ENTEROCOCCUS FAECALIS POLYNUCLEOTIDES AND POLYPEPTIDES

FIELD OF THE INVENTION

[0002] The present invention relates to the field of molecular biology. In particular, it relates to, among other things, nucleotide sequences of Enterococcus faecalis, 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

[0003] Enterococci have been recognized as being pathogenic for humans since the turn of the century when they were first described by Thiercelin in 1988 as microscopic organisms. The genus Enterococcus includes the species Enterococcus faecalis or E. faecalis which is the most common pathogen in the group, accounting for 80-90 percent of all enterococcal infections. See Lewis et al. (1990) Eur J. Clin Microbiol Infect Dis. 9:111-117.

[0004] The incidence of enterococcal infections has increased in recent years and enterococci are now the second most frequently reported nosocomial pathogens. Enterococcal infection is of particular concern because of its resistance to antibiotics. Recent attention has focused on enterococci not only because of their increasing role in nosocomial infections, but also because of their remarkable and increasing resistance to antimicrobial agents. These factors are mutually reinforcing since resistance allows enterococci to survive in an environment in which antimicrobial agents are heavily used; the hospital setting provides the antibiotics which eliminate or suppress susceptible bacteria, thereby providing a selective advantage for resistant organisms, and the hospital also provides the potential for dissemination of resistant enterococci via the usual routes of hand and environmental contamination.

[0005] Antimicrobial resistance can be divided into two general types, inherent or intrinsic property and that which is acquired. The genes for intrinsic resistance, like other other species characteristics, appear to reside on the chromosome. Acquired resistance results from either a mutation in the existing DNA or acquisition of new DNA. The various inherent traits expressed by enterococci include resistance to semisynthetic penicillinase-resistant penicillins, cephalosporins, low levels of aminoglycosides, and low levels of clindamycin. Examples of acquired resistance include resistance to chloramphenicol, erythromycin, high levels of clindamycin, tetracycline, high levels of aminoglycosides, penicillin by means of penicillinase, fluoroquinolones, and vancomycin. Resistance to high levels of penicillin without penicillinase and resistance to fluoroquinolones are not known to be plasmid or transposon mediated and presumably are due to mutation(s).

[0006] Although the main reservoir for enterococci in humans is the gastrointestinal tract, the bacteria can also reside in the gallbladder, urethra and vagina.

[0007]

E. faecalis
has emerged as an important pathogen in endocarditis, bacteremia, urinary tract infections (UTIs), intraabdominal infections, soft tissue infections, and neonatal sepsis (Lewis 1990, supra). In the 1970s and 1980s enterococci became firmly established as major nosocomial pathogens. They are now the fourth leading cause of hospital-acquired infection and the third leading cause of bacteremia in the United States. Fatality ratios for enterococcal bactermia range from 12% to 68%, with death due to enterococcal sepsis in 4 to 50% of these cases. See Emori, T. G. (1993) Clin. Microbiol. Rev. 6:428-442.

[0008] The ability of enterococci to colonize the gastrointestinal tract, plus the many intrinsic and acquired resistance traits, means that these organisms, which usually seem to have relatively low intrinsic virulence, are given an excellent opportunity to become secondary invaders. Since nosocomial isolates of enterococci have displayed resistance to essentially every useful antimicrobial agent, it will likely become increasingly difficult to successfully treat and control enterococcal infections. Particularly when the various resistance genes come together in a single strain, an event almost certain to occur at some time in the future.

[0009] The etiology of diseases mediated or exacerbated by Enterococcus faecalis, involves the programmed expression of E. faecalis genes, and that characterizing these genes and their patterns of expression would dramatically add to our understanding of the organism and its host interactions. Knowledge of the E. faecalis gene and genomic organization would improve our understanding of disease etiology and lead to improved and new ways of preventing, treating and diagnosing diseases. Thus, there is a need to characterize the genome of E. faecalis and for polynucleotides of this organism.

SUMMARY OF THE INVENTION

[0010] The present invention is based on the sequencing of fragments of the Enterococcus faecalis genome. The primary nucleotide sequences which were generated are provided in SEQ ID NOS: 1-982.

[0011] The present invention provides the nucleotide sequence of hundreds of contigs of the Enterococcus faecalis 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:1-982.

[0012] The present invention further provides nucleotide sequences which are at least 95%, 96%, 97%, 98%, and 99%, identical to the nucleotide sequences of SEQ ID NOS:1-982.

[0013] The nucleotide sequence of SEQ ID NOS:1-982, a representative fragment thereof, or a nucleotide sequence which is at least 95% identical to the nucleotide sequence of SEQ ID NOS:1-982 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.

[0014] 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 Enterococcus faecalis genome.

[0015] Another embodiment of the present invention is directed to fragments of the Enterococcus faecalis genome having particular structural or functional attributes. Such fragments of the Enterococcus faecalis 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 Enterococcus faecalis in a sample, hereinafter referred to as diagnostic fragments or DFs.

[0016] Each of the ORFs in fragments of the Enterococcus faecalis genome disclosed in Tables 1-3, and the EMFs found 5′ prime of the initiation codon, 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.

[0017] The present invention further includes recombinant constructs comprising one or more fragments of the Enterococcus faecalis 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 Enterococcus faecalis has been inserted.

[0018] The present invention further provides host cells containing any of the isolated fragments of the Enterococcus faecalis 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.

[0019] 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.

[0020] The invention further provides methods of obtaining homologs of the fragments of the Enterococcus faecalis 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.

[0021] The invention further provides antibodies which selectively bind polypeptides and proteins of the present invention. Such antibodies include both monoclonal and polyclonal antibodies.

[0022] 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.

[0023] 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.

[0024] In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the above-described assays.

[0025] 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.

[0026] 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.

[0027] The present genomic sequences of Enterococcus faecalis will be of great value to all laboratories working with this organism and for a variety of commercial purposes. Many fragments of the Enterococcus faecalis genome will be immediately identified by similarity searches against GenBank or protein databases and will be of immediate value to Enterococcus faecalis researchers and for immediate commercial value for the production of proteins or to control gene expression.

[0028] 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

[0029]
FIG. 1 is a block diagram of a computer system (102) that can be used to implement computer-based systems of the present invention.

[0030]
FIG. 2 is a schematic diagram depicting the data flow and computer programs used to collect, assemble, edit and annotate the contigs of the Enterococcus faecalis 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 Sequis runs on a Macintosh platform and parses the feature data extracted from the sequence files by Factura to the Unix based Enterococcus faecalis 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 1% 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 GeneMark, described in Borodovsky, M. and McIninch, J. D. (1993) Comput. Chem., 17:123 133. The ORFs are searched against E. faecalis 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

[0031] The present invention is based on the sequencing of fragments of the Enterococcus faecalis genome and analysis of the sequences. The primary nucleotide sequences generated by sequencing the fragments are provided in SEQ ID NOS: 1-982. (As used herein, the “primary sequence” refers to the nucleotide sequence represented by the IUPAC nomenclature system.)

[0032] In addition to the aforementioned Enterococcus faecalis polynucleotide and polynucleotide sequences, the present invention provides the nucleotide sequences of SEQ ID NOS: 1-982, or representative fragments thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan.

[0033] As used herein, a “representative fragment of the nucleotide sequence depicted in SEQ ID NOS:1-982” refers to any portion of the SEQ ID NOS: 1-982 which is not presently represented within a publicly available database. Preferred representative fragments of the present invention are Enterococcus faecalis open reading frames (ORFs), expression modulating fragment (EMFs) and fragments which can be used to diagnose the presence of Enterococcus faecalis in a 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:1-982 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 Enterococcus faecalis proteins.

[0034] The present invention is further directed to nucleic acid molecules encoding portions or fragments of the nucleotide sequences described herein. Fragments include portions of the nucleotide sequences of Table 1-3 and SEQ ID NOS:1-982, at least 10 contiguous nucleotides in length selected from any two integers, one of which representing a 5′ nucleotide position and a second of which representing a 3′ nucleotide position, where the first nucleotide for each nucleotide sequence in SEQ ID NOS:1-982 is position 1. That is, every combination of a 5′ and 3′ nucleotide position that a fragment at least 10 contiguous nucleotides in length could occupy is included in the invention. At least means a fragment may be 10 contiguous nucleotide bases in length or any integer between 10 and the length of an entire nucleotide sequence of SEQ ID NOS:1-982 minus 1. Therefore, included in the invention are contiguous fragments specified by any 5′ and 3′ nucleotide base positions of a nucleotide sequences of SEQ ID NOS:1-982 wherein the contiguous fragment is any integer between 10 and the length of an entire nucleotide sequence minus 1.

[0035] Further, the invention includes polynucleotides comprising fragments specified by size, in nucleotides, rather than by nucleotide positions. The invention includes any fragment size, in contiguous nucleotides, selected from integers between 10 and the length of an entire nucleotide sequence minus 1. Preferred sizes of contiguous nucleotide fragments include 20 nucleotides, 30 nucleotides, 40 nucleotides, 50 nucleotides. Other preferred sizes of contiguous nucleotide fragments, which may be useful as diagnostic probes and primers, include fragments 50-300 nucleotides in length which include, as discussed above, fragment sizes representing each integer between 50-300. Larger fragments are also useful according to the present invention corresponding to most, if not all, of the nucleotide sequences shown in SEQ ID NOS:1-982. The preferred sizes are, of course, meant to exemplify not limit the present invention as all size fragments, representing any integer between 10 and the length of an entire nucleotide sequence minus 1, of each SEQ ID NO:, are included in the invention.

[0036] The present invention also provides for the exclusion of any fragment, specified by 5′ and 3′ base positions or by size in nucleotide bases as described above for any nucleotide sequence of SEQ ID NOS:1-982. Any number of fragments of nucleotide sequences in SEQ ID NOS:1-982, specified by 5′ and 3′ base positions or by size in nucleotides, as described above, may be excluded from the present invention.

[0037] While the presently disclosed sequences of SEQ ID NOS:1-982 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:1-982. However, once the present invention is made available (i.e., once the information in SEQ ID NOS:1-982 and Tables 1-3 has been made available), resolving a rare sequencing error in SEQ ID NOS: 1-982 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 polynucleotides 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.

[0038] Even if all of the very rare sequencing errors in SEQ ID NOS: 1-982 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:1-982.

[0039] 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 Enterococcus faecalis strains that can be used to prepare E. faecalis 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 E. faecalis strain that provided the DNA of the present Sequence Listing, Strain V586, kindly provided by Dr. Michael Gilmore, University of Oklahoma, has been deposited in the ATCC, as a convenience to those of skill in the art. The E. faecalis strain V586 was deposited May 2, 1997 at the ATCC, 10801 University Blvd. Manassas, Va. 20110-2209, and given accession number 55969. The provision of the deposits is not a waiver of any rights of the inventors or their assignees in the present subject matter.

[0040] The nucleotide sequences of the genomes from different strains of Enterococcus faecalis differ somewhat. However, the nucleotide sequences of the genomes of all Enterococcus faecalis strains will be at least 95% identical, in corresponding part, to the nucleotide sequences provided in SEQ ID NOS: 1-982. Nearly all will be at least 99% identical and the great majority will be 99.9% identical.

[0041] The present application is further directed to nucleic acid molecules at least 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleic acid sequence shown in SEQ ID NOS: 1-982. The above nucleic acid sequences are included irrespective of whether they encode a polypeptide having E. faecalis activity. This is because even where a particular nucleic acid molecule does not encode a polypeptide having E. faecalis activity, one of skill in the art would still know how to use the nucleic acid molecule, for instance, as a hybridization probe. Uses of the nucleic acid molecules of the present invention that do not encode a polypeptide having E. faecalis activity include, inter alia, isolating an E. faecalis gene or allelic variants thereof from a DNA library, and detecting E. faecalis mRNA expression samples, environmental samples, suspected of containing E. faecalis by Northern Blot analysis.

[0042] Preferred, are nucleic acid molecules having sequences at least 90%, 95%, 96%, 97%, 98% or 99% identical to the nucleic acid sequence shown in SEQ ID NOS: 1-982, which do, in fact, encode a polypeptide having E. faecalis protein activity By “a polypeptide having E. faecalis activity” is intended polypeptides exhibiting activity similar, but not necessarily identical, to an activity of the E. faecalis protein of the invention, as measured in a particular biological assay suitable for measuring activity of the specified protein.

[0043] Due to the degeneracy of the genetic code, one of ordinary skill in the art will immediately recognize that a large number of the nucleic acid molecules having a sequence at least 90%, 95%, 96%, 97%, 98%, or 99% identical to the nucleic acid sequences shown in SEQ ID NOS: 1-982 will encode a polypeptide having E. faecalis protein activity. In fact, since degenerate variants of these nucleotide sequences all encode the same polypeptide, this will be clear to the skilled artisan even without performing the above described comparison assay. It will be further recognized in the art that, for such nucleic acid molecules that are not degenerate variants, a reasonable number will also encode a polypeptide having E. faecalis protein activity. This is because the skilled artisan is fully aware of amino acid substitutions that are either less likely or not likely to significantly effect protein function (e.g., replacing one aliphatic amino acid with a second aliphatic amino acid), as further described below.

[0044] The biological activity or function of the polypeptides of the present invention are expected to be similar or identical to polypeptides from other bacteria that share a high degree of structural identity/similarity. Tables 1 and 2 lists accession numbers and descriptions for the closest matching sequences of polypeptides available through Genbank. It is therefore expected that the biological activity or function of the polypeptides of the present invention will be similar or identical to those polypeptides from other bacterial genuses, species, or strains listed in Tables 1 and 2.

[0045] By a polynucleotide having a nucleotide sequence at least, for example, 95% “identical” to a reference nucleotide sequence of the present invention, it is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the E. faecalis polypeptide. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted, inserted, or substituted with another nucleotide. The query sequence may be an entire sequence shown in SEQ ID NOS: 1-982, the ORF (open reading frame), or any fragment specified as described herein.

[0046] As a practical matter, whether any particular nucleic acid molecule or polypeptide is at least 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence of the presence invention can be determined conventionally using known computer programs. A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. See Brutlag et al. (1990) Comp. App. Biosci. 6:237-245. In a sequence alignment the query and subject sequences are both DNA sequences. An RNA sequence can be compared by first converting U's to T's. The result of said global sequence alignment is in percent identity. Preferred parameters used in a FASTDB alignment of DNA sequences to calculate percent identity arc: Matrix=Unitary, k-tuple=4, Mismatch Penalty=1, Joining Penalty=30, Randomization Group Length=0, Cutoff Score=1, Gap Penalty=5, Gap Size Penalty 0.05, Window Size=500 or the length of the subject nucleotide sequence, whichever is shorter.

[0047] If the subject sequence is shorter than the query sequence because of 5′ or 3′ deletions, not because of internal deletions, a manual correction must be made to the results. This is because the FASTDB program does not account for 5′ and 3′ truncations of the subject sequence when calculating percent identity. For subject sequences truncated at the 5′ or 3′ ends, relative to the query sequence, the percent identity is corrected by calculating the number of bases of the query sequence that are 5′ and 3′ of the subject sequence, which are not matched/aligned, as a percent of the total bases of the query sequence. Whether a nucleotide is matched/aligned is determined by results of the FASTDB sequence alignment. This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score. This corrected score is what is used for the purposes of the present invention. Only nucleotides outside the 5′ and 3′ nucleotides of the subject sequence, as displayed by the FASTDB alignment, which are not matched/aligned with the query sequence, are calculated for the purposes of manually adjusting the percent identity score.

[0048] For example, a 90 nucleotide subject sequence is aligned to a 100 nucleotide query sequence to determine percent identity. The deletions occur at the 5′ end of the subject sequence and therefore, the FASTDB alignment does not show a matched/alignment of the first 10 nucleotides at 5′ end. The 10 unpaired nucleotides represent 10% of the sequence (number of nucleotides at the 5′ and 3′ ends not matched/total number of nucleotides in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 nucleotides were perfectly matched the final percent identity would be 90%. In another example, a 90 nucleotide subject sequence is compared with a 100 nucleotide query sequence. This time the deletions are internal deletions so that there are no nucleotides on the 5′ or 3′ of the subject sequence which are not matched/aligned with the query. In this case the percent identity calculated by FASTDB is not manually corrected. Once again, only nucleotides 5′ and 3′ of the subject sequence which are not matched/aligned with the query sequence are manually corrected for. No other manual corrections are to made for the purposes of the present invention.

[0049] Computer Related Embodiments

[0050] The nucleotide sequences provided in SEQ ID) NOS: 1-982, 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:1-982 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, which contains a nucleotide sequence of the present invention; i.e., a nucleotide sequence provided in SEQ ID NOS:1-982, 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:1-982. Such a manufacture provides a large portion of the Enterococcus faecalis genome and parts thereof (e.g., a Enterococcus faecalis open reading frame (ORF)) in a form which allows a skilled artisan to examine the manufacture using means not directly applicable to examining the Enterococcus faecalis genome or a subset thereof as it exists in nature or in purified form.

[0051] 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.

[0052] 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.

[0053] 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:1-982, 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: 1-982 the present invention enables the skilled artisan routinely to access the provided sequence information for a wide variety of purposes.

[0054] 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 Enterococcus faecalis genome which contain homology to ORFs or proteins from both Enterococcus faecalis and from other organisms. Among the ORFs discussed herein are protein encoding fragments of the Enterococcus faecalis genome useful in producing commercially important proteins, such as enzymes used in fermentation reactions and in the production of commercially useful metabolites, proteins to be used as vaccines or in the generation of immuno-therapeutic reagents, or as drug screening targets.

[0055] 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 Enterococcus faecalis genome.

[0056] 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 system are suitable for use in the present invention.

[0057] 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.

[0058] 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.

[0059] 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 (NCBI). 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.

[0060] 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.

[0061] 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 arc 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).

[0062] 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 Enterococcus faecalis 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.

[0063] 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 Enterococcus faecalis genome. In the present examples, implementing software which implement the BLAST algorithm, described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410, is used to identify open reading frames within the Enterococcus faecalis 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.

[0064]
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.

[0065] 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.

[0066] Biochemical Embodiments

[0067] Other embodiments of the present invention are directed to isolated fragments of the Enterococcus faecalis genome. The fragments of the Enterococcus faecalis genome of the present invention include, but are not limited to fragments which encode peptides, 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 Enterococcus faecalis in a sample, hereinafter diagnostic fragments (DFs).

[0068] As used herein, an “isolated nucleic acid molecule” or an “isolated fragment of the Enterococcus faecalis 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:1-982, 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.

[0069] 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.

[0070] In one embodiment, Enterococcus faecalis DNA can be enzymatically sheared to produce fragments of 15-20 kb in length. These fragments can then be used to generate a Enterococcus faecalis 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:1-982. Well known and routine techniques of PCR cloning then can be used to isolate the ORF from the lambda DNA library or Enterococcus faecalis genomic DNA. Thus, given the availability of SEQ ID NOS:1-982, 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:1-982 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.

[0071] 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. Each sequence of SEQ ID NOS:1-982, however, begins and ends with a termination codon. For purposes of numbering and reference to polynucleotide and polypeptide sequences the entire sequence of each sequence of SEQ ID NOS:1-982 is included with the first nucleotide being position 1. Therefore, for reference purposes the numbering used in the present invention is that provided in the sequence listing for SEQ ID NOS:1-982.

[0072] Tables 1, 2, and 3 list ORFs in the Enterococcus faecalis 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.

[0073] Table 1 sets out ORFs in the Enterococcus faecalis 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 March, 1997.

[0074] Table 2 sets out ORFs in the Enterococcus faecalis 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 March, 1997.

[0075] Table 3 sets out ORFs in the Enterococcus faecalis contigs of the present invention that do not match significantly, by BLASTP analysis, a polypeptide sequence available through GenBank in March, 1997.

[0076] 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 coordinate of the first nucleotide of the ORF, counting from the 5′ end of the contig strand; the fourth column indicates the coordinate of the final nucleotide of the ORF, counting from the 5′ end of the contig strand.

[0077] In Tables 1 and 2, column five lists the Reference for the closest matching sequence available through GenBank. These reference numbers are the database 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.

[0078] In Table 1, column seven provides the nucleotide BLAST percent identity score from the comparison of the ORF and the GenBank sequence, column eight indicates the length in nucleotides of the highest scoring segment pair identified by the BLAST identity analysis, and column nine provides the total length of the ORF in nucleotides.

[0079] In Table 2, column seven provides the protein BLAST percent similarity of the highest scoring segment pair identified, column eight provides the percent identity of the highest scoring segment pair, and column nine provides the total length of the ORF in nucleotides.

[0080] 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.

[0081] 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 Enterococcus faecalis 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.

[0082] 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.

[0083] 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.

[0084] EMF sequences can be identified within the contigs of the Enterococcus faecalis 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 Enterococcus faecalis 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.

[0085] 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.

[0086] 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.

[0087] As used herein, a “diagnostic fragment,” DF, means a series of nucleotide molecules which selectively hybridize to Enterococcus faecalis sequences. DFs can be readily identified by identifying unique sequences within contigs of the Enterococcus faecalis 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.

[0088] 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:1-982, a representative fragment thereof, or a nucleotide sequence at least 99% and preferably 99.9% identical to SEQ ID NOS:1-982, 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.

[0089] 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 Enterococcus faecalis origin isolated by using part or all of the fragments in question as a probe or primer.

[0090] Each of the ORFs of the Enterococcus faecalis 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 Enterococcus faecalis. 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 Enterococcus faecalis. Also particularly preferred are ORFs that can be used to distinguish between strains of Enterococcus faecalis, particularly those that distinguish medically important strain, such as drug-resistant strains.

[0091] 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). Antisense 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)).

[0092] The present invention further provides recombinant constructs comprising one or more fragments of the Enterococcus faecalis 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 Enterococcus faecalis 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.

[0093] 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, pBS SK (+ or −), pBS KS (+ or −), 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).

[0094] 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.

[0095] The present invention further provides host cells containing any one of the isolated fragments of the Enterococcus faecalis 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.

[0096] 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).

[0097] A host cell containing one of the fragments of the Enterococcus faecalis 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.

[0098] Preferred nucleic acid fragments of the present invention are the ORFs depicted in Tables 2 and 3 which encode proteins.

[0099] 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.

[0100] 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.

[0101] 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. Preferred polypeptides and proteins of the present invention are polypeptides and proteins coded for by the polynucleotides of SEQ ID NOS:1-982, wherein the polypeptides and proteins are coded in the same frame as the termination codon at the end of each sequence of SEQ ID NOS:1-982. 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.

[0102] The polypeptides of the present invention arc preferably provided in an isolated form, and preferably are substantially purified. A recombinantly produced version of the E. faecalis polypeptide can be substantially purified by the one-step method described by Smith et al. (1988) Gene 67:31-40. Polypeptides of the invention also can be purified from natural or recombinant sources using antibodies directed against the polypeptides of the invention in methods which are well known in the art of protein purification.

[0103] The invention further provides for isolated E. faecalis polypeptides comprising an amino acid sequence selected from the group including: (a) the amino acid sequence of a full-length E. faecalis polypeptide having the complete amino acid sequence from the first methionine codon to the termination codon of each sequence listed in SEQ ID NOS:1-982, wherein said termination codon is at the end of each SEQ ID NO: and said first methionine is the first methionine in frame with said termination codon; and (b) the amino acid sequence of a full-length E. faecalis polypeptide having the complete amino acid sequence in (a) excepting the N-terminal methionine.

[0104] The polypeptides of the present invention also include polypeptides having an amino acid sequence at least 80% identical, more preferably at least 90% identical, and still more preferably 95%, 96%, 97%, 98% or 99% identical to those described in (a) and (b) above.

[0105] The present invention is further directed to polynucleotide encoding portions or fragments of the amino acid sequences described herein as well as to portions or fragments of the isolated amino acid sequences described herein. Fragments include portions of the amino acid sequences described herein, are at least 5 contiguous amino acid in length, are selected from any two integers, one of which representing a N-terminal position. The initiation codon of the polypeptides of the present inventions position 1. The initiation codon (position 1) for purposes of the present invention is the first methionine codon of each sequence of SEQ ID NOS:1-982 which is in frame with the termination codon at the end of each said sequence. Every combination of a N-terminal and C-terminal position that a fragment at least 5 contiguous amino acid residues in length could occupy, on any given amino acid sequence encoded by a sequence of SEQ ID NOS:1-982 is included in the invention, i.e., from initiation codon up to the termination codon. At least means a fragment may be 5 contiguous amino acid residues in length or any integer between 5 and the number of residues in a full length amino acid sequence minus 1. Therefore, included in the invention are contiguous fragments specified by any N-terminal and C-terminal positions of amino acid sequence set forth in SEQ ID NOS:1-982 wherein the contiguous fragment is any integer between 5 and the number of residues in a full length sequence minus 1.

[0106] Further, the invention includes polypeptides comprising fragments specified by size, in amino acid residues, rather than by N-terminal and C-terminal positions. The invention includes any fragment size, in contiguous amino acid residues, selected from integers between 5 and the number of residues in a full length sequence minus 1. Preferred sizes of contiguous polypeptide fragments include about 5 amino acid residues, about 10 amino acid residues, about 20 amino acid residues, about 30 amino acid residues, about 40 amino acid residues, about 50 amino acid residues, about 100 amino acid residues, about 200 amino acid residues, about 300 amino acid residues, and about 400 amino acid residues. The preferred sizes are, of course, meant to exemplify, not limit, the present invention as all size fragments representing any integer between 5 and the number of residues in a full length sequence minus I are included in the invention. The present invention also provides for the exclusion of any fragments specified by N-terminal and C-terminal positions or by size in amino acid residues as described above. Any number of fragments specified by N-terminal and C-terminal positions or by size in amino acid residues as described above may be excluded.

[0107] The above fragments need not be active since they would be useful, for example, in immunoassays, in epitope mapping, epitope tagging, to generate antibodies to a particular portion of the protein, as vaccines, and as molecular weight markers.

[0108] Further polypeptides of the present invention include polypeptides which have at least 90% similarity, more preferably at least 95% similarity, and still more preferably at least 96%, 97%, 98% or 99% similarity to those described above.

[0109] A further embodiment of the invention relates to a polypeptide which comprises the amino acid sequence of a E. faecalis polypeptide having an amino acid sequence which contains at least one conservative amino acid substitution, but not more than 50 conservative amino acid substitutions, not more than 40 conservative amino acid substitutions, not more than 30 conservative amino acid substitutions, and not more than 20 conservative amino acid substitutions. Also provided are polypeptides which comprise the amino acid sequence of a E. faecalis polypeptide, having at least one, but not more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 conservative amino acid substitutions.

[0110] By a polypeptide having an amino acid sequence at least, for example, 95% “identical” to a query amino acid sequence of the present invention, it is intended that the amino acid sequence of the subject polypeptide is identical to the query sequence except that the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid sequence. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a query amino acid sequence, up to 5% of the amino acid residues in the subject sequence may be inserted, deleted, (indels) or substituted with another amino acid. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.

[0111] As a practical matter, whether any particular polypeptide is at least 90%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequences encoded by the sequences of SEQ ID NOS:1-982, as described herein, can be determined conventionally using known computer programs. A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al., (1990) Comp. App. Biosci. 6:237-245. In a sequence alignment the query and subject sequences are both amino acid sequences. The result of said global sequence alignment is in percent identity. Preferred parameters used in a FASTDB amino acid alignment are: Matrix=PAM 0, k-tuple=2, Mismatch Penalty=1, Joining Penalty-20, Randomization Group Length=0, Cutoff Score=1, Window Size=sequence length, Gap Penalty=5, Gap Size Penalty=0.05, Window Size=500 or the length of the subject amino acid sequence, whichever is shorter.

[0112] If the subject sequence is shorter than the query sequence due to N- or C-terminal deletions, not because of internal deletions, the results, in percent identity, must be manually corrected. This is because the FASTDB program does not account for N- and C-terminal truncations of the subject sequence when calculating global percent identity. For subject sequences truncated at the N- and C-termini, relative to the query sequence, the percent identity is corrected by calculating the number of residues of the query sequence that are N- and C-terminal of the subject sequence, which are not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. Whether a residue is matched/aligned is determined by results of the FASTDB sequence alignment. This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score. This final percent identity score is what is used for the purposes of the present invention. Only residues to the N- and C-terminal of the subject sequence, which are not matched/aligned with the query sequence, are considered for the purposes of manually adjusting the percent identity score. That is, only query amino acid residues outside the farthest N- and C-terminal residues of the subject sequence.

[0113] For example, a 90 amino acid residue subject sequence is aligned with a 100 residue query sequence to determine percent identity. The deletion occurs at the N-terminus of the subject sequence and therefore, the FASTDB alignment does not match/align with the first 10 residues at the N-terminus. The 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C-termini not matched/total number of residues in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 residues were perfectly matched the final percent identity would be 90%. In another example, a 90 residue subject sequence is compared with a 100 residue query sequence. This time the deletions are internal so there are no residues at the N- or C-termini of the subject sequence which are not matched/aligned with the query. In this case the percent identity calculated by FASTDB is not manually corrected. Once again, only residue positions outside the N- and C-terminal ends of the subject sequence, as displayed in the FASTDB alignment, which are not matched/aligned with the query sequence are manually corrected. No other manual corrections are to made for the purposes of the present invention.

[0114] The above polypeptide sequences are included irrespective of whether they have their normal biological activity. This is because even where a particular polypeptide molecule does not have biological activity, one of skill in the art would still know how to use the polypeptide, for instance, as a vaccine or to generate antibodies. Other uses of the polypeptides of the present invention that do not have E. faecalis activity include, inter alia, as epitope tags, in epitope mapping, and as molecular weight markers on SDS-PAGE gels or on molecular sieve gel filtration columns using methods known to those of skill in the art.

[0115] As described below, the polypeptides of the present invention can also be used to raise polyclonal and monoclonal antibodies, which are useful in assays for detecting E. faecalis protein expression or as agonists and antagonists capable of enhancing or inhibiting E. faecalis protein function. Further, such polypeptides can be used in the yeast two-hybrid system to “capture” E. faecalis protein binding proteins which are also candidate agonists and antagonists according to the present invention. See, e.g., Fields et al. (1989) Nature 340:245-246.

[0116] 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.

[0117] “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.

[0118] “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 Enterococcus faecalis 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.

[0119] 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.

[0120] “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.

[0121] 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, 2nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), the disclosure of which is hereby incorporated by reference in its entirety.

[0122] 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.

[0123] 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.

[0124] 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.

[0125] 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.

[0126] 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.

[0127] 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.

[0128] 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.

[0129] 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.

[0130] 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.

[0131] The invention further provides methods of obtaining homologs from other strains of Enterococcus faecalis, of the fragments of the Enterococcus faecalis 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 Enterococcus faecalis is defined as a homolog of a fragment of the Enterococcus faecalis 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 Enterococcus faecalis 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.

[0132] 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.

[0133] Region specific primers or probes derived from the nucleotide sequence provided in SEQ ID NOS:1-982 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:1-982 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)).

[0134] When using primers derived from SEQ ID NOS:1-982 or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS: 1-982, one skilled in the art will recognize that by employing high stringency conditions (e.g., annealing at 50-60° C. in 6×SSPC and 50% formamicle, and washing at 50-65° C. in 0.5×SSPC) 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×SSPC and 40-45% formamide, and washing at 42° C. in 0.5×SSPC), sequences which are greater than 40-50% homologous to the primer will also be amplified.

[0135] When using DNA probes derived from SEQ ID NOS:1-982, or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS:1-982, 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×SSPC and 50% formamide, and washing at 50-65° C. in 0.5×SSPC), 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×SSPC and 40-45% formamide, and washing at 42° C. in 0.5×SSPC), sequences having regions which are greater than 35-45% homologous to the probe will be obtained.

[0136] 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 Enterococcus faecalis.

[0137] Illustrative Uses of Compositions of the Invention

[0138] 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 Enterococcus faecalis 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.

[0139] 1. Biosynthetic Enzymes

[0140] 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.

[0141] The various metabolic pathways present in Enterococcus faecalis 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:1-982.

[0142] 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.

[0143] 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).

[0144] The metabolism of sugars is an important aspect of the primary metabolism of Enterococcus faecalis. 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).

[0145] 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.

[0146] 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).

[0147] 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)).

[0148] 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.

[0149] 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.

[0150] 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.

[0151] 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).

[0152] Another category of useful proteins encoded by the ORFs of the present invention include enzymes involved in nucleic acid synthesis, repair, and recombination.

[0153] 2. Generation of Antibodies

[0154] 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.

[0155]

E. faecalis
protein-specific antibodies for use in the present invention can be raised against the intact E. faecalis protein or an antigenic polypeptide fragment thereof, which may be presented together with a carrier protein, such as an albumin, to an animal system (such as rabbit or mouse) or, if it is long enough (at least about 25 amino acids), without a carrier.

[0156] As used herein, the term “antibody” (Ab) or “monoclonal antibody” (Mab) is meant to include intact molecules, single chain whole antibodies, and antibody fragments. Antibody fragments of the present invention include Fab and F(ab′)2 and other fragments including single-chain Fvs (scFv) and disulfide-linked Fvs (sdFv). Also included in the present invention are chimeric and humanized monoclonal antibodies and polyclonal antibodies specific for the polypeptides of the present invention. The antibodies of the present invention may be prepared by any of a variety of methods. For example, cells expressing a polypeptide of the present invention or an antigenic fragment thereof can be administered to an animal in order to induce the production of sera containing polyclonal antibodies. For example, a preparation of E. faecalis polypeptide or fragment thereof is prepared and purified to render it substantially free of natural contaminants. Such a preparation is then introduced into an animal in order to produce polyclonal antisera of greater specific activity.

[0157] In a preferred method, the antibodies of the present invention are monoclonal antibodies or binding fragments thereof. Such monoclonal antibodies can be prepared using hybridoma technology. See, e.g., Harlow et al., ANTIBODIES: A LABORATORY MANUAL, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling, et al., in: MONOCLONAL ANTIBODIES AND T-CELL HYBRIDOMAS 563-681 (Elsevier, N.Y., 1981). Fab and F(ab′)2 fragments may be produced by proteolytic cleavage, using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(ab′)2 fragments). Alternatively, E. faecalis polypeptide-binding fragments, chimeric, and humanized antibodies can be produced through the application of recombinant DNA technology or through synthetic chemistry using methods known in the art.

[0158] Alternatively, additional antibodies capable of binding to the polypeptide antigen of the present invention may be produced in a two-step procedure through the use of anti-idiotypic antibodies. Such a method makes use of the fact that antibodies are themselves antigens, and that, therefore, it is possible to obtain an antibody which binds to a second antibody. In accordance with this method, E. faecalis polypeptide-specific antibodies arc used to immunize an animal, preferably a mouse. The splenocytes of such an animal are then used to produce hybridoma cells, and the hybridoma cells are screened to identify clones which produce an antibody whose ability to bind to the E. faecalis polypeptide-specific antibody can be blocked by the E. faecalis polypeptide antigen. Such antibodies comprise anti-idiotypic antibodies to the E. faecalis polypeptide-specific antibody and can be used to immunize an animal to induce formation of further E. faecalis polypeptide-specific antibodies.

[0159] Antibodies and fragements thereof of the present invention may be described by the portion of a polypeptide of the present invention recognized or specifically bound by the antibody. Antibody binding fragements of a polypeptide of the present invention may be described or specified in the same manner as for polypeptide fragements discussed above., i.e., by N-terminal and C-terminal positions or by size in contiguous amino acid residues. Any number of antibody binding fragments, of a polypeptide of the present invention, specified by N-terminal and C-terminal positions or by size in amino acid residues, as described above, may also be excluded from the present invention. Therefore, the present invention includes antibodies the specifically bind a particularly described fragement of a polypeptide of the present invention and allows for the exclusion of the same.

[0160] Antibodies and fragements thereof of the present invention may also be described or specified in terms of their cross-reactivity. Antibodies and fragements that do not bind polypeptides of any other species of Enterococcus other than E. faecalis are included in the present invention. Likewise, antibodies and fragements that bind only species of Enterococcus, i.e. antibodies and fragements that do not bind bacteria from any genus other than Enterococcus, are included in the present invention.

[0161] 3. Diagnostic and Detection Assays and Kits

[0162] The present invention further relates to methods for assaying enterococcal infection in an animal by detecting the expression of genes encoding enterococcal polypeptides of the present invention. The methods comprise analyzing tissue or body fluid from the animal for Enterococcus-specific antibodies, nucleic acids, or proteins. Analysis of nucleic acid specific to Enterococcus is assayed by PCR or hybridization techniques using nucleic acid sequences of the present invention as either hybridization probes or primers. See, e.g., Sambrook et al. Molecular cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 2nd ed., 1983, page 54 reference); Eremeeva et al. (1994) J. Clin. Microbiol. 32:803-810 (describing differentiation among spotted fever group Rickettsiae species by analysis of restriction fragment length polymorphism of PCR-amplified DNA) and Chen et al. 1994 J. Clin. Microbiol. 32:589-595 (detecting B. burgdorferi nucleic acids via PCR).

[0163] Where diagnosis of a disease state related to infection with Enterococcus has already been made, the present invention is useful for monitoring progression or regression of the disease state whereby patients exhibiting enhanced Enterococcus gene expression will experience a worse clinical outcome relative to patients expressing these gene(s) at a lower level.

[0164] By “biological sample” is intended any biological sample obtained from an animal, cell line, tissue culture, or other source which contains Enterococcus polypeptide, mRNA, or DNA. Biological samples include body fluids (such as saliva, blood, plasma, urine, mucus, synovial fluid, etc.) tissues (such as muscle, skin, and cartilage) and any other biological source suspected of containing Enterococcus polypeptides or nucleic acids. Methods for obtaining biological samples such as tissue are well known in the art.

[0165] The present invention is useful for detecting diseases related to Enterococcus infections in animals. Preferred animals include monkeys, apes, cats, dogs, birds, cows, pigs, mice, horses, rabbits and humans. Particularly preferred are humans.

[0166] Total RNA can be isolated from a biological sample using any suitable technique such as the single-step guanidinium-thiocyanate-phenol-chloroform method described in Chomczynski et al. (1987) Anal. Biochem. 162:156-159. mRNA encoding Enterococcus polypeptides having sufficient homology to the nucleic acid sequences identified in SEQ ID NOS:1-982 to allow for hybridization between complementary sequences are then assayed using any appropriate method. These include Northern blot analysis, S1 nuclease mapping, the polymerase chain reaction (PCR), reverse transcription in combination with the polymerase chain reaction (RT-PCR), and reverse transcription in combination with the ligase chain reaction (RT-LCR).

[0167] Northern blot analysis can be performed as described in Harada et al. (1990) Cell 63:303-312. Briefly, total RNA is prepared from a biological sample as described above. For the Northern blot, the RNA is denatured in an appropriate buffer (such as glyoxal/dimethyl sulfoxide/sodium phosphate buffer), subjected to agarose gel electrophoresis, and transferred onto a nitrocellulose filter. After the RNAs have been linked to the filter by a UV linker, the filter is prehybridized in a solution containing formamide, SSC, Denhardt's solution, denatured salmon sperm, SDS, and sodium phosphate buffer. A E. faecalis polynucleotide sequence shown in SEQ ID NOS:1-982 labeled according to any appropriate method (such as the 32P-multiprimed DNA labeling system (Amersham)) is used as probe. After hybridization overnight, the filter is washed and exposed to x-ray film. DNA for use as probe according to the present invention is described in the sections above and will preferably at least 15 nucleotides in length.

[0168] S1 mapping can be performed as described in Fujita et al. (1987) Cell 49:357-367. To prepare probe DNA for use in S1 mapping, the sense strand of an above-described E. faecalis DNA sequence of the present invention is used as a template to synthesize labeled antisense DNA. The antisense DNA can then be digested using an appropriate restriction endonuclease to generate further DNA probes of a desired length. Such antisense probes are useful for visualizing protected bands corresponding to the target mRNA (i.e., mRNA encoding Enterococcus polypeptides).

[0169] Levels of mRNA encoding Enterococcus polypeptides are assayed, for e.g., using the RT-PCR method described in Makino et al. (1990) Technique 2:295-301. By this method, the radioactivities of the “amplicons” in the polyacrylamide gel bands are linearly related to the initial concentration of the target mRNA. Briefly, this method involves adding total RNA isolated from a biological sample in a reaction mixture containing a RT primer and appropriate buffer. After incubating for primer annealing, the mixture can be supplemented with a RT buffer, cNTPs, DTT, RNase inhibitor and reverse transcriptase. After incubation to achieve reverse transcription of the RNA, the RT products are then subject to PCR using labeled primers. Alternatively, rather than labeling the primers, a labeled dNTP can be included in the PCR reaction mixture. PCR amplification can be performed in a DNA thermal cycler according to conventional techniques. After a suitable number of rounds to achieve amplification, the PCR reaction mixture is electrophoresed on a polyacrylamide gel. After drying the gel, the radioactivity of the appropriate bands (corresponding to the mRNA encoding the Enterococcus polypeptides of the present invention) are quantified using an imaging analyzer. RT and PCR reaction ingredients and conditions, reagent and gel concentrations, and labeling methods are well known in the art. Variations on the RT-PCR method will be apparent to the skilled artisan. Other PCR methods that can detect the nucleic acid of the present invention can be found in PCR PRIMER: A LABORATORY MANUAL (C. W. Dieffenbach et al. eds., Cold Spring Harbor Lab Press, 1995).

[0170] The polynucleotides of the present invention., including both DNA and RNA, may be used to detect polynucleotides of the present invention or Enterococcal species including E. faecalis using bio chip technology. The present invention includes both high density chip arrays (>1000 oligonucleotides per cm2) and low density chip arrays (<1000 oligonucleotides per cm2). Bio chips comprising arrays of polynucleotides of the present invention may be used to detect Enterococcal species, including E. faecalis, in biological and environmental samples and to diagnose an animal, including humans, with an E. faecalis or other Enterococcal infection. The bio chips of the present invention may comprise polynucleotide sequences of other pathogens including bacteria, viral, parasitic, and fungal polynucleotide sequences, in addition to the polynucleotide sequences of the present invention, for use in rapid differential pathogenic detection and diagnosis. The bio chips can also be used to monitor an E. faecalis or other Enterococcal infections and to monitor the genetic changes (deletions, insertions, mismatches, etc.) in response to drug therapy in the clinic and drug development in the laboratory. The bio chip technology comprising arrays of polynucleotides of the present invention may also be used to simultaneously monitor the expression of a multiplicity of genes, including those of the present invention. The polynucleotides used to comprise a selected array may be specified in the same manner as for the fragements, i.e., by their 5′ and 3′ positions or length in contigious base pairs and include from. Methods and particular uses of the polynucleotides of the present invention to detect Enterococcal species, including E. faecalis, using bio chip technology include those known in the art and those of: U.S. Pat. Nos. 5,510,270, 5,545,531, 5,445,934, 5,677,195, 5,532,128, 5,556,752, 5,527,681, 5,451,683, 5,424,186, 5,607,646, 5,658,732 and World Patent Nos. WO/9710365, WO/9511995, WO/9743447, WO/9535505, each incorporated herein in their entireties.

[0171] Biosensors using the polynucleotides of the present invention may also be used to detect, diagnose, and monitor E. faecalis or other Enterococcal species and infections thereof. Biosensors using the polynucleotides of the present invention may also be used to detect particular polynucleotides of the present invention. Biosensors using the polynucleotides of the present invention may also be used to monitor the genetic changes (deletions, insertions, mismatches, etc.) in response to drug therapy in the clinic and drug development in the laboratory. Methods and particular uses of the polynucleotides of the present invention to detect Enterococcal species, including E. faecalis, using biosenors include those known in the art and those of: U.S. Pat. Nos. 5,721,102, 5,658,732, 5,631,170, and World Patent Nos. WO97/35011, WO/97/20203, each incorporated herein in their entireties.

[0172] Thus, the present invention includes both bio chips and biosensors comprising polynucleotides of the present invention and methods of their use.

[0173] Assaying Enterococcus polypeptide levels in a biological sample can occur using any art-known method, such as antibody-based techniques. For example, Enterococcus polypeptide expression in tissues can be studied with classical immunohistological methods. In these, the specific recognition is provided by the primary antibody (polyclonal or monoclonal) but the secondary detection system can utilize fluorescent, enzyme, or other conjugated secondary antibodies. As a result, an immunohistological staining of tissue section for pathological examination is obtained. Tissues can also be extracted, e.g., with urea and neutral detergent, for the liberation of Enterococcus polypeptides for Western-blot or dot/slot assay. See, e.g., Jalkanen, M. et al. (1985) J. Cell. Biol. 101:976-985; Jalkanen, M. et al. (1987) J. Cell . Biol. 105:3087-3096. In this technique, which is based on the use of cationic solid phases, quantitation of a Enterococcus polypeptide can be accomplished using an isolated Enterococcus polypeptide as a standard. This technique can also be applied to body fluids.

[0174] Other antibody-based methods useful for detecting Enterococcus polypeptide gene expression include immunoassays, such as the ELISA and the radioimmunoassay (RIA). For example, a Enterococcus polypeptide-specific monoclonal antibodies can be used both as an immunoabsorbent and as an enzyme-labeled probe to detect and quantify a Enterococcus polypeptide. The amount of a Enterococcus polypeptide present in the sample can be calculated by reference to the amount present in a standard preparation using a linear regression computer algorithm. Such an ELISA is described in Iacobelli et al. (1988) Breast Cancer Research and Treatment 11:19-30. In another ELISA assay, two distinct specific monoclonal antibodies can be used to detect Enterococcus polypeptides in a body fluid. In this assay, one of the antibodies is used as the immunoabsorbent and the other as the enzyme-labeled probe.

[0175] The above techniques may be conducted essentially as a “one-step” or “two-step” assay. The “one-step” assay involves contacting the Enterococcus polypeptide with immobilized antibody and, without washing, contacting the mixture with the labeled antibody. The “two-step” assay involves washing before contacting the mixture with the labeled antibody. Other conventional methods may also be employed as suitable. It is usually desirable to immobilize one component of the assay system on a support, thereby allowing other components of the system to be brought into contact with the component and readily removed from the sample. Variations of the above and other immunological methods included in the present invention can also be found in Harlow et al., ANTIBODIES: A LABORATORY MANUAL, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988).

[0176] Suitable enzyme labels include, for example, those from the oxidase group, which catalyze the production of hydrogen peroxide by reacting with substrate. Glucose oxidase is particularly preferred as it has good stability and its substrate (glucose) is readily available. Activity of an oxidase label may be assayed by measuring the concentration of hydrogen peroxide formed by the enzyme-labeled antibody/substrate reaction. Besides enzymes, other suitable labels include radioisotopes, such as iodine (125I, 121I), carbon (14C), sulphur (35S), tritium (3H), indium (112In), and technetium (99mTc), and fluorescent labels, such as fluorescein and rhodamine, and biotin.

[0177] Further suitable labels for the Enterococcus polypeptide-specific antibodies of the present invention are provided below. Examples of suitable enzyme labels include malate dehydrogenase, Enterococcal nuclease, delta-5-steroid isomerase, yeast-alcohol dehydrogenase, alpha-glycerol phosphate dehydrogenase, triose phosphate isomerase, peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-6-phosphate dehydrogenase, glucoamylase, and acetylcholine esterase.

[0178] Examples of suitable radioisotopic labels include 3H, 111In, 125I, 131I, 32P, 35S, 14C, 51 Cr, 57To, 58Co, 59Fe, 75Se, 152Eu, 90Y, 67Cu, 217Ci, 211At, 212Pb, 47Sc, 109Pd, etc. 111In is a preferred isotope where in vivo imaging is used since its avoids the problem of dehalogenation of the 125I or 131I-labeled monoclonal antibody by the liver. In addition, this radionucleotide has a more favorable gamma emission energy for imaging. See, e.g., Perkins et al. (1985) Eur. J. Nucl. Med. 10:296-301; Carasquillo et al. (1987) J. Nucl. Med. 28:281-287. For example, 111In coupled to monoclonal antibodies with 1-(P-isothiocyanatobenzyl)-DPTA has shown little uptake in non-tumors tissues, particularly the liver, and therefore enhances specificity of tumor localization. See, Esteban et al. (1987) J. Nucl. Med. 28:861-870.

[0179] Examples of suitable non-radioactive isotopic labels include 157Gd, 55Mn, 162Dy, 52Tr, and 56Fe.

[0180] Examples of suitable fluorescent labels include an 152Eu label, a fluorescein label, an isothiocyanate label, a rhodamine label, a phycoerythrin label, a phycocyanin label, an allophycocyanin label, an o-phthaldehyde label, and a fluorescamine label.

[0181] Examples of suitable toxin labels include, Pseudomonas toxin, diphtheria toxin, ricin, and cholera toxin.

[0182] Examples of chemiluminescent labels include a luminal label, an isoluminal label, an aromatic acridinium ester label, an imidazole label, an acridinium salt label, an oxalate ester label, a luciferin label, a luciferase label, and an aequorin label.

[0183] Examples of nuclear magnetic resonance contrasting agents include heavy metal nuclei such as Gd, Mn, and iron.

[0184] Typical techniques for binding the above-described labels to antibodies are provided by Kennedy et al. (1976) Clin. Chim. Acta 70:1-31, and Schurs et al. (1977) Clin. Chim. Acta 81:1-40. Coupling techniques mentioned in the latter are the glutaraldehyde method, the periodate method, the dimaleimide method, the m-maleimidobenzyl-N-hydroxy-succinimide ester method, all of which methods are incorporated by reference herein.

[0185] In a related aspect, the invention includes a diagnostic kit for use in screening serum containing antibodies specific against E. faecalis infection. Such a kit may include an isolated E. faecalis antigen comprising an epitope which is specifically immunoreactive with at least one anti-E. faecalis antibody. Such a kit also includes means for detecting the binding of said antibody to the antigen. In specific embodiments, the kit may include a recombinantly produced or chemically synthesized peptide or polypeptide antigen. The peptide or polypeptide antigen may be attached to a solid support.

[0186] In a more specific embodiment, the detecting means of the above-described kit includes a solid support to which said peptide or polypeptide antigen is attached. Such a kit may also include a non-attached reporter-labeled anti-human antibody. In this embodiment, binding of the antibody to the E. faecalis antigen can be detected by binding of the reporter labeled antibody to the anti-E. faecalis polypeptide antibody.

[0187] In a related aspect, the invention includes a method of detecting E. faecalis infection in a subject. This detection method includes reacting a body fluid, preferably serum, from the subject with an isolated E. faecalis antigen, and examining the antigen for the presence of bound antibody. In a specific embodiment, the method includes a polypeptide antigen attached to a solid support, and serum is reacted with the support. Subsequently, the support is reacted with a reporter-labeled anti-human antibody. The support is then examined for the presence of reporter-labeled antibody.

[0188] The solid surface reagent employed in the above assays and kits is prepared by known techniques for attaching protein material to solid support material, such as polymeric beads, dip sticks, 96-well plates or filter material. These attachment methods generally include non-specific adsorption of the protein to the support or covalent attachment of the protein, typically through a free amine group, to a chemically reactive group on the solid support, such as an activated carboxyl, hydroxyl, or aldehyde group. Alternatively, streptavidin coated plates can be used in conjunction with biotinylated antigen(s).

[0189] The polypeptides and antibodies of the present invention, including fragments thereof, may be used to detect Enterococcal species including E. faecalis using bio chip and biosensor technology. Bio chip and biosensors of the present invention may comprise the polypeptides of the present invention to detect antibodies, which specifically recognize Enterococcal species, including E. faecalis. Bio chip and biosensors of the present invention may also comprise antibodies which specifically recognize the polypeptides of the present invention to detect Enterococcal species, including E. faecalis or specific polypeptides of the present invention. Bio chips or biosensors comprising polypeptides or antibodies of the present invention may be used to detect Enterococcal species, including E. faecalis, in biological and environmental samples and to diagnose an animal, including humans, with an E. faecalis or other Enterococcal infection. Thus, the present invention includes both bio chips and biosensors comprising polypeptides or antibodies of the present invention and methods of their use. The bio chips of the present invention may further comprise polypeptide sequences of other pathogens including bacteria, viral, parasitic, and fungal polypeptide sequences, in addition to the polypeptide sequences of the present invention, for use in rapid differential pathogenic detection and diagnosis. The bio chips of the present invention may further comprise antibodies or fragements thereof specific for other pathogens including bacteria, viral, parasitic, and fungal polypeptide sequences, in addition to the antibodies or fragements thereof of the present invention, for use in rapid differential pathogenic detection and diagnosis. The bio chips and biosensors of the present invention may also be used to monitor an E. faecalis or other Enterococcal infection and to monitor the genetic changes (amio acid deletions, insertions, substitutions, etc.) in response to drug therapy in the clinic and drug development in the laboratory. The bio chip and biosensors comprising polypeptides or antibodies of the present invention may also be used to simultaneously monitor the expression of a multiplicity of polypeptides, including those of the present invention. The polypeptides used to comprise a bio chip or biosensor of the present invention may be specified in the same manner as for the fragements, i.e., by their N-terminal and C-terminal positions or length in contigious amino acid residue. Methods and particular uses of the polypeptides and antibodies of the present invention to detect Enterococcal species, including E. faecalis, or specific polypeptides using bio chip and biosensor technology include those known in the art, those of the U.S. patent Nos. and World Patent Nos. listed above for bio chips and biosensors using polynucleotides of the present invention, and those of: U.S. Pat. Nos. 5,658,732, 5,135,852, 5,567,301, 5,677,196, 5,690,894 and World Patent Nos. WO9729366, WO9612957, each incorporated herein in their entireties.

[0190] 4. Screening Assay for Binding Agents

[0191] 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 Enterococcus faecalis fragment and contigs herein described.

[0192] In general, such methods comprise steps of:

[0193] (a) contacting an agent with an isolated protein encoded by one of the ORFs of the present invention, or an isolated fragment of the Enterococcus faecalis genome; and

[0194] (b) determining whether the agent binds to said protein or said fragment.

[0195] 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.

[0196] 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.

[0197] 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.

[0198] 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.

[0199] 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.

[0200] 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.

[0201] 5. Pharmaceutical Compositions and Vaccines

[0202] The present invention further provides pharmaceutical agents which can be used to modulate the growth or pathogenicity of Enterococcus faecalis, 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.

[0203] As used herein, a pharmaceutical agent is said to “modulate the growth and/or pathogenicity of Enterococcus faecalis 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.

[0204] 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.

[0205] 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.

[0206] 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.

[0207] 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.

[0208] 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 in 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.

[0209] 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.

[0210] 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.

[0211] 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.

[0212] 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.

[0213] 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.

[0214] 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, 16th 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.

[0215] 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).

[0216] 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.

[0217] In addition, the agents of the present invention may be employed in conjunction with other therapeutic compounds.

[0218] The present invention also provides vaccines comprising one or more polypeptides of the present invention. Heterogeneity in the composition of a vaccine may be provided by combining E. faecalis polypeptides of the present invention. Multi-component vaccines of this type are desirable because they are likely to be more effective in eliciting protective immune responses against multiple species and strains of the Enterococcus genus than single polypeptide vaccines.

[0219] Multi-component vaccines are known in the art to elicit antibody production to numerous immunogenic components. See, e.g., Decker et al. (1996) J. Infect. Dis. 174:S270-275. In addition, a hepatitis B, diphtheria, tetanus, pertussis tetravalent vaccine has recently been demonstrated to elicit protective levels of antibodies in human infants against all four pathogenic agents. See, e.g., Axistegui, J. et al. (1997) Vaccine 15:7-9.

[0220] The present invention in addition to single-component vaccines includes multi-component vaccines. These vaccines comprise more than one polypeptide, immunogen or antigen. Thus, a multi-component vaccine would be a vaccine comprising more than one of the E. faecalis polypeptides of the present invention.

[0221] Further within the scope of the invention are whole cell and whole viral vaccines. Such vaccines may be produced recombinantly and involve the expression of one or more of the E. faecalis polypeptides described in SEQ ID NOS:1-982. For example, the E. faecalis polypeptides of the present invention may be either secreted or localized intracellular, on the cell surface, or in the periplasmic space. Further, when a recombinant virus is used, the E. faecalis polypeptides of the present invention may, for example, be localized in the viral envelope, on the surface of the capsid, or internally within the capsid. Whole cells vaccines which employ cells expressing heterologous proteins are known in the art. See, e.g., Robinson, K. et al. (1997) Nature Biotech. 15:653-657; Sirard, J. et al. (1997) Infect. Immun. 65:2029-2033; Chabalgoity, J. et al. (1997) Infect. Immun. 65:2402-2412. These cells may be administered live or may be killed prior to administration. Chabalgoity, J. et al., supra, for example, report the successful use in mice of a live attenuated Salmonella vaccine strain which expresses a portion of a platyhelminth fatty acid-binding protein as a fusion protein on its cells surface.

[0222] A multi-component vaccine can also be prepared using techniques known in the art by combining one or more E. faecalis polypeptides of the present invention, or fragments thereof, with additional non-Enterococcal components (e.g., diphtheria toxin or tetanus toxin, and/or other compounds known to elicit an immune response). Such vaccines are useful for eliciting protective immune responses to both members of the Enterococcus genus and non-Enterococcal pathogenic agents.

[0223] The vaccines of the present invention also include DNA vaccines. DNA vaccines are currently being developed for a number of infectious diseases. See, et al., Boyer, et al. (1997) Nat. Med. 3:526-532; reviewed in Spier, R. (1996) Vaccine 14:1285-1288. Such DNA vaccines contain a nucleotide sequence encoding one or more E. faecalis polypeptides of the present invention oriented in a manner that allows for expression of the subject polypeptide. For example, the direct administration of plasmid DNA encoding B. burgdorgeri OspA has been shown to elicit protective immunity in mice against borrelial challenge. See, Luke et al. (1997) J. Infect. Dis. 175:91-97.

[0224] The present invention also relates to the administration of a vaccine which is co-administered with a molecule capable of modulating immune responses. Kim et al. (1997) Nature Biotech. 15:641-646, for example, report the enhancement of immune responses produced by DNA immunizations when DNA, sequences encoding molecules which stimulate the immune response are co-administered. In a similar fashion, the vaccines of the present invention may be co-administered with either nucleic acids encoding immune modulators or the immune modulators themselves. These immune modulators include granulocyte macrophage colony stimulating factor (GM-CSF) and CD86.

[0225] The vaccines of the present invention may be used to confer resistance to Enterococcal infection by either passive or active immunization. When the vaccines of the present invention are used to confer resistance to Enterococcal infection through active immunization, a vaccine of the present invention is administered to an animal to elicit a protective immune response which either prevents or attenuates a Enterococcal infection. When the vaccines of the present invention are used to confer resistance to Enterococcal infection through passive immunization, the vaccine is provided to a host animal (e.g., human, dog, or mouse), and the antisera elicited by this antisera is recovered and directly provided to a recipient suspected of having an infection caused by a member of the Enterococcus genus.

