Streptococcus pneumoniae polynucleotides and sequences

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No:

6420135 -

Application no:

08961527 -

Filed date:

1997-10-30 -

Issue date:

2002-07-16

Abstract:

The present invention provides polynucleotide sequences of the genome of Streptococcus pneumoniae, polypeptide sequences encoded by the polynucleotide sequences, corresponding polynucleotides and polypeptides, vectors and hosts comprising the polynucleotides, and assays and other uses thereof. The present invention further provides polynucleotide and polypeptide sequence information stored on computer readable media, and computer-based systems and methods which facilitate its use.

US Classes:

Inventors:

Agents:

Assignees:

Claims:

What is claimed is:

1. An isolated polynucleotide fragment comprising the nucleic acid sequence of an ORF selected from the group consisting of: (a) ORF ID NO:9 of Contig ID NO:5, represented by nucleotides 12592-13197 of SEQ ID NO:5; (b) ORF ID NO:1 of Contig ID NO:46, represented by nucleotides 2-1267 of SEQ ID NO:46; (c) ORF ID NO:5 of Contig ID NO:58, represented by nucleotides 6565-7356 of SEQ ID NO:58; (d) ORF ID NO:3 of Contig ID NO:78, represented by nucleotides 1108-3636 of SEQ ID NO:78; (e) ORF ID NO:3 of Contig ID NO:94, represented by nucleotides 951-2741 of SEQ ID NO:94; (f) ORF ID NO:4 of Contig ID NO:94, represented by nucleotides 3006-5444 of SEQ ID NO:94; (g) ORF ID NO:3 of Contig ID NO:32, represented by nucleotides 1885-1076 of SEQ ID NO:32; (h) ORF ID NO:4 of Contig ID NO:92, represented by nucleotides 1753-3276 of SEQ ID NO:92; (i) ORF ID NO:2 of Contig ID NO:89, represented by nucleotides 1007-1627 of SEQ ID NO:89; and (j) ORF ID NO:1 of Contig ID NO:287, represented by nucleotides 2-871 of SEQ ID NO:287.

2. The isolated polynucleotide of claim 1, wherein said polynucleotide comprises a heterologous polynucleotide sequence.

3. The isolated polynucleotide of claim 2, wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.

4. A method for making a recombinant vector comprising inserting the isolated polynucleotide of claim 1 into a vector.

5. A nucleic acid sequence complimentary to the polynucleotide of claim 1.

6. A recombinant vector comprising the isolated polynucleotide of claim 1.

7. The recombinant vector of claim 6, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

8. A recombinant host cell comprising the isolated polynucleotide of claim 1.

9. The recombinant host cell of claim 8, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

10. An isolated polynucleotide fragment comprising a nucleic acid sequence which hybridizes under hybridization conditions, comprising hybridization in 5×SSC and 50% formamide at 50-65° C. and washing in a wash buffer consisting of 0.5×SSC at 65° C., to the complementary strand of an ORF selected from the group consisting of: (a) ORF ID NO:9 of Contig ID NO:5, represented by nucleotides 12592-13197 of SEQ ID NO:5; (b) ORF ID NO:1 of Contig ID NO:46, represented by nucleotides 2-1267 of SEQ ID NO:46; (c) ORF ID NO:5 of Contig ID NO:58, represented by nucleotides 6565-7356 of SEQ ID NO:58; (d) ORF ID NO:3 of Contig ID NO:78, represented by nucleotides 1108-3636 of SEQ ID NO:78; (e) ORF ID NO:4 of Contig ID NO:94, represented by nucleotides 3006-5444 of SEQ ID NO:94; (f) ORF ID NO:3 of Contig ID NO:32, represented by nucleotides 1885-3876 of SEQ ID NO:32; (g) ORF ID NO:4 of Contig ID NO:92, represented by nucleotides 1753-3276 of SEQ ID NO:92; (h) ORF ID NO:2 of Contig ID NO:89, represented by nucleotides 1007-1627 of SEQ ID NO:89; and (i) ORF ID NO:1 of Contig ID NO:287, represented by nucleotides 2-871 of SEQ ID NO:287.

11. An isolated polynucleotide complementary to the polynucleotide of claim 10.

12. An isolated polynucleotide comprising at least 50 contiguous nucleotides of an ORF selected from the group consisting of: (a) ORF ID NO:9 of Contig ID NO:5, represented by nucleotides 12592-13197 of SEQ ID NO:5; (b) ORF ID NO:1 of Contig ID NO:46, represented by nucleotides 2-1267 of SEQ ID NO:46; (c) ORF ID NO:5 of Contig ID NO:58, represented by nucleotides 6565-7356 of SEQ ID NO:58; (d) ORF ID NO:3 of Contig ID NO:78, represented by nucleotides 1108-3636 of SEQ ID NO:78; (e) ORF ID NO:3 of Contig ID NO:94, represented by nucleotides 951-2741 of SEQ ID NO:94; (f) ORF ID NO:4 of Contig ID NO:94, represented by nucleotides 3006-5444 of SEQ ID NO:94; (g) ORF ID NO:3 of Contig ID NO:32, represented by nucleotides 1885-3876 of SEQ ID NO:32; (h) ORF ID NO:4 of Contig ID NO:92, represented by nucleotides 1753-3276 of SEQ ID NO:92; (i) ORF ID NO:2 of Contig ID NO:89, represented by nucleotides 1007-1627 of SEQ ID NO:89; and (j) ORF ID NO:1 of Contig ID NO:287, represented by nucleotides 2-871 of SEQ ID NO:287.

13. An isolated polynucleotide complementary to the polynucleotide of claim 12.

14. An isolated polynucleotide comprising at least 100 contiguous nucleotides of an ORF selected from the group consisting of: (a) ORF ID NO:9 of Contig ID NO:5, represented by nucleotides 12592-13197 of SEQ ID NO:5; (b) ORF ID NO:1 of Contig ID NO:46, represented by nucleotides 2-1267 of SEQ ID NO:46; (c) ORF ID NO:5 of Contig ID NO:58, represented by nucleotides 6565-7356 of SEQ ID NO:58; (d) ORF ID NO:3 of Contig ID NO:78, represented by nucleotides 1108-3636 of SEQ ID NO:78; (e) ORF ID NO:3 of Contig ID NO:94, represented by nucleotides 951-2741 of SEQ ID NO:94; (f) ORF ID NO:4 of Contig ID NO:94, represented by nucleotides 3006-5444 of SEQ ID NO:94; (g) ORF ID NO:3 of Contig ID NO:32, represented by nucleotides 1885-3876 of SEQ ID NO:32; (h) ORF ID NO:4 of Contig ID NO:92, represented by nucleotides 1753-3276 of SEQ ID NO:92; (i) ORF ID NO:2 of Contig ID NO:89, represented by nucleotides 1007-1627 of SEQ ID NO:89; and (j) ORF ID NO:1 of Contig ID NO:287, represented by nucleotides 2-871 of SEQ ID NO:287.

15. An isolated polynucleotide complementary to the polynucleotide of claim 14.

16. The isolated polynucleotide of claim 1, wherein the selected ORF is (a).

17. The isolated polynucleotide of claim 1, wherein the selected ORF is (b).

18. The isolated polynucleotide of claim 1, wherein the selected ORF is (c).

19. The isolated polynucleotide of claim 1, wherein the selected ORF is (d).

20. The isolated polynucleotide of claim 1, wherein the selected ORF is (e).

21. The isolated polynucleotide of claim 1, wherein the selected ORF is (f).

22. The isolated polynucleotide of claim 1, wherein the selected ORF is (g).

23. The isolated polynucleotide of claim 1, wherein the selected ORF is (h).

24. The isolated polynucleotide of claim 1, wherein the selected ORF is (i).

25. The isolated polynucleotide of claim 1, wherein the selected ORF is (j).

26. The isolated polynucleotide of claim 10, wherein the selected ORF is (a).

27. The isolated polynucleotide of claim 10, wherein the selected ORF is (b).

28. The isolated polynucleotide of claim 10, wherein the selected ORF is (c).

29. The isolated polynucleotide of claim 10, wherein the selected ORF is (d).

30. The isolated polynucleotide of claim 10, wherein the selected ORF is (e).

31. The isolated polynucleotide of claim 10, wherein the selected ORF is (f).

32. The isolated polynucleotide of claim 10, wherein the selected ORF is (g).

33. The isolated polynucleotide of claim 10, wherein the selected ORF is (h).

34. The isolated polynucleotide of claim 10, wherein the selected ORF is (i).

35. The isolated polynucleotide of claim 12, wherein the selected ORF is (a).

36. The isolated polynucleotide of claim 12, wherein the selected ORF is (b).

37. The isolated polynucleotide of claim 12, wherein the selected ORF is (c).

38. The isolated polynucleotide of claim 12, wherein the selected ORF is (d).

39. The isolated polynucleotide of claim 12, wherein the selected ORF is (e).

40. The isolated polynucleotide of claim 12, wherein the selected ORF is (f).

41. The isolated polynucleotide of claim 12, wherein the selected ORF is (g).

42. The isolated polynucleotide of claim 12, wherein the selected ORF is (h).

43. The isolated polynucleotide of claim 12, wherein the selected ORF is (i).

44. The isolated polynucleotide of claim 12, wherein the selected ORF is (j).

45. The isolated polynucleotide of claim 14, wherein the selected ORF is (a).

46. The isolated polynucleotide of claim 14, wherein the selected ORF is (b).

47. The isolated polynucleotide of claim 14, wherein the selected ORF is (c).

48. The isolated polynucleotide of claim 14, wherein the selected ORF is (d).

49. The isolated polynucleotide of claim 14, wherein the selected ORF is (e).

50. The isolated polynucleotide of claim 14, wherein the selected ORF is (f).

51. The isolated polynucleotide of claim 14, wherein the selected ORF is (g).

52. The isolated polynucleotide of claim 14, wherein the selected ORF is (h).

53. The isolated polynucleotide of claim 14, wherein the selected ORF is (i).

54. The isolated polynucleotide of claim 14, wherein the selected ORF is (j).

55. The isolated polynucleotide of claim 10, wherein said polynucleotide comprises a heterologous polynucleotide sequence.

56. The isolated polynucleotide of claim 55, wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.

57. A method for making a recombinant vector comprising inserting the isolated polynucleotide of claim 10 into a vector.

58. A recombinant vector comprising the isolated polynucleotide of claim 10.

59. The recombinant vector of claim 58, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

60. A recombinant host cell comprising the isolated polynucleotide of claim 10.

61. The recombinant host cell of claim 60, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

62. The isolated polynucleotide of claim 12, wherein said polynucleotide comprises a heterologous polynucleotide sequence.

63. The isolated polynucleotide of claim 62, wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.

64. A method for making a recombinant vector comprising inserting the isolated polynucleotide of claim 12 into a vector.

65. A recombinant vector comprising the isolated polynucleotide of claim 12.

66. The recombinant vector of claim 65, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

67. A recombinant host cell comprising the isolated polynucleotide of claim 12.

68. The recombinant host cell of claim 67, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

69. The isolated polynucleotide of claim 14, wherein said polynucleotide comprises a heterologous polynucleotide sequence.

70. The isolated polynucleotide of claim 69, wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.

71. A method for making a recombinant vector comprising inserting the isolated polynucleotide of claim 14 into a vector.

72. A recombinant vector comprising the isolated polynucleotide of claim 14.

73. The recombinant vector of claim 72, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

74. A recombinant host cell comprising the isolated polynucleotide of claim 14.

75. The recombinant host cell of claim 74, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

76. An isolated polynucleotide fragment comprising a nucleic acid sequence encoding an amino acid sequence encoded by an ORF selected from the group consisting of: (a) ORF ID NO:3 of Contig ID NO:78, represented by nucleotides 1108-3636 of SEQ ID NO:78; (b) ORF ID NO:3 of Contig ID NO:94, represented by nucleotides 951-2741 of SEQ ID NO:94; and (c) ORF ID NO:1 of Contig ID NO:287, represented by nucleotides 2-871 of SEQ ID NO:287.

77. The isolated polynucleotide of claim 76, wherein the selected ORF is (a).

78. The isolated polynucleotide of claim 76, wherein the selected ORF is (b).

79. The isolated polynucleotide of claim 76, wherein the selected ORF is (c).

80. The isolated polynucleotide of claim 76, wherein said polynucleotide comprises a heterologous polynucleotide sequence.

81. The isolated polynucleotide of claim 80, wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.

82. A method for making a recombinant vector comprising inserting the isolated polynucleotide of claim 76 into a vector.

83. A nucleic acid sequence complimentary to the polynucleotide of claim 76.

84. A recombinant vector comprising the isolated polynucleotide of claim 76.

85. The recombinant vector of claim 84, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

86. A recombinant host cell comprising the isolated polynucleotide of claim 76.

87. The recombinant host cell of claim 86, wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.

88. A method for producing a polypeptide, comprising: (a) culturing a host cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of claim 76; and (b) recovering the polypeptide from the cell culture.

Text:

FIELD OF THE INVENTION

The present invention relates to the field of molecular biology. In particular, it relates to, among other things, nucleotide sequences of Streptococcus pneumoniae, contigs, ORFs, fragments, probes, primers and related polynucleotides thereof, peptides and polypeptides encoded by the sequences, and uses of the polynucleotides and sequences thereof, such as in fermentation, polypeptide production, assays and pharmaceutical development, among others.

BACKGROUND OF THE INVENTION

Streptococcus pneumoniae has been one of the most extensively studied microorganisms since its first isolation in 1881. It was the object of many investigations that led to important scientific discoveries. In 1928, Griffith observed that when heat-killed encapsulated pneumococci and live strains constitutively lacking any capsule were concomitantly injected into mice, the nonencapsulated could be converted into encapsulated pneumococci with the same capsular type as the heat-killed strain. Years later, the nature of this “transforming principle,” or carrier of genetic information, was shown to be DNA. (Avery, O. T., et al., J. Exp. Med., 79:137-157 (1944)).

In spite of the vast number of publications on S. pneumoniae many questions about its virulence are still unanswered, and this pathogen remains a major causative agent of serious human disease, especially community-acquired pneumonia. (Johnston, R. B., et al., Rev. Infect. Dis. 13(Suppl. 6):S509-517 (1991)). In addition, in developing countries, the pneumococcus is responsible for the death of a large number of children under the age of 5 years from pneumococcal pneumonia. The incidence of pneumococcal disease is highest in infants under 2 years of age and in people over 60 years of age. Pneumococci are the second most frequent cause (after Haemophilus influenzae type b) of bacterial meningitis and otitis media in children. With the recent introduction of conjugate vaccines for H. influenzae type b, pneumococcal meningitis is likely to become increasingly prominent. S. pneumoniae is the most important etiologic agent of community-acquired pneumonia in adults and is the second most common cause of bacterial meningitis behind Neisseria meningitidis.

The antibiotic generally prescribed to treat S. pneumoniae is benzylpenicillin, although resistance to this and to other antibiotics is found occasionally. Pneumococcal resistance to penicillin results from mutations in its penicillin-binding proteins. In uncomplicated pneumococcal pneumonia caused by a sensitive strain, treatment with penicillin is usually successful unless started too late. Erythromycin or clindamycin can be used to treat pneumonia in patients hypersensitive to penicillin, but resistant strains to these drugs exist. Broad spectrum antibiotics (e.g., the tetracyclines) may also be effective, although tetracycline-resistant strains are not rare. In spite of the availability of antibiotics, the mortality of pneumococcal bacteremia in the last four decades has remained stable between 25 and 29%. (Gillespie, S. H., et al., J. Med. Microbiol. 28:237-248 (1989).

S. pneumoniae is carried in the upper respiratory tract by many healthy individuals. It has been suggested that attachment of pneumococci is mediated by a disaccharide receptor on fibronectin, present on human pharyngeal epithelial cells. (Anderson, B. J., et al., J. Immunol. 142:2464-2468 (1989). The mechanisms by which pneumococci translocate from the nasopharynx to the lung, thereby causing pneumonia, or migrate to the blood, giving rise to bacteremia or septicemia, are poorly understood. (Johnston, R. B., et al., Rev. Infect. Dis. 13(Suppl. 6):S509-517 (1991).

Various proteins have been suggested to be involved in the pathogenicity of S. pneumoniae, however, only a few of them have actually been confirmed as virulence factors. Pneumococci produce an IgA1 protease that might interfere with host defense at mucosal surfaces. (Kornfield, S. J., et al., Rev. Inf. Dis. 3:521-534 (1981). S. pneumoniae also produces neuraminidase, an enzyme that may facilitate attachment to epithelial cells by cleaving sialic acid from the host glycolipids and gangliosides. Partially purified neuraminidase was observed to induce meningitis-like symptoms in mice; however, the reliability of this finding has been questioned because the neuraminidase preparations used were probably contaminated with cell wall products. Other pneumococcal proteins besides neuraminidase are involved in the adhesion of pneumococci to epithelial and endothelial cells. These pneumococcal proteins have as yet not been identified. Recently, Cundell et al., reported that peptide permeases can modulate pneumococcal adherence to epithelial and endothelial cells. It was, however, unclear whether these permeases function directly as adhesions or whether they enhance adherence by modulating the expression of pneumococcal adhesions. (DeVelasco, E. A., et al., Micro. Rev. 59:591-603 (1995). A better understanding of the virulence factors determining its pathogenicity will need to be developed to cope with the devastating effects of pneumococcal disease in humans.

Ironically, despite the prominent role of S. pneumoniae in the discovery of DNA, little is known about the molecular genetics of the organism. The S. pneumoniae genome consists of one circular, covalently closed, double-stranded DNA and a collection of so-called variable accessory elements, such as prophages, plasmids, transposons and the like. Most physical characteristics and almost all of the genes of S. pneumoniae are unknown. Among the few that have been identified, most have not been physically mapped or characterized in detail. Only a few genes of this organism have been sequenced. (See, for instance current versions of GENBANK and other nucleic acid databases, and references that relate to the genome of S. pneumoniae such as those set out elsewhere herein.)

It is clear that the etiology of diseases mediated or exacerbated by S. pneumoniae, infection involves the programmed expression of S. pneumoniae genes, and that characterizing the genes and their patterns of expression would add dramatically to our understanding of the organism and its host interactions. Knowledge of S. pneumoniae genes and genomic organization would improve our understanding of disease etiology and lead to improved and new ways of preventing, ameliorating, arresting and reversing diseases. Moreover, characterized genes and genomic fragments of S. pneumoniae would provide reagents for, among other things, detecting, characterizing and controlling S. pneumoniae infections. There is a need to characterize the genome of S. pneumoniae and for polynucleotides of this organism.

SUMMARY OF THE INVENTION

The present invention is based on the sequencing of fragments of the Streptococcus pneumoniae genome. The primary nucleotide sequences which were generated are provided in SEQ ID NOS:1-391.

The present invention provides the nucleotide sequence of several hundred contigs of the Streptococcus pneumoniae genome, which are listed in tables below and set out in the Sequence Listing submitted herewith, and representative fragments thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan. In one embodiment, the present invention is provided as contiguous strings of primary sequence information corresponding to the nucleotide sequences depicted in SEQ ID NOS:1-391.

The present invention further provides nucleotide sequences which are at least 95% identical to the nucleotide sequences of SEQ ID NOS:1-391.

The nucleotide sequence of SEQ ID NOS:1-391, a representative fragment thereof, or a nucleotide sequence which is at least 95% identical to the nucleotide sequence of SEQ ID NOS; 1-391 may be provided in a variety of mediums to facilitate its use. In one application of this embodiment, the sequences of the present invention are recorded on computer readable media. Such media includes, but is not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media.

The present invention further provides systems, particularly computer-based systems which contain the sequence information herein described stored in a data storage means. Such systems are designed to identify commercially important fragments of the Streptococcus pneumoniae genome.

Another embodiment of the present invention is directed to fragments of the Streptococcus pneumoniae genome having particular structural or functional attributes. Such fragments of the Streptococcus pneumoniae genome of the present invention include, but are not limited to, fragments which encode peptides, hereinafter referred to as open reading frames or ORFs, fragments which modulate the expression of an operably linked ORF, hereinafter referred to as expression modulating fragments or EMFs, and fragments which can be used to diagnose the presence of Streptococcus pneumoniae in a sample, hereinafter referred to as diagnostic fragments or DFs.

Each of the ORFs in fragments of the Streptococcus pneumoniae genome disclosed in Tables 1-3, and the EMFs found 5′ to the ORFs, can be used in numerous ways as polynucleotide reagents. For instance, the sequences can be used as diagnostic probes or amplification primers for detecting or determining the presence of a specific microbe in a sample, to selectively control gene expression in a host and in the production of polypeptides, such as polypeptides encoded by ORFs of the present invention, particular those polypeptides that have a pharmacological activity.

The present invention further includes recombinant constructs comprising one or more fragments of the Streptococcus pneumoniae genome of the present invention. The recombinant constructs of the present invention comprise vectors, such as a plasmid or viral vector, into which a fragment of the Streptococcus pneumoniae has been inserted.

The present invention further provides host cells containing any of the isolated fragments of the Streptococcus pneumoniae genome of the present invention. The host cells can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic cell, such as a yeast cell, or a procaryotic cell such as a bacterial cell.

The present invention is further directed to isolated polypeptides and proteins encoded by ORFs of the present invention. A variety of methods, well known to those of skill in the art, routinely may be utilized to obtain any of the polypeptides and proteins of the present invention. For instance, polypeptides and proteins of the present invention having relatively short, simple amino acid sequences readily can be synthesized using commercially available automated peptide synthesizers. Polypeptides and proteins of the present invention also may be purified from bacterial cells which naturally produce the protein. Yet another alternative is to purify polypeptide and proteins of the present invention from cells which have been altered to express them.

The invention further provides methods of obtaining homologs of the fragments of the Streptococcus pneumoniae genome of the present invention and homologs of the proteins encoded by the ORFs of the present invention. Specifically, by using the nucleotide and amino acid sequences disclosed herein as a probe or as primers, and techniques such as PCR cloning and colony/plaque hybridization, one skilled in the art can obtain homologs.

The invention further provides antibodies which selectively bind polypeptides and proteins of the present invention. Such antibodies include both monoclonal and polyclonal antibodies.

The invention further provides hybridomas which produce the above-described antibodies. A hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.

The present invention further provides methods of identifying test samples derived from cells which express one of the ORFs of the present invention, or a homolog thereof. Such methods comprise incubating a test sample with one or more of the antibodies of the present invention, or one or more of the DFs of the present invention, under conditions which allow a skilled artisan to determine if the sample contains the ORF or product produced therefrom.

In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the above-described assays.

Specifically, the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the antibodies, or one of the DFs of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of bound antibodies or hybridized DFs.

Using the isolated proteins of the present invention, the present invention further provides methods of obtaining and identifying agents capable of binding to a polypeptide or protein encoded by one of the ORFs of the present invention. Specifically, such agents include, as further described below, antibodies, peptides, carbohydrates, pharmaceutical agents and the like. Such methods comprise steps of: (a) contacting an agent with an isolated protein encoded by one of the ORFs of the present invention; and (b) determining whether the agent binds to said protein.

The present genomic sequences of Streptococcus pneumoniae will be of great value to all laboratories working with this organism and for a variety of commercial purposes. Many fragments of the Streptococcus pneumoniae genome will be immediately identified by similarity searches against GenBank or protein databases and will be of immediate value to Streptococcus pneumoniae researchers and for immediate commercial value for the production of proteins or to control gene expression.

The methodology and technology for elucidating extensive genomic sequences of bacterial and other genomes has and will greatly enhance the ability to analyze and understand chromosomal organization. In particular, sequenced contigs and genomes will provide the models for developing tools for the analysis of chromosome structure and function, including the ability to identify genes within large segments of genomic DNA, the structure, position, and spacing of regulatory elements, the identification of genes with potential industrial applications, and the ability to do comparative genomic and molecular phylogeny.

DESCRIPTION OF THE FIGURES

FIG. 1 is a block diagram of a computer system (102) that can be used to implement computer-based systems of present invention.

FIG. 2 is a schematic diagram depicting the data flow and computer programs used to collect, assemble, edit and annotate the contigs of the Streptococcus pneumoniae genome of the present invention. Both Macintosh and Unix platforms are used to handle the AB 373 and 377 sequence data files, largely as described in Kerlavage et al., Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, 585, IEEE Computer Society Press, Washington D.C. (1993). Factura (AB) is a Macintosh program designed for automatic vector sequence removal and end-trimming of sequence files. The program Loadis runs on a Macintosh platform and parses the feature data extracted from the sequence files by Factura to the Unix based Streptococcus pneumoniae relational database. Assembly of contigs (and whole genome sequences) is accomplished by retrieving a specific set of sequence files and their associated features using Extrseq, a Unix utility for retrieving sequences from an SQL database. The resulting sequence file is processed by seq_filter to trim portions of the sequences with more than 2% ambiguous nucleotides. The sequence files were assembled using TIGR Assembler, an assembly engine designed at The Institute for Genomic Research (TIGR) for rapid and accurate assembly of thousands of sequence fragments. The collection of contigs generated by the assembly step is loaded into the database with the lassie program. Identification of open reading frames (ORFs) is accomplished by processing contigs with zorf or GenMark. The ORFs are searched against S. pneumoniae sequences from GenBank and against all protein sequences using the BLASTN and BLASTP programs, described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990)). Results of the ORF determination and similarity searching steps were loaded into the database. As described below, some results of the determination and the searches are set out in Tables 1-3.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

The present invention is based on the sequencing of fragments of the Streptococcus pneumoniae genome and analysis of the sequences. The primary nucleotide sequences generated by sequencing the fragments are provided in SEQ ID NOS:1-391. (As used herein, the “primary sequence” refers to the nucleotide sequence represented by the IUPAC nomenclature system.)

In addition to the aforementioned Streptococcus pneumoniae polynucleotide and polynucleotide sequences, the present invention provides the nucleotide sequences of SEQ ID NOS:1-391, or representative fragments thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan.

As used herein, a “representative fragment of the nucleotide sequence depicted in SEQ ID NOS:1-391” refers to any portion of the SEQ ID NOS:1-391 which is not presently represented within a publicly available database. Preferred representative fragments of the present invention are Streptococcus pneumoniae open reading frames (ORFs), expression modulating fragment (EMFs) and fragments which can be used to diagnose the presence of Streptococcus pneumoniae in sample (DFs). A non-limiting identification of preferred representative fragments is provided in Tables 1-3. As discussed in detail below, the information provided in SEQ ID NOS:1-391 and in Tables 1-3 together with routine cloning, synthesis, sequencing and assay methods will enable those skilled in the art to clone and sequence all “representative fragments” of interest, including open reading frames encoding a large variety of Streptococcus pneumoniae proteins.

While the presently disclosed sequences of SEQ ID NOS:1-391 are highly accurate, sequencing techniques are not perfect and, in relatively rare instances, further investigation of a fragment or sequence of the invention may reveal a nucleotide sequence error present in a nucleotide sequence disclosed in SEQ ID NOS:1-391. However, once the present invention is made available (i.e., once the information in SEQ ID NOS:1-391 and Tables 1-3 has been made available), resolving a rare sequencing error in SEQ ID NOS:1-391 will be well within the skill of the art. The present disclosure makes available sufficient sequence information to allow any of the described contigs or portions thereof to be obtained readily by straightforward application of routine techniques. Further sequencing of such polynucleotide may proceed in like manner using manual and automated sequencing methods which are employed ubiquitous in the art. Nucleotide sequence editing software is publicly available. For example, Applied Biosystem's (AB) AutoAssembler can be used as an aid during visual inspection of nucleotide sequences. By employing such routine techniques potential errors readily may be identified and the correct sequence then may be ascertained by targeting further sequencing effort, also of a routine nature, to the region containing the potential error.

Even if all of the very rare sequencing errors in SEQ ID NOS:1-391 were corrected, the resulting nucleotide sequences would still be at least 95% identical, nearly all would be at least 99% identical, and the great majority would be at least 99.9% identical to the nucleotide sequences of SEQ ID NOS:1-391.

As discussed elsewhere herein, polynucleotides of the present invention readily may be obtained by routine application of well known and standard procedures for cloning and sequencing DNA. Detailed methods for obtaining libraries and for sequencing are provided below, for instance. A wide variety of Streptococcus pneumoniae strains that can be used to prepare S. pneumoniae genomic DNA for cloning and for obtaining polynucleotides of the present invention are available to the public from recognized depository institutions, such as the American Type Culture Collection (ATCC). While the present invention is enabled by the sequences and other information herein disclosed, the S. pneumoniae strain that provided the DNA of the present Sequence Listing, Strain 7/87 14.8.91, has been deposited in the ATCC, as a convenience to those of skill in the art. As a further convenience, a library of S. pneumoniae genomic DNA, derived from the same strain, also has been deposited in the ATCC. The S. pneumoniae strain was deposited on Oct. 10, 1996, and was given Deposit No. 55840, and the cDNA library was deposited on Oct. 11, 1996 and was given Deposit No. 97755. The genomic fragments in the library are 15 to 20 kb fragments generated by partial Sau3A1 digestion and they are inserted into the BamHI site in the well-known lambda-derived vector lambda DASH II (Stratagene, La Jolla, Calif.). The provision of the deposits is not a waiver of any rights of the inventors or their assignees in the present subject matter.

The nucleotide sequences of the genomes from different strains of Streptococcus pneumoniae differ somewhat. However, the nucleotide sequences of the genomes of all Streptococcus pneumoniae strains will be at least 95% identical, in corresponding part, to the nucleotide sequences provided in SEQ ID NOS:1-391. Nearly all will be at least 99% identical and the great majority will be 99.9% identical.

Thus, the present invention further provides nucleotide sequences which are at least 95%, preferably 99% and most preferably 99.9% identical to the nucleotide sequences of SEQ ID NOS:1-391, in a form which can be readily used, analyzed and interpreted by the skilled artisan.

Methods for determining whether a nucleotide sequence is at least 95%, at least 99% or at least 99.9% identical to the nucleotide sequences of SEQ ID NOS:1-391 are routine and readily available to the skilled artisan. For example, the well known fasta algorithm described in Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85: 2444 (1988) can be used to generate the percent identity of nucleotide sequences. The BLASTN program also can be used to generate an identity score of polynucleotides compared to one another.

COMPUTER RELATED EMBODIMENTS

The nucleotide sequences provided in SEQ ID NOS:1-391, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 99% and most preferably at least 99.9% identical to a polynucleotide sequence of SEQ ID NOS:1-391 may be “provided” in a variety of mediums to facilitate use thereof. As used herein, provided refers to a manufacture, other than an isolated nucleic acid molecule, wich contains a nucleotide sequence of the present invention; i.e., a nucleotide sequence provided in SEQ ID NOS:1-391, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 99% and most preferably at least 99.9% identical to a polynucleotide of SEQ ID NOS:1-391. Such a manufacture provides a large portion of the Streptococcus pneumoniae genome and parts thereof (e.g., a Streptococcus pneumoniae open reading frame (ORF)) in a form which allows a skilled artisan to examine the manufacture using means not directly applicable to examining the Streptococcus pneumoniae genome or a subset thereof as it exists in nature or in purified form.

In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, “computer readable media” refers to any medium which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories, such as magnetic/optical storage media. A skilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. Likewise, it will be clear to those of skill how additional computer readable media that may be developed also can be used to create analogous manufactures having recorded thereon a nucleotide sequence of the present invention.

As used herein, “recorded” refers to a process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently know methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention. A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and MicroSoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data-processor structuring formats (e.g., text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.

Computer software is publicly available which allows a skilled artisan to access sequence information provided in a computer readable medium. Thus, by providing in computer readable form the nucleotide sequences of SEQ ID NOS:1-391, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 99% and most preferably at least 99.9% identical to a sequence of SEQ ID NOS:1-391 the present invention enables the skilled artisan routinely to access the provided sequence information for a wide variety of purposes.

The examples which follow demonstrate how software which implements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993)) search algorithms on a Sybase system was used to identify open reading frames (ORFs) within the Streptococcus pneumoniae genome which contain homology to ORFs or proteins from both Streptococcus pneumoniae and from other organisms. Among the ORFs discussed herein are protein encoding fragments of the Streptococcus pneumoniae genome useful in producing commercially important proteins, such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.

The present invention further provides systems, particularly computer-based systems, which contain the sequence information described herein. Such systems are designed to identify, among other things, commercially important fragments of the Streptococcus pneumoniae genome.

As used herein, “a computer-based system” refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based systems are suitable for use in the present invention.

As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means.

As used herein, “data storage means” refers to memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.

As used herein, “search means” refers to one or more programs which are implemented on the computer-based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of the present genomic sequences which match a particular target sequence or target motif. A variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, MacPattern (EMBL), BLASTN and BLASTX (NCBIA). A skilled artisan can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems.

As used herein, a “target sequence” can be any DNA or amino acid sequence of six or more nucleotides or two or more amino acids. A skilled artisan can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 100 amino acids or from about 30 to 300 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.

As used herein, “a target structural motif,” or “target motif,” refers to any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzymic active sites and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).

A variety of structural formats for the input and output means can be used to input and output the information in the computer-based systems of the present invention. A preferred format for an output means ranks fragments of the Streptococcus pneumoniae genomic sequences possessing varying degrees of homology to the target sequence or target motif. Such presentation provides a skilled artisan with a ranking of sequences which contain various amounts of the target sequence or target motif and identifies the degree of homology contained in the identified fragment.

A variety of comparing means can be used to compare a target sequence or target motif with the data storage means to identify sequence fragments of the Streptococcus pneumoniae genome. In the present examples, implementing software which implement the BLAST and BLAZE algorithms, described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990), is used to identify open reading frames within the Streptococcus pneumoniae genome. A skilled artisan can readily recognize that any one of the publicly available homology search programs can be used as the search means for the computer-based systems of the present invention. Of course, suitable proprietary systems that may be known to those of skill also may be employed in this regard.

FIG. 1 provides a block diagram of a computer system illustrative of embodiments of this aspect of present invention. The computer system 102 includes a processor 106 connected to a bus 104. Also connected to the bus 104 are a main memory 108 (preferably implemented as random access memory, RAM) and a variety of secondary storage devices 110, such as a hard drive 112 and a removable medium storage device 114. The removable medium storage device 114 may represent, for example, a floppy disk drive, a CD-ROM drive, a magnetic tape drive, etc. A removable storage medium 116 (such as a floppy disk, a compact disk, a magnetic tape, etc.) containing control logic and/or data recorded therein may be inserted into the removable medium storage device 114. The computer system 102 includes appropriate software for reading the control logic and/or the data from the removable medium storage device 114, once it is inserted into the removable medium storage device 114.

A nucleotide sequence of the present invention may be stored in a well known manner in the main memory 108, any of the secondary storage devices 110, and/or a removable storage medium 116. During execution, software for accessing and processing the genomic sequence (such as search tools, comparing tools, etc.) reside in main memory 108, in accordance with the requirements and operating parameters of the operating system, the hardware system and the software program or programs.

BIOCHEMICAL EMBODIMENTS

Other embodiments of the present invention are directed to isolated fragments of the Streptococcus pneumoniae genome. The fragments of the Streptococcus pneumoniae genome of the present invention include, but are not limited to fragments which encode peptides and polypeptides, hereinafter open reading frames (ORFs), fragments which modulate the expression of an operably linked ORF, hereinafter expression modulating fragments (EMFs) and fragments which can be used to diagnose the presence of Streptococcus pneumoniae in a sample, hereinafter diagnostic fragments (DFs).

As used herein, an “isolated nucleic acid molecule” or an “isolated fragment of the Streptococcus pneumoniae genome” refers to a nucleic acid molecule possessing a specific nucleotide sequence which has been subjected to purification means to reduce, from the composition, the number of compounds which are normally associated with the composition. Particularly, the term refers to the nucleic acid molecules having the sequences set out in SEQ ID NOS:1-391, to representative fragments thereof as described above, to polynucleotides at least 95%, preferably at least 99% and especially preferably at least 99.9% identical in sequence thereto, also as set out above.

A variety of purification means can be used to generate the isolated fragments of the present invention. These include, but are not limited to methods which separate constituents of a solution based on charge, solubility, or size.

In one embodiment, Streptococcus pneumoniae DNA can be enzymatically sheared to produce fragments of 15-20 kb in length. These fragments can then be used to generate a Streptococcus pneumoniae library by inserting them into lambda clones as described in the Examples below. Primers flanking, for example, an ORF, such as those enumerated in Tables 1-3 can then be generated using nucleotide sequence information provided in SEQ ID NOS:1-391. Well known and routine techniques of PCR cloning then can be used to isolate the ORF from the lambda DNA library or Streptococcus pneumoniae genomic DNA. Thus, given the availability of SEQ ID NOS:1-391, the information in Tables 1, 2 and 3, and the information that may be obtained readily by analysis of the sequences of SEQ ID NOS:1-391 using methods set out above, those of skill will be enabled by the present disclosure to isolate any ORF-containing or other nucleic acid fragment of the present invention.

The isolated nucleic acid molecules of the present invention include, but are not limited to single stranded and double stranded DNA, and single stranded RNA.

As used herein, an “open reading frame,” ORF, means a series of triplets coding for amino acids without any termination codons and is a sequence translatable into protein.

Tables 1, 2, and 3 list ORFs in the Streptococcus pneumoniae genomic contigs of the present invention that were identified as putative coding regions by the GeneMark software using organism-specific second-order Markov probability transition matrices. It will be appreciated that other criteria can be used, in accordance with well known analytical methods, such as those discussed herein, to generate more inclusive, more restrictive, or more selective lists.

Table 1 sets out ORFs in the Streptococcus pneumoniae contigs of the present invention that over a continuous region of at least 50 bases are 95% or more identical (by BLAST analysis) to a nucleotide sequence available through GenBank in October, 1997.

Table 2 sets out ORFs in the Streptococcus pneumoniae contigs of the present invention that are not in Table 1 and match, with a BLASTP probability score of 0.01 or less, a polypeptide sequence available through GenBank in October, 1997.

Table 3 sets out ORFs in the Streptococcus pneumoniae contigs of the present invention that do not match significantly, by BLASTP analysis, a polypeptide sequence available through GenBank in October, 1997.

In each table, the first and second columns identify the ORF by, respectively, contig number and ORF number within the contig; the third column indicates the first nucleotide of the ORF (actually the first nucleotide of the stop codon immediately preceeding the ORF), counting from the 5′ end of the contig strand; and the fourth column, “stop (nt)” indicates the last nucleotide of the stop codon defining the 3′ end of the ORF.

In Tables 1 and 2, column five, lists the Reference for the closest matching sequence available through GenBank. These reference numbers are the databases entry numbers commonly used by those of skill in the art, who will be familiar with their denominators. Descriptions of the nomenclature are available from the National Center for Biotechnology Information. Column six in Tables 1 and 2 provides the gene name of the matching sequence; column seven provides the BLAST identity score and column eight the BLAST similarity score from the comparison of the ORF and the homologous gene; and column nine indicates the length in nucleotides of the highest scoring segment pair identified by the BLAST identity analysis.

Each ORF described in the tables is defined by “start (nt)” (5′)and “stop (nt)” (3′)nucleotide position numbers. These position numbers refer to the boundaries of each ORF and provide orientation with respect to whether the forward or reverse strand is the coding strand and which reading frame the coding sequence is contained. The “start” position is the first nucleotide of the triplet encoding a stop codon just 5′ to the ORF and the “stop” position is the last nucleotide of the triplet encoding the next in-frame stop codon (i.e., the stop codon at the 3′ end of the ORF). Those of ordinary skill in the art appreciate that preferred fragments within each ORF described in the table include fragments of each ORF which include the entire sequence from the delineated “start” and “stop” positions excepting the first and last three nucleotides since these encode stop codons. Thus, polynucleotides set out as ORFs in the tables but lacking the three (3) 5′ nucleotides and the three (3) 3′ nucleotides are encompassed by the present invention. Those of skill also appreciate that particularly preferred are fragments within each ORF that are polynucleotide fragments comprising polypeptide coding sequence. As defined herein, “coding sequence” includes the fragment within an ORF beginning at the first in-frame ATG (triplet encoding methionine) and ending with the last nucleotide prior to the triplet encoding the 3′ stop codon. Preferred are fragments comprising the entire coding sequence and fragments comprising the entire coding sequence, excepting the coding sequence for the N-terninal methionine. Those of skill appreciate that the N-terminal methionine is often removed during post-translational processing and that polynucleotides lacking the ATG can be used to facilitate production of N-termainal fusion proteins which may be benefical in the production or use of genetically engineered proteins. Of course, due to the degeneracy of the genetic code many polynucleotides can encode a given polypeptide. Thus, the invention further includes polynucleotides comprising a nucleotide sequence encoding a polypeptide sequence itself encoded by the coding sequence within an ORF described in Tables 1-3 herein. Further, polynucleotides at least 95%, preferably at least 99% and especially preferably at least 99.9% identical in sequence to the foregoing polynucleotides, are contemplated by the present invention.

Polypeptides encoded by polynucleotides described above and elsewhere herein are also provided by the present invention as are polypeptide comprising a an amino acid sequence at least about 95%, preferably at least 97% and even more preferably 99% identical to the amino acid sequence of a polypeptide encoded by an ORF shown in Tables 1-3. These polypeptides may or may not comprise an N-terminal methionine.

The concepts of percent identity and percent similarity of two polypeptide sequences is well understood in the art. For example, two polypeptides 10 amino acids in length which differ at three amino acid positions (e.g., at positions 1, 3 and 5) are said to have a percent identity of 70%. However, the same two polypeptides would be deemed to have a percent similarity of 80% if, for example at position 5, the amino acids moieties, although not identical, were “similar” (i.e., possessed similar biochemical characteristics). Many programs for analysis of nucleotide or amino acid sequence similarity, such as fasta and BLAST specifically list percent identity of a matching region as an output parameter. Thus, for instance, Tables 1 and 2 herein enumerate the percent identity of the highest scoring segment pair in each ORF and its listed relative. Further details concerning the algorithms and criteria used for homology searches are provided below and are described in the pertinent literature highlighted by the citations provided below.

It will be appreciated that other criteria can be used to generate more inclusive and more exclusive listings of the types set out in the tables. As those of skill will appreciate, narrow and broad searches both are useful. Thus, a skilled artisan can readily identify ORFs in contigs of the Streptococcus pneumoniae genome other than those listed in Tables 1-3, such as ORFs which are overlapping or encoded by the opposite strand of an identified ORF in addition to those ascertainable using the computer-based systems of the present invention.

As used herein, an “expression modulating fragment,” EMF, means a series of nucleotide molecules which modulates the expression of an operably linked ORF or EMF.

As used herein, a sequence is said to “modulate the expression of an operably linked sequence” when the expression of the sequence is altered by the presence of the EMF. EMFs include, but are not limited to, promoters, and promoter modulating sequences (inducible elements). One class of EMFs are fragments which induce the expression or an operably linked ORF in response to a specific regulatory factor or physiological event.

EMF sequences can be identified within the contigs of the Streptococcus pneumoniae genome by their proximity to the ORFs provided in Tables 1-3. An intergenic segment, or a fragment of the intergenic segment, from about 10 to 200 nucleotides in length, taken from any one of the ORFs of Tables 1-3 will modulate the expression of an operably linked ORF in a fashion similar to that found with the naturally linked ORF sequence. As used herein, an “intergenic segment” refers to fragments of the Streptococcus pneumoniae genome which are between two ORF(s) herein described. EMFs also can be identified using known EMFs as a target sequence or target motif in the computer-based systems of the present invention. Further, the two methods can be combined and used together.

The presence and activity of an EMF can be confirmed using an EMF trap vector. An EMF trap vector contains a cloning site linked to a marker sequence. A marker sequence encodes an identifiable phenotype, such as antibiotic resistance or a complementing nutrition auxotrophic factor, which can be identified or assayed when the EMF trap vector is placed within an appropriate host under appropriate conditions. As described above, a EMF will modulate the expression of an operably linked marker sequence. A more detailed discussion of various marker sequences is provided below. A sequence which is suspected as being an EMF is cloned in all three reading frames in one or more restriction sites upstream from the marker sequence in the EMF trap vector. The vector is then transformed into an appropriate host using known procedures and the phenotype of the transformed host in examined under appropriate conditions. As described above, an EMF will modulate the expression of an operably linked marker sequence.

As used herein, a “diagnostic fragment,” DF, means a series of nucleotide molecules which selectively hybridize to Streptococcus pneumoniae sequences. DFs can be readily identified by identifying unique sequences within contigs of the Streptococcus pneumoniae genome, such as by using well-known computer analysis software, and by generating and testing probes or amplification primers consisting of the DF sequence in an appropriate diagnostic format which determines amplification or hybridization selectivity.

The sequences falling within the scope of the present invention are not limited to the specific sequences herein described, but also include allelic and species variations thereof. Allelic and species variations can be routinely determined by comparing the sequences provided in SEQ ID NOS:1-391, a representative fragment thereof, or a nucleotide sequence at least 95%, preferrably at least 99% and most at least preferably 99.9% identical to SEQ ID NOS:1-391, with a sequence from another isolate of the same species. Furthermore, to accommodate codon variability, the invention includes nucleic acid molecules coding for the same amino acid sequences as do the specific ORFs disclosed herein. In other words, in the coding region of an ORF, substitution of one codon for another which encodes the same amino acid is expressly contemplated. Any specific sequence disclosed herein can be readily screened for errors by resequencing a particular fragment, such as an ORF, in both directions (i.e., sequence both strands). Alternatively, error screening can be performed by sequencing corresponding polynucleotides of Streptococcus pneumoniae origin isolated by using part or all of the fragments in question as a probe or primer.

Preferred DFs of the present invention comprise at least about 17, preferrably at least about 20, and more preferrably at least about 50 contiguous nucleotides within an ORF set out in Tables 1-3. Most highly preferred DFs specifically hybridize to a polynucleotide containing the sequence of the ORF from which they are derived. Specific hybridization occurs even under stringent conditions defined elsewhere herein.

Each of the ORFs of the Streptococcus pneumoniae genome disclosed in Tables 1, 2 and 3, and the EMFs found 5′ to the ORFs, can be used as polynucleotide reagents in numerous ways. For example, the sequences can be used as diagnostic probes or diagnostic amplification primers to detect the presence of a specific microbe in a sample, particularly Streptococcus pneumoniae. Especially preferred in this regard are ORFs such as those of Table 3, which do not match previously characterized sequences from other organisms and thus are most likely to be highly selective for Streptococcus pneumoniae. Also particularly preferred are ORFs that can be used to distinguish between strains of Streptococcus pneumoniae, particularly those that distinguish medically important strain, such as drug-resistant strains.

