EP0966529A1

EP0966529A1 - Novel prokaryotic polynucleotides, polypeptides and their uses

Info

Publication number: EP0966529A1
Application number: EP97949731A
Authority: EP
Inventors: Richard Lloyd Warren, Jr.
Original assignee: SmithKline Beecham Corp
Current assignee: SmithKline Beecham Corp
Priority date: 1996-11-25
Filing date: 1997-11-24
Publication date: 1999-12-29
Also published as: WO1998023738A2; JP2001510990A

Description

NOVEL PROKARYOTIC POLYNUCLEOTIDES, POLYPEPTIDES AND THEIR USES FIELD OF THE INVENTION

This invention relates to newly identified polynucleotides and polypeptides, and their production and uses, as well as their variants, agonists and antagonists, and their uses. In particular, in these and in other regards, the invention relates to novel polynucleotides and polypeptides set forth in Table 1. BACKGROUND OF THE INVENTION

The Staphylococci make up a medically important genera of microbes. They are known to produce two types of disease, invasive and toxigenic. Invasive infections are characterized generally by abscess formation effecting both skin surfaces and deep tissues. Stapylococcus aureus (herein "S. aureus") is the second leading cause of bacteremia in cancer patients. Osteomyelitis, septic arthritis, septic thrombophlebitis and acute bacterial endocarditis are also relatively common. There are at least three clinical conditions resulting from the toxigenic properties of Staphylococci. The manifestation of these diseases result from the actions of exotoxins as opposed to tissue invasion and bacteremia. These conditions include: Staphylococcal food poisoning, scalded skin syndrome and toxic shock syndrome.

While certain Staphylococcal proteins associated with pathogenicity have been identified, e.g., coagulase, hemolysins, leucocidins and exo and enterotoxins, very little is known concerning the temporal expression of such genes during infection and disease progression in a mammalian host. Discovering the sets of genes the bacterium is likely to be expressing at the different stages of infection, particularly when an infection is established, provides critical information for the screening and characterization of novel antibacterials which can interrupt pathogenesis. In addition to providing a fuller understanding of known proteins, ^'such an approach will identify previously unrecognised targets.

GUG is used as an initating nucleotide, rather than ATG, for a significant number of mRNA's in both Gram positive and Gram negative bacteria. Statistics on the frequency of NTG codons in the start codon for several bacterial species are available on line via computer (http://biochem.otago.ac. nz:800/Transterm/home_page.html). A discussion of initiation codons in B. subtilis is set forth in Vellanoweth, RL.1993 in Bacillus subtilis and other Gram Positive Bacteria, Biochemistry, Physiology and Molecular Genetics, Sonenshein, Hoch, Losick Eds. Amer. Soc. Microbiol, Washington DC. p. 699-71 1. Vellenworth indicates a major difference between B. subtilis and the i gram-negative organisms is in the choice of initiation codon. 91 % of the sequenced E. coli genes start with AUG. By contrast, about 30% of B. subtilis and other clostridial branch gened start with UUG or GUG. Moreover, CUG functions as a start codon in B. subtilis. Mutations of an AUG initiation codon to GUG or UUG often cause decreased expression in B. subtilis and E. coli. Generally, translation efficiency is higher with AUG initiation codons. A strong Shine-Delgarno ribosome binding site, however, can compensate almost fully for a weak initiation codon. It has been reported that genes with a range of expression levels have initiation codons other than ATG in gram positives (Vellanoweth, RL.1993 in Bacillus subtilis and other Gram Positive Bacteria, Biochemistry, Physiology and Molecular Genetics, Sonenshein, Hoch, Losick Eds. Amer. Soc. Microbiol, Washington DC. p. 699-71 1).

Provided herein are ORF sequences from genes possessing GUG initiation codons and proteins expressed therefrom to be used for screening for antimicrobial compounds. Clearly, there is a need for polypeptide and polynucleotide sequences that may be used to screen for antimicrobial compound and which may also be used to determine the roles of such sequences in pathogenesis of infection, dysfunction and disease. There is also need, therefore, for identification and characterization of such sequences which may play a role in preventing, ameliorating or correcting infections, dysfunctions or diseases.

The polypeptides of the invention have amino acid sequence homology to a known protein(s) as set forth in Table 1. SUMMARY OF THE INVENTION

It is an object of the invention to provide polypeptides that have been identified as novel polypeptides by homology between an amino acid sequence selected from the group consisting of the sequences set out in Table 1 and a known amino acid sequence or sequences of other proteins such as the protein identities listed in Table 1.

It is a further object of the invention to provide polynucleotides that encode novel polypeptides, particularly polynucleotides that encode polypeptides of Staphylococcus aureus.

In a particularly preferred embodiment of the invention the polynucleotide comprises a region encoding a polypeptide comprising a sequence sequence selected from the group consisting of the sequences set out in Table 1, or a variant of any of these sequences.

In another particularly preferred embodiment of the invention there is a novel protein from Staphylococcus aureus comprising an amino acid sequence selected from the group consisting of the sequences set out in Table 1, or a variant of any of these sequences. In accordance with another aspect of the invention there is provided an isolated nucleic acid molecule encoding a mature polypeptide expressible by the Staphylococcus aureus WCUH29 strain contained in the deposited strain.

A further aspect of the invention there are provided isolated nucleic acid molecules encoding a polypeptide of the invention, particularly Staphylococcus aureus polypeptide, and including mRNAs, cDNAs, genomic DNAs. Further embodiments of the invention include biologically, diagnostically, prophylactically, clinically or therapeutical ly useful variants thereof, and compositions comprising the same.

In accordance with another aspect of the invention, there is provided the use of a polynucleotide of the invention for therapeutic or prophylactic purposes, in particular genetic immunization. Among the particularly preferred embodiments of the invention are naturally occurring allelic variants of a polypeptide of the invention and polypeptides encoded thereby.

Another aspect of the invention there are provided novel polypeptides of Staphylococcus aureus as well as biologically, diagnostically, prophylactically, clinically or therapeutically useful variants thereof, and compositions comprising the same.

Among the particularly preferred embodiments of the invention are variants of the polypeptides of the invention encoded by naturally occurring alleles of their genes.

In a preferred embodiment of the invention there are provided methods for producing the aforementioned polypeptides.

In accordance with yet another aspect of the invention, there are provided inhibitors to such polypeptides, useful as antibacterial agents, including, for example, antibodies.

In accordance with certain preferred embodiments of the invention, there are provided products, compositions and methods for assessing expression of the polypeptides and polynucleotides of the invention, treating disease, for example, infections of the upper respiratory tract (e.g.', otitis media, bacterial tracheitis, acute epiglottitis, thyroiditis), lower respiratory (e.g., empyema, lung abscess), cardiac (e.g., infective endocarditis), gastrointestinal (e.g., secretory diarrhoea, splenic absces, retroperitoneal abscess), CNS (e.g., cerebral abscess), eye (e.g., blepharitis, conjunctivitis, keratitis, endophthalmitis, preseptal and orbital cellulitis, darcryocystitis), kidney and urinary tract (e.g., epididymitis, intrarenal and perinephric absces, toxic shock syndrome), skin (e.g., impetigo, folliculitis, cutaneous abscesses, cellulitis, wound infection, bacterial myositis) bone and joint (e.g., septic arthritis, osteomyelitis), assaying genetic variation, and administering a polypeptide or polynucleotide of the invention to an organism to raise an immunological response against a bacteria, especially a Staphylococcus aureus bacteria. In accordance with certain preferred embodiments of this and other aspects of the invention there are provided polynucleotides that hybridize to a polynucleotide sequence of the invention, particularly under stringent conditions.

In certain preferred embodiments of the invention there are provided antibodies against polypeptides of the invention.

In other embodiments of the invention there are provided methods for identifying compounds which bind to or otherwise interact with and inhibit or activate an activity of a polypeptide or polynucleotide of the invention comprising: contacting a polypeptide or polynucleotide of the invention with a compound to be screened under conditions to permit binding to or other interaction between the compound and the polypeptide or polynucleotide to assess the binding to or other interaction with the compound, such binding or interaction being associated with a second component capable of providing a detectable signal in response to the binding or interaction of the polypeptide or polynucleotide with the compound; and determining whether the compound binds to or otherwise interacts with and activates or inhibits an activity of the polypeptide or polynucleotide by detecting the presence or absence of a signal generated from the binding or interaction of the compound with the polypeptide or polynucleotide.

In accordance with yet another aspect of the invention, there are provided agonists and antagonists of the polypeptides and polynucleotides of the invention, preferably bacteriostatic or bacteriocidal agonists and antagonists.

In a further aspect of the invention there are provided compositions comprising a polynucleotide or a polypeptide of the invention for administration to a cell or to a multicellular organism.

Various changes and modifications within the spirit and scope of the disclosed invention will become readily apparent to those skilled in the art from reading the following descriptions and from reading the other parts of the present disclosure. GLOSSARY

The following definitions are provided to facilitate understanding of certain terms used frequently herein.

"Host cell" is a cell which has been transformed or transfected, or is capable of transformation or transfection by an exogenous polynucleotide sequence.

"Identity," as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, "identity" also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. "Identity" and "similarity" can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology, Lesk, A.M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D.W., ed.. Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A.M., and Griffin, H.G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991 : and Carillo, H., and Lipman, D., SIAM J. Applied Math., 48: 1073 (1988). Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Preferred computer program methods to determine identity and similarity between two sequences include, but are not limited to, the GCG program package (Devereux, J., et al., Nucleic Acids Research 12(1): 387 (1984)), BLASTP, BLASTN, and FASTA (Atschul, S.F. et al., J. Molec. Biol. 215: 403-410 (1990). The BLAST X program is publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al, NCBI NLM NIH Bethesda, MD 20894; Altschul, S., et al, J. Mol. Biol. 215: 403-410 (1990). As an illustration, by a polynucleotide having a nucleotide sequence having at least, for example, 95% "identity" to a reference nucleotide sequence it is intended that the nucleotide sequence of the tested 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. 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 or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These mutations of the reference sequence may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more [SEQ ID NO: ] contiguous groups within the reference sequence. Analogously , by a polypeptide having an amino acid sequence having at least, for example, 95% identity to a reference amino acid sequence is intended that the test amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. 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 [SEQ ID NO: ] contiguous groups within the reference sequence.

"Isolated" means altered "by the hand of man" from its natural state, i.e., if it occurs in nature, it has been changed or removed from its original environment, or both. For example, a polynucleotide or a polypeptide naturally present in a living organism is not "isolated," but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is "isolated", as the term is employed herein.

"Polynucleotide(s)" generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. "Polynucleotide(s)" include, without limitation, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions or single-, double- and triple-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded, or triple-stranded regions, or a mixture of single- and double-stranded regions. In addition, "polynucleotide" as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules. One of the molecules of a triple-helical region often is an oligonucleotide. As used herein, the term "polynucleotide(s)" also includes DNAs or RNAs as described above that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotide(s)" as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term "polynucleotide(s)" as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including, for example, simple and complex cells. "Polynucleotide(s)" also embraces short polynucleotides often referred to as oligonucleotide(s).

"Polypeptide(s)" refers to any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds. "Polypeptide(s)" refers to both short chains, commonly referred to as peptides, oligopeptides and oligomers and to longer chains generally referred to as proteins. Polypeptides may contain amino acids other than the 20 gene encoded amino acids. "Polypeptide(s)" include those modified either by natural processes, such as processing and other post-translational modifications, but also by chemical modification techniques. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature, and they are well known to those of skill in the art. It will be appreciated that the same type of modification may be present in the same or varying degree at several sites in a given polypeptide. Also, a given polypeptide may contain many types of modifications. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains, and the amino or carboxyl termini. Modifications include, for example, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, glycosylation, lipid attachment, sulfation, gamma- carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins, such as arginylation, and ubiquitination. See, for instance, PROTEINS - STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993) and Wold, F., Posttranslational Protein Modifications: Perspectives and Prospects, pgs. 1-12 in POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic Press, New York (1983); Seifter et al., Meth. Enzymol. 182:626-646 (1990) and Rattan et al., Protein Synthesis: Posttranslational Modifications and Aging, Ann. N.Y. Acad. Sci. 663: 48-62 (1992). Polypeptides may be branched or cyclic, with or without branching. Cyclic, branched and branched circular polypeptides may result from post-translational natural processes and may be made by entirely synthetic methods, as well. "Variant(s)" as the term is used herein, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties. A typical variant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide. Changes in the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide changes may result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptide encoded by the reference sequence, as discussed below. A typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide. Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall and, in many regions, identical. A variant and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions in any combination. A substituted or inserted amino acid residue may or may not be one encoded by the genetic code. A variant of a polynucleotide or polypeptide may be a naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally. Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques, by direct synthesis, and by other recombinant methods known to skilled artisans. DESCRIPTION OF THE INVENTION

Each of polynucleotide and polypeptide sequences provided herein may be used in the discovery and development of antibacterial compounds. Upon expression of the sequences with the appropriate initiation and termination codons the encoded polypeptide can be used as a target for the screening of antimicrobial drugs. Additionally, the DNA sequences encoding preferably the amino terminal regions of the encoded protein or the Shine-Delgarno region can be used to construct antisense sequences to control the expression of the coding sequence of interest. Furthermore, many of the sequences disclosed herein also provide regions upstream and downstream from the encoding sequence. These sequences are useful as a source of regulatory elements for the control of bacterial gene expression. Such sequences are conveniently isolated by restriction enzyme action or synthesized chemically and introduced, for example, into promoter identification strains. These strains contain a reporter structural gene sequence located downstream from a restriction site such that if an active promoter is inserted, the reporter gene will be expressed.

Although each of the sequences may be employed as described above, this invention also provides several means for identifying particularly useful target genes. The first of these approaches entails searching appropriate databases for sequence matches in related organisms. Thus, if a homologue exists, the Streptococcal-like form of this gene would likely play an analogous role. For example, a Streptococcal protein identified as homologous to a cell surface protein in another organism would be useful as a vaccine candidate. To the extent such homologies have been identified for the sequences disclosed herein they are reported along with the encoding sequence.

Each of the DNA sequences provided herein may be used in the discovery and development of antibacterial compounds. Because each of the sequences contains an open reading frame (ORF) with an appropriate initiation and termination codons, the encoded protein upon expression can be used as a target for the screening of antimicrobial drugs. Additionally, the DNA sequences encoding the amino terminal regions of the encoded protein can be used to construct antisense sequences to control the expression of the coding sequence of interest. Furthermore, many of the sequences disclosed herein also provide regions upstream and downstream from the encoding sequence. These sequences are useful as a source of regulatory elements for the control of bacterial gene expression. Such sequences are conveniently isolated by restriction enzyme action or synthesized chemically and introduced, for example, into promoter identification strains. These strains contain a reporter structural gene sequence located downstream from a restriction site such that if an active promoter is inserted, the reporter gene will be expressed.