[0226] The ability to label antibodies, or fragments of antibodies, with toxin molecules provides an additional method for treating Enterococcal infections when passive immunization is conducted. In this embodiment, antibodies, or fragments of antibodies, capable of recognizing the E. faecalis polypeptides disclosed herein, or fragments thereof, as well as other Enterococcus proteins, are labeled with toxin molecules prior to their administration to the patient. When such toxin derivatized antibodies bind to Enterococcus cells, toxin moieties will be localized to these cells and will cause their death.

[0227] The present invention thus concerns and provides a means for preventing or attenuating a Enterococcal infection resulting from organisms which have antigens that are recognized and bound by antisera produced in response to the polypeptides of the present invention. As used herein, a vaccine is said to prevent or attenuate a disease if its administration to an animal results either in the total or partial attenuation (i.e., suppression) of a symptom or condition of the disease, or in the total or partial immunity of the animal to the disease.

[0228] The administration of the vaccine (or the antisera which it elicits) may be for either a “prophylactic” or “therapeutic” purpose. When provided prophylactically, the compound(s) are provided in advance of any symptoms of Enterococcal infection. The prophylactic administration of the compound(s) serves to prevent or attenuate any subsequent infection. When provided therapeutically, the compound(s) is provided upon or after the detection of symptoms which indicate that an animal may be infected with a member of the Enterococcus genus. The therapeutic administration of the compound(s) serves to attenuate any actual infection. Thus, the E. faecalis polypeptides, and fragments thereof, of the present invention may be provided either prior to the onset of infection (so as to prevent or attenuate an anticipated infection) or after the initiation of an actual infection.

[0229] The polypeptides of the invention, whether encoding a portion of a native protein or a functional derivative thereof, may be administered in pure form or may be coupled to a macromolecular carrier. Example of such carriers are proteins and carbohydrates. Suitable proteins which may act as macromolecular carrier for enhancing the immunogenicity of the polypeptides of the present invention include keyhole limpet hemacyanin (KLH) tetanus toxoid, pertussis toxin, bovine serum albumin, and ovalbumin. Methods for coupling the polypeptides of the present invention to such macromolecular carriers are disclosed in Harlow et al., ANTIBODIES: A LABORATORY MANUAL, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988).

[0230] A composition is said to be “pharmacologically or physiologically acceptable” if its administration can be tolerated by a recipient animal and is otherwise suitable for administration to that animal. 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.

[0231] While in all instances the vaccine of the present invention is administered as a pharmacologically acceptable compound, one skilled in the art would recognize that the composition of a pharmacologically acceptable compound varies with the animal to which it is administered. For example, a vaccine intended for human use will generally not be co-administered with Freund's adjuvant. Further, the level of purity of the E. faecalis polypeptides of the present invention will normally be higher when administered to a human than when administered to a non-human animal.

[0232] As would be understood by one of ordinary skill in the art, when the vaccine of the present invention is provided to an animal, it may be in a composition which may contain salts, buffers, adjuvants, or other substances which are desirable for improving the efficacy of the composition. Adjuvants are substances that can be used to specifically augment a specific immune response. These substances generally perform two functions: (1) they protect the antigen(s) from being rapidly catabolized after administration and (2) they nonspecifically stimulate immune responses.

[0233] Normally, the adjuvant and the composition are mixed prior to presentation to the immune system, or presented separately, but into the same site of the animal being immunized. Adjuvants can be loosely divided into several groups based upon their composition. These groups include oil adjuvants (for example, Freund's complete and incomplete), mineral salts (for example, ALK(SO4)2, AlNa(SO4)2, AlNH4(SO4), silica, kaolin, and carbon), polynucleotides (for example, poly IC and poly AU acids), and certain natural substances (for example, wax D from Mycobacterium tuberculosis, as well as substances found in Corynebacterium parvum, or Bordetella pertussis, and members of the genus Brucella. Other substances useful as adjuvants are the saponins such as, for example, Quil A. (Superfos A/S, Denmark). Preferred adjuvants for use in the present invention include aluminum salts, such as AlK(SO4)2, AlNa(SO4)2, and AlNH4(SO4). Examples of materials suitable for use in vaccine compositions are provided in REMINGTON'S PHARMACEUTICAL SCIENCES 1324-1341 (A. Osol, ed, Mack Publishing Co, Easton, Pa., (1980) (incorporated herein by reference).

[0234] The therapeutic compositions of the present invention can be administered parenterally by injection, rapid infusion, nasopharyngeal absorption (intranasopharangeally), dermoabsorption, or orally. The compositions may alternatively be administered intramuscularly, or intravenously. Compositions for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Carriers or occlusive dressings can be used to increase skin permeability and enhance antigen absorption. Liquid dosage forms for oral administration may generally comprise a liposome solution containing the liquid dosage form. Suitable forms for suspending liposomes include emulsions, suspensions, solutions, syrups, and elixirs containing inert diluents commonly used in the art, such as purified water. Besides the inert diluents, such compositions can also include adjuvants, wetting agents, emulsifying and suspending agents, or sweetening, flavoring, or perfuming agents.

[0235] Therapeutic compositions of the present invention can also be administered in encapsulated form. For example, intranasal immunization using vaccines encapsulated in biodegradable microsphere composed of poly(DL-lactide-co-glycolide). See, Shahin, R. et al. (1995) Infect. Immun. 63:1195-1200. Similarly, orally administered encapsulated Salmonella typhimurium antigens can also be used. Allaoui-Attarki, K. et al. (1997) Infect. Immun. 65:853-857. Encapsulated vaccines of the present invention can be administered by a variety of routes including those involving contacting the vaccine with mucous membranes (e.g., intranasally, intracolonicly, intraduodenally).

[0236] Many different techniques exist for the timing of the immunizations when a multiple administration regimen is utilized. It is possible to use the compositions of the invention more than once to increase the levels and diversities of expression of the immunoglobulin repertoire expressed by the immunized animal. Typically, if multiple immunizations are given, they will be given one to two months apart.

[0237] According to the present invention, an “effective amount” of a therapeutic composition is one which is sufficient to achieve a desired biological effect. Generally, the dosage needed to provide an effective amount of the composition will vary depending upon such factors as the animal's or human's age, condition, sex, and extent of disease, if any, and other variables which can be adjusted by one of ordinary skill in the art.

[0238] The antigenic preparations of the invention can be administered by either single or multiple dosages of an effective amount. Effective amounts of the compositions of the invention can vary from 0.01-1,000 μg/ml per dose, more preferably 0.1-500 μg/ml pcr dose, and most preferably 10-300 μg/ml per dose.

[0239] 6. Shot-Gun Approach to Megabase DNA Sequencing

[0240] The present invention further demonstrates that a large genome 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.

[0241] 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

[0242] Libraries and Sequencing

[0243] 1. Shotgun Sequencing Probability Analysis

[0244] 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, P0, 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 P0=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, P0=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.

[0245] 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.

[0246] The treatment above is essentially that of Lander and Waterman, Genomics 2: 231 (1988).

[0247] 2. Random Library Construction

[0248] 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.

[0249]

Enterococcus faecalis
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.

[0250] 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.

[0251] 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 (1), 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.

[0252] 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%).

[0253] 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.

[0254] 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 MgCl2 (1 M), and 1 ml MgSO4/100 ml SOB agar. The 15 μl top layer is poured just prior to plating. Our titer is approximately 100 colonies/10 μl aliquot of transformation.

[0255] 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.

[0256] 3. Random DNA Sequencing

[0257] 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.

[0258] Templates are also prepared from an Enterococcus faecalis lambda genomic library in the vector DASH II (Stratagene). In particular, Enterococcus faecalis 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 fractionated by sucrose density gradient centrifugation. Fractions of the sucrose gradient containing 15 to 25 kb are recovered in a final volume of 6 ul. One μl of fragments is used with 1 μl of lambda 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. An amplified library is prepared by infecting restructure NM539 host E. coli cells eitn approximately 1×104 phage particles and recovering the progeny phages particles. The recovered phage is stored frozen in 7% dimethylsulfoxide. The phage titer is approximately 1×109 pfu/ml.

[0259] For high throughput sequencing of individual lambda phage clones, 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.

[0260] 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 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.

[0261] 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.

[0262] 4. Protocol for Automated Cycle Sequencing

[0263] The sequencing was 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.

[0264] Two sequencing protocols are used: one for (lye-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.

[0265] 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.

[0266] Informatics

[0267] 1. Data Management

[0268] 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 is 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.

[0269] 2. Assembly

[0270] An assembly engine (TIGR Assembler) developed for the rapid and accurate assembly of thousands of sequence fragments is 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 10 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).

[0271] The process resulted in 982 contigs as represented by SEQ ID NOs:1-982.

[0272] 3. Identifying Genes

[0273] The predicted coding regions of the Enterococcus faecalis 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 Enterococcus faecali nucleotide sequences front GenBank (March, 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.

[0274] Illustrative Applications

[0275] 1. Production of an Antibody to a Enterococcus faecalis Protein

[0276] 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.

[0277] 2. Monoclonal Antibody Production by Hybridoma Fusion

[0278] 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, New York. Section 21-2 (1989).

[0279] 3. Polyclonal Antibody Production by Immunization

[0280] 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).

[0281] 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)

[0282] 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 enterococcal 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.

[0283] 4. Preparation of PCR Primers and Amplification of DNA

[0284] Various fragments of the Enterococcus faecalis genome, such as those of Tables 1-3 and SEQ ID NOS:1-982 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.

[0285] 5. Isolation of a Selected DNA Clone From the Deposited Sample of E. faecalis

[0286] Three approaches can be used to isolate a E. faecalis clone comprising a polynucleotide of the present invention from any E. faecalis genomic DNA library. The E. faecalis strain V586 has been deposited as a convenient source for obtaining a E. faecalis strain although a wide varity of strains E. faecalis strains can be used which are known in the art.

[0287]

E. faecalis
genomic DNA is prepared using the following method. A 20 ml overnight bacterial culture grown in a rich medium (e.g., Trypticase Soy Broth, Brain Heart Infusion broth or Super broth), pelleted, ished two times with TES (30 mM Tris-pH 8.0, 25 mM EDTA, 50 mM NaCl), and resuspended in 5 ml high salt TES (2.5M NaCl). Lysostaphin is added to final concentration of approx 50 ug/ml and the mixture is rotated slowly 1 hour at 37 C. to make protoplast cells. The solution is then placed in incubator (or place in a shaking water bath) and warmed to 55 C. Five hundred micro liter of 20% sarcosyl in TES (final concentration 2%) is then added to lyse the cells. Next, guanidine HCl is added to a final concentration of 7M (3.69 g in 5.5 ml). The mixture is swirled slowly at 55 C. for 60-90 min (solution should clear). A CsCl gradient is then set up in SW41 ultra clear tubes using 2.0 ml 5.7M CsCl and overlaying with 2.85M CsCl. The gradient is carefully overlayed with the DNA-containing GuHCl solution. The gradient is spun at 30,000 rpm, 20 C. for 24 hr and the lower DNA band is collected. The volume is increased to 5 ml with TE buffer. The DNA is then treated with protease K (10 ug/ml) overnight at 37 C., and precipitated with ethanol. The precipitated DNA is resuspended in a desired buffer.

[0288] In the first method, a plasmid is directly isolated by screening a plasmid E. faecalis genomic DNA library using a polynucleotide probe corresponding to a polynucleotide of the present invention. Particularly, a specific polynucleotide with 30-40 nucleotides is synthesized using an Applied Biosystems DNA synthesizer according to the sequence reported. The oligonucleotide is labeled, for instance, with 32P-γ-ATP using T4 polynucleotide kinase and purified according to routine methods. (See, e.g., Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring, N.Y. (1982).) The library is transformed into a suitable host, as indicated above (such as XL-1 Blue (Stratagene)) using techniques known to those of skill in the art. See, e.g., Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL (Cold Spring Harbor, N.Y. 2nd ed. 1989); Ausubel et al., CURRENT PROTOCALS IN MOLECULAR BIOLOGY (John Wiley and Sons, N.Y. 1989). The transformants are plated on 1.5% agar plates (containing the appropriate selection agent, e.g., ampicillin) to a density of about 150 transformants (colonies) per plate. These plates are screened using Nylon membranes according to routine methods for bacterial colony screening. See, e.g., Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL (Cold Spring Harbor, N.Y. 2nd ed. 1989); Ausubel et al., CURRENT PROTOCALS IN MOLECULAR BIOLOGY (John Wiley and Sons, N.Y. 1989) or other techniques known to those of skill in the art.

[0289] Alternatively, two primers of 15-25 nucleotides derived from the 5′ and 3′ ends of a polynucleotide of SEQ ID NOS:1-982 arc synthesized and used to amplify the desired DNA by PCR using a E. faecalis genomic DNA prep as a template. PCR is carried out under routine conditions, for instance, in 25 μl of reaction mixture with 0.5 ug of the above DNA template. A convenient reaction mixture is 1.5-5 mM MgCl2, 0.01% (w/v) gelatin, 20 μM each of dATP, dCTP, dGTP, dTTP, 25 pmol of each primer and 0.25 Unit of Taq polymerase. Thirty five cycles of PCR (denaturation at 94° C. for 1 min. annealing at 55° C. for 1 min; elongation at 72° C. for 1 min) are performed with a Perkin-Elmer Cetus automated thermal cycler. The amplified product is analyzed by agarose gel electrophoresis and the DNA band with expected molecular weight is excised and purified. The PCR product is verified to be the selected sequence by subcloning and sequencing the DNA product.

[0290] Finally, overlapping oligos of the DNA sequences of SEQ ID NOS:1-982 can be chemically synthesized and used to generate a nucleotide sequence of desired length using PCR methods known in the art.

[0291] 6(a). Expression and Purification Enterococcal polypeptides in E. coli

[0292] The bacterial expression vector pQE60 was used for bacterial expression of some of the polypeptide fragements of the present invention which were used in the soft tissue and systemic infection models discussed below. (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311). pQE60 encodes ampicillin antibiotic resistance (“Ampr”) and contains a bacterial origin of replication (“ori”), an IPTG inducible promoter, a ribosome binding site (“RBS”), six codons encoding histidine residues that allow affinity purification using nickel-nitrilo-tri-acetic acid (“Ni-NTA”) affinity resin (QIAGEN, Inc., supra) and suitable single restriction enzyme cleavage sites. These elements are arranged such that an inserted DNA fragment encoding a polypeptide expresses that polypeptide with the six His residues (i.e., a “6× His tag”) covalently linked to the carboxyl terminus of that polypeptide.

[0293] The DNA sequence encoding the desired portion of a E. faecalis protein of the present invention was amplified from E. faecalis genomic DNA using PCR oligonucleotide primers which anneal to the 5′ and 3′ sequences coding for the portions of the E. faecalis polynucleotide shown in SEQ ID NOS:1-982. Additional nucleotides containing restriction sites to facilitate cloning in the pQE60 vector are added to the 5′ and 3′ sequences, respectively.

[0294] For cloning the mature protein, the 5′ primer has a sequence containing an appropriate restriction site followed by nucleotides of the amino terminal coding sequence of the desired E. faecalis polynucleotide sequence in SEQ ID NOS:1-982. One of ordinary skill in the art would appreciate that the point in the protein coding sequence where the 5′ and 3′ primers begin may be varied to amplify a DNA segment encoding any desired portion of the complete protein shorter or longer than the mature form. The 3′ primer has a sequence containing an appropriate restriction site followed by nucleotides complementary to the 3′ end of the polypeptide coding sequence of SEQ ID NOS:1-982, excluding a stop codon, with the coding sequence aligned with the restriction site so as to maintain its reading frame with that of the six His codons in the pQE60 vector.

[0295] The amplified E. faecalis DNA fragment and the vector pQE60 were digested with restriction enzymes which recognize the sites in the primers and the digested DNAs were then ligated together. The E. faecalis DNA was inserted into the restricted pQE60 vector in a manner which places the E. faecalis protein coding region downstream from the IPTG-inducible promoter and in-frame with an initiating AUG and the six histidine codons.

[0296] The ligation mixture was transformed into competent E. coli cells using standard procedures such as those described by Sambrook et al., supra.. E. coli strain M15/rep4, containing multiple copies of the plasmid pREP4, which expresses the lac repressor and confers kanamycin resistance (“Kanr”), was used in carrying out the illustrative example described herein. This strain, which was only one of many that are suitable for expressing a E. faecalis polypeptide, is available commercially (QIAGEN, Inc., supra). Transformants were identified by their ability to grow on LB agar plates in the presence of ampicillin and kanamycin. Plasmid DNA was isolated from resistant colonies and the identity of the cloned DNA confirmed by restriction analysis, PCR and DNA sequencing.

[0297] Clones containing the desired constructs were grown overnight (“O/N”) in liquid culture in LB media supplemented with both ampicillin (100 μg/ml) and kanamycin (25 μg/ml). The O/N culture was used to inoculate a large culture, at a dilution of approximately 1:25 to 1:250. The cells were grown to an optical density at 600 nm (“OD600”) of between 0.4 and 0.6. Isopropyl-β-D-thiogalactopyranoside (“IPTG”) was then added to a final concentration of 1 mM to induce transcription from the lac repressor sensitive promoter, by inactivating the lacI repressor. Cells subsequently were incubated further for 3 to 4 hours. Cells then were harvested by centrifugation.

[0298] The cells were then stirred for 3-4 hours at 4° C. in 6M guanidine-HCl, pH 8. The cell debris was removed by centrifugation, and the supernatant containing the E. faecalis polypeptide was loaded onto a nickel-nitrilo-tri-acetic acid (“Ni-NTA”) affinity resin column (QIAGEN, Inc., supra). Proteins with a 6× His tag bind to the Ni-NTA resin with high affinity were purified in a simple one-step procedure (for details see: The QIAexpressionist, 1995, QIAGEN, Inc., supra). Briefly the supernatant was loaded onto the column in 6 M guanidine-HCl, pH 8, the column was first washed with 10 volumes of 6 M guanidine-HCl, pH 8, then washed with 10 volumes of 6 M guanidine-HCl pH 6, and finally the E. faecalis polypeptide was eluted with 6 M guanidine-HCl, pH 5.

[0299] The purified protein was then renatured by dialyzing it against phosphate-buffered saline (PBS) or 50 mM Na-acetate, pH 6 buffer plus 200 mM NaCl. Alternatively, the protein could be successfully refolded while immobilized on the Ni-NTA column. The recommended conditions are as follows: renature using a linear 6M-1M urea gradient in 500 mM NaCl, 20% glycerol, 20 mM Tris/HCl pH 7.4, containing protease inhibitors. The renaturation should be performed over a period of 1.5 hours or more. After renaturation the proteins can be eluted by the addition of 250 mM immidazole. Immidazole was removed by a final dialyzing step against PBS or 50 mM sodium acetate pH 6 buffer plus 200 mM NaCl. The purified protein was stored at 4° C. or frozen at −80° C.

[0300] Some of the polypeptide of the present invention were prepared using a non-denaturing protein purification method. For these polypeptides, the cell pellet from each liter of culture was resuspended in 25 mls of Lysis Buffer A at 4° C. (Lysis Buffer A=50 mM Na-phosphate, 300 mM NaCl, 10 mM 2-mercaptoethanol, 10% Glycerol, pH 7.5 with 1 tablet of Complete EDTA-free protease inhibitor cocktail (Boehringer Mannheim #1873580) per 50 ml of buffer). Absorbance at 550 nm was approximately 10-20 O.D./ml. The suspension was then put through three freeze/thaw cycles from −70° C. (using a ethanol-dry ice bath) up to room temperature. The cells were lysed via sonication in short 10 sec bursts over 3 minutes at approximately 80 W while kept on ice. The sonicated sample was then centrifuged at 15,000 RPM for 30 minutes at 4° C. The supernatant was passed through a column containing 1.0 ml of CL-4B resin to pre-clear the sample of any proteins that may bind to agarose non-specifically, and the flow-through fraction was collected.

[0301] The pre-cleared flow-through was applied to a nickel-nitrilo-tri-acetic acid (“Ni-NTA”) affinity resin column (Quiagen, Inc., supra). Proteins with a 6× His tag bind to the Ni-NTA resin with high affinity and can be purified in a simple one-step procedure. Briefly, the supernatant was loaded onto the column in Lysis Buffer A at 4° C., the column was first washed with 10 volumes of Lysis Buffer A until the A280 of the eluate returns to the baseline. Then, the column was washed with 5 volumes of 40 mM Imidazole (92% Lysis Buffer A/8% Buffer B) (Buffer B=50 mM Na-Phosphate, 300 mM NaCl, 10% Glycerol, 10 mM 2-mercaptoethanol, 500 mM Imidazole, pH of the final buffer should be 7.5). The protein was eluted off of the column with a series of increasing Imidazole solutions made by adjusting the ratios of Lysis Buffer A to Buffer B. Three different concentrations were used: 3 volumes of 75 mM Imidazole, 3 volumes of 150 mM Imidazole, 5 volumes of 500 mM Imidazole. The fractions containing the purified protein were analyzed using 8%, 10% or 14% SDS-PAGE depending on the protein size. The purified protein was then dialyzed 2× against phosphate-buffered saline (PBS) in order to place it into an easily workable buffer. The purified protein was stored at 4° C. or frozen at −80°.

[0302] The following alternative method may be used to purify E. faecalis expressed in E coli when it is present in the form of inclusion bodies. Unless otherwise specified, all of the following steps are conducted at 4-10° C.

[0303] Upon completion of the production phase of the E. coli fermentation, the cell culture is cooled to 4-10° C. and the cells are harvested by continuous centrifugation at 15,000 rpm (Heraeus Sepatech). On the basis of the expected yield of protein per unit weight of cell paste and the amount of purified protein required, an appropriate amount of cell paste, by weight, is suspended in a buffer solution containing 100 mM Tris, 50 mM EDTA, pH 7.4. The cells are dispersed to a homogereous suspension using a high shear mixer.

[0304] The cells are then lysed by passing the solution through a microfluidizer (Microfuidics, Corp. or APV Gaulin, Inc.) twice at 4000-6000 psi. The homogenate is then mixed with NaCl solution to a final concentration of 0.5 M NaCl, followed by centrifugation at 7000×g for 15 min. The resultant pellet is washed again using 0.5M NaCl, 100 mM Tris, 50 mM EDTA, pH 7.4.

[0305] The resulting washed inclusion bodies are solubilized with 1.5 M guanidine hydrochloride (GuHCl) for 2-4 hours. After 7000×g centrifugation for 15 min., the pellet is discarded and the E. faecalis polypeptide-containing supernatant is incubated at 4° C. overnight to allow further GuHCl extraction.

[0306] Following high speed centrifugation (30,000×g) to remove insoluble particles, the GuHCl solubilized protein is refolded by quickly mixing the GuHCl extract with 20 volumes of buffer containing 50 mM sodium, pH 4.5, 150 mM NaCl, 2 mM EDTA by vigorous stirring. The refolded diluted protein solution is kept at 4° C. without mixing for 12 hours prior to further purification steps.

[0307] To clarify the refolded E. faecalis polypeptide solution, a previously prepared tangential filtration unit equipped with 0.16 μm membrane filter with appropriate surface area (e.g., Filtron), equilibrated with 40 mM sodium acetate, pH 6.0 is employed. The filtered sample is loaded onto a cation exchange resin (e.g., Poros HS-50, Perseptive Biosystems). The column is washed with 40 mM sodium acetate, pH 6.0 and eluted with 250 mM, 500 mM, 1000 mM, and 1500 mM NaCl in the same buffer, in a stepwise manner. The absorbance at 280 mm of the effluent is continuously monitored. Fractions are collected and further analyzed by SDS-PAGE.

[0308] Fractions containing the E. faecalis polypeptide are then pooled and mixed with 4 volumes of water. The diluted sample is then loaded onto a previously prepared set of tandem columns of strong anion (Poros HQ-50, Perseptive Biosystems) and weak anion (Poros CM-20, Perseptive Biosystems) exchange resins. The columns are equilibrated with 40 mM sodium acetate, pH 6.0. Both columns are washed with 40 mM sodium acetate, pH 6.0, 200 mM NaCl. The CM-20 column is then eluted using a 10 column volume linear gradient ranging from 0.2 M NaCl, 50 mM sodium acetate, pH 6.0 to 1.0 M NaCl, 50 mM sodium acetate, pH 6.5. Fractions are collected under constant A280 monitoring of the effluent. Fractions containing the E. faecalis polypeptide (determined, for instance, by 16% SDS-PAGE) are then pooled.

[0309] The resultant E. faecalis polypeptide exhibits greater than 95% purity after the above refolding and purification steps. No major contaminant bands are observed from Commassie blue stained 16% SDS-PAGE gel when 5 μg of purified protein is loaded. The purified protein is also tested for endotoxin/LPS contamination, and typically the LPS content is less than 0.1 ng/ml according to LAL assays.

[0310] 6(b). Alternative Expression and Purification Enterococcal Polypeptides in E. coli

[0311] The vector pQE10 was alternatively used to clone and express some of the polypeptides of the present invention for use in the soft tissue and systemic infection models discussed below. The difference being such that an inserted DNA fragment encoding a polypeptide expresses that polypeptide with the six His residues (i.e., a “6× His tag”) covalently linked to the amino terminus of that polypeptide. The bacterial expression vector pQE10 (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311) was used in this example. The components of the pQE10 plasmid are arranged such that the inserted DNA sequence encoding a polypeptide of the present invention expresses the polypeptide with the six His residues (i.e., a “6× His tag”)) covalently linked to the amino terminus.

[0312] The DNA sequences encoding the desired portions of a polypeptide of SEQ ID NOS:1-982 were amplified using PCR oligonucleotide primers from genomic E. faecalis DNA. The PCR primers anneal to the nucleotide sequences encoding the desired amino acid sequence of a polypeptide of the present invention. Additional nucleotides containing restriction sites to facilitate cloning in the pQE10 vector were added to the 5′ and 3′ primer sequences, respectively.

[0313] For cloning a polypeptide of the present invention, the 5′ and 3′ primers were selected to amplify their respective nucleotide coding sequences. One of ordinary skill in the art would appreciate that the point in the protein coding sequence where the 5′ and 3′ primers begins may be varied to amplify a DNA segment encoding any desired portion of a polypeptide of the present invention. The 5′ primer was designed so the coding sequence of the 6× His tag is aligned with the restriction site so as to maintain its reading frame with that of E. faecalis polypeptide. The 3′ was designed to include an stop codon. The amplified DNA fragment was then cloned, and the protein expressed, as described above for the pQE60 plasmid.

[0314] The DNA sequences encoding the amino acid sequences of SEQ ID NOS:1-982 may also be cloned and expressed as fusion proteins by a protocol similar to that described directly above, wherein the pET-32b(+) vector (Novagen, 601 Science Drive, Madison, Wis. 53711) is preferentially used in place of pQE10.

[0315] The above methods are not limited to the polypeptide fragements actually produced. The above method, like the methods below, can be used to produce either full length polypeptides or desired fragements therof.

[0316] 6(c). Alternative Expression and Purification of Enterococcal Polypeptides in E. coli

[0317] The bacterial expression vector pQE60 is used for bacterial expression in this example (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311). However, in this example, the polypeptide coding sequence is inserted such that translation of the six His codons is prevented and, therefore, the polypeptide is produced with no 6× His tag.

[0318] The DNA sequence encoding the desired portion of the E. faecalis amino acid sequence is amplified from an E. faecalis genomic DNA prep the deposited DNA clones using PCR oligonucleotide primers which anneal to the 5′ and 3′ nucleotide sequences corresponding to the desired portion of the E. faecalis polypeptides. Additional nucleotides containing restriction sites to facilitate cloning in the pQE60 vector are added to the 5′ and 3′ primer sequences.

[0319] For cloning a E. faecalis polypeptides of the present invention, 5′ and 3′ primers are selected to amplify their respective nucleotide coding sequences. One of ordinary skill in the art would appreciate that the point in the protein coding sequence where the 5′ and 3′ primers begin may be varied to amplify a DNA segment encoding any desired portion of a polypeptide of the present invention. The 3′ and 5′ primers contain appropriate restriction sites followed by nucleotides complementary to the 5′ and 3′ ends of the coding sequence respectively. The 3′ primer is additionally designed to include an in-frame stop codon.

[0320] The amplified E. faecalis DNA fragments and the vector pQE60 are digested with restriction enzymes recognizing the sites in the primers and the digested DNAs are then ligated together. Insertion of the E. faecalis DNA into the restricted pQE60 vector places the E. faecalis protein coding region including its associated stop codon downstream from the IPTG-inducible promoter and in-frame with an initiating AUG. The associated stop codon prevents translation of the six histidine codons downstream of the insertion point.

[0321] The ligation mixture is transformed into competent E. coli cells using standard procedures such as those described by Sambrook et al. E. coli strain M15/rep4, containing multiple copies of the plasmid pREP4, which expresses the lac repressor and confers kanamycin resistance (“Kanr”), is used in carrying out the illustrative example described herein. This strain, which is only one of many that are suitable for expressing E. faecalis polypeptide, is available commercially (QIAGEN, Inc., supra). Transformants are identified by their ability to grow on LB plates in the presence of ampicillin and kanamycin. Plasmid DNA is isolated from resistant colonies and the identity of the cloned DNA confirmed by restriction analysis, PCR and DNA sequencing.

[0322] Clones containing the desired constructs are grown overnight (“O/N”) in liquid culture in LB media supplemented with both ampicillin (100 μg/ml) and kanamycin (25 μg/ml). The O/N culture is used to inoculate a large culture, at a dilution of approximately 1:25 to 1:250. The cells are grown to an optical density at 600 nm (“OD600”) of between 0.4 and 0.6. isopropyl-b-D-thiogalactopyranoside (“IPTG”) is then added to a final concentration of 1 mM to induce transcription from the lac repressor sensitive promoter, by inactivating the lacI repressor. Cells subsequently are incubated further for 3 to 4 hours. Cells then are harvested by centrifugation.

[0323] To purify the E. faecalis polypeptide, the cells are then stirred for 3-4 hours at 4° C. in 6M guanidine-HCl, pH 8. The cell debris is removed by centrifugation, and the supernatant containing the E. faecalis polypeptide is dialyzed against 50 mM Na-acetate buffer pH 6, supplemented with 200 mM NaCl. Alternatively, the protein can be successfully refolded by dialyzing it against 500 mM NaCl, 20% glycerol, 25 mM Tris/HCl pH 7.4, containing protease inhibitors. After renaturation the protein can be purified by ion exchange, hydrophobic interaction and size exclusion chromatography. Alternatively, an affinity chromatography step such as an antibody column can be used to obtain pure E. faecalis polypeptide. The purified protein is stored at 4° C. or frozen at −80° C.

[0324] The following alternative method may be used to purify E. faecalis polypeptides expressed in E coli when it is present in the form of inclusion bodies. Unless otherwise specified, all of the following steps are conducted at 4-10° C.

[0325] Upon completion of the production phase of the E. coli fermentation, the cell culture is cooled to 4-10 ° C. and the cells are harvested by continuous centrifugation at 15,000 rpm (Heracus Sepatech). On the basis of the expected yield of protein per unit weight of cell paste and the amount of purified protein required, an appropriate amount of cell paste, by weight, is suspended in a buffer solution containing 100 mM Tris, 50 mM EDTA, pH 7.4. The cells are dispersed to a homogeneous suspension using a high shear mixer.

[0326] The cells ware then lysed by passing the solution through a microfluidizer (Microfuidics, Corp. or APV Gaulin, Inc.) twice at 4000-6000 psi. The homogenate is then mixed with NaCl solution to a final concentration of 0.5 M NaCl, followed by centrifugation at 7000×g for 15 min. The resultant pellet is washed again using 0.5M NaCl, 100 mM Tris, 50 mM EDTA, pH 7.4.

[0327] The resulting washed inclusion bodies are solubilized with 1.5 M guanidine hydrochloride (GuHCl) for 2-4 hours. After 7000×g centrifugation for 15 min., the pellet is discarded and the E. faecalis polypeptide-containing supernatant is incubated at 4° C. overnight to allow further GuHCl extraction.

[0328] Following high speed centrifugation (30,000×g) to remove insoluble particles, the GuHCl solubilized protein is refolded by quickly mixing the GuHCl extract with 20 volumes of buffer containing 50 mM sodium, pH 4.5, 150 mM NaCl, 2 mM EDTA by vigorous stirring. The refolded diluted protein solution is kept at 4° C. without mixing for 12 hours prior to further purification steps.

[0329] To clarify the refolded E. faecalis polypeptide solution, a previously prepared tangential filtration unit equipped with 0.16 μm membrane filter with appropriate surface area (e.g., Filtron), equilibrated with 40 mM sodium acetate, pH 6.0 is employed. The filtered sample is loaded onto a cation exchange resin (e.g., Poros HS-50, Perseptive Biosystems). The column is washed with 40 mM sodium acetate, pH 6.0 and eluted with 250 mM, 500 mM, 1000 mM, and 1500 mM NaCl in the same buffer, in a stepwise manner. The absorbance at 280 mm of the effluent is continuously monitored. Fractions are collected and further analyzed by SDS-PAGE.

[0330] Fractions containing the E. faecalis polypeptide are then pooled and mixed with 4 volumes of water. The diluted sample is then loaded onto a previously prepared set of tandem columns of strong anion (Poros HQ-50, Perseptive Biosystems) and weak anion (Poros CM-20, Perseptive Biosystems) exchange resins. The columns are equilibrated with 40 mM sodium acetate, pH 6.0. Both columns are washed with 40 mM sodium acetate, pH 6.0, 200 mM NaCl. The CM-20 column is then eluted using a 10 column volume linear gradient ranging from 0.2 M NaCl, 50 mM sodium acetate, pH 6.0 to 1.0 M NaCl, 50 mM sodium acetate, pH 6.5. Fractions are collected under constant A280 monitoring of the effluent. Fractions containing the E. faecalis polypeptide (determined, for instance, by 16% SDS-PAGE) are then pooled.

[0331] The resultant E. faecalis polypeptide exhibits greater than 95% purity after the above refolding and purification steps. No major contaminant bands are observed from Commassie blue stained 16% SDS-PAGE gel when 5 μg of purified protein is loaded. The purified protein is also tested for endotoxin/LPS contamination, and typically the LPS content is less than 0.1 ng/ml according to LAL assays.

[0332] 6(d). Cloning and Expression of E. faecalis in Other Bacteria

[0333]

E. faecalis
polypeptides can also be produced in: E. faecalis using the methods of S. Skinner et al., (1988) Mol. Microbiol. 2:289-297 or J. I. Moreno (1996) Protein Expr. Purif. 8(3):332-340; Lactobacillus using the methods of C. Rush et al., 1997 Appl. Microbiol. Biotechnol. 47(5):537-542; or in Bacillus subtilis using the methods Chang et al., U.S. Pat. No. 4,952,508.

[0334] 7. Cloning and Expression in COS Cells

[0335] A E. faecalis expression plasmid is made by cloning a portion of the DNA encoding a E. faecalis polypeptide into the expression vector pDNAI/Amp or pDNAIII (which can be obtained from Invitrogen, Inc.). The expression vector pDNAI/amp contains: (1) an E. coli origin of replication effective for propagation in E. coli and other prokaryotic cells; (2) an ampicillin resistance gene for selection of plasmid-containing prokaryotic cells; (3) an SV40 origin of replication for propagation in eukaryotic cells; (4) a CMV promoter, a polylinker, an SV40 intron; (5) several codons encoding a hemagglutinin fragment (i.e., an “HA” tag to facilitate purification) followed by a termination codon and polyadenylation signal arranged so that a DNA can be conveniently placed under expression control of the CMV promoter and operably linked to the SV40 intron and the polyadenylation signal by means of restriction sites in the polylinker. The HA tag corresponds to an epitope derived from the influenza hemagglutinin protein described by Wilson et al. 1984 Cell 37:767. The fusion of the HA tag to the target protein allows easy detection and recovery of the recombinant protein with an antibody that recognizes the HA epitope. pDNAIII contains, in addition, the selectable neomycin marker.

[0336] A DNA fragment encoding a E. faecalis polypeptide is cloned into the polylinker region of the vector so that recombinant protein expression is directed by the CMV promoter. The plasmid construction strategy is as follows. The DNA from a E. faecalis genomic DNA prep is amplified using primers that contain convenient restriction sites, much as described above for construction of vectors for expression of E. faecalis in E. coli. The 5′ primer contains a Kozak sequence, an AUG start codon, and nucleotides of the 5′ coding region of the E. faecalis polypeptide. The 3′ primer, contains nucleotides complementary to the 3′ coding sequence of the E. faecalis DNA, a stop codon, and a convenient restriction site.

[0337] The PCR amplified DNA fragment and the vector, pDNAI/Amp, are digested with appropriate restriction enzymes and then ligated. The ligation mixture is transformed into an appropriate E. coli strain such as SURE™ (Stratagene Cloning Systems, La Jolla, Calif. 92037), and the transformed culture is plated on ampicillin media plates which then are incubated to allow growth of ampicillin resistant colonies. Plasmid DNA is isolated from resistant colonies and examined by restriction analysis or other means for the presence of the fragment encoding the E. faecalis polypeptide

[0338] For expression of a recombinant E. faecalis polypeptide, COS cells are transfected with an expression vector, as described above, using DEAE-dextran, as described, for instance, by Sambrook et al. (supra). Cells are incubated under conditions for expression of E. faecalis by the vector.

[0339] Expression of the E. faecalis-HA fusion protein is detected by radiolabeling and immunoprecipitation, using methods described in, for example Harlow et al., supra.. To this end, two days after transfection, the cells are labeled by incubation in media containing 35S-cysteine for 8 hours. The cells and the media are collected, and the cells are washed and the lysed with detergent-containing RIPA buffer: 150 mM NaCl, 1% NP-40, 0.1% SDS, 1% NP-40, 0.5% DOC, 50 mM TRIS, pH 7.5, as described by Wilson et al. (supra ). Proteins are precipitated from the cell lysate and from the culture media using an HA-specific monoclonal antibody. The precipitated proteins then are analyzed by SDS-PAGE and autoradiography. An expression product of the expected size is seen in the cell lysate, which is not seen in negative controls.

[0340] 8. Cloning and Expression in CHO Cells

[0341] The vector pC4 is used for the expression of E. faecalis polypeptide in this example. Plasmid pC4 is a derivative of the plasmid pSV2-dhfr (ATCC Accession No. 37146). The plasmid contains the mouse DHFR gene under control of the SV40 early promoter. Chinese hamster ovary cells or other cells lacking dihydrofolate activity that are transfected with these plasmids can be selected by growing the cells in a selective medium (alpha minus MEM, Life Technologies) supplemented with the chemotherapeutic agent methotrexate. The amplification of the DHFR genes in cells resistant to methotrexate (MTX) has been well documented. See, e.g., Alt et al., 1978, J. Biol. Chem. 253:1357-1370; Hamlin et al., 1990, Biochem. et Biophys. Acta, 1097:107-143; Page et al., 1991, Biotechnology 9:64-68. Cells grown in increasing concentrations of MTX develop resistance to the drug by overproducing the target enzyme, DHFR, as a result of amplification of the DHFR gene. If a second gene is linked to the DHFR gene, it is usually co-amplified and over-expressed. It is known in the art that this approach may be used to develop cell lines carrying more than 1,000 copies of the amplified gene(s). Subsequently, when the methotrexate is withdrawn, cell lines are obtained which contain the amplified gene integrated into one or more chromosome(s) of the host cell.

[0342] Plasmid pC4 contains the strong promoter of the long terminal repeat (LTR) of the Rouse Sarcoma Virus, for expressing a polypeptide of interest, Cullen, et al. (1985) Mol. Cell. Biol. 5:438-447; plus a fragment isolated from the enhancer of the immediate early gene of human cytomegalovirus (CMV), Boshart, et al., 1985, Cell 41:521-530. Downstream of the promoter are the following single restriction enzyme cleavage sites that allow the integration of the genes: Bam HI, Xba I, and Asp 718. Behind these cloning sites the plasmid contains the 3′ intron and polyadenylation site of the rat preproinsulin gene. Other high efficiency promoters can also be used for the expression, e.g., the human β-actin promoter, the SV40 early or late promoters or the long terminal repeats from other retroviruses, e.g., HIV and HTLVI. Clontech's Tet-Off and Tet-On gene expression systems and similar systems can be used to express the E. faecalis polypeptide in a regulated way in mammalian cells (Gossen et al., 1992, Proc. Natl. Acad. Sci. USA 89:5547-5551. For the polyadenylation of the mRNA other signals, e.g., from the human growth hormone or globin genes can be used as well. Stable cell lines carrying a gene of interest integrated into the chromosomes can also be selected upon co-transfection with a selectable marker such as gpt, G418 or hygromycin. It is advantageous to use more than one selectable marker in the beginning, e.g., G418 plus methotrexate.

[0343] The plasmid pC4 is digested with the restriction enzymes and then dephosphorylated using calf intestinal phosphates by procedures known in the art. The vector is then isolated from a 1% agarose gel. The DNA sequence encoding the E. faecalis polypeptide is amplified using PCR oligonucleotide primers corresponding to the 5′ and 3′ sequences of the desired portion of the gene. A 5′ primer containing a restriction site, a Kozak sequence, an AUG start codon, and nucleotides of the 5′ coding region of the E. faecalis polypeptide is synthesized and used. A 3′ primer, containing a restriction site, stop codon, and nucleotides complementary to the 3′ coding sequence of the E. faecalis polypeptides is synthesized and used. The amplified fragment is digested with the restriction endonucleases and then purified again on a 1% agarose gel. The isolated fragment and the dephosphorylated vector are then ligated with T4 DNA ligase. E. coli HB101 or XL-1 Blue cells are then transformed and bacteria are identified that contain the fragment inserted into plasmid pC4 using, for instance, restriction enzyme analysis.

[0344] Chinese hamster ovary cells lacking an active DHFR gene are used for transfection. Five μg of the expression plasmid pC4 is cotransfected with 0.5 μg of the plasmid pSVneo using a lipid-mediated transfection agent such as Lipofectin™ or LipofectAMINE.™ (LifeTechnologies Gaithersburg, Md.). The plasmid pSV2-neo contains a dominant selectable marker, the neo gene from Tn5 encoding an enzyme that confers resistance to a group of antibiotics including G418. The cells are seeded in alpha minus MEM supplemented with 1 mg/ml G418. After 2 days, the cells are trypsinized and seeded in hybridoma cloning plates (Greiner, Germany) in alpha minus MEM supplemented with 10, 25, or 50 ng/ml of methotrexate plus 1 mg/ml G418. After about 10-14 days single clones are trypsinized and then seeded in 6-well petri dishes or 10 ml flasks using different concentrations of methotrexate (50 nM, 100 nM, 200 nM, 400 nM, 800 nM). Clones growing at the highest concentrations of methotrexate are then transferred to new 6-well plates containing even higher concentrations of methotrexate (1 μM, 2 μM, 5 μM, 10 mM, 20 mM). The same procedure is repeated until clones are obtained which grow at a concentration of 100-200 μM. Expression of the desired gene product is analyzed, for instance, by SDS-PAGE and Western blot or by reversed phase HPLC analysis.

[0345] 9. Quantitative Murine Soft Tissue Infection Model for E. faecalis

[0346] Compositions of the present invention, including polypeptides and peptides, are assayed for their ability to function as vaccines or to enhance/stimulate an immune response to a bacterial species (e.g., E. faecalis) using the following quantitative murine soft tissue infection model. Mice (e.g., NIH Swiss female mice, approximately 7 weeks old) are first treated with a biologically protective effective amount, or immune enhancing/stimulating effective amount of a composition of the present invention using methods known in the art, such as those discussed above. See, e.g., Harlow et al., ANTIBODIES: A LABORATORY MANUAL, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988). An example of an appropriate starting dose is 20 ug per animal.

[0347] The desired bacterial species used to challenge the mice, such as E. faecalis, is grown as an overnight culture. The culture is diluted to a concentration of 5×108 cfu/ml, in an appropriate media, mixed well, serially diluted, and titered. The desired doses are further diliuted 1:2 with sterilized Cytodex 3 microcarrier beads preswollen in sterile PBS (3 g/100 ml). Mice are anesthetize briefly until docile, but still mobile and injected with 0.2 ml of the Cytodex 3 bead/bacterial mixture into each animal subcutaneously in the inguinal region. After four days, counting the day of injection as day one, mice are sacrificed and the contents of the abscess is excised and placed in a 15 ml conical tube containing 1.0 ml of sterile PBS. The contents of the abscess is then enzymatically treated and plated as follows.

[0348] The abscess is first disrupted by vortexing with sterilized glass beads placed in the tubes. 3.0 mls of prepared enzyme mixture (1.0 ml Collagenase D (4.0 mg/ml), 1.0 ml Trypsin (6.0 mg/ml) and 8.0 mls PBS) is then added to each tube followed by a 20 min. incubation at 37 C. The solution is then centrifuged and the supernatant drawn off. 0.5 ml dH20 is then added and the tubes are vortexed and then incubated for 10 min. at room temperature. 0.5 ml media is then added and samples are serially diluted and plated onto agar plates, and grown overnight at 37 C. Plates with distinct and separate colonies are then counted, compared to positive and negative control samples, and quantified. The method can be used to identify composition and determine appropriate and effective doses for humans and other animals by comparing the effective doses of compositions of the present invention with compositions known in the art to be effective in both mice and humans. Doses for the effective treatment of humans and other animals, using compositions of the present invention, are extrapolated using the data from the above experiments of mice. It is appreciated that further studies in humans and other animals may be needed to determine the most effective doses using methods of clinical practice known in the art.

[0349] 10. Murine Systemic Neutropenic Model for E. faecalis Infection Compositions of the present invention, including polypeptides and peptides, are assayed for their ability to function as vaccines or to enhance/stimulate an immune response to a bacterial species (e.g., E. faecalis) using the following qualitative murine systemic neutropenic model. Mice (e.g., NIH Swiss female mice, approximately 7 weeks old) are first treated with a biologically protective effective amount, or immune enhancing/stimulating effective amount of a composition of the present invention using methods known in the art, such as those discussed above. See, e.g., Harlow et al., ANTIBODIES: A LABORATORY MANUAL, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988). An example of an appropriate starting dose is 20 ug per animal. Mice are then injected with 250-300 mg/kg cyclophosphamide intraperitonially. Counting the day of C.P. injection as day one, the mice are left untreated for 5 days to begin recovery of PMNL'S.

[0350] The desired bacterial species used to challenge the mice, such as E. faecalis, is grown as an overnight culture. The culture is diluted to a concentration of 5×108 cfu/ml, in an appropriate media, mixed well, serially diluted, and titered. The desired doses are further diliuted 1:2 in 4% Brewer's yeast in media. Mice are injected with the bacteria/brewer's yeast challenge intraperitonially. The Brewer's yeast solution alone is used as a control. The mice are then monitered twice daily for the first week following challenge, and once a day for the next week to ascertain morbidity and mortality. Mice remaining at the end of the experiment are sacrificed. The method can be used to identify compositions and determine appropriate and effective doses for humans and other animals by comparing the effective doses of compositions of the present invention with compositions known in the art to be effective in both mice and humans. Doses for the effective treatment of humans and other animals, using compositions of the present invention, are extrapolated using the data from the above experiments of mice. It is appreciated that further studies in humans and other animals may be needed to determine the most effective doses using methods of clinical practice known in the art.

[0351] The disclosure of all publications (including patents, patent applications, journal articles, laboratory manuals, books, or other documents) cited herein are hereby incorporated by reference in their entireties.

[0352] The present invention is not to be limited in scope by the specific embodiments described herein, which are intended as single illustrations of individual aspects of the invention. Functionally equivalent methods and components are within the scope of the invention, in addition to those shown and described herein and will become apparant to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims.

1TABLE 1E. faecalis-Coding regions containing known sequencesContigOrfStartStopPercentHSP ntIDID(nt)(nt)Match AccessionMatch Gene NameIndentlength324231226gb|U24692|“Enterococcus faecalis pyrimidine99229biosynthesis D (pyrD) gene, complete cds”47141708516216gb|M81466|“Enterococcus faecalis RecA protein (recA)98308gene, partial cds”521501441emb|X62755|SFNPRGS.faecalis npr gene for NADH peroxidase98137452224561494emb|X62755|SFNPRGS.faecalis npr gene for NADH peroxidase1002096112358gb|U35369|“Enterococcus faecalis vancomycin99318resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”6124671975gb|U35369|“Enterococcus faecalis vancomycin981297resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”61317491967gb|U35369|“Enterococcus faecalis vancomycin100136resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB),Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”61419902949gb|U35369|“Enterococcus faecalis vancomycin100960resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), DAla:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”61521122399gb|U35369|“Enterococcus faecalis vancomycin100288resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”61629223794gb|U35369|“Enterococcus faecalis vancomycin100873resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”61736714762gb|U35369|“Enterococcus faecalis vancomycin991092resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”61843123860gb|U35369|“Enterococcus faecalis vancomycin100453resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”61946535783gb|U35369|“Enterococcus faecalis vancomycin1001131resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”611057506397gb|U35369|“Enterococcus faecalis vancomyc2-fl99648resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”611171586784gb|U35369|“Enterococcus faecalis vancomycin100161resistance genes, response regulator(vanRB), protein histidine kinase (vanSB),D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanX>”6713809gb|U24692”“Enterococcus faecalis pyrimidine98807biosynthesis D (pyrD) gene, complete cds”6727811512gb|U24692|“Enterococcus faecalis pyrimidine9392biosynthesis D (pyrD) gene, complete cds”6911228gb|U60038|“Enterococcus faecalis major cold-shock100136protein (cspA) gene, partial cds”72151581419737emb|X62656|EFASP1“E.faecalis plasmid pPD1 aspl and URFs922504pd57, pd125 and pd113 genes”72161973920155emb|X62657|EFORF3E.faecalis plasmid pAD1 DNA for orf3963417513365emb|Z19137|EFPTSHGNE.faecalis of ptsH gene encoding HPr100267831287667432emb|X78425|EFPBP5E.faecalis pbp5 gene98416831388699699emb|X78425|EFPBP5E.faecalis pbp5 gene998198314961210913emb|X78425|EFPBP5E.faecalis pbp5 gene99120383151094311746emb|X78425|EFPBP5E.faecalis pbp5 gene9728684216573558emb|X86176|EFRPODDNEE.faecalis dnaE and rpoD gene9979784336494773emb|X86176|EFRPODDNEE.faecalis dnaE and rpoD gene99112584449137000emb|X86176|EFRPODDNEE.faecalis dnaE and rpoD gene99301104240182900gb|U36195|“Enterococcus faecalis pyrAa gene, partial93310cds”108758755183gb|M58002|“Streptococcus faecalis bacterial cell98252wall hydrolase gene, complete cds”145881937234gb|U03756|“Enterococcus faecalis endocarditis99960specific antigen gene, complete cds”145988368147gb|U03756|“Enterococcus faecalis endocarditis100132specific antigen gene, complete cds”147320963418emb|X68847|SFNOXAAS.faecalis nox gene for NADH oxidase991301154421602492emb|X17O92|PPRRAPlasmid pAM-beta-1 (from S.faecalis)93294replication region DNA1541059356294gb|U17153|“Enterococcus faecalis plasmid pjh199355tetracycline resistant (tetL) gene,complete cds”1541162796584gb|U17153|“Enterococcus faecalis plasmid pjh19889tetracycline resistant (tetL) gene,complete cds”1541278827097gb|U86375|“Enterococcus faecalis ermB regulator and99736adenine methylase (ermB) genes, completecds”1541387508043gb|U17153|“Enterococcus faecalis plasmid pjh199498tetracycline resistant (tetL) gene,complete cds”15911581483gb|M58002|“Streptococcus faecalis bacterial cell981323wall hydrolase gene, complete cds”1592807157gb|M58002|“Streptococcus faecalis bacterial cell99651wall hydrolase gene, complete cds”159313952192gb|M58002|“Streptococcus faecalis bacterial cell93350wall hydrolase gene, complete cds”21622821841gb|M90060|“Streptococcus faecalis H+ ATPase a811558(atpB),b (atpF),c (atpE),alpha (atpA),beta (atpD),gamma (atpG),delta (atpH),andepsilon (atpC) subunits, complete cds”216428092967gb|M90060|“Streptococcus faecalis H+ATPase a86132(atpB),b (atpF),c (atpE),alpha (atpA),beta (atpD) ,gamma (atpG) ,delta (atpH) ,andepsilon (atpC) subunits, complete cds”216529404244gb|M90060|“Streptococcus faecalis H+ ATPase a831293(atpB),b (atpF),c (atpE),alpha (atpA),beta (atpD) ,gamma (atpG) ,delta (atpH) ,andepsilon (atpC) subunits, complete cds”238318142218gb|M38386|“Streptococcus faecalis mtlF enzymeIII,96302mannitol-mtlD-phosphate- dehydrogenase”238421822670gb|M38386|“Streptococcus faecalis mtlF enzymeIII,98480mannitol-mtlD-phosphate- dehydrogenase”238526343839gb|M38386|“Streptococcus faecalis mtlF enzymeIII,96459mannitol-mtlD-phosphate- dehydrogenase”26121397510emb|Z12296|EFSPREGE.faecalis sprE gene for serine proteinase98888homologue261324741413dbj|D85393|ENEGE1E“Enterococcus faecalis DNA for gelatinase,981051complete cds”261429742417dbj|D85393|ENEGE1E“Enterococcus faecalis DNA for gelatinase,97516complete cds”275314721044gb|L23802|“Enterococcus faecalis pore forming, cell98422wall enzyme, regulatory, anddehydroquinase homologue proteins(ebsA,ebsB,ebsC,and ebsD) genes, completecds with repeat region”275415812018gb|L23802|“Enterococcus faecalis pore forming, cell97438wall enzyme, regulatory, anddehydroguinase homologue proteins(ebsA, ebsB, ebsC, and ebsD) genes, completecds with repeat region”2755 27892148gb|L23802|“Enterococcus faecalis pore forming, cell98642wall enzyme, regulatory, anddehydroquinase homologue proteins(ebsA, ebsB, ebsC, and ebsD) genes, completecds with repeat region”275634752660gb|L23802|“Enterococcus faecalis pore forming, cell98790wall enzyme, regulatory, anddehydroquinase homologue proteins(ebsA, ebsB, ebsC, and ebsD) genes, completecds with repeat region”28721565558emb|X17092|PPRRAPlasmid pAM-beta-1 (from S.faecalis)97991replication region DNA287320491582emb|X17092|PPRRAPlasmid pAM-beta-1 (from S.faecalis)97461replication region DNA287626393346gb|U17153|“Enterococcus faecalis plasmid pjh199498tetracycline resistant (tetL) gene,complete cds”2941145194211gb|U17153|“Enterococcus faecalis plasmid pjh110050tetracycline resistant (tetL) gene,complete cds”302111755emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy831755302223102687emb|X17214|SFPASA1S. faecalis plasmid pAD1 asal gene for100378aggregation substance and ORF 1302328653329emb|X17214|SPPASA1S. faecalis plasmid pAD1 asal gene for99463aggregation substance and ORF 1316427242110gb|M13771|“Streptococcus faecalis 6′-aminoglycoside100248acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”346522242880emb|X62755|SFNPRGS.faecalis npr gene for NADH peroxidase983513492686907dbj|D78257|D78257“Enterococcus faecalis plasmid pYI17 genes83200for BacA, BacB, ORF3, ORF4, ORF5, ORF6,ORF7, ORF8, ORF9, ORF10, ORF11,partialcds”355131166emb|X17214|SFPASA1S. faecalis plasmid pAD1 asal gene for971100aggregation substance and ORF 1355211021548emb|X17214|SFPASA1S. faecalis plasmid pAD1 asal gene for94432aggregation substance and ORF 1355316632037emb|X62657|EFORF3E.faecalis plasmid pAD1 DNA for orf399337355420352445emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading99411frames”355525582851emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading96280frames”355628383299emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading97430frames”355732363739emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading97279frames”355836964529emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading97537frames”355945875870emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading98718frames”3551058436490emb|X96977|EFPAD1OR9“E.faecalis plasmid pAD1, open reading99224frames”3551164716890emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading96361frames”3551268817204emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading98324frames”3551371918231emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading98984frames”3551482188496emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading99279frames”3551584128885emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading100474frames”3551794799952emb|X96977|EFPAD1ORF“E.faecalis plasmid pADl, open reading98417frames”36513380gb|M13771|“Streptococcus faecalis 6′-aminoglycoside100248acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”370111299dbj|D78016|ENEPPD1A“Enterococcus faecalis Plasmid pPD1 genes731267for REPB, REPA, TRAC, TRAB, TRAA, iPD1,TRAE, TRAF, complete cds and partial cds”40739632162gb|U38590|“Enterococcus faecalis plasmid pCF10 PrgN,98257PrgO, and PrgP genes, complete cds”407538114131gb|U38590|“Enterococcus faecalis plasmid pCF10 PrgN,86317PrgO, and PrgP genes, complete cds”417142419gb|UOO681|“Enterococcus faecalis plasmid pADi TraB98304(traB) gene, complete cds (traC) and(repA) genes, partial cds”417231341gb|U00681|“Enterococcus faecalis plasmid pADl TraB97198(traB) gene, complete cds (traC) and(repA) genes, partial cds”4173440754gb|U00681|“Enterococcus faecalis plasmid pAD1 TraB100219(traB) gene, complete cds (traC) and(repA) genes, partial cds”4261112462emb|Z49243|EF4110SODE.faecalis partial sod gene for superoxide98291dismutase (strain = BM4110)4262628419emb|Z49243|EF4110SODE.faecalis partial sod gene for superoxide100148dismutase (strain = BM4110)4263456725emb|Z49243|EF4110SODE.faecalis partial sod gene for superoxide100148dismutase (strain = BM4110)429184079emb|X62658|EFSEA1E.faecalis plasmid pADl seal gene and orfy9873742921087767emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy99321429427652460gb|U17153|“Enterococcus faecalis plasmid pjh19889tetracycline resistant (tetL) gene,complete cds”429531662750gb|U17153|“Enterococcus faecalis plasmid pjhl99413tetracycline resistant (tetL) gene,complete cds”435527312324gb|M38052|“Enterococcus faecalis cytolysin B9797transport protein gene, complete cds”459213301067gb|M1377|“Streptococcus faecalis 6′-aminoglycoside99248acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”506112424emb|X17214|SFPASA1S. faecalis plasmid pADi asal gene for991144aggregation substance and ORF 1514314961113gb|M13771|“Streptococcus faecalis 6′-aminoglycoside100248acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”527217331371gb|U17153|“Enterococcus faecalis plasmid pjhl98153tetracycline resistant (tetL) gene,complete cds”54413094gb|U38590|“Enterococcus faecalis plasmid pCF10 PrgN,95306PrgO, and PrgP genes, complete cds”56113761dbj|D78016|ENEPPD1A“Enterococcus faecalis Plasmid pPD1 genes77528for REPB, REPA, TRAC, TRAB, TRAA, iPD1,TRAE, TRAF, complete cds and partial cds”56127721566gb|U00681|“Enterococcus faecalis plasmid pAD1 TraB99795(traB) gene, complete cds (traC) and(repA) genes, partial cds”56638742037dbj|D78016|ENEPPD1A“Enterococcus faecalis Plasmid pPD1 genes901160for REPB, REPA, TRAC, TRAB, TRAA, iPD1,TRAE, TPAF, complete cds and partial cds”58113983emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading100393frames”5812908540emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading100369frames”59715737gb|M38052|“Enterococcus faecalis cytolysin B99566transport protein gene, complete cds”59721247516gb|M38052|“Enterococcus faecalis cytolysin B97701transport protein gene, complete cds”604732652903gb|U17153|“Enterococcus faecalis plasmid pjhl100143tetracycline resistant (tetL) gene,complete cds”61811534gb|M13771|“Streptococcus faecalis 6′-aminoglycoside99470acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”622186416gb|M13771|“Streptococcus faecalis 6′-aminoglycoside99849acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”62221317862gb|M13771|“Streptococcus faecalis 6′-aminoglycoside99256acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”622315861311gb|M13771|“Streptococcus faecalis l 6′-aminoglycoside99248acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”624656418001gb|U66286|“Enterococcus faecalis gyrase A (gyrA)98219gene, partial cds”6351516953dbj|D78257|D78257“Enterococcus faecalis plasmid pYI17 genes94404for BacA, BacB, ORF3, ORF4, ORF5, ORF6,ORF7, ORF8, ORF9, ORF10, ORF11,partialcds38 63529201222dbj|D78257|D78257“Enterococcus faecalis plasmid pYI17 genes83299for BacA, BacB, ORF3, ORF4, ORF5, ORF6,ORF7, ORF8, ORF9, ORF10, ORF11,partialcds”63713545emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs92506pd57, pd125 and pd113 genes65821198365gb|M38052|“Enterococcus faecalis cytolysin B100819transport protein gene, complete ods”658314461189gb|M38052|“Enterococcus faecaliscytolysin B98258transport protein gene, complete cds”664149065emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy884236642737417emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy9432174315614dbj|78016|ENEPPD1A“Enterococcus faecalis Plasmid pPD1 genes87305for REPB, REPA, TRAC, TRAB, TRAA, iPD1,TRAE, TRAF, complete cds and partial cds”74721139324gb|M38052|“Enterococcus faecalis cytolysin B99691transport protein gene, complete cds”7473577783gb|M38052|“Enterococcus faecalis cytolysin B100207transport protein gene, complete cds”747414741133gb|M13771|“Streptococcus faecalis 6′-aminoglycoside99248acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds”77714013gb|M38052|Enterococcus faecalis cytolysin B100335transport protein gene, complete cds”8161793512gb|M13771|“Streptococcus faecalis 6-aminoglycoside100243acetyltransferase phosphotransferase(AAC(6′)-APH(2′)) bifunctional resistanceprotein, complete cds“842141889emb|X17214|SFPASA1S. faecalis plasmid pAD1 asal gene for91303aggregation substance and ORF 18422856605emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy92246847114813emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy9214798641361106emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy93945864215713550emb|X62656|EFASP1“E.faecalisplasmid pPD1 asp1 and URFs961979pd57, pd125 and pd113 genes”87212633gb|U17153|“Enterococcus faecalis plasmid pjh198261tetracycline resistant (tetL) gene,complete cds”8741833693dbj|D31675|ENE16RNA8“Enterococcus faecalis 16S ribosomal RNA,10098partial sequence”_________878130230gb|U17153|“Enterococcus faecalis plasmid pjh19494tetracycline resistant (tetL) gene,complete cds”8782263445gb|U17153|“Enterococcus faecalis plasmid pjh199181tetracycline resistant (tetL) gene,complete cds”921174826emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy9561292914842emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy9940994613422emb|X62657|EFORF3E.faecalis plasmid pAD1 DNA for orf3993419462420830emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading98411frames”94638661123emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading96230frames”9471112498emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs96378pd57, pd125 and pd113 genes”951148426emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy9535395613545emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs96543pd57, pd125 and pd113 genes”9562524721emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs94161pd57, pd125 and pd113 genes”95716162emb|X96977|EFPAD1ORF“E.faecalis plasmid pAD1, open reading99615frames”957242686emb|X96977|EFPAD1ORF“E.facalis plasmid pAD1, open reading99595frames”96811456emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs96366pd57, pd125 and pd113 genes”9682339641emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs95158pd57, pd125 and pd113 genes9683395658emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs94126pd57, pd125 and pd113 genes”97715943emb|X17214|SFPASA1S. faecalis plasmid pAD1 asal gene for99847aggregation substance and ORF 198213762emb|X62658|EFSEA1E.faecalis plasmid pAD1 seal gene and orfy95365985185471emb|X62656|EFASP1“E.faecalis plasmid pPD1 asp1 and URFs91362pd57, pd125 and pd113 genes”

