores which go across the membrane which becomes permeable for a number of substances. It should be noted that proteins which do not have transmembrane domains may also be anchored by the intermediacy of fatty acids in the cytoplasmic membrane, it being possible for the breaking of the bond between the protein and its anchor in some cases to be responsible for the release of the peptide outside the bacterium.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis transmembrane polypeptide or one of its representative fragments, having between 1 and 3 transmembrane domains and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF2; ORF3; ORF5; ORF8; ORF9; ORF10; ORF11; ORF12; ORF17; ORF21; ORF26; ORF27; ORF28; ORF29; ORF30; ORF31; ORF33; ORF35; ORF37; ORF39; ORF40; ORF41; ORF42; ORF43; ORF44; ORF45; ORF46; ORF47; ORF48; ORF49; ORF52; ORF53; ORF55; ORF56; ORF58; ORF65; ORF66; ORF68; ORF70; ORF74; ORF75; ORF76; ORF78; ORF79; ORF81; ORF82; ORF83; ORF86; ORF91; ORF92; ORF94; ORF97; ORF100; ORF102; ORF103; ORF105; ORF106; ORF107; ORF109; ORF110; ORF111; ORF112; ORF113; ORF114; ORF115; ORF116; ORF117; ORF120; ORF122; ORF123; ORF130; ORF134; ORF135; ORF137; ORF140; ORF141; ORF143; ORF144; ORF145; ORF147; ORF148; ORF149; ORF150; ORF151; ORF155; ORF156; ORF162; ORF163; ORF164; ORF165; ORF166; ORF167; ORF168; ORF169; ORF170; ORF171; ORF173; ORF175; ORF176; ORF177; ORF181; ORF183; ORF184; ORF186; ORF187; ORF188; ORF190; ORF191; ORF192; ORF194; ORF195; ORF196; ORF197; ORF198; ORF199; ORF201; ORF202; ORF204; ORF206; ORF207; ORF209; ORF212; ORF213; ORF217; ORF219; ORF220; ORF221; ORF222; ORF223; ORF224; ORF225; ORF227; ORF228; ORF231; ORF232; ORF234; ORF236; ORF237; ORF243; ORF244; ORF245; ORF247; ORF248; ORF249; ORF252; ORF254; ORF257; ORF260; ORF261; ORF263; ORF265; ORF266; ORF267; ORF270; ORF271; ORF272; ORF274; ORF276; ORF277; ORF278; ORF279; ORF282; ORF283; ORF284; ORF285; ORF287; ORF289; ORF290; ORF291; ORF294; ORF298; ORF305; ORF306; ORF310; ORF311; ORF313; ORF315; ORF316; ORF319; ORF320; ORF322; ORF323; ORF325; ORF326; ORF327; ORF328; ORF330; ORF331; ORF332; ORF333; ORF334; ORF335; ORF336; ORF338; ORF339; ORF340; ORF341; ORF344; ORF345; ORF348; ORF349; ORF350; ORF351; ORF352; ORF353; ORF356; ORF357; ORF358; ORF361; ORF362; ORF366; ORF367; ORF368; ORF370; ORF372; ORF373; ORF375; ORF377; ORF378; ORF379; ORF380; ORF382; ORF383; ORF384; ORF385; ORF387; ORF389; ORF390; ORF391; ORF393; ORF396; ORF398; ORF399; ORF403; ORF404; ORF406; ORF407; ORF413; ORF414; ORF417; ORF418; ORF420; ORF421; ORF424; ORF426; ORF427; ORF428; ORF430; ORF433; ORF434; ORF435; ORF436; ORF437; ORF440; ORF443; ORF446; ORF448; ORF450; ORF451; ORF454; ORF455; ORF457; ORF458; ORF459; ORF463; ORF464; ORF466; ORF467; ORF468; ORF469; ORF470; ORF473; ORF474; ORF475; ORF476; ORF477; ORF479; ORF480; ORF481; ORF483; ORF484; ORF485; ORF486; ORF487; ORF488; ORF491; ORF493; ORF496; ORF497; ORF498; ORF500; ORF501; ORF503; ORF504; ORF508; ORF512; ORF513; ORF514; ORF519; ORF521; ORF523; ORF524; ORF526; ORF527; ORF529; ORF530; ORF531; ORF532; ORF534; ORF536; ORF537; ORF538; ORF540; ORF541; ORF542; ORF543; ORF544; ORF545; ORF546; ORF547; ORF551; ORF552; ORF553; ORF555; ORF558; ORF559; ORF560; ORF561; ORF562; ORF566; ORF567; ORF568; ORF569; ORF571; ORF572; ORF574; ORF575; ORF576; ORF580; ORF582; ORF585; ORF587; ORF589; ORF592; ORF593; ORF595; ORF596; ORF597; ORF599; ORF601; ORF602; ORF603; ORF604; ORF608; ORF609; ORF610; ORF611; ORF615; ORF616; ORF617; ORF618; ORF621; ORF622; ORF623; ORF624; ORF625; ORF628; ORF632; ORF633; ORF634; ORF635; ORF637; ORF638; ORF640; ORF641; ORF643; ORF646; ORF648; ORF649; ORF651; ORF652; ORF653; ORF654; ORF655; ORF658; ORF664; ORF665; ORF666; ORF668; ORF669; ORF670; ORF671; ORF672; ORF673; ORF674; ORF676; ORF677; ORF678; ORF680; ORF682; ORF683; ORF684; ORF686; ORF688; ORF689; ORF690; ORF691; ORF692; ORF693; ORF695; ORF696; ORF698; ORF701; ORF703; ORF704; ORF705; ORF706; ORF707; ORF709; ORF710; ORF711; ORF712; ORF713; ORF714; ORF715; ORF717; ORF718; ORF720; ORF721; ORF722; ORF724; ORF726; ORF728; ORF729; ORF730; ORF731; ORF732; ORF733; ORF734; ORF737; ORF738; ORF739; ORF740; ORF742; ORF743; ORF744; ORF745; ORF746; ORF748; ORF750; ORF751; ORF752; ORF753; ORF754; ORF755; ORF757; ORF758; ORF759; ORF760; ORF764; ORF766; ORF768; ORF769; ORF771; ORF772; ORF773; ORF774; ORF775; ORF776; ORF777; ORF778; ORF779; ORF780; ORF781; ORF782; ORF783; ORF786; ORF787; ORF788; ORF789; ORF790; ORF793; ORF798; ORF800; ORF802; ORF803; ORF806; ORF808; ORF809; ORF810; ORF811; ORF813; ORF814; ORF817; ORF820; ORF822; ORF824; ORF825; ORF827; ORF828; ORF829; ORF830; ORF833; ORF834; ORF835; ORF837; ORF838; ORF839; ORF840; ORF841; ORF842; ORF843; ORF845; ORF848; ORF849; ORF850; ORF851; ORF852; ORF854; ORF855; ORF856; ORF857; ORF859; ORF860; ORF862; ORF863; ORF864; ORF866; ORF869; ORF872; ORF873; ORF874; ORF878; ORF879; ORF880; ORF881; ORF883; ORF884; ORF885; ORF886; ORF887; ORF892; ORF893; ORF894; ORF895; ORF897; ORF899; ORF900; ORF901; ORF904; ORF906; ORF909; ORF910; ORF912; ORF914; ORF917; ORF920; ORF921; ORF922; ORF923; ORF924; ORF925; ORF926; ORF927; ORF930; ORF933; ORF934; ORF935; ORF936; ORF937; ORF940; ORF941; ORF942; ORF943; ORF944; ORF945; ORF947; ORF948; ORF951; ORF952; ORF953; ORF954; ORF955; ORF956; ORF957; ORF958; ORF960; ORF961; ORF962; ORF963; ORF964; ORF966; ORF967; ORF969; ORF970; ORF971; ORF973; ORF974; ORF979; ORF980; ORF981; ORF982; ORF984; ORF988; ORF989; ORF990; ORF991; ORF995; ORF996; ORF999; ORF1001; ORF1003; ORF1004; ORF1005; ORF1006; ORF1007; ORF1009; ORF1010; ORF1011; ORF1012; ORF1013; ORF1014; ORF1016; ORF1017; ORF1018; ORF1020; ORF1021; ORF1025; ORF1026; ORF1027; ORF1029; ORF1030; ORF1031; ORF1035; ORF1036; ORF1037; ORF1038; ORF1039; ORF1040; ORF1044; ORF1045; ORF1047; ORF1048; ORF1050; ORF1051; ORF1052; ORF1053; ORF1055; ORF1056; ORF1057; ORF1058; ORF1061; ORF1062; ORF1063; ORF1064; ORF1065; ORF1066; ORF1068; ORF1069; ORF1072; ORF1074; ORF1076 and one of their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis transmembrane polypeptide or one of its representative fragments, having between 4 and 6 transmembrane domains and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF7; ORF14; ORF16; ORF32; ORF34; ORF36; ORF38; ORF50; ORF57; ORF59; ORF61; ORF62; ORF63; ORF64; ORF67; ORF69; ORF72; ORF77; ORF80; ORF84; ORF87; ORF93; ORF95; ORF99; ORF108; ORF119; ORF125; ORF126; ORF129; ORF131; ORF136; ORF139; ORF146; ORF152; ORF154; ORF160; ORF161; ORF172; ORF179; ORF182; ORF185; ORF200; ORF203; ORF205; ORF239; ORF242; ORF250; ORF1253; ORF256; ORF259; ORF262; ORF268; ORF275; ORF281; ORF286; ORF288; ORF292; ORF295; ORF296; ORF297; ORF299; ORF300; ORF308; ORF314; ORF317; ORF318; ORF324; ORF342; ORF343; ORF355; ORF360; ORF374; ORF376; ORF386; ORF388; ORF392; ORF394; ORF395; ORF402; ORF405; ORF411; ORF415; ORF416; ORF422; ORF423; ORF429; ORF432; ORF441; ORF442; ORF444; ORF449; ORF452; ORF456; ORF460; ORF461; ORF465; ORF471; ORF472; ORF482; ORF489; ORF492; ORF494; ORF495; ORF502; ORF505; ORF506; ORF509; ORF516; ORF517; ORF520; ORF525; ORF533; ORF539; ORF549; ORF554; ORF557; ORF563; ORF570; ORF573; ORF581; ORF590; ORF591; ORF600; ORF607; ORF612; ORF613; ORF620; ORF626; ORF629; ORF630; ORF639; ORF644; ORF647; ORF656; ORF659; ORF661; ORF685; ORF687; ORF699; ORF700; ORF708; ORF716; ORF719; ORF725; ORF747; ORF749; ORF756; ORF765; ORF767; ORF794; ORF796; ORF797; ORF799; ORF801; ORF807; ORF821; ORF823; ORF826; ORF847; ORF853; ORF861; ORF870; ORF871; ORF875; ORF882; ORF888; ORF889; ORF898; ORF902; ORF903; ORF911; ORF916; ORF931; ORF939; ORF975; ORF976; ORF978; ORF983; ORF986; ORF987; ORF992; ORF993; ORF1000; ORF1002; ORF1008; ORF1019; ORF1022; ORF1032; ORF1034; ORF1046; ORF1054; ORF1060; ORF1071 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis transmembrane polypeptide or one of its representative fragments, having at least 7 transmembrane domains and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF4; ORF6; ORF13; ORF20; ORF51; ORF71; ORF88; ORF118; ORF128; ORF132; ORF133; ORF158; ORF159; ORF174; ORF180; ORF189; ORF210; ORF211; ORF214; ORF215; ORF226; ORF229; ORF233; ORF235; ORF240; ORF246; ORF251; ORF255; ORF273; ORF354; ORF364; ORF369; ORF371; ORF397; ORF401; ORF409; ORF412; ORF419; ORF439; ORF453; ORF462; ORF490; ORF510; ORF51; ORF518; ORF535; ORF548; ORF550; ORF564; ORF565; ORF578; ORF579; ORF614; ORF631; ORF636; ORF650; ORF662; ORF667; ORF679; ORF681; ORF702; ORF727; ORF741; ORF763; ORF791; ORF792; ORF815; ORF816; ORF832; ORF846; ORF858; ORF865; ORF867; ORF868; ORF877; ORF891; ORF896; ORF907; ORF908; ORF918; ORF919; ORF932; ORF959; ORF977; ORF994; ORF998; ORF1024; ORF1028; ORF1042; ORF1067; ORF1070; ORF1073 and one of their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis surface exposed polypeptide (e.g., an outer membrane protein) or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences:
ORF 2, ORF 3, ORF 21, ORF 22, ORF 23, ORF 53, ORF 77, ORF 187, ORF 203, ORF 383, ORF 477, ORF 478, ORF 479, ORF 481, ORF 482, ORF 483, ORF 484, ORF 485, ORF 486, ORF 487, ORF 488, ORF 489, ORF 490, ORF 571, ORF 572, ORF 573, ORF 593, ORF 670, ORF 693, ORF 742, ORF 749, ORF 801, ORF 817, ORF 818, ORF 819, ORF 820, ORF 851, ORF 902, ORF 923, ORF 1035, ORF 1036, ORF 1037, ORF 1038, ORF 1069, ORF 1070, ORF 1071, ORF 1073, ORF 1076, ORF 1095, ORF 1096, ORF 1141, ORF 1181, and their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis lipoprotein or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences:
ORF 29, ORF 42, ORF 66, ORF 72, ORF 76, ORF 78, ORF 148, ORF 154, ORF 180, ORF 182, ORF 184, ORF 187, ORF 200, ORF 242, ORF 245, ORF 250, ORF 253, ORF 272, ORF 274, ORF 275, ORF 308, ORF 350, ORF 362, ORF 383, ORF 394, ORF 396, ORF 399,
ORF 422, ORF 488, ORF 535, ORF 568, ORF 573, ORF 578, ORF 593, ORF 607, ORF 625, ORF 662, ORF 669, ORF 688, ORF 690, ORF 716, ORF 773, ORF 778, ORF 781, ORF 783, ORF 788, ORF 817, ORF 848, ORF 851, ORF 853, ORF 857, ORF 875, ORF 877, ORF 886, ORF 898, ORF 902, ORF 923, ORF 938, ORF 976, ORF 978, ORF 990, ORF 1005, ORF 1021, ORF 1035, ORF 1069, ORF 1083, ORF 1088, ORF 1089, ORF 1091, ORF 1092, ORF 1095, ORF 1096, ORF 1100, ORF 1105, ORF 1108, ORF 1117, ORF 1120, ORF 1121, ORF 1124, ORF 1128, ORF 1133, ORF 1135, ORF 1139, ORF 1140, ORF 1157, ORF 1159, ORF 1163, ORF 1165, ORF 1167, ORF 1168, ORF 1169, ORF 1171, ORF 1173, ORF 1174, ORF 1177, ORF 1180, ORF 1181, ORF 1186, ORF 1194, ORF 1197, and their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide involved in lipopolysaccharide (LPS) biosynthesis, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences: ORF 17, ORF 201, ORF 691, ORF 807, ORF 936, ORF 983, ORF 1019, ORF 1077 and one of their representative fragments.
Preferably the invention relates to additional LPS-related nucleotide sequences according to the invention, characterized in that they encode:
(a) a Chlamydia trachomatis KDO (3-deoxy-D-manno-octulosonic acid)-related polypeptide or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences: ORF 41, ORF 242, ORF 269, ORF 772, and one of their representative fragments;
(b) a Chlamydia trachomatis phosphomannomutase-related polypeptide or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequence: ORF 139, and one of its representative fragments;
(c) a Chlamydia trachomatis phosphoglucomutase-related polypeptide or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequence: ORF 567, and one of its representative fragments; and
(d) a Chlamydia trachomatis lipid A component-related polypeptide or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences: ORF 4, ORF 933, ORF 934, ORF 935, ORF 1185, and one of their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis Type III or other, non-Type III secreted polypeptides or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences: ORF 180, ORF 181, ORF 207, ORF 208, ORF 372, ORF 391, ORF 399, ORF 477, ORF 486, ORF 749, ORF 758, ORF 819, ORF 878, ORF 888, ORF 896, ORF 897, ORF 900, ORF 902, ORF 923, ORF 1015, ORF 1018, ORF 1059, ORF 1060, ORF 1069, ORF 1071, ORF 1073, ORF 1076, ORF 1189, and their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide containing RGD (Arg-Gly-Asp) attachment sites or one of its representative fragments:
(a) RGD-containing proteins that are outer membrane proteins, are more likely to play a role in cell attachment. ORFs that encoded a protein containing an RGD sequence and also were classified as outer membrane proteins are ORF 488, ORF 489, ORF 571, ORF 572, ORF 573 or ORF 716, and its representative fragments.
(b) The outer membrane of Chlamydia is made of cysteine-rich proteins that form a network of both intra and inter molecular disulfide links. This contributes to the integrity of the membrane since Chlamydia lacks the peptidoglycan layer that other gram-negative bacteria have Cysteine-rich proteins that have the RGD sequence are also considered to be potential vaccine candidates. Cysteine-rich proteins were defined as proteins that had more than 3.0% cysteine in their primary amino acid sequence, above the mean genomic ORF cysteine content. The corresponding ORF is: ORF 1144 and one of its representative fragments.
(c) The outer membrane of Chlamydia may also contain small proteins that have cysteines in their N- and C-terminus that may contribute to the network formed by disulfide linkages. These proteins may be anchored in the outer membrane via their N-terminus and may have their C-terminus exposed, which then can interact with the host cells. Alternatively, these proteins may be anchored in the outer membrane via both N- and C-terminus and may have regions in the middle that may be exposed which can in turn interact with the host cells. ORFs encoding polypeptides that contain cysteines in their first 30 amino acids and also contain an RGD sequence are: ORF 101, ORF 122, ORF 308, ORF 488, ORF 489, ORF 571, ORF 572, ORF 573, ORF 651, ORF 679, ORF 680, ORF 705, ORF 716, ORF 763, ORF 870, ORF 878, ORF 879, ORF 995, ORF 1028, ORF 1029, ORF 1176, and one of their representative fragments.
(d) RGD-containing ORFs homologous to RGD-containing ORFs from Chlamydia pneumoniae are:
ORF 28, ORF 101, ORF 125, ORF 155, ORF 156, ORF 286, ORF 571, ORF 572, ORF 573, ORF 763, ORF 870, and one of their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis cell wall anchored surface polypeptide or one of its representative fragments, said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences: ORF 662, ORF 681, ORF 1182, ORF 1192, and their representative fragments.
Preferably, the invention relates to the nucleotide sequences according to the invention, characterized in that they encode Chlamydia trachomatis polypeptides not found in Chlamydia pneumoniae (Blastp P>e−10), said nucleotide sequences comprising a nucleotide sequence chosen from the following sequences: ORF 2, ORF 18, ORF 60, ORF 66, ORF 67, ORF 68, ORF 69, ORF 70, ORF 81, ORF 89, ORF 107, ORF 108, ORF 109, ORF 134, ORF 147, ORF 191, ORF 194, ORF, 216, ORF 217, ORF 218, ORF 219, ORF 220, ORF 221, ORF 222, ORF 223, ORF 224, ORF 225, ORF 228, ORF 235, ORF 257, ORF 276, ORF 277, ORF 278, ORF 279, ORF 280, ORF 281, ORF 282, ORF 283, ORF 284, ORF 285, ORF 289, ORF 291, ORF 298, ORF 313, ORF 314, ORF 315, ORF 316, ORF 334, ORF 335, ORF 336, ORF 337, ORF 338, ORF 339, ORF 340, ORF 381, ORF 393, ORF 413, ORF 418, ORF 419, ORF 420, ORF 421, ORF 422, ORF 423, ORF 436, ORF 460, ORF 475, ORF 476, ORF 480, ORF 485, ORF 487, ORF 491, ORF 492, ORF 493, ORF 494, ORF 496, ORF 500, ORF 504, ORF 514, ORF 527, ORF 559, ORF 569, ORF 570, ORF 575, ORF 580, ORF 582, ORF 593, ORF 598, ORF 632, ORF 640, ORF 651, ORF 671, ORF 690, ORF 694, ORF 698, ORF 710, ORF 722, ORF 723, ORF 724, ORF 770, ORF 771, ORF 782, ORF 783, ORF 784, ORF 790, ORF 795, ORF 798, ORF 805, ORF 810, ORF 817, ORF 829, ORF 830, ORF 864, ORF 866, ORF 876, ORF 887, ORF 892, ORF 899, ORF 913, ORF 921, ORF 933, ORF 938, ORF 949, ORF 956, ORF 1010, ORF 1017, ORF 1018, ORF 1027, ORF 1030, ORF 1037, ORF 1038, ORF 1047, ORF 1072, ORF 1074, ORF 1075, ORF 1078, ORF 1079, ORF 1081, ORF 1083, ORF 1084, ORF 1087, ORF 1088, ORF 1089, ORF 1091, ORF 1092, ORF 1094, ORF 1095, ORF 1096, ORF 1098, ORF 1104, ORF 1105, ORF 1106, ORF 1108, ORF 1110, ORF 1114, ORF 1115, ORF 1116, ORF 1117, ORF 1119, ORF 1128, ORF 1132, ORF 1133, ORF 1135, ORF 1136, ORF 1139, ORF 1140, ORF 1141, ORF 1142, ORF 1144, ORF 1148, ORF 1151, ORF 1155, ORF 1157, ORF 1159, ORF 1161, ORF 1162, ORF 1165, ORF 1166, ORF 1167, ORF 1168, ORF 1169, ORF 1171, ORF 1172, ORF 1173, ORF 1174, ORF 1175, ORF 1176, ORF 1177, ORF 1178, ORF 1180, ORF 1181, ORF 1183, ORF 1184, ORF 1186, ORF 1187, ORF 1188, ORF 1192, ORF 1194, ORF 1197, and their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the intermediate metabolism, in particular in the metabolism of sugars and/or of cofactors, such as for example triose phosphate isomerase or pyruvate kinase, and in that they comprise a nucleotide sequence chosen from the following sequences: ORF10; ORF44; ORF45; ORF46; ORF47; ORF93; ORF101; ORF102; ORF103; ORF106; ORF107; ORF120; ORF121; ORF130; ORF135; ORF140; ORF143; ORF144; ORF145; ORF158; ORF159; ORF160; ORF161; ORF192; ORF193; ORF196; ORF197; ORF198; ORF199; ORF227; ORF229; ORF236; ORF236; ORF239; ORF243; ORF245; ORF264; ORF265; ORF297; ORF331; ORF333; ORF359; ORF360; ORF374; ORF404; ORF405; ORF405; ORF410; ORF415; ORF415; ORF416; ORF417; ORF432; ORF460; ORF461; ORF462; ORF495; ORF513; ORF515; ORF566; ORF566; ORF566; ORF589; ORF613; ORF645; ORF646; ORF647; ORF652; ORF653; ORF654; ORF672; ORF673; ORF674; ORF682; ORF684; ORF692; ORF700; ORF725; ORF801; ORF802; ORF835; ORF836; ORF837; ORF860; ORF861; ORF862; ORF863; ORF869; ORF869; ORF925; ORF964; ORF983 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the intermediate metabolism of nucleotides or nucleic acids, such as for example CTP synthetase or GMP synthetase, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF142; ORF142; ORF169; ORF256; ORF268; ORF325; ORF352; ORF366; ORF435; ORF444; ORF528; ORF529; ORF530; ORF548; ORF549; ORF601; ORF602; ORF617; ORF619; ORF644; ORF745; ORF971; ORF972; ORF1023 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of nucleic acids, such as for example DNA polymerases or DNA topoisomerases, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF5; ORF12; 0182; ORF96; ORF97; ORF98; ORF99; ORF100; ORF105; ORF118; ORF136; ORF137; ORF163; ORF190; ORF204; ORF259; ORF260; ORF262; ORF290; ORF300; ORF301; ORF302; ORF387; ORF427; ORF434; ORF441; ORF444; ORF471; ORF595; ORF596; ORF597; ORF599; ORF600; ORF605; ORF612; ORF624; ORF625; ORF650; ORF657; ORF658; ORF702; ORF703; ORF704; ORF708; ORF719; ORF766; ORF767; ORF775; ORF779; ORF787; ORF, 788; ORF794; ORF841; ORF842; ORF883; ORF884; ORF907; ORF918; ORF924; ORF928; ORF929; ORF962; ORF962; ORF963; ORF969; ORF970; ORF975; ORF979; ORF995; ORF1031; ORF1032 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of amino acids or polypeptides, such as for example serine hydroxymethyl transferase or the proteins which load amino acids onto transfer RNAs, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF27; ORF41; ORF55; ORF56; ORF57; ORF59; ORF62; ORF63; ORF64; ORF65; ORF119; ORF132; ORF240; ORF241; ORF277; ORF278; ORF279; ORF382; ORF406; ORF428; ORF442; ORF446; ORF447; ORF453; ORF454; ORF541; ORF542; ORF591; ORF608; ORF609; ORF610; ORF618; ORF648; ORF649; ORF660; ORF661; ORF677; ORF717; ORF765; ORF797; ORF871; ORF875; ORF920; ORF922; ORF937; ORF998; ORF1020; ORF1021; ORF1034; ORF1044; ORF1046; ORF1049 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of polypeptides, such as for example protein kinases or proteases, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF21; ORF22; ORF23; ORF24; ORF25; ORF26; ORF75; ORF84; ORF86; ORF92; ORF133; ORF151; ORF152; ORF157; ORF179; ORF209; ORF307; ORF326; ORF343; ORF344; ORF345; ORF371; ORF429; ORF519; ORF557; ORF586; ORF587; ORF630; ORF656; ORF706; ORF707; ORF730; ORF751; ORF752; ORF786; ORF847; ORF885; ORF923; ORF978; ORF1039; ORF1048 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of fatty acids, such as for example succinyl-CoA-synthesizing proteins or phosphatidylserine synthetase, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF4; ORF15; ORF16; ORF141; ORF173; ORF205; ORF205; ORF206; ORF207; ORF208; ORF312; ORF355; ORF415; ORF550; ORF558; ORF560; ORF561; ORF574; ORF574; ORF577; ORF578; ORF590; ORF614; ORF772; ORF808; ORF809; ORF904; ORF905; ORF905; ORF933; ORF934; ORF934; ORF936 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the synthesis of the wall, such as for example KDO transferase, and the proteins responsible for the attachment of certain sugars onto the exposed proteins, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF87; ORF196; ORF242; ORF269; ORF628; ORF629; ORF634; ORF635; ORF637; ORF638; ORF1019 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the transcription, translation and/or maturation process, such as for example initiation factors, RNA polymerases or certain chaperone proteins, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF112; ORF113; ORF332; ORF212; ORF213; ORF350; ORF362; ORF363; ORF364; ORF407; ORF451; ORF546; ORF643; ORF744; ORF746; ORF833; ORF868; ORF981; ORF982; ORF1003; ORF1011; ORF1042 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis ribosomal polypeptide or one of its representative fragments, such as for example the ribosomal proteins L21, L27 and S10, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF114; ORF115; ORF116; ORF328; ORF361; ORF375; ORF445; ORF543; ORF584; ORF585; ORF743; ORF813; ORF941; ORF942; ORF944; ORF946; ORF947; ORF948; ORF950; ORF951; ORF952; ORF953; ORF954; ORF955; ORF955; ORF957; ORF958; ORF960; ORF961; ORF1040; ORF1041; ORF1043; ORF1063; ORF1064 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis transport polypeptide or one of its representative fragments, such as for example the proteins for transporting amino acids, sugars and certain oligopeptides, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF6; ORF50; ORF51; ORF80; ORF125; ORF126; ORF128; ORF129; ORF215; ORF246; ORF248; ORF249; ORF251; ORF252; ORF253; ORF255; ORF271; ORF275; ORF293; ORF309; ORF323; ORF324; ORF398; ORF401; ORF449; ORF511; ORF512; ORF564; ORF565; ORF667; ORF679; ORF680; ORF711; ORF712; ORF713; ORF714; ORF715; ORF730; ORF731; ORF736; ORF737; ORF738; ORF870; ORF908; ORF919; ORF977; ORF987; ORF988; ORF992; ORF993; ORF994; ORF1028; ORF1029 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the virulence process, such as for example the proteins analogous to the Escherichia coli vacB protein, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF20; ORF815; ORF816; ORF898; ORF1059; ORF1060 and one of their representative fragments.
Preferably, the invention also relates to the nucleotide sequences according to the invention, characterized in that they encode a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the secretory system and/or which is secreted, such as for example proteins homologous to proteins in the secretory system of certain bacteria such as the Salmonellae or the Yersiniae, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF758; ORF888; ORF889; ORF890; ORF891; ORF896; ORF897; ORF898 and one of their representative fragments.
Preferably, the invention also relates to nucleotide sequences according to the invention, characterized in that they encode a polypeptide specific to Chlamydiae or one of its representative fragments, and in that they comprise a nucleotide sequence chosen from the following sequences:
ORF22; ORF29; ORF31; ORF32; ORF34; ORF35; ORF39; ORF40; ORF43; ORF48; ORF49; ORF50; ORF52; ORF53; ORF54; ORF72; ORF77; ORF78; ORF87; ORF90; ORF95; ORF108; ORF1101; ORF111; ORF122; ORF123; ORF124; ORF127; ORF138; ORF144; ORF146; ORF153; ORF155; ORF164; ORF166; ORF175; ORF182; ORF184; ORF186; ORF187; ORF188; ORF202; ORF210; ORF247; ORF258; ORF266; ORF267; ORF270; ORF273; ORF274; ORF295; ORF296; ORF305; ORF306; ORF309; ORF318; ORF319; ORF322; ORF326; ORF342; ORF357; ORF376; ORF379; ORF380; ORF388; ORF390; ORF400; ORF431; ORF433; ORF438; ORF443; ORF456; ORF457; ORF458; ORF464; ORF468; ORF470; ORF473; ORF486; ORF489; ORF497; ORF501; ORF503; ORF504; ORF508; ORF512; ORF521; ORF522; ORF523; ORF524; ORF533; ORF535; ORF536; ORF537; ORF538; ORF539; ORF540; ORF554; ORF563; ORF572; ORF579; ORF595; ORF603; ORF604; ORF606; ORF607; ORF615; ORF616; ORF622; ORF641; ORF642; ORF659; ORF668; ORF670; ORF693; ORF695; ORF696; ORF699; ORF703; ORF704; ORF716; ORF726; ORF728; ORF739; ORF742; ORF747; ORF750; ORF751; ORF755; ORF757; ORF759; ORF761; ORF762; ORF763; ORF764; ORF773; ORF780; ORF781; ORF789; ORF800; ORF803; ORF804; ORF818; ORF820; ORF822; ORF823; ORF824; ORF827; ORF828; ORF839; ORF849; ORF850; ORF851; ORF852; ORF855; ORF856; ORF857; ORF858; ORF859; ORF860; ORF861; ORF862; ORF863; ORF865; ORF868; ORF869; ORF870; ORF871; ORF872; ORF873; ORF874; ORF875; ORF877; ORF878; ORF880; ORF882; ORF884; ORF886; ORF893; ORF901; ORF906; ORF910; ORF912; ORF915; ORF916; ORF917; ORF926; ORF929; ORF933; ORF965; ORF967; ORF968; ORF984; ORF986; ORF989; ORF990; ORF996; ORF997; ORF1001; ORF1002; ORF1013; ORF1016; ORF1031; ORF1033; ORF1035; ORF1049; ORF1051; ORF1052; ORF1054; ORF1056; ORF1057; ORF1058; ORF1062; ORF1070; ORF1071; ORF1073 and one of their representative fragments.
Also forming part of the invention are polypeptides encoded by the polynucleotides of the invention, as well as fusion polypeptides comprising such polypeptides. In one embodiment, the polypeptides and fusion polypeptides immunoreact with seropositive serum of an individual infected with Chlamydia trachomatis. For example, described below, are polypeptide sequences exhibiting particularly preferable characteristics. For each group of preferred polypeptides described below, it is to be understood that in addition to the individual polypeptides listed, in instances wherein such polypeptides are encoded as part of “combined” ORFs, such “combined” polypeptides are also to be included within the preferred group.
The subject of the invention is also a polypeptide according to the invention, characterized in that it is a polypeptide of the cellular envelope, preferably of the outer cellular envelope, of Chlamydia trachomatis or one of its representative fragments. According to the invention, the said polypeptide is preferably chosen from the polypeptides having the following sequences:
SEQ ID No. 3; SEQ ID No. 19; SEQ ID No. 51; SEQ ID No. 189; SEQ ID No. 212; SEQ ID No. 213; SEQ ID No. 324; SEQ ID No. 477; SEQ II) No. 478; SEQ ID No. 479; SEQ ID No. 481; SEQ ID No. 482; SEQ ID No. 483; SEQ ID No. 484; SEQ ID No. 486; SEQ ID No. 488; SEQ ID No. 489; SEQ ID No. 490; SEQ ID No. 572; SEQ ID No. 573; SEQ ID No. 742; SEQ ID No. 817; SEQ ID No. 818; SEQ ID No. 820; SEQ ID No. 1035; SEQ ID No. 1036; SEQ ID No. 1037; SEQ ID No. 1038; SEQ ID No. 1070; SEQ ID No. 1071; SEQ ID No. 1073 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis transmembrane polypeptide or one of its representative fragments, having between 1 and 3 transmembrane domains, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 2; SEQ ID No. 3; SEQ ID No. 5; SEQ ID No. 8; SEQ ID No. 9; SEQ ID No. 10; SEQ ID No. 1; SEQ ID No. 12; SEQ ID No. 17; SEQ ID No. 21; SEQ ID No. 26; SEQ ID No. 27; SEQ ID No. 28; SEQ ID No. 29; SEQ ID No. 30; SEQ ID No. 31; SEQ ID No. 33; SEQ ID No. 35; SEQ ID No. 37; SEQ ID No. 39; SEQ ID No. 40; SEQ ID No. 41; SEQ ID No. 42; SEQ ID No. 43; SEQ ID No. 44; SEQ ID No. 45; SEQ ID No. 46; SEQ ID No. 47; SEQ ID No. 48; SEQ ID No. 49; SEQ ID No. 52; SEQ ID No. 53; SEQ ID No. 55; SEQ ID No. 56; SEQ ID No. 58; SEQ ID No. 65; SEQ ID No. 66; SEQ ID No. 68; SEQ ID No. 70; SEQ ID No. 74; SEQ ID No. 75; SEQ ID No. 76; SEQ ID No. 78; SEQ ID No. 79; SEQ ID No. 81; SEQ ID No. 82; SEQ ID No. 83; SEQ ID No. 86; SEQ ID No. 91; SEQ ID No. 92; SEQ ID No. 94; SEQ ID No. 97; SEQ ID No. 100; SEQ ID No. 102; SEQ ID No. 103; SEQ ID No. 105; SEQ ID No. 106; SEQ ID No. 107; SEQ ID No. 109; SEQ ID No. 110; SEQ ID No. 111; SEQ ID No. 112; SEQ ID No. 113; SEQ ID No. 114; SEQ ID No. 115; SEQ ID No. 116; SEQ ID No. 117; SEQ ID No. 120; SEQ ID No. 122; SEQ ID No. 123; SEQ ID No. 130; SEQ ID No. 134; SEQ ID No. 135; SEQ ID No. 137; SEQ ID No. 140; SEQ ID No. 141; SEQ ID No. 143; SEQ ID No. 144; SEQ ID No. 145; SEQ ID No. 147; SEQ ID No. 148; SEQ ID No. 149; SEQ ID No. 150; SEQ ID No. 151; SEQ ID No. 155; SEQ ID No. 156; SEQ ID No. 162; SEQ ID No. 163; SEQ ID No. 164; SEQ ID No. 165; SEQ ID No. 166; SEQ ID No. 167; SEQ ID No. 168; SEQ ID No. 169; SEQ ID No. 170; SEQ ID No. 171; SEQ ID No. 173; SEQ ID No. 175; SEQ ID No. 176; SEQ ID No. 177; SEQ ID No. 181; SEQ ID No. 183; SEQ ID No. 184; SEQ ID No. 186; SEQ ID No. 187; SEQ ID No. 188; SEQ ID No. 190; SEQ ID No. 191; SEQ ID No. 192; SEQ ID No. 194; SEQ ID No. 195; SEQ ID No. 196; SEQ ID No. 197; SEQ ID No. 198; SEQ ID No. 199; SEQ ID No. 201; SEQ ID No. 202; SEQ ID No. 204; SEQ ID No. 206; SEQ ID No. 207; SEQ ID No. 209; SEQ ID No. 212; SEQ ID No. 213; SEQ ID No. 217; SEQ ID No. 219; SEQ ID No. 220; SEQ ID No. 221; SEQ ID No. 222; SEQ ID No. 223; SEQ ID No. 224; SEQ ID No. 225; SEQ ID No. 227; SEQ ID No. 228; SEQ ID No. 231; SEQ ID No. 232; SEQ ID No. 234; SEQ ID No. 236; SEQ ID No. 237; SEQ ID No. 243; SEQ ID No. 244; SEQ ID No. 245; SEQ ID No. 247; SEQ ID No. 248; SEQ ID No. 249; SEQ ID No. 252; SEQ ID No. 254; SEQ ID No. 257; SEQ ID No. 260; SEQ ID No. 261; SEQ ID No. 263; SEQ ID No. 265; SEQ ID No. 266; SEQ ID No. 267; SEQ ID No. 270; SEQ ID No. 271; SEQ ID No. 272; SEQ ID No. 274; SEQ ID No. 276; SEQ ID No. 277; SEQ ID No. 278; SEQ ID No. 279; SEQ ID No. 282; SEQ ID No. 283; SEQ ID No. 284; SEQ ID No. 285; SEQ ID No. 287; SEQ ID No. 289; SEQ ID No. 290; SEQ ID No. 291; SEQ ID No. 294; SEQ ID No. 298; SEQ ID No. 305; SEQ ID No. 306; SEQ ID No. 310; SEQ ID No. 311; SEQ ID No. 313; SEQ ID No. 315; SEQ ID No. 316; SEQ ID No. 319; SEQ ID No. 320; SEQ ID No. 322; SEQ ID No. 323; SEQ ID No. 325; SEQ ID No. 326; SEQ ID No. 327; SEQ ID No. 328; SEQ ID No. 330; SEQ ID No. 331; SEQ ID No. 332; SEQ ID No. 333; SEQ ID No. 334; SEQ ID No. 335; SEQ ID No. 336; SEQ ID No. 338; SEQ ID No. 339; SEQ ID No. 340; SEQ ID No. 341; SEQ ID No. 344; SEQ ID No. 345; SEQ ID No. 348; SEQ ID No. 349; SEQ ID No. 350; SEQ ID No. 351; SEQ ID No. 352; SEQ ID No. 353; SEQ ID No. 356; SEQ ID No. 357; SEQ ID No. 358; SEQ ID No. 361; SEQ ID No. 362; SEQ ID No. 366; SEQ ID No. 367; SEQ ID No. 368; SEQ ID No. 370; SEQ ID No. 372; SEQ ID No. 373; SEQ ID No. 375; SEQ ID No. 377; SEQ ID No. 378; SEQ ID No. 379; SEQ ID No. 380; SEQ ID No. 382; SEQ ID No. 383; SEQ ID No. 384; SEQ ID No. 385; SEQ ID No. 387; SEQ ID No. 389; SEQ ID No. 390; SEQ ID No. 391; SEQ ID No. 393; SEQ ID No. 396; SEQ ID No. 398; SEQ ID No. 399; SEQ ID No. 403; SEQ ID No. 404; SEQ ID No. 406; SEQ ID No. 407; SEQ ID No. 413; SEQ ID No. 414; SEQ ID No. 417; SEQ ID No. 418; SEQ ID No. 420; SEQ ID No. 421; SEQ ID No. 424; SEQ ID No. 426; SEQ ID No. 427; SEQ ID No. 428; SEQ ID No. 430; SEQ ID No. 433; SEQ ID No. 434; SEQ ID No. 435; SEQ ID No. 436; SEQ ID No. 437; SEQ ID No. 440; SEQ ID No. 443; SEQ ID No. 446; SEQ ID No. 448; SEQ ID No. 450; SEQ ID No. 451; SEQ ID No. 454; SEQ ID No. 455; SEQ ID No. 457; SEQ ID No. 458; SEQ ID No. 459; SEQ ID No. 463; SEQ ID No. 464; SEQ ID No. 466; SEQ ID No. 467; SEQ ID No. 468; SEQ ID No. 469; SEQ ID No. 470; SEQ ID No. 473; SEQ ID No. 474; SEQ ID No. 475; SEQ ID No. 476; SEQ ID No. 477; SEQ ID No. 479; SEQ ID No. 480; SEQ ID No. 481; SEQ ID No. 483; SEQ ID No. 484; SEQ ID No. 485; SEQ ID No. 486; SEQ ID No. 487; SEQ ID No. 488; SEQ ID No. 491; SEQ ID No. 493; SEQ ID No. 496; SEQ ID No. 497; SEQ ID No. 498; SEQ ID No. 500; SEQ ID No. 501; SEQ ID No. 503; SEQ ID No. 504; SEQ ID No. 508; SEQ ID No. 512; SEQ ID No. 513; SEQ ID No. 514; SEQ ID No. 519; SEQ ID No. 521; SEQ ID No. 523; SEQ ID No. 524; SEQ ID No. 526; SEQ ID No. 527; SEQ ID No. 529; SEQ ID No. 530; SEQ ID No. 531; SEQ ID No. 532; SEQ ID No. 534; SEQ ID No. 536; SEQ ID No. 537; SEQ ID No. 538; SEQ ID No. 540; SEQ ID No. 541; SEQ ID No. 542; SEQ ID No. 543; SEQ ID No. 544; SEQ ID No. 545; SEQ ID No. 546; SEQ ID No. 547; SEQ ID No. 551; SEQ ID No. 552; SEQ ID No. 553; SEQ ID No. 555; SEQ ID No. 558; SEQ ID No. 559; SEQ ID No. 560; SEQ ID No. 561; SEQ ID No. 562; SEQ ID No. 566; SEQ ID No. 567; SEQ ID No. 568; SEQ ID No. 569; SEQ ID No. 571; SEQ ID No. 572; SEQ ID No. 574; SEQ ID No. 575; SEQ ID No. 576; SEQ ID No. 580; SEQ ID No. 582; SEQ ID No. 585; SEQ ID No. 587; SEQ ID No. 589; SEQ ID No. 592; SEQ ID No. 593; SEQ ID No. 595; SEQ ID No. 596; SEQ ID No. 597; SEQ ID No. 599; SEQ ID No. 601; SEQ ID No. 602; SEQ ID No. 603; SEQ ID No. 604; SEQ ID No. 608; SEQ D No. 609; SEQ ID No. 610; SEQ ID No. 611; SEQ ID No. 615; SEQ ID No. 616; SEQ ID No. 617; SEQ ID No. 618; SEQ ID No. 621; SEQ ID No. 622; SEQ ID No. 623; SEQ ID No. 624; SEQ ID No. 625; SEQ ID No. 628; SEQ ID No. 632; SEQ ID No. 633; SEQ ID No. 634; SEQ ID No. 635; SEQ ID No. 637; SEQ ID No. 638; SEQ ID No. 640; SEQ ID No. 641; SEQ ID No. 643; SEQ ID No. 646; SEQ ID No. 648; SEQ ID No. 649; SEQ ID No. 651; SEQ ID No. 652; SEQ ID No. 653; SEQ ID No. 654; SEQ ID No. 655; SEQ ID No. 658; SEQ ID No. 664; SEQ ID No. 665; SEQ ID No. 666; SEQ ID No. 668; SEQ ID No. 669; SEQ ID No. 670; SEQ ID No. 671; SEQ ID No. 672; SEQ ID No. 673; SEQ ID No. 674; SEQ ID No. 676; SEQ ID No. 677; SEQ ID No. 678; SEQ ID No. 680; SEQ ID No. 682; SEQ ID No. 683; SEQ ID No. 684; SEQ ID No. 686; SEQ ID No. 688; SEQ ID No. 689; SEQ ID No. 690; SEQ ID No. 691; SEQ ID No. 692; SEQ ID No. 693; SEQ ID No. 695; SEQ ID No. 696; SEQ ID No. 698; SEQ ID No. 701; SEQ ID No. 703; SEQ ID No. 704; SEQ ID No. 705; SEQ ID No. 706; SEQ ID No. 707; SEQ ID No. 709; SEQ ID No. 710; SEQ ID No. 711; SEQ ID No. 712; SEQ ID No. 713; SEQ ID No. 714; SEQ ID No. 715; SEQ ID No. 717; SEQ ID No. 718; SEQ ID No. 720; SEQ ID No. 721; SEQ ID No. 722; SEQ ID No. 724; SEQ ID No. 726; SEQ ID No. 728; SEQ ID No. 729; SEQ ID No. 730; SEQ ID No. 731; SEQ ID No. 732; SEQ ID No. 733; SEQ ID No. 734; SEQ ID No. 737; SEQ ID No. 738; SEQ ID No. 739; SEQ ID No. 740; SEQ ID No. 742; SEQ ID No. 743; SEQ ID No. 744; SEQ ID No. 745; SEQ ID No. 746; SEQ ID No. 748; SEQ ID No. 750; SEQ ID No. 751; SEQ ID No. 752; SEQ ID No. 753; SEQ ID No. 754; SEQ ID No. 755; SEQ ID No. 757; SEQ ID No. 758; SEQ ID No. 759; SEQ ID No. 760; SEQ ID No. 764; SEQ ID No. 766; SEQ ID No. 768; SEQ ID No. 769; SEQ ID No. 771; SEQ ID No. 772; SEQ ID No. 773; SEQ ID No. 774; SEQ ID No. 775; SEQ ID