It is believed that bacteria possess a number of ways of regulating gene expression levels, especially in subtle degrees, and the interplay between ribosome binding site and inititation codon is utilized for this purpose for these genes. It is also believed that such genes will be important targets for antimicrobial drug discovery, particularly since pathogenesis genes are believed undergo gene expression regulation during in the pathogenesis process. Therefore, the invention provides ORF sequences possessing a GTG (GUG ) initiation codon and protein targets expressed thereform.

Although each of the sequences may be employed as described above, this invention also provides several means for identifying particularly useful target genes. The first of these approaches entails searching appropriate databases for sequence matches in related organisms. Thus, if a homologue exists, the Staphylococcal-like form of this gene would likely play an analogous role. For example, a Staphylococcal protein identified as homologous to a cell surface protein in another organism would be useful as a vaccine candidate. To the extent such homologies have been identified for the sequences disclosed herein they are reported along with the encoding sequence. ORF Gene Expression

Recently techniques have become available to evaluate temporal gene expression in bacteria, particularly as it applies to viability under laboratory and infection conditions. A number of methods can be used to identify genes which are essential to survival per se, or essential to the establishment/maintenance of an infection. Identification of an ORF unknown by one of these methods yields additional information about its function and permits the selection of such an ORF for further development as a screening target. Briefly, these approaches include:

1) Signature Tagged Mutagenesis (STM): This technique is described by Hensel et aj., Science 269: 400-403(1995), the contents of which is incoφorated by reference for background puφoses. Signature tagged mutagenesis identifies genes necessary for the establishment/maintenance of infection in a given infection model.

The basis of the technique is the random mutagenesis of target organism by various means (e.g., transposons) such that unique DNA sequence tags are inserted in close proximity to the site of mutation. The tags from a mixed population of bacterial mutants and bacteria recovered from an infected hosts are detected by amplification, radiolabeling and hybridisation analysis. Mutants attenuated in virulence are revealed by absence of the tag from the pool of bacteria recovered from infected hosts.

In Staphylococcus aureus, because the transposon system is less well developed, a more efficient way of creating the tagged mutants is to use the insertion-duplication mutagenesis technique as described by Morrison et al., J. Bacteriol. 159:870 (1984) the contents of which is incoφorated by reference for background puφoses.

2) In Vivo Expression Technology (IVET): This technique is described by Camilli et a]., Proc. Natl Acad. Sri. USA. 91:2634-2638 (1994), the contents of which is incoφorated by reference for background puφoses. IVET identifies genes up-regulated during infection when compared to laboratory cultivation, implying an important role in infection. ORF identified by this technique are implied to have a significant role in infection establishment maintenance.

In this technique random chromosomal fragments of target organism are cloned upstream of a promoter-less recombinase gene in a plasmid vector. This construct is introduced into the target organism which carries an antibiotic resistance gene flanked by resolvase sites. Growth in the presence of the antibiotic removes from the population those fragments cloned into the plasmid vector capable of supporting transcription of the recombinase gene and therefore have caused loss of antibiotic resistance. The resistant pool is introduced into a host and at various times after infection bacteria may be recovered and assessed for the presence of antibiotic resistance. The chromosomal fragment carried by each antibiotic sensitive bacterium should carry a promoter or portion of a gene normally upregulated during infection. Sequencing upstream of the recombinase gene allows identification of the up regulated gene.

3) Differential display: This technique is described by Chuang et al., L Bacteriol. 175:2026-2036 (1993), the contents of which is incoφorated by reference for background puφoses. This method identifies those genes which are expressed in an organism by identifying mRNA present using randomly-primed RT-PCR. By comparing pre-infection and post infection profiles, genes up and down regulated during infection can be identified and the RT-PCR product sequenced and matched to ORF 'unknowns'.

4) Generation of conditional lethal mutants by transposon mutagenesis: This technique, described by de Lorenzo, V. et al., Gene 123: 17-24 (1993); Neuwald, A. F. et a]., Gene 125: 69-73(1993); and Takiff, H. E. et aL, J. Bacteriol. 174:1544- 1553(1992), the contents of which is incoφorated by reference for background puφoses, identifies genes whose expression are essential for cell viability.

In this technique transposons carrying controllable promoters, which provide transcription outward from the transposon in one or both directions, are generated. Random insertion of these transposons into target organisms and subsequent isolation of insertion mutants in the presence of inducer of promoter activity ensures that insertions which separate promoter from coding region of a gene whose expression is essential for cell viability will be recovered. Subsequent replica plating in the absence of inducer identifies such insertions, since they fail to survive. Sequencing of the flanking regions of the transposon allows identification of site of insertion and identification of the gene disrupted. Close monitoring of the changes in cellular processes/moφhology during growth in the absence -of inducer yields information on likely function of the gene. Such monitoring could include flow cytometry (cell division, lysis, redox potential, DNA replication), incoφoration of radiochemically labeled precursors into DNA, RNA, protein, lipid, peptidoglycan, monitoring reporter enzyme gene fusions which respond to known cellular stresses.

5) Generation of conditional lethal mutants by chemical mutagenesis: This technique is described by Beckwith, J.. Methods in Enzymology 204:

3-18(1991), the contents of which are incoφorated herein by reference for background puφoses. In this technique random chemical mutagenesis of target organism, growth at temperature other than physiological temperature (permissive temperature) and subsequent replica plating and growth at different temperature (e.g. 42°C to identify ts, 25"C to identify cs) are used to identify those isolates which now fail to grow (conditional mutants). As above close monitoring of the changes upon growth at the non-permissive temperature yields information on the function of the mutated gene. Complementation of conditional lethal mutation by library from target organism and sequencing of complementing gene allows matching with unknown ORF.

6) RT-PCR: Staphylococcus aureus messenger RNA is isolated from bacterial infected tissue e.g. 48 hour murine lung infections, and the amount of each mRNA species assessed by reverse transcription of the RNA sample primed with random hexanucleotides followed by PCR with gene specific primer pairs. The determination of the presence and amount of a particular mRNA species by quantification of the resultant PCR product provides information on the bacterial genes which are transcribed in the infected tissue. Analysis of gene transcription can be carried out at different times of infection to gain a detailed knowledge of gene regulation in bacterial pathogenesis allowing for a clearer understanding of which gene products represent targets for screens for novel antibacterials. Because of the gene specific nature of the PCR primers employed it should be understood that the bacterial mRNA preparation need not be free of mammalian RNA. This allows the investigator to carry out a simple and quick RNA preparation from infected tissue to obtain bacterial mRNA species which are very short lived in the bacterium (in the order of 2 minute halflives). Optimally the bacterial mRNA is prepared from infected murine lung tissue by mechanical disruption in the presence of TRIzole (GIBCO-BRL) for very short periods of time, subsequent processing according to the manufacturers of TRIzole reagent and DNAase treatment to remove contaminating DNA. Preferably the process is optimised by finding those conditions which give a maximum amount of Staphylococcus aureus 16S ribosomal RNA as detected by probing Northerns with a suitably labelled sequence specific oligonucleotide probe. Typically a 5' dye labelled primer is used in each PCR primer pair in a PCR reaction which is terminated optimally between 8 and 25 cycles. The PCR products are separated on 6% polyacrylamide gels with detection and quantification using GeneScanner (manufactured by ABI).

Each of these techniques may have advantages or disadvantage depending on the particular application. The skilled artisan would choose the approach that is the most relevant with the particular end use in mind. Use of the of these technologies when applied to the ORFs of the present invention enables identification of bacterial proteins expressed during infection, inhibitors of which would have utility in anti-bacterial therapy.

The invention relates to novel polypeptides and polynucleotides as described in greater detail below. In particular, the invention relates to polypeptides and polynucleotides of Staphylococcus aureus, which is related by amino acid sequence homology to known polypeptide as set forth in Table 1. The invention relates especially to compounds having the nucleotide and amino acid sequence selected from the group consisting of the sequences set out in Table 1, and to the nucleotide sequences of the DNA in the deposited strain and amino acid sequences encoded thereby.

Deposited materials

S. aureus WCUH 29 has been deposited at the National Collection of Industrial and Marine Bacteria Ltd. (NCDVIB), Aberdeen, Scotland under number NCIMB 40771 on 11 September 1995.

The Staphylococcus aureus strain deposit is referred to herein as "the deposited strain" or as "the DNA of the deposited strain."

The deposited strain contains the full length genes comprising the polynucleotides set forth in Table 1. The sequence of the polynucleotides contained in the deposited strain, as well as the amino acid sequence of the polypeptide encoded thereby, are controlling in the event of any conflict with any description of sequences herein.

The deposit of the deposited strain has been made under the terms of the Budapest Treaty on the Intemational Recognition of the Deposit of Micro-organisms for Puφoses of Patent Procedure. The strain will be irrevocably and without restriction or condition released to the public upon the issuance of a patent. The deposited strain is provided merely as convenience to those of skill in the art and is not an admission that a deposit is required for enablement, such as that required under 35 U.S.C. §112.

A license may be required to make, use or sell the deposited strain, and compounds derived therefrom, and no such license is hereby granted.

Polypeptides

The polypeptides of the invention include the polypeptides set forth in Table 1 (in particular the mature polypeptide) as well as polypeptides and fragments, particularly those which have the biological activity of a polypeptide of the invention, and also those which have at least 50%, 60% or 70% identity to a polypeptide sequence selected from the group consisting of the sequences set out in Table 1 or the relevant portion, preferably at least 80% identity to a^~ polypeptide sequence selected from the group consisting of the sequences set out in Table 1 , and more preferably at least 90% similarity (more preferably at least 90% identity) to a polypeptide sequence selected from the group consisting of the sequences set out in Table 1, and still more preferably at least 95% similarity (still more preferably at least 95% identity) to a polypeptide sequence selected from the group consisting of the sequences set out in Table 1 , and also include portions of such polypeptides with such portion of the polypeptide generally containing at least 30 amino acids and more preferably at least 50 amino acids.

The invention also includes polypeptides of the formula:

X-(R₁)_m-(R₂)-(R₃)_n-Y wherein, at the amino terminus, X is hydrogen, and at the carboxyl terminus, Y is hydrogen or a metal, R i and R3 are any amino acid residue, m is an integer between 1 and 2000, n is an integer between 1 and 2000, and R₂ is an amino acid sequence of the invention, particularly an amino acid sequence selected from the group set forth in Table 1. In the formula above R₂ is oriented so that its amino terminal residue is at the left, bound to Ri and its carboxy terminal residue is at the right, bound to R3. Any stretch of amino acid residues denoted by either R group, where m and/or n is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer. In preferred embodiments m and/or n is an integer between 1 and 1000 or 2000.

A fragment is a variant polypeptide having an amino acid sequence that entirely is the same as part but not all of the amino acid sequence of the aforementioned polypeptides. As with polypeptides, fragments may be "free-standing," or comprised within a larger polypeptide of which they form a part or region, most preferably as a single continuous region, a single larger polypeptide.

Preferred fragments include, for example, truncation polypeptides having a portion of the amino acid sequence of Table 1, or of variants thereof, such as a continuous series of residues that includes the amino terminus, or a continuous series of residues that includes the carboxyl terminus: Degradation forms of the polypeptides of the invention in a host cell, particularly a Staphylococcus aureus, are also preferred. Further preferred are fragments characterized by structural or functional attributes such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions.

Also preferred are biologically active fragments which are those fragments that mediate activities of polypeptides of the invention, including those with a similar activity or an improved activity, or with a decreased undesirable activity. Also included are those fragments that are antigenic or immunogenic in an animal, especially in a human. Particularly preferred are fragments comprising receptors or domains of enzymes that confer a function essential for viability of Staphylococcus aureus or the ability to initiate, or maintain cause disease in an individual, particularly a human.

Variants that are fragments of the polypeptides of the invention may be employed for producing the corresponding full-length polypeptide by peptide synthesis; therefore, these variants may be employed as intermediates for producing the full-length polypeptides of the invention.

In addition to the standard single and triple letter representations for amino acids, the term "X" or "Xaa" is also used. "X" and "Xaa" mean that any of the twenty naturally occuring amino acids may appear at such a designated position in the polypeptide sequence.

Polynucleotides

The nucleotide sequences disclosed herein can be obtained by synthetic chemical techniques known in the art or can be obtained from S. aureus WCUH 29 by probing a DNA preparation with probes constructed from the particular sequences disclosed herein. Alternatively, oligonucleotides derived from a disclosed sequence can act as PCR primers in a process of PCR-based cloning of the sequence from a bacterial genomic source. It is recognised that such sequences will also have utility in diagnosis of the stage of infection and type of infection the pathogen has attained.

To obtain the polynucleotide encoding the protein using the DNA sequence given herein typically a library of clones of chromosomal DNA of S.aureus WCUH 29 in E. coli or some other suitable host is probed with a radiolabelled oligonucleotide, preferably a 17mer or longer, derived from the partial sequence. Clones carrying DNA identical to that of the probe can then be distinguished using high stringency washes. By sequencing the individual clones thus identified with sequencing primers designed from the original sequence it is then possible to extend the sequence in both directions to determine the full gene sequence. Conveniently such sequencing is performed using denatured double stranded DNA prepared from a plasmid clone. Suitable techniques are described by Maniatis, T., Fritsch, E.F. and Sambrook, J. in MOLECULAR CLONING, A Laboratory . Manual, 2nd edition, 1989, Cold Spring Harbor Laboratory (see: Screening By Hybridization 1.90 and Sequencing Denatured Double-Stranded DNA Templates 13.70).

Moerover, another aspect of the invention relates to isolated polynucleotides that encode the polypeptides of the invention having a deduced amino acid sequence selected from the group consisting of the sequences in Table 1 and polynucleotides closely related thereto and variants thereof.

Using the information provided herein, such as the polynucleotide sequences set out in Table 1, a polynucleotide of the invention encoding polypeptide may be obtained using standard cloning and screening methods, such as those for cloning and sequencing chromosomal DNA fragments from bacteria using Staphylococcus aureus WCUH29 cells as starting material, followed by obtaining a full length clone. For example, to obtain a polynucleotide sequence of the invention, such as a sequence set forth in Table 1 , typically a library of clones of chromosomal DNA of Staphylococcus aureus WCUH29 in E.coli or some other suitable host is probed with a radiolabeled oligonucleotide, preferably a 17-mer or longer, derived from a partial sequence. Clones carrying DNA identical to that of the probe can then be distinguished using stringent conditions. By sequencing the individual clones thus identified with sequencing primers designed from the original sequence it is then possible to extend the sequence in both directions to determine the full gene sequence. Conveniently, such sequencing is performed using denatured double stranded DNA prepared from a plasmid clone. Suitable techniques are described by Maniatis, T., Fritsch, E.F. and Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, 2nd Ed.; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989). (see in particular Screening By Hybridization 1.90 and Sequencing Denatured Double-Stranded DNA Templates 13.70). Illustrative of the invention, the polynucleotides set out in Table 1 were discovered in a DNA library derived from Staphylococcus aureus WCUH29.