In addition, the fragments of the present invention, as broadly described, can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which methods are based on the binding of a polynucleotide sequence to DNA or RNA. Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Information from the sequences of the present invention can be used to design antisense and triple helix-forming oligonucleotides. Polynucleotides suitable for use in these methods are usually 20 to 40 bases in length and are designed to be complementary to a region of the gene involved in transcription, for triple-helix formation, or to the mRNA itself, for antisense inhibition. Both techniques have been demonstrated to be effective in model systems, and the requisite techniques are well known and involve routine procedures. Triple helix techniques are discussed in, for example, Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991). Antisence techniques in general are discussed in, for instance, Okano, J. Neurochem. 56:560 (1991) and Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)).

The present invention further provides recombinant constructs comprising one or more fragments of the Streptococcus pneumoniae genomic fragments and contigs of the present invention. Certain preferred recombinant constructs of the present invention comprise a vector, such as a plasmid or viral vector, into which a fragment of the Streptococcus pneumoniae genome has been inserted, in a forward or reverse orientation. In the case of a vector comprising one of the ORFs of the present invention, the vector may further comprise regulatory sequences, including for example, a promoter, operably linked to the ORF. For vectors comprising the EMFs of the present invention, the vector may further comprise a marker sequence or heterologous ORF operably linked to the EMF.

Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available for generating the recombinant constructs of the present invention. The following vectors are provided by way of example. Useful bacterial vectors include phagescript, PsiX174, pBluescript SK, pBS KS, pNH8a, pNH16a, pNH18a, pNH46a (available from Stratagene); pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (available from Pharmacia). Useful eukaryotic vectors include pWLneo, pSV2cat, pOG44, pXT1, pSG (available from Stratagene) pSVK3, pBPV, pMSG, pSVL (available from Pharmacia).

Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art.

The present invention further provides host cells containing any one of the isolated fragments of the Streptococcus pneumoniae genomic fragments and contigs of the present invention, wherein the fragment has been introduced into the host cell using known methods. The host cell can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or a procaryotic cell, such as a bacterial cell.

A polynucleotide of the present invention, such as a recombinant construct comprising an ORF of the present invention, may be introduced into the host by a variety of well established techniques that are standard in the art, such as calcium phosphate transfection, DEAE, dextran mediated transfection and electroporation, which are described in, for instance, Davis, L. et al., BASIC METHODS IN MOLECULAR BIOLOGY (1986).

A host cell containing one of the fragments of the Streptococcus pneumoniae genomic fragments and contigs of the present invention, can be used in conventional manners to produce the gene product encoded by the isolated fragment (in the case of an ORF) or can be used to produce a heterologous protein under the control of the EMF. The present invention further provides isolated polypeptides encoded by the nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. By “degenerate variant” is intended nucleotide fragments which differ from a nucleic acid fragment of the present invention (e.g., an ORF) by nucleotide sequence but, due to the degeneracy of the Genetic Code, encode an identical polypeptide sequence.

Preferred nucleic acid fragments of the present invention are the ORFs and subfragments thereof depicted in Tables 2 and 3 which encode proteins.

A variety of methodologies known in the art can be utilized to obtain any one of the isolated polypeptides or proteins of the present invention. At the simplest level, the amino acid sequence can be synthesized using commercially available peptide synthesizers. This is particularly useful in producing small peptides and fragments of larger polypeptides. Such short fragments as may be obtained most readily by synthesis are useful, for example, in generating antibodies against the native polypeptide, as discussed further below.

In an alternative method, the polypeptide or protein is purified from bacterial cells which naturally produce the polypeptide or protein. One skilled in the art can readily employ well-known methods for isolating polypeptides and proteins to isolate and purify polypeptides or proteins of the present invention produced naturally by a bacterial strain, or by other methods. Methods for isolation and purification that can be employed in this regard include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography.

The polypeptides and proteins of the present invention also can be purified from cells which have been altered to express the desired polypeptide or protein. As used herein, a cell is said to be altered to express a desired polypeptide or protein when the cell, through genetic manipulation, is made to produce a polypeptide or protein which it normally does not produce or which the cell normally produces at a lower level. Those skilled in the art can readily adapt procedures for introducing and expressing either recombinant or synthetic sequences into eukaryotic or prokaryotic cells in order to generate a cell which produces one of the polypeptides or proteins of the present invention.

Any host/vector system can be used to express one or more of the ORFs of the present invention. These include, but are not limited to, eukaryotic hosts such as HeLa cells, CV-1 cell, COS cells, and Sf9 cells, as well as prokaryotic host such as E. coli and B. subtilis. The most preferred cells are those which do not normally express the particular polypeptide or protein or which expresses the polypeptide or protein at low natural level.

“Recombinant,” as used herein, means that a polypeptide or protein is derived from recombinant (e.g., microbial or mammalian) expression systems. “Microbial” refers to recombinant polypeptides or proteins made in bacterial or fungal (e.g., yeast) expression systems. As a product, “recombinant microbial” defines a polypeptide or protein essentially free of native endogenous substances and unaccompanied by associated native glycosylation. Polypeptides or proteins expressed in most bacterial cultures, e.g., E. coli, will be free of glycosylation modifications; polypeptides or proteins expressed in yeast will have a glycosylation pattern different from that expressed in mammalian cells.

“Nucleotide sequence” refers to a heteropolymer of deoxyribonucleotides. Generally, DNA segments encoding the polypeptides and proteins provided by this invention are assembled from fragments of the Streptococcus pneumoniae genome and short oligonucleotide linkers, or from a series of oligonucleotides, to provide a synthetic gene which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon.

“Recombinant expression vehicle or vector” refers to a plasmid or phage or virus or vector, for expressing a polypeptide from a DNA (RNA) sequence. The expression vehicle can comprise a transcriptional unit comprising an assembly of (1) a genetic regulatory elements necessary for gene expression in the host, including elements required to initiate and maintain transcription at a level sufficient for suitable expression of the desired polypeptide, including, for example, promoters and, where necessary, an enhancer and a polyadenylation signal; (2) a structural or coding sequence which is transcribed into mRNA and translated into protein, and (3) appropriate signals to initiate translation at the beginning of the desired coding region and terminate translation at its end. Structural units intended for use in yeast or eukaryotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an N-terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.

“Recombinant expression system” means host cells which have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry the recombinant transcriptional unit extra chromosomally. The cells can be prokaryotic or eukaryotic. Recombinant expression systems as defined herein will express heterologous polypeptides or proteins upon induction of the regulatory elements linked to the DNA segment or synthetic gene to be expressed.

Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2^nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), the disclosure of which is hereby incorporated by reference in its entirety.

Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiae TRP1 gene, and a promoter derived from a highly expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), alpha-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an N-terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product.

Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and, when desirable, provide amplification within the host.

Suitable prokaryotic hosts for transformation include strains of E. coli, B. subtilis, Salmonella typhimurium and various species within the genera Pseudomonas and Streptomyces. Others may, also be employed as a matter of choice.

As a representative but non-limiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (available form Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (available from Promega Biotec, Madison, Wis., USA). These pBR322 “backbone” sections are combined with an appropriate promoter and the structural sequence to be expressed.

Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter, where it is inducible, is derepressed or induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period to provide for expression of the induced gene product. Thereafter cells are typically harvested, generally by centrifugation, disrupted to release expressed protein, generally by physical or chemical means, and the resulting crude extract is retained for further purification.

Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described in Gluzman, Cell 23:175 (1981), and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines.

Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, enhancer, splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

Recombinant polypeptides and proteins produced in bacterial culture is usually isolated by initial extraction from cell pellets, followed by one or more salting-out, aqueous ion exchange or size exclusion chromatography steps. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps.

The present invention further includes isolated polypeptides, proteins and nucleic acid molecules which are substantially equivalent to those herein described. As used herein, substantially equivalent can refer both to nucleic acid and amino acid sequences, for example a mutant sequence, that varies from a reference sequence by one or more substitutions, deletions, or additions, the net effect of which does not result in an adverse functional dissimilarity between reference and subject sequences. For purposes of the present invention, sequences having equivalent biological activity, and equivalent expression characteristics are considered substantially equivalent. For purposes of determining equivalence, truncation of the mature sequence should be disregarded.

The invention further provides methods of obtaining homologs from other strains of Streptococcus pneumoniae, of the fragments of the Streptococcus pneumoniae genome of the present invention and homologs of the proteins encoded by the ORFs of the present invention. As used herein, a sequence or protein of Streptococcus pneumoniae is defined as a homolog of a fragment of the Streptococcus pneumoniae fragments or contigs or a protein encoded by one of the ORFs of the present invention, if it shares significant homology to one of the fragments of the Streptococcus pneumoniae genome of the present invention or a protein encoded by one of the ORFs of the present invention. Specifically, by using the sequence disclosed herein as a probe or as primers, and techniques such as PCR cloning and colony/plaque hybridization, one skilled in the art can obtain homologs.

As used herein, two nucleic acid molecules or proteins are said to “share significant homology” if the two contain regions which possess greater than 85% sequence (amino acid or nucleic acid) homology. Preferred homologs in this regard are those with more than 90% homology. Especially preferred are those with 93% or more homology. Among especially preferred homologs those with 95% or more homology are particularly preferred. Very particularly preferred among these are those with 97% and even more particularly preferred among those are homologs with 99% or more homology. The most preferred homologs among these are those with 99.9% homology or more. It will be understood that, among measures of homology, identity is particularly preferred in this regard.

Region specific primers or probes derived from the nucleotide sequence provided in SEQ ID NOS:1-391 or from a nucleotide sequence at least 95%, particularly at least 99%, especially at least 99.5% identical to a sequence of SEQ ID NOS:1-391 can be used to prime DNA synthesis and PCR amplification, as well as to identify colonies containing cloned DNA encoding a homolog. Methods suitable to this aspect of the present invention are well known and have been described in great detail in many publications such as, for example, Innis et al., PCR Protocols, Academic Press, San Diego, Calif. (1990)).

When using primers derived from SEQ ID NOS:1-391 or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS:1-391, one skilled in the art will recognize that by employing high stringency conditions (e.g., annealing at 50-60° C. in 6×SSC and 50% formamide, and washing at 50-65° C. in 0.5×SSC) only sequences which are greater than 75% homologous to the primer will be amplified. By employing lower stringency conditions (e.g., hybridizing at 35-37° C. in 5×SSC and 40-45% formamide, and washing at 42° C. in 0.5×SSC), sequences which are greater than 40-50% homologous to the primer will also be amplified.

When using DNA probes derived from SEQ ID NOS:1-391, or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS:1-391, for colony/plaque hybridization, one skilled in the art will recognize that by employing high stringency conditions (e.g., hybridizing at 50-65° C. in 5×SSC and 50% formamide, and washing at 50-65° C. in 0.5×SSC), sequences having regions which are greater than 90% homologous to the probe can be obtained, and that by employing lower stringency conditions (e.g., hybridizing at 35-37° C. in 5×SSC and 40-45% formamide, and washing at 42° C. in 0.5×SSC), sequences having regions which are greater than 35-45% homologous to the probe will be obtained.

Any organism can be used as the source for homologs of the present invention so long as the organism naturally expresses such a protein or contains genes encoding the same. The most preferred organism for isolating homologs are bacteria which are closely related to Streptococcus pneumoniae.

ILLUSTRATIVE USES OF COMPOSITIONS OF THE INVENTION

Each ORF provided in Tables 1 and 2 is identified with a function by homology to a known gene or polypeptide. As a result, one skilled in the art can use the polypeptides of the present invention for commercial, therapeutic and industrial purposes consistent with the type of putative identification of the polypeptide. Such identifications permit one skilled in the art to use the Streptococcus pneumoniae ORFs in a manner similar to the known type of sequences for which the identification is made; for example, to ferment a particular sugar source or to produce a particular metabolite. A variety of reviews illustrative of this aspect of the invention are available, including the following reviews on the industrial use of enzymes, for example, BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY HANDBOOK, 2nd Ed., MacMillan Publications, Ltd. NY (1991) and BIOCATALYSTS IN ORGANIC SYNTHESES, Tramper et al., Eds., Elsevier Science Publishers, Amsterdam, The Netherlands (1985). A variety of exemplary uses that illustrate this and similar aspects of the present invention are discussed below.

1. Biosynthetic Enzymes

Open reading frames encoding proteins involved in mediating the catalytic reactions involved in intermediary and macromolecular metabolism, the biosynthesis of small molecules, cellular processes and other functions includes enzymes involved in the degradation of the intermediary products of metabolism, enzymes involved in central intermediary metabolism, enzymes involved in respiration, both aerobic and anaerobic, enzymes involved in fermentation, enzymes involved in ATP proton motor force conversion, enzymes involved in broad regulatory function, enzymes involved in amino acid synthesis, enzymes involved in nucleotide synthesis, enzymes involved in cofactor and vitamin synthesis, can be used for industrial biosynthesis.

The various metabolic pathways present in Streptococcus pneumoniae can be identified based on absolute nutritional requirements as well as by examining the various enzymes identified in Table 1-3 and SEQ ID NOS:1-391.

Of particular interest are polypeptides involved in the degradation of intermediary metabolites as well as non-macromolecular metabolism. Such enzymes include amylases, glucose oxidases, and catalase.

Proteolytic enzymes are another class of commercially important enzymes. Proteolytic enzymes find use in a number of industrial processes including the processing of flax and other vegetable fibers, in the extraction, clarification and depectinization of fruit juices, in the extraction of vegetables' oil and in the maceration of fruits and vegetables to give unicellular fruits. A detailed review of the proteolytic enzymes used in the food industry is provided in Rombouts et al., Symbiosis 21:79 (1986) and Voragen et al. in Biocatalysts In Agricultural Biotechnology, Whitaker et al., Eds., American Chemical Society Symposium Series 389:93 (1989).

The metabolism of sugars is an important aspect of the primary metabolism of Streptococcus pneumoniae. Enzymes involved in the degradation of sugars, such as, particularly, glucose, galactose, fructose and xylose, can be used in industrial fermentation. Some of the important sugar transforming enzymes, from a commercial viewpoint, include sugar isomerases such as glucose isomerase. Other metabolic enzymes have found commercial use such as glucose oxidases which produces ketogulonic acid (KGA). KGA is an intermediate in the commercial production of ascorbic acid using the Reichstein's procedure, as described in Krueger et al., Biotechnology 6(A , Rhine et al., Eds., Verlag Press, Weinheim, Germany (1984).

Glucose oxidase (GOD) is commercially available and has been used in purified form as well as in an immobilized form for the deoxygenation of beer. See, for instance, Hartmeir et al., Biotechnology Letters 1:21 (1979). The most important application of GOD is the industrial scale fermentation of gluconic acid. Market for gluconic acids which are used in the detergent, textile, leather, photographic, pharmaceutical, food, feed and concrete industry, as described, for example, in Bigelis et al., beginning on page 357 in GENE MANIPULATIONS AND FUNGI; Benett et al., Eds., Academic Press, New York (1985). In addition to industrial applications, GOD has found applications in medicine for quantitative determination of glucose in body fluids recently in biotechnology for analyzing syrups from starch and cellulose hydrosylates. This application is described in Owusu et al., Biochem. et Biophysica. Acta. 872:83 (1986), for instance.

The main sweetener used in the world today is sugar which comes from sugar beets and sugar cane. In the field of industrial enzymes, the glucose isomerase process shows the largest expansion in the market today. Initially, soluble enzymes were used and later immobilized enzymes were developed (Krueger et al., Biotechnology, The Textbook of Industrial Microbiology, Sinauer Associated Incorporated, Sunderland, Mass. (1990)). Today, the use of glucose-produced high fructose syrups is by far the largest industrial business using immobilized enzymes. A review of the industrial use of these enzymes is provided by Jorgensen, Starch 40:307 (1988).

Proteinases, such as alkaline serine proteinases, are used as detergent additives and thus represent one of the largest volumes of microbial enzymes used in the industrial sector. Because of their industrial importance, there is a large body of published and unpublished information regarding the use of these enzymes in industrial processes. (See Faultman et al., Acid Proteases Structure Function and Biology, Tang, J., ed., Plenum Press, New York (1977) and Godfrey et al., Industrial Enzymes, MacMillan Publishers, Surrey, UK (1983) and Hepner et al., Report Industrial Enzymes by 1990, Hel Hepner & Associates, London (1986)).

Another class of commercially usable proteins of the present invention are the microbial lipases, described by, for instance, Macrae et al., Philosophical Transactions of the Chiral Society of London 310:227 (1985) and Poserke, Journal of the American Oil Chemist Society 61:1758 (1984). A major use of lipases is in the fat and oil industry for the production of neutral glycerides using lipase catalyzed inter-esterification of readily available triglycerides. Application of lipases include the use as a detergent additive to facilitate the removal of fats from fabrics in the course of the washing procedures.

The use of enzymes, and in particular microbial enzymes, as catalyst for key steps in the synthesis of complex organic molecules is gaining popularity at a great rate. One area of great interest is the preparation of chiral intermediates. Preparation of chiral intermediates is of interest to a wide range of synthetic chemists particularly those scientists involved with the preparation of new pharmaceuticals, agrochemicals, fragrances and flavors. (See Davies et al., Recent Advances in the Generation of Chiral Intermediates Using Enzymes, CRC Press, Boca Raton, Fla. (1990)). The following reactions catalyzed by enzymes are of interest to organic chemists: hydrolysis of carboxylic acid esters, phosphate esters, amides and nitrites, esterification reactions, trans-esterification reactions, synthesis of amides, reduction of alkanones and oxoalkanates, oxidation of alcohols to carbonyl compounds, oxidation of sulfides to sulfoxides, and carbon bond forming reactions such as the aldol reaction.

When considering the use of an enzyme encoded by one of the ORFs of the present invention for biotransformation and organic synthesis it is sometimes necessary to consider the respective advantages and disadvantages of using a microorganism as opposed to an isolated enzyme. Pros and cons of using a whole cell system on the one hand or an isolated partially purified enzyme on the other hand, has been described in detail by Bud et al., Chemistry in Britain (1987), p. 127.

Amino transferases, enzymes involved in the biosynthesis and metabolism of amino acids, are useful in the catalytic production of amino acids. The advantages of using microbial based enzyme systems is that the amino transferase enzymes catalyze the stereo-selective synthesis of only L-amino acids and generally possess uniformly high catalytic rates, A description of the use of amino transferases for amino acid production is provided by Roselle-David, Methods of Enzymology 136:479 (1987).

Another category of useful proteins encoded by the ORFs of the present invention include enzymes involved in nucleic acid synthesis, repair, and recombination.

2. Generation of Antibodies

As described here, the proteins of the present invention, as well as homologs thereof, can be used in a variety of procedures and methods known in the art which are currently applied to other proteins. The proteins of the present invention can further be used to generate an antibody which selectively binds the protein. Such antibodies can be either monoclonal or polyclonal antibodies, as well fragments of these antibodies, and humanized forms.

The invention further provides antibodies which selectively bind to one of the proteins of the present invention and hybridomas which produce these antibodies. A hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.

In general, techniques for preparing polyclonal and monoclonal antibodies as well as hybridomas capable of producing the desired antibody are well known in the art (Campbell, A. M., Monoclonal Antibody Technology: Laboratory Techniques In Biochemistry And Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1984); St. Groth et al., J. Immunol. Methods 35. 1-21 (1980), Kohler and Milstein, Nature 256:495-497 (1975)), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today 4:72 (1983), pgs. 77-96 of Cole et al., in Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc. (1985)). Any animal (mouse, rabbit, etc.) which is known to produce antibodies can be immunized with the pseudogene polypeptide. Methods for immunization are well known in the art. Such methods include subcutaneous or interperitoneal injection of the polypeptide. One skilled in the art will recognize that the amount of the protein encoded by the ORF of the present invention used for immunization will vary based on the animal which is immunized, the antigenicity of the peptide and the site of injection.

The protein which is used as an immunogen may be modified or administered in an adjuvant in order to increase the proteins antigenicity. Methods of increasing the antigenicity of a protein are well known in the art and include, but are not limited to coupling the antigen with a heterologous protein (such as globulin or galactosidase) or through the inclusion of an adjuvant during immunization.

For monoclonal antibodies, spleen cells from the immunized animals are removed, fused with myeloma cells, such as SP2/0-Ag14 myeloma cells, and allowed to become monoclonal antibody producing hybridoma cells.

Any one of a number of methods well known in the art can be used to identify the hybridoma cell which produces an antibody with the desired characteristics. These include screening the hybridomas with an ELISA assay, western blot analysis, or radioimmunoassay (Lutz et al., Exp. Cell Res. 175.109-124 (1988)),

Hybridomas secreting the desired antibodies are cloned and the class and subclass is determined using procedures known in the art (Campbell, A. M., Monoclonal Antibody Technology: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1984)).

Techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies to proteins of the present invention.

For polyclonal antibodies, antibody containing antisera is isolated from the immunized animal and is screened for the presence of antibodies with the desired specificity using one of the above-described procedures.

The present invention further provides the above-described antibodies in detectably labelled form. Antibodies can be detectably labelled through the use of radioisotopes, affinity labels (such as biotin, avidin, etc.), enzymatic labels (such as horseradish peroxidase, alkaline phosphatase, etc.) fluorescent labels (such as FITC or rhodamine, etc.), paramagnetic atoms, etc. Procedures for accomplishing such labeling are well-known in the art, for example see Sternberger et al., J. Histochem. Cytochem. 18:315 (1970); Bayer, E. A. et al., Meth. Enzym. 62:308 (1979); Engval, E. et al., Immunol. 109:129 (1972); Goding, J. W., J. Immunol.

Meth. 13:215 (1976)).

The labeled antibodies of the present invention can be used for in vitro, in vivo, and in situ assays to identify cells or tissues in which a fragment of the Streptococcus pneumoniae genome is expressed.

The present invention further provides the above-described antibodies immobilized on a solid support. Examples of such solid supports include plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, acrylic resins and such as polyacrylamide and latex beads. Techniques for coupling antibodies to such solid supports are well known in the art (Weir, D. M. et al., “Handbook of Experimental Immunology” 4th Ed., Blackwell Scientific Publications, Oxford, England, Chapter 10 (1986); Jacoby, W. D. et al., Meth. Enzym. 34 Academic Press, N.Y. (1974)). The immobilized antibodies of the present invention can be used for in vitro, in vivo, and in situ assays as well as for immunoaffinity purification of the proteins of the present invention.

3. Diagnostic Assays and Kits

The present invention further provides methods to identify the expression of one of the ORFs of the present invention, or homolog thereof, in a test sample, using one of the DFs or antibodies of the present invention.

In detail, such methods comprise incubating a test sample with one or more of the antibodies or one or more of the DFs of the present invention and assaying for binding of the DFs or antibodies to components within the test sample.

Conditions for incubating a DF or antibody with a test sample vary, Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the DF or antibody used in the assay. One skilled in the art will recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the DFs or antibodies of the present invention. Examples of such assays can be found in Chard, T., An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G. R. et al., Techniques in Immunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of Enzyme Immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985).

The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized.

In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention.

Specifically, the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the DFs or antibodies of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound DF or antibody.

In detail, a compartmentalized kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the antibodies used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc.), and containers which contain the reagents used to detect the bound antibody or DF.

Types of detection reagents include labelled nucleic acid probes, labelled secondary antibodies, or in the alternative, if the primary antibody is labelled, the enzymatic, or antibody binding reagents which are capable of reacting with the labelled antibody. One skilled in the art will readily recognize that the disclosed DFs and antibodies of the present invention can be readily incorporated into one of the established kit formats which are well known in the art.

4. Screening Assay for Binding Agents

Using the isolated proteins of the present invention, the present invention further provides methods of obtaining and identifying agents which bind to a protein encoded by one of the ORFs of the present invention or to one of the fragments and the Streptococcus pneumoniae fragment and contigs herein described.

In general, such methods comprise steps of:

(a) contacting an agent with an isolated protein encoded by one of the ORFs of the present invention, or an isolated fragment of the Streptococcus pneumoniae genome; and

(b) determining whether the agent binds to said protein or said fragment,

The agents screened in the above assay can be, but are not limited to, peptides, carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents can be selected and screened at random or rationally selected or designed using protein modeling techniques.

For random screening, agents such as peptides, carbohydrates, pharmaceutical agents and the like are selected at random and are assayed for their ability to bind to the protein encoded by the ORF of the present invention.

Alternatively, agents may be rationally selected or designed. As used herein, an agent is said to be “rationally selected or designed” when the agent is chosen based on the configuration of the particular protein. For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the like capable of binding to a specific peptide sequence in order to generate rationally designed antipeptide peptides, for example see Hurby et al., “Application of Synthetic Peptides: Antisense Peptides,” in Synthetic Peptides, A User's Guide, W. H. Freeman, NY (1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or pharmaceutical agents, or the like.

In addition to the foregoing, one class of agents of the present invention, as broadly described, can be used to control gene expression through binding to one of the ORFs or EMFs of the present invention. As described above, such agents can be randomly screened or rationally designed/selected. Targeting the ORF or EMF allows a skilled artisan to design sequence specific or element specific agents, modulating the expression of either a single ORF or multiple ORFs which rely on the same EMF for expression control.

One class of DNA binding agents are agents which contain base residues which hybridize or form a triple helix by binding to DNA or RNA. Such agents can be based on the classic phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl or polymeric derivatives which have base attachment capacity.

Agents suitable for use in these methods usually contain 20 to 40 bases and are designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense—Okano, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems. Information contained in the sequences of the present invention can be used to design antisense and triple helix-forming oligonucleotides, and other DNA binding agents.

5. Pharmaceutical Compositions and Vaccines

The present invention further provides pharmaceutical agents which can be used to modulate the growth or pathogenicity of Streptococcus pneumoniae, or another related organism, in vivo or in vitro. As used herein, a “pharmaceutical agent” is defined as a composition of matter which can be formulated using known techniques to provide a pharmaceutical compositions. As used herein, the “pharmaceutical agents of the present invention” refers the pharmaceutical agents which are derived from the proteins encoded by the ORFs of the present invention or are agents which are identified using the herein described assays.

As used herein, a pharmaceutical agent is said to “modulate the growth pathogenicity of Streptococcus pneumoniae or a related organism, in vivo or in vitro,” when the agent reduces the rate of growth, rate of division, or viability of the organism in question. The pharmaceutical agents of the present invention can modulate the growth or pathogenicity of an organism in many fashions, although an understanding of the underlying mechanism of action is not needed to practice the use of the pharmaceutical agents of the present invention. Some agents will modulate the growth by binding to an important protein thus blocking the biological activity of the protein, while other agents may bind to a component of the outer surface of the organism blocking attachment or rendering the organism more prone to act the bodies nature immune system. Alternatively, the agent may comprise a protein encoded by one of the ORFs of the present invention and serve as a vaccine. The development and use of a vaccine based on outer membrane components are well known in the art.

As used herein, a “related organism” is a broad term which refers to any organism whose growth can be modulated by one of the pharmaceutical agents of the present invention, In general, such an organism will contain a homolog of the protein which is the target of the pharmaceutical agent or the protein used as a vaccine. As such, related organisms do not need to be bacterial but may be fungal or viral pathogens.

The pharmaceutical agents and compositions of the present invention may be administered in a convenient manner, such as by the oral, topical, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal or intradermal routes. The pharmaceutical compositions are administered in an amount which is effective for treating and/or prophylaxis of the specific indication. In general, they are administered in an amount of at least about 1 mg/kg body weight and in most cases they will be administered in an amount not in excess of about 1 g/kg body weight per day. In most cases, the dosage is from about 0.1 mg/kg to about 10 g/kg body weight daily, taking into account the routes of administration, symptoms, etc.

The agents of the present invention can be used in native form or can be modified to form a chemical derivative. As used herein, a molecule is said to be a “chemical derivative” of another molecule when it contains additional chemical moieties not normally a part of the molecule. Such moieties may improve the molecule's solubility, absorption, biological half life, etc. The moieties may alternatively decrease the toxicity of the molecule, eliminate or attenuate any undesirable side effect of the molecule, etc. Moieties capable of mediating such effects are disclosed in, among other sources, REMINGTON'S PHARMACEUTICAL SCIENCES (1980) cited elsewhere herein.

For example, such moieties may change an immunological character of the functional derivative, such as affinity for a given antibody. Such changes in immunomodulation activity are measured by the appropriate assay, such as a competitive type immunoassay. Modifications of such protein properties as redox or thermal stability, biological half-life, hydrophobicity, susceptibility to proteolytic degradation or the tendency to aggregate with carriers or into multimers also may be effected in this way and can be assayed by methods well known to the skilled artisan.

The therapeutic effects of the agents of the present invention may be obtained by providing the agent to a patient by any suitable means (e.g., inhalation, intravenously, intramuscularly, subcutaneously, enterally, or parenterally). It is preferred to administer the agent of the present invention so as to achieve an effective concentration within the blood or tissue in which the growth of the organism is to be controlled. To achieve an effective blood concentration, the preferred method is to administer the agent by injection. The administration may be by continuous infusion, or by single or multiple injections.

In providing a patient with one of the agents of the present invention, the dosage of the administered agent will vary depending upon such factors as the patient's age, weight, height, sex, general medical condition, previous medical history, etc. In general, it is desirable to provide the recipient with a dosage of agent which is in the range of from about 1 pg/kg to 10 mg/kg (body weight of patient), although a lower or higher dosage may be administered. The therapeutically effective dose can be lowered by using combinations of the agents of the present invention or another agent.

As used herein, two or more compounds or agents are said to be administered “in combination” with each other when either (1) the physiological effects of each compound, or (2) the serum concentrations of each compound can be measured at the same time. The composition of the present invention can be administered concurrently with, prior to, or following the administration of the other agent.

The agents of the present invention are intended to be provided to recipient subjects in an amount sufficient to decrease the rate of growth (as defined above) of the target organism.

The administration of the agent(s) of the invention may be for either a “prophylactic” or “therapeutic” purpose. When provided prophylactically, the agent(s) are provided in advance of any symptoms indicative of the organisms growth. The prophylactic administration of the agent(s) serves to prevent, attenuate, or decrease the rate of onset of any subsequent infection. When provided therapeutically, the agent(s) are provided at (or shortly after) the onset of an indication of infection. The therapeutic administration of the compound(s) serves to attenuate the pathological symptoms of the infection and to increase the rate of recovery.

The agents of the present invention are administered to a subject, such as a mammal, or a patient, in a pharmaceutically acceptable form and in a therapeutically effective concentration, A composition is said to be “pharmacologically acceptable” if its administration can be tolerated by a recipient patient. Such an agent is said to be administered in a “therapeutically effective amount” if the amount administered is physiologically significant. An agent is physiologically significant if its presence results in a detectable change in the physiology of a recipient patient.

The agents of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby these materials, or their functional derivatives, are combined in a mixture with a pharmaceutically acceptable carrier vehicle. Suitable vehicles and their formulation, inclusive of other human proteins, e.g., human serum albumin, are described, for example, in REMINGTON'S PHARMACEUTICAL SCIENCES, ₁₆^th Ed., Osol, A., Ed., Mack Publishing, Easton Pa. (1980). In order to form a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of one or more of the agents of the present invention, together with a suitable amount of carrier vehicle.

Additional pharmaceutical methods may be employed to control the duration of action. Control release preparations may be achieved through the use of polymers to complex or absorb one or more of the agents of the present invention. The controlled delivery may be effectuated by a variety of well known techniques, including formulation with macromolecules such as, for example, polyesters, polyamino acids, polyvinyl, pyrrolidone, ethylenevinylacetate, methylcellulose, carboxymethylcellulose, or protamine, sulfate, adjusting the concentration of the macromolecules and the agent in the formulation, and by appropriate use of methods of incorporation, which can be manipulated to effectuate a desired time course of release. Another possible method to control the duration of action by controlled release preparations is to incorporate agents of the present invention into particles of a polymeric material such as polyesters, polyamino acids, hydrogels, poly(lactic acid) or ethylene vinylacetate copolymers. Alternatively, instead of incorporating these agents into polymeric particles, it is possible to entrap these materials in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization with, for example, hydroxymethylcellulose or gelatine-microcapsules and poly(methylmethacylate) microcapsules, respectively, or in colloidal drug delivery systems, for example, liposomes, albumin microspheres, microemulsions, nanoparticles, and nanocapsules or in macroemulsions. Such techniques are disclosed in REMINGTON'S PHARMACEUTICAL SCIENCES (1980).

The invention further provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

In addition, the agents of the present invention may be employed in conjunction with other therapeutic compounds.

6. Shot-Gun Approach to Megabase DNA Sequencing

The present invention further demonstrates that a large sequence can be sequenced using a random shotgun approach. This procedure, described in detail in the examples that follow, has eliminated the up front cost of isolating and ordering overlapping or contiguous subclones prior to the start of the sequencing protocols.

Certain aspects of the present invention are described in greater detail in the examples that follow. The examples are provided by way of illustration. Other aspects and embodiments of the present invention are contemplated by the inventors, as will be clear to those of skill in the art from reading the present disclosure.

ILLUSTRATIVE EXAMPLES

Libraries and Sequencing

1. Shotgun Sequencing Probability Analysis

The overall strategy for a shotgun approach to whole genome sequencing follows from the Lander and Waterman (Landerman and Waterman, Genomics 2:231 (1988)) application of the equation for the Poisson distribution. According to this treatment, the probability, P, that any given base in a sequence of size L, in nucleotides, is not sequenced after a certain amount, n, in nucleotides, of random sequence has been determined can be calculated by the equation P=e^−m, where m is L/n, the fold coverage. For instance, for a genome of 2.8 Mb, m=1 when 2.8 Mb of sequence has been randomly generated (1×coverage). At that point, P=e^−1=0.37. The probability that any given base has not been sequenced is the same as the probability that any region of the whole sequence L has not been determined and, therefore, is equivalent to the fraction of the whole sequence that has yet to be determined, Thus, at one-fold coverage, approximately 37% of a polynucleotide of size L, in nucleotides has not been sequenced. When 14 Mb of sequence has been generated, coverage is 5× for a 2.8 Mb and the unsequenced fraction drops to 0.0067 or 0.67%. 5×coverage of a 2.8 Mb sequence can be attained by sequencing approximately 17,000 random clones from both insert ends with an average sequence read length of 410 bp.

Similarly, the total gap length, G, is determined by the equation G=Le^−m, and the average gap size, g, follows the equation, g=L/n. Thus, 5×coverage leaves about 240 gaps averaging about 82 bp in size in a sequence of a polynucleotide 2.8 Mb long.

The treatment above is essentially that of Lander and Waterman, Genomics 2: 231 (1988).

2. Random Library Construction

In order to approximate the random model described above during actual sequencing, a nearly ideal library of cloned genomic fragments is required. The following library construction procedure was developed to achieve this end.

Streptococcus pneumoniae DNA is prepared by phenol extraction. A mixture containing 200 μg DNA in 1.0 ml of 300 mM sodium acetate, 10 mM Tris-HCl, 1 mM Na-EDTA, 50% glycerol is processed through a nebulizer (IPI Medical Products) with a stream of nitrogen adjusted to 35 Kpa for 2 minutes. The sonicated DNA is ethanol precipitated and redissolved in 500 μl TE buffer.

To create blunt-ends, a 100 μl aliquot of the resuspended DNA is digested with 5 units of BAL31 nuclease (New England BioLabs) for 10 min at 30° C. in 200 μl BAL31 buffer. The digested DNA is phenol-extracted, ethanol-precipitated, redissolved in 100 μl TE buffer, and then size-fractionated by electrophoresis through a 1.0% low melting temperature agarose gel. The section containing DNA fragments 1.6-2.0 kb in size is excised from the gel, and the LGT agarose is melted and the resulting solution is extracted with phenol to separate the agarose from the

DNA. DNA is ethanol precipitated and redissolved in 20 μl of TE buffer for ligation to vector.

A two-step ligation procedure is used to produce a plasmid library with 97% inserts, of which >99% were single inserts. The first ligation mixture (50 ul) contains 2 μg of DNA fragments, 2 μg pUC18 DNA (Pharmacia) cut with SmaI and dephosphorylated with bacterial alkaline phosphatase, and 10 units of T4 ligase (GIBCO/BRL) and is incubated at 14° C. for 4 hr. The ligation mixture then is phenol extracted and ethanol precipitated, and the precipitated DNA is dissolved in 20 μl TE buffer and electrophoresed on a 1.0% low melting agarose gel. Discrete bands in a ladder are visualized by ethidium bromide-staining and UV illumination and identified by size as insert (I), vector (v), v+I, v+2i, v+3i, etc. The portion of the gel containing v+I DNA is excised and the v+I DNA is recovered and resuspended into 20 μl TE. The v+I DNA then is blunt-ended by T4 polymerase treatment for 5 min. at 37° C. in a reaction mixture (50 ul) containing the v+I linears, 500 μM each of the 4 dNTPs, and 9 units of T4 polymerase (New England BioLabs), under recommended buffer conditions. After phenol extraction and ethanol precipitation the repaired v+I linears are dissolved in 20 μl TE, The final ligation to produce circles is carried out in a 50 μl reaction containing 5 μl of v+I linears and 5 units of T4 ligase at 14° C. overnight. After 10 min. at 70° C. the following day, the reaction mixture is stored at −20° C.

This two-stage procedure results in a molecularly random collection of single-insert plasmid recombinants with minimal contamination from double-insert chimeras (<1%) or free vector (<3%).

Since deviation from randomness can arise from propagation the DNA in the host, E. coli host cells deficient in all recombination and restriction functions (A. Greener, Strategies 3 (1):5 (1990)) are used to prevent rearrangements, deletions, and loss of clones by restriction. Furthermore, transformed cells are plated directly on antibiotic diffusion plates to avoid the usual broth recovery phase which allows multiplication and selection of the most rapidly growing cells.

Plating is carried out as follows. A 100 μl aliquot of Epicurian Coli SURE II Supercompetent Cells (Stratagene 200152) is thawed on ice and transferred to a chilled Falcon 2059 tube on ice. A 1.7 μl aliquot of 1.42 M beta-mercaptoethanol is added to the aliquot of cells to a final concentration of 25 mM. Cells are incubated on ice for 10 min. A 1 μl aliquot of the final ligation is added to the cells and incubated on ice for 30 min. The cells are heat pulsed for 30 sec. at 42° C. and placed back on ice for 2 min. The outgrowth period in liquid culture is eliminated from this protocol in order to minimize the preferential growth of any given transformed cell. Instead the transformation mixture is plated directly on a nutrient rich SOB plate containing a 5 ml bottom layer of SOB agar (5% SOB agar: 20 g tryptone, 5 g yeast extract, 0.5 g NaCl, 1.5% Difco Agar per liter of media). The 5 ml bottom layer is supplemented with 0.4 ml of 50 mg/ml ampicillin per 100 ml SOB agar. The 15 ml top layer of SOB agar is supplemented with 1 ml X-Gal (2%), 1 ml MgCl (1 M), and 1 ml MgSO/100 ml SOB agar. The 15 ml top layer is poured just prior to plating. Our titer is approximately 100 colonies/10 μl aliquot of transformation.

All Colonies are picked for template preparation regardless of size. Thus, only clones lost due to “poison” DNA or deleterious gene products are deleted from the library, resulting in a slight increase in gap number over that expected.

3. Random DNA Sequencing

High quality double stranded DNA plasmid templates are prepared using a “boiling bead” method developed in collaboration with Advanced Genetic Technology Corp. (Gaithersburg, Md.) (Adams et al., Science 252:1651 (1991); Adams et al., Nature 355:632 (1992)). Plasmid preparation is performed in a 96-well format for all stages of DNA preparation from bacterial growth through final DNA purification. Template concentration is determined using Hoechst Dye and a Millipore Cytofluor. DNA concentrations are not adjusted, but low-yielding templates are identified where possible and not sequenced.

Templates are also prepared from two Streptococcus pneumoniae lambda genomic libraries. An amplified library is constructed in the vector Lambda GEM-12 (Promega) and an unamplified library is constructed in Lambda DASH II (Stratagene). In particular, for the unamplified lambda library, Streptococcus pneumoniae DNA (>100 kb) is partially digested in a reaction mixture (200 ul) containing 50 μg DNA, 1×Sau3AI buffer, 20 units Sau3AI for 6 min. at 23° C. The digested DNA was phenol-extracted and electrophoresed on a 0.5% low melting agarose gel at 2V/cm for 7 hours. Fragments from 15 to 25 kb are excised and recovered in a final volume of 6 ul. One μl of fragments is used with 1 μl of DASHII vector (Stratagene) in the recommended ligation reaction. One μl of the ligation mixture is used per packaging reaction following the recommended protocol with the Gigapack II XL Packaging Extract (Stratagene, #227711). Phage are plated directly without amplification from the packaging mixture (after dilution with 500 μl of recommended SM buffer and chloroform treatment). Yield is about 2.5×10³ pfu/ul. The amplified library is prepared essentially as above except the lambda GEM-12 vector is used. After packaging, about 3.5×10⁴ pfu are plated on the restrictive NM539 host. The lysate is harvested in 2 ml of SM buffer and stored frozen in 7% dimethylsulfoxide. The phage titer is approximately 1×10⁹ pfu/ml.

Liquid lysates (100 μl) are prepared from randomly selected plaques (from the unamplified library) and template is prepared by long-range PCR using T7 and T3 vector-specific primers.

Sequencing reactions are carried out on plasmid and/or PCR templates using the AB Catalyst LabStation with Applied Biosystems PRISM Ready Reaction Dye Primer Cycle Sequencing Kits for the M13 forward (M13-21) and the M13 reverse (M13RP1) primers (Adams et al., Nature 368:474 (1994)). Dye terminator sequencing reactions are carried out on the lambda templates on a Perkin-Elmer 9600 Thermocycler using the Applied Biosystems Ready Reaction Dye Terminator Cycle Sequencing kits. T7 and SP6 primers are used to sequence the ends of the inserts from the Lambda GEM-12 library and T7 and T3 primers are used to sequence the ends of the inserts from the Lambda DASH II library. Sequencing reactions are performed by eight individuals using an average of fourteen AB 373 DNA Sequencers per day. All sequencing reactions are analyzed using the Stretch modification of the AB 373, primarily using a 34 cm well-to-read distance. The overall sequencing success rate very approximately is about 85% for M13-21 and M13RP1 sequences and 65% for dye-terminator reactions. The average usable read length is 485 bp for M13-21 sequences, 445 bp for M13RP1 sequences, and 375 bp for dye-terminator reactions.

Richards et al., Chapter 28 in AUTOMATED DNA SEQUENCING AND ANALYSIS, M. D. Adams, C. Fields, J. C. Venter, Eds., Academic Press, London, (1994) described the value of using sequence from both ends of sequencing templates to facilitate ordering of contigs in shotgun assembly projects of lambda and cosmid clones. We balance the desirability of both-end sequencing (including the reduced cost of lower total number of templates) against shorter read-lengths for sequencing reactions performed with the M13RP1 (reverse) primer compared to the M13-21 (forward) primer. Approximately one-half of the templates are sequenced from both ends. Random reverse sequencing reactions are done based on successful forward sequencing reactions. Some M13RP1 sequences are obtained in a semi-directed fashion: M13-21: sequences pointing outward at the ends of contigs are chosen for M13RP1 sequencing in an effort to specifically order contigs.

4. Protocol for Automated Cycle Sequencing

The sequencing is carried out using ABI Catalyst robots and AB 373 Automated DNA Sequencers. The Catalyst robot is a publicly available sophisticated pipetting and temperature control robot which has been developed specifically for DNA sequencing reactions. The Catalyst combines pre-aliquoted templates and reaction mixes consisting of deoxy- and dideoxynucleotides, the thermostable Taq DNA polymerase, fluorescently-labelled sequencing primers, and reaction buffer. Reaction mixes and templates are combined in the wells of an aluminum 96-well thermocycling plate. Thirty consecutive cycles of linear amplification (i.e., one primer synthesis) steps are performed including denaturation, annealing of primer and template, and extension; i. e., DNA synthesis. A heated lid with rubber gaskets on the thermocycling plate prevents evaporation without the need for an oil overlay.

Two sequencing protocols are used: one for dye-labelled primers and a second for dye-labelled dideoxy chain terminators. The shotgun sequencing involves use of four dye-labelled sequencing primers, one for each of the four terminator nucleotide. Each dye-primer is labelled with a different fluorescent dye, permitting the four individual reactions to be combined into one lane of the 373 DNA Sequencer for electrophoresis, detection, and base-calling. ABI currently supplies pre-mixed reaction mixes in bulk packages containing all the necessary non-template reagents for sequencing. Sequencing can be done with both plasmid and PCR-generated templates with both dye-primers and dye-terminators with approximately equal fidelity, although plasmid templates generally give longer usable sequences.

Thirty-two reactions are loaded per AB373 Sequencer each day, for a total of 960 samples. Electrophoresis is run overnight following the manufacturer's protocols, and the data is collected for twelve hours. Following electrophoresis and fluorescence detection, the ABI 373 performs automatic lane tracking and base-calling. The lane-tracking is confirmed visually. Each sequence electropherogram (or fluorescence lane trace) is inspected visually and assessed for quality. Trailing sequences of low quality are removed and the sequence itself is loaded via software to a Sybase database (archived daily to 8 mm tape). Leading vector polylinker sequence is removed automatically by a software program. Average edited lengths of sequences from the standard ABI 373 are around 400 bp and depend mostly on the quality of the template used for the sequencing reaction. ABI 373 Sequencers converted to Stretch Liners provide a longer electrophoresis path prior to fluorescence detection and increase the average number of usable bases to 500-600 bp.

Informatics

1. Data Management

A number of information management systems for a large-scale sequencing lab have been developed. (For review see, for instance, Kerlavage et al., Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, IEEE Computer Society Press, Washington D. C., 585 (1993)) The system used to collect and assemble the sequence data was developed using the Sybase relational database management system and was designed to automate data flow wherever possible and to reduce user error. The database stores and correlates all information collected during the entire operation from template preparation to final analysis of the genome. Because the raw output of the ABI 373 Sequencers was based on a Macintosh platform and the data management system chosen was based on a Unix platform, it was necessary to design and implement a variety of multi-user, client-server applications which allow the raw data as well as analysis results to flow seamlessly into the database with a minimum of user effort.