[0353]

2

TABLE 2

E. faecalis
- Putative coding regions of novel proteins similar to known proteins

Contig
ORF
Start
Stop

ID
ID
(nt)
(nt)
Match accession
Match gene name
% Sim
% Ident

137
3
3208
2003
gi|152947
transposase [Staphylococcus aureus]
100
100

154
14
9166
9750
gi|141861
traA gene product [Plasmid pAD1]
100
100

276
16
11268
11047
gnl|PID|e284733
C34B7.1 [Caenorhabditis elegans]
100
71

287
1
485
234
gi|152947
transposase [Staphylococcus aureus]
100
100

287
7
3454
3765
gi|152947
transposase [Staphylococcus aureus]
100
100

292
6
3001
4185
gi|488330
alpha-amylase [unidentified cloning
100
100

vector]

429
3
2013
1654
gi|141863
regulatory protein [Plasmid pAD1]
100
100

604
3
1243
1043
gi|559860
clyLs [Plasmid pAD1]
100
98

604
4
1492
1268
gi|559859
clyL1 [PLasmid pAD1]
100
100

656
7
7592
6834
gi|488339
alpha-amylase [unidentified cloning
100
100

vector]

658
1
312
4
gi|152947
transposase [Staphylococcus aureus]
100
100

674
3
1236
1589
gi|1196996
unknown protein [Transposon Tn10]
100
98

700
1
375
4
gi|152947
transposase [Staphylococcus aureus]
100
100

961
1
1
450
gi|152947
transposase [Staphylococcus aureus]
100
100

72
17
20153
21040
gi|150556
surface protein [Plasmid pCF10]
99
99

99
5
3117
1933
gi|1006839
malic enzyme [Streptococcus bovis]
99
99

154
3
1995
1491
gi|149482
transposase [Lactococcus lactis]
99
99

326
3
3030
1714
pir|S16989|S16989
dihydrolipaomide S-acetyltransferase (EC
99
98

2.3.1.12)-Enterococcus faecalis

407
6
4636
4235
gi|141859
replication-associated protein [Plasmid
99
99

pAD1]

692
1
3
485
gi|559861
clyM [Plasmid pAD1]
99
99

99
6
3904
3134
gi|1146122
L-malate permease [Streptococcus bovis]
98
98

326
4
3358
3002
pir|S16989|S16989
dihydrolipoamide S-acetyltransferase (EC
98
97

2.3.1.12)-Enterococcus faecalis

346
1
606
4
gi|1146122
L-malate permease [Streptococcus bovis]
98
98

367
31
14415
13999
gi|1644226
ribosomal protein S10 [Bacillus subtilis]
98
88

367
6
2797
2495
gi|142459
initiation factor 1 [Bacillus subtilis]
97
88

407
9
5454
4894
gi|141858
replication-associated protein [Plasmid
97
97

pAD1]

497
6
3514
3762
gi|532552
ORF19 [Enterococcus faecalis]
97
87

558
1
1
399
gi|46638
ORF 2 (AA 1-236) [Staphylococcus aureus]
97
97

829
1
169
2
gnl|PID|e283110
femD [Staphylococcus aureus]
97
86

407
8
4970
4599
gi|141858
replication-associated protein [Plasmid
96
96

pAD1]

777
2
1102
380
gi|559861
clyM [Plasmid pAD1]
96
96

23
33
20797
21126
gnl|PID|e223402
DNA topoisomerase IV C submit
95
80

[Streptococcus pneumoniae]

32
5
3454
3071
gi|147194
phnA protein [Escherichia coli]
95
87

95
8
5493
6875
gi|391682
Na+ −ATPase beta subunit [Enterococcus
95
89

hirae
]

138
25
16587
16745
gi|143136
L-lactate dehydrogenase [Bacillus
95
70

megaterium
]

367
20
9198
8797
gi|40150
L14 protein (AA 1-122) [Bacillus subtilis]
95
90

367
21
9519
9223
gi|1044973
ribosomal protein L17 [Bacillus subtilis]
95
89

439
2
846
1241
gi|488334
alpha-amylase [unidentified cloning
95
94

vector]

604
1
792
4
gi|559861
clyM [Plasmid pAD1]
95
93

722
1
1
504
gi|47453
ribosomal protein S12 [Streptococcus
95
94

pneumoniae
]

17
8
7317
7676
gi|532554
ORF21 [Enterococcus faecalis]
94
86

95
2
1288
1791
gi|416405
Na+−ATPase K subunit [Enterococcus hirae]
94
88

97
3
2481
1432
gi|1750264
heat shock protein 70 [Streptococcus
94
90

pneumoniae
]

117
5
2700
3842
gi|467376
unknown [Bacillus subtilis]
94
89

327
3
3283
3762
gi|153566
ORF (19K protein) [Enterococcus faecalis]
94
87

327
5
4782
5054
gi|153568
H+ ATPase [Enterococcus faecalis]
94
82

387
4
3608
1728
gi|153661
translational initiation factor IF2
94
88

[Enterococcus faecium] sp|P18311|IF2_ENTFC

INITIATION FACTOR IF-2.

455
1
2
259
gi|532549
ORF16 [Enterococcus faecali]
94
82

97
2
1444
677
gi|450684
dnaK gene product [Lactococcus lactis]
93
83

188
2
1690
1911
gi|43865
nifJ gene product [Klebsiella pneumoniae]
93
78

216
6
4234
4680
gi|153574
H+ ATPase [Enterococcus faecalis]
93
86

298
2
2798
1221
gi|143012
GMP synthetase [Bacillus subtilis]
93
86

329
2
1538
771
gi|153826
adhesin B [Streptococcus sanguis]
93
83

367
15
7675
7247
gi|1044978
ribosomal protein S8 [Bacillus subtilis]
93
82

722
2
527
1030
gi|1644222
ribosomal protein S7 [Bacillus subtilis]
93
83

803
1
657
151
gi|1196998
unknown protein [Transposon Tn10]
93
93

962
1
130
636
gi|152947
transposase [Staphylococcus aureus]
93
92

237
12
6056
6385
gi|963038
Arpυ [Enterococcus hirae]
92
76

309
4
8218
4541
gi|402363
RNA polymerase beta-subunit [Bacillus
92
82

subtilis
] sp |P37870| RPOB_BACSU DNA-

DIRECTED RNA POLYMERASE BETA CHAIN (EC

.7.7.6) (TRANSCRIPTASE BETA CHAIN) (RNA

POLYMERASE BETA SUBUNIT).

329
4
2529
1717
gi|310632
hydrophobic membrane protein
92
78

[Streptococcus gordonii]

sp|P42361|P29K_STRGC 29 KD MEMBRANE

PROTEIN IN PSAA 5′REGION ORF1).

367
4
1942
1544
gi|142462
ribosomal protein S11 [Bacillus subtilis]
92
82

367
8
3648
3457
pir|C44859|C44859
adenylate kinase - Bacillus sp. (fragment)
92
88

367
12
6183
5641
gi|1044981
ribosomal protein S5 [Bacillus subtilis]
92
81

367
17
8427
7885
pir51 A29102|R5BS5F
ribosomal protein L5 - Bacillus
92
83

stearothermophilus

527
1
1404
373
gi|153092
replication protein [Staphylococcus
92
81

aureus
]

701
1
2
352
gi|143793
tyrosyl-tRNA synthetase [Bacillus
92
74

caldotenax
]

23
28
17420
17566
sp|P45692|EUTX_SAL
ETHANOLAMINE UTILIZATION PROTEIN EUTX
91
73

TY
(FRAGMENT).

57
5
4129
4701
gi|15958l0
type-I signal peptidase SpsB
91
67

[Staphylococcus aureus]

57
12
13281
13970
gnl|PID|e254999
phenylalany-tRNA synthetase beta subunit
91
75

[Bacillus subtilis]

156
5
4609
6474
gi|1303804
YqeQ [Bacillus subtilis]
91
79

216
3
1848
2765
gi|153572
H+ ATPase [Enterococcus faecalis]
91
81

367
24
10802
10128
gi|1165309
S3 [Bacillus subtilis]
91
78

415
1
452
883
pir|B56272|B56272
probable pheromone-responsive regulatory
91
90

protein R - Enterococcus faecalis plasmid

pCF10

466
2
1313
2065
gi|142443
adenylosuccinate synthetase [Bacillus
91
79

subtilis
]sp|P29726|PURA_BACSU

ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4)

IMP--ASPARTATE LIGASE).

545
1
1
345
gi|532549
ORF16 [Enterococcus faecalis]
91
80

572

1 8
652
gi|347998
uracil phosphoribosyltransferase
91
78

[Streptococcus salivarius]

sp|P36399|UPP_STRSL PROBABLE URACIL

PHOSPHORIBOSYLTRANSFERASE (EC .4.2.9) (UMP

PYROPHOSPHORYLASE) (UPRTASE).

599
1
8
343
gi|42029
ORF1 gene product [Escherichia coli]
91
75

600
2
585
779
pir|B48396|B48396
ribosomal protein L33 - Bacillus
91
81

stearothermophilus

652
1
394
2
gi|535662
transposase [Insertion sequence IS1251]
91
81

1
4
3465
2557
gi|1644224
elongation factor Tu [Bacillus subtilis]
90
83

17
19
14844
17297
gi|532549
ORF16 [Enterococcus faecalis]
90
77

52
3
2650
2811
gi|473902
alpha-acetolactate synthase [Lactococcus
90
68

lactis
]

74
9
5870
5469
gi|1653508
hypothetical protein [Synechocystis sp.]
90
52

75
3
1177
2091
gi|153615
phosphoenolpyruvate:sugar
90
83

phosphotransferase system enzyme I

Streptococcus salivarius
]

117
10
6591
8126
gi|924848
inosine monophosphate dehydrogenase
90
80

[Streptococcus pyogenes] pir|JC4372 |JC4372

IMP dehydrogenase (EC 1.1.1.205) -

Streptococcus yogenes

276
1
577
95
gi|530798
LysB [Bacteriophage phi-LC3]
90
72

287
5
2611
2441
gi|1333835
copS gene product [Streptococcus pyogenes]
90
78

290
1
1
708
gi|897795
30S ribosomal protein [Pediococcus
90
75

acidilactici
] sp|P49668|RS2_PEDAC 30S

RIBOSOMAL PROTEIN S2.

309
3
4401
1093
gnl|PID|e187579
DNA-directed RNA polymerase [Listeria
90
81

innocua]

367
22
9731
9513
pir|A02825|R5BS29
ribosomal protein L29 - Bacillus
90
76

stearothermophilus

452
4
2224
2508
gi|434759
ORF [Homo sapiens]
90
54

455
2
2776
323
gi|532549
ORF16 [Enterococcus faecalis]
90
77

623
1
3
221
gi|460259
enolase [Bacillus subtilis]
90
80

624
5
3612
5615
gnl|PID|e2O8213
DNA gyrase [Streptococcus pneumoniae]
90
81

853
2
752
282
gnl|PID|e13389
translation initiation factor IF3 (AA 1-
90
82

172) [Bacillus stearothermophilus]

966
1
1
462
gi|532549
ORF16 [Enterococcus faccalis]
90
83

1
3
2596
2219
gi|1661195
elongation factor-Tu [Streptococcus
89
78

mutans
]

1
5
4314
3556
gi|1644223
elongation factor G [Bacillus subtilis]
89
79

23
21
13990
14295
gi|466518
pduA [Salmonella typhimurium]
89
75

23
32
19927
20799
gnl|PID|e208211
DNA topoisomerase IV [Streptococcus
89
83

pneumoniae
]

42
2
349
1989
gi|287871
groEL gene product [Lactococcus lactis]
89
79

45
15
11835
12167
gi|150554
surface exclusion protein [Plasmid pCF10]
89
68

53
2
685
1797
gnl|PID|e221213
ClpX protein [Bacillus subtilis]
89
81

86
4
3374
4024
gi|537286
triosephosphate isomerase [Lactococcus
89
78

lactis
]

95
7
3677
5506
gi|912449
Na+ −ATPase alpha subunit [Enterococcus
89
80

hirae
]

128
18
11348
11013
gi|466473
cellobiose phosphotransferase enzyme II′
89
60

[Bacillus tearothermophilus]

132
1
180
2180
gi|153854
uvs402 protein [Streptococcus pneumoniae]
89
78

342
1
783
4
gi|1041115
TRAC [Plasmid pPD1]
89
79

367
23 10146
9691
sp|P14577|RL16—BAC
50S RIBOSOMAL PROTEIN L16.
89
80

SU

367
27
12377
11541
gi|1165306
L2 [Bacillus subtilis]
89
79

435
4
2424
2215
gi|559863
clyA [Plasmid pA1]
89
89

466
3
1972
2736
gi|467328
adenylosuccinate synthetase [Bacillus
89
75

subtilis
]

512
3
999
1607
gi|1477776
ClpP [Bacillus subtilis]
89
73

518
1
1
174
gi|786163
Ribosomal Protein L10 [Bacillus subtilis]
89
76

604
2
1000
713
gi|559861
clyM [Plasmid pAD1]
89
89

615
2
888
691
gi|467469
unknown [Bacillus subtilis]
89
75

677
2
992
429
gi|1389732
S-adenosylmethionine synthetase [Bacillus
89
76

subtilis
]

677
3
1315
950
gi|1020317
S-adenosylmethionine synthetase
89
73

[Staphylococcus aureus]

722
3
1102
1278
pir|PW0010|PW0010
translation elongation factor G - Bacillus
89
72

stearothermophilus
(fragment)

850
1
464
3
gi|142521
deoxyribodipyrimidine photolyase [Bacillus
89
72

subtilis
]gnl|PID|e255102

deoxyribodipyrimidine photolyase [Bacillus

ubtilis
]

17
5
3711
4751
gi|532554
ORF21 [Enterococcus faecalis]
88
72

37
5
3322
3717
gi|1216488
uncharacterized open reading frame;
88
75

hypothetical protein displaying similarity

to a Bacillus subtilis hypothetical

protein (Ylm [Streptococcus mutans]

39
6
2454
2630
sp|P49865|NTPR_ENT
NTPR PROTEIN (FRAGMENT).
88
77

HR

48
3
1740
2666
gi|557492
dihydroxynapthoic acid (DHNA) synthetase
88
75

[Bacillus subtilis] gi|143186

dihydroxynapthoic acid (DHNA) synthetase

[Bacillus ubtilis]

63
5
2753
3607
gi|1064814
homologous to sp:PHOP_BACSUB [Bacillus
88
77

subtilis
]

86
2
1004
2047
gi|153763
plasmin receptor [Streptococcus pyogenes]
88
79

104
6
6431
6213
gi|431231
uracil permease [Bacillus caldolyticus]
88
60

110
19
18174
16891
gi|217040
acid glycoprotein [Streptococcus pyogenes]
88
72

145
10
9040
8834
gi|393268
29-kiloDalton protein [Streptococcus
88
71

pneumoniae
]sp|P42362|P29K_STRPN 29 KD

MEMBRANE PROTEIN IN PSAA 5′REGION ORF1).

151
1
1620
316
gi|143366
adenylosuccinate lyase (PUR-B) [Bacillus
88
78

subtilis
] pir|C29326|WZBSDS

adenylosuccinate lyase (EC 4.3.2.2) -

Bacillus ubtilis

171
10
9676
10119
gi|1591672
phosphate transport system ATP-binding
88
63

protein [Methanococcus jannaschii]

190
3
1997
975
gi|532554
ORF21 [Enterococcus faecalis]
88
76

229
6
5712
5954
gi|143648
ribosomal protein L28 [Bacillus subtilis]
88
70

270
2
895
1869
gi|1303828
YqfJ p8 Bacillus subtilis]
88
75

275
7
3761
3552
gi|425474
SMDR1 [Schistosoma mansoni]
88
72

293
1
614
3
gi|1783246
highly homologous to many ATP-binding
88
80

transport proteins; hypothetical [Bacillus

subtilis
]

367
1
485
72
gi|142464
ribosomal protein L17 [Bacillus subtilis]
88
76

367
5
2335
1961
gi|1044989
ribosomal protein S13 [Bacillus subtilis]
88
80

367
16
7887
7681
pir|S48688|S48688
ribosomal protein S14 - Bacillus
88
83

stearothermophilus

598
1
1006
23
gi|565287
transposase-like protein of PS3IS
88
66

[thermophilic bacterium PS3]

pir|JC4292|JC4292 insertion sequence

element 1341 - thermophilic acterium PS-3

600
3
1640
882
gi|763052
integrase [Bacteriophage T270]
88
68

669
1
2
514
gi|153801
enzyme scr-II [Streptococcus mutans]
88
75

808
2
624
394
gi|1574781
exodeoxyribonuclease V (recB) [Haemophilus
88
77

influenzae]

871
1
714
229
gi|1574120
branched-chain-amino-acid transaminase
88
79

[Haemophilus influenzae]

979
1
1
384
gnl|PID|e187579
DNA-directed RNA polymerase [Listeria
88
78

innocua
]

983
1
34
282
gi|40026
homologous to E.coli gidA [Bacillus
88
78

subtilis
]

47
5
6799
5810
gi|532204
prs [Listeria monocytogenes]
87
79

69
3
2033
750
gi|1377831
unknown [Bacillus subtilis]
87
74

73
2
1432
167
gi|143434
Rho Factor [Bacillus subtilis]
87
76

76
5
2412
3740
gi|496283
lysin [Bacteriophage Tuc2009]
87
75

88
3
1600
2016
gnl|PID|e137596
heat shock induced protein HtpO
87
75

[Lactobacillus leichmannii]

89
7
6003
5608
gi|1695686
pyruvate carboxylase [Bacillus
87
77

stearothermophilus
]

93
1
283
119
gi|1124825
unknown protein [Chlamydia trachomatis]
87 56

104
1
2945
3
gnl|PID|e199387
carbamoyl-phosphate synthase
87
75

[Lactobacillus plantarum]

124
4
3191
2274
gi|995767
UDP-glucose pyrophosphorylase
87
76

[Streptococcus pyogenes]

273
2
608
1108
gi|1184680
polynucleotide phosphorylase [Bacillus
87
76

subtilis]

293
2
1020
532
gi|153741
ATP-binding protein [Streptococcus mutans]
87
74

326
5
4534
3533
gi|143378
pyruvate decarboxylase (E-1) beta subunit
87
74

[Bacillus subtilis] gi|1377836 pyruvate

decarboxylase E-1 beta subunit [Bacillus

ubtilis]

334
3
3182
3340
pir|A36324|A36324
growth arrest-specific protein - mouse
87
50

337
1
1382
186
gi|308861
GTG start codon [Lactococcus lactis]
87
75

338
8
6925
5723
gi|149575
L(+)-lactate dehydrogenase [Lactobacillus
87
73

casei
] sp|P00343|LDH_LACCA L-LACTATE

DEHYDROGENASE (EC 1.1.1.27). (SUB −326)

367
18
8782
8450
pir|A02819|R5BS24
ribosomal protein L24 - Bacillus
87
70

stearothermophilus

388
2
410
183
gnl|PID|e225674
unknown [Schizosaccharomyces pombe]
87
75

440
1
466
1797
gi|520754
putative [Bacillus subtilis]
87
75

508
1
694
137
gi|496558
orfX [Bacillus subtilis]
87
73

654
3
530
802
pir|A47079|A47079
heat shock protein DnaJ - Lactococcus
87
70

lactis

18
1
3
413
gi|46912
ribosomal protein L13 [Staphylococcus
86
70

carnosus]

18
2
406
819
pir|S08564|R3BS9
ribosomal protein S9 - Bacillus
86
73

stearothermophilus

50
1
84
1148
gi|452398
threonine synthase [Bacillus sp.]
86
74

74
14
10547
10080
gi|1314299
ORF6; putative glutamyl-tRNA-transferase;
86
74

similar to glutamyl-tRNA-transferase from

Bacillus subtilis
[Listeria monocytogenes]

95
5
3176
3406
gi|487276
Na+ −ATPase subunit C [Enterococcus hirae]
86
62

114
8
9216
10313
gi|853776
peptide chain release factor 1 [Bacillus
86
69

subtilis
] pir|S55437|S55437 peptide chain

release factor 1 - Bacillus ubtilis

115
2
501
899
gi|551879
ORF 1 [Lactococcus lactis]
86
70

164
26
25639
25842
pir|S34762|S34762
L-serine dehydratase beta chain -
86
81

Clostridium sp

243
2
2143
1082
gi|143607
sporulation protein [Bacillus subtilis]
86
70

255
1
2
196
gi|755604
unknown [Bacillus subtilis]
86
64

257
3
3565
983
gi|928832
0RF259; putative [Lactococcus lactis phage
86
66

BK5-T]

273
3
943
1314
gi|1184680
polynucleotide phosphorylase [Bacillus
86
65

subtilis
]

288
2
554
1087
gi|153033
tagatose 6-phosphate isomerase
86
74

[Staphylococcus aureus] pir|B38158|B38158

galactose-6-phosphate isomerase 19K chain

- taphylococcus aureus

327
7
5183
5722
gi|153569
H+ ATPase [Enterococcus faecalis]
86
71

345
7
5111
5620
gi|1314294
ORF1; putative 17 kDa protein [Listeria
86
63

monocytogenes)

350
3
1900
2781
gi|511015
dihydroorotate dehydrogenase A
86
73

[Lactococcus lactis] sp|P54321|PYDA_LACLC

DIHYDROOROTATE DEHYDROCENASE A (EC

1.3.3.1) DIHYDROOROTATE OXIDASE A)

(DHODEHASE A).

383
3
3328
4233
gi|1657517
hypothetical protein [Escherichia coli]
86
59

367
25
11216
10851
gi|116538
L22 [Bacillus subtilis]
86
68

367
26
11534
11220
gi|1165307
S19 [Bacillus subtilis]
86
77

367
30
13995
13453
gi|1165303
L3 [Bacillus subtilis]
86
75

393
1
1
660
sp|P33898|G3P3_ECO
GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE C
86
77

LI
(EC 1.2.1.12) (GAPDH-C).

396
1
1
192
gi|944942
RipX [Bacillus subtilis]
86
77

438
3
1279
1560
gi|1001878
CspL protein [Listeria monocytogenes]
86
75

510
1
1008
199
gi|473795
‘ORF’ [Escherichia coli]
86
71

510
2
1912
962
gi|473794
‘ORF’ [Escherichia coli]
86
76

539
1
705
4
gi|467477
unknown [Bacillus subtilis]
86
79

570
2
2069
1023
gi|881511
Ccpa protein [Lactobacillus casei]
86
72

654
2
240
575
pir|A47079|A47079
heat shock protein DnaJ - Lactococcus
86
77

lactis

677
1
431
102
gi|1389732
S-adenosylmethionine synthetase [Bacillus
86
80

subtilis
]

984
1
1
147
pir|A56922|A56922
transcription factor shn - fruit fly
86
73

(Drosophila melanogaster)

5
11
7720
8487
gi|41015
aspartate-tRNA ligase [Escherichia coli]
85
71

34
2
2133
1711
gi|47828
pyruvate kinase [Bacillus
85
75

stearothermophilus
]

97
4
2666
2517
pir|S39341|S3934l
grpE protein - Lactococcus lactis
85
66

103
2
1263
946
gi|143364
phosphoribosyl aminoimidazole carboxylase
85
68

I (PUR-E) [Bacillus ubtilis]

103
3
1465
1169
gi|143364
phosphoribosyl aminoimidazole carboxylase
85
67

I (PUR-E) [Bacillus ubtilis]

129
3
2395
3258
gi|143766
(thrSv) (EC 6.1.1.3) [Bacillus subtilis]
85
67

129
4
3240
4445
gi|143766
(thrSv) (EC 6.1.1.3) [Bacillus subtilis]
85
78

188
1
86
1447
gnl|PID|e214721
glutamine synthetase [Staphylococcus
85
71

aureus
]

217
3
673
1086
gi|520540
unknown [Bacillus subtilis]
85
72

241
2
1715
1086
gi|495089
recombinase [Staphylococcus aureus]
85
68

285
2
712
993
gi|40014
pot. ORF 446 (aa 1-446) [Bacillus
85
77

subtilis
]

293
3
1149
1595
gi|755604
unknown [Bacillus subtilis]
85
66

300
2
2738
2220
gi|289261
comE ORF2 [Bacillus subtilis]
85
72

305
2
1853
2695
pir|S09411|S09411
spoIIIE protein - Bacillus subtilis
85
70

322
1
1
171
gi|153562
aspartate beta-semialdehyde dehydrogenase
85
67

(EC 1.2.1.11) Streptococcus mutans]

327
4
4056
4784
gi|153567
H+ ATPase [Enterococcus faecalis]
85
66

367
10
5417
4959
pir|A02795|R5BS15
ribosomal protein L15 - Bacillus
85
76

stearothermophilus

383
3
3168
2953
gnl|PID|e274577
csp [Lactobacillus plantarum]
85
79

404
3
3069
2101
gi|143402
recombination protein (ttg start codon)
85
72

[Bacillus subtilis] gi|1303923 RecN

[Bacillus subtilis]

469
1
2
724
gi|508979
GTP-binding protein [Bacillus subtilis]
85
78

488
1
1
996
gi|532548
ORF15 [Enterococcus faecalis]
85
67

535
5
6468
4849
gi|634107
kdpB [Escherichia coli]
85
68

584
3
732
562
gi|467374
single strand DNA binding protein
85
75

[Bacillus subtilis]sp|P37455|SSB_BACSU

SINGLE-STRAND BINDING PROTEIN (SSB) HELIX-

DESTABILIZING PROTEIN).

695
1
78
500
gi|499384
orf189 [Bacillus subtilis]
85
75

836
1
1
357
gi|153801
enzyme scr-II [Streptococcus mutans]
85
69

17
20
17212
18813
gi|532548
ORF15 [Enterococcus faecalis]
84
68

23
31
18728
19987
gnl|PID|e208211
DNA topoisomerase IV [Streptococcus
84
68

pneumoniae
]

34
3
3112
2144
gi|143312
6-phospho-1-fructokinase (gtg start codon;
84
69

EC 2.7.1.11) [Bacillus tearothermophilus]

36
1
1
1152
gi|1644223
elongation factor G [Bacillus subtilis]
84
73

49
12
6730
8190
gi|456319
74kDa protein [Bacteriophage FC1]
84
65

51
2
1379
1663
gi|468207
Submitter comments: A Mg2+ transporting P-
84
71

type ATPase highly omologous with mgtB

ATPase at 80 min on Salmonella chromosome.

ediates the influx of Mg2+ only.

Transcription regulated by xtracellular

Mg2+ [Salmonella typhimurium]

95
6
3330
3707
gi|487277
Na+ −ATPase subunit C [Enterococcus hirae]
84
64

104
5
6250
5459
gnl|PID|e199440
aspartate carbamoyltransferase, aspartate
84
65

transcarbamylase,

carbamylaspartotranskinase [Lactobacillus

plantarum
]

105
6
4605
5273
gi|467411
recombination protein [Bacillus subtilis]
84
65

114
11
12278
12997
gi|556886
serine hydroxymethyltransferase [Bacillus
84
74

subtilis
]pir|S49363|S49363 serine

hydroxymethyltransferase - Bacillus

ubtilis

117
2
705
1484
gi|580906

B.subtilis
genes rpmH, rnpA, 50kd, gidA
84
70

and gidB [Bacillus subtilis] gi|467381

regulation of SpoOJ and 0rf283 (probable)

[Bacillus ubtilis]

121
2
1274
2119
gi|290643
ATPase [Enterococcus hirae]
84
67

121
6
5016
5219
gi|153765
DNA polymerase I [Streptococcus
84
66

pneumoniae
]

128
27
22456
20453
gi|437916
isoleucyl-tRNA synthetase [Staphylococcus
84
71

aureus
]

130
1
2
133
gi|1237013
ORF2 [Bacillus subtilis]
84
74

138
35
26712
25777
gi|143795
transfer RNA-Tyr synthetase [Bacillus
84
69

subtilis
]

164
28
26378
27277
gnl|PID|e247026
orf6 [Lactobacillus sake]
84
72

171
1
158
2719
gi|499335
secA protein [Staphylococcus carnosus]
84
68

210
5
4870
3884
gi|950062
hypothetical yeast protein 1 [Mycoplasma
84
75

capricolum
] pir|S48578|S48578 hypothetical

protein - Mycoplasma capricolum SGC3)

(fragment)

217
7
5222
3546
gi|143597
CTP synthetase [Bacillus subtilis]
84
68

243
1
1088
126
gi|143608
sporulation protein [Bacillus subtilis]
84
70

275
1
578
48
gi|1103865
formyl-tetrahydrofolate synthetase
84
72

[Streptococcus mutans]

281
1
333
698
gi|1303962
YqjK [Bacillus subtilis]
84
68

292
23
18340
18038
gi|142988
membrane transport protein [Bacillus
84
61

stearothermophilus
] pir|A42478|A42478

glutamine transport protein glnQ -

[Bacillus tearothermophilus]

309
2
1114
722
gi|1644219
RNA polymerase beta′ subunit [Bacillus
84
72

subtilis
]

315
1
668
3
gi|149601
thymidylate synthase (EC 2.1.1.45)
84
72

[Lactobacillus casei]

334
6
5375
6862
gi|1354211
PET112-like protein [Bacillus subtilis]
84
71

338
10
7585
10479
gi|467444
transcription-repair coupling factor
84
68

[Bacillus subtilis] sp|P37474|MFD_BACSU

TRANSCRIPTION-REPAIR COUPLING FACTOR

(TRCF).

338
14
12713
13018
gi|467448
unknown [Bacillus subtilis]
84
64

340
3
1068
2273
gi|40046
phosphoglucose isomerase A (AA 1-449)
84
69

[Bacillus stearothermophilus]

ir|S15936|NUBSSA glucose-6-phosphate

isornerase (EC 5.3.1.9) A - cillus

stearothermophilus

375
2
1430
1780
gi|1402531
ORE10 [Enterococcus faecalis]
84
64

381
1
2
1279
gnl|PID|e208212
DNA topoisomerase IV [Streptococcus
84
67

pneumoniae
]

421
1
5
151
gi|710632
beta-glucosidase [Bacillus subtilis]
84
73

421
3
1229
1465
gi|710632
beta-glucosidase [Bacillus subtilis]
84
65

445
1
1080
190
gi|46985
glucose-1-phosphate thymidylyltransferase
84
71

[Salmonella enterica] ir|S23342|S23342

hypothetical protein 6.1 - Salmonella

choleraesuis p|P55254|RFBA_SALAN GLUCOSE-

1-PHOSPHATE THYMIDYLYLTRANSFERASE (EC

7.7.24) (DTDP-GLUCOSE SYNTHASE) (DTDP-

GLUCOSE PYROPHOSPHO

466
9
10467
11006
gi|147403
mannose permease subunit II-P-Man
84
61

[Escherichia coli]

497
2
469
1680
gi|1220529
methyl transferase [Streptococcus
84
72

pneumoniae
]

545
2
309
2171
gi|532548
ORF15 [Enterococcus faecalis]
84
68

550
5
2744
2265
gi|455528
ORF2 [Streptococcus thermophilus
84
54

bacteriophage
]

637
5
2679
3545
gnl|PID|e236571
cell wall anchoring signal [Enterococcus
84
72

faecalis
]

653
3
1023
736
gi|1408584
LtrC [Lactococcus lactis lactis]
84
72

674
1
763
254
gi|467452
unknown [Bacillus subtilis]
84
66

788
1
165
500
gi|1196907
daunorubicin resistance protein
84
66

[Streptomyces peucetius]

675
1
1
621
gi|467470
lysyl-tRNA thynthetase [Bacillus subtilis]
83
71

763
2
374
640
gi|145851
envM [Escherichia coli]
83
61

774
1
658
2
gi|1256145
YbbP [Bacillus subtilis]
83
60

3
1
58
327
gi|312443
carbamoyl-phosphate synthase (glutamine-
82
70

hydrolysing) [Bacillus aldolyticus]

5
10
6389
7708
sp|P30053|SY_STREQ
HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21)
82
71

(HISTIDINE--TRNA LIGASE) (HISRS).

27
4
1906
1145
gi|1303960
YgjI [Bacillus subtilis]
82
71

32
2
1333
965
gi|1303839
YqfR [Bacillus subtilis]
82
60

34
1
1643
324
gnl|PID|e218042
pyruvate kinase [Lactobacillus
82
68

delbrueckii
]

55
9
4182
5054
gi|1685110
tetrahydrofolate
82
70

dehydrogenase/cyclohydrolase

[Streptococcus thermophilus]

62
7
4644
4210
gi|143723
putative [Bacillus subtilis]
82
66

88
2
995
1624
gi|535349
CodW [Bacillus subtilis]
82
66

94
7
4790
3432
gi|1146247
asparaginyl-tRNA synthetase [Bacillus
82
67

subtilis
]

110
23
21590
20742
gi|467403
seryl-tRNA synthetase [Bacillus subtilis]
82
69

114
7
8623
9228
gi|703442
thyrmidine kinase [Streptococcus gordonii]
82
68

123
6
4499
4996
gi|467356
unknown [Bacillus subtilis]
82
68

130
3
1413
2381
gi|308851
ATP binding protein [Lactococcus lactis]
82
64

144
3
3292
2339
gnl|PID|e183449
putative ATP-binding protein of ABC-type
82
62

[Bacillus subtilis]

144
7
5331
5110
gi|335495
A23R; putative [Vaccinia virus]
82
47

159
4
2533
5010
gi|143148
transfer RNA-Leu synthetase [Bacillus
82
71

subtilis
]

159
6
5845
5387
gi|467354
unknown [Bacillus subtilis]
82
55

171
8
8510
9349
gi|1591672
phosphate transgport system ATP-binding
82
61

protein [Methanococcus jannaschii]

222
5
2158
3402
gi|143444
RNase PH [Bacillus subtilis]
82
66

254
6
1621
1112
gi|49316
ORF2 gene product [Bacillus subtilis]
82
61

279
12
9839
8442
gi|1237019
Srb [Bacillus subtilis]
82
67

288
1
22
546
gi|149393
lacA [Lactococcus lactis]
82
73

345
8
5608
8118
gi|442360
ClpC adenosine triphosphatase [Bacillus
82
63

subtilis
]

367
3
1472
1110
gi|142463
RNA polymerase alpha-core-subunit
82
75

[Bacillus subtilis]

367
9
4961
3660
gi|44073
SecY protein [Lactococcus lactis]
82
65

367
28
12719
12411
pir|A02815|R5BS23
ribosomal protein L23 - Bacillus
82
66

stearothermophilus

367
29
13330
12701
gi|1165304
L4 [Bacillus subtilis]
82
67

379
5
4396
3107
gi|887820
UUG start; possible frameshift at end?
82
71

[Escherichia coli]

393
2
1145
711
gi|1303993
YqkL [Bacillus subtilis]
82
67

416
1
3
650
gi|475113
sucrase [Pediococcus pentosaceus]
82
69

477
1
1
1209
gi|309663
signaling protein [Plasmid pCF10]
82
62

497
7
3760
4275
gi|532551
ORF18 [Enterococcus faecalis]
82
67

535
3
4275
1666
gi|1747434
KdpD [Clostridium acetobutylicum]
82
62

587
1
488
108
gi|1303840
YgfS [Bacillus subtilis]
82
71

623
2
122
1348
gi|460259
enolase [Bacillus subtilis]
82
67

656
1
1
1908
gi|1184680
polynucleotide phosphorylase [Bacillus
82
69

subtilis]

687
1
227
1252
gi|40218
PRPP synthetase (AA 1-317) [Bacillus
82
64

subtilis
]

728
1
3
527
gi|1146183
putative [Bacillus subtilis]
82
65

741
1
3
704
gi|153804
sucrose-6-phosphate hydrolase
82
66

[Streptococcus mutans]

846
1
458
3
gnl|PID|e221400
tex gene product [Bordetella pertussis]
82
76

865
1
18
308
gi|416006
orf CJ01.2 [Campylobacter jejuni]
82
57

876
1
207
689
gi|1064795
function unknown [Bacillus subtilis]
82
62

925
1
436
128
gi|1773195
hypothetical [Escherichia coli]
82
74

983
2
280
474
gi|40026
homologous to E.coli gidA [Bacillus
82
78

subtilis
]

12
3
4778
5788
gi|1100074
tryptophanyl-tRNA synthetase [Clostridium
81
68

longisporum
]

31
4
2984
4456
gi|849026
hypothetical 54.6-kDa protein [Bacillus
81
68

subtilis
]

34
6
6707
6910
gi|606067
ORF_f444 [Escherichia coli]
81
54

37
1
1
144
gi|1303854
YggG [Bacillus subtilis]
81
59

37
3
2671
1958
gi|40056
phoP gene product [Bacillus subtilis]81
61

57
3
1733
3220
gi|1657506
hypothetical protein [Escherichia coli]
81
66

60
5
5564
4440
gi|143370
phosphoribosylpyrophosphate
81
63

amidotransferase (PUR-F; EC 2.4.2.14)

Bacillus subtilis
]

73
3
2706
1450
gi|853767
UDP-N-acetylglucosamine 1-
81
61

carboxyvinyltransferase [Bacillus ubtilis]

88
4
1977
2732
gnl|PID|e137596
heat shock induced protein HtpO
81
67

[Lactobacillus leichniannii]

88
5
2723
3040
gi|535350
CodX [Bacillus subtilis]
81
65

101
4
3091
2435
gi|1109687
ProZ [Bacillus subtilis]
81
60

101
7
5884
4661
gi|1109684
ProV [Bacillus subtilis]
81
64

101
9
7501
7965
gi|1001768
queuosine biosynthesis protein QueA
81
47

[Synechocystis sp.]

116
5
2766
3395
gi|1146234
dihydrodipicolinate reductase [Bacillus
81
66

subtilis]

121
5
4811
5074
gi|153765
DNA polymerase I [Streptococcus
81
64

pneumoniae
]

121
7
5203
7488
gi|153765
DNA polymerase I [Streptococcus
81
70

pneumoniae
]

127
5
5103
3826
gi|290561
o188 [Escherichia coli]
81
48

147
1
299
1279
gi|467462
cysteine synthetase A [Bacillus subtilis]
81
65

147
2
1370
1861
gnl|PID|e281583
hypothetical 16.4 kd protein [Bacillus
81
63

subtilis]

154
1
168
638
gi|149533
coniugated bile acid hydrolase
81
66

[Lactobacillus plantarum]

154
2
1074
1277
gnl|PID|e242898
aBIR [Lactococcus lactis]
81
59

158
14
13790
12324
gi|558559
pyrimidine nucleoside phosphorylase
81
71

[Bacillus subtilis]

164
5
2469
3035
gi|727436
putative 20-kDa protein [Lactococcus
81
61

lactis
]

223
8
5293
6153
gn1|PID|e254976
hypothetical protein [Bacillus subtilis]
81
66

238
1
185
937
gi|622991
mannitol transport protein [Bacillus
81
68

stearotherinophilus
]sp|P50852 PTMB_BACST

PTS SYSTEM, MANNITOL-SPECIFIC IIBC

COMPONENT EIIBC-MTL) (MANNITOL-PERMEASE

IIBC COMPONENT) (PHOSPHOTRANSFERASE NZYME

II, BC COMPONENT) (EC 2.7.1.69) (EII-MTL).

276
7
3109
2819
pir|A41207|A41207
collagen 13, nonfibrillar - freshwater
81
77

sponge (Ephvdatia muelleri) (fragrnent)

307
2
1983
3617
gi|153742
dextran glucosidase [Streptococcus mutans]
81
69

322
2
122
286
gi|296147
Asd protein [Bacillus subtilis]
81
63

326
6
5352
4513
gi|40041
pyruvate dehydrogenase (lipoamide)
81
69

[Bacillus stearothermophilus]

ir|S10798 DEBSPF pyruvate dehydrogenase

(lipoamide) (EC 1.2.4.1) pha chain -

Bacillus stearothermophilus

329
3
1774
1448
gi|1117994
surface antigen A variant precursor
81
72

[Streptococcus pneumoniae]

346
3
1056
1199
gi|536970
ORF_fS43 [Escherichia coli]
81
43

362
4
1131
2213
gi|1001826
cadmium-transporting ATPase [Synechocystis
81
64

sp.
]

391
3
1345
575
gi|1184967
ScrR [Streptococcus mutans]
81
66

441
3
1873
3447
gi|1742675
Phosphotransferase system enzyme II (EC
81
64

2.7.1.69) MalX [Escherichia coli]

556
2
1062
493
gi|1553037
RecN [Bacillus subtilis]
81
66

710
2
361
816
gi|1303840
YgfS [Bacillus subtilis]
81
68

804
1
403
2
gi|149533
conjugated bile acid hydrolase
81
68

[Lactobacillus_plantarum]

5
7
3311
4255
gi|407881
stringent response-like protein
80
62

[Streptococcus equisimilis]

pir|S39975|S39975 stringent response-like

protein - Streptococcus quisimilis

17
10
8283
8438
gi|1326394
B0218.7 gene product [Caenorhabditis
80
53

elegans
]

17
15
12258
12776
gi|532551
ORF18 [Enterococcus faecalis]
80
63

22
1
3
2180
gi|44027
Tma protein [Lactococcus lactis]
80
70

37
6
3707
5140
pir|B47154|B47154
signal recognition particle 54K chain
80
64

homolog Ffh - Bacillus subtilis

42
1
2
259
gi|1066157
chaperonin-10 [Thermus aquaticus
80
66

thermophilus]

49
16
11106
11309
gi|1136430
similar to hypothetical protein YM49959.11C
80
53

of S.cerevisiae. [Homo sapiens]

60
4
4465
3407
gi|143371
phosphoribosyl aminoimidazole synthetase
80
62

(PUR-M) [Bacillus subtilis]

pir|H29326|AJBSCL

phosphoribosylformyiglycinamidine cyclo-

ligase EC 6.3.3.1) Bacillus subtilis

60
9
9023
8745
pir|E29326|E29326
hypothetical protein (pur operon) -
80
50

Bacillus subtilis

66
1
1
783
gi|520753
DNA topoisornerase I [Bacillus subtilis]
80
66

80
3
2519
1821
gnl|PID|e236074
beta-phosphoglucomutase [Lactococcus
80
62

lactis
]

83
9
6268
5378
gi|1070079
R08B4.1 [Caenorhabditis elegans]
80
72

89
18
19093
18845
gi|39451
type III restriction endonuclease
80
72

[Bacillus cereus] ir|S15518|JC1116 type

III site-specific deoxyribonuclease (EC

1.21.5) - Bacillus cereus (fragment)

97
1
366
4
gi|148506
dnaJ [Erysipelothrix rhusiopathiae]
80
70

107
2
1094
591
sp|P37214|ERA_STRM
GTP-BINDING PROTEIN ERA HOMOLOG.
80
64

U

114
3
1474
5076
gi|43863
pyruvate-flavodoxin oxidoreductase
80
62

[Kiebsiella pneumoniae] ir|S01997|QQKBFP

pyruvate (flavodoxin) dehydrogenase (EC

1.2.99.-) Klebsiella pneumoniae

117
3
1456
2367
gi|40031
spoOJ93 gene product [Bacillus subtilis]
80
56

126
3
1857
709
gi|551854
ORF2 [Erwinia herbicola]
80
68

128
28
23265
22447
gi|437916
isoleucyl-tRNA synthetase [Staphylococcus
80
63

aureus
]

133
10
9128
9856
gi|520844
orf4 [Bacillus subtilis]
80
63

158
4
3926
2703
gi|944943
phosphopentomutase [Bacillus subtilis]
80
64

172
5
3732
3920
sp|P20182|YT14_STR
HYPOTHETICAL 29.1 KD PROTEIN IN TRANSPOSON 80 63

FR
TN4556.

180
16
15548
16393
gi|1773200
hypothotical protein [Escherichia coli]
80
66

181
10
8597
7407
gi|143806
AroF [Bacillus subtilis]
80
64

194
4
1580
1957
gi|47394
5-oxoprolyl-peptidase [Streptococcus
80
66

pyogenes
]

213
5
3515
4078
gnl|PID|e199384
pyrR gene product [Lactobacillus
80
65

plantarum
]

217
11
7724
8395
gi|1561567
Unknown [Bacillus subtilis]
80
65

218
6
4843
5331
gi|1574120
branched-chain-amino-acid transaminase
80
64

[Haemophilus influenzae]

225
8
6092
5829
gi|530459
similar to phosphotransferase EII
80
52

[Mycoplasma capricolum]

229
2
1170
178
gi|1502419
P1sX [Bacillus subtilis]
80
59

243
3
2545
2150
gi|1732315
transport system permease homolog
80
64

[Listeria monocytogenes]

275
2
694
939
gi|1256629
cold-shock protein [Bacillus subtilis]
80
65

307
3
3607
3888
gi|1321625
exo-alpha-1, 4-glucosidase [Bacillus
80
73

stearothermophilus

322
3
284
1090
gi|142828
aspartate semialdehyde dehydrogenase
80
62

[Bacillus subtilis] sp|Q04797|DHAS_BACSU

ASPARTATE- SEMIALDEHYDE DEHYDROGENASE (EC

.2.1.11)
(ASA DEHYDROGENASE).

349
1
2
616
gi|495089
recombinase [Staphylococcus aureus]
80
65

367
7
3511
2924
gi|44074
adenylate kinase [Lactococcus lactis]
80
64

386
7
4305
5306
gi|149396
lacD [Lactococcus lactis]
80
64

394
3
2642
3757
pir|B39096|B39096
alkaline phosphatase (EC 3.1.3.1) III
80
64

precursor - Bacillus subtilis

399
17
12070
13488
gi|1591862
oxaloacetate decarboxylase, alpha subunit
80
61

[Methanococcus jannaschii]

399
24
22979
24907
gi|40026
homologous to E.coli gidA [Bacillus
80
67

subtilis]

435
3
2217
2032
gi|559863
clyA [Plasmid pAD1]
80
78

466
1
3
1208
gi|467330
replicativo DNA helicaso [Bacillus
80
61

subtilis
]

475
4
3402
2947
gi|532547
ORF14 [Enterococcus faecalis]
80
68

491
4
3844
4392
gi|473892
large-conductance mechanosensitive channel
80
56

[Escherichia coli] gi|473420 yhdC

[Escherichia coli]

605
2
1252
338
gi|580875
ipa-57d gene product [Bacillus subtilis]
80
69

615
1
760
14
gi|467469
unknown [Bacillus subtilis]
80
66

668
1
117
587
pir|S16974|R5BS7F
ribosomal protein L9 - Bacillus
80
71

stearothermophilus

684
2
694
464
gi|786314
Highly similar to Glycogen debranching
80
33

enzyme 4-alpha-glucanotransferase, Swiss

Prot. accession number P35573)

Saccharomyces cerevisiae
]

767
1
1
480
gi|41828
istB gene product [Escherichia coli]
80
52

818
1
1
357
gi|743856
intrageneric coaggregation-relevant
80
66

adhesin [Streptococcus gordonii]

833
1
325
95
gi|1561567
Unknown [Bacillus subtilis]
80
68

934
1
394
56
gi|1001706
ABC transporter subunit [Synechocystis
80
63

sp.]

948
1
465
4
gi|1773196
similar to B. stearothermophilus N-
80
59

carbamyl-L-amino acid amidohydrolase

[Escherichia coli]

949
1
61
411
gi|1330380
Similar to cystathionine gamma-lyase
80
61

[Caenorhabditis elegans]

20
2
468
1262
gi|1256698
chitinase [Serratia marcescens]
79
67

22
3
2420
3238
gi|467460
unknown [Bacillus subtilis]
79
59

24
1
39
1109
gi|1303821
YgfE [Bacillus subtilis]
79
61

26
1
214
873
gi|403984
deoxyguanosine kinase/deoxyadenosine
79
68

kinase(I) subunit Lactobacillus

acidophilus
]

47
8
10268
8106
gi|153657
mismatch repair protein [Streptococcus
79
63

pneumoniae
] pir|A33589|A33589 mismatch

repair protein hexB - Streptococcus

neumoniae

48
9
9905
9198
gi|290566
f213 [Escherichia coli]
79
53

58
4
4677
3694
gi|1653179
hydrogenase subunit [Synechocystis sp.]
79
52

63
6
3605
5443
gi|1064813
homologous to sp:PHOR_BACSU [Bacillus
79
55

subtilis
]

88
8
5493
4771
gnl|PID|e208252
unidentified [Streptococcus pneumoniae]
79
57

146
8
6649
5609
gi|153676
tagatose 1,6-aldolase [Streptococcus
79
63

mutans
]

149
4
2554
1976
gi|1216490
DNA/pantothenate metabolism flavoprotein
79
64

[Streptococcus mutans]

158
2
1859
1143
gi|1276873
DeoD [Streptococcus thermophilus]
79
67

179
19
19022
18417
gi|467372
3′-exo-deoxyribonuclease [Bacillus
79
61

subtilis
]

222
2
982
230
gi|142988
membrane transport protein [Bacillus
79
59

stearothemophilus] pir|A42478|A42478

glutamine transport protein glnQ -

Bacillus tearothermophilus

228
6
4060
3401
gi|413950
ipa-26d gene product [Bacillus subtilis]
79
55

229
3
3270
1219
gnl|PID|e186699
MmsA [Streptococcus pneumoniae]
79
62

238
7
5750
5100
gi|596046
L8003.16 gene product [Saccharomyces
79
55

cerevisiae
]

269
10
6664
5489
gi|1303788
YgeH [Bacillus subtilis]
79
63

274
1
1
1143
gi|153062
helicase [Staphylococcus aureus]
79
65

290
9
7364
8779
gi|466882
pps1; B1496_c2_189 [Mycobacterium leprae]
79
64

292
22
18122
17595
gi|1303951
YgiZ [Bacillus subtilis]
79
61

316
3
864
2003
gi|1146207
putative [Bacillus subtilis]
79
58

326
2
1772
360
gi|40044
dihydrolipoamide dehydrogenase [Bacillus
79
65

stearothermophilus] ir|S13839|813839

dihydrolipoamide dehydrogenase (EC

1.8.1.4) - cillus stearothermophilus

363
5
5738
7180
gi|1657519
hypothetical protein [Eseherichia coli]
79
63

367
11
5668
5447
gi|216337
ORE for L30 ribosmnal protein [Bacillus
79
63

subtilis
]

375
5
4346
3393
gi|1644203
unknown [Bacillus subtilis]
79
62

406
2
666
1481
gi|49316
ORF2 gene product [Bacillus subtilis]
79
58

460
7
4973
5860
gi|1276664
acetyl-CoA carboxylase carboxytransferase
79
62

beta subunit [Porphyra purpurea]

486
1
380
3
gi|1256618
transport protein [Bacillus subtilis]
79
63

488
3
987
1997
gi|532547
ORE14 [Enterococcus faecalis]
79
69

500
2
1358
681
gi|535662
transposase [Insertion sequence IS1251]
79
75

523
3
1803
820
gi|142981
ORF5; This ORF includes a region (aa23-
79
62

103) containing a potential ron-sulphur

centre homologous to a region of

Rhodospirillum rubrum
nd Chromatium

vinosum; putative [Bacillus

stearothermophilus] pir|PQ0299|PQ0299

hypothetical protein 5 (gidA 3′ region) -

552
2
2401
902
gi|887851
ORF_o479 [Escherichia coli]
79
63

587
2
622
434
gi|1303840
YgfS [Bacillus subtilis]
79
66

612
1
1
378
gi|1064791
function unknown [Bacillus subtilis]
79
56

654
1
2
286
pir|A47079|A47079
heat shock protein DnaJ - Lactococcus
79
75

lactis

701
2
325
534
gi|143793
tyrosyl-tRNA synthetase [Bacillus
79
63

caldotenax
]

708
2
369
566
gi|488430
alcohol dehydrogenase 2 [Entamoeba
79 66

histolytica
]

840
1
140
1078
gi|1573250
aspartate aminotransferase (aspC)
79
65

[Haemophilus influenzae]

5
9
5555
6049
gi|407880
ORF1 [Streptococcus equisimilis]
78
58

33
4
3755
4597
gi|1742846
NH(3)-dependent NAD(+) synthetase (EC
78
64

6.3.5.1) (Nitrogen-regulatory protein)

[Escherichia coli]

60
7
8100
5854
gi|143369
phosphoribosylformyl glycinamidine
78
62

synthetase II (PUR-Q) [Bacillus ubtilis]

65
4
3407
2625
gi|1661179
high affinity branched chain amino acid
78
67

transport protein [Streptococcus mutans]

76
7
5760
4747
gi|1161061
dioxygenase [Methylobacterium extorguens]
78
62

81
11
7141
6824
gi|1072380
ORF3 [Lactococcus lactis]
78
67

83
5
2559
2843
gi|1256896
L9606.1 gene product [Saccharomyces
78
52

cerevisiae
]

85
4
4298
3288
gi|142612
branched chain alpha-keto acid
78
61

dehydrogenase El-beta [Bacillus ubtilis]

85
8
6723
6307
gi|1303941
YqiV [Bacillus subtilis]
78
62

88
10
6477
6689
gi|222585
nucleocapsid protein [Sialodacryoadenitis
78
57

virus
]

93
5
1838
2641
gi|405133
putative [Bacillus subtilis]
78
51

117
1
3
707
gi|40027
homologous to E.coli gidB [Bacillus
78
64

subtilis
]

117
11
9624
8338
gi|467403
seryl-tRNA synthetase [Bacillus subtilis]
78
63

132
2
2323
2024
gi|683484
fusion protein [Mumps virus]
78
63

133
3
2241
3413
gi|405622
unknown [Bacillus subtilis]
78
63

150
2
568
1425
gnl|PID|e185373
ceuD gene product [Campylobacter coil]
78
52

155
2
604
1182
gi|285628
transcription antitermination factor NusG
78
61

[Bacillus subtilis] pir|S39859|539859

transcription antitermination factor NusG

- acillus subtilis

156
2
308
2629
gi|1573874
ATP-dependent protease binding subunit
78
59

(clpB) [Haemophilus influenzae]

158
3
2719
1868
gi|1638804
purine nucleoside phosphorylase [Bacillus
78
64

stearothermophilus
]

160
5
2058
3050
gi|1161061
dioxygenase [Methylobacterium extorguens]
78
60

161
3
1466
3295
gnl|PID|e280490
unknown [Streptococcus pneumoniae]
78
62

169
1
2
2206
gi|1072361
pyruvate-formate-lyase [Clostridium
78
61

pasteurianum
]

171
2
2833
3897
sp|P28367|
PROBABLE PEPTIDE CHAIN RELEASE FACTOR 2
78
64

RF2_BACS
(RF-2) (FRAGMENT).