The DNA sequences set out in Table 1 each contains at least one open reading frame encoding a protein having at least about the number of amino acid residues set forth in Table 1. The start and stop codons of each open reading frame (herein "ORF") DNA are the first three and the last three nuclotides of each polynucleotide set forth in Table 1.

Certain polynucleotides and polypeptides of the invention are structurally related to known proteins as set forth in Table 1. These proteins exhibit greatest homology to the homologue listed in Table 1 from among the known proteins.

The invention provides a polynucleotide sequence identical over its entire length to each coding sequence in Table 1. Also provided by the invention is the coding sequence for the mature polypeptide or a fragment thereof, by itself as well as the coding sequence for the mature polypeptide or a fragment in reading frame with other coding sequence, such as those encoding a leader or secretory sequence, a pre-, or pro- or prepro- protein sequence. The polynucleotide may also contain non-coding sequences, including for example, but not limited to non-coding 5' and sequences, such as the transcribed, non-translated sequences, termination signals, ribosome binding sites, sequences that stabilize mRNA, introns, polyadenylation signals, and additional coding sequence which encode additional amino acids. For example, a marker sequence that facilitates purification of the fused polypeptide can be encoded. In certain embodiments of the invention, the marker sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and described in Gentz et al, Proc. Natl. Acad. Sci., USA 86: 821- 824 (1989), or an HA tag (Wilson et al., Cell 37: 767 (1984). Polynucleotides of the invention also include, but .are not limited to, polynucleotides comprising a structural gene and its naturally associated sequences that control gene expression.

The invention also includes polynucleotides of the formula:

X-(R₁)_m-(R₂)-(R₃)_n-Y wherein, at the 5' end of the molecule, X is hydrogen, and at the 3' end of the molecule, Y is hydrogen or a metal, R _j and R3 is any nucleic acid residue, m is an integer between 1 and 3000, n is an integer between 1 and 3000, and R₂ is a nucleic acid sequence of the invention, particularly a nucleic acid sequence selected from the group set forth in Table 1. In the polynucleotide formula above R₂ is oriented so that its 5' end residue is at the left, bound to R_j and its 3' end residue is at the right, bound to R3. Any stretch of nucleic acid residues denoted by either R group, where m and/or n is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer. In a preferred embodiment m and or n is an integer between 1 and 1000, or 2000 or 3000.

The term "polynucleotide encoding a polypeptide" as used herein encompasses polynucleotides that include a sequence encoding a polypeptide of the invention, particularly a bacterial polypeptide and more particularly a polypeptide of the Staphylococcus aureus having an amino acid sequence set out in Table 1. The term also encompasses polynucleotides that include a single continuous region or discontinuous regions encoding the polypeptide (for example,- interrupted by integrated phage or an insertion sequence or editing) together with additional regions, that also may contain coding and/or non-coding sequences.

The invention further relates to variants of the polynucleotides described herein that encode for variants of the polypeptide having the deduced amino acid sequence of Table 1. Variants that are fragments of the polynucleotides of the invention may be used to synthesize full-length polynucleotides of the invention.

Further particularly preferred embodiments are polynucleotides encoding polypeptide variants, that have the amino acid sequence of a polypeptide of Table 1 in which several, a few, 5 to 10, 1 to 5, 1 to 3, 2, 1 or no amino acid residues are substituted, deleted or added, in any combination. Especially preferred among these are silent substitutions, additions and deletions, that do not alter the properties and activities of such polynucleotide.

Further preferred embodiments of the invention are polynucleotides that are at least 50%, 60% or 70% identical over their entire length to a polynucleotide encoding a polypeptide having the amino acid sequence set out in Table 1 , and polynucleotides that are complementary to such polynucleotides. Alternatively, most highly preferred are polynucleotides that comprise a region that is at least 80% identical over its entire length to a polynucleotide encoding a polypeptide of the deposited strain and polynucleotides complementary thereto. In this regard, polynucleotides at least 90% identical over their entire length to the same are particularly preferred, and among these particularly preferred polynucleotides, those with at least 95% are especially preferred. Furthermore, those with at least 97% are highly preferred among those with at least 95%, and among these those with at least 98% and at least 99% are particularly highly preferred, with at least 99% being the more preferred.

A preferred embodiment is an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of: a polynucleotide having at least a 50% identity to a polynucleotide encoding a polypeptide comprising the amino acid sequence of Table 1 and obtained from a prokaryotic species other than S. aureus; and a polynucleotide encoding a polypeptide comprising an amino acid sequence which is at least 50% identical to the amino acid sequence of Table 1 and obtained from a prokaryotic species other than S. aureus.

Preferred embodiments are polynucleotides that encode polypeptides that retain substantially the same biological function or activity as the mature polypeptide encoded by the DNA of Table 1.

The invention further relates to polynucleotides that hybridize to the herein above- described sequences. In this regard, the invention especially relates to polynucleotides that hybridize under stringent conditions to the herein above-described polynucleotides. As herein used, th^'e terms "stringent conditions" and "stringent hybridization conditions" mean hybridization will occur only if there is at least 95% and preferably at least 97% identity between the sequences. An example of stringent hybridization conditions is overnight incubation at 42°C in a solution comprising: 50% formamide, 5x SSC (150mM NaCI, 15mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5x Denhardt's solution, 10% dextran sulfate, and 20 micrograms/ml denatured, sheared salmon sperm DNA, followed by washing the hybridization support in O. lx SSC at about 65°C. Hybridization and wash conditions are well known and exemplified in Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., ( 1989), particularly Chapter 1 1 therein. The invention also provides a polynucleotide consisting essentially of a polynucleotide sequence obtainable by screening an appropriate library containing the complete gene for a polynucleotide sequence set forth in Table 1 under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence or a fragment thereof; and isolating said DNA sequence. Fragments useful for obtaining such a polynucleotide include, for example, probes and primers described elsewhere herein.

As discussed additionally herein regarding polynucleotide assays of the invention, for instance, polynucleotides of the invention as discussed above, may be used as a hybridization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding a polypeptide and to isolate cDNA and genomic clones of other genes that have a high sequence similarity to a polynucleotide set forth in Table 1. Such probes generally will comprise at least 15 bases. Preferably, such probes will have at least 30 bases and may have at least 50 bases. Particularly preferred probes will have at least 30 bases and will have 50 bases or less.

For example, the coding region of each gene that comprises or is comprised by a polynucleotide set forth in Table 1 may be isolated by screening using a DNA sequence provided in Table 1 to synthesize an oligonucleotide probe. A labeled oligonucleotide having a sequence complementary to that of a gene of the invention is then used to screen a library of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybridizes to.

The polynucleotides and polypeptides of the invention may be employed, for example, as research reagents and materials for discovery of treatments of and diagnostics for disease, particularly human disease, as further discussed herein relating to polynucleotide assays.

Polynucleotides of the invention that are oligonucleotides derived from the a polynucleotide or polypeptide sequence set forth in Table 1 may be used in the processes herein as described, but preferably for PCR, to determine whether or not the polynucleotides identified herein in whole or in part are transcribed in bacteria in infected tissue. It is recognized that such sequences will also have utility in diagnosis of the stage of infection and type of infection the pathogen has attained.

The invention also provides polynucleotides that may encode a polypeptide that is the mature protein plus additional amino or carboxyl-terminal amino acids, or amino acids interior to the mature polypeptide (when the mature form has more than one polypeptide chain, for instance). Such sequences may play a role in processing of a protein from precursor to a mature form, may allow protein transport, may lengthen or shorten protein half-life or may facilitate manipulation of a protein for assay or production, among other things. As generally is the case in vivo, the additional amino acids may be processed away from the mature protein by cellular enzymes.

A precursor protein, having the mature form of the polypeptide fused to one or more prosequences may be an inactive form of the polypeptide. When prosequences are removed such inactive precursors generally are activated. Some or all of the prosequences may be removed before activation. Generally, such precursors are called proproteins.

In addition to the standard A, G, C, T/U representations for nucleic acid bases, the term "N" is also used. "N" means that any of the four DNA or RNA bases may appear at such a designated position in the DNA or RNA sequence, except it is preferred that N is not a base that when taken in combination with adjacent nucleotide positions, when read in the correct reading frame, would have the effect of generating a premature termination codon in such reading frame.

In sum, a polynucleotide of the invention may encode a mature protein, a mature protein plus a leader sequence (which may be referred to as a preprotein), a precursor of a mature protein having one or more prosequences that are not the leader sequences of a preprotein, or a preproprotein, which is a precursor to a proprotein, having a leader sequence and one or more prosequences, which generally are removed during processing steps that produce active and mature forms of the polypeptide.

Vectors, host cells, expression

The invention also relates to vectors that comprise a polynucleotide or polynucleotides of the invention, host cells that are genetically engineered with vectors of the invention and the production of polypeptides of the invention by recombinant techniques. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the invention.

For recombinant production, host cells can be genetically engineered to incoφorate expression systems or portions thereof or polynucleotides of the invention. Introduction of a polynucleotide into the host cell can be effected by methods described in many standard laboratory manuals, such as Davis et al., BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), such as, calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction and infection. Representative examples of appropriate hosts include bacterial cells, such as staphylococci, staphylococci, enterococci E. coli, streptomyces and Bacillus subtilis cells; fungal cells, such as yeast cells and Aspergillits cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293 and Bowes melanoma cells; and plant cells.

A great variety of expression systems can be used to produce the polypeptides of the invention. Such vectors include, among others, chromosomal, episomal and vims-derived vectors, e.g., vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from vimses such as baculoviruses, papova vimses, such as SV40, vaccinia vimses, adenoviruses, fowl pox viruses, pseudorabies vimses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids. The expression system constructs may contain control regions that regulate as well as engender expression. Generally, any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide in a host may be used for expression in this regard. The appropriate DNA sequence may be inserted into the expression system by any of a variety of well-known and routine techniques, such as, for example, those set forth in Sambrook etal., MOLECULAR CLONING, A LABORATORY MANUAL, (supra).

For secretion of the translated protein into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment, appropriate secretion signals may be incoφorated into the expressed polypeptide. These signals may be endogenous to the polypeptide or they may be heterologous signals.

Polypeptides of the invention can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, and lectin chromatography. Most preferably, high performance liquid chromatography is employed for purification. Well known techniques for refolding protein may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or purification.

Diagnostic Assays

This invention is also related to the use of the polynucleotides of the invention for use as diagnostic reagents. Detection of such polynucleotides in a eukaryote, particularly a mammal, and especially a human, will provide a diagnostic method for diagnosis of a disease. Eukaryotes (herein also "individual(s)"), particularly mammals, and especially humans, infected with an organism comprising a gene of the invention may be detected at the nucleic acid level by a variety of techniques.

Nucleic acids for diagnosis may be obtained from an infected individual's cells and tissues, such as bone, blood, muscle, cartilage, and skin. Genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR or other amplification technique prior to analysis. RNA or cDNA may also be used in the same ways. Using amplification, characterization of the species and strain of prokaryote present in an individual, may be made by an analysis of the genotype of the prokaryote gene. Deletions and insertions can be detected by a change in size of the amplified product in comparison to the genotype of a reference sequence. Point mutations can be identified by hybridizing amplified DNA to labeled polynucleotide sequences of the invention. Perfectly matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences in melting temperatures. DNA sequence differences may also be detected by alterations in the electrophoretic mobility of the DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing. See, e.g., Myers et al., Science, 230: 1242 (1985). Sequence changes at specific locations also may be revealed by nuclease protection assays, such as RNase and S 1 protection or a chemical cleavage method. See, e.g., Cotton et al., Proc. Natl. Acad. Sci., USA, 85: 4397-4401 (1985).

Cells carrying mutations or polymoφhisms in the gene of the invention may also be detected at the DNA level by a variety of techniques, to allow for serotyping, for example. For example, RT-PCR can be used to detect mutations. It is particularly preferred to used RT-PCR in conjunction with automated detection systems, such as, for example, GeneScan. RNA or cDNA may also be used for the same puφose, PCR or RT-PCR. As an example, PCR primers complementary to a nucleic acid encoding a polypeptide of the invention can be used to identify and analyze mutations. These primers may be used for, among other things, amplifying a DNA of the invention isolated from a sample derived from an individual. The primers may be used to amplify the gene isolated from an infected individual such that the gene may then be subject to various techniques for elucidation of the DNA sequence. In this way, mutations in the DNA sequence may be detected and used to diagnose infection and to serotype and/or classify the infectious agent.

The invention further provides a process for diagnosing disease, preferably bacterial infections, more preferably infections by Staphylococcus aureus, and most preferably disease, such as, infections of the upper respiratory tract (e.g., otitis media, bacterial tracheitis, acute epiglottitis, thyroiditis), lower respiratory (e.g., empyema, lung abscess), cardiac (e.g., infective endocarditis), gastrointestinal (e.g., secretory diarrhoea, splenic absces, retroperitoneal abscess), CNS (e.g., cerebral abscess), eye (e.g., blepharitis, conjunctivitis, keratitis, endophthalmitis, preseptal and orbital cellulitis, darcryocystitis), kidney and urinary tract (e.g., epididymitis, intrarenal and perinephric absces, toxic shock syndrome), skin (e.g., impetigo, folliculitis, cutaneous abscesses, cellulitis, wound infection, bacterial myositis) bone and joint (e.g., septic arthritis, osteomyelitis), comprising determining from a sample derived from an individual a increased level of expression of polynucleotide having the sequence of Table 1. Increased or decreased expression of a polynucleotide of the invention can be measured using any on of the methods well known in the art for the quantitation of polynucleotides, such as, for example, amplification, PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods.

In addition, a diagnostic assay in accordance with the invention for detecting over- expression of a polypeptide of the invention compared to normal control tissue samples may be used to detect the presence of an infection, for example. Assay techniques that can be used to determine levels of a protein, in a sample derived from a host are well-known to those of skill in the art. Such assay methods include radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays.

Antibodies

The polypeptides of the invention or variants thereof, or cells expressing them can be used as an immunogen to produce antibodies immunospecific for such polypeptides. "Antibodies" as used herein includes monoclonal and polyclonal antibodies, chimeric, single chain, simianized antibodies and humanized antibodies, as well as Fab fragments, including the products of an Fab immunolglobulin expression library.