2. Assembly

An assembly engine (TIGR Assembler) developed for the rapid and accurate assembly of thousands of sequence fragments was employed to generate contigs. The TIGR assembler simultaneously clusters and assembles fragments of the genome. In order to obtain the speed necessary to assemble more than 10⁴ fragments, the algorithm builds a hash table of 12 bp oligonucleotide subsequences to generate a list of potential sequence fragment overlaps. The number of potential overlaps for each fragment determines which fragments are likely to fall into repetitive elements. Beginning with a single seed sequence fragment, TIGR Assembler extends the current contig by attempting to add the best matching fragment based on oligonucleotide content. The contig and candidate fragment are aligned using a modified version of the Smith-Waterman algorithm which provides for optimal gapped alignments (Waterman, M. S., Methods in Enzymology 164:765 (1988)). The contig is extended by the fragment only if strict criteria for the quality of the match are met. The match criteria include the minimum length of overlap, the maximum length of an unmatched end, and the minimum percentage match. These criteria are automatically lowered by the algorithm in regions of minimal coverage and raised in regions with a possible repetitive element. The number of potential overlaps for each fragment determines which fragments are likely to fall into repetitive elements. Fragments representing the boundaries of repetitive elements and potentially chimeric fragments are often rejected based on partial mismatches at the ends of alignments and excluded from the current contig. TIGR Assembler is designed to take advantage of clone size information coupled with sequencing from both ends of each template. It enforces the constraint that sequence fragments from two ends of the same template point toward one another in the contig and are located within a certain range of base pairs (definable for each clone based on the known clone size range for a given library).

The process resulted in 391 contigs as represented by SEQ ID NOs:1-391.

3. Identifying Genes

The predicted coding regions of the Streptococcus pneumoniae genome were initially defined with the program GeneMark, which finds ORFs using a probabilistic classification technique. The predicted coding region sequences were used in searches against a database of all nucleotide sequences from GenBank (October, 1997), using the BLASTN search method to identify overlaps of 50 or more nucleotides with at least a 95% identity. Those ORFs with nucleotide sequence matches are shown in Table 1. The ORFs without such matches were translated to protein sequences and compared to a non-redundant database of known proteins generated by combining the Swiss-prot, PIR and GenPept databases. ORFs that matched a database protein with BLASTP probability less than or equal to 0.01 are shown in Table 2. The table also lists assigned functions based on the closest match in the databases. ORFs that did not match protein or nucleotide sequences in the databases at these levels are shown in Table 3.

Illustrative Applications

1. Production of an Antibody to a Streptococcus pneumoniae Protein

Substantially pure protein or Polypeptide is isolated from the transfected or transformed cells using any one of the methods known in the art. The protein can also be produced in a recombinant prokaryotic expression system, such as E. coli, or can be chemically synthesized. Concentration of protein in the final preparation is adjusted, for example, by concentration on an Amicon filter device, to the level of a few micrograms/ml Monoclonal or polyclonal antibody to the protein can then be prepared as follows.

2. Monoclonal Antibody Production by Hybridoma Fusion

Monoclonal antibody to epitopes of any of the peptides identified and isolated as described can be prepared from murine hybridomas according to the classical method of Kohler, G. and Milstein, C., Nature 256:495 (1975) or modifications of the methods thereof. Briefly, a mouse is repetitively inoculated with a few micrograms of the selected protein over a period of a few weeks. The mouse is then sacrificed, and the antibody producing cells of the spleen isolated. The spleen cells are fused by means of Polyethylene glycol with mouse myeloma cells, and the excess unfused cells destroyed by growth of the system on selective media comprising aminopterin (HAT media). The successfully fused cells are diluted and aliquots of the dilution placed in wells of a microtiter plate where growth of the culture is continued. Antibody-producing clones are identified by detection of antibody in the supernatant fluid of the wells by immunoassay procedures, such as ELISA, as originally described by Engvall, E., Meth. Enzymol. 70:419 (1980), and modified methods thereof. Selected positive clones can be expanded and their monoclonal antibody product harvested for use. Detailed procedures for monoclonal antibody production are described in Davis, L. et al., Basic Methods in Molecular Biology, Elsevier, N.Y. Section 21-2 (1989).

3. Polyclonal Antibody Production by Immunization

Polyclonal antiserum containing antibodies to heterogenous epitopes of a single protein can be prepared by immunizing suitable animals with the expressed protein described above, which can be unmodified or modified to enhance immunogenicity. Effective polyclonal antibody production is affected by many factors related both to the antigen and the host species. For example, small molecules tend to be less immunogenic than others and may require the use of carriers and adjuvant. Also, host animals vary in response to site of inoculations and dose, with both inadequate or excessive doses of antigen resulting in low titer antisera. Small doses (ng level) of antigen administered at multiple intradermal sites appears to be most reliable. An effective immunization protocol for rabbits can be found in Vaitukaitis, J. et al., J. Clin. Endocrinol. Metab. 33:988-991 (1971).

Booster injections can be given at regular intervals, and antiserum harvested when antibody titer thereof, as determined semi-quantitatively, for example, by double immunodiffusion in agar against known concentrations of the antigen, begins to fall. See, for example, Ouchterlony, O. et al., Chap. 19 in: Handbook of Experimental Immunology, Wier, D., ed, Blackwell (1973). Plateau concentration of antibody is usually in the range of 0.1 to 0.2 mg/ml of serum (about 12M). Affinity of the antisera for the antigen is determined by preparing competitive binding curves, as described, for example, by Fisher, D., Chap. 42 in: Manual of Clinical Immunology, second edition, Rose and Friedman, eds., Amer. Soc. For Microbiology, Washington, D. C. (1980)

Antibody preparations prepared according to either protocol are useful in quantitative immunoassays which determine concentrations of antigen-bearing substances in biological samples; they are also used semi-quantitatively or qualitatively to identify the presence of antigen in a biological sample. In addition, antibodies are useful in various animal models of pneumococcal disease as a means of evaluating the protein used to make the antibody as a potential vaccine target or as a means of evaluating the antibody as a potential immunotherapeutic or immunoprophylactic reagent.

4. Preparation of PCR Primers and Amplification of DNA

Various fragments of the Streptococcus pneumoniae genome, such as those of Tables 1-3 and SEQ ID NOS:1-391 can be used, in accordance with the present invention, to prepare PCR primers for a variety of uses. The PCR primers are preferably at least 15 bases, and more preferably at least 18 bases in length. When selecting a primer sequence, it is preferred that the primer pairs have approximately the same G/C ratio, so that melting temperatures are approximately the same. The PCR primers and amplified DNA of this Example find use in the Examples that follow.

5. Gene expression from DNA Sequences Corresponding to ORFs

A fragment of the Streptococcus pneumoniae genome provided in Tables 1-3 is introduced into an expression vector using conventional technology. Techniques to transfer cloned sequences into expression vectors that direct protein translation in mammalian, yeast, insect or bacterial expression systems are well known in the art. Commercially available vectors and expression systems are available from a variety of suppliers including Stratagene (La Jolla, Calif.), Promega (Madison, Wis.), and Invitrogen (San Diego, Calif.). If desired, to enhance expression and facilitate proper protein folding, the codon context and codon pairing of the sequence may be optimized for the particular expression organism, as explained by Hatfield et al., U.S. Pat. No. 5,082,767, incorporated herein by this reference.

The following is provided as one exemplary method to generate polypeptide(s) from cloned ORFs of the Streptococcus pneumoniae genome fragment. Bacterial ORFs generally lack a poly A addition signal. The addition signal sequence can be added to the construct by, for example, splicing out the poly A addition sequence from pSG5 (Stratagene) using BglI and SalI restriction endonuclease enzymes and incorporating it into the mammalian expression vector pXT1 (Stratagene) for use in eukaryotic expression systems. pXT1 contains the LTRs and a portion of the gag gene of Moloney Murine Leukemia Virus. The positions of the LTRs in the construct allow efficient stable transfection. The vector includes the Herpes Simplex thymidine kinase promoter and the selectable neomycin gene. The Streptococcus pneumoniae DNA is obtained by PCR from the bacterial vector using oligonucleotide primers complementary to the Streptococcus pneumoniae DNA and containing restriction endonuclease sequences for PstI incorporated into the 5′ primer and BglII at the 5′ end of the corresponding Streptococcus pneumoniae DNA 3′ primer, taking care to ensure that the Streptococcus pneumoniae DNA is positioned such that its followed with the poly A addition sequence. The purified fragment obtained from the resulting PCR reaction is digested with PstI, blunt ended with an exonuclease, digested with BglII, purified and ligated to pXT1, now containing a poly A addition sequence and digested BglII.

The ligated product is transfected into mouse NIH 3T3 cells using Lipofectin (Life Technologies, Inc., Grand Island, N.Y.) under conditions outlined in the product specification. Positive transfectants are selected after growing the transfected cells in 600 ug/ml G418 (Sigma, St. Louis, Mo.). The protein is preferably released into the supernatant. However if the protein has membrane binding domains, the protein may additionally be retained within the cell or expression may be restricted to the cell surface. Since it may be necessary to purify and locate the transfected product, synthetic 15-mer peptides synthesized from the predicted Streptococcus pneumoniae DNA sequence are injected into mice to generate antibody to the polypeptide encoded by the Streptococcus pneumoniae DNA.

Alternatively and if antibody production is not possible, the Streptococcus pneumoniae DNA sequence is additionally incorporated into eukaryotic expression vectors and expressed as, for example, a globin fusion. Antibody to the globin moiety then is used to purify the chimeric protein. Corresponding protease cleavage sites are engineered between the globin moiety and the polypeptide encoded by the Streptococcus pneumoniae DNA so that the latter may be freed from the formed by simple protease digestion. One useful expression vector for generating globin chimerics is pSG5 (Stratagene). This vector encodes a rabbit globin. Intron II of the rabbit globin gene facilitates splicing of the expressed transcript, and the polyadenylation signal incorporated into the construct increases the level of expression. These techniques are well known to those skilled in the art of molecular biology. Standard methods are published in methods texts such as Davis et al., cited elsewhere herein, and many of the methods are available from the technical assistance representatives from Stratagene, Life Technologies, Inc., or Promega. Polypeptides of the invention also may be produced using in vitro translation systems such as in vitro Express™ Translation Kit (Stratagene).

While the present invention has been described in some detail for purposes of clarity and understanding, one skilled in the art will appreciate that various changes in form and detail can be made without departing from the true scope of the invention.

All patents, patent applications and publications referred to above are hereby incorporated by reference.

Stop< td/>< td/>< td/>< td/>Streptococcus pneumoniae malA gene, complete cds; malR gene, complete cdsStreptococcus pneumoniae malA gene, complete cds; malR gene, complete cdsStreptococcus pneumoniae peptide methionine sulfoxide reductase (msrA) andStreptococcus pneumoniae peptide methionine sulfoxide reductase (msrA) andS. pneumoniae autolysin (lytA) gene, complete cds< td>S. pneumoniae autolysin (lytA) gene, complete cds< td>Streptococcus pneumoniae ORF, complete cdsStreptococcus pneumoniae ORF, complete cdsStreptococcus pneumoniae ORF, complete cdsStreptococcus pneumoniae ORF, complete cds< td>Streptococcus pneumoniae ORF, complete cds< td>Streptococcus pneumoniae Exp7 gene, partial cds< tr>S. pneumoniae mismatch repair protein (hexA) gene, complete cdsS. pneumoniae mismatch repair protein (hexA) gene, complete cdsStreptococcus pneumoniae hyaluronidase gene, complete cdsStreptococcus pneumoniae hyaluronidase gene, complete cdsS. pneumoniae DpnI gene region encoding dpnC and dpnD, complete cds< td>S. pneumoniae DpnII gene region encoding dpnM, dpnA, dpnB, complete cds< td>S. pneumoniae exodeoxyribonuclease (exoA) gene, complete cdsS. pneumoniae exodeoxyribonuclease (exoA) gene, complete cds< td>Streptococcus pneumoniae Exp8 gene, partial cds< td/>< td>Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase< td/>< td/>< tr>Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase< td/>< td/>< td/>< td>99< td>S. pneumoniae mismatch repair protein (hexA) gene, comptete cds< td/>< td/>< td/>< td/>< tr>Streptococcus pneumoniae uvs402 protein gene, complete cds< td>Streptococcus pneumoniae uvs402 protein gene, complete cds< td/>< td/>163S. pneumoniae malX and malM genes encoding membrane protein and< td>Streptococcus pneumoniae Exp4 gene, partial cdsStreptococcus pneumoniae formate acetyltransferase (exp72) gene, partial< td/>< td/>< td>Streptococcus pneumoniae pneumococcal surface protien A PspA (pspA) gene,< td>S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnoseS. pneumoniae recP gene, complete cds< td>Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase< td/>< td/>< td>257< td/>< tr>< td/>

TABLE 1
S. pneumoniae - Coding regions containing known sequences
Contig	ORF	Start	match		percent	HSP nt	ORF nt
ID	ID	(nt)	(nt)< /td>	acession	match gene name	ident	length	length
1	1	437	1003	gb|U41735|	Streptococcus pneumoniae peptide methionine sulfoxide reductase (msrA) and	92	200	567
					homoserine kinase homolog (thrB) genes, complete cds
2	5	6169	5720	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	96	450	450
				sequence IS1202 transposase gene, complete cds
2	6	6592	6167	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	98	426	426
					biosynthesis genes and aliA gene
3	11	9770	9147	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	94	624	624
					biosynthesis genes and aliA gene
3	12	10489	967 1	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	91	819	819
					biosynthesis genes and aliA gene
3	13	11546	120 19	gb|U43526|	Streptococcus pneumoniae neuraminidase B (nanB) gene, complete cds, and	99	474	474
					neuraminidase (nanA) gene, partial cds
3	14	12017	1337 5	gb|U43526|	Streptococcus pneumoniae neuraminidase B (nanB) gene, complete cds, and	99	1359	1359
< td/>				neuraminidase (nanA) gene, partial cds
3	15	13421	1433 8	gb|U43526|	Streptococcus pneumoniae neuraminidase B (nanB) gene, complete cds, and	99	918	918
					neuraminidase (nanA) gene, partial cds
3	16	14329	1517 1	gb|U43526|	Streptococcus pneumoniae neuraminidase B (nanB) gene, complete cds, and	99	843	843
					neuraminidase (nanA) gene, partial cds
3	17	15132	1728 2	gb|U43526|	Streptococcus pneumoniae neutaminidase B (nanB) gene, complete cds, and	99	2151	2151
< td/>				neuraminidase (nanA) gene, partial cds
3	18	17267	1839 7	gb|U43526|	Streptococcus pneumoniae neuraminidase B (nanB) gene, complete cds, and	99	1069	1131
< td/>				neuraminidase (nanA) gene, partial cds
4	1	46	1188	emb|Y11463|SPDN	Streptococcus pneumoniae dnaG, rpoD, cpoA genes and ORF3 and ORF5	99	1143	1143
4	2	1198	2529	emb|Y11463|SPDN	Streptococcus pneumoniae dnaG, rpoD, cpoA genes and ORF3 and ORF5	99	876	1332
5< /td>	7	11297	11473	gb|U41735|	Streptococcus pneumoniae peptide methionine sulfoxide reductase (msrA) and	82	175	177
					homoserine kinase homolog (thrB) genes, complete cds
6	7	7125	7364	emb|Z77726|SPIS	S. pneumoniae DNA for insertion sequence IS1318 (1372 bp)	93	238	240
6	8	7322	7570	emb|Z77725|SPIS	S. pneumoniae DNA for insertion sequence IS1381 (966 bp)	95	160	249
6	9	7533	7985	emb|Z77725|SPIS	S. pneumoniae DNA for insertion sequence IS1381 (966 bp)	99	453	453
6	23	20197	19733	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	96	465	465
					biosynthesis genes and aliA gene
7	10	8305	7682	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	95	624	624
					biosynthesis genes and aliA gene
7	11	9024	8206	emb|Z83335|SPZ8	S. pneumonia dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	95	819	819
					biosynthesis genes and aliA gene
10	13	9304	807 8	gb|L29323|	Streptococcus pneumoniae methyl transferase (mtr) gene cluster, complete	93	513	1227
				cds
11	2	548	919	emb|Z79691|SOOR	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	99	316	372
11	3	892	1980	emb|Z79691|SOOR< /td>	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	99	1089	1089
11	5	3040	3477	emb|Z79691|SO OR	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	99	259	438
11	6	3480	3247	emb|Z79691|SOOR	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	99	234	234
11	7	3601	4557	emb|Z79691|SOOR	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	98	957	957
11	8	4506	4886	emb|Z79691|SOOR	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	99	381	381
11	9	4884	7142	emb|X16367|SPPB	Streptococcus pneumoniae pbpX gene for penicillin binding protein 2X	99	2259	2259
11< /td>	10	7132	8124	emb|X16367|SPPB	Streptococcus pneumoniae pbpX gene for penicillin binding protein 2X	98	70	993
13	1	53	1126	gb|M31296|	S. pneumoniae recP gene, complete cds	99	437	1074
14< /td>	3	1837	2148	emb|Z83335|SPZ8< /td>	S. pneumoniae desB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	87	96	312
					bisynthesis genes and aliA gene
14	4	2518	2108	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	98	411	411
				(purC) genes, complete cds
15	9	8942	8511< /td>	gb|U09239|	Streptococcus pneumoniae type 19F capsular polysaccharide biosynthesis	89	340	432
					operon, (cps19 fABCDEFGHIJKLMNO) genes, complete cds, and aliA gene,
					partial cds
17	7	3910	3458< /td>	emb|Z77726|SPIS	S. pneumoniae DNA for insertion sequence IS1318 (1372 bp)	98	453	453
17	8	4304	3873	emb|Z77727|SPIS	S. pneumoniae DNA for insertion sequence IS1318 (823 bp)	96	382	432
19	1	41	529	emb|X94909|SPIG	S. pneumoniae iga gene	75	368	489
19< /td>	2	554	757	gb|L07752|	Streptococcus pneumoniae attachment site (attB), DNA sequence	99	167	204
19	3	946	1827	gb|L07752|	Streptococcus pneumoniae attachment site (attB), DNA sequence	94	100	882
20	1	937	182	gb|U33315|	Streptoccus pneumoniae orfL gene, partial cds, competence stimulating	99	756	756
					peptide precursor (comC), histidine protein kinase (comD) and response
					regulator (comE) genes, complete cds, tRNA-Arg and tRNA-Gln genes
20	2	2271	931	gb|U33315|	Streptococcus pneumoniae orfL gene, partial cds, competence stimulating	98	1341	1341
					peptide precursor (comC), histidine protein kinase (comD) and response
					regulator (comE) genes, complete cds, tRNA-Arg and tRNA-Gln genes
20	3	3175	268 4	gb|U76218|	Streptococcus pneumoniae competence stimulating peptide precursor ComC	99	492	492
				(comC), histidine kinase homolog ComD (comD), and response regulator
					homolog ComE (comE) genes, complete cds
20	4	3322	4527< /td>	gb|AF000658|	Streptococcus pneumoniae R801 tRNA-Arg gene, partial sequence, and putative	99	1206	1206
				serine protease (sphtra), SPSpoJ (spspoJ), initiator protein (spdnaa) and
					beta subunit of DNA polymerase III (spdnan) genes, complete cds
20	5	4573	5343< /td>	gb|AF000658|	Streptococcus pneumoniae R801 tRNA-Arg gene, partial sequence, and putative	99	771	771
					serine protease (sphtra), SPSpoJ (spspoJ), initiator protein (Spdnaa) and
					beta subunit of DNA polymerase III (spdnan) genes, complete cds
20	6	5532	6917< /td>	gb|AF000658|	Streptococcus pneumoniae R801 tRNA-Arg gene, partial sequence, and putative	99	1386	1386
				serine protease (sphtra), SPSpoJ (spspoJ), initiator protein (spdnaa) and
					beta subunit of DNA polymerase III (spdnan) genes, complete cds
20	7	6995	8212< /td>	gb|AF000658|	Streptococcus pneumoniae R801 tRNA-Arg gene, partial sequence, and putative	99	1218	1218
				serine protease (sphtra), SPSpoJ (spspoJ), initiator protein (spdnaa) and
					beta subunit of DNA polymerase III (spdnan) genes, complete cds
20	8	8214	8471< /td>	gb|AF000658|	Streptococcus pneumoniae R801 tRNA-Arg gene, partial sequence, and putative	98	258	258
					serine protease (sphtra), SPSpoJ (spspoJ), initiator protein (spdnaa) and
					beta subunit of DNA polymerase III (spdnan) genes, complete cds
20	9	8534	9670< /td>	gb|AF000658|	Streptococcus pneumoniae R801 tRNA-Arg gene, partial sequence, and putative	99	134	1137
				serine protease (sphtra), SPSpoJ (spspoJ), initiator protein (spdnaa) and
					beta subunit of DNA polymerase III (spdnan) genes, complete cds
22	14	11887	122 67	emb|Z77726|SPIS	S. pneumoniae DNA for insertion sequence IS1318 (1372 bp)	99	226	381
22	15	12708	12256	emb|Z77727|SPI S	S. pneumoniae DNA for insertion sequence IS1318 (823 bp)	97	353	453
22	16	13165	12662	emb|Z77726|SPI S	S. pneumoniae DNA for insertion sequence IS1318 (1372 bp)	98	504	504
22	23	18398	18910	emb|Z86112|SPZ 8	S. pneumoniae genes encoding galacturonosyl transferase and transposase and	95	463	513
					insertion sequence IS1515
22	24	18829	19299	emb|Z86112|SPZ8	S. pneumoniae genes encoding galacturonosyl transferase and transposase and	99	443	471
					insertion sequence IS1515
23	5	5624	42 03	emb|X52474|SPPL	S. pneumoniae ply gene for pneumolysin	99	1422	1422
23	6	6063	5629	gb|M177 17|	S. pneumoniae pneumolysin gene, complete cds	98	197	435
26	1	5500	2	emb|X94909|SPIG	S. pneumoniae iga gene	87	3487	5499
2 6	2	5823	5584	gb|U47687|	Streptococcus pneumoniae immunoglobulin A1 protease (iga) gene, complete	99	151	240
					cds
26	3< /td>	6878	5685	gb|U47687|	Streptococcus pneumoniae immunoglobulin A1 protease (iga) gene, complete	100	50	1194
				cds
26	8	14498	14854	emb|Z83335|SPX8	S. pnuemoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	99	338	357
					biosynthesis genes and aliA gene
26	9	14763	149 24	emb|Z83335|SPZ8	S. pnuemoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	100	94	162
					biosynthesis genes and aliA gene
26	10	14922	15 173	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	97	242	252
				sequence IS1202 transposase gene, complete cds
28	1	80	505	emb|Z83335|SPZ8	S. pnuemoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	99	426	426
					biosynthesis genes and aliA gene
28	2	503	952	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	97	450	450
				sequence IS1202 transposase gene, complete cds
28	3	780	1298	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	96	181	519
				sequence IS1202 transposase gene, complete cds
34	1	207	1523	gb|L08611|	Streptococcus pneumoniae maltose/maltodextrin uptake (malX) and two	99	1317	1317
< td/>				maltodextrin permease (malC and MalD) genes, complete cds
34	2	1477	2367< /td>	gb|L08611|	Streptococcus pneumoniae maltose/maltodextrin uptake (malX) and two	96	795	891
					maltodextrin permease (malC and MalD) genes, complete cds
34	3	2593	3420< /td>	gb|L21856|	Streptococcus pneumoniae malA gene, complete cds; malR gene, complete cds	96	446	828
34	4	2790	2647	gb|L21856|	98	137	144
34	5	3418	4416	gb|L21856|	96	999	999
34	9	7764	7507	gb|U41735|	93	201	258
					homoserine kinase homolog (thrB) genes, complete cds
34	16	10562	102 57	emb|X63602|SPBO	S. pneumoniae mmsA-Box	92	238	306
35	4	1176	1439	em b|Z83335|SPX8	S. pnuemoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	87	248	264
					biosynthesis genes and aliA gene
35	5	1458	1961	gb|U09239|	Streptococcus pneumoniae type 19F capsular polysaccharide biosynthesis	98	264	504
					operon, (cps19 fABCDEFGHIJKLMNO) genes, complete cds, and aliA gene,
					partial cds
35	17	16172	154 77	emb|X85787|SPCP	S. pneumoniae dexB, cps14A, cps14B, cps14C, cps14D, cps14E, cps14F, cps14G,	97	696	696
					cps14H, cps14I, cps14J, cps14K, cps14L, tasA genes
35	18	16961	1 6170	emb|Z83335|SPX8	S. pnuemoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	86	792	792
					biosynthesis genes and aliA gene
35	19	17620	16 871	gb|U09239|	Streptococcus pneumoniae type 19F capsular polysaccharide biosynthesis	83	750	750
					operon, (cps19fABCDEFGHIJKLMNO) genes, complete cds, and aliA gene,
					partial cds
35	20	19061	176 04	emb|X85787|SPCP	S. pneumoniae dexB, cps14A, cpsl4B, cps14C, cps14D, cps14E, cps14F, cps14G,	94	1458	1458
				cps14H, cps14I, cps14J, cps14K, cps14L, tasA genes
36	19	18960	1 8352	gb|U40786|	Streptococcus pneumoniae surface antigen A variant precursor (psaA) and 18	99	609	609
					kDa protein genes, complete cds, and ORF1 gene, partial cds
36	20	19934	189 66	gb|U53509|	Streptococcus pneumoniae surface adhesin A precursor (psaA) gene, complete	99	969	969
					cds
37	1< /td>	2743	179	emb|Z67739|SPPA	S. pneumoniae parC, parE and transposase genes and unknown orf	99	2565	2565
37	2	2985	2824	emb|Z67739|SPPA	S. pneumoniae parC, parE and transposase genes and unknown orf	100	162	162
37< /td>	3	5034	3070	emb|Z67739|SPPA< /td>	S. pneumoniae parC, parE and transposase genes and unknown orf	99	1965	1965
37	4	5134	5790	emb|Z67739|SPPA	S. pneumoniae parC, parE and transposase genee and unknown orf	99	657	657
37	5	6171	5833	emb|Z67739|SPPA	S. pneumoniae parC, parE and transpoaase genes and unknown orf	96	339	339
38	19	12969	13268	gb|M28679|	S. pneumoniae promoter region DNA	100	64	300
39	2	1256	2137	gb|U41735|	99	882	882
					homoserine kinase homolog (thrB) genes, complete cds
39	3	2405	3370< /td>	gb|U41735|	Streptococcus pneumoniae peptide methionine sulfoxide reductase (msrA) and	99	966	966
					homoserine kinase homolog (thrB) genes, complete cds
40	9	5253	7208< /td>	gb|M29686|	S. pneumoniae mismatch repair (hexB) gene, complete cds	99	1956	1956
41	1	3	1037	emb|Z17307|SPRE	S. pneumoniae recA gene encoding RecA	99	1027	1035
4 1	2	1328	2713	emb|Z34303|SPC I	Streptococcus pneumoniae cin operon encoding the cinA, recA, dinF, lytA	99	1386	3386
					genes, and downstream sequences
41	3	3083	4045	gb|M13812|	S. pneumoniae autolysin (lytA) gene, complete cds	99	963	963
41	4	3272	3096	gb|M13812|	100	177	177
41< /td>	5	3603	3860	gb|M13812|	100	258	258
41< /td>	6	4755	5162	gb|L36660|	98	408	408
41	7	5270	5716	gb|L36660|	98	447	447
41	8	6112	6918	gb|L36660|	98	431	807
41	9	6916	7119	gb|L36660|	100	204	204
41< /td>	10	7082	7660	gb|L36660|	Streptococcus pneumoniae ORF, complete cds	97	552	579
41	11	7680	7979	gb|L36660|	98	81	300
41	12	9169	8717	emb|Z77727|SPIS	S. pneumoniae DNA for insertion sequence IS1318 (823 bp)	97	353	453
41	13	9533	9132	emb|Z77725|SPIS< /td>	S. pneumoniae DNA for insertion sequence IS1381 (966 bp)	95	160	402
41	14	9669	9475	emb|Z82001|SPZ8< /td>	S. pneumoniae pcpA gene and open reading frames	100	189	195
44	5	7190	7555	emb|Z82001|SP Z8	S. pneumoniae pcpA gene and open reading frames	99	366	366
4 4	6	8059	7607	emb|Z77726|SPI S	S. pneumoniae DNA for insertion sequence IS1318 (1372 bp)	97	453	453
44	7	8423	8022	emb|Z77725|SPIS	S. pneumoniae DNA for insertion sequence IS1381 (966 bp)	95	160	402
44	8	8559	8365	emb|Z82001|SPZ8	S. pneumoniae pcpA gene and open reading frames	100	189	195
48	9	6480	4687	gb|L39074|	Streptococcus pneumoniae pyruvate oxidase (spxB) gene, complete cds	99	1794	1794
49	2	231	2603	gb|L20561|	100	216	2373
53	6	2407	2156	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucomidase gene and insertion	97	242	252
				sequence IS1202 transposase gene, complete cds
53	7	2566	2405< /td>	emb|Z83335|SPZ8	S. pneuaoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	100	94	162
					biosynthesis genes and aliA gene
53	8	2831	2475	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	99	338	357
					biosynthesis genes and aliA gene
54	13	12409	11 105	emb|Z83335|SPZ8	S. pneuaoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	67	591	1305
					biosynthesis genes and aliA gene
55	22	20488	19 949	emb|Z84379|HSZ8	S. pneumoniae dfr gene (isolate 92)	99	540	540
61	11	11864	9900	emb|Z16082|PNAL	Streptococcus pneumoniae aliB gene	98	1965	1965
6 3	1	3	239	gb|M18729|	S. pneumoniae mismatch repair protein (hexA) gene, complete cds	100	237	237
63< /td>	2	233	2611	gb|M18729|	99	2330	2379
63	3	2557	2823	gb|M18729|	S. pneumoniae mismatch repair protein (hexA) gene, complete cds	99	266	267
63	4	2958	4664	gb|M18729|	95	69	1707
67	6	3770	3399	gb|L20670|	96	372	372
67	7	7161	4171	gb|L20670|	99	2938	2991
70	1	1	702	gb|M14340|	S. pneumoniae DpnI gene region encoding dpnC and dpnD, complete cds	100	693	702
70< /td>	2	678	1160	gb|M14340|	100	483	483
70< /td>	3	2490	1210	gb|M14339|	98	462	1281
70< /td>	7	4230	4424	gb|J04234|	99	147	195
70	8	5197	4316	gb|J04234|	99	881	882
70	13	8108	9874	gb|L20562|	93	234	1767
71< /td>	22	27964	28341	emb|X63602|SP BO	S. pneumoniae mmsA-Box	93	233	378
72	5	4607	3552	em b|Z26850|SPAT	S. pneumoniae (M222) genes for ATPase a subunit, ATPase b subunit and ATPase	97	102	1056
					c subunit
73	1	471	13 3	emb|X63602|SPBO	S. pneumoniae mmsA-Box	91	193	339
73	3	3658	977	gb| J04479|	S. pneumoniae DNA polymerase I (polA) gene, complete cds	99	2682	2682
73	8	4864	5379	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	98	318	516
				(purC) genes, complete cds
77	3	2622	1999< /td>	emb|Z83335|SPZ8	S. penumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	95	624	624
					biosynthesis genes and aliA gene
77	4	3341	2523	emb|Z83335|SPZ8	S. penumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	91	819	819
					biosynthesis genes and aliA gene
78	1	341	3	emb|X77249|SPR6	S. pneumoniae (R6) ciaR/ciaH genes	99	339	339
78	2	1095	325	emb|X77249|SPR6< /td>	S. pneumoniae (R6) ciaR/ciaH genes	99	771	771
82	10	11436	10816	gb|U90721|	Streptococcus pneumoniae signal peptidase I (spi) gene, complete cds	97	621	621
82	11	12402	11434	gb|U93576|	Streptococcus pneumoniae ribonuclease HII (rnhB) gene, complete cds	98	953	969
82	12	12381	12704	gb|U93576|	Streptococcus pneumoniae ribonuclease HII (rnhB) gene, complete cds	100	51	324
83	8	3212	3550	emb|Z77727|SPIS	S. pneumoniae DNA for insertion sequence IS1318 (823 bp)	97	290	339
83	10	4662	6851	gb|M36180|	99	2190	2190
					(purC) genes, complete cds
83	11	6849	8213	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	99	1365	1365
					(purC) genes, complete cds
83	12	8236	9090	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	99	855	855
				(purC) genes, complete cds
83	13	9283	1301 7	gb|L15190|	Streptococcus pneumoniae SAICAR synthetase (purC) gene, complete cds	100	107	3735
83	23	22147	23313	gb|L36923|	Streptococcus pneumoniae beta-N-acetylhexosaminidase (strH) gene, complete	98	218	1167
				cds
83	2 4	23268	23450	gb|L36923|	Streptococcus pneumoniae beta-N-acetylhexosaminidase (strH) gene, complete	98	172	183
					cds
83	25	27527	23505	gb|L36923|	Streptococcus pneumoniae beta-N-acetylhexosaminidase (strH) gene, complete	99	3826	4023
				cds
83	26	28472	27771	gb|L36923|	Streptococcus pneumoniae beta-N-acetylhexosaminidase (strH) gene, complete	99	416	702
					cds
84	4< /td>	4554	6173	emb|Z83335|SPZB	S. pneumoniae dexB, cap1]A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	98	697	1620
					biosynthesis genes and aliA gene
87	6	5951	5316	emb|Z77725|SPIS	S. pneumoniae DNA for insertion sequence IS1381 (966 bp)	96	439	636
88	5	2957	3511	gb|M36180|	94	555	555
				(purC) genes, complete cds
88	6	3466	4269< /td>	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	94	804	804
				(purC) genes, complete cds
89	13	9878	1009 3	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	97	211	216
				(purC) genes, complete cds
89	14	10062	104 12	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1(A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	97	335	351
					biosynthesis genes and aliA gene
93	10	5303	494 1	emb|X63602|SPBO	S. pneumoniae mmsA-Box	89	237	363
97	4	1708	1520	gb |U41735|	Streptococcus pneumoniae peptide methionine sulfoxide reductase (msrA) and	91	140	189
					homoserine kinase homolog (thrB) genes, complete cds
99	1	89	700	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	93	592	612
					biosynthesis genes and aliA gene
99	2	1773	775< /td>	emb|X17337|SPAM	Streptococcus pneumoniae ami locus conferring aminopterin resistance	99	998	999
3	2794	1712	emb|X17337 |SPAM	Streptococcus pneumoniae ami locus conferring aminopterin resistance	99	1083	1083
99	4	3732	2788	emb|X173 37|SPAM	Streptococcus pneumoniae ami locus conferring aminopterin resistance	100	945	945
99	5	5249	3714	emb|X1733 7|SPAM	Streptococcus pneumoniae ami locus conferring aminopterin resistance	100	1536	1536
99	6	7262	5277	emb|X17 337|SPAM	Streptococcus pneumoniae ami locus conferring aminopterin resistance	99	1986	1986
101	1	216	1538	emb|X542 25|SPEN	S. pneumoniae epuA and endA genes for 7 kDa protein and membrane	99	146	1323
				endonuclease
101	2	1492	1719	emb|X54225|SPEN	S. pneumoniae epuA and endA genes for 7 kDa protein and membrane	99	228	228
					endonuclease
101< /td>	3	1694	1855	emb|X54225|SPEN< /td>	S. pneumoniae epuA and endA genes for 7 kDa protein and membrane	100	162	162
				endonuclease
101	4	1701	2582	emb|X54225|SPEN	S. pneumponiae epuA and endA genes for 7 kDa protein and membrane	100	882	882
				endonuclease
103	7	5556	5041	emb|Z95914|SPZ9	Streptococcus pneumoniae sodA gene	100	396	516
10 4	2	1347	1556	emb|Z77727|SPI S	S. pneumoniae DNA for insertion sequence IS1318 (823 bp)	83	206	210
105< /td>	5	5381	5028	emb|Z67739|SPPA< /td>	S. pneumoniae parC, parE and transposase genes and unknown orf	98	353	354
105< /td>	6	6089	5379	emb|Z67739|SPPA< /td>	S. pneumoniae parC, parE and transposase genes and unknown orf	98	84	711
107	4	2785	1880	emb|X16022|SPPE	S. pneumoniae penA gene	98	72	906
107< /td>	5	2913	4988	emb|X16022|SPPE< /td>	S. pneumoniae penA gene	99	1692	2076
1 07	6	4981	5595	emb|X13136|SP PE	Streptococcus pneumoniae penA gene for penicillin binding protein 2B	91	107	615
					lacking N-term, (penicillin resistant strain)
108	9	9068	8718	emb|Z67739|SPPA	S. pneumoniae parC, parE and transposase genes and unknown orf	95	342	351
108< /td>	12	11308	10922	emb|Z67739|SP PA	S. pneumoniae parC, parE and transposase genes and unknown orf	99	199	387
109< /td>	3	2768	2241	emb|Z77725|SPIS< /td>	S. pneumoniae DNA for insertion sequence IS1381 (966 bp)	96	61	528
109	4	2688	2855	emb|Z77726|SPIS	S. pneumoniae DNA for insertion sequence IS3318 (1372 bp)	96	148	168
109< /td>	5	2862	3269	emb|Z77727|SPIS< /td>	S. pneumoniae DNA for insertion sequence IS1318 (823 bp)	97	353	408
109< /td>	6	5320	3584	gb|M18729|	100	371	1737
11 3	1	431	3	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	95	429	429
				(purC) genes, complete cds
113	10	9788	853 2	emb|X99400|SPDA	S. pneumoniae dacA gene and ORF	99	1257	1257
11 3	11	9870	10985	emb|X99400|S PDA	S. pneumoniae dacA gene and ORF	99	1116	1116
11 4	3	2530	2030	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	95	481	501
				(purC) genes, complete cds
115	11	11303	10 932	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	97	372	372
				sequence IS1202 transposase gene, complete cds
117	1	897	3302< /td>	emb|X72967|SPNA	S. pneumoniae nanA gene	99	2402	2408
1 17	2	3277	3831	emb|X72967|SP NA	S. pneumoniae nanA gene	99	237	555
117	3	4327	3899	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	98	429	429
				(purC) genes, complete cds
121	2	1369	1941	gb|U72720|	Streptococcus pneumoniae heat shock protein 70 (dnaK) gene, complete cds	99	202	573
					and DnaJ (dnaJ) gene, partial cds
121	3	2412	4253	gb|U72720|	Streptococcus pneumoniae heat shock protein 70 (dnaK) gene, complete cds	99	1842	1842
< td/>				and DnaJ (dnaJ) gene, partial cds
122	8	5066	5587	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	64	451	522
				sequence IS1202 transposase gene, complete cds
125	1	1811	189< /td>	gb|H36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	92	99	1623
				(purC) genes, complete cds
128	15	12496	11 204	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	91	705	1293
					biosynthesis genes and aliA gene
134	1	1	492	emb|Y10818|SPY1	S. pneumoniae spsA gene	99	203	492
134	2	556	2652	gb|AF019904|	Streptococcus pneumoniae choline binding protein A (cbpA) gene, partial cds	86	685	2097
134	3	1160	837	emb|Y10818|SPY1< /td>	S. pneumoniae spsA gene	86	324	324
134	4	3952	2882	gb|AF019904|	Streptococcus pneumoniae choline binding protein A (cbpA) gene, partial cds	98	215	1071
134	8	7992	9848	gb|U12567|	Streptococcus pneumoniae P13 glycerol-3-phosphate dehydrogenase (glpD)	99	285	1857
					gene, partial cds, and glycerol uptake facilitator (glpF) and ORF3 genes,
					complete cds
134	9	9846	1062 2	gb|U12567|	Streptococcus pneunoniae P13 glycerol-3-phosphate dehydrogenase (glpD)	99	570	777
					gene, partial cds, and glycerol uptake facilitator (glpF) and ORF3 genes,
					complete cds
134	10	10805	11 122	gb|U12567|	Streptococcus pneumoniae P13 glycerol-3-phosphate dehydrogenase (glpD)	100	318	318
					gene, partial cds, and glycerol uptake facilitator (glpF) and ORF3 genes,
					complete cds
137	13	7970	844 3	gb|U09239|	Streptococcus pneumoniae type 19F capsular polysaccharide biosynthesis	90	420	474
					operon, (cps19 fABCDEFGHIJKLMNO) genes, complete cds, and aliA gene,
					partial cds
137	14	8590	877 5	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1 [A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	94	174	186
					biosynthesis genes and aliA gene
137	15	8773	89 67	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	98	195	195
					biosynthesis genes and aliA gene
137	16	9223	96 87	emb|Z77726|SPIS	S. pneumoniae DNA for insertion sequence IS1318 (1372 bp)	96	446	465
137< /td>	17	9641	10051	emb|Z77727|SPI S	S. pneumoniae DNA for insertion sequence IS1318 (823 bp)	96	293	411
139< /td>	10	12998	12702	emb|X63602|SP BO	S. pneumoniae mmsA-Box	90	234	297
141	8	7805	8938	e mb|Z49988|SPMM	Streptococcus pneumoniae mmsA gene	99	338	1134
14 1	9	8936	10972	emb|Z49988|SP MM	Streptococcus pneumoniae mmsA gene	99	2037	2037
1 41	10	11472	12467	emb|Z49988 |SPMM	Streptococcus pneumoniae mmsA gene	100	76	996
142	2	257	814	gb|M80215|	98	174	558
142< /td>	3	787	957	gb|M80215|	Streptococcus pneumoniae uvs402 protein gene, complete cds	100	142	171
142	4	980	3022	gb|M80215|	95	1997	2043
14 2	5	3020	3595	gb|M80215|	Streptococcus pneumoniae uvs402 protein gene, complete cds	100	153	576
145	1	1	219	emb|Z35135|SPAL	S. pneumoniae aliA gene for amiA-like gene A	97	185	219
145	2	171	1994	gb|L20556|	Streptococcus pneumoniae plpA gene, partial cds	99	1811	1824
14 5	3	2287	7599	emb|Z47210|SPD E	S. pneumoniae dexB, cap3A, cap3B and cap3C genes and orfs	99	1052	5313
1 45	4	9934	7766	gb|M90527|	Streptococcus pneumoniae penicillin binding protein (ponA) gene, complete	99	2169	2169
				cds
145	5	10488	9922	gb|M90527|	Streptococcus pneumoniae penicillin binding protein (ponA) gene, complete	99	512	567
					cds
146	1	159	4	emb|Z82002|SPZ8	S. pneumoniae pcpB and pcpC genes	98	156	156
14 6	2	344	90	emb|Z82002|SPZ8	S. pneumoniae pcpB and pcpC genes	98	255	255
14 6	16	11795	10794	emb|Z82002| SPZ8	S. pneumoniae pcpB and pcpC genes	85	276	1002
1 47	11	10678	10202	emb|Z21702 |SPUN	S. pneumoniae ung gene and mutX genes encoding uracil-DNA glycosylase and 8-	98	477	477
					oxodGTP nucleoside triphosphatase
147	12	11338	10676	emb|Z21702|SPUN	S. pneumoniae ung gene and mutX genes encoding uracil-DNA glycosylase and 8-	99	663	663
					oxodGTP nucleoside triphosphatase
148	12	9009< /td>	8815	gb|U41735|	Streptococcu s pneumoniae peptide methionine sulfoxide reductase (msrA) and	90	180	195
					homoserine kinase homolog (thrB) genes, complete cds
156	4	1154	1402	emb|X63602|SPBO	S. pneumoniae mmsA-Box	94	185	249
159	13	9048	8521	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	98	526	528
				(purC) genes, complete cds
160	1	1	147	emb|Z26851|SPAT	S. pneumoniae (R6) genes for ATPase a subunit, ATPase b subunit and ATPase c	100	142	147
					subunit
160	2	179	898	emb|Z26851|SPAT	S. pneumoniae (R6) genes for ATPase a subunit, ATPase b subunit and ATPase c	99	720	720
					subunit
160	3	906	1406	emb|Z26850|SPAT	S. pneumoniae (M222) genes for ATPase a subunit, ATPase b subunit and ATPase	95	501	501
					c subunit
160	4	1373	1942	emb|Z26850|SPAT	S. pneumoniae (M222) genes for ATPase a subunit, ATPase b subunit and ATPase	87	306	570
					c subunit
161	1	1	984	emb|X77249|SPR6	S. pneumoniae (R6) ciaR/ciaH genes	99	984	984
16 1	7	6910	7497	emb|X83917|SPG Y	S. pneumoniae orflgyrB and gyrB gene encoding DNA gyrase B subunit	99	437	588
161	8	7443	9386	emb|X83917|S PGY	S. pneumoniae orflgyrB and gyrB gene encoding DNA gyrase B subunit	98	1912	1944
1	2	2155	gb|L20559|	Streptococcus pneumoniae Exp5 gene, partial cds	98	327	2154
165	1	32	1618	gb|J01796|	99	1587	1587
< td/>				amylomaltase, complete cds, and malP gene encoding phosphorylase
165	2	1608	3902	gb|J01796|	S. pneumoniae malX and malM genes encoding membrane protein and	100	280	2295
< td/>				amylomaltase, complete cds, and malP gene encoding phosphorylase
166	1	378	4	emb|Y11463|SPDN	Streptococcus pneumoniae dnaG, rpoD, cpoA genes and ORF3 and ORF5	100	375	375
16 6	2	1507	320	emb|Y11463|SPDN	Streptocgccus pneumoniae dnaG, rpoD, cpoA genes and ORF3 and ORF5	99	1188	1188
1 66	3	3240	1432	emb|Y11463|SP DN	Streptococcus pneumoniae dnaG, rpoD, cpoA genes and ORF3 and ORF5	99	563	1809
16 7	1	1077	328	emb|Z71552|SPAD	Streptococcus pneumoniae adcCBA operon	94	155	750
1 67	2	1844	999	emb|Z71552|SPA D	Streptococcus pneumoniae adcCBA operon	98	405	846
1 67	3	2714	1842	emb|Z71552|SP AD	Streptococcus pneumoniae adcCBA operon	97	604	873
1 67	4	3399	2641	emb|Z71552|SP AD	Streptococcus pneumoniae adcCBA operon	99	703	759
1 68	1	1	2259	gb|L20558|	99	282	2259
170	10	7338	7685	emb|Z77726|SPI S	S. pneumoniae DNA for insertion sequence IS1318 (1372 bp)	95	315	348
172< /td>	6	2462	4981	gb|47625|	97	365	2520
					cds
175	1	373	20	gb|M36180|	S treptococcus pneumoniae transposase (comA and comB) and SAICAR synthetase	89	353	354
				(purC) genes, complete cds
175	4	1843	3621	emb|Z47210|SPDE	S. pneumoniae dexB, cap3A, cap3B and cap3C genes and orfs	95	89	1779
176	5	3984	2980	emb|Z67739|SPPA	S. pneumoniae parC, parE and transposase genes and unknown orf	100	573	1005
17 8	1	3	425	emb|Z67739|SPPA	S. pneumoniae parC, parE and transposase genes and unknown orf	95	423	423
179< /td>	1	426	70	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	99	338	357
					biosynthesis genes and aliA gene
180	3	3084	185 5	emb|X95718|SPGY	S. pneumoniae gyrA gene	99	381	1230
18 6	1	714	4	emb|Z79691|SOOR	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	98	59	711
186	2	2254	608	emb|Z79691|SOOR< /td>	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	98	315	1647
1 86	3	707	880	emb|Z79691|SOOR	S. pneumoniae yorf[A,B,C,D,E], ftsL, pbpX and regR genes	98	174	174
18 9	1	2	259	gb|U72720|	Streptococcus pneumoniae heat shock protein 70 (dnaK) gene, complete cds	99	258	258
					and DnaJ (dnaJ) gene, partial cds
189	2	600	385	gb|U72720|	Streptococcus pneumoniae heat shock protein 70 (dnaK) gene, complete cds	98	204	216
					and DnaJ (dnaJ) gene, partial cds
189	3	1018	851< /td>	gb|U72720|	Streptococcus pneumoniae heat shock protein 70 (dnaK) gene, complete cds	99	168	168
					and DnaJ (dnaJ) gene, partial cds
189	4	1012	2154	gb|U72720|	Streptococcus pneumoniae heat shock protein 70 (dnaK) gene, complete cds	99	1062	1143
< td/>				and DnaJ (dnaJ) gene, partial cds
191	9	7829	7524	emb|X63602|SPBO	S. pneumoniae mmsA-Box	95	234	306
194	1	1	729	gb|M3 6180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	91	728	729
				(purC) genes, complete cds
199	2	1117	881< /td>	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	96	211	237
					biosynthesis genes and aliA gene
199	4	1499	176 2	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	89	248	264
					biosynthesis genes and aliA gene
199	5	1781	228 4	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	98	504	504
					biosynthesis genes and aliA gene
203	1	1977	337	gb|L20563|	Streptococcus pneumoniae Exp9 gene, partial cds	99	342	1641
204	1	1145	3	gb|L36131|	Streptococcus pneumoniae exp10 gene, complete cds, recA gene, 5′ end	99	1143	1143
20 8	1	59	2296	gb|U89711|	90	471	2238
					complete cds
213	3	2455	2123	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	96	332	333
					biosynthesis genes and aliA gene
216	1	368	12	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	99	338	357
					biosynthesis genes and aliA gene
216	3	2650	232 7	gb|M28678|	S. pneumoniae promoter sequence DNA	98	86	324
222	1	417	4	emb|Z83335|SPZ8	94	414	414
					biosynthesis genes and aliA gene
227	3	5266	423 8	emb|AJ000336|SP	Streptococcus pneumoniae 1dh gene	99	1029	1029
2 39	1	1	804	gb|M31296|	95	484	804
247< /td>	3	1625	1807	gb|M36180|	94	178	183
				(purC) genes, complete cds
249	3	921	1364< /td>	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	94	443	444
					biosynthesis genes and aliA gene
253	1	362	3	gb|M36180]	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	99	360	360
				(purC) genes, complete cds
253	5	1238	2050	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	95	420	813
					biosynthesis genes and aliA gene
253	6	2069	257 2	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	97	504	504
					biosynthesis genes and aliA gene
254	1	3	800	emb|Z82002|SPZ8	S. pneumoniae pcpB and pcpC genes	97	531	798
25 5	2	798	1841	emb|Z82002|SPZ8	S. pneumoniae pcpB and pcpC genes	97	672	1044
2 55	3	2493	1969	emb|Z67739|SP PA	S. pneumoniae parC, parE and transposase genes and unknown orf	92	435	525
257< /td>	2	985	770	emb|X17337|SPAM	Streptococcus pneumoniae ami locus conferring aminopterin resistance	96	117	216
3	1245	907	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	97	339	339
				(purC) genes, complete cds
267	2	495	1208< /td>	gb|U16156|	Streptococcus pneumoniae dihydropteroate synthase (sulA), dihydrofolate	95	84	714
					synthetase (sulB), guanosine triphosphate cyclohydrolase (sulC), aldolase-
					pyrophos phokinase (sulD) genes, complete cds
267	3	1291	2277	gb|U16156|	Streptococcus pneumoniae dihydropteroate synthase (sulA), dihydrofolate	97	755	987
					synthetase (sulB), guanosine triphosphate cyclohydrolase (sulC), aldolase-
					pyrophos phokinase (sulD) genes, complete cds
267	4	2261	3601	gb|U16156|	Streptococcus pneumoniae dihydropteroate synthase (sulA), dihydrofolate	98	1341	1341
					synthetase (sulB), guanosine triphosphate cyclohydrolase (sulC), aldolase-
					pyrophos phokinase (sulD) genes, complete cds
267	5	3561	4136	gb|U16156|	Streptococcus pneumoniae dihydropteroate synthase (sulA), dihydrofolate	99	576	576
					synthetase (sulB), guanosine triphosphate cyclohydrolase (sulC), aldolase-
					pyrophos phokinase (sulD) genes, complete cds
267	6	4164	4949	gb|U16156|	Streptococcus pneumoniae dihydropteroate synthase (sulA), dihydrofolate	99	748	786
					synthetase (sulB), guanosine triphosphate cyclohydrolase (sulC), aldolase-
					pyrophos phokinase (sulD) genes, complete cds
267	7	5544	5140	gb|U16156|	Streptococcus pneumoniae dihydropteroate synthase (sulA), dihydrofolate	100	186	405
					synthetase (sulB), guanosine triphosphate cyclohydrolase (sulC), aldolase-
					pyrophos phokinase (sulD) genes, complete cds
268	4	1793	1990	emb|X63602|SPBO	S. pneumoniae mmsA-Box	89	194	198
271	1	562	104	gb| 429686|	S. pneumoniae mismatch repair (hexB) gene, complete cds	93	160	459
291< /td>	1	75	524	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	96	450	450
				sequence IS1202 transposase gene, complete cds
291	2	1001	525< /td>	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	87	205	477
					biosynthesis genes and aliA gene
291	3	807	559< /td>	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	90	170	249
					biosynthesis genes and aliA gene
291	4	1374	109 9	gb|M36180|	Streptococcus pneumoniae transposase, (comA and comB) and SAICAR synthetase	85	264	276
				(purC) genes, complete cds
293	1	3	1673	emb|Z67740|SPGY	S. pneumoniae gyrB gene and unknown orf	98	553	1671
296	1	1434	151	emb|Z47210|SPDE< /td>	S. pneumoniae dexB, cap3A, cap3B and cap3C genes and orfs	99	430	1284
31 7	1	157	510	emb|Z67739|SPPA< /td>	S. pneumoniae parC, parE and transposase genes and unknown orf	89	353	354
325< /td>	2	1237	485	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	91	299	753
					biosynthesis genes and aliA gene
326	1	1	462	emb|Z82001|SPZ8	S. pneumoniae pcpA gene and open reading frames	100	233	462
327	1	603	64	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K) genes, dTDP-rhamnose	94	89	540
					biosynthesis genes and aliA gene
334	1	153	545< /td>	gb|U41735|	Streptococcus pneumoniae peptide methionine sulfoxide reductase (msrA) and	87	91	393
					homoserine kinase homolog (thrB) genes, complete cds
336	1	308	93	emb|Z26850|SPAT	S. pneumoniae (M222) genes for ATPase a subunit, ATPase b subunit and ATPase	97	102	216
					c subunit
360	1	1	519	emb|Z67739|SPPA	S. pneumoniae parC, parE and transposase genes and unknown orf	95	435	519
360< /td>	4	1598	1960	emb|Z83335|SPZ8< /td>	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	94	353	363
					biosynthesis genes and aliA gene
362	1	673	2	emb|Z83335|SPZ8	S. pneumoniae dexB, cap1[A,B,C,D,E,F,G,H,I,J,K] genes, dTDP-rhamnose	95	63	672
					biosynthesis genes and aliA gene
362	2	1168	728	gb|U04047|	Streptococcus pneumoniae SSZ dextran glucosidase gene and insertion	96	441	441
				sequence IS1202 transposase gene, complete cds
384	1	347	111	emb|X85787|SPCP	S. pneumoniae dexB, cps14A, cps14B, cps14C, cpsl4D, cps14E, cps14F, cps14G,	94	54	237
					cps14H, cps14I, cps14J, cps14K, cps14L, tasA genes