No. 776; SEQ ID No. 777; SEQ ID No. 778; SEQ ID No. 779; SEQ ID No. 780; SEQ ID No. 781; SEQ ID No. 782; SEQ ID No. 783; SEQ ID No. 786; SEQ ID No. 787; SEQ ID No. 788; SEQ ID No. 789; SEQ ID No. 790; SEQ ID No. 793; SEQ ID No. 798; SEQ ID No. 800; SEQ ID No. 802; SEQ ID No. 803; SEQ ID No. 806; SEQ ID No. 808; SEQ ID No. 809; SEQ ID No. 810; SEQ ID No. 811; SEQ ID No. 813; SEQ ID No. 814; SEQ ID No. 817; SEQ ID No. 820; SEQ ID No. 822; SEQ ID No. 824; SEQ ID No. 825; SEQ ID No. 827; SEQ ID No. 828; SEQ ID No. 829; SEQ ID No. 830; SEQ ID No. 833; SEQ ID No. 834; SEQ ID No. 835; SEQ ID No. 837; SEQ ID No. 838; SEQ ID No. 839; SEQ ID No. 840; SEQ ID No. 841; SEQ ID No. 842; SEQ ID No. 843; SEQ ID No. 845; SEQ ID No. 848; SEQ ID No. 849; SEQ ID No. 850; SEQ ID No. 851; SEQ ID No. 852; SEQ ID No. 854; SEQ ID No. 855; SEQ ID No. 856; SEQ ID No. 857; SEQ ID No. 859; SEQ ID No. 860; SEQ ID No. 862; SEQ ID No. 863; SEQ ID No. 864; SEQ ID No. 866; SEQ ID No. 869; SEQ ID No. 872; SEQ ID No. 873; SEQ ID No. 874; SEQ ID No. 878; SEQ ID No. 879; SEQ ID No. 880; SEQ ID No. 881; SEQ ID No. 883; SEQ ID No. 884; SEQ ID No. 885; SEQ ID No. 886; SEQ ID No. 887; SEQ ID No. 892; SEQ ID No. 893; SEQ ID No. 894; SEQ ID No. 895; SEQ ID No. 897; SEQ ID No. 899; SEQ H) No. 900; SEQ ID No. 901; SEQ ID No. 904; SEQ ID No. 906; SEQ ID No. 909; SEQ ID No. 910; SEQ ID No. 912; SEQ ID No. 914; SEQ ID No. 917; SEQ ID No. 920; SEQ ID No. 921; SEQ ID No. 922; SEQ ID No. 923; SEQ ID No. 924; SEQ ID No. 925; SEQ ID No. 926; SEQ ID No. 927; SEQ ID No. 930; SEQ ID No. 933; SEQ ID No. 934; SEQ ID No. 935; SEQ ID No. 936; SEQ ID No. 937; SEQ ID No. 940; SEQ ID No. 941; SEQ ID No. 942; SEQ ID No. 943; SEQ ID No. 944; SEQ ID No. 945; SEQ ID No. 947; SEQ ID No. 948; SEQ ID No. 951; SEQ ID No. 952; SEQ ID No. 953; SEQ ID No. 954; SEQ ID No. 955; SEQ ID No. 956; SEQ ID No. 957; SEQ ID No. 958; SEQ ID No. 960; SEQ ID No. 961; SEQ ID No. 962; SEQ ID No. 963; SEQ ID No. 964; SEQ ID No. 966; SEQ ID No. 967; SEQ ID No. 969; SEQ ID No. 970; SEQ ID No. 971; SEQ ID No. 973; SEQ ID No. 974; SEQ ID No. 979; SEQ ID No. 980; SEQ ID No. 981; SEQ ID No. 982; SEQ ID No. 984; SEQ ID No. 988; SEQ ID No. 989; SEQ ID No. 990; SEQ ID No. 991; SEQ ID No. 995; SEQ ID No. 996; SEQ ID No. 999; SEQ ID No. 1001; SEQ ID No. 1003; SEQ ID No. 1004; SEQ ID No. 1005; SEQ ID No. 1006; SEQ ID No. 1007; SEQ ID No. 1009; SEQ ID No. 1010; SEQ ID No. 1011; SEQ ID No. 1012; SEQ ID No. 1013; SEQ ID No. 1014; SEQ ID No. 1016; SEQ ID No. 1017; SEQ ID No. 1018; SEQ ID No. 1020; SEQ ID No. 1021; SEQ ID No. 1025; SEQ ID No. 1026; SEQ ID No. 1027; SEQ ID No. 1029; SEQ ID No. 1030; SEQ ID No. 1031; SEQ ID No. 1035; SEQ ID No. 1036; SEQ ID No. 1037; SEQ ID No. 1038; SEQ ID No. 1039; SEQ ID No. 1040; SEQ ID No. 1044; SEQ ID No. 1045; SEQ ID No. 1047; SEQ ID No. 1048; SEQ ID No. 1050; SEQ ID No. 1051; SEQ ID No. 1052; SEQ ID No. 1053; SEQ ID No. 1055; SEQ ID No. 1056; SEQ ID No. 1057; SEQ ID No. 1058; SEQ ID No. 1061; SEQ ID No. 1062; SEQ ID No. 1063; SEQ ID No. 1064; SEQ ID No. 1065; SEQ ID No. 1066; SEQ ID No. 1068; SEQ ID No. 1069; SEQ ID No. 1072; SEQ ID No. 1074; SEQ ID No. 1076 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis transmembrane polypeptide or one of its representative fragments, having between 4 and 6 transmembrane domains, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 7; SEQ ID No. 14; SEQ ID No. 16; SEQ ID No. 32; SEQ ID No. 34; SEQ ID No. 36; SEQ ID No. 38; SEQ ID No. 50; SEQ ID No. 57; SEQ ID No. 59; SEQ ID No. 61; SEQ ID No. 62; SEQ ID No. 63; SEQ ID No. 64; SEQ ID No. 67; SEQ ID No. 69; SEQ ID No. 72; SEQ ID No. 77; SEQ ID No. 80; SEQ ID No. 84; SEQ ID No. 87; SEQ ID No. 93; SEQ ID No. 95; SEQ ID No. 99; SEQ ID No. 108; SEQ ID No. 119; SEQ ID No. 125; SEQ ID No. 126; SEQ ID No. 129; SEQ ID No. 131; SEQ ID No. 136; SEQ ID No. 139; SEQ ID No. 146; SEQ ID No. 152; SEQ ID No. 154; SEQ ID No. 160; SEQ ID No. 161; SEQ ID No. 172; SEQ ID No. 179; SEQ ID No. 182; SEQ ID No. 185; SEQ ID No. 200; SEQ ID No. 203; SEQ ID No. 205; SEQ ID No. 239; SEQ ID No. 242; SEQ ID No. 250; SEQ ID No. 253; SEQ ID No. 256; SEQ ID No. 259; SEQ ID No. 262; SEQ ID No. 268; SEQ ID No. 275; SEQ ID No. 281; SEQ ID No. 286; SEQ ID No. 288; SEQ ID No. 292; SEQ ID No. 295; SEQ ID No. 296; SEQ ID No. 297; SEQ ID No. 299; SEQ ID No. 300; SEQ ID No. 308; SEQ ID No. 314; SEQ ID No. 317; SEQ ID No. 318; SEQ ID No. 324; SEQ ID No. 342; SEQ ID No. 343; SEQ ID No. 355; SEQ ID No. 360; SEQ ID No. 374; SEQ ID No. 376; SEQ ID No. 386; SEQ ID No. 388; SEQ ID No. 392; SEQ ID No. 394; SEQ ID No. 395; SEQ ID No. 402; SEQ ID No. 405; SEQ ID No. 411; SEQ ID No. 415; SEQ ID No. 416; SEQ ID No. 422; SEQ ID No. 423; SEQ ID No. 429; SEQ ID No. 432; SEQ ID No. 441; SEQ ID No. 442; SEQ ID No. 444; SEQ ID No. 449; SEQ ID No. 452; SEQ ID No. 456; SEQ ID No. 460; SEQ ID No. 461; SEQ ID No. 465; SEQ ID No. 471; SEQ ID No. 472; SEQ ID No. 482; SEQ ID No. 489; SEQ ID No. 492; SEQ ID No. 494; SEQ ID No. 495; SEQ ID No. 502; SEQ ID No. 505; SEQ ID No. 506; SEQ ID No. 509; SEQ ID No. 516; SEQ ID No. 517; SEQ ID No. 520; SEQ ID No. 525; SEQ ID No. 533; SEQ ID No. 539; SEQ ID No. 549; SEQ ID No. 554; SEQ ID No. 557; SEQ ID No. 563; SEQ ID No. 570; SEQ ID No. 573; SEQ ID No. 581; SEQ ID No. 590; SEQ ID No. 591; SEQ ID No. 600; SEQ ID No. 607; SEQ ID No. 612; SEQ ID No. 613; SEQ ID No. 620; SEQ ID No. 626; SEQ ID No. 629; SEQ ID No. 630; SEQ ID No. 639; SEQ ID No. 644; SEQ ID No. 647; SEQ ID No. 656; SEQ ID No. 659; SEQ ID No. 661; SEQ ID No. 685; SEQ ID No. 687; SEQ ID No. 699; SEQ ID No. 700; SEQ ID No. 708; SEQ ID No. 716; SEQ ID No. 719; SEQ ID No. 725; SEQ ID No. 747; SEQ ID No. 749; SEQ ID No. 756; SEQ ID No. 765; SEQ ID No. 767; SEQ ID No. 794; SEQ ID No. 796; SEQ ID No. 797; SEQ ID No. 799; SEQ ID No. 801; SEQ ID No. 807; SEQ ID No. 821; SEQ ID No. 823; SEQ ID No. 826; SEQ ID No. 847; SEQ ID No. 853; SEQ ID No. 861; SEQ ID No. 870; SEQ ID No. 871; SEQ ID No. 875; SEQ ID No. 882; SEQ ID No. 888; SEQ ID No. 889; SEQ ID No. 898; SEQ ID No. 902; SEQ ID No. 903; SEQ ID No. 911; SEQ ID No. 916; SEQ ID No. 931; SEQ ID No. 939; SEQ ID No. 975; SEQ ID No. 976; SEQ ID No. 978; SEQ ID No. 983; SEQ ID No. 986; SEQ ID No. 987; SEQ ID No. 992; SEQ ID No. 993; SEQ ID No. 1000; SEQ ID No. 1002; SEQ ID No. 1008; SEQ ID No. 1019; SEQ ID No. 1022; SEQ ID No. 1032; SEQ ID No. 1034; SEQ ID No. 1046; SEQ ID No. 1054; SEQ ID No. 1060; SEQ ID No. 1071 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis transmembrane polypeptide or one of its representative fragments, having at least 7 transmembrane domains, and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 4; SEQ ID No. 6; SEQ ID No. 13; SEQ ID No. 20; SEQ ID No. 51; SEQ ID No. 71; SEQ ID No. 88; SEQ ID No. 118; SEQ ID No. 128; SEQ ID No. 132; SEQ ID No. 133; SEQ ID No. 158; SEQ ID No. 159; SEQ ID No. 174; SEQ ID No. 180; SEQ ID No. 189; SEQ ID No. 210; SEQ ID No. 211; SEQ ID No. 214; SEQ ID No. 215; SEQ ID No. 226; SEQ ID No. 229; SEQ ID No. 233; SEQ ID No. 235; SEQ ID No. 240; SEQ ID No. 246; SEQ ID No. 251; SEQ ID No. 255; SEQ ID No. 273; SEQ ID No. 354; SEQ ID No. 364; SEQ ID No. 369; SEQ ID No. 371; SEQ ID No. 397; SEQ ID No. 401; SEQ ID No. 409; SEQ ID No. 412; SEQ ID No. 419; SEQ ID No. 439; SEQ ID No. 453; SEQ ID No. 462; SEQ ID No. 490; SEQ ID No. 510; SEQ ID No. 511; SEQ ID No. 518; SEQ ID No. 535; SEQ ID No. 548; SEQ ID No. 550; SEQ ID No. 564; SEQ ID No. 565; SEQ ID No. 578; SEQ ID No. 579; SEQ ID No. 614; SEQ ID No. 631; SEQ ID No. 636; SEQ ID No. 650; SEQ ID No. 662; SEQ ID No. 667; SEQ ID No. 679; SEQ ID No. 681; SEQ ID No. 702; SEQ ID No. 727; SEQ ID No. 741; SEQ ID No. 763; SEQ ID No. 791; SEQ ID No. 792; SEQ ID No. 815; SEQ ID No. 816; SEQ ID No. 832; SEQ ID No. 846; SEQ ID No. 858; SEQ ID No. 865; SEQ ID No. 867; SEQ ID No. 868; SEQ ID No. 877; SEQ ID No. 891; SEQ ID No. 896; SEQ ID No. 907; SEQ ID No. 908; SEQ ID No. 918; SEQ ID No. 919; SEQ ID No. 932; SEQ ID No. 959; SEQ ID No. 977; SEQ ID No. 994; SEQ ID No. 998; SEQ ID No. 1024; SEQ ID No. 1028; SEQ ID No. 1042; SEQ ID No. 1067; SEQ ID No. 1070; SEQ ID No. 1073 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis surface exposed polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQ ID No. 53, SEQ ID No. 77, SEQ ID No. 187, SEQ ID No. 203, SEQ ID No. 383, SEQ ID No. 477, SEQ ID No. 478, SEQ ID No. 479, SEQ ID No. 481, SEQ ID No. 482, SEQ ID No. 483, SEQ ID No. 484, SEQ ID No. 485, SEQ ID No. 486, SEQ ID No. 487, SEQ ID No. 488, SEQ ID No. 489, SEQ ID No. 490, SEQ ID No. 571, SEQ ID No. 572, SEQ ID No. 573, SEQ ID No. 593, SEQ ID No. 670, SEQ ID No. 693, SEQ ID No. 742, SEQ ID No. 749, SEQ ID No. 801, SEQ ID No. 817, SEQ ID No. 818, SEQ ID No. 819, SEQ ID No. 820, SEQ ID No. 851, SEQ ID No. 902, SEQ ID No. 923, SEQ ID No. 1035, SEQ ID No. 1036, SEQ ID No. 1037, SEQ ID No. 1038, SEQ ID No. 1069, SEQ ID No. 1070, SEQ ID No. 1071, SEQ ID No. 1073, SEQ ID No. 1076, SEQ ID No. 1095, SEQ ID No. 1096, SEQ ID No. 1141, SEQ ID No. 1181, and their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis lipoprotein or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 29, SEQ ID No. 42, SEQ ID No. 66, SEQ ID No. 72, SEQ ID No. 76, SEQ ID No. 78, SEQ ID No. 148, SEQ ID No. 154, SEQ ID No. 180, SEQ ID No. 182, SEQ ID No. 184, SEQ ID No. 187, SEQ ID No. 200, SEQ ID No. 242, SEQ ID No. 245, SEQ ID No. 250, SEQ ID No. 253, SEQ ID No. 272, SEQ ID No. 274, SEQ ID No. 275, SEQ ID No. 308, SEQ ID No. 350, SEQ ID No. 362, SEQ ID No. 383, SEQ ID No. 394, SEQ ID No. 396, SEQ ID No. 399, SEQ ID No. 422, SEQ ID No. 488, SEQ ID No. 535, SEQ ID No. 568, SEQ ID No. 573, SEQ ID No. 578, SEQ ID No. 593, SEQ ID No. 607, SEQ ID No. 625, SEQ ID No. 662, SEQ ID No. 669, SEQ ID No. 688, SEQ ID No. 690, SEQ ID No. 716, SEQ ID No. 773, SEQ ID No. 778, SEQ ID No. 781, SEQ ID No. 783, SEQ ID No. 788, SEQ ID No. 817, SEQ ID No. 848, SEQ ID No. 851, SEQ ID No. 853, SEQ ID No. 857, SEQ ID No. 875, SEQ ID No. 877, SEQ ID No. 886, SEQ ID No. 898, SEQ ID No. 902, SEQ ID No. 923, SEQ ID No. 938, SEQ ID No. 976, SEQ ID No. 978, SEQ ID No. 990, SEQ ID No. 1005, SEQ ID No. 1021, SEQ ID No. 1035, SEQ ID No. 1069, SEQ ID No. 1083, SEQ ID No. 1088, SEQ ID No. 1089, SEQ ID No. 1091, SEQ ID No. 1092, SEQ ID No. 1095, SEQ ID No. 1096, SEQ ID No. 1100, SEQ ID No. 1105, SEQ ID No. 1108, SEQ ID No. 1117, SEQ ID No. 1120, SEQ ID No. 1121, SEQ ID No. 1124, SEQ ID No. 1128, SEQ ID No. 1133, SEQ ID No. 1135, SEQ ID No. 1139, SEQ ID No. 1140, SEQ ID No. 1157, SEQ ID No. 1159, SEQ ID No. 1163, SEQ ID No. 1165, SEQ ID No. 1167, SEQ ID No. 1168, SEQ ID No. 1169, SEQ ID No. 1171, SEQ ID No. 1173, SEQ ID No. 1174, SEQ ID No. 1177, SEQ ID No. 1180, SEQ ID No. 1181, SEQ ID No. 1186, SEQ ID No. 1194, SEQ ID No. 1197, and their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis polypeptide involved in lipopolysaccharide (LPS) biosynthesis, and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 17, SEQ ID No. 201, SEQ ID No. 691, SEQ ID No. 807, SEQ ID No. 936, SEQ ID No. 983, SEQ ID No. 1019, SEQ ID No. 1077, and their representative fragments.
Preferably, the invention relates to additional LPS-related polypeptides according to the invention, in that it is:
(a) a Chlamydia trachomatis KDO (3-deoxy-D-manno-octylosonic acid)-related polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 41, SEQ ID No. 242, SEQ ID No. 269, SEQ ID No. 772, and one of their representative fragments;
(b) a Chlamydia trachomatis phosphomannomutase-related polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequence: SEQ ID No. 139, and its representative fragments;
(c) a Chlamydia trachomatis phosphoglucomutase-related polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequence: SEQ ID No. 567 and its representative fragments; and
(d) a Chlamydia trachomatis lipid A component-related polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 4, SEQ ID No. 933, SEQ ID No. 934, SEQ ID No. 935, SEQ ID No. 1185, and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments that contains an RGD sequence and is also an outer membrane protein, and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 488, SEQ ID No. 489, SEQ ID No. 571, SEQ ID No. 572, SEQ No. 573, SEQ ID No. 716 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments that is cysteine-rich and contains RGD sequence, and in that it is chosen from the polypeptides having the following sequence: SEQ ID No. 144 and one of its representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis outer membrane polypeptide that contains cysteines in their first 30 amino acids and also contain an RGD sequence, and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 101, SEQ ID No. 122, SEQ ID No. 308, SEQ ID No. 488, SEQ ID No. 489, SEQ ID No. 571, SEQ ID No. 572, SEQ ID No. 573, SEQ ID No. 651, SEQ ID No. 679, SEQ ID No. 680, SEQ ID No. 705, SEQ ID No. 716, SEQ ID No. 763, SEQ ID No. 870, SEQ ID No. 878, SEQ ID No. 879, SEQ ID No. 995, SEQ ID No. 1028, SEQ ID No. 1029, SEQ ID No. 1176, and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments that contains RGD sequences homologous to Chlamydia pneumoniae polypeptides containing RGD sequences, and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 28, SEQ ID No. 101, SEQ ID No. 125, SEQ ID No. 155, SEQ ID No. 156, SEQ ID No. 286, SEQ ID No. 571, SEQ ID No. 572, SEQ ID No. 573, SEQ ID No. 763, SEQ ID No. 870, and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis Type III or non-Type III secreted polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 180, SEQ ID No. 181, SEQ ID No. 207, SEQ ID No. 208, SEQ ID No. 372, SEQ ID No. 391, SEQ ID No. 399, SEQ ID No. 477, SEQ ID No. 486, SEQ ID No. 749, SEQ ID No. 758, SEQ ID No. 819, SEQ ID No. 878, SEQ ID No. 888, SEQ ID No. 896, SEQ ID No. 897, SEQ ID No. 900, SEQ ID No. 902, SEQ ID No. 923, SEQ ID No. 1015, SEQ ID No. 1018, SEQ ID No. 1059, SEQ ID No. 1060, SEQ ID No. 1069, SEQ ID No. 1071, SEQ ID No. 1073, SEQ ID No. 1076, SEQ ID No. 1189, and their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis cell wall anchored surface polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 662, SEQ ID No. 681, SEQ ID No. 1182, SEQ ID No. 1192, and their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments not found in Chlamydia pneumoniae (Blastp P>e−10) and in that it is chosen from the polypeptides having the following sequences: SEQ ID No. 2, SEQ ID No. 18, SEQ ID No. 60, SEQ ID No. 66, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 70, SEQ ID No. 81, SEQ ID No. 89, SEQ ID No. 107, SEQ ID No. 108, SEQ ID No. 109, SEQ ID No. 134, SEQ ID No. 147, SEQ ID No. 191, SEQ ID No. 194, SEQ ID No. 216, SEQ ID No. 217, SEQ ID No. 218, SEQ ID No. 219, SEQ ID No. 220, SEQ ID No. 221, SEQ ID No. 222, SEQ ID No. 222, SEQ ID No. 223, SEQ ID No. 224, SEQ ID No. 225, SEQ ID No. 228, SEQ ID No. 235, SEQ ID No. 257, SEQ ID No. 276, SEQ ID No. 277, SEQ ID No. 278, SEQ ID No. 279, SEQ ID No. 280, SEQ ID No. 281, SEQ ID No. 282, SEQ ID No. 283, SEQ ID No. 284, SEQ ID No. 285, SEQ ID No. 289, SEQ ID No. 291, SEQ ID No. 298, SEQ ID No. 284, SEQ ID No. 313, SEQ ID No. 314, SEQ ID No. 315, SEQ ID No. 316, SEQ ID No. 334, SEQ ID No. 335, SEQ ID No. 336, SEQ ID No. 337, SEQ ID No. 338, SEQ ID No. 339, SEQ ID No. 340, SEQ ID No. 381, SEQ ID No. 393, SEQ ID No. 413, SEQ ID No. 418, SEQ ID No. 419, SEQ ID No. 419, SEQ ID No. 420, SEQ ID No. 421, SEQ ID No. 422, SEQ ID No. 423, SEQ ID No. 436, SEQ ID No. 460, SEQ ID No. 475, SEQ ID No. 476, SEQ ID No. 480, SEQ ID No. 485, SEQ ID No. 487, SEQ ID No. 491, SEQ ID No. 492, SEQ ID No. 493, SEQ ID No. 494, SEQ ID No. 496, SEQ ID No. 500, SEQ ID No. 504, SEQ ID No. 514, SEQ ID No. 527, SEQ ID No. 559, SEQ ID No. 569, SEQ ID No. 570, SEQ ID No. 575, SEQ ID No. 580, SEQ ID No. 582, SEQ ID No. 593, SEQ ID No. 598, SEQ ID No. 632, SEQ ID No. 640, SEQ ID No. 651, SEQ ID No. 671, SEQ ID No. 690, SEQ ID No. 694, ID No. 698, SEQ ID No. 710, SEQ ID No. 722, SEQ ID No. 723, SEQ ID No. 724, SEQ ID No. 770, SEQ ID No. 771, SEQ ID No. 782, SEQ ID No. 783, SEQ ID No. 784, SEQ ID No. 790, SEQ ID No. 795, SEQ ID No. 798, SEQ ID No. 805, SEQ ID No. 810, SEQ ID No. 817, SEQ ID No. 829, SEQ ID No. 830, SEQ ID No. 864, SEQ ID No. 866, SEQ ID No. 876, SEQ ID No. 887, SEQ ID No. 892, SEQ ID No. 899, SEQ ID No. 913, SEQ ID No. 921, SEQ ID No. 933, SEQ ID No. 938, SEQ ID No. 949, SEQ ID No. 956, SEQ ID No. 1010, SEQ ID No. 1017, SEQ ID No. 1018, SEQ ID No. 1027, SEQ ID No. 1030, SEQ ID No. 1037, SEQ ID No. 1038, SEQ ID No. 1047, SEQ ID No. 1072, SEQ ID No. 1074, SEQ ID No. 1075, SEQ ID No. 1078, SEQ ID No. 1079, SEQ ID No. 1081, SEQ ID No. 1083, SEQ ID No. 1084, SEQ ID No. 1087, SEQ ID No. 1088, SEQ ID No. 1089, SEQ ID No. 1091, SEQ ID No. 1092, SEQ ID No. 1094, SEQ ID No. 1095, SEQ ID No. 1096, SEQ ID No. 1098, SEQ ID No. 1104, SEQ ID No. 1105, SEQ ID No. 1106, SEQ ID No. 1108, SEQ ID No. 110, SEQ ID No. 1114, SEQ ID No. 1115, SEQ ID No. 1116, SEQ ID No. 1117, SEQ ID No. 1119, SEQ D No. 1128, SEQ ID No. 1132, SEQ ID No. 1133, SEQ ID No. 1135, SEQ ID No. 1136, SEQ ID No. 1139, SEQ ID No. 1140, SEQ ID No. 1141, SEQ ID No. 1142, SEQ ID No. 1144, SEQ ID No. 1148, SEQ ID No. 1151, SEQ ID No. 1155, SEQ ID No. 1157, SEQ ID No. 1159, SEQ ID No. 1161, SEQ ID No. 1162, SEQ ID No. 1165, SEQ ID No. 1166, SEQ ID No. 1167, SEQ ID No. 1168, SEQ ID No. 1169, SEQ ID No. 1171, SEQ ID No. 1172, SEQ ID No. 1173, SEQ ID No. 1174, SEQ ID No. 1175, SEQ ID No. 1176, SEQ ID No. 1177, SEQ ID No. 1178, SEQ ID No. 1180, SEQ ID No. 1181, SEQ ID No. 1183, SEQ ID No. 1184, SEQ ID No. 1186, SEQ ID No. 1187, SEQ ID No. 1188, SEQ ID No. 1192, SEQ ID No. 1194, SEQ ID No. 1197, and their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the intermediate metabolism, in particular in the metabolism of sugars and/or of cofactors, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 10; SEQ ID No. 44; SEQ ID No. 45; SEQ ID No. 46; SEQ ID No. 47; SEQ ID No. 93; SEQ D No. 101; SEQ ID No. 102; SEQ ID No. 103; SEQ ID No. 106; SEQ ID No. 107; SEQ ID No. 120; SEQ ID No. 121; SEQ ID No. 130; SEQ ID No. 135; SEQ ID No. 140; SEQ ID No. 143; SEQ ID No. 144; SEQ ID No. 145; SEQ ID No. 158; SEQ ID No. 159; SEQ ID No. 160; SEQ ID No. 161; SEQ ID No. 192; SEQ ID No. 193; SEQ ID No. 196; SEQ ID No. 197; SEQ ID No. 198; SEQ ID No. 199; SEQ ID No. 227; SEQ ID No. 229; SEQ ID No. 236; SEQ ID No. 236; SEQ ID No. 239; SEQ ID No. 243; SEQ ID No. 245; SEQ ID No. 264; SEQ ID No. 265; SEQ ID No. 297; SEQ ID No. 331; SEQ ID No. 333; SEQ ID No. 359; SEQ ID No. 360; SEQ ID No. 374; SEQ ID No. 404; SEQ ID No. 405; SEQ ID No. 405; SEQ ID No. 410; SEQ ID No. 415; SEQ ID No. 415; SEQ ID No. 416; SEQ ID No. 417; SEQ ID No. 432; SEQ ID No. 460; SEQ ID No. 461; SEQ ID No. 462; SEQ ID No. 495; SEQ ID No. 513; SEQ ID No. 515; SEQ ID No. 566; SEQ ID No. 566; SEQ ID No. 566; SEQ ID No. 589; SEQ ID No. 613; SEQ ID No. 645; SEQ ID No. 646; SEQ ID No. 647; SEQ ID No. 652; SEQ ID No. 653; SEQ ID No. 654; SEQ ID No. 672; SEQ ID No. 673; SEQ ID No. 674; SEQ ID No. 682; SEQ ID No. 684; SEQ ID No. 692; SEQ ID No. 700; SEQ ID No. 725; SEQ ID No. 801; SEQ ID No. 802; SEQ ID No. 835; SEQ ID No. 836; SEQ ID No. 837; SEQ ID No. 860; SEQ ID No. 861; SEQ ID No. 862; SEQ ID No. 863; SEQ ID No. 869; SEQ ID No. 869; SEQ ID No. 925; SEQ ID No. 964; SEQ ID No. 983 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the intermediate metabolism of nucleotides or nucleic acids, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 142; SEQ ID No. 142; SEQ ID No. 169; SEQ ID No. 256; SEQ ID No. 268; SEQ ID No. 325; SEQ ID No. 352; SEQ ID No. 366; SEQ ID No. 435; SEQ ID No. 444; SEQ ID No. 528; SEQ ID No. 529; SEQ ID No. 530; SEQ ID No. 548; SEQ ID No. 549; SEQ ID No. 601; SEQ ID No. 602; SEQ ID No. 617; SEQ ID No. 619; SEQ ID No. 644; SEQ ID No. 745; SEQ ID No. 971; SEQ ID No. 972; SEQ ID No. 1023 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of nucleic acids, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 5; SEQ ID No. 12; SEQ ID No. 82; SEQ ID No. 96; SEQ ID No. 97; SEQ ID No. 98; SEQ ID No. 99; SEQ ID No. 100; SEQ ID No. 105; SEQ ID No. 118; SEQ ID No. 136; SEQ ID No. 137; SEQ ID No. 163; SEQ ID No. 190; SEQ ID No. 204; SEQ ID No. 259; SEQ ID No. 260; SEQ ID No. 262; SEQ ID No. 290; SEQ H) No. 300; SEQ ID No. 301; SEQ ID No. 302; SEQ ID No. 387; SEQ ID No. 427; SEQ ID No. 434; SEQ ID No. 441; SEQ ID No. 444; SEQ ID No. 471; SEQ ID No. 595; SEQ ID No. 596; SEQ ID No. 597; SEQ ID No. 599; SEQ ID No. 600; SEQ ID No. 605; SEQ ID No. 612; SEQ ID No. 624; SEQ ID No. 625; SEQ ID No. 650; SEQ ID No. 657; SEQ ID No. 658; SEQ ID No. 702; SEQ ID No. 703; SEQ ID No. 704; SEQ ID No. 708; SEQ ID No. 719; SEQ ID No. 766; SEQ ID No. 767; SEQ ID No. 775; SEQ ID No. 779; SEQ ID No. 787; SEQ ID No. 788; SEQ ID No. 794; SEQ ID No. 841; SEQ ID No. 842; SEQ ID No. 883; SEQ ID No. 884; SEQ ID No. 907; SEQ ID No. 918; SEQ ID No. 924; SEQ ID No. 928; SEQ ID No. 929; SEQ ID No. 962; SEQ ID No. 962; SEQ ID No. 963; SEQ ID No. 969; SEQ ID No. 970; SEQ ID No. 975; SEQ ID No. 979; SEQ ID No. 995; SEQ ID No. 1031; SEQ ID No. 1032 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of amino acids or polypeptides, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 27; SEQ ID No. 41; SEQ ID No. 55; SEQ ID No. 56; SEQ ID No, 57; SEQ ID No. 59; SEQ ID No. 62; SEQ ID No. 63; SEQ ID No. 64; SEQ ID No. 65; SEQ ID No. 119; SEQ ID No. 132; SEQ ID No. 240; SEQ ID No. 241; SEQ ID No. 277; SEQ ID No. 278; SEQ ID No. 279; SEQ ID No. 382; SEQ ID No. 406; SEQ ID No. 428; SEQ ID No. 442; SEQ ID No. 446; SEQ ID No. 447; SEQ ID No. 453; SEQ ID No. 454; SEQ ID No. 541; SEQ ID No. 542; SEQ ID No. 591; SEQ ID No. 608; SEQ ID No. 609; SEQ ID No. 610; SEQ ID No. 618; SEQ ID No. 648; SEQ ID No. 649; SEQ ID No. 660; SEQ ID No. 661; SEQ ID No. 677; SEQ ID No. 717; SEQ ID No. 765; SEQ ID No. 797; SEQ ID No. 871; SEQ ID No. 875; SEQ ID No. 920; SEQ ID No. 922; SEQ ID No. 937; SEQ ID No. 998; SEQ ID No. 1020; SEQ ID NO. 1021; SEQ ID No. 1034; SEQ ID No. 1044; SEQ ID No. 1046; SEQ D No. 1049 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of polypeptides, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 21; SEQ ID No. 22; SEQ ID No. 23; SEQ ID No. 24; SEQ ID No. 25; SEQ ID No. 26; SEQ ID NO. 75; SEQ ID No. 84; SEQ ID No. 86; SEQ ID NO. 92; SEQ ID NO. 133; SEQ ID No. 151; SEQ ID No. 152; SEQ ID No. 157; SEQ ID No. 179; SEQ ID No. 209; SEQ ID No. 307; SEQ ID No. 326; SEQ ID No. 343; SEQ ID No. 344; SEQ ID No. 345; SEQ ID No. 371; SEQ ID No. 429; SEQ ID No. 519; SEQ ID No. 557; SEQ ID No. 586; SEQ ID No. 587; SEQ ID No. 630; SEQ ID No. 656; SEQ ID No. 706; SEQ ID No. 707; SEQ ID No. 730; SEQ ID No. 751; SEQ ID No. 752; SEQ ID No. 786; SEQ ID No. 847; SEQ ID No. 885; SEQ ID No. 923; SEQ ID No. 978; SEQ ID No. 1039; SEQ ID No. 1048 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the metabolism of fatty acids, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 4; SEQ ID No. 15; SEQ ID No. 16; SEQ ID No. 141; SEQ ID No. 173; SEQ ID No. 205; SEQ ID No. 205; SEQ ID No. 206; SEQ ID No. 207; SEQ ID No. 208; SEQ ID No. 312; SEQ ID No. 355; SEQ ID No. 415; SEQ ID No. 550; SEQ ID No. 558; SEQ ID No. 560; SEQ ID No. 561; SEQ ID No. 574; SEQ ID No. 574; SEQ ID No. 577; SEQ ID No. 578; SEQ ID No. 590; SEQ ID No. 614; SEQ ID No. 772; SEQ ID No. 808; SEQ ID No. 809; SEQ ID No. 904; SEQ ID No. 905; SEQ ID No. 905; SEQ ID No. 933; SEQ ID No. 934; SEQ ID No. 934; SEQ ID No. 936 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the synthesis of the wall, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 87; SEQ ID No. 196; SEQ ID No. 242; SEQ ID No. 269; SEQ ID No. 628; SEQ ID No. 629; SEQ ID No. 634; SEQ ID No. 635; SEQ ID No. 637; SEQ ID No. 638; SEQ ID No. 1019 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the transcription, translation and/or maturation process, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 112; SEQ ID No. 113; SEQ ID No. 332; SEQ ID No. 212; SEQ ID No. 213; SEQ ID No. 350; SEQ ID No. 362; SEQ ID No. 363; SEQ ID No. 364; SEQ ID No. 407; SEQ ID No. 451; SEQ ID No. 546; SEQ ID No. 643; SEQ ID No. 744; SEQ ID No. 746; SEQ ID No. 833; SEQ ID No. 868; SEQ ID No. 981; SEQ ID No. 982; SEQ ID No. 1003; SEQ ID No. 1011; SEQ ID No. 1042 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis ribosomal polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 114; SEQ ID No. 115; SEQ ID No. 116; SEQ ID No. 328; SEQ ID No. 361; SEQ ID No. 375; SEQ ID No. 445; SEQ ID No. 543; SEQ ID No. 584; SEQ ID No. 585; SEQ ID No. 743; SEQ ID No. 813; SEQ ID No. 941; SEQ ID No. 942; SEQ ID No. 944; SEQ ID No. 946; SEQ ID No. 947; SEQ ID No. 948; SEQ ID No. 950; SEQ ID No. 951; SEQ ID No. 952; SEQ ID No. 953; SEQ ID No. 954; SEQ ID No. 955; SEQ ID No. 955; SEQ ID No. 957; SEQ ID No. 958; SEQ ID No. 960; SEQ ID No. 961; SEQ ID No. 1040; SEQ ID No. 1041; SEQ ID No. 1043; SEQ ID No. 1063; SEQ ID No. 1064 and one of their fragments.
Preferably, the invention also relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis transport polypeptide or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 6; SEQ ID No. 50; SEQ ID No. 51; SEQ ID No. 80; SEQ ID No. 125; SEQ ID No. 126; SEQ ID No. 128; SEQ ID No. 129; SEQ ID No. 215; SEQ ID No. 246; SEQ ID No. 248; SEQ ID No. 249; SEQ ID No. 251; SEQ ID No. 252; SEQ ID No. 253; SEQ ID No. 255; SEQ ID No. 271; SEQ ID No. 275; SEQ ID No. 293; SEQ ID No. 309; SEQ ID No. 323; SEQ ID No. 324; SEQ ID No. 398; SEQ ID No. 401; SEQ ID No. 449; SEQ ID No. 511; SEQ ID No. 512; SEQ ID No. 564; SEQ ID No. 565; SEQ ID No. 667; SEQ ID No. 679; SEQ ID No. 680; SEQ ID No. 711; SEQ ID No. 712; SEQ ID No. 713; SEQ ID No. 714; SEQ ID No. 715; SEQ ID No. 730; SEQ ID No. 731; SEQ ID No. 736; SEQ ID No. 737; SEQ ID No. 738; SEQ ID No. 870; SEQ ID No. 908; SEQ ID No. 919; SEQ ID No. 977; SEQ ID No. 987; SEQ ID No. 988; SEQ ID No. 992; SEQ ID No. 993; SEQ ID No. 994; SEQ ID No. 1028; SEQ ID No. 1029 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the virulence process, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 20; SEQ ID No. 815; SEQ ID No. 816; SEQ ID No. 898; SEQ ID No. 1059; SEQ ID No. 1060 and one of their representative fragments.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a Chlamydia trachomatis polypeptide or one of its representative fragments which is involved in the secretory system and/or which is secreted, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 758; SEQ ID No. 888; SEQ ID No. 889; SEQ ID No. 890; SEQ ID No. 891; SEQ ID No. 896; SEQ ID No. 897; SEQ ID No. 898 and one of their representative fragments.
The secreted polypeptides, including the Type III and other, non-Type III secreted polypeptides, of the present invention, as well as the corresponding nucleotide sequences, may be detected by techniques known to persons skilled in the art, such as for example the techniques using cloning combined with vectors allowing the expression of the said polypeptides fused to export markers such as the luc gene for luciferase or the PhoA gene for alkaline phosphatase.
Preferably, the invention relates to a polypeptide according to the invention, characterized in that it is a polypeptide specific to Chlamydiae or one of its representative fragments, and in that it is chosen from the polypeptides having the following sequences:
SEQ ID No. 22; SEQ ID No. 29; SEQ ID No. 31; SEQ ID No. 32; SEQ ID No. 34; SEQ ID No. 35; SEQ ID No. 39; SEQ ID No. 40; SEQ ID No. 43; SEQ ID No. 48; SEQ ID No. 49; SEQ ID No. 50; SEQ ID No. 52; SEQ ID No. 53; SEQ ID No. 54; SEQ ID No. 72; SEQ ID No. 77; SEQ ID No. 78; SEQ ID No. 87; SEQ ID No. 90; SEQ ID No. 95; SEQ ID No. 108; SEQ ID No. 110; SEQ ID No. 111; SEQ ID No. 122; SEQ ID No. 123; SEQ ID No. 124; SEQ ID No. 127; SEQ ID No. 138; SEQ ID No. 144; SEQ ID No. 146; SEQ ID No. 153; SEQ ID No. 155; SEQ ID No. 164; SEQ ID No. 166; SEQ H No. 175; SEQ ID No. 182; SEQ ID No. 184; SEQ ID No. 186; SEQ ID No. 187; SEQ ID No. 188; SEQ ID No. 202; SEQ ID No. 210; SEQ ID No. 247; SEQ ID No. 258; SEQ ID No. 266; SEQ ID No. 267; SEQ ID No. 270; SEQ ID No. 273; SEQ ID No. 274; SEQ ID No. 295; SEQ ID No. 296; SEQ ID No. 305; SEQ ID No. 306; SEQ ID No. 309; SEQ ID No. 318; SEQ ID No. 319; SEQ ID No. 322; SEQ ID No. 326; SEQ ID No. 342; SEQ ID No. 357; SEQ ID No. 376; SEQ ID No. 379; SEQ ID No. 380; SEQ ID No. 388; SEQ ID No. 390; SEQ ID No. 400; SEQ ID No. 431; SEQ ID No. 433; SEQ ID No. 438; SEQ ID No. 443; SEQ ID No. 456; SEQ ID No. 457; SEQ ID No. 458; SEQ ID No. 464; SEQ ID No. 468; SEQ ID No. 470; SEQ ID No. 473; SEQ ID No. 486; SEQ ID No. 489; SEQ ID No. 497; SEQ ID No. 501; SEQ ID No. 503; SEQ ID No. 504; SEQ ID No. 508; SEQ ID No. 512; SEQ ID No. 521; SEQ ID No. 522; SEQ ID No. 523; SEQ ID No. 524; SEQ ID No. 533; SEQ ID No. 535; SEQ ID No. 536; SEQ ID No. 537; SEQ ID No. 538; SEQ ID No. 539; SEQ ID No. 540; SEQ ID No. 554; SEQ ID No. 563; SEQ ID No. 572; SEQ ID No. 579; SEQ ID No. 595; SEQ ID No. 603; SEQ ID No. 604; SEQ ID No. 606; SEQ ID No. 607; SEQ ID No. 615; SEQ ID No. 616; SEQ ID No. 622; SEQ ID No. 641; SEQ ID No. 642; SEQ ID No. 659; SEQ ID No. 668; SEQ ID No. 670; SEQ ID No. 693; SEQ ID No. 695; SEQ ID No. 696; SEQ ID No. 699; SEQ ID No. 703; SEQ ID No. 704; SEQ ID No. 716; SEQ ID No. 726; SEQ ID No. 728; SEQ ID No. 739; SEQ ID No. 742; SEQ ID No. 747; SEQ ID No. 750; SEQ ID No. 751; SEQ ID No. 755; SEQ ID No. 757; SEQ ID No. 759; SEQ ID No. 761; SEQ ID No. 762; SEQ ID No. 763; SEQ ID No. 764; SEQ ID No. 773; SEQ ID No. 780; SEQ ID No. 781; SEQ ID No. 789; SEQ ID No. 800; SEQ ID No. 803; SEQ ID No. 804; SEQ ID No. 818; SEQ ID No. 820; SEQ ID No. 822; SEQ ID No. 823; SEQ ID No. 824; SEQ ID No. 827; SEQ ID No. 828; SEQ ID No. 839; SEQ ID No. 849; SEQ ID No. 850; SEQ ID No. 851; SEQ ID No. 852; SEQ ID No. 855; SEQ ID No. 856; SEQ ID No. 857; SEQ ID No. 858; SEQ ID No. 859; SEQ ID No. 860; SEQ ID No. 861; SEQ ID No. 862; SEQ ID No. 863; SEQ ID No. 865; SEQ ID No. 868; SEQ ID No. 869; SEQ ID No. 870; SEQ ID No. 871; SEQ ID No. 872; SEQ ID No. 873; SEQ ID No. 874; SEQ ID No. 875; SEQ ID No. 877; SEQ ID No. 878; SEQ ID No. 880; SEQ ID No. 882; SEQ ID No. 884; SEQ ID No. 886; SEQ ID No. 893; SEQ ID No. 901; SEQ ID No. 906; SEQ ID No. 910; SEQ ID No. 912; SEQ ID No. 915; SEQ ID No. 916; SEQ ID No. 917; SEQ ID No. 926; SEQ ID No. 929; SEQ ID No. 933; SEQ ID No. 965; SEQ ID No. 967; SEQ ID No. 968; SEQ ID No. 984; SEQ ID No. 986; SEQ ID No. 989; SEQ ID No. 990; SEQ ID No. 996; SEQ ID No. 997; SEQ ID No. 1001; SEQ ID No. 1002; SEQ ID No. 1013; SEQ ID No. 016; SEQ ID No. 1031; SEQ ID No. 1033; SEQ ID No. 1035; SEQ ID No. 1049; SEQ ID No. 1051; SEQ ID No. 1052; SEQ ID No. 1054; SEQ ID No. 1056; SEQ ID No. 1057; SEQ ID No. 1058; SEQ ID No. 1062; SEQ ID No. 1070; SEQ ID No. 1071; SEQ ID No. 1073 and one of their representative fragments.
In general, in the present invention, the functional group to which a polypeptide of the invention belongs, as well as its corresponding nucleotide sequence, may be determined either by comparative analogy with sequences already known, or by the use of standard techniques of biochemistry, of cytology combined with the techniques of genetic engineering such as immunoaffinity, localization by immunolabelling, differential extraction, measurement of enzymatic activity, study of the activity inducing or repressing expression or the study of expression in E. coli. 
It is clearly understood, on the one hand, that, in the present invention, the nucleotide sequences (ORF) and the amino acid sequences (SEQ ID No. 2 to SEQ ID No. 1197) which are listed by functional group, are not exhaustive within the group considered. Moreover, it is also clearly understood that, in the present invention, a nucleotide sequence (ORF) or an amino acid sequence mentioned within a given functional group may also be part of another group taking into account, for example, the interrelationship between the groups listed. Accordingly, and as an example of this interrelationship, an exported and/or secreted polypeptide as well as its coding nucleotide sequence may also be involved in the Chlamydia trachomatis virulence process by modifying the defense mechanism of the infected host cell, or a transmembrane polypeptide or its coding nucleotide sequence is also part of the polypeptides or coding nucleotide sequences of the cellular envelope.
The subject of the present invention is also the nucleotide and/or polypeptide sequences according to the invention, characterized in that the said sequences are recorded on a medium, called recording medium, whose type and nature facilitate the reading, the analysis and the exploitation of the said sequences. These media may of course also contain other information extracted from the present invention, such as in particular the analogies with already known sequences, such as those mentioned in Table 1 of the present description, and/or may contain, in addition, information relating to the nucleotide and/or polypeptide sequences of other microorganisms so as to facilitate the comparative analysis and the exploitation of the results obtained.
Among these recording media, computer-readable media, such as magnetic, optical, electrical and hybrid media such as, for example, floppy disks, CD-ROMs or recording cassettes, are preferred in particular.
The invention also relates to nucleotide sequences which can be used as primer or probe, characterized in that the said sequences are chosen from the nucleotide sequences according to the invention.
The invention relates, in addition, to the use of a nucleotide sequence according to the invention, as primer or probe, for the detection and/or amplification of nucleic acid sequences.
The nucleotide sequences according to the invention may thus be used to amplify nucleotide sequences, in particular by the PCR technique (polymerase chain reaction) (Erlich, 1989; Innis et al., 1990; Rolfs et al., 1991, and White et al., 1997).
These oligodeoxyribonucleotide or oligoribonucleotide primers correspond to representative nucleotide fragments, and are advantageously at least 8 nucleotides, preferably at least 12 nucleotides, 15 nucleotides and still more preferably at least 20 nucleotides long.
Other techniques for amplifying the target nucleic acid may be advantageously used as alternatives to PCR.
The nucleotide sequences of the invention, in particular the primers according to the invention, may also be used in other methods for amplifying a target nucleic acid, such as:

    
    
        the TAS (Transcription-based Amplification System) technique described by Kwoh et al. in 1989;
        the 3SR (Self-Sustained Sequence Replication) technique described by Guatelli et al. in 1990;
        the NASBA (Nucleic Acid Sequence Based Amplification) technique described by Kievitis et al. in 1991;
        the SDA (Strand Displacement Amplification) technique (Walker et al., 1992);
        the TMA (Transcription Mediated Amplification) technique.
    
    


The polynucleotides of the invention may also be used in techniques for amplifying or for modifying the nucleic acid serving as probe, such as:

    
    
        the LCR (Ligase Chain Reaction) technique described by Landegren et al. in 1988 and perfected by Barany et al. in 1991, which uses a thermostable ligase;
        the RCR (Repair Chain Reaction) technique described by Segev in 1992;
        the CPR (Cycling Probe Reaction) technique described by Duck et al. in 1990;
        the Q-beta-replicase amplification technique described by Miele et al. in 1983 and perfected in particular by Chu et al. in 1986, Lizardi et al. in 1988, and then by Burg et al. as well as by Stone et al. in 1996.
    
    


The invention also relates to the nucleotide sequences of fragments which can be obtained by amplification with the aid of at least one primer according to the invention. The present invention encompasses both hybridization probes and primers. In general, the complementary probes should be of the length sufficient to form a stable hybrid complex with the target sequences. Primers, while complementary to the target sequences need not form stable hybridization complexes with the target sequences alone. Rather, primers form stable complexes with the target sequences in the presence of polymerase to permit extension of the primer.
In the case where the target polynucleotide to be detected is possibly an RNA, for example an mRNA, it will be possible to use, prior to the use of an amplification reaction with the aid of at least one primer according to the invention or to the use of a method of detection with the aid of at least one probe of the invention, a reverse transcriptase-type enzyme so as to obtain a cDNA from the RNA contained in the biological sample. The cDNA obtained will then serve as target for the primer(s) or the probe(s) used in the amplification or detection method according to the invention.
The detection probe will be chosen so that it hybridizes with the target sequence or the amplicon generated from the target sequence. Such a detection probe will advantageously have as sequence a sequence of at least 12 nucleotides, 15 nucleotides, in particular of at least 20 nucleotides, and preferably at least 100 nucleotides.
The invention also comprises the nucleotide sequences which can be used as probe or primer according to the invention, characterized in that they are labelled with a radioactive compound or with a nonradioactive compound.
The nonlabelled nucleotide sequences may be used directly as probes or primers; however, the sequences are generally labelled with a radioactive element (32P, 35S, 3H, 125I) or with a nonradioactive molecule (biotin, acetylaminofluorene, digoxigenin, 5-bromo-deoxyuridine, fluorescein) so as to obtain probes which can be used in numerous applications.
Examples of nonradioactive labelling of nucleotide sequences are described, for example, in French patent No. 78,10975 or by Urdea et al. or by Sanchez-Pescador et al. in 1988.
In the latter case, one of the labelling methods described in patents FR-2 422 956 and FR-2 518 755 may also be used.
The invention also relates to the nucleotide sequences of fragments which can be obtained by hybridization with the aid of at least one probe according to the invention.
The hybridization technique may be performed in various ways (Matthews et al., 1988). The most common method consists in immobilizing the nucleic acid extracted from C. trachomatis cells on a support (such as nitrocellulose, nylon, polystyrene) and in incubating, under well-defined conditions, the target nucleic acid immobilized with the probe. After hybridization, the excess probe is removed and the hybrid molecules formed are detected by the appropriate method (measurement of the radioactivity, of the fluorescence or of the enzymatic activity linked to the probe).
The invention also comprises the nucleotide sequences according to the invention, characterized in that they are covalently or noncovalently immobilized on a support.
According to another advantageous embodiment of the nucleic sequences according to the invention, the latter may be used immobilized on a support and may thus serve to capture, through specific hybridization, the target nucleic acid obtained from the biological sample to be tested. If necessary, the solid support is separated from the sample and the hybridization complex formed between the so-called capture probe and the target nucleic acid is then detected by means of a second probe, called detection probe, labelled with an easily detectable element.
The nucleotide sequences according to the invention may also be used in new analytical systems, DNA chips, which allow sequencing, the study of mutations and of the expression of genes, and which are currently of interest given their very small size and their high capacity in terms of number of analyses.
The principle of the operation of these chips is based on molecular probes, most often oligo-nucleotides, which are attached onto a miniaturized surface, generally of the order of a few square centimetres. During an analysis, a sample containing fragments of a target nucleic acid to be analysed, for example DNA or RNA labelled, for example, after amplification, is deposited onto the DNA chip in which the support has been coated beforehand with probes. Bringing the labelled target sequences into contact with the probes leads to the formation, through hybridization, of a duplex according to the rule of pairing defined by J. D. Watson and F. Crick. After a washing step, analysis of the surface of the chip allows the effective hybridizations to be located by means of the signals emitted by the labels tagging the target. A hybridization fingerprint results from this analysis which, by appropriate computer processing, will make it possible to determine information such as the presence of specific fragments in the sample, the determination of sequences and the presence of mutations.
The chip consists of a multitude of molecular probes, precisely organized or arrayed on a solid support whose surface is miniaturized. It is at the centre of a system where other elements (imaging system, microcomputer) allow the acquisition and interpretation of a hybridization fingerprint.
The hybridization supports are provided in the form of flat or porous surfaces (pierced with wells) composed of various materials. The choice of a support is determined by its physicochemical properties, or more precisely, by the relationship between the latter and the conditions under which the support will be placed during the synthesis or the attachment of the probes or during the use of the chip. It is therefore necessary, before considering the use of a particular support (R. S. Matson et al., 1994), to consider characteristics such as its stability to pH, its physical strength, its reactivity and its chemical stability as well as its capacity to nonspecifically bind nucleic acids. Materials such as glass, silicon and polymers are commonly used. Their surface is, in a first step, called “functionalization”, made reactive towards the groups which it is desired to attach thereon. After the functionalization, so-called spacer molecules are grafted onto the activated surface. Used as intermediates between the surface and the probe, these molecules of variable size render unimportant the surface properties of the supports, which often prove to be problematic for the synthesis or the attachment of the probes and for the hybridization.
Among the hybridization supports, there may be mentioned glass which is used, for example, in the method of in situ synthesis of oligonucleotides by photochemical addressing developed by the company Affymetrix (E. L. Sheldon, 1993), the glass surface being activated by silane. Genosensor Consortium (P. Mérel, 1994) also uses glass slides carrying wells 3 mm apart, this support being activated with epoxysilane.
Polymers or silicon may also be mentioned among these hybridization supports. For example, the Andrein Mirzabekov team has developed a chip consisting of polyacrylamide squares polymerized on a silanized glass surface (G. Yershov et al., 1996). Several teams use silicon, in particular the IFOS laboratory of Ecole Centrale of Lyon which uses a silicon semiconductor substrate which is p-doped by introducing it into its crystalline structure atoms whose valency is different from that of silicon. Various types of metals, in particular gold and platinum, may also be used as support (Genosensor Consortium (K. Beattie et al., 1993)).
The probes according to the invention may be synthesized directly in situ on the supports of the DNA chips. This in situ synthesis may be carried out by photochemical addressing (developed by the company Affymax (Amsterdam, Holland) and exploited industrially by its subsidiary Affymetrix (United States)) or based on the VLSIPS (very large scale immobilized polymer synthesis) technology (S. P. A. Fodor et al., 1991) which is based on a method of photochemically directed combinatory synthesis and the principle of which combines solid-phase chemistry, the use of photolabile protecting groups and photolithography.
The probes according to the invention may be attached to the DNA chips in various ways such as electrochemical addressing, automated addressing or the use of probe printers (T. Livache et al., 1994; G. Yershov et al., 1996; J. Derisi et al., 1996, and S. Borman, 1996).
The revealing of the hybridization between the probes of the invention, deposited or synthesized in situ on the supports of the DNA chips, and the sample to be analysed, may be determined, for example, by measurement of fluorescent signals, by radioactive counting or by electronic detection.
The use of fluorescent molecules such as fluorescein constitutes the most common method of labelling the samples. It allows direct or indirect revealing of the hybridization and allows the use of various fluorochromes.
Affymetrix currently provides an apparatus or a scanner designed to read its “Gene Chip” chips. It makes it possible to detect the hybridizations by scanning the surface of the chip in confocal microscopy (R. J. Lipshutz et al., 1995). Other methods of detecting fluorescent signals have been tested: coupling of an epifluorescence microscope and a CCD camera (G. Yershov et al., 1996), the use of an optical fibre collecting system (E. L. Sheldon, 1993). A conventional method consists in carrying out an end labelling, with phosphorus 32, of the target sequences, by means of an appropriate apparatus, the Phosphorimager (marketed by Molecular Dynamics). The electronic detection is based on the principle that the hybridization of two nucleic acid molecules is accompanied by physical phenomena which can be quantified under certain conditions (system developed by Ecole Centrale of Lyon and called GEN-FET (GEN field effect transistor)). Genosensor Consortium and the company Beckman Instruments who are developing an electronic chip “Permittivity Chips” may also be mentioned (K. Beattie et al., 1993).
The nucleotide sequences according to the invention may thus be used in DNA chips to carry out the analysis of mutations. This analysis is based on the production of chips capable of analysing each base of a nucleotide sequence according to the invention. It is possible, in particular to this end, to use the microsequencing techniques on a DNA chip. The mutations are detected by extending immobilized primers which hybridize to the template of sequences analysed, just at the position adjacent to that of the mutated nucleotide to be detected. A single-stranded template, RNA or DNA, of the sequences to be analysed will be advantageously prepared according to conventional methods, from products amplified according to PCR-type techniques. The templates of single-stranded DNA, or of RNA thus obtained are then deposited on the DNA chip, under conditions allowing their specific hybridization to the immobilized primers. A thermostable polymerase, for example Tth or T7 DNA polymerase, specifically extends the 3′ end of the immobilized primer with a labelled nucleotide analogue complementary to the nucleotide at the position of the variable site. For example a thermal cycling is performed in the presence of fluorescent dideoxyribonucleotides. The experimental conditions will be adapted in particular to the chips used, to the immobilized primers, to the polymerases used and to the labelling system chosen. One advantage of microsequencing, compared with techniques based on the hybridization of probes, is that it makes it possible to identify all the variable nucleotides with optimal discrimination under homogeneous reaction conditions; used on DNA chips, it allows optimal resolution and specificity for the routine and industrial detection of mutations in multiplex.
The nucleotide sequences according to the invention may also be used in DNA chips to carry out the analysis of the expression of the Chlamydia trachomatis genes. This analysis of the expression of Chlamydia trachomatis genes is based on the use of chips where probes of the invention, chosen for their specificity to characterize a given gene, are present (D. J. Lockhart et al., 1996; D. D. Shoemaker et al., 1996). For the methods of analysis of gene expression using the DNA chips, reference may, for example, be made to the methods described by D. J. Lockhart et al. (1996) and Sosnowsky et al. (1997) for the synthesis of probes in situ or for the addressing and the attachment of previously synthesized probes. The target sequences to be analysed are labelled and in general fragmented into sequences of about 50 to 100 nucleotides before being hybridized onto the chip. After washing as described, for example, by D. J. Lockhart et al. (1996) and application of different electric fields (Sosnowsky et al., 1997), the labelled compounds are detected and quantified, the hybridizations being carried out at least in duplicate. Comparative analyses of the signal intensities obtained with respect to the same probe for different samples and/or for different probes with the same sample, determine the differential expression of RNA or of DNA derived from the sample.
The nucleotide sequences according to the invention may, in addition, be used in DNA chips where other nucleotide probes specific for other microorganisms are also present, and may allow the carrying out of a serial test allowing rapid identification of the presence of a microorganism in a sample.
Accordingly, the subject of the invention is also the nucleotide sequences according to the invention, characterized in that they are immobilized on a support of a DNA chip.
The DNA chips, characterized in that they contain at least one nucleotide sequence according to the invention, immobilized on the support of the said chip, also form part of the invention.
The said chips will preferably contain several probes or nucleotide sequences of the invention of different length and/or corresponding to different genes so as to identify, with greater certainty, the specificity of the target sequences or the desired mutation in the sample to be analysed.
Accordingly, the analyses carried out by means of primers and/or probes according to the invention, immobilized on supports such as DNA chips, will make it possible, for example, to identify, in samples, mutations linked to variations such as intraspecies variations. These variations may be correlated or associated with pathologies specific to the variant identified and will make it possible to select the appropriate treatment.
The invention thus comprises a DNA chip according to the invention, characterized in that it contains, in addition, at least one nucleotide sequence of a microorganism different from Chlamydia trachomatis, immobilized on the support of the said chip; preferably, the different microorganism will be chosen from an associated microorganism, a bacterium of the Chlamydia family, and a variant of the species Chlamydia trachomatis. 
Another subject of the present invention is a vector for the cloning and/or the expression of a sequence, characterized in that it contains a nucleotide sequence according to the invention.
Among the said vectors according to the invention, the vectors containing a nucleotide sequence encoding a polypeptide of the cellular, preferably outer, envelope of Chlamydia trachomatis or one of its representative fragments, are preferred.
In a specific embodiment, the vectors contain a nucleotide sequence encoding a Chlamydia trachomatis secreted polypeptide or one of its representative fragments or encoding a transport polypeptide, a surface exposed polypeptide, a lipoprotein or one of its representative fragments, a polypeptide involved in lipopolysaccharide (LPS) biosynthesis, a Type III or non-Type III secreted polypeptide, a polypeptide containing RGD attachment sites, a cell wall anchored surface polypeptide, a polypeptide not found in Chlamydia pneumoniae, a ribosomal polypeptide or a polypeptide involved in secretion, transcription, translation, maturation of proteins, a polypeptide involved in the synthesis of the wall, a polypeptide involved in the virulence, a polypeptide involved in the intermediate metabolism, in particular in the metabolism of sugars and/or of cofactors, a polypeptide involved in the metabolism of nucleotides, of amino acids, of nucleic acids or of fatty acids of Chlamydia trachomatis or one of their representative fragments, or a polypeptide specific to Chlamydiae, are also preferred.
According to the invention, the vectors comprise the elements necessary to allow the expression and/or the secretion of the said nucleotide sequences in a given host cell, and also form part of the invention.
The vector should, in this case, comprise a promoter, signals for initiation and for termination of translation, as well as appropriate regions for regulation of transcription. It should be capable of being stably maintained in the host cell and may optionally possess particular signals specifying the secretion of the translated protein. These different elements are chosen according to the host cell used. To this effect, the nucleotide sequences according to the invention may be inserted into autonomously-replicating vectors within the chosen host, or integrative vectors in the chosen host.
Any of the standard methods known to those skilled in the art for the insertion of DNA fragments into a vector may be used to construct expression vectors containing a chimeric gene consisting of appropriate transcriptional/translational control signals and the protein coding sequences. These methods may include in vitro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination).
Expression of a polypeptide, peptide or derivative, or analogs thereof encoded by a polynucleotide sequence in SEQ ID No. 1 or ORFs contained within SEQ ID No. 1 may be regulated by a second nucleic acid sequence so that the protein or peptide is expressed in a host transformed with the recombinant DNA molecule. For example, expression of a protein or peptide may be controlled by any promoter/enhancer element known in the art. Promoters which may be used to control expression include, but are not limited to, the CMV promoter, the SV40 early promoter region (Bernoist and Chambon, 1981, Nature 290:304-310), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto, et al., 1980, Cell 22:787-797), the herpes thymidine kinase promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445), the regulatory sequences of the metallothionein gene (Brinster et al., 1982, Nature 296:39-42); prokaryotic expression vectors such as the β-lactamase promoter (VIIIa-Kamaroff, et al., 1978, Proc. Natl. Acad. Sci. U.S.A. 75:3727-3731), or the tac promoter (DeBoer, et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:21-25); see also “Useful proteins from recombinant bacteria” in Scientific American, 1980, 242:74-94; plant expression vectors comprising the nopaline synthetase promoter region (Herrera-Estrella et al., 1983, Nature 303:209-213) or the cauliflower mosaic virus 35S RNA promoter (Gardner, et al., 1981, Nucl. Acids Res. 9:2871), and the promoter of the photosynthetic enzyme ribulose biphosphate carboxylase (Herrera-Estrella et al., 1984, Nature 310:115-120); promoter elements from yeast or other fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, alkaline phosphatase promoter, and the following animal transcriptional control regions, which exhibit tissue specificity and have been utilized in transgenic animals: elastase I gene control region which is active in pancreatic acinar cells (Swift et al., 1984, Cell 38:639-646; Ornitz et al., 1986, Cold Spring Harbor Symp. Quant. Biol. 50:399-409; MacDonald, 1987, Hepatology 7:425-515); insulin gene control region which is active in pancreatic beta cells (Hanahan, 1985, Nature 315:115-122), immunoglobulin gene control region which is active in lymphoid cells (Grosschedl et al., 1984, Cell 38:647-658; Adames et al., 1985, Nature 318:533-538; Alexander et al., 1987, Mol. Cell. Biol. 7:1436-1444), mouse mammary tumor virus control region which is active in testicular, breast, lymphoid and mast cells (Leder et al., 1986, Cell 45:485-495), albumin gene control region which is active in liver (Pinkert et al., 1987, Genes and Devel. 1:268-276), alpha-fetoprotein gene control region which is active in liver (Krumlauf et al., 1985, Mol. Cell. Biol. 5:1639-1648; Hammer et al., 1987, Science 235:53-58; alpha 1-antitrypsin gene control region which is active in the liver (Kelsey et al., 1987, Genes and Devel. 1:161-171), beta-globin gene control region which is active in myeloid cells (Mogram et al., 1985, Nature 315:338-340; Kollias et al., 1986, Cell 46:89-94; myelin basic protein gene control region which is active in oligodendrocyte cells in the brain (Readhead et al., 1987, Cell 48:703-712); myosin light chain-2 gene control region which is active in skeletal muscle (Sani, 1985, Nature 314:283-286), and gonadotropic releasing hormone gene control region which is active in the hypothalamus (Mason et al., 1986, Science 234:1372-1378).
The vectors according to the invention are, for example, vectors of plasmid or viral origin. In a specific embodiment, a vector is used that comprises a promoter operably linked to a protein or peptide-encoding nucleic acid sequence in SEQ ID No. 1, or ORFs contained within SEQ ID No. 1, one or more origins of replication, and, optionally, one or more selectable markers (e.g., an antibiotic resistance gene). Expression vectors comprise regulatory sequences that control gene expression, including gene expression in a desired host cell. Preferred vectors for the expression of the polypeptides of the invention include the pET-type plasmid vectors (Promega) or pBAD plasmid vectors (Invitrogen). Furthermore, the vectors according to the invention are useful for transforming host cells so as to clone or express the nucleotide sequences of the invention.
Expression can also be achieved using targeted homologous recombination to activate Chlamydia trachomatis genes present in the cloned genomic DNA. A heterologous regulatory element may be inserted into a stable cell line or cloned microorganism, such that it is operatively linked with an endogenous Chlamydia trachomatis gene present in the cloned genome, using techniques, such as targeted homologous recombination, which are well known to those of skill in the art (See, e.g., Chappel, U.S. Pat. No. 4,215,051 and Skoultchi, WO 91/06667 each of which is incorporated herein in its entirety).
Expression vector/host cell systems containing inserts of polynucleotide sequences in SEQ ID No. 1 or ORFs within SEQ ID No. 1, which encode polypeptides, peptides or derivatives, or analogs thereof; can be identified by three general approaches: (a) nucleic acid hybridization, (b) presence or absence of “marker” gene functions, and (c) expression of inserted sequences. In the first approach, the presence of a polynucleotide sequence inserted in an expression vector can be detected by nucleic acid hybridization using probes comprising sequences that are homologous to an inserted polynucleotide sequence. In the second approach, the recombinant vector/host system can be identified and selected based upon the presence or absence of certain “marker” gene functions (e.g., thymidine kinase activity, resistance to antibiotics, transformation phenotype, occlusion body formation in baculovirus, etc.) caused by the insertion of a polynucleotide sequence in the vector. For example, if the polynucleotide sequence in SEQ ID No. 1 or ORFs within SEQ ID No. 1 is inserted within the marker gene sequence of the vector, recombinants containing the insert can be identified by the absence of the marker gene function. In the third approach, recombinant expression vectors can be identified by assaying the product of the polynucleotide sequence expressed by the recombinant. Such assays can be based, for example, on the physical or functional properties of the expressed polypeptide in in vitro assay systems, e.g., binding with antibody, promotion of cell proliferation.
Once a particular recombinant DNA molecule is identified and isolated, several methods known in the art may be used to propagate it. The clones identified may be introduced into an appropriate host cell by standard methods, such as for example lipofection, electroporation, and heat shock. Once a suitable host system and growth conditions are established, recombinant expression vectors can be propagated and prepared in quantity.
The invention also encompasses the host cells transformed by a vector according to the invention. These cells may be obtained by introducing into host cells a nucleotide sequence inserted into a vector as defined above, and then culturing the said cells under conditions allowing the replication and/or the expression of the transfected nucleotide sequence.
The host cell may be chosen from eukaryotic or prokaryotic systems, such as for example bacterial cells (Olins and Lee, 1993), but also yeast cells (Buckholz, 1993), as well as animal cells, in particular cultures of mammalian cells (Edwards and Aruffo, 1993), and in particular Chinese hamster ovary (CHO) cells, but also insect cells in which methods using baculoviruses for example may be used (Luckow, 1993).
Furthermore, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Expression from certain promoters can be elevated in the presence of certain inducers; thus, expression of the genetically engineered polypeptide may be controlled. Furthermore, different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification (e.g., glycosylation, phosphorylation) of proteins. Appropriate cell lines or host systems can be chosen to ensure the desired modification and processing of the foreign protein expressed. For example, expression in a bacterial system can be used to produce an unglycosylated core protein product. Expression in yeast will produce a glycosylated product. Expression in mammalian cells can be used to ensure “native” glycosylation of a heterologous protein. Furthermore, different vector/host expression systems may effect processing reactions to different extents.
A preferred host cell for the expression of the proteins of the invention consists of prokaryotic cells, such as Gram negative bacteria.
A further preferred host cell according to the invention is a bacterium belonging to the Chlamydia family, more preferably belonging to the species Chlamydia trachomatis or chosen from a microorganism associated with the species Chlamydia trachomatis. 
In other specific embodiments, the polypeptides, peptides or derivatives, or analogs thereof may be expressed as a fusion, or chimeric protein product (comprising the protein, fragment, analog, or derivative joined via a peptide bond to a heterologous protein sequence (of a different protein)). Such a chimeric product can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other by methods known in the art, in the proper coding frame, and expressing the chimeric product by methods commonly known in the art. Alternatively, such a chimeric product may be made by protein synthetic techniques, e.g., by use of a peptide synthesizer.
Genomic sequences can be cloned and expressed as translational gene products (i.e., peptides, polypeptides, and proteins) or transcriptional gene products (i.e., antisense and ribozymes).
The invention further relates to the intracellular production of an antisense nucleic acid sequence of SEQ ID No. 1 by transcription from an exogenous sequence. For example, a vector can be introduced in vivo such that it is taken up by a cell, within which cell the vector or a portion thereof is transcribed, producing an antisense nucleic acid (RNA) of the invention. Such a vector would contain a sequence encoding an antisense nucleic acid. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in mammalian cells. Expression of the sequence encoding the antisense RNA can be by any promoter known in the art to act in mammalian, preferably human, cells. Such promoters can be inducible or constitutive. Such promoters include but are not limited to: the CMV promoter, the SV40 early promoter region (Bemoist and Chambon, 1981, Nature 290:304-310), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto et al., 1980, Cell 22:787-797), the herpes thymidine kinase promoter (Wagner et al, 1981, Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445), the regulatory sequences of the metallothionein gene (Brinster et al., 1982, Nature 296:39-42), etc.
In a specific embodiment, the antisense oligonucleotide comprises catalytic RNA, or a ribozyme (see, e.g., PCT International Publication WO 90/11364, published Oct. 4, 1990; Sarver et al., 1990, Science 247:1222-1225). In another embodiment, the oligonucleotide is a 2′-β-methylribonucleotide (Inoue et al., 1987, Nucl. Acids Res. 15:6131-6148), or a chimeric RNA-DNA analog (Inoue et al., 1987, FEBS Lett. 215:327-330).
In another embodiment, the antisense nucleic acids of the invention comprise a sequence complementary to at least a portion of an RNA transcript of a polynucleotide sequence in SEQ ID No. 1. However, absolute complementarity, although preferred, is not required. A sequence “complementary to at least a portion of an RNA,” as referred to herein, means a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex; in the case of double-stranded antisense nucleic acid sequence, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid. Generally, the longer the hybridizing nucleic acid, the more base mismatches with an RNA transcribed from SEQ ID No. 1 may contain and still form a stable duplex (or triplex, as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.
The invention also relates to the animals, except humans, comprising one of the above-described transformed cells according to the invention.
The production of transgenic animals according to the invention overexpressing one or more of the Chlamydia trachomatis genes will be preferably carried out on rats, mice or rabbits according to methods well known to persons skilled in the art such as viral or nonviral transfections. The transgenic animals overexpressing one or more of the said genes may be obtained by transfection of multiple copies of the said genes under the control of a powerful promoter of a ubiquitous nature, or which is selective for one type of tissue. The transgenic animals may also be obtained by homologous recombination on embryonic stem cells, transfer of these stem cells to embryos, selection of the chimeras affected at the level of the reproductive lines, and growth of the said chimeras.
The transformed cells as well as the transgenic animals according to the invention can be used in methods of preparing the recombinant polypeptide.
It is now possible to produce recombinant polypeptides in a relatively large quantity by genetic engineering using the cells transformed with expression vectors according to the invention or using transgenic animals according to the invention.
The methods of preparing a polypeptide of the invention in recombinant form, characterized in that they use a vector and/or a cell transformed with a vector according to the invention and/or a transgenic animal comprising one of the said transformed cells according to the invention, are themselves included in the present invention.
Among the said methods of preparing a polypeptide of the invention in recombinant form, the methods of preparation using a vector, and/or a cell transformed with the said vector and/or a transgenic animal comprising one of the said transformed cells, containing a nucleotide sequence encoding a polypeptide of the cellular envelope of Chlamydia trachomatis or one of its representative fragments, more preferably encoding a polypeptide of the outer cellular envelope of Chlamydia trachomatis or one of its fragment, are preferred.
Among the said methods of preparing a polypeptide of the invention in recombinant form, the methods of preparation using a vector, and/or a cell transformed with the said vector and/or a transgenic animal comprising one of the said transformed cells, containing a nucleotide sequence encoding a Chlamydia trachomatis secreted polypeptide or one of its representative fragments, or encoding a transport polypeptide, a surface exposed polypeptide, a lipoprotein or one of its representative fragments, a polypeptide involved in lipopolysaccharide biosynthesis, a Type III or other secreted polypeptide, a polypeptide containing RGD attachment sites, a cell wall anchored surface polypeptide, a polypeptide not found in Chlamydia pneumoniae, a ribosomal polypeptide or a polypeptide involved in secretion, transcription, translation, maturation of proteins, a polypeptide involved in the synthesis of the wall, a polypeptide involved in the virulence, a polypeptide involved in the intermediate metabolism, in particular in the metabolism of sugars and/or of cofactors, a polypeptide involved in the metabolism of nucleotides, of amino acids, of nucleic acids or of fatty acids of Chlamydia trachomatis or one of their representative fragments, or a polypeptide specific to Chlamydiae, are also preferred.
The recombinant polypeptides obtained as indicated above may be provided either in glycosylated or nonglycosylated form and may or may not have the natural tertiary structure.
A preferred variant consists in producing a recombinant polypeptide fused to a “carrier” protein (chimeric protein). The advantage of this system is that it allows a stabilization and a reduction in proteolysis of the recombinant product, an increase in solubility during renaturation in vitro and/or a simplification of purification when the fusion partner has affinity for a specific ligand.
More particularly, the invention relates to a method of preparing a polypeptide of the invention comprising the following steps:
a) culture of the transformed cells under conditions allowing the expression of a recombinant polypeptide having a nucleic acid sequence according to the invention;
b) where appropriate, recovery of the said recombinant polypeptide.
When the method of preparing a polypeptide of the invention uses a transgenic animal according to the invention, the recombinant polypeptide is then extracted from the said animal.
The subject of the invention is also a polypeptide capable of being obtained by a method of the invention as described above.
The invention also comprises a method of preparing a synthetic polypeptide, characterized in that it uses an amino acid sequence of polypeptides according to the invention.
The invention also relates to a synthetic polypeptide obtained by a method according to the invention.
Polypeptides according to the invention may also be prepared by conventional techniques in the field of peptide synthesis under conditions suitable to produce the polypeptides encoded by the polynucleotide of the invention. This synthesis may be carried out in and recovered from a homogeneous solution or on a solid phase.
For example, the synthesis technique in a homogeneous solution described by Houbenweyl in 1974 may be used.
This method of synthesis consists in successively condensing, in pairs, the successive amino acids in the required order, or in condensing amino acids and fragments previously formed and already containing several amino acids in the appropriate order, or alternatively several fragments thus previously prepared, it being understood that care will have been taken to protect beforehand all the reactive functional groups carried by these amino acids or fragments, with the exception of the amine functional groups of one and the carboxyl functional groups of the other or vice versa, which should normally take part in the formation of the peptide bonds, in particular after activation of the carboxyl functional group, according to methods well known in peptide synthesis.
According to another preferred technique of the invention, the one described by Merrifield is used.
To manufacture a peptide chain according to the Merrifield method, a highly porous polymer resin is used, onto which the first C-terminal amino acid of the chain is attached. This amino acid is attached onto a resin via its carboxyl group and its amine functional group is protected. The amino acids which will constitute the peptide chain are thus attached, one after another, onto the amine group, each time deprotected beforehand, of the portion of the peptide chain already formed, and which is attached to the resin. When the entire peptide chain desired is formed, the protecting groups are removed from the various amino acids constituting the peptide chain and the peptide is detached from the resin with the aid of an acid.
The invention relates, in addition, to hybrid (fusion) polypeptides having at least one polypeptide or one of its representative fragments according to the invention, and a sequence of a polypeptide capable of eliciting an immune response in humans or animals.
Advantageously, the antigenic determinant is such that it is capable of eliciting a humoral and/or cellular response.
An antigenic determinant may be identified by screening expression libraries of the Chlamydia trachomatis genome with antibodies contained in the serum of patients infected with a bacterium belonging to the species Chlamydia trachomatis. An antigenic determinant may comprise a polypeptide or one of its fragments according to the invention, in glycosylated form, used in order to obtain immunogenic compositions capable of inducing the synthesis of antibodies directed against multiple epitopes. The said polypeptides or their glycosylated fragments also form part of the invention.
These hybrid molecules may consist, in part, of a carrier molecule for polypeptides or for their representative fragments according to the invention, combined with a portion which may be immunogenic, in particular an epitope of the diphtheria toxin, the tetanus toxin, a hepatitis B virus surface antigen (patent FR7921811), the poliomyelitis virus VP1 antigen or any other viral or bacterial toxin or antigen.
The methods of synthesizing the hybrid molecules include the methods used in genetic engineering to construct hybrid nucleotide sequences encoding the desired polypeptide sequences. Reference may be advantageously made, for example, to the technique for producing genes encoding fusion proteins described by Minton in 1984.
The said hybrid nucleotide sequences encoding a hybrid polypeptide as well as the hybrid polypeptides according to the invention, characterized in that they are recombinant polypeptides obtained by the expression of the said hybrid nucleotide sequences, also form part of the invention.
The invention also comprises the vectors characterized in that they contain one of the said hybrid nucleotide sequences. The host cells transformed by the said vectors, the transgenic animals comprising one of the said transformed cells as well as the methods of preparing recombinant polypeptides using the said vectors, the said transformed cells and/or the said transgenic animals of course also form part of the invention.
The polypeptides according to the invention, the antibodies according to the invention described below and the nucleotide sequences according to the invention may advantageously be used in in vitro and/or in vivo methods for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis, in a biological sample (biological tissue or fluid) which is likely to contain them. These methods, depending on the specificity of the polypeptides, of the antibodies and of the nucleotide sequences according to the invention which will be used, may in particular detect and/or identify the bacterial variants belonging to the species Chlamydia trachomatis as well as the associated microorganisms capable of being detected by the polypeptides, the antibodies and the nucleotide sequences according to the invention which will be chosen. It may, for example, be advantageous to choose a polypeptide, an antibody or a nucleotide sequence according to the invention, which is capable of detecting any bacterium of the Chlamydia family by choosing a polypeptide, an antibody and/or a nucleotide sequence according to the invention which is specific to the family or, on the contrary, it will be most particularly advantageous to target a variant of the species Chlamydia trachomatis, which is responsible, for example, for the induction or the worsening of pathologies specific to the targeted variant, by choosing a polypeptide, an antibody and/or a nucleotide sequence according to the invention which is specific to the said variant.
The polypeptides according to the invention may advantageously be used in a method for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, in a biological sample (biological tissue or fluid) which is likely to contain them, characterized in that it comprises the following steps:
a) bringing this biological sample into contact with a polypeptide or one of its representative fragments according to the invention (under conditions allowing an immunological reaction between the said polypeptide and the antibodies which may be present in the biological sample);

b) detecting the antigen-antibody complexes which may be formed.

Preferably, the biological sample consists of a fluid, for example a human or animal serum, blood or biopsies.
Any conventional procedure may be used to carry out such a detection of the antigen-antibody complexes which may be formed.
By way of example, a preferred method uses immunoenzymatic procedures based on the ELISA technique, immunofluorescence procedures or radioimmunological procedures (RIA), and the like.
Accordingly, the invention also relates to the polypeptides according to the invention, labelled with the aid of a suitable label such as a label of the enzymatic, fluorescent or radioactive type.
Such methods comprise, for example, the following steps:

    
    
        deposition of defined quantities of a polypeptide composition according to the invention into the wells of a microtitre plate,
        introduction, into the said wells, of increasing dilutions of serum, or of a different biological sample as defined above, which has to be analysed,
        incubation of the microplate,
        introduction, into the wells of the microtitre plate, of labelled antibodies directed against human or animal immunoglobulins, these antibodies having been labelled with the aid of an enzyme selected from those which are capable of hydrolyzing a substrate, thereby modifying the absorption of the radiation of the latter, at least at a defined wavelength, for example at 550 nm,
        detection, by comparison with a control, of the quantity of substrate hydrolyzed.
    
    


The invention also relates to a kit or set for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, characterized in that it comprises the following components:

    
    
        a polypeptide according to the invention,
        where appropriate, the reagents for constituting the medium appropriate for the immunological or specific reaction,
        the reagents allowing the detection of the antigen-antibody complexes produced by the immunological reaction between the polypeptide(s) of the invention and the antibodies which may be present in the biological sample, it being possible for these reagents also to carry a label, or to be capable of being recognized in turn by a labelled reagent, more particularly in the case where the polypeptide according to the invention is not labelled,
        where appropriate, a reference biological sample (negative control) free of antibodies recognized by a polypeptide according to the invention,
        where appropriate, a reference biological sample (positive control) containing a predetermined quantity of antibodies recognized by a polypeptide according to the invention.
    
    


According to the invention, the polypeptides, peptides, fusion proteins or other derivatives, or analogs thereof encoded by a polynucleotide sequence in SEQ ID No. 1, may be used as an immunogen to generate antibodies which immunospecifically bind such an immunogen. Such antibodies may include, but are not limited to, polyclonal and monoclonal antibodies, humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab′)2 fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies, and epitope-binding fragments of any of the above. In a specific embodiment, the antibody to a polypeptide, peptide or other derivative, or analog thereof encoded by a polynucleotide sequence in SEQ ID No. 1 is a bispecific antibody (see generally, e.g. Fanger and Drakeman, 1995, Drug News and Perspectives 8: 133-137). Such a bispecific antibody is genetically engineered to recognize both (1) an epitope and (2) one of a variety of “trigger” molecules, e.g. Fe receptors on myeloid cells, and CD3 and CD2 on T cells, that have been identified as being able to cause a cytotoxic T-cell to destroy a particular target. Such bispecific antibodies can be prepared either by chemical conjugation, hybridoma, or recombinant molecular biology techniques known to the skilled artisan.
Various procedures known in the art may be used for the production of polyclonal antibodies to a polypeptide, peptide or other derivative, or analog thereof encoded by a polynucleotide sequence in SEQ ID No. 1. For the production of antibody, various host animals can be immunized by injection with a polypeptide, or peptide or other derivative, or analog thereof, including but not limited to rabbits, mice, rats, etc. Various adjuvants, depending on the host species, may be used to increase the immunological response, including but not limited to StimulonTM QS-21 (Aquila Biopharmaceuticals, Inc., Framingham, Mass.), MPLTM (3-O-deacylated monophosphoryl lipid A; RIBI ImmunoChem Research, Inc., Hamilton, Mont.), aluminum phosphate, IL-12 (Genetics Institute, Cambridge, Mass.), Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, BCG (bacille Calmette-Guerin), and Corynebacterium parvum. Alternatively, polyclonal antibodies may be prepared by purifying, on an affinity column onto which a polypeptide according to the invention has been previously attached, the antibodies contained in the serum of patients infected with a bacterium belonging to the species Chlamydia trachomatis. 
For preparation of monoclonal antibodies directed toward a polypeptide, peptide or other derivative, or analog, any technique which provides for the production of antibody molecules by continuous cell lines in culture may be used. For example, the hybridoma technique originally developed by Kohler and Milstein (1975, Nature 256:495-497), as well as the trioma technique, the human B-cell hybridoma technique (Kozbor et al., 1983, Immunology Today 4:72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). In an additional embodiment of the invention, monoclonal antibodies can be produced in germ-free animals utilizing technology described in PCT/US90/02545. In another embodiment of the invention, transgenic non-human animals can be used for the production of human antibodies utilizing technology described in WO 98/24893 and WO 96/33735. According to the invention, human antibodies may be used and can be obtained by using human hybridomas (Cote et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:2026-2030) or by transforming human B cells with EBV virus in vitro (Cole et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, pp. 77-96). In fact, according to the invention, techniques developed for the production of “chimeric antibodies”, (Morrison et al., 1984, PROC. NATL. ACAD. SCI. U.S.A. 81:6851-6855; Neuberger et al., 1984, Nature 312:604-608; Takeda et al., 1985, Nature 314:452-454) by splicing the genes from a mouse antibody molecule specific for a polypeptide, peptide or other derivative, or analog together with genes from a human antibody molecule of appropriate biological activity can be used; such antibodies are within the scope of this invention.
According to the invention, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce polypeptide or peptide-specific single chain antibodies. An additional embodiment of the invention utilizes the techniques described for the construction of Fab expression libraries (Huse et al., 1989, Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for polypeptides, derivatives, or analogs.
Antibody fragments which contain the idiotype of the molecule can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)2 fragment which can be produced by pepsin digestion of the antibody molecule; the Fab′ fragments which can be generated by reducing the disulfide bridges of the F(ab′)2 fragment, the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent, and Fv fragments.
In addition, techniques have been developed for the production of chimerized (See, e.g., Boss, M. et al., U.S. Pat. No. 4,816,397; and Cabilly, S. et al., U.S. Pat. No. 5,585,089 each of which is incorporated herein by reference in its entirety) humanized antibodies (See, e.g., Queen, U.S. Pat. No. 5,585,089, which is incorporated herein by reference in its entirety.) An immunoglobulin light or heavy chain variable region consists of a “framework” region interrupted by three hypervariable regions, referred to as complementarily determining regions (CDRs). The extent of the framework region and CDRs have been precisely defined (See, “Sequences of Proteins of Immunological Interest”, Kabat, E. et al., U.S. Department of Health and Human Services (1983)). Briefly, humanized antibodies are antibody molecules from non-human species having one or more CDRs from the non-human species and a framework from a human immunoglobulin molecule.
The antibodies of the invention may also be labelled in the same manner as described above for the nucleic probes of the invention such as an enzymatic, fluorescent or radioactive type labelling.
The invention relates, in addition, to a method for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism in a biological sample, characterized in that it comprises the following steps:
a) bringing the biological sample (biological tissue or fluid) into contact with a mono- or polyclonal antibody according to the invention (under conditions allowing an immunological reaction between the said antibodies and the polypeptides of the bacterium belonging to the species Chlamydia trachomatis or to an associated microorganism which may be present in the biological sample, that is, under conditions suitable for the formation of immune complexes);

b) detecting the antigen-antibody complex which may be formed.

Also falling within the scope of the invention is a kit or set for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, characterized in that it comprises the following components:

    
    
        a polyclonal or monoclonal antibody according to the invention, labelled where appropriate;
        where appropriate, a reagent for constituting the medium appropriate for carrying out the immunological reaction;
        a reagent allowing the detection of the antigen-antibody complexes produced by the immunological reaction, it being possible for this reagent also to carry a label, or to be capable of being recognized in turn by a labelled reagent, more particularly in the case where the said monoclonal or polyclonal antibody is not labelled;
        where appropriate, reagents for carrying out the lysis of the cells in the sample tested.
    
    


The principle of the DNA chip which was explained above may also be used to produce protein “chips” on which the support has been coated with a polypeptide or an antibody according to the invention, or arrays thereof, in place of the DNA. These protein “chips” make it possible, for example, to analyse the biomolecular interactions (BIA) induced by the affinity capture of target analytes onto a support coated, for example, with proteins, by surface plasma resonance (SPR). Reference may be made, for example, to the techniques for coupling proteins onto a solid support which are described in EP 524 800 or to the methods describing the use of biosensor-type protein chips such as the BLAcore-type technique (Pharmacia) (Arlinghaus et al., 1997, Krone et al., 1997, Chatelier et al., 1995). These polypeptides or antibodies according to the invention, capable of specifically binding antibodies or polypeptides derived from the sample to be analysed, may thus be used in protein chips for the detection and/or the identification of proteins in samples. The said protein chips may in particular be used for infectious diagnosis and may preferably contain, per chip, several polypeptides and/or antibodies of the invention of different specificity, and/or polypeptides and/or antibodies capable of recognizing microorganisms different from Chlamydia trachomatis. 
Accordingly, the subject of the present invention is also the polypeptides and the antibodies according to the invention, characterized in that they are immobilized on a support, in particular of a protein chip.
The protein chips, characterized in that they contain at least one polypeptide or one antibody according to the invention immobilized on the support of the said chip, also form part of the invention.
The invention comprises, in addition, a protein chip according to the invention, characterized in that it contains, in addition, at least one polypeptide of a microorganism different from Chlamydia trachomatis or at least one antibody directed against a compound of a microorganism different from Chlamydia trachomatis, immobilized on the support of the said chip.
The invention also relates to a kit or set for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, or for the detection and/or the identification of a microorganism characterized in that it comprises a protein chip according to the invention.
The subject of the present invention is also a method for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism in a biological sample, characterized in that it uses a nucleotide sequence according to the invention.
More particularly, the invention relates to a method for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism in a biological sample, characterized in that it comprises the following steps:
a) where appropriate, isolation of the DNA from the biological sample to be analysed, or optionally production of a cDNA from the RNA in the biological sample;
b) specific amplification of the DNA of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism with the aid of at least one primer according to the invention;
c) detection of the amplification products.
These may be detected, for example, by the molecular hybridization technique using a nucleic probe according to the invention. This probe will be advantageously labelled with a nonradioactive (cold probe) or radioactive element.
For the purposes of the present invention, “DNA in the biological sample” or “DNA contained in the biological sample” will be understood to mean either the DNA present in the biological sample considered, or optionally the cDNA obtained after the action of a reverse transcriptase-type enzyme on the RNA present in the said biological sample.
Another aim of the present invention consists in a method according to the invention, characterized in that it comprises the following steps:
a) bringing a nucleotide probe according to the invention into contact with a biological sample, the DNA contained in the biological sample having, where appropriate, been previously made accessible to hybridization, under conditions allowing the hybridization of the probe to complementary base pairs of the DNA of a bacterium belonging to the species Chlamydia trachomatis or to an associated microorganism;

b) detecting the hybridization complex formed between the nucleotide probe and the DNA in the biological sample.

The present invention also relates to a method according to the invention, characterized in that it comprises the following steps:
a) bringing a nucleotide probe immobilized on a support according to the invention into contact with a biological sample, the DNA in the sample having, where appropriate, been previously made accessible to hybridization, under conditions allowing the hybridization of the probe to the DNA of a bacterium belonging to the species Chlamydia trachomatis or to an associated microorganism;

b) bringing the hybrid formed between the nucleotide probe immobilized on a support and the DNA contained in the biological sample, where appropriate after removal of the DNA in the biological sample which has not hybridized with the probe, into contact with a labelled nucleotide probe according to the invention;

c) detecting the new hybrid formed in step b).