Antibodies generated against the polypeptides of the invention can be obtained by administering the polypeptides or epitope-bearing fragments, analogues or cells to an animal, preferably a nonhuman, using routine protocols. For preparation of monoclonal antibodies, any technique known in the art that provides antibodies produced by continuous cell line cultures can be used. Examples include various techniques, such as those in Kohler, G. and Milstein, C, Nature 256: 495-497 (1975); Kozbor et al., Immunology Today 4: 72 (1983); Cole et al., pg. 77- 96 in MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985).

Techniques for the production of single chain antibodies (U.S. Patent No. 4,946,778) can be adapted to produce single chain antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized antibodies.

Alternatively phage display technology may be utilized to select antibody genes with binding activities towards the polypeptide either from repertoires of PCR amplified v- genes of lymphocytes from humans screened for possessing recognition of a polypeptide of the invention or from naive libraries (McCafferty, J. et al., (1990), Nature 348, 552-554; Marks, J. et al., (1992) Biotechnology 10, 779-783). The affinity of these antibodies can also be improved by chain shuffling (Clackson, T. et al., (1991) Nature 352, 624-628).

If two antigen binding domains are present each domain may be directed against a different epitope - termed 'bispecific' antibodies.

The above-described antibodies may be employed to isolate or to identify clones expressing the polypeptides to purify the polypeptides by affinity chromatography.

Thus, among others, antibodies against a polypeptide of the invention may be employed to treat infections, particularly bacterial infections and especially infections of the upper respiratory tract (e.g., otitis media, bacterial tracheitis, acute epiglottitis, thyroiditis), lower respiratory (e.g., empyema, lung abscess), cardiac (e.g., infective endocarditis), gastrointestinal (e.g., secretory diarrhoea, splenic absces, retroperitoneal abscess), CNS (e.g., cerebral abscess), eye (e.g., blepharitis, conjunctivitis, keratitis, endophthalmitis, preseptal and orbital cellulitis, darcryocystitis), kidney and urinary tract (e.g., epididymitis, intrarenal and perinephric absces, toxic shock syndrome), skin (e.g., impetigo, folliculitis, cutaneous abscesses, cellulitis, wound infection, bacterial myositis) bone and joint (e.g., septic arthritis, osteomyelitis).

Polypeptide variants include antigenically, epitopically or immunologically equivalent variants that form a particular aspect of this invention. The term "antigenically equivalent derivative" as used herein encompasses a polypeptide or its equivalent which will be specifically recognized by certain antibodies which, when raised to the protein or polypeptide according to the invention, interfere with the immediate physical interaction between pathogen and mammalian host. The term "immunologically equivalent derivative" as used herein encompasses a peptide or its equivalent which when used in a suitable formulation to raise antibodies in a vertebrate, the antibodies act to interfere with the immediate physical interaction between pathogen and mammalian host.

The polypeptide, such as an antigenically or immunologically equivalent derivative or a fusion protein thereof is used as an antigen to immunize a mouse or other animal such as a rat or chicken. The fusion protein may provide stability to the polypeptide. The antigen may be associated, for example by conjugation, with an immunogenic carrier protein for example bovine serum albumin (BSA) or keyhole limpet haemocyanin (KLH). Alternatively a multiple antigenic peptide comprising multiple copies of the protein or polypeptide, or an antigenically or immunologically equivalent polypeptide thereof may be sufficiently antigenic to improve immunogenicity so as to obviate the use of a carrier.

Preferably, the antibody or variant thereof is modified to make it less immunogenic in the individual. For example, if the individual is human the antibody may most preferably be "humanized"; where the complimentarity determining region(s) of the hybridoma-derived antibody has been transplanted into a human monoclonal antibody , for example as described in Jones, P. et al. (1986), Nature 321, 522-525 or Tempest et al.,(1991) Biotechnology 9, 266-273.

The use of a polynucleotide of the invention in genetic immunization will preferably employ a suitable delivery method such as direct injection of plasmid DNA into muscles (Wolff et al., Hum Mol Genet 1992, 1 :363, Maπthoφe et al., Hum. Gene Ther. 1963:4, 419), delivery of DNA complexed with specific protein carriers (Wu et al., J Biol Chem. 1989: 264,16985), coprecipitation of DNA with calcium phosphate (Benvenisty & Reshef, PNAS, 1986:83,9551), encapsulation of DNA in various forms of liposomes (Kaneda et al., Science 1989:243,375), particle bombardment (Tang et al., Nature 1992, 356: 152, Eisenbraun et al., DNA Cell Biol 1993, 12:791) and in vivo infection using cloned retroviral vectors (Seeger et al., PNAS 1984:81,5849).

Antagonists and agonists - assays and molecules

Polypeptides of the invention may also be used to assess the binding of small molecule substrates and ligands in, for example, cells, cell-free preparations, chemical libraries, and natural product mixtures. These substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics. See, e.g., Coligan et al, Current Protocols in Immunology 1(2): Chapter 5 (1991).

The invention also provides a method of screening compounds to identify those which enhance (agonist) or block (antagonist) the action of a polypeptides or polynucleotides of the invention, particularly those compounds that are bacteriostatic and/or bacteriocidal. The method of screening may involve high-throughput techniques. For example, to screen for agonists or antagoists, a synthetic reaction mix, a cellular compartment, such as a membrane, cell envelope or cell wall, or a preparation of any thereof, comprising a polypeptide of the invention and a labeled substrate or ligand of such polypeptide is incubated in the absence or the presence of a candidate molecule that may be an agonist or antagonist of a polypeptide of the invention. The ability of the candidate molecule to agonize or antagonize a polypeptide of the invention is reflected in decreased binding of the labeled ligand or decreased production of product from such substrate. Molecules that bind gratuitously, i.e., without inducing the effects of a polypeptide of the invention are most likely to be good antagonists. Molecules that bind well and increase the rate of product production from substrate are agonists. Detection of the rate or level of production of product from substrate may be enhanced by using a reporter system. Reporter systems that may be useful in this regard include but are not limited to colorimetric labeled substrate converted into product, a reporter gene that is responsive to changes in polynucleotide or polypeptide activity, and binding assays known in the art.

Another example of an assay for antagonists of polypeptides of the invention is a competitive assay that combines any such polypeptide and a potential antagonist with a compound which binds such polypeptide, natural substrates or ligands, or substrate or ligand mimetics, under appropriate conditions for a competitive inhibition assay. A polypeptide of the invention can be labeled, such as by radioactivity or a colorimetric compound, such that the number of such polypeptide molecules bound to a binding molecule or converted to product can be determined accurately to assess the effectiveness of the potential antagonist.

Potential antagonists include small organic molecules, peptides, polypeptides and antibodies that bind to a polynucleotide or polypeptide of the invention and thereby inhibit or extinguish its activity. Potential antagonists also may be small organic molecules, a peptide, a polypeptide such as a closely related protein or antibody that binds the same sites on a binding molecule, such as a binding molecule, without inducing activities induced by a polypeptide of the invention, thereby preventing the action of such polypeptide by excluding it from binding.

Potential antagonists include a small molecule that binds to and occupies the binding site of the polypeptide thereby preventing binding to cellular binding molecules, such that normal biological activity is prevented. Examples of small molecules include but are not limited to small organic molecules, peptides or peptide-like molecules. Other potential antagonists include ^• antisense molecules (see Okano, J. Neurochem. 56: 560 (1991); OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton, FL (1988), for a description of these molecules). Preferred potential antagonists include compounds related to and variants of a polypeptide of the invention.

Each of the DNA sequences provided herein may be used in the discovery and development of antibacterial compounds. The encoded protein, upon expression, can be used as a target for the screening of antibacterial drugs. Additionally, the DNA sequences encoding the amino terminal regions of the encoded protein or Shine-Delgarno or other translation facilitating sequences of the respective mRNA can be used to construct antisense sequences to control the expression of the coding sequence of interest.

The invention also provides the use of the polypeptide, polynucleotide or inhibitor of the invention to interfere with the initial physical interaction between a pathogen and mammalian host responsible for sequelae of infection. In particular the molecules of the invention may be used: in the prevention of adhesion of bacteria, in particular gram positive bacteria, to mammalian extracellular matrix proteins on in-dwelling devices or to extracellular matrix proteins in wounds; to block protein-mediated mammalian cell invasion by, for example, initiating phosphorylation of mammalian tyrosine kinases (Rosenshine et al., Infect. Iinmun. 60:221 1 (1992); to block bacterial adhesion between mammalian extracellular matrix proteins and bacterial proteins that mediate tissue damage and; to block the normal progression of pathogenesis in infections initiated other than by the implantation of in-dwelling devices or by other surgical techniques.

The antagonists and agonists of the invention may be employed, for instance, to inhibit and treat disease, such as, infections of the upper respiratory tract (e.g., otitis media, bacterial tracheitis, acute epiglottitis, thyroiditis), lower respiratory (e.g., empyema, lung abscess), cardiac (e.g., infective endocarditis), gastrointestinal (e.g., secretory diarrhoea, splenic absces, retroperitoneal abscess), CNS (e.g., cerebral abscess), eye (e.g., blepharitis, conjunctivitis, keratitis, endophthalmitis, preseptal and orbital cellulitis, darcryocystitis), kidney and urinary tract (e.g., epididymitis, intrarenal and perinephric absces, toxic shock syndrome), skin (e.g., impetigo, folliculitis, cutaneous abscesses, cellulitis, wound infection, bacterial myositis) bone and joint (e.g., septic arthritis, osteomyelitis).

Helicobacter pylori (herein H. pylori) bacteria infect the stomachs of over one-third of the world's population causing stomach cancer, ulcers, and gastritis (International Agency for Research on Cancer (1994) Schistosomes, Liver Flukes and Helicobacter Pylori (International Agency for Research on Cancer, Lyon, France; http://www.uicc.ch/ecp/ecp2904.htm). Moreover, the international Agency for Research on Cancer recently recognized a cause-and-effect relationship between H. pylori and gastric adenocarcinoma, classifying the bacterium as a Group I (definite) carcinogen. Preferred antimicrobial compounds of the invention found using screens provided by the invention, particularly broad-spectrum antibiotics, should be useful in the treatment of H. pylori infection. Such treatment should decrease the advent of H. pylori-m^' άaceά cancers, such as gastrointestinal carcinoma. Such treatment should also cure gastric ulcers and gastritis.

Vaccines Another aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal which comprises inoculating the individual with a polypeptide of the invention, or a fragment or variant thereof, adequate to produce antibody and/ or T cell immune response to protect said individual from infection, particularly bacterial infection and most particularly Staphylococcus aureus infection. Also provided are methods whereby such immunological response slows bacterial replication. Yet another aspect of the invention relates to a method of inducing immunological response in an individual which comprises delivering to such individual a nucleic acid vector to direct expression of a polynucleotide or polypeptide of the invention, or a fragment or a variant thereof, for expressing such polynucleotide or polypeptide, or a fragment or a variant thereof in vivo in order to induce an immunological response, such as, to produce antibody and/ or T cell immune response, including, for example, cytokine-producing T cells or cytotoxic T cells, to protect said individual from disease, whether that disease is already established within the individual or not. One way of administering the gene is by accelerating it into the desired cells as a coating on particles or otherwise. Such nucleic acid vector may comprise DNA, RNA, a modified nucleic acid, or a DNA/RNA hybrid.

A further aspect of the invention relates to an immunological composition which, when introduced into an individual capable or having induced within it an immunological response, induces an immunological response in such individual to a polynucleotide of the invention or protein coded therefrom, wherein the composition comprises a recombinant polynucleotide or protein coded therefrom comprising DNA which codes for and expresses an antigen of said polynucleotide or protein coded therefrom. The immunological response may be used therapeutically or prophylactically and may take the form of antibody immunity or cellular immunity such as that arising from CTL or CD4+ T cells.

A polypeptide of the invention or a fragment thereof may be fused with co-protein which may not by itself produce antibodies, but is capable of stabilizing the first protein and producing a fused protein which will have immunogenic and protective properties. Thus fused recombinant protein, preferably further comprises an antigenic co-protein, such as Iipoprotein D from Hemophilus influenzae, Glutathione-S-transferase (GST) or beta- galactosidase, relatively large co-proteins which solubilize the protein and facilitate production and purification thereof. Moreover, the co-protein may act as an adjuvant in the sense of providing a generalized stimulation of the immune system. The co-protein may be attached to either the amino or carboxy terminus of the first protein. Provided by this invention are compositions, particularly vaccine compositions, and methods comprising the polypeptides or polynucleotides of the invention and immunostimulatory DNA sequences, such as those described in Sato, Y. et al. Science 273: 352 (1996).

Also, provided by this invention are methods using the described polynucleotide or particular fragments thereof which have been shown to encode non-variable regions of bacterial cell surface proteins in DNA constructs used in such genetic immunization experiments in animal models of infection with Staphylococcus aureus will be particularly useful for identifying protein epitopes able to provoke a prophylactic or therapeutic immune response. It is believed that this approach will allow for the subsequent preparation of monoclonal antibodies of particular value from the requisite organ of the animal successfully resisting or clearing infection for the development of prophylactic agents or therapeutic treatments of bacterial infection, particularly Staphylococcus aureus infection, in mammals, particularly humans.

The polypeptide may be used as an antigen for vaccination of a host to produce specific antibodies which protect against invasion of bacteria, for example by blocking adherence of bacteria to damaged tissue. Examples of tissue damage include wounds in skin or connective tissue caused, e.g., by mechanical, chemical or thermal damage or by implantation of indwelling devices, or wounds in the mucous membranes, such as the mouth, mammary glands, urethra or vagina.

The invention also includes a vaccine formulation which comprises an immunogenic recombinant protein of the invention together with a suitable carrier. Since the protein may be broken down in the stomach, it is preferably administered parenterally, including, for example, administration that is subcutaneous, intramuscular, intravenous, or intradermal. Formulations suitable for parenteral administration include aqueous and non- aqueous -sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the bodily fluid, preferably the blood, of the individual; and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use. The vaccine formulation may also include adjuvant systems for enhancing the immunogenicity of the formulation, such as oil-in water systems and other systems known in the art. The dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation.

While the invention has been described with reference to certain protein, such as, for example, those set forth in Table 1, it is to be understood that this covers fragments of the naturally occurring protein and similar proteins with additions, deletions or substitutions which do not substantially affect the immunogenic properties of the recombinant protein.

Compositions, kits and administration

The invention also relates to compositions comprising the polynucleotide or the polypeptides discussed above or their agonists or antagonists. The polypeptides of the invention may be employed in combination with a non-sterile or sterile carrier or carriers for use with cells, tissues or organisms, such as a pharmaceutical carrier suitable for administration to a subject. Such compositions comprise, for instance, a media additive or a therapeutically effective amount of a polypeptide of the invention and a pharmaceutically acceptable carrier or excipient. Such carriers may include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol and combinations thereof. The formulation should suit the mode of administration. The invention further relates to diagnostic and pharmaceutical packs and kits comprising one or more containers filled with one or more of the ingredients of the aforementioned compositions of the invention.