Stop< tr>< /tr>< td>189< td>gi|987050< /tr>< td>sp|P37214|ERA_S< td>gi|46606< td>gi|208225< td>gi|149396< td>gi|703442gi|287871< /tr>< /tr>< td>gi|2323342< td>pir|A45434|A45419447 96862623< td>gnl|PID|e134943< td>912< td>771< /tr>< td>gi|1196921gnl|PID|e228283< td>gi|1661193< td>gi|2160707< td>gi|2149909< td>gi|1044989< td>876< /tr>gnl|PID|d102006< tr>< tr>< /tr>< td>gi|104498014144 < td>gi|311707< tr>< td>gi|1500567< td>1350   3< td>pir|S06097|S060< td>pir|S08564|R3BSgi|146402198< /tr>gi|1685111< td>gi|1216490< td>gnl|PID|e305362< td>828< td>gi|1183884< td>pir|A02815|R5BS< td>1104 19457 < /tr>< td>gnl|PID|d101091< td>gi|506700< tr>< td>gi|897795< td>gi|143328< tr>< td>gi|580914< td>gi|142463< tr>< td>gi|149402gi|1174237gi|580902< td>6322< td>gnl|PID|d100306< td>gi|1916729< td>gi|520738< td>gi|1708640< tr>< td>gi|148921726< td>gi|2293302< td>gi|511015< td>gnl|PID|e334776< td>774< td>3869< td>12881 < td/>< td>gi|944944< td>gi|1674310< td>gi|143795< td>gnl|PID|d100959< td>gi|551880< td>gi|431272< tr>< tr>< td>gi|149520< td>gi|2293211< tr>< tr>< td>gi|1146219< td>gnl|PID|e323529< td>711< td>1071 < td>38710082 < td>gi|1119198192< td>gnl|PID|e257631< td>gi|1573373< td/>< td>gi|666983gnl|PID|e265580gi|857631< tr>< tr>< tr>< tr>< td/>< td>ribosome releasing factor [Synechocystis sp.]< tr>< td>gi|829615< td>gi|472327< tr>< tr>< tr>< tr>< tr>< td>gi|580900< td>gi|1353874< td/>< td>gi|39478< td>gi|662792gi|11612193812< tr>1954< td>762< td>gnl|PID|e275074< td>gi|1573037< td>7888< td>gi|2293312< tr>< /tr>< /tr>gi|1353874< td>gi|580887< tr>< /tr>< td>3247gnl|PID|e257629< td>gnl|PID|d101314< td>gnl|PID|d100581< td>966< /tr>gi|148945251< td>gi|1790131< tr>< td>786< td>gnl|PID|d101732< td>pir|B54545|B545spore coat protein [Bacillus subtilis]< tr>< td>1026 1728 < /tr>< td>717< tr>< td>gnl|PID|d10133012740 < td>gnl|PID|e264711< td>gi|1142714< /tr>< tr>< td>gi|1161933< /tr>< td>gi|153841< tr>< td>gi|1842438< tr>1083 < tr>< td>219< td/>1101 < td>gi|2098719< td> 89< /tr>gi|609332< td>gi|726288TPP-dependent acetoin dehydrogenase alpha-subunit [Clostridium< td>2270< tr>< td>gi|517210< td>gnl|PID|e325010< td>gi|14804294519< td>861< tr>< td/>gi|1575577< tr>< td>657< td>gi|49315< td>gnl|PID|e265529< td>gi|1762328< td>gnl|PID|d102036< td>gi|15738264949< td>pir|JC1151|JC11< td>gi|1322245< td>gnl|PID|d100964< td>gi|581307< /tr>< td>gi|1573393gnl|PID|e217602< /tr>gi|1377843< td>gi|722339< td>gi|2098719< td>gi|1052803< td>gi|7171< tr>< td>gnl|PID|e324217< /tr>< td>gi|722339gi|1877424gi|2252843< td>168< td>9538< td>gi|2314379< tr>< /tr>YqeG [Bacillus subtilis]< td>gi|1573024< td>pir|S41509|S415< td>657< td>gnl|PID|e254644< td>200< tr>< tr>< tr>< tr>< tr>putative cel operon regulator [Bacillus subtilis]< td>gi|1209527< td>gi|1787043< tr>< td>363< tr>< td>gnl|PID|d100417< tr>< td>pir|JC1151|JC11< tr>< td>gi|149569< /tr>16951 < td>gnl|PID|d100587< td>7372< tr>< tr>< td>gnl|PID|e334782gnl|PID|d101876< td>Pgm [Treponema pallidum]< td>gnl|PID|e313022< tr>< td>gnl|PID|e308090< tr>< td>gi|580841< td>180< td>246< /tr>40< td>(AB001488) FUNCTION UNKNOWN, SIMILAR PRODUCT IN< td>7213< td>8836< td/>360< td>gi|666062< tr>< /tr>gi|39478291gi|153794< td>648< td>gi|473901gi|167475< td>gnl|PID|e246727< tr>< td>gi|466474< td>pir|JC1151|JC11< td>939< td>gi|1553692079< td>gi|559882< td>gi|1591393< td>45618627 < tr>< td>1008 < td>28701 < td>gi|995560< /tr>< td>gi|600431< /tr>< tr>< td>gi|147402< tr>< td>492< td>gi|1592090< /tr>13191 < /tr>< td>gnl|PID|d100247gi|2182397< /tr>pir|S5790451 S579< td>3< tr>< td>gnl|PID|e316518< td>gi|1088261< tr>< td>gi|896042< tr>< td>gi|535052< td>gi|1196504< td>gnl|PID|d101741< td>gi|396844< td>gi|396397< tr>< td>gi|160671488212103 < tr>< /tr>< td>recombinase [Moraxella bovis]< /tr>< tr>< td/>< td>gnl|PID|e313074S antigen precursor [Plasmodium falciparum]< /tr>gnl|PID|e316029< tr>< td>gi|563366< td>gi|149581< /tr>< /tr>< td>orf2 [Lactobacillus helveticus]< td>gi|2317740< td>1896 < tr>< td>gi|471234gi|153733< td>gnl|PID|e245024< td>gi|497647< tr>gi|2314455< td>gnl|PID|d101316< td>probable copper-transporting atpase [Escherichia coli]< tr>< td>gi|1633572< td>11550 < tr>< tr>< tr>< td>gnl|PID|d100974< td/>< td>7179< td>1125 < td>15770 < /tr>gi|2275264< td>gi|1066016gi|895747< td>gi|1216475gi|152271< td>gi|1786983< td/>< td>gi|393396< td>gnl|PID|e285322< /tr>< td>gi|39573< td/>< td>549< td>gnl|PID|e290649< tr>< /tr>< td/>< td>P20 (AA 1-178) [Bacillus licheniformis]< td>pir|A37024|A370< td>gnl|PID|d100964< td>615< td/>< tr>gi|1469286< td>232< td>gi|1673744< /tr>< /tr>< tr>18256 < tr>< td>340< /tr>