According to an advantageous embodiment of the method for the detection and/or the identification defined above, it is characterized in that, prior to step a), the DNA in the biological sample is primer-extended and/or amplified beforehand with the aid of at least one primer according to the invention.
The invention relates, in addition, to a kit or set for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, characterized in that it comprises the following components:
a) a nucleotide probe according to the invention;
b) where appropriate, the reagents necessary for carrying out a hybridization reaction;
c) where appropriate, at least one primer according to the invention as well as the reagents (e.g., polymerase and/or deoxynucleotide triphosphates) necessary for a DNA amplification reaction.
The invention also relates to a kit or set for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, characterized in that it comprises the following components:
a) a nucleotide probe, called capture probe, according to the invention;
b) an oligonucleotide probe, called detection probe, according to the invention;
c) where appropriate, at least one primer according to the invention as well as the reagents (e.g., polymerase and/or deoxynucleotide triphosphates) necessary for a DNA amplification reaction.
The invention also relates to a kit or set for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, characterized in that it comprises the following components:
a) at least one primer according to the invention;
b) where appropriate, the reagents necessary for carrying out a DNA amplification reaction;
c) where appropriate, a component which makes it possible to check the sequence of the amplified fragment, more particularly an oligonucleotide probe according to the invention.
The invention relates, in addition, to a kit or set for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis or to an associated microorganism, or for the detection and/or the identification of a microorganism characterized in that it comprises a DNA chip according to the invention.
The invention also relates to a method or to a kit or set according to the invention for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis, characterized in that the said primer and/or the said probe according to the invention are chosen from the nucleotide sequences specific to the species Chlamydia trachomatis, in that the said polypeptides according to the invention are chosen from the polypeptides specific to the species Chlamydia trachomatis and in that the said antibodies according to the invention are chosen from the antibodies directed against the polypeptides according to the invention chosen from the polypeptides specific to the species Chlamydia trachomatis. 
Preferably, the said method or the said kit or set above according to the invention, for the detection and/or the identification of bacteria belonging to the species Chlamydia trachomatis is characterized in that the said primer and/or the said probe or the said polypeptides are chosen from the nucleotide sequences or polypeptides according to the invention which have been identified as being specific to the species Chlamydia trachomatis and in that the said antibodies according to the invention are chosen from the antibodies directed against the polypeptides according to the invention chosen from the polypeptides identified as being specific to the species Chlamydia trachomatis. 
The invention relates, in addition, to a method or a kit or set according to the invention for the diagnosis of predispositions to, or of a condition caused by, genital diseases which are induced or worsened by a Chlamydia trachomatis infection.
The invention also relates to a method or a kit or set according to the invention for the diagnosis of predispositions to, or of conditions caused by, eye diseases induced or worsened by a Chlamydia trachomatis infection.
The invention also relates to a method or a kit or set according to the invention for the diagnosis of predispositions to, or of conditions caused by, systemic diseases, in particular of the lymphatic system, which are induced or worsened by a Chlamydia trachomatis infection.
According to another aspect, the subject of the invention is the use of polypeptides according to the invention, of cells transformed with a vector according to the invention and/or of transformed animals according to the invention, for the biosynthesis or the biodegradation of organic or inorganic compounds.
As has been mentioned above, the nucleotide sequences of the invention were identified by homology with sequences known to encode, for example, polypeptides or fragments of enzymatic polypeptides involved in the biosynthesis or the biodegradation of organic or inorganic molecules.
It is thus possible to use the said polypeptides of the invention in a similar manner for the biosynthesis or the biodegradation of organic or inorganic compounds of industrial or therapeutic interest (called compounds of interest).
Among these polypeptides, there may be mentioned in particular the enzymes involved in metabolism, such as the proteolytic enzymes, amino transferases, glucose metabolism, or the enzymes which may be used in the biosynthesis of sugars, amino acids, fatty acids, polypeptides, nucleotides, nucleic acids or any other organic or inorganic compound or in the biodegradation of organic or inorganic compounds.
Among these polypeptides, there may be mentioned, in addition, the mutated or modified enzymes corresponding to mutated or modified polypeptides according to the invention which may also be used for the biosynthesis or the biodegradation of organic or inorganic compounds at the industrial level, such as, for example, the production of compounds of interest, the reprocessing of manufacturing residues applied to the food industries, to the papermaking industry or to the chemical and pharmaceutical industries.
The methods of biosynthesis or biodegradation of organic or inorganic compounds, characterized in that they use a polypeptide or one of its representative fragments according to the invention, transformed cells according to the invention and/or a transformed animal according to the invention, also form part of the invention.
The invention relates, in addition, to the use of a nucleotide sequence according to the invention, of a polypeptide according to the invention, of an antibody according to the invention, of a cell according to the invention, and/or of a transformed animal according to the invention, for the selection of an organic or inorganic compound capable of modulating, regulating, inducing or inhibiting the expression of genes, and/or of modifying the cellular replication of eukaryotic or prokaryotic cells or capable of inducing, inhibiting or worsening the pathologies linked to an infection by Chlamydia trachomatis or one of its associated microorganisms.
The invention also comprises screening assays that comprise methods of selecting compounds capable of binding to a polypeptide, fusion polypeptide, or one of its representative fragments according to the invention, capable of binding to a nucleotide sequence according to the invention, or capable of recognizing an antibody according to the invention, and/or capable of modulating, regulating, inducing or inhibiting the expression of genes, and/or of modifying the growth or the cellular replication of eukaryotic or prokaryotic cells, or capable of inducing, inhibiting or worsening, in an animal or human organism, the pathologies linked to an infection by Chlamydia trachomatis or one of its associated microorganisms, characterized in that it comprises the following steps:
a) bringing the said compound into contact with the said polypeptide, the said nucleotide sequence, with a transformed cell according to the invention and/or administering the said compound to a transformed animal according to the invention;
b) determining the capacity of the said compound to bind with the said polypeptide or the said nucleotide sequence, or to modulate, regulate, induce or inhibit the expression of genes, or to modulate growth or cellular replication, or to induce, inhibit or worsen in the said transformed animal, the pathologies linked to an infection by Chlamydia trachomatis or one of its associated microorganisms.
The transformed cells and/or animals according to the invention may advantageously serve as a model and may be used in methods for studying, identifying and/or selecting compounds capable of being responsible for pathologies induced or worsened by Chlamydia trachomatis, or capable of preventing and/or of treating these pathologies such as, for example, genital, eye or systemic diseases, especially of the lymphatic system. In particular, the transformed host cells, in particular bacteria of the Chlamydia family whose transformation with a vector according to the invention may, for example, increase or inhibit its infectivity, or modulate the pathologies usually induced or worsened by the infection, may be used to infect animals in which the onset of pathologies will be monitored. These nontransformed animals, infected for example with transformed Chlamydia bacteria, may serve as a study model. In the same manner, the transformed animals according to the invention may, for example, exhibit predispositions to genital and/or eye and/or systemic diseases, especially of the lymphatic system, and thus be used in methods for selecting compounds capable of preventing and/or of treating the said diseases. The said methods using the said transformed cells and/or transformed animals form part of the invention.
The compounds capable of being selected may be organic compounds such as polypeptides or carbohydrates or any other organic or inorganic compounds already known, or new organic compounds produced using molecular modelling techniques and obtained by chemical or biochemical synthesis, these techniques being known to persons skilled in the art.
The said selected compounds may be used to modulate the growth and/or the cellular replication of Chlamydia trachomatis or any other associated microorganism and thus to control infection by these microorganisms. The said compounds according to the invention may also be used to modulate the growth and/or the cellular replication of all eukaryotic or prokaryotic cells, in particular tumour cells and infectious microorganisms, for which the said compounds will prove active, the methods which make it possible to determine the said modulations being well known to persons skilled in the art.
Compound capable of modulating the growth of a microorganism is understood to designate any compound which makes it possible to act, to modify, to limit and/or to reduce the development, the growth, the rate of proliferation and/or the viability of the said microorganism.
This modulation may be achieved, for example, by an agent capable of binding to a protein and thus of inhibiting or of potentiating its biological activity, or capable of binding to a membrane protein of the outer surface of a microorganism and of blocking the penetration of the said microorganism into the host cell or of promoting the action of the immune system of the infected organism directed against the said microorganism. This modulation may also be achieved by an agent capable of binding to a nucleotide sequence of a DNA or RNA of a microorganism and of blocking, for example, the expression of a polypeptide whose biological or structural activity is necessary for the growth or for the reproduction of the said microorganism.
Associated microorganism is understood to designate in the present invention any microorganism whose gene expression may be modulated, regulated, induced or inhibited, or whose growth or cellular replication may also be modulated by a compound of the invention. Associated microorganism is also understood to designate in the present invention any microorganism containing nucleotide sequences or polypeptides according to the invention. These microorganisms may, in some cases, contain polypeptides or nucleotide sequences identical or homologous to those of the invention may also be detected and/or identified by the detection and/or identification methods or kit according to the invention and may also serve as a target for the compounds of the invention.
The invention relates to the compounds capable of being selected by a method of selection according to the invention.
The invention also relates to a pharmaceutical composition comprising a compound chosen from the following compounds: a nucleotide sequence according to the invention; a polypeptide or fusion polypeptide according to the invention; a vector according to the invention; an antibody according to the invention; and a compound capable of being selected by a method of selection according to the invention, optionally in combination with a pharmaceutically acceptable vehicle or carrier.
An effective quantity is understood to designate a sufficient quantity of the said compound or antibody, or of a polypeptide of the invention, which makes it possible to modulate the growth of Chlamydia trachomatis or of an associated microorganism.
The invention also relates to a pharmaceutical composition according to the invention for the prevention or the treatment of an infection by a bacterium belonging to the species Chlamydia trachomatis or by an associated microorganism.
The invention relates, in addition, to an immunogenic and/or vaccine composition, characterized in that it comprises one or more polypeptides according to the invention and/or one or more hybrid polypeptides according to the invention.
The invention also comprises the use of a transformed cell according to the invention, for the preparation of a vaccine composition.
The invention also relates to a vaccine composition, characterized in that it contains a nucleo-tide sequence according to the invention, a vector according to the invention and/or a transformed cell according to the invention.
The invention also relates to the vaccine compositions according to the invention, for the prevention or the treatment of an infection by a bacterium belonging to the species Chlamydia trachomatis or by an associated microorganism.
The invention also relates to the use of DNA encoding polypeptides of Chlamydia trachomatis, in particular antigenic determinants, to be formulated as vaccine compositions. In accordance with this aspect of the invention, the DNA of interest is engineered into an expression vector under the control of regulatory elements, which will promote expression of the DNA, i.e., promoter or enhancer elements. In one preferred embodiment, the promoter element may be cell-specific and permit substantial transcription of the DNA only in predetermined cells. The DNA may be introduced directly into the host either as naked DNA (U.S. Pat. No. 5,679,647 incorporated herein by reference in their entirety) or formulated in compositions with other agents which may facilitate uptake of the DNA including viral vectors, i.e., adenovirus vectors, or agents which facilitate immunization, such as bupivacaine and other local anesthetics (U.S. Pat. No. 5,593,972 incorporated herein by reference in their entirety), saponins (U.S. Pat. No. 5,739,118 incorporated herein by reference in their entirety) and cationic polyamines (published international application WO 96/10038 incorporated herein by reference in their entirety).
The DNA sequence encoding the antigenic polypeptide and regulatory element may be inserted into a stable cell line or cloned microorganism, using techniques, such as targeted homologous recombination, which are well known to those of skill in the art, and described e.g., in Chappel, U.S. Pat. No. 4,215,051; Skoultehi, WO 91/06667 each of which is incorporated herein by reference in its entirety.
Such cell lines and microorganisms may be formulated for vaccine purposes. In yet another embodiment, the DNA sequence encoding the antigenic polypeptide and regulatory element may be delivered to a mammalian host and introduced into the host genome via homologous recombination (See, Chappel, U.S. Pat. No. 4,215,051; Skoultchi, WO 91/06667 each of which is incorporated herein by reference in its entirety.
Preferably, the immunogenic and/or vaccine compositions according to the invention intended for the prevention and/or the treatment of an infection by Chlamydia trachomatis or by an associated microorganism will be chosen from the immunogenic and/or vaccine compositions comprising a polypeptide or one of its representative fragments corresponding to a protein, or one of its representative fragments, of the cellular envelope of Chlamydia trachomatis. The vaccine compositions comprising nucleotide sequences will also preferably comprise nucleotide sequences encoding a polypeptide or one of its fragments corresponding to a protein, or one of its representative fragments, of the cellular envelope of Chlamydia trachomatis. 
Among these preferred immunogenic and/or vaccine compositions, the most preferred are those comprising a polypeptide or one of its representative fragments, or a nucleotide sequence or one of its representative fragments whose sequences are chosen from the nucleotide or amino acid sequences identified in this functional group and listed above.
The polypeptides of the invention or their representative fragments entering into the immunogenic compositions according to the invention may be selected by techniques known to persons skilled in the art, such as for example on the capacity of the said polypeptides to stimulate T cells, which results, for example, in their proliferation or the secretion of interleukins, and which leads to the production of antibodies directed against the said polypeptides.
In mice, in which a weight dose of the vaccine composition comparable to the dose used in humans is administered, the antibody reaction is tested by collecting serum followed by a study of the formation of a complex between the antibodies present in the serum and the antigen of the vaccine composition, according to the customary techniques.
According to the invention, the said vaccine compositions will be preferably in combination with a pharmaceutically acceptable vehicle and, where appropriate, with one or more appropriate immunity adjuvants.
Various types of vaccines are currently available for protecting humans against infectious diseases: attenuated live microorganisms (M. bovis—BCG for tuberculosis), inactivated microorganisms (influenza virus), acellular extracts (Bordetella pertussis for whooping cough), recombinant proteins (hepatitis B virus surface antigen), polysaccharides (pneumococci). Experiments are underway on vaccines prepared from synthetic peptides or from genetically modified microorganisms expressing heterologous antigens. Even more recently, recombinant plasmid DNAs carrying genes encoding protective antigens were proposed as an alternative vaccine strategy. This type of vaccination is carried out with a particular plasmid derived from an E. coli plasmid which does not replicate in vivo and which encodes only the vaccinal protein. Animals were immunized by simply injecting the naked plasmid DNA into the muscle. This technique leads to the expression of the vaccine protein in situ and to a cell-type (CTL) and a humoral type (antibody) immune response. This double induction of the immune response is one of the main advantages of the technique of vaccination with naked DNA.
The vaccine compositions of the present invention can be evaluated in in vitro and in vivo animal models prior to host, e.g., human, administration. For example, in vitro neutralization assays such as those described by Peterson et al. (1988) can be utilized. The assay described by Peterson et al. (1988) is suitable for testing vaccine compositions directed toward either Chlamydia trachomatis or Chlamydia pneumoniae. 
Briefly, hyper-immune antisera is diluted in PBS containing 5% guinea pig serum, as a complement source. Chlamydiae (104 IFU; inclusion forming units) are added to the antisera dilutions. The antigen-antibody mixtures are incubated at 37° C. for 45 minutes and inoculated into duplicate confluent Hep-2 or HeLa cell monolayers contained in glass vials (e.g., 15 by 45 mm), which have been washed twice with PBS prior to inoculation. The monolayer cells are infected by centrifugation at 1000×g for 1 hour followed by stationary incubation at 37° C. for 1 hour. Infected monolayers are incubated for 48 or 72 hours, fixed and stained with a Chlamydiae specific antibody, such as anti-MOMP for C. trachomatis, etc. Inclusion-bearing cells are counted in ten fields at a magnification of 200×. Neutralization titer is assigned based on the dilution that gives 50% inhibition as compared to control monolayers/IFU.
The efficacy of vaccine compositions can be determined in vivo by challenging animal models of Chlamydia trachomatis infection, e.g., guinea pigs or mice, with the vaccine compositions. For example, in vivo vaccine composition challenge studies in the guinea pig model of Chlamydia trachomatis infection can be performed. Briefly, female guinea pigs weighing 450 to 500 g are housed in an environmentally controlled room with a 12 hour light-dark cycle and immunized with vaccine compositions via a variety of immunization routes. Post-vaccination, guinea pigs are infected in the genital tract with the agent of guinea pig inclusion conjunctivitis (GPIC), which has been grown in HeLa or McCoy cells (Rank et al. (1988)). Each animal receives approximately 1.4×107 inclusion forming units (IFU) contained in 0.05 ml of sucrose-phosphate-glutamate buffer, pH 7.4 (Schacter, J. (1980)). The course of infection monitored by determining the percentage of inclusion-bearing cells by indirect immunofluorescence with GPIC specific antisera, or by Giemsa-stained smear from a scraping from the genital tract (Rank et al. (1988)). Antibody titers in the serum is determined by an enzyme-linked immunosorbent assay.
Alternatively, in vivo vaccine composition challenge studies can be performed in the murine model of Chlamydia trachomatis (Morrison et al., 1995). Briefly, female mice 7 to 12 weeks of age receive 2.5 mg of depoprovera subcutaneously at 10 and 3 days before vaginal infection. Post-vaccination, mice are infected in the genital tract with 1,500 inclusion-forming units of Chlamydia trachomatis contained in 5 ml of sucrose-phosphate-glutamate buffer, pH. 7.4. The course of infection is monitored by determining the percentage of inclusion-bearing cells by indirect immunofluorence with Chlamydia trachomatis specific antisera, or by a Giemsa-stained smear from a scraping from the genital tract of an infected mouse. The presence of antibody titers in the serum of a mouse is determined by an enzyme-linked immunosorbent assay.
The vaccine compositions comprising nucleotide sequences or vectors into which the said sequences are inserted are in particular described in International Application No. WO 90/11092 and also in International Application No. WO 95/11307.
The nucleotide sequence constituting the vaccine composition according to the invention may be injected into the host after having been coupled to compounds which promote the penetration of this polynucleotide inside the cell or its transport up to the cell nucleus. The resulting conjugates may be encapsulated into polymeric microparticles, as described in International Application No. WO 94/27238 (Medisorb Technologies International).
According to another embodiment of the vaccine composition according to the invention, the nucleotide sequence, preferably a DNA, is complexed with the DEAE-dextran (Pagano et al., 1967) or with nuclear proteins (Kaneda et al., 1989), with lipids (Felgner et al., 1987) or encapsulated into liposomes (Fraley et al., 1980) or alternatively introduced in the form of a gel facilitating its transfection into the cells (Midoux et al., 1993, Pastore et al., 1994). The polynucleotide or the vector according to the invention may also be in suspension in a buffer solution or may be combined with liposomes.
Advantageously, such a vaccine will be prepared in accordance with the technique described by Tacson et al. or Huygen et al. in 1996 or alternatively in accordance with the technique described by Davis et al. in International Application No. WO 95/11307.
Such a vaccine may also be prepared in the form of a composition containing a vector according to the invention, placed under the control of regulatory elements allowing its expression in humans or animals. It is possible, for example, to use, as vector for the in vivo expression of the polypeptide antigen of interest, the plasmid pcDNA3 or the plasmid pcDNA1/neo, both marketed by Invitrogen (R & D Systems, Abingdon, United Kingdom). It is also possible to use the plasmid V1Jns.tPA, described by Shiver et al. in 1995. Such a vaccine will advantageously comprise, in addition to the recombinant vector, a saline solution, for example a sodium chloride solution.
The immunogenic compositions of the invention can be utilized as part of methods of immunization, wherein such methods comprise administering to a host, e.g., a human host, an immunizing amount of the immunogenic compositions of the invention. In a preferred embodiment, the method of immunizing is a method of immunizing against Chlamydia trachomatis. 
A pharmaceutically acceptable vehicle is understood to designate a compound or a combination of compounds entering into a pharmaceutical or vaccine composition which does not cause side effects and which makes it possible, for example, to facilitate the administration of the active compound, to increase its life and/or its efficacy in the body, to increase its solubility in solution or alternatively to enhance its preservation. These pharmaceutically acceptable vehicles are well known and will be adapted by persons skilled in the art according to the nature and the mode of administration of the active compound chosen.
As regards the vaccine formulations, these may comprise appropriate immunity adjuvants which are known to persons skilled in the art, such as, for example, aluminum hydroxide, a representative of the family of muramyl peptides such as one of the peptide derivatives of N-acetyl-muramyl, a bacterial lysate, or alternatively incomplete Freund's adjuvant, StimulonTM QS-21 (Aquila Biopharmaceuticals, Inc., Framingham, Mass.), MPLTM (3-O-deacylated monophosphoryl lipid A; RIBI ImmunoChem Research, Inc., Hamilton, Mont.), aluminum phosphate, IL-12 (Genetics Institute, Cambridge, Mass.).
Preferably, these compounds will be administered by the systemic route, in particular by the intravenous route, by the intranasal, intramuscular, intradermal or subcutaneous route, or by the oral route. More preferably, the vaccine composition comprising polypeptides according to the invention will be administered several times, spread out over time, by the intradermal or subcutaneous route.
Their optimum modes of administration, dosages and galenic forms may be determined according to criteria which are generally taken into account in establishing a treatment adapted to a patient, such as for example the patient's age or body weight, the seriousness of his general condition, tolerance of the treatment and the side effects observed.
The invention comprises the use of a composition according to the invention for the treatment or the prevention of genital diseases which are induced or worsened by Chlamydia trachomatis. 
Finally, the invention comprises the use of a composition according to the invention for the treatment or the prevention of eye diseases which are induced or worsened by the presence of Chlamydia trachomatis. 
Finally, the invention comprises the use of a composition according to the invention for the treatment or the prevention of systemic diseases, especially of the lymphatic system, which are induced or worsened by the presence of Chlamydia trachomatis. 
Other characteristics and advantages of the invention appear in the following examples and figures:



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1: Line for the production of Chlamydia trachomatis sequences (SEQ ID NO: 5182)
FIG. 2: Analysis of the sequences and assembling (SEQ ID NO: 5182)
FIG. 3: Finishing techniques
FIG. 3a): Assembly map
FIG. 3b): Determination and use of the orphan ends of the contigs



EXAMPLES
Cells. The Chlamydia trachomatis LGV2 strain used is identified to have over 98% homology with the outer membrane protein sequences omp1 (CHTMOMPA) and omp2 (CHTOMP2A) of the Chlamydia trachomatis serovar L2/434/Bu strain.
The Chlamydia trachomatis LGV2 strain is cultured on mouse fibroblasts (McCoy cells), obtained from the American Type Culture Collection, under the reference ATCC CRL-1696.
Culture of the cells. The mouse fibroblasts are cultured in 75-ml cell culture flasks (Corning). The culture medium is Dulbecco's modified cell culture medium (Gibco BRL No. 04101965) supplemented with MEM amino acids (Gibco BRL-No. 04301140) L (5 ml per 500 ml of medium) and 5% foetal calf serum (Gibco BRL No. 10270 batch 40G8260K) without antibiotics or antifungals.
The cell culture stock is maintained in the following manner. The cell cultures are examined under an inverted microscope. 24 hours after confluence, each cellular lawn is washed with PBS (Gibco BRL No. 04114190), rinsed and then placed for 5 min in an oven in the presence of 3 ml of trypsine (Gibco BRL No. 25200056). The cellular lawn is then detached and then resuspended in 120 ml of culture medium, the whole is stirred in order to make the cellular suspension homogeneous. 30 ml of this suspension are then distributed per cell culture flask. The flasks are kept in a CO2 oven (5%) for 48 hours at a temperature of 37° C. The cell stock is maintained so as to have available daily 16 flasks of subconfluent cells. It is these subconfluent cells which will be used so as to be infected with Chlamydia. 25-ml cell culture flasks are also used, these flasks are prepared in a similar manner but the volumes used for maintaining the cells are the following: 1 ml of trypsine, 28 ml of culture medium to resuspend the cells, 7 ml of culture medium are used per 25-ml flask.
Infection of the cells with Chlamydia. Initially, the Chlamydiae are obtained frozen (at −70° C.), in suspension in a volume of 1 millilitre. This preparation is slowly thawed, 500 μl are collected and brought into contact with subconfluent cells, which are obtained as indicated above, in a 25-ml cell culture flask, containing 1 ml of medium, so as to cover the cells. The flask is then centrifuged at 2000 rpm in a “swing” rotor for microtitre plates, the centrifuge being maintained at a temperature of 35° C. After centrifugation, the two flasks are placed in an oven at 35° C. for three hours. 6 ml of culture medium containing cycloheximide (1 μg/ml) are then added and the flask is stored at 35° C. After 48 hours, the level of infection is evaluated by direct immunofluorescence and by the cytopathogenic effect caused to the cells.
Direct immunofluorescence. Starting with infected cells, which were obtained as indicated above, a cellular smear is deposited with a Pasteur pipette on a microscope slide. The cellular smear is fixed with acetone for 10 minutes; after draining the acetone, the smear is covered with 30 μl of muline monoclonal antibodies directed against MOMP (major outer membrane protein) of Chlamydia (Syva, Biomérieux) labelled with fluorescein isothiocyanate. The whole is then incubated in a humid chamber at a temperature of 37° C. The slides are then rinsed with water, slightly dried, and then after depositing a drop of mounting medium, a coverslip is mounted before reading. The reading is carried out with the aid of a fluorescence microscope equipped with the required filters (excitation at 490 nm, emission at 520 nm).
Harvesting of the Chlamydia trachomatis. After checking the infection by direct immuno-fluorescence, carried out as indicated above, the culture flasks are opened under a sterile cabinet, sterile glass beads with a diameter of the order of a millimeter are placed in the flask. The flask is closed and then vigorously stirred while being maintained horizontally, the cellular lawn at the bottom, so that the glass beads can have a mechanical action on the cellular lawn. Most of the cells are thus detached or broken; the effect of the stirring is observed under an optical microscope so as to ensure proper release of Chlamydiae.
Large-scale infection of the cell cultures. The product of the Chlamydiae harvest (culture medium and cellular debris) is collected with a pipette, and distributed into three cell culture flasks containing subconfluent L cells, obtained as indicated above. The cells thus inoculated are placed under gentle stirring (swing) in an oven at 35° C. After one hour, the flasks are kept horizontally in an oven so that the culture medium covers the cells for 3 hours. 30 ml of culture medium containing actydione (1 μg/ml) are then added to each of the flasks. The culture flasks are then stored at 35° C. for 48 hours. The cells thus infected are examined under an optical microscope after 24 hours, the cytopathogenic effect is evaluated by the appearance of cytoplasmic inclusions which are visible under an inverted optical microscope. After 48 hours, the vacuoles containing the Chlamydiae occupy the cytoplasm of the cell and push the cell nucleus sideways. At this stage, numerous cells are spontaneously destroyed and have left free elementary bodies in the culture medium. The Chlamydiae are harvested as described above and are either frozen at −80° C. or used for another propagation.
Purification of the Chlamydiae. The product of the Chlamydia harvests, stored at −80° C., is thawed on a water bath at room temperature. After thawing, each tube is vigorously stirred for one minute and immersed for one minute in an ultrasound tank (BRANSON 1200); the tubes are then stirred by inverting before being centrifuged for 5 min at 2000 rpm. The supernatant is carefully removed and kept at cold temperature (ice). The supernatant is vigorously stirred and then filtered on nylon filters having pores of 5 microns in diameter on a support (Nalgene) allowing a delicate vacuum to be established under the nylon filter. For each filtration, three nylon filters are superposed; these filters are replaced after every 40 ml of filtrate. Two hundred milliliters of filtration product are kept at cold temperature, and then after stirring by inverting, are centrifuged at 10,000 rpm for 90 min, the supernatant is removed and the pellet is taken up in 10 ml of 10 mM Tris, vigorously vortexed and then centrifuged at 10,000 rpm for 90 min. The supernatant is removed and the pellet is taken up in a buffer (20 mM Tris pH 8.0, 50 mM KCl, 5 mM MgCl2) to which 800 units of DNAse I (Boehringer) are added. The whole is kept at 37° C. for one hour. One ml of 0.5 M EDTA is then added, and the whole is vortexed and frozen at −20° C.
Preparation of the DNA. The Chlamydiae purified above are thawed and subjected to a proteinase K (Boehringer) digestion in a final volume of 10 ml. The digestion conditions are the following: 0.1 mg/ml proteinase K, 0.1% SDS at 55° C., stirring every 10 min. The product of digestion is then subjected to a double extraction with phenol-chloroform, two volumes of ethanol are added and the DNA is directly recovered with a Pasteur pipette having one end in the form of a hook. The DNA is dried on the edge of the tube and then resuspended in 500 μl of 2 mM Tris pH 7.5. The DNA is stored at 4° C. for at least 24 hours before being used for the cloning.
Cloning of the DNA. After precipitation, the DNA is quantified by measuring the optical density at 260 nm. Thirty μg of Chlamydia DNA are distributed into 10 tubes of 1.5 ml and diluted in 300 μl of water. Each of the tubes is subjected to 10 applications of ultrasound lasting for 0.5 sec in a sonicator (Unisonix XL2020). The contents of the 10 tubes are then grouped and concentrated by successive extractions with butanol (Sigma B1888) in the following manner: two volumes of butanol are added to the dilute DNA mixture. After stirring, the whole is centrifuged for five minutes at 2500 rpm and the butanol is removed. This operation is repeated until the volume of the aqueous phase is less than 1 ml. The DNA is then precipitated in the presence of ethanol and of 0.5 M sodium acetate pH 5.4, and then centrifuged for thirty minutes at 15,000 rpm at cold temperature (4° C.). The pellet is washed with 75% ethanol, centrifuged for five minutes at 15,000 rpm and dried at room temperature. A tenth of the preparation is analysed on a 0.8% agarose gel. Typically, the size of the DNA fragments thus prepared is between 200 and 8000 base pairs.
To allow the cloning of the DNA obtained, the ends are repaired. The DNA is distributed in an amount of 10 μg/tube, in the following reaction medium: 100 μl final volume, 1× buffer (Biolabs 201L), 0.5 μl BSA 0.05 mg/ml, 0.1 mM dATP, 0.1 mM each of dGTP, dCTP or dTTP, 60,000 IU T4 DNA polymerase. The reaction is incubated for thirty minutes at 16° C. The contents of each of the tubes are then grouped before carrying out an extraction with phenol-chloroform and then precipitating the aqueous phase as described above. After this step, the DNA thus prepared is phosphorylated. For that, the DNA is distributed into tubes in an amount of 10 μg per tube, and then in a final volume of 50 μl, the reaction is prepared in the following manner: 1 mM ATP, 1× kinase buffer, 10 IU T4 polynucleotide kinase (Biolabs 201L). The preparation is incubated for thirty minutes at 37° C. The contents of the tubes are combined and a phenol-chloroform extraction and then a precipitation are carried out in order to precipitate the DNA. The latter is then suspended in 1 μl of water and then the DNA fragments are separated according to their size on a 0.8% agarose gel (1×TAE). The DNA is subjected to an electric field of 5 V/cm and then visualized on a UV table. The fragments whose size varies between 1200 and 2000 base pairs are selected by cutting out the gel. The gel fragment thus isolated is placed in a tube and then the DNA is purified with the Qiaex kit (20021 Qiagen), according to the procedure provided by the manufacturer.
Preparation of the vector. 14 μg of the cloning vector pGEM-5Zf (Proméga P2241) are diluted in a final volume of 150 μl and are subjected to digestion with the restriction enzyme EcoRV 300 IU (Biolabs 195 S) according to the protocol and with the reagents provided by the manufacturer. The whole is placed at 37° C. for 150 min and then distributed in the wells of a 0.8% agarose gel subjected to an electric field of 5 V/cm. The linearized vector is visualized on a UV table, isolated by cutting out the gel and then purified by the Qiaex kit (Qiagen 20021) according to the manufacturer's recommendations. The purification products are grouped in a tube, the volume is measured and then half the volume of phenol is added and the whole is vigorously stirred for 1 min. Half the volume of chloroform-isoamyl alcohol 24:1 is added and vigorously stirred for 1 min. The whole is centrifuged at 15,000 rpm for 5 min at 4° C., the aqueous phase is recovered and transferred into a tube. The DNA is precipitated in the presence of 0.3 M sodium acetate, pH 5.4 and 3 volumes of ethanol and placed at −20° C. for 1 hour. The DNA is then centrifuged at 15,000 rpm for 30 min at 4° C., the supernatant is removed while preserving the pellet, washed twice with 70% ethanol. After drying at room temperature, the DNA is suspended in 25 μl of water.
Phosphorylation of the vector. 25 μl of the vector prepared in the preceding step are diluted in a final volume of 500 μl of the following reaction mixture:
After repair, the DNA is subjected to a phenol-chloroform extraction and a precipitation, the pellet is then taken up in 10 μl of water, the DNA is quantified by measuring the optical density at 260 nm. The quantified DNA is ligated into the vector PGEm-5Zf(+) prepared by the restriction enzyme EcoRV and dephosphorylated (see preparation of the vector). The ligation is carried out under three conditions which vary in the ratio between the number of vector molecules and the number of insert molecules. Typically, an equimolar ratio, a ratio of 1:3 and a ratio of 3:1 are used for the ligations which are, moreover, carried out under the following conditions: vector PGEm-5Zf(+) 25 ng, cut DNA, ligation buffer in a final volume of 20 μl with T4 DNA ligase (Amersham E70042X); the whole is then placed in a refrigerator overnight and then a phenol-chloroform extraction and a precipitation are carried out in a conventional manner. The pellet is taken up in 5 μl of water.
Transformation of the Bacteria. Plating of the Bacteria
Petri dishes containing LB Agar medium containing ampicillin (50 μg/ml), Xgal (280 μg/ml) [5-bromo-4-chloro-indolyl-beta-D-galactopyranoside (Sigma B-4252)], IPTG (140 μg/ml) [isopropyl-beta-D-thiogalactoside (Sigma I-6758)] are used, 50 and 100 μl of bacteria are plated for each of the ligations. The Petri dishes are placed upside down at 37° C. for 15 to 16 hours in an oven. The number of “recombinant” positive clones is evaluated by counting the white colonies and the blue colonies which are thought to contain the vector alone.
Evaluation of the “recombinant” positive clones. Ninety-four white colonies and two blue colonies are collected with the aid of sterile cones and are deposited at the bottom of the wells of plates designed for carrying out the amplification techniques. 30 μl of the following reaction mixture are added to each well: 1.7 mM MgCl2, 0.2 mM each of dATP, dCTP, dGTP and dTTP, two synthetic oligonucleotides corresponding to sequences flanking the cloning site on either side and orienting the synthesis of the DNA in a convergent manner (0.5 mM RP and PU primers, 1 U TAQ polymerase (GibcoBRL 18038-026)).
The colonies thus prepared are subjected to a temperature of 94° C. for 5 min and then to 30 thermal cycles composed of the following steps: 94° C. for 40 s, 50° C. for 30 s, 72° C. for 180 s. The reaction is then kept for 7 min at 72° C. and then kept at 4° C.
The amplification products are deposited on an agarose gel (0.8%), stained with ethidium bromide, subjected to electrophoresis, and then analysed on an ultraviolet table. The presence of an amplification fragment having a size greater than 500 base pairs indicates the presence of an insert. The bacterial clones are then prepared so as to study the sequence of their insert.
Sequencing. To sequence the inserts of the clones obtained as above, these were amplified by PCR on bacteria cultures carried out overnight using the primers for the vectors flanking the inserts. The sequence of the ends of these inserts (on average 500 bases on each side) was determined by automated fluorescent sequencing on an ABI 377 sequencer, equipped with the ABI Prism DNA Sequencing Analysis software (version 2.1.2).
Analysis of the sequences. The sequences obtained by sequencing in a high-yield line (FIG. 1) are stored in a database; this part of the production is independent of any treatment of the sequences. The sequences are extracted from the database, avoiding all the regions of inadequate quality, that is to say the regions for which uncertainties are observed on the sequence at more than 95%. After extraction, the sequences are introduced into a processing line, the diagram of which is described in FIG. 2. In a first path of this processing line, the sequences are assembled by the Gap4 software from R. Staden (Bonfield et al., 1995) (OS UNIX/SUN Solaris); the results obtained by this software are kept in the form of two files which will be used for a subsequent processing. The first of these files provides information on the sequence of each of the contigs obtained. The second file represents all the clones participating in the composition of all the contigs as well as their positions on the respective contigs.
The second processing path uses a sequence assembler (TIGR-Asmg assembler UNIX/SUN Solaris); the results of this second processing path are kept in the form of a file in the TIGR-Asmg format which provides information on the relationship existing between the sequences selected for the assembly. This assembler is sometimes incapable of linking contigs whose ends overlap over several hundreds of base pairs.
The results obtained from these two assemblers are compared with the aid of the BLAST program, each of the contigs derived from one assembly path being compared with the contigs derived from the other path.
For the two processing paths, the strict assembly parameters are fixed (95% homology, 30 superposition nucleotides). These parameters avoid 3 to 5% of the clones derived from eukaryotic cells being confused with sequences obtained from the clones derived from Chlamydia trachomatis. The eukaryotic sequences are however preserved during the course of this project; the strategy introduced, which is described below, will be designed, inter alia, not to be impeded by these sequences derived from contaminating clones.
The results of these two assemblers are processed in a software developed for this project. This software operates on a Windows NT platform and receives, as data, the results derived from the STADEN software and/or the results derived from the TIGR-Asmg assembler, the software, results, after processing of the data, in the determination of an assembly map which gives the proximity relationship and the orientation of the contigs in relation to one another (FIG. 3a). Using this assembly map, the software determines all the primers necessary for finishing the project. This treatment, which will be detailed below, has the advantage of distinguishing the isolated sequences derived from the contaminations, by the DNA eukaryotic cells, of the small-sized sequences clearly integrated into the project by the relationships which they establish with contigs. In order to allow, without any risk of error, the arrangement and the orientation of the contigs in relation to one another, a statistical evaluation of the accuracy of the names “naming” of sequence is made from the results of “contigation”. This evaluation makes it possible to give each of the clone plates, as well as each of the subsets of plates, a weight which is inversely proportional to probable error rate existing in the “naming” of the sequences obtained from this plate or from a subset of this plate. In spite of a low error rate, errors may occur throughout the steps of production of the clones and of the sequences. These steps are numerous, repetitive and although most of them are automated, others, like the deposition in the sequencers, are manual; it is then possible for the operator to make mistakes such as the inversion of two sequences. This type of error has a repercussion on the subsequent processing of the data, by resulting in relationships (between the contigs) which do not exist in reality, then in attempts at directed sequencing between the contigs which will end in failure. It is because of this that the evaluation of the naming errors is of particular importance since it allows the establishment of a probabilistic assembly map from which it becomes possible to determine all the clones which will serve as template to obtain sequences separating two adjacent contigs. Table 2 of parent U.S. Application Ser. No. 60/107,077 filed Nov. 4, 1998, French application 97-15041 filed Nov. 28, 1997 and French application 97-16034 filed Dec. 17, 1997, each of which is incorporated by reference herein in its entirety, gives the clones and the sequences of the primers initially used during the initial operations.
To avoid the step which consists in ordering and then preparing the clones by conventional microbiological means, outer and inner primers oriented towards the regions not yet sequenced are defined by the software. The primers thus determined make it possible to prepare, by PCR, a template covering the nonsequenced region. It is the so-called outer primers (the ones most distant from the region to be sequenced) which are used to prepare this template. The template is then purified and a sequence is obtained on each of the two strands during 2 sequencing reactions which each use one of the 2 inner primers. In order to facilitate the use of this approach, the two outer primers and the two inner primers are prepared and then stored on the same position of 4 different 96-well plates. The two plates containing the outer primers are used to perform the PCRs which serve to prepare the templates. These templates will be purified on purification columns preserving the topography of the plates. Each of the sequences are obtained using primers situated on one and then on the other of the plates containing the inner primers. This distribution allows a very extensive automation of the process and results in a method which is simple to use for finishing the regions not yet sequenced. Table 3 of parent U.S. Application Ser. No. 60/107,077 filed Nov. 4, 1998, French application 97-15041 filed Nov. 28, 1997 and French application 97-16034 filed Dec. 17, 1997, each of which is incorporated by reference herein in its entirety, gives the names and the sequences of the primers used for finishing Chlamydia trachomatis. 
Finally, a number of contigs exist in a configuration where one of their ends is not linked to any other contig end (FIG. 3b) by a connecting clone relationship (a connecting clone is defined as a clone having one sequence end on a contig and the other end of its sequence on another contig; furthermore, this clone must be derived from a plate or a subset of plates with adequate naming quality). For the Chlamydia trachomatis project, this particular case occurred 37 times. Two adjacent PCR primers orienting the synthesis of the DNA towards the end of the consensus sequence are defined for each of the orphan ends of the consensus sequence. The primer which is closest to the end of the sequence is called the inner primer whereas the primer which is more distant from the end of the sequence is called the outer primer. The outer primers are used to explore the mutual relationship between the orphan ends of the different contigs. The presence of a single PCR product and the possibility of amplifying this product unambiguously using the inner primers evokes the probable relationship between the contigs on which the primers which allowed the amplification are situated. This relationship will be confirmed by sequencing and will allow the connection between the orphan ends of the consensus sequences. This strategy has made it possible to obtain a complete map of the Chlamydia trachomatis chromosome and then to finish the project.
Quality control. All the bases not determined with certainty in the chromosomal sequence were noted and the density of uncertainties was measured on the entire chromosome. The regions with a high density of uncertainties were noted and the PCR primers spanning these regions were drawn and are represented in Table 4 of parent U.S. Application Ser. No. 60/107,077 filed Nov. 4, 1998, French application 97-15041 filed Nov. 28, 1997 and French application 97-16034 filed Dec. 17, 1997 each of which is incorporated by reference herein in its entirety.
Data banks. Local reorganizations of major public banks were used. The protein bank used consists of the nonredundant fusion of the Genpept bank (automated translation of GenBank, NCBI; Benson et al., 1996).
The entire BLAST software (public domain, Altschul et al., 1990) for searching for homologies between a sequence and protein or nucleic data banks was used. The significance levels used depend on the length and the complexity of the region tested as well as the size of the reference bank. They were adjusted and adapted to each analysis.
The results of the search for homologies between a sequence according to the invention and protein or nucleic data banks are presented and summarized in Table 1 below.
Table 1: List of coding chromosome regions and homologies between these regions and the sequence banks.
Legend to Table 1: Open reading frames are identified with the GenMark software version 2.3A (GenePro), the template used is Chlamydia trachomatis of order 4 on a length of 196 nucleotides with a window of 12 nucleotides and a minimum signal of 0.5. These reading frames are numbered in order of appearance on the chromosome, starting with ORF2 (ORF column). The positions of the beginning and of the end are then given in column 2 (position). When the position of the beginning is greater than the position of the end, this means that the region is encoded by the strand complementary to the sequence which was given in the sequence SEQ ID No. 1.
All the putative products were subjected to a search for homology on GENPEPT (release 103 for SEQ ID No. 2 to SEQ ID No. 1076 and release 108 for SEQ ID No. 1077 to SEQ ID No. 1197 with the BLASTp software (Altschul et al. 1990), with, as parameters, the default parameters with the exception of the expected value E set at 10−5 (for SEQ ID No. 2 to SEQ ID No. 1076) and P value set at e−10 (for SEQ ID No. 1077 to SEQ ID No. 1197). Subsequently, only the identities greater than 30% (1% column) were taken into account. The description of the most homologous sequence is given in the Homology column; the identifier for the latter sequence is given in the ID column and the animal species to which this sequence belongs is given in the Species column. The Homology score is evaluated by the sum of the blast scores for each region of homology and reported in the Score column.
Materials and methods: transmembrane domains. The DAS software was used as recommended by the authors (Cserzo et al., 1997).
This method uses, to predict the transmembrane domains, templates derived from a sampling of selected proteins. All the regions for which a “Cutoff” greater than 1.5 was found by the program were taken into account.
Additional ORF Finder Programs. For this analysis, two additional ORF finder programs were used to predict potential open reading frames of a minimum length of 74 amino acids; Glimmer (Salzberg, Delcher, A., Kasif, S., and W. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:544-548.), and an in-house written program. The in-house program used a very simple search algorithm. The analysis required that the genomic DNA sequence text be in the 5′ to 3′ direction, the genome is circular, and that TAA, TAG, and TGA are stop codons. The search parameters were as follows:
(1) A search for an ORF that started with a GTG codon was performed. If no GTG codons were found, then a search for an ATG codon was performed. However, if a GTG codon was found, then a search downstream for a ATG codon was performed. All start and stop nucleotide positions were recorded.
(2) A search for an ORF that started with a TTG codon was performed. If no TTG codons were found, then a search for a ATG codon was performed. However, if a TTG codon was found, then a search downstream for a ATG codon was performed. All start and stop nucleotide positions were recorded.
(3) The analysis described in steps 1 and 2 were repeated for the opposite strand of DNA sequence.
(4) A search for ORFs that determined all ORF lengths using start and stop positions in the same reading frames was performed.
(5) All ORFs whose DNA length was less than 225 nucleotides were eliminated from the search.
Surface Exposed Protein Search Criteria. Potential cell surface vaccine targets are outer membrane proteins such as porins, lipoproteins, adhesions and other non-integral proteins. In Chlamydia psittaci, the major immunogens is a group of putative outer membrane proteins (POMPs) and no homologs have been found in Chlamydia trachomatis and Chlamydia trachomatis by traditional analysis (Longbottom, D., Russell, M., Dunbar, S. M., Jones, G. E., and A. J. Herring. 1998. Molecular Cloning and Characterization of the Genes Coding for the Highly Immunogenic Cluster of 90-Kilodalton Envelope Proteins from Chlamydia psittaci Subtype That Causes Abortion in Sheep. Infect Immun 66:1317-1324.) However, utilizing the criteria described below, several ORFs encoding outer membrane proteins have been identified in Chlamydia trachomatis, all of which may represent vaccine candidates. Any ORF which met any one of the criteria described below were considered to encode a surface exposed protein.
Protein homology searches of the translated ORFs were done using the Blastp 2.0 tool (Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402). An ORF was labeled surface exposed if the translated ORF had homology to a known, or hypothetical, or putative surface exposed protein with a P score less than e−10.
Most, if not all, proteins that are localized to the membrane of bacteria, via a secretory pathway, contain a signal peptide. The software program SignalP, was used to analyze the amino acid sequence of an ORF for such a signal peptide (Nielsen, H., Engelbrecht. J., Brunak, S., and G. von Heijne. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 10:1-6.) The first 60 N-terminal amino acids of each ORF were analyzed by SignalP using the Gram-negative software database. The output generates four separate values, maximum C, maximum Y, maximum S, and mean S. The S-score, or signal region, is the probability of the position belonging to the signal peptide. The C-score, or cleavage site, is the probability of the position being the first in the mature protein. The Y-score is the geometric average of the C-score and a smoothed derivative of the S-score. A conclusion of either a Yes or No is given next to each score. If all four conclusions are Yes and the C-terminal amino acid is either a phenylalanine (F) or a tyrosine (Y), the ORF was labelled outer membrane (Struyve, M., Moons, M., and J. Tommassen. 1991. Carboxy-terminal Phenylalanine is Essential for the Correct Assembly of a Bacterial Outer Membrane Protein. J. Mol. Biol. 218:141-148.)
The program called Psort was used to determine the localization of a protein based on its signal sequence, recognition of transmembrane segments, and analysis of its amino acid composition (Nakai, K., and M. Kanehisa. 1991. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 11:95-110.) An ORF is considered to be an outer membrane protein if the output data predicts the ORF encoded protein as outer membrane with a certainty value of 0.5 or better and whose value is at least twice as large as the next predicted localized certainty value.
Finally, ORFs that were not predicted to be outer membrane or surface exposed, based on the above criteria, were further analyzed. The Blastp output data for these ORFs were searched using various general and specific keywords, suggestive of known cell surface exposed proteins. An ORF was labeled surface exposed if the keywords matched had a Blastp hit with a P score less than e−10, and there was no better data indicating otherwise. The following is a list of the searched keywords:

















Adhesion
Adhesin
Invasin



Invasion
Extension
Omp



Outer Surface
Porin
Outer Membrane



Cell Surface
Cell Wall
Pilin



Flagellar sheath
Cir
ChuA



CopB
ExeD
FadL



FecA
FepA
FhuA



FmdC
FomA
FrpB



GspD
HemR
HgbA



Hgp
HmbR
HmuR



HMW
HrcC
Hrp



InvG
LamB
LbpA



LcrQ
Lmp1
MxiD



MOMP
PilE
HpaA



NolW
NspA
OpcP



OpnP
Opr
OspA



PhoE
PldA
Por



PscC
PulD
PupA



QuiX
RafY
ScrY



SepC
ShuA
SomA



SpiA
Tbp1
Yop



YscC
mip
Tol



Pilus
BtuB










Those ORFs that did not meet the minimum requirement for being an outer membrane protein based on the above search criteria but which were homologous to identified outer membrane ORFs in Chlamydia pneumoniae were included. The Chlamydia pneumoniae genome (French patent application No. 97-14673, filed 21 Nov. 1997) was analyzed using the above search criteria and a number of outer membrane ORFs were identified. These Chlamydia pneumoniae ORFs were then tested against the Chlamydia trachomatis genome using Blastp. Any Chlamydia trachomatis ORF with a Blastp P value less than e−10 against a Chlamydia pneumoniae outer membrane was included in this section, if there was no better data indicating otherwise. A list of ORFs in the Chlamydia trachomatis genome encoding putative surface exposed proteins is set forth above in the specification.