U

180
15
14851
15567
gi|1773199
hypothetical proteinh [Escherichia coli]
78
67

185
1
1142
3
pir|C33496|C33496
hisC homolog - Bacillus subtilis
78
59

188
3
1863
4178
gnl|PID|e256969
nifJ gene product [Enterobacter
78
62

agglomerans
]

216
7
5136
5600
gnl|PID|e276830
UDP-N-acetylglucosamine 1-
78
60

carboxyvinyltransferase [Bacillus

subtilis
]

216
8
5531
6508
gnl|PID|e276830
UDP-N-acetylglucosamine 1-
78
63

carboxyvinyltransferase [Bacillus

subtilis
]

238
26
24515
25387
gi|396681
rhamnulose-1-phosphate aldolase
78
56

[Escherichia coli]

256
6
4189
6237
gi|467427
methionyl-tRNA synthetase [Bacillus
78
67

subtills
]

292
4
2063
2353
gi|1742823
Proton/sodium-glutamate symport protein
78
62

(Glutamate-aspartate carrier protein)

[Escherichia coli]

305
1
268
1872
gi|143582
spoIIIEA protein [Bacillus subtilis]
78
58

337
2
2332
1448
gi|308861
GTG start codon [Lactococcus lactis]
78
63

338
2
606
1466
gi|1773142
similar to the 20.2kd protein in TETB-EXOA
78
66

region of B. subtilis [Escherichia coli]

362
1
109
429
gi|150719
cadmium resistance protein [Plasmid pI258]
78
51

379
3
2878
1922
gi|887824
ORF_o310 [Escherichia coli]
78
60

446
2
962
1636
gi|537235
Kenn Rudd identifies as gpmB [Escherichia
78
43

coli
]

495
5
3038
3502
gi|634107
kdpB [Escherichia coli]
78
58

502
3
3077
1470
gi|1652592
peptide-chain-release factor 3
78
58

[Synechocystis sp.]

523
1
2
616
gi|289288
lexA [Bacillus subtilis]
78
59

571
1
99
365
gnl|PID|e249644
YneP [Bacillus subtilis]
78
65

573
3
1258
1971
gi|1731683
component II of heptaprenyl diphosphate
78
50

synthase [Bacillus stearothermophilus]

575
2
434
168
gi|58831
The experimental evidence that this
78
47

sequence codes for a complete gag otein is

that transfection of the viral genome

results in oduction of infectious virus

[Cas-Br-E murine leukemia virus]

p|P27460|GAG_MLVCB GAG POLYPROTEIN

(CONTAINS: CORE PROTEIN P15; N

607
1
148
708
gi|530410
Ala-tRNA synthetase [Mycoplasma
78
63

capricolum
]

655
2
300
899
gi|147404
mannose permease subunit II-M-Man
78
60

[Escherichia coli]

704
1
181
2
gi|467430
unknown [Bacillus subtilis]
78
63

708
1
1
378
gi|443985
alcohol dehydrogenase [Entamoeba
78
61

histolytica
]

732
1
661
2
gi|1064791
function umknown [Bacillus subtilis]
78
55

785
1
2
679
gi|556014
DP-N-acetyl muramate-alanine ligase
78
59

[Bacillus subtilis]

786
1
2
172
gi|536992
SugES [Escherichia coli]
78
60

820
2
1602
1144
gi|153749
UDPglucose 4-epimerase [Streptococcus
78
60

thermophilus
] pir|A44509|A44509 UDPglucose

4-epimerase (EC 5.1.3.2) - treptococcus

thermophilus

887
1
337
2
gi|495046
tripeptidase [Lactococcus lactis]
78
70

970
2
395
234
gi|1652190
Fat protein [Synechocystis sp.]
78
51

4
7
6069
5656
gi|1573482
high affinity ribose transport protein
77
51

(rbsD) [Haemophilus influenzae]

45
16
12065
14047
gi|666069
orf2 gene product [Lactobacillus
77
51

leichmannii
]

49
13
8199
9992
gnl|PID|e228615
homologous to yqcC of the skin element
77
59

[Bacillus subtilis]

60
2
2895
1300
gi|143373
phosphoribosyl aminoimidazole carboxy
77
63

formyl ormyltransferase/inosine

monophosphate cyclohydrolase (PUR-H(J))

Bacillus subtilis
]

70
6
5118
3874
gi|912464
No definition line found [Escherichia
77
53

coli
]

70
7
5172
5756
gi|288413
glutamate dehydrogenase (NADP+)
77
65

[Corynebacterium glutamicum]

pir|S32227|S32227 glutamate dehydrogenase

(NADP+) (EC 1.4.1.4) - orynebacterium

glutamicum

74
10
7303
5864
gi|289284
cysteinyl-tRNA synthetase [Bacillus
77
62

subtilis
]

74
12
9559
8078
gi|289282
glutamyl-tRNA synthetase [Bacillus
77
57

subtilis
]

88
6
3013
3843
gi|535351
CodY [Bacillus subtilis]
77
57

89
6
5749
2510
gi|1695686
pyruvate carboxylase [Bacillus
77
62

stearothemophilus
]

91
1
396
728
gi|1184044
L-glutamine:D-fructose-6-P
77
66

amidotransferase precursor [Thermus

aguaticus thermophilus
]

98
4
3992
5710
gi|984804
transmembrane protein [Bacillus subtilis]
77
56

124
1
2
940
gnl|PID|e199002
prolidase PepQ [Lactobacillus deibrueckii]
77
60

158
5
4845
4171
gi|435297
unknown [Lactococcus lactis]
77
48

162
6
7426
5882
gi|142992
glycerol kinase (glpK) (BC 2.7.1.30)
77
60

[Bacillus subtilis] pir|B45868|B45868

glycerol kinase (EC 2.7.1.30) - Bacillus

subtilis sp|P18157|GLPK_BACSU GLYCEROL

KINASE (EC 2.7.1.30) (ATP:GLYCEROL -

PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK).

164
1
179
1102
gi|882532
ORF_o294 [Escherichia coli]
77
57

164
22
24158
23646
gi|1573564
hypothetical [Haemophilus influenzae]
77
36

171
6
6656
7639
gi|1303855
YggH [Bacillus subtilis]
77
59

171
9
9198
9683
gi|1591672
phosphate transport system ATP-binding
77
57

protein [Methanococcus jannaschii]

202
4
2967
3422
gi|147782
ruvA protein (gtg start) [Escherichia
77
50

coli
]

202
6
3662
4693
gi|147783
ruvB protein [Escherichia coli]
77
58

213
1
3
1046
gi|1103865
formyl-tetrahydrofolate synthetase
77
63

[Streptococcus mutans]

217
10
6870
7742
gi|414014
ipa-90d gene product [Bacillus subtilis]
77
50

223
5
4171
4902
gnl|PID|e254974
autolysin response regulator [Bacillus
77
55

subtilis
]

223
7
5024
5473
gnl|PID|e254975
hypothetical protein [Bacillus subtilis]
77
58

228
10
7747
6035
gi|467409
DNA polymerase III subunit [Bacillus
77
61

subtilis
]

229
15
16711
14261
gnl|PID|e290286
priA [Bacillus subtilis]
77
62

232
3
1742
1437
gi|142708
comG3 gene product [Bacillus subtilis]
77
50

238
25
23174
24511
pir|B48649|B48649
L-rhamnose isomerase (EC 5.3.1.14)
77
59

Escherichia coli

238
32
29472
28708
gi|451072
di-tripeptide transporter [Lactococcus
77
56

lactis
]

244
4
3591
2809
gi|1773173
similar to M. jannaschii MJ0938
77
60

[Escherichia coli]

269
5
3890
3522
gi|1303793
YgeL [Bacillus subtilis]
77
55

276
6
2840
2328
pir|PC1127|PC1127
hypothetical 110 protein (lytA 5′ region)
77
50

- Lactococcus lactis phage US3 (fragment)

291
1
119
916
gi|556014
UDP-N-acetyl muramate-alanine ligase
77
63

[Bacillus subtilis]

304
2
941
2020
gnl|PID|e285001
CTORF239 [Staphylococcus aureus]
77
62

305
4
3618
4394
gi|709993
hypothetical protein [Bacillus subtilis]
77
54

327
8
5697
6005
gi|153570
H+ ATPase [Enterococcus faecalis]
77
61

341
4
1206
1937
gi|1303951
YqiZ [Bacillus subtilis]
77
62

360
1
429
4
gi|897754
nonstructural protein NSP3 [Human
77
38

rotavirus
]

362
3
541
1239
gi|1001826
cadmium-transporting ATPase [Synechocystis
77
60

sp
.]

363
9
13917
12652
gi|1574390
C4-dicarboxylate transport protein
77
55

[Haemophilus influenzae]

367
14
7218
6679
pir|A02766|RSBS0F
ribosomal protein L6 - Bacillus
77
63

stearothermophilus

386
8
5456
5776
gnl|PID|e281578
hypothetical 12.2 kd protein [Bacillus
77
61

subtilis
]

394
4
3706
4167
pir|B39096|B39096
alkaline phosphatase (EC 3.1.3.1) III
77
55

precursor - Bacillus subtilis

402
1
710
3
gi|533105
unknown [Bacillus subtilis]
77
59

408
2
1357
584
gi|666983
putative ATP binding subunit [Bacillus
77
58

subtilis
]

460
6
3562
4938
gi|1055246
biotin carboxylase [Bacillus subtilis]
77
60

466
7
8657
9253
gi|147402
mannose permease subunit III-Man
77
61

[Escherichia coli]

475
5
3794
3234
gi|532547
ORF14 [Enterococcus faecalis]
77
68

498
1
1
603
gi|410137
ORFX13 [Bacillus subtilis]
77
58

515
1
107
574
gi|1303815
YgeY [Bacillus subtilis]
77
60

518
6
2980
4518
gi|1402515
membrane-spanning transporter protein
77
56

[Clostridium perfringens]

523
5
2527
2333
gi|149601
thymidylate synthase (EC 2.1.1.45)
77
66

[Lactobacillus casei]

526
2
1782
436
gi|1750124
xylose isomerase [Bacillus subtilis
77
62

552
7
6809
6135
gi|534045
antiterminator [Bacillus subtilis]
77
51

607
3
778
936
gi|1015321
alanyl-tRNA synthetase [Homo sapiens]
77
51

624
3
2289
2555
gnl|PID|e187971
orf121 gene product [Lactococcus lactis]
77
57

781
1
15
485
gi|580883
ipa-88d gene product [Bacillus subtilis]
77
65

850
2
895
572
gi|142520
thioredoxin [Bacillus subtilis]
77
59

853
1
186
4
gi|39962
ribosomal protein L35 (AA 1-66) [Bacillus
77
66

stearothermophilus
] ir|S05347|R5BS35

ribosomal protein L35 - Bacillus

earothermophilus

944
1
2
172
gi|425467
transposase [Lactobacillus helveticus]
77
50

10
1
1
258
gnl|PID|e234078
hom [Lactococcus lactis]
76
63

12
4
7650
5842
gnl|PID|e254877
unknown [Mycobacterium tuberculosis]
76
57

17
29
29022
28153
gi|1500003
mutator mutT protein [Methanococcus
76
47

jannaschii]

23
15
8897
10285
gi|153960
ethanolamine ammonia-lyase (eutB)
76
64

[Salmonella typhimurium] pir|A36570|A36570

ethanolamine ammonia-lyase (EC 4.3.1.7)

55K chain Salmonella typhimurium

29
2
1024
500
gi|40011
ORF17 (AA 1-161) [Bacillus subtilis]
76
61

33
1
14
1552
gi|148304
beta-1,4-N-acetylmuramoylhydrolase
76
60

[Enterococcus hirae] pir|A42296|A42296

lysozyme 2 (EC 3.2.1.-) precursor -

Enterococcus irae
(ATCC 9790)

34
7
7432
6965
gi|44067
ORF1 C-terminal [Lactococcus lactis]
76
59

45
8
3708
4166
gi|1303698
BltD [Bacillus subtilis]
76
56

47
9
12849
10270
gi|1002520
MutS [Bacillus subtilis]
76
59

55
8
3614
4105
gi|1303915
YghZ [Bacillus subtilis]
76
53

55
11
6385
6642
gi|216583
ORF1 [Escherichia coli]
76
45

57
14
17283
16597
gi|1183887
integral membrane protein [Bacillus
76
56

subtilis
]

59
6
3112
2426
gi|392872
repressor protein [Pasteurella multocida]
76
47

64
1
1242
46
gi|483941
blt gene product [Bacillus subtilis]
76
55

67
3
1370
2146
gnl|PID|e199390
orotate phosphoribosyltransferase
76
57

[Lactobacillus plantarum]

69
2
837
334
gi|1377831
unknown [Bacillus subtilis]
76
57

70
1
164
1588
gi|895751
putative 6-phospho-beta-glucosidase
76
60

[Bacillus subtilis] pir|S57762|S57762

probable 6-phospho-beta-glucosidase -

Bacillus ubtilis

74
11
7826
7269
pir|E53402|E53402
serine O-acetyltransferase (EC 2.3.1.30) -
76
54

Bacillus stearothermophilus

74
13
10073
9588
gi|289281
unknown [Bacillus subtilis]
76
60

85
11
7809
7102
gi|457634
butyrate kinase [Clostridium
76
61

acetobutylicum]

94
8
6036
4801
gi|142538
aspartate aminotransferase [Bacillus sp.]
76
57

94
14
17174
12801
gi|40060
DNA polymerase III (AA 1-1437) [Bacillus
76
62

subtilis] p|P13267|DP3A_BACSU DNA

POLYMERASE III, ALPHA CHAIN (EC 2.7.7.7).

94
15
19140
17407
gi|1573733
prolyl-tRNA synthetase (proS) [Haemophilus
76
54

influenzae
]

95
1
1
1290
gi|472918
v-type Na-ATPase [Enterococcus hirae]
76
59

95
4
2367
3194
gi|487276
Na+ ″ATPase subunit C [Enterococcus hirae]
76
48

99
1
1
171
gi|1353874
unknown [Rhodobacter capsulatus]
76
52

100
5
5414
5064
gi|1591962

M. jannaschii
predicted coding region
76
46

MJ1322 [Methanococcus jannaschii]

100
27
23165
21198
gi|216151
DNA polymerase (gene L; ttg start codon)
76
62

[Bacteriophage SPO2] gi|579197 SPO2 DNA

polymerase (aa 1-648) [Bacteriophage SPO2]

pir|A21498|DJBPS2 DNA-directed DNA

polymerase (EC 2.7.7.7) - phage PO2

106
1
1511
264
gi|1750108
YnbA [Bacillus subtilis]
76
61

116
4
2480
2854
gi|755602
unknown [Bacillus subtilis]
76
60

116
6
3299
3625
gi|1146234
dihydrodipicolinate reductase [Bacillus
76
56

subtilis
]

122
5
3029
3619
gi|467436
unknown [Bacillus subtilis]
76
52

123
10
9109
10389
gi|1773196
similar to B. stearothermophilus N-
76
61

carbamyl-L-amino acid amidohydrolase

[Escherichia coli]

124
5
4087
3182
gi|974332
NAD(P)H-dependent dihydroxyacetone-
76
58

phosphate reductase [Bacillus ubtilis]

130
5
3341
4294
gi|308853
transmembrane protein [Lactococcus lactis]
76
55

132
3
2265
5117
gi[1673889
(AE000022) Mycoplasma pneumoniae,
76
59

excinuclease ABC subunit A; similar to

Swiss-Prot Accession Number P07671, from

E. coli
[Mycoplasma pneumoniae]

138
34
25849 25409
gi|143795
transfer RNA-Tyr synthetase [Bacillus
76
56

subtilis
]

139
1
3
350
gnl|PID|e191395
mobilisation protein [Lactococcus lactis]
76
65

141
1
2
544
gi|662792
single-stranded DNA binding protein
76
64

[unidentified eubacterium]

155
9
7612
7058
gnl|PID|e247026
orf6 [Lactobacillus sake]
76
57

164
4
1889
2416
gi|727436
putative 20-kDa protein [Lactococcus
76
55

lactis
]

181
5
3475
2288
gi|1147744
PSR [Enterococcus hirae]
76
53

181
8
6281
4986
gi|683583
5-enolpyruvylshikimate-3-phosphate
76
62

synthase [Lactococcus lactis]

pir|S52580|S52580 3-phosphoshikirnate 1-

carboxyvinyltransferase (EC .5.1.19) -

Lactococcus lactis

197
7
7662
8102
gi|1783253
homologous to many ATP-binding transport
76
58

proteins; hypothetical [Bacillus subtilis]

222
16
10780
11298
gi|1591856
hypothetical protein (SP:P15889)
76
64

[Methanococcus jannaschii]

229
1
1
138
gi|148316
NaH-antiporter protein [Enterococcus
76
47

hirae
]

233
6
3946
3341
gi|1591652
hypothetical protein (SP:P31065)
76
60

[Methanococcus jannaschii]

238
2
844
1848
gi|622991
mannitol transport protein [Bacillus
76
64

stearothermophilus
] sp|P508521|PTMB_BACST

PTS SYSTEM, MANNITOL-SPECIFIC IIBC

COMPONENT EIIBC-MTL) (MANNITOL- PERMEASE

IIBC COMPONENT) (PHOSPHOTRANSFERASE NZYME

II, BC COMPONENT) (EC 2.7.1.69) (EII-MTL).

238
9
7235
7957
gi|1592142
ABC transporter, probable ATP-binding
76
49

subunit [Methanococcus jannaschii]

249
2
543
1235
gi|143156
membrane bound protein [Bacillus subtilis]
76
45

262
3
4131
2692
gnl|PID|e281591
catalase [Bacillus subtilis]
76
65

265
1
2
400
gi|141858
replication-associated protein [Plasmid
76
52

pAD1]

271
13
8175
10844
gi|397973
Mg2+ transport ATPase [Salmonella
76
57

typhimurium
]

323
4
4128
4568
gnl|PID|e249023
T19B10.3 [Caenorhabditis elegans]
76
60

329
5
3270
2560
gi|310631
ATP binding protein [Streptococcus
76
54

gordonii
]

356
1
971
3
gi|971479
orf3 gene product [Lactobacillus
76
52

371
1
1564
944
gi|1750125
xylulose kinase [Bacillus subtilis]
76
57

375
6
5137
4238
gi|1644202
unknown [Bacillus subtilis]
76
58

382
2
508
2769
gi|442360
ClpC adenosine triphosphatase [Bacillus
76
60

subtilis
]

399
11
7811
8845
gi|1572970
acetate:SH-citrate lyase ligase (AMP)
76
54

[Haemophilus influenzae]

399
13
9126
10034
gi|1572968
citrate lyase beta chain (acyl lyase
76
57

subunit) (citE) [Haemophilus influenzae]

485
1
3
1262
gi|564018
dihydrofolate synthetase [Streptococcus
76
54

pneumoniae
]

486
2
970
344
gi|1256617
adenine phosphoribosyltransferase
76
61

[Bacillus subtilis]

536
1
220
2
gi|437389
transposase [Lactococcus lactis]
76
59

552
3
3969
2491
gi|882609
6-phospho-beta-glucosidase [Escherichia
76
63

coli

634
2
697
918
gi|1022725
unknown [Staphylococcus haemolyticus]
76
52

684
3
1191
688
gi|1256653
DNA-binding protein [Bacillus subtilis]
76
65

752
1
1111
929
gi|407907
ORF2 [Staphylococcus xylosus]
76
46

822
1
548
237
gi|144313
6.0 kd ORF [Plasmid ColE1]
76
73

923
1
2
421
gi|153843
trypsin-resistant surface T6 protein
76
57

(tee6) precursor [Streptococcus yogenes]

953
2
534
187
gi|1592339
hypothetical protein (PIR:S52522)
76
44

[Methanococcus jannaschii]

965
2
564
343
gi|1098898
CTRP [Plasmodium falciparum]
76
69

7
4
3754
4161
gi|495046
tripeptidase [Lactococcus lactis]
75
61

25
1
2
580
gi|1575577
DNA-binding response regulator [Thermotoga
75
57

maritima
]

45
7
3090
3350
gi|1673663
(AE000003) Mycoplasma pneumoniae,
75
35

E07_orf166 Protein [Mycoplasma pneumoniae]

47
6
7526
6957
gi|1673843
(AE000019) Mycoplasma pneumoniae, pilB
75
58

homolog; similar to GenBank Accession

Number E64124, from H. influenzae

[Mycoplasma pneumoniae]

51
1
15
1520
sp|P39168|ATM_ECO
MG(2+) TRANSPORT ATPASE, P-TYPE 1 (EC
75
58

LI
3.6.1.-).

54
11
3761
3579
gi|1504026
similar to C.elegans protein (Z37093)
75
56

[Homo sapiens]

55
5
1648
2562
gi|1303901
YghT [Bacillus subtilis]
75
58

56
8
5873
5358
gi|895749
putative cellobiose phosphotransferase
75
49

enzyme II″ [Bacillus ubtilis]

58
2
2707
1916
gi|1658403
formate dehydrogenase alpha subunit
75
58

[Moorella thermoacetica]

71
1
110
1429
gi|1304007
LysA [Bacillus subtilis]
75
58

74
5
3436
3074
gi|467433
unknown [Bacillus subtilis]
75
61

74
8
5491
4631
gi|467483
unknown [Bacillus subtilis]
75
60

77
1
3
992
gi|1653966
47 kD protein [Synechocystis sp.]
75
34

81
1
26
862
gi|1064809
homologous to sp:HTRA_ECOLI [Bacillus
75
55

subtilis
]

89
11
11651
9801
gi|1573881
hypothetical [Haemophilus influenzae]
75
51

96
3
2521
1643
gi|1531619
NodB [Rhizobium sp.]
75
54

98
9
11494
10199
gi|1573043
hypothetical [Haemophilus influenzae]
75
53

110
12
11326
10283
gi|1184121
auxin-induced protein [Vigna radiata]
75
51

117
13
11200
9944
gi|457635
vancomycin histidine protein kinase
75
51

[Enterococcus faecium] gi|801884 vanS

[Transposon Tn1546]

122
6
3812
5206
gi|467439
temperature sensitive cell division
75
59

[Bacillus subtilis]

128
12
8262
7921
gi|466473
cellobiose phosphotransferase enzyme II′
75
48

[Bacillus tearothermophilus]

128
38
31848
30733
gi|216300
peptidoglycan synthesis enzyme [Bacillus
75
56

subtilis
] sp|P37585 MURG_BACSU MURO

PROTEIN UPD-N-ACETYLGLUCOSAMINE--N-

ACETYLMURAMYL-

PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL

N-ACETYLGLUCOSAMINE RANSFERASE).

129
2
1916
2134
gnl|PID|e267624
Unknown, highly similar to Pseudomonas
75
47

putida 4-oxalocrotonate tautomerase

[Bacillus subtilis]

130
4
2375
3343
gi|495179
transmembrane protein [Lactococcus lactis]
75
55

133
1
3
1514
gnl|PID|e254877
unknown [Mycobacterium tuberculosis]
75
54

158
13
12326
11634
gi|809660
deoxyribose-phosphate aldolase [Bacillus
75
66

subtilis
] pir|S49455|S49455 deoxyribose-

phosphate aldolase (EC 4.1.2.4) - acillus

subtilis

162
13
14285
12543
gi|1653222
cation-transporting ATPase PacL
75
60

[Synechocystis sp.]

170
2
1280
921
sp|P07999|DHGB_BAC
GLUCOSE 1-DEHYDROGENASE B (EC 1.1.1.47). 75
62

ME

171
7
7618
8523
gi|1303856
YagI [Bacillus subtilisi
75
52

179
14
14668
15255
gi|457177
alkyl hydroperoxide reductase [Salmonella
75
55

typhimurium] sp|P19479|AHPC
_SALTY ALKYL

HYDROPEROXIDE REDUCTASE C22 PROTEIN (EC

.6.4.-). {SUB 2-187)}

181
6
4470
3604
gi|683585
prephenate dehydratase [Lactococcus
75
49

lactis
]

191
1
183
560
gnl|PID|e261991
putative orf [Bacillus subtilis]
75
57

197
3
2117
3592
gi|1783250
h omologous to cytochrome d ubiquinol
75
60

oxidase subunit I; hypothetical [Bacillus

subtilis
]

215
3
2545
2201
gn|PID|e284996
ORF136 [Staphylococcus aureus]
75
54

216
1
2
256
gi|153570
H+ ATPase [Enterococcus faecalis]
75
53

223
4
2406
4193
gi|862312
lytS gene product [Staphylococcus aureus]
75
56

227
5
3004
3567
gi|144729
butanol dehydrogenase [Clostridium
75
53

acetobutylicum
] sp|Q04944|ADHA_CLOAB NADH-

DEPENDENT BUTANOL DEHYDROGENASE A (EC

.1.1.-)
(BDH I).

228
9
6032
5700
gi|467410
unknown [Bacillus subtilis]
75
59

229
16
17081
16848
gi|207398
tropomyosin T class IVd alpha-3 [Rattus
75
42

norvegicus
]

238
8
6038
7237
gi|141927
czcB gene product [Alcaligenes eutrophus]
75
39

244
10
7795
7460
gi|467419
unknown [Bacillus subtilis]
75
56

247
1
7
1431
gi|577569
PepV [Lactobacillus delbrueckii]
75
54

250
5
3416
3201
gi|1580783
sperm receptor [Strongylocentrotus
75
50

purpuratus

256
1
2
562
gi|709991
hypothetical protein [Bacillus subtilis]
75
56

262
2
1031
2479
gi|142783
DNA photolyase [Bacillus firmus]
75
59

263
1
222
890
gi|148304
beta-1,4-N-acetylmuramoylhydrolase
75
60

[Enterococcus hirae] pir|A42296|A42296

lysozyme 2 (EC 3.2.1.-) precursor -

Enterococcus irae
(ATCC 9790)

266
5
2224
1982
gnl|PID|e253211
ORF YDLO65c [Saccharomyces cerevisiae]
75
50

269
2
1477
707
gi|1736647
ORF_ID:o347#4; similar to [SwissProt
75
61

Accession Number P44634] [Escherichia

coli
]

276
11
7415
4593
gnl|PID|e221269
tail protein [Bacteriophage CP-1]
75
54

279
17
14992
14651
gi|1389549
ORF3 [Bacillus subtilis]
75
61

292
11
7829
8470
gi|160693
sporozoite surface protein [Plasmodium
75
50

yoelii
]

295
2
489
1157
gi|533099
endonuclease III [Bacillus subtilis]
75
59

307
4
3804
4889
gi|1321625
exo-alpha-1, 4-glucosidase [Bacillus
75
60

stearothermophilus
]

322
4
1088
1996
gi|310303
mosA [Rhizobium meliloti]
75
63

331
1
1
294
gi[1016092
ribosomal protein S14 [Cyanophora
75
57

paradoxa
]

334
7
6860
7969
gi|409286
bmrU [Bacillus subtilis]
75
45

340
1
3
743
gi|288413
glutamate dehydrogenase (NADP+)
75
60

[Corynebacterium glutamicum]

pir|S32227|S32227 glutamate dehydrogenase

(NADP+) (EC 1.4.1.4) - orynebacterium

glutamicum

343
2
1497
778
gi|46602
putative transposase (AA 1 - 224)
75
54

[Staphylococcus aureus] ir|S12093|S12093

probable IS431mec protein - Staphylococcus

aureus
p|P19380|TRA2_STAAU TRANSPOSASE FOR

INSERTION SEQUENCE-LIKE ELEMENT 431MEC.

372
3
865
1629
gi|146282
gut operon repressor (gutR) [Escherichia
75
58

coli
]

372
7
6614
5307
gnl|PID|e255128
trigger factor [Bacillus subtilis]
75
62

387
3
1721
1353
gi|580902
ORF6 gene product [Bacillus subtilis]
75
53

399
30
28774
29805
gi|146278
glucitol-specific enzyme II (gutA)
75
61

[Escherichia coli] pir|A26725|WQEC2S

phosphotransferase system enzyme II (EC

.7.1.69), sorbitol-specific, factor II -

Escherichia coli sp|P05705|PTHB_ECOLI PTS

SYSTEM, GLUCITOL/SORBITOL-SPECIFIC IIBC

OMPONENT (EIIBC-GUT)

399
33
31077
32768
gi|517205
67 kDa Myosin-crossreactive streptococcal
75
59

antigen [Streptococcus yogenes]

404
6
4994
4332
gi|1303921
YqiF [Bacillus subtilis]
75
64

404
7
4984
4829
gi|1303921
YgiF [Bacillus subtilis]
75
60

419
1
320
3
gi|496283
lysin [Bacteriophage Tuc2009]
75
67

431
3
1139
759
sp|P46351|YZGD_BAC
HYPOTHETICAL 45.4 KD PROTEIN IN THIAMINASE
75
60

SU
I 5′REGION.

473
1
166
2
gnl|PID|e229299
R04D3.8[Caenorhabditis elegans]
75
35

481
1
1
351
gi|1573766
phosphoglyceromutase (gpmA) [Haemophilus
75
64

influenzae
]

492
1
440
3
gi|806487
ORF211; putative [Lactococcus lactis]
75
57

595
1
705
181
gi|147485
queA [Escherichia coli]
75
51

619
2
879
319
gi|1063246
low homology to P14 protein of Heamophilus
75
59

influenzar
and 14.2 kDa protein of

Escherichia coli
[Bacillus subtilis]

663
1
15
1544
gi|475112
enzyme IIabc [Pediococcus pentosaceus]
75
54

701
4
662
946
gi|143793
tyrosyl-tRNA synthetase [Bacillus
75
60

caldotenax
]

719
1
970
419
gi|727436
putative 20-kDa protein [Lactococcus
75
56

lactis
]

886
1
101
409
gi|143150
levR [Bacillus subtilis]
75
59

939
1
403
191
gi|425467
transposase [Lactobacillus helveticus]
75
53

984
2
66
227
gi|1652190
Fat protein [Synechocystis sp.]
75
48

17
2
2592
2924
gi|532556
ORF23 [Enterococcus faecalis]
74
53

17
25
24449
25639
gi|1458228
mutY homolog [Homo sapiens]
74
50

21
7
4729
5229
gi|726320
putative protein of unknown function
74
57

encoded by the IS200-like lement [Yersinia

pestis
]

32
9
5819
4488
gi|1498962

M. jannaschii
predicted coding region
74
41

MJ0188 [Methanococcus jannaschii]

38
1
707
3
gi|142152
sulfate permease (gtg start codon)
74
53

[Synechococcus PCC6301] pir|A30301|GRYCS7

sulfate transport protein - Synechococcus

sp.
PCC 7942)

44
1
1
927
gi|1377823
aminopeptidase [Bacillus subtilis]
74
63

60
8
8747
8070
gi|143368
phosphoribosylformyl glycinamidine
74
63

synthetase I (PUR-L; gtg start odon)

[Bacillus subtilis]

72
8
7388
7119
gnl|PID|e209004
glutaredoxin-like protein [Lactococcus
74
53

lactis
]

91
4
1031
2257
gi|726480
L-glutamine-D-fructose-6-phosphate
74
58

amidotransferase [Bacillus ubtilis]

105
7
5553
5855
gi|467418
unknown [Bacillus subtilis]
74
63

110
18
16903
15842
gi|45288
arcB (AA 11336) [Pseudomonas aeruginosa]
74
57

112
3
1112
636
gi|887824
ORF_o310 [Esoherichia coli]
74
53

123
8
6105
7619
gi|1773191
similar to Pseudomonas sp. ORF5
74
60

[Escherichia coli]

128
1
2
1315
gi|143961
pyruvate phosphate dikinase [Clostridium
74
58

symbiosum] pir|A36231|KIQAPO

pyruvate, orthophosphate dikinase (EC

2.7.9.1) - lostridium symbiosum

128
26
18866
20401
gi|1303961
YgjJ [Bacillus subtilis]
74
57

150
5
4653
5303
gi|495046
tripeptidase [Lactococcus lactis]
74
53

159
8
7500
6850
gi|581098
GlnQ (AA 1-240); gtg start [Escherichia
74
53

coli
]

179
1
1259
57
gi|537080
ribonucleoside triphosphate reductase
74
62

[Escherichia coli] pir|A47331|A47331

oxygen-sensitive ribonucleoside-

triphosphate eductase (BC 1.17.4.-)-

Escherichia coli

183
2
1669
224
gi|1146200
DNA or RNA helicase, DNA-dependent ATPase
74
53

[Bacillus subtilis]

213
4
2265
3200
gi|1373157
orf-X; hypothetical protein; Method:
74
63

conceptual translation supplied by author

[Bacillus subtilis]

229
13
13774
12806
gnl|PID|e290288
Met-tRNAi formyl transferase [Bacillus
74
55

subtilis
]

238
31
28648
28052
gi|451072
di-tripeptide transporter [Lactococcus
74
56

244
8
6409
5552
gi|467422
unknown [Bacillus subtilis]
74
60

249
1
7
411
gi|1591758
diaminopimelate epimerase [Methanococcus
74
51

jannaschii]

270
3
1832
3955
gi|1303829
YgfK [Bacillus subtilis]
74
55

276
3
1668
1357
gi|496282
holin [Bacteriophage Tuc2009]
74
54

288
9
5807
5076
gi|530063
glycerol uptake facilitator [Streptococcus
74
60

pneumoniae
] sp|P52281|GLPF_STRPN GLYCEROL

UPTAKE FACILITATOR PROTEIN.

292
21
16780
17547
gi|1573646
Mg(2+) transport ATPase protein C (mgtC)
74
42

(SP:P22037) [Haemophilus influenzae]

297
1
682
11
gnl|PID|e255093
hypothetical protein [Bacillus subtilis]
74
54

298
3
3562
3095
gi|1303970
YqjS [Bacillus subtilis]
74
46

321
10
5081
6028
pir|A32950|A32950
probable reductase protein - Leishmania
74
56

major

327
2
904
3285
gi|1573876
virulence associated protein homolog
74
53

(vacB) [Haemophilus influenzae]

334
5
3942
5432
gi|1652678
amidase [Synechocystis sp.]
74
57

341
13
13007
12069
gi|39881
ORF 311 (AA 1-311) [Bacillus subtilis]
74
53

362
7
3529
5274
gnl|PID|e255093
hypothetical protein [Bacillus subtilis]
74
58

376
3
1282
2346
gi|1773090
transfer RNA-guanine transglycosylase
74
59

[Escherichia coli]

421
2
48
1400
gi|710632
beta-glucosidase [Bacillus subtilis]
74
58

471
1
815
3
gi|854234
cymG geno product [Klebsiella oxytoca]
74
53

480
2
263
607
gi|1303994
YgkM [Bacillus subtilis]
74
48

518
7
4409
5002
gi|145821
EBG enzyme alpha subunit [Escherichia
74
47

coli
]

539
8
6607
7179
gi[1165295
D3703.8p [Saccharomyces cerevisiae]
74
57

542
1
750
4
gi[1064810
function unknown [Bacillus subtilis]
74
56

559
1
1204
5
gi|43821
nifJ protein (AA 1-1171) [Klebsiella
74
58

pneumoniae
] p|P03833|NIFJ_KLEPN PYRUVATE-

FLAVODOXIN OXIDOREDUCTASE (BC -.-.-)

579
3
1373
1624
gi[1237013
ORF2 [Bacillus subtilis]
74
46

624
4
2518
3669
gi[467394
recombination protein [Bacillus subtilis]
74
56

688
1
623
3
gi[662880
novel hemolytic factor [Bacillus cereus]
74
48

763
1
106
441
gi|153955
envM protein [Salmonella typhimurium]
74
46

811
1
3
158
gi|309662
pheromone binding protein [Plasmid pCF10]
74
57

852
1
2
601
gi|309662
pheromone binding protein [Plasmid pCF10]
74
53

935
1
976
2
gi|467403
seryl-tRNA synthetase [Bacillus subtilis]
74
59

22
2
2178
2471
gi|467460
unknown [Bacillus subtilis]
73
61

24
2
1126
3150
gi|1303822
YqfF [Bacillus subtilis]
73
54

33
6
6638
6970
gi|536971
ORF_o76 [Esoherichia coli]
73
56

48
1
621
1241
gnl|PID|e274111
aggregation promoting protein
73
67

[Lactobacillus gasseri]

48
6
5327
7225
gi|1185289
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-
73
56

carboxylate synthase [Bacillus subtilis]

50
2
1097
2008
gi|1498295
homoserine kinase homolog [Streptococcus
73
55

pneumoniae
]

52
4
2793
4334
gi|473902
alpha-acetolactate synthase [Lactococcus
73
59

lactis
]

55
1
1
261
gi|396365
alternate name yjbA [Escherichia coli]
73
36

60
6
5935
5549
gi|551881
amidophosphoribosyltransferase
73
57

[Lactobacillus casei] pir|PC1136|PC1136

purF protein - Lactobacillus casei

(fragment) sp|P35853|PUR1_LACCA

AMIDOPHOSPHORIBOSYLTRANSFEFASE (SC

2.4.2.14) GLUTAMINE

PHOSPHORIBOSYLPYROPHOSPHATE

AMIDOTRANSFERASE) (ATASE) FRAGMENT

74
2
477
1355
gnl|PID|e233567
unknown [Mycobacterium tuberculosis]
73
54

81
19
14213
13845
gi|606073
ORF_o169 [Escherichia coli]
73
52

93
7
2861
4075
gi|405134
acetate kinase [Bacillus subtilis]
73
56

100
1
1057
2
gi|1353561
ORF44 [Bacteriophage rlt]
73
52

100
41
28872
28627
gi|188492
heat shock-induced protein [Homo sapiens]
73
42

104
4
5558
5274
gi|312440
aspartate carbamoyltransferase [Bacillus
73
55

caldolyticus] pir|S34318|S34318 aspartate

carbamoyltransferase (EC 2.1.3.2) -

acillus caldolyticus

119
5
3264
3638
gi|473707
positive regulator for virulence factors
73
39

[Clostridium perfringens]

123
17
16156
15665
gi|1303703
YrkD [Bacillus subtilis]
73
37

123
18
16133
16465
gi|1303893
YghL [Bacillus subtilis]
73
43

124
3
2165
1722
gi|486661
TMnm related protein [Saccharomyces
73
45

cerevisiae
]

127
6
5778
5101
gi|290561
o188 [Escherichia coli]
73
48

128
10
6896
7201
pir|S37387|s37387
internalin A precursor - Listeria
73
53

monocytogenes

137
2
980
1954
gi|1276882
EpsI [Streptococcus thermophilus]
73
56

141
3
942
2777
gi|467336
unknown [Bacillus subtilis]
73
49

146
7
5611
4739
gi|149395
lacC [Lactococcus lactis]
73
56

154
6
3566
4621
gi|1354775
pfoS/R [Treponema pallidum]
73
46

155
8
7136
6726
gnl|PID|e247026
orf6 [Lactobacillus sake]
73
61

158
8
8693
7119
gi|1674275
(AE000056) Mycoplasma pneumonlae,
73
45

hypothetical ABC transporter (yjcW)

homolog; similar to Swiss-Prot Accession

Number P32721, from E. coli [Mycoplasma

pneumoniae]

162
4
4039
3305
gi|142997
glycerol uptake facilitator [Bacillus
73
55

subtilis
]

165
4
3962
3105
gi|882736
ORFf278 [Escherichia coli]
73
58

171
3
3952
4689
gnl|PID|e63527
FtsE [Mycobacterium tuberculosis]
73
56

171
5
5673
6596
gi|1303854
YqgG [Bacillus subtilis]
73
59

179
9
9302
10414
gnl|PID|e254984
hypothetical protein [Bacillus subtilis]
73
55

180
1
24
1151
gi|43985
nifS-like gene [Lactobacillus delbrueckii]
73
56

181
12
10036
9674
gnl|PID|e220317
chorismate mutase [Staphylococcus xylosus]
73
50

181
13
10713
10003
gi|39813
phospho-2-dehydro-3-deoxyheptonate
73
56

aldolase [Bacillus subtilis]

ir|S21418|S21418 phospho-2-dehydro-3-

deoxyheptonate aldolase (EC 1.2.15) -

Bacillus subtilis

183
3
2716
1667
gi|1146199
putative [Bacillus subtilis]
73
36

198
1
869
108
gi|142854
homologous to E. coli radC gene product
73
47

and to unidentified protein rom

Staphylococcus aureus
[Bacillus subtilis]

210
1
956
3
gnl|PID|e281310
acetyl coenzyme A acetyltransferase
73
54

(thiolase) [Thermoanaerobacterium

thermosaccharolyticum]

230
1
1
171
gi|304143
S-layer protein [Bacillus circulans]
73
46

235
1
715
2
gi|1732315
transport system permease homolog
73
49

[Listeria monocytogenes]

235
2
888
676
gi|551726
sporulation protein [Bacillus subtilis]
73
54

242
4
3290
3517
gnl|PID|e236570
orf6 gene product [Enterococcus faecalis]
73
30

242
8
5914
6492
gi|1742340
HipB protein. [Escherichia coli]
73
49

250
3
3037
2411
gi|1174238
TipB [Pseudomonas fluorescens]
73
57

254
5
1124
792
gi|580900
ORF3 gene product [Bacillus subtilis]
73
52

269
9
5507
5154
gi|1303790
YqeI [Bacillus subtilis]
73
60

269
12
7989
7345
gi|285621
undefined open reading frame [Bacillus
73
54

stearothermophilus
]

284
1
1
915
gi|455528
ORF2 [Streptococcus thermophilus
73
54

bacteriophage]

290
3
1932
2678
gnl|PID|e248883
unknown [Mycobacterium tuberculosis]
73
57

295
8
4521
4739
gi|145478
putative [Escherichia coli]
73
56

296
1
2
1846
gnl|PID|e249642
transketolase [Bacillus subtilis]
73
59

310
4
3488
3036
gi|1591900
nucleoside diphosphate kinase
73
48

[Methanococcus jannaschii]

313
1
17
778
gi|1658371
cyclic beta-1,2-glucan modification
73
60

protein [Rhizobium meliloti]

314
3
2642
2067
gi|1330343
C34D4.12 gene product [Caenorhabditis
73
56

elegans

325
1
492
4
gi|407908
EIIscr [Staphylococcus xylosus]
73
56

345
19
20549
21901
gi|443691
glutathione reductase [Streptococcus
73
59

thermophilus]

359
4
3280
2252
gi|1001478
hypothetical protein [Synechocystis sp.]
73
50

374
1
884
3
gi|435123
PacL [Synechococcus sp.]
73
58

379
6
5676
4339
gi|887822
possible frameshift at end to join to next
73
57

ORF? [Escherichia coli]

383
4
3815
3387
gi|1651732
mutator MutT protein [Synechocystis sp.]
73
52

392
4
3454
5202
gi|294587
minimal change nephritis transmembrane
73
56

glycoprotein [Rattus orvegicus]

394
5
4267
5250
gi|49011
amidinotransferase II [Streptomyces
73
42

griseus
]

395
10
4252
4608
gi|1591139

M. jannaschii
predicted coding region
73
48

MJ0435 [Methanococcus jannaschii]

397
1
885
4
gnl|PID|e249658
GriA [Bacillus subtilis]
73
56

399
15
10007
11569
gi|565619
citrate lyase alpha-subunit [Klebsiella
73
54

pneumoniae
] pir|S60776|560776 citrate

(pro-3S)-lyase (EC 4.1.3.6) alpha chain -

lebsiella pneumoniae

416
2
660
1649
gi|475114
regulatory protein [Pediococcus
73
50

pentosaceus
]

436
6
4124
3540
gi|727436
putative 20-kDa protein [Lactococcus
73
53

lactis
]

446
3
1618
4260
gi|882711
exonuclease V alpha-subunit [Escherichia
73
48

coli
]

462
1
819
43
gi|1399011
immunogenic secreted protein precursor
73
63

(Streptococcus pyogenes ]

482
5
3181
2501
gi|1072419
glcB gene product [Staphylococcus
73
55

carnosus
]

495
4
1340
3031
gi|146547
kdpA [Escherichia coli]
73
55

523
4
2354
1821
pir|A00392|RDSODF
dihydrofolate reductase (EC 1.5.1.3) -
73
54

Enterococcus faecium

543
5
3099
2893
gi|19743
nsGRP-2 [Nicotiana sylvestris]
73
53

567
1
9
740
gi|1147601
cyclophilin isoform 4 [Caenorhabditis
73
54

elegans
]

629
1
945
4
gi|1006620
ABC transporter [Synechocystis sp.]
73
46

714
2
344
556
gi|1045872
ATP-binding protein [Mycoplasma
73
61

genitalium
]

747
1
320
3
gi|437389
transposase [Lactococcus lactis]
73
56

764
1
3
515
gi|532554
ORF21 [Enterococcus faecalis]
73
50

766
1
683
3
gi|1673788
(AE000015) Mycoplasma pneumoniae,
73
52

fructose-bisphosphate aldolase; similar to

Swiss-Prot Accession Number P13243, from

B. subtilis
[Mycoplasma pneumoniae]

880
1
198
4
gi|309661
regulatory protein [Plasmid pCF10]
73
50

897
1
3
170
gi|807976
unknown [Saccharomyces cerevisiae]
73
57

5
1
223
2
gnl|PID|e255315
unknown [Mycobacterium tuberculosis]
72
56

8
5
4158
4799
gi|587088
shikimate kinase [Bacillus subtilis]
72
54

19
6
2600
2833
gi|34844
embryonic myosin heavy chain (AA 1 - 1940)
72
38

[Homo sapiens] ir|S04090|S04090 myosin

heavy chain, skeletal muscle, embryonic -

man

19
25
12872
14605
gnl|PID|e242896
orf5 [Bacteriophage A2]
72
52

21
4
2777
2598
gi|54115
skeletal muscle chloride channel [Mus
72
45

musculus domesticus
]

23
7
3702
4847
gi|144714
NADPH-dependent butanol dehydrogenase
72
48

[Clostridium acetobutylicum]

pir|JU0053|JJU0053 NADPH-dependent butanol

dehydrogenase - lostridium acetobutylicum

32
1
1073
3
gi|1303839
YqfR [Bacillus subtilis]
72
50

39
8
4137
3244
pir|A32950|A32950
probable reductase protein - Leishmania
72
55

major

43
3
969
1919
gi|290494
o287 [Escherichia coli]
72
46

45
2
911
1567
gi|1039479
ORFU [Lactococcus lactis]
72
50

55
6
2549
2896
gi|755602
unknown [Bacillus subtilis]
72
51

55
7
3178
3660
gi|1303914
YghY [Bacillus subtilis]
72
49

60
1
1302
34
gi|143374
phosphoribosyl glycinamide synthetase
72
59

(PUR-D; gtg start codon) Bacillus

subtilis
]

60
3
3422
2838
gi|143372
phosphoribosyl glycinamide
72
48

formyltransferase (PUR-N) [Bacillus

ubtilis
]

60
10
9771
9010
gi|143367
phosphoribosyl aminoidazole
72
57

succinocarboxamide synthetase (PUR-C; tg

start codon) [Bacillus subtilis]

70
5
3615
3833
sp|P43672|YCBH_ECO
HYPOTHETICAL 14.4 KD PROTEIN IN PYRD-PQIA
72
48

LI
INTERGENIC REGION.

79
2
632
841
gi|1652343
ABC transporter [Synechocystis sp.]
72
47

85
2
1843
770
gi|1354775
pfoS/R [Treponema pallidum]
72
45

87
1
2
745
gi|42029
ORF1 gene product [Escherichia coli]
72
47

88
1
124
1047
gi|535348
CodV [Bacillus subtilis]
72
50

88
7
3862
4752
gi|149413
ORF [Lactococcus lactis]
72
51

91
2
611
877
gi|726480
L-glutamine-D-fructose-6-phosphate
72
57

amidotransferase [Bacillus ubtilis]

98
16
16302
15163
gi|147326
transport protein [Escherichia coli]
72
57

101
6
4676
4023
gi|1109685
ProW [Bacillus subtilis]
72
53

104
3
5331
3982
gi|312441
dihydroorotase [Bacillus caldolyticus]
72
58

114
10
11165
12205
gi|556881
Similar to Saccharomyces cerevisiae SUA5
72
60

protein [Bacillus subtilis]

pir|S49358|S49358 ipc-29d protein -

Bacillus subtilis
sp|P39153|YWLC_BACSU

HYPOTHETICAL 37.0 KD PROTEIN IN SPOIIR-

GLYC NTERGENIC REGION.

128
19
14325
11560
gi|143150
levR [Bacillus subtilis]
72
58

130
2
382
1437
gi|308850
ATP binding protein [Lactoccus lactis]
72
55

135
4
5012
3693
gi|413940
ipa-16d gene product [Bacillus subtilis]
72
56

150
6
5114
5878
gi|495046
tripeptidase [Lactococcus lactis]

154
9
5850
5677
gi|425467
transposase [Lactobacillus helveticus]
72
52

168
4
1375
1563
gi|1652869
NADH dehydrogenase [Synechocystis sp.]
72
55

173
5
2879
4024
gnl|PID|e254877
unknown [Mycobacterium tuberculosis]
72
57

179
2
1608
2399
gi|709993
hypothetical protein [Bacillus subtilis]
72
45

179
6
7584
7844
gi|1161934
DltC [Lactobacillus casei]
72
54

180
21
19948
21105
gi|1773197
similar to M. fervidus malate
72
55

dehydrogenase [Escherichia coli]

182
1
3
413
gi|1146182
putative [Bacillus subtilis]
72
48

200
23
13106
12789
gi|1707358
polyprotein precurser [Soybean mosaic
72
34

virus]

204
6
2462
2289
gi|1200525
dihydrolipoamide acetyltransferase
72
61

[Pseudomonas aeruginosa]

204
9
6374
5187
gi|1732040
alcohol dehydrogenase [Actinobacillus
72
56

pleuropneumoniae
]

205
1
463
71
gi|42029
ORF1 gene product [Escherichia coli]
72
57

210
7
6433
5279
gi|142978
glycerol dehydrogenase [Bacillus
72
46

stearothermophilus
]
pir I JQ1474 I JQ1474

glycerol dehydrogenase (EC 1.1.1.6) -

Bacillus tearothermophilus

213
6
4086
5141
gi|431231
uracil permease [Bacillus caldolyticus]
72
51

223
1
99
833
gi|1573615
ATP-binding protein (abc) [Haemophilus
72
47

influenzae
]

227
1
26
886
gi|1070015
protein-dependent [Bacillus subtilis]
72
52

228
4
2047
2481
gi|467339
unknown [Bacillus subtilis]
72
50

238
17 14728
15582
gi|882736
ORF_f278 [Escherichia coli]
72
59

250
6
4169
4765
gi|437389
transposase [Lactococcus lactis]
72
56

258
7
5296
7089
gi|192185
acid beta-galactosidase [Mus musculus]
72
53

266
3
2024
1773
gi|145149
ORFd [Escherichia coli]
72
50

269
8
5142
4477
gi|1303791
YgeJ [Bacillus subtilis]
72
45

276
13
9843
8152
gnl|PID|e59644
predicted 86.4kd protein; 52Kd observed
72
48

[Mycobacteriophage 15]

278
2
965
1573
gi|425467
transposase [Lactobacillus helveticus]
72
52

279
2
1305
340
gnl|PID|e198981
ttg start [Campylobacter coli]
72
47

283
4
1668
2045
gi|1353563
ORF46 [Bacteriophage rlt]
72
48

286
2
789
2606
gi|1651216
Pz-peptidase [Bacillus licheniformis]
72
52

290
4
2676
3239
gi|1653645
ribosome releasing factor [Synechocystis
72
56

sp.
]

301
2
1762
899
gi|606013
CG Site No. 829 [Escherichia coli]
72
57

362
2
377
688
gi|1001826
cadmium-transporting ATPase [Synechocystis
72
53

sp
.]

369
1
582
142
gi|153745
mannitol-specific enzyme III
72
47

[Streptococcus mutans]pir|B44798|844798

mannitol-specific factor III, MtlF -

treptococcus mutans

379
2
1934
1527
gi|1055071
C23G10.2 gene product [Caenorhabditis
72
51

elegans
]

384
2
694
1098
gi|1208474
hypothetical protein [Synechocystis sp.]
72
49

388
1
291
4
gi|1673836
(AE000018) Mycoplasma pneumoniae,
72
43

osmotically inducible protein; similar to

Swiss-Prot Accession Number P23929, from

E. coli
[Mycoplasma pneumoniae]

401
6
3995
5137
gi|508242
ORF 6, putative Galf synthesis pathway
72
62

protein [Escherichia coli] gi|510253 orf6

[Escherichia coli]

404
2
2119
776
gi|466474
cellobiose phosphotransferase enzyme II′
72
48

[Bacillus tearothermophilus]

416
4
3461
1980
gi|710632
beta-glucosidase [Bacillus subtilis]
72
55

416
7
6285
5551
gnl|PID|e269549
Unknown [Bacillus subtilis]
72
52

419
3
759
505
gi|928830
ORF75; putative [Lactococcus lactis phage
72
47

BK5-T]

441
4
3420
4676
gi|1732195
beta-cystathionase [Vibrio furnissii]
72
54

460
3
1385
2641
gi|1652389
beta ketoacyl-acyl carrier protein
72
55

synthase [Synechocystis sp.]

460
5
3129
3560
gnl|PID|e289141
similar to hydroxymyristoyl-(acyl carrier
72
54

protein) dehydratase [Bacillus subtilis]

460
8
5817
6023
gi|285621
undefined open reading frame [Bacillus
72
57

stearothermophilus
]

462
2
1591
785
gi|148304
beta-1,4-N-acetylmuramoylhydrolase
72
51

[Enterococcus hirae] pir|A42296|A42296

lysozyme 2 (EC 3.2.1.-) precursor -

Enterococcus irae (ATCC 9790)

467
1
2
706
gi|148711
6-aminohexanoate-cyclic-dimer hydrolase
72
50

[Flavobacterium sp.] gi|488343 6-

aminohexanoate-cyclic-dimer hydrolase

[Flavobacterium p.]

469
3
1144
1419
gi|466474
cellobiose phosphotransferase enzyme II″
72
48

[Bacillus tearothermophilusi]

493
1
1124
240
sp|IP5O848IYPW&BAC
HYPOTHETICAL 58.2 KD PROTEIN IN KDGT-XPT
72
58

SU
INTERGENIC REGION.

536
2
379
218
gi|437389
transposase [Lactococcus lactis]
72
58

543
1
574
86
gi|290513
f470 [Escherichia coli]
72
47

592
1
57
680
gi|987092
ABC-transporter [Streptomyces
72
55

hygroscopicus]

666
2
551
967
gi|1064786
function unknown [Bacillus subtilis]
72
48

762
1
974
273
gi|304928
pantothenate synthetase [Escherichia coli]
72
55

792
1
401
3
pir|A36933|A36933
diacyiglycerol kinase homolog -
72
50

Streptococcus mutans

873
1
183
4
gnl|PID|e258329
oxaloacetate decarboxylase alpha-chain
72
55

[Legionella pneumophila]

4
4
3799
3155
gi|496943
ORF [Saccharomyces cerevisiae]

10
2
180
977
gnl|PID|e234078
hom [Lactococcus lactis]
71
49

16
7
4922
6097
gi|534982
phosphoglucomutase [Spinacia oleracea]
71
54

21
6
4148
3972
gi|1736645
Proline/betaine transporter (Proline
71
50

porter II) (PPII) . [Escherichia coli]

23
27
16452
17459
gi|1408503
yxeR gene product [Bacillus subtilis]
71
52

25
7
5812
6669
gi|413943
ipa-19d gene product [Bacillus subtilis]
71
58

31
1
80
946
gi|534045
antiterminator [Bacillus subtilis]
71
47

39
3
755
1297
sp|P09997|YIDA_ECO
HYPOTHETICAL 29.7 KD PROTEIN IN IBPA-GYRB
71
50

LI
INTERGENIC REGION.

39
7
2537
3193
pir|C43748|C43748
hypothetical protein (pepX 3′ region) -
71
54

Lactococcus lactis
subsp. lactis

45
10
5119
5484
gi|606044
ORF_o130; Geneplot suggests frameshift,
71
51

none found [Escherichia oil]

48
10
11722
10148
gi|20432
4-cournarate:CoA ligase Pc4Cl-1 (AA 1-544)
71
39

[Petroselinum crispum] ir|S0l667|S01667 4-

coumarate--CoA ligase (EC 6.2.1.12) (clone

4CL-1) - parsley

55
4
1470
1709
gi|1303901
YqhT [Bacillus subtilis]
71
54

57
10
12899
13060
gi|40053
phenylalanyl-tRNA synthetase alpha subunit
71
45

[Bacillus subtilis] ir|S11730|YFBSA

phenylalanine--tRNA ligase (EC 6.1.1.20)

alpha ain - Bacillus subtilis

58
3
3743
2571
gi|1658403
formate dehydrogenase alpha subunit
71
51

[Moorella thermoacetica]

68
11
8225
8602
gi|793910
surface antigen [Homo sapiens]
71
49

74
4
2908
2042
gi|467435
unknown [Bacillus subtilis]
71
55

85
3
3267
1966
gi|142613
branched chain alpha-keto acid
71
56

dehydrogenase E2 [Bacillus subtilis]

gi|1303944 BfmBB [Bacillus subtilis]

111
8
5737
4253
gi|1256135
YbbF [Bacillus subtilis]
71
50

111
9
6590
5730
gi|1573762
glucokinase regulator [Haemophilus
71
53

influenzae
]

120
1
111
353
gnl|PID|e235823
unknown [Schizosaccharmyces pombe]
71
52

123
11
10387
11196
gi|1773195
hypothetical [Escherichia coli]
71
55

151
3
4045
3098
gi|1256618
transport protein [Bacillus subtilis]
71
51

172
6
3949
4806
gi|1262288
CdsA [Brucella abortus]
71
56

172
7
5264
6448
gi|40100
rodC (tag3) polypeptide (AA 1-746)
71
52

[Bacillus subtilis] ir|S06049|S06049 rode

protein - Bacillus subtilis

p|P13485|TAGF_BACSU TEICHOIC ACID

BIOSYNTHESIS PROTEIN F.