TABLE 2
S. pneumoniae - Putative coding regions of novel proteins similar to known proteins
Contig	ORF	Start	match		%	%	length
ID	ID	(nt)	(nt)	acession	match gene name	sim	ident	(nt)
228	2	1760	1942	pir|F60663|F606	translation elongation factor Tu - Streptococcus oralis	100 	100 	183
319	1	 2	 205	gi|984927	neomycin phosphotransferase [Cloning vector pBSL99]	100 	100 	204
260	1	 2	1138	pir|F60663|F606	translatio n elongation factor Tu - Streptococcus oralis	99	98	1137 
 25	2	 486	1394	gi|1574495	hypothetical [Haemophilus influenzae]	98	96	909
 94	2	 685	1002	gi|310627	phosphoenolpyruvate:sugar phosphotransferase system HPr	98	93	318
					[Streptococcus mutans]
312	1	  190	 2	gi|347999	ATP-dependent protease proteolytic subunit [Streptococcus	98	95
					sal ivarius]
329	1	 1	 807	gi|924848	inosine monophosphate dehydrogenase [Streptococcus pyogenes]	98	94	807
336	2	 290	 589	lacZ gene product [unidentified cloning vector]	98	98	300
1 81	9	5948	7366	gi|153855	phospho-beta-D-galactosidase (EC 3.2.1.85) [Lactococcus lactis	97	94	1419 
					cremoris]
312	2	1044	  361	gi|347998	uracil phosphoribosyltransferase [Streptococcus salivarius]	97	88	684
 32	8	6575	7486	GTP-BINDING PROTEIN ERA HOMOLOG.	96	91	912
 94	3	 951	2741	gi|15361 5	phosphoenolpyruvate:sugar phosphotransferase system enzyme I	96	92	1791 
				[Streptococcus salivarius]
127	1	 1	 168	gicremoris]581299	initia tion factor IF-1 [Lactococcus lactis]	96	89	168
128	14 	10438 	11154 	gicremoris]1276873	DeoD [Streptococcus thermophilus]	96	93	717
181	4	1362	1598	lacD polypeptide (AA 1-326) [Staphylococcus aureus]	96	80	237
218	1	 1	 834	gi|1743856	intrageneric coaggregation-relevant adhesin [Streptococcus gordonii]	96	93	834
319	2	 115	 441	heat-shock protein 82/neomcyn phosphotransferase fusion protein	96	96	327
					(hsp82-neo) [unidentified cloning vector]
 54	12 	8622	10967 	gnl|PID|d100972	Pyruvate formate-lyase [Streptococcus mutans]	95	89	2346 
181	2	 606	1289	lacD [Lactococcus lactis]	95	89	684
 46	3	3410	3045	g i|1850606	YlxM [Streptococcus mutans]	94	86	366
 89	10 	7972	7337	thymidine kinase [Streptococcus gordonii]	94	86	636
148	9	6431	7354	g i|995767	UDP-glucose pyrophosphorylase [Streptococcus pyogenes]	94	85	924
160	7	4430	5848	g i|153573	H+ ATPase [Enterococcus faecalis]	94	87	1419 
2	3	4598	3513	gi|153763	plasmin receptor [Streptococcus pyogenes]	93	86	1086 
 12	8	7877	6204	gi|1103865	formyl-tetrahydrofolate synthetase [Streptococcus mutans]	93	84	1674 
 65	11 	4734	5120	gi|40150	L14 protein (AA 1-122) [Bacillus subtilis]	93	87	387
 68	1	53	1297	gi|47341	antitumor protein [Streptococcus pyogenes]	93	87	1245 
 80	1	 3	 299	gnl|PID|d101166	ribosoma l protein S7 [Bacillus subtilis]	93	84	297
127	3	 695	1093	gi|142462	ribosomal protein S11 [Bacillus subtilis]	93	86	399
160	5	1924	3462	g i|1773264	ATPase, alpha subunit [Streptococcus mutans]	93	85	1539 
211	5	3757	3047	gi|535273	aminopeptidase C [Streptococcus thermophilus]	93	82	711
262	1	16	 564	gi|149394	lacB [Lactococcus lactis]	93	90	549
366	1	 197	 3	gi|295259	tryptophan synthase beta subunit [Synechocystis sp.]	93	91	195
 2 5	3	1392	1976	gi|1574496	hypothetical [Haemophilus influenzae]	92	80	585
 36	21 	20781 	19 927 	gi|310632	hydrophobic membrane protein [Streptococcus gordonii]	92	86	855
181	3	1265	1534	g i|149396	lacD [Lactococcus lactis]	92	83	270
181	7	3662	4060	gi| 149410	enzyme III [Lactococcus lactis]	92	83	399
 32	4	5631	3937	g nl|PID|e294090	fibronectin-binding protein-like protein A [Streptococcus gordonii]	91	85	1695 
 46	2	3054	1462	gi|1850607	signal recognition particle Ffh [Streptococcus mutans]	91	84	1593 
 65	10 	4442	4726	pir|S17865|S178	ribosomal protein S17 - Bacillus stearothermophilus	91	80	285
 77	2	 260	1900	groEL gene product [Lactococcus lactis]	91	82	1641 
 84	1	 2	2056	gi|871784	Clp-like ATP-dependent protease binding subunit [Bos taurus]	91	79	2055 
 99	8	10750 	9272	gi|153740	sucrose phosphorylase [Streptococcus mutans]	91	84	1479 
 99	9	11947 	11072⠀‚	gi|153739	membrane protein [Streptococcus mutans]	91	78	876
127	5	2065	2469	pir |SO7223|R5BS	ribosomal protein L17 - Bacillus stearothermophilus	91	78	4 05
132	6	9539	9390< /td>	gi|143065	hubst [Bacillus stearothermophilus]	91	89	150
137	8	4765	6153	gnl|PID|d100347	Na+ - ATPase beta subunit [Enterococcus hirae]	91	79	1389 
151	7	11119 	9734	gi|1815634	glutamine synthetase type 1 [Streptococcus agalactiae]	91	82	1386 < /td>
201	2	1798	 278	gi|1108998	dextran glucosidase DexS [Streptococcus suis]	91	79	1521 
222	2	 673	1839	gi|153741	ATP-binding protein [Streptococcus mutans]	91	85	1167 
293	5	4113	4400	gi|1196921	unknown protein [Insertion sequence IS861]	91	71	288
†‚32	7	6166	6570	pir|A36933|A 369	diacylglycerol kinase homolog - Streptococcus mutans	90	77	405
 33	2	 841	527	g i|1196921	unknown protein [Insertion sequence IS861]	90	70	315
†‚48	27 	20908 	19757 	gnl|PID|e274705	lactate oxidase [Streptococcus iniae]	90	80	1152 
 55	21 	19777 	185 15 	gnl|PID|e221213	ClpX protein [Bacillus subtilis]	90	75	1263 
 56	2	 717	 977	gi|1710133	flagellar filament cap [Borrelia burgdorferi]	90	50	261
 65	1	 1	 606	gi|1165303	L3 [Bacillus subtilis]	90	75	606
114	1	 2	 988	gi|153562	aspartate beta-semialdehyde dehydrogenase (EC 1.2.1.11)	90	80	987
					[Streptococcus mutans]
120	1	134 5	 827	gi|407880	ORF1 [Streptococcus equismilis]	90	75	519
159	12 	7690	8298	gi|143012	GMP synthetase [Bacillus subtilis]	90	84	609
166	4	4076	3282	g i|1661179	high affinity branched chain amino acid transport protein	90	78	795
					[Streptococcus mutans]
183	1	28	1395	gi|308858	ATP:pyruvate 2-O-phosphotransferase [Lactococcus lactis]	90	76	1368 
191	3	2891	1662	gi|149521	tryptophan synthase beta subunit [Lactococcus lactis]	90	78	1230 
198	2	1551	 436	(AF014460) CcpA [Streptococcus mutans]	90	76	1116 
305	1	37	 783	gi|1573551	asparagine synthethase A (asnA) [Haemophilus influenzae]	90	80	747
8	3	2285	3343	gi|149434	putative [Lactococcus lactis]	89	78	1059 
 46	8	7577	7362	ribosomal protein L19 - Bacillus stearothermophilus	89	76	216
 49	9	8363	10342 	gi|153792	recP peptide [Streptococcus pneumoniae]	89	83	1980 < /td>
 51	14 	18410 	gi|308857	ATP:D-fructose 6-phosphate 1-phosphotransferase [Lactococcus	89	81	1038 
					l actis]
 57	11 	10669 	gnl|PID|d100932	H2O- forming NADH Oxidase [Streptococcus mutans]	89	77	984
 65	5	2418	2786	g i|1165307	S19 [Bacillus subtilis]	89	81	369
 65	8	3806	4225	sp|P14577|RL16—	50S RIBOSOMAL PROTEIN L16.	89	82	420
 6 5	18 	8219	8719	gi|143417< /td>	ribosomal protein S5 [Bacillus stearothermophilus]	89	76	501
 73	9	6337	53 15	gi|532204	prs [Listeria monocytogens]	89	70	1023†‚
 76	3	3360	1465	gnl|PID|e200671	lepA gene product [Bacillus subtilis]	89	76	1896 
 99	10 	12818 	11919 	gi|153738	membrane protein [Streptococcus mutans]	89	73	900
120	2	3552	1300	gi| 407881	stringent response-like protein [Streptococcus equisimilis]	89	79	2253 
122	5	4512	2791	gnl|PID|e280490	unknown [Streptococcus pneumoniae]	89	81	1722 < /td>
176	1	 669	 4	gi|47394	5-oxoprolyl-peptidase [Streptococcus pyogenes]	89	78	666
177	6	3050	3934	g i|912423	putative [Lactococcus lactis]	89	71	885
181	8	4033	5751	gi| 149411	enzyme III [Lactococcus lactis]	89	80	1719 
211	4	3149	2793	gi|535273	aminopeptidase C [Streptococcus thermophilus]	89	70	408
361	1	 431	 838	gi|1196922	unknown protein [Insertion sequence IS861]	89	70	408
†‚34	17 	11839 	10535 	sp|P30053[SYH_S	HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21)	88	78	1305 
					(HISTIDINE--TRNA LIGASE) (HISRS)
 38	3	1646	gi|2058544	putative ABC transporter subunit ComYA [Streptococcus gordonii]	88	78	978
 54	1	 3	 227	gnl|PID|d101320	YggU [Bacillus subtilis]	88	66	225
 57	2	 611	1468	putative reductase 1 [Saccharomyces cerevisiae]	88	75	858
 65	13 	5497	6069	pir|A29102|R5BS	ribosomal protein L5 - Bacillus stearothermophilus	88	75	5 73
 65	20 	9030	9500	gi|2078381	ribosomal protein L15 [Staphylococcus aureus]	88	83	471
 78	3	3636	1108	g nl|PID|d100781	lysyl-aminopeptidase [Lactococcus lactis]	88	80	2529 
106	12 	12965 	1205 4 	gi|2407215	(AF017421) putative heat shock protein HtpX [Streptococcus	88	72
					gor donii]
107	2	 2 19	962	gnl|PID|e339862	putative acylneuraminate lyase [Clostridium tertium]	88	75	744
111	8	14073 	10420 	gi|402363	RNA polymerase beta-subunit [Bacillus subtilis]	88	74	3654 
126	9	13096 	12062⠀‚	gnl|PID|e311468	unknown [Bacillus subtilis]	88	74	1035 
140	17 	19143 	18 874 	gi|1573659	H. influenzae predicted coding region HI0659 [Haemophilus	88	61	270
					influ enzae]
144	1	 3 94	555	gnl|PID|e274705	lactate oxidase [Streptococcus iniae]	88	75	162
148	4	2723	3493	gi|1 59672	phosphate transport system ATP-binding protein [Methanococcus	88	68
					jan naschii]
160	8	58 53	6278	gi|1773267	ATPase, epsilon subunit [Streptococcus mutans]	88	65	426
177	4	1770	2885	gi| 149426	putative [Lactococcus lactis]	88	72	1116 
211	6	4149	3613	gi|535273	aminopeptidase C [Streptococcus thermophilus]	88	74	528
231	4	 580	 957	gi|40186	homologous to E. coli ribosomal protein L27 [Bacillus subtilis]	88	78	378
260	5	2387	2998	g i|1196922	unknown protein [Insertion sequence IS861]	88	69	612
29 1	6	2017	3375	gnl|PID|d10057 1	adenylosuccinate synthetase [Bacillus subtilis]	88	75	1359 
319	4	 658	 317	gi|603578	serine/threonine kinase [Phytophthora capsici]	88	88	342
 40	5	4353	4514	gi|153672	lactose repressor [Streptococcus mutans]	87	56	162
 49	10 	10660 	10929⠀‚	gi|1196921	unknown protein [Insertion sequence IS861]	87	72	270
†‚65	7	3140	3808	gi|1165309	S3 [Bacillus subtilis]	87	73	669
 65	15 	6623	7039	gi|1044978	ribosomal protein S8 [Bacillus subtilis]	87	73	417
 75	8	5411	6625	gi|1877422	galactokinase [Streptococcus mutans]	87	78	1215 
 80	2	 703	2805	gnl|PID|d101166	elongation factor G [Bacillus subtilis]	87	76	2103 
 82	1	 541	 248	gi|1196921	unknown protein [Insertion sequence IS861]	87	69	294
14 0	23 	25033 	23897 	gn l|PID|e254999	phenylalany-tRNA synthetase beta subunit [Bacillus subtilis]	87	74	1137 
214	14 	10441 	85 16	gi|2281305	glucose inhibited division protein homolog GidA [Lactococcus lactis	87	75	1926 
					cremoris]
220	2	2742	  874	gnl|PID|e324358	product highly similar to elongation factor EF-G [Bacillus subtilis]	87	73	1869 
260	4	2096	2389	unknown protein [Insertion sequence IS861]	87	72	294
32 3	1	27	 650	gi|897795	30S ribosomal protein [Pediococcus acidilactici]	87	73	624
357	1	 154	 570	gi|1044978	ribosomal protein S8 [Bacillus subtilis]	87	73	417
 49	11 	10927 	1144 5 	gi|1196922	unknown protein [Insertion sequence IS861]	86	63	519
†‚59	12 	7461	9224	gi|95105 1	relaxase [Streptococcus pneumoniae]	86	68	1764 < /td>
 65	4	1553	2401	pir|A02759|R5BS	ribosomal protein L2 - Bacillus stearothermophilus	86	77	849
 65	23 	10957 	11610  	gi|44074	adenylate kinase [Lactococcus lactis]	86	76	654
 82	4	4374	4856	g i|153745	mannitol-specific enzyme III [Streptococcus mutans]	86	72	483
102	4	4270	4986	gnl |PID|e264705	OMP decarboxylase [Lactococcus lactis]	86	76	717
106	6	7824	6880	gnl |PID|e137598	aspartate transcarbamylase [Lactobacillus leichmannii]	86	68	945
107	1	 1	 273	gnl|PID|e339862	putative acylneuraminate lyase [Clostridium tertium]	86	71	273
111	7	10432 	6710	DNA-dependent RNA polymerase [Streptococcus pyogenes]	86	80	3723 
131	9	5704	4892	polipoprotein diacylglycerol transferase [Streptococcus mutans]	86	71	813
134	7	6430	7980	gi| 2388637	glycerol kinase [Enterococcus faecalis]	86	73	1551 
146	11 	7473	6583	gi|1591731	melvalonate kinase [Methanococcus jannaschii]	86	72	891
153	2	 595	2010	dipeptidase [Lactococcus lactis]	86	78	1416 
154	1	 2	1435	gi|1857246	6-phosphoglucon ate dehydrogenase [Lactococcus lactis]	86	74	1434 
161	5	5025	6284	gi|47529	Unknown [Streptococcus salivarius]	86	66	1260 < /td>
184	1	 2	1483	gi|642667	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	86	73	1482 
					[Streptococcus mutans]
210	8	365 9	6571	gi|153661	translational initiation factor IF2 [Enterococcus faecium]	86	76	2913 
250	1	 2	 187	gi|1573551	asparagine synthetase A (asnA) [Haemophilus influenzae]	86	68	186
 36	4	2644	3909	cell division protein [Enterococcus faecalis]	85	73	1266 
 38	4	2475	3587	gi|2058545	putative ABC transporter subunit ComYB [Streptococcus gordonii]	85	72	1113 
 38	5	3577	3915	gi|2058546	ComYC [Streptococcus gordonii]	85	80	339
 57	5	2797	3789	gnl|PID|d101316	YqfJ [Bacillus subtilis]	85	72	993
 82	5	4915	6054	gi|153746	mannitol-phosphate dehydrogenase [Streptococcus mutans]	85	68	1140 
 83	15 	14690 	15 793 	gi|143371	phosphoribosyl aminoimidazole synthetase (PUR-M) [Bacillus	85	69	11 04 
					subt ilis]
 87	2	141 7	2388	gi|1184967	ScrR [Streptococcus mutans]	85	69	972
108	3	2666	3154	gi| 153566	ORF (19K protein) [Enterococcus faecalis]	85	67	489
127	2	 312	 692	ribosomal protein S13 [Bacillus subtilis]	85	72	381
128	3	1534	2409	g i|1685110	tetrahydrofolate dehydrogenase/cyclohydrolase [Streptococcus	85	71
					the rmophilus]
137	7	2962	4767	gnl|PID|d100347	Na+ -ATPase alpha subunit [Enterococcus hirae]	85	74	1806 
170	2	2622	 709	(AB001488) FUNCTION UNKNOWN, SIMILAR PRODUCT IN E.	85	70	1914 
					COLI, H. INFLUENZAE AND NEISSERIA MENINGITIDIS.
					[Bacillus subtilis]
187	5	3 760	4386	gi|727436	putative 20-kDa protein [Lactococcus lactis]	85	65	627
233	2	 728	1873	g i|1163116	ORF-5 [Streptococcus pneumoniae]	85	67	1146 < /td>
234	3	 962	1255	gi|2293155	(AF008220) YtiA [Bacillus subtilis]	85	61	294
240	1	 309	1931	gi|143597	CTP synthetase [Bacillus subtilis]	85	70	1623 
6	1	 199	1521	gi|508979	GTP-binding protein [Bacillus subtilis]	84	72	1323 
 10	4	4375	3443	gnl|PID|e339862	putative acylneuraminate lyase [Clostridium tertium]	84	70	933
 14	1	63	2093	gi|520753	DNA topoisomerase I [Bacillus subtilis]	84	69	2031 
 19	4	1793	2593	gi|2352484	(AF005098) RNAseH II (Lactococcus lactis)	84	68	801
 20	17 	17720 	19687⠀‚	gnl|PID|d100584	cell division protein [Bacillus subtilis]	84	71	1968 
 22	28 	21723 	20884 	gi|299163	alanine dehydrogenase [Bacillus subtilis]	84	68	840
 30	10 	7730	6792	gnl|PID|d100296	fructokinase [Streptococcus mutans]	84	75	939
 33	9	5650	5300	g i|147194	phnA protein [Escherichia coli]	84	71	351
 36	22 	21551 	20772 	gi|310631	ATP binding protein [Streptococcus gordonii]	84	72	780
 48	4	2837	2505	gi|882609	6-phospho-beta-glucosidase [Escherichia coli]	84	69	333
 58	1	41	1516	gi|450849	amylase [Streptococcus bovis]	84	73	1476 
 59	10 	6715	7116	gi|951053	ORF10, putative [Streptococcus pneumoniae]	84	74	402
 62	1	21	 644	gi|806487	ORF211, putative [Lactococcus lactis]	84	66	624
 65	17 	7779	8207	ribosomal protein L18 [Bacillus subtilis]	84	73	429
 65	21 	9507	10397 	gi|44073	SecY protein [Lactococcus lactis]	84	68	891
106	4	5474	2262	gnl |PID|e199387	carbamoyl-phosphate synthase [Lactobacillus plantarium]	84	73	3213 < /td>
159	1	47	 4	gi|806487	ORF211; putative [Lactococcus lactis]	84	63	144
163	4	4690	5910	gi| 2293164	(AF008220) SAM synthase [Bacillus subtilis]	84	69	1221 
192	1	46	1308	gi|495046	tripeptidase [Lactococcus lactis]	84	73	1263 
348	1	 671	 6	gi|1787753	(AE000245) f346; 70 pct identical to 336 amino acids of	84	71	666
					ADH1_ZYMMO SW; F20368 but has 10 additional N-ter residues
					[ Escherichia coli]
3	4	1572	1375	gi|143766	(thrSv) (EC 6.1.1.3) [Bacillus subtilis]	83	65	2004 
9	6	3893	3417	gnl|PID|d10057 6	single strand DNA binding protein [Bacillus subtilis]	83	68	477
 17	15 	7426	8457	gi|520738	comA protein [Streptococcus pneumoniae]	83	66	1032 < /td>
 20	12 	13860 	gnl|PID|d100583	unknown [Bacillus subtilis]	83	61	285
 23	4	3358	2606	gi|1788294	(AE000290) o238; This 238 aa orf is 40 pct identical (5 gaps) to 231	83	74	753
					residues of an approx. 248 as protein YEBC_ECOLI SW; P24237
					[Es cherichia coli]
 28	6	330 4	3005	gi|1573659	H. influenzae predicted coding region HI0659 [Haemophilus influenzae]	83	57	300
 35	7	5108	3867	hypothetical nucleotide binding protein [Acholeplasma laidlawii]	83	63	1242 
 55	19 	17932 	17528 	gi|537085	ORF_f141 [Escherichia coli]	83	59	405
 55	20 	18539 	17919 	gi|496558	orfx [Bacillus subtilis]	83	69	621
 65	6	2795	3142	gi|1165308	L22 [Bacillus subtilis]	83	64	348
 68	6	6877	6683	gi|1213494	immunoglobulin A1 protease [Streptococcus pneumoniae]	83	54	195
 87	15 	15112 	14 771	gnl|PID|e323522	putative rpoZ protein [Bacillus subtilis]	83	54	342
 96	12 	8963	9631	gi|47394	5-oxoprolyl-peptidase [Streptococcus pyogenes]	83	73	669
 98	1	 3	 263	go|1183885	glutamine-bin ding subunit [Bacillus subtilis]	83	55	261
120	4	7170	5233	g i|310630	zinc metalloprotease [Streptococcus gordonii]	83	72	1938 
127	7	2998	4347	M. jannaschii predicted coding region MJ1665 [Methanococcus	83	72
					jannaschii]
137	1	 440	gi|472918	v-type Na-ATPase [Enterococcus hirae]	83	60	438
160	6	3466	4356	gi|1 773265	ATPase, gamma subunit [Streptococcus mutans]	83	67	891
214	4	2278	2964	gi| 663279	transposase [Streptococcus pneumoniae]	83	72	687
226	3	2367	2020	gi|142154	thioredoxin [Synechococcus PCC6301]	83	58	348
303	1	 3	1049	gi|40046	phosphoglucose isomerase A (AA 1-449) [Bacillus	83	67	10 47 
					stea rothermophilus]
303	2	1155	1931	gi|289282	glutamyl-tR NA synthetase [Bacillus subtilis]	83	67	777
6	17 	15370 	14318 	gi |633147	ribose-phosphate pyrophosphokinase [Bacillus caldolyticus]	82	64	1053†‚
7	1	 299	96	gi|143648	ribosomal protein L28 [Bacillus subtilis]	82	69	204
9	3	1479	1090	gi|385178	unknown [Bacillus subtilis]	82	46	390
9	7	4213	3899	gnl|PID|d10057 6	ribosomal protein S6 [Bacillus subtilis]	82	60	315
 12	6	4688	3942	gnl|PID|d100571	unknown [Bacillus subtilis]	82	68	747
 22	17 	13422 	1483 7 	gi|520754	putative [Bacillus subtilis]	82	69	1416 
 22	18 	14897 	15658 	gnl|PID|d101929	uridine monophosphate kinase [Synechocystis sp.]	82	62	762
 3 3	16 	11471 	10641 	gn l|PID|d101190	ORF4 [Streptococcus mutans]	82	68	831
 35	9	7400	6255	g i|1881543	UDP-N-acetylglucosamine-2-epimerase [Streptococcus pneumoniae]	82	68	1146 < /td>
 40	10 	8003	75 33	gi|1173519	riboflavin synthase beta subunit [Actinobacillus pleuropneumoniae]	82	68	47 1
 48	32 	23159 	23437 	gi|1930092	outer membrane protein [Campylobacter jejuni]	82	61	279
 52	14 	13833 	14765⠀‚	gi|142521	deoxyribodipyrimidine photolyase [Bacillus subtilis]	82	61	933
 60	4	4737	1849	gnl|PID|d102221	(AB001610) urvA [Deinococcus radiodurans]	82	66	2889 
 62	4	2131	1457< /td>	gi|2246749	(AF009622) thioredoxin reductase (Listeria monocytogenes]	82	63	675
 71	11 	16586 	17518 	gnl|PID|e322063	ss-1,4-galactosylt ransferase [Streptococcus pneumoniae]	82	60	933
 73	13 	9222	7837	gnl|PID|d100586	unknown [Bacillus subtilis]	82	65	1386 
 74	1	 1	3771	gnl|PID|d101199	alkaline amylopullulanase [Bacillus sp.]	82	68	3771 
 83	9	3696	3983	gnl|PID|e3 05362	unnamed protein product [Streptococcus thermophilus]	82	52	288
 86	13 	10776 	9394	gi|683583	5-enolpyruvylshikimate-3-phos phate synthase [Lactococcus lactis]	82	67	1383 
 89	12 	8295	9752	gi|40025	homologous to E. coli 50K [Bacillus subtilis]	82	66	1458 
115	9	10347 	8812	gnl|PID|d102090	(AV003927) phospho-beta-galactosidase [Lactobacillus gasseri]	82	74	1536 
118	1	 1	1332	gnl|PID|d100579	seryl-tRNA synthetase [Bacillus subtilis]	82	71	1332 
151	1	4657	6246	type I site-specific deoxyribonuclease (EC 3.1.21.3) CfrA chain S -	82	66	1590 
				Citrobacter freundii
173	6	41 83	3503	gi|2313836	(AE000584) conserved hypothetical protein [Helicobacter pylori]	82	68	681
177	12 	5481	7442	gnl|PID|d101999	(AV001341) NcrB [Escherichia coli]	82	58	1962 
193	2	 178	 576	ribosomal protein S9 - Bacillus stearothermophilus	82	70	399
245	2	 258	 845	EcoA type I restriction-modification enzyme S subunit [Escherichia	82	68	588
					coli< /i>]
9	5	3400	3146	gnl|PID|d10057 6	ribosomal protein S18 [Bacillus subtilis]	81	66	255
 16	7	7484	8413	gi|1100074	tryptophanyl-tRNA synthetase [Clostridium longisporum]	81	70	930
 20	11 	10308 	1 3820 	gnl|PID|d100583	transcription-repair coupling factor [Bacillus subtilis]	81	63	3513 
 38	2	1232	1606	gi|2058543	putative DNA binding protein [Streptococcus gordonii]	81	63	375
 45	2	3061	1751	gi|460259	enolase [Bacillus subtilis]	81	67	1311 
 46	1	 2	1267	gi|431231	uracil permease [Bacillus caldolyticus]	81	61	1266†‚
 48	3	2453	1440	gnl|PID|d100453	Mannosephosphate Isomerase [Streptococcus mutans]	81	70	1014 
 54	2	1106	 336	gi|154752	transport protein [Agrobacterium tumefaciens]	81	64	771
 65	22 	10306 	1 0821 	gi|44073	SecY protein [Lactococcus lactis]	81	66	516
 89	4	3874	2603	g i|556886	Sering hydroxymethyltransferase [Bacillus subtilis]	81	69	1272 
 99	16 	19126 	18929 	gi|2313526	(AE000557) H. pylori predicted coding region HP0411 [Helicobacter	81	75
					pylo ri]
106	7	8373	7822	gnl|PID|e199384	pyrR [Lactobacillus plantarum]	81	61	552
108	6	5054	6877	gi|1469939	group B oligopeptidase PepB [Streptococcus agalactiae]	81	66	1824 < /td>
113	15 	15899 	18283 	pir|S09411|S094	spoIIIE protein - Bacillus subtilis	81	65	2385 
128	5	3359	3634	orf1091 [Streptococcus thermophilus]	81	69	276
151	1	 830	3211	gi|304896	EcoE type I restriction-modification enzyme R subunit [Escherichia	81	59	2382 
					c oli]
159	11 	67 22	7837	gi|2239288	GMP synthetase [Bacillus subtilis]	81	69	1116 
170	1	 739	 458	gnl|PID|d102006	(AB001488) FUNCTION UNKNOWN [Bacillus subtilis]	81	55	282
191	2	1759	 893	gi|149522	tryptophan synthase alpha subunit [Lactococcus lactis]	81	65	867
214	3	2290	1994	gi| 157587	reverse transcriptase endonuclease [Drosophila virilis]	81	43	297
217	4	4415	4008	gi |466473	cellobiose phosphotransferase enzyme II′ [Bacillus	81	59	40 8
					stearoth ermophilus]
262	2	 569	 868	gi|153675	tagatose 6-P kinase [Streptococcus mutans]	81	68	300
299	1	 663	 4	gnl|PIDp51 e301154	StySKI methylase [Salmonella enterica]	81	60	660
366	2	 376	83	gi|149521	tryptophan synthase beta subunit [Lactococcus lactis]	81	65	294
 12	10 	8766	9242	DNA/pantothenate metabolism flavoprotein [Streptococcus mutans]	80	64	477
 17	11 	6050	5748	unnamed protein product [Streptococcus thermophilus]	80	67	303
 17	16 	8455	9066	gi|703126	leucocin A translocator [Leuconostoc gelidum]	80	59	612
 18	3	2440	1613	gi|1591672	phosphate transport system ATP-binding protein [Methanococcus	80	58
					jan naschii]
 27	3	4248	1579	gi|452309	valyl-tRNA synthetase [Bacillus subtilis]	80	69	2670 
 28	7	3671	3288	gi|1573660	H. influenzae predicted coding region HI0660 [Haemophilus	80	63	384
					influ enzae]
 32	2	†‚902	1933	gnl|PID|e264499	dihydrooro tate dehydrogenase B [Lactococcus lactis]	80	66	1032 
 39	1	 	1266	gnl|PID|e2340478	hom [Lactococcus lactis]	80	63	1266 
 52	5	4363	3593	ATP-binding subunit [Bacillus subtilis]	80	57	771
 54	5	4550	4744	gi|2198820	(AF004225) Cux/CDP(1B1); Cus/CDP homeoprotein [Mus musculus]	80	60	195
 59	11 	7109	7486	gi|951052	ORF9, putative [Streptococcus pneumoniae]	80	68	378
 65	3	1230	1550	ribosomal protein L23 - Bacillus stearothermophilus	80	69	3 21
 65	12 	5174	5503	pir|A02819|R5BS	ribosomal protein L24 - Bacillus stearothermophilus	80	70	3 30
 66	9	9884	106 87 	gi|2313836	(AE000584) conserved hypothetical protein [Helicobacter pylori]	80	66	804
 82	2	 648	2438	gi|622991	mannitol transport protein [Bacillus stearothermophilus]	80	65	1791 
 85	1	 950	 630	gi|528995	polyketide synthase [Bacillus subtilis]	80	46	321
 89	8	6870	5779	gi|853776	peptide chain release factor 1 [Bacillus subtilis]	80	63	1092 
 93	12 	8718	7438	gnl|PID|d101959	hypothetical protein [Synechocystis sp.]	80	60	1281 
106	5	6854	5751	gnl|PID|e199 386	glutaminase of carbomoyl-phosphate synthase [Lactobacillus	80	65
					plantarum]
109	2	2160	1450	gi|40056	phoP gene product [Bacillus subtilis]	80	59	711
124	9	4246	3953	g nl|PID|d102254	30S ribosomal protein S16 [Bacillus subtilis]	80	65	294
128	8	5148	6428	g i|2281308	phosphopentomutase [Lactococcus lactis cremoris]	80	66	1281 
337	19 	12665 	11 376 	gi|159109	NADP-dependent glutamate dehydrogenase [Glardia intestinalis]	80	68	1290†‚
140	19 	19699 	gi|517210	putative transposase [Streptococcus pyogenes]	80	70	243
158	2	2474	 984	gi|1877423	galactose-1-P-uridyl transferase [Streptococcus mutans]	80	65	1491 
171	10 	7474	7728	gi|397800	cyclophilin C-associated protein [Mus musculus]	80	60	255
181	1	 2	 619	gi|149395	lacC [Lactococcus lactis]	80	66	618
313	1	27	 539	gi|143467	ribosomal protein S4 [Bacillus subtilis]	80	80	513
329	2	1652	 858	gi|533080	RecF protein [Streptococcus pyogenes]	80	63	795
371	1	 2	 958	gi|442360	ClpC adenosine triphosphates [Bacillus subtilis]	80	58	957
8	7	4312	5580	gi|149435	putative [Lactococcus lactis]	79	64	1269 
 23	1	1175	 135	gi|1542975	AbcB [Thermoanaerobacterium thermosulfurigenes]	79	61	1041 
 33	14 	9244	8201	gnl|PID|e253891	UDP-glocuse 4-epimerase [Bacillus subtilis]	79	62	1044 
 36	3	1242	2633	gnl|PID|e324218	ftsA [Enterococcus hirae]	79	58	1392 
 38	13 	7155	8378	gi|405134	acetate kinase [Bacillus subtilis]	79	58	1224 
 55	7	9011	8229	gi|1146234	dihydroipicolinate reductase [Bacillus subtilis]	79	56	783
 65	19 	8661	8915	gi|2078380	ribosomal protein L30 [Staphylococcus aureus]	79	68	255
 69	4	3678	2128	g nl|PID|e311452	unknown [Bacillus subtilis]	79	64	1551 
 69	9	7881	7279	gi|677850	hypothetical protein [Staphylococcus aureus]	79	59	603
 72	10 	8491	9783	hypothetical protein [Synechocystis sp.]	79	62	1293 
 80	3	2906	7300	gi|143342< /td>	polymerase III [Bacillus subtilis]	79	65	4395 
 82	14 	13326 	15689 	gnl|PID|e255093	hypothetical protein [Bacillus subtilis]	79	65	2364 
 86	13 	12233 	11118 	gi|683582	prephenate dehydrogenase [Lactococcus lactis]	79	58	1116 
 92	3	 940	1734	gi|537286	triosephosphate isomerase [Lactococcus lactis]	79	65	795
 98	6	4023	4742	g nl|PID|d100262	LivG protein [Salmonella typhimurium]	79	63	720
 99	12 	16315 	1 4150 	gi|153736	a-galactosidase [Streptococcus mutans]	79	64	2166 
107	7	5684	6406	gi|460080	D-alanine:D-alanine ligase-related protein [Enterococcus faecalis]	79	58	723
113	9	6858	8303	g i|466882	ppsl; B1496_C2_189 [Mycobacterium leprae]	79	64	1446 
151	10 	13424 	1221 3 	gi|450686	3-phosphoglycerate kinase [Thermotoga maritima]	79	60	1212 
162	2	1158	3017	CapD [Staphylococcus aureus]	79	67	1860 
177	5	2876	3052	gi|912423	putative [Lactococcus lactis]	79	61	177
177	8	4198	4563	gi| 149429	putative [Lactococcus lactis]	79	61	366
187	3	2728	2907	gnl |PID|d102002	(AB001488) FUNCTION UNKNOWN [Bacillus subtilis]	79	53	180
189	7	3589	4350	g nl|PID|e183449	putative ATP-binding protein of ABC-type [Bacillus subtilis]	79	61	762
191	5	4249	3449	g i|149519	indoleglycerol phosphate synthase [Lactococcus lactis]	79	66	801
211	3	1805	2737	gi| 147404	mannose permease subunit II-M-Man [Escherichia coli]	79	57	933
212	3	3863	3621	gnl|P ID|e209004	glutaredoxin-like protein [Lactococcus lactis]	79	58	243
215	1	 987	 715	gi|1183242	(AF008220) arginine succinate synthase [Bacillus subtilis]	79	64	273
323	2	 530	 781	30S ribosomal protein [Pedicoccus acidilactici]	79	67	252
380	1	 694	 2	gi|1184680	polynucleotide phosphorylase [Bacillus subtilis]	79	64	693
384	2	 655	 239	phoP protein (put.); putative [Bacillus subtilis]	79	59	417
6	3	2820	4091	gi|853767	UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus	78	62	12 72 
					subt ilis]
8	1	50	1786	gi|149432	putative [Lactococcus lactis]	78	63	1737 
9	1	 351	 124	gi|897793< /td>	y98 gene product [Pediococcus acidilactici]	78	59	228
 15	8	7364	8314	gnl|PID|d100585	cystein synthetase [Bacillus subtilis]	78	63	951
 20	10 	9783	10310 	gnl|PID|d100583	stage V sporulation [Bacillus subtilis]	78	58	573
 20	16 	17165 	1771 3 	gi|49105	hypoxanthine phosphoribosyltransferase [Lactococcus lactis]	78	59	549
 22	22 	17388 	18416⠀‚	gnl|PID|d101315	Ygfe [Bacillus subtilis]	78	60	1029 
 22	27 	20971 	20612 	gi|299163	alanine dehydrogenase [Bacillus subtilis]	78	59	360
 34	8	7407	7105	gi|41015	aspartate-tRNA ligase [Escherichia coli]	78	55	303
 35	8	6257	5196	gi| 1657644	Cap8E [Staphylococcus aureus]	78	60	1062 
 40	11 	9287	8001	gi|1173518	GTP cyclohydrase II 3,4-dihydroxy-2-butanone-4-phosphate	78	58	1287 
					syn thase [Actinobacillus pleuropneumoniae]
 48	3 1 	22422 	23183 	gi|2314330	(AE000623) glutamine ABC transporter, ATP-binding protein (glnQ)	78	58	762
< td/>				[Helicobacter pylori]
 52	2	2 101	1430	gi|1183887	integral membrane protein [Bacillus subtilis]	78	54	672
 55	14 	13605 	1271 2 	gnl|PID|d102026	(AB002150) YbbP [Bacillus subtilis]	78	58	894
 55	17 	16637 	1561 2 	gnl|PID|e313027	hypothetical protein [Bacillus subtilis]	78	51	1026 
 71	14 	19756 	19598 	gi|179764	calcium channel alpha-1D subunit [Homo sapiens]	78	57	159
 74	11 	15031 	14018  	gi|1573279	Holliday junction DNA helicase (rubB) [Haemophilus influenzae]	78	57	1014 < /td>
 75	9	6623	7972	gi|1877423	galactose-1-P-uridyl transferase [Streptococcus mutans]	78	62	1350 
 81	12 	12125 	13 906 	gi|1573607	L-fucose isomerase (fucI) [Haemophilus influenzae]	78	66	1782 < /td>
 82	3	2423	4417	gi|153744	ORF X; putative [Streptococcus mutans]	78	64	1995 
 83	18 	16926 	18 500 	gi|143373	phosphoribosyl aminoimidazole carboxy formyl	78	63	1575 
				formyltransferase/inosine monophosphate cyclohydrolase (PUR-H(J))
					[< i>Bacillus subtilis]
 83	20 	20212 	20775 	gi|143364	pho sphoribosyl aminoimidazole carboxylase I (PUR-E) [Bacillus	78	64	56 4
					subtilis ]
 92	2	 165< /td>	 878	gnl|PID|d101190	ORF2 [Streptococcus mutans]	78	62	714
 98	8	5863	6909	g i|2331287	(AF013188) release factor 2 [Bacillus subtilis]	78	63	1047 
113	3	1071	2741	dnaZX [Bacillus subtilis]	78	64	1671 
127	4	1133	2071	RNA polymerase alpha-core-subunit [Bacillus subtilis]	78	59	939
132	1	2782	 497	gi|1561763	pullulanase [Bacteroides thetaiotaomicron]	78	58	22 86 
135	4	2698	35 37	gi|1788036	(AE000269) NH3-dependent AND synthetase [Escherichia coli]	78	66	840
140	24 	26853 	25423 	gi|1100077	phospho-beta-glucosidase [Clostridium longisporum]	78	64	1431 
150	5	4690	4514	gi|149464	amino peptidase [Lactococcus lactis]	78	42	177
152	1	 1	 795	gi|639915	NADH dehydrogenase subunit [Thunbergia alata]	78	43	795
162	4	4997	4110	gnl| PID|e323528	putative YhaP protein [Bacillus subtilis]	78	64	888
181	10 	8651	7947	lactose repressor (lacR; alt.) [Lactococcus lactis]	78	48	705
200	4	3627	4958	gnl |PID|d100172	invertase [Zymomonas mobilis]	78	61	1332 
203	3	3230	3015	CycK [Pseudomonas fluorescens]	78	57	216
210	9	6789	7172	ORF6 gene product [Bacillus subtilis]	78	42	384
214	6	3810	2797	g nl|PID|d102049	P. haemolytica o-sialoglycoproptein endopeptidase; P36174 (660)	78	60	1014 
					transmembrane [Bacillus subtilis]
214	13 	8163	gi|1377831	unknown [Bacillus subtilis]	78	62	1842 
217	1	 9	2717	gi|488430	alcohol dehydrogenase 2 [Entamoeba histolytica]	78	64	2709 
222	3	2316	3098	gi|15733047	spore gemination and vegetative growth protein (gerC2)	78	65	783
					[Haemophilus influenzae]
268	1	 742	 8	gi|517210	putative transposase [Streptococcus pyogenes]	78	65	735
276	1	 223	 753	ribosomal protein L1 [Bacillus subtilis]	78	65	531
312	3	1567	1079	g i|289261	comE ORF2 [Bacillus subtilis]	78	54	489
339	1	 117	 794	CadD [Staphylococcus aureus]	78	53	678
342	2	 762	 265	gi|1842439	phosphatidylglycerophosphate synthase [Bacillus subtilis]	78	59	498
383	1	 737	 3	gi|1184680	polynucleotide phosphorylase [Bacillus subtilis]	78	64	735
7	15 	11923 	11018 	gi |1399855	carboxyltransferase beta subunit [Synechococcus PCC7942]	77	63	906
8	2	1698	2255	gi|149433	putative [Lactococcus lactis]	77	59	558
 17	14 	6948	7550	comA protein [Streptococcus pneumoniae]	77	60	603
 30	12 	9761	8967	gi|1000451	TreP [Bacillus subtilis]	77	43	795
 36	14 	11421 	1213 1 	gi|1573766	phosphoglyceromutase (gpmA) [Haemophilus influenzae]	77	64	711
 55	3	3836	4096	YeaB [Bacillus subtilis]	77	55	261
 61	8	8377	8054	gi|1890649	multidrug resistance protein LmrA [Lactococcus lactis]	77	51	324
 65	2	 607	1254	gi|40103	ribosomal protein L4 [Bacillus stearothermophilus]	77	63	648
 68	8	7509	72 40	gi|47551	MRP [Streptococcus suis]	77	68	270
 69	1	1083	 118	g nl|PID|e311493	unknown [Bacillus subtilis]	77	57	966
 77	5	4583	4026	gnl|PID51 e281578	hypothetical 12.2 kd protein [Bacillus subtilis]	77	60	558
 83	14 	13104 	1455 2 	gi|1590947	amidophosphoribosyltransfera se [Methanococcus jannaschii]	77	56	1449
 94	4	3006	5444	gnl|PID|e329895	(AJ000496) cyclic nucleotide-gated channel beta subunit [Rattus	77	66	2439
					norvegicu s]
 96	11 	85 18	8880	gi|551879	ORF 1 [Lactococcus lactis]	77	62	363
 99	11 	14082 	12799⠀‚	gi|153737	sugar-binding protein [Streptococcus mutans]	77	61	1284 
106	2	 361	1176	LicD protein [Haemophilus influenzae]	77	51	816
108	4	3152	4030	gi|1574730	tellurite resistance protein (tehB) [Haemophilus influenzae]	77	58	879
118	4	3520	3131	gi|1573900	D-alanine permease (dagA) [Haemophilus influenzae]	77	57	390
124	4	1796	1071	gi|1573162	tRNA (guanine-N1)-methyltransferase (trmD) [Haemorphilus	77	58
					infl uenzae]
126	4	590 9	4614	gnl|PID|d101163	Srb [Bacillus subtilis]	77	62	1296 
128	2	 630	1373	gnl|PID|d101328	YqiZ [Bacillus subtilis]	77	58	744
130	1	 1	1287	gnl|PID|e325013	hypothetic al protein [Bacillus subtilis]	77	61	1287 
139	5	4388	3639	(AF008220) YtqA [Bacillus subtilis]	77	59	750
140	11 	10931 	9582	gi|289284	cysteinyl-tRNA synthetase [Bacillus subtilis]	77	64	1350 
140	18 	19451 	19 263 	gi|517210	putative transposase [Streptococcus pyogenes]	77	66	189
141	2	 976	1683	gnl|PID|e157887	URF5 (aa 1-573) [Drosophila yakuba]	77	50	708
141	4	2735	5293	gi| 556258	secA [Listeria monocytogenes]	77	59	2559⠀‚
144	2	 671	217 3	gnl|PID|d100585	lysyl-tRNA thynthetase [Bacillus subtilis]	77	61	1503 
163	5	6412	7398	dihydroorotate dehydrogenase A [Lactococcus lactis]	77	62	987
164	10 	7841	7074	gni|PID|d100964	homologue of iron dicitrate transport ATP-binding protein FecE of	77	52	768
					E. coli [Bacillus subtilis]
191	8	7 257	5791	gi|149516	anthranilate synthase alpha subunit [Lactococcus lactis]	77	57	1467 
198	8	5377	5177	gi|1573856	hypothetical [Haemophilus influenzae]	77	66	201
213	1	 202	 462	gi|1743860	Brac2 ]Mus musculus]	77	50	261
250	2	 231	 509	YlbH protein [Bacillus subtilis]	77	60	279
289	3	1737	1276	g nl|PID|d100947	Ribosomal Protein L10 [Bacillus subtilis]	77	62	462
292	2	1399	 668	gi|143004	transfer RNA-Gln synthetase [Bacillus stearothermophilus]	77	58	732
7	3	2734	1166	gnl|PID|d10182 4	peptide-chain-release factor 3 [Synechocystis sp.]	76	53	1569 
7	23 	18474 	18235 	gi |455157	acyl carrier protein [Crypotomas phi]	76	57	240
9	8	5706	4342	gi|1146247	asparaginyl-tRNA synthetase [Bacillus subtilis]	76	61	1365 
 10	5	4531	4385	gnl|PID|e314495	hypothetical protein [Clostridium perfringens]	76	53	147
 18	2	1615	 842	gi|1591672	phosphate transport system ATP-binding protein [Methanococcus	76	56
					jan naschii]
 22	37 	27796 	28173 	gnl|PID|e13389	translation initiation factor IF3 (AA 1-172) [Bacillus	76	64	37 8
					stearoth ermophilus]
 35	6	2682	gi|1773346	Cap5G [Staphylococcus aureus]	76	61	1188 
 48	28 	21113 	21 787 	gi|2314328	(AE000623) glutamine ABC transporter, permease protein (glnP)	76	52	675
< td/>				[Helicobacter pylori]
 52	12 	13786 	gi|142521	deoxy ribodipyrimidine photolyase [Bacillus subtilis]	76	58	906
 55	10 	11521 	1057 1 	gnl|PID|e283110	femD [Staphylococcus aureus]	76	61	951
 57	8	7824	6559	g i|290561	o188 [Escherichia coli]	76	47	1266 
 62	5	2406	2095	gnl|PID|e313024	hypothetical protein [Bacillus subtilis]	76	59	312
 65	9	4223	4441	gi|40148	L29 protein (AA 1-66) [Bacillus subtilis]	76	58	219
 68	2	1328	2371	gnl|PID|e284233	anabolic ornithine carbamoyltransferase [Lactobacillus plantarum]	76	61	1044 
 69	8	7297	6005	gnl|PID|d101420	Pyrimidine nucleoside phosphorylase [Bacillus stearothermophilus]	76	61	1293 
 73	12 	7839	7267	gnl|PID|e243629	unknown [Mycobacterium tubercolosis]	76	53	573
 74	5	8433	7039	gnl|PID|d102048	C. thermocellum beta-glucosidase; P2208 (985) [Bacillus subtilis]	76	60	1395 
 80	5	7643	7936	gi|2314030	(AE000599) conserved hypothetical protein [Helicobacter pylori]	76	61	294
 82	15 	16019 	16996⠀‚	gi|1573900	D-alanine permease (dagA) [Haemophilus influenzae]	76	56	978
 83	19 	18616 	19 884 	gi|143374	phosphoribosyl glycinamide synthetase (PUR-D; gtg start condon)	76	60	1269 
				[Bacillus subtilis]
 86	14 	13409 	12231 	gi|143806	Aro F [Bacillus subtilis]	76	58	1179 
 87	1	 3	1442	gi|153804	sucrose-6-phosph ate hydrolase [Streptococcus mutans]	76	59	1440 
 87	16 	15754 	15 110 	gnl|PID|e323500	putative Gmk protein [Bacillus subtilis]	76	56	645
 93	4	1769	1539	gi|1574820	1,4-alpha-glucan branching enzyme (glgB) [Haemophilus influenzae]	76	46	231
 94	1	51	 365	gi|144313	6.0 kd ORF [Plasmid ColE1]	76	73	315
11 6	2	2151	1678	gi|153841	pneumococcal surface protein A [Streptococcus pneumoniae]	76	59	474
123	6	3442	5895	gi|1314297	ClpC ATPase [Listeria monocytogenes]	76	59	2454⠀‚
126	2	2156	2932< /td>	gnl|PID|d101328	YqiZ [Bacillus subtilis]	76	61	777
128	10 	6973	7797	purine nucleoside phosphorylase [Bacillus subtilis]	76	60	825
131	11 	6186	5812	(AE000058) Mycoplasma pneumoniae, MG085 homolog, from	76	47	375
					M. genitalium [Mycoplasma pneumoniae]
139	4	3641	3192	gi|2293302	(AF008220) YtgA [Bacillus subtilis]	76	53	450
140	14 	14872 	12536⠀‚	gi|1184680	polynucleotide phosphorylase [Bacillus subtilis]	76	62	2337 
143	2	2583	3905	transfer RNA-Tyr synthetase [Bacillus subtilis]	76	61	1323 
170	6	5095	6114	ycgQ [Bacillus subtilis]	76	44	1020 
180	2	1927	 557	gi|40019	ORF 821 (aa 1-821) [Bacillus subtilis]	76	53	1371 
191	7	5815	5228	anthranilate synthase beta subunit [Lactococcus lactis]	76	61	588
195	3	3829	2444	gi| 2149905	D-glutamic acid adding enzyme [Enterococcus faecalis]	76	60	1386 
200	3	1914	3629	lysis protein [Bacillus subtilis]	76	58	1716 
201	1	 431	 207	gi|2208998	dextran glucosidase DexS [Streptococcus suis]	76	57	225
214	2	1283	2380	gi|55 3278	transposase [Streptococcus pneumoniae]	76	55	1098 < /td>
225	3	2338	3411	gi|1552775	ATP-binding protein [Escherichia coli]	76	56	1074 
233	1	 2	 724	gi|1163115	neuraminidase B [Streptococcus pneumoniae]	76	60	723
347	1	 523	38	gi|537033	ORF_f356 [Escherichia coli]	76	60	486
356	2	 842	 165	g i|2149905	D-glutamic acid adding enzyme [Enterococcus faecalis]	76	61	678
366	3	 734	 348	phosphoribosyl anthranilate isomerase [Lactococcus lactis]	76	69	387
5	8	12599 	11484 	gi|157 4293	fimbrial transcription regulation repressor (pilB) [Haemophilus	75	61	1116 
					i nfluenzae]
6	13 	12553 	11894 	gn l|PID|d102050	ydiH [Bacillus subtilis]	75	51	660
9	10 	7282	6062	gi|142538< /td>	aspartate aminotransferase [Bacillus sp.]	75	55	1221 
 10	12 	8080	7940	gi|149 493	SCRFI methylase [Lactococcus lactis]	75	56	141
 18	5	4266	3301	g nl|PID|d101319	YqgH [Bacillus subtilis]	75	52	966
 22	4	1838	2728	gi|1373157	orf-X; hypothetical protein; Method: conceptual translation supplied	75	62	891
					by author [Bacillus subtilis]
 30	11 	9015	7828	gi|153801	enzyme scr-II [Streptococcus mutans]	75	64	1188 
 31	5	2362	2030	(AF008220) putative thioredoxin [Bacillus subtilis]	75	53	333
 32	9	7484	8359	gnl|PID|d100560	formamidopyrimidine-DNA glycosylase [Streptococcus mutans]	75	61	876
 33	4	1735	1448	g i|413976	ipa-52r gene product [Bacillus subtilis]	75	53	288
 33	10 	6470	5769	gi|533105	unknown [Bacillus subtilis]	75	56	702
 33	12 	6878	7183	pir|A00205|FECL	ferredoxin [4Fe-4S] - Clostridium thermaceticum	75	56	306
 36	1	 181	 2	gi|2088739	(AF003141) strong similarity to the FABP/P2/CRBP/CRABP family	75	43	180
< td/>				of transporters [Caenorhabditis elegans]
 38	22 	14510 	15379 	gi|1574058	hyp othetical [Haemophilus influenzae]	75	56	870
 48	33 	23398 	24 066 	gi|1930092	outer membrane protein [Campylobacter jejuni]	75	56	669
 51	1	 2	 319	gi|43985	nifS-like gene [Lactobacillus delbrueckii]	75	55	318
 51	10 	8318	11683  	gi|537192	CG Site No. 620; alternate gene names hs, hsp, hsr, rm; apparent	75	50	3366 
					frameshift in GenBank Accession Number X06545 [Escherichia coli]
 54	18 	19566 	20759 	gi|666069	orf2 gene product [Lactobacillus leichmannii]	75	58	1194 
 57	9	8448	7822< /td>	gi|290561	o188 [Escherichia coli]	75	50	627
 65	14 	6072	6356	gi|606241	30S ribosomal subunit protein S14 [Escherichia coli]	75	64	285
 70	4	3071	2472	gi| 1256617	adenine phosphoribosyltransferase [Bacillus subtilis]	75	57	600
 71	24 	30399 	2940 4 	gi|1574390	C4-dicarboxylate transport protein [Haemophilus influenzae]	75	57	996
 73	2	 910	 455	gnl|PID|e249656	YneT [Bacillus subtilis]	75	57	456
 79	1	1810	 491	28.2% of identity to the Escherichia coli GTP-binding protein Era;	75	59	1320 
					putative [Bacillus subtilis]
 82	5	6360	6536	gi|1655715	BztD [Rhodobacter capsulatus]	75	55	177
 83	6	1938	2975	putative PlsX protein [Bacillus subtilis]	75	56	1038 
 93	11 	7368	5317	gi|39989	methionyl-tRNA synthetase [Bacillus stearothermophilus]	75	58	2052 
 93	13 	9409	8699	gi|1591493	glutamine transport ATP-binding protein Q [Methanococcus	75	54
					jan naschii]
 95	1	1795	 47	gnl|PID|e323510	Ylov protein [Bacillus subtilis]	75	57	1749 
103	2	 362	1186	gnl|PID|e266928	unknown [Mycobacterium tuberculosis]	75	64	825
104	1	 691	 915	gi|460026	repressor protein [Streptococcus pneumoniae]	75	54	225
113	5	2951	3883	gnl|PID|d101119	ABC transporter subunit [Synechocystis sp.]	75	55	933
121< /td>	1	 320	1390	gi|2145131	repressor of class I heat shock gene expression HrcA [Streptococcus	75	58
					mutans]
127	6	26 14	3000	gi|1500451	M. jannaschii predicted coding region MJ1558 [Methanococcus	75	44
					jan naschii]
137	18 	10687 	gi|393116	P-glyc oprotein 5 [Entamoeba histolytica]	75	52	606
149	11 	8499	9338	gnl|PID|d100582	unknown [Bacillus subtilis]	75	55	840
151	6	9100	7673	g i|40467	HsdS polypeptide, part of CfrA family [Citrobacter freundii]	75	57	1428 
158	1	 986	 3	gnl|PID|e253891	UDP-glucose 4-epimerase [Bacillus subtilis]	75	63	984
172	8	5653	6774	g i|142978	glycerol dehydrogenase [Bacillus stearothermophilus]	75	56	1122 
172	9	7139	9730	gnl|PID|e268456	unknown [Mycobacterium tuberculosis]	75	58	2592†‚
173	1	 261	79	gnl|PID|e236469	C10C5.6 [Caenorhabditis elegans]	75	50	183
185	3	3066	2014	gi |1574806	spermidine/putrescine transport ATP-binding protein (potA)	75	56	1053 
				[Haemophilus influenzae]
191	6	5235	4213	gi|149518	phosphoribosyl anthranilate transferase [Lactococcus lactis]	75	61	1023 
226	2	1774	1181	gi|2314588	(Ae000642) conserved hypothetical protein [Helicobacter pylori]	75	65	594
231	1	 1	 153	gi|40173	homolog of E. coli ribosomal protein L21 [Bacillus subtilis]	75	57	153
234	1	 2	 418	gi|2293259	(AF008220) YtqI [Bacillus subtilis]	75	59	417
279	1	 552	 151	unknown protein [Bacillus subtilis]	75	50	402
291	7	3558	3827	g i|40011	ORF17 (AA 1-161) [Bacillus subtilis]	75	48	270
375	2	 137	628	gi|410137	ORFX13 [Bacillus subtilis]	75	58	492
6	20 	16721 	17560 	gi |2293323	(AF008220) YtdI [Bacillus subtilis]	74	53	840
7	6	4682	6052	gi|1354211	PET112-like protein [Bacillus subtilis]	74	60	1371 
 18	4	3341	2427	gnl|PID|d101319	YqgI [Bacillus subtilis]	74	54	915
 21	6	5885	4800	gi|1072381	glutamyl-aminopeptidase [Lactococcus lactis]	74	59	1086 
 24	2	 739	 548	gi|2314762	(AE000655) ABC transporter, permease protein (yaeE) [Helicobacter	74	46
					pylori]
 25	1	 2	 367	gnl|PID|d100932	H2O-form ing NADH Oxidase [Streptococcus mutans]	74	63	366
 38	18 	11432 	12964⠀‚	gi|537034	ORF_o488 [Escherichia coli]	74	57	1533 
 48	10 	8924	6669	gi|1513069	P-type adenosine triphosphatase [Listeria monocytogenes]	74	53	2256⠀‚
 55	11 	11964 	11401 	gnl|PID|e283110	femD [Staphylococcus	74	64	564
					au reus]
 61	2	178 2	 427	gi|2293216	(AF008220) putative UDP-N-acetylmuramate-alanine ligase [Bacillus	74	55	13 56 
					subt ilis]
 76	10 	9414	8065	gnl|PID|d101325	YaiB [Bacillus subtilis]	74	54	1350 
 83	2	 666	 926	pir|C33496|C334	hisC homolog - Bacillus subtilis	74	55	261
 86	9	8985	8080	gi|683585	prephenate dehydratase [Lactococcus lactis]	74	55	906
102	5	5005	5652	gi| 143394	OMP-PRPP transferase [Bacillus subtilis]	74	57	648
103	5	4364	3267	g nl|PID|e323524	YloN protein [Bacillus subtilis]	74	62	1098 
108	7	6864	7592	methyltransferase [Lactococcus lactis]	74	56	729
131	2	 478	 146	gnl|PID|d101320	YqgZ [Bacillus subtilis]	74	45	333
133	2	1380	 919	gnl|PID|e313025	hypothetical protein [Bacillus subtilis]	74	60	462
137	9	6167	6787	g nl|PID|d100479	Na+ -ATPase subunit D [Enterococcus hirae]	74	53	621
149	4	3008	3883	gnl| PID|d100581	high level kasgamycin resistance [Bacillus subtilis]	74	55	876
157	2	 243	 824	methylated-DNA--protein-cysteine methyltransferase (dat1)	74	48	582
< td/>				[Haemophilus influenzae]
164	6	3515	4249	gi|410131	ORFX7 [Bacillus subtilis]	74	48	735
167	7	5446	5201	g i|413927	ipa-3r gene product [Bacillus subtilis]	74	55	246
171	1	 1	1818	gnl|PID|d102251	beta-galac tosidase [Bacillus circulans]	74	62	1818 
172	4	1064	2392	gi|466474	cellobiose phosphotransferase enzyme II″ [Bacillus	74	50	13 29 
					stea rothermophilus]
185	1	 326	 3	gi|1573646	Mg(2+) transport ATPase protein C (mgtC) (SP:P22037)	74	68	324
				[Haemophilus influenzae]
188	2	1089	2018	gi|1573008	ATP dependent translocator homolog (msbA) [Haemophilus	74	44	930
					influ enzae]
189	11 	6491	7174	gi|1661199	sakacin A production response regulator [Streptococcus mutans]	74	60	684
210	2	 520	1287	g i|2293207	(AF008220) YtmQ [Bacillus subtilis]	74	60	768
261	1	 836	 192	putative ATP binding subunit [Bacillus subtilis]	74	55	645
263	3	1619	3655	g i|663232	Similarity with S. cerevisiae hypothetical 137.7 kD protein in	74	42	2037 
< td/>				subtelomeric Y′ repeat region [Saccharomyces cerevisiae]
265	2	 844	1227	gi|49272	Asparaginase [Bacillus licheniformis]	74	64	384
368	1	 1	 942	gi|603998	unknown [Saccharomyces cerevisiae]	74	39	942
7	16 	13357 	11921 	gn l|PID|d101324	YqhX [Bacillus subtilis]	73	57	1437 
 17	10 	5706	5449	gnl|PID|e305362	unnamed protein product [Streptococcus thermophilus]	73	47	258
 31	2	 522	 244	gnl|PID|d100576	single strand DNA binding protein [Bacillus subtilis]	73	55	279
 32	6	5667	6194	gnl|PID|d101315	YqfG [Bacillus subtilis]	73	58	528
 34	15 	10281 	9790	gnl|PID|d102151	(AB001684) ORF42c [Chlorella vulgaris]	73	46	492
 40	12 	9876	9226	gi|1173517	riboflavin synthase alpha subunit [Actinobacillus pleuropneumoniae]	73	55	65 1
 55	2	3592	 8 39	gnl|PID|d101887	cation-transporting ATPase PacL [Synechocystis sp.]	73	60	2754 
 55	18 	17494 	16586 	unknown [Mycobacterium tuberculosis]	73	52	909
 65	16 	7213	7767	gi|143419	ribosomal protein L6 [Bacillus stearothermophilus]	73	60	555
 66	3	3300	36 59	gnl|PID|e269883	LacF [Lactobacillus casei]	73	52	360
 70	10 	5557	5733	envelope protein [Human immunodeficiency virus type 1]	73	60	177
 71< /td>	4	6133	8262	gnl|PID|e322063< /td>	ss-1,4-galactosyltransferase [Streptococcus pneumoniae]	73	45	2130 < /td>
 72	1	 3	 851	gi|1183177	(AF008220) transporter [Bacillus subtilis]	73	50	849
 76	7	7019	6195	gnl|PID|d101325	YqiF [Bacillus subtilis]	73	66	825
 76	12 	10009 	9533	gi|1573086	uridine kinase (uridine monophosphokinase) (udk) [Haemophilus	73	54	477
					influ enzae]
 80	7	81 13	9372	gi|1377823	aminopeptidase [Bacillus subtilis]	73	60	1260 
 97	5	3389	1668	gnl|PID|d101954	dihydroxyacid dehydratase [Synechocytis sp.]	73	54	1722 
 98	9	6912	7619	gnl|PID|e3 14991	FtsE [Mycobacterium tuberculosis]	73	54	708
108	11 	10928 	10 440 	gi|388109	regulatory protein [Enterococcus faecalis]	73	54	489
128	6	3632	4222	g i|1685111	orf1091 [Streptococcus thermophilus]	73	63	591
138	2	1575	 394	gi|147326	transport protein [Escherichia coli]	73	60	1182 
140	13 	12538 	11903⠀‚	pir|E53402|E534	serine O-acetyltransferase (EC 2.3.1.30) - Bacillus	73	55	636
					stearothe rmophilus
162	5	5 701	4991	gnl|PID|e323511	putative YhaQ protein [Bacillus subtilis]	73	50	711
164	4	2323	2790	g i|1592076	hypothetical protein (SP:P25768) [Methanococcus jannaschii]	73	52	468
164	8	4815	5546	gi|410137	ORFX13 [Bacillus subtilis]	73	56	732
170	5	4394	5302	g nl|PID|d100959	homologue of unidentified protein of E. coli [Bacillus subtilis]	73	46	909
178	7	3893	4855	g i|46242	nodulation protein B, 5′end [Rhizobium loti]	73	56	963
204	6	5096	4278	gnl|P ID|e214719	PlcR protein [Bacillus thuringiensis]	73	41	819
213	2	 832	2037	gi|156296	ribosomal protein S1 homolog; sequence specific DNA-binding	73	55	1206 
					protein [Leuconostoc lactis]
231	2	84	 287	gi|40173	homolog of E. coli ribosomal protein L21 [Bacillus subtilis]	73	61	204
237	1	 2	 505	gi|1773151	adenine phosphoribosyltransferase [Escherichia coli]	73	51	504
269	1	 2	 691	gnl|PID|d101328	YqiX [Bacillus subtilis]	73	36	690
289	2	1272	 832	pir|A02771|R7MC	ribosomal protein L/L12 - Micrococcus luteus	73	66	441
343	1	14	 484	gi|1788125	(AE000276) hypothetical 30.4 kD protein in manZ-cpsC intergenic	73	47	471
				region [Escherichia coli]
356	1	 22 2	 4	gi|2149905	D-glutamic acid adding enzyme [Enterococcus faecalis]	73	50	219
7	5	3165	4691	gnl|PID|d10183 3	amidase [Synechocystis sp.]	72	52	1527 
7	9	7195	7647	gi|146976	nusB [Escherichia coli]	72	54	453
7	17 	13743 	13300 	gn l|PID|e289141	similar to hydroxymyristoyl-(acyl carrier protein) dehydratase	72	59	444
				[Bacillus subtilis]
 22	19 	15367 	16224 	gnl|PID|d101929	72	51	588
 3 3	17 	12111 	11425 	gn l|PID|d101190	ORF3 [Streptococcus mutans]	72	55	687
 34	7	7147	5627	g i|396501	aspartyl-tRNA synthetase [Thermus thermophilus]	72	52	1521†‚
 38	23 	15372 	16085 	pir|H64108|H641	L-ribulose-phos phate 4-epimerase (araD) homolog - Haemophilus	72	54	714
					influe nzae (strain Rd KW20)
 39	5	5094	6905	gnl|PID|e254877	unknown [Mycobacterium tuberculosis]	72	56	1812†‚
 40	6	4469	4636	gi|153672	lactose repressor [Streptococcus mutans]	72	58	168
 48	2	1459	1253	g i|310380	inhibin beta-A-subunit [Ovis aries]	72	33	207
 48	29 	21729 	22424†‚	gi|2314329	(AE000623) glutamine ABC transporter, permease protein (glnP)	72	49	696
< td/>				[Helicobacter pylori]
 50	5	4 529	3288	gi|1750108	YnbA [Bacillus subtilis]	72	54	1242 
 51	3	1044	2282	gi|2293230	(AF008220) YtbJ [Bacillus subtilis]	72	54	1239 
 52	13 	13681 	13938 	gi|142521	deoxyribodipyrimidine photolyase [Bacillus subtilis]	72	45	258
 55	1	 841	35	gi|882518	ORF_o304; GTG start [Escherichia coli]	72	59	807
 75	5	2832	3191	gnl |PID|e209886	mercuric resistance operon regulatory protein [Bacillus subtilis]	72	44	360
 76	6	6229	5771	gi|142450	ahrC protein [Bacillus subtilis]	72	53	459
 79	5	5065	4592	gi|2293279	(AF008220) YtcG [Bacillus subtilis]	72	46	474
 87	14 	14726 	1230 9 	gnl|PID|e323502	putative PriA protein [Bacillus subtilis]	72	52	2418 
 91	1	 444	 662	gi|500691	MY01 gene product [Saccharomyces cerevisiae]	72	50	219
 91	7	4516	4764	skeletal muscle sodium channel alpha-subunit [Equus caballus]	72	38	249
 95	2	2004	1717	gnl|PID|e323527	putative Asp23 protein [Bacillus subtilis]	72	40	288
109	1	1452	 118	gi|143331	alkaline phosphatase regulatory protein [Bacillus subtilis]	72	52	1335 
126	1	 3	2192	gnl|PID|d101831	glutamine- binding periplasmic protein [Synechocystis sp.]	72	46	2190 
130	3	1735	2478	gi|2415396	(AF015775) carboxypeptidase [Bacillus subtilis]	72	53	744
137	6	2585	2929	g i|472922	v-type Na-ATPase [Enterococcus hirae]	72	46	345
140	10 	9601	9203	gi|49224	URF 4 [Synechococcus sp.]	72	48	399
146< /td>	5	1906	1247	gnl|PID|e324945< /td>	hypothetical protein [Bacillus subtilis]	72	45	660
147	2	2084	1083	g nl|PID|e325016	hypothetical protein [Bacillus subtilis]	72	56	1002 
147	5	6156	5146	TPP-dependent acetoin dehydrogenase beta-subunit [Clostridium	72	56	1011 
					m agnum]
148	8	5381	6433	gi|974332	NAD(P)H-dependent dihydroxyacetone-phosphate reductase [Bacillus	72	54	10 53 
					subt ilis]
148	14 	1 0256 	9675	gnl|PID|d101319	YqgN [Bacillus subtilis]	72	50	582
159	8	4005	4949	g i|1788770	(AE000330) o463; 24 pct identical (44 gaps) to 338 residues from	72	43	945
					penicillin-binding protein 4*, PBPE_BACSU SW; P32959 (451 aa)
					[Esche richia coli]
172	10 	9 907	10620 	gi|763387	unknown [Saccharomyces cerevisiae]	72	55	714
220	3	2862	3602	gi|1574175	hypothetical [Haemophilus influenzae]	72	50	741
267	1	 3	 449	gi|290513	f470 [Escherichia coli]	72	48	447
281	2	 899	 540	g nl|PID|d100964	homologue of aspartokinase 2 alpha and beta subunits LysC of	72	45	360
					B. subtilis [Bacillus subtilis]
290	1	1 018	14	gi|474195	This ORF is homologous to a 40.0 kd hypothetical protein in the htrB	72	54	1005 
					3′ region from E. coli, Accession Number X61000 [Mycoplasma-like
					o rganism]
300	1	63	 587	gi|746399	transcription elongation factor [Escherichia coli]	72	50	525
316	1	1326	 4	gi|158127	protein kinase C [Drosophila melanogaster]	72	40	1323†‚
342	1	 227	 3	gnl|PID|d101164	unknown [Bacillus subtilis]	72	54	225
354	1	 1	1005	gnl|PID|d102048	C. thermocellum beta-glucosidase; P26208 (985) [Bacillus subtilis]	72	52	1005 
6	10 	8134	10467 	gnl|PI D|e264229	unknown [Mycobacterium tuberculosis]	71	57	2334†‚
7	20 	16231 	15464 	gi |18046	3-oxoacyl-[acyl-carrier protein] reductase [Cuphea lanceolata]	71	52	768
 15	1	1297	 2	gnl|PID|d100571	replicative DNA helicase [Bacillus subtilis]	71	51	1296 
 15	4	4435	3869	gi|499384	orf189 [Bacillus subtilis]	71	47	567
 18	6	5120	4218	gnl|PID|d101318	YqgG [Bacillus subtilis]	71	51	903
 29	1	 1	 540	gi|17773142	similar to the 20.2kd protein in TETB-EXOA region of B. subtilis	71	56	540
					[Escherichia coli]
 38	20 	13327 	13830 	gi|537036	ORF_o15 8 [Escherichia coli]	71	48	504
 51	12 	15015 	12676 	gi|149528	dipeptidyl peptidase IV [Lactococcus lactis]	71	59	2340 
 55	23 	21040 	20 585 	gi|2343285	(AF015453) surface located protein [Lactobacillus rhamonus]	71	58	456
 60	2	 705	 265	gnl|PID|d101320	YqgZ [Bacillus subtilis]	71	44	441
 71	18 	24679 	2622 6 	gi|580920	rodD (gtaA) polypeptide (AA 1-673) [Bacillus subtilis]	71	44	1548 
 71	25 	30587 	30360 	gi|606028	ORF_o414; Geneplot suggests frameshift near start but none found	71	50	228
				[Escherichia coli]
 72	6	523 9	6729	gi|580835	lysine decarboxylase [Bacillus subtilis]	71	48	1491 
 72	14 	11991 	12878 	gi|624085	similar to rat beta-alanine synthetase encoded by GenBank Accession	71	54	888
					Number S27881; contains ATP/GTP binding motif [Paramecium
				bursaria Chlorella virus 1]
 73	11 	7269	7033	gi|1906594	PN1 [Rattus norvegicus]	71	42	237
 74	6	10385 	8517	gi|1573733	prolyl-tRNA synthetase (proS) [Haemophilus influenzae]	71	52	1869 < /td>
 81	9	5772	6578	gi|147404	mannose permease subunit II-M-Man [Escherichia coli]	71	45	807
 86	5	4602	3604	gnl |PID|e322063	ss-1,4-galactosyltransferase [Streptococcus pneumoniae]	71	53	999
105	4	3619	4707	gi|2323341	(AF014460) PepQ [Streptococcus mutans]	71	58	1089 
106	13 	13557 	1295 5 	gi|1519287	LemA [Listeria monocytogenes]	71	48	603
114	2	1029	1979	gi|310303	mosA [Rhizobium meliloti]	71	55	951
122	2	 564	1205	gi|1649037	glutamine transport ATP-binding protein GLNQ [Salmonella	71	50	642
					typhim urium]
132	5	9018	7063	gnl|PID|d102049	H. influenzae hypothetical ABC transporter; P44808 (974)	71	51	1956 
					[Bacillus subtilis]
140	1	1 141	 227	gi|1673788	(AE00015) Mycoplasma pneumonia, fructose-bisphosphate aldolase;	71	49	915
					similar to Swiss-Prot Accession Number P13243, from B. subtilis
					[Mycoplasma pneumoniae]
140	5	5635	4973	gnl|PID|d100964	homologue of hypothetical protein in a rapamycin synthesis gene	71	48	663
					cluster of Streptomyces hygroscopicus [Bacillus subtilis]
141	7	7 369	7845	gnl|PID|d102005	(AB001488) FUNCTION UNKNOWN, SIMILAR PRODUCT IN	71	51	477
					E. COLI AND MYCOPLASMA PNEUMONIAE. [Bacillus subtilis]
193	1	 1	 165	gi|46912	ribosomal protein L13 [Staphylococcus carnosus]	71	59	165
194	3	2205	1594	g i|535351	CodY [Bacillus subtilis]	71	52	612
199	3	1510	1319	g i|2182574	(AE000090) Y4pE [Rhizobium sp. NGR234]	71	45	192
2 08	2	2616	3752	gi|1787378	(AE000213) hypothetical protein in purB 5′ region [Escherichia coli]	71	57	1137 
209	2	2022	1141	g i|41432	fepC gene product [Escherichia coli]	71	46	882
210	5	1911	3071	gi|49 316	ORF2 gene product [Bacillus subtilis]	71	45	1161 
210	6	3069	3386	ORF3 gene product [Bacillus subtilis]	71	48	318
212	2	3561	1381	g i|557567	ribonucleotide reductase R1 subunit [Mycobacterium tubercolosis]	71	53	2181†‚
233	3	2003	2920	gnl|PID|d101320	YqgR [Bacillus subtilis]	71	50	918
244	1	13	1053	gnl|PID|d100964	homologue of aspartokinase 2 alpha and beta subunits LysC or	71	55	1041 
< td/>				B. subtilis [Bacillus subtilis]
251	2	1 008	1874	gi|755601	unknown [Bacillus subtilis]	71	46	867
282	2	 906	 712	unknown [Rhodobacter capsulatus]	71	46	195
312	4	2137	1565	gnl|PID|d102245	(AB005554) yxbF [Bacillus subtilis]	71	34	573
338	1	 3	 683	gi|1591045	hypothetical protein (SP:P31466) [Methanococcus jannaschii]	71	48	681
346	1	 3	 164	gi|1591234	hypothetical protein (SP:P42297) [Methanococcus jannaschii]	71	36	162
374	1	 619	 2	gi|397526	clumping factor [Staphylococcus aureus]	71	23	618
377	1	 688	 2	gi|397526	clumping factor [Staphylococcus aureus]	71	23	687
3	8	7419	6958	gnl|PID|e26948 6	Unknown [Bacillus subtilis]	70	42	462
3	10 	8395	9075	gnl|PID|e2 55543	putative iron dependant repressor [Staphylococcus epidermidis]	70	46	681
7	14 	11024 	10254 	gn l|PID|d100290	undefined open reading frame [Bacillus stearothermophilus]	70	55	771
7	18 	14213 	13719 	gn l|PID|d101090	biotin carboxyl carrier protein of acetyl-CoA carboxylase	70	56	495
				[Synechocystis sp.]
9	2	1057	 287	gnl|PID|d100 581	unknown [Bacillus subtilis]	70	52	771
 12	4	2610	1789	gnl|PID|d101195	yycJ [Bacillus subtilis]	70	52	822
 21	2	2586	1846	gi|2293447	(AF008930) ATPase [Bacillus subtilis]	70	54	741
 22	13 	10955 	1151 2 	gi|1165295	Ydr540cp [Saccharomyces cerevisiae]	70	50	558
 30	6	4315	3980	ATP binding protein of transport ATPase [Bacillus firmus]	70	51	336
 31	1	 370	 113	single-stranded DNA binding protein [unidentified eubacterium]	70	36	258
 33	15 	10639 	9521	homolgous to D-amino acid dehydrogenase enzyme [Pseudomonas	70	50	1119 
					a eruginosa]
 38	6	4312	gi|2058547	ComYD [Streptococcus gordonii]	70	48	501
 38	25 	17986 	1847 7 	gi|537033	ORF_f356 [Escherichia coli]	70	58	492
 40	13 	11054 	9846	gi|1173516	riboflavin-specific deaminase [Actinobacillus pleuropneumoniae]	70	52	12 09 
 42	2	 722	gi|1146183	putative [Bacillus subtilis]	70	51	1233 
 43	3	2373	1612	gi|1591493	glutamine transport ATP-binding protein Q [Methanococcus	70	48
					jan naschii]
 45	8	9197	8049	gnl|PID|d102036	subunit of ADP-glucose pyrophosphorylase [Bacillus	70	54	11 49 
					stea rothermophilus]
 59	2	 567	 956	gnl|PID|d100302	neopullulanase [Bacillus sp.]	70	42	390
 6 0	3	1874	 795	gnl|PID|e276 466	aminopeptidase P [Lactococcus lactis]	70	48	1080 
 61	4	5553	2437	SNF [Bacillus cereus]	70	51	3117 
 61	7	7914	6802	cystathionine gamma-synthase (metB) [Haemophilus influenzae]	70	52	1113 < /td>
 63	7	5372	7222	gnl|PID|d100974	unknown [Bacillus subtilis]	70	54	1851 
 68	7	7126	6962	gi|1263014	emm18.1 gene product [Streptococcus pyogenes]	70	37	165
 72	12 	10081 	1091 1 	gi|2313093	(AE000524) carboxynorspermidine decarboxylase (nspC)	70	56	831
< td/>				[Helicobacter pylori]
 75	10 	8124	gi|1877423	galactose-1- P-uridyl transferase [Streptococcus mutans]	70	59	237
 79	3	3424	2525	g i|39881	ORK 311 (AA 1-311) [Bacillus subtilis]	70	47	900
 87	10 	9369	7324	gnl|PID|e323506	putative Pkn2 protein [Bacillus subtilis]	70	52	2046 
 96	14 	10640 	11788 	gi|1573209	tRNA-guanine transglycosylase (tgt) [Haemophilus influenzae]	70	52	1149 < /td>
113	2	 574	1086	gi|433630	A180 [Saccharomyces cerevisiae]	70	59	513
123	5	2901	3461	gnl|PID|d100585	unknown [Bacillus subtilis]	70	45	561
125	5	4593	4282	g nl|PID|e276474	capacitative calcium entry channel 1 [Bos taurus]	70	35	312
129	5	4500	3454	gnl |PID|d101314	YqeT [Bacillus subtilis]	70	47	1047 
133	3	2608	1394	(AF008220) YtfP [Bacillus subtilis]	70	50	1215 
135	1	 420	 662	gnl|PID|e265530	yorfE [Streptococcus pneumoniae]	70	47	243
137	3	 438	 932	gi|472919	v-type Na-ATPase [Enterococcus hirae]	70	57	495
138	1	 440	 1	gi|147336	transmembrane protein [Escherichia coli]	70	42	438
140	16 	18796 	16364 	gi|976441	N5-methyltetrahydrofolate homocysteine methyltransferase	70	53	2433 
					[Saccharomyces cerevisiae]
167	10 	8263	6695	gi|149535	D-alanine activating enzyme [lactobacillus casei]	70	52	1569 
204	4	3226	2747	gnl|PID|d102049	E. coli hypothetical protein; P31805 (267) [Bacillus subtilis]	70	51	480
207	3	2627	2869	g nl|PID|e309213	racGAP [Dictyostelium discoidem]	70	45	243
282	3	1136	 882	unknown [Rhodobacter capsulatus]	70	50	255
6	21 	17554 	18453 	gn l|PID|e233879	hypothetical protein [Bacillus subtilis]	69	44	900
6	22 	18482 	19474 	gi |580883	ipa-88d gene product [Bacillus subtilis]	69	53	990
 22	6	4682	5824	gi|2209379	(AF006720) ProJ [Bacillus subtilis]	69	48	1143 
 22	9	7992	8651	gnl|PID|d100580	unknown [Bacillus subtilis]	69	51	660
 22	12 	9871	10767 	gnl|PID|d100581	unknown [Bacillus subtilis]	69	51	897
 27	7	5857	5348	gnl|PID|d102012	(AB001488) FUNCTION UNKNOWN. [Bacillus subtilis]	69	28	510
 36	10 	7294	10116 	gi|437916	isoleucyl-tRNA synthetase [Staphylococcus aureus]	69	53	2823 
 38	1	 2	1090	gi|141900	alcohol dehydrogenase (EC 1.1.1.1) [Alcaligenes eutrophus]	69	48	1089 
 40	14 	11333 	11944 	gi|1573280	Holliday junction DNA helicase (ruvA) [Haemophilus influenzae]	69	44	612
 40	15 	11942 	12 517 	gi|1573653	DNA-3-methyladenine glycosidase I (tagI) [Haemophilus influenzae]	69	50	576
 45	6	6947	5490	starch (bacterial glycogen) synthase [Bacillus subtilis]	69	47	1458 
 48	34 	24932 	24153 	gnl|PID|e233870	hypothetical protein [Bacillus subtilis]	69	36	780
 49	6	6183	6521	gi|396297	similar to phosphotransferase system enzyme II [Escherichia coli]	69	50	339
 49	8	7586	8338	gi| 396420	similar to Alcaligenes eutrophus pHG1 D-ribulose-5-phosphate 3	69	49	753
	< td/>			epimerase [Escherichia coli]
 55	6	826 2	7033	gi|1146238	poly(A) polymerase [Bacillus subtilis]	69	50	1230 
 59	3	 954	2333	gnl|PID|e313038	hypothetical protein [Bacillus subtilis]	69	54	1380 
 62	3	1170	1418	gnl|PID|d101915	hypothetical protein [Synechocystis sp.]	69	49	249
 6 3	8	7298	7762	gi|293017	ORF3 (put.); putative [Lactococcus lactis]	69	42	465
 66	4	3657	5081	g i|153755	phospho-beta-D-galactosidase (EC 3.2.1.85) [Lactococcus lactis	69	49	1425 
					cremoris]
 66	5	5126	6 829	gi|433809	enzyme II [Streptococcus mutans]	69	46	1704 
 71	6	10017 	10664⠀‚	gnl|PID|e322063	ss-1,4-galactosyltransfer ase [Streptococcus pneumoniae]	69	39	648
 71	21 	27730 	27 966 	gnl|PID|d400649	DE-cadherin [Drosophila melanogaster]	69	30	237
 77	1	 1	 237	gi|287870	groES gene product [Lactococcus lactis]	69	44	237
 81	5	3622	4101	g i|1573605	fucose operon protein (fucU) [Haemophilus influenzae]	69	52	480
 83	1	40	 714	pir|C33496|C334	hisC homolog - Bacillus subtilis	69	46	675
 83	16 	15742 	16335  	gi|143372	phosphoribosyl glycinamide formyltransferase (PUR-N) [Bacillus	69	46	59 4
					subtilis ]
 85	2	1212	 916	gi|194097	IFN-response element binding factor 1 [Mus musculus]	69	48	297
 91	5	3678	4274	gi|1574712	anaerobic ribonuleoside-triphosphate reductase activating protein	69	44	597
					(nrdG) [Haemophilus influenzae]
 98	5	4032	gnl|PID|d100262	LivF protein [Salmonella typhimurium]	69	51	786
108	5	4085	5056	transcription factor [Lactococcus lactis]	69	49	972
126	3	3078	4568	gnl |PID|d101329	YqjJ [Bacillus subtilis]	69	49	1491 
131	6	4121	2889	YqeR [Bacillus subtilis]	69	47	1233 
136	2	1505	2299	unknown [Bacillus subtilis]	69	47	795
149	5	3852	4763	g nl|PID|e323525	YloQ protein [Bacillus subtilis]	69	50	912
149	12 	9336	10655 	gi|151571	Homology with E. coli and P. aeruginosa lysA gene; product of	69	52	1320 
< td/>				unknown function; putative [Pseudomonas syringae]
153	4	3 191	3829	gi|1710373	BrnQ [Bacillus subtilis]	69	44	639
169	3	 849	2324	gnl|PID|d100582	temperature sensitive cell division [Bacillus subtilis]	69	49	1476 
180	1	 566	 3	gi|488339	alpha-amylase [unidentified cloning vector]	69	50	564
2 12	1	1196	 231	gi|1395209< /td>	ribonucleotide reductase R2-2 small subunit [Mycobacterium	69	53
					tub erculosis]
226	1	 2	 661	pir|JQ2285|JQ22	nodulin- 26 - soybean	69	41	660
2 33	5	3249	4766	gi|472918	v-type Na-ATPase [Enterococcus hirae]	69	56	1518 
235	3	 660	1766	methylase [Haemophilus influenzae]	69	43	1107 < /td>
243	2	 865	2361	gnl|PID|d100225	ORF5 [Barley yellow dwarf virus]	69	69	1497 
3	2899	1967	gi|2289231	macrolide-efflux protein [Streptococcus agalactiae]	69	51	933
310	1	 1	 282	gnl|PID|e322442	peptide deformylase [Clostridium beijerinckii]	69	55	282
369	1	 868	 2	gi|397526	clumping factor [Staphylococcus aureus]	69	55	282
370	1	 749	 3	gi|397526	clumping factor [Staphylococcus aureus]	69	21	747
379	1	44	 280	gnl|PID|d100649	DE-cadheri n [Drosophila melanogaster]	69	30	237
388	1	 260	72	gi|1787524	(AE000225) hypothetical 32.7 kD protein in trpL-btuR intergenic	69	44	189
				region [Escherichia coli]
1	2	2006	3040	gnl|PID|d10180 9	ABC transporter [Synechocystis sp.]	68	43	1035 
 12	5	3958	2600	gi|2182992	histidine kinase [Lactococcus lactis cremoris]	68	45	1359 
 15	2	1790	1311	pir|S16974|R5BS	ribosomal protein L9 - Bacillus stearothermophilus	68	56	4 80
 16	6	7353	570 1	gi|1787041	(AE000184) o530; This 530 aa orf is 33 pct identical (14 gaps) to 525	68	45	1653 
					residues of an approx. 640 aa protein YHES_HAEIN SW; P44808
					[Es cherichia coli]
 17	12 	6479	6805	gi|553165	acetylcholinest erase [Homo sapiens]	68	68	327
 20	13 	14128 	14505  	gi|142700	P competence protein (ttg start codon) (put.); putative [Bacillus	68	40	37 8
					subtilis ]
 22	32 	246 12 	25397 	gi|289262	comE ORF3 [Bacillus subtilis]	68	36	786
 30	7	4548	4288	gi|311388	ORF1 [Azorhizobium caulinodans]	68	46	261
 36	5	3911	4585	gi|1573041	hypothetical [Haemophilus influenzae]	68	54	675
 46	6	5219	6040	(AE000446) hypothetical 29.7 kD protein in ibpA-gyrB intergenic	68	47	822
				region [Escherichia coli]
 54	10 	6235	7086	gi|882579	CF Site No. 29739 [Escherichia coli]	68	55	852
 55	5	7069	5165	gnl |PID|d101914	ABC transporter [Synechocystis sp.]	68	45	1905 
 71	3	6134	5613	gi|1573353	outer membrane integrity protein (tolA) [Haemophilus influenzae]	68	50	522
 71	10 	15342 	16 613 	gi|580866	ipa-12d gene product [Bacillus subtilis]	68	31	1272 
 71	12 	17560 	18792 	gi|44073	SecY protein [Lactococcus lactis]	68	35	1233 
 71	17 	22295 	24 703 	gi|1762349	involved in protein export [Bacillus subtilis]	68	50	2409 
 73	16 	10208 	9729	gi|1353537	dUTPase [Bacteriophage rit]	68	51	480
 8 6	18 	17198 	16011 	gi |413943	ipa-19d gene product [Bacillus subtilis]	68	53	1188 
 87	17 	17491 	15866 	gi|150209	ORF 1 [Mycoplasma mycoides]	68	43	1626 
 89	6	5139	1454	gi|1498824	M. jannaschii predicted coding region MJ0062 [Methanococcus	68	40
					jan naschii]
 89	11 	8021	8242	gi|150974	4-oxalocroto nate tautomerase [Pseudomonas putida]	68	43	222
 97	8	6755	5394	g i|2367358	(AE000491) hypothetical 52.9 kD protein in aidB-rspF intergenic	68	41	1362 
					region [Escherichia coli]
 98	3	141 8	2308	gni|PID|d100261	LivA protein [Salmonella typhimurium]	68	40	891
 99	13 	16414 	1 7280 	gi|455363	regulatory protein [Streptococcus mutans]	68	50	867
115	3	5054	3693	gi| 466474	cellobiose phosphotransferase enzyme II″ [Bacillus	68	44	13 62 
					stea rothermophilus]
124	7	3394	3221	gnl|PID|d100702	cut14 protein [Schizosaccharomyces pombe]	68	56	174
125	2	2923	1922	gi|4 50566	transmembrane protein [Bacillus subtilis]	68	50	1002 
132	2	4858	2888	DNA ligase [Synechocystis sp.]	68	52	1971 
140	7	7765	7580	gi|1209711	unknown [Saccharomyces cerevisiae]	68	47	186
150	1	 539	 3	gi|402490	ADP-ribosylarginine hydrolase [Mus musculus]	68	59	537
164	1	58	 867	gnl|PID|e255114	glutamate racemase [Bacillus subtilis]	68	49	810
164	2	 819	1835	gnl|PID|e255117	hypothetical protein [Bacillus subtilis]	68	50	1017 
169	7	3946	4104	hypothetical protein - Lactococcus lactis subsp. lactis plasmid pSL2	68	40	159
170< /td>	4	4247	4396	gi|304146	68	52	150
171	8	6002	7054	g i|38722	precursor (aa −20 to 381) [Acinetobacter calcoaceticus]	68	54	1053⠀‚
198	3	2473	1871< /td>	gnl|PID|e313075	hypothetical protein [Bacillus subtilis]	68	46	603
211	2	 969	1802	gi|1439528	EIIC-man [Lactobacillus curvatus]	68	45	834
214	8	4926	4231	g nl|PID|d102049	H. influenzae hypothetical protein, P43990 (182) [Bacillus subtilis]	68	50	696
217	6	4955	5170	g nl|PID|e326966	similar to B. vulgaris CMS-associated mitochondrial . . . (reverse	68	36	216
					transcriptase) [Arabidopsis thaliana]
218	7	3 930	4745	go|2293198	(AF008220) YtgP [Bacillus subtilis]	68	38	816
220	6	4628	4338	g nl|PID|e325791	(AJ000005) orf1 [Bacillus magaterium]	68	51	291
236	1	 746	 108	gi|410137	ORFX13 [Bacillus subtilis]	68	46	639
237	2	 675	1451	gi|396348	homoserine transsuccinylase [Escherichia coli]	68	49	777
250	4	 771	1229	gi| 310859	ORF2 [Synechococcus sp.]	68	50	459
254< /td>	1	 517	 155	gi|1787105	(AE000189) o648 was o669; This 669 aa orf is 40 pct identical (1	68	44	363
					gaps) to 217 residues of an approx. 232 as protein YBBA_HAEIN
					SW; P45247 [Escherichia coli]
337	1	 1	 774	gnl|PID|e261990	putative orf [Bacillus subtilis]	68	47	774
345	1	 3	 653	gi|149513	thymidylate sythase (EX 2.1.1.45) [Lactococcus lactis]	68	61	651
386	2	 417	 4	gi|1573353	outer membrane integrity protein (tolA) [Haemophilus influenzae]	68	51	414
2	4	5722	4697	gi|1592141	M. jannaschii predicted coding region MJ1507 [Methanococcus	67	26
					jannaschii]
3	6	5397	4591	gi|2293175	(AF008220) signal transduction regulator [Bacillus subtilis]	67	44	807
5	2	2301	 574	gi‘2313385	(AE000547) para-aminobenzoate synthetase (pabB) [Helicobacter	67	48
					pylori]
6	19 	16063 	16758 	gi |413931	ipa-7d gene product [Bacillus subtilis]	67	41	696
 22	8	7094	7897	gi|1928962	pyrroline-5-carboxylate reductase [Actinidia deliciosa]	67	51	804
 29	10 	8335	9072	go|468745	gtcR gene product [Bacillus brevis]	67	41	738
 31	3	1379	 585	gi|2425123	(AF019986) PksB [Dictyostelium discoideum]	67	49	795
 32	11 	8849	10150⠀‚	gi|42029	ORF1 gene product [Escherichia coli]	67	47	1302 
 36	16 	14830 	1554 6 	gi|1592142	ABC transporter, probable ATP-binding subunit [Methanococcus	67	43
					jan naschii]
 38	9	4958	5392	gnl|PID|e214803	T2283.3 [Caenorhabditis elegans]	67	47	435
 38	21 	13775 	14512  	gi|537037	ORF_o216 [Escherichia coli]	67	52	738
 45	9	10428 	9181	gi|551710	branching enzyme (glgB) (EC 2.4.1.18) [Bacillus stearothermophilus]	67	51	1248 
 48	23 	18334†‚	17514 	gi|413949	ipa-25d gene product [Bacillus subtilis]	67	50	831
 50	2	1773	 952	YqjQ [Bacillus subtilis]	67	55	822
 53	1	 431	 3	gi|1574291	fimbrial transcription regulation repressor (pilB) [Haemophilus	67	40	429
					influ enzae]
 55	13 	11946 	gnl|PID|e252990	ORF YDL037c [Saccharomyces cerevisiae]	67	51	795
 61	9	9210	8329	ATP-binding cassette transporter A [Staphylococcus aureus]	67	50	882
 71	2	5614	6117	g i|1197667	vitellogenin [Anolis pulchellus]	67	36	504
 81	7	4489	4983	phosphoenolpyruvate:mannose phosphotransferase element IIB	67	42	495
					[Lactobacillus curvatus]
 83	7	2957	3214	gi|1276746	Acyl carrier protein [Porphyra purpurea]	67	37	258
 86	8	8140	6809	gi|1147744	PSR [Enterococcus hirae]	67	45	1332 
 97	3	 986	1366	gnl|PID|d102235	(AB000631) unnamed protein product [Streptococcus mutans]	67	43	381
102	1	 601	1413	g i|682765	mccB gene product [Escherichia coli]	67	36	813
106	3	1109	1987	gi|14 8921	LicD protein [Haemophilus influenzae]	67	43	879
115	4	5982	5656	gi|8955750	putative cellobiose phosphotransferase enzyme III [Bacillus subtilis]	67	44	327
115	7	8421	8077	g i|466473	cellobiose phosphotransferase enzyme II′ [Bacillus	67	51	34 5
					stearoth ermophilus]
127	13 	8127	7021	gi|147326	transport protein [Escherichia coli]	67	45	1107 
136	3	2215	2859	g nl|PID|d100581	unknown [Bacillus subtilis]	67	49	645
140	21 	23317 	20906⠀‚	gnl|PID|d101912	phenylalanyl-tRNA synthetase [Synechocystis sp.]	67	43	2412 
146	6	2894	1893	gi|2182994	histidine kinase [Lactococcus lactis cremoris]	67	44	1002 
151	8	11476 	11117⠀‚	gnl|PID|d100085	ORF129 [Bacillus cereus]	67	48	360
160	10 	7453	8646	gi|2281317	OrfB; similar to a Streptococcus pneumoniae putative membrane	67	46	1194 
					protein encoded by GenBank Accession Number X99400;
					inactivati on of the OrfB gene leads to UV-sensitivity and to decrease
					of homologous recombination (plasmidic test) [Lactococcus 1
163	3	3099	4505	gnl|PID|d101317	YqfR [Bacillus subtilis]	67	47	1407 
167	8	6704	5454	DibB [Lactobacillus casei]	67	45	1251 
169	4	2322	2879	gnl|PID|d101331	YqkG [Bacillus subtilis]	67	41	558
171	11 	7656	8384	pneumococcal surface protein A [Streptococcus pneumoniae]	67	50	729
188	3	1930	3723	gi|1542975	AbcB [Thermoanaerobacterium thermosulfurigenes]	67	46	1794 
189	6	3599	3141	gnl|PID|e325178	Hypothetical protein [Bacillus subtilis]	67	52	459
205	3	1663	2211	g i|606073	ORF_o169 [Escherichia coli]	67	47	549
207	4	2896	3456	gi|22 76374	DtxR/iron regulated lipoprotein precursor [Corynebacterium	67	49	561
					d iphtheriae]
217	3	4086	3703	gi|895750	putative cellobiose phosphotransferase enzyme III [Bacillus subtilis]	67	42	384
246	2	 291	 662	unknown [Bacillus subtilis]	67	43	372
252	1	 2	 745	gi|2341768	PspA [Streptococcus pneumoniae]	67	41	744
265	3	1134	1811	gi|2313847	(AE000585) L-asparaginase II (ansB) [Helicobacter pylori]	67	42	678
295	1	 1	 375	gi|2276374	DtxR/iron regulated lipoprotein precursor [Corynebacterium	67	43	375
					d iphtheriae]
1	7	4898	5146	gnl|PID|e25517 9	unknown [Mycobacterium tuberculosis]	66	56	249
3	1	 389	 3	gnl|PID|e269548	Unknown [Bacillus subtilis]	66	48	387
3	20 	19267 	20805 	gi |39956	IIGlc [Bacillus subtilis]	68	50	1539 
4	3	2545	2718	gi|1787564	(AE000228) phage shock protein C [Escherichia coli]	66	36	174
5	9	13197 	12592 	gi|157 4291	fimbrial transcription regulation repressor (pilB) [Haemophilus	66	46	606
					influ enzae]
9	4	2872	1451	gnl|PID|e26692 8	unknown [Mycobacterium tuberculosis]	66	43	1422†‚
 12	2	1469	1200	gi|520407	orf2; GTG start codon [Bacillus thuringiensis]	66	42	270
 15	12 	10979 	9897	gi|2314738	(AE0000653) translation elongation factor EF-Ts (tsf) [Helicobacter	66	49
					pylori]
 16	2	1 312	 734	gnl|PID|d102245	(AB005554 ) yxbF [Bacillus subtilis]	66	35	579
 22	3	1372	1851	gi|1480916	signal peptidase type II [Lactococcus lactis]	66	38	480
 22	7	5828	7096	g nl|PID|e206261	gamma-glutamyl phosphate reductase [Streptococcus thermophilus]	66	51	1269†‚
 22	20 	16194 	17138 	gnl|PID|e281914	YitL [Bacillus subtilis]	66	50	945
 30	2	 530	 976	gi|2314379	(AE000627) ABC transporter, ATP-binding protein (yhcG)	66	40	447
< td/>				[Helicobacter pylori]
 32	1	⠀‚199	 984	gi|312444	ORF2 [Bacillus caldolyticus]	66	49	786
 33	13 	8352	7234	gi|1387979	44% identity over 302 residues with hypothetical protein from	66	44	1119 
					Synechocystis sp, accession D64006_CD; expression induced by
					environmental stress; some similarity to glycosyl transferases; two
					potential membrane-spanning helices [Bacillus subtil
 34	6	56 58	4708	gnl|PID|e250724	orf2 [Lactobacillus sake]	66	39	951
 34	14 	9792	9574	gi|1590997	M jannaschii predicted coding region MJ0272 [Methanococcus	66	48
					jan naschii]
 35	16 	15163 	14501 	gi|1773352	Cap 5M [Staphylococcus aureus]	66	46	663
 36	9	6173	6976	g i|1518680	minicell-associated protein DivIVA [Bacillus subtilis]	66	35	804
 36	11 	10396 	1082 4 	bbs|155344	insulin activator factor, INSAF [human, Pancreatic insulinoma,	66	43	429
				Peptide Partial, 744 aa] [Homo sapiens]
 48	1	28	1419	gnl|PID|e325204	hypothetical protein [Bacillus subtilis]	66	50	1392 