Identification of Putative Lipoproteins in the Genome of Chlamydia trachomatis. Lipoproteins are the most abundant post-translationally modified bacterial secretory proteins (Pugsley, A. P. 1993. The complete general secretory pathway in Gram-negative bacteria. Microbiol. Rev. 57:50-108). The characteristic features of lipoproteins are a thiol-linked diacylglyceride and an amine-linked monoacyl group on the cysteine that becomes the amino-terminal residue after signal peptide cleavage by Signal Peptidase II. (Pugsley, A. P. 1993. The complete general secretory pathway in Gram-negative bacteria. Microbiol. Rev. 57:50-108). The identification of putative lipoproteins from the genomic sequencing of Chlamydia trachomatis was done by examining the deduced amino acid sequence of identified ORFs for the presence of a signal peptide with a Signal Peptidase II cleavage site analogous to the consensus sequence for prolipoprotein modification and processing reactions (Hayashi, S., and H. C. Wu. 1992. Identification and characterization of lipid-modified proteins in bacteria, p. 261-285. In N. M. Hooper and A. J. Turner (ed.) Lipid modification of proteins: A practical approach. Oxford University Press, New York; Sutcliffe, I. C. and R. R. B. Russell. 1995. Lipoproteins of Gram-positive bacteria. J. Bacteriol. 177:1123-1128).
The deduced amino acid sequences of Chlamydia trachomatis ORFs were initially screened for the most basic of lipoprotein characteristics, a cysteine in the first 30 amino acids of the deduced protein. ORFs with a standard start codon (ATG, GTG, or TTG) and having one or more of the following characteristics were selected for direct analysis of their first 30 amino acids:
(a) Significant Signal P value (at least two out-of-the four values are Yes)
(b) PSORT value indicating membrane passage (IM-inner membrane, Peri-periplasm, or OM-outer membrane)
(c) Identification of the word lipoprotein among the ORF Blastp data set.
(d) A Blastp value of <e−10 with a putative lipoprotein from Chlamydia pneumoniae (French application No. 97-14673 filed 21 Nov. 1997).
The first 30 amino acids encoded by each ORF in this set were analyzed for the characteristics commonly found in lipoprotein signal peptides (Pugsley, A. P. 1993. The complete general secretory pathway in Gram-negative bacteria. Microbiol. Rev. 57:50-108; Hayashi, S., and H. C. Wu. 1992. Identification and characterization of lipid-modified proteins in bacteria, p. 261-285. In N. M. Hooper and A. J. Turner (ed.) Lipid modification of proteins: A practical approach. Oxford University Press, New York; Sutcliffe, I. C. and R. R. B. Russell. 1995. Lipoproteins of Gram-positive bacteria. J. Bacteriol. 177:1123-1128.) Putative lipoprotein signal peptides were required to have a cysteine between amino acid 10 and 30 and reach a minimum score of three based on the following criteria for lipoprotein signal peptides:

    
    
        (a) Identification of specific amino acids in specific positions around the cysteine which are part of the consensus Signal Peptidase II cleavage site (Hayashi, S., and H. C. Wu. 1992. Identification and characterization of lipid-modified proteins in bacteria, p. 261-285. In N. M. Hooper and A. J. Turner (ed.) Lipid modification of proteins: A practical approach. Oxford University Press, New York); Sutcliffe, I. C. and R. R. B. Russell. 1995. Lipoproteins of Gram-positive bacteria. J. Bacteriol. 177:1123-1128). Since the identification of the cleavage site is the most important factor in identifying putative lipoproteins, each correctly positioned amino acid contributed toward reaching the minimum score of three.
        (b) A hydrophobic region rich in alanine and leucine prior to the cleavage site (Pugsley, A. P. 1993. The complete general secretory pathway in Gram-negative bacteria. Microbiol. Rev. 57:50-108) contributed toward reaching the minimum score of three.
        (c) A short stretch of hydrophilic amino acids greater than or equal to 1, usually lysine or arginine, following the N-terminal methionine (Pugsley, A. P. 1993. The complete general secretory pathway in Gram-negative bacteria. Microbiol. Rev. 57:50-108) contributed toward reaching the minimum score of three.

A list of ORFs in the Chlamydia trachomatis genome encoding putative lipoproteins is set forth above in the specification.

    
    


LPS-Related ORFs of Chlamydia trachomatis. Lipopolysaccharide (LPS) is an important major surface antigen of Chlamydia cells. Monoclonal antibodies (Mab) directed against LPS of Chlamydia pneumoniae have been identified that can neutralize the infectivity of Chlamydia pneumoniae both in vitro and in vivo (Peterson et al. 1988). Similar results are expected utilizing monoclonal antibodies against LPS of Chlamydia trachomatis. LPS is composed of lipid A and a core oligosaccharide portion and is phenotypically of the rough type (R-LPS) (Lukacova, M., Baumann, M., Brade, L., Mamat, U., Brade, H.1994. Lipopolysaccharide Smooth-Rough Phase Variation in Bacteria of the Genus Chlamydia. Infect. Immun. June 62(6):2270-2276.) The lipid A component is composed of fatty acids which serve to anchor LPS in the outer membrane. The core component contains sugars and sugar derivatives such as a trisaccharide of 3-deoxy-D-manno-octulosonic acid (KDO) (Reeves, P. R., Hobbs, M., Valvano, M. A., Skurnik, M., Whitfield, C., Coplin, D., Kido, N., Klena, J., Maskell, D., Raetz, C. R. H., Rick, P. D. 1996. Bacterial Polysaccharide Synthesis and Gene Nomenclature pp. 10071-10078, Elsevier Science Ltd.). The KDO gene product is a multifunctional glycosyltransferase and represents a shared epitope among the Chlamydia. For a review of LPS biosynthesis see, e.g., Schnaitman, C. A., Klena, J. D. 1993. Genetics of Lipopolysaccharide Biosynthesis in Enteric Bacteria. Microbiol. Rev. 57:655-682.
A text search of the ORF Blastp results identified several genes that are involved in Chlamydial LPS production with a P score less than e−10. The following key-terms were used in the text search: KDO, CPS (Capsular Polysaccharide Biosynthesis), capsule, LPS, rfa, rfb, rfc, rfe, rha, rhl, core, epimerase, isomerase, transferase, pyrophosphorylase, phosphatase, aldolase, heptose, manno, glucose, lpxB, fibronectin, fibrinogen, fucosyltransferase, lic, lgt, pgm, tolC, rol, ChoP, phosphorylcholine, waaF, PGL-Tb1. A list of ORFs in the Chlamydia trachomatis genome encoding putative polypeptides involved in LPS biosynthesis is set forth above in the specification.
Type III And Other Secreted Products. Type III secretion enables gram-negative bacteria to secrete and inject pathogenicity proteins into the cytosol of eukaryotic host cells (Hueck, C. J., 1998. Type III Protein Secretion Systems in Bacterial Pathogens of Animals and Plants. In Microbiology and Molecular Biology Reviews. 62:379-433.) These secreted factors often resemble eukaryotic signal transduction factors, thus enabling the bacterium to redirect host cell functions (Lee, C. A., 1997. Type III secretion systems: machines to deliver bacterial proteins into eukaryotic cells? Trends Microbiol. 5:148-156.) In an attempt to corrupt normal cellular functions, Chlamydial pathogenicity factors injected into the host cytosol will nonetheless, as cytoplasmic constituents be processed and presented in the context of the Major Histocompatibility Complex (MHC class I). As such, these pathogenicity proteins represent MHC class I antigens and will play an important role in cellular immunity. Also included in this set are secreted non-type III products that may play a role as vaccine components.
A text search of the ORF Blastp results identified genes that are involved in Chlamydia trachomatis protein secretion with a P score less than e−10. The following key-terms were used in the text search in an effort to identify surface localized or secreted products: Yop, Lcr, Ypk, Exo, Pcr, Pop, Ipa, Vir, Ssp, Spt, Esp, Tir, Hrp, Mxi, hemolysin, toxin, IgA protease, cytolysin, tox, hap, secreted and Mip.
Chlamydia trachomatis ORFs that did not meet the above keyword search criteria, but have homologs in Chlamydia pneumoniae that do meet the search criteria are included herein. The Chlamydia pneumoniae genome (French patent application No. 97-14673, filed 21 Nov. 1997) was analyzed using the above search criteria and a number of ORFs were identified. These Chlamydia pneumoniae ORFs were tested against the Chlamydia trachomatis genome using Blastp. Any Chlamydia pneumoniae ORF with a Blastp P value <e10 against a Chlamydia trachomatis homolog, identified using the above search criteria, was included. A list of ORFs in the Chlamydia trachomatis genome encoding putative secreted proteins is set forth above in the specification.
Chlamydia trachomatis RGD Recognition Sequence. Proteins that contain Arg-Gly-Asp (RGD) attachment site, together with integrins that serve as their receptor constitute a major recognition system for cell adhesion. The RGD sequence is the cell attachment site of a large number of adhesive extracellular matrix, blood, and cell surface proteins and nearly half of the known integrins recognize this sequence in their adhesion protein ligands. There are many RGD containing microbial proteins such as the penton protein of adenovirus, the coxsackie virus, the foot and mouth virus and pertactin, a 69 kDa (kilodalton) surface protein of Bordetella pertussis, that serve as ligands through which these microbes bind to integrins on the cell surfaces and gain entry into the cell. The following provides evidence supporting the importance of RGD in microbial adhesion:
a) The adenovirus penton base protein has a cell rounding activity and when penton base was expressed in E. coli, it caused cell rounding and cells adhered to polystyrene wells coated with the protein. Mutant analysis showed that both these properties required an RGD sequence. Virus mutants with amino acid substitutions in the RGD sequence, showed much less adherence to HeLa S3 cells, and also were delayed in virus reproduction (Bai, M., Harfe, B., and Freimuth, P. 1993. Mutations That Alter an RGD Sequence in the Adenovirus Type 2 Penton Base Protein Abolish Its Cell-Rounding Activity and Delay Virus Reproduction in Flat Cells. J. Virol. 67:5198-5205).
b) It has been shown that attachment and entry of coxsackie virus A9 to GMK cells were dependent on an RGD motif in the capsid protein VP1. VP1 has also been shown to bind αvβ3 integrin, which is a vitronectin receptor (Roivainen, M., Piirainen, L., Hovi, T., Virtanen, I., Riikonen, T., Heino, J., and Hyypia, T. 1994. Entry of Coxsackievirus A9 into Host Cells: Specific Interactions with αvβ3 Integrin, the Vitronectin Receptor Virology, 203:357-65).
c) During the course of whooping cough, Bordetella pertussis interacts with alveolar macrophages and other leukocytes on the respiratory epithelium. Whole bacteria adheres by means of two proteins, filamentous hemagglutinin (FHA) and pertussis toxin. FHA interacts with two classes of molecules on macrophages, galactose containing glycoconjugates and the integrin CR3. The interaction between CR3 and FHA involves recognition of RGD sequence at the positions 1097-1099 in FHA (Relman, D., Tuomanen, E., Falkow, S., Golenbock, D. T., Saukkonen, K., and Wright, S. D. “Recognition of a Bacterial Adhesin by an Integrin: Macrophage CR3 Binds Filamentous Hemagglutinin of Bordetella Pertussis.” Cell, 61:1375-1382 (1990)).
d) Pertactin, a 69 kDa outer membrane protein of Bordetella pertussis, has been shown to promote attachment of Chinese hamster ovary cells (CHO). This attachment is mediated by recognition of RGD sequence in pertactin by integrins on CHO cells and can be inhibited by synthetic RGD containing peptide homologous to the one present in pertactin (Leininger, E., Roberts, M., Kenimer, J. G., Charles, I. G., Fairweather, N., Novotny, P., and Brennan, M. J. 1991. Pertactin, an Arg-Gly-Asp containing Bordetella pertussis surface protein that promotes adherence of mammalian cells Proc. Natl. Acad. Sci. USA, 88:345-349).
e) The RGD sequence is highly conserved in the VP1 protein of foot and mouth disease virus (FMDV). Attachment of FMDV to baby hamster kidney cells (BHK) has been shown to be mediated by VP1 protein via the RGD sequence. Antibodies against the RGD sequence of VP1 blocked attachment of virus to BHK cells (Fox, G., Parry, N. R., Barnett, P. V., McGinn, B., Rowland, D. J., and Brown, F. 1989. The Cell Attachment Site on Foot-and-Mouth Disease Virus Includes the Amino Acid Sequence RGD (Arginine-Glycine-Aspartic Acid) J. Gen. Virol., 70:625-637).
It has been demonstrated that bacterial adherence can be based on interaction of a bacterial adhesin RGD sequence with an integrin and that bacterial adhesins can have multiple binding site characteristic of eukaryotic extracellular matrix proteins. RGD recognition is one of the important mechanisms used by microbes to gain entry into eukaryotic cells.
The complete deduced protein sequence of the Chlamydia trachomatis genome was searched for the presence of RGD sequence. There were a total of 38 ORFs that had one or more RGD sequences. Not all RGD containing proteins mediate cell attachment. It has been shown that RGD containing peptides that have proline immediately following the RGD sequence are inactive in cell attachment assays (Pierschbacher & Ruoslahti. 1987. Influence of stereochemistry of the sequence Arg-Gly-Asp-Xaa on binding specificity in cell adhesion. J. Biol. Chem. 262:17294-98). ORFs that had RGD, with proline as the amino acid following the RGD sequence were excluded from the list. Also, RGD sequence may not be available at the surface of the protein or may be present in a context that is not compatible with integrin binding. Since not all RGD-containing proteins are involved in cell attachment, several other criteria were used to refine the list of RGD-containing proteins. A list of ORFs in the Chlamydia trachomatis genome encoding polypeptides with RGD recognition sequence(s) is set forth above in the specification.
Non-Chlamydia pneumoniae ORFs. Chlamydia trachomatis ORFs were compared to the ORFs in the Chlamydia pneumoniae genome (French patent application No. 97-14673, filed 21 Nov. 1997) using Blastp. Any Chlamydia trachomatis ORF with a Blastp “P” value greater than e−10 (i.e. >e−10) against Chlamydia pneumoniae ORFs are included in this section. A list of ORFs in the Chlamydia trachomatis genome which are not found in Chlamydia pneumoniae is set forth above in the specification.
Cell Wall Anchor Surface ORFs. Many surface proteins are anchored to the cell wall of Gram-positive bacteria via the conserved LPXTG motif (Schneewind, O., Fowler, A., and Faull, K. F. 1995. Structure of the Cell Wall Anchor of Surface Proteins in Staphylococcus aureus. Science 268:103-106). A search of the proteins encoded by the Chlamydia trachomatis ORFs was done using the motif LPXTG. A list of ORFs in the Chlamydia trachomatis genome encoding polypeptides anchored to the cell wall is set forth above in the specification.
ECACC Deposits. Samples of Chlamydia trachomatis were deposited with the European Collection of Cell Cultures (ECACC), Salisbury, Wiltshire SP4 OJG, UK on Nov. 26, 1998 and assigned the accession number 98112618. Cells can be grown, harvested and purified, and DNA can be prepared as discussed above. In order to enable recovery of specific fragments of the chromosome, one can run targeted PCR reactions, whose amplification products can then be sequenced and/or cloned into any suitable vector, according to standard procedures known to those skilled in the art.
In addition, a pool of clones covering the Chlamydia trachomatis genome was deposited with the ECACC on Nov. 26, 1998 and assigned accession number 98112617. The pool of clones contains a series of clones, which when taken together, cover the whole chromosome, with a redundancy of slightly more than ten. The total number of clones in the sample is 13,572.
Table 4 lists groups of oligonucleotides to be used to amplify each of ORFs 2-1197 according to standard procedures known to those skilled in the art. Such oligonucleotides are listed as SEQ ID Nos. 1198 to 5981. For each ORF, the following is listed: one forward primer positioned 2,000 bp upstream of the beginning of the ORF; one forward primer positioned 200 bp upstream of the beginning of the ORF; one reverse primer positioned 2,000 bp downstream at the end of ORF, which is 2,000 bp upstream of the end site of the ORF on the complementary strand; and one reverse primer 200 bp downstream at the end of ORF, which is 200 bp upstream of the end site of the ORF on the complementary strand. The corresponding SEQ ID Nos. for the primers are listed in Table 4, where Fp is the proximal forward primer; Fd is the distal forward primer; Bp is the proximal reverse primer; and Bd is the distal reverse primer. The positions of the 5′ ends of each of these primers on the nucleotide sequence of SEQ ID No. 1 are shown in Table 5.
The present invention is not to be limited in scope by the specific embodiments described herein, which are intended as single illustrations of individual aspects of the invention, and functionally equivalent methods and components are within the scope of the invention. Indeed, various modifications of the invention, in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims.
All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.














TABLE 1





ORF
begin
stop
Homology
ID
Species
Score
I %






















ORF2
501
208
putative






ORF3
3276
505
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
379
37


ORF4
5068
3242
lipid A disaccharide synthetase (lpxB)
U32786
Haemophilus influenzae
285
40


ORF5
6400
5126
poly(A) polymerase
AE000123
Escherichia coli
552
46


ORF6
7977
6619
D-alanine permease (dagA)
U32770
Haemophilus influenzae
265
36


ORF7
8582
8082
signal peptidase II
X78084
Staphylococcus carnosus
174
36


ORF8
8995
8591
YteA
AF008220
Bacillus subtilis
157
43


ORF9
9440
8979
ORF 168
D28752
Synechococcus sp.
318
42


ORF10
9828
10430
unknown
Z80108
Mycobacterium tuberculosis
324
46


ORF11
10367
11254
hypothetical protein (SP: P39587)
U67605
Methanococcus jannaschii
152
38


ORF12
11245
11916
rRNA methylase
D90913
Synechocystis sp.
209
40


ORF13
12068
13324
hypothetical
U32691
Haemophilus influenzae
367
45


ORF14
13532
14413
neutral amino acid transporter B0.
U75284
Oryctolagus cuniculus
410
39


ORF15
14807
15019
dihydrolipoamide acetyltransferase
L38646
Saccharopolyspora erythraea
324
47


ORF16
14932
15969
branched chain alpha-keto
M97391
Bacillus subtilis
577
44





acid dehydrogenase E2






ORF17
15995
16501
ORF_o328
U18997
Escherichia coli
223
44


ORF18
16467
16138
putative






ORF19
18190
17417
putative outer membrane protein
U80956
Borrelia burgdorferi
86
36


ORF20
20521
18437
ORF-2
D11024
Shigella flexneri
642
37


ORF21
22202
20814
dnaK like protein (AA 1-660)
X52175
Chlamydia trachomatis
2214
99


ORF22
22602
22153
ORF, 82 kDa protein
L22180
Chlamydia trachomatis
558
89


ORF23
22804
22478
heat shock protein
M62819
Chlamydia trachomatis
503
99


ORF24
23183
22824
GrpE-like protein
L25105
Chlamydia trachomatis
580
98


ORF25
23394
23110
GrpE-like protein
L25105
Chlamydia trachomatis
373
87


ORF26
24569
23394
has homology to putative heat shock proteins 
L25105
Chlamydia trachomatis
1999
99





of Bacillus subtilis and Clostridium 









acetobutylicum; ORFA; putative






ORF27
26383
24641
aminoacyl-tRNA synthetase
L25105
Chlamydia trachomatis
3044
99


ORF28
26640
27710
ORFB; putative
L25105
Chlamydia trachomatis
1298
99


ORF29
28780
27725
putative






ORF30
29957
28740
hypothetical protein
D64004
Synechocystis sp.
786
46


ORF31
30721
30032
putative






ORF32
31281
30520
putative






ORF33
31436
31780
putative
L46591
Bartonella bacilliformis
126
45


ORF34
33356
31800
putative






ORF35
33901
33314
putative






ORF36
34116
35027
Yer156cp
U18917
Saccharomyces cerevisiae
175
32


ORF37
34988
35359
F21C3.3
Z71261
Caenorhabditis elegans
245
44


ORF38
35167
35919
putative






ORF39
35923
36996
putative






ORF40
37810
37013
putative






ORF41
38207
39085
DAPH synthase-chorismate mutase
AF008220
Bacillus subtilis
529
48


ORF42
39151
39927
arginine binding protein
X67753
Escherichia coli
192
44


ORF43
39923
40756
putative






ORF44
40760
42007
hypothetical protein MTCY154.05c
Z98209
Mycobacterium tuberculosis
663
43


ORF45
42175
43116
phosphoglucoisomerase-like protein
L40822
Chlamydia trachomatis
681
95


ORF46
42999
43802
phosphoglucoisomerase-like protein
L40822
Chlamydia trachomatis
959
91


ORF47
44211
45227
NADP-malate dehydrogenase
L40958
Flaveria bidentis
755
42


ORF48
46072
45275
putative






ORF49
46340
45975
putative






ORF50
46895
46506
putative






ORF51
47955
46882
membrane protein (arcD)
M33223
Pseudomonas aeruginosa
892
47


ORF52
48585
48178
putative






ORF53
50072
48630
putative






ORF54
50710
50099
putative






ORF55
52439
50925
dehydroquinate dehydratase/shikimate
L32794
Nicotiana tabacum
142
36





dehydrogenase






ORF56
53484
52348
3-dehydroquinate synthase
D90911
Synechocystis sp.
462
39


ORF57
54536
53466
chorismate synthase
X67516
Synechocystis sp.
801
56


ORF58
55086
54595
shikimate kinase II
M13045
Escherichia coli
154
38


ORF59
56350
55031
5-enolpyruvylshikimate 3-phosphate synthase
U67500
Methanococcus jannaschii
355
37


ORF60
55659
56084
putative






ORF61
56847
58235
putative






ORF62
58423
59181
dihydrodipicolinate reductase
U47017
Pseudomonas syringae pv.
350
40







tabaci




ORF63
59185
60195
aspartate-semialdehyde dehydrogenase
U67476
Methanococcus jannaschii
590
44


ORF64
60188
61483
aspartokinase III
U00006
Escherichia coli
312
41


ORF65
61496
62353
dihydrodipicolinate synthetase (dapA)
AE000609
Helicobacter pylori
345
42


ORF66
62500
63141
putative






ORF67
63396
63983
hypothetical protein
Y14084
Bacillus subtilis
148
42


ORF68
64628
64071
putative






ORF69
64285
64656
putative






ORF70
64944
64609
putative






ORF71
65347
67269
unknown
D26185
Bacillus subtilis
733
44


ORF72
67656
68873
putative






ORF73
68877
69233
KsgA
Z94752
Mycobacterium tuberculosis
156
38


ORF74
69212
69721
high level kasgamycin resistance
D26185
Bacillus subtilis
306
43


ORF75
69958
70455
polypeptide deformylase
Y10305
Calothrix PCC7601
272
43


ORF76
70701
71006
protein translocation protein, low 
U32727
Haemophilus influenzae
90
32





temperature (secG)






ORF77
73191
71086
putative






ORF78
74900
73497
putative






ORF79
75463
74876
homologous to unidentified E. coli protein
M96343
Bacillus subtilis
283
34


ORF80
77124
75502
o530; This 530 aa ORF is 33 pct identical 
AE000184
Escherichia coli
1447
42





(14 gaps) to 525 residues of an approx.









640 aa protein YHES_HAEIN SW: P44808






ORF81
77000
77299
putative






ORF82
78095
77145
integrase-recombinase protein (xerC)
U32750
Haemophilus influenzae
495
38


ORF83
79065
78154
hypothetical protein
D64001
Synechocystis sp.
400
40


ORF84
81971
79878
LON protease homolog
U88087
Arabidopsis thaliana
1927
48


ORF85
82639
83271
putative






ORF86
83792
84850
DnaJ
U58360
Salmonella typhimurium
822
42


ORF87
84876
86921
putative






ORF88
88650
87313
putative






ORF89
87440
87805
putative






ORF90
88400
88747
putative






ORF91
88717
89265
putative






ORF92
89355
89732
Hpr protein
X12832
Bacillus subtilis
128
32


ORF93
89735
91447
PTS enzyme I
U12340
Bacillus stearothermophilus
671
34


ORF94
91749
91435
ORF107
X17014
Bacillus subtilis
120
35


ORF95
92392
91745
putative






ORF96
93138
92344
dnaZX-like ORF put. DNA polymerase III
X06803
Bacillus subtilis
542
53


ORF97
94134
93361
excinuclease ABC subunit A (uvrA)
AE000583
Helicobacter pylori
326
36


ORF98
94637
94071
excinuclease ABC subunit A (uvrA)
AE000583
Helicobacter pylori
487
40


ORF99
98299
94628
UvrA
D49911
Thermus thermophilus
2090
44


ORF100
98715
98113
excinuclease ABC subunit A (uvrA)
AE000583
Helicobacter pylori
319
42


ORF101
100228
98741
pyruvate kinase
U83196
Chlamydia trachomatis
2411
97


ORF102
101347
100337
hypothetical protein
D90903
Synechocystis sp.
494
37


ORF103
102210
101323
YqiE
D84432
Bacillus subtilis
471
49


ORF104
102485
102210
putative






ORF105
104315
102726
exonuclease VII, large subunit (xseA)
U32723
Haemophilus influenzae
634
51


ORF106
105075
104254
triose phosphate isomerase
L29475
Bacillus subtilis
558
48


ORF107
105259
105894
phosphoribosylanthranilate isomerase
U18969
Arabidopsis thaliana
300
38


ORF108
107429
108460
putative






ORF109
108665
108955
putative






ORF110
109459
109013
putative






ORF111
110366
109704
putative






ORF112
111330
112520
elongation factor Tu
L22216
Chlamydia trachomatis
2007
100


ORF113
112915
113463
transcription antitermination protein (nusG)
U32754
Haemophilus influenzae
313
37


ORF114
113566
113994
ribosomal protein L11
D13303
Bacillus subtilis
443
59


ORF115
114020
114604
ribosomal protein L1
Z11839
Thermotoga maritima
528
54


ORF116
114720
115253
ribosomal protein L10
Z11839
Thermotoga maritima
143
38


ORF117
115362
115676
rpl12 (AA 1-128)
X53178
Synechocystis PCC6803
254
62


ORF118
116022
119795
DNA-directed RNA polymerase beta chain
X64172
Staphylococcus aureus
2675
61


ORF119
119823
124010
DNA-directed RNA polymerase
U32733
Haemophilus influenzae
3486
50





beta′ chain (rpoC)






ORF120
124065
124988
transaldolase
L19437
Homo sapiens
677
50


ORF121
124873
125106
transaldolase
U67611
Homo sapiens
121
44


ORF122
126261
125536
putative






ORF123
126328
126930
putative






ORF124
127138
127785
putative






ORF125
127924
129714
A1 isoform of vacuolar H+-ATPase subunit A
U22077
Gallus gallus
1062
45


ORF126
129720
131033
membrane ATPase
X79516
Haloferax volcanii
790
48


ORF127
131018
131629
putative






ORF128
131834
133156
Na+-ATPase subunit I
D17462
Enterococcus hirae
188
34


ORF129
133075
133584
v-type Na-ATPase
X76913
Enterococcus hirae
110
38


ORF130
133625
133999
v-type Na-ATPase
X76913
Enterococcus hirae
89
32


ORF131
133861
134508
putative






ORF132
134638
137454
valyl-tRNA synthetase
D64006
Synechocystis sp.
1763
51


ORF133
137442
140276
PknD
Z95209
Mycobacterium tuberculosis
452
44


ORF134
140733
140335
putative






ORF135
141799
141077
porphobilinogen deaminase
U22968
Yersinia pestis
282
38


ORF136
143240
141780
unknown
D26185
Bacillus subtilis
1113
53


ORF137
143829
143128
ORF3
D64116
Bacillus subtilis
356
39


ORF138
143923
144393
putative






ORF139
144548
146326
unknown
Z47210
Streptococcus pneumoniae
741
44


ORF140
146413
147078
manganese superoxide dismutase precursor
D12984
Caenorhabditis elegans
625
56


ORF141
147140
148075
acetyl-CoA carboxylase beta subunit (accD)
AE000604
Helicobacter pylori
704
52


ORF142
148115
148549
Dut
Z96072
Mycobacterium tuberculosis
277
53


ORF143
148524
149027
enzyme IIANtr
U18997
Escherichia coli
168
44


ORF144
149000
149305
putative






ORF145
149187
149708
enzyme IIANtr
U18997
Escherichia coli
169
43


ORF146
149712
150911
putative






ORF147
152044
151004
putative






ORF148
152664
151999
putative






ORF149
152900
153352
hypothetical
U32702
Haemophilus influenzae
292
47


ORF150
153389
153997
hypothetical protein in purB 5′ region
AE000213
Escherichia coli
555
49


ORF151
155276
153984
ClpC adenosine triphosphatase
U02604
Bacillus subtilis
986
45


ORF152
156544
155231
ClpC adenosine triphosphatase
U02604
Bacillus subtilis
1535
53


ORF153
156806
157525
putative






ORF154
157489
158955
Unknown
Y08559
Bacillus subtilis
99
39


ORF155
159104
159961
putative






ORF156
159916
161220
putative






ORF157
161183
161593
glycine cleavage protein homolog
U12980
Saccharomyces cerevisiae
175
35


ORF158
162354
161623
unidentified protein of Na+-
D49364
Vibrio alginolyticus
524
51





translocating NADH-quinone reductase






ORF159
163013
162363
NADH: ubiquinone oxidoreductase
Z37111
Vibrio alginolyticus
543
55


ORF160
163941
162994
NADH:ubiquinone oxidoreductase
U32702
Haemophilus influenzae
287
54





(GP: Z37111_4)






ORF161
165505
164474
NADH:ubiquinone oxidoreductase
Z37111
Vibrio alginolyticus
449
45





subunit B






ORF162
166686
166093
H. pylori predicted coding region HP1542
AE000652
Helicobacter pylori
111
33


ORF163
168171
166729
pot. ORF 446 (aa 1-446)
X02369
Bacillus subtilis
722
42


ORF164
169249
168848
putative






ORF165
169586
170431
hypothetical protein
D90906
Synechocystis sp.
462
48


ORF166
170780
171334
putative






ORF167
171333
172376
penicillin-binding protein 2
M26645
Neisseria flavescens
210
47


ORF168
172309
172722
penicillin-binding protein 2
M26645
Neisseria flavescens
176
44


ORF169
173048
174496
murE gene product
Z15056
Bacillus subtilis
789
43


ORF170
174399
174968
N-acetylmuramoyl-L-alanine amidase (amiA)
AE000589
Helicobacter pylori
177
41


ORF171
175267
175710
integration host factor beta subunit
L35259
Pseudomonas aeruginosa
110
38


ORF172
175714
177009
putative






ORF173
177423
178115
carboxyltransferase alpha subunit
U59236
Synechococcus PCC7942
558
50


ORF174
178084
180021
ATP dependent translocator homolog (msbA)
U32691
Haemophilus influenzae
453
41


ORF175
180704
180048
putative






ORF176
181398
180631
H. pylori predicted coding region HP0152
AE000536
Helicobacter pylori
256
34


ORF177
182594
181398
contains similarity to DNA polymerase III, 
AF007270
Arabidopsis thaliana
173
50





alpha chain (SP: P47277)






ORF178
182895
183656
putative Ptc1 protein
Y13937
Bacillus subtilis
371
53


ORF179
183665
184786
NifS2
AF008220
Bacillus subtilis
452
43


ORF180
186007
184796
similar to [SwissProt 
D90888
Escherichia coli
93
30





Accession Number P37908]






ORF181
186848
186000
hypothetical
U32728
Haemophilus influenzae
154
35


ORF182
187270
186749
putative






ORF183
187426
187809
regulatory protein for beta-lactamase
D90902
Synechocystis sp.
96
36


ORF184
189481
188798
putative






ORF185
189693
190352
prolipoprotein diacylglyceryl transferase
AJ000977
Rhodobacter sphaeroides
99
38


ORF186
190235
190510
putative






ORF187
190785
191786
putative






ORF188
191790
192464
putative






ORF189
192392
193183
60 kDa inner-membrane protein
AE000645
Helicobacter pylori
373
40


ORF190
193254
194630
DnaA
D89066
Staphylococcus aureus
545
43


ORF191
195046
194690
putative






ORF192
195184
197031
glycogen phosphorylase B
U47025
Homo sapiens
1758
56


ORF193
197018
197635
glycogen phosphorylase (AA 1-790)
X16931
Escherichia coli
580
53


ORF194
197762
198208
unknown
X86470
Saccharomyces cerevisiae
148
42


ORF195
198963
197668
F23B12.5
Z77659
Caenorhabditis elegans
795
50


ORF196
199957
198962
pyruvate dehydrogenase E1 beta subunit
U09137
Arabidopsis thaliana
856
48


ORF197
200327
199941
pyruvate dehydrogenase E1
U38804
Porphyra purpurea
170
31





component, alpha subunit






ORF198
200685
200266
pyruvate dehydrogenase
U81808
Thiobacillus
302
60





complex E1 alpha subunit

ferrooxidans




ORF199
200962
200585
TPP-dependent acetoin
L31844
Clostridium magnum
127
43





dehydrogenase alpha-subunit






ORF200
201169
202377
putative






ORF201
203441
202380
UDP-3-O-[3-hydroxymyristoyl]glucosamine
U70214
Escherichia coli
577
38





N-acyltransferase






ORF202
203998
203471
putative






ORF203
206449
204059
OMP1 precursor
U51683
Brucella abortus
83
31


ORF204
207425
206811
recombination protein
D90916
Synechocystis sp.
334
40


ORF205
207506
208528
beta-ketoacyl-acyl carrier protein synthase III
M77744
Escherichia coli
706
50


ORF206
208545
209471
malonyl-CoA:Acyl carrier protein transacylase
U59433
Bacillus subtilis
522
48


ORF207
209471
210214
3-ketoacyl-acyl carrier protein reductase
U59433
Bacillus subtilis
616
51


ORF208
210586
210816
acyl carrier protein (acpP)
U32701
Haemophilus influenzae
220
57


ORF209
211332
210883
protein kinase type II
J02934
Rattus norvegicus
150
31





regulatory subunit (, EC 2.7.1.37)






ORF210
212978
211374
putative






ORF211
214134
212875
unknown
AF017105
Chlamydia psittaci
852
63


ORF212
214710
214168
inclusion membrane protein C
AF017105
Chlamydia psittaci
231
43


ORF213
215143
214754
inclusion membrane protein B
AF017105
Chlamydia psittaci
181
47


ORF214
216705
215236
sodium-dependent transporter
AF017105
Chlamydia psittaci
1341
70


ORF215
217917
216892
amino acid transporter
AF017105
Chlamydia psittaci
1027
60


ORF216
217088
217441
putative






ORF217
218364
218702
putative






ORF218
218695
219009
putative






ORF219
219179
219748
putative






ORF220
219891
220430
putative






ORF221
220499
221074
putative






ORF222
221137
221541
putative






ORF223
221601
222092
putative






ORF224
222472
223290
putative






ORF225
223423
223818
LAGLI-DADG endonuclease
U57090
Chlamydia trachomatis
619
99


ORF226
224278
225171
YqfU
D84432
Bacillus subtilis
530
46


ORF227
225749
225174
phenylacrylic acid decarboxylase
U67467
Methanococcus jannaschii
334
52


ORF228
225334
225549
Ydr537cp
U43834
Saccharomyces cerevisiae
96
42


ORF229
226654
225749
4-hydroxybenzoate octaprenyltransferase
U61168
Bacillus firmus
321
36


ORF230
227299
226769
putative






ORF231
227646
227161
stationary-phase survival protein (surE)
AE000602
Helicobacter pylori
274
48


ORF232
228457
227750
f311; This 311 aa ORF is 22 pct identical 
AE000232
Escherichia coli
246
36





(13 gaps) to 186 residues of an approx.









488 aa protein YACA_BACSU









SW: P37563; pyu1 of D21139






ORF233
230001
228607
GadC
AF005098
Lactococcus lactis
740
35


ORF234
231074
230151
f374; This 374 aa ORF is 30 pct identical 
AE000299
Escherichia coli
985
65





(9 gaps) to 102 residues of an approx.









512 aa protein FLIC_SALMU SW: P06177






ORF235
231348
233006
putative






ORF236
233059
233829
orf2
D88555
Methanobacterium
351
52







thermoautotrophicum




ORF237
233801
234265
hypothetical protein
D90906
Synechocystis sp.
151
37


ORF238
234282
234854
ORF_o211
U28377
Escherichia coli
105
54


ORF239
236300
235227
glutamate 1-semialdehyde 2,1aminomutase
X82072
Pseudomonas aeruginosa
650
52


ORF240
236314
238209
leucine tRNA synthetase
AF008220
Bacillus subtilis
1836
61


ORF241
238164
238769
leucine tRNA synthetase
AF008220
Bacillus subtilis
410
46


ORF242
238769
240061
3-deoxy-D-manno-2-octulosonic 
Z22659
Chlamydia trachomatis
2240
100





acid (Kdo) transferase






ORF243
242022
240313
pyrophosphate-dependent
Z32850
Ricinus communis
1021
43





phosphofructokinase beta subunit






ORF244
242846
241941
putative






ORF245
244480
242798
pyrophosphate-dependent
Z32850
Ricinus communis
1017
42





phosphofructokinase beta subunit






ORF246
245897
244479
YflS
D86417
Bacillus subtilis
951
42


ORF247
246877
245924
putative






ORF248
247731
246985
ATP binding protein
L18760
Lactococcus lactis
442
47


ORF249
248585
247743
sporulation protein
M57689
Bacillus subtilis
532
38


ORF250
249420
248569
sporulation protein
M57689
Bacillus subtilis
601
38


ORF251
250383
249766
sporulation protein
M57689
Bacillus subtilis
464
47


ORF252
251186
250545
oligopeptide permease homolog AII
AF000366
Borrelia burgdorferi
119
31


ORF253
252111
251095
sporulation protein
M57689
Bacillus subtilis
317
36


ORF254
253088
252066
P. haemolytica o-sialoglycoprotein
D88802
Bacillus subtilis
601
46





endopeptidase; P36175 (660) transmembrane






ORF255
255153
256718
Mg2+ transporter
D90905
Synechocystis sp.
103
35


ORF256
256762
257844
tRNA guanine transglycosylase
L33777
Zymomonas mobilis
482
44


ORF257
257911
258690
putative






ORF258
258780
259187
putative






ORF259
259193
261604
subunit B of DNA gyrase
Y07916
Salmonella typhimurium
1925
58


ORF260
261622
264129
DNA gyrase
L47978
Aeromonas salmonicida
1963
45


ORF261
264125
264742
unknown
D26185
Bacillus subtilis
307
37


ORF262
264741
265628
replication protein (dnaX)
U32802
Haemophilus influenzae
162
35


ORF263
266416
265631
putative isozyme of glucose-6-P-
U14553
Anabaena sp.
218
47





dehydrogenase; developmentally regulated









gene in heterocyst development






ORF264
266938
266426
glucose 6-phosphate dehydrogenase
U83195
Chlamydia trachomatis
914
99


ORF265
267961
266942
glucose 6-phosphate dehydrogenase
U83195
Chlamydia trachomatis
1770
99


ORF266
268320
268066
ORF3
U15192
Chlamydia trachomatis
403
100


ORF267
268510
268205
ORF3
U15192
Chlamydia trachomatis
320
91


ORF268
270116
268500
CTP synthetase
U15192
Chlamydia trachomatis
2828
100


ORF269
270892
270095
CMP-2-keto-3-deoxyoctulosonic acid
U15192
Chlamydia trachomatis
1313
100





synthetase






ORF270
271191
271613
putative






ORF271
272219
272932
nitrate transporter
X61625
Synechococcus sp.
300
34


ORF272
272884
273588
putative






ORF273
274816
273596
putative






ORF274
274821
275666
putative






ORF275
277689
276103
ORF_f535
U28377
Escherichia coli
396
38


ORF276
278268
278816
putative






ORF277
279771
279013
tryptophan synthase alpha subunit
M15826
Pseudomonas aeruginosa
357
37


ORF278
280777
279767
tryptophan synthetase
M91661
Coprinus cinereus
1042
62


ORF279
281603
281295
tryptophan repressor
L26582
Enterobacter aerogenes
151
35


ORF280
282104
281787
putative






ORF281
284335
282794
putative






ORF282
284460
284795
putative






ORF283
284817
285674
putative






ORF284
285637
286137
putative






ORF285
286357
286677
putative






ORF286
286681
287898
hypothetical protein
U88070
Chlamydia psittaci
99
35


ORF287
288127
289227
comE ORF1
D64002
Synechocystis sp.
90
46


ORF288
289744
290679
hypothetical protein
U88070
Chlamydia psittaci
246
36


ORF289
290828
291535
putative






ORF290
291514
292230
endonuclease
U09868
Escherichia coli
160
37


ORF291
292326
293048
putative






ORF292
293330
294853
putative






ORF293
295684
295010
glutamine transport ATP-binding protein Q
U67524
Methanococcus jannaschii
407
38


ORF294
296336
295692
H. influenzae predicted coding region HI1555
U32830
Haemophilus influenzae
134
37


ORF295
297238
296243
putative






ORF296
297791
298735
putative






ORF297
298905
300458
similar to putative oxygenase of S. fradiae
U73857
Escherichia coli
82
40


ORF298
302152
300527
putative






ORF299
304917
302071
putative






ORF300
306157
304973
DNA ligase
M74792
Thermus aquaticus
745
41







thermophilus




ORF301
306494
306111
DNA LIGASE (EC 6.5.1.2)
D90870
Escherichia coli
197
40





(POLYDEOXYRIBONUCLEOTIDE









SYNTHASE (NAD+)).






ORF302
306963
306436
Mycoplasma pneumoniae, DNA ligase; 
AE000047
Mycoplasma pneumoniae
292
37





similar to Swiss-Prot Accession Number









P15042, from E. coli






ORF303
308773
306977
unknown
Z84395
Mycobacterium tuberculosis
316
52


ORF304
309881
309276
putative






ORF305
310720
309872
putative






ORF306
311570
310716
putative






ORF307
312451
311972
Preprotein translocase SecA subunit.
D90832
Escherichia coli
123
86


ORF308
313435
314364
sporulation protein
M57689
Bacillus subtilis
202
37


ORF309
314340
314738
putative






ORF310
315526
314741
orfX gene product
X58778
Klebsiella pneumoniae
169
45


ORF311
316507
315665
Similar to Saccharomyces cerevisiae 
Z38002
Bacillus subtilis
147
41





SUA5 protein






ORF312
317284
316529
serine esterase [Spirulina platensis, 
S70419
Spirulina platensis
167
58





C1, Peptide, 207 aa]






ORF313
317592
317338
putative






ORF314
318470
317499
putative






ORF315
317599
317874
putative






ORF316
318947
318477
putative






ORF317
319342
320142
ORF2
L35036
Chlamydia psittaci
802
60


ORF318
320544
321497
putative






ORF319
321485
321937
putative






ORF320
321901
322362
putative






ORF321
322301
323140
putative






ORF322
323144
324913
putative






ORF323
325621
324977
YqiZ
D84432
Bacillus subtilis
430
43


ORF324
326268
325621
integral membrane protein homolog
U97348
Lactobacillus fermentum
343
44


ORF325
326469
327203
adenylate kinase
AB000111
Synechococcus sp.
371
46


ORF326
327281
328150
putative






ORF327
328605
328204
RpsI
Z95389
Mycobacterium tuberculosis
315
55


ORF328
329066
328734
50S ribosomal subunit protein L13
U18997
Escherichia coli
269
60


ORF329
329663
329292
YqhX
D84432
Bacillus subtilis
297
56


ORF330
330666
329608
biotin carboxylase
L14862
Anabaena sp.
1089
58


ORF331
331161
330670
YqhW
D84432
Bacillus subtilis
208
52


ORF332
331731
331177
elongation factor P
D64001
Synechocystis sp.
297
33


ORF333
332404
331721
putative CfxE protein
Y13937
Bacillus subtilis
483
55


ORF334
332779
333021
putative






ORF335
333005
333589
putative






ORF336
334357
333806
putative






ORF337
334089
334361
putative






ORF338
335142
334729
putative






ORF339
335195
335602
putative






ORF340
335673
335194
putative






ORF341
336334
335903
putative






ORF342
337378
336338
putative






ORF343
339947
337347
ATP-dependent protease binding subunit
M29364
Escherichia coli
2005
53


ORF344
340507
341847
Pz-peptidase
D88209
Bacillus licheniformis
508
39


ORF345
341783
342022
group B oligopeptidase PepB
U49821
Streptococcus agalactiae
140
48


ORF346
342249
342470
hypA protein
M31739
Chlamydia trachomatis
361
99


ORF347
342597
343370
heat shock protein
L12004
Chlamydia trachomatis
1271
99


ORF348
343361
344032
hypB protein
M31739
Chlamydia trachomatis
1051
100


ORF349
343956
344225
hypB protein
M31739
Chlamydia trachomatis
344
100


ORF350
344357
345142
orf 3′of chaperonin homolog
S40172
Chlamydia psittaci
344
63





hypB [Chlamydia psittaci, pigeon strain 









P-1041, Peptide Partial, 98 aa]






ORF351
345934
345161
o247; This 247 aa ORF is 51 pct identical 
AE000174
Escherichia coli
387
41





(0 gaps) to 117 residues of an approx.









160 aa protein YPH7_CHRVI SW: P45371






ORF352
347102
346080
mutY homolog
U63329
Homo sapiens
492
46


ORF353
347113
347940
hypothetical 36.0 kD protein in rne-rpmF 
AE000209
Escherichia coli
397
44





intergenic region






ORF354
350164
348146
putative






ORF355
350423
351283
enoyl-acyl carrier protein reductase 
S60064
Brassica napus
909
64





[Brassica napus, Peptide, 385 aa]






ORF356
352207
351314
hypothetical protein
D90914
Synechocystis sp.
113
42


ORF357
352727
352245
putative






ORF358
353709
353305
FUNCTION UNKNOWN, SIMILAR
AB001488
Bacillus subtilis
213
40





PRODUCT IN E. COLI AND









MYCOPLASMA PNEUMONIAE.