190
7
3454
3122
gi|532556
ORF23 [Enterococcus faecalis]
71
52

195
24
9850
11871
gi|405564
traE [Plasmid pSK41]
71
45

215
4
3361
2711
gi|1573086
uridine kinase (uridine monophosphokinase)
71
51

(udk) [Haemophilus influenzae]

218
2
1456
2613
gnl|PID|e254644
membrane protein [Streptococcus
71
41

pneumoniae
]

222
3
1205
2053
gnl|PID|e255114
glutamate racemase [Bacillus subtilis]
71
56

222
4
1611
1387
gi|1001195
phosphate transport system permease
71
57

protein PstA [Synechocystis sp.]

222
14
8852
9853
gi|466720
No definition line found [Escherichia
71
53

coli
]

238
22
19256
20578
gi|595299
YgiK [Salmonella typhimurium]
71
50

255
3
2692
1061
gnl|PID|e254877
unknown [Mycobacterium tuberculosis]
71
55

265
5
2960
1581
gi|1039479
ORFU [Lactococcus lactis]
71
58

276
2
1359
538
gi|496283
lysin [Bacteriophage Tuc2009]
71
63

290
5
3552
4379
gi|1016162
ABC transporter subunit [Cyanophora
71
49

paradoxa
]

290
7
5659
6912
gi|1001708
NifS [Synechocystis sp.]
71
56

292
3
948
2156
gn1|PID|e233874
hypothetical protein [Bacillus subtilis]
71
55

318
4
3229
2285
gi|1256138
YbbI [Bacillus subtilis]
71
54

333
1
145
741
gi|293011
unknown protein [Lactococcus lactis]
71
50

344
1
76
396
gi|853775
unknown [Bacillus subtilis]
71
53

350
1
138
1394
gi|1652389
beta ketoacyl-acyl carrier protein
71
57

synthase [Synechocystis sp.]

363
4
4184
5674
gi|1657518
similar to fdrA gene of E. coli
71
54

[Escherichia coli]

364
5
5319
6563
gi|1657522
hypothetical protein [Escherichia coli]
71
46

367
13
6539
6162
gi|44225
ribosomal protein L18 (AA 1-116)
71
51

[Mycoplasma capricolum] ir|S02847|R5YM18

ribosomal protein L18 - Mycoplasma

capricolum
GC3)

379
7
6884
5655
gi|887821
ORF_o398 [Escherichia coli]
71
50

399
9
6528
7664
gi|154198
oxaloacetate decarboxylase [Salmonella
71
50

typhimurium
] pir|C44465|C44465 sodium ion

pump oxaloacetate decarboxylase ubunit

beta - Salmonella typhimurium

399
18
13540
14778
gi|143165
malic enzyme (EC 1.1.1.38) [Bacillus
71
46

stearothermophilus
] pir|A33307|DEBSXS

malate dehydrogenase oxaloacetate-

decarboxylating) (EC 1.1.1.38) - Bacillus

tearothermophilus

404
4
3769
3029
gi|143402
recombination protein (ttg start codon)
71
48

[Bacillus subtilis] gi|1303923 RecN

[Bacillus subtilis]

464
1
1532
216
gi|895749
putative cellobiose phosphotransferase
71
40

enzyme II″ [Bacillus ubtilis]

464
3
2088
2846
gi|1486242
unknown [Bacillus subtilis]
71
39

481
2
954
409
gi|144729
butanol dehydrogenase [Clostridium
71
58

acetobutylicum] sp|Q04944|ADHA
_CLOAB NADH-

DEPENDENT BUTANOL DEHYDROGENASE A (EC

.1.1.-) (BDH I).

482
4
2503
1841
gi|1072418
gicA gene product [Staphylococcus
71
58

carnosus
]

496
2
1636
848
gi|1001226
methionine aminopeptidase [Synechocystis
71
51

sp
.]

503
2
1624
650
gi|39478
ATP binding protein of transport ATPases
71
49

[Bacillus firmus] ir|S15486|S15486 ATP-

binding protein - Bacillus firmus

p|26946|YATR_BACFI HYPOTHETICAL ABC

TRANSPORTER ATP-BINDNG OTEIN.

513
2
1590
982
gnl|PID|e202290
unknown [Lactobacillus sake]
71
46

530
1
2
1534
gi|1542974
AbcA [Thermoanaerobacterium
71
52

thermosulfurigenes
]

537
1
706
365
gi|929972
ORFB; similar to B. anthracis SterneL
71
57

element ORFB; putative S150-like

transposase [Bacillus anthracis]

553
1
304
1287
gi|1653479
regulatory components of sensory
71
48

transduction system [Synechocystis sp.]

573
9
5560
5090
gi|143799
MtrA [Bacillus subtilis]
71
59

583
1
21
341
gi|1064791
function umknown [Bacillus subtilis]
71
50

584
2
638
276
gi|662792
single-stranded DNA binding protein
71
58

[unidentified eubacterium]

585
1
282
809
gi|666972
ORF 168 [Synechococcus sp.]
71
46

611
1
985
2
gi|1039479
ORFU [Lactococcus lactis]
71
55

616
1
350
3
gi|1088272
nitrogen fixation protein [Bacillus
71
52

cereus
]

624
1
61
399
gi|40014
pot. ORF 446 (aa 1-446) [Bacillus
71
53

subtilis
]

624
2
608
1732
gi|40015
pot. ORF 378 (aa 1-378) [Bacillus
71
51

subtilis
]

659
1
76
582
gi|1591045
hypothetical protein (SP:P31466)
71
51

[Methanococcus jannaschii]

668
2
836
1030
gi|467330
replicative DNA helicase [Bacillus
71
60

subtilis
]

683
1
582
118
gnl|PID|e264663
CinA [Streptococcus pneumoniae]
71
55

701
3
411
797
gi|143795
transfer RNA-Tyr synthetase [Bacillus
71
51

subtilis
]

720
1
1
351
gi|1595810
type-I signal peptidase SpsB
71
55

[Staphylococcus aureus]

724
2
1020
415
gnl|PID|e239621
ORF YNL218w [Saccharomyces cerevisiae]
71
51

790
2
658
383
gi|1783253
homologous to many ATP-binding transport
71
48

proteins; hypothetical [Bacillus subtilis]

799
1
505
906
gi|580866
ipa-12d gene product [Bacillus subtilis]
71
45

974
2
139
333
gi|1778531
H10021 homolog [Escherichia coli]

980
1
156
497
gi|437389
transposase [Lactococcus lactis]

4
3
3170
2418
gi|1001805
hypothetical protein [Synechocystis sp.]
70
55

17
21
18642
21527
gi|145821
EBG enzyme alpha subunit [Escherichia
70
53

coli]

19
8
2894
3952
gi|1353527
ORF10 [Bacteriophage rlt]
70
58

23
6
2640
3230
gi|699336
C. freundli orfW homologue [Mycobacterium
70
43

leprae
] sp|P53523|Y02Y_MYCLE HYPOTHETICAL

20.9 KD PROTEIN U471A.

27
3
1011
493
gi|1001644
regulatory components of sensory
70
44

transduction system [Synechocystis sp.]

31
2
1095
1337
gi|1100076
PTS-dependent enzyme II [Clostridium
70
55

longisporum
]

32
10
6527
5817
gi|1591789

M. jannaschii
predicted coding region
70
51

MJ1163 [Methanococcus jannaschii]

33
7
6930
7235
gi|536972
ORF_o90a [Escherichia coli]
70
45

35
2
500
2533
gi|43819
nagE gene product [Klebsiella pneumoniae]
70
50

47
13
15837
14512
gi|150209
ORF 1 [Mycoplasma mycoides]
70
44

49
15
10409
11179
gi|853751
N-acetylmuramoyl-L-alanine amidase
70
54

[Bacteriophage A511]

57
7
8365
12189
gi|142440
ATP-dependent nuclease [Bacillus subtilis]
70
48

57
16
18656
18033
gi|388565
major cell-binding factor [Campylobacter
70
52

jejuni
]

59
9
4985
7060
gnl|PID|e254877
unknown [Mycobacterium tuberculos]
70
49

72
6
6771
4600
gi|557567
ribonucleotide reductase R1 subunit
70
53

[Mycobacterium tuberculosis]

sp|P50640|RIR1_MYCTU RIBONUCLEOSIDE-

DIPHOSPHATE REDUCTASE ALPHA HAIN (EC

1.17.4.1) (RIBONUCLEOTIDE REDUCTASE) (R1

SUBUNIT) FRAGMENT).

76
8
5960
6343
gi|1063251
no homologous protein [Bacillus subtilis]
70
52

81
16
12529
11723
gi|1732200
PTS permease for rnannose subunit IIPMan
70
52

[Vibrio furnissii]

98
7
8974
7874
gi|1573045
hypothetical [Haemophilus influenzae]
70
46

110
2
1353
502
gi|1399848
unknown [Synechococcus PCC7942]
70
52

123
7
5009
5527
gi|143284
negative regulator pal 1 [Bacillus
70
51

subtilis
]

123
22
19729 20412 gi|1591493
glutamine transport ATP-binding protein Q
70 48

[Methanococcus jannaschii]

133
6
5905
6498
gi|746399
transcription elongation factor
70
50

[Escherichia coli]

134
1
1
384
gi|1146242
aspartate 1-decarboxylase [Bacillus
70
49

subtilis
]

138
10
8543
7953
gi|467371
LACI family of transcriptional repreesor
70
50

(probable) [Bacillus ubtilis]

160
3
1263
1520
gi|1468939
meso-2,3-butanediol dehydrogenase (D-
70
45

acetoin forming) [Klebsiella pneumoniae]

174
3
2279
1572
gi|413931
ipa-7d gene product [Bacillus subtilis]
70
44

177
2
2104
1022
gnl|PID|e186242
D-mannonate hydrolase [Thermotoga
70
52

neapolitana
]

178
2
1320
532
gi|499659
K+ channel protein [Panulirus interruptus]
70
51

180
18
17770
18729
gi|887824
ORF_o310 [Escherichia coli]
70
50

180
22
21072
22526
gi|1573294
hypothetical [Haemophilus influenzae]
70
40

181
9
7409
6279
sp|P20692|TYRA_BAC
PREPHENATE DEHYDROGENASE (EC 1.3.1.12)
70
49

SU
(PDH).

197
5
4529
6340
gi|1783252
homologous to many ATP-binding transport
70
47

proteins including Swissprot:CYDD_ECOLI;

hypothetical [Bacillus subtilis]

200
21
12419
11820
gi|290943
HindIII modification methyltransferase
70
47

[Haemophilus influenzae]

sp|P43871|MTH3_HAEIN MODIFICATION

METHYLASE HINDIII (SC 2.1.1.72) ADENINE-

SPECIFIC METHYLTRANSFERASE HINDIII)

(M.HINDIII)

210
4
3877
3269
gi|602683
orfC [Mycoplasma capricolum]
70
47

217
2
405
707
gi|153767
ORF [Streptococcus pneumoniae]
70
56

222
8
4940
6046
gi|537033
ORF_f356 [Escherichia coli]
70
54

222
15
9825
10553
gi|537039
ORF_o228a [Escherichia coli]
70
56

227
4
1871
2893
gi|1070014
protein-dependent [Bacillus subtilis]
70
44

228
2
1343
792
gi|1742730
Protein AraJ precursor. [Escherichia coli]
70
50

228
5
3470
2574
gi|1573390
hypothetical [Haemophilus influenzae]
70
54

231
2
2470
1238
gi|1574085

H. influenzae
predicted coding region
70
48

HI1048 [Haemophilus influenzae]

235
4
2779
2138
gi|309662
pheromone binding protein [Plasmid pCF10]
70
46

239
4
5807
6409
gi|682765
mccB gene product [Escherichia coli]
70
41

248
1
3
350
gi|143725
putative [Bacillus subtilis]
70
52

254
4
838
497
gi|49318
ORF4 gene product [Bacillus subtilis]
70
48

256
3
1737
2612
gi|596092
putative multiple membrane domain protein;
70
51

possible TTG initiation odon at position

1064, near putative RBS at position 1052

Streptococcus pyogenes
]

279
15
14547
14224
gi|1389549
ORF3 [Bacillus subtilis]
70
50

283
6
2279
3190
gi|853751
N-acetylmuralmoyl-L-alanine amidase
70
52

[Bacteriophage A511]

292
8
5557
6534
gi|474195
This ORF is homologous to a 40.0 kd 70
50

hypothetical protein in the htrB ′ region

from E. coli, Accession Number X61000

[Mycoplasma-like rganism]

294
8
2776
3375
gi|1750126
YncB [Bacillus subtilis]
70
47

294
10
3742
4020
gi|984581
YafQ [Escherichia coli]
70
50

299
1
905
132
gi|606309
ORF_o265; gtg start [Escherichia coli]
70
40

300
3
3200
2784
gi|289260
comE ORF1 [Bacillus subtilis]
70
50

301
9
8564
7590
gi|1303865
YqgR [Bacillus subtilis]
70
52

336
2
661
921
gi|202864
[Rat alternatively spliced mRNA.], gene
70
47

product [Rattus norvegicus]

339
1
269
3
gi|786163
Ribosomal Protein L10 [Bacillus subtilis]
70
50

351
9
4760
4359
gi|799235
dTDP-6-deoxy-L-lyxo-4-hexulose reductase
70
45

[Escherichia coli]

399
28
28203
28793
gi|146278
glucitol-specfic enzyme II (gutA)
70
52

[Escherichia coli] pir|A26725|WQEC2S

phosphotransferase system enzyme II (EC

.7.1.69), sorbitol-specific, factor II -

Escherichia coli
sp|P05705|PTHB_ECOLI PTS

SYSTEM, GLUCITOL/SORBITOL-SPECIFIC IIBC

OMPONENT (EIIBC-GUT)

406
1
1
552
gi|49315
ORF1 gene product [Bacillus subtilis]
70
50

436
5
2417
2193
gi|773665
transposase [Lactococcus lactis]
70
36

482
3
1887
1660
gi|48680
ptsG-like product [Bacillus subtilis]
70
47

529
3
6587
7030
gi|1022726
unknown [Staphylococcus haemolyticus]
70
44

535
2
1702
965
gi|1747435
KdpE [Clostridium acetobutylicum]
70
52

543
2
1248
547
gi|1591045
hypothetical protein (SP:P31466)
70
47

[Methanococcus jannaschii]

543
8
4084
3878
gi|511976
SERP gene gene product [Plasmodium
70
60

falciparum
]

560
3
1037
876
gi|558458
acidic 82 kDa protein [Homo sapiens]
70
40

573
4
1920
2258
gi|336639
prephytoene pyrophosphate dehydrogenase
70
32

[Cyanophora paradoxa] gi|1016130 prenyl

transferase [Cyanophora paradoxa]

pir|A40433|A40433 prephytoene

pyrophosphatase dehydrogenase (crtE)

omolog - Cyanophora paradoxa

599
2
244
573
gi|42029
ORF1 gene product [Escherichia coli]
70
49

608
3
867
556
gi|475032
formamidopyrimidine-DNA glycosylase
70
53

[Streptococcus mutans] sp|P55045|FPG_STRMU

FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (EC

.2.2.23) (FAPY-DNA GLYCOSYLASE).

636
1
2
628
gi|606309
ORF_o265; gtg start [Escherichia coli]
70
50

670
2
2157
1828
gi|1657698
hyaluronan receptor [Homo sapiens]
70
41

702
1
103
870
gi|149490
sucrose-6-phosphate hydrolase [Lactococcus
70
51

lactis
] pir|JH0754|JH0754 sucrose-6-

phosphate hydrolase (EC 3.2.1.-) -

actococcus lactis

726
2
725
480
gnl|PID|e240103
unknown ORF [Saccharomnyces cerevisiae]
70
41

854
1
1
207
gi|532653
thermonuclease [Staphylococcus hyicus]
70
51

901
1
238
447
gi|172022
myosin 1 isoform (MYO2) [Saccharomyces
70
20

cerevisiae]

940
1
1
318
gi|1039479
ORFU [Lactococcus lactis]
70
56

1
2
2112
1213
gi|413976
ipa-52r gene product [Bacillus subtilis]
69
51

8
2
2196
778
gi|1510108
ORF-1 [Agrobacterium tumefaciens]
69
50

8
9
7949
6654
gi|1196907
daunorubicin resistance protein
69
44

[Streptomyces peucetius]

16
3
1618
2574
gi|1109684
ProV [Bacillus subtilis]
69
53

17
26
25781
26944
gi|485275
53.6 kDa protein [Streptococus
69
44

pneumoniae
]

17
35
32300
32770
gi|1574146
pfs protein (pfs) [Haemophilus influenzae]
69
53

23
30
18107 18538
gnl|PID|e249656
YneT [Bacillus subtilis]
69
59

25
8
6653
6994
gi|413943
ipa-19d gene product [Bacillus subtilis]
69
46

37
2
2042
186
gi|143331
alkaline phosphatase regulatory protein
69
52

[Bacillus subtilis] pir|A27650|A27650

regulatory protein phoR - Bacillus

subtilis sp|P23545|PHOR_BACSU ALKALINE

PHOSPHATASE SYNTHESIS SENSOR PROTEIN HOR

(EC 2.7.3.-).

39
2
528
767
gi|1408493
homologous to SwissProt:YIDA_ECOLI
69
52

hypothetical protein [Bacillus subtilis]

56
6
4809
3457
gi|1591610
probable ATP-dependent helicase
69
45

[Methanococcus jannaschii]

67
5
3042
3938
gi|1658188
oxidative stress transcriptional regulator
69
39

[Erwinia carotovora]

68
3
684
1529
gnl|PID|e214719
P1cR protein [Bacillus thuringiensis]
69
45

72
4
2099
3394
gi|882672
ORF_o313 [Escherichia coli]
69
37

81
15
11820
10915
gi|1732201
PTS permease for mannose subunit IIBMan
69
44

[pi Vibria furnissii]

83
20
14001
15800
gi|1230668
Similar to Arginyl-tRNA synthetase (Swiss
69
44

Prot. accession number P11875)

[Saccharomyces cerevisiae]

85
6
6309
5299
sp|P54533|DLD2_BAC
LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF
69
46

SU
BRANCHED-CHAIN ALPHA-KETO ACID

DEHYDROGENASE COMPLEX (EC 1.8.1.4)

(DIHYDROLIPOAMIDE DEHYDROGENASE) (LPD-

VAL).

86
3
2084
3367
gi|143318
phosphoglycerate kinase [Bacillus
69
53

megaterium
]

94
2
1401
751
gi|755216
N-acetylmuramidase [Lactococcus lactis]
69
41

94
16
20498
19197
gi|1208948
unknown [Escherichia coli]
69
47

98
8
10201
9029
gi|563934
similar to E. coli hypothetical protein:
69
51

PIR Accession Number Q0614] [Bacillus

subtilis
]

109
4
2350
1316
gi|396501
aspartyl-tRNA synthetase [Thermus
69
56

aquaticus thermophilus
] pir|S33743|533743

aspartate--tRNA ligase (EC 6.1.1.12) -

Thermus quaticus

114
1
83
1522
gi|1658402
formate dehydrogenase beta subunit
69
45

[Moorella thermoacetica]

123
9
7617
8984
gi|1773192
similar to S. cerevisiae dal1 [Escherichia
69
50

coli
]

128
11
7940
7578
gi|895750
putative cellobiose phosphotransferase
69
53

enzyme III [Bacillus ubtilis]

130
10
8764
9036
gi|1641
put. Na(+)/glucose co-transporter (AA 1-
69
47

662) [Oryctolagus cuniculus] |1717

cortical sodium-D-glucose cotransporter

[Oryctolagus iculus]

138
26
16721
17545
pir|A25805|A25805
L-lactate dehydrogenase (EC 1.1.1.27) -
69
55

Bacillus subtilis

139
2
310
1083
gi|1408587
relaxase [Lactococcus lactis lactis]
69
46

139
9
5196
4984
gi|473955
DNA-binding protein [Lactobacillus sp.]
69
34

142
9
5559
4564
gi|623073
ORF360; putative [Bacteriophage LL-H]
69
47

155
6
4658
5818
gi|1591260
endoglucanase [Methanococcus jannaschii]
69
48

158
12
11671
11201
gi|606744
cytidine deaminase [Bacillus subtilis]
69
52

162
5
5888
4032
gi|142993
glycerol-3-phosphate dehydrogenase (glpD)
69
54

(EC 1.1.99.5) [Bacillus ubtilis]

180
2
1901
1203
gi|1575577
DNA-binding response regulator [Thermotoga
69
49

maritima
]

197
4
3571
4602
gi|1783251
homologous to cytochrome d ubiquino
169
46

oxidase subunit II; hypothetical [Bacillus
C

subtilis
]

197
6
6283
7701
gi|1783253
homologous to many ATP-binding transport.
69
49

proteins; hypothetical [Bacillus subtilis]

222
1
201
10
gi|149901
gene codes for a 19 kDa protein
69
50

[Mycobacterium avium] sp|P46733|19KD_MYCAV

19 KD LIPOPROTEIN ANTIGEN PRECURSOR.

223
28
23857
24567
gnl|PID|e269548
Unknown [Bacillus subtilis]
69
53

228
3
2031
1285
gi|1742730
Protein AraJ precursor. [Escherichia coli]
69
45

229
8
7390
6698
gi|1162980
ribulose-5-phosphate 3-epimer [Spinacia
69
52

oleracea
]

238
27
25243
25695
gi|305005
ORF_f104 [Escherichia coli]
69
53

253
3
1067
921
gi|1591278
aspartokinase I [Methanococcus jannaschii]
69
39

260
4
2110
3105
gi|580841
F1 [Bacillus subtilis]
69
45

268
3
2287
1910
gi|460026
repressor protein [Streptococcus
69
48

pneumoniae
]

269
7
4532
4083
gi|1303792
YqeK [Bacillus subtilis]
69
50

271
15
11040
12236
gi|1303805
YqeR [Bacillus subtilis]
69
48

271
16
12444
12809
gi|435490
orf1 gene product [Lactococcus lactis]
69
46

281
3
1277
2068
gi|1303968
YgjQ [Bacillus subtilis]
69
50

281
6
5004
5534
gi|1773151
adenine phosphoribosyltransferase
69
54

[Escherichia coli]

292
24
19939
18398
gi|1652664
glutamine-binding periplasmic protein
69
45

[Synechocystis sp.]

323
3
2708
4243
gi|179401
beta-D-galactosidase precursor (EC
69
56

3.2.1.23) [Homo sapiens] gi|179423 beta-

galactosidase precursor (EC 3.2.1.23)

[Homo sapiens] pir|A32688|A32611 beta-

galactosidase (EC 3.2.1.23) precursor -

uman

330
2
1388
2353
gi|1303783
YgeC [Bacillus subtilis]
69
48

332
1
2
223
gi|1653594
hemolysin [Synechocystis sp.]
69
50

338
9
7035
7607
gi|467442
stage V sporulation [Bacillus subtilis]
69
55

341
1
1
408
gi|1477741
histidine periplasmic binding protein P29
69
50

[Campylobacter jejuni]

368
2
972
598
gi|516826
rat GCP360 [Rattus rattus]
69
33

375
4
3405
2599
gi|1215693
putative orf; GT9_orf434 [Mycoplasma
69
38

pneumoniae
]

386
1
2
166
gi|1549376
putative protein [Synechococcus PCC7942]
69
42

396
4
1248
1715
gi|410132
ORFX8 [Bacillus subtilis]
69
50

398
4
2763
2927
gi|466475
putative phospho-beta-glucosidase
69
55

[Bacillus stearothermophilus]

pir|D49898|D49898 cellobiose

phosphotransferase system celC - acillus

stearothermophilus

421
5
2950
3471
gi|1574625

H. influenzae
predicted coding region
69
45

H11074 [Haemophilus influenzae]

423
4
2408
2893
gnl|PID|e163522
rnhB [Haemophilus influenzae]
69
55

436
3
1763
1521
gi|155032
ORF B [Plasmid pEa34]
69
37

452
1
3
341
gi|1591139

M. jannaschii
predicted coding region
69
52

MJ0435 [Methanococcus jannaschii]
69
52

470
3
1816
2181
gi|437389
transposase [Lactococcus lactis]
69
56

471
2
2003
813
gi|854233
cymF gene product [Klebsiella oxytoca]
69
49

478
1
822
4
gi|142521
deoxyribodipyrimidine photolyase [Bacillus
69
63

subtilis
] gnl|PID|e255102

deoxyribodipyrimidine photolyase [Bacillus

ubtilis
]

490
4
1447
1289
gi|699379
glvr-1 protein [Mycobacterium leprae]
69
41

518
2
213
605
pir|S00076|RSBS12
ribosomal protein L12 - Bacillus
69
59

stearotherrnophilus

536
4
1471
1653
gi|1146240
ketopantoate hydroxymethyltransferase
69
53

[Bacillus subtilis]

539
5
3796
5091
gi|973231
gamma-glutamyl phosphate reductase
69
54

[Lycopersicon esculentum]

566
1
1
231
gi|45741
ORFE [Enterococcus faecalis]
69
50

579
5
2729
3595
gi|145887
malonyl coenzyme A-acyl carrior protein
69
49

transacylase [Escherichia oli]

583
2
373
912
gi|1064791
function umknown [Bacillus subtilis]
69
55

605
1
254
3
pir|S39743|S39743
hypothetical protein - Bacillus subtilis
69
37

630
2
1659
1231
gi|153672
lactose repressor [Streptococcus mutans]
69
47

634
1
36
731
gi|1022725
unknown [Staphylococcus haemolyticus]
69
53

662
1
486
73
gi|467431
high level kasgamycin resistance [Bacillus
69
55

subtilis
] sp|P37468|KSGA_BACSU

DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-)

S-ADENOSYLMETHIONINE-6-N′, N′-

ADENOSYL(RRNA) DIMETHYLTRANSFERASE) 16S

RRNA DIMETHYLASE) (HIGH LEVEL KASUGAMYCIN

RESISTANCE PROTEIN SGA) (K

689
1
340
26
gi|1017817
membrane spanning protein [Streptomyces
69
41

coelicolor]

756
2
300
500
gi|520596
Mre2 protein [Saccharomyces cerevisiae]
69
46

792
2
855
460
gi|1303823
YqfG [Bacillus subtilis]
69
55

916
1
4
789
gnl|PID|e253114
ornithine carbamoyltransferase [Pyrococcus
69
57

furiosus
]

7
3
2609
3748
gi|1303836
YgfO [Bacillus subtilis]
68
50

16
5
4165
4689
gi|142450
ahrC protein [Bacillus subtilis]
68
46

17
16
12826
13071
gi|222681
RNA polymerase [Tomato spotted wilt virus]
68
50

17
32
31402
31572
gi|1303984
YgkG [Bacillus subtilis]
68
44

17
33
31509
32009
gi|1303984
YgkG [Bacillus subtilis]
68
50

29
1
19
282
gi|1234787
up-regulated by thyroid hormone in
68
37

tadpoles; expressed specifically in the

tail and only at metamorphosis; membrane

bound or extracellular protein; C-terminal

basic region [Xenopus laevis]

29
3
1087
1950
gi|407878
leucine rich protein [Streptococcus
68
45

equisimilis
]

45
1
204
959
gi|1039479
ORFU [Lactococcus lactis]
68
50

47
7
8108
7527
gi|142853
homologous to unidentified E. coli protein
68
46

[Bacillus subtilis] gi|143161 maf

[Bacillus subtilis]

52
6
4304
5050
gnl|PID|e124050
alpha-acetolactate decarboxylase
68
53

[Lactococcus lactis]

58
5
5961
4807
gi|466365
potential NAD-reducing hydrogenase subunit
68
49

[Desulfovibrio ructosovorans]

68
8
4036
4743
gi|1673727
(AE000009) Mycoplasma pneumoniae,
68
44

glutamine transport ATP-binding protein;

similar to Swiss-Prot Accession Number

P10346, from E. coli [Mycoplasma

pneumoniae
]

72
5
4441
3434
gi|1395209
ribonucleotide reductase R2-2 small
68
52

subunit [Mycobacterium tuberculosis]

80
1
836
3
gi|474176
regulator protein [Staphylococcus xylosus]
68
48

81
2
793
1359
gi|1064809
homologous to sp:HTRA_ECOLI [Bacillus
68
48

subtilis
]

85
9
6911
6711
gi|144893
butyrate kinase [Clostridium
68
55

acetobutylicum
]

89
8
7184
5970
gi|1469784
putative cell division protein ftsW
68
44

[Enterococcus hirae]

91
3
828
1076
gi|726480
L-glutarnine-D-fructose-6-phosphate
68
53

amidotransferase [Bacillus ubtilis]

103
1
1019
3
gi|143365
phosphoribosyl aminoimidazole carboxylase
68
50

II (PUR-K; ttg start odon) [Bacillus

subtilis
]

106
2
2441
1509
gi|146860
delta-2-isopentenyl pyrophosphate
68
47

transferase [Escherichia coli] gi|537012

tRNA delta-2-isopentenylpyrophosphate

(IPP) transferase Escherichia coli]

112
1
558
100
gnl|PID|e242290
carbamate kinase [Clostridium perfringens]
68
50

116
3
2383
1496
gi|755601
unknown [Bacillus subtilis]
68
42

119
3
2136
1201
gi|1171125
thioredoxin reductase [Clostridium
68
49

litorale
]

121
4
3697
4650
gi|790945
aryl-alcohol dehydrogenase [Bacillus
68
48

subtilis
]

123
26
24262
24801
gi|537235
Kenn Rudd identifies as gpmB [Escherichia
68
51

coli
]

123
27
24887
25888
gi|143150
levR [Bacillus subtilis]
68
51

126
4
2773
1844
gi|551854
ORF2 [Erwinia herbicola]
68
54

131
1
150
1058
gi|1387979
44% identity over 302 residues with
68
44

hypothetical protein from Synechocystis

sp, accession D64006_CD; expression

induced by environmental stress; some

similarity to glycosyl transferases; two

potential membrane-spanning helices

[Bacillus subtil

134
3
2154
1804
sp|P39213|YI91_SHI
INSERTION ELEMENT IS911 HYPOTHETICAL 12.7
68
43

DY
KD PROTEIN.

138
19
12285
12656
gi|1438847
homologue of hypothetical 17.6 kDa protein
68
43

in rplI-cpdB intergenic region of E. coli

[Bacillus subtilis]

151
2
2784
1654
gi|143365
phosphoribosyl aminoimidazole carboxylase
68
45

II(PUR-K; ttg start odon) [Bacillus

subtilis
]

164
23
24352
24119
gi|1573564
hypothetical [Haemophilus influenzae]
68
40

166
2
970
1260
gi|151968
nifS [Rhodobacter sphaeroides]
68
41

172
2
1320
2015
gi|1208965
hypothetical 23.3 kd protein [Escherichia
68
46

coli
]

175
1
900
451
gi|468207
Submitter comments: A Mg2+ transporting P-
68
47

type ATPase highly omologous with mgtB

ATPase at 80 min on Salmonella chromosome.

ediates the influx of Mg2+ only.

Transcription regulated by xtracellular

Mg2+ [Salmonella typhimurium]

180
14
12551
14956
gi|565641
FdrA protein [Escherichia coli]
68
49

186
1
3
686
gi|405804
transposase [Streptococcus thermophilus]
68
51

200
1
239
3
gi|468016
immunoglobulin heavy chain binding protein
68
42

[Giardia intestinalis]

201
4
4468
3686
gi|304013
abcA [Aeromonas salmonicida]
68
50

204
10
6833
6468
gi|488430
alcohol dehydrogenase 2 [Entamoeba
68
51

histolytica
]

214
3
3360
2491
gi|928834
integrase [Lactococcus lactis phage BK5-T]
68
50

229
9
8277
7375
gi|1574569
hypothetical [Haemophilus influenzae]
68
41

229
14
14288
13740
gnl|P1D|e290287
polypeptide deformylase [Bacillus
68
50

subtilis
]

230
5
4593
3532
gi|143002
proton glutamate symport protein [Bacillus
68
29

caldotenax
] pir|S26246|S526246

glutamate/aspartate transport protein -

Bacillus aldotenax

244
1
1
891
gi|537080
ribonucleoside triphosphate reductase
68
54

[Escherichia coli] pir|A47331|A47331

oxygen-sensitive ribonucleoside-

triphosphate eductase (EC 1.17.4.-) -

Escherichia coli

244
5
4249
3551
gi|1773172
hypothetical protein [Escherichia coli]
68
46

244
7
5670
5212
gi|467423
unknown [Bacillus subtilis]
68
43

264
9
3925
3734
gi|914991
Similar to hemoglobinase [Saccharomyces
68
44

cerevisiae
] pir|S59796|S59796 hypothetical

protein D9798.2 - yeast Saccharomyces

cerevisiae
)

271
7
3484
4686
gi|1469784
putative cell division protein ftsW
68
50

[Enterococcus hirae]

271
11
6817
6548
gi|413948
ipa-24d gene product [Bacillus subtilis]
68
50

288
3
1638
1333
gi|562039
NADH dehydrogenase, subunit 2
68
50

[Acanthamoeba castellanii]

pir|S53835|S53835 NADH dehydrogenase chain

2 - Acanthamoeba astellanii mitochondrion

(SGC6)

295
6
3537
4472
gi|555668
glycosylasparaginase precursor
68
41

[Flavobacterium meningosepticum]

296
2
3143
1950
gi|1742630
Bicyclomycin resistance protein
68
34

(Sulfonamide resistance protein)

[Escherichia coli]

301
3
3271
1760
gi|413960
ipa-36d galT gene product [Bacillus
68
53

subtilis
]

315
3
2230
905
gi|1653498
ABC transporter [Synechocystis sp.]
68
47

318
2
1285
854
gi|43940
EIII-F Sor PTS [Klebsiella pneumoniae]
68
39

320
2
1178
621
gi|664842
sister of P-glycoprotein [Sus scrofa
68
46

domestica]

331
2
342
566
pir|B48396|B48396
ribosomal protein L33 - Bacillus
68
59

stearothermophilus

336
1
1
663
gi|1006591
cation-transporting ATPase PacL
68
44

[Synechocystis sp.]

338
6
4004
5035
gi|155276
aldehyde dehydrogenase [Vibrio cholerae]
68
51

338
12
10404
11165
gi|467444
transcription-repair coupling factor
68
46

[Bacillus subtilis] sp|P37474|MF_BACSU

TRANSCRIPTION-REPAIR COUPLING FACTOR

(TRCF).

341
3
743
1222
gi|1183886
integral membrane protein [Bacillus
68
45

subtilis
]

351
6
2992
2561
gi|580881
ipa-73d gene product [Bacillus subtilis]
68
53

363
8
12517
9950
gi|1652980
H(+)-transporting ATPase [Synechocystis
68
46

sp
.]

368
3
1269
1736
gnl|PID|e209005
homologous to ORF2 in nrdEF operons of
68
37

E.coli
and S.typhimurium [Lactococcus

lactis
]

386
11
6564
6115
gi|765072
ORF3 [Staphylococcus aureus]
68
46

395
3
935
729
gi|5521
ORF 3 (AA 1-90) [Bacteriophaqe phi-105]
68
34

399
8
6073
6519
gi|153584
biotin carboxyl carrier protein
68
53

[Streptococcus mutans]

sp|P29337|BCCP_STRMU BIOTIN CARBOXYL

CARRIER PROTEIN (BCCP).

408
3
2289
1336
gi|41572
GlnP (AA 1-219) [Escherichia coli]
68
40

420
1
559
2
gi|1592142
ABC transporter, probable ATP-binding
68
51

subunit [Methanococcus jannaschii]

423
2
254
1294
gi|1773109
similar to S. typhimurium apbA
68
47

[Escherichia coli]

423
3
1465
2421
gi|1653032
hypothetical protein [Synechocystis sp.]
68
40

428
1
859
2
gi|1652454
hypothetical protein [Synechocystis sp.]
68
48

432
7
4626
3901
gi|1573285
hypothetical [Haemophilus influenzae]
68
55

434
1
90
1889
gi|1542975
AbcB [Thermoanaerobacterium
68
50

thermosulfurigenes
]

441
5
4674
5156
gi|467437
unknown [Bacillus subtilis]
68
48

455
4
3835
4080
gi|19815
luminal binding protein (BiP) [Nicotiana
68
40

tabacum
]

530
2
394
546
gi|763326
unknown [Saccharomnyces cerevisiae]
68
42

531
2
810
622
gi|1146183
putative [Bacillus subtilis]
68
51

537
3
1353
1192
gi|929968
ORFA; similar to B. anthracis WeyAR
68
56

element ORFA; putative ransposase

[Bacillus anthracis]

539
3
2725
2231
gi|1353537
dUTPase [Bacteriophage rlt]
68
53

569
1
3
446
gi|146544
18 kD protein [Eschenichia coli]
68
47

591
2
656
174
gi|1039479
ORFU [Lactococcus lactis]
68
42

652
2
739
1032
gi|1303715
YrkP [Bacillus subtilis]
68
50

671
2
436
1617
gi|413959
ipa-35d galK gene product [Bacillus
68
50

subtilis
]

684
1
466
2
gnl|PID|e248400
orfRM1 gene product [Bacillus subtilis]
68
40

693
1
2
787
gi|405804
transposase [Streptococcus thermophilus]
68
46

700
2
772
596
gi|153801
enzyme scr-II [Streptococcus mutans]
68
50

735
1
118
609
gi|969027
gamma-aminobutyrate permease [Bacillus
68
40

subtilis
] sp|P46349|GABP_BACSU GABA

PERMEASE (4-AMINO BUTYRATE TRANSPORT

ARRIER) (GAMA-AMINOBUTYRATE PERMEASE).

750
1
2
529
gi|893358
PgsA [Bacillus subtilis]
68
54

762
2
1588
950
gi|1146240
ketopantoate hydroxymethyltransferase
68
49

[Bacillus subtilis]

790
1
407
3
gi|142224
attachment protein ChvA (ttg strart codon)
68
55

[Agrobacterium umefaciens]

882
1
3
278
gi|57572
glyceraldehyde-3-phosphate dehydrogenase
68
48

(NADP+) (phosphorylating) attus rattus]

950
1
140
568
gi|882736
ORF_f278 [Escherichia coli]
68
53

969
2
554
339
gi|1118031
similar to neural cell adhesion molecules
68
47

and neuroglians in their IG-like C2-type

domains [Caenorhabditis elegans]

970
1
297
73
gi|474404
cyclophilin [Tolypocladium inflatum]
68
40

1
1
1103
3
gi|48790
ORF 3 [Pseudomonas putAda]
67
50

29
10
7156
6614
sp|P36672|PTTB_ECO
PTS SYSTEM, TREHALOSE-SPECIFIC IIBC
67
52

LI
COMPONENT (EIIBC-TRE) (TREHALOSE- PERMEASE

IIBC COMPONENT) (PHOSPHOTRANSFERASE ENZYME

II, BC COMPONENT) (EC 2.7.1.69) (EII-TRE).

48
8
8035
9141
gi|975627
N-acylamino acid racemase [Amycolatopsis
67
48

sp
.]

55
12
6621
7439
gi|391610
farnesyl diphosphate synthase [Bacillus
67
47

stearothermophilus
] pir|JX0257|JX0257

geranyltranstransferase (BC 2.5.1.10) -

Bacillus tearothermophilus

57
13
13972
16401
gnl|PID|e255138
phenylalanyl-tRNA synthetase beta subunit
67
47

[Bacillus subtilis]

63
4
1917
2729
gi|1321629
MIP related protein of E. coli
67
47

[Escherichia coli]

68
12
8600
8923
gi|793910
surface antigen [Homo sapiens]
67
43

72
7
7138
6740
gnl|PID|e209005
homologous to ORF2 in nrdEF operons of
67
39

E.coli
and S.typhimurium [Lactococcus

lactis
]

72
10
8309
9433
gi|1199515
ferrous iron transport protein B
67
41

[Escherichia coli]

85
5
5315
4296
gi|142611
branched chain alpha-keto acid
67
52

dehydrogenase E1-alpha [Bacillus ubtilis]

101
5
4149
3100
gi|1109686
ProX [Bacillus subtilis]
67
48

110
4
2335
1292
gi|1066343
mu-crystallin [Homo sapiens]
67
48

114
12
12936
13520
gi|146218
serine hydroxymethyltransferase
67
50

[Escherichia coli]

115
5
3137
2010
gi|1256150
YbaR [Bacillus subtilis]
67
47

115
6
3199
2792
gi|1652593
hypothetical protein [Synechocystis sp.]
67
45

123
25
22739
24208
gi|148711
6-aminohexanoate-cyclic-dimer hydrolase
67
50

[Flavobacterium sp.] gi|488343 6-

aminohexanoate-cyclic-dimer hydrolase

[Flavobacterium p.]

124
6
5139
4267
gi|1016770
prolipoprotein diacyiglyceryl transferase
67
50

[Staphylococcus aureus]

125
2
1306
221
gi|853743
L-alanoyl-D-glutamate peptidase
67
50

[Bacteriophage A118]

128
36
29462
28737
gi|142940
ftsA [Bacillus subtilis]
67
46

138
27
17602
18183
gi|1256639
putative [Bacillus subtilis]
67
50

138
31
21578
20097
gi|143245
Na+/H+ antiporter [Bacillus firmus]
67
42

138
33
25165
23249
gi|1498811

M. jannaschii
predicted coding region
67
45

MJ0050 [Methanococcus jannaschii]

138
36
28690
27362
gnl|PID|e269549
Unknown [Bacillus subtilis]
67
47

144
4
3271
3717
gi|1753229
PKCI [Borrelia burgdorferi]
67
52

145
3
1435
2511
gi|1573615
ATP-binding protein (abc) [Haemophilus
67
47

influenzae
]

146
5
4657
2804
gi|1045034
beta-galactosidase [Xanthomonas campestris
67
51

pv. manihotis]

149
3
1978
1367
gi|806536
membrane protein [Bacillus
67
51

acidopullulyticus
]

156
1
3
365
gnl|PID|e265539
ClpB-homologue [Thermus aquaticus
67
42

thermophilus
]

158
15
14863
13766 gi|1573487
rbs repressor (rbsR) [Haemophilus
67
40

influenzae
]

158
17 16483
15959
gi|677850
hypothetical protein [Staphylococcus
67
51

aureus
]

159
7
6872
6006
gi|1303949
YqiX [Bacillus subtilis]
67
41

159
9
8103
7498
gi|1303950
YqiY [Bacillus subtilis]
67
41

165
11
9846
9004
gi|606079
ORF_o267 [Escherichia coli]
67
36

169
2
2151
3047
gi|42371
pyruvate formate-lyase activating enzyme
67
44

(AA 1-246) [Escherichia li]

179
13
13648
14451
gnl|PID|e257631
methyltransferase [Lactococcus lactis]
67
45

180
28
28656
29801
gi|666005
hypothetical protein [Bacillus subtilis]
67
48

194
6
2774
4231
gi|143245
Na+/H+ antiporter [Bacillus firmus]
67
41

194
10
6472
8259
gi|622991
mannitol transport protein [Bacillus
67
50

stearothermophilus
] sp|P50852|PTMB_BACST

PTS SYSTEM, MANNITOL-SPECIFIC IIBC

COMPONENT EIIBC-MTL) (MANNITOL- PERMEASE

IIBC COMPONENT) (PHOSPHOTRANSFERASE NZYME

II, BC COMPONENT) (EC 2.7.1.69) (EII-MTL).

204
5
1924
3006
gi|1235684
mevalonate pyrophosphate decarboxylase
67
50

[Saccharomyces cerevisiae]

214
1
42
1196
gi|606013
CG Site No. 829 [Escherichia coli]
67
36

219
2
524
850
gnl|PID|e257628
ORF [Lactococcus lactis]
67
42

223
15
13640
14407
gi|496520
orf iota [Streptococcus pyogenes]
67
54

227
3
1011
1892
gi|1070013
protein-dependent [Bacillus subtilis]
67
37

233
12
9340
8339
gi|507880
xanthine dehydrogenase [Gallus gallus]
67
50

238
10
7951
9183
gi|1653948
hypothetical protein [Synechocystis sp.]
67
45

246
3
783
1430
gnl|PID|e233869
hypothetical protein [Bacillus subtilis]
67
47

256
2
570
1601
gi|709992
hypothetical protein [Bacillus subtilisl
67
36

266
2
1266
835
gi|963038
ArpU [Enterococcus hirae]
67
42

285
1
3
809
gi|40014
pot. ORF 446 (aa 1-446) [Bacillus
67
53

subtilis
]

288
10
6838
5801
gi|1651806
hypothetical protein [Synechocystis sp.]
67
45

301
10
8822
8562
gi|1303864
YqgQ [Bacillus subtilis]
67
43

312
5
2377
2595
gi|709991
hypothetical protein [Bacillus subtilis]
67
52

353
1
3
1472
gi|151259
HMG-CoA reductase (EC 1.1.1.88)
67
48

[Pseudomonas mevalonii] pir|A44756|A44756

hydroxymethylglutaryl-CoA reductase (EC

1.1.1.88) Pseudomonas sp.

359
2
984
439
gi|1773190
similar to E. coli yhaE [Escherichia coli]
67
45

359
3
2244
982
gi|1001478
hypothetical protein [Synechocystis sp.]
67
30

364
8
8469
7816
gi|496943
ORF [Saccharomyces cerevisiae]
67
50

386
12
6625
7833
gnl|PID|e254644
membrane protein [Streptococcus
67
36

pneumoniae
]

394
2
497
2635
gnl|PID|e25593
hypothetical protein [Bacillus subtilis]
67
45

399
6
5410
3971
gi|665994
hypothetical protein [Bacillus subtilis]
67
45

414
1
1
1227
gi|1621027
high affinity potassium transporter
67
40

[Debaryomyces occidentalis]

453
2
618
391
gi|537189
ORF_f132 [Escherichia coli]
67
45

458
1
825
226
gnl|PID|e189917
ORF 28.5 [Escherichia coli]
67
45

460
2
644
1387
gi|1502421
3-ketoacyl-acyl carrier protein reductase
67
48

[Bacillus subtilis]

460
4
2622
3131
gi|1399830
biotin carboxyl carrier protein
67
53

[Synechococcus PCC7942]

474
1
1456
77
gi|495277
histidine kinase [Streptococcus
67
54

pneumoniae]

488
6
3892
3032
gi|437389
transposase [Lactococcus lactis]
67
47

490
1
460
2
gi|1742830
ORF_ID:o326#2; similar to [SwissProt
67
43

Accession Number P37794] [Eseherichia

coli
]

582
1
2
787
gi|1408485
yxdM gene product [Bacillus subtilis]
67
38

629
2
1280
915
gi|1006620
ABC transporter [Synechocystis sp.]
67
50

633
2
941
390
gnl|PID|e221400
tex gene product [Bordetella pertussis]
67
54

655
1
47
313
gi|147403
mannose permease subunit Il-P-Man
67
48

[Escherichia coli]

671
3
1630
2415
sp|P13226|GALE_STR
UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2)
67
52

LI
(GALACTOWALDENASE).

682
2
1428
595
gi|147404
mannose permease subunit II-M-Man
67
42

[Escherichia coli]

704
3
977
411
gi|467428
unknown [Bacillus subtilis]
67
45

711
1
590
168
gi|471236
orf3 [Haemophilus influenzae]
67
37

784
1
253
2
gnl|PID|e236287
site-specific DNA-methyltransferase
67
44

[Bacillus_stearothermophilus]

907
1
209
3
gi|5119
topoisomerase I [Schizosaccharomyces
67
42

pombe
]

908
1
275
96
gi|1591045
hypothetical protein (SP:P31466)
67
46

[Methanococcus jannaschii]

960
1
499
98
gi|405804
transposase [Streptococcus thermophilus]
67
50

963
1
259
2
pir|S34632|S34632
dnaJ protein homolog - human
67
54

964
1
164
628
bbs|173803
CD4+ T cell-stimulating antigen [Listeria
67
49

monocytogenes, 85E0-1167, Peptide Partial,

268 aa] [Listeria monocytogenes]

5
4
1438
2403
gi|1303810
YgeT [Bacillus subtilis]
66
50

7
1
24
1727
gi|145220
alanyl-tRNA synthetase [Escherichia coli]
66
50

7
2
1858
2646
gi|687599
orfA1; transposon insertion into orfA1
66
58

impairs growth and virulence f L.

monocytogenes [Listeria monocytogenes]

8
1
3
707
gi|1303830
YgfL [Bacillus subtilis]
66
45

9
1
182
1051
gi|467399
IMP dehydrogenase [Bacillus subtilis]
66
51

17
11
8383
8598
gi|457336
Pv200 [Plasmodium vivax]
66
42

18
14
5903
6136
gi|294706
trfA [Plasmid RK2]
66
50

23
12
5951
6895
gi|1652472
ethylene response sensor protein
66
51

[Synechocystis sp.]

23
17
11198
11881
gi|466517
pduB [Salmonella typhimurium]
66
44

23
19
12395
13501
gi|145206
pduB [Salmonella typhimurium]
66
47

34
5
5987
6232
gi|397360
yNucR endo-exonuclease [Saccharomyces
66
46

cerevisiae
]

43
2
782
1018
gi|513417
non-structural polyprotein of pSP6-SFV4
66
46

[unidentified]

43
5
3757
2324
gnl|PID|e154145
penicillin binding protein 4
66
44

[Staphylococcus_aureus]

56
4
2351
1662
gi|49272
Asparaginase [Bacillus licheniformis]
66
44

57
2
950
1735
gi|1657505
hypothetical protein [Escherichia coli]
66
46

57
4
3117
3932
gi|1657507
hypothetical protein [Escherichia coli]
66
41

57
8
12269
12646
gi|1622733
orf108; unknown function [Butyrivibrio
66
44

fibrisolvens
]

62
2
547
1302
gi|413967
ipa-43d gene product [Bacillus subtilis]
66
50

62
5
2633
1905
gi|475110
fructokinase [Pediococcus pentosace]
66
51

74
7
4661
4086
gi|467484
unknown [Bacillus subtilis]
66
47

81
18
13878
13717
gi|146724
enzyme III-Man function protein (manX
66
35

(ptsL)) [Escherichia coli] gi|41976 manX

gene product (AA 1-315) [Escherichia coli]

94
17
20780
21253
gi|142955
glucose dehydrogenase (EC 1.1.1.47)
66
47

[Bacillus subtilis] pir|S36090|S36090

glucose 1-dehydrogenase (EC 1.1.1.47) -

Bacillus ubtilis

98
15
15165
14338
gi|147327
transport protein [Escherichia coli]
66
34

105
3
1726
3183
gnl|PID|e205173
orf1 gene product [Lactobacillus
66
45

helveticus
]

110
17
15811
14804
gi|887824
ORF_o310 [Escherichia coli]
66
52

112
2
712
443
gnl|PID|e242290
carbainate kinase [Clostridium perfringens]
66
51

123
1
1
540
gi|1573538

H. influenzae
predicted coding region
66
39

H10552 [Haemophilus influenzae]

123
33
30312
31460
gi|1498930

M. jannaschii
predicted coding region
66
48

MJ0158 [Methanococcus jannaschii]

125
8
4914
4474
gi|1736749
Exopolysaccharide production protein PSS.
66
54

[Escherichia_coli]

128
25
18201
18878
gnl|PID|e255543
putative iron dependant repressor
66
48

[Staphylococcus epidermidis]

131
3
2311
3213
gi|38969
lacF gene product [Agrobacterium
66
37

radiobacter
]

131
5
3588
3394
gi|1303823
YqfG [Bacillus subtilis]
66
29

135
1
1214
45
gi|1498930

M. jannaschii
predicted coding region
66
48

MJ0158 [Methanococcus jannaschii]

135
10
7764
7405
gi|530825
OVT1 [Onchocerca volvulus]
66
47

144
13
12859
10739
pir|A40614|A40614
penicillin-binding protein pbpF - Bacillus
66
47

subtilis

145
5
3224
4063
gi|349531
lipoprotein [Pasteurella haemolytica]
66
45

146
2
1497
619
gi|147404
mannose permease subunit II-M-Man
66
38

[Escherichia coli]

149
2
1097
1282
gi|1762962
FemA [Staphylococcus simulans]
66
38

150
3
1443
2417
gnl|PID|e185374
ceuE gene product [Campylobacter coli]
66
46

150
8
6487
6903
gi|1377842
unknown [Bacillus subtilis]
66
43

164
20
21846
22646
gi|1279769
FdhC [Methanobacterium thermoformicicum]
66
57

164
25
24555
25688
pir|A43577|A43577
regulatory protein pfoR - Clostridium
66
47

perfringens

178
1
383
3
gi|763052
integrase [Bacteriophage T270]
66
47

195
19
8698
8516
bbs|169008
homeobox gene [Drosophila sp.]
66
55

207
1
166
1554
gi|619724
MgtE [Bacillus firmus]
66
39

207
3
2312
2010
gi|1204258
soluble protein [Escherichia coli]
66
44

211
3
1523
1729
gi|289932
MHC class II beta chain [Cyphotilapia
66
66

frontosa
]

213
3
1811
2308
gi|153045
prolipoprotein signal peptidase
66
40

[Staphylococcus aureus] pir|S20433|S20433

lsp protein - Staphylococcus aureus

sp|P31024|LSPA_STAAU LIPOPROTEIN SIGNAL

PEPTIDASE (EC 3.4.23.36) PROLIPOPROTEIN

SIGNAL PEPTIDASE) (SIGNAL PEPTIDASE II)

(SPASE II).

221
7
2524
3468
gi|1353527
ORF10 [Bacteriophage rlt]
66
44

222
13
8272
8988
gi|466719
No definition line found [Eschenichia
66
48

coli
]

223
18
15210
15971
gi|496520
orf iota [Streptococcus pyogenes]
66
57

232
5
3494
2715
gi|142706
comG1 gene product [Bacillus subtilis]
66
41

235
3
1774
734
gi|580897
OppB gene product [Bacillus subtilis]
66
47

244
2
906
1520
gi|15354
ORF 55.9 [Bacteriophage T4]
66
46

259
3
2355
1867
gi|56312
Gephyrin [Rattus norvegicus]
66
55

271
1
1
675
gi|1574748
tRNA pseudouridine 55 synthase (truB)
66
53

[Haemophilus influenzae]

277
1
1
927
gi|1303799
YqeN [Bacillus subtilis]
66
45

291
5
4587
3547
gnl|PID|e257609
sugar-binding transport protein
66
46

[Anaerocellum thermophilum]

292
25
20451
19912
gi|1649035
high-affinity periplasmic glutamine
66
50

binding protein [Salmonella typhimurium]

300
1
2302
77
gi|289262
comE ORF3 [Bacillus subtilis]
66
46

301
4
4290
3265
sp|P13226|GALE_STR
UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2)
66
51

LI
(GALACTOWALDENASE).

301
5
4516
4689
gnl|PID|e212164
PSII, protein N [Odontella sinensis]
66
58

314
1
360
4
gi|467452
unknown [Bacillus subtilis]
66
43

15
4
2559
2209
gi|1653498
ABC transporter [Synechocystis sp.]
66
44

320
3
2406
1081
gnl|PID|e250352
unknown [Mycobacterium tuberculosis]
66
35

332
2
157
921
gi|1303875
YghB [Bacillus subtilis]
66
44

334
2
1001
3076
gi|1651660
DNA ligase [Synechocystis sp.]
66
48

338
1
2
616
gi|845686
ORF-27 [Staphylococcus aureus]
66
54

338
7
5011
5496
gi|912476
No definition line found [Escherichia
66
48

coli
]

341
5
1935
3107
gi|142538
aspartate aminotransferase [Bacillus sp.]
66
44

343
3
2548
2045
gnl|PID|e289147
similar to single strand binding protein
66
44

[Bacillus subtilis]

345
20
22093
22461
gi|1657795
dihydroneopterin aldolase
66
45

[Methylobacterium extorquens]

353
3
2621
2379
gnl|PID|e257628
ORF [Lactococcus lactis]
66
52

365
4
5117
4779
gi|1742868
Mutator MutT protein (7,8-dihydro-8-
66
54

oxoguanine-triphosphatase) (8-oxo-dgtpase)

(EC 3.6.1.-) (DGTP pyrophosphohydrolase).

[Escherichia coli]

376
1
3
1076
gi|1778517
glycerol dehydrogenase homolog
66
45

[Escherichia coli]

394
7
5980
5648
gi|486358
ORF YKL202w [Saccharomyces cerevisiae]
66
38

421
4
1469
2539
gi|606375
ORF_f345 [Escherichia coli]
66
48

475
6
3978
3763
gi|532547
ORF14 [Enterococcus faecalis]
66
48

491
8
7710
7081
gi|1000453
TreR [Bacillus subtilis]
66
49

526
1
392
3
gi|1750125
xylulose kinase [Bacillus subtilis]
66
49

552
6
6147
5917
gi|1432152
PTS antiterminator [Klebsiella oxytoca]
66
37

571
2
560
1153
gi|1773132
multidrug resistance-like ATP-binding
66
38

protein Mdl [Esoherichia coli]

575
3
1075
539
gi|1651722
guanylate kinase [Synechocystis sp.]
66
48

608
2
631
113
gi|1213334
OrfX; hypothetical 22.5 KD protein
66
41

downstream of type IV prepilin leader

peptidase gene; Method: conceptual

translation supplied by author [Vibrio

vulnificus
]

640
1
877
2
sp|P50487|YCPX_CLO
HYPOTHETICAL PROTEIN IN CPE 5′REGION
66
36

PE
(FRAGMENT)

734
1
2
343
gi|1653602
hypothetical protein [Synechocystis sp.]
66
43

802
1
2
292
gnl|PID|e280516
voltage-gated sodium channel [Mus
66
58

musculus
]

812
2
343
531
gi|511075
ORF2 [Streptococcus agalactiae]
66
51

823
1
1
393
gi|1303843
YqfV [Bacillus subtilis]
66
42

891
1
82
402
gi|567769
ORF5; predicted protein shows similarity
66
52

to ATP-binding transport roteins AmiE and

AmiF of Streptococcus pneumoniae;

disruptulon of RF5 leads to aminopterin

resistance [Streptococcus parasanguis]
66
52

5
6
2630
3154
gi|1303811
YqeU [Bacillus subtilis]
65
50

16
1
2
628
gi|1742303
Acyl carrier protein phosphodiesterase
65
43

(ACP phosphodiesterase) (fragment),

[Escherichia coli]

18
6
3360
2518
gi|601880
rep protein [Bacillus borstelensis]
65
40

21
11
7933
7706
gi|1500521

M. jannaschii
predicted coding region
65
32

MJ1623 [Methanococcus jannaschii]

23
20
13459
13881
gi|488430
alcohol dehydrogenase 2 [Entamoeba
65
43

histolytica
]

23
25
15987
16178
gnl|PID|e248966
F32D8.5 [Caenorhabditis elegans]
65
50

27
2
526
302
gi|1001644
regulatory components of sensory
65
44

transduction system [Synechocystis sp.]