 48	7	3810	4112	gi|2182574	(AE000090) Y4pE [Rhizobium sp. NGR234]	66	40	303
⠀‚52	4	3595	2789	gi|388565	major cell-binding factor [Campylobacter jejuni]	66	52	807
 54	3	2662	1076	g nl|PID|d101831	glutamine-binding periplasmic protein [Synechocystis sp.]	66	43	1587 
 61	10 	9740	9183	gnl|PI D|e154144	mdr gene product [Staphylococcus aureus]	66	44	558
 72	13 	10893 	11993⠀‚	gi|2313129	(AE000526) H. pylori predicted coding region HP0049 [Helicobacter	66	44
					pylori]
 74	9	1 3267 	12476 	gi|1573941	hypothet ical [Haemophilus influenzae]	66	43	792
 75	1	 2	 868	gi|1574631	nicotinamide mononucleotide transporter (pnuC) [Haemophilus	66	48	867
					influ enzae]
 75	7	53 03	4275	gi|41312	put. EBG repressor protein [Escherichia coli]	66	40	1029 
 82	7	6813	8123	gnl|PID|e255128	trigger factor [Bacillus subtilis]	66	53	1311 
 83	3	 905	1219	pir|C33496|C334	hisC homolog - Bacillus subtilis	66	44	315
 86	10 	9407	8925	gi|683584	shikimate kinase [Lactococcus lactis]	66	41	483
 88	10 	7001	6060	putative fimbrial-associated protein [Actinomyces naeslundii]	66	52	942
1	 951	 4	gi|410118	ORFX19 [Bacillus subtilis]	66	41	948
 93	7	3661	2711	gi|1787936	(Ae000260) f298; This 298 as orf is 51 pct identical (5 gaps) to 297	66	49	951
					residue of an approx. 304 as protein YCSN_BACSU SW; P42972
					[Es cherichia coli]
104	3	1805< /td>	3049	gi|1469784	putative cell division protein ftsW [Enterococcus hirae]	66	48	1245 
106	14 	13576 	14253  	gi|40027	homologous to E. coli gidB [Bacillus subtilis]	66	52	678
107	3	 965	1864	gi|144858	ORF A [Clostridium perfringens]	66	49	900
112	7	5718	6593	DprA [Haemophilus influenzae]	66	43	876
115	1	 3	 302	gi|727367	Hyrlp [Saccharomyces cerevisiae]	66	56	300
122	1	 3	 566	gnl|PID|d101328	YqiY [Bacillus subtilis]	66	36	564
126	8	11759 	11046 	gnl|PID|d101163	ORF3 [Bacillus subtilis]	66	48	714
128	11 	8201	8431	growth associated protein GAP-43 [Xenopus laevis]	66	41	231
131	8	4894	4508	gi| 486661	TMnm related protein [Saccharomyces cerevisiae]	66	39	387
140	3	3236	2574	gi|40056	phoP gene product [Bacillus subtilis]	66	36	663
140	15 	16318 	15434⠀‚	gi|1658189	5,10-methylenetetrahydrofolate reductase [Erwinia carotovara]	66	48	885
146	12 	7926	7636	gnl|PID|d101140	transposase [Synechocystis sp.]	66	42	291
147< /td>	6	7137	6154	gi|472326	66	48	984
					magnu m]
149	6	4435	5430	gnl|PID|d101887	pentose-5-phosphat e-3-epimerase [Synechocystis sp.]	66	46	996
149< /td>	13 	10754 	11575 	gi|4 2371	pyruvate formate-lyase activating enzyme (AA 1-246) [Escherichia	66	42	822
					coli< /i>]
186	4	2578	gnl|PID|d101199	ORF11 [Enterococcus faecalis]	66	4	309
207	2	2340	2597	gn l|PID|e321893	envelope glycoprotein gp160 [Human immunodeficiency virus	66	46	258
				type 1]
210	7	3358	3678< /td>	gi|49318	ORF4 gene product [Bacillus subtilis]	66	46	321
217	8	5143	5355	g i|49538	thrombin receptor [Cricetulus longicaudatus]	66	38	213
220	4	3875	3642	gi|466648	alternate name ORFD of L23635 [Escherichia coli]	66	33	234
223	1	1070	 138	gnl |PID|e247187	zinc finger protein [Bacteriophage phigle]	66	45	933
224	2	1864	2640	gi| 1176399	putative ABC transporter subunit [Staphylococcus epidermidis]	66	41	777
243	1	 3	 872	dbj||AB000617_2	(AB00061 7) YcdH [Bacillus subtilis]	66	45	870
268	2	 891	 568	putative transposase [Streptococcus pyogenes]	66	60	324
322	1	 2	 643	gi|1499836	Zn protease [Methanococcus jannaschii]	66	40	642
5	10 	13909 	13178 	gi |1574292	hypothetical [Haemophilus influenzae]	65	34	732
6	11 	10465 	11190 	gi |142854	homologous to E. coli radC gene product and to unidentified protein	65	48	726
					from Staphylococcus aureus [Bacillus subtilis]
7	2	 647	 405	pir|C64146 |C641	hypothetical protein HI0259 - Haemophilus influenzae (strain RD	65	42	243
					KW20)
7	7	6246	6821	gni|PID|d10132 3	YqhU [Bacillus subtilis]	65	50	576
 10	2	1873	1397	gi|1163111	ORF-1 [Streptococcus pneumoniae]	65	54	477
 16	3	1428	2222	hypothetical protein [Bacillus subtilis]	65	45	795
 21	4	3815	3357	gnl|PID|e314910	hypothetical protein [Staphylococcus sciuri]	65	40	459
 22	34 	25776 	26384⠀‚	gi|1123030	CpxA [Actinobacillus pleuropneumoniae]	65	42	60 9
 43	2	1648	 2 90	gi|1044826	F14E5.1 [Caenorhabditis elegans]	65	38	1359 
 48	13 	10062 	1 0856 	gi|1573390	hypothetical [Haemophilus influenzae]	65	45	795
 48	22 	17521 	16 883 	gi|1573391	hypothetical [Haemophilus influenzae]	65	37	639
 48	25 	19027 	18 533 	gnl|PID|e264484	YCR020c, len:215 [Saccharomyces cerevisiae]	65	38	495
 49	3	3856	5334	putative transcriptional regulator [Bacillus stearothermophilus]	65	32	1479 
 50	6	5337	gi|171963	tRNA isopentenyl transferase [Saccharomyces cerevisiae]	65	42	819
 52	15 	14728 	15 588 	gi|1499745	M. jannaschii predicted coding region MJ0912 [Methanococcus	65	46
					jan naschii]
 59	7	3963	4745	gi|496514	orf zeta [Streptococcus pyogenes]	54	42	783
 68	3	2500	3483	gi|887824	ORF_o310 [Escherichia coli]	65	46	984
 69	3	2171	1077	gnl |PID|e311453	unknown [Bacillus subtilis]	65	42	1095 
 69	7	6029	5325	gi|809660	deoxyribose-phosphate aldolase [Bacillus subtilis]	65	55	705
 71	5	8536	9783	gi|1573224	glycosyl transferase lgtC (GP:U14554_4) [Haemophilus influenzae]	65	42	1248 < /td>
 72	8	7664	8527	gnl|PID|e267589	Unknown, highly similar to several spermidine synthases [Bacillus	65	39	86 4
					subtilis ]
 76	5	5773	4097	gnl|PID|d101723	DNA REPAIR PROTEIN RECN (RECOMBINATION PROTEIN	65	44	1677 
				N). [Escherichia coli]
 76	9	809 9	7875	gi|1574276	exodeoxyribonuclea se, small subunit (xseB) [Haemophilus	65	38	225
					influ enzae]
 84	2	28 70	2352	gi|2313188	(AE000532) conserved hypothetical protein [Helicobacter pylori]	65	41	519
 86	15 	14495 	13407⠀‚	gnl|PID|d101880	3-dehydroquinate synthase [Synechocystis sp.]	65	44	1089 
 87	3	3706	2423	gi|151259< /td>	HMG-CoA reductase (EC 1.1.1.88) [Pseudomonas mevalonii]	65	51	1284 
 88	3	2425	2736	gi|1098510	unknown [Lactococcus lactis]	65	30	213
 89	2	1627	1007	g nl|PID|d102008	(AB001488) SIMILAR TO ORF14 OF ENTEROCOCCUS	65	41	621
					FAECA LIS TRANSPOSON TN916. [Bacillus subtilis]
111	6	6 635	6186	gnl|PID|e246063	NM23/nucleo side diphosphate kinase [Xenopus laevis]	65	50	450
116	1	 3	1016	gnl|PID|d101125	queuosine biosynthesis protein QueA [Synechocystis sp.]	65	44	1014 
123	1	69	 389	gi|498839	ORF2 [Clostridium perfringens]	65	36	321
123	7	6522	7190	DNA-binding response regulator [Thermotoga maritima]	65	39	669
125	3	3821	2859	g nl|PID|e257609	sugar-binding transport protein [Anaerocellum thermophilum]	65	47	963
137	12 	8015	7818	gi|2182574	(AE000090) Y4pE [Rhizobium sp. NGR234]	65	41	198
1 47	4	5021	3884	gi|472329	dihydrolipoamide acetyltransferase [Clostridium magnum]	65	47	1137 
148	2	1053	1931	gnl|PID|d101319	YqgH [Bacillus subtilis]	65	42	879
151	2	3212	4687	g i|304987	EcoE type I restriction modification enzyme M subunit [Escherichia	65	50	1476 
					coli]
156	2	 730	 437	gi|310893	membrane protein [Theileria parva]	65	47	294
164	7	4256	4837	gi|4 10132	ORFX8 [Bacillus subtilis]	65	48	582
169	5	3192	3914	g i|1552737	similar to purine nucleoside phosphorylase (deoD) [Escherichia coli]	65	41	723
176	4	2951	2220	gnl|P ID|e339500	oligopeptide binding lipoprotein [Streptococcus pneumoniae]	65	43	732
195	4	4556	3900	gi|1592142	ABC transporter, probable ATP-binding subunit [Methanococcus	65	40
					jan naschii]
196	1	†‚160	1572	gnl|PID|d102004	(AB001488) PROBABLE UDP-N-	65	51	1413 
				ACETYLMURAMOYLALANYL-D-GLUTAMYL-2 ,6-
					DIAMINOLIGASE (EC 6.3.2.15). [Bacillus subtilis]
204	2	2 246	1215	gi|143156	membrane bound protein [Bacillus subtilis]	65	37	1032 
210	4	1544	1891	ORF1 gene product [Bacillus subtilis]	65	48	348
242	2	1625	 723	gi|1787540	(AE000226) f249; This 249 aa orf is 32 pct identical (8 gaps) to 244	65	42	903
					residues of an approx. 272 as protein AGAR_ECOLI SW: P42902
					[Es cherichia coli]
284	1	 1	 900	gi|559861	clyM [Plasmid pAD1]	65	36	900
304	1	 2	 574	gnl|PID|e290934	unknown [Mycobacterium tuberculosis]	65	52	573
315	1	 2	1483	gi|790694	mannuronan C-5-epimerase [Azotobacter vinelandi]	65	57	1482 
120	1	 3	 569	gnl|PID|d102048	K. aerogenes, histidine utilization repressor; P12380 (199) DNA	65	46	567
					binding [Bacillus subtilis]
358	1	 1	 309	gnl|PID|e323508	YloS protein [Bacillus subtilis]	65	55	309
2	7	7571	6696	gi|1498753	nicotinate-nucleotide pyrophosphorylase [Rhodospirillum rubrum]	64	47	876
6	6	5924	6802	gnl|PID|d10111 1	methionine aminopeptidase [Synechocystis sp.]	64	52	879
8	4	3417	3686	gi|1045935	DNA helicase II [Mycoplasma genitalium]	64	58	270
 11	4	3249	2689	OrfB [Streptococcus pneumoniae]	64	46	561
 15	7	6504	7145	Ycr59c/YigZ homolog [Bacillus subtilis]	64	45	642
 22	11 	9548	9895	gnl|PID|d100581	unknown [Bacillus subtilis]	64	38	348
 22	30 	22503 	2317 4 	gi|289260	comE ORF1 [Bacillus subtilis]	64	44	672
 26	7	14375 	14199 	gi|409286	bmrU [Bacillus subtilis]	64	30	177
 27	2	1510	1334	gi|40795	DdeI methylase [Desulfovibrio vulgaris]	64	51	177
 29	2	 614	 297	gi|2326168	type VII collagen [Mus musculus]	64	50	318
 35	2	 368	 721	pir|JC1151|JC11	hypothetical 20.3K protein (insertion sequence IS1131) -	64	50	354
	< td/>			Agrobacterium tumefaciens (strain PO22) plasmid Ti
 40	1	 3	 449	gi|46970	epiD gene product [Staphylococcus epidermidis]	64	41	447
 40	7	4683	4976	gnl|PID|e325792	(AJ000005) glucose kinase [Bacillus megaterium]	64	45	294
 45	7	8068	6920	subunit of ADP-glucose pyrophosphorylase [Bacillus	64	40	11 49 
					stea rothermophilus]
 51	2	 301	1059	gi|43985	nifS-lik e gene [Lactobacillus delbrueckii]	64	54	759
 51	13 	15251 	1 8397 	gi|2293260	(Af008220) DNA-polymerase III alpha-chain [Bacillus subtilis]	64	46	3147 
 53	3	1157	 555	gi|1574292	hypothetical [Haemophilus influenzae]	64	47	603
 58	2	4236	1606	alanyl-tRNA synthetase (alaS) [Haemophilus influenzae]	64	51	2631 < /td>
 66	1	 3	1259	gi|895749	putative cellobiose phosphotransferase enzyme II″ [Bacillus subtilis]	64	42	1257 
 68	5	5213	6556	gi|436965	[malA] gene products [Bacillus stearothermophilus]	64	47	1344 
 69	6	5356	gnl|PID|d101316	Cdd [Bacillus subtilis]	64	52	408
 74	4	5948	5038	gi|726480	L-glutamine-D-fructose-6-phosphate amidotransferase [Bacillus	64	50	19 11 
					subt ilis]
 75	3	128 3	1465	bbs|133379	TLS-CHOP = fusion protein (CHOP = C/EBP transcription factor,	64	57	183
					TLS = nuclear RNA-binding protein) (human, myxoid liposarcomas
					cells , Peptide Mutant, 462 aa) [Homo sapiens]
 81	13 	14016 	14231 	gi|143175	meth anol dehydrogenase alpha-10 subunit [Bacillus sp.]	64	35	216
 8 3	22 	21851 	22090 	gn l|PID|d01315	YqfA [Bacillus subtilis]	64	44	240
 87	11 	10046 	9300	gnl|PID|e323505	putative Ptcl protein [Bacillus subtilis]	64	43	747
 98	7	5032	5706	gnl|PID|e233880	hypothetical protein [Bacillus subtilis]	64	38	675
105	1	 2	1276	gi|1657503	similar to S. aureus mercury(II) reductase [Escherichia coli]	64	45	1275 
113	7	5136	6410	g nl|PID|d101119	NifS [Synechocystis sp.]	64	50	1275 
119	1	 2	1297	gnl|PID|e320520	hypothetic al protein [Natronobacterium pharaonis]	64	37	1296 
123	3	1125	2156	gnl|PID|e253284	ORF YDL44w [Saccharomyces cerevisiae]	64	40	1032 < /td>
124	5	2331	1780	gnl|PID|d101884	hypothetical protein [Synechocystis sp.]	64	50	552
129< /td>	4	3467	2709	gnl|PID|d101314< /td>	YqeU [Bacillus subtilis]	64	52	759
131	1	 152	 3	gi|1377841	unknown [Bacillus subtilis]	64	42	150
137	11 	7196	7549	hypothetical 20.3K protein (insertion sequence IS1131) -	64	50	354
	< td/>			Agrobacterium tumefaciens (strain PO22) plasmid Ti
139	3	3226	2651< /td>	gi|2293301	(AF008220) YtqB [Bacillus subtilis]	64	44	576
146	10 	6730	5648	mevalonate pyrophosphate decarboxylase [Rattus norvegicus]	64	45	1083 < /td>
147	1	 2	1018	gnl|PID|e137033	unknown gene product [Lactobacillus leichmannii]	64	46	1017 
148	11 	8430	878 3	gi|2130630	(AF000430) dynamin-like protein [Homo sapiens]	64	28	354
156	7	4313	3612	gn l|PID|d102050	transmembrane [Bacillus subtilis]	64	31	702
157	4	1299	2114	g nl|PID|d100892	homologous to Gln transport system permease proteins [Bacillus	64	43	81 6
					subtilis ]
162	6	5880	6362	gi|517204	ORF1, putative 42 kDa protein [Streptococcus pyogenes]	64	58	483
164	13 	9707	8769	homologue of ferric anguibactin transport system permerase protein	64	40	939
					FatD of V. anguillarum [Bacillus subtilis]
175	5	3 906	3598	gi|534045	antiterminator [Bacillus subtilis]	64	39	693
189	10 	6154	6507	response regulator [Lactobacillus plantarum]	64	33	354
191	4	3519	2863	gi|149520	phosphoribosyl anthranilate isomerase [Lactococcus lactis]	64	46	657
202	1	76	1140	gnl|PID|e293806	o-acetylhomo serine sulfhydrylase [Leptospira meyeri]	64	47	1065 
224	1	 234	1571	collagenase (prtC) [Haemophilus influenzae]	64	42	1338 < /td>
231	3	 291	 647	gi|40174	ORF X [Bacillus subtilis]	64	43	357
253	3	 709	1089	pir|JC1151|HC11	hypothetical 20.3K protein (insertion sequence IS1131) -	64	50	381
	< td/>			Agrobacterium tumefaciens (strain PO22) plasmid Ti
265	1	 820	 2	gi|1377832	unknown [Bacillus subtilis]	64	31	819
297	1	 1	 660	gi|1590871	collagenase [Methanococcus jannaschii]	64	48	660
328	1	 263	21	gi|992651	Gln4p [Saccharomyces cerevisiae]	64	41	243
5	4	8730	8098	gi|556885	Unknown [Bacillus subtilis]	64	48	633
 10	6	5178	4483	gi|1573101	hypothetical [Haemophilus influenzae]	63	40	696
 12	11 	9324	9902	gi|806536	membrane protein [Bacillus acidopullulyticus]	63	42	5 79
 15	10 	8897	9187	gi|722339	unknown [Acetobacter xylinum]	63	40	291
 17	2	1031	 309	PlnU [Lactobacillus plantarum]	63	32	723
 18	8	7778	6975	unknown [Bacillus subtilis]	63	45	804
 26	4	9780	7078	gi|142440	ATP-dependent nuclease [Bacillus subtilis]	63	46	2703 
 29	5	3488	4192	gi|1377829	unknown [Bacillus subtilis]	63	35	705
 34	11 	8830	7988	gnl|PID|d101198	ORF8 [Enterococcus faecalis]	63	45	843
 35	3	1187	 876	unknown [Acetobacter xylinum]	63	39	312
 48	15 	12509 	11691  	gi|1573389	hypothetical [Haemophilus influenzae]	63	41	819
 51	11 	12719 	12 189 	gi|142450	ahrC protein [Bacillus subtilis]	63	35	531
 55	4	3979	5022	gi|1708640	YeaB [Bacillus subtilis]	63	41	1044 
 55	15 	13669 	14670 	gnl|PID|e311502	thioredoxine reductase [Bacillus subtilis]	63	44	1002 
 68	10 	9242	8919	sp|P37686|YIAY—	HYP OTHETICAL 40.2 KD PROTEIN IN AVTA-SELB	63	40	324
					INTERGENIC REGION (F382)
 86	7	6554	5685	gi|1574382	lic-1 operon protein (licD) [Haemophilus influenzae]	63	41	870
 88	8	6085	5180	putative fimbrial-associated protein [Actinomyces naeslundii]	63	43	906
 96	8	5858	6484	orflgyrb gene product [Streptococcus pneumoniae]	63	38	627
100	1	 240	1940	fucosidase [Dictyostelium discoideum]	63	36	1701 < /td>
104	4	3063	5765	gi|144985	phosphoenolpyrubate carboxylase [Corynebacterium glutamicum]	63	46	2703 < /td>
106	8	9189	8554	gi|533099	endonuclease II [Bacillus subtilis]	63	45	636
122	6	4704	4886	g nl|PID|d101139	transposase [Synechosystis sp.]	63	39	183
128< /td>	7	4517	5203	gnl|PID|d101434< /td>	orf2 [Methanobacterium thermoautotrophicum]	63	50	687
137	4	 963	1 547	gi|472920	v-type Na-ATPase [Enterococcus hirae]	63	27	585
142	7	4100	4585	gnl| PID|e313025	hypothetical protein [Bacillus subtilis]	63	44	486
159	5	1741	2571	g i|1787043	(AE000184) f271; This 271 aa orf is 24 pct identical (16 gaps) to 265	63	39	831
					residues of an approx. 272 aa protein YIDA_ECOLI SW: PO9997
					[Es cherichia coli]
171	12 	8 803	14406 	gnl|PID|e324918	Iga1 protease [Streptococcus sanguis]	63	48	5604 
177	1	 3	 347	gi|1773150	hypothetical 14.8kd protein [Escherichia coli]	63	34	345
178	2	 423	 917	g i|722339	unknown [Acetobacter xylinum]	63	41	495
178	3	 794	1012	gi|1591582	cobalamin biosynthesis protein N [Methanococcus jannaschii]	63	36	219
195	1	1377	 175	ftsQ [Enterococcus hirae]	63	33	1203 
234	5	1739	1527	gi|1591582	cobalamin biosynthesis protein N [Methanococcus jannaschii]	63	36	213
249	1	81	 257	gi|1000453	TreR [Bacillus subtilis]	63	41	177
283	1	 127	1347	gi|396486	ORF8 [Bacillus subtilis]	63	44	1221 
293	3	2804	3466	unknown [Acetobacter xylinum]	63	37	663
311	1	 905	 486	UDP-galactose 4-epimerase [Streptococcus mutans]	63	46	420
324	1	 2	 556	gi|1477741	histidine periplasmic binding protein P29 [Campylobacter jejuni]	63	36	555
365	1	 219	13	gi|2252843	(AF013293) No definition line found [Arabidopsis thaliana]	63	33	207
382	1	88	 378	gi|722339	unknown [Acetobacter xylinum]	63	40	291
385	3	 364	 158	(AF013293) No definition line found [Arabidopsis thaliana]	63	33	207
2	1	2495	 288	gnl|PID|e325 007	penicillin-binding protein [Bacillus subtilis]	62	42	2208 
3	23 	23374 	24231 	gn l|PID|e254993	hypothetical protein [Bacillus subtilis]	62	35	858
6	16 	14320 	13193 	gn l|PID|e349614	nifS-like protein [Mycobacterium leprae]	62	37	1128 
7	8	6819	7232	gnl|PID|d10132 4	YqhY [Bacillus subtilis]	62	32	414
7	19 	15466 	14207 	gn l|PID|d101804	beta ketoacyl-acyl carrier protein syntase [Synechocystis sp.]	62	43	1260 
7	21 	17155 	16229 	gn l|PID|e323514	putative FabD protein [Bacillus subtilis]	62	46	927
7	24 	19526 	18519 	gi |1276434	beta-ketoacyl-ACP synthase III [Cuphea wrightii]	62	37	1008 
 12	7	5904	4702	gi|1573768	A/G-specific adenine glycosylase (mutY) [Haemophilus influenzae]	62	43	1203 < /td>
 12	9	8032	8793	gi|1591587	pantothenate metabolism flavoprotein [Methanococcus jannaschii]	62	33	762
 15	11 	9678	9328	pir|JC1151|JC11	hypothetical 20.3K protein (insertion sequence IS1131) -	62	43	351
	< td/>			Agrobacterium tumefaciens (strain PO22) plasmid Ti
 17	4	2609	244 2	gi|1591081	M. jannaschii predicted coding region MJ0374 [Methanococcus	62	43
					jan naschii]
 17	5	3053	2835	gi|149570	role in the expression of lactacin F, part of the laf operon	62	44	219
< td/>				[Lactobacillus sp.]
 22	10 	8627	gnl|PID|d100580	similar to B. subtilis DnaH [Bacillus subtilis]	62	43	912
 30	3	 865	2043	(AE000627) ABC transporter, ATP-binding protein (yhcG)	62	43	1179 
				[Helicobacter pylori]
 33	5	2 235	1636	gi|413976	ipa-52r gene product [Bacillus subtilis]	62	44	600
 38	11 	5689	6123	gi|148231	o251 [Escherichia coli]	62	34	435
 40	17 	14272 	13328 	gnl|PID|d101904	hypothetical protein [Synechocystis sp.]	62	43	945
 4 2	1	 3	 311	gi|1146182	putative [Bacillus subtilis]	62	41	309
 44	2	1267	4005	gi|1786952	(AE000176) o877; 100 pct identical to the first 86 residues of the 100	62	43	2739 
					aa hypothetical protein fragment YBGB_ECOLI SW: P54746
					[Es cherichia coli]
 48	12 	9732	9304	gi|662920	repressor protein [Enterococcus hirae]	62	32	429
 51	8	5664	7181	gn l|PID|e301153	StySKI methylase [Salmonella enterica]	62	44	1518 
 52	3	2791	2099	gi|1183886	integral membrane protein [Bacillus subtilis]	62	41	693
 55	16 	15702 	1470 4 	gnl|PID|e313028	hypothetical protein [Bacillus subtilis]	62	40	999
 59	6	3418	3984	gi|2065483	unknown [Lactococcus lactis lactis]	62	32	567
 63	5	4997	4809	g i|149771	pilin gene inverting protein (PivML) [Moraxella lacunata]	62	28	189
 70	14 	10002 	1073 9 	gi|992977	hplG gene product [Bordetella pertussis]	62	45	738
 71	13 	18790 	203 82 	gi|1280135	coded for by C. elegans cDNA cm21e6; coded for by C. elegans	62	62	1593 
					cDNA cm01e2; similar to melibiose carrier protein
					(thiomethy lgalactoside permease II) [Caenorhabditis elegans]
 71	28 	32217 	32768 	gnl|PID|d101312	62	35	552
 74	7	11666 	10383 	gi|1552753	hypothetical [Escherichia coli]	62	38	1284 
 80	8	9370	9609	gnl|PID|d102002	(AB001488) FUNCTION UNKNOWN. [Bacillus subtilis]	62	46	240
 97	10 	9068	7041	gi|882463	protein-N(pi)-phosphohistidine-sugar phosphotransferase [Escherichia	62	42	2028 
					c oli]
 98	4	2306	3268	gnl|PID|d101496	BraE (integral membrane protein) [Pseudomonas aeruginosa]	62	42	963
102	3	2823	3539	gnl|PID|e313010	hypothetical protein [Bacillus subtilis]	62	24	717
103	3	2795	1242	g nl|PID|d102049	H. influenzae hypothetical ABC transporter; P44808 (974)	62	41	1554 
					[Bacillus subtilis]
111	2	2 035	3462	gi|581297	NisP [Lactococcus lactis]	62	44	1428 
112	4	3154	4080	gi|1574379	lic-1 operon protein (licA) [Haemophilus influenzae]	62	39	927
112	6	4939	5649	gi|1574381	lic-1 operon protein (licC) [Haemophilus influenzae]	62	39	711
124	3	1137	 721	anaerobic ribonucleoside-triphosphate reductase (nrdD) [Haemophilus	62	45	417
					influ enzae]
124	6	3162	2329	gi|609076	leucyl aminopeptidase [Lactobacillus delbrueckii]	62	40	834
126	7	11073 	7516	gnl|PID|d101163	ORF4 [Bacillus subtilis]	62	38	3558 
129	6	4983	4540	zinc finger protein EF6 - Chilo iridescent virus	62	48	444
131	7	4510	4103	gi|1857245	unknown [Lactococcus lactis]	62	42	408
149	2	1923	2579	gi| 1592142	ABC transporter, probable ATP-binding subunit [Methanococcus	62	41
					jan naschii]
149	7	53 60	6055	gnl|PID|e323508	YloS protein [Bacillus subtilis]	62	40	696
156	1	 450	 238	membrane protein [Streptococcus pneumoniae]	62	40	213
156	6	3606	2935	gnl|PID|d102050	transmembrane [Bacillus subtilis]	62	37	672
171	2	1779	2291	g i|43941	EIII-B Sor PTS [Klebsiella pneumoniae]	62	35	513
172	2	 385	 723	gi|895750	putative cellobiose phosphotransferase enzyme III [Bacillus subtilis]	62	39	339
173	3	2599	 893	gi|1591732	cobalt transport ATP-binding protein O [Methanococcus jannaschii]	62	42	1707 < /td>
179	2	 492	1754	gi|1574071	H. influenzae predicted coding region HI1038 [Haemophilus influenzae]	62	38	1263 < /td>
181	6	2856	3707	gi|1777435	LacT [Lactobacillus casei]	62	42	852
185	2	2074	 311	gi |2182397	(AE00073) Y4fN [Rhizobium sp. NGR234]	62	41	1764 
2	1061	1984	gi|450566	transmembrane protein [Bacillus subtilis]	62	37	924
202	3	2583	3473	g i|42219	P35 gene product (AA 1-314) [Escherichia coli]	62	41	891
210	3	1374	1565	gi|49 315	ORF1 gene product [Bacillus subtilis]	62	45	192
211	1	 3	 971	gi|147402	mannose permease subunit III-Man [Escherichia coli]	62	43	969
223	2	1495	1034	gnl|P ID|d101190	ORF2 [Streptococcus mutans]	62	41	462
228	1	34	 909	gi|530063	glycerol uptake facilitator [Streptococcus pneumoniae]	62	44	876
234	2	90	 917	gi|2293259	(AF008220) YtqI [Bacillus subtilis]	62	38	828
282	5	1765	1487	g nl|PID|e273475	galactokinase [Arabidopsis thaliana]	62	33	279
375	1	 1	 159	gi|1674231	(AE000052) Mycoplasma pneumoniae, hypothetical protein homolog;	62	40	159
					similar to Swiss-Prot Accession Number P35155, form B. subtilis
					[Mycoplasma pneumoniae]
385	5	 584	 357	gi|1573353	outer membrane integrity protein (tolA) [Haemophilus influenzae]	62	47	228
3	19 	18550 	19269 	gi |606162	ORF_f229 [Escherichia coli]	61	41	720
7	4	2725	3225	gi|2114425	similar to Synechocystis sp. hypothetical protein, encoded by	61	42	501
					GenBank Accession Number D64006 [Bacillus subtilis]
 17	6	3326	3054	gi|149569	lactacin F [Lactobacillus sp.]	61	43	273
 4 4	3	4061	4957	gnl|PID|d10106 8	xylose repressor [Synechocystis sp.]	61	38	897
 5 4	11 	8388	7234	gnl|PID|d1 01329	YqjH [Bacillus subtilis]	61	42	1155 
 57	6	3974	6037	gnl|PID|d101316	YqfK [Bacillus subtilis]	61	42	2064 
 58	5	7356	6565	sp|P45169|POTC—	SPERMID INE/PUTRESCINE TRANSPORT SYSTEM PERMEASE	61	34	792
					PROTEIN POTC.
 67	1	 3	 692	gi|537108	ORF_f254 [Escherichia coli]	61	46	690
 68	9	8816	7890	gi| 19501	pPLX12 gene product (AA 1-184) [Lupinus polyphyllus]	61	41	927
 70	15 	10737 	1 2008 	gi|992976	bplF gene product [Bordetella pertussis]	61	44	1272 
 72	11 	9759	102 02 	gnl|PID|d101833	carboxynorspermidine decarboxylase [Synechocystis sp.]	61	36	444
 7 6	8	7881	7003	gnl|PID|d10030 5	farnesyl disphosphate syntase [Bacillus stearothermophilus]	61	45	879
 87	4	4914	36 97	gi|528991	unknown [Bacillus subtilis]	61	42	1218 
 87	13 	12311 	11361 	gi|1789683	(AE000407) methionyl-tRNA formultransferase [Escherichia coli]	61	44	951
 91	2	 731	2989	g i|537080	ribonucleoside triphosphate reductase [Escherichia coli]	61	45	2259 
105	3	2711	3499	g nl|PID|d101851	hypothetical protein [Synechocystis sp.]	61	44	789
115< /td>	6	7986	6478	gi|895747	61	36	1491 
123	8	7181	8518	protein histidine kinase [Enterococcus faecalis]	61	40	1338 
126	6	7525	6725	(AE000184) f271; This 271 as orf is 24 pct identical (16 gaps) to 265	61	38	801
					residues of an approx. 272 as protein YIDA_ECOLI SW; PO9997
					[Es cherichia coli]
128	1	11 1	 639	gnl|PID|d101328	YqiY [Bacillus subtilis]	61	41	639
139	7	4794	5054	g i|1022726	unknown [Staphylococcus haemolyticus]	61	41	261
139	9	12632 	5913	gnl|PID|e270014	beta-galactosidase [Thermoanaerobacter ethanolicus]	61	41	6720 
143	1	2552	42	gi|520541	penicillin-binding proteins 1A and 1B [Bacillus subtilis]	61	42	2511 
148	16 	12125 	11 424 	gi|1552743	tetrahydrodipicolinate N-succinyltransferase [Escherichia coli]	61	42	702
162	3	4112	3456	gnl|P ID|d101829	phosphoglycolate phosphatase [Synechocystis sp.]	61	30	657
172< /td>	3	 727	1077	gnl|PID|d10204 8	B. subtilis, cellobiose phosphotransferase system, celA; P46318 (220)	61	44	351
				[Bacillus subtilis]
177	3	1 101	1772	gnl|PID|d100574	unknown [Bacillus subtilis]	61	43	672
202	2	1278	2585	g i|1045831	hypothetical protein (GB:L18965_6) [Mycoplasma genitalium]	61	36	1308 < /td>
224	3	2782	3144	gi|1591144	M. jannaschii predicted coding region MJ0440 [Methanococcus	61	30
					jan naschii]
225	4	33 95	3766	gi|1552774	hypothetical [Escherichia coli]	61	40	372
249	2	 212	 802	g i|1000453	TreR [Bacillus subtilis]	61	42	591
254	2	 843	 484	ORF120 [Escherichia coli]	61	36	360
257	1	 3	 350	gnl|PID|e255315	unknown [Mycobacterium tuberculosis]	61	42	348
293	4	3971	3657	hypothetical 20.3K protein (insertion sequence IS1131) -	61	45	315
	< td/>			Agrobacterium tumefaciens (strain PO22) plasmid Ti
301	1	 949	17	gi|2291209	(AF016424) contains similarity to acyltransferases [Caenorhabditis	61	33	933
					el egans]
373	1	1066	287	gi|393396	Tb-292 membrane associated protein [Trypanosoma brucei subgroup]	61	38	780
3	24 	24473 	24955 	gi |537093	ORF_o153b [Escherichia coli]	60	27	483
6	5	4636	5739	gi|2293258	(AF008220) YtoI [Bacillus subtilis]	60	35	1104 
6	12 	11936 	11187 	gi |293017	ORF3 (put.); putative [Lactococcus lactis]	60	44	750
 17	13 	6708	6484	lactacin F [Lactobacillus sp.]	60	32	225
 1 8	7	6977	5670	gi|1788140	(AE000278) o481; This 481 as orf is 35 pct identical (19 gaps) to 309	60	43	1308 
					residues of an approx. 856 aa protein NOL1_HUMAN SW: P46087
					[Es cherichia coli]
 20	15 	15878 	17167 	gnl|PID|d100584	u nknown [Bacillus subtilis]	60	44	1290 
 22	1	 1	 243	gnl|PID|d102050	transmem brane [Bacillus subtilis]	60	36	243
 32	10 	8296	8964	gi|2293275	(AF008220) YtaG [Bacillus subtilis]	60	37	669
 38	15 	8837	9697	gi|40023	B. subtilis genes rpmH, rnpA, 50kd, gidA and gidB [Bacillus subtilis]	60	35	861
 43	6	6610	5944	gi|171787	protein kinase 1 [Saccharomyces cerevisiae]	60	36	2667 < /td>
 44	1	 1	1269	gnl|PID|e235823	unknown [Schizosaccharomyces pombe]	60	44	1269 
 45	10 	11138 	103 68 	gi|397488	1,4-alpha-glucan branching enzyme [Bacillus subtilis]	60	43	771
 48	19 	15766 	1437 8 	gnl|PID|e205173	orf1 [Lactobacillus helveticus]	60	39	1389 < /td>
 48	21 	16727 	gnl|PID|d102041	(AB002668) unnamed protein product [Haemophilus	60	32	225
					actin omycetemcomitans]
 50	1	 2	 898	gnl|PID|e246537	ORF286 protein [Pseudomonas stutzeri]	60	31	897
 62	2	 638	1177	unknown [Bacillus subtilis]	60	42	540
 68	4	3590	5203	gi|1573583	H. influenzae predicted coding region HI0594 [Haemophilus	60	36	1614 
					i nfluenzae]
 70	11 	5781	6182	gnl|PID|d102014	(AB0 01488) SIMILAR TO YDFR GENE PRODUCT OF THIS	60	33	402
					ENTRY (YDFR_BACSU) [Bacillus subtilis]
 70	12 	6343	8133	gnl|PID|e324970	hypot hetical protein [Bacillus subtilis]	60	38	1791 
 71	8	11701 	1415 7 	gi|580866	ipa-12d gene product [Bacillus subtilis]	60	33	2457 
 74	8	12509 	1166 4 	gnl|PID|d101832	phosphatidate cytidylyltransferase [Synechocystis sp.]	60	45	846
 7 6	4	4116	3367	gi|2352096	orf; similar to serine/threonine protein phosphatase [Fervidobacterium	60	39	750
					islandicum]
 80	4	7665	gi|1786420	(AE000131) f86; 100 pct identical to GB: ECODINJ_6	60	30	294
					ACCESSION: D38582 [Bacillus subtilis]
 81	6	4073	4522	gi|147402	mannose permease subunit III-Man [Escherichia coli]	60	35	450
 86	1	 940	 155	gi|143177	putative [Bacillus subtilis]	60	26	786
 92	1	 1	 192	gi|396348	homoserine transsuccinylase [Escherichia coli]	60	45	192
 93	14 	10619 	9384	gi|1788389	(AE000297) o464; This 464 aa orf is 33 pct identical (9 gaps) to 331	60	27	1236 
					residues of an approx. 416 aa protein MTRC_NEIGO SW: P43505
					[Es cherichia coli]
 94	5	554 8	8121	gnl|PID|e329895	(AJ000496) cyclic nucleotide-gated channel beta subunit [Rattus	60	50	2574  
					norveg icus]
 97	7	539 7	4533	gi|1591396	transketolase′ [Methanococcus jannaschii]	60	43	864
102	2	2081	2833	gnl|PID|e320929	hypothetical protein [Mycobacterium tuberculosis]	60	43	753
106	9	9773	9183	YlbN protein [Bacillus subtilis]	60	31	591
113	8	6361	6837	g i|466875	nifU; BB1496_C1_157 [Mycobacterium laprae]	60	43	477
115	2	2755	 524	g nl|PID|e328143	(AJ000332) Glucosidase II [Homo sapiens]	60	32	2232 
122	7	4763	5068	transposase [Synechocystis sp.]	60	39	306
127< /td>	8	4510	5283	gi|1777938	60	38	774
138	4	3082	2672	g nl|PID|e325196	hypothetical protein [Bacillus subtilis]	60	36	411
139	1	 177	 4	gnl|PID|d100680	ORF [Thermus thermophilus]	60	39	174
139	11 	14520 	13 009 	gi|537145	ORF_f437 [Escherichia coli]	60	30	1512 
140	2	2592	1249	g i|1209527	protein histidine kinase [Enterococcus faecalis]	60	37	1344 
141	1	 210	1049	gi|463181	E5 ORF from bp 3842 to 4081; putative [Human papillomavirus	60	34	840
					type 33]
141	5	5368	6405	gi|145362	tyrosine-sensitive DAHP synthase (aroF) [Escherichia coli]	60	41	1038 
142	6	3558	4049	g i|600711	putative [Bacillus subtilis]	60	37	492
148	10 	7742	8713	hypothetical protein [Bacillus subtilis]	60	27	972
153	5	3667	4278	g i|2293322	(AF008220) branch-chain amino acid transporter [Bacillus subtilis]	60	42	612
155	1	1413	 748	gi|2104504	putative UDP-glucos dehydrogenase [Escherichia coli]	60	40	666
158	3	3116	2472	gnl|P ID|d100872	a negative regulator of pho regulon [Pseudomonas aeruginosa]	60	37	645
159	3	 778	3386	product highly similar to Bacillus anthracis CapA [Bacillus subtilis]	60	48	609
163	7	8049	8468	g nl|PID|d101313	YqeN [Bacillus subtilis]	60	38	420
170	3	4130	2688	g i|1574179	H. influenzae predicted coding region HI1244 [Haemophilus	60	39	1443 
					i nfluenzae]
171	7	4717	5901	gi|606076	ORF_o384 [Escherichia coli]	60	44	1185 
183	3	2440	2135	g i|1877427	repressor [Streptococcus pyogenes phage T12]	60	38	306
191< /td>	10 	9444	8428	gi|415664	catabolite control protein [Bacillus megaterium]	60	42	1017 < /td>
200	1	 139	1083	gi|438462	transmembrane protein [Bacillus subtilis]	60	37	945
201	3	3895	1928	g i|475112	enzyme IIabe [Pediococcus pentosaceus]	60	39	1968 
214	15 	10930 	10439 	gi|1573407	hypothetical [Haemophilus influenzae]	60	39	492
218	4	2145	2363	gi|608520	myosin heavy chain kinase A [Dictyostelium discoideum]	60	31	219
226	4	2518	2351	gi|437705	hyaluronidase [Streptococcus pneumoniae]	60	53	168
242	1	 725	 3	gi|43938	Sor regulator [Klebsiella pneumoniae]	60	41	723
245	1	 1	 288	gi|304897	EcoE type I restriction modification enzyme M subunit [Escherichia	60	56	288
					coli< /i>]
251	1	 905	45	gi|671632	unknown [Staphylococcus aureus]	60	36	861
259	1	 969	82	gi|153794	rgg [Streptococcus gordonii]	60	32	888
260	2	1492	1662	p ir|S31840|S318	probable transposase - Bacillus stearothermophilus	60	26	1 71
274	1	 836	96	gi|1592173	N-ethylammeline chlorohydrolase [Methanococcus jannaschii]	60	40	741
308	1	 463	 2	gi|1787397	(AE000214) o157 [Escherichia coli]	60	43	462
318	1	 3	 308	gnl|PID|e137594	xerC recombinase [Lactobacillus leichmannii]	60	42	306
344	1	73	 522	gi|509672	repressor protein [Bacteriophage Tuc2009]	60	32	450
5	1	 576	 4	gi|2293147	(AF008220) YtxM [Bacillus subtilis]	59	31	573
7	22 	18140 	17142 	gn l|PID|e280724	unknown [Mycobacterium tuberculosis]	59	39	999
 10	1	1413	 4	gi|1353880	sialidase L [Macrobdella decora]	59	41	1410 
 15	6	6463	5156	F1 [Bacillus subtilis]	59	35	1308 
 22	2	 479	1393	gi|142469	als operom regulatory protein [Bacillus subtilis]	59	34	915
 22	5	2698	4614	gnl|PID|e280623	PCPA [Streptococcus pneumoniae]	59	44	1917 < /td>
 30	1	 208	558< /td>	gnl|PID|e233868	hypothetical protein [Bacillus subtilis]	59	37	351
 30	4	3678	2455	gnl|PID|e202290	unknown [Lactobacillus sake]	59	33	1224 
 35	13 	12201 	1107 1 	gnl|PID|e238664	hypothetical protein [Bacillus subtilis]	59	35	1131 
 35	14 	13288 	12182 	gi|1657647	Cap8H [Staphylococcus aureus]	59	39	1107 
 36	18 	18076 	17 897 	gi|1500535	M. jannaschii predicted coding region MJ1635 [Methanococcus	59	33
					jan naschii]
 38	12 	6172	7137	gi|2293239	(AF008220) YtxK [Bacillus subtilis]	59	34	966
 42	3	1952	3361	gi|1684845	pinin [Canis familiaris]	59	40	1410 < /td>
 50	3	2678	1728	gnl|PID|d101329	YqjK [Bacillus subtilis]	59	41	951
 56	5	1870	2388	gnl|PID|e137594	xerC recombinase [Lactobacillus leichmannii]	59	41	519
 61	6	6812	5628	gnl|PID|e311516	aminotransferase [Bacillus subtilis]	59	40	1185 
 67	5	2382	3023	gi|1146190	2-keto-3-deoxy-6-phosphogluconate aldolase [Bacillus subtilis]	59	36	642
 69	10 	8567	8899	gi|1573628	antothenate kinase (coaA) [Haemophilus influenzae]	59	38	333
 87	12 	11383 	10 055 	gnl|PID|e323504	putative Fmu protein [Bacillus subtilis]	59	44	1325 
113	14 	13927 	15 894 	gi|1673731	(AE000010) Mycoplasma pneumoniae, fructose-permease IIBC	59	43	1968 
					component; similar to Swiss-Prot Accession Number P20966, from
					E. coli [Mycoplasma pneumoniae]
115	8	8766	8521	gi|1590886	M. jannaschii predicted coding region MJ0110 [Methanococcus	59	38
					jan naschii]
119	2	19 66	1526	gnl|PID|e209005	homologous to ORF2 in nrdEF operons of E. coli and S. typhimurim	59	43	441
					[Lactococcus lactis]
128	17 	13438 	13178 	gnl|PID|e279632	u nknown [Mycobacterium tuberculosis]	59	38	261
140	22 	23903 	23 388 	gi|482922	protein with homology to pail repressor of B. subtilis [Lactobacillus	59	516
					< HIL>delbrueckii]
148	1 3 	9697	9014	gnl|PID|d102005	59	32	684
					H. INFLUENZAE AND SYNECHOCYSTIS. [Bacillus subtilis]
149	10 	8244	gi|710422	cmp-binding-f actor 1 [Staphylococcus aureus]	59	40	1032 
164	9	6993	6013	gnl|PID|d100965	ferric anguibactin-binding protein precursor FabT of V. anguillarum	59	41	981
					[Bacillus subtilis]
164	12 	7823	gni|PID|d100964	homolog ue of ferric anguibactin transport system permerase protein	59	35	1014 
				FatC of V. anguillarum [Bacillus subtilis]
177	2	4 01	1072	gi|289759	coded for by C. elegans cDNA CE2G3 (GenBank:Z14728); putative	59	40	672
					[Caenorhabditis elegans]
177	7	38 41	4200	gi|2313445	(AE000551) H. pylori predicted coding region HP0342 [Helicobacter	59	38
					pylo ri]
183	4	2768	2508	gi|509672	repressor protein [Bacteriophage Tuc2009]	59	50	261
186	6	3398	2820	gi |606080	ORF_o290; Geneplot suggests frameshift linking to o267, not found	59	38	579
				[Escherichia coli]
190	3	3120< /td>	1711	gi|1613768	histidine protein kinase [Streptococcus pneumoniae]	59	32	1410 < /td>
194	2	1621	1019	gnl|PID|d100579	unknown [Bacillus subtilis]	59	40	603
198	7	5205	4306	g nl|PID|e313073	hypothetical protein [Bacillus subtilis]	59	38	900
220	5	4362	3958	g nl|PID|d101322	YqhL [Bacillus subtilis]	59	46	405
242	3	1573	2367	g i|1787045	(AE000184) f308; This 308 aa orf is 35 pct identical (35 gaps) to 305	59	42	795
					residues of an approx. 296 aa protein PFLC_ECOLI SW: P32675
					[Es cherichia coli]
247	2	1154< /td>	1480	gi|40073	ORF107 [Bacillus subtilis]	59	39	327
256	1	 868	 2	gnl|PID|d101924	hemolysin [Synechocystis sp.]	59	39	867
258< /td>	1	65	 820	gi|2246532	ORF 73, contains large complex repeat CR 73 (Kaposi's	59	20	756
					sarcoma-associated herpesvirus]
270	1	 386	1126	gnl|PID|d102092	YfnB [Bacillus subtilis]	59	40	741
281	1	 552	 166	putative [Lactococcus lactis]	59	31	387
309	1	 3	 479	gi|405879	yeiH [Escherichia coli]	59	38	477
363	1	 2	1894	gi|915208	gastric mucin [Sus scrofa]	59	31	1893 
387	2	 425	84	gi|160671	S antigen precursor [Plasmodium falciparum]	59	44	342
5	5	11223 	10465 	gnl|PI D|d101812	LumQ [Synechocystis sp.]	58	29	759
 2 9	4	2098	3513	gnl|PID|d10047 9	Na+ -ATPase subunit J [Enterococcus hirae]	58	39	1416 
 30	5	4058	3651	ATP binding protein of transport ATPases [Bacillus firmus]	58	34	408
 33	6	2983	2210	g nl|PID|d101164	unknown [Bacillus subtilis]	58	45	774
 36	8	5316	6179	gi|1518679	orf [Bacillus subtilis]	58	32	864
 43	5	5926	3971	gi|1788150	(AE000278) protease II [Escherichia coli]	58	37	1956 
 46	5	3704	5221	gnl|PID|e267329	Unknown [Bacillus subtilis]	58	42	1518 
 48	14 	11722 	11066 	gnl|PID|d101771	thiamin biosynthetic bifunctional enzyme [Synechocystis sp.]	58	34	657
 5 2	1	1229	 3	gnl|PID|d101291	reductase [Pseudomonas aeruginosa]	58	35	1227 < /td>
 53	2	 702	 4 12	gi|2313357	(AE000545) cytochrome c biogenesis protein (ccdA) [Helicobacter	58	25
					pylo ri]
 58	4	6586< /td>	5498	gi|147329	transport protein [Escherichia coli]	58	41	1089 
 69	5	4934	3807	gnl|PID|e311492	unknown [Bacillus subtilis]	58	41	1128 
 71	27 	31357 	32277 	gi|2408014	hypothetical protein [Schizosaccharomyces pombe]	58	33	921
 72	4	3586	2882	gi |18694	nodulin-21 (AA 1-201) [Glycine max]	58	34	705
 7 4	3	4937	4230	gi|2293252	(AF008220) YtmO [Bacillus subtilis]	58	33	708
 79	4	4594	3422	gi|1217989	ORF3 [Streptococcus pneumoniae]	58	44	1173 < /td>
 82	8	10585 	81 71	gi|882711	exonuclease V alpha-subunit [Escherichia coli]	58	38	2415 
 86	17 	16017 	1533 7 	gi|47642	5-dehydroquinate hydrolyase (3-dehydroquinase) [Salmonella typhi]	58	32	681
 97	2	 931	 560	rgg [Streptococcus gordonii]	58	32	372
108	2	 358	2724	gi|537020	vacB gene product [Escherichia coli]	58	37	2367 
111	5	4593	5240	g i|1592142	ABC transporter, probable ATP-binding subunit [Methanococcus	58	36
					jan naschii]
120	3	44 21	5110	gni|PID|d101320	YqgX [Bacillus subtilis]	58	47	690
128	16 	13131 	12673⠀‚	gi|662919	ORF U [Enterococcus hirae]	58	42	459
132	3	6174	4939	gi|1 800301	macrolide-efflux determinant [Streptococcus pneumoniae]	58	35	1236 < /td>
133	1	 111	 890	gnl|PID|e269488	Unknown [Bacillus subtilis]	58	36	780
160	11 	8615	9865	ORF1 [Lactococcus lactis]	58	39	1251 
161	6	6268	6849	gnl|PID|d101024	DJ-1 protein [Homo sapiens]	58	32	582
169	1	 214	 2	gnl|PID|d100447	translation elongation factor-3 [Chlorella virus]	58	31	213
18 7	1	 487	 2	gi|475114	regulatory protein [Pediococcus pentosaceus]	58	38	486
187	6	4384	4620	dessication-related protein [Craterostigma plantagineum]	58	55	237
190	2	1464	1640	competence pheromone [Streptococcus gordonii]	58	38	177
192	2	2012	1344	g nl|PID|d100556	rat GCP360 [Rattus rattus]	58	44	669
206	1	1292	 696	g nl|PID|e202579	product similar to WrbA [Lactobacillus sake]	58	35	597
216	2	2333	 555	gnl |PID|e325036	hypothetical protein [Bacillus subtilis]	58	33	1779 
217	5	5250	4321	cellobiose phosphotransferase enzyme II″ [Bacillus	58	38	93 0
					stearoth ermophilus]
217	7	5636	5106	gnl|PID|d102048	B . subtilis cellobiose phosphotransferase system celB; P46317 (998)	58	44	531
				transmembrane [Bacillus subtilis]
232	1	 2	 811	gi|1573777	cell division ATP-binding protein (ftsE) [Haemophilus influenzae]	58	39	810
264	1	 2	 715	gi|973330	NatA [Bacillus subtilis]	58	32	714
280	1	33	 767	gi|1786187	(AE000111) hypothetical 29.6 kD protein in thrC-talB intergenic	58	31	735
				region [Escherichia coli]
306	1	 84 5	 3	gnl|PID|e334780	YlbL protein [Bacillus subtilis]	58	47	843
360	3	1556	1092	s p|P46351|YZGD—	HYPOTHETICAL 45.4 KD PROTEIN IN THIAMINASE I	58	32	465
	< td/>			5′REGION
363	5< /td>	2160	1867	gi|160671	S antigen precursor [Plasmodium falciparum]	58	51	294
372	1	 806	 3	gi|393394	Tb-291 membrane associated protein [Trypanosoma brucei subgroup]	58	37	804
382	2	 749	 519	hypothetical 20.3K protein (insertion sequence IS1131) -	58	41	231
	< td/>			Agrobacterium tumefaciens (strain PO22) plasmid Ti
3	0	8409	7471	gi|1499745	M. jannaschii predicted coding region MJ0912 [Methanococcus	57	38
					jan naschii]
 10	10 	7674	7507	gi|1737169	homologue to SKP1 [Arabidopsis thaliana]	57	30	168
 11	1	 2	 412	gnl|PID|d100139	ORF [Acetobacter pasteurianus]	57	42	411
 31	4	2032	1388	gi|2293213	(AF008220) YtpR [Bacillus subtilis]	57	37	645
 33	11 	6931	6449	gnl|PID|e324949	hypothetical protein [Bacillus subtilis]	57	36	483
 45	5	5446	5060	gi|1592204	phosphoserine phosphatase [Methanococcus jannaschii]	57	44	387
 49	7	6523	7632	PTS enzyme-II fructose [Xanthomonas campestris]	57	35	1110 < /td>
 52	5	4520	6850	gi|1574144	single-stranded-DNA-specific exonuclease (recJ) [Haemophilus	57	35	2331 
					i nfluenzae]
 53	5	1795	gi|1843580	replicase-ass ociated polyprotein [oat blue dwarf virus]	57	46	285
†‚63	6	5312	4995	gi|2182608	(AE000094) Yr4J [Rhizobium sp. NGR234]	57	39	318
⠀‚72	15 	13883 	13059 	gnl|PID|d100892	homologous to SwissPrto:YIDA_ECOLI hypothetical protein	57	40	825
					[Bacillus subtilis]
 79	2	2561	1815	gnl|PID|d100965	homologue of NADPH-flavin oxidoreductase Frp of V. harveyi	57	44	747
					[Bacillus subtilis]
 82	9	9596	9763	gi|1206045	short region of similarity to glycerophosphoryl diester	57	35	168
					phosphodiesterases [Caenorhabditis elegans]
 86	16 	15371 	14493 	gi|1787983	(AE 000264) o288; 92 pct identical (1 gaps) to 222 residues of	57	34	879
					fragment YDIB_ECOLI SW: P28244 (223 aa) [Escherichia coli]
 93	3	169 5	1177	gi|1500003	mutator mutT protein [Methanococcus jannaschii]	57	33	519
 96	6	3026	4519	threonine synthase [Arabidopsis thaliana]	57	43	1494 
 99	14 	17211 	18212 	gi|773349	BirA protein [Bacillus subtilis]	57	44	1002 
112	8	7448	7903	M. jannaschii predicted coding region MJ0678 [Methanococcus	57	30
					jan naschii]
113	16 	18328 	pir|A45605|A456	mature-parasite-infected erythrocyte surface antigen MESA -	57	22	300
	< td/>			Plasmodium falciparum
123	2	 343	1110	pir|F64149|F641	hypothet ical protein HI0335 - Haemophilus influenzae (strain Rd	57	38	768
					KW20)
123	4	2108	2884	gnl|PID|d102148	(AB001 684) sulfate transport system permease protein [Chlorella	57	39	7 77
					vulgari s]
127	10 	6477	5587	gi|1573082	nitrogenase C (nifC) [Haemophilus influenzae]	57	35	891
128	13 	9251	9790	gi|153692	pneumolysin [Streptococcus pneumoniae]	57	38	540
131	4	2139	1363	gi|42081	nagD gene product (AA 1-250) [Escherichia coli]	57	36	777
136	1	 214	1221	bbs |148453	SpA = endocarditis immunodominant antigen [Streptococcus	57	44
					sorbinus, MUCOB 263, Peptide, 1566 aa) [Streptococcus sobrinus]
140	25 	26851 	gi|505576	beta- glucoside permease [Bacillus subtilis]	57	38	1851 
141	6	6395	7438	unknown [Schizosaccharomyces pombe]	57	41	1044 
144	3	3231	2785	gnl|PID|d100139	ORF [Acetobacter pasteurianus]	57	42	447
155	4	5454	4564	glycosyl transerase [Erwinia amylovora]	57	34	891
159	9	4877	5854	gi|290509	o307 [Escherichia coli]	57	35	978
167	11 	9710	9429	g nl|PID|d100139	ORF [Acetobacter pasteurianus]	57	42	462
171	6	4023	4436	mannose permease subunit III-Man [Escherichia coli]	57	29	414
178	4	2170	1076	gnl|P ID|d102004	(AB001488) ATP-DEPENDENT RNA HELICASE DEAD	57	39	1095 
					HOMOLOG. [Bacillus subtilis]
190	1	⠀‚145	1455	gi|149420	export/processi ng protein [Lactococcus lactis]	57	30	1311 
198	1	 298	95	gi|522268	unidentified ORF22 [Bacteriophage bIL67]	57	36	204
20 3	2	3195	2110	gnl|PID|e28391 5	orf c01003 [Sulfolobus solfataricus]	57	41	1086†‚
205	1	40	 507	gi|1439527	EIIA-man [Lactobacillus curvatus]	57	28	468
214	7	4243	3797	g nl|PID|d102049	H. influenzae, ribosomal protein alanine acetyltransferase; P44305	57	48	447
< td/>				(189) [Bacillus subtilis]
268	3	1 767	1276	gi|43979	L. curvatus small cryptic plasmid gene for rep protein [Lactobacillus	57	36
					curvatus]
351	1	 324	34	gnl|PID|e275871	T03F6.b [Caenorhabditis elegans]	57	31	291
386	1	226	 2	gi|160671	S antigen precursor [Plasmodium falciparum]	57	45	225
5	5	10486 	8777	gi|405857< /td>	yehU [Escherichia coli]	56	33	1710 
8	5	3674	3910	gi|467199	pksC; L518_F1_2 [Mycobacterium laprae]	56	39	237
 10	3	3442	1874	g nl|PID|d101907	sodium-coupled permease [Synechocystis sp.]	56	36	1569 
 21	1	1880	 333	gi|23139 49	(AE000593) osmoprotection protein (proWX) [Helicobacter pylori]	56	33	1548 
 22	29 	21968 	22 456 	gnl|PID|d102001	(AB001488) PROBABLE ACETYLTRANSFERASE. [Bacillus	56	37	48 9
					subtilis ]
 27	1	1361	 3	gi|215132	ea59 (525) [Bacteriophage lambda]	56	30	1359 
 28	9	4667	4278	DNA repair protein RAD2 [Methanococcus jannaschii]	56	29	390
 33	1	 3	 386	gnl|PID|d100139	ORF [Acetobacter pasteurianus]	56	41	384
 36	7	5122	5397	pir|PQ0053|PQ00	hypothetical protein (proC 3′ region) - Pseudomonas aeruginosa	56	28	276
					(strain PAO) (fragment)
 40	4	3137	4318	gi|1800301	macrolide-efflux determinate [Streptococcus pneumoniae]	56	27	1182 < /td>
 40	16 	12511 	gnl|PID|e217602	PlnU [Lactobacillus plantarum]	56	38	681
 48	17 	13775 	130 23 	gi|143729	transcription activator [Bacillus subtilis]	56	35	753
 75	4	1674	2594	gnl|PID|d102036	membrane protein [Bacillus stearothermophilus]	56	25	921
 85	3	1842	14 59	gnl|PID|d100139	ORF [Acetobacter pasteurianus]	56	41	384
 89	7	5815	4940	gi|853777	product similar to E. coli PRFA2 protein [Bacillus subtilis]	56	42	876
105	2	1360	2718	g nl|PID|d101913	hypothetical protein [Synechocystis sp.]	56	37	1359 
112	3	2151	3194	gi|537201	ORF_o345 [Escherichia coli]	56	31	1044 
113	4	2754	2963	g nl|PID|d100340	ORF [Plum pox virus]	56	28	210
12 2	3	1203	2054	gi|1649035	high-affinity periplasmic glutamine binding protein [Salmonella	56	30	852
					typhim urium]
124	8	3939	3694	gnl|PID|e248893	unknown [Mycobacterium tuberculosis]	56	27	246
125	4	4403	4107	human non-muscle myosin heavy chain [Homo sapiens]	56	32	297
127	11 	6608	6405	(AE000073) Y4fN [Rhizobium sp. NGR234]	56	35	204
1 34	5	4769	3849	gnl|PID|d1018 70	hypothetical protein [Synechocystis sp.]	56	39	921
137< /td>	10 	6814	7245	gi|1592011	sulfate permease (cysA) [Methanococcus jannaschii]	56	34	432
142	8	5019	4582	pir|A47071|A470	orf1 immediately 5′ of nifS - Bacillus subtilis	56	29	438
146	8	4676	3660	gn l|PID|d101911	hypothetical protein [Synechocystis sp.]	56	32	1017 
148	3	1906	2739	gnl|PID|d101 099	phosphate transport system permease protein PstA	56	36	834
					[Synechocystis sp.]
150	4	4449	274 3	gnl|PID|e304628	probably site-specific recombinase of the resolvase family enzyme	56	27	1707 
				[Bacteriophage TP21]
172	1	 2	 208	gi|1787791	(AE000249) f317; This 317 aa orf is 27 pct identical (16 gaps) to 301	56	34	207
					residues of an approx. 320 as protein YXXC_BACSU SW: P39140
					[Es cherichia coli]
172	7	4979< /td>	5668	gi|396293	similar to Bacillus subtilis hypoth. 20 kDa protein, in tsr 3′ region	56	40	690
< td/>				[Escherichia coli]
186	7	3732< /td>	3367	gi|1732200	PTS permease for mannose subunit IIPMan [Vibrio furnissii]	56	36	366
187	2	2402	 819	virR49 protein - Streptococcus pyogenes (strain CS101, serotype	56	35	1584 
					M49)
204	2772	2239	gi|606376	ORF _o162 [Escherichia coli]	56	35	534
206	2	3342	1633	gi|55 9861	clyM [Plasmid pAD1]	56	38	1710 
219	3	1689	1096	gi|1146197< /td>	putative [Bacillus subtilis]	56	27	594
230	2	 409	1485	pir|C60328|C603	hypothetical protein 2 (sr 5′ region) - Streptococcus mutans (strain	56	40	1077 
					OMZ175, serotype f)
233	4	2930	3268< /td>	gi|1041785	rhoptry protein [Plasmodium yoelii]	56	24	339
273	2	1543	2724	gi| 143089	iep protein [Bacillus subtilis]	56	32	1182 
353	1	 1	 516	gnl|PID|e325000	hypothet ical protein [Bacillus subtilis]	56	41	516
359	1	87	 641	gi|1786952	(AE000176) o877; 100 pct identical to the first 86 residues of the	56	35	555
					100 aa hypothetical protein fragment YBGB_ECOLI SW: P54746
					[Es cherichia coli]
363	7	4482< /td>	4198	gi|1573353	outer membrane integrity protein (tolA) [Haemophilus influenzae]	56	38	285
376	1	 2	 508	gnl|PID|e325031	hypothet ical protein [Bacillus subtilis]	56	33	507
 18	1	 836	 177	gnl|PID|d100872	a negative regulator of pho regulon [Pseudomonas aeruginosa]	55	31	660
 28	4	1824	1618	STAT protein [Dicytostelium discoideum]	55	40	207
 29	6	4496	5041	unknown protein [Anabaena sp.]	55	31	546
 3 8	16 	9695	10702 	gi|580 905	B. subtilis genes rpmH, rnpA, 50kd, gidA and gibB [Bacillus subtilis]	55	31	1008 
 49	5	5727	6182	gi|1786951	(AE000176) heat-responsive regulatory protein [Escherichia coli]	55	29	456
 51	4	2381	3241	gnl |PID|d101293	YbbA [Bacillus subtilis]	55	42	861
 52	9	9640	10866 	gi|153016	ORF 419 protein [Staphylococcus aureus]	55	23	1227 
 53	4	1813	1349	OspF [Borrelia burgdorferi]	55	30	465
 60	5	4794	5756	gi|1499876	magnesium and cobalt transport protein [Methanococcus jannaschii]	55	38	963
 71	9	14176 	15408⠀‚	gi|1857120	glycosyl transferase [Neisseria meningitidis]	55	41	1233†‚
 75	5	3189	4229	gnl|PID|e108780	NAD alcohol dehydrogenase [Bacillus subtilis]	55	44	1041 
108	10 	10488 	98 20	gnl|PID|e324997	hypothetical protein [Bacillus subtilis]	55	36	669
113	12 	12273 	13037⠀‚	gnl|PID|e311496	unknown [Bacillus subtilis]	55	34	765
113	13 	13007 	13945⠀‚	gi|1573423	1-phosphofructokinase (fruK) [Haemophilus influenzae]	55	39	939
126	5	6764	5907	gi|1790131	(AE000446) hypothetical 29.7 kD protein in ibpA-gyrB intergenic	55	37	858
				region [Escherichia coli]
129	3	2719< /td>	 902	gnl|PID|d101425	Pz-peptidase [Bacillus licheniformis]	55	35	1818⠀‚
138	3	2593	1610< /td>	gi|142833	ORF2 [Bacillus subtilis]	55	37	984
140	6	6916	5633	g nl|PID|d100964	homologue of hypothetical protein in a rapamycin synthesis gene	55	26	1284 
					cluster of Streptomyces hygroscopicus [Bacillus subtilis]
147	3	3 854	2136	gi|472330	dihydrolipoamide dehydrogenase [Clostridium magnum]	55	39	1719 
147	10 	10204 	8921	gnl|PID|e73078	dihydroorotase [Lactobacillus leichmannii]	55	38	1284 
148	5	3430	4119	gi|290572	peripheral membrane protein U [Escherichia coli]	55	29	690
148	6	4171	4650	gi|69 5769	transposase [Xanthobacter autotrophicus]	55	37	480
149	14 	12564 	1 1650 	gnl|PID|d101329	YqjG [Bacillus subtilis]	55	32	915
156	3	1113	 550	gi|2314496	(AE000634) conserved hypothetical integral membrane protein	55	34	564
					[Helicobacter pylori]
159	10 	6625	5897	gi|290533	similar to E. coli ORF adjacent to suc operon; similar to gntH class of	55	29	729
					regulatory proteins [Escherichia coli]
164	3	1784< /td>	2332	gnl|PID|e255118	hypothetical protein [Bacillus subtilis]	55	37	549
164	5	2772	3521	g i|40348	put. resolvase Tnp I (AA 1-284) [Bacillus thuringiensis]	55	35	750
164	11 	7428	7216< /td>	gnl|PID|e249407	unknown [Mycobacterium tuberculosis]	55	38	213
167	5	3860	3345	involved in protein secretion [Bacillus subtilis]	55	28	516
186	5	2880	2563	g i|606080	ORF_o290; Geneplot suggests frameshift linking to o267, not found	55	35	318
				[Escherichia coli]
189	8	4311< /td>	5396	gnl|PID|e183450	hypothetical EcsB protein [Bacillus subtilis]	55	32	1086 
192	5	3270	3079	vitellogenin convertase [Aedes aegypti]	55	38	192
195	2	2454	1384	gi |1574693	transferase, peptidoglycan synthesis (murG) [Haemophilus	55	33	1071 
					i nfluenzae]
198	4	3013	2471	gnl|PID|e313074	hypothetic al protein [Bacillus subtilis]	55	29	543
214	1	 373	 744	transposase [Synechocystis sp.]	55	33	372
219< /td>	2	1115	 456	gi|288301	ORF2 gene product [Bacillus megaterium]	55	30	660
263	7	3742	3443	gi|18137	cgcr-4 product [Chlamydomonas reinhardtii]	55	48	300
285	1	 2	 829	gnl|PID|d100974	unknown [Bacillus subtilis]	55	40	828
286	1	 650	 249	ORF (18 kDa) [Vibrio cholerae]	55	31	402
297	2	1229	1696	g i|150848	prtc [Porphyromonas gingivalis]	55	39	468
309	2	 218	 982	gi|1574491	hypothetical [Haemophilus influenzae]	55	35	765
328	2	 646	 224	gi|571500	prohibition [Saccharomyces cerevisiae]	55	27	423
330	1	1340	 474	soxS [Escherichia coli]	55	29	867
364	3	2538	1546	gi|39 3394	Tb-291 membrane associated protein [Trypanosoma brucei subgroup]	55	36	993
368	3	 941	 105	S antigen precursor [Plasmodium falciparum]	55	40	837
3	5	4604	3624	gi|2293176	(AF008220) signal transduction protein kinase [Bacillus subtilis]	54	26	981
9	11 	7746	7246	gi|1146245	putative [Bacillus subtilis]	54	38	501
 38	24 	16213 	1793 7 	gi|1480429	putative transcriptional regulator [Bacillus stearothermophilus]	54	27	1725 
 40	8	5076	gi|39989	methionyl-tRNA synthetase [Bacillus stearothermophilus]	5	35	1 95
 43	4	3980	236 7	gnl|PID|e148611	ABC transporter [Lactobacillus helveticus]	54	25	1614 < /td>
 52	10 	10844 	gi|1762962	FemA [Staphylococcus simulans]	54	29	1260 
 57	1	 3	 512	gi|558177	endo-1,4-beta- xylanase [Cellulomonas fimi]	54	36	510
 58	3	4749	4246	gnl |PID|d101237	hypothetical [Bacillus subtilis]	54	29	504
 71	7	10684 	11703 	gi|510255	orf3 [Escherichia coli]	54	31	1020 
 71	20 	27546 	2773 7 	gi|202543	serotonin receptor [Rattus novegicus]	54	31	192
 72	2	 844	1098	gi|148613	arnB gene product [Plasmid F]	54	37	255
 72< /td>	7	7438	6695	gi|1196496	54	38	744
 74	10 	14043 	13465†‚	gi|1200342	ORF 3 gene product [Bradyrhizobium japonicum]	54	32	579
 74	12 	16483 	159 95 	gi|2317798	maturase-related protein [Pseudomonas alcaligenes]	54	30	489
 86	3	2877	2155	gi|46988	orf9.6 possibly encodes the O unit polymerase [Salmonella enterica]	54	34	723
 89	5	4433	3921	gi|147211	phnO protein [Escherichia coli]	54	41	513
 90	1	 3	 464	gi|2317798	maturase-rela ted protein [Pseudomonas alcaligenes]	54	30	462
 96	10 	8058	8510< /td>	gnl|PID|d102015	(AB001488) SIMILAR TO SALMONELLA TYPHIMURIUM SLYY	54	32	453
					GENE REQUIRED FOR SURVIVAL IN MACROPHAGE.
					[ Bacillus subtilis]
 97	6	4662	3604	gi|1591394	transketolase⠀³ [Methanococcus jannaschii]	54	30	1059 < /td>
106	11 	10406 	12010 	gi|1606286	ORD_o637 [Escherichia coli]	54	32	1605 
147	8	8663	7404	g nl|PID|d101615	ORF_ID:o319#7; similar to (SwissProt Accession Number P37340)	54	35	1260 
				[Escherichia coli]
171	4	2477< /td>	3223	gi|1439528	EIIC-man [Lactobacillus curvatus]	54	36	747
174	2	2068	1787	g nl|PID|d100518	motor protein [Homo sapiens]	54	35	282
188	1	 526	1188	gnl|PID|e250352	unknown [Mycobacterium tuberculosis]	54	31	663
198	5	3582	2884	hypothetical protein [Bacillus subtilis]	54	33	699
207	1	 1	1641	gnl|PID|d101813	hypothetic al protein [Synechocystis sp.]	54	24	1641 
210	1	 2	 655	gi|2293206	(AF008220) YtmP [Bacillus subtilis]	54	29	654
225	2	 966	2357	gnl|PID|e330194	R11H6.1 [Caenorhabditis elegans]	54	39	1392 
241	1	1681	 347	gnl|PID|d101813	hypothetical protein [Synechocystis sp.]	54	26	1335 
263	2	 907	1395	gnl|PID|d1 01886	transposase [Synechocystis sp.]	54	30	489
263< /td>	6	3450	2977	gi|160671	54	47	474
277	3	2517	1363	gi|1196926	unknown protein [Streptococcus mutans]	54	30	1155 
307	1	 828	 4	gi|2293198	(AF008220) YtgP [Bacillus subtilis]	54	28	825
325	1	19	 768	gi|2182507	(AE000083) Y41H (Rhizobium sp. NGR234)	54	37	750
3 32	2	 898	 590	gi|159181 5	ADP-ribosylglycohydrolase (draG) [Methanococcus jannaschii]	54	32	309
385	4	 240	 479	gi|530878	amino acid feature: N-glycosylation sites, aa 41 . . . 43, 46 . . . 48,	54	49	240
					51 . . . 53, 72 . . . 74, 107 . . . 109, 128 . . . 130, 132 . . . 143,
					158 . . . 160, 153 . . . 165, amino acid feature: Rod protein domain,
					aa 169 . . . 340; amino acid feature: globular protein domai
7	25 	19702 	19493 	gn l|PID|e255111	hyptothetical protein [Bacillus subtilis]	53	32	210
 23	3	2497	2033	gnl|PID|d102015	(AB001488) SIMILAR TO SALMONELLA TYPHIMURIUM SLYY	53	25	465
					GENE REQUIRED FOR SURVIVAL IN MACROPHAGE.
					[ Bacillus subtilis]
 29	11 	9042	10121 	gi|143331	alkalin e phosphatase regulatory protein [Bacillus subtilis]	53	31	1080 
 33	3	1479	1009	pir|S10655|S106	hypothetical protein X - Pyrococcus woesei (fragment)	53	33	471
 36	6	4583	5134	unknown [Mycobacterium tuberculosis]	53	30	552
 38	14 	8521	8898	gi|580904	homologous to E. coli rnpA [Bacillus subtilis]	53	30	378
 52	7	7007	8686	gi|1377831	unknown [Bacillus subtilis]	53	29	1680 
 54	17 	17555 	19564 	gi|666069	orf2 gene product [Lactobacillus leichmannii]	53	36	2010 
 56	1	 1	 681	gi|1592266	restriction modification system S subunit [Methanococcus jannaschii]	53	32	681
 57	10	9431	8487	gi|1788543	(AE000310) f351; Residues 1-121 are 100 pct identical to	53	31	945
					YOJL_ECOLI SW; P33944 (122 aa) and aa 152-351 are 100 pct
					identical to YOJK_ECOLI SW; P33943 [Escherichia coli]
 61	1	  429	 4	gnl|PID|e236467	B0024.13 [Caenorhabditis elegans]	53	33	426
 71	1	5772	 4	gi|393394	Tb-291 membrane associated protein [Trypanosoma brucei subgroup]	53	33	5769 
 72	3	 894	2840	gi|2293178	(AF008220) YtsD [Bacillus subtilis]	53	27	1947 
 73	14 	9793	9212	gi|1778556	putative cobalamin synthesis protein [Escherichia coli]	53	32	582
 88	7	5217	4342	gi| 2098719	putative fimbrial-associated protein [Actinomyces naeslundii]	53	38	876
 93	5	2395	1688	gluconate oxidoreductase [Gluconobacter oxydans]	53	33	708
 96	9	6632	7762	gi|517204	ORF1, putative 42 kDa protein [Streptococcus pyogenes]	53	42	1131 
108	8	7629	8600	maturation protein [Lactobacillus paracasei]	53	32	972
128	9	6412	6972	gnl|PID|e317237	unknown [Mycobacterium tuberculosis]	53	36	561
128	12 	8429	9253	gi|311070	pentraxin fusion protein [Xenopus laevis]	53	31	825
14	1	 3	 950	pir|A61607|A616	probable hemolysin precursor - Streptococcus agalactiae (strain	53	36	948
					74-360)
1 63	2	2162	3022	gi|1755150	nocturnin [Xenopus laevis]	53	30	861
171	3	2304	2624	gi| 1732200	PTS permease for mannose subunit IIPMan [Vibrio furnissii]	53	32	321
182	5	3785	3051	gnl|PID|d100572	unknown [Bacillus subtilis]	53	35	735
209	3	2948	1935	g i|1778505	ferric enterobactin transport protein [Escherichia coli]	53	28	1014 
218	5	3884	2406	g i|140162	murE gene product [Bacillus subtilis]	53	34	1479 
250	3	 473	 790	gnl|PID|e334776	YlbH protein [Bacillus subtilis]	53	30	318
275	1	 1	1611	gnl|PID|d101314	YqeW [Bacillus subtilis]	53	35	1611 
332	1	 544	 2	gi|409286	bmrU [Bacillus subtilis]	53	31	543
2	2	2543	3445	gnl|PID|e23387 9	hypothetical protein [Bacillus subtilis]	52	39	903
3	22 	22402 	23376 	gi |38969	lacF gene product [Agrobacterium radiobacter]	52	36	975
5	3	8094	2356	gnl|PID|e32491 5	IgAl protease [Streptococcus sanguis]	52	32	5739 
 22	26 	19961 	2 0212 	gi|152901	ORF 3 [Spirochaeta aurantia]	52	35	252
 22	31 	23140 	2466 6 	gi|289262	comE ORF3 [Bacillus subtilis]	52	32	1527 
 27	6	5397	4801	gi|39573	P20 (AA 1-178) [Bacillus licheniformis]	52	35	597
 35	10 	8604	735 7	gi|508241	putative O-antigen transporter [Escherichia coli]	52	27	1248 
 45	4	4801	3662	gnl|PID|d102243	(AB005554) homologs are found in E. coli and H. influenzae; see	52	36	1140 
					SWISS_PROT ACC#: P42100 [Bacillus subtilis]
 48	18 	14385 	13726 	gnl|PID|e205174	52	25	660
 49	4	5321	5755	(AF013987) nitrogen regulatory IIA protein [Vibrio cholerae]	52	19	435
 54	4	2773	4668	gi|1500472	M. jannaschii predicted coding region MJ1577 [Methanococcus	52	36
					jannaschii]
 54	6	5250	4969	gi|2182453	(AE000079) Y4iO [Rhizobium sp. NGR234]	52	40	282
⠀‚66	6	8400	6955	gi|43140	TrkG protein [Escherichia coli]	52	30	1446 
 71	26 	30659 	3131 2 	gnl|PID|e314993	unknown [Mycobacterium tuberculosis]	52	23	654
 75	2	1673	1035	gnl|PID|d102271	(AB001683) FarA [Streptomyces sp.]	52	27	639
 8 1	3	1439	2893	gnl|PID|e31145 8	rhamnulose kinase [Bacillus subtilis]	52	32	1455 
 81	8	4987	5781	gi|147403	mannose permease subunit II-P-Man [Escherichia coli]	52	37	795
 83	21 	20687 	21853 	gi|143365	phosphoribosyl aminoimidazole carboxylase II (PUR-K; ttg start	52	37	1167 
					codon) [Bacillus subtilis]
 86	6	5785	4592	gi|1276879	EpsF [Streptococcus thermophilus]	52	26	1194†‚
 86	20 	19390 	17861 	gi|454844	ORF 3 [Schistosoma mansoni]	52	26	1530 
 96	13 	10540 	9 659	gi|288299	ORF1 gene product [Bacillus megaterium]	52	33	882
111	1	 2	2026	gi|148309	cytolysin B transport protein [Enterococcus faecalis]	52	27	2025 
112	2	1457	2167	orf1 [Haemophilus influenzae]	52	33	711
118	3	2931	2365	bbs|151233	Mip = 24 kda macrophage infectivity potentiator protein [Legionella	52	33	567
					pneumo phila, Philadelphia-1, Peptide, 184 aa] [Legionella
				pneumophila]
122	9	5646	5951	gi|8214	myosin heavy chain [Drosophila melanogaster]	52	36	306
122	11 	6159	6374	gi|434025	dihydrolipoamide acetyltransferase [Pelobacter carinolicus]	52	52	216
134	6	4880	6313	M protein trans-acting positive regulator [Streptococcus pyogenes]	52	43	1434 
135	3	1238	2716	unknown [Mycobacterium tuberculosis]	52	35	1479†‚
141	3	1681	2319	gnl|PID|d100573	unknown [Bacillus subtilis]	52	32	639
161	4	2562	5024	g i|1146243	22.4% identity with Escherichia coli DNA-damage inducible	52	36	2463 
					protein . . . ; putative [Bacillus subtilis]
173	2	⠀‚968	 183	gi|1215693	putative orf; GT9_orf434 [Mycoplasma pneumoniae]	52	30	786
198	6	4400	3567	gnl|PID|e313010	hypothetical protein [Bacillus subtilis]	52	26	834
210	12 	8844	9107	DNA gyrase subunit B [Mycoplasma genitalium]	52	38	264
214	10 	5264	5431	gi|550697	envelope protein [Human immunodeficiency virus type 1]	52	36	168
225	1	15	 884	gi|1552773	hypothetical [Escherichia coli]	52	34	870
230	1	39	 362	gnl|PID|d100582	unknown [Bacillus subtilis]	52	28	324
287	1	 871	 2	gnl|PID|e335028	protease/peptidase [Mycobacterium leprae]	52	29	870
363	2	1305	 4	gi|393394	Tb-291 membrane associated protein [Trypanosoma brucei subgroup]	52	32	1302 
 23	2	2048	1173	gnl|PID|e254943	unknown [Mycobacterium tuberculosis]	51	30	876
 29	3	 742	1521	gi|929900	5′-methylthioadenosine phosphorylase [Sulfolobus solfataricus]	51	31	780
 45	1	 410	1597	gi|1877429	integrase [Streptococcus pyogenes phage T12]	51	32	1188 
 48	26 	19227 	18946 	(AE000633) transcriptional regulator (tenA) [Helicobacter pylori]	51	33	282
 73	5	4276	4016	g i|474177	alpha-D-1,4-glucosidase [Staphylococcus xylosus]	51	31	261
 81	11 	8935	12057 < /td>	gi|311070	pentraxin fusion protein [Xenopus laevis]	51	31	2123 
 83	5	1195	1986	yqfI [Bacillus subtilis]	51	33	792
 98	10 	7531	8538	gi|41500	ORF 3 (AA 1-352); 38 kD (put. ftsX) [Escherichia coli]	51	28	1008 
113	6	3908	5173	g i|466882	pps1; B1496_C2_189 [Mycobacterium leprae]	51	27	1266 
124	1	 326	57	gi|2191168	(AF007270) contains similarity to myosin heavy chain [Arabidopsis	51	32	270
					thali ana]
129	10 	72 86	6816	gi|1046241	orf14 [Bacteriophage HP1]	51	30	471
143< /td>	3	4963	3983	gi|1354935	51	26	981
148	15 	11359 	10226 	gi|2293256	(AF008220) putative hippurate hydrolase [Bacillus subtilis]	51	36	1134 
149	8	6003	7313	Herpesvirus saimiri ORF73 homolog [Kaposi's sarcoma-associated	51	21	1311 
					herpes-like virus]
151	9	12092 	gnl|PID|e281580	hypothetical 40.7 kd protein [Bacillus subtilis]	51	34	543
159	6	2555	3208	g i|146944	CMP-N-acetylneuraminic acid synthetase [Escherichia coli]	51	36	654
174	1	1797	 4	gi|1773166	probable copper-transporting atpase [Escherichia coli]	51	28	1794 
265	4	2231	1773	g nl|PID|e256400	anti-P. falciparum antigenic polypeptide [Saimiri sciureus]	51	18	459
277	2	 643	1311	pir|S32915|S329	pilD protein - Neisseria gonorrhoeae	51	33	669
350	1	 890	 3	gi|290509	o307 [Escherichia coli]	51	30	888
363	4	1228	4485	gi|17 07247	partial CDS [Caenorhabditis elegans]	51	23	3258 
367	1	1701	 4	gi|393394	Tb-291 membrane associated protein [Tyrpanosoma brucei subgroup]	51	32	1698 
 15	5	5174	4497	gnl|PID|e58151	F3 [Bacillus subtilis]	50	38	678
 16	4	2220	2582	gnl|PID|e325010	hypothetical protein [Bacillus subtilis]	50	29	363
 19	5	2591	4159	gi|1552733	similar to voltage-gated chloride channel protein [Escherichia coli]	50	30	1569 
 25	4	2701	1997	gi|887849	ORF_f219 [Escherichia coli]	50	27	705
 35	1	 211	 417	gnl|PID|e236697	unknown [Saccharomyces cerevisiae]	50	33	207
 39	4	3416	5152	unknown [Bacillus subtilis]	50	27	1737 
 51	7	4000	5181	gi|1592027	carbamoyl-phosphate synthase, pyrimidine-specific, large subunit	50	27	1182 
				[Methanococcus jannaschii]
 51	9	8303	gi|1591847	type I restriction-modification enzyme, S subunit [Methanococcus	50	28
					jannaschii]
 52	8	8740	9534	gi|144297	acetyl esterase (XynC) [Caldocellum saccharolyticum]	50	34	795
 52	16 	16951 	gi|2108229	basic surface protein [Lactobacillus fermentum]	50	34	822
 57	7	6031	6336	60S ribosomal protein L7B [Schizosaccharomyces pombe]	50	40	306
 71	23 	29348 	28383†‚	gnl|PID|d101328	YqjA [Bacillus subtilis]	50	30	966
 86	12 	11155 	1076 9 	gnl|PID|e324964	hypothetical protein [Bacillus subtilis]	50	24	387
 93	2	1205	 330	similar to Escherichia coli pyruvate, water dikinse, Swiss-Prot	50	24	876
				Accession Number P23538 [Pyrococcus furiosus]
 96	5	1673	2959	gnl|PID|e322433	gamma-glu tamylcysteine synthetase [Brassica juncea]	50	29	1287 
 98	2	 218	1171	gi|151110	leucine-, isoleucine-, and valine-binding protein [Pseduomonas	50	30	954
					aerug inosa]
103	4	3303	2785	gi|154330	O-antigen ligase [Salmonella typhimurium]	50	31	519
115	5	6480	5980	putative cel operon regulatro [Bacillus subtilis]	50	26	501
129	11 	7559	7305	skeletal muscle ryanodine receptor [Homo sapiens]	50	32	255
129	13 	8192	7965	319-kDA protein [Rhizobium meliloti]	50	30	228
151	5	7634	6819	g i|40348	put. resolvase Tnp I (AA 1-284) [Bacillus thuringiensis]	50	35	816
153	1	 1	 597	gnl|PID|d102015	(AB00148 8) SIMILAR TO NITROREDUCTASE. [Bacillus subtilis]	50	29	597
155	5	5986	5432	g i|1276880	EspsG [Streptococcus thermophilus]	50	28	555
160	9	7390	6323	(AE000179) o331; 92 pct identical to the 333 as hypothetical protein	50	30	1068 
				YBHE_ECOLI SW: P52697; 26 pct identical (7 gaps) to 167
					residues of the 373 as protein MLE_TRICU SW: P46057;
					SW: P52697 [Escherichia coli]
163	6	7396< /td>	8091	gnl|PID|d101313	YqeN [Bacillus subtilis]	50	22	696
167	6	5232	3940	g i|413926	ipa-2r gene product [Bacillus subtilis]	50	27	1293 
169	2	 807	 130	gnl|PID|e304540	endolysin [Bacertiophage Bastille]	50	35	678
171	5	3158	4025	g i|606080	ORF_o290; Geneplot suggests frameshift linking to o267, not found	50	27	858
				[Escherichia coli]
210	13 	8 151	8414	gi|330038	HRV 2 polyprotein [Human rhinovirus]	50	25	264
364	1	1538	 135	Tb-292 membrane associated protein [Trypanosoma brucei subgroup]	50	31	1404 
 10	7	5911	5090	gi|144859	ORF B [Clostridium perfringens]	49	24	822
 26	5	10754 	9768< /td>	gi|142440	ATP-dependent nuclease [Bacillus subtilis]	49	31	987
 66	7	9777	8398	gi|414170	trkA gene product [Methanosarcina mazeii]	49	26	1380 
 77	6	5364	4648	RecX protein [Mycobacterium smegmatis]	49	28	717
 82	13 	12689 	132 49 	gnl|PID|e255091	hypothetical protein [Bacillus subtilis]	49	20	561
 93	9	4866	4531	gi|40067	X gene product [Bacillus sphaericus]	49	26	336
112	5	4019	4948	gi|1574380	lic-1 operon protein (licB) [Haemophilus influenzae]	49	27	930
129	7	6058	4949	gnl|PID|e267587	Unknown [Bacillus subtilis]	49	35	1110 
135	5	3875	4438	P20 (AA 1-178) [Bacillus licheniformis]	49	25	564
154	2	1423	1953	gnl|PID|d101102	regulatory components of sensory transduction system	49	29	531
< td/>				[Synechocystis sp.]
156	5	2878	163 7	gnl|PID|d101732	hypothetical protein [Synechocystis sp.]	49	25	1242 
173	5	3500	2940	gi|490324	LORF X gene product [unidentified]	49	30	561
182	1	1057	 2	gi|331002	first methionine codon in the ECLF1 ORF [Saimirine herpesvirus 2]	49	25	1056 
192	6	5352	3667	gi|2 394472	(AF024499) contains similarity to homeobox domains	49	23	1686 
				[Caenorhabditis elegans]
253	4	11 29	1350	gi|531116	SIR4 protein [Saccharomyces cerevisiae]	49	23	222
277	1	 600	 136	gi|396844	ORF (18 kDa) [Vibrio cholerae]	49	32	465
327	3	1435	 887	gi|733524	phosphatidylinositol-4,5-diphosphate 3-kinase [Dictyostelium	49	24
					dis coideum]
365	3	14 36	 132	gi|393394	Tb-291 membrane associated protein [Trypanosoma brucei subgroup]	49	31	1305 
 33	7	4461	3277	gi|145644	codes for a protein of unknown function [Escherichia coli]	48	26	1185 
 40	2	 652	1776	ornithine decarboxylase [Nicotiana tabacum]	48	29	1125 
 67	4	1377	2384	gi|1772652	2-keto-3-deoxygluconate kinase [Haloferax alicantei]	48	30	1008 
 74	2	4269	3871	gi|12182678	(AE000101) Y4vJ [Rhizobium sp. NGR234]	48	27	399
⠀‚81	2	1326	 541	gi|153672	lactose repressor [Streptococcus mutans]	48	33	786
 81	4	2981	3646	g i|146042	fuculose-1-phosphate aldolase (fucA) [Escherichia coli]	48	30	666
 97	1	 602	51	gi|153794	rgg [Streptococcus gordonii]	48	29	552
110	1	 1	3132	gi|1381114	prtB gene product [Lactobacillus delbrueckii]	48	23	3132 
131	5	2914	2147	gnl|PID|e183811	Acyl-ACP thioesterase [Brassica napus]	48	27	768
133	4	3494	2628	gnl| PID|e261988	putative ORF [Bacillus subtilis]	48	27	867
139	6	4231	4599	g i|1098388	2K470.1 gene product [Caenorhabditis elegans]	48	23	369
139	8	5036	5665	gi |1022725	unknown [Staphylococcus haemolyticus]	48	29	630
140	12 	11936 	11 007 	gnl|PID|d102049	H. influenzae, ribosomal protein alanine acetyltransferase; P44305	48	27	930
< td/>				(189) [Bacillus subtilis]
146	9	5 670	4654	gi|1591731	melvalonate kinase [Methanococcus jannaschii]	48	24	1017 < /td>
161	3	1280	2374	gnl|PID|d101578	Collagenase precursor (EC 3.4.—.—), [Escherichia coli]	48	24	1095 
172	11 	10581 	11048⠀‚	gnl|PID|d101132	hypothetical protein [Synechocystis sp.]	48	27	468
182< /td>	4	2930	2586	gi|40067	X gene product [Bacillus sphaericus]	48	37	345
210	15 	10786 	1119 6 	sp|P13940|LE29—	LATE EMBRYOGENESIS ABUNDANT PROTEIN D029 (LEA	48	30	411
					D-29)
214	12†‚	6231	6482	gi|40389	non-tox ic components [Clostridium botulinum]	48	26	252
221	1	 704	 3	gi|11573364	H. influenzae predicted coding region HI0392 [Haemophilus	48	27	702
					influenzae]
227	2	 647	3928	gi|1673693	(AE000005) Mycoplasma pneumoniae, C09_orf718 Protein	48	30	3282 
				[Mycoplasma pneumoniae]
253	2	 480	 758	gnl|PID|e236697	unkno wn [Saccharomyces cerevisiae]	48	31	279
363	3	1874	1122	gi|18137	cgcr-4 product [Chlamydomonas reinhardtii]	48	40	753
389	1	 505	 2	gi|18137	cgcr-4 product [Chlamydomonas reinhardtii]	48	38	504
3	21 	20879 	22258 	gn i|PID|e264778	putative maltose-binding protein [Streptomyces coelicolor]	47	33	1380 < /td>
6	4	4089	4658	gi|39573	47	23	570
 15	3	3736	1760	gnl|PID|d100572	unknown [Bacillus subtilis]	47	25	1977 
 35	15 	14516 	13263 	gi|17773351	Cap5L [Staphylococcus aureus]	47	20	1254 
 51	6	3547	4002	32K antigen precursor - Mycobacterium tuberculosis	47	38	456
 55	8	10154 	9273< /td>	gi|39848	U3 [Bacillus subtilis]	47	26	882
 92	4	1753	3276	gnl|PID|e280611	PCPC [Streptococcus pneumoniae]	47	35	1524 < /td>
127	9	5589	5386	gi|1786458	(AE000134) f120; This 120 aa orf is 76 pct identical (0 gaps) to 42	47	32	204
					residues of an approx. 48 aa protein Y127_HAEIN SW: P43949
					[Es cherichia coli]
130	2	1232< /td>	1759	gnl|PID|e266555	unknown [Mycobacterium tuberculosis]	47	23	528
140	4	4951	3542	homologue of hypothetical protein in a rapamycin synthesis gene	47	24	1410 
					cluster of Streptomyces hygroscopicus [Bacillus subtilis]
151	4	6 814	6200	gi|1522674	M. jannaschii predicted coding region MJ3CL41 [Methanococcus	47	27
					jan naschii]
157	3	†‚803	1174	gnl|PID|d101320	YqgZ [Bacillus subtilis]	47	25	372
178	5	3267	2155	g i|2367190	(AE000390) o334; sequence change joins ORFs ygjR & ygjS from	47	30	1113 
					earlier version (YGJR_ECOLI SW: P42599 and YGJS_ECOLI SW:
					P42600) [Escherichia coli]
273	1	 2	1549	gnl|PID|e254973	autolysin sensor kinase [Bacillus subtilis]	47	32	1548 
300	2	 880	 644	gi|1835755	zinc finger protein Png-1 [Mus muculus]	47	22	237
 54	14 	14182 	12638  	pir|S43609|S436	rofA protein - Streptococcus pyogenes	46	24	1545 
 88	1	 2	1018	gnl|PID|e223891	xylose repressor [Anaerocellum thermophilum]	46	27	1017†‚
 96	7	4553	5860	gnl|PID|d101652	ORF_ID:0347#5; similar to (SwissProt Accession Number P45272)	46	23	1308 
				[Escherichia coli]
112	1	1127< /td>	 3	gi|2209215	(AF004325) putative oligosaccharide repeat unit transporter	46	24	1125 
					[Streptococcus pneumoniae]
122	13 	7308	7982	gi|1054776	hr44 gene product [Homo sapiens]	46	34	675
127	14 	9198	8125	afuA gene product [Actinobacillus pleuropneumoniae]	46	28	10 74 
132	4	7093	61 97	gi|153794	rgg [Streptococcus gordonii]	46	26	897
140	8	8220	7723	g i|1235795	pullulanase [Thermoanaerobacterium thermosulfurigenes]	46	21	498
140	9	9205	8315	gi|407878	leucine rich protein [Streptococcus equisimilis]	46	27	891
162	1	 1	1125	gi|1143209	ORF7; Method: conceptual translation supplied by author [Shigella	46	25	11 25 
					sonn ei]
199	1	 1	 585	gi|1947171	(AF000299) No definition line found [Caenorhabditis elegans]	46	28	585
223	3	1971	1477	sp |P02562|MYSS—	MYOSIN HEAVY CHAIN, SKELETAL MUSCLE (FRAGMENTS)	46	27	495
2	 760	1608	gi|1016 112	ycf38 gene product [Cyanophora paradoxa]	46	28	849
292	1	 687	 220	(AE000011) Mycoplasma pneumoniae, cytidine deaminase; similar to	46	29	468
					GenBank Accession Number C53312, from M. pirum [Mycoplasma
				pneumoniae]
 30	8	5843	6472	g i|1788049	(AE000270) o235; This 235 aa orf is 29 pct identical (10 gaps) to 198	45	24	630
					residues of an approx. 216 as protein YTXB_BACSU SW: P06568
					[Es cherichia coli]
 48	6	346 1	3868	gi|722339	unknown [Acetobacter xylinum]	45	29	408
 60	1	 307	 2	gi|1699079	coded for by C. elegans cDNA yk41h4.3; coded for by C. elegans	45	36	306
					cDNA yk148g10.5; coded for by C. elegans cDNA yk152g5.5; coded
					for by C. elegans cDNA yk59a10.5; coded for by C. elegans cDNA
					yk4 1h4.5; coded for by C. elegans cDNA cm20g10; coded
 72	16	14371 	14874 	gi|1321900	NADH dehydrogenase (ubiquinone) [Artemia franciscana]	45	25	504
 99	7	9158	7941	gi|152192	mutation causes a succinoglucan-minus phenotype; ExoQ is	45	28	1218 
< td/>				atransmembrane protein; third gene of the exoYFQ operon;; putative
					[ Rhizobium meliloti]
127	12	7046	6606	bbs|153689	HitB = iron utilization protein [Haemophilus influenzae, type b,	45	24	441
					DL42, NTHI TN106, Peptide, 506 aa] [Haemophilus influenzae]
137	5	1561	2619	gi|472921	v-type Na-ATPase [Enterococcus hirae]	45	33	1059 
209	1	 774	 364	gi|304141	restriction endonuclease beta [Bacillus coagulans]	45	28	411
314	1	 604	 2	gi|1480457	latex allergen [Hevea brasiliensis]	45	31	603
 20	18 	19782 	20288 	gi|433942	ORF [Lactococcus lactis]	44	26	507
 87	8	7030	6452	g i|537207	ORF_f277 [Escherichia coli]	44	26	579
166	5	4909	4037	gnl|P ID|e308082	membrane transport protein [Bacillus subtilis]	44	25	873
247	1	 818	75	gnl|PID|d100718	ORF1 [Bacillus sp.]	44	20	744
 3 2	3	1885	3876	gi|2351768	PspA [Streptococcus pneumoniae]	43	24	1992 < /td>
 36	17 	15467 	gi|1045739	M. genitalium predicted coding region MG064 [Mycoplasma	43	26	2790 
					ge nitalium]
 54	15 	14656 	17343 	gi|520541	pen icillin-binding proteins 1A and 1B [Bacillus subtilis]	43	27	2688 
 67	2	 696	1352	gi|536934	yjcA gene product [Escherichia coli]	43	29	657
139	2	2416	 338	gi| 396400	similar to eukaryotic Na+/H+ exchangers [Escherichia coli]	43	24	2079 
298	1	 3	 809	gi|413972	ipa-48r gene product [Bacillus subtilis]	43	24	807
387	1	47	 427	gi|2315652	(AF016669) No definition line found [Caenorhbditis elegans]	43	30	381
185	4	4221	3127	gi |2182399	(AE000073) Y4fP [Rhizobium sp. NGR234]	41	25	1095 
1	 582	70	gnl|PID|e218681	CDP-diacylglycerol synthetase [Arabidopsis thaliana]	41	20	513
363	6	4205	1914	g i|1256742	R27-2 protein [Trypanosoma cruzi]	41	27	2292 
368	2	 2	 943	gi|21783	LMW glutenin (AA 1-356) [Triticum aestivum]	41	34	942
155	3	4489	2861	g i|42023	member of ATP-dependent transport family, very similar to mdr	40	18	1629 
					proteins and hemolysin B, export protein [Escherichia coli]
365	2	95	1438	gi|1633572	Herpesvir us saimiri ORF73 homolog [Kaposi's sarcoma-associated	40	21	1344 
					herpes-like virus]
1	3	2979	3860	gnl|PID|d10190 8	hypothetical protein [Synechocystis sp.]	39	26	882
1	5	3814	4647	gnl|PID|d10196 1	hypothetical protein [Synechocystis sp.]	39	19	834
 2 6	6	14035 	10724 	gi|142 439	ATP-dependent nuclease [Bacillus subtilis]	38	20	3312 
 47	1	 3	4916	gi|632549	NF-180 [Petromyzon marinus]	36	23	4914 