ORF359
354218
353670
NADPH thioredoxin reductase
Z23108
Arabidopsis thaliana
577
60


ORF360
354721
354140
Thioredoxin Reductase (NADPH)
D45049
Neurospora crassa
417
60


ORF361
354966
356672
30S ribosomal protein S1
D90729
Escherichia coli
1305
44


ORF362
356700
357377
NusA
U74759
Chlamydia trachomatis
948
100


ORF363
357326
358093
NusA
U74759
Chlamydia trachomatis
1216
100


ORF364
358035
360743

U74759
Chlamydia trachomatis
3311
98


ORF365
360753
361121
ORF6 gene product
Z18631
Bacillus subtilis
116
32


ORF366
361162
361884
tRNA pseudouridine 55 synthase
D90917
Synechocystis sp.
362
42


ORF367
361826
362746
protein X
M35367
Pseudomonas fluorescens
192
49


ORF368
363859
362816
hypothetical GTP-binding
AE000219
Escherichia coli
978
52





protein in pth 3′ region






ORF369
364116
365195
cds1 gene product
U88070
Chlamydia psittaci
1631
88


ORF370
365198
365587
cds2 gene product
U88070
Chlamydia psittaci
516
93


ORF371
365479
367320
cds2 gene product
U88070
Chlamydia psittaci
2817
87


ORF372
367341
368603
copN gene product
U88070
Chlamydia psittaci
585
37


ORF373
368644
369081
scc1 gene product
U88070
Chlamydia psittaci
528
67


ORF374
369088
370251
No definition line found
U88070
Chlamydia psittaci
1362
62


ORF375
370769
371086
ribosomal protein L28 (rpL28)
U32776
Haemophilus influenzae
182
46


ORF376
371203
372816
hypothetical protein
U88070
Chlamydia psittaci
1926
68


ORF377
373119
373529
hypothetical protein
U88070
Chlamydia psittaci
286
49


ORF378
373614
374204
hypothetical protein
U88070
Chlamydia psittaci
379
48


ORF379
374736
374224
putative






ORF380
376391
374703
putative






ORF381
377062
376748
corresponds to a 97 amino 
L40838
Chlamydia trachomatis
490
98





acid long polypeptide






ORF382
377853
378737
methylenetetrahydrofolate dehydrogenase
D64000
Synechocystis sp.
678
51


ORF383
378626
379048
putative






ORF384
379017
379403
hypothetical
U32702
Haemophilus influenzae
137
45


ORF385
380009
379641
small protein
D90914
Synechocystis sp.
216
51


ORF386
380187
381470
DNA polymerase III beta-subunit (dnaN)
U32780
Haemophilus influenzae
76
39


ORF387
381473
382567
recombination protein
D26185
Bacillus subtilis
477
35


ORF388
382704
383702
putative






ORF389
383945
383655
hypothetical
U70214
Escherichia coli
134
35


ORF390
385217
383949
putative






ORF391
385507
385178
conserved hypothetical
AE000606
Helicobacter pylori
185
45





secreted protein






ORF392
386845
385706
hypothetical protein
D64000
Synechocystis sp.
686
41


ORF393
386127
386627
putative






ORF394
387372
386872
ORF1; putative
M26130
Streptococcus parasanguis
150
35


ORF395
387823
387338
ytgD
AF008220
Bacillus subtilis
168
42


ORF396
388250
387816
TroR
U55214
Treponema pallidum
134
40


ORF397
389169
388237
putative protein of 299 amino acids
U30821
Cyanophora paradoxa
164
31


ORF398
389955
389173
TroB
U55214
Treponema pallidum
592
51


ORF399
390988
389945
YtgA
AF008220
Bacillus subtilis
282
30


ORF400
391514
391810
putative






ORF401
392410
393996
adenine nucleotide translocase
Z49227
Arabidopsis thaliana
1295
56


ORF402
394170
395354
lepA gene product
X91655
Bacillus subtilis
1235
60


ORF403
395309
395992
GTP-binding membrane protein (lepA)
AE000552
Helicobacter pylori
543
54


ORF404
396538
396059
phosphogluconate dehydrogenase
U30255
Homo sapiens
411
55


ORF405
397507
396542
6-phosphogluconate dehydrogenase
AB006102
Candida albicans
908
51


ORF406
398753
397401
tyrosyl-tRNA synthetase
M13148
Bacillus caldotenax
844
45


ORF407
399688
398909
whiG-Stv gene product
X68709
Streptoverticillium
463
41







griseocarneum




ORF408
400167
399778
FLHA gene product
X63698
Bacillus subtilis
134
35


ORF409
401224
400034
flbF
M73782
Caulobacter crescentus
355
39


ORF410
401776
402021
ferredoxin IV
M59855
Rhodobacter capsulatus
98
54


ORF411
402126
403220
putative






ORF412
403348
405180
GcpE
D90908
Synechocystis sp.
995
49


ORF413
403788
403276
putative






ORF414
405165
405920
YfiH
U50134
Escherichia coli
166
43


ORF415
407049
405955
dihydrolipoamide transsuccinylase 
M27141
Bacillus subtilis
833
61





(odhB; EC 2.3.1.61)






ORF416
409773
407056
alpha-ketoglutarate dehydrogenase
U41762
Rhodobacter capsulatus
1537
50


ORF417
410532
411416
YqeR
D84432
Bacillus subtilis
496
44


ORF418
411707
413410
putative






ORF419
413433
412606
putative






ORF420
413404
413952
putative






ORF421
413841
415112
putative






ORF422
414379
413978
putative






ORF423
416664
415177
putative






ORF424
417456
416740
unknown
Z94752
Mycobacterium tuberculosis
172
36


ORF425
418053
417721
putative






ORF426
418603
418031
putative






ORF427
419531
418647
Hc2 nucleoprotein
L10193
Chlamydia trachomatis
1661
92


ORF428
420190
419672
[karp] gene products
M86605
Chlamydia trachomatis
612
96


ORF429
421171
420245
aminopeptidase
D17450
Mycoplasma salivarium
269
41


ORF430
421988
421518
putative
L39923
Mycobacterium leprae
165
36


ORF431
422486
423043
putative






ORF432
423226
425079
glycogen operon protein GlgX
D90908
Synechocystis sp.
1229
55


ORF433
426054
425146
putative






ORF434
426985
426245
Holliday junction specific DNA helicase
D83138
Pseudomonas aeruginosa
633
53


ORF435
427248
427817
deoxycytidine triphosphate deaminase (dcd)
AE000554
Helicobacter pylori
612
63


ORF436
429560
429886
putative






ORF437
430360
429857
biotin apo-protein ligase
U27182
Saccharomyces cerevisiae
173
38


ORF438
430637
430323
putative






ORF439
430933
431787
putative






ORF440
431658
431987
putative






ORF441
432232
434475
exonuclease V alpha-subunit
U29581
Escherichia coli
289
53


ORF442
436308
434620
methionyl-tRNA synthetase
AB004537
Schizosaccharomyces pombe
817
54


ORF443
436574
436272
putative






ORF444
437685
436567
RNAseH II
AF005098
Lactococcus lactis
395
47


ORF445
438262
437894
ribosomal protein L19
X72627
Synechocystis sp.
287
47


ORF446
439127
438285
tRNA (guanine-N1)-methyltransferase (trmD)
U32705
Haemophilus influenzae
374
56


ORF447
439339
438986
tRNA (guanine-N1)-methyltransferase (trmD)
U32705
Haemophilus influenzae
199
57


ORF448
439705
439358
ribosomal protein S16 (rpS16)
U32705
Haemophilus influenzae
168
39


ORF449
441042
439699
signal recognition particle protein
AE000347
Escherichia coli
865
40


ORF450
441911
441042
product similar to E. coli PRFA2 protein
Z49782
Bacillus subtilis
314
37


ORF451
442593
441898
polypeptide chain release factor 1 (prfA)
U32830
Haemophilus influenzae
708
62


ORF452
444505
446388
leader peptidase I
D90904
Synechocystis sp.
268
44


ORF453
448068
446452
isoleucyl-tRNA synthetase
U04953
Homo sapiens
704
49


ORF454
449575
447932
isoleucyl-tRNA synthetase
U04953
Homo sapiens
1687
55


ORF455
450546
451076
putative






ORF456
451623
451144
putative






ORF457
452593
451517
putative






ORF458
453195
452632
putative






ORF459
453567
454868
product similar to E. coli PhoH protein
Z97025
Bacillus subtilis
820
50


ORF460
455430
454972
CydB
Z95554
Mycobacterium tuberculosis
105
31


ORF461
456047
455367
cyanide insensitive terminal oxidase
Y10528
Pseudomonas aeruginosa
388
38


ORF462
457384
456047
cyanide insensitive terminal oxidase
Y10528
Pseudomonas aeruginosa
537
52


ORF463
457659
458450
YbbP
AB002150
Bacillus subtilis
324
42


ORF464
458508
459632
putative






ORF465
459839
461203
HtrB protein
X61000
Escherichia coli
77
31


ORF466
461624
461196
unknown
U87792
Bacillus subtilis
114
38


ORF467
461887
462621
hypothetical protein
Z75208
Bacillus subtilis
148
51


ORF468
463758
462895
putative






ORF469
464048
464629
putative






ORF470
464721
465848
putative






ORF471
467420
466113
PET112
D90913
Synechocystis sp.
892
48


ORF472
468891
467419
amidase
U49269
Moraxella catarrhalis
1051
46


ORF473
469280
468906
putative






ORF474
469349
469675
putative






ORF475
471226
469826
putative






ORF476
471624
471106
putative






ORF477
471954
473267
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
173
33


ORF478
473252
473695
POMP90A precursor
U65942
Chlamydia psittaci
175
39


ORF479
473982
474527
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
193
38


ORF480
475198
474602
putative






ORF481
476527
475613
POMP91A
U65942
Chlamydia psittaci
100
38


ORF482
478640
476517
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
537
40


ORF483
479084
478665
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
234
35


ORF484
479723
479088
putative outer membrane protein
U72499
Chlamydia psittaci
313
40


ORF485
480012
479668
putative






ORF486
481466
479895
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
391
38


ORF487
481732
481496
putative






ORF488
481864
483429
POMP90A precursor
U65942
Chlamydia psittaci
114
40


ORF489
483402
484964
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
77
34


ORF490
484898
487864
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
506
39


ORF491
485725
485222
putative






ORF492
488204
489247
putative






ORF493
488571
488233
putative






ORF494
489440
490456
putative






ORF495
492765
490507
branching enzyme
M31544
Synechococcus PCC6301
1624
57


ORF496
492357
492893
putative






ORF497
493744
492737
putative






ORF498
493875
494675
YqkM
D84432
Bacillus subtilis
230
44


ORF499
494573
494869
xprB
M54884
Escherichia coli
245
48


ORF500
494835
495365
putative






ORF501
495174
494872
putative






ORF502
495687
496634
putative






ORF503
496295
497176
putative






ORF504
497703
498515
putative






ORF505
498280
499239
putative






ORF506
499215
500732
putative






ORF507
501710
500790
penicillin tolerance protein (lytB)
U32781
Haemophilus influenzae
702
50


ORF508
502863
501808
putative






ORF509
503675
502692
putative






ORF510
505002
503722
hypothetical protein
Z96072
Mycobacterium tuberculosis
102
42


ORF511
505739
506986
hypothetical protein in pth-prs intergenic 
AE000219
Escherichia coli
740
44





region






ORF512
506999
507439
putative






ORF513
508404
507649
fumarate hydratase
AF013216
Myxococcus xanthus
611
54


ORF514
508291
508590
putative






ORF515
508915
508478
fumarase
D64000
Synechocystis sp.
386
57


ORF516
509600
510691
thiamine-repressed protein (nmt1)
U32720
Haemophilus influenzae
82
31


ORF517
511039
511527
putative






ORF518
511547
512185
hypothetical protein (SP: P46851)
U67608
Methanococcus jannaschii
208
39


ORF519
512382
513092
methionine amino peptidase
M15106
Escherichia coli
384
46


ORF520
514287
513055
putative






ORF521
514789
515244
putative






ORF522
514994
515269
putative






ORF523
515553
515804
putative






ORF524
515808
516422
putative






ORF525
516476
517171
putative






ORF526
517927
517400
orf150 gene product
X95938
Porphyromonas gingivalis
340
51


ORF527
518096
518380
30S ribosomal protein S15
D90901
Synechocystis sp.
245
52


ORF528
518403
518822
polynucleotide phosphorylase
AF010578
Pisum sativum
306
49


ORF529
518923
519516
polyribonucleotide phophorylase
U52048
Spinacia oleracea
387
47


ORF530
519577
520497
polynucleotide phosphorylase
U18997
Escherichia coli
860
54


ORF531
521986
520718
ATP-binding protein
U01376
Escherichia coli
970
49


ORF532
522131
521886
cell division protein (ftsH)
U32812
Haemophilus influenzae
314
76


ORF533
523495
522143
putative






ORF534
524591
523623
ORF327 gene product
U38804
Porphyra purpurea
148
44


ORF535
524652
525746
putative






ORF536
525731
526078
putative






ORF537
525939
526400
putative






ORF538
526301
526735
putative






ORF539
528323
526851
putative






ORF540
528861
528292
putative






ORF541
529723
529142
phenylalanyl-tRNA synthetase alpha subunit
X53057
Bacillus subtilis
476
52


ORF542
530166
529624
phenylalany-tRNA synthetase beta subunit
Z75208
Bacillus subtilis
164
40


ORF543
530543
530223
ribosomal protein L20 (AA 1-119)
X16188
Bacillus stearothermophilus
230
47


ORF544
531378
530737
unknown
Z85982
Mycobacterium tuberculosis
452
50


ORF545
532370
533272
UDP-N-acetylenolpyruvylglucosamine
U86147
Synechococcus PCC7942
488
43





reductase






ORF546
533849
533244
YtqB
AF008220
Bacillus subtilis
273
38


ORF547
534672
533944
hypothetical protein MTCY08D5.03c
Z92669
Mycobacterium tuberculosis
170
35


ORF548
535915
534878
ribonucleoside diphosphate reductase, 
AE000553
Helicobacter pylori
397
33





beta subunit (nrdB)






ORF549
539153
535956
ribonucleoside-diphosphate reductase 
AE000581
Helicobacter pylori
1447
51





1 alpha subunit (nrdA)






ORF550
539731
540519
phosphatidylserine synthase (pssA)
AE000614
Helicobacter pylori
226
49


ORF551
540523
540969
putative






ORF552
540906
541805
hypothetical 54.7 kD protein in udp 3′ region 
AE000459
Escherichia coli
82
39





precursor (o475)






ORF553
543255
541825
Ydr430cp; CAI: 0.15
U33007
Saccharomyces cerevisiae
130
48


ORF554
544133
543222
putative






ORF555
544565
544179
hypA gene product
X86493
Clostridium perfringens
221
46


ORF556
544762
544487
orf1 gene product
X70951
Saccharomyces cerevisiae
153
38


ORF557
546423
544951
serine protease (htrA)
AE000610
Helicobacter pylori
981
46


ORF558
547480
546584
succinyl coenzyme A synthetase alpha subunit
U23408
Dictyostelium discoideum
869
63


ORF559
546789
547382
putative






ORF560
547901
547476
putative succinyl-coA synthetase beta chain
AJ000975
Bacillus subtilis
388
55


ORF561
548634
547900
succinate--CoA ligase (ADP-forming)
X54073
Thermus aquaticus flavus
498
46


ORF562
548692
549459
cell division protein (ftsY)
AE000588
Helicobacter pylori
330
46


ORF563
550385
549663
putative






ORF564
551611
550421
Tyrosine-specific transport
D90832
Escherichia coli
508
40





protein (Tyrosine permease).






ORF565
553041
551797
tyrosine-specific transport protein (tyrP)
U32730
Haemophilus influenzae
353
36


ORF566
554946
553096
L-glutamine:D-fructose-6-P
U17352
Thermus aquaticus
1324
45





amidotransferase precursor

thermophilus




ORF567
556300
554927
hypothetical
U32824
Haemophilus influenzae
1009
51


ORF568
556524
556904
putative






ORF569
558126
557314
putative






ORF570
557810
558235
putative






ORF571
559215
558310
putative






ORF572
561349
559196
POMP91A
U65942
Chlamydia psittaci
245
39


ORF573
562931
561150
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
130
38


ORF574
564083
563121
putative PlsX protein
Y13937
Bacillus subtilis
519
45


ORF575
563593
563943
putative






ORF576
565379
566953
ORF_f495; orfF of ECMRED, uses 2nd start
U18997
Escherichia coli
874
39


ORF577
567079
567966
glycerol-3-phosphate acyltransferase
M80571
Cucumis sativus
594
45


ORF578
568021
570399
insulin-degrading enzyme
M58465
Drosophila melanogaster
334
42


ORF579
571269
572021
putative






ORF580
572519
572755
putative






ORF581
573519
572731
unknown
Z94752
Mycobacterium tuberculosis
203
35


ORF582
572879
573427
putative






ORF583
574160
573660
putative heat shock protein ORF; putative
M62820
Chlamydia trachomatis
315
83


ORF584
574426
574184
ribosomal protein S18 homolog; putative
M62820
Chlamydia trachomatis
384
99


ORF585
574781
574446
ribosomal protein S6 (rps6)
AE000630
Helicobacter pylori
176
39


ORF586
575243
574923
peptidyl-tRNA hydrolase
U31570
Chlamydia trachomatis
358
78


ORF587
575458
575057
peptidyl-tRNA hydrolase
U31570
Chlamydia trachomatis
393
81


ORF588
575849
575469
partial ctc gene product (AA 1-186)
X16518
Bacillus subtilis
94
37


ORF589
576545
578023
glycogen (starch) synthase
D90899
Synechocystis sp.
695
48


ORF590
578673
578017
phosphatidylglycerophosphate synthase
U87792
Bacillus subtilis
243
48


ORF591
579012
582104
glycyl-tRNA synthetase
U20547
Chlamydia trachomatis
5054
99


ORF592
582697
582206
putative






ORF593
583122
582811
putative






ORF594
583514
583182
putative






ORF595
583869
583438
putative






ORF596
584435
583827
dnaG
AB001896
Staphylococcus aureus
298
41


ORF597
584967
584299
DNA primase
U13165
Listeria monocytogenes
339
41


ORF598
585297
585016
putative






ORF599
585240
586610
DNA mismatch repair protein
D90909
Synechocystis sp.
673
42


ORF600
586484
587758
DNA mismatch repair protein
U71154
Aquifex pyrophilus
845
50


ORF601
587786
589408
excinuclease ABC subunit C (uvrC)
U32691
Haemophilus influenzae
719
46


ORF602
589198
589578
exinuclease ABC subunit C
U29587
Rhodobacter sphaeroides
156
42


ORF603
590061
589630
putative






ORF604
590739
591272
putative






ORF605
592406
592765
homologous to E. coli rnpA
X62539
Bacillus subtilis
117
34


ORF606
593145
592849
putative






ORF607
593900
593121
putative






ORF608
594138
595637
cys-tRNA synthetase (cysS)
U32693
Haemophilus influenzae
991
49


ORF609
596122
595640
lysyl-tRNA synthetase
D90906
Synechocystis sp.
375
53


ORF610
596864
596154
lysine--tRNA ligase
X70708
Thermus aquaticus
571
52







thermophilus




ORF611
597731
597282
putative






ORF612
598524
600809
putative PriA protein
Y13937
Bacillus subtilis
1097
38


ORF613
601876
600734
L-alanine - pimelyl CoA ligase
U51868
Bacillus subtilis
242
42


ORF614
603523
601910
2-acylglycerophosphoethanolamine
L14681
Escherichia coli
388
42





acyltransferase/acyl carrier protein synthetase






ORF615
603794
603531
putative






ORF616
604413
603757
putative






ORF617
604549
605610
3′(2′),5-diphosphonucleoside
U33283
Oryza sativa
254
45





3′(2′) phosphohydrolase






ORF618
606619
605582
leucine dehydrogenase
X79068
Thermoactinomyces
638
49







intermedius




ORF619
606843
607493
inorganic pyrophosphatase
X57545
Arabidopsis thaliana
291
37


ORF620
609068
608031
beta-ketoacyl-ACP synthase
L13242
Ricinus communis
1069
57


ORF621
609652
609296
HI0034 homolog
U82598
Escherichia coli
196
36


ORF622
611860
610109
putative






ORF623
611812
612927
conserved hypothetical protein
AE000579
Helicobacter pylori
780
41


ORF624
613597
612938
trna delta(2)-isopentenylpyrophosphate
Z98209
Mycobacterium
244
37





transferase

tuberculosis




ORF625
613952
613692
delta2-isopentenylpyrophosphate
Z11831
Escherichia coli
134
54





tRNA transferase






ORF626
614315
615244
putative






ORF627
615396
615683
unknown
Z74024
Mycobacterium tuberculosis
93
47


ORF628
617711
615864
D-alanine:D-alanine ligase
U39788
Enterococcus hirae
555
38


ORF629
618313
617510
UDP-N-acetylmuramate-alanine ligase (murC)
U32794
Haemophilus influenzae
448
47


ORF630
619338
618361
transferase, peptidoglycan synthesis (murG)
U32793
Haemophilus influenzae
380
39


ORF631
620416
619247
spoVE gene product (AA 1-366)
X51419
Bacillus subtilis
538
37


ORF632
619863
620261
putative






ORF633
621184
620420
hypothetical protein
Y14079
Bacillus subtilis
313
44


ORF634
621690
621154
murD gene product (AA 1-438)
X51584
Escherichia coli
221
43


ORF635
622399
621674
MurD
Z95388
Mycobacterium tuberculosis
228
41


ORF636
623466
622414
ORF-Y (AA 1-360)
X51584
Escherichia coli
543
45


ORF637
624178
623570
PROBABLE UDP-N-
AB001488
Bacillus subtilis
103
43





ACETYLMURAMOYLALANYL-D-









GLUTAMYL-2,6-DIAMINOLIGASE









(EC 6.3.2.15).






ORF638
624918
624073
UDP-N-acetylmuramoylalanyl-D
X62437
Synechocystis sp.
243
33





glutamyl-2,6-diaminopimelate--D-alanyl-D-









alanine ligase






ORF639
625346
626665
chaperonin 60
U56021
Thermoanaerobacter brockii
136
31


ORF640
626514
626900
putative






ORF641
626954
627853
putative






ORF642
627822
628124
putative






ORF643
628715
628146
elongation factor P
U14003
Escherichia coli
467
55


ORF644
628932
629801
AMP nucleosidase (EC 3.2.2.4).
D90837
Escherichia coli
278
47


ORF645
630406
629804
transketolase
Z73234
Bacillus subtilis
361
46


ORF646
630960
630298
transketolase
Z73234
Bacillus subtilis
460
47


ORF647
631799
630915
transketolase 1 (TK 1) (tktA)
U32783
Haemophilus influenzae
756
47


ORF648
637488
638084
alanyl-tRNA synthetase
X59956
Rhizobium leguminosarum
436
56


ORF649
638036
640207
alanyl-tRNA synthetase
X95571
Thiobacillus ferrooxidans
1121
39


ORF650
640221
643472
transcription-repair
U32805
Haemophilus influenzae
1426
46





coupling factor (trcF) (mfd)






ORF651
640627
640220
putative






ORF652
643485
644495
uroporphyrinogen decarboxylase
M97208
Bacillus subtilis
416
40


ORF653
644471
645430
putative oxygen-independent
U06779
Salmonella typhimurium
638
43





coproporphyrinogen III oxidase






ORF654
645394
645840
oxygen independent
D90912
Synechocystis sp.
283
42





coprophorphyrinogen III oxidase






ORF655
645840
647111
hemY
M97208
Bacillus subtilis
133
38


ORF656
649676
647109
phosphoprotein
L25078
Chlamydia trachomatis
2043
99


ORF657
649970
650344
Hcl
M60902
Chlamydia trachomatis
603
100


ORF658
650418
651722
pCTHom1 gene product
M94254
Chlamydia trachomatis
1735
100


ORF659
651686
652171
putative






ORF660
652516
652908
phenolhydroxylase component
U32702
Haemophilus influenzae
263
41


ORF661
652799
653593
phenolhydroxylase component
U32702
Haemophilus influenzae
456
51


ORF662
659884
661851
YtpT
AF008220
Bacillus subtilis
709
52


ORF663
661740
662282
spoIIIEB protein
M17445
Bacillus subtilis
330
43


ORF664
662286
663074
yycJ
D78193
Bacillus subtilis
405
38


ORF665
662951
663730
C41G7.4
Z81048
Caenorhabditis elegans
200
36


ORF666
664212
663745
hypothetical protein MTCY180.08
Z97193
Mycobacterium tuberculosis
194
38


ORF667
665619
664255
D-alanine glycine permease (dagA)
AE000603
Helicobacter pylori
205
34


ORF668
666083
665727
putative






ORF669
666423
665782
putative






ORF670
666831
668117
putative






ORF671
668121
668375
putative






ORF672
668470
668174
riboflavin synthase beta chain (ribE)
U32810
Haemophilus influenzae
192
40


ORF673
669533
668616
GTP cyclohydrolase II/3,4-dihydroxy-2-
AJ000053
Arabidopsis thaliana
800
51





butanone-4-phoshate synthase






ORF674
669892
669485
unnamed protein product
A38767
Saccharomyces cerevisiae
288
49


ORF675
670780
669998
ribG gene product
L09228
Bacillus subtilis
191
42


ORF676
671241
670732
riboflavin-specific deaminase
U27202
Actinobacillus
314
51







pleuropneumoniae




ORF677
671182
672447
seryl-tRNA synthetase
X91007
Haloarcula marismortui
736
49


ORF678
672692
673231
putative






ORF679
673204
674562
ATPase
L28104
Transposon Tn5422
565
41


ORF680
674612
675232
unknown
Z74025
Mycobacterium tuberculosis
340
43


ORF681
675327
676463
rod-shape-determining protein
M22857
Escherichia coli
442
37


ORF682
677027
676476
biotin [acetyl-CoA carboxylase] ligase
L02354
Paracoccus denitrificans
169
49


ORF683
678422
677700
ORFX13
L09228
Bacillus subtilis
426
43


ORF684
678717
679508
2,3-bisphosphoglycerate
M23068
Homo sapiens
494
47


ORF685
679342
680502
synthesis of [Fe—S] cluster (nifS)
AE000542
Helicobacter pylori
150
33


ORF686
680579
681280
NifU
AF001780
Cyanothece PCC 8801
101
31


ORF687
681539
682558
putative






ORF688
682554
683087
putative






ORF689
683164
684465
ORF 4
M72718
Bacillus subtilis
708
36


ORF690
684774
684418
putative






ORF691
684839
686203
AgX-1 antigen [human,
S73498
Homo sapiens
338
37





infertile patient, testis, Peptide, 505 aa]






ORF692
686197
687204
L-glycerol 3-phosphate dehydrogenase
U00039
Escherichia coli
577
38


ORF693
687341
688360
putative






ORF694
688432
688193
putative






ORF695
689616
688432
putative






ORF696
689960
689631
putative






ORF697
690487
689846
putative






ORF698
690717
690463
putative






ORF699
691871
690672
putative






ORF700
693837
692041
phosphoenolpyruvate carboxykinase
M59372
Neocallimastix frontalis
1818
59


ORF701
694934
693837
MreB protein
M96343
Bacillus subtilis
961
56


ORF702
697263
694942
SNF
X98455
Bacillus cereus
1073
50


ORF703
698084
697170
putative






ORF704
698392
697979
putative






ORF705
698792
700117
trigger factor (tig)
AE000591
Helicobacter pylori
84
34


ORF706
700269
700895
proteosome major subunit
AF013216
Myxococcus xanthus
615
59


ORF707
700912
702165
ATP-dependent protease ATPase subunit
L18867
Escherichia coli
1183
55


ORF708
702183
703412
poly(A) polymerase
L47709
Bacillus subtilis
362
38


ORF709
703522
705000
hypothetical protein
D90912
Synechocystis sp.
809
41


ORF710
705011
705604
putative






ORF711
706159
705704
Preprotein translocase subunit
AF022186
Cyanidium caldarium
165
44


ORF712
706521
706138
secA
X99401
Bacillus firmus
155
42


ORF713
708103
706496
SecA
U66081
Mycobacterium smegmatis
1044
58


ORF714
708398
708078
cp-SecA; chloroplast SecA homolog
U71123
Zea mays
258
69


ORF715
708610
708248
SecA
U21192
Streptomyces lividans
179
42


ORF716
710278
708872
putative






ORF717
711164
710262
phosphatidylserine decarboxylase
U72715
Chlamydia trachomatis
1548
99


ORF718
711432
712763
homologous to E. coli 50K
X62539
Bacillus subtilis
713
54


ORF719
712767
713438
ultraviolet N-glycosylase/AP lyase
U22181
Micrococcus luteus
273
45


ORF720
714232
713651
putative






ORF721
714632
714120
putative






ORF722
715592
714834
putative






ORF723
715854
715558
putative






ORF724
716937
715921
putative






ORF725
718357
717149
3-phosphoglycerate kinase
U83197
Chlamydia trachomatis
2049
100


ORF726
718500
718862
putative






ORF727
719797
718499
phosphate permease (YBR296C)
U32834
Haemophilus influenzae
997
42


ORF728
720273
719782
putative






ORF729
720452
720144
H. influenzae predicted coding region HI1603
U32834
Haemophilus influenzae
164
37


ORF730
720613
721575
dciAD
X56678
Bacillus subtilis
722
41


ORF731
721559
722356
was dppE
U00039
Escherichia coli
477
44


ORF732
723248
722397
chromosome partitioning protein ParB
U87804
Caulobacter crescentus
388
50


ORF733
724598
723378
NifS protein.
D90811
Escherichia coli
805
39


ORF734
725763
724576
hypothetical protein
D64004
Synechocystis sp.
154
41


ORF735
726519
725767
Multidrug resistance protein
D90811
Escherichia coli
607
54





1 (P-glycoprotein 1).






ORF736
726819
726538
ABC transporter subunit
D64004
Synechocystis sp.
266
58


ORF737
727493
726753
ABC transporter subunit
D64004
Synechocystis sp.
854
71


ORF738
727984
727469
ABC transporter subunit
D64004
Synechocystis sp.
531
55


ORF739
728778
728329
putative






ORF740
729346
728759
antiviral protein
L36940
Saccharomyces cerevisiae
115
33


ORF741
732639
729442
penicillin-binding protein 2 (pbp2)
U32688
Haemophilus influenzae
208
43


ORF742
733246
734427
major outer membrane protein precursor
M14738
Chlamydia trachomatis
2045
99


ORF743
734814
735659
ribosomal protein S2
U60196
Chlamydia trachomatis
1269
76


ORF744
735644
736504
elongation factor Ts
U60196
Chlamydia trachomatis
1278
90


ORF745
736520
737254
UMP kinase
U60196
Chlamydia trachomatis
1153
94


ORF746
737254
737787
ribosome-releasing factor
U60196
Chlamydia trachomatis
760
92


ORF747
737942
738679
putative






ORF748
738838
739740
ORF3; putative 39 kDa protein
U40604
Listeria monocytogenes
116
31


ORF749
742057
740060
XcpQ
X68594
Pseudomonas aeruginosa
453
37


ORF750
742869
742045
putative






ORF751
743378
742824
putative






ORF752
744298
743306
unknown
Z80233
Mycobacterium tuberculosis
137
40


ORF753
744714
744430
putative
M69228
Caulobacter crescentus
117
38


ORF754
744985
744611
putative






ORF755
745557
744958
putative






ORF756
746412
745561
putative






ORF757
746772
746416
putative






ORF758
748269
746944
PscN
AF010151
Pseudomonas aeruginosa
1220
55


ORF759
748966
748274
putative






ORF760
749426
748965
putative






ORF761
749702
749433
putative






ORF762
750029
749721
putative






ORF763
752307
750007
putative






ORF764
752913
752503
putative






ORF765
754659
753616
NAD(P)H:glutamyl-transfer RNA reductase
M57676
Bacillus subtilis
172
40


ORF766
755000
756814
DNA gyrase subunit B
U35453
Clostridium acetobutylicum
970
38


ORF767
756796
758301
gyrA
X92503
Mycobacterium smegmatis
409
49


ORF768
758691
758446
unknown
Z74024
Mycobacterium tuberculosis
107
34


ORF769
759787
759338
SfhB
U50134
Escherichia coli
241
48


ORF770
760242
759871
putative






ORF771
760538
760188
putative






ORF772
760966
761772
3-deoxy-D-manno-octulosonate
U72493
Chlamydia trachomatis
1350
99





8-phosphate synthetase






ORF773
761759
762142
unknown
U72493
Chlamydia trachomatis
536
94


ORF774
762267
762983
ATP binding protein
U72493
Chlamydia trachomatis
1197
99


ORF775
764465
763335
chlanectin coding region
M17875
Chlamydia trachomatis
239
100


ORF776
764857
764438
putative






ORF777
766068
764821
unknown function
Z32530
Chlamydia trachomatis
1803
99


ORF778
766643
766065
unknown function
Z32530
Chlamydia trachomatis
704
100


ORF779
768091
766934
RecA
U16739
Chlamydia trachomatis
1753
100


ORF780
768785
768252
unknown function
Z32530
Chlamydia trachomatis
904
99


ORF781
770092
768791
unknown function
Z32530
Chlamydia trachomatis
2249
100


ORF782
770138
770470
putative






ORF783
770661
770185
putative






ORF784
770924
770634
putative






ORF785
772010
771330
putative






ORF786
772390
773391
unknown
D26185
Bacillus subtilis
486
35


ORF787
774221
773427
ORF_f169
U18997
Escherichia coli
263
51


ORF788
776035
774191
DNA topoisomerase I
L27797
Bacillus subtilis
1357
52


ORF789
776663
777706
putative






ORF790
777195
776953
putative






ORF791
779222
777732
ORF_f397
U29581
Escherichia coli
93
40


ORF792
779321
781552
putative






ORF793
781297
782442
putative






ORF794
782447
785524
exonuclease V (AA 1-1180)
X04581
Escherichia coli
557
49


ORF795
785532
786002
putative






ORF796
786580
785546
MreC protein
M31792
Escherichia coli
81
64


ORF797
787741
786611
aspartate aminotransferase precursor
M12105
Gallus gallus
700
42


ORF798
787620
788021
putative






ORF799
790124
787920
GreA
U02878
Rickettsia prowazekii
84
33


ORF800
790160
790609
putative






ORF801
790634
792016
NADH:ubiquinone oxidoreductase subunit A
Z37111
Vibrio alginolyticus
409
37


ORF802
793084
792059
delta_aminolevulinic acid dehydratase
L24386
Bradyrhizobium japonicum
867
52


ORF803
793343
794056
putative






ORF804
794046
794957
putative






ORF805
795401
795144
putative






ORF806
795575
796255
ompR gene product
X92405
Neisseria meningitidis
103
32


ORF807
796278
797015
glucose-1-phosphate thymidylyltransferase
U67553
Methanococcus jannaschii
216
36


ORF808
796979
797365
YqiD
D84432
Bacillus subtilis
184
58


ORF809
797260
797856
farnesyl diphosphate synthase
D13293
Bacillus stearothermophilus
107
37


ORF810
797772
798086
putative






ORF811
798426
797935
Orf39.9
X61000
Escherichia coli
290
51


ORF812
798925
798416
This ORF is homologous to a 40.0 kd 
L22217
Mycoplasma-like
150
46





hypothetical protein in the htrB 3′ region 

organism







from E. coli, Accession Number X61000






ORF813
799301
799927
ribosomal protein S4 (rps4)
AE000633
Helicobacter pylori
407
46


ORF814
800892
800029
apurinic/apyrimidinic endonuclease
U40707
Caenorhabditis elegans
397
35


ORF815
801062
802129
mviB homolog
U50732
Chlamydia trachomatis
1716
97


ORF816
802023
802673
mviB homolog
U50732
Chlamydia trachomatis
973
97


ORF817
802851
803246
lorf2; possible membrane-bound protein
U50732
Chlamydia trachomatis
280
100


ORF818
803105
804220
76 kDa protein
L23921
Chlamydia pneumoniae
775
59


ORF819
804307
805356
putative






ORF820
805290
806282
76 kDa protein
L23921
Chlamydia pneumoniae
125
50


ORF821
806453
808081
putative






ORF822
808026
809009
putative






ORF823
810461
809079
putative






ORF824
811605
810328
putative






ORF825
811725
812342
putative






ORF826
812329
813522
putative






ORF827
813455
813772
putative






ORF828
813732
814334
putative






ORF829
815213
814314
putative






ORF830
814878
814396
putative






ORF831
815733
815428
30S ribosomal protein S20
Z67753
Odontella sinensis
150
38


ORF832
816116
817456
KIAA0336
AB002334
Homo sapiens
90
32


ORF833
817608
819320
RNA polymerase sigma-subunit
J05546
Chlamydia trachomatis
2868
100


ORF834
819324
819713
putative






ORF835
819704
820402
dihydropterin pyrophosphokinase/
Y08611
Pisum sativum
310
45





dihydropteroate synthase






ORF836
820375
821061
dihydropteroate synthase
X68068
Neisseria meningitidis
100
48


ORF837
821043
821537
dihydrofolate reductase
Z84379
Streptococcus pneumoniae
168
45


ORF838
821646
822239
M. jannaschii predicted coding region MJ0768
U67522
Methanococcus jannaschii
139
41


ORF839
822182
822931
putative






ORF840
824355
823045
nitrogen metabolism regulator
M58480
Thiobacillus ferrooxidans
133
58


ORF841
825894
824359
helicase
M63176
Staphylococcus aureus
893
50


ORF842
826322
825879
helicase
M63176
Staphylococcus aureus
282
47


ORF843
826340
827026
ipa-57d gene product
X73124
Bacillus subtilis
602
52


ORF844
827014
827250
putative






ORF845
827856
827230
hypothetical
U32712
Haemophilus influenzae
302
45


ORF846
828007
829275
19/20 residue stretch (32-51) identical to 
L19954
Bacillus subtilis
442
37





N-terminal putative signal sequence of









unknown, partly cloned B. subtilis









gene.; putative






ORF847
829355
830953
heat shock protein GroEL
U55047
Bradyrhizobium japonicum
418
36


ORF848
831119
831748
bas1 protein
Z34917
Hordeum vulgare
516
47


ORF849
832152
831751
putative






ORF850
832744
832214
putative






ORF851
833446
832805
putative






ORF852
833802
833368
putative






ORF853
834679
833879
putative






ORF854
835452
834661
putative






ORF855
835778
835371
putative






ORF856
836482
835775
putative






ORF857
836602
837264
putative






ORF858
837209
838699
putative






ORF859
838760
839575
putative






ORF860
839942
840583
putative






ORF861
840445
841713
putative






ORF862
841659
842459
putative






ORF863
842523
843068
putative






ORF864
843495
843031
putative






ORF865
843239
846196
putative






ORF866
844137
843802
putative






ORF867
848043
846217
putative






ORF868
850123
848150
putative






ORF869
851645
850230
putative






ORF870
853696
851669
putative






ORF871
854836
853700
putative






ORF872
855525
854920
putative






ORF873
856240
855437
putative






ORF874
857183
856233
putative






ORF875
859439
857451
putative






ORF876
859946
859587
putative






ORF877
859642
860640
putative






ORF878
861599
860724
putative






ORF879
862053
861580
putative






ORF880
863540
862098
putative






ORF881
863930
863571
putative






ORF882
864697
863996
putative






ORF883
864923
866248
DNA mismatch repair protein (mutL)
U32692
Haemophilus influenzae
506
47


ORF884
866303
866605
putative






ORF885
866665
867732
YqhT
D84432
Bacillus subtilis
444
39


ORF886
867810
869090
putative






ORF887
869094
869357
putative






ORF888
869270
871372
fimbrial assembly protein
L13865
Pseudomonas aeruginosa
181
40


ORF889
871299
872582
xpsE gene product
X59079
Xanthomonas campestris
825
56


ORF890
872429
872860
secretion protein XcpR
Y09102
Acinetobacter calcoaceticus
213
48


ORF891
872773
873915
ORF_o398
U18997
Escherichia coli
271
33


ORF892
873812
873360
putative






ORF893
874028
874438
putative






ORF894
874778
875386
putative






ORF895
875774
876382
putative






ORF896
877872
877000
secretion system apparatus, SsaT
X99944
Salmonella typhimurium
174
34


ORF897
878172
877876
yscS
L25667
Yersinia pseudotuberculosis
172
44


ORF898
879098
878172
pathogenicity protein
M64094
Xanthomonas campestris
464
46


ORF899
878883
879161
putative






ORF900
879842
879105
PscL
U56077
Pseudomonas aeruginosa
141
34


ORF901
880885
880052
putative






ORF902
881863
880889
HrcJ
U56662
Erwinia amylovora
236
43


ORF903
882904
881948
ORF YOR196c
Z75104
Saccharomyces cerevisiae
685
44


ORF904
883794
882901
dihydrolipoamide dehydrogenase
L31844
Clostridium magnum
578
38


ORF905
884296
883661
YqiV
D84432
Bacillus subtilis
437
44


ORF906
884996
884508
putative






ORF907
888777
885166
helicase of the snf2/rad54 family
D90916
Synechocystis sp.
824
43


ORF908
890172
888940
sodium-coupled branched-
D49784
Clostridium perfringens
230
35





chain amino acid carrier






ORF909
891164
890325
putative Fmu protein
Y13937
Bacillus subtilis
220
41


ORF910
891463
891116
putative






ORF911
893278
891968
DD-carboxypeptidase
M85047
Bacillus subtilis
302
39


ORF912
893356
893808
putative






ORF913
893909
893643
putative






ORF914
894276
893821
hypothetical protein
D90908
Synechocystis sp.
155
39


ORF915
894778
894248
putative






ORF916
895892
895050
putative






ORF917
895951
896829
putative






ORF918
900783
897064
DNA polymerase III alpha-subunit (dnaE)
AE000646
Helicobacter pylori
1974
43


ORF919
902032
900791
UhpC protein
M17102
Escherichia coli
1117
52


ORF920
902659
903876
histidine--tRNA ligase
Z17214
Streptococcus equisimilis
686
47


ORF921
903731
903471
putative






ORF922
903860
905605
aspartyl-tRNA synthetase
D90910
Synechocystis sp.
1339
51


ORF923
905725
906474
mip-like protein
X66126
Chlamydia trachomatis
1196
98


ORF924
906493
906945
spoU
L40369
Chlamydia trachomatis
607
100


ORF925
907306
907001
trxA
L39892
Chlamydia psittaci
380
76


ORF926
908101
908742
putative






ORF927
908721
909194
hypothetical protein
D90914
Synechocystis sp.
150
37


ORF928
909198
909584
DNA polymerase III
Z48003
Staphylococcus aureus
181
40


ORF929
909583
909951
putative






ORF930
910081
910569
VdlD
U94318
Helicobacter pylori
197
43


ORF931
910615
910944
putative






ORF932
910948
912261
acid-inducible gene
L13845
Sinorhizobium meliloti
145
50


ORF933
912399
912629
putative






ORF934
912595
913218
UDP-3-O-acyl-GlcNAc deacetylase
U67855
Pseudomonas aeruginosa
309
39


ORF935
913203
913676
(3R)-hydroxymyristol acyl
D90910
Synechocystis sp.
302
59





carrier protein dehydrase






ORF936
913691
914485
UDP-N-acetylglucosamine acyltransferase
L22690
Rickettsia rickettsii
503
38


ORF937
914516
915136
methionyl-tRNA formyltransferase
X63666
Escherichia coli
407
42


ORF938
915144
915467
putative






ORF939
915629
916633
putative






ORF940
916051
916539
putative






ORF941
916965
917627
ribosomal protein L3 (rpL3)
U32761
Haemophilus influenzae
470
48


ORF942
917612
918304
50S ribosomal protein L4
AB000111
Synechococcus sp.
210
43


ORF943
918323
918655
ribosomal protein L23
Z21677
Thermotoga maritima
116
47


ORF944
918682
919533
rpl2
M74770
Mycoplasma-like organism
800
48


ORF945
919542
919829
Mycoplasma pneumoniae, ribosomal protein 
AE000061
Mycoplasma pneumoniae
315
68





S19; similar to GenBank Accession









Number S36895, from M. bovis






ORF946
919723
920157
ribosomal protein L22
Z21677
Thermotoga maritima
240
49


ORF947
920184
920840
ribosomal protein S3 (rpS3)
U32761
Haemophilus influenzae
605
57


ORF948
920866
921294
ribosomal protein L16
Z21677
Thermotoga maritima
434
62


ORF949
921272
921514
ribosomal protein CtrL29e
M80325
Chlamydia trachomatis
343
99


ORF950
921510
921758
ribosomal protein S17e
M80325
Chlamydia trachomatis
419
100


ORF951
921778
922143
ribosomal protein CtrL14e
M80325
Chlamydia trachomatis
618
100


ORF952
922159
922491
ribosomal protein CtrL24e
M80325
Chlamydia trachomatis
568
100


ORF953
922496
923035
ribosomal protein CtrL5e
M80325
Chlamydia trachomatis
793
99


ORF954
923160
923453
ribosomal protein CtrS8e
M80325
Chlamydia trachomatis
487
98


ORF955
923484
924032
ribosomal protein L6
M60652
Chlamydia trachomatis
927
100


ORF956
924048
924425
ribosomal protein CtrL18e
M80325
Chlamydia trachomatis
605
99


ORF957
924443
924937
ribosomal protein CtrS5e
M80325
Chlamydia trachomatis
814
99


ORF958
924933
925364
ribosomal protein CtrL15e
M80325
Chlamydia trachomatis
740
99


ORF959
925390
926760
homolog
L25077
Chlamydia trachomatis
2254
99


ORF960
926819
927184
ribosomal protein S13
L33834
Chlamydia trachomatis
604
100


ORF961
927209
927604
ribosomal protein S11
L33834
Chlamydia trachomatis
646
98


ORF962
927577
928155
RNA polymerase alpha-subunit
L33834
Chlamydia trachomatis
847
97


ORF963
928100
928759
RNA polymerase alpha-subunit
L33834
Chlamydia trachomatis
1040
98


ORF964
929222
930244
glyceraldehyde-3-phosphate dehydrogenase
U83198
Chlamydia trachomatis
1735
99


ORF965
930222
930656
putative






ORF966
930608
931078
putative






ORF967
931367
931666
putative






ORF968
931549
931959
putative






ORF969
932070
932579
crossover junction
U32717
Haemophilus influenzae
250
41





endodeoxyribonuclease (ruvC)






ORF970
932602
933201
Holliday junction DNA helicase (ruvA)
U32716
Haemophilus influenzae
258
38


ORF971
933319
933621
nucleoside diphosphate kinase (ndk)
AE000540
Helicobacter pylori
264
60


ORF972
933522
933785
nucleoside 5′-diphosphate
J05207
Myxococcus xanthus
186
64





phosphotransferase (EC 2.7.4.6)






ORF973
934546
933848
hypothetical protein (GB: U14003_297)
U39706
Mycoplasma genitalium
156
36


ORF974
936377
934539
homologous to E. coli gidA
X62540
Pseudomonas putida
1562
51


ORF975
938081
936666
replicative DNA helicase
D26185
Bacillus subtilis
848
41


ORF976
938538
939098
phosphatidylglycerophosphate
AE000610
Helicobacter pylori
120
33





synthase (pgsA)






ORF977
939329
940933
adenine nucleotide translocase
Z49227
Arabidopsis thaliana
668
40


ORF978
941031
942068
putative protease
AF008220
Bacillus subtilis
265
36


ORF979
942082
944685
DNA polymerase
D12982
Bacillus caldotenax
1334
42


ORF980
944634
945287
T05G5.5
Z27079
Caenorhabditis elegans
198
32


ORF981
945287
946294
‘The first ATG in the open reading frame 
L27278
Pseudomonas fluorescens
882
68





was chosen as the initiation codon.’






ORF982
946293
946676
‘The first GTG in the open reading frame 
L27276
Deinococcus radiodurans
417
65





was chosen as the initiation codon.’