Polypeptides and other compounds of the invention may be employed alone or in conjunction with other compounds, such as therapeutic compounds.

The pharmaceutical compositions may be administered in any effective, convenient manner including, for instance, administration by topical, oral, anal, vaginal, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal or intradermal routes among others.

In therapy or as a prophylactic, the active agent may be administered to an individual as an injectable composition, for example as a sterile aqueous dispersion, preferably isotonic.

Alternatively the composition may be formulated for topical application for example in the form of ointments, creams, lotions, eye ointments, eye drops, ear drops, mouthwash, impregnated dressings and sutures and aerosols, and may contain appropriate conventional additives, including, for example, preservatives, solvents to assist drug penetration, and emollients in ointments and creams. Such topical formulations may also contain compatible conventional carriers, for example cream or ointment bases, and ethanol or oleyl alcohol for lotions. Such carriers may constitute from about 1 % to about 98% by weight of the formulation; more usually they will constitute up to about 80% by weight of the formulation.

For administration to mammals, and particularly humans, it is expected that the daily dosage level of the active agent will be from 0.01 mg/kg to 10 mg/kg, typically around 1 mg/kg. The physician in any event will determine the actual dosage which will be most suitable for an individual and will vary with the age, weight and response of the particular individual. The above dosages are exemplary of the average case. There can, of course, be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention.

In-dwelling devices include surgical implants, prosthetic devices and catheters, i.e., devices that are introduced to the body of an individual and remain in position for an extended time. Such devices include, for example, artificial joints, heart valves, pacemakers, vascular grafts, vascular catheters, cerebrospinal fluid shunts, urinary catheters, continuous ambulatory peritoneal dialysis (CAPD) catheters.

The composition of the invention may be administered by injection to achieve a systemic effect against relevant bacteria shortly before insertion of an in-dwelling device. Treatment may be continued after surgery during the in-body time of the device. In addition, the composition could also be used to broaden perioperative cover for any surgical technique to prevent bacterial wound infections, especially Staphylococcus aureus wound infections.

Many orthopedic surgeons consider that humans with prosthetic joints should be considered for antibiotic prophylaxis before dental treatment that could produce a bacteremia. Late deep infection is a serious complication sometimes leading to loss of the prosthetic joint and is accompanied by significant morbidity and mortality. It may therefore be possible to extend the use of the active agent as a replacement for prophylactic antibiotics in this situation.

In addition to the therapy described above, the compositions of this invention may be used generally as a wound treatment agent to prevent adhesion of bacteria to matrix proteins exposed in wound tissue and for prophylactic use in dental treatment as an alternative to, or in conjunction with, antibiotic prophylaxis.

Alternatively, the composition of the invention may be used to bathe an indwelling device immediately before insertion. The active agent will preferably be present at a concentration of 1 μg/ml to lOmg/ml for bathing of wounds or indwelling devices. A vaccine composition is conveniently in injectable form. Conventional adjuvants may be employed to enhance the immune response. A suitable unit dose for vaccination is 0.5-5 microgram/kg of antigen, and such dose is preferably administered 1-3 times arrt! with an interval of 1-3 weeks. With the indicated dose range, no adverse toxicological effects will be observed with the compounds of the invention which would reclude their administration to suitable individual*.

Each reference disclosed herein is incoφorated by reference herein in its entirety. Any patent application to which this application claims priority is also incoφorated by reference herein in its entirety. TABLES

Certain pertinent data for each of the polypeptides and polynucleotides set forth in Table 1 are summarized in the following Table.

TABLE 1

Provided in this Table are listed homologues of each polypeptide encoded by each ORF of the invention based on a comparison of the sequences of in Table 1 with sequences available in the public domain (see the description after the ">" symbol). Where no significant homologue was detected "unknown" appears as the decription. Preferred polypeptides encoded by the ORFs of the invention, particularly full length proteins either obtained using such ORFs or encoded entirely by such ORFs, are ones that have a biological function of the homologue listed, among other functions. The analysis used to determine each homologue listed in Table 1 was either BlastP, BlastX or MPSearch, each of which is well known. The SEQ ID NO: of each DNA sequence in Table 1 appears before the contig number, which contig number is preceded by the word "contig". The SEQ ID NO: of each protein (polypeptide) sequence of each sequence in Table 1 appears bfore the score value and beneath the heading "Plus Strand HSPs" or "Minus Strand HSPs". In some instances the DNA sequence encodes more than one protein sequence and so is listed more than once. Other pertinent information is provided regarding the comparison of the published sequence with each sequence of the invention, such as, the score, percent identity, probability score, etc. This information is standard information provided by known homology scoring algorithms.

TABLE 1

[SEQ ID NO: ] contig [0092 ] Length: 582 Check: 5031 .. 98/23738

1 TTTATATCGT TTTTAATAAT CGGTCTATAT ATGTTTATCG AAATCATCGG

51 CGGTCTCCTT GCTAACAGCT TGGCATTACT ATCTGACGGT ATCCATATGT

101 TTAGCGACAC ATTCTCATTA GGTGTTGCAC TTGTCGCATT TATTTATGCT

151 GAAAAGAATG CCACAACTAC AAAAACATTT GGTTATAAAC GTTTCGAAGT

201 ACTCGCAGCG TTATTTAACG GTGTAACGCT TTTTGTAATA AGTATTTTGA

251 TTGTTTTTGA AGCGATTAAA CGTTTCTTTG TTCCTTCTGA AGTTCAATCA

301 AAAGAAATGT TAATCATTAG TATTATCGGT TTAATTGTCA ATATCGTTGT

351 TGCATTCTTT ATGTTTAAAG GCGGCGACAC TTCACACAAT TTAAATATGC

401 GTGGTGCTTT TCTACATGTT ATCGGAGACT TATTAGGTTC AGTTGGCGCC

451 ATTACTGCAG CTATTTTAAT TTGGGCATTT GGATGGACAA TCGCCGATCC

501 TATCGCAAGT ATTTTAGTTT CCGTTATTAT TTTAAAAAGT GCTTGGGGTA

551 TCACAAAATC TTCAATTAAC ATTTTAATGG AA

gnl I PID|e 90 2 (X98 51) czcD gene produce [Alcaligenes eutrop us] Length = 316

Plus Strand HSPs:

[SEQ ID NO: 1 score = 275 (126.5 bits), Expect = 9.7e-52, Sum P(2) = 9.7e-52 Identities = 50/130 (38%), Positives = 85/130 (65%), Frame = +1

Query: 4 ISFLIIGLYMFIEIIGGLLANΞLALLSDGIHMFSDTFSLGVALVAFIYAEKNATTTKTFG 183

1+ + G ++ E++GG++ SLAL+ΞD HM +DT +L +AL A A++ A +TFG Sbjct: 19 IALALTGTFLIAEWGGVMTKΞLALISDAAHMLTDTVALAIALAAIAIAKRPADKKRTFG 78

Query: 184 YKRFEVLAALFNGVTLFVISILIVFEAIKRFFVPSEVQSKEMLIISIIGLIVNIWAFFM 363

Y RFE+LAA FN + LF ++I I++EA R P +++S M +++++GLI+N++ + Sbjct: 79 YYRFEILAAAFNALLLFGVAIYILYEAYLRLKSPPQIESTGMFWAVXGLIINLISMRML 138

Query: 364 FKGGDTSHNL 393

G +S N+ Sbjct: 139 SSGQSSSLNV 148

[SEQ ID NO: 1 score = 154 (70.8 bits). Expect = 9.7e-52, Sum P(2) = 9.7e-52 Identities = 30/67 (44%), Positives = 44/67 (65%), Frame = +1

Query: 382 SHNLNMRGAFLHVIGDLLGSVGAITAAILIWAFG TIADPIASILVSVIILKSA GITKS 561

S +LN++GA+L V DLLGSVG I AI+I GW D ++L+ + +L W + KS Sbjct: 143 SSSLNVKGAYLEVWΞDLLGΞVGVIAGAIIIRFTGWAPVDΞAIAVLIGLWVLPRT ILLKS 202

Query: 562 SINILME 582

S+N+L+E Sbjct: 203 SLNVLLE 209 >sp|P13512|CZCD_ALCEU CATION EFFLUX SYSTEM PROTEIN CZCD. >pir||D33830 cation efflux system membrane protein czcD - Alcaligenes eutrophus >gi 1141929 (M26073) czcD gene product [Alcaligenes eutrophus) Length = 199

Plus Strand HSPs:

[SEQ ID NO: ] score = 275 (126.5 bits), Expect = 2.5e-49, Sum P(2) = 2.5e-49 Identities = 50/130 (38%), Positives = 85/130 (65%), Frame = +1

Query: 4 ISFLIIGLYMFIEIIGGLLANΞLALLSDGIHMFSDTFΞLGVALVAFIYAEKNATTTKTFG 183

1+ + G ++ E++GG++ ΞLAL+SD H +DT +L +AL A A++ A +TFG Sbjct: 19 IALALTGTFLIAEWGGVMTKSLALISDAAHMLTDTVALAIALAAIAIAKRPADKKRTFG 78

Query: 184 YKRFEVLAALFNGVTLFVIΞILIVFEAIKRFFVPSEVQΞKEMLIIΞIIGLIVNIWAFFM 363

Y RFE+LAA FN + LF ++I I++EA R P •P-÷+S M +++++GLI+N++ + Sbjct: 79 YYRFEILAAAFNALLLFGVAIYILYEAYLRLKSPPQIESTGMFWAVLGLIINLIΞMRML 138

Query: 364 FKGGDTSHNL 393

G +S N+ Sbjct: 139 SSGQSSSLNV 148

[SEQ ID NO: ] score = 122 (56.1 bits), Expect = 2.5e-49, Sum P(2) = 2.5e-49 Identities = 24/55 (43%), Positives = 34/55 (61%), Frame = +1

Query: 382 SHNLNMRGAFLHVIGDLLGSVGAITAAILI AFGWTIADPIASILVSVIILKSAW 546

S +LN++GA+L V DLLGSVG I AI+I GW D ++L+ + +L Sbjct: 143 SSΞLNVKGAYLEV ΞDLLGSVGVIAGAIIIRFTGWAWVDΞAIAVLIGLWVLPRTW 197

[SEQ ID NO: ] contig[0090] Length: 654 Check: 3187

.1 GGTAGTTTCT GTATAAAACC AACAGTATCT GAAATAATTA AATTAAATCC

51 ATCATTTATT TGAATTTGTC GTGTTTTAGG ATCTAACGTT GCAAATAATT

101 GATCTTTTTC ATACGTCTCT TCATTTGCTA AAACATTAAA CCATGATGAT

151 TTACCAGCAT TTGTATAACC AACTAAAGCT ACTTGAAACA CCTGATTTTG

201 ATTTCTTTTA TTTCGATATC TTTCGCGATG TTCTTCTACC GTCCGCAATT

251 GATGTTTAAT TTCATTCATA CGAGTTCGAA TATGTCTGCG ATCCATCTCT

301 AACTTCGTTT CACCAGGGCC TCTAGTTCCA ATACCGCCAC CTAAACGAGA

351 AAGACTTTTA CCATGGCCTT GCAATCTAGG TAATAAATAA TCAAGTTGTG

401 CTAGCTCTAC TTGCAATTTA CCTTCTTTAC TTCTTGCTCT TAATGCAAAT

451 ATTTCAAGAA TCAACTGAGT TCTATCAATA ATTTTTACAC CTAAAGCTTC

501 ATTTAGTGAT TTGGATTGTG CAGTCGTTAA TTCATCATTT GTGATGACTA

551 CATCAATATC TTTGAAACTC AATAAATGCT TGAATTTCTT CAATTTTACC 601 TTTACCAACA TAATATTTGC GATCTACACG ATCTCTGTTT TGAGTAATTT 651

>gi|l653117 (D90911) GTP-binding protein HflX [Synechocystis sp.J Length = 534

Minus Strand HSPs:

[SEQ ID NO: ) score = 491 (225.9 bits), Expect = 1.5e-69, Sum P(3) = 1.5e-69 Identities = 95/171 (55%), Positives = 131/171 (76%), Frame = -2

Query: 554 DWITNDELTTAQSKSLNEALGVKIIDRTQLILEIFALRARSKEGKLQVELAQLDYLLPR 375

++V+ + +L+ AQ ++L + GV++IDRT+LIL+IFA RA+S+ GKLQVELAQL+YLLP+ Sbjct: 240 NLWFDRDLSAAQVRNLEQRCGVRVIDRTELILDIFAQRAQSRAGKLQVELAQLEYLLPK 299

Query: 374 LQGHGKΞLSRLGGGIGTRGPGETKLEMDRRHIRTRMNEIKHQLRTVEEHRERYRNKRNQN 195

L G G+ +SRLGGGIGTRGPGETKLE +RR I++R+ +++ Q+ ++ HR R RN+R Q Sbjct: 300 LVGRGQGMSRLGGGIGTRGPGETKLETERRTIQSRIAKLQKQVNELQSHRSRLRNQRQQQ 359

Query: 194 QVFQVALVGYTNAGKSSWFNVLANEETYEKDQLFATLDPKTRQIQINDGFN 42

V VA+VGYTNAGKS+ N L + Y DQLFATLDP TR++ + D N Sbjct: 360 AVPTVAIVGYTNAGKΞTLLNALTQADIYAADQLFATLDPTTRRLSLLDPEN 410

[SEQ ID NO: ] score = 49 (22.5 bits), Expect = 1.5e-69, Sum P(3) = 1.5e-69 Identities = 9/25 (36%), Positives = 16/25 (64%), Frame = -1

Query: 642 QNRDRVDRKYYVGKGKIEEIQAFIE 568

QNR + + VG+GK+EE+ ++ Sbjct: 211 QNRSKPHPQTWGEGKVEELALAVQ 235

[SEQ ID NO: ] score = 47 (21.6 bits), Expect = 1.5e-69, Sum P(3) = 1.5e-69 Identities = 8/13 (61%), Positives = 12/13 (92%), Frame = -2

Query: 41 LIISDTVGFIQKL 3

++++DTVGFI KL Sbjct: 416 ILLTDTVGFIHKL 428

[SEQ ID NO: ] contig[0089] Length: 597 Check: 9759 ..