29
9
6770
5727
sp|P36672|PTTB_ECO
PTS SYSTEM, TREHALOSE-SPECIFIC IIBC
65
45

LI
COMPONENT (EIIBC-TRE) (TREHALOSE- PERMEASE

IIBC COMPONENT) (PHOSPHOTRANSFERASE ENZYME

II, BC COMPONENT) (BC 2.7.1.69) (EII-TRE).

31
5
4611
5207
gi|171625
guanylate kinase [Saccharomyces
65
39

cerevisiae
]

32
7
4085
3915
gi|150158
29 kD protein [Mycoplasma genitalium]
65
51

33
8
7396
7638
gi|1573421
protein translocation protein, low
65
26

temperature (secG) [Haemophilus

influenzae
]

35
1
2
499
gi|1737500
transcription antiterminator [Bacillus
65
40

stearothermophilus
]

45
6
2537
3037
gi|511455
unknown [Coxiella burnetii]
65
37

46
3
1028
2254
gi|1001642
dGTP triphosphohydrolase [Synechocystis
65
43

sp
.]

47
12
14524
14264
gi|150209
ORF 1 [Mycoplasma mycoides]
65
34

50
3
2866
2051
gi|1303830
YgfL [Bacillus subtilis]
65
40

57
11
12955
13332
gnl|PID|e254999
phenylalany-tRNA synthetase beta subunit
65
51

[Bacillus subtilis]

62
1
2
484
gi|1573470

H. influenzae
predicted coding region
65
57

H10491 [Haemophilus influenzae]

68
1
49
282
gi|1573250
aspartate aminotransferase (aspC)
65
52

[Haemophilus influenzae]

72
2
567
1325
gi|466645
alternate name yhiD [Escherichia coli]
65
40

81
5
3711
2938
gi|1732200
PTS permease for mannose subunit IIPMan
65
43

[Vibria furnissii]

83
18
12506
12745
pir|D64042|D64042
ribosomal-protein-alanine
65
50

acetyltransferase (rimI) homolog -

Haemophilus influenzae
(strain Rd KW20)

100
38
28229
28032
gi|183075
glial fibrillary acidic protein [Homo
65
43

sapiens
]

105
1
912
106
pir|S15248|YQBZCD
fimC protein - Dichelobacter nodosus
65
46

(serotype D)

106
5
6097
5102
gi|1143204
ORF2; Method: conceptual translation
65
44

supplied by author [Shigella sonnei]

109
3
1165
899
gi|1573390
hypothetical [Haemophilus influenzae]

110
7
5579
4257
pir|B44514|B44514
hypothetical protein 1 (vnfA 5′ region) -
65
43

Azotobacter vinelandii
]

120
3
1249
1632
sp|P54746|YBGB_ECO
HYPOTHETICAL PROTEIN IN HRSA 3′REGION
65
48

LI
(FRAGMENT).

122
2
896
1654
gi|1335913
unknown [Erysipelothrix rhusiopathiae]
65
48

145
4
2509
3210
gi|1208965
hypothetical 23.3 kd protein [Eseherichia
65
40

coli
]

149
7
4407
3502
gi|145173
35 kDa protein [Escherichia coli]
65
46

154
8
5738
4926
gi|405804
transposase [Streptococcus thermophilis]
65
47

155
1
306
512
gi|285627

E.coli
SecE homologous protein [Bacillus
65
48

subtilis] pir|S39858|S39858 secE protein

homolog - Bacillus subtilis

sp|Q06799|SECE_BACSU PREPROTEIN

TRANSLOCASE SECE SUBUNIT.

158
1
150
1103
gi|289272
ferrichrome-binding protein [Bacillus
65
40

subtilis
]

158
16
14885
15946
gi|467172
add; L308_C2_206 [Mycobacterium leprae]
65
36

173
4
2103
2912
gnl|PID|e254877
unknown [Mycobacterium tuberculosis]
65
41

173
12
9749
9054
gi|1652864
hypothetical protein [Synechocystis sp.]
65
50

179
16
15674
17035
gi|1171125
thioredoxin reductase [Clostridium
65
41

litorale
]

180
26
26911
28266
sp|P13692|P54_ENTF
P54 PROTEIN PRECURSOR.
65
39

C

193
6
2893
3795
gi|39787
adaA [Bacillus subtilis]
65
45

194
5
1843
2238
gi|47394
5-oxoprolyl-peptidase [Streptococcus
65
48

pyogenes
]

199
1
894
82
gi|1591118
nitrate transport ATP-binding protein
65
46

[Methanococcus jannaschii]

200
24
13441
13136
gi|144926
toxin A [Clostridium difficile]
65
39

202
3
2925
1846
gi|413968
ipa-44d gene product [Bacillus subtilis]
65
46

203
1
797
3
gi|1377832
unknown [Bacillus subtilis]
65
45

204
3
1065
1472
gi|1008996
unknown [Schizosaccharomyces pombe]
65
51

205
4
1029
1685
gi|148989
truncated tetracycline resistance
65
42

repressor (non-functional) Haemophilus

parainfluenzae
]

206
8
5037
4807
pir|D60110|D60110
repetitive protein antigen 3 - Trypanosoma
65
41

cruzi
(fragment)

217
1
411
4
gi|1146181
putative [Bacillus subtilis]
65
43

217
4
1092
3065
gi|984229
penicillin-binding protein 1a
65
48

[Streptococcus pneumoniae]

223
27
23445
23879
gnl|PID|e269486
Unknown [Bacillus subtilis]
65
47

225
6
5138
3984
gi|39956
IIGlc [Bacillus subtilis]
65
47

229
5
5528
5130
gi|1303914
YghY [Bacillus subtilis]
65
33

229
10
10697
8517
gnl|PID|e266933
unknown [Mycobacterium tuberculosis]
65
46

233
3
2413
1526
gi|1887825
ORF_f541 [Escherichia coli]
65
46

236
4
6975
4789
gi|405863
yohA [Escherichia coli]
65
43

237
4
1460
1816
gi|305080
myosin heavy chain [Entamoeba histolytica]
65
42

238
24
21690
23228
gi|305008
rhamnulokinase [Escherichia coli]
65
49

242
3
2192
3280
gnl|PID|e221269
tail protein [Bacteriophage CP-1]
65
37

244
6
5172
4228
gi|1653197
hypothetical protein [Synechocystis sp.]
65
51

259
5
3684
2779
gi|559900
F49E2.1 [Caenorhabditis elegans]
65
39

259
6
4243
3749
gi|1743887
molybdopterin cofactor biosynthesis enzyme
65
50

[Bradyrhizobium laponicum]

260
1
140
478
gi|895748
putative cellobiose phosphotransferase
65
55

enzyme II [Bacillus ubtilis]

269
6
4113
3907
gi|1303792
YgeK [Bacillus subtilis]
65
39

271
12
7731
6772
gi|1657534
cyn operon transcriptional activator
65
45

[Escherichia coli]

275
9
6413
5361
gi|1773132
multidrug resistance-like ATP-binding
65
48

protein Mdl [Escherichia coli]

276
4
1813
1583
gi|1504014
similar to myosin heavy chain: Containing
65
34

ATP/GTP-binding site motif A(P-loop) [Homo

sapiens
]

279
14
14254
10625
gi|1237015
ORF4 [Bacillus subtilis]
65
45

281
2
692
1279
gi|1303962
YgjK [Bacillus subtilis]
65
50

295
5
2279
3388
gi|436965
[malA] gene products [Bacillus
65
41

stearothermophilus
] pir|543914|S43914

hypothetical protein 1 - Bacillus

tearothermophilus

298
1
63
1142
gi|928834
integrase [Lactococcus lactis phage BK5-T]
65
44

301
8
7592
7176
gi|1303893
YqhL [Bacillus subtilis]
65
50

311
3
4658
5701
gnl|PID|e221269
tail protein [Bacteriophage CP-1]
65
40

326
1
2
247
gi|466520
pocR [Salmonella typhimurium]
65
38

329
1
789
523
gi|1303895
YqhN [Bacillus subtilis]
65
36

345
5
3363
3641
gi|895749
putative cellobiose phosphotransferase
65
51

enzyme II″ [Bacillus ubtilis]

369
3
1635
1207
gi|1480429
putative transcriptional regulator
65
45

[Bacillus stearothermophilus]

373
2
815
1630
gi|1277032
unknown [Bacillus subtilis]
65
41

379
9
11301
8275
gi|887828
was o492p and o826p before splice
65
49

[Escherichia coli]

386
13
7903
8145
gnl|PID|e217382
M7.9 [Caenorhabditis elegans]
65
39

395
4
1028
1231
gi|1592033

M. jannaschii
predicted coding region
65
30

MJ1387 [Methanococcus jannaschii]

396
3
1000
1272
gi|1045900
hypothetical protein (GB:L09228_17)
65
44

[Mycoplasma genitalium]

422
3
2050
1262
gi|405907
yejD [Escherichia coli]
65
50

438
1
44
358
gi|530798
LysB [Bacteriophage phi-LC3]
65
39

460
1
119
646
gi|1502420
malonyl-CoA:Acyl carrier protein
65
46

transacylase [Bacillus subtilis]

463
1
870
121
gi|1651917
tRNA(m1G37)methyltramsferase
65
47

[Synechocystis sp.]

468
1
2
823
gi|216457
ORF [Escherichia coli]
65
46

470
1
34
816
gi|530798
LysB [Bacteriophage phi-LC3]
65
47

476
1
21
830
gi|1006591
cation-transporting ATPase PacL
65
46

[Synechocystis sp.]

510
7
4875
6092
gi|143150
levR [Bacillus subtilis]
65
46

565
2
686
339
gi|143833
PBSX repressor [Bacillus subtilis]
65
51

566
2
198
743
gi|496501
RepS [Streptococcus pyogenes]
65
34

604
5
1875
2078
gi|1590997

M. jannaschii
predicted coding region
65
49

MJ0272 [Methanococcus jannaschii]

608
1
194
3
gnl|PID|e290940
unknown [Mycobacterium tuberculosis]
65
35

648
1
60
953
gi|1591145
hypothetical protein (HI0902)
65
31

[Methanococcus jannaschii]

657
4
2531
1620
gi|1500015
amidase [Methanococcus jannaschii]
65
46

691
1
2
718
gnl|PID|e248400
orfRM1 gene product [Bacillus subtilis]
65
48

704
2
474
175
gi|467428
unknown [Bacillus subtilis]
65
50

758
2
408
683
gi|451201
ORF1 [Bacillus subtilis]
65
44

778
1
833
3
gi|410137
ORFX13 [Bacillus subtilis]
65
40

793
1
1
564
gi|912436
oligo-1,6-glucosidase [Bacillus
65
40

thermoglucosidasius
] pir|A41707|A41707

oligo-1,6-glucosidase (BC 3.2.1.10) -

Bacillus hemoglucosidasius

827
1
364
2
gi|852076
MrgA [Bacillus subtilis]
65
33

856
1
209
3
gi|1575605
4-methyl-5-nitrocatechol oxygenase
65
45

[Burkholderia sp.]

890
1
966
745
pir|A44803|A44803
pG1 protein - human (fragment)
65
63

4
1
2
958
gnl|PID|e265530
yorfE [Streptococcus pneumoniae]
64
43

5
8
4212
5579
gi|407881
stringent response-like protein
64
47

[Streptococcus equisimilis]

pir|539975|539975 stringent response-like

protein - Streptococcus quisimilis

8
4
4047
3304
gi|1573150
dihydrolipoamide acetyltransferase (acoC)
64
37

[Haemophilus influenzae]

17
14
11709
10393
gi|155109
ORF 1B [Thermus aguaticus thermophilus]
64
37

19
12
6499
6801
gi|1303755
YqbO [Bacillus subtilis]
64
32

23
1
1
303
gi|1022963
dextransucrase [Leuconostoc mesenteroides]
64
50

28
4
7059
6505
gi|1568609
18kDA protein [Streptococcus pneumoniae]
64
45

31
3
1316
2986
gi|1100076
PTS-dependent enzyme II [Clostridium
64
47

longisporum
]

47
2
2665
3408
gi|1742154
Phosphoglycolate phosphatase (EC
64
52

3.1.3.18). [Escherichia coli]

48
2
1699
1310
gi|142702
A competence protein 2 [Bacillus subtilis]
64
41

54
8
2750
2352
gi|951052
ORF9, putative [Streptococcus pneumoniae]
64
31

57
15
18035
17274
gi|1183886
integral membrane protein [Bacillus
64
40

subtilis
]

62
4
1968
1699
gi|475110
fructokinase [Pediococcus pentosaceus]
64
52

100
42
29329
29039
gi|951048
excisionase [Streptococcus pneumoniae]
64
37

102
4
3726
4805
gi|215331
morphogenesis protein [Bacteriophage phi-
64
43

29]

106
3
3296
2439
gi|1303930
YgiK [Bacillus subtilis]
64
44

123
12
12960
11314
sp|P37047|YAEG_ECO
HYPOTHETICAL 44.3 KD PROTEIN IN HTRA-DAPD
64
40

LI
INTERGENIC REGION.

128
2
1285
1614
gi|143961
pyruvate phosphate dikinase [Clostridium
64
52

symbiosum
] pir|A36231|KIQAPO

pyruvate, orthophosphate dikinase (EC

2.7.9.1) - lostridium symbiosum

128
8
6178
4757
gi|40665
beta-glucosidase [Clostridium
64
41

thermocellum
]

133
2
1748
2248
gi|1591027
ferripyochelin binding protein
64
46

[Methanococcus jannaschii]

150
1
35
673
gnl|PID|e185372
ceuC gene product [Campylobacter coli]
64
38

158
6
6038
5040
gi|1045801
hypothetical protein (SP:P32720)
64
35

[Mycoplasma genitalium]

164
7
3620
4903
gnl|PID|e283116
unknown similar to quinolon resistance
64
41

protein NorA [Bacillus subtilis]

171
11
10107
10784
gi|1591668
phosphate transport system regulatory
64
40

protein [Methanococcus jannaschii]

179
4
4826
6373
gi|149535
D-alanine activating enzyme [Lactobacillus
64
51

casei
]

181
4
2251
1364
gi|671632
unknown [Staphylococcus aureus]
64
38

190
11
11302
10355
gi|599850
orf1 gene product [Lactobacillus sake]
64
33

195
37
15344
16033
gi|1736499
Lysostaphin precursor (BC 3.5.1.-).
64
49

[Escherichia coli]

199
4
4000
5631
gi|746574
similar to M. musculus transport system
64
37

membrane protein, Nramp PIR:A40739) and S.

cerevisiae
SMF1 protein (PIR:A45154)

Caenorhabditis elegans
]

202
1
1
1560
gi|309662
pheromone binding protein [Plasmid pCF10]
64
45

204
7
3000
4115
gi|1591731
melvalonate kinase [Methanococcus
64
41

jannaschii
]

208
1
308
1090
gi|473821
‘tetrahydrodipicolinate N-
64
42

succinyltransferase’ [Escherichia coli]

gi|1552743 tetrahydrodipicolinate N-

succinyltransferase Escherichia coli]

216
9
6501
6698
gi|47373
7 kDa protein [Streptococcus pneumoniae]
64
35

221
18
8268
8513
gi|1389837
complement regulatory protein [Trypanosoma
64
28

cruzi
]

231
4
2964
2632
gnl|PID|e279941
muconate cycloisomerase [Rhodococcus
64
37

erythropolis
]

234
2
751
302
gnl|PID|e194709
N-terminal part of a protein of unknown
64
42

function [Chlamydia psittaci]

238
18
15580
16392
gi|537108
ORE_f254 [Escherichia coli]
64
44

245
1
14
868
gi|153247
endo-beta-N-acetylglucosaminidase H
64
51

[Streptomyces plicatus]pir|A00903|RBSMHP

mannosyl-glycoprotein ndo-beta-N-

acetyiglucosaminidase (EC 3.2.1.96) H

precursor - treptomyces plicatus

272
2
584
1144
gi|580781
signal peptidase [Bacillus licheniformis]
64
47

281
5
2659
5019
gi|147550
recJ [Escherichia coli]
64
46

290
12
9496
10371
gi|45713

P.putida
genes rpmH, rnpA, 9k, 60k, 50k,
64
42

gidA, gidB, uncI and uncB seudomonas

putida]

298
4
4029
3466
gi|147780
rts gene product [Escherichia coli]
64
43

301
20
16216
15977
gi|170482
prosystemin [Solanum lycopersicum]
64
57

301
21
17732
17391
gi|405804
transposase [Streptococcus thermophilus]
64
52

307
1
198
1964
gi|1255196
BSMA [Bacillus stearothermophilus]
64
48

320
5
3441
3070
gi|972900
ArtP [Haemophilus influenzae]
64
38

341
9
7690
6413
gi|1161380
IcaA [Staphylococcus epidermidis]
64
30

345
6
3589
4848
gi|902932
L-methionine gamma-lyase [Pseudomonas
64
45

putida
]

348
1
453
22
gi|1591957

M. jannaschii
predicted coding region
64
32

MJ1318 [Methanococcus jannaschii]

350
2
1372
1830
gnl|PID|e289141
similar to hydroxyrnyristoyl-(acyl carrier
64
44

protein) dehydratase [Bacillus subtilis]

351
7
3291
2917
gi|49013
dTDP-dihydrostreptose synthase
64
46

[Streptomyces griseus] ir|S18618|SYSMPG

dTDP-dihydrostreptose synthase -

Streptomyces iseus

352
2
780
1028
gi|173431
H+−ATPase [Schizosaccharomyces pombe]
64
38

386
10
5952
6161
gnl|PID|e243284
ORF YGLO56c [Saccharomyces cerevisiae]
64
50

398
2
1233
1808
gi|147920
3-methyladenine-DNA glycosylase I (tag)
64
47

[Escherichia coli]

399
12
8761
9159
gi|1778534
H10024 homolog [Escherichia coli]
64
40

409
1
657
1607
gi|1773157
ferrochelatase [Escherichia coli]
64
41

446
1
266
775
gi|563845
orf gene product [Bacillus circulans]
64
53

462
4
1714
1959
gi|169461
serine proteinase inhibitor [Populus
64
50

trichocarpa
× Populus eltoides]

466
6
5621
8539
gi|143150
levR [Bacillus subtilis]
64
43

501
2
891
1469
gi|467109
rim; 30S Ribosomal protein S18 alanine
64
44

acetyltransferase; 229_C1_170

[Mycobacterium leprae]

512
1
1
279
gi|1651948
hypothetical protein [Synechocystis sp.]
64
35

516
1
466
2
gi|155027
6′-N-acetyltransferase [Transposon Tn2426]
64
35

516
2
556
759
gi|1653387
nitrogen assimilation regulatory protein
64
58

[Synechocystis sp.]

523
2
904
662
gi|159464
armadillo protein [Musca domestica]
64
45

537
2
1083
844
gi|929966
truncated ORFB due to a basepair deletion;
64
42

similar to B. anthracis terneR element

ORFB [Bacillus anthracis]

549
1
309
4
gi|1279769
FdhC [Methanobacterium thermoformicicum]
64
48

552
4
5960
3945
gi|1100076
PTS-dependent enzyme II [Clostridium
64
47

longisporum
]

556
1
3
224
gi|727437
putative 37-kDa protein [Lactococcus
64
49

lactis
]

557
2
767
1120
gnl|PID|e257629
transcription factor [Lactococcus lactis]
64
44

602
1
428
156
gi|520407
orf2; GTG start codon [Bacillus
64
50

thuringiensis]

603
1
1
165
gi|1621445
sporulation protein Cse15 [Bacillus
64
32

subtilis
]

626
1
3
992
gi|1574715
thioredoxin reductase (trxB) [Haemophilus
64
40

influenzae
]

628
2
240
446
gi|1165281
Smg [Borrelia burgdorferi]
64
41

723
1
23
829
gi|1620648
surface protein Rib [Streptococcus
64
50

agalactiae
]

739
1
4
378
gi|143835
PBSX repressor [Bacillus subtilis]
64
37

748
1
139
765
gi|498816
ORF7; homology to regions 4.1 and 4.2 of
64
35

sigma factors [Bacillus ubtilis]

758
1
3
410
gi|451201
ORF1 [Bacillus subtilis]
64
34

808
1
368
3
gi|142833
ORF2 [Bacillus subtilis]
64
47

818
2
415
663
gi|854020
U41, major DNA binding protein [Human
64
40

herpesvirus
6]

906
1
2
433
gi|1303865
YggR [Bacillus subtilis]
64
44

17
28
28175
27612
gi|151824
ORF5 [Plasmid R46]
63
34

19
18
9546
9722
gi|288661
ORF5 product [Bacteriophage P2]
63
45

39
5
1841
2329
gi|1573292
hypothetical [Haemophilus influenzae]
63 47

41
1
1531
2
gi|580896
nodB protein (aa 1-219) [Bradyrhizobium
63
43

sp
.]

55
10
5052
6410
gi|1303917
YgiB [Bacillus subtilis]
63
42

80
2
1852
824
gi|38722
precursor (aa −20 to 381) [Acinetobacter
63
42

calcoaceticus
] ir|A29277|A29277 aldose 1-

epimerase (EC 5.1.3.3) - Acinetobacter

lcoaceticus

81
10
6724
6221
gi|1591234
hypothetical protein (SP:P42297)
63
40

[Methanococcus jannaschii]

81
14
9175
10848
gi|309662
pheromone binding protein [Plasmid pcF10]
63
44

86
1
2
1006
gi|143316
[gap]gene products [Bacillus megaterium]
63
43

89
13
12929
12639
gi|1377841
unknown [Bacillus subtilis]
63
44

98
14
14365
13502
sp|P45169|POTC_HAE
SPERMIDINE/PUTRESCINE TRANSPORT SYSTEM
63
37

IN
PERMEASE PROTEIN POTC.

100
24
20444
17985
gi|563258
virulence-associated protein E
63
44

[Dichelobacter nodosus]

102
2
2441
2599
gi|1619835
MOB [Bacillus thuringiensis israelens]
63
28

110
22
19725
20705
gi|1763011
lysophospholipase homolog [Homo sapiens]
63
48

115
1
481
92
gi|467360
unknown [Bacillus subtilis]
63
38

128
30
25257
24397
gi|1518679
orf [Bacillus subtilis]
63
39

138
18
12236
11580
gi|405516
This ORF is homologous to nitroreductase
63
39

from Enterobacter cloacae, ccession Number

A38686, and Salmonella, Accession Number

P15888 Mycoplasma-like organism]

143
2
167
1096
pir|S39416|S39416
metallothionein 10-I - blue mussel
63
63

158
9
10023
8893
bbs|173803
CD4+ T cell-stimulating antigen [Listeria
63
48

monocytogenes
, 85EO-1167, Peptide Partial,

268 aa] [Listeria monocytogenes]

164
6
3041
3301
gi|1573583

H. influenzae
predicted coding region
63
31

H10594 [Haemophilus influenzae]

164
18
18502
21708
gi|1015903
ORF YJR151c [Saccharomyces cerevisiae]
63
45

165
3
3084
2278
gi|537108
ORF_f254 [Escherichia coli]
63
45

166
1
83
1045
gi|762778
NifS gene product [Anabaena azollae]
63
49

168
3
638
1489
gi|805022
Ndilp [Saccharomyces cerevisiae]
63
32

171
12
10655
10810
gi|152403
phosphate regulatory protein [Rhizobium
63
50

meliloti
]

172
1
242
1336
gi|1552775
ATP-binding protein [Escherichia coli]
63
45

179
11
11236
12111
gnl|PID|e245033
unknown [Mycobacterium tuberculosis]
63
42

179
15
15289
15765
gi|1353197
thioredoxin reductase [Eubacterium
63
44

acidaminophilum
]

180
3
3412
1892
gi|1064813
homologous to sp:PHOR_BACSU [Bacillus
63
40

subtilis
]

180
7
7063
7926
gi|1657516
hypothetical protein [Escherichia coli]
63
41

187
1
1
729
gi|1651957
hypothetical protein [Synechocystis sp.]
63
34

195
17
7717
8280
gi|431928
MunI methyltransferase [Mycoplasma sp.]
63
44

202
8
5311
6165
gi|606162
ORF_f229 [Escherichia coli]
63
48

202
10
7848
8681
gi|606018
ORF_o783 [Escherichia coli]
63
47

208
3
2979
2341
gi|1006613
hypothetical protein [Synechocystis sp.]
63
40

221
3
874
1146
gnl|PID|e265530
yorfE [Streptococcus pneumoniae]
63
42

227
2
856
1254
gi|438459
homologous to E. coli hydrophobic Fe-
63
41

uptake components FepD, FecD; utative

[Bacillus subtilis]

231
3
2618
2448
gi|606248
30S ribosomal subunit protein S3
63
42

[Escherichia coli]

233
9
6773
6144
gi|887827
ORF_o192 [Escherichia coli]
63
41

234
1
348
70
gi|494958
ExpZ [Bacillus subtilis]
63
32

240
2
1230
721
gnl|PID|e252616
DcuC protein [Escherichia coli]
63
38

244
9
7512
6508
gi|467421
similar to B. subtilis DnaH [Bacillus
63
43

subtilis
] sp|P37540|YAAS_BACSU

HYPOTHETICAL 37.6 KD PROTEIN IN XPAC-ABRB

NTERGENIC REGION.

255
5
3600
2818
gi|1486244
unknown [Bacillus subtilis]
63
47

258
1
3
449
gi|1041115
TRAC [Plasmid pPD1]
63
38

259
4
2842
2342
gnl|PID|e290788
unknown [Mycobacterium tuberculos]
63
42

265
8
3313
3480
gi|694074
emml gene product [Streptococcus pyogenes]
63
42

276
18
12505
11654
gi|601878
beta-1,3-glucanase bg1H [Bacillus
63
36

circulans
]

294
5
2012
2275
gi|288661
ORF5 product [Bacteriophage P2]
63
40

301
7
7063
6704
gnl|PID|e290998
unknown [Mycobacteriurn tuberculos]
63
41

345
2
2279
2725
gi|413940
ipa-16d gene product [Bacillus subtilis]
63
39

351
8
4361
3306
gi|398120
TDP-glucose oxireductase [Xanthomonas
63
47

campestris
]

359
1
526
14
gi|1001605
3-hydroxyisobutyrate dehydrogenase
63
36

[Synechocystis sp.]

364
6
6741
7277
gi|1736473
ORF_ID:o335#13; similar to [SwissProt
63
42

Accession Number P36088] [Escherichia

coli
]

378
2
683
1414
gi|529016
aminoglycoside 6-adenylyltransferase
63
41

[Bacillus subtilis] pir|JU0059|XXBSG

aminoglycoside 6-adenylyltransferase (EC

2.7.7.-) Bacillus subtilis

392
2
783
1646
gi|1772644
orfR gene product [Bacillus subtilis]
63
34

399
2
574
1407
gi|40023

B.subtilis
genes rpmH, rnpA, 50kd, gidA
63
42

and gidB [Bacillus subtilis] i|467388

stage III sporulation [Bacillus subtilis]

ir|S18073|S18073 spoIIIJ protein -

Bacillus subtilis

403
1
754
2
gi|1303938
YqiS [Bacillus subtilis]
63
52

404
5
4149
3745
gi|142450
ahrC protein [Bacillus subtilis]
63
42

430
1
2
1222
gi|1046082

M. genitalium
predicted coding region
63
40

MG372 [Mycoplasma genitalium]

432
1
3
1241
gi|1001328
UDP-MurNac-tripeptide synthetase
63
33

[Synechocystis sp.]

432
4
1970
3016
gi|1161061
dioxygenase [Methylobacterium extorquens]
63
41

463
2
1324
851
gi|1573163
hypothetical [Haemophilus influenzae]
63
40

466
4
2843
3730
gnl|PID|e261988
putative ORF [Bacillus subtilis]
63
41

472
1
527
3
gi|556885
Unknown [Bacillus subtilis]
63
50

517
3
2803
1646
gi|531265
lipophilic protein which affects bacterial
63
38

lysis rate and ethicillin resistance level

[Staphylococcus aureus] pir|A55856|A55856

llm protein - Staphylococcus aureus

538
1
206
3
gi|172657
serine-protein kinase [Saccharomyces
63
47

cerevisiae
]

539
4
2997
3851
gi|973230
gamma-glutatnyl kinase [Lycopersicon
63
43

esculentum
]

565
3
756
1010
gi|1303724
YgaF [Bacillus subtilis]
63
51

573
7
4518
3709
gi|1652352
dihydropteroate pyrophosphorylase
63
45

[Synechocystis sp.]

579
2
361
1344
gi|1573114
beta-ketoacyl-acyl carrier protein
63
41

synthase III (fabH) [Haemophilus

influenzae
]

593
2
390
1037
gi|409286
bmrU [Bacillus subtilis]
63
33

707
1
647
171
gi|511596
interleukin-2 [Canis familiaris]
63
33

714
1
2
268
gnl|PID|e213832
putative inner membrane protein [Bacillus
63
38

licheniformis]

724
1
562
239
gnl|PID|e255315
unknown [Mycobacterium tuberculosis]
63
49

759
1
681
4
gi|437639
[Plasmodium falciparum 3′end.], gene
63
28

product [Plasmodium alciparum]

794
1
981
313
gi|451201
ORF1 [Bacillus subtilis]
63
37

811
2
609
184
gi|150553
regulatory protein [Plasmid pCF10]
63
30

835
1
2
262
gi|1736496
RpiR protein. [Escherichia coli]
63
41

11
1
2
1144
gi|143150
levR [Bacillus subtilis]
62
48

12
5
8710
7673
gi|1486244
unknown ]Bacillus subtilis]
62
43

15
3
1167
2957
gi|1592101
adenine deaminase [Methanococcus
62
40

jannaschii
]

16
4
2572
4092
gi|1109685
ProW [Bacillus subtilis]
62
37

23
4
1279
2067
gi|41432
fepC gene product [Escherichia coli]
62
35

23
26
16176
16454
gi|154499
carbon dioxide concentrating mechanism
62
41

protein [Synechococcus sp.]

pir|C36904|C36904 carbon dioxide

concentrating mechanism protein cmL -

Synechococcus sp
. (PCC 7942)

31
6
5322
5774
gi|532309
25 kDa protein [Escherichia coli]
62
38

68
4
1606
2778
gi|1732203
GlcNAc 6-P deacetylase [Vibrio furnissii]
62
44

72
1
1
540
gi|1573097
glucosamine-6-phosphate deaminase protein
62
26

(nagB) [Haemophilus influenzae]

76
3
1937
2227
gi|928830
ORF75; putative [Lactococcus lactis phage
62
34

BK5 -T]

83
16
11700
12272
gi|1592161
N-terminal acetyltransferase complex,
62
33

subunit ARD1 [Methanococcus jannaschii]

83
19
12685
13737
gi|1653193
sialoglycoprotease [Synechocystis sp.]
62
42

91
6
3232
3789
gi|1762962
FemA [Staphylococcus simulans]
62
37

100
43
29676
29317
gi|963033
orf1 gene product [Enterococcus hirae]
62
45

101
8
7410
6481
gi|1161061
dioxygenase [Methylobacterium extorguens]
62
45

110
3
653
871
gi|992683
mdm2-D [Homo sapiens]
62
37

110
8
8440
5810
gi|784897
beta-N-acetylhexosaminidase [Streptococcus
62
46

pneumoniae
] pir|A56390|A56390 mannosyl-

glycoprotein ndo-beta-N-

acetylglucosaminidase (EC 3.2.1.96)

precursor - treptococcus pneumoniae

111
2
1057
287
gnl|PID|e253280
ORF YDL238c [Saccharomyces cerevisiae]
62
45

114
5
6886
7662
gi|152719
flavocytochrome c [Shewanella
62
37

putrefaciens
]

115
4
1401
1994
gi|1303978
YgkA [Bacillus subtilis]
62
46

118
1
545
225
gi|39431
oligo-1,6-glucosidase [Bacillus cereus]
62
40

119
8
4625
4356
gi|1522673
type I restriction enzyme [Methanococcus
62
33

jannaschii
]

120
2
257
1270
gnl|PID|e235823
unknown [Schizosaccharomyces pombe]
62
41

121
8
7543
8034
gi|39475
formamidopyrimidine-DNA glycosylase
62
48

[Bacillus firmus] ir|A11489|S11489

formamidopyrimidine-DNA glycosidase (EC

3.2.2.23) Bacillus firmus

123
2
1677
592
gi|882252
conjugated bile acid hydrolase
62
40

[Clostridium perfringens]

sp|P54965|CBH_CLOPE CHOLOYLOLYCINE

HYDROLASE (EC 3.5.1.24) CONJUGATED BILE

ACID HYDROLASE) (CBAH) (BILE SALT

HYDROLASE).

128
16
10895
9408
gi|1742834
PTS system, cellobiose-specific IIC
62
43

component (EIIC-CEL) (Cellobiose- permease

IIC component) (Phosphotransferase enzyme

II, C component) . [Escherichia coli]

128
29
24254
23544
gi|1518680
minicell-associated protein DivIVA
62
37

[Bacillus subtilis]

128
35
28843
28103
gi|142940
ftsA [Bacillus subtilis]
62
42

133
4
3434
4165
gnl|PID|e235174
unknown [Mycobacterium tuberculosis]
62
38

134
2
1679
933
gi|155032
ORF B [Plasmid pEa34]
62
36

146
6
4923
4651
gi|153675
tagatose 6-P kinase [Streptococcus mutans]
62
48

149
5
3318
2527
gi|1591587
pantothenate metabolism flavoprotein
62
35

[Methanococcus jannaschii]

152
9
4830
5747
gi|1652461
lactose transport system permease protein
62
39

LacF [Synechocystis sp.]

163
2
1341
544
gi|533098
DnaD protein [Bacillus subtilis]
62
41

164
14
9567
9322
gi|1118060
coded for by C. elegans cDNA yk3d11.5;
62
27

coded for by C. elegans cDNA yk5f4.5

[Caenorhabditis elegans]

172
8
6613
7146
gi|915199
ggaB [Bacillus subtilis]
62
33

173
13 11127
9736
gi|1653484
hypothetical protein [Synechocystis sp.]
62
44

177
1
1077
364
gi|1572994
2-keto-3-deoxy-6-phosphogluconate aldolase
62
38

(eda) [Haemophilus influenzae]

178
4
1683
1318
gnl|PID|e155310
Orf2 [Bacteriophage TP901-1]
62
51

179
5
6425
7576
gi|1161933
DltB [Lactobacillus casei]
62
44

180
13
12470
10842
sp|P37047|YAEG_ECO
HYPOTHETICAL 44.3 KD PROTEIN IN HTRA-DAPD
62
38

LI
INTERGENIC REGION.

181
14
11649
10735
gi|1742758
Shikimate 5-dehydrogenase (EC 1.1.1.25).
62
41

[Escherichia coli]

197
2
516
1442
gi|623476
transcriptional activator [Providencia
62
34

stuartii
] sp|P43463|AARP_PROST

TRANSCRIPTIONAL ACTIVATOR AARP.

206
5
2728
1790
gnl|PID|e265638
unknown [Mycobacterium tuberculosis]
62
37

210
2
938
2290
gi|528991
unknown [Bacillus subtilis]
62
41

221
15
7083
7280
gnl|PID|e219154
K08F4.5 [Caenorhabditis elegans]
62
44

222
11
7141
8022
gi|537034
ORF_o488 [Escherichia coli]
62
39

223
9
6924
6358
gnl|PID|e283128
unknown, highly similar to E. coli YecD
62
42

hypothtical 21.8 KD protein in aspS

5′region and to isochorismatase [Bacillus

subtilis
]

225
4
2055
2885
gi|18724
pyrroline-5-carboxylate reductase (AA 1-
62
39

274) [Glycine max] ir|S10186|S10186

pyrroline-5-carboxylate reductase (EC

1.5.1.2) - ybean

229
11
11428
10670
gnl|PID|e235745
hypothetical protein [Mycobacterium
62
36

leprae
]

231
1
1244
3
gi|48808
dciAE gene product [Bacillus subtilis]
62
45

233
1
801
4
gi|143391
ORF2 [Bacillus subtilis]
62
42

233
13
10471
9431
gi|887825
ORF_f541 [Escherichia coli]
62
35

242
1
3
149
gi|532549
ORF16 [Enterococcus faecalis]
62
44

255
2
443
1009
gi|639789
ORF9 [Mycoplasma pneumoniae]
62
44

266
6
2349
2158
gnl|PID|e194945
yeast sds22 homolog [Homo sapiens]
62
37

270
1
3
314
gi|1303827
YqfI [Bacillus subtilis]
62
35

270
7
5136
4447
gi|1303958
YgIG [Bacillus subtilis]
62
41

279
1
271
2
gnl|PID|e185372
ceuC gene product [Campylobacter coli]
62
44

301
11
9598
8798
gi|1303863
YggP [Bacillus subtilis]
62
45

306
2
750
1202
gi|148771
ribosomal protein HmaS4 [Haloarcula
62
41

marismortui
]

308
3
2328
1684
gnl|PID|e238666
hypothetical protein [Bacillus subtilis]
62
40

309
5
8806
8573
gi|1591861

M. jannaschii
predicted coding region
62
37

MJ1230 [Methanococcus jannaschii]

318
3
2278
1283
gi|1256134
YbbE [Bacillus subtilis]
62
37

321
3
1433
1792
gi|606080
ORF_o290; Geneplot suggests frameshift
62
37

linking to o267, not found Escherichia

coli
]

338
13
11175
12770
gi|467446
similar to SpoVB [Bacillus subtilis]
62
38

345
11
10519
11793
gi|1736789
Collagenase precursor (EC 3.4.-.-).
62
40

[Escherichia coli]

345
21
22459
22947
gi|1657794
6-hydroxymethyl-7,8-dihydropterin
62
47

pyrophosphokinase [Methylobacterium

extorguens
]

358
1
902
36
gi|409241
penicillin-binding protein 2
62
44

[Staphylococcus aureus]

362
6
2930
3493
gnl|PID|e255091
hypothetical protein [Bacillus subtilis]
62
37

363
2
3242
1581
gnl|PID|e254997
hypothetical protein [Bacillus subtilis]
62
40

365
2
400
1770
gi|143150
levR [Bacillus subtilis]
62
42

372
5
2525
4489
gi|1045736
fructose-permease IIBC component
62
43

[Mycoplasma genitalium]

373
1
3
851
gi|438462
transmembrane protein [Bacillus subtilis]
62
36

375
1
2
1336
gi|732813
branched-chain amino acid carrier
62
43

[Lactobacillus delbrueckii]

pir|S60180|S60180 branched-chain amino

acid carrier brnQ - actobacillus

delbrueckii

375
3
2592
1831
gi|1644206
unknown [Bacillus subtilis]
62
43

391
2
142
510
gi|151776
ORF3 [Escherichia coli]
62
31

396
2
254
1051
gi|410131
ORFX7 [Bacillus subtilis]
62
41

423
1
197
6
pir|A33592|A33592
repressor protein catM - Acinetobacter
62
38

calcoaceticus

436
1
704
3
gi|455376
unidentified reading frame L (ORFL)
62
32

(putative); putative [Transposon n10]

466
8
9320
10480
gi|147402
mannose permease subunit III-Man
62
44

[Escherichia coli]

488
5
2175
2927
gi|532546
ORF13 [Enterococcus faecalis]
62
40

510
4
2572
3078
gi|43941
EIII-B Sor PTS [Klebsiella pneumoniae]
62
35

517
2
1533
736
gi|559388
epsX gene product [Acinetobacter
62
53

calcoaceticus
]

519
1
2
1084
gi|1652876
hypothetical protein [Synechocystis sp.]
62
41

535
1
353
69
gi|1196922
unknown protein [Insertion sequence IS861]
62
33

579
1
1
363
gi|535052
involved in protein secretion [Bacillus
62
22

subtilis
]

656
5
5351
5956
gnl|PID|e290931
unknown [Mycobacterium tuberculosis]
62
40

666
1
445
128
gi|483940
transcription regulator [Bacillus
62
42

subtilis
]

682
1
597
172
gi|146724
enzyme III-Man function protein (manX
62
37

(ptsL)) [Escherichia coli] gi|41976 manX

gene product (AA 1-315) [Escherichia coli]

771
1
3
365
gi|1773086
similar to S. typhimurium ProY
62
44

[Escherichia coli]

831
1
390
94
gnl|PID|e255000
hypothetical protein [Bacillus subtilis]
62
55

15
5
4421
5260
gnl|PID|e214719
PlcR protein [Bacillus thuringiensis]
61
38

16
6
4705
4938
gi|758425
complement component C3 [Xenopus
61
44

laevis/gilli
]

23
16
10279
11214
sp|P19265|EUTC_SAL
ETHANOLAMINE ANMONIA-LYASE LIGHT CHAIN (EC
61
46

TY
4.3.1.7).

33
2
1789
2205
gi|413958
ipa-34d gene product [Bacillus subtilis]
61
36

33
5
4756
6594
gi|1001823
cadmium-transporting ATPase [Synechocystis
61
38

sp.]

37
4
2813
3295
gi|1256140
YbbK [Bacillus subtilis]
61
51

37
7
5973
5215
gnl|PID|e269488
Unknown [Bacillus subtilis]
61
33

49
4
1567
1839
gnl|PID|e139445
major tail protein [Bacteriophage B1]
61
43

56
1
108
641
gi|1574067

H. influenzae
predicted coding region
61
35

H11034 [Haemophilus influenzae]

59
1
1
1002
gi|763513
ORF4; putative [Streptomyces
61
37

violaceoruber
]

69
7
4837
5523
gnl|PID|e254877
unknown [Mycobacterium tuberculosis]
61
34

72
11
9262
10476
gi|1591272
ferrous iron transport protein B
61
45

[Methanococcus jannaschii]

83
2
731
1549
gi|755152
highly hydrophobic integral membrane
61
41

protein [Bacillus subtilis]

sp|P42953|TAGG_BACSU TEICHOIC ACID

TRANSLOCATION PERMEASE PROTEIN AGG.

87
2
2067
925
gi|1573129
hypothetical [Haemophilus influenzae]
61
46

103
5
2689
3495
gi|1685111
orf1091 [Streptococcus thermophilus]
61
45

110
13
11455
11820
gi|100182S5 transcriptional repressor SmtB
61
42

[Synechocystis sp.]

110
15
14048
12588
gi|1573583

H. influenzae
predicted coding region
61
38

H10594 [Haemophilus influenzae]

111
3
1675
1055
gnl|PID|e253280
ORF YDL238c [Saccharomyces cerevisiae]
61
34

111
4
1838
2518
gi|1574513
hypothetical [Haemophilus influenzae]
61
50

111
5
2535
3158
gi|537235
Kenn Rudd identifies as gpmB [Escherichia
61
40

coli
]

121
1
3
1397
gi|290643
ATPase [Enterococcus hirae]
61
50

123
28
25608
27734
gi|143150
levR [Bacillus subtilis]
61
39

125
5
3455
2589
gi|148921
LicD protein [Haemophilus influenzae]
61
47

128
14
9382
9146
gi|575361
protein kinase PkpA [Phycomyces
61
38

blakesleeanus
]

138
32
23151
21628
gi|1184262
GadC [Shigella flexneri]
61
34

144
8
6311
5325
gi|710422
cmp-binding-factor 1 [Staphylococcus
61
39

aureus
]

171
4
4601
5566
gi|41500
ORF 3 (AA 1-352); 38 kD (put. ftsX)
61
31

[Escherichia coli]

172
3
2006
2848
gi|303560
ORF271 [Escherichia coli]
61
42

173
7
5146
6228
gi|1256134
YbbE [Bacillus subtilis]
61
31

197
8
9183
8182
gi|143803
GerC3 [Bacillus subtilis]
61
33

217
5
3007
3462
gi|1749414
unnamed protein product
61
43

[Schizosaccharomyces pombe]

217
8
6099
5464
gi|143456
rpoE protein (ttg start codon) [Bacillus
61
37

subtilis
]

222
6
3400
3927
gnl|PID|e255118
hypothetical protein [Bacillus subtilis]
61
41

225
3
1946
981
gi|1574660
xylose operon regluatory protein (xylR)
61
43

[Haemophilus influenzae]

237
2
203
952
gi|1019108
alternate start at bp 59; ORF
61
52

[Bacteriophage phi-80]

237
7
3058
3279
gnl|PID|e246904
ORF YPL169c [Saccharomyces cerevisiae]
61
32

262
1
20
913
gnl|PID|e214719
PlcR protein [Bacillus thuringiensis]
61
35

271
17
12725
13504
gi|143057
ORF39 [Bacillus subtilis]
61
31

275
8
5370
3697
gi|1542975
AbcB [Thermoanaerobacterium
61
41

thermosulfurigenes
]

280
2
692
3079
gi|1001352
ABC transporter [Synechocystis sp.]
61
42

294
7
2276
2767
gi|662792
single-stranded DNA binding protein
61
44

[unidentified eubacterium]

301
12
9965
9519
gi|1303861
YqgN [Bacillus subtilis]
61
41

308
1
1471
26
gi|1276882
EpsI [Streptococcus thermophilus]
61
36

314
2
475
1662
gi|975351
PatB [Bacillus subtilis]
61
42

321
9
3762
4193
gi|1732202
PTS permease for mannose subunit IIIMan N
61
40

terminal domain [Vibrio furnissii]

323
5
5118
5537
gi|532540
ORF7 [Enterococcus faecalis]
61
28

324
7
4800
5156
gi|146122
H-protein [Escherichia coli]
61
39

338
3
1456
1989
pir|A47071|A47071
orfi immediately 5′ of nifS - Bacillus
61
43

subtilis

341
2
342
947
gi|1736577
Octopine transport system permease protein
61
41

OccM. [Escherichia coli]

349
3
1788
1363
pir|G64143|G64143
hypothetical protein HI0143 - Haemophilus
61
38

influenzae
(strain Rd KW20)

369
2
1261
587
gi|153744
ORF X; putative [Streptococcus mutans]
61
33

371
2
1801
1562
gi|48836
xylulokinase [Staphylococcus xylosus]
61
40

372
4
1575
2543
gi|149395
lacC [Lactococcus lactis]
61
43

379
11
12683
11727
gi|887829
D21141 uses 2nd start; frame determined by
61
40

Lac fusion [Escherichia oli]

383
5
5625
3820
gi|624072
similar to Escherichia coli
61
36

glycerophosphoryl diester

hosphodiesterase, Swiss-Prot Accession

Number p10908 [Paramecium ursaria

Chlorella virus 1]

395
2
771
517
gnl|PID|e276251
T23G11.6 [Caenorhabditis elegans]
61
42

399
20
15621
15812
gi|472527
protein phosphatase 1 [Schizosaccharomyces
61
44

pombe
]

413
1
3
749
gnl|PID|e289144
ywpE [Bacillus subtilis]
61
42

427
1
1079
288
gi|403373
glycerophosphoryl diester
61
42

phosphodiesterase [Bacillus subtilis]

pir|S37251|S37251 glycerophosphoryl

diester phosphodiesterase - acillus

subtilis

436
4
2045
1761
gi|48669
pot. ORF B [Shigella sonnei]
61
38

437
1
1158
244
gi|580866
ipa-12d gene product [Bacillus subtilis]
61
47

482
2
1676
1167
bbs|158786
4A11 antigen, sperm tail membrane
61
42

antigen=putative sucrose-specific

phosphotransferase enzyme II homolog

[mice, testis, Peptide Partial, 172 aa]

[Mus sp.]

490
3
1291
1094
gnl|PID|e248473
putative phosphate permease [Arabidopsis
61
35

thaliana
]

514
1
687
142
gi|1742775
msm operon regulatory protein.
61
36

[Escherichia coli]

541
1
758
3
gi|1591732
cobalt transport ATP-binding protein 0
61
39

[Methanococcus jannaschii]

551
3
2163
1600
gi|671632
unknown [Staphylococcus aureus]
61
38

603
2
163
564
gi|1408587
relaxase [Lactococcus lactis lactis]
61
39

637
8
4539
4769
gi|143559
subtilin [Bacillus subtilis]
61
38

765
1
34
681
gi|408888
orfA 5′ of intG [Lactobacillus
61
40

bacteriophage
phi adh] pir|PN0468|PN0468

hypothetical protein 106 - Lactobacillus

gasseri
fragment)

773
1
53
1207
gi|143841
xylose repressor [Bacillus subtilis]
61
36

798
1
175
381
gi|187572
located at OATL1 [Homo sapiens]
61
32

5
2
303
998
gi|1783264
homologous to DNA glycosylases;
60
50

hypothetical [Bacillus subtilis]

8
8
5891
6550
gi|1777939
Pfs [Treponema pallidum]
60
40

11
7
4096
4935
gi|147404
mannose permease subunit II-M-Man
60
41

[Escherichia coli]

11
8
4919
5254
gi|467125
glmS; L-Glucosamine:D-fructose-6-Phosphate
60
30

aminotransferase; 229_C3_238

[Mycobacterium leprae]

17
9
7736
8203
gi|496514
orf zeta [Streptococcus pyogenes]
60
42

20
1
3
443
gi|861137
chitin binding protein [Streptomyces
60
40

olivaceoviridis
] pir|S55001|S55001 CHB1

protein - Streptomyces olivaceoviridis

{SUB −30}

21
3
1970
684
gi|1778520
hypothetical protein [Escherichia coli]
60
43

23
11
5357
5953
gi|619066
NAST [Azotobacter vinelandii]
60
31

34
4
6662
3279
gi|153952
polymerase III polymerase subunit (dnaE)
60
37

[Salmonella typhimurium]
pir|A45915|A45915

DNA-directed DNA polymerase (EC 2.7.7.7)

III lpha chain - Salmonella typhimurium

39
1
47
466
gi|1561567
Unknown [Bacillus subtilis]
60
35

39
4
1855
1361
gi|298045
Orf154 [Streptomyces ambofaciens]
60
41

48
4
2554
4128
gi|1255259
o-succinylbenzoic acid (OSB) CoA ligase
60
40

[Staphylococcus aureus]

56
9
6682
5795
gi|413940
ipa-16d gene product [Bacillus subtilis]
60
40

65
3
2105
2593
gi|1573061
hypothetical [Haemophilus influenzae]
60
34

72
9
7854
8330
gi|606343
CG Site No. 28964 [Escherichia coli]
60
39

81
3
2053
1406
gi|1574770
phenylalanyl-tRNA synthetase beta-subunit
60
46

(pheT) [Haemophilus influenzae]

81
4
2987
2130
gi|147404
mannose permease subunit II-M-Man
60
34

[Escherichia coli]

81
12
8280
7150
gnl|PID|e254984
hypothetical protein [Bacillus subtilis]
60
44

83
22
16887
16537
gi|509672
repressor protein [Bacteriophage Tuc2009]
60
33

89
1
698
60
gi|840838
hypothetical 21.7 kDa protein in ftsY 5′
60
36

region [Pseudomonas eruginosa]

89
12
12641
11856
gi|1377843
unknown [Bacillus subtilis]
60
40

89
17
18879
15844
gi|666069
orf2 gene product [Lactobacillus
60
37

leichmannii
]

94
6
2281
3384
gi|468760
ORF334 [Rhizobium meliloti]
60
36

98
1
12
1970
gi|1652892
ABC transporter [Synechocystis sp.]
60
38

99
3
978
1460
gi|473955
DNA-binding protein [Lactobacillus sp.]
60
31

100
35
26818
26333
gi|347851
junctional sarcoplasmic reticulum
60
48

glycoprotein [Oryctolagus uniculus]

100
45
30072
30449
gi|143547
Sin regulatory protein (ttg start codon)
60
43

[Bacillus subtilis] gi|1303886 SinR

[Baciilus subtilis]

102
8
5923
6561
gi|1633572

Herpesvirus saimiri
ORF73 homolog
60
25

[Kaposi's sarcoma-associated herpes-like

virus]

109
1
362
3
pir|S10655|S10655
hypothetical protein X - Pyrococcus woesei
60
33

(fragment)

110
16
14806
14087
pir|JH0364|JH0364
hypothetical protein 176 (SAGP 5′ region)
60
35

- Streptococcus pyogenes

110
20
18929
18414
gi|142450
ahrC protein [Bacillus subtilis]
60
39

110
21
19124
19624
gi|142450
ahrC protein [Bacillus subtilis]
60
40

111
1
289
2
gi|1256618
transport protein [Bacillus subtilis]
60
31

122
7
5627
9589
gi|217191
5′-nucleotidase precursor [Vibrio
60
39

parahaemolyticus
]

123
5
4390
3659
gi|1197667
vitellogenin [Anolis pulchellus]
60
27

123
20
18102
18407
gi|1303705
YrkF [Bacillus subtilis]
60
34

128
32
26229
25492
gi|1652485
hypothetical protein [Synechocystis sp.]
60
29

129
5
4421
6259
gi|1303853
YggF [Bacillus subtilis]
60
36

131
2
1112
2338
gi|699112
ugpC gene product [Mycobacterium leprae]
60
41

131
4
3194
4036
gi|296356
putative membrane transport protein
60
32

[Clostridium perfringens]

pir|A56641|A56641 probable membrane

transport protein - Clostridium erfringens

131
8
6669
7901
gi|537054
2′,3′-cyclic-nucleotide 2′-
60
40

phosphodiesterase [Escherichia coli]

pir|S56438|s56438 2′,3′-cyclic-nucleotide

2-phosphodiesterase (EC .1.4.16) -

Escherichia coli

133
11
9854
10240
gnl|PID|e249654
YneR [Bacillus subtilis]
60
37

138
7
6793
6263
gi|1486247
unknown [Bacillus subtilis]
60
48

146
4
2831
2328
gi|39979
P18 [Bacillus subtilis]
60
38

149
6
3504
3316
gi|145173
35 kDa protein [Escherichia coli]
60
47

154
5
2599
3558
gi|1773109
similar to S. typhimurium apbA
60
41

[Escherichia coli]

155
5
3061
4701
gi|388269
traC [Plasmid pAD1]
60
38

155
11
8565
8927
gi|1197460
MtfB [Escherichia coli]
60
39

158
10
11123
10032
gi|581809
tmbC gene product [Treponema pallidum]
60
39

165
7
6131
5700
gi|1439527
EIIA-man [Lactobacillus curvatus]
60
35

172
4
3169
3810
gi|1001342
hypothetical protein [Synechocystis sp.]
60
42

174
2
1574
762
gi|1045808
hypothetical protein (GB:U00021_19)
60
35

[Mycoplasma genitalium]

181
7
4975
4460
gi|683584
shikimate kinase [Lactococcus lactis]
60
33

183
6
2719
2955
gi|1146198
ferredoxin [Bacillus subtilis]
60
37

189
2
3528
2221
gi|396301
matches PS00041: Bacterial regulatory
60
35

proteins, araC family ignature

[Escherichia coli]

193
5
3121
2600
gi|39788
adaB [Bacillus subtilis]
60
49

195
11
4623
6569
gnl|PID|e250887
potential coding region [Clostridium
60
39

difficile
]

202
2
1837
1607
gi|693939
membrane ATPase [Haloferax volcanii]
60
32

206
7
4794
3754
gi|1574702
hypothetical [Haemophilus influenzae]
60
42

209
2
1308
433
pir|A38587|A38587
collagen, corneal - chicken (fragment)
60
51

220
3
4263
1213
gi|437706
alternative truncated translation product
60
41

from E.coli [Streptococcus neumoniae]

222
9
6019
6522
gi|882463
protein-N(pi)-phosphohistidine-sugar
60
47

phosphotransferase [Escherichia oli]

222
12
8001
8336
gi|537035
ORF_o101 [Escherichia coli]
60
33

233
2
1294
827
gi|145091
flavodoxin [Desulfovibrio salexigens]
60
39

242
11
7370
7627
gi|1353404
cytochrome oxidase subunit I [Metridium
60
28

senile
]

249
3
1109
1768
gi|143156
membrane bound protein [Bacillus subtilis]
60
41

251
3
4053
1933
gi|1235662
RfbC [Myxococcus xanthus]
60
42

256
4
2614
3867
gi|532612
ecotropic retrovirus receptor [Mus
60
37

musculus
]

260
2
1539
802
gi|1208447
metahloprotease transporter [Serratia
60
35

marcescens
]

261
5
4528
3179
gnl|PID|e246728
histidine kinase [Streptococcus gordonii]
60
25

269
3
2723
1563
gi|1591618

M. jannaschii
predicted coding region
60
39

MJ0951 [Methanococcus jannaschii]

269
4
3541
2780
gi|1303794
YgeM [Bacillus subtilis]
60
36

269
11
7164
6595
gi|1303787
YgeG [Bacillus subtilis]
60
38

271
2
677
1651
gnl|PID|e269877
riboflavin kinase [Bacillus subtilis]
60
43

271
3
1639
2247
gi|537148
ORF_f181 [Escherichia coli]
60
41

271
18
13502
13762
pir|S3934|S39341
grpE protein - Lactococcus lactis
60
40

277
2
1662
979
gi|1773109
similar to S. typhimurium apbA
60
41

[Escherichia coli]

279
13
10627
9773
gi|290545
f270 [Escherichia coli]
60
41

290
2
790
1695
gi|152886
elongation factor Ts (tsf) [Spiroplasma
60
38

citri
]

291
4
3571
2612
gnl|PID|e257610
sugar-binding transport protein
60
40

[Anaerocellum thermophilum]

295
3
1309
2094
gi|1000453
TreR [Bacillus subtilis]
60
37

301
15
11063
11344
gi|535274
ORF1 [Streptococcus thermophilus]
60
36

310
3
2903
1266
gi|809765
aspartate aminotransferase (AA 1-402)
60
44

[Sulfolobus solfataricus]

pir|S07088|S07088 aspartate transaminase

(EC 2.6.1.1) - Sulfolobus olfataricus

316
2
319
119
bbs|115298
polyprotein(coat protein) [raspberry
60
28

ringspot virus RRV, Peptide, 1107 aa]

[Raspberry ringspot virus]

320
4
3085
2483
gi|143002
proton glutamate symnport protein [Bacillus
60
26

caldotenax
] pir|S26246|S26246

glutamate/aspartate transport protein -

Bacillus aldotenax

323
1
1
681
gi|1477486
transposase [Burkholderia cepacia]
60
44

330
4
3361
4488
gi|1778517
glycerol dehydrogenase homolog
60
48

[Escherichia coli]

356
3
2471
2205
gi|57633
neuronal myosin heavy chain [Rattus
60
40

rattus
]

362
5
2458
2925
gnl|PID|e255090
hypothetical protein [Bacillus subtilis]
60
36

364
4
4096
5349
gi|1657522
hypothetical protein [Escherichia coli]
60
41

383
1
654
4
gn|PID|e288399
F56H6.k [Caenorhabditis elegans]
60
39

383
2
2208
853
gi|143536
sigma factor 54 [Bacillus subtilis]
60
37

386
2
130
510
gi|1046053
hypothetical protein (SP:P32049)
60
42

[Mycoplasma genitalium]

399
26
25892
27757
gi|895747
putative cel operon regulator [Bacillus
60
30

subtilis
]

399
27
27721
28239
gi|146281
gut operon activator (gutM) [Escherichia
60
35

coli
]

401
4
2081
3523
gi|142833
ORF2 [Bacillus subtilis]
60
36

405
2
1353
763
gi|633113
ORF3 [Streptococcus sobrinus]
60
42

407
7
4380
4589
gi|1674126
(AE000043) Mycoplasma pneumoniae, MG280
60
39

homolog, from M. genitalium [Mycoplasma

pneumoniae]

408
1
12
539
gi|455006
orf6 [Rhodococcus fascians]
60
42

421
7
4113
3925
gi|60020
ORF31 (AA1-868) [Human herpesvirus 3]
60
43

452
3
712
2223
gi|532554
ORF21 [Enterococcus faecalis]
60
38

462
3
2066
1551
gi|1015903
ORE YJR151c [Sacoharomyces cerevisiae]
60
37

480
1
12
272
gi|468715
sss gene product [Pseudomonas aeruginosa]
60
34

487
1
1091
3
gi|388269
traC [Plasmid pAD1]
60
39

490
5
2108
1479
gi|699379
glvr-1 protein [Mycobacterium leprae]
60
29

507
1
221
751
gi|1303952
YqjA [Bacillus subtilis]
60
37

511
1
449
63
gi|391610
farnesyl diphosphate synthase [Bacillus
60
42

stearothermophilus
] pir|JX0257|JX0257

geranyltranstransferase (EC 2.5.1.10) -

Bacillus tearothermophilus

551
2
1521
604
gi|1256648
putative [Bacillus subtilis]
60
37

552
1
887
63
gi|537235
Kenn Rudd identifies as gpmB [Escherichia
60
40

coli
]

610
1
1
792
gi|1321625
exo-alpha-1, 4-glucosidase [Bacillus
60
45

stearothermophilus]

642
1
402
214
gi|992964
thioredoxin [Arabidopsis thaliana]
60
36

646
1
642
265
gi|1041115
TRAC [Plasmid pPD1]
60
32

661
2
305
943
gi|1651536
3-oxoacyl-[acyl-carrier-protein] reductase
60
37

[Escherichia coli]

678
1
536
3
gi|532554
ORF21 [Enterococcus faecalis]
60
39

716
1
799
305
gi|886040
ORFtxel [Clostridium difficile]
60
38

717
1
2
472
gi|1402529
ORF8 [Enterococcus faecalis]
60
31

727
1
516
82
gi|471283
ORF [Synechococcus PCC6301]
60
41

770
1
327
4
gi|467451
unknown [Bacillus subtilis]
60
33

843
1
234
4
gi|2819
transferase (GAL10) (AA 1 - 687)
60
37

[Kluyveromyces lactis] r|S01407|XUVKG

UDPglucose 4-epimerase (EC 5.1.3.2) -

yeast uyveromyces marxianus var. lactis)

21
1
341
3
gi|1778519
hypothetical protein [Escherichia coli]
59
47

23
2
290
1303
gi|1407800
ABC-type permease [Yersinia pestis]
59
36

23
13
6720
7388
gi|1652472
ethylene response sensor protein
59
37

[Synechocystis sp.]