ORF983
947105
948454
ADPglucose pyrophosphorylase
M31616
Oryza sativa
755
44


ORF984
948522
949277
putative






ORF985
949277
949594
YlbH protein
Z98682
Bacillus subtilis
223
41


ORF986
949849
950676
putative






ORF987
950680
951330
ferrochelatase
M59288
Mus musculus
260
42


ORF988
951281
951643
ferrochelatase
D26106
Cucumis sativus
178
47


ORF989
951788
952798
putative






ORF990
953581
954264
putative






ORF991
954426
955157
putative






ORF992
955754
957940
orf4 gene product
X93084
Methanosarcina barkeri
130
41


ORF993
957837
959312
OppB gene product
X56347
Bacillus subtilis
327
38


ORF994
959299
961050
dipeptide ABC transporter,
AE000548
Helicobacter pylori
263
39





permease protein (dppC)






ORF995
961562
961053
methylated DNA protein
U67593
Methanococcus
109
39





cysteine methyltransferase

jannaschii




ORF996
962575
961487
putative






ORF997
961979
961584
putative






ORF998
964914
962545
phenylalanyl-tRNA synthetase beta subunit
Z75208
Bacillus subtilis
775
37


ORF999
964941
965708
putative






ORF1000
967023
966193
unknown
Z48008
Saccharomyces cerevisiae
492
44


ORF1001
967444
968061
putative






ORF1002
968903
968064
putative






ORF1003
970685
969528
transcriptional activator of pilA
Z12154
Pseudomonas aeruginosa
849
45


ORF1004
971806
971024
sensor protein
L39904
Myxococcus xanthus
147
30


ORF1005
973053
972388
putative






ORF1006
974546
973746
unknown
D64126
Bacillus subtilis
500
50


ORF1007
975223
974558
unknown
D26185
Bacillus subtilis
141
44


ORF1008
976193
975207
hypothetical protein in htrA
AE000126
Escherichia coli
142
42





dapD intergenic region






ORF1009
976520
976254
unknown
Z49939
Saccharomyces cerevisiae
183
39


ORF1010
976588
976899
putative






ORF1011
976886
977635
peptide release factor 2
X99401
Bacillus firmus
534
44


ORF1012
977661
977933
release factor 2
AF013188
Bacillus subtilis
187
52


ORF1013
977918
978433
putative






ORF1014
978619
978984
spore coat protein CotRC
D50551
Bacillus subtilis
355
52


ORF1015
978933
979331
hypothetical
U32717
Haemophilus influenzae
199
40


ORF1016
981197
979389
putative






ORF1017
979711
980112
putative






ORF1018
982116
981148
putative






ORF1019
982321
983598
UDP-N-acetylglucosamine
U32788
Haemophilus influenzae
593
38





enolpyruvyl transferase (murZ)






ORF1020
984488
983862
arginyl-tRNA-synthetase
D64006
Synechocystis sp.
347
44


ORF1021
985381
984371
arginyl-tRNA-synthetase
D64006
Synechocystis sp.
782
58


ORF1022
986103
985399
hypothetical protein
D90915
Synechocystis sp.
224
35


ORF1023
986693
986046
No definition line found
U00021
Mycobacterium leprae
286
50


ORF1024
987607
986693
o298; This 298 aa ORF is 33 pct identical 
AE000238
Escherichia coli
132
46





(24 gaps) to 248 residues of an approx.









256 aa protein CDSA_ECOLI SW: P06466






ORF1025
988119
987616
conserved hypothetical protein
AE000627
Helicobacter pylori
343
49


ORF1026
988253
987936
hypothetical protein (HI0920)
U67577
Methanococcus jannaschii
110
38


ORF1027
988831
989163
putative






ORF1028
989693
993442
protein-export membrane protein SecD
D64000
Synechocystis sp.
447
38


ORF1029
993408
993785
protein-export membrane protein
U83136
Rhodobacter sphaeroides
240
43


ORF1030
993835
993416
putative






ORF1031
993882
994262
putative






ORF1032
994226
995656
RecJ recombination protein
U41759
Chlamydia psittaci
880
66


ORF1033
996036
996611
unknown
U41759
Chlamydia psittaci
533
75


ORF1034
996885
998267
glutamyl-tRNA synthetase homolog
U41759
Chlamydia psittaci
2018
83


ORF1035
998962
999225
9-kDa cysteine-rich outer membrane protein
M35148
Chlamydia trachomatis
504
100


ORF1036
999375
1001033
outer membrane protein 2
M23001
Chlamydia trachomatis
2857
100


ORF1037
1001211
1001516
15-kDa serine-rich outer membrane protein
M35148
Chlamydia trachomatis
276
94


ORF1038
1001392
1001664
15-kDa serine-rich outer membrane protein
M35148
Chlamydia trachomatis
438
97


ORF1039
1003721
1001823
ORF of prc gene (alt.)
D00674
Escherichia coli
486
42


ORF1040
1004459
1004845
StrA
M86701
Haemophilus influenzae
454
70


ORF1041
1004990
1005382
ribosomal protein S7
Z11567
Chlamydia trachomatis
662
99


ORF1042
1005391
1007496
translation elongation factor EF-G (fusA)
AE000625
Helicobacter pylori
2147
62


ORF1043
1007486
1007821
ribosomal protein S10
Z21676
Spirulina platensis
350
68


ORF1044
1007802
1008698
NADPH-sulfite reducatase
M23008
Escherichia coli
113
48





flavoprotein component






ORF1045
1009426
1009121
unknown
Z92774
Mycobacterium tuberculosis
102
42


ORF1046
1010534
1012054
serine hydroxymethyltransferase
Z38002
Bacillus subtilis
1021
55


ORF1047
1012397
1011942
putative






ORF1048
1012042
1012635
ATP-dependent Clp protease
D90915
Synechocystis sp.
365
44





proteolytic subunit






ORF1049
1012593
1012862
putative






ORF1050
1012811
1013440
diaminopimelate epimerase (dapF)
U32759
Haemophilus influenzae
108
40


ORF1051
1013456
1014055
putative






ORF1052
1013977
1014489
putative






ORF1053
1015224
1014529
hypothetical 28.1 kD protein
AE000459
Escherichia coli
263
38





in udp-rfaH intergenic region






ORF1054
1016002
1015145
putative






ORF1055
1017120
1015939
conserved hypothetical protein
AE000579
Helicobacter pylori
428
42


ORF1056
1017766
1017245
putative






ORF1057
1018911
1017916
putative






ORF1058
1019191
1018580
putative






ORF1059
1020199
1019831
hemolysin
AE000647
Helicobacter pylori
164
33


ORF1060
1021007
1020114
unknown
Z95208
Mycobacterium tuberculosis
201
36


ORF1061
1021569
1021075
putative






ORF1062
1022411
1022097
putative






ORF1063
1023344
1023667
50S ribosomal subunit protein L21
U18997
Escherichia coli
218
43


ORF1064
1023701
1023949
50S ribosomal protein L27
U38804
Porphyra purpurea
251
64


ORF1065
1023976
1024776
ORF_f390
U18997
Escherichia coli
603
51


ORF1066
1024704
1025045
GTP-binding protein (obg)
U32769
Haemophilus influenzae
161
37


ORF1067
1025881
1024967
hypothetical protein
D90903
Synechocystis sp.
439
35


ORF1068
1026546
1025839
YcdI
AB000617
Bacillus subtilis
312
40


ORF1069
1027379
1026546
adhesion protein
D90903
Synechocystis sp.
354
35


ORF1070
1030604
1027929
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
95
49


ORF1071
1033252
1030508
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
75
36


ORF1072
1031733
1032086
putative






ORF1073
1037037
1033456
putative 98 kDa outer membrane protein
U72499
Chlamydia psittaci
160
46


ORF1074
1035674
1035910
putative






ORF1075
1036175
1036507
putative






ORF1076
68 (com)
1036967
putative






ORF1077
16591
16989
GutQ/KpsF Family Sugar-P Isomerase
AE001313
Chlamydia trachomatis
658
97


ORF1078
31779
31408
putative






ORF1079
56502
56834
hypothetical protein
AE001309
Chlamydia trachomatis
284
95


ORF1080
56686
56913
hypothetical protein
AE001309
Chlamydia trachomatis
303
94


ORF1081
64748
65074
hypothetical protein (possible 357R?)
AE001309
Chlamydia trachomatis
501
100


ORF1082
73482
73195
Predicted OMP [leader (19) peptide]
AE001308
Chlamydia trachomatis
476
100


ORF1083
78482
78736
putative






ORF1084
79803
79411
hypothetical protein
AE001307
Chlamydia trachomatis
583
98


ORF1085
82333
81959
Lon ATP-dependent protease
AE001307
Chlamydia trachomatis
607
99


ORF1086
87313
86999
hypothetical protein
AE001307
Chlamydia trachomatis
534
100


ORF1087
109929
109456
hypothetical protein
AE001305
Chlamydia trachomatis
529
98


ORF1088
111599
111351
putative






ORF1089
112069
111734
putative






ORF1090
112666
112911
hypothetical protein
AE001305
Chlamydia trachomatis
395
94


ORF1091
114017
113715
putative






ORF1092
120757
120464
putative






ORF1093
125133
125522
predied ferredoxin
AE001303
Chlamydia trachomatis
631
97


ORF1094
131888
131604
putative






ORF1095
144164
144427
putative






ORF1096
150698
150369
putative






ORF1097
164385
163948
NADH (Ubiquinone) Dehydrogenase
AE001300
Chlamydia trachomatis
755
100


ORF1098
165690
166115
hypothetical protein
AE001300
Chlamydia trachomatis
724
99


ORF1099
168742
168425
hypothetical protein
AE001300
Chlamydia trachomatis
356
96


ORF1100
170509
170793
hypothetical protein
AE001300
Chlamydia trachomatis
489
100


ORF1101
177145
177474
AcCoA Carboxylase/Transferase Alpha
AE001299
Chlamydia trachomatis
518
99


ORF1102
188295
188023
hypothetical protein
AE001298
Chlamydia trachomatis
451
100


ORF1103
188791
188330
hypothetical protein
AE001298
Chlamydia trachomatis
733
97


ORF1104
190629
190336
putative






ORF1105
197313
197083
putative






ORF1106
210914
211384
putative






ORF1107
235160
234852
Glutamate Aminomutase
AE001295
Chlamydia trachomatis
507
97


ORF1108
237227
236913
putative






ORF1109
249733
249446
Oligopeptide Permease
AE001293
Chlamydia trachomatis
512
100


ORF1110
253493
253158
hypothetical protein
AE001293
Chlamydia trachomatis
318
63


ORF1111
253701
254789
hypothetical protein
AE001293
Chlamydia trachomatis
1860
99


ORF1112
271633
271932
hypothetical protein
AE001291
Chlamydia trachomatis
512
100


ORF1113
275666
276070
Disulfide bond Oxidoreductase
AE001291
Chlamydia trachomatis
700
99


ORF1114
277931
278218
putative






ORF1115
282741
282481
hypothetical protein
AE001290
Chlamydia trachomatis
422
99


ORF1116
293178
293489
Phospholipase D Endonuclease Superfamily
AE001289
Chlamydia trachomatis
433
95


ORF1117
303155
303469
putative






ORF1118
309297
308965
hypothetical protein
AE001287
Chlamydia trachomatis
422
95


ORF1119
312219
312536
putative






ORF1120
312853
312602
hypothetical protein
AE001287
Chlamydia trachomatis
338
99


ORF1121
313167
312772
hypothetical protein
AE001287
Chlamydia trachomatis
616
98


ORF1122
320224
320598
hypothetical protein
AE001286
Chlamydia trachomatis
628
98


ORF1123
340249
340503
Oligopeptidase
AE001285
Chlamydia trachomatis
444
100


ORF1124
352839
353324
hypothetical protein
AE001284
Chlamydia trachomatis
751
98


ORF1125
373475
373699
Phopholipase D Superfamily
AE001282
Chlamydia trachomatis
378
100





[leader (33) peptide}






ORF1126
377316
377756
hypothetical protein
AE001282
Chlamydia trachomatis
764
99


ORF1127
379268
379657
hypothetical protein
AE001282
Chlamydia trachomatis
535
100


ORF1128
395098
394823
putative






ORF1129
401594
401142
Flagellar Secretion Protein
AE001280
Chlamydia trachomatis
698
100


ORF1130
410045
410539
hypothetical protein
AE001279
Chlamydia trachomatis
767
100


ORF1131
411425
411658
Coproporphyrinogen III Oxidase
AE001279
Chlamydia trachomatis
399
99


ORF1132
414937
414416
putative






ORF1133
422889
423212
Glycogen Hydrolase (debranching)
AE001278
Chlamydia trachomatis
206
100


ORF1134
427842
428183
hypothetical protein
AE001278
Chlamydia trachomatis
610
100


ORF1135
428732
429451
hypothetical protein
AE001278
Chlamydia trachomatis
1010
98


ORF1136
442557
442799
hypothetical protein
AE001277
Chlamydia trachomatis
649
94


ORF1137
443628
444041
L31 Ribosomal Protein
AE001277
Chlamydia trachomatis
538
96


ORF1138
443678
443166
putative






ORF1139
445901
446155
putative






ORF1140
467981
468262
putative






ORF1141
471869
472108
Putative Outer Membrane Protein I
AE001361
Chlamydia trachomatis
370
100


ORF1142
488032
488337
Membrane Thiol Protease
AE001360
Chlamydia trachomatis
483
96


ORF1143
497179
497694
Low Calcium Response Protein H
AE001359
Chlamydia trachomatis
864
95


ORF1144
500474
500202
putative






ORF1145
508968
509561
ABC transporter permease
AE001358
Chlamydia trachomatis
964
100


ORF1146
510845
511264
hypothetical protein
AE001358
Chlamydia trachomatis
360
89


ORF1147
526525
526848
hypothetical protein
AE001356
Chlamydia trachomatis
242
81


ORF1148
531318
531863
hypothetical protein
AE001356
Chlamydia trachomatis
127
100


ORF1149
556826
557224
hypothetical protein
AE001354
Chlamydia trachomatis
683
99


ORF1150
564971
564537
hypothetical protein
AE001353
Chlamydia trachomatis
534
100


ORF1151
566963
567232
Glycerol-3-P Acyltransferase
AE001353
Chlamydia trachomatis
220
53


ORF1152
570351
570890
Insulinase family/Protease III
AE001353
Chlamydia trachomatis
925
100


ORF1153
571072
571332
hypothetical protein
AE001353
Chlamydia trachomatis
441
99


ORF1154
576025
575801
General Stress Protein
AE001352
Chlamydia trachomatis
273
97


ORF1155
590363
590650
hypothetical protein
AE001351
Chlamydia trachomatis
442
100


ORF1156
597868
598593
hypothetical protein
AE001350
Chlamydia trachomatis
1176
98


ORF1157
606889
606626
putative






ORF1158
608031
607786
hydrolase/phosphatase homolog
AE001349
Chlamydia trachomatis
434
99


ORF1159
610110
610391
putative






ORF1160
632703
633353
putative






ORF1161
637213
637482
putative






ORF1162
650517
649924
putative






ORF1163
652317
652562
Phenolhydrolase/NADH
AE001345
Chlamydia trachomatis
324
99





ubiquinone oxidoreductase






ORF1164
654753
655325
putative






ORF1165
661118
660810
putative






ORF1166
677596
677057
hypothetical protein
AE001343
Chlamydia trachomatis
864
98


ORF1167
679528
679253
putative






ORF1168
732536
732210
putative






ORF1169
742069
742383
putative






ORF1170
759318
758782
(Pseudouridine Synthase)
AE001336
Chlamydia trachomatis
909
98


ORF1171
760282
760521
putative






ORF1172
771313
770894
hypothetical protein
AE001335
Chlamydia trachomatis
661
96


ORF1173
772115
772408
hypothetical protein
AE001335
Chlamydia trachomatis
520
99


ORF1174
788137
788457
putative






ORF1175
816302
815967
putative






ORF1176
846606
846914
putative






ORF1177
867803
868054
putative






ORF1178
875386
875658
hypothetical protein
AE001327
Chlamydia trachomatis
268
86


ORF1179
876445
876915
hypothetical protein
AE001327
Chlamydia trachomatis
747
99


ORF1180
884548
884312
putative






ORF1181
891859
891467
hypothetical protein
AE001326
Chlamydia trachomatis
551
95


ORF1182
900770
900417
putative






ORF1183
902553
902269
putative






ORF1184
908046
907783
putative






ORF1185
912313
912567
Myristoyl GlcNac Deacetylase
AE001324
Chlamydia trachomatis
195
97


ORF1186
935451
935741
putative






ORF1187
946961
946692
hypothetical protein
AE001322
Chlamydia trachomatis
410
99


ORF1188
953193
952783
hypothetical protein
AE001322
Chlamydia trachomatis
593
100


ORF1189
966199
965873
hypothetical protein
AE001321
Chlamydia trachomatis
542
98


ORF1190
969298
968765
putative






ORF1191
971009
970731
2-Component Sensor
AE001320
Chlamydia trachomatis
467
97


ORF1192
972162
972404
putative






ORF1193
973119
973508
Phosphoglycolate Phosphatase
AE001320
Chlamydia trachomatis
647
98


ORF1194
998649
998404
putative






ORF1195
1004280
1003882
hypothetical protein
AE001317
Chlamydia trachomatis
571
99


ORF1196
1010200
1009532
hypothetical protein
AE001317
Chlamydia trachomatis
1132
99


ORF1197
1029174
1029482
putative





















TABLE 2







SEQ ID NO
begin
stop
preferred start





















2
501
208
501



3
3276
505
3153



4
5068
3242
5062



5
6400
5126
6400



6
7977
6619
7977



7
8582
8082
8582



8
8995
8591
8995



9
9440
8979
9440



10
9828
10430
9828



11
10367
11254
10430



12
11245
11916
11245



13
12068
13324
12068



14
13532
14413
13538



15
14807
15019
14807



16
14932
15969
14977



17
15995
16501
16004



18
16467
16138
16377



19
18190
17417
18178



20
20521
18437
20518



21
22202
20814
22166



22
22602
22153
22509



23
22804
22478
22795



24
23183
22824
23180



25
23394
23110
23394



26
24569
23394
24569



27
26383
24641
26383



28
26640
27710
26640



29
28780
27725
28729



30
29957
28740
29957



31
30721
30032
30628



32
31281
30520
31254



33
31436
31780
31436



34
33356
31800
33344



35
33901
33314
33874



36
34116
35027
34116



37
34988
35359
35027



38
35167
35919
35377



39
35923
36996
36031



40
37810
37013
37765



41
38207
39085
38252



42
39151
39927
39157



43
39923
40756
39959



44
40760
42007
40772



45
42175
43116
42229



46
42999
43802
43128



47
44211
45227
44217



48
46072
45275
46066



49
46340
45975
46331



50
46895
46506
46865



51
47955
46882
47955



52
48585
48178
48558



53
50072
48630
50012



54
50710
50099
50692



55
52439
50925
52430



56
53484
52348
53478



57
54536
53466
54536



58
55086
54595
55104



59
56350
55031
56350



60
55659
56084
55722



61
56847
58235
56931



62
58423
59181
58423



63
59185
60195
59194



64
60188
61483
60191



65
61496
62353
61496



66
62500
63141
62518



67
63396
63983
63396



68
64628
64071
64580



69
64285
64656
64285



70
64944
64609
64938



71
65347
67269
65347



72
67656
68873
67815



73
68877
69233
68892



74
69212
69721
69323



75
69958
70455
69970



76
70701
71006
70725



77
73191
71086
73185



78
74900
73497
74891



79
75463
74876
75463



80
77124
75502
77124



81
77000
77299
77012



82
78095
77145
78095



83
79065
78154
79065



84
81971
79878
81965



85
82639
83271
82642



86
83792
84850
83921



87
84876
86921
84888



88
88650
87313
88383



89
87440
87805
87458



90
88400
88747
88409



91
88717
89265
88729



92
89355
89732
89355



93
89735
91447
89735



94
91749
91435
91749



95
92392
91745
92323



96
93138
92344
92874



97
94134
93361
93945



98
94637
94071
94577



99
98299
94628
98113



100
98715
98113
98715



101
100228
98741
100195



102
101347
100337
101323



103
102210
101323
102210



104
102485
102210
102479



105
104315
102726
104315



106
105075
104254
105075



107
105259
105894
105271



108
107429
108460
107486



109
108665
108955
108683



110
109459
109013
109456



111
110366
109704
110363



112
111330
112520
111330



113
112915
113463
112918



114
113566
113994
113566



115
114020
114604
114020



116
114720
115253
114807



117
115362
115676
115380



118
116022
119795
116040



119
119823
124010
119823



120
124065
124988
124065



121
124873
125106
124873



122
126261
125536
126243



123
126328
126930
126331



124
127138
127785
127147



125
127924
129714
127942



126
129720
131033
129720



127
131018
131629
131021



128
131834
133156
131852



129
133075
133584
133096



130
133625
133999
133628



131
133861
134508
133948



132
134638
137454
134638



133
137442
140276
137472



134
140733
140335
140727



135
141799
141077
141799



136
143240
141780
143240



137
143829
143128
143820



138
143923
144393
143923



139
144548
146326
144548



140
146413
147078
146425



141
147140
148075
147152



142
148115
148549
148115



143
148524
149027
148524



144
149000
149305
149033



145
149187
149708
149187



146
149712
150911
149769



147
152044
151004
151966



148
152664
151999
152592



149
152900
153352
152924



150
153389
153997
153425



151
155276
153984
155228



152
156544
155231
156544



153
156806
157525
156809



154
157489
158955
157534



155
159104
159961
159104



156
159916
161220
159916



157
161183
161593
161228



158
162354
161623
162354



159
163013
162363
163013



160
163941
162994
163941



161
165505
164474
165505



162
166686
166093
166686



163
168171
166729
168171



164
169249
168848
169189



165
169586
170431
169607



166
170780
171334
170783



167
171333
172376
171390



168
172309
172722
172309



169
173048
174496
173048



170
174399
174968
174399



171
175267
175710
175267



172
175714
177009
175735



173
177423
178115
177468



174
178084
180021
178084



175
180704
180048
180635



176
181398
180631
181398



177
182594
181398
182594



178
182895
183656
182895



179
183665
184786
183665



180
186007
184796
186007



181
186848
186000
186791



182
187270
186749
187240



183
187426
187809
187429



184
189481
188798
189442



185
189693
190352
189693



186
190235
190510
190280



187
190785
191786
190824



188
191790
192464
191811



189
192392
193183
192500



190
193254
194630
193263



191
195046
194690
195037



192
195184
197031
195193



193
197018
197635
197024



194
197762
198208
197669



195
198963
197668
198954



196
199957
198962
199945



197
200327
199941
200306



198
200685
200266
200598



199
200962
200585
200962



200
201169
202377
201184



201
203441
202380
203441



202
203998
203471
203989



203
206449
204059
206434



204
207425
206811
207410



205
207506
208528
207506



206
208545
209471
208545



207
209471
210214
209471



208
210586
210816
210586



209
211332
210883
211293



210
212978
211374
212972



211
214134
212875
214134



212
214710
214168
214701



213
215143
214754
215128



214
216705
215236
216705



215
217917
216892
217911



216
217088
217441
217202



217
218364
218702
218364



218
218695
219009
218785



219
219179
219748
219260



220
219891
220430
219912



221
220499
221074
220505



222
221137
221541
221176



223
221601
222092
221616



224
222472
223290
222487



225
223423
223818
223423



226
224278
225171
224278



227
225749
225174
225749



228
225334
225549
225328



229
226654
225749
226654



230
227299
226769
227170



231
227646
227161
227646



232
228457
227750
228439



233
230001
228607
229854



234
231074
230151
231062



235
231348
233006
231366



236
233059
233829
233059



237
233801
234265
233801



238
234282
234854
234288



239
236300
235227
236300



240
236314
238209
236314



241
238164
238769
238185



242
238769
240061
238769



243
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727
719797
718499
719776