1 GAAACGACAT ACAACTTCAT CATCCATGAA ACGACCATTT TCATCTAATT

51 TAGAGTTTGC TTGTGCTACA ACATAGCTAT CTTCTTCGTC AGCTGTTAAA

101 TAGTCAATTT GATCAGTGAT AGCATGTGTA TCTAAATCAA CTTTACGATA

151 TGGTGTTTCA ATAAAGCCGA ATTCATTTAC ACGTGCATAA CTTGATAATG O 98/23738

201 AGTTAATCAA TCCAATGTTT GGTCCCTCAG GTGTTTCAAT TGGACACATA

251 CGGCCATAGT GAGAGTAGTG AACGTCACGT ACTTCCATTT GAGCACGTTC

301 ACGTGT AAA CCACCAGGTC CTAATGCTGA TAGACGACGT TTATGCGTTA

351 ACTCAGCTAA TGGGTTTGCT TGGTCCATGA ATTGTGATAA TTGAGAGCTA

401 CCAAAGAATT CTTTAATAGA TGCAATAACA GGTCGAATAT TAATTAATTG

451 TTGAGGTGTG ATAGACTCAG TATCTTGAAT TGACATTCTT TCACGTAACA

501 ACTCTTTCCA TTCTTGATAA ACCGATACGG AATTGGTTTT GGTAGTAATT

551 CACCTACAGA ACGTAACGAC GGTTACCTAA ATGGTCAATA TCATCTG

>sp|P47768|RPOB_STAAU DNA-DIRECTED RNA POLYMERASE BETA CHAIN (TRANSCRIPTASE BETA CHAIN) (RNA POLYMERASE BETA SUBUNIT) . >gi | 677851 (X64172) DNA-directed RNA polymerase beta chain [Staphylococcus aureus] >prf I |2107219B RNA polymerase: SUBUNIT=beta [Staphylococcus aureus) >prf I |2113202B RNA polymerase :SUBUNIT=beta [Staphylococcus aureus) Length = 1182

Minus Strand HSPs:

[SEQ ID NO: ] score = 855 (393.3 bits). Expect = l.Se-123, Sum P(2) = 1.5e-123 Identities = 165/169 (97%), Positives = 168/169 (99%) , Frame = -1

Query: 507 KELLRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLS 328

+ ++RERMSIQDTESITPQQLINIRPVIASIKEFFGΞΞQLSQFMDQANPLAELTHKRRLS Sbjct: 427 ERWRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLS 486

Query: 327 ALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPY 148

ALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINΞLSSYARVNEFGFIETPY Sbjct: 487 ALGPGGLTRERAQMEVRDVHYΞHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPY 546

Query: 147 RKVDLDTHAITDQIDYLTADEEDSYWAQANSKLDENGRFMDDEWCRF 1

RKVDLDTHAITDQIDYLTADEEDSYWAQANSKLDENGRFMDDEWCRF Sbjct: 547 RKVDLDTHAITDQIDYLTADEEDSYWAQANSKLDENGRFMDDEWCRF 595

[SEQ ID NO: ] score = 114 (52.4 bits) , Expect = 1.5e-123, Sum P(2) = 1.5e-123 Identities = 25/33 (75%) , Positives = 25/33 (75%) , Frame = -3

Query: 595 DDIDHLGNRRYVL*VNYYQNQFRIGLSRMERW 497

DDIDHLGNRR QNQFRIGLSRMERW

Sbjct: 398 DDIDHLGNRRLRSVGELLQNQFRIGLSRMERW 430

>sp|P37870|RPOB_BACSU DNA-DIRECTED RNA POLYMERASE BETA CHAIN (TRANSCRIPTASE

BETA CHAIN) (RNA POLYMERASE BETA SUBUNIT) . >gi|402363 (L24376) RNA polymerase beta-subunit [Bacillus subtilis] Length = 1193

Minus Strand HSPs:

[SEQ ID NO: ] score = 744 (342.2 bits). Expect = 4.2e-108, Sum P(2) = 4.2e-108 Identities = 141/169 (83%), Positives = 156/169 (92%), Frame = -1

Query: 507 KELLRERMSIQDTEΞITPQQLINIRPVIAΞIKEFFGΞSQLΞQFMDQANPLAELTHKRRLS 328

+ ++RERMSIQDT +ITPQQLINIRPVIASIKEFFGSSQLSQFMDQ NPLAELTHKRRLS Sbjct: 428 ERWRERMΞIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLS 487

Query: 327 ALGPGGLTRERAQMEVRDVHYΞHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPY 148

ALGPGGLTRERA MEVRDVHYΞHYGRMCPIETPEGPNIGLINSLSSYA+VN FGFIETPY Sbjct: 488 ALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLΞSYAKVNRFGFIETPY 547

Query: 147 RKVDLDTHAITDQIDYLTADEEDSYWAQANSKLDENGRFMDDEWCRF 1

R+VD +T +T +IDYLTADEED+YWAQAN++LD+ G F+DD +V RF Sbjct: 548 RRVDPETGKVTGRIDYLTADEEDNYWAQANARLDDEGAFIDDSIVARF 596

[SEQ ID NO: ] score = 114 (52.4 bits), Expect = 4.2e-108, Sum P(2) = 4.2e-108 Identities = 25/33 (75%), Positives = 25/33 (75%), Frame = -3

Query: 595 DDIDHLGNRRYVL*VNYYQNQFRIGLSRMERW 497

DDIDHLGNRR QNQFRIGLSRMERW Sbjct: 399 DDIDHLGNRRLRSVGELLQNQFRIGLSRMERW 431

[SEQ ID NO: ] contig[0088] Length: 599 Check: 1701

1 CCGTTTTGTA ATTAAAATCT TAATAAAACA TAACAAGAAC GCTTTAGATT

51 GTTTTGTAAC AGAAAGTAAT TCATACCAAA AAACACCAAG CAACCGAAAC

101 GTTACTTGGT GTCATTACAA ATGTAATATT ATTTTAAATT ATGTCACTAC

151 TTTAAATACT TTTTATTTCC AAACCTTCAT CGCCCCATGC GTGCATGCCG

201 CCTTCGACAT TTACGGCATC AATGCCATTT GCCTCTAAAT ATTCTACAAC

251 TTTAGCGCTT CGAACTCCAC CAGCACATAC AATATAATAT ATTTCATTTT

301 TATTAAATGA ATTTAAATTA TCCGGAATGG TATCCATTGG AATCAACTTT

351 GCATTAGGAA TATATCCCAT TGCTGTTTCT TCGTCAGTAC GAACATCAAC

401 AATTTGAACT GGTTTAGATT CAAAAAGTTT GTTTTTTAAT TCATCTGTAG

451 TAATTGACTT CATTTCAAAG TCCTCCTTAA AACATTATTT AGCTACAATA

501 TTGACTAATT TTTGAGGAAC AGCGATGACT TTCATGATGT CTTTACCTTC

551 AATACTCGCT TTAACATTGT CATTAGATAA GGCAATTTCT TGCATTTCT

>gi 11303705 (D84432) YrkF [Bacillus subtilis] Length = 185 Minus Strand HSPs.

[SEQ ID NO ] score = 111 (51 1 bits) Expect = 2 5e-06 P = 2 5e-06 Identities = 24/81 (29%) Positives = 38/81 (46%) Frame = -2

Query 454 ITTDELKNKLFESKPVQIVDVRTDEETAMGYIPNAKLIPMDTIPDNLNSFNKNEIYYIVC 275

1+ + K K+ + + I+DVR EE +IP IP+ + N N+N+ YI+C Sbjct 90 IΞLEAFKQKVDSDESLNILDVREIEEYEKAHIPGWHIPLGEVEKRANELNENDEIYIIC 149

Query 27 AGGVRSAKWEYLEANGIDAV 212

G RS ++ G V Sbjct 150 HSGRRSEMAARTMKKQGFKKV 170

>sp|P36430|ΞYL_BACSU LEUCYL-TRNA SYNTHETASE (LΞUCINE--TRNA LIGASE) (LEURΞ)

>pιr| |A41882 leucine—tRNA ligase (EC 6 1 1 4) - Bacillus subtilis gι 1143148 (M88581) transfer RNA-Leu synthetase [Bacillus subtilis) Length = 804

Minus Strand HSPs

[SEQ ID NO ] score = 100 (46 0 bits) Expect = 0 00016 P = 0 00016 Identities = 19/36 (52%), Positives = 29/36 (80%), Frame = -2

Query 598 EMQEIALSNDNVKASIEGKDIMKVIAVPQKLVNIVA 491

+++++A +++ VK +EGK I K+IAVP KLVNIVA Sbjct 768 QLEQLAQADEKVKEQLEGKTIRKIIAVPGKLVNIVA 803

>gι 11303893 (D84432) YqhL [Bacillus subtilis] Length = 126

Minus Strand HSPs-

[SEQ ID NO ] score = 95 (43 7 bits) Expect = 0 00035, P = 0 00035 Identities = 19/64 (29%), Positives = 31/64 (48%), Frame = -2

Query 415 KPVQIVDVRTDEETAMGYIPNAKLIPMDTIPDNLNSFNKNEIYYIVCAGGVRSAKWEYL 236

+ Q++DVR E G+I A+ IP+ + N ++ Y+ C VRS + + L Sbjct 41 RKAQLIDVREPNEFEGGHILGARNIPLSQLKQRKNEIRTDKPVYLYCQNSVRSGRAAQTL 100

Query 235 EANG 224 NG Sbjct: 101 RKNG 104

>gi|1653525 (D90914) molybdopterin biosynthesis MoeB protein [Synechocystis sp.) Length = 392

Minus Strand HSPs:

[SEQ ID NO: ] score = 78 (35.9 bits), Expect = 0.00087, Sum P(2) = 0.00087 Identities = 15/34 (44%), Positives = 21/34 (61%), Frame = -2

Query: 277 CAGGVRSAKWEYLEANGIDAVNVEGGMHAWGDE 176

C G RS K + L+ GI+ +NV+GG+ AW E Sbjct: 351 CKLGGRSTKALSLLKEAGIEGINVKGGITAWSRE 384

[SEQ ID NO: ] score = 48 (22.1 bits), Expect = 0.00087, Sum P(2) = 0.00087 Identities = 10/34 (29%), Positives = 18/34 (52%), Frame = -2

Query: 421 ESKPVQIVDVRTDEETAMGYIPNAKLIPMDTIPD 320

+ K ++DVR E + IP + L+P+ I + Sbjct: 296 QEKDFILLDVRNPNEYDIARIPGSVLVPLPDIEE 329

[SEQ ID NO: ] contig[0087] Length: 1685 Check: 4913 ..

1 ATAAGATAAC CATTAAGATA ATTGGAATAA CGTTGCTATT TTATAAAATT

51 AATTAAGTAT CTTTGACAGT CATCTTAGCC TCTTATTTAA GGAAAAAGCT

101 TTATGCTTAA AATAAGTCTT TTTTAGTGAA ATTAATGCAT CTCATATAAT

151 TATTTGCTAT TTATACGAAA GCAGAATCTC CAGTCAAAGC GCGTCCAATT

201 ACTAAGGCAT TAATTTCATG TGT CCTTCG TACGTGTAAA TCGCTTCTGC

251 ATCAGAGAAG AAACGTGCAA TATCATAATC GTCAGCTAGT ATGCCATTAC

301 CACCTGTAAT ACCGCGGCCC ATAGCTACTG TCTCACGCAA ACGTAAGGCA

351 TTCATCATCT TCGCCGTTGA AGTTGCAACC TCGTCATATT CACCATGTGC

401 TTGCATATTA GCTAATTGAG CACATGTTGC CATTGCTTGA GCTAAATTAC

451 CTTGCATCAT TGCTAGCTTT TCTTGTATTA ACTGATATTT ACTAATTGGT

501 TTGCCGAATT GCTTACGCTC AGTGACATAA TCTAATGTGG CACGTAAAGC

551 GCCAGCCATA CCACCTGTAG CCATATAAGC AACGCCTGCT CTCGTTGAAT

601 AAAGAATTTT GGCAATATCT TTAAAGCTTG TTATGTTTTG TAAGCGATCC

651 GCTTCATCTA CTTTGACATT AGTTAATTTA ATTAGTGCGT TAGGAACAAT

701 GCGAAGTGCG ATTTTATTAT CAATGACTTC AATATCGACG CCATCTTGTT

751 CTGGTCTGAC TACAAAGCAA TGGGGTTTGC CAGTTTTTTT ATTTACTGCG

801 AATACTGGAA TGACATCAGA TACATGTGCA CCACCAATCC ATTTCTTTTC

851 ACCATTGATA ACCCAAGTAT CGCCTTGGCG TTCAGCGACT GTTTCAAGAC

901 CTCCCGCAAC GTCCGAACCG TGTTCTGGTT CAGTTAAAGC AAAGCATGTA 98/23738

951 GGCAGTTCAT GTGACTGTAA TTTAGGTACA TATTTCGCAA TTTGTTCTTT

1001 GCTACCTCCG AAATAGGAAG TGTTATGCCC TAAACCTTGG TGAACACCGA

1051 GTAGGGTAGC TAAGGAAATA TCAAATCGCG CGAGTAGGTA AGACATGAAA

1101 AACTGAAATA GTTGACTAGG CATTTTGGCG TTTGGACGAT CCTTGTAAAG

1151 TAATGGATTG TTAAAATAAT TTAATTCTCC CAGATCTTTA AAATAGTCCT

1201 CGGGTACAGT AGCGTCTATC CAATGTTGAT TAATATTTTC ACGGTACTTA

1251 CTTTCTAGCA ATGAATCTAC TTGTTGTAAA AATTCGACTT CACCGTCTGT

1301 TAAACCTTTA GCAATACTAA GTACATCTTC AGGAAATAAT GTTTTTAAGA

1351 CCGTTTCTTT TTCAAATGTC ATATAAATTC CTCCTAAAAA TAATATGAAT

1401 ACTAATGTGA AATGCATTTA ATTCAAAAAC AACACGCTTT ATTTGTAAAC

1451 GCTTACACTA AATGTCAAAA ATTTTTATCA CCTTTAAAGT GTTTGTGAGA

1501 CTTTGTCATT CATCATTTGT CGAATCGCAA GTTTATCTGG TTTCTGCGTA

1551 CTGTTTAACG GCATATGTGT CACTGGTACA TACATTCTTG GGACTTTATA

1601 ACCTGCTAAA CGACTTCGCA TATGTTGATC TAAAATTTCA GCGTAATGAG

1651 TTCATCTTCG CGAAGTATAA TGGCTGCAGC AATTG

>gi 11657621 (U72505) G6p [Arabidopsis thaliana] Length = 436

Minus Strand HSPs:

[SEQ ID NO: ] score = 357 (164.2 bits) , Expect = 1.8e-66, Sum P(3) = 1.8e-66 Identities = 80/209 (38%) , Positives = 116/209 (55%) , Frame = -2