< tr>< tr>< tr>< tr>< tr>< td/>< td/>1050< td>3< /tr>5< td/>< td/>42695< td/>7< td>2416< td>1165< td>6< td>4< /tr>19 < td/>< tr>< td>23951< td> 9044924< tr>< td> 10210 14840 14 < td>13 < /tr>25573 6312< tr>< td> 5464923< td/>< tr>< td>28612< td>23306 600< td>2116 310< td>121858 494< td/>< td> 607 342< td> 705 44 636

TABLE 3
S. pneumoniae - Putative coding regions of novel proteins not similar
to known proteins
	Contig	ORF	Start	Stop
	ID	ID	(nt)	(nt)
	1	4	3428	3009
	2	6	4611	4964
	3	2	 818	 994
	3	3	1182	1574
	3	7	5382	6497
	3	25 	25046 	25396 
	3	26 	25625 	26317 
	6	2	1519	1689
	6	14 	12875 	12618 
	6	15 	13215 	12841 
	6	18 	15977 	15390 
	7	12 	9955	9419
	7	13 	10161 	9910
8	6	3915	4280
	9	9	6024	5704
	 10	8	6909	6298
	 10	9	7136	6888
 10	11 	7968	7672
	 12	1	1140	 4
	 12	3	1779	1456
	 14	2	1913< /td>	1434
	 16	1	 1	 243
	 16	5	5675	3087
	 17	1	 324	34
	 17	3	1451
	 17	9	4890	4465
	 20	14 	14544 	15893 
	 21	3359	2589
	 21	5	4802	4482
	  22	21 	17099 	17362 
	 22	25 	19467 	19 982 
	 22	33 	255 40 	25764 
	 22	3 5 	26388 	26218 
	 22	36 	26382 	27572 
	 23	7	6655	6032
	 23	8	7132	66 53
	 24	1	36	 518
	 25	5	3009	2641
	 27	4< /td>	4819	4223
	 27	4789	4956
	 28	5	3017	1797
	 2 8	8	4272	3850
	 28	10 	5028	4597
 28	11 	5746	5072
	 29	7	5596	4919
	 29	8	5039	551 8
	 29	9	5595	8207
	 30	9	6511	6263
	 31	6	2664	2344
	 32	5	5203	5538
	 33	8	5327	4668
	 34	10  	8024	7740
	 34	12 	9360	8641
	 34	13 	9667	9377
 34	18 	13104 	11902†‚
	 35	11 	9688	8588
	 35	12 	11073 	9670
	 36	2< /td>	 334	1041
	 36	12 	11120 	10893 
	 36	13 	10993 	11388 < /td>
	 36	15 	12172 	14595 
	 38	7	4577
	 38	8	4480	5001
	 38	10 	5517	5711
	 38< /td>	17 	10732 	11376 
	 40	3	1728	3143
	 43	1	 172	  5
	 43	7	8884	8732
	 43	8	9568	9071
	 44	4	4831	6831
	 45	3	3204	3665
	 46	4	3875	3468
	 46	7< /td>	6074	7081
	 48	3196	3582
	 48	8	4579	4229
	 4 8	11 	9323	8922
	 48	16 	13042 	12494 
	 48	20 	16342 	15764 
	 48	24 	17971 	18351 
	 48	30 	21979 	21776 
 49	1	 209	  3
	 50	4	3307	2672
	 51	5	3239	3598
	 52	11 	12146 	12883 
	 54	5588	5187
	 54	8	6013	5459
	 5 4	9	6004	6210
	 54	16 	17685 	17506 
	 55	9	10515 	101 23 
	 55	12 	1194 7 	12141 
	 56	3< /td>	 935	1387
	 56	4	1496	1939
	 57< /td>	3	1624	2130
	†‚57	4	2100	2501
 58	6	7541	7335
	 59	1	  2	 430
	 59	4	2736
	 59	5	2734	3063
	 59	8	4743	5549
	 59	9	5459	5929
	 60	6	5741	6451
	⠀‚61	3	2395	1772
< td> 61	5	3316	3176
 64	1	2722	 2
	 66	2	1180	3147
	 66	8	9082< /td>	9495
	 67	3	1 343	1182
	 69	2	 980
	 70	5	4059	3922
	 70	4215	4057
	 70	9	5268	5504
	  71	15 	20351 	21901 
	 71	16 	21859 	22 338 
	 71	19 	262 04 	27556 
	 72	9	8458	8081
	 73	3815	4216
	 73	6	4214	4582
	  73	7	4369	4773
	 73	10 	7183	6428
	 73	15 	9462	9668
	 76	1	 524	 1 95
	 76	2	 867	 535
	 76	11 	8602	9210
	 80	6	7924	8109
	 81	1	 244	  2
	 81	10 	6631	8931
	 83	4	1872	1150
	 83	17 	16810 	16460 
	 84	3	4464	2929
	 8 6	2	2147	1092
	 86	4	3606	2875
	 86	19 	16767 	17114 
	 87	5	5326	500 0
	 87	7	6459	6001
	 87	9	7224	7006
	 87	18 	17930 	17670 
	 87	18275 	17928 
	 88	2	1619	1840
 88	4	2711	2878
	 88	9	6252	6016
	 89	3	2634	1621
	 89	9	7371	686 8
	 90	2	 899
	 90	3	1143	 952
	 91	3	2959	3141
	 91	4	3170	3691
	 91	6< /td>	4253	4573
	 93	 391	  2
	 93	6	2648	2379
	 93	8	4533	3712
	 96	1	  3	 182
	 96	2	 632
	 96	3	1407	1147
	 96	4	1250	1420
	 97	9	7043	6753
	⠀‚99	15 	18522 	18692 
	 99	17 	19717 	19541 
	100	2	4094	1980
	103	1	48	 299
	103	6	4373
	104	5	6142	6735
	105	7	6098	6517
	106	1< /td>	 1	 363
	106	10 < /td>	9832	10212 
	108	1	 2	 268
	111	3	3417	3788
	111	4	3809	4606
	115	10  	10854 	10438 
	116	3	2873	2121
118	2	2274	1357
	122	4	2698	2333
	122	10 	5858	6199
	122	12 	6301	7416
	124	2	 346	 69 0
	128	4	2544	3 368
	129	1	 689
	129	2	1011	 724
	129	8	64 54	6056
	129	9	6540	6277
	129	12 	7809	7621
	131	3< /td>	1433	 756
	131	5972	5673
	134< /td>	11 	11838 	11209 
	135	2	 625	1140
	136	4	2913	3830
	137	2	 325	 134< /td>
	139	12 	14027 	14521 
	139	13 	14532 
	139	15363 	14875 
	140	20 	19822 	20838 
	142	1	  1	 285
	146	3	 760	 479
	146	4	1149	 778
	146	7	3604	2885
	146	8223	9401
	146	14 	9399	10676 
146	15 	10052 	9750
	147	7	7488	7276
	147	9	8913	8647
	148	7	5298	4765
	149	1	 2	1936
	149	3	2880
	149	9	6258	6070
	150	2	1355	 579
	150	3	2556	1909
	153	2061	2642
	154	3	1953	1741
	155	2	2181	1411
	156< /td>	8	4550	4311
	15 7	1	37	 294
	159	2	 780
	159	4< /td>	1384	1722
	159	7	3271	4017
	161	1332	1018
	165	3	5535	4945
	166	6	5406	4972
	167< /td>	9	6075	6395
	16 9	5	2828	3205
	170	7	6485	6243
170	8	6964	6362
	170	9	7303	6962
	170	11 	8790	7906
	171	9	7150	7476
	172	5	2298	1948
	173	4	2913	2677
	175	2	 659	 83 5
	175	3	 893	1789
	176	2	1487
	176	3	2200	1466
	177	9	4686	4925
	177	10 	5177
	177	11 < /td>	5111	5347
	177	13 	7396	8703
	178	6	3452	3724
	181< /td>	5	1853	2473
	18 2	2	2112	1102
	182	3	2617	2006
183	2	2126	2320
	185	5	4683	4219
	185	6	4846	4634
187	4	2940	3557
	188	4	3686	4363
	188	5	4183	4821
	188	6	5882	6493
	189	5	3143	2844
	189	9	5956	5564
	191	1	 618	 4
	191	11 	10357†‚	10001 
	192	3	2268
	192	4	3081	2878
	192	7	6800	5331
	193	3	 997	 839
	194	4	2315	2127
	195	5	6249	4543
	195	6	6620	6231
	1 96	2	1553	1849
	197	1	 1	 861
	198	9	6844	6644
	200	5	5329	5769
	200	6< /td>	5993	6595
	204	5	3914	3276
	205	 447	1709
	209	4	2038	2460
	209< /td>	5	2458	2682
	21 0	10 	7370	8230
	210	13 	9029	10441 
	210	14 	10439 	107 05 
	214	5	2581
	214	9	5065	5277
	214	11 	59 96	5754
	217	2	 541	 194
	218	2	 914	1432
	218	3	1430	1972
	218	3639	3821
	219	1	 458	39
	220	1	 869
	223	4	2617	1964
	227	1	  1	 510
	234	4	1539	1312
	234	6	1838
	235	1	52	 312
	235	2	 687
	238	1< /td>	 660	64
	246	1	  1	 270
	248	1	  3	 362
	248	2	 443	1222
	254	3	2789	 792
	258	2	1179	1616
	260	3	1770	2123
	263	 653	 177
	263	4	2244	1900
	2 63	5	3569	2973
	266	1	 1	 342
	266	2	 177	1022
	270	2< /td>	1124	1681
	272	1	 857	 186
	275	2	1684	2295
	278< /td>	1	 2	 406
	282	1	 714	 391
	282	4	1463	1134
	287	1119	 826
	288	1	 540	  4
	289	1	 684	 4
	291	5	1589
	293	2	2539	2925
	294	1	21	 608
	296	2	 700
	296	3< /td>	 670	 843
	302	1	 261	 530
	30 9	3	 559	 350
	310	2	 249	1889
316	2	2087	1818
	317	2	1048	 584
	318	2	 313	 777
	319	3	 477	  133
	327	2	 912
	331	1	  1	 549
	333	1	  2	 535
	333	2	 465	82
	333	3	 127
	341	1	1
	345	2	 895	 701
	346	2	 750	 199
	349	1	  1	 198
	350	2	81	 413
	355	1	 973
	358	2	 448
	360	2< /td>	 948	 628
	364	2	1639	1265
	378	1	 345	1004
	37 9	2	 683	 510
	381	1	 109	 693
	385	1	 150	  4
	385	2	 269	  30