728
720273
719782
720147



729
720452
720144
720452



730
720613
721575
720613



731
721559
722356
721571



732
723248
722397
723239



733
724598
723378
724580



734
725763
724576
725760



735
726519
725767
726519



736
726819
726538
726801



737
727493
726753
727466



738
727984
727469
727984



739
728778
728329
728718



740
729346
728759
729334



741
732639
729442
732639



742
733246
734427
733246



743
734814
735659
734814



744
735644
736504
735644



745
736520
737254
736520



746
737254
737787
737254



747
737942
738679
738122



748
738838
739740
738862



749
742057
740060
741982



750
742869
742045
742824



751
743378
742824
743348



752
744298
743306
744292



753
744714
744430
744660



754
744985
744611
744931



755
745557
744958
745548



756
746412
745561
746409



757
746772
746416
746697



758
748269
746944
748269



759
748966
748274
748954



760
749426
748965
749411



761
749702
749433
749681



762
750029
749721
750020



763
752307
750007
752307



764
752913
752503
752901



765
754659
753616
754659



766
755000
756814
755000



767
756796
758301
756832



768
758691
758446
758688



769
759787
759338
759787



770
760242
759871
760188



771
760538
760188
760529



772
760966
761772
760966



773
761759
762142
761759



774
762267
762983
762267



775
764465
763335
764312



776
764857
764438
764821



777
766068
764821
765972



778
766643
766065
766643



779
768091
766934
768091



780
768785
768252
768785



781
770092
768791
770062



782
770138
770470
770150



783
770661
770185
770631



784
770924
770634
770894



785
772010
771330
772010



786
772390
773391
772390



787
774221
773427
774215



788
776035
774191
776035



789
776663
777706
776894



790
777195
776953
777177



791
779222
777732
779180



792
779321
781552
779360



793
781297
782442
781351



794
782447
785524
782447



795
785532
786002
785697



796
786580
785546
786580



797
787741
786611
787729



798
787620
788021
787782



799
790124
787920
790064



800
790160
790609
790178



801
790634
792016
790634



802
793084
792059
793084



803
793343
794056
793370



804
794046
794957
794079



805
795401
795144
795395



806
795575
796255
795575



807
796278
797015
796311



808
796979
797365
796979



809
797260
797856
797395



810
797772
798086
797805



811
798426
797935
798393



812
798925
798416
798916



813
799301
799927
799301



814
800892
800029
800892



815
801062
802129
801062



816
802023
802673
802041



817
802851
803246
802920



818
803105
804220
803111



819
804307
805356
804331



820
805290
806282
805356



821
806453
808081
806498



822
808026
809009
808098



823
810461
809079
810437



824
811605
810328
811590



825
811725
812342
811824



826
812329
813522
812398



827
813455
813772
813455



828
813732
814334
813780



829
815213
814314
815207



830
814878
814396
814975



831
815733
815428
815733



832
816116
817456
816170



833
817608
819320
817608



834
819324
819713
819342



835
819704
820402
819713



836
820375
821061
820453



837
821043
821537
821043



838
821646
822239
821667



839
822182
822931
822221



840
824355
823045
824352



841
825894
824359
825891



842
826322
825879
826322



843
826340
827026
826340



844
827014
827250
827014



845
827856
827230
827856



846
828007
829275
828025



847
829355
830953
829358



848
831119
831748
831140



849
832152
831751
832140



850
832744
832214
832666



851
833446
832805
833446



852
833802
833368
833742



853
834679
833879
834661



854
835452
834661
835365



855
835778
835371
835775



856
836482
835775
836470



857
836602
837264
836617



858
837209
838699
837209



859
838760
839575
838760



860
839942
840583
839951



861
840445
841713
840451



862
841659
842459
841686



863
842523
843068
842541



864
843495
843031
843447



865
843239
846196
843335



866
844137
843802
844077



867
848043
846217
848022



868
850123
848150
850099



869
851645
850230
851504



870
853696
851669
853672



871
854836
853700
854809



872
855525
854920
855468



873
856240
855437
856240



874
857183
856233
857006



875
859439
857451
859430



876
859946
859587
859916



877
859642
860640
859660



878
861599
860724
861599



879
862053
861580
862038



880
863540
862098
863531



881
863930
863571
863927



882
864697
863996
864688



883
864923
866248
864923



884
866303
866605
866336



885
866665
867732
866665



886
867810
869090
867864



887
869094
869357
869094



888
869270
871372
869336



889
871299
872582
871359



890
872429
872860
872555



891
872773
873915
872773



892
873812
873360
873668



893
874028
874438
874067



894
874778
875386
874796



895
875774
876382
875843



896
877872
877000
877866



897
878172
877876
878157



898
879098
878172
879098



899
878883
879161
878886



900
879842
879105
879809



901
880885
880052
880885



902
881863
880889
881863



903
882904
881948
882901



904
883794
882901
883761



905
884296
883661
884296



906
884996
884508
884984



907
888777
885166
888771



908
890172
888940
890172



909
891164
890325
891146



910
891463
891116
891427



911
893278
891968
893278



912
893356
893808
893386



913
893909
893643
893894



914
894276
893821
894276



915
894778
894248
894760



916
895892
895050
895874



917
895951
896829
895963



918
900783
897064
900774



919
902032
900791
902158



920
902659
903876
902659



921
903731
903471
903731



922
903860
905605
903860



923
905725
906474
905725



924
906493
906945
906493



925
907306
907001
907306



926
908101
908742
908131



927
908721
909194
908724



928
909198
909584
909201



929
909583
909951
909670



930
910081
910569
910090



931
910615
910944
910636



932
910948
912261
910951



933
912399
912629
912399



934
912595
913218
912595



935
913203
913676
913218



936
913691
914485
913691



937
914516
915136
914522



938
915144
915467
915162



939
915629
916633
915629



940
916051
916539
916159



941
916965
917627
916965



942
917612
918304
917612



943
918323
918655
918323



944
918682
919533
918682



945
919542
919829
919542



946
919723
920157
919723



947
920184
920840
920184



948
920866
921294
920866



949
921272
921514
921272



950
921510
921758
921510



951
921778
922143
921778



952
922159
922491
922159



953
922496
923035
922496



954
923160
923453
923160



955
923484
924032
923484



956
924048
924425
924057



957
924443
924937
924443



958
924933
925364
924933



959
925390
926760
925390



960
926819
927184
926819



961
927209
927604
927209



962
927577
928155
927577



963
928100
928759
928127



964
929222
930244
929243



965
930222
930656
930258



966
930608
931078
930665



967
931367
931666
931406



968
931549
931959
931558



969
932070
932579
932070



970
932602
933201
932602



971
933319
933621
933319



972
933522
933785
933522



973
934546
933848
934546



974
936377
934539
936377



975
938081
936666
938081



976
938538
939098
938595



977
939329
940933
939506



978
941031
942068
941076



979
942082
944685
942082



980
944634
945287
944673



981
945287
946294
945287



982
946293
946676
946368



983
947105
948454
947132



984
948522
949277
948546



985
949277
949594
949277



986
949849
950676
949888



987
950680
951330
950701



988
951281
951643
951290



989
951788
952798
951803



990
953581
954264
953602



991
954426
955157
954429



992
955754
957940
955766



993
957837
959312
957867



994
959299
961050
959317



995
961562
961053
961562



996
962575
961487
962545



997
961979
961584
961979



998
964914
962545
964914



999
964941
965708
964956



1000
967023
966193
966984



1001
967444
968061
967459



1002
968903
968064
968792



1003
970685
969528
970685



1004
971806
971024
971785



1005
973053
972388
973026



1006
974546
973746
974546



1007
975223
974558
975214



1008
976193
975207
976193



1009
976520
976254
976511



1010
976588
976899
976588



1011
976886
977635
976934



1012
977661
977933
977682



1013
977918
978433
977933



1014
978619
978984
978619



1015
978933
979331
978987



1016
981197
979389
981197



1017
979711
980112
979753



1018
982116
981148
982107



1019
982321
983598
982321



1020
984488
983862
984296



1021
985381
984371
985381



1022
986103
985399
986046



1023
986693
986046
986693



1024
987607
986693
987607



1025
988119
987616
987942



1026
988253
987936
988247



1027
988831
989163
988834



1028
989693
993442
989693



1029
993408
993785
993408



1030
993835
993416
993754



1031
993882
994262
993906



1032
994226
995656
994259



1033
996036
996611
996036



1034
996885
998267
996885



1035
998962
999225
998962



1036
999375
1001033
999393



1037
1001211
1001516
1001214



1038
1001392
1001664
1001443



1039
1003721
1001823
1003721



1040
1004459
1004845
1004459



1041
1004990
1005382
1004990



1042
1005391
1007496
1005391



1043
1007486
1007821
1007453



1044
1007802
1008698
1007841



1045
1009426
1009121
1009426



1046
1010534
1012054
1010534



1047
1012397
1011942
1012241



1048
1012042
1012635
1012057



1049
1012593
1012862
1012593



1050
1012811
1013440
1012829



1051
1013456
1014055
1013468



1052
1013977
1014489
1013977



1053
1015224
1014529
1015206



1054
1016002
1015145
1015963



1055
1017120
1015939
1017120



1056
1017766
1017245
1017658



1057
1018911
1017916
1018893



1058
1019191
1018580
1019110



1059
1020199
1019831
1020196



1060
1021007
1020114
1020992



1061
1021569
1021075
1021557



1062
1022411
1022097
1022402



1063
1023344
1023667
1023344



1064
1023701
1023949
1023701



1065
1023976
1024776
1023976



1066
1024704
1025045
1024704



1067
1025881
1024967
1025845



1068
1026546
1025839
1026546



1069
1027379
1026546
1027373



1070
1030604
1027929
1030328



1071
1033252
1030508
1033249



1072
1031733
1032086
1031823



1073
1037037
1033456
1037016



1074
1035674
1035910
1035674



1075
1036175
1036507
1036268



1076
68(comp)
1036967
38



1077
16591
16989
16597



1078
31779
31408
31764



1079
56502
56834
56520



1080
56686
56913
56686



1081
64748
65074
64790



1082
73482
73195
73482



1083
78482
78736
78506



1084
79803
79411
79773



1085
82333
81959
82333



1086
87313
86999
87523



1087
109929
109456
109716



1088
111599
111351
111599



1089
112069
111734
111988



1090
112666
112911
112666



1091
114017
113715
113978



1092
120757
120464
120757



1093
125133
125522
125133



1094
131888
131604
131837



1095
144164
144427
144191



1096
150698
150369
150635



1097
164385
163948
164385



1098
165690
166115
165408



1099
168742
168425
168742



1100
170509
170793
170509



1101
177145
177474
177145



1102
188295
188023
188295



1103
188791
188330
188791



1104
190629
190336
190626



1105
197313
197083
197307



1106
210914
211384
210956



1107
235160
234852
235160



1108
237227
236913
237188



1109
249733
249446
249904



1110
253493
253158
253493



1111
253701
254789
253701



1112
271633
271932
271633



1113
275666
276070
275666



1114
277931
278218
277976



1115
282741
282481
282738



1116
293178
293489
293181



1117
303155
303469
303185



1118
309297
308965
309297



1119
312219
312536
312246



1120
312853
312602
312844



1121
313167
312772
313167



1122
320224
320598
320224



1123
340249
340503
340249



1124
352839
353324
352839



1125
373475
373699
373475



1126
377316
377756
377316



1127
379268
379657
379268



1128
395098
394823
395077



1129
401594
401142
401594



1130
410045
410539
410045



1131
411425
411658
411425



1132
414937
414416
414937



1133
422889
423212
422964



1134
427842
428183
427842



1135
428732
429451
428732



1136
442557
442799
442524



1137
443628
444041
443628



1138
443678
443166
443678



1139
445901
446155
445901



1140
467981
468262
468023



1141
471869
472108
471869



1142
488032
488337
488044



1143
497179
497694
497101



1144
500474
500202
500471



1145
508968
509561
508968



1146
510845
511264
510845



1147
526525
526848
526525



1148
531318
531863
531444



1149
556826
557224
556826



1150
564971
564537
564971



1151
566963
567232
566963



1152
570351
570890
570351



1153
571072
571332
571072



1154
576025
575801
576025



1155
590363
590650
590363



1156
597868
598593
597868



1157
606889
606626
606889



1158
608031
607786
608031



1159
610110
610391
610143



1160
632703
633353
632703



1161
637213
637482
637255



1162
650517
649924
650517



1163
652317
652562
652317



1164
654753
655325
654753



1165
661118
660810
661118



1166
677596
677057
677578



1167
679528
679253
679477



1168
732536
732210
732536



1169
742069
742383
742069



1170
759318
758782
759318



1171
760282
760521
760282



1172
771313
770894
771391



1173
772115
772408
772115



1174
788137
788457
788137



1175
816302
815967
816302



1176
846606
846914
846612



1177
867803
868054
867806



1178
875386
875658
875395



1179
876445
876915
876445



1180
884548
884312
884548



1181
891859
891467
891859



1182
900770
900417
900728



1183
902553
902269
902529



1184
908046
907783
908007



1185
912313
912567
912313



1186
935451
935741
935451



1187
946961
946692
946940



1188
953193
952783
953145



1189
966199
965873
966184



1190
969298
968765
969298



1191
971009
970731
971009



1192
972162
972404
972165



1193
973119
973508
973119



1194
998649
998404
998625



1195
1004280
1003882
1004280



1196
1010200
1009532
1010200



1197
1029174
1029482
1029180





















TABLE 4






ORF-


ORF-


ORFGenset
oligosFd
ORFoligosFp
ORFoligosBd
oligosBp



















2
1199
1198
3591
3590


3
1201
1200
3593
3592


4
1203
1202
3595
3594


5
1205
1204
3597
3596


6
1207
1206
3599
3598


7
1209
1208
3601
3600


8
1211
1210
3603
3602


9
1213
1212
3605
3604


10
1215
1214
3607
3606


11
1217
1216
3609
3608


12
1219
1218
3611
3610


13
1221
1220
3613
3612


14
1223
1222
3615
3614


15
1225
1224
3617
3616


16
1227
1226
3619
3618


17
1229
1228
3621
3620


18
1231
1230
3623
3622


19
1233
1232
3625
3624


20
1235
1234
3627
3626


21
1237
1236
3629
3628


22
1239
1238
3631
3630


23
1241
1240
3633
3632


24
1243
1242
3635
3634


25
1245
1244
3637
3636


26
1247
1246
3639
3638


27
1249
1248
3641
3640


28
1251
1250
3643
3642


29
1253
1252
3645
3644


30
1255
1254
3647
3646


31
1257
1256
3649
3648


32
1259
1258
3651
3650


33
1261
1260
3653
3652


34
1263
1262
3655
3654


35
1265
1264
3657
3656


36
1267
1266
3659
3658


37
1269
1268
3661
3660


38
1271
1270
3663
3662


39
1273
1272
3665
3664


40
1275
1274
3667
3666


41
1277
1276
3669
3668


42
1279
1278
3671
3670


43
1281
1280
3673
3672


44
1283
1282
3675
3674


45
1285
1284
3677
3676


46
1287
1286
3679
3678


47
1289
1288
3681
3680


48
1291
1290
3683
3682


49
1293
1292
3685
3684


50
1295
1294
3687
3686


51
1297
1296
3689
3688


52
1299
1298
3691
3690


53
1301
1300
3693
3692


54
1303
1302
3695
3694


55
1305
1304
3697
3696


56
1307
1306
3699
3698


57
1309
1308
3701
3700


58
1311
1310
3703
3702


59
1313
1312
3705
3704


60
1315
1314
3707
3706


61
1317
1316
3709
3708


62
1319
1318
3711
3710


63
1321
1320
3713
3712


64
1323
1322
3715
3714


65
1325
1324
3717
3716


66
1327
1326
3719
3718


67
1329
1328
3721
3720


68
1331
1330
3723
3722


69
1333
1332
3725
3724


70
1335
1334
3727
3726


71
1337
1336
3729
3728


72
1339
1338
3731
3730


73
1341
1340
3733
3732


74
1343
1342
3735
3734


75
1345
1344
3737
3736


76
1347
1346
3739
3738


77
1349
1348
3741
3740


78
1351
1350
3743
3742


79
1353
1352
3745
3744


80
1355
1354
3747
3746


81
1357
1356
3749
3748


82
1359
1358
3751
3750


83
1361
1360
3753
3752


84
1363
1362
3755
3754


85
1365
1364
3757
3756


86
1367
1366
3759
3758


87
1369
1368
3761
3760


88
1371
1370
3763
3762


89
1373
1372
3765
3764


90
1375
1374
3767
3766


91
1377
1376
3769
3768


92
1379
1378
3771
3770


93
1381
1380
3773
3772


94
1383
1382
3775
3774


95
1385
1384
3777
3776


96
1387
1386
3779
3778


97
1389
1388
3781
3780


98
1391
1390
3783
3782


99
1393
1392
3785
3784


100
1395
1394
3787
3786


101
1397
1396
3789
3788


102
1399
1398
3791
3790


103
1401
1400
3793
3792


104
1403
1402
3795
3794


105
1405
1404
3797
3796


106
1407
1406
3799
3798


107
1409
1408
3801
3800


108
1411
1410
3803
3802


109
1413
1412
3805
3804


110
1415
1414
3807
3806


111
1417
1416
3809
3808


112
1419
1418
3811
3810


113
1421
1420
3813
3812


114
1423
1422
3815
3814


115
1425
1424
3817
3816


116
1427
1426
3819
3818


117
1429
1428
3821
3820


118
1431
1430
3823
3822


119
1433
1432
3825
3824


120
1435
1434
3827
3826


121
1437
1436
3829
3828


122
1439
1438
3831
3830


123
1441
1440
3833
3832


124
1443
1442
3835
3834


125
1445
1444
3837
3836


126
1447
1446
3839
3838


127
1449
1448
3841
3840


128
1451
1450
3843
3842


129
1453
1452
3845
3844


130
1455
1454
3847
3846


131
1457
1456
3849
3848


132
1459
1458
3851
3850


133
1461
1460
3853
3852


134
1463
1462
3855
3854


135
1465
1464
3857
3856


136
1467
1466
3859
3858


137
1469
1468
3861
3860


138
1471
1470
3863
3862


139
1473
1472
3865
3864


140
1475
1474
3867
3866


141
1477
1476
3869
3868


142
1479
1478
3871
3870


143
1481
1480
3873
3872


144
1483
1482
3875
3874


145
1485
1484
3877
3876


146
1487
1486
3879
3878


147
1489
1488
3881
3880


148
1491
1490
3883
3882


149
1493
1492
3885
3884


150
1495
1494
3887
3886


151
1497
1496
3889
3888


152
1499
1498
3891
3890


153
1501
1500
3893
3892


154
1503
1502
3895
3894


155
1505
1504
3897
3896


156
1507
1506
3899
3898


157
1509
1508
3901
3900


158
1511
1510
3903
3902


159
1513
1512
3905
3904


160
1515
1514
3907
3906


161
1517
1516
3909
3908


162
1519
1518
3911
3910


163
1521
1520
3913
3912


164
1523
1522
3915
3914


165
1525
1524
3917
3916


166
1527
1526
3919
3918


167
1529
1528
3921
3920


168
1531
1530
3923
3922


169
1533
1532
3925
3924


170
1535
1534
3927
3926


171
1537
1536
3929
3928


172
1539
1538
3931
3930


173
1541
1540
3933
3932


174
1543
1542
3935
3934


175
1545
1544
3937
3936


176
1547
1546
3939
3938


177
1549
1548
3941
3940


178
1551
1550
3943
3942


179
1553
1552
3945
3944


180
1555
1554
3947
3946


181
1557
1556
3949
3948


182
1559
1558
3951
3950


183
1561
1560
3953
3952


184
1563
1562
3955
3954


185
1565
1564
3957
3956


186
1567
1566
3959
3958


187
1569
1568
3961
3960


188
1571
1570
3963
3962


189
1573
1572
3965
3964


190
1575
1574
3967
3966


191
1577
1576
3969
3968


192
1579
1578
3971
3970


193
1581
1580
3973
3972


194
1583
1582
3975
3974


195
1585
1584
3977
3976


196
1587
1586
3979
3978


197
1589
1588
3981
3980


198
1591
1590
3983
3982


199
1593
1592
3985
3984


200
1595
1594
3987
3986


201
1597
1596
3989
3988


202
1599
1598
3991
3990


203
1601
1600
3993
3992


204
1603
1602
3995
3994


205
1605
1604
3997
3996


206
1607
1606
3999
3998


207
1609
1608
4001
4000


208
1611
1610
4003
4002


209
1613
1612
4005
4004


210
1615
1614
4007
4006


211
1617
1616
4009
4008


212
1619
1618
4011
4010


213
1621
1620
4013
4012


214
1623
1622
4015
4014


215
1625
1624
4017
4016


216
1627
1626
4019
4018


217
1629
1628
4021
4020


218
1631
1630
4023
4022


219
1633
1632
4025
4024


220
1635
1634
4027
4026


221
1637
1636
4029
4028


222
1639
1638
4031
4030


223
1641
1640
4033
4032


224
1643
1642
4035
4034


225
1645
1644
4037
4036


226
1647
1646
4039
4038


227
1649
1648
4041
4040


228
1651
1650
4043
4042


229
1653
1652
4045
4044


230
1655
1654
4047
4046


231
1657
1656
4049
4048


232
1659
1658
4051
4050


233
1661
1660
4053
4052


234
1663
1662
4055
4054


235
1665
1664
4057
4056


236
1667
1666
4059
4058


237
1669
1668
4061
4060


238
1671
1670
4063
4062


239
1673
1672
4065
4064


240
1675
1674
4067
4066


241
1677
1676
4069
4068


242
1679
1678
4071
4070


243
1681
1680
4073
4072


244
1683
1682
4075
4074


245
1685
1684
4077
4076


246
1687
1686
4079
4078


247
1689
1688
4081
4080


248
1691
1690
4083
4082


249
1693
1692
4085
4084


250
1695
1694
4087
4086


251
1697
1696
4089
4088


252
1699
1698
4091
4090


253
1701
1700
4093
4092


254
1703
1702
4095
4094


255
1705
1704
4097
4096


256
1707
1706
4099
4098


257
1709
1708
4101
4100


258
1711
1710
4103
4102


259
1713
1712
4105
4104


260
1715
1714
4107
4106


261
1717
1716
4109
4108


262
1719
1718
4111
4110


263
1721
1720
4113
4112


264
1723
1722
4115
4114


265
1725
1724
4117
4116


266
1727
1726
4119
4118


267
1729
1728
4121
4120


268
1731
1730
4123
4122


269
1733
1732
4125
4124


270
1735
1734
4127
4126


271
1737
1736
4129
4128


272
1739
1738
4131
4130


273
1741
1740
4133
4132


274
1743
1742
4135
4134


275
1745
1744
4137
4136


276
1747
1746
4139
4138


277
1749
1748
4141
4140


278
1751
1750
4143
4142


279
1753
1752
4145
4144


280
1755
1754
4147
4146


281
1757
1756
4149
4148


282
1759
1758
4151
4150


283
1761
1760
4153
4152


284
1763
1762
4155
4154


285
1765
1764
4157
4156


286
1767
1766
4159
4158


287
1769
1768
4161
4160


288
1771
1770
4163
4162


289
1773
1772
4165
4164


290
1775
1774
4167
4166


291
1777
1776
4169
4168


292
1779
1778
4171
4170


293
1781
1780
4173
4172


294
1783
1782
4175
4174


295
1785
1784
4177
4176


296
1787
1786
4179
4178


297
1789
1788
4181
4180


298
1791
1790
4183
4182


299
1793
1792
4185
4184


300
1795
1794
4187
4186


301
1797
1796
4189
4188


302
1799
1798
4191
4190


303
1801
1800
4193
4192


304
1803
1802
4195
4194


305
1805
1804
4197
4196


306
1807
1806
4199
4198


307
1809
1808
4201
4200


308
1811
1810
4203
4202


309
1813
1812
4205
4204


310
1815
1814
4207
4206


311
1817
1816
4209
4208


312
1819
1818
4211
4210


313
1821
1820
4213
4212


314
1823
1822
4215
4214


315
1825
1824
4217
4216


316
1827
1826
4219
4218


317
1829
1828
4221
4220


318
1831
1830
4223
4222


319
1833
1832
4225
4224


320
1835
1834
4227
4226


321
1837
1836
4229
4228


322
1839
1838
4231
4230


323
1841
1840
4233
4232


324
1843
1842
4235
4234


325
1845
1844
4237
4236


326
1847
1846
4239
4238


327
1849
1848
4241
4240


328
1851
1850
4243
4242


329
1853
1852
4245
4244


330
1855
1854
4247
4246


331
1857
1856
4249
4248


332
1859
1858
4251
4250


333
1861
1860
4253
4252


334
1863
1862
4255
4254


335
1865
1864
4257
4256


336
1867
1866
4259
4258


337
1869
1868
4261
4260


338
1871
1870
4263
4262


339
1873
1872
4265
4264


340
1875
1874
4267
4266


341
1877
1876
4269
4268


342
1879
1878
4271
4270


343
1881
1880
4273
4272


344
1883
1882
4275
4274


345
1885
1884
4277
4276


346
1887
1886
4279
4278


347
1889
1888
4281
4280


348
1891
1890
4283
4282


349
1893
1892
4285
4284


350
1895
1894
4287
4286


351
1897
1896
4289
4288


352
1899
1898
4291
4290


353
1901
1900
4293
4292


354
1903
1902
4295
4294


355
1905
1904
4297
4296


356
1907
1906
4299
4298


357
1909
1908
4301
4300


358
1911
1910
4303
4302


359
1913
1912
4305
4304


360
1915
1914
4307
4306


361
1917
1916
4309
4308


362
1919
1918
4311
4310


363
1921
1920
4313
4312


364
1923
1922
4315
4314


365
1925
1924
4317
4316


366
1927
1926
4319
4318


367
1929
1928
4321
4320


368
1931
1930
4323
4322


369
1933
1932
4325
4324


370
1935
1934
4327
4326


371
1937
1936
4329
4328


372
1939
1938
4331
4330


373
1941
1940
4333
4332


374
1943
1942
4335
4334


375
1945
1944
4337
4336


376
1947
1946
4339
4338


377
1949
1948
4341
4340


378
1951
1950
4343
4342


379
1953
1952
4345
4344


380
1955
1954
4347
4346


381
1957
1956
4349
4348


382
1959
1958
4351
4350


383
1961
1960
4353
4352


384
1963
1962
4355
4354


385
1965
1964
4357
4356


386
1967
1966
4359
4358


387
1969
1968
4361
4360


388
1971
1970
4363
4362


389
1973
1972
4365
4364


390
1975
1974
4367
4366


391
1977
1976
4369
4368


392
1979
1978
4371
4370


393
1981
1980
4373
4372


394
1983
1982
4375
4374


395
1985
1984
4377
4376


396
1987
1986
4379
4378


397
1989
1988
4381
4380


398
1991
1990
4383
4382


399
1993
1992
4385
4384


400
1995
1994
4387
4386


401
1997
1996
4389
4388


402
1999
1998
4391
4390


403
2001
2000
4393
4392


404
2003
2002
4395
4394


405
2005
2004
4397
4396


406
2007
2006
4399
4398


407
2009
2008
4401
4400


408
2011
2010
4403
4402


409
2013
2012
4405
4404


410
2015
2014
4407
4406


411
2017
2016
4409
4408


412
2019
2018
4411
4410


413
2021
2020
4413
4412


414
2023
2022
4415
4414


415
2025
2024
4417
4416


416
2027
2026
4419
4418


417
2029
2028
4421
4420


418
2031
2030
4423
4422


419
2033
2032
4425
4424


420
2035
2034
4427
4426


421
2037
2036
4429
4428


422
2039
2038
4431
4430


423
2041
2040
4433
4432


424
2043
2042
4435
4434


425
2045
2044
4437
4436


426
2047
2046
4439
4438


427
2049
2048
4441
4440


428
2051
2050
4443
4442


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2053
2052
4445
4444


430
2055
2054
4447
4446


431
2057
2056
4449
4448


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2059
2058
4451
4450


433
2061
2060
4453
4452


434
2063
2062
4455
4454


435
2065
2064
4457
4456


436
2067
2066
4459
4458


437
2069
2068
4461
4460


438
2071
2070
4463
4462


439
2073
2072
4465
4464


440
2075
2074
4467
4466


441
2077
2076
4469
4468


442
2079
2078
4471
4470


443
2081
2080
4473
4472


444
2083
2082
4475
4474


445
2085
2084
4477
4476


446
2087
2086
4479
4478


447
2089
2088
4481
4480


448
2091
2090
4483
4482


449
2093
2092
4485
4484


450
2095
2094
4487
4486


451
2097
2096
4489
4488


452
2099
2098
4491
4490


453
2101
2100
4493
4492


454
2103
2102
4495
4494


455
2105
2104
4497
4496


456
2107
2106
4499
4498


457
2109
2108
4501
4500


458
2111
2110
4503
4502


459
2113
2112
4505
4504


460
2115
2114
4507
4506


461
2117
2116
4509
4508


462
2119
2118
4511
4510


463
2121
2120
4513
4512


464
2123
2122
4515
4514


465
2125
2124
4517
4516


466
2127
2126
4519
4518


467
2129
2128
4521
4520


468
2131
2130
4523
4522


469
2133
2132
4525
4524


470
2135
2134
4527
4526


471
2137
2136
4529
4528


472
2139
2138
4531
4530


473
2141
2140
4533
4532


474
2143
2142
4535
4534


475
2145
2144
4537
4536


476
2147
2146
4539
4538


477
2149
2148
4541
4540


478
2151
2150
4543
4542


479
2153
2152
4545
4544


480
2155
2154
4547
4546


481
2157
2156
4549
4548


482
2159
2158
4551
4550


483
2161
2160
4553
4552


484
2163
2162
4555
4554


485
2165
2164
4557
4556


486
2167
2166
4559
4558


487
2169
2168
4561
4560


488
2171
2170
4563
4562


489
2173
2172
4565
4564


490
2175
2174
4567
4566


491
2177
2176
4569
4568


492
2179
2178
4571
4570


493
2181
2180
4573
4572


494
2183
2182
4575
4574


495
2185
2184
4577
4576


496
2187
2186
4579
4578


497
2189
2188
4581
4580


498
2191
2190
4583
4582


499
2193
2192
4585
4584


500
2195
2194
4587
4586


501
2197
2196
4589
4588


502
2199
2198
4591
4590


503
2201
2200
4593
4592


504
2203
2202
4595
4594


505
2205
2204
4597
4596


506
2207
2206
4599
4598


507
2209
2208
4601
4600


508
2211
2210
4603
4602


509
2213
2212
4605
4604


510
2215
2214
4607
4606


511
2217
2216
4609
4608


512
2219
2218
4611
4610


513
2221
2220
4613
4612


514
2223
2222
4615
4614


515
2225
2224
4617
4616


516
2227
2226
4619
4618


517
2229
2228
4621
4620


518
2231
2230
4623
4622


519
2233
2232
4625
4624


520
2235
2234
4627
4626


521
2237
2236
4629
4628


522
2239
2238
4631
4630


523
2241
2240
4633
4632


524
2243
2242
4635
4634


525
2245
2244
4637
4636


526
2247
2246
4639
4638


527
2249
2248
4641
4640


528
2251
2250
4643
4642


529
2253
2252
4645
4644


530
2255
2254
4647
4646


531
2257
2256
4649
4648


532
2259
2258
4651
4650


533
2261
2260
4653
4652


534
2263
2262
4655
4654


535
2265
2264
4657
4656


536
2267
2266
4659
4658


537
2269
2268
4661
4660


538
2271
2270
4663
4662


539
2273
2272
4665
4664


540
2275
2274
4667
4666


541
2277
2276
4669
4668


542
2279
2278
4671
4670


543
2281
2280
4673
4672


544
2283
2282
4675
4674


545
2285
2284
4677
4676


546
2287
2286
4679
4678


547
2289
2288
4681
4680


548
2291
2290
4683
4682


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2293
2292
4685
4684


550
2295
2294
4687
4686


551
2297
2296
4689
4688


552
2299
2298
4691
4690


553
2301
2300
4693
4692


554
2303
2302
4695
4694


555
2305
2304
4697
4696


556
2307
2306
4699
4698


557
2309
2308
4701
4700


558
2311
2310
4703
4702


559
2313
2312
4705
4704


560
2315
2314
4707
4706


561
2317
2316
4709
4708


562
2319
2318
4711
4710


563
2321
2320
4713
4712


564
2323
2322
4715
4714


565
2325
2324
4717
4716


566
2327
2326
4719
4718


567
2329
2328
4721
4720


568
2331
2330
4723
4722


569
2333
2332
4725
4724


570
2335
2334
4727
4726


571
2337
2336
4729
4728


572
2339
2338
4731
4730


573
2341
2340
4733
4732


574
2343
2342
4735
4734


575
2345
2344
4737
4736


576
2347
2346
4739
4738


577
2349
2348
4741
4740


578
2351
2350
4743
4742


579
2353
2352
4745
4744


580
2355
2354
4747
4746


581
2357
2356
4749
4748


582
2359
2358
4751
4750


583
2361
2360
4753
4752


584
2363
2362
4755
4754


585
2365
2364
4757
4756


586
2367
2366
4759
4758


587
2369
2368
4761
4760


588
2371
2370
4763
4762


589
2373
2372
4765
4764


590
2375
2374
4767
4766


591
2377
2376
4769
4768


592
2379
2378
4771
4770


593
2381
2380
4773
4772


594
2383
2382
4775
4774


595
2385
2384
4777
4776


596
2387
2386
4779
4778


597
2389
2388
4781
4780


598
2391
2390
4783
4782


599
2393
2392
4785
4784


600
2395
2394
4787
4786


601
2397
2396
4789
4788


602
2399
2398
4791
4790


603
2401
2400
4793
4792


604
2403
2402
4795
4794


605
2405
2404
4797
4796


606
2407
2406
4799
4798


607
2409
2408
4801
4800


608
2411
2410
4803
4802


609
2413
2412
4805
4804


610
2415
2414
4807
4806


611
2417
2416
4809
4808


612
2419
2418
4811
4810


613
2421
2420
4813
4812


614
2423
2422
4815
4814


615
2425
2424
4817
4816


616
2427
2426
4819
4818


617
2429
2428
4821
4820


618
2431
2430
4823
4822


619
2433
2432
4825
4824


620
2435
2434
4827
4826


621
2437
2436
4829
4828


622
2439
2438
4831
4830


623
2441
2440
4833
4832


624
2443
2442
4835
4834


625
2445
2444
4837
4836


626
2447
2446
4839
4838


627
2449
2448
4841
4840


628
2451
2450
4843
4842


629
2453
2452
4845
4844


630
2455
2454
4847
4846


631
2457
2456
4849
4848


632
2459
2458
4851
4850


633
2461
2460
4853
4852


634
2463
2462
4855
4854


635
2465
2464
4857
4856


636
2467
2466
4859
4858


637
2469
2468
4861
4860


638
2471
2470
4863
4862


639
2473
2472
4865
4864


640
2475
2474
4867
4866


641
2477
2476
4869
4868


642
2479
2478
4871
4870


643
2481
2480
4873
4872


644
2483
2482
4875
4874


645
2485
2484
4877
4876


646
2487
2486
4879
4878


647
2489
2488
4881
4880


648
2491
2490
4883
4882


649
2493
2492
4885
4884


650
2495
2494
4887
4886


651
2497
2496
4889
4888


652
2499
2498
4891
4890


653
2501
2500
4893
4892


654
2503
2502
4895
4894


655
2505
2504
4897
4896


656
2507
2506
4899
4898


657
2509
2508
4901
4900


658
2511
2510
4903
4902


659
2513
2512
4905
4904


660
2515
2514
4907
4906


661
2517
2516
4909
4908


662
2519
2518
4911
4910


663
2521
2520
4913
4912


664
2523
2522
4915
4914


665
2525
2524
4917
4916


666
2527
2526
4919
4918


667
2529
2528
4921
4920


668
2531
2530
4923
4922


669
2533
2532
4925
4924


670
2535
2534
4927
4926


671
2537
2536
4929
4928


672
2539
2538
4931
4930


673
2541
2540
4933
4932


674
2543
2542
4935
4934


675
2545
2544
4937
4936


676
2547
2546
4939
4938


677
2549
2548
4941
4940


678
2551
2550
4943
4942


679
2553
2552
4945
4944


680
2555
2554
4947
4946


681
2557
2556
4949
4948


682
2559
2558
4951
4950


683
2561
2560
4953
4952


684
2563
2562
4955
4954


685
2565
2564
4957
4956


686
2567
2566
4959
4958


687
2569
2568
4961
4960


688
2571
2570
4963
4962


689
2573
2572
4965
4964


690
2575
2574
4967
4966


691
2577
2576
4969
4968


692
2579
2578
4971
4970


693
2581
2580
4973
4972


694
2583
2582
4975
4974


695
2585
2584
4977
4976


696
2587
2586
4979
4978


697
2589
2588
4981
4980


698
2591
2590
4983
4982


699
2593
2592
4985
4984


700
2595
2594
4987
4986


701
2597
2596
4989
4988


702
2599
2598
4991
4990


703
2601
2600
4993
4992


704
2603
2602
4995
4994


705
2605
2604
4997
4996


706
2607
2606
4999
4998


707
2609
2608
5001
5000


708
2611
2610
5003
5002


709
2613
2612
5005
5004


710
2615
2614
5007
5006


711
2617
2616
5009
5008


712
2619
2618
5011
5010


713
2621
2620
5013
5012


714
2623
2622
5015
5014


715
2625
2624
5017
5016


716
2627
2626
5019
5018


717
2629
2628
5021
5020


718
2631
2630
5023
5022


719
2633
2632
5025
5024


720
2635
2634
5027
5026


721
2637
2636
5029
5028


722
2639
2638
5031
5030


723
2641
2640
5033
5032


724
2643
2642
5035
5034


725
2645
2644
5037
5036


726
2647
2646
5039
5038


727
2649
2648
5041
5040


728
2651
2650
5043
5042


729
2653
2652
5045
5044


730
2655
2654
5047
5046


731
2657
2656
5049
5048


732
2659
2658
5051
5050


733
2661
2660
5053
5052


734
2663
2662
5055
5054


735
2665
2664
5057
5056


736
2667
2666
5059
5058


737
2669
2668
5061
5060


738
2671
2670
5063
5062


739
2673
2672
5065
5064


740
2675
2674
5067
5066


741
2677
2676
5069
5068


742
2679
2678
5071
5070


743
2681
2680
5073
5072


744
2683
2682
5075
5074


745
2685
2684
5077
5076


746
2687
2686
5079
5078


747
2689
2688
5081
5080


748
2691
2690
5083
5082


749
2693
2692
5085
5084


750
2695
2694
5087
5086


751
2697
2696
5089
5088


752
2699
2698
5091
5090


753
2701
2700
5093
5092


754
2703
2702
5095
5094


755
2705
2704
5097
5096


756
2707
2706
5099
5098


757
2709
2708
5101
5100


758
2711
2710
5103
5102


759
2713
2712
5105
5104


760
2715
2714
5107
5106


761
2717
2716
5109
5108


762
2719
2718
5111
5110


763
2721
2720
5113
5112


764
2723
2722
5115
5114


765
2725
2724
5117
5116


766
2727
2726
5119
5118


767
2729
2728
5121
5120


768
2731
2730
5123
5122


769
2733
2732
5125
5124


770
2735
2734
5127
5126


771
2737
2736
5129
5128


772
2739
2738
5131
5130


773
2741
2740
5133
5132


774
2743
2742
5135
5134


775
2745
2744
5137
5136


776
2747
2746
5139
5138


777
2749
2748
5141
5140


778
2751
2750
5143
5142


779
2753
2752
5145
5144


780
2755
2754
5147
5146


781
2757
2756
5149
5148


782
2759
2758
5151
5150


783
2761
2760
5153
5152


784
2763
2762
5155
5154


785
2765
2764
5157
5156


786
2767
2766
5159
5158


787
2769
2768
5161
5160


788
2771
2770
5163
5162


789
2773
2772
5165
5164


790
2775
2774
5167
5166


791
2777
2776
5169
5168


792
2779
2778
5171
5170


793
2781
2780
5173
5172


794
2783
2782
5175
5174


795
2785
2784
5177
5176


796
2787
2786
5179
5178


797
2789
2788
5181
5180


798
2791
2790
5183
5182


799
2793
2792
5185
5184


800
2795
2794
5187
5186


801
2797
2796
5189
5188


802
2799
2798
5191
5190


803
2801
2800
5193
5192


804
2803
2802
5195
5194


805
2805
2804
5197
5196


806
2807
2806
5199
5198


807
2809
2808
5201
5200


808
2811
2810
5203
5202


809
2813
2812
5205
5204


810
2815
2814
5207
5206


811
2817
2816
5209
5208


812
2819
2818
5211
5210


813
2821
2820
5213
5212


814
2823
2822
5215
5214


815
2825
2824
5217
5216


816
2827
2826
5219
5218


817
2829
2828
5221
5220


818
2831
2830
5223
5222


819
2833
2832
5225
5224


820
2835
2834
5227
5226


821
2837
2836
5229
5228


822
2839
2838
5231
5230


823
2841
2840
5233
5232


824
2843
2842
5235
5234


825
2845
2844
5237
5236


826
2847
2846
5239
5238


827
2849
2848
5241
5240


828
2851
2850
5243
5242


829
2853
2852
5245
5244


830
2855
2854
5247
5246


831
2857
2856
5249
5248


832
2859
2858
5251
5250


833
2861
2860
5253
5252


834
2863
2862
5255
5254


835
2865
2864
5257
5256


836
2867
2866
5259
5258


837
2869
2868
5261
5260


838
2871
2870
5263
5262


839
2873
2872
5265
5264


840
2875
2874
5267
5266


841
2877
2876
5269
5268


842
2879
2878
5271
5270


843
2881
2880
5273
5272


844
2883
2882
5275
5274


845
2885
2884
5277
5276


846
2887
2886
5279
5278


847
2889
2888
5281
5280


848
2891
2890
5283
5282


849
2893
2892
5285
5284


850
2895
2894
5287
5286


851
2897
2896
5289
5288


852
2899
2898
5291
5290


853
2901
2900
5293
5292


854
2903
2902
5295
5294


855
2905
2904
5297
5296


856
2907
2906
5299
5298


857
2909
2908
5301
5300


858
2911
2910
5303
5302


859
2913
2912
5305
5304


860
2915
2914
5307
5306


861
2917
2916
5309
5308


862
2919
2918
5311
5310


863
2921
2920
5313
5312


864
2923
2922
5315
5314


865
2925
2924
5317
5316


866
2927
2926
5319
5318


867
2929
2928
5321
5320


868
2931
2930
5323
5322


869
2933
2932
5325
5324


870
2935
2934
5327
5326


871
2937
2936
5329
5328


872
2939
2938
5331
5330


873
2941
2940
5333
5332


874
2943
2942
5335
5334


875
2945
2944
5337
5336


876
2947
2946
5339
5338


877
2949
2948
5341
5340


878
2951
2950
5343
5342


879
2953
2952
5345
5344


880
2955
2954
5347
5346


881
2957
2956
5349
5348


882
2959
2958
5351
5350


883
2961
2960
5353
5352


884
2963
2962
5355
5354


885
2965
2964
5357
5356


886
2967
2966
5359
5358


887
2969
2968
5361
5360


888
2971
2970
5363
5362


889
2973
2972
5365
5364


890
2975
2974
5367
5366


891
2977
2976
5369
5368


892
2979
2978
5371
5370


893
2981
2980
5373
5372


894
2983
2982
5375
5374


895
2985
2984
5377
5376


896
2987
2986
5379
5378


897
2989
2988
5381
5380


898
2991
2990
5383
5382


899
2993
2992
5385
5384


900
2995
2994
5387
5386


901
2997
2996
5389
5388


902
2999
2998
5391
5390


903
3001
3000
5393
5392


904
3003
3002
5395
5394


905
3005
3004
5397
5396


906
3007
3006
5399
5398


907
3009
3008
5401
5400


908
3011
3010
5403
5402


909
3013
3012
5405
5404


910
3015
3014
5407
5406


911
3017
3016
5409
5408


912
3019
3018
5411
5410


913
3021
3020
5413
5412


914
3023
3022
5415
5414


915
3025
3024
5417
5416


916
3027
3026
5419
5418


917
3029
3028
5421
5420


918
3031
3030
5423
5422


919
3033
3032
5425
5424


920
3035
3034
5427
5426


921
3037
3036
5429
5428


922
3039
3038
5431
5430


923
3041
3040
5433
5432


924
3043
3042
5435
5434


925
3045
3044
5437
5436


926
3047
3046
5439
5438


927
3049
3048
5441
5440


928
3051
3050
5443
5442


929
3053
3052
5445
5444


930
3055
3054
5447
5446


931
3057
3056
5449
5448


932
3059
3058
5451
5450


933
3061
3060
5453
5452


934
3063
3062
5455
5454


935
3065
3064
5457
5456


936
3067
3066
5459
5458


937
3069
3068
5461
5460


938
3071
3070
5463
5462


939
3073
3072
5465
5464


940
3075
3074
5467
5466


941
3077
3076
5469
5468


942
3079
3078
5471
5470


943
3081
3080
5473
5472


944
3083
3082
5475
5474


945
3085
3084
5477
5476


946
3087
3086
5479
5478


947
3089
3088
5481
5480


948
3091
3090
5483
5482


949
3093
3092
5485
5484


950
3095
3094
5487
5486


951
3097
3096
5489
5488


952
3099
3098
5491
5490


953
3101
3100
5493
5492


954
3103
3102
5495
5494


955
3105
3104
5497
5496


956
3107
3106
5499
5498


957
3109
3108
5501
5500


958
3111
3110
5503
5502


959
3113
3112
5505
5504


960
3115
3114
5507
5506


961
3117
3116
5509
5508


962
3119
3118
5511
5510


963
3121
3120
5513
5512


964
3123
3122
5515
5514


965
3125
3124
5517
5516


966
3127
3126
5519
5518


967
3129
3128
5521
5520


968
3131
3130
5523
5522


969
3133
3132
5525
5524


970
3135
3134
5527
5526


971
3137
3136
5529
5528


972
3139
3138
5531
5530


973
3141
3140
5533
5532


974
3143
3142
5535
5534


975
3145
3144
5537
5536


976
3147
3146
5539
5538


977
3149
3148
5541
5540


978
3151
3150
5543
5542


979
3153
3152
5545
5544


980
3155
3154
5547
5546


981
3157
3156
5549
5548


982
3159
3158
5551
5550


983
3161
3160
5553
5552


984
3163
3162
5555
5554


985
3165
3164
5557
5556


986
3167
3166
5559
5558


987
3169
3168
5561
5560


988
3171
3170
5563
5562


989
3173
3172
5565
5564


990
3175
3174
5567
5566


991
3177
3176
5569
5568


992
3179
3178
5571
5570


993
3181
3180
5573
5572


994
3183
3182
5575
5574


995
3185
3184
5577
5576


996
3187
3186
5579
5578


997
3189
3188
5581
5580


998
3191
3190
5583
5582


999
3193
3192
5585
5584


1000
3195
3194
5587
5586


1001
3197
3196
5589
5588


1002
3199
3198
5591
5590


1003
3201
3200
5593
5592


1004
3203
3202
5595
5594


1005
3205
3204
5597
5596


1006
3207
3206
5599
5598


1007
3209
3208
5601
5600


1008
3211
3210
5603
5602


1009
3213
3212
5605
5604


1010
3215
3214
5607
5606


1011
3217
3216
5609
5608


1012
3219
3218
5611
5610


1013
3221
3220
5613
5612


1014
3223
3222
5615
5614


1015
3225
3224
5617
5616


1016
3227
3226
5619
5618


1017
3229
3228
5621
5620


1018
3231
3230
5623
5622


1019
3233
3232
5625
5624


1020
3235
3234
5627
5626


1021
3237
3236
5629
5628


1022
3239
3238
5631
5630


1023
3241
3240
5633
5632


1024
3243
3242
5635
5634


1025
3245
3244
5637
5636


1026
3247
3246
5639
5638


1027
3249
3248
5641
5640


1028
3251
3250
5643
5642


1029
3253
3252
5645
5644


1030
3255
3254
5647
5646


1031
3257
3256
5649
5648


1032
3259
3258
5651
5650


1033
3261
3260
5653
5652


1034
3263
3262
5655
5654


1035
3265
3264
5657
5656


1036
3267
3266
5659
5658


1037
3269
3268
5661
5660


1038
3271
3270
5663
5662


1039
3273
3272
5665
5664


1040
3275
3274
5667
5666


1041
3277
3276
5669
5668


1042
3279
3278
5671
5670


1043
3281
3280
5673
5672


1044
3283
3282
5675
5674


1045
3285
3284
5677
5676


1046
3287
3286
5679
5678


1047
3289
3288
5681
5680


1048
3291
3290
5683
5682


1049
3293
3292
5685
5684


1050
3295
3294
5687
5686


1051
3297
3296
5689
5688


1052
3299
3298
5691
5690


1053
3301
3300
5693
5692


1054
3303
3302
5695
5694


1055
3305
3304
5697
5696


1056
3307
3306
5699
5698


1057
3309
3308
5701
5700


1058
3311
3310
5703
5702


1059
3313
3312
5705
5704


1060
3315
3314
5707
5706


1061
3317
3316
5709
5708


1062
3319
3318
5711
5710


1063
3321
3320
5713
5712


1064
3323
3322
5715
5714


1065
3325
3324
5717
5716


1066
3327
3326
5719
5718


1067
3329
3328
5721
5720


1068
3331
3330
5723
5722


1069
3333
3332
5725
5724


1070
3335
3334
5727
5726


1071
3337
3336
5729
5728


1072
3339
3338
5731
5730


1073
3341
3340
5733
5732


1074
3343
3342
5735
5734


1075
3345
3344
5737
5736


1076
3347
3346
5739
5738


1077
3349
3348
5741
5740


1078
3351
3350
5743
5742


1079
3353
3352
5745
5744


1080
3355
3354
5747
5746


1081
3357
3356
5749
5748


1082
3359
3358
5751
5750


1083
3361
3360
5753
5752


1084
3363
3362
5755
5754


1085
3365
3364
5757
5756


1086
3367
3366
5759
5758


1087
3369
3368
5761
5760


1088
3371
3370
5763
5762


1089
3373
3372
5765
5764


1090
3375
3374
5767
5766


1091
3377
3376
5769
5768


1092
3379
3378
5771
5770


1093
3381
3380
5773
5772


1094
3383
3382
5775
5774


1095
3385
3384
5777
5776


1096
3387
3386
5779
5778


1097
3389
3388
5781
5780


1098
3391
3390
5783
5782


1099
3393
3392
5785
5784


1100
3395
3394
5787
5786


1101
3397
3396
5789
5788


1102
3399
3398
5791
5790


1103
3401
3400
5793
5792


1104
3403
3402
5795
5794


1105
3405
3404
5797
5796


1106
3407
3406
5799
5798


1107
3409
3408
5801
5800


1108
3411
3410
5803
5802


1109
3413
3412
5805
5804


1110
3415
3414
5807
5806


1111
3417
3416
5809
5808


1112
3419
3418
5811
5810


1113
3421
3420
5813
5812


1114
3423
3422
5815
5814


1115
3425
3424
5817
5816


1116
3427
3426
5819
5818


1117
3429
3428
5821
5820


1118
3431
3430
5823
5822


1119
3433
3432
5825
5824


1120
3435
3434
5827
5826


1121
3437
3436
5829
5828


1122
3439
3438
5831
5830


1123
3441
3440
5833
5832


1124
3443
3442
5835
5834


1125
3445
3444
5837
5836


1126
3447
3446
5839
5838


1127
3449
3448
5841
5840


1128
3451
3450
5843
5842


1129
3453
3452
5845
5844


1130
3455
3454
5847
5846


1131
3457
3456
5849
5848


1132
3459
3458
5851
5850


1133
3461
3460
5853
5852


1134
3463
3462
5855
5854


1135
3465
3464
5857
5856


1136
3467
3466
5859
5858


1137
3469
3468
5861
5860


1138
3471
3470
5863
5862


1139
3473
3472
5865
5864


1140
3475
3474
5867
5866


1141
3477
3476
5869
5868


1142
3479
3478
5871
5870


1143
3481
3480
5873
5872


1144
3483
3482
5875
5874


1145
3485
3484
5877
5876


1146
3487
3486
5879
5878


1147
3489
3488
5881
5880


1148
3491
3490
5883
5882


1149
3493
3492
5885
5884


1150
3495
3494
5887
5886


1151
3497
3496
5889
5888


1152
3499
3498
5891
5890


1153
3501
3500
5893
5892


1154
3503
3502
5895
5894


1155
3505
3504
5897
5896


1156
3507
3506
5899
5898


1157
3509
3508
5901
5900


1158
3511
3510
5903
5902


1159
3513
3512
5905
5904


1160
3515
3514
5907
5906


1161
3517
3516
5909
5908


1162
3519
3518
5911
5910


1163
3521
3520
5913
5912


1164
3523
3522
5915
5914


1165
3525
3524
5917
5916


1166
3527
3526
5919
5918


1167
3529
3528
5921
5920


1168
3531
3530
5923
5922


1169
3533
3532
5925
5924


1170
3535
3534
5927
5926


1171
3537
3536
5929
5928


1172
3539
3538
5931
5930


1173
3541
3540
5933
5932


1174
3543
3542
5935
5934


1175
3545
3544
5937
5936


1176
3547
3546
5939
5938


1177
3549
3548
5941
5940


1178
3551
3550
5943
5942


1179
3553
3552
5945
5944


1180
3555
3554
5947
5946


1181
3557
3556
5949
5948


1182
3559
3558
5951
5950


1183
3561
3560
5953
5952


1184
3563
3562
5955
5954


1185
3565
3564
5957
5956


1186
3567
3566
5959
5958


1187
3569
3568
5961
5960


1188
3571
3570
5963
5962


1189
3573
3572
5965
5964


1190
3575
3574
5967
5966


1191
3577
3576
5969
5968


1192
3579
3578
5971
5970


1193
3581
3580
5973
5972


1194
3583
3582
5975
5974


1195
3585
3584
5977
5976


1196
3587
3586
5979
5978


1197
3589
3588
5981
5980


















TABLE 5





SEQ ID
Or.
position

















1198
F
1038449


1199
F
1036517


1200
F
250


1201
F
1036965


1202
F
3011


1203
F
1123


1204
F
4907


1205
F
2996


1206
F
6379


1207
F
4483


1208
F
7837


1209
F
5961


1210
F
8351


1211
F
6467


1212
F
8705


1213
F
6834


1214
F
9598


1215
F
7709


1216
F
10134


1217
F
8248


1218
F
10990


1219
F
9060


1220
F
11823


1221
F
9946


1222
F
13236


1223
F
11410


1224
F
14529


1225
F
12643


1226
F
14668


1227
F
12813


1228
F
15747


1229
F
13844


1230
F
15903


1231
F
14019


1232
F
17198


1233
F
15298


1234
F
18218


1235
F
16263


1236
F
20595


1237
F
18692


1238
F
21932


1239
F
19969


1240
F
22259


1241
F
20338


1242
F
22605


1243
F
20659


1244
F
22890


1245
F
20987


1246
F
23150


1247
F
21244


1248
F
24413


1249
F
22506


1250
F
26379


1251
F
24476


1252
F
27498


1253
F
25602


1254
F
28476


1255
F
26621


1256
F
29785


1257
F
27860


1258
F
30276


1259
F
28363


1260
F
31184


1261
F
29287


1262
F
31574


1263
F
29650


1264
F
33095


1265
F
31184


1266
F
33840


1267
F
31949


1268
F
34769


1269
F
32869


1270
F
34915


1271
F
32961


1272
F
35696


1273
F
33793


1274
F
36794


1275
F
34893


1276
F
37960


1277
F
36085


1278
F
38924


1279
F
37017


1280
F
39704


1281
F
37754


1282
F
40541


1283
F
38615


1284
F
41945


1285
F
40054


1286
F
42779


1287
F
40859


1288
F
43991


1289
F
42061


1290
F
45056


1291
F
43155


1292
F
45755


1293
F
43821


1294
F
46272


1295
F
44382


1296
F
46654


1297
F
44763


1298
F
47926


1299
F
46059


1300
F
48403


1301
F
46485


1302
F
49871


1303
F
47980


1304
F
50706


1305
F
48792


1306
F
52129


1307
F
50199


1308
F
53247


1309
F
51346


1310
F
54376


1311
F
52462


1312
F
54790


1313
F
52890


1314
F
55404


1315
F
53540


1316
F
56602


1317
F
54695


1318
F
58151


1319
F
56284


1320
F
58965


1321
F
57039


1322
F
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1920
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1927
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1928
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1930
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1931
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1932
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1933
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1935
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1936
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1937
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1938
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1939
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1940
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1941
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1943
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1946
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1950
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1956
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1957
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1958
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1960
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1961
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1962
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1963
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1964
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1965
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1966
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1967
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1968
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1969
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1970
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1971
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1972
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1973
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1974
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1975
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1976
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1977
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1978
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1979
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1980
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1981
F
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1982
F
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1983
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1984
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1985
F
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1986
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1987
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1988
F
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1989
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1990
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1991
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1992
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1993
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1994
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1995
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1996
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1997
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1998
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1999
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2000
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2001
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2002
F
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2003
F
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2004
F
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2005
F
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2006
F
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2007
F
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2008
F
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2009
F
396790


2010
F
399550


2011
F
397659


2012
F
399797


2013
F
397915


2014
F
401527


2015
F
399623


2016
F
401907


2017
F
399960


2018
F
403017


2019
F
401131


2020
F
403017


2021
F
401131


2022
F
404910


2023
F
403010


2024
F
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2025
F
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2026
F
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2027
F
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2028
F
410291


2029
F
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2030
F
411488


2031
F
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2032
F
412379


2033
F
410487


2034
F
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2035
F
411263


2036
F
413606


2037
F
411626


2038
F
413721


2039
F
411859


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5565
B
954930


5566
B
954509


5567
B
956384


5568
B
955397


5569
B
957278


5570
B
958191


5571
B
960060


5572
B
959570


5573
B
961432


5574
B
961273


5575
B
963183


5576
B
961837


5577
B
963749


5578
B
962823


5579
B
964695


5580
B
962199


5581
B
964099


5582
B
965286


5583
B
967118


5584
B
965928


5585
B
967828


5586
B
967261


5587
B
969179


5588
B
968345


5589
B
970181


5590
B
969123


5591
B
971023


5592
B
970973


5593
B
972849


5594
B
972081


5595
B
973933


5596
B
973279


5597
B
975173


5598
B
974803


5599
B
976683


5600
B
975459


5601
B
977346


5602
B
976431


5603
B
978335


5604
B
976740


5605
B
978640


5606
B
977175


5607
B
979042


5608
B
977855


5609
B
979768


5610
B
978153


5611
B
980060


5612
B
978655


5613
B
980553


5614
B
979204


5615
B
981104


5616
B
979554


5617
B
981465


5618
B
981423


5619
B
983319


5620
B
980363


5621
B
982289


5622
B
982361


5623
B
984236


5624
B
983818


5625
B
985718


5626
B
984720


5627
B
986608


5628
B
985607


5629
B
987553


5630
B
986323


5631
B
988223


5632
B
986925


5633
B
988825


5634
B
987850


5635
B
989749


5636
B
988354


5637
B
990252


5638
B
988474


5639
B
990393


5640
B
989437


5641
B
991305


5642
B
993662


5643
B
995596


5644
B
994015


5645
B
995906


5646
B
994084


5647
B
995955


5648
B
994523


5649
B
996382


5650
B
995903


5651
B
997791


5652
B
996831


5653
B
998764


5654
B
998505


5655
B
1000417


5656
B
999445


5657
B
1001345


5658
B
1001253


5659
B
1003169


5660
B
1001751


5661
B
1003637


5662
B
1001954


5663
B
1003786


5664
B
1004003


5665
B
1005872


5666
B
1005114


5667
B
1006999


5668
B
1005620


5669
B
1007561


5670
B
1007761


5671
B
1009618


5672
B
1008052


5673
B
1009941


5674
B
1008954


5675
B
1010818


5676
B
1009679


5677
B
1011621


5678
B
1012274


5679
B
1014193


5680
B
1012682


5681
B
1014550


5682
B
1012855


5683
B
1014755


5684
B
1013104


5685
B
1014996


5686
B
1013698


5687
B
1015571


5688
B
1014289


5689
B
1016181


5690
B
1014730


5691
B
1016653


5692
B
1015459


5693
B
1017377


5694
B
1016272


5695
B
1018122


5696
B
1017377


5697
B
1019285


5698
B
1018043


5699
B
1019888


5700
B
1019146


5701
B
1021064


5702
B
1019421


5703
B
1021323


5704
B
1020440


5705
B
1022319


5706
B
1021269


5707
B
1023161


5708
B
1021789


5709
B
1023722


5710
B
1022638


5711
B
1024535


5712
B
1023900


5713
B
1025787


5714
B
1024169


5715
B
1026083


5716
B
1024996


5717
B
1026938


5718
B
1025295


5719
B
1027165


5720
B
1026136


5721
B
1028031


5722
B
1026823


5723
B
1028699


5724
B
1027642


5725
B
1029524


5726
B
1030824


5727
B
1032737


5728
B
1033510


5729
B
1035372


5730
B
1032306


5731
B
1034209


5732
B
1037275


5733
B
1162


5734
B
1036130


5735
B
1038037


5736
B
1036727


5737
B
149


5738
B
225


5739
B
2104


5740
B
17209


5741
B
19109


5742
B
32032


5743
B
33899


5744
B
57057


5745
B
58954


5746
B
57141


5747
B
59033


5748
B
65406


5749
B
67210


5750
B
73871


5751
B
75741


5752
B
78956


5753
B
80903


5754
B
80042


5755
B
81944


5756
B
82642


5757
B
84491


5758
B
87820


5759
B
89658


5760
B
110184


5761
B
112086


5762
B
111873


5763
B
113837


5764
B
112302


5765
B
114206


5766
B
113165


5767
B
115093


5768
B
114270


5769
B
116158


5770
B
121039


5771
B
122904


5772
B
125742


5773
B
127643


5774
B
132170


5775
B
134028


5776
B
144647


5777
B
146547


5778
B
150960


5779
B
152837


5780
B
164761


5781
B
166686


5782
B
166362


5783
B
168305


5784
B
168970


5785
B
170889


5786
B
171056


5787
B
173021


5788
B
177747


5789
B
179629


5790
B
188605


5791
B
190552


5792
B
189016


5793
B
190924


5794
B
190871


5795
B
192749


5796
B
197533


5797
B
199449


5798
B
211604


5799
B
213554


5800
B
235455


5801
B
237385


5802
B
237448


5803
B
239387


5804
B
250266


5805
B
252155


5806
B
253731


5807
B
255663


5808
B
255115


5809
B
256969


5810
B
272158


5811
B
274093


5812
B
276317


5813
B
278190


5814
B
278470


5815
B
280366


5816
B
283005


5817
B
284873


5818
B
293718


5819
B
295643


5820
B
303690


5821
B
305624


5822
B
309538


5823
B
311476


5824
B
312791


5825
B
314685


5826
B
313073


5827
B
314977


5828
B
313506


5829
B
315343


5830
B
320823


5831
B
322730


5832
B
340723


5833
B
342638


5834
B
353562


5835
B
355444


5836
B
373944


5837
B
375838


5838
B
377997


5839
B
379877


5840
B
379877


5841
B
381778


5842
B
395318


5843
B
397228


5844
B
401846


5845
B
403782


5846
B
410759


5847
B
412677


5848
B
411878


5849
B
413779


5850
B
415199


5851
B
417099


5852
B
423479


5853
B
425332


5854
B
428421


5855
B
430332


5856
B
429678


5857
B
431571


5858
B
443036


5859
B
444947


5860
B
444280


5861
B
446161


5862
B
443964


5863
B
445811


5864
B
446392


5865
B
448276


5866
B
468498


5867
B
470382


5868
B
472328


5869
B
474285


5870
B
488594


5871
B
490459


5872
B
497914


5873
B
499837


5874
B
500718


5875
B
502596


5876
B
509811


5877
B
511702


5878
B
511485


5879
B
513385


5880
B
527090


5881
B
529014


5882
B
532083


5883
B
533999


5884
B
557487


5885
B
559357


5886
B
565191


5887
B
567099


5888
B
567452


5889
B
569355


5890
B
571110


5891
B
573047


5892
B
571557


5893
B
573461


5894
B
576288


5895
B
578181


5896
B
590890


5897
B
592770


5898
B
598813


5899
B
600714


5900
B
607146


5901
B
609012


5902
B
608260


5903
B
610162


5904
B
610621


5905
B
612514


5906
B
633573


5907
B
635473


5908
B
637702


5909
B
639603


5910
B
650757


5911
B
652667


5912
B
652808


5913
B
654682


5914
B
655545


5915
B
657446


5916
B
661392


5917
B
663292


5918
B
677837


5919
B
679716


5920
B
679748


5921
B
681674


5922
B
732909


5923
B
734756


5924
B
742639


5925
B
744503


5926
B
759613


5927
B
761510


5928
B
760782


5929
B
762671


5930
B
771617


5931
B
773519


5932
B
772628


5933
B
774528


5934
B
788703


5935
B
790577


5936
B
816591


5937
B
818443


5938
B
847145


5939
B
849042


5940
B
868276


5941
B
870177


5942
B
875887


5943
B
877779


5944
B
877137


5945
B
879035


5946
B
884780


5947
B
886680


5948
B
892172


5949
B
894073


5950
B
900990


5951
B
902955


5952
B
902780


5953
B
904687


5954
B
908266


5955
B
910218


5956
B
912811


5957
B
914730


5958
B
935988


5959
B
937863


5960
B
947227


5961
B
949089


5962
B
953426


5963
B
955397


5964
B
966421


5965
B
968345


5966
B
969548


5967
B
971477


5968
B
971390


5969
B
973279


5970
B
972661


5971
B
974581


5972
B
973730


5973
B
975665


5974
B
998885


5975
B
1000774


5976
B
1004572


5977
B
1006449


5978
B
1010507


5979
B
1012353


5980
B
1029707


5981
B
1031628









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## Claims

1. An isolated polynucleotide encoding an open reading frame (ORF) of a Chlamydia trachomatis genome, said ORF comprising SEQ ID NO: 52 (ORF 52), SEQ ID NO: 347 (ORF 347) or SEQ ID NO: 508 (ORF 508).

2. The isolated polynucleotide according to claim 1, wherein said polynucleotide encodes SEQ ID NO: 52 (ORF 52).

3. The isolated polynucleotide according to claim 1, wherein SEQ ID NO: 52 is encoded by a polynucleotide fully complementary to nucleotides 48585 to 48178 of SEQ ID NO: 1.

4. The isolated polynucleotide according to claim 1, wherein said polynucleotide encodes SEQ ID NO: 347 (ORF 347).

5. The isolated polynucleotide according to claim 1, wherein SEQ ID NO: 347 is encoded by nucleotides 342597 to 343370 of SEQ ID NO: 1.

6. The isolated polynucleotide according to claim 1, wherein said polynucleotide encodes SEQ ID NO: 508 (ORF 508).

7. The isolated polynucleotide according to claim 1, wherein SEQ ID NO: 508 is encoded by a polynucleotide fully complementary to nucleotides 502863 to 501808 of SEQ ID NO: 1.

8. An isolated vector comprising a polynucleotide encoding an open reading frame (ORF) of a Chlamydia trachomatis genome, said ORF comprising SEQ ID NO: 52 (ORF 52), SEQ ID NO: 347 (ORF 347) or SEQ ID NO: 508 (ORF 508).

9. The isolated vector according to claim 8, wherein said polynucleotide encodes SEQ ID NO: 52 (ORF 52).

10. The isolated vector according to claim 8, wherein SEQ ID NO: 52 is encoded by a polynucleotide fully complementary to nucleotides 48585 to 48178 of SEQ ID NO 1.

11. The isolated vector according to claim 8, wherein said polynucleotide encodes SEQ ID NO: 347 (ORF 347).

12. The isolated vector according to claim 8, wherein SEQ ID NO: 347 is encoded by nucleotides 342597 to 343370 of SEQ ID NO: 1.

13. The isolated vector according to claim 8, wherein said polynucleotide encodes SEQ ID NO: 508 (ORF 508).

14. The isolated vector according to claim 8, wherein SEQ ID NO: 508 is encoded by a polynucleotide fully complementary to nucleotides 502863 to 501808 of SEQ ID NO: 1.

15. An isolated genetically engineered host cell comprising a polynucleotide encoding an open reading frame (ORF) of a Chlamydia trachomatis genome, said ORF comprising SEQ ID NO: 52 (ORF 52), SEQ ID NO: 347 (ORF 347) or SEQ ID NO: 508 (ORF 508).

16. The host cell according to claim 15, wherein said polynucleotide encodes SEQ ID NO: 52 (ORF 52).

17. The host cell according to claim 15, wherein SEQ ID NO: 52 is encoded by nucleotides 48585 to 48178 of SEQ ID NO: 1.

18. The host cell according to claim 15, wherein said polynucleotide encodes SEQ ID NO: 347 (ORF 347).

19. The host cell according to claim 15, wherein SEQ ID NO: 347 is encoded by nucleotides 342597 to 343370 of SEQ ID NO: 1.

20. The host cell according to claim 15, wherein said polynucleotide encodes SEQ ID NO: 508 (ORF 508).

21. The host cell according to claim 15, wherein SEQ ID NO: 508 is encoded by a polynucleotide fully complementary to nucleotides 502863 to 501808 of SEQ ID NO: 1.

22. A method for producing a polypeptide, comprising:
(a) culturing a genetically engineered host cell according to claim 15 under conditions suitable to produce a polypeptide; and
(b) recovering the polypeptide from the culture.

23. The method according to claim 22, wherein said genetically engineered host cell comprises a polynucleotide that encodes SEQ ID NO: 52 (ORF 52).

24. The method according to claim 22, wherein SEQ ID NO: 52 is encoded by nucleotides 48585 to 48178 of SEQ ID NO: 1.

25. The method according to claim 22, wherein said polynucleotide encodes SEQ ID NO: 347 (ORF 347).

26. The method according to claim 22, wherein SEQ ID NO: 347 is encoded by nucleotides 342597 to 343370 of SEQ ID NO: 1.

27. The method according to claim 22, wherein said polynucleotide encodes SEQ ID NO: 508 (ORF 508).

28. The method according to claim 22, wherein SEQ ID NO: 508 is encoded by a polynucleotide fully complementary to nucleotides 502863 to 501808 of SEQ ID NO: 1.