23
18
11892
12413
gi|825627
malor carboxysome shell protein
59
42

[Thiobacillus neapolitanus]

pir|S60136|S60136 malor carboxysome shell

protein - Thiobacillus eapolitanus

29
4
1989
2852
gi|1742383
ORF_D:o276#3; similar to [PIR Accession
59
48

Number S11432] [Escherichia coli]

32
8
4504
4064
gi|1046081
hypothetical protein (GB:D26185_10)
59
33

[Mycoplasma genitalium]

37
9
6670
6284
gi|290561
o188 [Escherichia coli]
59
44

47
1
2
2743
gnl|PID|e248792
unknown [Mycobacterium tuberculosis]
59
46

48
5
4017
5492
gi|1185288
isochorismate synthase [Bacillus subtilis]
59
40

49
5
1797
2093
gi|496280
structural protein [Bacteriophage Tuc2009]
59
41

59
8
3324
5057
gi|1486244
unknown |Bacillus subtilis]
59
35

72
14
13937
13434
gi|532540
ORF7 [Enterococcus faecalis]
59
25

81
20
14659
14219
gi|39978
P16 [Bacillus subtilis]
59
38

98
2
1961
2617
gi|41519
P30 protein (AA 1-240) [Escherichia coli]
59
39

102
3
2542
3774
gi|1674376
(AE000062) Mycoplasma pneumoniae, MG148
59
30

homolog, from M. genitalium [Mycoplasma

pneumoniae]

116
2
907
1458
gi|1146225
putative [Bacillus subtilis]
59
37

116
7
3532
4842
gi|1146238
poly(A) polymerase [Bacillus subtilis]
59
41

128
20
15626
14310
gi|1001719
ATP-dependent RNA helicase DeaD
59
34

[Synechocystis sp.]

134
4
3158
3850
gi|1477486
transposase [Burkholderia cepacia]
59
40

137
1
1
999
gi|1065948
similar to thymidine diphosphoglucose 4,6-
59
40

dehydratase [Caenorhabditis elegans]

138
8
7489
6827
gnl|PID|e264435
Putative orf YCLX8c, len:192
59
36

[Saccharomyces cerevisiae]

140
1
3
656
gnl|PID|e254943
unknown [Mycobacterium tuberculosis]
59
32

165
13
10427
9849
gi|1732199
PTS permease for mannose subunit IIIMan C
59
37

terminal domain [Vibrio furnissii]

167
1
2
1045
gi|1573128
hypothetical [Haemophilus influenzae]
59
38

173
2
430
2160
gi|1486244
unknown [Bacillus subtilis]
59
31

179
10
10432
11199
gi|288299
ORF1 gene product [Bacillus megaterium]
59
34

179
12
12117
13148
gi|1045964
hypothetical protein (GB:U14003_297)
59
41

[Mycoplasma genitalium]

181
11
9684
8575
gi|1653152
3-dehydroquinate synthase [Synechocystis
59
41

sp
.]

223
24
20736
21974
gi|1573051
succinyl-diaminopimelate desuccinylase
59
48

(dapE) [Haemophilus influenzae]

229
12
12818
11421
gi|1652035
fmu and fmv protein [Synechocystis sp.]
59
39

244
3
2836
1565
gi|1303959
YqjH [Bacillus subtilis]
59
45

265
9
4116
3868
gi|311100
translational activator [Saccharomyces
59
28

cerevisiae
]

272
1
1
546
gi|490320
Y gene product [unidentified]
59
41

279
16
14774
14370
gi|1389549
ORF3 [Bacillus subtilis]
59
46

283
8
3222
3401
gi|153047
lysostaphin (ttg start codon)
59
43

[Staphylococcus simulans]

pir|A25881|A25881 lysostaphin precursor -

Staphylococcus simulans

sp|P10547|LSTP_STASI LYSOSTAPHIN PRECURSOR

(EC 3.5.1.-).

288
5
2617
3144
gi|1142714
phosphoenolpyruvate:mannose
59
45

phosphotransferase element IIB

[Lactobacillus curvatus]

292
19
14837
16792
gi|495646
ATPase [Transposon Tn5422]
59
40

295
1
49
495
gi|533098
DnaD protein [Bacillus subtilis]
59
39

315
2
907
653
gi|1574802
hypothetical [Haemophilus influenzae|
59
38

318
6
4549
4058
gi|43941
EIII-B Sor PTS [Klebsiella pneumoniae]
59
35

345
3
2707
3507
gi|895749
putative cellobiose phosphotransferase
59
38

enzyme II″ [Bacillus ubtilis]

351
5
2646
2371
gi|1666506
RfbC [Leptospira interrogans]
59
30

355
21
15237
17222
gi|515738
ORF2; putative [Oenococcus oeni]
59
35

384
1
14
754
gi|1162959
homologous to HI0365 in Haemophilus
59
34

influenzae
; ORF1 [Pseudomonas aeruginosa]

385
1
3
533
gi|1146197
utative [Bacillus subtilis]
59
36

394
13
13137
12160
gnl|PID|e243582
ORF YGR263c [Saccharomyces cerevisiae]
59
36

399
1
224
580
gi|580904
homologous to E.coli rnpA [Bacillus
59
38

subtilis
]

412
1
3
2927
gi|1620648
surface protein Rib [Streptococcus
59
43

agalactiae
]

412
2
2918
3559
gi|1620648
surface protein Rib [Streptococcus
59
43

agalactiae
]

416
6
5283
3940
gi|1100076
PTS-dependent enzyme II [Clostridium
59
38

longisporum
]

437
2
1561
1136
gi|580866
ipa-12d gene product [Bacillus subtilis]
59
44

495
2
438
614
gi|1500472

M. jannaschii
predicted coding region
59
45

MJ1577 [Methanococcus jannaschii]

502
1
853
188
gi|1063248
No homologous protein [Bacillus subtilis]
59
25

573
8
5092
4493
gi|1573226
hypothetical [Haemophilus influenzae]
59
39

579
4
1716
2717
gnl|PID|e280724
unknown [Mycobacterium tuberculosis]
59
41

600
1
1
504
gi|49386
internal region of the penicillin-binding
59
40

protein 2B gene treptococcus pneumoniae]

616
3
904
533
gi|289265
[Bacillus sp. (KSM 64) endo-1,4-beta-
59
44

glucanase gene, complete cds.], ene

products [Bacillus sp.]

657
1
432
4
gi|1651338
PnuC protein [Escherichia coli]
59
37

699
1
416
165
gnl|PID|e199096
PepR1 [Lactobacillus deibrueckii]
59
23

713
4
3709
2660
gi|515738
ORF2; putative [Oenococcus oeni]
59
37

715
1
698
84
gi|1176399
EpiF [Staphylococcus epidermidis]
59
42

737
2
660
199
gi|666000
hypothetical protein [Bacillus subtilis]
59
43

744
1
395
3
gi|1732057
MUC.CL-1 [Trypanosoma cruzi]
59
45

746
1
3
554
gi|141858
replication-associated protein [Plasmid
59
36

pAD1]

869
1
2
250
gi|1432153
cellobiose-specific PTS permease
59
40

[Klebsiella oxytoca]

4
8
6948
6067
gi|147516
ribokinase [Escherichia coli]
58
42

11
6
3312
4121
gi|1732200
PTS permease for mannose subunit IIPMan
58
35

[Vibrio furnissii]

16
9
7684
6932
gnl|PID|e233879
hypothetical protein [Bacillus subtilis]
58
48

23
14
7440
8903
gi|142940
ftsA [Bacillus subtilis]
58
39

30
2
570
1283
gi|1644202
unknown [Bacillus subtilis]
58
37

48
7
7186
8037
gi|1573247
hypothetical [Haemophilus influenzae]
58
35

49
7
2395
2871
gnl|PID|e210884
c2 gene product [Bacteriophage B1]
58
34

54
1
1014
91
gi|46645
ORF (rlx) [Staphylococcus aureus]
58
46

55
3
1221
511
gi|726443
No definition line found [Caenorhabditis
58
41

elegans
]

58
1
1904
696
gi|1591564
molybdenum cofactor biosynthesis moeA
58
39

protein [Methanococcus jannaschii]

58
8
7238
6996
gi|1279769
FdhC [Methanobacterium thermoformicicum]
58
54

72
12
12117
10897
gi|763052
integrase [Bacteriophage T270]
58
37

77
2
1155
1910
gi|1245464
YfeA [Yersinia pestis]
58
34

78
1
2589
49
gi|40663
sialidase [Clostridium septicum]
58
40

88
9
5854
6528
gi|1619623
hemin binding protein [Yersinia
58
37

enterocolitica
]

93
6
2639
2863
gi|405133
putative [Bacillus subtilis]
58
33

98
13
13523
12432
gi|147329
transport protein [Escherichia coli]
58
41

100
12
8550
8224
gi|1736642
Invasin. [Escherichia coli]
58
47

102
7
5688
5969
gi|808869
human gcp372 [Homo sapiens]
58
30

105
5
3716
4501
gi|143729
transcription activator [Bacillus
58
40

subtilis
]

107
1
511
2
gi|1303827
YqfI [Bacillus subtilis]
58
34

108
2
1040
1732
gi|1592142
ABC transporter, probable ATP-binding
58
37

subunit [Methanococcus jannaschii]

114
6
7608
8444
gi|152719
flavocytochrome c [Shewanella
58
40

putrefaciens
]

117
14
11813
11115
gi|1575577
DNA-binding response regulator [Thermotoga
58
42

maritima
]

122
1
1
936
gi|393269
adhesion protein [Streptococcus
58
38

pneumoniae]

123
23
20379
21617
gi|1653948
hypothetical protein [Synechocystis sp.]
58
38

133
8
7362
8480
gi|143498
degS protein [Bacillus subtilis]
58
38

133
9
8437
9087
gi|143089
iep protein [Bacillus subtilis]
58
31

138
3
3551
2898
gi|216114
DNA polymerase [Bacteriophage SPO1]
58
41

138
5
5819
5049
gnl|PID|e289148
highly similar to phosphotransferase
58
38

system regulator [Bacillus subtilis]

138
17
11419
10379
gi|1674137
(A5000044) Mycoplasma pneumnoniae, lipoate
58
37

protein ligase; similar to Swiss-Prot

Accession Number P32099, from E. coli

[Mycoplasma pneumnoniae]

139
8
5002
4808
gi|153607
dpnD gene product [Streptococcus
58
43

pneumoniae]

146
9
7817
6627
gi|606076
ORF_o384 [Escherichia coli]
58
43

150
10
7529
7894
gi|141852
sialidase [Actinomyces viscosus]
58
28

152
10
5717
6637
gi|296356
putative membrane transport protein
58
36

[Clostridium perfringens]

pir|A56641|A56641 probable membrane

transport protein - Clostridium erfringens

162
10
11009
11185
gi|42655
pi protein [Escherichia coli]
58
37

164
3
1793
1608
gi|881499
parathion hydrolase (phosphotriesterase)-
58
41

related protein [Mus usculus]

165
6
5640
4975
gi|1146190
2-keto-3-deoxy-6-phosphogluconate aldolase
58
39

[Bacillus subtilis]

165
10
9038
8199
gi|606080
ORF_290; Geneplot suggests frameshift
58
35

linking to o267, not found Escherichia

coli
]

168
1
1
657
gi|413930
ipa-6d gene product [Bacillus subtilis]
58
41

170
1
923
234
gi|1573505
hypothetical [Haemophilus influenzae]
58
30

176
1
1
1101
gi|1652379
cation-transporting P-ATPase
58
30

[Synechocystis sp.]

180
12
10237
10410
gi|408123
V-ATPase 14kD subunit peptide [Drosophila
58
33

melanogaster]
pir|S38436|S38436 H+-

transporting ATPase (EC 3.6.1.35) 14K

chain - ruit fly (Drosophila melanogaster)

193
3
2077
1388
gi|1256633
putative [Bacillus subtilis]
58
39

193
4
2602
2075
gi|147920
3-methyladenine-DNA glycosylase I (tag)
58
33

[Escherichia coli]

194
9
6492
5500
sp|P09997|YIDA_ECO
HYPOTHETICAL 29.7 KD PROTEIN IN IBPA-GYRB
58
38

LI
INTERGENIC REGION.

201
5
5152
4466
gi|755152
highly hydrophobic integral membrane
58
28

protein [Bacillus subtilis]

sp|P42953|TAGG_BACSU TEICHOIC ACID

TRANSLOCATION PERMEASE PROTEIN AGG.

210
9
6546
7265
gi|466520
pocR [Salmonella typhimurium]
58
36

220
1
3
569
gi|467441
expressed at the end of exponential growyh
58
38

under condtions in which he enzymes of the

TCA cycle are repressed [Bacillus

subtilis
] sp|P14194|CTC_BACSU GENERAL

STRESS PROTEIN CTC. {SUB 2-204} gi|40219

partial ctc gene product (AA 1-186)

[Bacillus subtilis]

222
10
6520
7143
gi|1674024
(AE000033) Mycoplasma pneumoniae,
58
41

hypothetical protein (yjfS) homolog;

similar to Swiss-Prot Accession Number

P39301, from E. coli [Mycoplasma

pneumoniae
]

233
7
4984
3944
gi|147806
selenium metabolism protein [Escherichia
58
45

coli
]

238
14
12128
12910
gi|1736468
Pectin degradation repressor protein KdgR.
58
37

[Escherichia coli]

244
11
8102
7809
gi|467418
unknown [Bacillus subtilis]
58
37

246
1
1
276
gi|65291
receptor tyrosine kiase preprotein
58
32

[Xiphophorus sp.] ir|S06142|S06142 kinase-

related transforming protein (Tu) (EC

7.1.-) precursor - southern platyfish

255
4
2927
2559
gi|1652384
ABC transporter [Synechocystis sp.]
58
41

258
9
8025
8966
gi|147402
mannose permease subunit III-Man
58
35

[Escherichia coli]

259
2
1801
893
gi|1591564
molybdenum cofactor biosynthesis moeA
58
39

protein [Methanococcus jannaschii]

260
3
1754
2254
gi|580841
F1 [Bacillus subtilis]
58
38

271
4
2382
2738
gi|40067
X gene product [Bacillus sphaericus]
58
37

279
8
6237
6536
gi|1783243
homologous to jojc gene product (B.
58
34

subtilis; prf:2111327a); hypothetical

[Bacillus subtilis]

301
1
753
175
gi|499196
ORF1 [Streptomyces lincolnensis]
58
37

304
1
100
849
gi|1653322
hypothetical protein [Synechocystis sp.]
58
41

313
2
748
1650
gi|1658371
cyclic beta-1,2-glucan modification
58
36

protein [Rhizobium meliloti]

321
11
6033
6533
gi|1573292
hypothetical [Haemophilus influenzae]
58
34

322
6
3819
5069
gi|23897
5′-nucleotidase [Homo sapiens]
58
34

324
5
3259
4452
gi|1469784
putative cell division protein ftsW
58
37

[Enterococcus hirae]

328
1
1
270
gi|882579
CG Site No. 29739 [Escherichia coli]
58
43

330
8
6228
6758
gi|43941
EIII-B Sor PTS [Klebsiella pneumoniae]
58
37

334
4
3634
3963
gi|1001306
hypothetical protein [Synechocystis sp.]
58
34

345
17 18899
20044
gi|853809
ORF3 [Clostridium perfringens]
58
30

363
7
8475
9944
gi|348056
trans-acting positive regulator [Bacillus
58
33

anthracis
]

375
7
6472
5279
gi|1408501
homologous to N-acyl-L-amino acid
58
42

amidohydrolase of Bacillus

stearothermophilus
[Bacillus subtilis]

394
12
10689
12095
gi|537034
ORF_o488 [Escherichia coli]
58
32

399
3
1383
2198
gi|580905

B.subtilis
genes rpmH, rnpA, 50kd, gidA
58
36

and gidB [Bacillus subtilis]gi|580919 Jag

[Bacillus subtilis]

399
16
11544
12098
gi|1572965
hypothetical [Haemophilus influenzae]
58
39

399
19
14776
15654
gi|1778530
CitG homolog [Escherichia coli]
58
40

407
2
738
553
gi|170553
pyruvate kinase [Trichoderma reesei]
58
38

416
5
4045
3389
gi|475112
enzyme IIabc [Pediococcus pentosaceus]
58
41

449
4
1421
879
gi|928834
integrase [Lactococcus lactis phage BK5-T]
58
32

497
1
3
458
gi|160628
reticulocyte binding protein 2 [Plasmodium
58
30

vivax
]

594
1
285
4
gi|1353874
unknown [Rhodobacter capsulatus]
58
39

637
6
3451
2765
pir|D61615|D61615
sericin MG-1 - greater wax moth (fragment)
58
52

653
1
595
245
gi|1408585
LtrD [Lactococcus lactis lactis]
58
41

656
4
3713
5209
sp|P13692|P54_ENTF
P54 PROTEIN PRECURSOR.
58
37

C

656
6
5988
6467
gi|1017818
phosphotyrosine protein phosphatase
58
48

[Streptomyces coelicolor]

667
1
88
1467
bbs|177441
OsNramp1=Nramp1 homolog/Bcg product
58
40

homolog [Oryza sativa, indica, cv. IR 36,

etiolated shoots, Peptide, 517 aa] [Oryza

sativa
]

686
1
892
233
pir|A24255|A24255
chorion class A protein L11 precursor -
58
38

silkworm

706
1
1002
607
gi|1001762
hypothetical protein [Synechocystis sp.]
58
32

801
1
254
12
gnl|PID|e243641
unknown [Mycobacterium tuberculosis]
58
29

848
1
212
3
gnl|PID|e254644
membrane protein [Streptococcus
58
37

pneumoniae
]

975
1
3
422
gi|290545
f270 [Escherichia coli]
58
35

11
4
2345
2833
gi|1439527
EIIA-man [Lactobacillus curvatis]
57
46

16
2
1426
365
gi|780550
acetyl transferase [Rhizobium loti]
57
35

18
3
1593
925
gnl|PID|e137594
xerC recombinase [Lactobacillus
57
36

leichmannii
]

19
15
8058
8267
gi|1590922
cell division inhibitor [Methanococcus
57
42

jannaschii
]

19
23
11938
12318
gi|1294760
structural protein; orfL3; putative
57
46

[Bacteriophage phi-41]

25
9
7743
6958
gnl|PID|e255000
hypothetical protein [Bacillus subtilis]
57
40

47
3
3857
4462
gi|1353540
ORF23 [Bacteriophage rlt]
57
35

65
10
7100
8919
gi|496254
fibronectin/fibrinogen-binding protein
57
40

[Streptococcus pyogenes]

68
7
3923
3705
gi|336656
ribosomal protein secY [Cyanophora
57
28

paradoxa
]

70
4
2317
3645
pir|S11158|YESAEE
erythromycin resistance protein -
57
40

Staphylococcus epidermidis plasmid pULSOSO

76
1
55
1095
gi|1353562
Structural protein [Bacteriophage rlt]
57
41

91
11
9070
8849
gi|550321
beta-fructofuranosidase [Chenopodium
57
30

rubrum
]

94
4
1740
1495
gif 47406
penicillin-binding protein 1a
57
30

[Streptococcus pneumoniae]

ir|S28031|528031 penicillin-binding

protein 1a - Streptococcus eumoniae

(strain 456) (fragment)

98
6
7766
6849
gi|409286
bmrU [Bacillus subtilis]
57
31

100
22
17294
15912
gnl|PID|e289150
member of the SNF2 helicase family
57
30

[Bacillus subtilis]

102
1
66
2465
gi|405564
traE [Plasmid pSK41]
57
28

110
14
11757
12497
gi|854601
unknown [Schizosaccharomyces pombe]
57
38

114
9
10291
11139
gi|853777
product similar to E.coli PRFA2 protein
57
38

[Bacillus subtilis] pir|555438|S55438 ywkE

protein - Bacillus subtilis

sp|P45873|HEMK_BACSU POSSIBLE

PROTOPORPHYRINOGEN OXIDASE (EC .3.3.-).

115
3
955
1461
gi|396347
alternate name yjaB [Escherichia coli]
57
33

123
3
1925
2932
gi|1001731
low affinity sulfate transporter
57
39

[Synechocystis sp.]

124
7
6026
5118
gi|1674310
(AE000058) Mycoplasma pneumoniae, MG085
57
30

homolog, from M. genitalium [Mycoplasma

pneumoniae]

128
9
7530
6235
gi|413940
ipa-16d gene product [Bacillus subtilis]
57
36

128
31
25487
25206
gi|1651915
hypothetical protein [Synechocystis sp.]
57
42

128
33
26878
26150
gi|1001387
hypothetical protein [Synechocystis sp.]
57
30

128
37
30730
29600
gi|406877
DivIB protein [Bacillus licheniformis]
57
35

130
9
7408
8556
gi|343539
NADH dehydrogenase subunit 4 [Trypanosoma
57
27

brucei
]

144
1
1013
219
gi|1652518
hypothetical protein [Synechocystis sp.]
57
45

144
6
4145
5254
gi|149581
maturation protein [Lactobacillus
57
38

paracasei
]

146
1
617
192
gi|147402
mannose permease subunit III-Man
57
33

[Escherichia coli]

153
1
83
991
gi|147336
transmembrane protein [Escherichia coli]
57
33

160
8
4718
4134
gi|305333
zeta-crystallin [Cavia porcellus]
57
39

167
8
14891
14688
gi|206354
protein kinase C, zeta subspecies [Rattus
57
39

norvegicus
] pir|A30314|A30314 protein

kinase C (EC 2.7.1.-) zeta - rat

sp|P09217|KPCZ_RAT PROTEIN KINASE C, ZETA

TYPE (EC 2.7.1.-) NPKC-ZETA).

174
1
760
2
gnl|PID|e191403
ORFA gene product [Chloroflexus
57
42

aurantiacus
]

176
4
3347
3568
gi|1236529
cyclomaltodextrinase [Bacillus sp.]
57
46

194
8
4786
5457
gi|405516
This ORF is homologous to nitroreductase
57
26

from Enterobacter cloacae, ccession Number

A38686, and Salmonella, Accession Number

P15888 Mycoplasma-like organism]

199
3
3207
3764
gi|216350
ORF [Bacillus subtilis]
57
38

202
5
3356
3664
gi|1183841
Holliday junction binding protein
57
34

[Pseudomonas aeruginosa]

202
12
10911
10192
gi|971338
anaerobic regulatory protein [Bacillus
57
27

subtilis
]

205
3
1022
468
gi|1783240
hypothetical [Bacillus subtilis]
57
38

223
2
779
1501
gi|1208965
hypothetical 23.3 kd protein [Escherichia
57
32

coli
]

223
3
1499
2332
gi|303560
ORF271 [Escherichia coli]
57
35

223
11
8404
12198
gi|158079
period protein [Drosophila serrata]
57
40

237
9
3685
3906
gi|514919
phosphofructokinase [Drosophila
57
31

melanogaster
]

242
7
5760
5020
gi|1574596

H. influenzae
predicted coding region
57
33

HI1738 [Haemophilus influenzae]

250
2
1243
1485
gnl|PID|e275819
K08G2.8 [Caenorhabditis elegans]
57
47

276
28
16565
16332
gi|886375
variant-specific surface protein
57
47

[Plasmodium falciparum]

288
6
3157
3363
gi|147403
mannose permease subunit II-P-Man
57
39

[Escherichia coli]

289
1
141
818
gi|1742822
Phosphoglycolate phosphatase (EC
57
40

3.1.3.18). [Escherichia coli]

292
20
15930
15721
gi|854201
putative polymerase [Infectious bursal
57
47

disease virus]

294
4
1454
2014
gi|454303
LDJ2 gene product [Allium porrum]
57
41

295
4
2052
2342
pir|S48588|S48588
hypothetical protein - Mycoplasma
57
39

capricolum
(SGC3) (fragment)

301
14
10921
10148
gnl|PID|e262045
putative orf [Bacillus subtilis]
57
38

306
1
2
793
gi|216715
HpaI methyltransferase [Haemophilus
57
36

parainfluenzae] pir|S28681|S28681 site-

specific DNA-methyltransferase adenine-

specific) (EC 2.1.1.72) HpaI - Haemophilus

parainfluenzae sp|P29538|MTH1_HAEPA

MODIFICATION METHYLASE HPAI (EC 2.1.1.72)

ADENINE-SPECIFIC MET

306
8
5418
5663
gi|1591542

M. jannaschii
predicted coding region
57
42

MJ0857 [Methanococcus jannaschii]

308
2
1732
1487
gi|1518045
FlbF protein [Borrelia burgdorferi]
57
28

321
2
1030
1458
gi|606080
ORF_o290; Geneplot suggests frameshift
57
30

linking to o267, not found Escherichia

coli
]

351
4
2342
1587
gi|1591853

M. jannaschii
predicted coding region
57
37

MJ1222 [Methanococcus jannaschii]

355
30
20619
20861
gi|1136394
There are three putative hydrophobic
57
42

domains in the central region. [Homo

sapiens
]

364
10
9415
8852
gi|38722
precursor (aa −20 to 381) [Acinetobacter
57
32

calcoaceticus
] ir|29277|A29277 aldose 1-

epimerase (EC 5.1.3.3) - Acinetobacter

lcoaceticus

365
3
4715
1812
gi|914990
Similar to DEAD box family helicases
57
35

[Saccharomyces cerevisiae]

pir|S59797|S59797 hypothetical protein

P9798.1 - yeast Saccharomyces cerevisiae)

378
1
615
10
gi|1652989
hypothetical protein [Synechocystis sp.]
57
35

379
1
1457
114
gi|1256618
transport protein [Bacillus subtilis]
57
36

390
1
1426
2
gi|387880
collagen adhesin [Staphylococcus aureus]
57
37

422
1
2
409
gi|1591837

M. jannaschii
predicted coding region
57
37

MJ1207 [Methanococcus jannaschii]

447
1
397
131
gi|214566
keratin protein XK81 [Xenopus laevis]
57
33

454
2
1095
889
gi|1783256
sigma factor [Bacillus subtilis]
57
28

504
2
641
1426
gi|42081
nagD gene product (AA 1-250) [Escherichia
57
32

coli
]

524
2
963
577
gi|143724
putative [Bacillus subtilis]
57
43

535
4
4862
4305
gi|146549
kdpC [Escherichia coli]
57
40

547
2
426
719
gi|533098
DnaD protein [Bacillus subtilis]
57
33

548
1
316
717
gi|397973
Mg2+ transport ATPase [Salmonella
57
33

typhimurium
]

639
2
359
105
gnl|PID|e247390
P-type ATPase [Dictyostelium discoideum]
57
31

641
1
941
180
gnl|PID|e261990
putative orf [Bacillus subtilis]
57
36

686
3
1298
3259
gi|496506
orf gamma [Streptococcus pyogenes]
57
37

686
6
2200
2847
gi|404800
putative [Saccharopolyspora erythraea]
57
47

782
2
591
860
gi|1591270
alanyl-tRNA synthetase [Methanococcus
57
32

jannaschii
]

844
1
3
182
gi|849217
Weak similarity to Streptococcus Protein
57
34

V, a type-II IgG receptor PIR accession

number S17354) and Giardia lamblia median

body rotein (PIR accession number S33821)

[Saccharomyces cerevisiae]

pir|S61181|S61181 hypothetical protein

D9740.10 - yeast Sacchar

859
1
174
4
gi|1762584
polygalacturonase isoenzyme 1 beta subunit
57
28

homolog [Arabidopsis thaliana]

967
1
381
4
gi|309662
pheromone binding protein [Plasmid pCF10]
57
40

11
5
2817
3314
gi|43941
EIII-B Sor PTS [Klebsiella pneumoniae]
56
30

15
1
80
892
gi|1574803
spermidine/putrescine-binding periplasmic
56
32

protein precursor (potD) [Haemophilus

influenzae]

37
8
6327
6088
gi|290561
o188 [Escherichia coli]
56
41

44
2
1169
1360
gi|16096
peroxidase [Armoracia rusticana]
56
37

56
3
1881
1363
gi|49272
Asparaginase [Bacillus licheniformis]
56
33

65
1
102
887
gi|1377832
unknown [Bacillus subtilis]
56
41

75
9
5817
4306
gi|1235712
polyprotein [Infectious pancreatic
56
30

necrosis virus]

83
7
3260
4051
gi|1652645
phosphoglycolate phosphatase
56
30

[Synechocystis sp.]

95
3
1793
2389
pir|C53610|C53610
ntpE protein - Enterococcus hirae
56
28

100
3
5076
1915
gi|1353559
ORF42 [Bacteriophage rlt]
56
35

100
16
10581
10369
gi|868224
No definition line found [Caenorhabditis
56
35

elegans
]

100
48
31841
32770
gi|460025
ORF2, putative [Streptococcus pneumoniae]
56
38

108
5
4007
3336
gi|288301
ORF2 gene product [Bacillus megaterium]
56
34

109
2
1032
325
gi|413976
ipa-52r gene product [Bacillus subtilis]
56
36

119
7
3958
5304
gi|498842
VirS [Clostridium perfringens]
56
35

123
32
29479
30345
gi|39981
[Bacillus subtilis]
56
38

126
1
521
3
gi|147403
mannose permease subunit II-P-Man
56
29

[Escherichia coli]

130
6
4296
6104
gi|308854
oligopeptide binding protein [Lactococcus
56
33

lactis
]

131
7
5267
6613
gi|466589
CG Site No. 39 [Escherichia coli]
56
32

133
5
4358
5758
gi|1573431
ammnodeoxychonismate lyase (pabC)
56
40

[Haemophilus influenzae]

138
20
13680
12670
gi|1590951
UDP-glucose 4-epimerase [Methanococcus
56
40

jannaschii
]

138
29
19764
18823
gi|44864
H.8 outer membrane protein (AA −17 to 71)
56
33

[Neisseria gonorrhoeae] ir|S02720|S02720

outer membrane protein H.8 precursor -

Neisseria norrhoeae

145
7
5611
7179
gi|1652892
ABC transporter [Synechocystis sp.]
56
33

146
10
8545
7811
gi|41519
P30 protein (AA 1-240)
[Escherichia coli]
56
28

150
4
2979
4637
gi|309662
pheromone binding protein [Plasmid pCF10]
56
32

159
5
5362
5066
gi|576733
apocytochrome b [Trypanoplasma borreli]
56
43

164
13
8864
15031
gi|1654116
protein F2 [Streptococcus pyogenes]
56
43

179
7
7790
9118
gi|413926
ipa-2r gene product [Bacillus subtilis]
56
33

187
4
2239
1667
gi|1573061
hypothetical [Haemophilis influenzae]
56
18

200
19
11473
10724
gi|498817
ORF8; homologous to small subunit of phage
56
35

terminases [Bacillus ubtilis]

206
6
3766
2759
gi|474837
ORF1 [Thermoanaerobacterium
56
34

thermosulfurigenes
] sp|P3854|YAMB_THETU

HYPOTHETICAL 35.6 KD PROTEIN IN AMYB

5′REGION ORF1).

207
2
2091
1672
gi|1204258
soluble protein [Escherichia coli]
56
40

217
9
6661
6158
gi|1017427
elastic titin [Homo sapiens]
56
28

225
7
6007
5099
gi|1742675
Phosphotransferase system enzyme II (EC
56
46

2.7.1.69) MalX [Escherichia coli]

230
3
595
3153
gi|437706
alternative truncated translation product
56
34

from E.coli [Streptococcus neumoniae]

236
2
1486
515
gi|415664
catabolite control protein [Bacillus
56
35

megaterium] sp|P46828|CCPA
_BACME GLUCOSE-

RESISTANCE AMYLASE REGULATOR CATABOLITE

CONTROL PROTEIN).

236
7
9255
8599
gi|343544
ATPase 6 [Trypanosoma brucei]
56
48

238
15
13059
13718
gi|1146190
2-keto-3-deoxy-6-phosphogluconate aldolase
56
37

[Bacillus subtilis]

238
20
17734
18756
gi|1574060
hypothetical [Haemophilus influenzae]
56
32

238
23
21613
20726
gi|151361
member of the AraC/XylS family of
56
36

transcriptional regulators Pseudomonas

aeruginosa
]

242
6
4103
4477
gi|886858
nicotinic acetylcholine receptor
56
35

[Caenorhabditis elegans] pir|S57648|S57648

nicotinic acetylcholine receptor -

Caenorhabditis legans

260
5
3170
3781
gnl|PID|e58151
F3 [Bacillus subtilis]
56
43

279
6
5140
2831
gi|581100
gamma-glutamylcysteine synthetase (aa 1-
56
42

518) [Escherichia coli] pir|A24136|SYECEC

glutamate--cysteine ligase (EC 6.3.2.2) -

scherichia coli

279
9
6434
7228
gi|1783243
homologous to jojC gene product (B.
56
29

subtilis; prf:2111327a); hypothetical

[Bacillus subtilis]

292
14
10719
11504
gi|45738
ORFC [Enterococcus faecalis]
56
37

313
3
3039
1831
gi|474915
orf 337; translated orf similarity to SW:
56
31

BCR_ECOLI bicyclomycin esistance protein

of Escherichia coli [Coxiella burnetii]

pir|S44207|44207 hypothetical protein 337

- Coxiella burnetti {SUB -338}

313
5
4233
3589
gi|405883
yeiL [Escherichia coli]
56
30

322
5
1994
3715
gi|1377831
unknown [Bacillus subtilis]
56
34

353
2
2353
1310
gnl|PID|e254644
membrane protein [Streptococcus
56
26

pneumoniae
]

394
14
13289
14143
gi|142836
repressor protein [Bacillus subtilis]
56
30

399
32
30208
30891
gi|396293
similar to Bacillus subtilis hypoth. 20
56
38

kDa protein, in tsr 3′ egion [Escherichia

coli
]

402
2
1267
914
gi|170710
alpha-type gliadin precursor protein
56
45

[Triticum aestivum]

408
4
2825
2220
gnl|PID|e257696
collagen binding protein [Lactobacillus
56
36

reuteri
]

432
5
3105
3302
gi|11678
atpE gene product [Marchantia polymorpha]
56
33

443
2
844
1089
gi|1256138
YbbI [Bacillus subtilis]
56
36

499
2
875
1666
gi|1499876
magnesium and cobalt transport protein
56
30

[Methanococcus jannaschii]

510
6
3864
4733
gi|147404
mannose permease subunit II-M-Man
56
34

[Escherichia coli]

543
6
3706
3113
gi|563812
XCAP-C [Xenopus laevis]
56
32

609
2
390
653
gi|48745
principal sigma subunit (AA 1-442)
56
37

[Streptomyces coelicolor] ir|S11712|S11712

translation initiation factor sigma hrdB -

reptomyces coelicolor

626
2
1124
2104
gi|950197
unknown [Corynebacterium glutamicum]
56
40

787
1
2
634
gnl|PID|e283826
orf c04012 [Sulfolobus solfataricus]
56
26

820
1
1220
3
gi|44001
galactose-1-P-uridyl transferase
56
35

[Lactobacillus helveticus]

ir|B47032|B47032 galactose-1-phosphate

uridyl transferase - ctobacillus

helveticus

875
1
1
144
gi|455178
16K protein [Escherichia coli]
56
46

906
2
307
846
gi|144858
ORF A [Clostridium perfringens]
56
34

941
1
3
335
gi|160299
glutamic acid-rich protein [Plasmodium
56
23

falciparum] pir|A54514|A54514 glutamnic

acid-rich protein precursor - Plasmodium

alciparum

5
5
2451
2951
gi|1303811
YgeU [Bacillus subtilis]
55
39

8
10
8312
7947
gi|1196907
daunorubicin resistance protein
55
29

[Streptomyces peucetius]

17
24
23626
24465
gnl|PID|e285322
RecX rotein [Mycobacterium smegmatis]
55
28

17
31
31027
30344
gi″143830
xpaC [Bacillus subtilis]
55
22

17
34
31991
32302
gnl|PID|e229183
C11G6.3 [Caenorhabditis elegans]
55
34

30
1
2
478
pir|S10655|S10655
hypothetical protein X - Pyrococcus woesei
55
34

(fragment)

49
14
9998
10411
gi|455154
ORE D [Clostridium perfringens]
55
36

54
3
955
1332
gnl|PID|e238660
hypothetical protein [Bacillus subtilis]
55
32

54
10
3527
3231
pir|JQ0405|JQ0405
hypothetical 119.5K protein (uvrA region)
55
45

- Micrococcus luteus

67
4
2313
3044
gi|555750
unknown [Neisseria gonorrhoeae]
55
42

69
4
2250
2020
gnl|PID|e259955
K04G11.5 [Caenorhabditis elegans]
55
33

77
5
3954
2938
gi|1001634
hypothetical protein [Synechocystis sp.]
55
34

80
4
4806
2482
gi|466952
B1620_F1_30 [Mycobacterium leprae]
55
35

81
6
4212
3730
gi|606073
ORF_o169 [Escherichia coli]
55
34

83
1
66
737
gi|216064
morphogenesis protein B [Bacteriophage
55
36

PZA]

89
10
9486
7714
gi|148221
DNA-dependent ATPase, DNA helicase
55
35

[Escherichia coli] pir|JS0137|BVECRQ recQ

protein - Escherichia coli

91
5
2507
3289
gi|153015
FemA protein [Staphylococcus aureus]
55
35

100
14
9974
9393
gi|558603
synaptonemal complex protein 1 [Mus
55
30

musculus
]

116
1
1
909
gi|473901
ORF1 [Lactococcus lactis]
55
33

122
3
1801
2655
gi|1016216
putative protein of 299 amino acids
55
28

[Cyanophora paradoxa]

123
30
28191
28721
gi|1142714
phosphoenolpyruvate:mannose
55
29

phosphotransferase element IIB

[Lactobacillus curvatus]

128
22
16664
16029
gi|606025
ORF_o221 [Escherichia coli]
55
42

150
7
5949
6521
gi|39573
P20 (AA 1-178) [Bacillus licheniformis]
55
32

155
7
5767
6660
gi|1763974
DPPA [Bacillus methanolicus]
55
31

157
1
867
70
gi|1067010
M153.1 [Caenorhabditis elegans]
55
34

160
9
6090
4804
gi|1592141

M. jannaschii
predicted coding region
55
31

MJ1507 [Methanococcus jannaschii]

176
3
2060
3349
gi|153858
wall-associated protein [Streptococcus
55
37

mutans
]

201
2
3277
413
gi|1235662
RfbC [Myxococcus xanthus]
55
36

202
9
6199
8001
gi|606018
ORF_o783 [Escherichia coli]
55
42

222
7
4803
4021
gnl|PID|e289148
highly similar to phosphotransferase
55
40

system regulator [Bacillus subtilis]

238
12
11465
9942
gnl|PID|e266573
unknown [Mycobacterium tuberculosis]
55
27

238
13
11527
12027
gi|1129093
unknown protein [Bacillus sp.]
55
36

240
4
1988
1215
gnl|PID|e252616
DcuC protein [Escherichia coli]
55
34

246
2
433
792
gnl|PID|e233868
hypothetical protein [Bacillus subtilis]
55
25

253
5
1827
1549
gi|142540
aspartokinase II [Bacillus sp.]
55
48

259
1
895
74
gi|1006621
molybdate-binding periplasmic protein
55
37

[Synechocystis sp.]

267
1
1183
2
gi|882672
ORF_o313 [Escherichia coli]
55
27

292
16
12843
13325
gi|561746
cyclin-dependent protein kinase [Mus
55
26

musculus
]

294
9
3390
3752
gi|984582
DinJ [Escherichia coli]
55
26

300
5
3914
3582
gi|1591957

M. jannaschii
predicted coding region
55
38

MJ1318 [Methanococcus jannaschii]

305
3
2769
3527
gi|606309
ORF_o265; gtg start [Escherichia coli]
55
36

320
6
4479
3475
gi|1591732
cobalt transport ATP-binding protein O
55
32

[Methanococcus jannaschii]

355
24
18149
18322
gi|344751
MDV TK gene product [unidentified]
55
40

364
2
2083
386
gi|1573045
hypothetical [Haemophilus influenzae]
55
40

364
9
8796
8575
gnl|PID|e252108
ORF YOR255w [Saccharomyces cerevisiae]
55
27

379
8
8248
6872
gi|1330236
dihydropyrimidinase [Homo sapiens]
55
37

386
6
3847
4332
gi|976025
HrsA [Escherichia coli]
55
27

441
2
939
1730
gi|144859
ORF B [Clostridium perfringens]
55
28

482
6
3515
3156
gi|606162
ORF_f229 [Escherichia coli]
55
39

497
9
4885
5937
gi|1041637
replication initiator protein
55
33

[Staphylococcus xylosus]

546
1
1
1104
gi|467446
similar to SpoVB [Bacillus subtilis]
55
36

634
4
2132
1524
gi|431950
similar to a B.subtilis gene (GB:
55
27

BACHEMEHY_5) [Clostridium asteurianum]

660
2
249
401
gnl|PID|e254995
hypothetical protein [Bacillus subtilis]
55
35

671
1
288
58
gi|38722
precursor (aa −20 to 381) [Acinetobacter
55
33

calcoaceticus
] ir|A29277|A29277 aldose 1-

epimerase (EC 5.1.3.3) - Acinetobacter

lcoaceticus

686
2
245
1141
gi|1633572

Herpesvirus saimiri
ORF73 homolog
55
36

[Kaposi's sarcoma-associated herpes-like

virus]

713
3
2742
1438
gnl|PID|e8901
RESA NF7 Ag13 [Plasmodium falciparum]
55
25

815
1
2
226
gi|1113815
histidine kinase [Borrelia burgdorferi]
55
36

857
1
2
520
gi|143024
glucose-resistance amylase regulator
55
31

[Bacillus subtilis] pir|515318|S15318 ccpA

protein - Bacillus subtilis

sp|P25144 CCPA_BACSU GLUCOSE-RESISTANCE

AMYLASE REGULATOR CATABOLITE CONTROL

PROTEIN).

931
1
3
557
gi|1098508
putative spore germination apparatus
55
32

protein [Bacillus megaterium]

17
7
6379
7218
gnl|PID|e250887
potential coding region [Clostridium
54
35

difficile
]

21
9
7265
6348
gi|13441
NADH dehydrogenase subunit 4L [Phoca
54
29

vitulina
]

28
2
2727
3425
gi|1001792
hypothetical protein [Synechocystis sp.]
54
29

32
6
4044
3523
gi|1673660
(AE000002) Mycoplasma pneumoniae,
54
36

hypothetical 28K protein; similar to

GenBank Accession Number JS0068, from M.

pneumoniae
[Mycoplasma pneumoniae]

33
3
2274
3767
gnl|PID|e245024
unknown [Mycobacterium tuberculosis]
54
36

40
1
1
915
gi|773349
BirA protein [Bacillus subtilis]
54
32

49
6
2120
2485
gnl|PID|e139446
a2 gene product [Bacteriophage Bi]
54
38

54
17
8969
8661
gi|334068
ORF2 [Suid herpesvirus 1]
54
51

65
2
1311
2120
gi|537207
ORF_277 [Escherichia coli]
54
27

72
20
21986
22435
gi|928848
ORF70′; putative [Lactococcus lactis phage
54
34

BK5-T]

105
4
3039
3827
gnl|PID|e205174
orf2 gene product [Lactobacillus
54
30

helveticus
]

127
1
884
150
gi|726443
No definition line found [Caenorhabditis
54
31

elegans
]

148
1
1204
62
gi|467456
unknown [Bacillus subtilis]
54
37

156
4
4360
3167
gi|1032483
unidentified ORF downstream of hydrogenase
54
30

cluster; ORF5 [Anabaena variabilis]

160
4
1523
2077
gnl|PID|e255111
hypothetical protein [Bacillus subtilis]
54
27

160
7
4260
3745
gi|1184121
auxin-induced protein [Vigna radiata]
54
30

165
5
4996
3971
gi|1772652
2-keto-3-deoxygluconate kinase [Haloferax
54
36

alicantei
]

176
2
1044
1937
gi|162201
P-type ATPase [Trypanosoma brucei]
54
38

180
29
30833
29853
gnl|PID|e254644
membrane protein [Streptococcus
54
29

pneumoniae
]

200
16
7933
6656
gi|1574238
traN protein (traN) [Haemophilus
54
31

influenzae]

206
1
232
2
gi|1220501

Rickettsia tsutsugamushi
(strain Kp47)
54
31

gene, complete cds [Rickettsia

tsutsugamushi
]

220
4
5235
4342
gi|606080
ORF_o290; Geneplot suggests frameshift
54
31

linking to o267, not found Escherichia

coli
]

220
5
5821
5135
gi|43942
first subunit of EII-Sor [Klebsiella
54
36

pneumoniae]

223
20
17253
17747
gi|47932
tonB protein [Salmonella typhimurium]
54
38

228
7
4866
4033
gi|1736828
Thi4 protein [Escherichia coli]
54
34

229
4
5050
3371
gi|1046078

M. genitalium
predicted coding region
54
42

MG369 [Mycoplasma genitalium]

236
3
4777
1496
gi|152271
319-kDA protein [Rhizobium meliloti]
54
28

236
5
7822
6944
gnl|PID|e285031
Hyp1 protein [Hydra vulgaris]
54
20

238
30
27964
27746
gnl|PID|e217586
PlnM [Lactobacillus plantarum]
54
42

242
5
3508
4050
gi|149502
beta-lactamase [Lactococcus lactis]
54
35

257
1
296
120
gi|1498064
AtE1 [Arabidopsis thaliana]
54
50

257
6
6745
5633
gi|343949
var1(40.0) [Saccharomyces cerevisiae]
54
42

258
8
7839
7114
gi|41519
P30 protein (AA 1-240) [Escherichia coli]
54
31

276
20
13101
12880
gi|155322
icsB gene product [Plasmid pWR100]
54
37

280
1
618
106
gi|467356
unknown [Bacillus subtilis]
54
21

288
4
2183
2632
gi|39978
P16 [Bacillus subtilis]
54
39

316
1
3
767
gi|143264
membrane-associated protein [Bacillus
54
34

subtilis
]

318
7
5035
4565
gi|606080
ORF_o290; Geneplot suggests frameshift
54
28

linking to o267, not found Escherichia

coli
]

319
3
1393
2163
gi|148327
vancomycin response regulator
54
34

[Enterococcus faecium]

323
2
1256
2560
gi|413940
ipa-16d gene product [Bacillus subtilis]
54
26

364
7
7335
7724
gnl|PID|e250171
F18C12.1 [Caenorhabditis elegans]
54
31

386
5
2399
3844
gi|155369
PTS enzyme-II fructose [Xanthomonas
54
37

campestris
]

392
3
2004
3353
gi|872306
integral membrane protein [Streptomyces
54
32

pristinaespiralis
] pir|557509|S57509

integral membrane protein - Streptomyces

ristinaespiralis

424
5
1553
1371
gi|160316
major merozoite surface antigen
54
37

[Plasmodium falciparum]

sp|P50495|MSP1_PLAFP MEROZOITE SURFACE

PROTEIN 1 PRECURSOR MEROZOITE SURFACE

ANTIGENS) (PMMSA) (GP195)

445
2
1897
1178
gi|1781503
MigA [Pseudomonas aeruginosa]
54
31

452
5
2506
2805
gi|216292
neopullulanase [Bacillus sp.]
54
34

457
2
2178
1024
gi|405570
TraK protein shares sequence similarity
54
35

with a family of proteins ncoded on Gram-

negative gene transfer systems such as

TraD from the plasmid [Plasmid pSK41]

461
3
627
1418
gi|797332
MocD [Agrobacterium tumefaciens]
54
38

466
5
5419
3770
gi|1652892
ABC transporter [Synechocystis sp.]
54
29

475
3
2745
1990
gi|532546
ORF13 [Enterococcus faecalis]
54
35

495
1
2
295
gi|304990
ORF_o290 [Escherichia coli]
54
21

502
4
3518
3216
gi|1573270
hemolysin (tlyC) [Haemophilus influenzae]
54
33

510
5
3089
3931
gi|1732200
PTS permease for mannose subunit IIPMan
54
29

[Vibria furnissii]

570
1
1
930
gi|1001582
penicillin-binding protein 1A
54
31

[Synechocystis sp.]

573
6
2763
3164
gi|416197
homologous to plasmid R100 pemK gene
54
35

[Escherichia coli]

590
1
433
2
gi|532309
25 kDa protein [Escherichia coli]
54
33

643
2
1202
1477
gnl|PID|e125689
256 kD golgin [Homo sapiens]
54
29

705
1
2
682
gi|148921
LicD protein [Haemophilus influenzae]
54
39

730
1
370
167
gnl|PID|e245531
ORF YLR068w [Saccharornyces cerevisiae]
54
29

745
1
502
209
gi|581140
NADH dehydrogenase [Escherichia coli]
54
37

749
1
413
3
gi|664840
TagB [Dictyostelium discoideum]
54
44

932
1
3
320
gi|537207
ORF_f277 [Escherichia coli]
54
27

4
6
5671
4748
gi|216267
ORF2 [Bacillus megaterium]
53
34

16
8
6231
6806
gi|517105
spermidine acetyltransferase [Escherichia
53
35

coli]

17
1
2
2497
gi|387880
collagen adhesin [Staphylococcus aureus]
53
35

42
4
2942
3529
gi|1633572

Herpesvirus saimiri
ORF73 homolog
53
20

[Kaposi's sarcoma-associated herpes-like

virus]

69
6
3149
4879
gi|1486244
unknown [Bacillus subtilis]
53
30

72
3
1455
2063
gi|1592197

M. jannaschii
predicted coding region
53
32

MJ1576 [Methanococcus jannaschii]

79
1
83
592
gi|633757
pr2 [Mycoplasma hyopneumoniae]
53
28

83
8
5179
4412
gi|496100
unknown function; putative [Bacteriophage
53
39

phi-LC3]

85
10
7180
6764
gil 1303940
YgiU [Bacillus subtilis]
53
35

92
2
789
986
gi|1372996
Rho [Borrelia burgdorferi]
53
28

95
10
7546
7734
gi|162379
variant surface glycoprotein [Trypanosoma
53
28

brucei
]

99
4
1391
1861
gi|1499620

M. jannaschii
predicted coding region
53
34

MJ0798 [Methanococcus jannaschii]

100
44
29982
29749
gi|1590997

M. jannaschii
predicted coding region
53
35

MJ0272 [Methanococcus jannaschii]

102
5
4787
5089
gi|1399011
immunogenic secreted protein precursor
53
40

[Streptococcus pyogenes]

113
1
825
4
gnl|PID|e264148
unknown [Mycobacterium tuberculosis]
53
24

114
4
6555
5113
gi|487282
Na+ −ATPase subunit J [Enterococcus hirae]
53
33

119
6
3581
3994
gi|473707
positive regulator for virulence factors
53
31

[Clostridium perfringens]

123
19
16463
18115
gi|1591361
NADH oxidase [Methanococcus jannaschii]
53
33

136
1
381
4
gi|152744
IpaD protein [Shigella flexneri]
53
32

138
9
8079
7594
gi|467371
LACI family of transcriptional repreesor
53
29

(probable) [Bacillus ubtilis]

142
8
4594
4007
gi|755216
N-acetylmuramidase [Lactococcus lactis]
53
38

162
12
12482
11937
gi|1063250
low homology to P20 protein of Bacillus
53
36

lichiniformis
and bleomycin

acetyltransferase of Streptomyces

verticillus
[Bacillus subtilis]

163
1
546
31
gi|153767
ORF [Streptococcus pneumoniae]
53
34

163
7
4973
3453
gi|29468
beta-myosin heavy chain (1151 AA) [Homo
53
36

sapiens
]

167
2
1038
2006
gi|413930
ipa-6d gene product [Bacillus subtilis]
53
27

173
11
8865
7843
gi|1778569
YaaF homolog [Escherichia coli]
53
39

190
8
6842
3549
gi|387880
collagen adhesin [Staphylococcus aureus]
53
38

199
2
2725
950
gi|1652570
nitrate transport protein NrtB
53
32

[Synechocystis sp.]

200
13
6184
5954
gi|1652679
hypothetical protein [Synechocystis sp.]
53
40

200
17
9287
7890
gi|1574246

H. influenzae
predicted coding region
53
35

HI1409 [Haemophilus influenzae]

205
6
2048
3229
gi|148026
topoisomerase III [Escherichia coli]
53
32

211
2
270
1052
gi|483940
transcription regulator [Bacillus
53
30

subtilis
]

221
10
5119
5994
gi|1353529
ORF12 [Bacteriophage rlt]
53
44

232
7
4344
3925
gi|1665759
Similar to Schistosoma mansoni amino acid
53
35

permease (L25068). [Homo sapiens]

238
21
18705
19247
gi|1574062
hypothetical [Haemophilus influenzae]
53
30

239
1
2
1636
gi|433932
activator of (R)-hydroxyglutaryl-CoA
53
35

dehydratase [Acidaminococcus ermentans]

250
1
1469
318
gi|987094
membrane transport protein [Streptomyces
53
22

hygroscopicus
]

253
4
1759
1028
gi|537245
aspartokinase I-homoserine dehydrogenase I
53
35

[Escherichia coli] pir|556629|S56629

aspartate kinase (EC 2.7.2.4)/homoserine

ehydrogenase (EC 1.1.1.3) - Escherichia

coli

271
8
4649
5800
gi|413966
ipa-42d gene product [Bacillus subtilis]
53
27

276
26
15786
15112
gi|1699017
ErpB2 [Borrelia burgdorferi]
53
26

279
11
8309
7797
gi|1651934
hypothetical protein [Synechocystis sp.]
53
35

288
8
3997
4872
gi|43943
second subunit of EII-Sor [Klebsiella
53
32

pneumoniae
]

290
6
4391
5680
gi|466882
pps1; B1496_C2_189 [Mycobacterium leprae]
53
29

294
3
1197
1481
gi|173004
topoisomerase I [Saccharomyces cerevisiae]
53
40

330
3
2351
3367
gi|466691
No definition line found [Escherichia
53
34

coli
]

334
8
8172
9182
gi|1652483
hypothetical protein [Synechocystis sp.]
53
29

368
1
620
102
gi|487273
Na+ ATPase subunit I [Enterococcus hirae]
53
29

377
4
2424
2260
gi|221407
FPS [Fowlpox virus]
53
35

382
1
257
36
gi|1592016

M. jannaschii
predicted coding region
53
32

MJ1371 [Methanococcus jannaschii]

387
1
2
460
gi|1574317
repressor protein (GP:L22692_1)
53
30

[Haemophilus influenzae]

394
10
8379
10412
gi|882463
protein-N(pi)-phosphohistidine-sugar
53
34

phosphotransferase [Escherichia oli]

399
4
2349
3098
gi|453287
OmpR protein [Escherichia coli]
53
27

420
2
1378
719
gi|1437473
nitrate transporter [Bacillus subtilis]
53
28

441
6
5361
7937
gi|1592205

M. jannaschii
predicted coding region
53
38

MJ1595 [Methanococcus jannaschii]

461
1
6
512
gi|1651800
L-glutamine:D-fructose-6-P
53
29

amidotransferase [Synechocystis sp.]