SEQUENCE LISTING

The patent contains a lengthy “Sequence Listing” section. A copy of the “Sequence Listing” is available in electronic form from the USPTO

web site (http://seqdata.uspto.gov/sequence.html?DocID=06420135B1). An electronic copy of the “Sequence Listing” will also be available from the

USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

Field of search:

No:23.7 - Encodes a microbial polypeptide

No:325 - ANIMAL CELL, PER SE (E.G., CELL LINES, ETC.); COMPOSITION THEREOF; PROCESS OF PROPAGATING, MAINTAINING OR PRESERVING AN ANIMAL CELL OR COMPOSITION THEREOF; PROCESS OF ISOLATING OR SEPARATING AN ANIMAL CELL OR COMPOSITION THEREOF; PROCESS OF PREPARING A CO

No:69.1 - Recombinant DNA technique included in method of making a protein or polypeptide

No:320.1 - VECTOR, PER SE (E.G., PLASMID, HYBRID PLASMID, COSMID, VIRAL VECTOR, BACTERIOPHAGE VECTOR, ETC.)

No:252.3 - Transformants (e.g., recombinant DNA or vector or foreign or exogenous gene containing, fused bacteria, etc.)

No:24.32 - Probes for detection of microbial nucleotide sequences

Foreign documents:

EP0622081 / 1969-12-31

EP0687688 / 1969-12-31

WO/1993/010238 / 1969-12-31

WO/1995/006732 / 1969-12-31

WO/1995/014712 / 1969-12-31

WO/1995/031548 / 1969-12-31

WO/1996/005859 / 1969-12-31

WO/1996/008582 / 1969-12-31

WO/1996/016082 / 1969-12-31

WO/1996/033276 / 1969-12-31

WO/1997/043303 / 1969-12-31

WO/1998/018930 / 1969-12-31

WO/1998/026072 / 1969-12-31