497
3
1700
1960
gi|4328
RIF1 gene product [Saccharomyces
53
33

cerevisiae
]

503
1
669
4
gnl|PID|e202290
unknown [Lactobacillus sake]
53
30

538
2
1053
262
gi|1613769
response regulator [Streptococcus
53
30

pneumoniae
]

539
6
6172
5183
gi|567887
putative repressor [Streptomyces
53
32

peucetius
]

551
1
629
162
gi|1256649
putative [Bacillus subtilis]
53
26

557
1
9
695
gi|143177
putative [Bacillus subtilis]
53
31

569
2
418
1158
gi|1184684
MucD [Pseudomonas aeruginosa]
53
26

614
1
99
581
gi|485280
28.2 kDa protein [Streptococcus
53
32

pneumoniae
]

660
1
1
279
gnl|PID|e288480
R10E8.f [Caenorhabditis elegans]
53
34

776
1
3
635
gi|151352
mandelate racemase (EC 5.1.2.2)
53
33

[Pseudomonas putida]

11
2
1117
1656
gi|143150
levR [Bacillus subtilis]
52
29

17
6
5327
6559
gnl|PID|e250887
potential coding region [Clostridium
52
37

difficile
]

19
31
17760
17978
gi|1079556
dShc [Drosophila melanogaster]
52
42

19
38
20306
22627
gn|PID|e139448
host interacting protein [Bacteriophage
52
32

B1]

25
4
2662
2087
gi|1072067
PepE [Rhodobacter sphaeroides]
52
23

25
6
5596
3407
gi|1303866
YggS [Bacillus subtilis]
52
34

49
3
1135
1569
gi|496279
putative [Bacteriophage Tuc2009]
52
25

53
1
850
2
sp|P52697|YBHE_ECO
HYPOTHETICAL 30.2 KD PROTEIN IN MODC
52
35

LI
3′REGION.

54
9
10909
2687
gi|1633572

Herpesvirus saimiri
ORF73 homolog
52
30

[Kaposi's sarcoma-associated herpes-like

virus]

57
6
4779
8402
gi|142439
ATP-dependent nuclease [Bacillus subtilis]
52
31

58
6
6446
5949
gnl|PID|e255921
F53F4.10 [Caenorhabditis elegans]
52
31

72
13
13446
13195
gi|532541
ORF8 [Enterococcus faecalis]
52
37

81
17
13692
12520
gi|1732203
GlcNAc 6-P deacetylase [Vibrio furnissii]
52
35

84
1
3
1355
gi|64288
fast skeletal muscle Ca-ATPase [Rana
52
34

esculenta
]

100
2
1917
1027
gi|1353560
ORF43 [Bacteriophage rlt]
52
34

101
1
30
1862
gi|405957
yeeF [Escherichia coli]
52
24

106
8
8517
7600
gi|454904
rfbG gene product [Shigella flexneri]
52
41

108
1
1
1059
gnl|PID|e255337
unknown [Mycobacterium tuberculosis]
52
29

123
4
2899
3495
gi|1305720
prs-associated putative membrane protein
52
24

[Escherichia coli]

128
23
17561
16740
gi|473805
‘regulatory protein sfs1 involved in
52
32

maltose metabolism’ Escherichia coli]

130
8
6693
7481
gi|1552775
ATP-binding protein [Escherichia coli]
52
30

138
1
40
1359
gi|1045867
oligoendopeptidase F [Mycoplasma
52
31

genitalium
]

138
2
2757
1384
gi|1591425
hypothetical protein (GP:X91006_2)
52
26

[Methanococcus jannaschii]

138
6
6317
5940
gi|1486247
unknown [Bacillus subtilis]
52
36

142
10
7337
5466
gi|1151158
repeat organellar protein [Plasmodium
52
34

chabaudi
]

149
1
33
1133
gi|1762962
FemA [Staphylococcus simulans]
52
31

161
1
3
245
gi|151276
histidine utilization genes repressor
52
35

protein (hut) [Pseudomonas utida]

163
4
2048
1320
gi|1064810
function unknown [Bacillus subtilis]
52
27

164
8
4882
5103
gi|57251
precursor (AA −35 to 1766) [Rattus
52
38

norvegicus
]

165
9
7247
7474
gi|1652671
hypothetical protein [Synechocystis sp.]
52
28

178
5
1887
1681
gi|220704
cAMP-dependent protein kinase catalytic
52
36

subunit-beta [Rattus sp.]gi|191177 cAMP-

dependent protein kinase beta-catalytic

subunit Cricetulus sp.]

180
24
22536
23774
gi|581052
cytosine deaminase [Escherichia coli]
52
28

190
9
8891
7056
gi|1592079

M. jannaschii
predicted coding region
52
39

MJ1429 [Methanococcus jannaschii]

195
8
2000
2272
gi|868024
HIC-1 gene product [Homo sapiens]
52
52

202
11
9189
10145
gi|141861
traA gene product [Plasmid pAD1]
52
33

204
4
1361
2011
gi|1184118
mevalonate kinase [Methanobacterium
52
33

thermoautotrophicum
]

204
8
4018
5142
gnl|PID|e283860
carotenoid biosynthetic gene ERWCRTS
52
31

homolog [Sulfolobus solfataricus]

208
2
1112
2296
gi|1408501
homologous to N-acyl-L-amino acid
52
35

amidohydrolase of Bacillus

stearothermophilus
[Bacillus subtilis]

215
1
772
2
gi|1480429
putative transcriptional regulator
52
26

[Bacillus stearothemophilus]

218
4
4072
3425
gi|862630
glyceraldehyde-3-Phosphate dehydrogenase
52
35

[Buchnera aphidicola] sp|Q07234|G3P_BUCAP

GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE

(EC .2.1.12) (GAPDH).

228
1
1
741
gnl|PID|e264148
unknown [Mycobacterium tuberculosis]
52
29

230
2
149
634
gi|437705
hyaluronidase [Streptococcus pneumoniae]
52
28

233
8
6166
4982
gi|1001708
NifS [Synechocystis sp.]
52
31

240
3
725
967
gi|399655
Ca2+ regulatory protein [Saccharomyces
52
21

cerevisiae]sp ( P35206 I CSG2 YEAST CSG2

PROTEIN PRECURSOR.

288
7
3171
4028
gi|147403
mannose permease subunit II-P-Man
52
27

[Escherichia coli]

318
1
7
819
gi|1303849
YggB [Bacillus subtilis]
52
33

330
1
1062
154
gi|144859
ORF B [Clostridium perfringens]
52
29

330
9
6815
7213
gi|1439527
EIIA-man [Lactobacillus curvatus]
52
31

345
9
8348
9397
gi|606292
ORF_o696 [Escherichia coli]
52
27

398
3
2671
1877
gi|144859
ORF B [Clostridium perfringens]
52
29

411
1
992
3
gnl|PID|e283950
daunorubicin resistance ATP-binding
52
27

protein DrrA [Sulfolobus solfataricus]

422
2
1292
585
gi|537214
yjjG gene product [Escherichia coli]
52
32

436
2
1669
1205
gi|507323
ORF1 [Bacillus stearothermophilus]
52
29

450
1
119
754
gi|1573916
multidrug resistance protein (emrB)
52
32

[Haemophilus influenzae]

453
1
190
381
gi|182021
elastin [Homo sapiens]
52
40

455
7
5767
4634
gnl|PID|e155312
integrase [Bacteriophage TP901-1]
52
34

479
1
138
758
gi|1742859
ORF_ID:o327#7; similar to [SwissProt
52
27

Accession Number P54449] [Escherichia

coli
]

517
1
763
2
gi|152780
rhamnosyl transferase II [Shigella
52
29

dysenteriae
]

518
3
1735
848
gi|153858
wall-associated protein [Streptococcus
52
20

mutans
]

526
3
2297
1848
gi|147402
mannose permease subunit III-Man
52
27

[Escherichia coli]

617
1
1
462
gi|142863
replication initiation protein [Bacillus
52
35

subtilis
]

639
3
1068
259
gi|1591153
hypothetical protein (SP:P46348)
52
30

[Methanococcus jannaschii]

703
1
773
81
gi|793910
surface antigen [Homo sapiens]
52
31

737
1
235
2
gi|666000
hypothetical protein [Bacillus subtilis]
52
29

791
4
1368
1802
gnl|PID|e269549
Unknown [Bacillus subtilis]
52
28

825
1
1
300
gi|732538
No definition line found [Caenorhabditis
52
28

elegans
]

981
1
226
2
gi|951100
P45016a-ms1 [Mus spretus]
52
36

17
23
23542
22163
gi|1652483
hypothetical protein [Synechocystis sp.]
51
32

65
6
4302
3691
gi|397498
Membrane Ribose Binding Protein [Bacillus
51
31

subtilis] pir|S42714|S42714 membrane

ribose-binding protein - Bacillus ubtilis

69
5
2926
2537
gi|1773150
hypothetical 14.8kd protein [Escherichia
51
30

coli
]

92
1
973
44
gnl|PID|e243523
ORF YGR130c [Saccharomyces cerevisae]
51
29

103
6
5272
3593
gi|312940
threonine kinase [Streptococcus
51
32

equisimilis
]

111
7
4195
3317
pir|G64143|G64143
hypothetical protein HI0143 - Haemophilus
51
29

influenzae (strain Rd KW20)

115
7
4526
3414
gi|405879
yeiH [Escherichia coli]
51
27

123
29
27788
28207 gi|147402
mannose permease subunit III-Man
51
27

[Escherichia coli]

125
1
223
2
gi|4482
SLY1 gene product [Saccharomyces
51
37

cerevisiae]

128
21
16156
15638
gi|606026
ORF_o115 [Escherichia coli]
51
27

137
4
3207
5369
gi|1673692
(AE000005) Mycoplasma pneumoniae,
51
26

C09_orf422 Protein [Mycoplasma pneumoniae]

138
28
18295
18771
gi|149647
ORFZ [Listeria monocytogenes]
51
31

145
6
4054
5271
gi|1653860
N-acyl-L-amino acid amidohydrolase
51
41

[Synechocystis sp.]

155
4
3019
2273
gi|1486242
unknown [Bacillus subtilis]
51
41

180
8
7951
9189
gi|1657522
hypothetical protein [Escherichia coli]
51
32

186
2
859
1620
gi|511497
oleoyl-acyl carrier protein thioesterase
51
29

[Coriandrum sativum]

186
3
1644
2060
sp|P37348|YECE_ECO
HYPOTHETICAL PROTEIN IN ASPS 5 REGION
51
38

LI
(FRAGMENT).

194
3
1521
1276
gi|332697
fusion protein [Human parainfluenza virus
51
32

2]

195
7
1986
3767
gi|405570
TraK protein shares sequence similarity
51
28

with a family of proteins ncoded on Gram-

negative gene transfer systems such as

TraD from the plasmid [Plasmid pSK41]

197
1
3
494
gi|1592234
DNA topoisomerase I [Methanococcus
51
32

jannaschii
]

198
2
1521
862
gi|1196483
unknown protein [Lactobacillus casei]
51
32

238
16
13630
14730
gi|1772652
2-keto-3-deoxygluconate kinase [Haloferax
51
36

alicantei
]

257
5
5646
4513
pir|S43367|S43367
metallothionein - Green crab, common shore
51
38

crab

261
6
4950
4519
gi|581545
orf 4 [Staphylococcus aureus]
51
26

270
5
4480
4220
gi|1066975
F49E2.5a [Caenorhabditis elegans]
51
28

306
10
5928
6905
gi|1752736
gene required for phosphoylation of
51
28

oligosaccharides/ has high homology with

YJR061w [Saccharomyces cerevisiae]

324
3
1590
2405
gi|409925
VirR positive regulator [Streptococcus
51
25

pyogenes
]

328
2
632
309
gi|466475
putative phospho-beta-glucosidase
51
30

[Bacillus stearothermophilus]

pir|D49898|D49898 cellobiose

phosphotransferase system celC - acillus

stearothermophilus

340
2
898
1152
gi|40046
phosphoglucose isomerase A (AA 1-449)
51
39

[Bacillus stearothermophilus]

ir|S15936|NUBSSA glucose-6-phosphate

isomerase (EC 5.3.1.9) A - cillus

stearothermophilus

340
4
3617
2445
gi|763052
integrase [Bacteriophage T270]
51
33

379
10
11742
11311
gi|887829
D21141 uses 2nd start; frame determined by
51
34

Lac fusion [Escherichia oli]

380
1
2
1123
gi|309662
pheromone binding protein [Plasmid pCF10]
51
34

395
1
526
95
gi|490986
phi 105 repessor orf2 [unidentified]
51
27

424
4
2512
995
gi|1633572

Herpesvirus saimiri
ORF73 homolog
51
31

[Kaposi's sarcoma-associated herpes-like

virus]

444
1
737
483
gi|1245376
cardiac ryanodine receptor [Oryctolagus
51
34

cuniculus
]

483
1
1
642
gi|1303981
YgkD [Bacillus subtilis]
51
29

500
1
2
550
gi|987094
membrane transport protein [Streptomyces
51
23

hygroscopicus
]

525
3
492
983
pir|A57438|A57438
tryptophan-rich sensory protein -
51
38

Rhodobacter sphaeroides
(strain 2.4.1)

534
1
2
1165
gi|147516
ribokinase [Escherichia coli]
51
33

547
1
1
387
gi|1353528
ORF11 [Bacteriophage rlt]
51
33

553
2
1728
1330
pir|B55124|B55124
thioredoxin - Chlorobium sp.
51
27

574
1
2291
2476
bbs|129435
RprX=inner membrane signal-transducing
51
36

protein [Bacteroides fragilis, Peptide,

519 aa] [Bacteroides fragilis]

574
2
3145
3420
gi|1732202
PTS permease for mannose subunit IIIMan N
51
29

terminal domain [Vibrio furnissii]

594
2
530
225
gi|1657696
tryptophan hydroxylase [Gallus gallus]
51
40

605
3
1220
1936
gnl|PID|e289149
similar to B. subtilis YcsE hypothetical
51
32

protein [Bacillus subtilis]

609
1
1027
74
gi|1226279
strong similarity to Schistosoma amino
51
26

acid permease (GB:L25068) [Caenorhabditis

elegans
]

656
2
2033
2950
gi|143213
putative [Bacillus subtilis]
51
26

670
1
1508
369
gi|1652222
hypothetical protein [Synechocystis sp.]
51
25

673
1
2
1135
gi|532553
ORF20 [Enterococcus faecalis]
51
27

674
2
1158
778
gi|467451
unknown [Bacillus subtilis]
51
26

735
2
477
725
gi|757791
aromatic amino acid permease
51
38

[Corynebacterium glutamicum]

pir|S52754|S52754 aromatic amino acid

permease - Corynebacterium lutamicum

924
1
794
3
gi|40663
sialidase [Clostridium septicum]
51
35

4
5
3811
4728
gi|413948
ipa-24d gene product [Bacillus subtilis]
50
29

8
3
3310
2180
gi|1592205

M. jannaschii
predicted coding region
50
28

MJ1595 [Methanococcus jannaschii]

11
9
5269
5520
gi|1651800
L-glutamine:D-fructose-6-P
50
25

amidotransferase [Synechocystis sp.]

12
6
9045
8662
gnl|PID|e254943
unknown [Mycobacterium tuberculosis]
50
23

15
4
2911
4269
gi|1592173
N-ethylammeline chlorohydrolase
50
28

[Methanococcus jannaschii]

19
10
4934
5530
gi|825569
unknown [Saccharomyces cerevisiae]
50
20

28
5
7515
7057
gi|1230586
orf10; Method: conceptual translation
50
38

supplied by author [Vibrio cholerae O139]

45
9
4279
5019
gi|1591029
thioredoxin/glutaredoxin [Methanococcus
50
32

jannaschii
]

54
16
7739
7590
gi|1589837
cuticle preprocollagen [Meloidogyne
50
46

incognita
]

59
5
1551
2345
gi|144297
acetyl esterase (XynC) [Caldocellum
50
34

saccharolyticum
] pir|B37202|B37202

acetylesterase (EC 3.1.1.6) (XynC) -

Caldocellum accharolyticum

62
3
1650
1360
gnl|PID|e205266
LEA76 homologue type2 [Arabidopsis
50
31

thaliana
]

91
10
8858
7521
gi|758229
integrase [Bacteriophage phi-13]
50
31

112
5
3548
2133
gi|1184262
GadC [Shigella flexneri]
50
25

123
13
13099
14319
gi|178273
alanine:glyoxylate aminotransferase [Homo
50
31

sapiens
]

123
15
14395
15675
gi|467342
unknown [Bacillus subtilis]
50
28

123
31
28700
29494
gi|43942
first subunit of EII-Sor [Klebsiella
50
27

pneumoniae
]

124
2
1666
1061
gi|556016
similar to plant water stress proteins;
50
34

ORF2 [Bacillus subtilis gi|556016 similar

to plant water stress proteins; ORF2

[Bacillus ubtilis]

128
39
32767
31829
gi|39993
UDP-N-acetylmuramoylalanine--D-glutamate
50
33

ligase [Bacillus subtilis]

135
11
8803
7694
gi|895747
putative cel operon regulator [Bacillus
50
26

subtilis
]

138
21
14648
13653
gi|1591472
malic acid transport protein
50
26

[Methanococcus jannaschii]

146
3
2338
1415
gi|1732200
PTS permease for mannose subunit IIPMan
50
27

[Vibrio furnissii]

160
2
724
1302
gnl|PID|e264218
F54F3.4 [Caenorhabditis elegans]
50
30

164
15
15432
16364
gi|409286
bmrU Bacillus subtilis]
50
27

167
9
17082
15394
gi|143156
membrane bound protein [Bacillus subtilis]
50
30

179
3
2350
4485
gi|1408485
yxdM gene product [Bacillus subtilis]
50
24

180
30
31056
30643
gnl|PID|e254644
membrane protein [Streptococcus
50
27

pneumoniae
]

184
1
2
1015
gi|854232
cymE gene product [Klebsiella oxytoca]
50
24

194
7
4335
4817
gi|1256652
25% identity to the E.coli regulatory
50
30

protein MprA; putative [Bacillus subtilis]

195
29
11712
12422
gi|662263
ORF5 [Plasmid pIP501]
50
25

204
1
2
166
gi|328656
envelope polyprotein [Human
50
45

immunodeficiency virus type 1]

205
7
3118
3861
gi|437697
traE [Plasmid RP4]
50
31

216
11
7181
7750
gnl|PID|e254644
membrane protein [Streptococcus
50
30

pneumoniae
]

223
10
7036
8082
gi|606423
T09B9.1 [Caenorhabditis elegans]
50
30

223
22
19257
19799
gi|1256141
YbbL [Bacillus subtilis]
50
29

233
4
3102
2320
gi|887826
GUG start [Escherichia coli]
50
32

238
6
5102
3906
gi|1161219
hoinolgous to D-amino acid dehydrogenase
50
29

enzyme [Pseudomonas aeruginosa]

239
3
4449
5159
gi|41519
P30 protein (AA 1-240) [Escherichia coli]
50
31

242
2
147
2210
gi|160299
glutamic acid-rich protein [Plasmodium
50
30

falciparum
] pir|A54514|A54514 glutamic

acid-rich protein precursor - Plasmodium

alciparum

248
2
263
712
gi|143725
putative [Bacillus subtilis]
50
32

256
8
8531
7395
gnl|PID|e250452
C44H9.4 [Caenorhabditis elegans]
50
38

265
3
1150
893
gi|1402527
ORF6 [Enterococcus faecalis]
50
39

276
24
14203
14000
gi|1591019

M. jannaschii
predicted coding region
50
33

MJ0297 [Methanococcus jannaschii]

276
32
20601
19924
gi|1334905
BXLF2 late reading frame, encodes gp85;
50
29

homologous to RF 37 VZV and glycoprotein H

of HSV (gpIII of VZV) [Human herpesvirus

4]

286
1
1
747
gnl|PID|e257895
homology with truncated ORF2 of pepF2
50
32

[Lactococcus lactis]

301
17
11706
13313
gi|562039
NADH dehydrogenase, subunit 2
50
26

[Acanthamoeba castellanii]

pir|S53835|S53835 NADH dehydrogenase chain

2 - Acanthamoeba astellanii mitochondrion

(SGC6)

338
5
2206
3729
gi|829194
bacterial cell wall hydrolase
50
34

[Enterococcus faecalis] pir|A38109|A38109

autolysin - Enterococcus faecalis

sp|P37710|ALYS_ENTFA AUTOLYSIN (EC

3.5.1.28) N-ACETYLMURAMOYL-L-ALANINE

AMIDASE).

345
12
11781
13379
gnl|PID|e235181
unknown [Mycobacterium tuberculosis]
50
32

360
2
2879
408
gi|40782
bps2 gene product [Desulfurolobus
50
25

ambivalens
]

372
1
6
440
gi|1552733
similar to voltage-gated chloride channel
50
31

protein [Escherichia coli]

372
2
391
738
gi|1591749
TRK system potassium uptake protein A
50
23

[Methanococcus jannaschii]

377
3
2262
1846
gi|52797
kinesin heavy chain [Mus musculus]
50
22

392
1
433
2
gi|147213
phnP protein [Escherichia coli]
50
33

399
31
29803
30186
gi|146288
PTS enzyme III glucitol [Escherichia coli]
50
30

518
4
2885
2040
gi|475107
regulatory protein [Pediococcus
50
29

pentosaceus
]

528
1
3
665
gi|215098
excisionase [Bacteriophage 154a]
50
38

562
1
631
107
gi|1592205

M. jannaschii
predicted coding region
50
28

MJ1595 [Methanococcus jannaschii]

596
1
227
1153
gi|963039
orf gene product [Enterococcus hirae]
50
26

680
1
2
1090
gi|1050297
product p150Glued [Neurospora crassa]
50
27

755
1
2
430
gi|1736469
Tetracenomycin C resistance and export
50
33

protein. [Escherichia coli]

838
1
428
3
gi|530424
50S ribosomal protein [Mycoplasma
50
30

capricolum
]

14
2
3453
538
gi|47049
asa1 gene product (AA 1-1296)
49
25

[Enterococcus faecalis] ir|S10223|HMSO1F

aggregation protein asa1 - Enterococcus

faecalis
asmid pAD1

56
7
5367
4822
gi|924754
glycine reductase complex selenoprotein B
49
31

[Clostridium litorale]

68
9
4741
7389
gi|1591494

M. jannaschii
predicted coding region
49
21

MJ0797 [Methanococcus jannaschii]

94
10
9425
6633
gi|1146243
22.4% identity with Escherichia coli DNA-
49
30

damage inducible protein . . . ; putative

[Bacillus subtilis]

98
12
12306
11701
gi|1303784
YqeD [Bacillus subtilis]
49
26

117
7
4789
6228
gi|435493
orf4 gene product [Lactococcus lactis]
49
26

123
21
18576
19745
gi|298032
EF [Streptococcus suis]
49
29

125
4
2358
1594
gnl|PID|e237295
unknown [Saccharomyces cerevisiae]
49
27

125
6
4235
3453
gi|1573885
glycosyl transferase (lgtD) [Haemophilus
49
32

influenzae
]

144
5
3715
4062
gi|507130
emm64 gene product [Streptococcus
49
30

pyogenes
]

162
8
10472
9120
gi|47045
NADH oxidase [Enterococcus faecalis]
49
34

179
18
18426
17848
gi|40060
DNA polymerase III (AA 1-1437) [Bacillus
49
27

subtilis
] p|P13267|DP3A_BACSU DNA

POLYMEPASE III, ALPHA CHAIN (EC 2.7.7.7).

180
19
18727
19917
gi|143000
proton glutamate symport protein [Bacillus
49
31

stearothermophilus
] pir|S26247|S26247

glutamate/aspartate transport protein -

Bacillus tearothermophilus

224
1
145
1371
gi|1103862
TolA [Pseudomonas aeruginosa]
49
32

236
8
10955
9249
gi|431272
lysis protein [Bacillus subtilis]
49
28

278
1
757
2
gi|467478
unknown [Bacillus subtilis]
49
29

290
8
6860
7366
gi|466875
nifU; B1496_C1_157 [Mycobacterium leprae]
49
35

318
5
4065
3190
gi|144859
ORF B [Clostridium perfringens]
49
25

318
8
6052
5033
gi|1439528
EIIC-man [Lactobacillus curvatus]
49
30

335
1
534
40
gi|216861
24K membrane protein [Pseudomonas
49
24

aeruginosa
]

338
4
2861
2169
gnl|PID|e288536
F37H8.a [Caenorhabditis elegans]
49
30

346
4
1257
2273
gi|536970
ORF_f543 [Escherichia coli]
49
25

355
20
12902
15262
gi|292836
trichohyalin [Homo sapiens]
49
20

366
1
1
1437
gi|405857
yehU [Escherichia coli]
49
26

375
8
7663
6470
gi|1573546

H. influenzae
predicted coding region
49
30

H10561 [Haemophilus influenzae]

377
2
1624
392
gi|532553
ORF20 [Enterococcus faecalis]
49
27

399
5
3960
3142
gi|1742362
nta operon transcriptional regulator.
49
29

[Escherichia coli]

456
1
1070
342
gi|290533
similar to E. coli ORF adjacent to suc
49
27

operon; similar to gntR class f regulatory

proteins [Escherichia coli]

619
1
2
232
gi|665956
ribosomal protein S20 homolog [Aeromonas
49
41

sobria
] sp|P45786|RS20_AERHY 30S RIBOSOMAL

PROTEIN S20 (FRAGMENT).

sp|P45788|RS20_AERSO 30S RIBOSOMAL PROTEIN

S20 (FRAGMENT).

621
1
319
942
gi|149456
nisin-resistance protein [Lactococcus
49
29

lactis
]

630
1
3
1190
gi|537145
ORF_f437 [Escherichia coli]
49
34

736
1
859
2
gi|1592020
hypothetical protein (SP:P37555)
49
27

[Methanococcus jannaschii[

849
1
232
11
gi|145514
cyclopropane fatty acid synthase
49
35

[Escherichia coli]

47
11
14140
13307
gi|1045937

M. genitalium
predicted coding region
48
34

MG246 [Mycoplasma genitalium]

103
4
2492
1605
gi|1591514
membrane protein [Methanococcus
48
19

jannaschii
]

127
7
6836
5736
gi|1573128
hypothetical [Haemophilus influenzae]
48
24

138
22
14742
15590
gi|580884
ipa-89d gene product [Bacillus subtilis]
48
33

160
6
3048
3665
gi|1652295
serine esterase [Synechocystis sp.]
48
28

162
3
3048
2491
gn|143830
xpaC [Bacillus subtilis]
48
13

193
2
1257
310
gi|1591153
hypothetical protein (SP:P46348)
48
24

[Methanococcus jannaschii]

219
1
61
573
gnl|PID|e257628
ORF [Lactococcus lactis]
48
32

221
11
5952
6428
gi|1303733
YgaN [Bacillus subtilis]
48
31

232
4
2776
1712
gi|142707
comG2 gene product [Bacillus subtilis]
48
24

236
6
8618
7689
gi|550075
cephalosporin-C deacetylase [Bacillus
48
26

subtilis
]

238
28
25896
26825
gi|47906
rha regulatory protein [Salmonella
48
31

typhimurium
]

251
2
1935
640
gi|1143026
ORF10 [Spiroplasma virus]
48
30

252
1
2036
3
gnl|PID|e228699
homologous to yqb0 of the skin element
48
37

[Bacillus subtilis]

269
1
481
2
gi|1045975
sensory rhodopsin II transducer
48
28

[Mycoplasma genitalium]

315
5
4604
2649
gi|396400
similar to eukaryotic Na+/H+ exchangers
48
30

[Escherichia coli] sp|P32703|YJCE_ECOLI

HYPOTHETICAL 60.5 KD PROTEIN IN SOXR-ACS

NTERGENIC REGION (O549).

327
1
128
916
gi|216314
esterase [Bacillus stearothermophilus]
48
30

330
6
4486
5337
gi|43942
first subunit of EII-Sor [Klebsiella
48
21

pneumoniae
]

330
7
5325
6230
gi|147404
mannose permease subunit II-M-Man
48
33

[Escherichia coli]

345
10
9571
10521
gi|1736789
Collagenase precursor (EC 3.4.-.-).
48
26

[Escherichia coli]

509
1
1
444
gi|606376
ORF_o162 [Escherichia coli]
48
33

531
1
624
109
sp|P50848|YPWA_BAC
HYPOTHETICAL 58.2 KD PROTEIN IN KDGT-XPT
48
33

SU
INTERGENIC REGION.

549
3
962
369
gi|1001212
molybdenum cofactor biosynthesis protein C
48
32

[Synechocystis sp.]

725
1
3
500
gi|1151158
repeat organellar protein [Plasmodium
48
25

chabaudi
]

789
1
133
717
gi|42724
rhaS (AA 1-278) [Escherichia coli]
48
39

936
1
32
316
gi|532549
ORF16 [Enterococcus faecalis]
48
45

2
2
2662
449
gi|929878
J1027 gene product [Saccharomyces
47
20

cerevisiae
]

4
2
1002
2192
gi|763052
integrase [Bacteriophage T270]
47
29

21
8
6350
5355
gi|1066343
mu-crystallin [Homo sapiens]
47
29

25
3
915
2048
gi|1064813
homologous to sp:PHOR_BACSU [Bacillus
47
21

subtilis
]

59
2
953
1378
gi|872306
integral membrane protein [Streptomyces
47
26

pristinaespiralis
] pir|S57509|S57509

integral membrane protein - Streptomyces

ristinaespiralis

81
7
4970
4206
gi|1591754
hypothetical protein (SP:P39364)
47
22

[Methanococcus jannaschii]

82
3
1534
866
gi|397526
clumping factor [Staphylococcus aureus]
47
21

110
5
2313
3767
gil 151928
48 kDa protein [Rhodobacter sphaeroides]
47
26

150
11
7839
9107
gnl|PID|e275490
C30H6.k [Caenorhabditis elegans]
47
16

161
2
116
1450
gnl|PID|e283830
aminotransferase [Sulfolobus solfataricus]
47
23

165
8
8081
6129
gi|924925
heparinase III protein [Cytophaga
47
29

heparina
]

180
31
31515
31054
gi|1591753
N-acetylglucosamine-1-phosphate
47
29

transferase [Methanococcus jannaschii]

194
11
8247
9236
gi|1480429
putative transcriptional regulator
47
26

[Bacillus stearothermophilus]

225
2
1039
701
gi|212992
Protein sequence and annotation available
47
33

soon via Swiss-Prot; available at present

via e-mail from LABEIT@EMBL-Heidelberg.DE

[Homo sapiens]

232
1
196
969
gi|293033
integrase [Bacteriophage phi-LC3]
47
30

232
6
3687
3340
gi|142706
comGl gene product [Bacillus subtilis]
47
28

233
10
8424
6739
gi|887816
possible start 13 codons upstream, for
47
35

o765 [Escherichia coli]

346
2
706
1083
gi|536970
ORF_f543 [Escherichia coli]
47
27

352
1
112
843
gi|1591857
H+-transporting ATPase [Methanococcus
47
28

jannaschii
]

410
1
3
980
gi|1652869
NADH dehydrogenase [Synechocystis sp.]
47
30

465
2
1976
1749
gi|211659
p68 protein; c-rel proto-oncogene [Gallus
47
30

gallus
]

491
3
3752
2466
gi|881434
ORFP [Bacillus subtilis]
47
24

501
1
48
809
gi|467429
unknown [Bacillus subtilis]
47
33

532
1
3
287
gi|755724
alpha-toxin [Clostridium novyi]
47
32

578
1
707
81
gi|532547
ORF14 [Enterococcus faecalis]
47
30

605
4
2051
2470
gi|1783233
hypothetical [Bacillus subtilis]
47
22

626
3
2459
2169
gi|1573573
2′,3′-cyclic-nucleotide 2′-
47
44

phosphodiesterase (cpdB) [Haemophilus

influenzae
]

650
1
1042
341
gi|404802
integrase [Saccharopolyspora erythraea]
47
26

665
1
714
1175
gi|143655
sporulation protein [Bacillus subtilis]
47
22

754
2
1086
736
gi|143835
PBSX repressor [Bacillus subtilis]
47
27

845
1
2
241
gi|1303952
YqjA [Bacillus subtilis]
47
26

911
1
1
456
gi|1019640
ORFX (a homolog to the prgX gene of the
47
26

pheromone response plasmid pCF10);

putative [Plasmid pHKK701]

933
1
16
303
gi|331002
first methionine codon in the ECLF1 ORF
47
29

[Saimiriine herpesvirus 2] gi|60394 ORF

73; ECLF1 [Saimiriine herpesvirus 2]

17
17
13073
13675
gi|1304597
abortive phage resistance protein
46
27

[Lactococcus lactis]

19
11
5515
6393
gi|1353529
ORF12 [Bacteriophage rlt]
46
28

42
3
2460
3011
gi|1064814
homologous to sp:PHOP_BACEUB [Bacillus
46
33

subtilis
]

49
9
4042
5793
gnl|PID|e59644
predicted 86.4kd protein; S2Kd observed
46
22

[Mycobacteriophage 15]

74
6
4039
3434
gi|143542
PNA polymerase sigma-30 factor [Bacillus
46
27

licheniformis
] pir|B28625|SZBSSL

transcription initiation factor sigma H -

acillus licheniformis

89
14
14259
12967
gi|1499089

M. jannaschii
predicted coding region
46
32

MJ0305 [Methanococcus jannaschii]

89
15
15737
14427
gi|1653339
hypothetical protein [Synechocystis sp.]
46
22

94
13
12634
11132
gi|1402515
membrane-spanning transporter protein
46
23

[Clostnidium perfringens]

100
18
13493
11958
gi|15470
portal protein [Bacteriophage SPP1]
46
31

144
2
2364
1126
gnl|PID|e183450
hypothetical EcsB protein [Bacillus
46
25

subtilis
]

144
9
8977
6236
gi|710421
unknown [Staphylococcus aureus]
46
24

152
7
3397
4557
gnl|PID|e254991
hypothetical protein [Bacillus subtilis]
46
25

158
7
7144
5993
gi|1045800
ribose transport system permease protein
46
28

[Mycoplasma genitalium]

180
11
10882
10055
gi|303953
esterase [Acinetobacter calcoaceticus]
46
23

181
3
1173
976
gi|1591638

M. jannaschii
predicted coding region
46
36

MJ0975 [Methanococcus jannaschii]

240
1
715
221
gi|1766062
Ats1 [Schizosaccharomyces pombe]
46
28

254
2
499
2
gi|153661
translational initiation factor IF2
46
32

[Enterococcus faecium] sp|P18311|IF2_ENTFC

INITIATION FACTOR IF-2.

262
4
5276
4431
pir|A45605|A45605
mature-parasite-infected erythrocyte
46
20

surface antigen MESA - Plasmodium

falciparum

309
1
2
673
gi|1651714
type 4 prepilin peptidase [Synechocystis
46
40

sp
.]

312
1
18
872
gi|580884
ipa-89d gene product [Bacillus subtilis]
46
32

324
6
4450
4836
gi|1061418
ArsC [Plasmid R46]
46
28

345
1
2241
1333
gi|144859
ORF B [Clostridium perfringens]
46
24

386
4
1438
2421
gi|405894
1-phosphofructokinase [Escherichia coli]
46
31

395
8
3584
3853
gnl|PID|e120267
sucrose-phosphate synthase [Beta vulgaris]
46
25

491
2
2527
1169
gnl|PID|e267595
Unknown, similar to peptidases [Bacillus
46
29

subtilis
]

495
3
612
869
gi|406286
triose phosphate/phosphate translocator
46
27

[Flaveria pringlei] pir|537553|S37553

triose phosphate/3-

phosphoglycerate/phosphate ranslocator -

Flaveria pringlei

513
1
2
946
gi|143024
glucose-resistance amylase regulator
46
26

[Bacillus subtilis] pir|S15318|515318 ccpA

protein - Bacillus subtilis

sp|P25144|CCPA_BACSU GLUCOSE-RESISTANCE

AMYLASE REGULATOR CATABOLITE CONTROL

PROTEIN).

520
3
914
2674
gi|1163086
microfilarial sheath protein SHP3 [Brugia
46
27

malayi
]

554
1
3
788
gi|413972
ipa-48r gene product [Bacillus subtilis]
46
27

568
1
1574
3
gi|532549
ORF16 [Enterococcus faecalis]
46
28

809
1
506
135
gi|49021
surface exclusion protein (SEA1)
46
28

[Enterococcus faecalis] ir|522452|S22452

surface exclusion protein sea1 precursor -

terococcus faecalis plasmid pAD1

813
1
2
1090
gi|150556
surface protein [Plasmid pCF10]
46
34

78
2
4915
2516
gi|577295
The ha1225 gene product is related to
45
20

human alpha-glucosidase. [Homo apiens]

81
9
6123
5386
gi|147200
phnF protein [Escherichia coli]
45
28

85
1
120
761
gi|457514
gltC [Bacillus subtilis]
45
19

94
11
10681
9668
gi|289753
homology with nucleolin protein; putative
45
23

[Caenorhabditis elegans] pir|S44897|S44897

ZK1236.2 protein - Caenorhabditis elegans

sp|P34618|Y082_CAEEL HYPOTHETICAL 33.8 KD

PROTEIN ZK1236.2 IN HROMOSOME III.

108
3
2427
1789
gnl|PID|e263931
OrfD [Streptococcus pneumoniae]
45
27

108
4
3338
2352
gi|606150
ORF_f309 [Escherichia coli]
45
25

131
6
3981
5309
gi|1590845
hypothetical protein (PIR:551413)
45
36

[Methanococcus jannaschii]

144
11
10215
8944
gi|1001554
hypothetical protein [Synechocystis sp.]
45
30

164
11
8247
6736
gi|409925
VirR positive regulator [Streptococcus
45
22

pyogenes
]

192
1
1598
591
gi|1736826
Lysozyme M1 precursor (EC 3.2.1.17) (1,4-
45
27

b-N-acetylmuramidase M1). [Escherichia

coli
]

223
16
14409
15212
gi|1651958
hypothetical protein [Synechocystis sp.]
45
32

279
7
5236
5772
gi|1736514
Isochorismatase (EC 3.3.2.1) (2,3 dihydro-
45
29

2,3 dihydroxybenzoate synthase).

[Escherichia coli]

364
3
2419
4098
gi|309662
pheromone binding protein [Plasmid pCF10]
45
26

459
1
2
307
gi|1679640
ORFA [Mycoplasma mycoides mycoides SC]
45
27

491
1
1022
135
sp|P27434|YFGA_ECO
HYPOTHETICAL 36.2 KD PROTEIN IN NDK-GCPE
45
20

LI
INTERGENIC REGION.

496
1
847
2
gi|1208489
serum resistance locus BrkB [Synechocystis
45
19

sp
.]

542
2
1169
804
gi|1064811
function unknown [Bacillus subtilis]
45
28

63
3
1047
1919
gi|39848
U3 [Bacillus subtilis]
44
26

93
3
1108
1374
sp|Q4747|SRF2_SAC
SURFACTIN SYNTHETASE SUBUNIT 2.
44
27

SU

155
10
8354
7620
sp|P35136|SERA_BAC
D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC
44
29

SU
1.1.1.95) (PGDH).

215
2
2192
1134
gi|468760
ORF334 [Rhizobium meliloti]
44
31

303
1
466
2
gi|431950
similar to a B.subtilis gene (GB:
44
22

BACHEMEHY_5) [Clostridium asteurianum]

310
1
284
39
pir|S01294|S01294
intermediate filament protein B - Roman
44
26

snail

311
1
122
2668
gi|532549
ORF16 [Enterococcus faecalis]
44
27

320
1
709
2
gi|290801
member of super-family of ABC proteins
44
23

[Francisella tularensis (var. ovicida)]

341
14
13882
12998
gi|142863
replication initiation protein [Bacillus
44
16

subtilis
]

345
15
16445
18001
gi|151282
DL-hydantoinase [Pseudomonas sp.]
44
34

386
3
1340
570
sp|P46117|YARA_PRO
HYPOTHETICAL 31.5 KD PROTEIN IN AARA
44
19

ST
3′REGION.

862
1
483
4
gi|929796
precursor of the major merozoite surface
44
26

antigens [Plasmodium alciparum]

19
3
1695
1372
gi|603263
Ye1055p [Saccharomyces cerevisiae]
43
31

45
17
14045
14995
gnl|PID|e233895
hypothetical protein [Bacillus subtilis]
43
32

57
1
667
317
gi|664840
TagB [Dictyostelium discoideum]
43
22

71
2
1537
2568
gi|1303981
YgkD [Bacillus subtilis]
43
36

72
18
20511
20164
gi|349045
merozoite surface antigen 2 [Plasmodium
43
36

falciparum
]

94
9
6581
6039
gi|1146245
putative [Bacillus subtilis]
43
28

180
17
16391
17656
gi|290540
f445 [Escherichia coli]
43
24

252
2
2407
1829
gi|154381
chemoreceptor [Salmonella typhimurium]
43
19

276
30
19091
18480
gi|15470
portal protein [Bacteriophage SPP1]
43
23

311
2
2666
4639
gi|160299
glutamic acid-rich protein [Plasmodium
43
28

falciparum
] pir|A54514|A54514 glutamic

acid-rich protein precursor - Plasmodium

alciparum

631
2
1126
2328
gi|1519696
coded for by C. elegans cDNA yk126f9.5;
43
27

coded for by C. elegans cDNA yk159h6.3;

coded for by C. elegans cDNA yk126f9.3;

coded for by C. elegans cDNA yk159h6.5

[Caenorhabditis elegans]

11
3
1509
2342
gi|143150
levR [Bacillus subtilis]
42
21

45
14
10730
12028
gi|666069
orf2 gene product [Lactobacillus
42
23

leichmannii
]

72
19
21070
21981
gnl|PID|e236595
orf7 gene product [Enterococcus faecalis]
42
23

123
35
32205
32768
gi|1772652
2-keto-3-deoxygluconate kinase [Haloferax
42
27

alicantei
]

136
5
2737
2375
gi|153858
wall-associated protein [Streptococcus
42
27

mutans

167
4
2701
6540
gi|1519696
coded for by C. elegans cDNA yk126f9.5;
42
27

coded for by C. elegans cDNA yk159h6.3;

coded for by C. elegans cDNA yk126f9.3;

coded for by C. elegans cDNA yk159h6.5

[Caenorhabditis elegans]

195
31
12430
13155
pir|S33124|S33124
tpr protein - human
42
24

211
1
187
2
gi|1653346
GDP-mannose pyrophosphorylase
42
33

[Synechocystis sp.]

242
13
8089
12447
gi|951460
FIM-C.1 gene product [Xenopus laevis]
42
31

305
5
4354
5340
gi|1408485
yxdM gene product [Bacillus subtilis]
42
25

355
18
9964
12549
gi|532549
ORF16 [Enterococcus faecalis]
42
30

446
4
4428
5261
gi|47528
glucosyltransferase S [Streptococcus
42
25

salivarius
]

656
3
2866
3456
gi|142857
MreD protein [Bacillus subtilis]
42
25

686
11
3646
3921
pir|A44805|A44805
eggshell protein - fluke (Schistosoma
42
42

haematobium
) (subelone SH.E 2-1)

920
1
41
316
gi|532549
ORF16 [Enterococcus faecalis]
42
40

23
3
729
487
gi|414525
meiotin-1 [Lilium longiflorum]
41
41

456
5
3511
2324
gi|1591610
probable ATP-dependent helicase
41
21

[Methanococcus jannaschii]

98
17
16843
16274
gi|1742129
Immunity repressor protein. [Escherichia
41
23

coli
]

167
6
6734
9811
gnl|PID|e249616
F56H9.1 [Caenorhabditis elegans]
41
37

171
13
10879
11871
gi|331002
first methionine codon in the ECLF1 ORE
41
23

[Saimiriine herpesvirus 2] gi|60394 ORF

73; ECLF1 [Saimiriine herpesvirus 2]

181
2
1012
500
gi|455315
ORF 4 [Plasmid pIP404]
41
24

230
4
3664
3224
gi|498251
glutamate/aspartate transporter II [Homo
41
22

sapiens]

718
1
2
613
gi|984656
ORF3 [Salmonella typhimurium]
41
22

219
30
16391
17770
gi|806704
Upf2p [Saccharomyces cerevisiae]
40
21

164
16
16440
17951
gi|348056
trans-acting positive regulator [Bacillus
40
22

anthracis
]

200
12
5956
4841
gi|1574243

H. influenzae
predicted coding region
40
24

HI1405 [Haemophilus influenzae]

216
10
6799
7194
gi|146279
glucitol-specific enzyme III (gutB)
40
27

[Escherichia coli]

292
13
8633
10741
gi|1008233
ORF YJL076w [Saccharomyces cerevisiae]
40
18

345
13
14050
15333
gi|581051
cytosine permease [Escherichia coli]
40
25

521
1
177
1466
gi|289614
homology with glucose induced repressor,
40
18

GRR1; putative Caenorhabditis elegans]

64
3
2646
1855
gi|154924
spectinomycin adenyltransferase
39
27

[Transposon Tn554]

100
17
12037
10565
gi|1052806
product required for head morphogenesis
39
24

[Bacteriophage SPP1]

529
1
326
4939
gi|295671
selected as a weak suppressor of a mutant
39
19

of the subunit AC40 of DNA ependant RNA

polymerase I and III [Saccharomyces

cerevisiae
]

49
2
518
931
gi|166162
Bacteriophage phi-11 int gene activator
38
19

[Staphylococcus acteriophage phi 11]

54
19
11264
10854
gi|160186
circumsporozoite protein [Plasmodium
38
31

vivax
]

164
21
22793
23587
gi|603857
secreted acid phosphatase 2 (SAP2)
38
18

[Leishniania mexicana]

167
3
2322
2756
gi|435039
proline-rich cell wall protein [Gossypium
38
36

hirsutum
]

204
2
133
798
gi|396401
No definition line found [Escherichia
38
25

coli
]

475
2
761
1792
gi|1574532

H. influenzae
predicted coding region
38
27

HI1680 [Haemophilus influenzae]

164
19
20738
21385
gi|165704
[Rabbit smooth muscle myosin light chain
37
20

kinase mRNA, complete DS.], gene product

[Oryctolagus cuniculus]

394
6
5649
6395
gi|603857
secreted acid phosphatase 2 (SAP2)
36
16

[Leishmania mexicana]

958
1
1
459
gi|951460
FITA-C.1 gene product [Xenopus laevis]
36
28

399
21
16383
21359
gi|1707247
partial CDS [Caenorhabditis elegans]
34
13

150
12
9056
11740
gi|1015903
ORF YJR151c [Saccharomyces cerevisiae]
33
19

195
34
13017
15512
gi|632549
NF-180 [Petromyzon marinus]
33
18

[0354]

3

TABLE 3

E. faecalis-Putative coding regions of novel proteins not similar

to known proteins

Contig ID
ORF ID
Start (nt)
Stop (nt)

2
1
458
3

2
3
2208
2624

5
3
928
1440

8
6
4792
5877

8
7
5480
5262

12
1
2
832

12
2
771
4622

13
1
2
1684

14
1
531
130

15
2
862
1197

16
1
51
200

17
4
3309
3665

17
13
10079
10261

17
18
14431
13682

17
22
21525
21956

17
27
27055
27567

18
4
2172
1591

18
5
2524
2249

18
7
3467
3715

18
8
4082
3555

18
9
4333
4055

18
10
4395
4204

18
11
4498
4677

18
12
4656
5393

18
13
5878
5492

18
15
6296
6931

19
1
1047
676

19
2
1068
1247

19
4
1747
2031

19
5
2244
2612

19
7
2797
2943

19
9
3873
4730

19
13
6884
7420

19
14
7428
8042

19
16
9246
8425

19
17
9412
9615

19
19
9733
9918

19
20
10032
10334

19
21
10422
11009

19
22
11516
11944

19
24
12423
12881

19
26
14606
15427

19
27
15414
15848

19
28
15802
16134

19
29
16064
16393

19
32
17846
18052

19
33
18021
18356

19
34
18334
18684

19
35
18659
19036

19
36
18991
19677

19
37
19671
20132

19
39
22603
23337

19
40
23319
25580

21
2
762
262

21
5
3440
2925

21
10
7684
7241

23
5
2098
2652

23
8
4912
4709

23
9
4911
5246

23
10
5087
5353

23
22
14318
14926

23
23
14924
15565

23
24
15559
16083

23
29
17567
18022

25
2
553
1005

25
5
3363
2653

26
2
1220
1654

27
1
297
4

28
1
239
2833

29
5
3244
2822

29
6
4014
3301

29
7
4168
4557

29
8
5620
4595

32
3
2646
1375

32
4
2573
3010

39
9
4636
4986

40
2
1346
981

43
1
120
620

43
4
1972
2280

45
3
1557
1961

45
4
2012
2230

45
5
2218
2553

45
11
7226
5670

45
12
7270
10113

45
13
10013
10732

46
1
42
872

46
2
886
1125

46
4
2807
3100

47
4
5101
5625

47
10
13239
12847

49
1
106
504

49
8
2858
4132

49
10
5777
6193

49
11
6166
6720

52
5
3505
3110

52
7
5160
5603

52
8
5662
5459

54
2
400
729

54
4
1326
1610

54
5
2354
1335

54
6
1676
2080

54
7
2151
2576

54
12
4181
3954

54
13
5975
6289

54
14
6869
7144

54
15
7433
7107

54
18
9764
11086

55
2
252
440

56
2
1344
658

57
9
12450
12605

58
7
7066
6425

59
3
1350
952

59
4
1225
1515

59
7
2958
3200

62
6
4116
3007

63
1
77
364

63
2
455
1060

63
7
5422
5910

63
8
5870
6751

63
9
6688
7296

64
2
1849
1523

64
4
3183
2644

64
5
3422
3213

65
5
3787
3389

65
7
5043
4300

65
8
5354
4959

65
9
7005
6328

67
6
3719
4060

68
2
569
348

68
5
3234
2821

68
6
3808
3221

68
10
7495
8106

70
2
2102
1614

70
3
2019
2231

71
3
3362
3787

72
21
22464
22709

72
22
22690
23019

72
23
23013
23834

73
1
154
2

74
1
61
486

74
3
1334
1981

75
4
3227
2136

75
5
3994
3251

75
6
3348
3632

75
7
4519
4043

75
8
4296
4529

75
10
6518
5769

76
2
1079
1897

76
4
2113
2436

76
6
4737
4105

77
3
1874
2704

77
4
2665
2459

78
3
5814
5398

79
3
848
1645

79
4
2121
1642

81
8
5392
4961

81
13
8428
8874

81
21
15746
14802

82
1
858
4

82
2
198
383

83
3
2194
2604

83
4
2728
2405

83
6
2855
3172

83
10
7188
6184

83
11
7415
7065

83
17
12259
12561

83
21
15890
16456

83
23
16946
17251

84
5
7071
7949

85
7
6518
6174

89
2
1012
599

89
3
1382
939

89
4
2350
1370

89
5
2523
2314

89
9
7505
7182

89
16
15846
15673

89
19
20070
19045

90
1
3
689

91
7
3834
4127

91
8
4288
5268

91
9
7259
5748

91
12
9737
8973

91
13
10162
9731

92
3
1458
958

92
4
1934
1287

93
2
479
949

93
4
1344
1727

94
1
770
45

94
3
1460
1618

94
5
2279
1734

94
12
11000
10641

95
11
7674
7907

95
12
8604
8056

95
13
8725
8546

96
1
758
1018

96
2
1038
1469

98
5
6809
5994

98
10
10338
10652

98
11
10650
11558

99
2
232
513

100
4
3728
4048

100
6
5866
5378

100
7
6574
5921

100
8
6923
6534

100
9
7355
6921

100
10
7698
7339

100
11
8226
7744

100
13
9395
8514

100
15
10368
10102

100
19
14770
13505

100
20
15300
14758

100
21
15783
15298

100
23
17699
17292

100
25
20933
20625

100
26
21200
20946

100
28
23713
23156

100
29
23948
23691

100
30
24312
23965

100
31
24550
24287

100
32
24912
24565

100
33
25173
24910

100
34
26339
25158

100
36
27251
26994

100
37
27945
27232

100
39
28442
28227

100
40
28657
28403

100
46
30439
31146

100
47
31158
31712

101
2
850
464

101
3
2453
1899

102
6
5023
5616

102
9
6704
7111

103
7
5454
5296

105
2
1244
1828

106
4
5114
3294

106
6
7622
6168

106
7
6577
6867

108
6
5192
4158

110
1
2
454

110
6
3689
4207

110
9
9374
8553

110
10
9903
9361

110
11
10175
9843

111
6
3118
3267

112
4
2170
1043

114
2
1347
1135

116
8
4782
5147

117
4
2437
2670

117
6
3876
4640

117
8
5643
5927

117
9
6195
6488

117
12
9655
9837

119
1
3
500

119
2
670
1158

119
4
2730
2284

121
3
2276
3670

123
14
14304
14555

123
16
15305
15147

123
24
21896
22663

123
34
31458
32207

125
3
1581
1300

125
7
4516
4346

126
2
85
312

127
2
1047
787

127
3
2006
1299

127
4
3432
1924

128
4
3094
2747

128
5
3466
3305

128
6
4625
3507

128
7
4726
4550

128
13
8947
8522

128
15
9325
9582

128
17
10126
10380

128
24
17649
18038

129
1
276
1769

130
7
6478
6702

130
11
9386
9769

133
7
6622
7380

135
2
2289
1153

135
3
3380
2271

135
5
3778
3930

135
6
5835
5137

135
7
6649
5852

135
8
7021
6647

135
9
7420
7034

136
2
963
379

136
3
2009
939

136
4
2344
1973

138
4
5051
3636

138
11
8499
8753

138
12
8682
8536

138
13
8923
9270

138
14
9333
9887

138
15
9628
10308

138
16
10422
10216

138
23
15980
15678

138
24
16437
16063

138
30
19388
19828

139
3
1068
1466

139
4
3338
1983

139
5
3769
3317

139
6
4114
3818

139
7
4838
4236

139
10
5639
5175

142
1
369
106

142
2
1005
367

142
3
2140
980

142
4
2504
2127

142
5
2821
2474

142
6
3294
2806

142
7
4000
3635

143
1
650
3

143
3
1090
173

143
4
1044
433

144
10
7570
8403

144
12
10727
10335

145
1
188
30

145
2
775
978

150
9
6876
7166

150
13
11538
11242

152
1
35
445

152
2
405
914

152
3
912
1430

152
4
1349
2212

152
5
2210
2896

152
6
2739
3368

152
8
4479
4694

152
11
6647
7321

154
7
4557
4195

155
3
1227
2180

155
12
8726
9022

156
3
3179
2664

158
11
10876
11220

160
1
545
3

162
1
228
1349

162
2
2513
1653

162
7
9163
7664

162
9
10619
10990

162
11
11891
11427

163
3
1043
1234

163
5
3217
2021

163
6
3455
3198

163
8
5611
4931

163
9
5969
5580

163
10
6144
5926

164
2
1100
1687

164
9
5729
5259

164
10
6778
5639

164
12
8277
8450

164
17
18224
18526

164
24
24751
24536

164
27
25764
26369

165
1
17
481

165
2
2213
1389

165
12
9871
9689

165
14
11416
10367

166
3
1250
1669

167
5
3774
3439

167
7
10479
14498

167
10
17476
18768

168
2
665
393

172
9
7018
6701

172
10
7097
7930

173
1
2
412

173
3
2341
2024

173
6
4234
5055

173
9
7882
7295

173
10
7413
7571

173
14
12308
11748

174
4
2350
3021

174
5
3082
3498

178
3
866
1105

179
8
8115
7816

179
17
17407
17135

180
4
3524
4537

180
5
4686
5687

180
6
5897
6949

180
9
9721
9299

180
10
9996
9715

180
20
19805
19954

180
23
21808
21509

180
25
24127
26460

180
27
27977
27474

181
1
381
82

183
1
190
2

183
4
1849
2211

183
5
2350
2568

183
7
3592
2978

183
8
4176
3571

185
2
1260
1424

185
3
2722
1301

185
4
3612
2671

187
2
727
1302

187
3
1293
1745

187
5
2592
2173

189
1
18
2180

190
1
466
68

190
2
896
411

190
4
1878
2165

190
5
2740
2384

190
10
10281
8875

191
2
861
658

191
3
1096
827

192
2
1881
1564

193
1
316
2

193
7
4667
3813

194
1
30
641

194
2
608
1582

195
1
2
433

195
2
431
943

195
3
1055
465

195
4
972
1487

195
5
1507
1995

195
6
3314
1851

195
9
3089
3529

195
10
3521
3312

195
12
6604
6837

195
13
7049
6786

195
14
6825
7700

195
15
7682
7047

195
16
7202
7417

195
18
8278
9036

195
20
8583
8837

195
21
8871
9602

195
22
9251
9403

195
23
9600
10022

195
25
10020
10226

195
26
11229
10024

195
27
10659
10946

195
28
10944
11318

195
30
12449
12246

195
32
13212
12505

195
33
12558
12773

195
35
13673
14011

195
36
14811
14143

195
38
16061
16363

195
39
16320
16799

195
40
16515
16333

196
1
608
1411

197
9
9269
9553

200
2
1103
249

200
3
1335
1033

200
4
1769
1284

200
5
2124
1747

200
6
2792
2106

200
7
3073
2708

200
8
3510
3061

200
9
4126
3467

200
10
4350
4042

200
11
4847
4368

200
14
6487
6182

200
15
6681
6499

200
18
10749
9307

200
20
11787
11464

200
22
12859
12410

201
1
509
105

201
3
3704
3237

202
7
5296
4817

205
2
117
323

205
5
1669
2148

206
2
546
196

206
3
841
632

206
4
1622
777

206
9
5466
5035

209
1
472
86

209
3
1510
1280

210
3
3175
2363

210
6
5281
4868

210
8
5619
6002

211
4
1708
3756

212
1
919
2

213
2
1107
1826

214
2
2106
1237

214
4
3677
3132

217
6
3548
3162

218
1
1
1218

218
3
2731
3378

218
5
4188
4667

219
3
1386
910

219
4
1595
1344

220
2
794
1144

221
1
110
295

221
2
326
880

221
4
1496
1825

221
5
1907
2200

221
6
2169
2555

221
8
3425
4246

221
9
4233
5111

221
12
6419
6757

221
13
6751
6987

221
14
6911
7120

221
16
7400
7909

221
17
7963
8199

221
19
8597
9079

222
17
11376
11597

223
6
5328
5008

223
12
12189
13307

223
13
13291
13716

223
14
13601
13434

223
17
15331
15068

223
19
15940
17160

223
21
17710
19089

223
23
19800
20708

223
25
22857
22027

223
26
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3
270
467

981
2
154
405

984
3
164
337

SEQUENCE LISTING PLACE INDICATOR

[0355] PAGES 280 TO 2076, WHICH ARE THE COMPLETE SEQUENCE LISTINGS FOR THIS APPLICATION, ARE LOCATED IN THE FOUR (4) ATTACHED REDWELDS IDENTIFIED BY THE FOLLOWING INFORMATION ON THE INDIVIDUAL VOLUME COVER SHEETS:

[0356] Applicants: Kunsch et al.

[0357] Serial No.: Unassigned

[0358] Filed: Concurrently herewith

[0359] For: Enterococcos faecalis Polynucleotides and Polypeptides

[0360] Attorney Docket No. PB369

ENTEROCOCCUS FAECALIS POLYNUCLEOTIDES AND POLYPEPTIDES

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CPC

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Parent Case Info