Query: 907 AGGLETVAERQGDTWVINGEKKWIGGAHVSDVIPVFAVNKKTGKPHCFWRPEQDGVDIE 728

A GL T A + W ING+K+WIG + +D++ +FA N T + + F+V+ + G+

Sbjct: 183 ASGLGTTATKVEGGWKINGQKR IGNSTFADLLIIFARNTTTNQINGFIVKKDAPGLKAT 242

Query: 727 VIDNKIALRIVPNALIKLTNVKVDEADRLQNITSFKDIAKILYΞTRAGVAYMATGGMAGA 548

I NKI LR+V N I L NV V + DRL + SF+D +K+L +R VA+ G G Sbjct: 243 KIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQPIGISMGI 302

Query: ^• 547 LRATLDYVTERKQFGKPISKYQLIQEKLAMMQGNLAQAMATCAQLANMQAHGEYDEVATS 368

Y+ ERKQFG P++ +QL Q+KL M GN+ +L + G+ S

Sbjct: 303 YDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQMTPGQAS 362

Query: 367 TAKMMNALRLRETVAMGRGITGGNGILAD 281

K + + RET ++GR + GGNGILAD Sbjct: 363 LGKA ISSKARETASLGRELLGGNGILAD 391

[SEQ ID NO: ] score = 128 (58.9 bits) , Expect = 1.8e-66, Sum P(3) = 1.8e-66 Identities = 29/71 (40%) , Positives = 40/71 (56%), Frame = -2

Query: 1084 LARFDISLATLLGVHQGLGHNTSYFGGSKEQIAKYVPKLQSHELPTCFALTEPEHGSDVA 905 +AR D S +T + VH LG T GS+ Q KY+P L C+ALTEP++GSD + Sbjct: 125 IARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNGSDAS 184

Query: 904 GGLETVAERQG 872

G T + +G Sbjct: 185 GLGTTATKVEG 195

[SEQ ID NO: ) score = 114 (52.4 bits). Expect = 1.8e-66, Sum P(3) = 1.8e-66 Identities = 22/45 (48%), Positives = 31/45 (68%), Frame = -2

Query: 301 GNGILADDYDIARFFSDAEAIYTYEGTHEINALVIGRALTGDSAF 167

G + D+ +A+ F D E IYTYEGT++IN LV GR +TG ++F Sbjct: 384 GGNGILADFLVAKAFCDLEPIYTYEGTYDINTLVTGREVTGIASF 428

[SEQ ID NO: ) score = 38 (17.5 bits). Expect = 4.8e-06, Sum P(2) = 4.8e-06 Identities = 6/20 (30%), Positives = 13/20 (65%), Frame = -2

Query: 1558 LNSTQKPDKLAIRQMMNDKV 1499

L +T+ P+K+ +R + N + Sbjct: 239 LKATKIPNKIGLRMVQNGDI 258

[ SEQ ID NO : ] contig [ 0086 ] Length : 641 Check : 1648 . .

1 GAATTTTCCC CTCGGACGAC TATAAATATC ATTATTTTGA GGCAGTAATG

51 AGTCATGATC GTTATCTATA TTTTGTGATT CTTGACGTCT TTTTTTCTTT

101 CTATGAATCA AGTCATCATT TGAATCATTA TCTTCGCCGA ATAATTTATC

151 AAACCAGCTC ATATTTTCAC TACCTTCCTT AATTATTCAA AAAATGCTTG

201 TCCAATTTCA TAGCTGTCAT TTAATACCAT AATACCTTTT TCTTCAGGTG

251 CATTAGGTAA ATTCAATTCT TTCATTGAAC AAATCATACC GCTTGAGGCA

301 ACACCACGTA ATTCAGCATC TTTAATTACC ATACCGCTAG GCATCACTGC

351 ACCTACTTTA GCAACAACAA CTTTCTGTCC AGCTTCAACG TTAGGCGCGC

401 CACATACAAT TTGTAATGTG TCATTTCCAA CGTTTACATT TAGTACACTT

451 AATTTATCTG CATCAGGATG TTTGTCTTTA GTTTCAACGT AGCCAACTAC

501 AAATTTCGGT GATAGATCAG CATTTAATTT ATAATCAAAA CCAGCTTCTG

551 AAATACGCTT TTGGAATACA TTTACAAGTT CATCAGTTAA TTTAATATGA

601 CCTTTTTCTT CAATTGT AT ATCTTTTGAA ATTTCAAAAA T

>sp | Pl7922 | SYFB_BACSU PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN

(PHENYLALANINE--TRNA LIGASE BETA CHAIN) (PHERΞ) . >pir | | YFBSB phenylalanine--tRNA ligase (EC 6.1.1.20) beta chain - Bacillus subtilis >gi | 40054 (X53057 ) phenylalanyl-tRNA synthetase beta subunit (AA l-80 ) [Bacillus subtilis] Length = 804 Minus Strand HSPs:

[SEQ ID NO: ) score = 170 (78.2 bits), Expect = 9.4e-19, Sum P(2) = 9.4e-19 Identities = 32/53 (60%), Positives = 41/53 (77%), Frame = -1

Query: 416 LQIVCGAPNVEAGQKWVAKVGAVMPSGMVIKDAELRGVASSGMICΞMKELNL 258

+QI+CGAPNV+ GQKV VA VGAV+P IK A +RG S+GMICS++EL + Sbjct: 76 VQIICGAPNVDKGQKVAVATVGAVLPGNFKIKKANVRGEEΞNGMICSLQELGI 128

[SEQ ID NO: ] score = 64 (29.4 bits). Expect = 9.4e-19, Sum P(2) = 9.4e-19 Identities = 11/25 (44%), Positives = 20/25 (80%), Frame = -1

Query: 500 WGYVETKDKHPDADKLSVLNVNVG 426

V+G+V +++HP+ADKL+ V++G Sbjct: 47 VIGHVLEREQHPNADKLNKCLVDIG 71

[SEQ ID NO: ] contig[0085] Length: 675 Check: 7091 ..

1 TTCGGCACGA GACTTATATT AGACGGCTTA GAAGACCCGC ATAACTTGGG

51 ATCAATTTTA AGAACAGCCG ATGCAACGGG AGTTGATGGT GTTATTATTC

101 CTAAACGTCG TTCAGTTACA CTAACGCAAA CAGTTGCAAA AGCCTCAACA

151 GGTGCAATTG AACATGTACC AGTTATTCGA GTGACAAATT TAGCTAAAAC

201 TATCGATGAA CTAAAAGATA ATGGCTTTTG GGTAGCTGGC ACTGAAGCTA

251 ATAATGCAAC AGATTATAGA AATCTAGAAG CGGACATGTC ATTGGCTATT

301 GTAATTGGTA GCGAAGGACA GGGTATGAGT CGCCTAGTAA GTGATAAATG

351 CGATTTTTAT ATTAAGATTC CAATGGTTGG ACATGTAAAC AGTTTGAATG

401 CTTCGGTTGC AGCAAGTTTA ATGATGTACG AAGTATTTCG AAAAAGACAT

451 GATGTTGGAG AAATATAATG AAAGAACGTT ACTTAATCAT TGATGGATAC

501 AATATGATAG GACAATCACC AACGCTAAGC GCCATTGCAA AAGAGAATTT

551 AGAAGAAGCT AGAATGCCAT TAATAGATGC AATTGCAAAT TATAATGCAG

601 TTATTCAGAT GAAATTATTT GTGTTTTTCG ATGCTTATGA CCAATCGGGT

651 GTTGAAAGAA AATACATGTT TTCAT

>sp|Q06753|YACO_BACSU HYPOTHETICAL 27.5 KD PROTEIN IN CYSS 3 'REGION. >gi| 467483 (D26185) unknown [Bacillus subtilis] Length = 249

Plus Strand HSPs:

[SEQ ID NO: ] score = 555 (255.3 bits), Expect = 5.9e-72, P = 5.9e-72 Identities = 104/150 (69%), Positives = 127/150 (84%), Frame = +1

Query: 13 LILDGLEDPHNLGSILRTADATGVDGVIIPKRRSVTLTQTVAKASTGAIEHVPVIRVTNL 192 LILD LEDPHNLGSI+RTADA G G++IPKRR+V LT TVAKASTGAIEH+PV RVTNL Sbjct: 100 LILDELEDPHNLGSIMRTADAVGAHGIVIPKRRAVGLTTTVAKASTGAIEHIPVARVTNL 159

Query: 193 AKTIDELKDNGFWVAGTEANNATDYRNLEADMSLAIVIGΞEGQGMSRLVSDKCDFYIKIP 372

A+T++E+K+ G WV GT+A+ D+RN++ +M LA+VIGSEG+GM RLV +KCDF IK+P Sbjct: 160 ARTLEEMKERGIWWGTDASAREDFRNMDGNMPLALVIGSEGKGMGRLVKEKCDFLIKLP 219

Query: 373 MVGHVNSLNAΞVAASLMMYEVFRKRHDVGE 462

M G V SLNASVAA L+MYEV+RKR+ VGE Sbjct: 220 MAGKVTSLNASVAAGLLMYEVYRKRNPVGE 249

[ SEQ ID NO : ] contig [ 0084 ] Length : 496 Check : 7190 . .

1 GGAGAGTGAG GGATTCGAAC CCTCGAGACG CTTGTGGCGC CTACACACTT

51 TCCAGGCGTG CTCCTTCGGC CAACTCGGAC AACTCTCCTC AATAATAAAT

101 ATGTAATAAA AAAACAGAAG CGATATTTCA CTTCTGTTTG TATGACTCCT

151 ACGGGACTCG AACCCGTGTT ACCGCCGTGA AAGGGCGGTG TCTTAACCGC

201 TTGACCAAGG AGCCATGGCT CCACAGGTAG GACTCGAACC TACGACCGAT

251 CGGTTAACAG CCGATAGCTC TACCACTGAG CTACTGTGGA ATAATAATAG

301 AAAATAATGG AGCGGGTGAT GGGAATCGAA CCCACAACAT CAGCTTGGAA

351 GGCTGAGGTT TTGCCATTAA ACTACACCCG CTAATGTAAA CGATTATGGG

401 GCGGCTGAAA GGGATCAACC CTCGAATGTC GGAACCACAA TCCGATGTGT

451 TAACCACTTC ACCACAACCG CCATGAATTA AGAATGGTTC AGGACA

>pir | | A05066 hypothetical protein 75 - common tobacco chloroplast >gi | 11786 (X02441 ) unidenti fied reading frame ORF 75 [Nicotiana tabacum] >gi | 11880 (Z00044 ) ORF75 [Nicotiana tabacum) >gi | 473681 (M23767 ) ORF 75 ; putative [Nicotiana tabacum) >gi | 1223679 (Z00044) ORF75 [Nicotiana tabacum) >prf | | 1211235CK ORF 75 [Nicotiana tabacum] Length = 75

Minus Strand HSPs :

[SEQ ID NO : ] score = 94 (43 . 2 bits ) . Expect = 1 . 2e-05 , P = 1 .2e-05 Identities = 22/27 (81%) , Positives = 23/27 (85%) , Frame = -2

Query: 300 LLLFHSSSWELSAVNRSWGSSPTCG 220

LLLF SSSWE SAVNR WGS+PT G Sbjct : 38 LLLFLSSSWERSAVNRLWGΞNPTWG 64

>gi 1 1147586 (X93084 ) molybdenum formylmethanofuran dehydrogenase subunit fmdE [Methanosarcina barkeri ] >prf | | 2206350D formylmethanofuran dehydrogenase [Methanosarcina barkeri ) Length = 204

Minus Strand HSPs:

[SEQ ID NO: ] score = 56 (25.8 bits). Expect = 3.5, Sum P(2) = 0.97 Identities = 12/34 (35%), Positives = 17/34 (50%), Frame = -3

Query: 221 EPWLLGQAVKTPPFHGGNTGSSPVGVIQTEVKYR 120

+P LL Q K PFHG T + +G+ + R Sbjct: 21 DPELLSQIKKWPFHGFLTΞGALIGIQMLNIARR 54

[SEQ ID NO: ] score = 39 (17.9 bits), Expect = 3.5, Sum P(2) = 0.97 Identities = 7/17 (41%), Positives = 9/17 (52%), Frame = -2

Query: 102 IFIIEESCPSWPKEHAW 52

I + E +PK HAW Sbjct: 119 IILDPEKTKDYPKLHAW 135

[SEQ ID NO: ] contig[0083] Length: 976 Check: 1235 ..

1 TGCGCCATTG TATGCGTTAA GTGCAATAAG TTATGAAAAA GAATTAATGG

51 GGTGAATATT TATGTCAACA GTTGCGTTTC ACACATTAGG TTGTAAAGTA

101 AACCATTATG AAACTGAAGC AATCTGGCAA TTATTTAAAG AAGCAAACTA

151 TGAGCGCGTT GACTTTGAAG CGAATGCTGA TGTATTTGTT ATTAATACTT

201 GTACAGTAAC GAATACAGGT GATAAAAAAA GTCGTCAAAT AATTAGACGT

251 GCAATAAGAC AAAATCCTGA TGCTGTAATC TGTGTAACAG GTTGTTATGC

301 GCAAACTTCA TCAGCTGAAA TTATGGAAAT TCCTGGTGTC GATGTAGTAG

351 TTGGTACACA AGATAGACAT AAACTATTAG GTTACATTGA TGAATTCCGT

401 AAAGAACGCC AACCAATTAA TGGTGTTGGA AATATCATGA AAAATCGTAA

451 ATATGAAGAA TTAGATGTTC CATATTTTAC AGATAGAACA CGTGCGTCAT

501 TAAAAATTCA AGAAGGTTGT AACAACTTCT GCACATTCTG TATTATTCCA

551 TGGGCTCGTG GCTTAATGCG TTCAAGAGAT CCGGAAAAAG TAGTTGAACA

601 AGCGACGCAA CTAGTGAATT CAGGATATAA GGAAATTGTT TTGACGGGAA

651 TTCATACAGG TGGATATGGT CAAGATTTAA AAGATTATAA CTTGGCCCAA

701 TTATTACGTG ATCTTGAAAC GATTAATGGA TTAGAACGAA TTCGAATTTC

751 TTCAATTGAA GCAAGTCAAC TTACAGATGA AGTAATTGAC GTTTTAGAAC

801 GTTCAACAAA AGTTGTGCGT CATTTGCATA TTCCATTACA ATCTGGTTCA

851 GATACAGTAT TAAAACGTAT GAGACGTAAG TATACAATGG ATAGATTTTC

901 AGAACGATTA ACAAAATTGC ATAAAGCTTT ACCAGACTTG GCAGTTACGA

951 GTGATGTAAT TGTTGGTTTC

>gi 11303812 (D84432) YqeV [Bacillus subtilis] Length = 451 Plus Strand HSPs:

[SEQ ID NO: J score = 1014 (466.4 bits), Expect = 2.1e-181, Sum P(2) = 2.1e-181 Identities = 186/220 (84%), Positives = 205/220 (93%), Frame = +2

Query: 62 MΞTVAFHTLGCKVNHYETEAIWQLFKEANYERVDFEANADVFVINTCTVTNTGDKKSRQI 241

M+TVAFHTLGCKVNHYETEAIWQLFKEA YER DFE ADV+VINTCTVTNTGDKKSRQ+ Sbjct: 1 MATVAFHTLGCKVNHYETEAIWQLFKEAGYERRDFEQTADVYVINTCTVTNTGDKKSRQV 60

Query: 242 IRRAIRQNPDAVICVTGCYAQTSSAEIMEIPGVDVWGTQDRHKLLGYIDEFRKERQPIN 421

IRRAIRQNPD VICVTGCYAQTS AEIM IPGVD+WGTQDR K+LGYID++R+ERQPIN Sbjct: 61 IRRAIRQNPDGVICVTGCYAQTΞPAEIMAIPGVDIWGTQDREKMLGYIDQYREERQPIN 120

Query: 422 GVGNIMKNRKYEELDVPYFTDRTRAΞLKIQEGCNNFCTFCIIPWARGLMRSRDPEKWEQ 601

GV NIMK R YEΞLDVP FTDRTRASLKIQEGCNNFCTFCIIPWARGL+RSRDPE+V++Q Sbjct: 121 GVΞNIMKARVYΞELDVPAFTDRTRAΞLKIQEGCNNFCTFCIIPWARGLLRSRDPEEVIKQ 180

Query: 602 ATQLVNSGYKEIVLTGIHTGGYGQDLKDYNLAQLLRDLET 721

A QLV++GYKEIVLTGIHTGGYG+D+KDYN A+LL +L+T Sbjct: 181 AQQLVDAGYKEIVLTGIHTGGYGEDMKDYNFAKLLSELDT 220

[SEQ ID NO: ] score = 338 (155.5 bits), Expect = 2.1e-181, Sum P(2) = 2.1e-181 Identities = 66/85 (77%), Positives = 78/85 (91%), Frame = +2

Query: 722 INGLERIRIΞΞIEASQLTDEVIDVLERΞTKWRHLHIPLQSGSDTVLKRMRRKYTMDRFS 901

+ G++RIRIΞSIEASQ+TDEVI+VL+RS K+V HLHIP+QSGS+TVLKRMRRKYTM+ F+ Sbjct: 222 VEGVKRIRIΞSIEASQITDEVIEVLDRΞDKIVNHLHIPIQSGSNTVLKRMRRKYTMEFFA 281

Query: 902 ERLTKLHKALPDLAVTΞDVIVGFPG 976

+RL KL KALP LAVTSDVIVGFPG Sbjct: 282 DRLNKLKKALPGLAVTSDVIVGFPG 306

[SEQ ID NO: ] contig[0082] Length: 692 Check: 333

1 GCAAGATTAC CTGCCTCTTT TTTAGTTATT AAATATGCGT GTTAATTCTT

51 GGTAATAGTG TTACTGAGAC GCATTACGAA GAAATTTATC TTGATTTTCC

101 TTTTTTAAAA AGAAGTGAAG ATATCCTATA AAGACTCTAA GTACTATTAC

151 AGTGGCTAAT AACACTTCGA TAAACAAAAG ACTTTCCAAA TATCTGGAAA

201 CATAAGTACA GGCAAACTGT TCTTTAAAGC AGTTGCTGAG ATTACTAAAG

251 GGAATGTGAA AGCTGAAAAT ACGGGCGAAA AAGGTTCTTT TAGTAATTTA

301 GGCAATTGTA TAATGATATA AAAATAAAAT ATTTGAGCTA ATATTAAAAA

351 TATAATTACG ATAAAAGCAT TCGCCTTAGG AAAGGCTATA ACATATGCTG

401 CAGCGACTAA AGAAAATGGT GCACAAATTG TCGATGTGTT CGGTTTGATT

451 GACGTCTGCA ATGGAAATGC TTTTAATCGC TTGAAAACAA TAGGTAAGAC

501 AATACAAGTA GCTACAAAGC CATATATTAC TGTTAATTGA CCTATGAAAA 551 AACATCCGCT AACGGGTGCC GTCAATCCTG CGATAGCAAT ACCAATAAAA 601 AGTACAGTCC CACGAAAGGA TAAACATTTT CCAAGTGAAA AATCTTTTAA 651 ATATTTTATG AAAAAAATAA TCATATGCCT CATAATT

>gi 11216394 (U40265) ATPase subunit 6 [Trypanoso a cruzi] Length = 174

Minus Strand HSPs:

[SEQ ID NO: ] score = 41 (18.9 bits). Expect = 2.3, Sum P(3) = 0.90 Identities = 8/19 (42%), Positives = 14/19 (73%), Frame = -3

Query: 162 LLATVIVLRVFIGYLHFFL 106

LL++ +L +F +L_^FFL Sbjct: 148 LLSSHFLLLMFFDFLYFFL 166

[SEQ ID NO: ] score = 41 (18.9 bits), Expect = 2.3, Sum P(3) = 0.90 Identities = 10/41 (24%), Positives = 18/41 (43%), Frame = -3

Query: 510 YLYCLTYCFQAIKSISIADVNQTEHIDNLCTIFFSRCΞICY 388

+LY +++ F + N DN +FF R +C+ Sbjct: 87 FLYYMSFLFLFCFLLDFFLFNNLLVGDNFMDVFFIRFLLCF 127

[SEQ ID NO: ] score = 38 (17.5 bits), Expect = 2.3, Sum P(3) = 0.90 Identities = 8/19 (42%), Positives = 13/19 (68%), Frame = -2

Query: 643 IFHLENVYPFVGLYFLLVL 587

+F L ++Y F+GL L+L Sbjct: 40 LFCLFDLYLFIGLCLFLLL 58

[SEQ ID NO: ] contig[0081] Length: 961 Check: 1121 ..

•1 CCCGGCACAG GTGCTTGCAA CTATTGTAGG TGGTTGGGGA TCTACACTTG

51 TAAATATTGG TTTAATTATT TCGGTACTAG GTGCATGGTT AGGATGGACA

101 TTGCTTGCTG GTGAATTACC TTTCATTGTT GCAAAAGATG GATTATTTCC

151 AAAGTGGTTT GCTAAAGAAA ATAAAAATGG AGCACCTGTA AATGCACTGC

201 TTATTACCAA TATATTAGTA CAATTATTTT TAATAAGTAT GCTATTTACA

251 CAGAGTGCGT ATCAATTTGC ATTTTCACTA GCATCAAGTG CTATTTTATA

301 CCCTTACATG TTCAGTGCAT TTTACCAAGT TAAATACACT TTAGAGCATC

351 GACAGCAAGC AACTACTAAA CAATGGACGA TTGGCATCAT AGCCTCAATT

401 TATGCTATAT GGCTTATATA TGCAGCAGGT ATCAATTACT TATTATTGAC

451 GATGTTACTT TATATTCCAG CTCTTCTTGT TTATTCAATC GTTCAAAAGA

501 ATAATCAGAC ACGTTTGATT AAATCAGACT ATATTCTTTT TATGATTATT

551 ATCGTACTTG CAGTTATCGG ATTAATTAAG TTATTGATGG GAACGATAAA 601 TGTTTTTTAA AAGGAGCGAC AAAAATATGA AAGAGAAAAT TGTCATTGCA

651 TTAGGCGGTA ATGCGATACA GACAAAAGAA GCAACAGCTG AAGCACAACA

701 AACAGCTATT AGACGTGCGA TGCAAAACCT TAAACCTTTA TTTGATTCAC

751 CAGCGCGTAT TGTCATTTCA CATGGTAATG GCCCACAAAT TGGAAGTTTA

801 TTAATCCAAC AAGCTAAATC GAACAGTGAC ACAACGCCGG CAATGCCATT

851 GGATACTTGT GGTGCAATGT CACAGGGTAT GATAGGCTAT TGGTTGGAAA

901 CTGAAATCAA TCGCATTTTA ACTGAAATGA A AGTGATAG AACTGTAGGC

951 ACAATCGTTA C

>gnl|PID|e242289 (X97768) arginine ornithine antiporter [Clostridium perf ringens] Length = 476

Plus Strand HSPs:

[SEQ ID NO: ] score = 321 (147.7 bits) , Expect = 9.8e-56, Sum P(3) = 9.8e-56 Identities = 63/113 (55%) , Positives = 79/113 (69%) , Frame = +2

Query: 5 AQVLATIVGGWGSTLVNIGLIIΞVLGAWLGWTLLAGELPFIVAKDGLFPKWFAKENKNGA 184

A VL VG WG+ L+N+GLIIΞ+ G+ LGW LLA E+P++ AKDG+ PK FAK NK G Sbjct: 269 AYVLEFAVGKWGAVLINLGLIISLFGSLLGWALLAAEIPYVAAKDGVLPKVFAKLNKKGT 328

Query: 185 PVNALLITNILVQLFLISMLFTQSAYQFAFΞLASΞAILYPYMFSAFYQVKYTL 343

P +L+ITN+LVQ FLI L S YQ +S+AS+AIL PY+ SA Y K L Sbjct: 329 PSGΞLIITNLLVQAFLILTLWSSTYQALYSVASTAILVPYLLSAMYGFKLAL 381

[SEQ ID NO: ] score = 108 (49.7 bits) , Expect = 9.8e-56, Sum P(3) = 9.8e-56 Identities = 22/56 (39%) , Positives = 32/56 (57%) , Frame = +2

Query: 338 TLEHRQQATTKQWTIGIIAΞIYAIWLIYAAGINYLLLTMLLYIPALLVYSIVQKNN 505

T + T+ G IA++YAIWL YAA + YLLL +LY ++ + I +K N

Sbjct: 385 TYDKNPTGRTRDKIFGGIATVYAIWLCYAAELKYLLLCFILYAVGIIFFYIGKKQN 440

[SEQ ID NO: ] score = 58 (26.7 bits) , Expect = 9.8e-56, Sum P(3) = 9.8e-56 Identities = 10/29 (34%) , Positives = 20/29 (68%), Frame = +2

Query: 518 IKSDYILFMIIIVLAVIGLIKLLMGTINV 604

+ + IL +I++V+A+I ++ L GTI + Sbjct: 448 VGKEKILAIIVLVIAIIAIVMLFNGTITI 476

[SEQ ID NO: ] contig[0080] Length: 886 Check: 2263

1 TAGCAAAGAA GAATGGCTAA GTATGTCTCT TGCAGAAAGA CAAAAAGCTG 51 AAAAAGCATT TCGACACGAA GTTAAAAATA TGGACGATGT AAGAATGCCC 101 TTCTCAAGTG TCCATGACGC CCAAGTAAAA TTATATAATG TTGTATATTC

151 TTATAACGGC ATTAAACGTA ATTTTAAACA AGTTGAAAAT GAAGGATTCT

201 AATATCATTT CGTTTATATA TAGCAGACAT GATAGAATTT TATATGTAAA

251 TCTTGTAGGT AATCGTTTTA AAAATAATAT AAGTATGACT AAAGCCACAT

301 CCAATATAGG ACGTGGCTTT TAGTATCGTT CCAGATTTGT GGGGAGTTAG

351 GGTTTACTTA ATTAAAGGGG TCTGCCCTCA ATTGCTCACC AACGAGGGCA

401 AGTTACATCA ATCACACTTC AATTGCCGCC GACTAGGGGT AGTAATCATT

451 GGCAATAAGA ACTAGTTAGT GACTAACGAT TTACGTTCCA TAGCAAAGTG

501 ATACAAACGC TCAGCATCAA TGTAAGGCAT AGAATCAATA GTTAGGTAAC

551 CATCTTTGAT GTCACCAATT AATCCTTGAT TTACACCAGT GTTCACGTAA

601 ATATCATAGC TACTTACGTC TGAGAAAATA AGCGCTTCAA TCTCTTTTCT

651 CATAATCATC ACTCCAATGT TTATATATTA TTTATATAAA CTCTCTCGTC

701 TCTCTCTATT TATTAACTTC TTACAAGTCT AATATTACAT GAATTTCCAA

751 ATAAATAAAG AGGTTTGTGA TGTATTTCAC AAATTTATCA CTATTTTGGA

801 AAATTAAGAA ATAGTTAATT ATATAAAAGT TTAATAAGTC AGAAAATATG

851 A AAAATGTA GATGTTCTTT AGACATTAAA AGCTTC

gnl|PID|e249013 (Z74042) T11F9.12 [Caenorhabdi is elegans] Length = 409

Minus Strand HSPs:

[SEQ ID NO: ] score = 71 (32.7 bits). Expect = 3.2, P = 0.96 Identities = 15/44 (34%), Positives = 24/44 (54%), Frame = -3

Query: 656 IMRKEIEALIFSDVSSYDIYVNTGVNQGLIGDIKDGYLTIDSMP 525

++ E +fF+D SSYD V T GL+ K +T+D +P Sbjct: 169 LLTLENNFWFTDESSYDFWKTRTKLGLMDKTKVHKITLDDLP 212

[SEQ ID NO: ] contig[0079] Length: 708 Check: 3242 ..

•1 TGCATCGATT ACTAATTTTA AAGCGAGTAA GACATTTCCA TTGCAACAAT

51 TATCACAAGA TGATGTATTC GCACAAATTA AAAATGAAAT GTTAAGTGAG

101 AATTTATTTT CGGCTGTTAA AATTTATGGC ACATTTAAAC ATATGCATGT

151 ACGAATGATG CCTGCTCAGC AACCGCCATA TACACGTTTG ATTGATTCAG

201 CACGCAGACA ACCTGAGGAA AAAAGACAAG ATATTCGTGG TGCCATTGTT

251 GGATTTTTTA CACCAGAATT ATTTCATGGC GTAGGGTCTG CTGGTTTTCA

301 TATACATTTT GCGGATGATG AAAGAGCTTA TGGTGGACAT GTTCTTGACT

351 TTGAAGTGGA TGACGTTGTC GTTGAGATAC AAAACTTTGG AAACATTCCA

401 ACAACATTTC CCGGTAAATA ACGAGACGTT TGTTAAAGCG AAAATAGACT

451 ATAAAGATGT GGCAGAAGAA ATTAGAGAAG CTGAATAGTC TAA ATAATT

501 AAAAGACCTT AGCGATATTA GGACAGGTGG TTCTAAATGC ATCGTTAAGG

551 TCTTTTTATA TTATATATGT GCTTACATAT TTTGTTGAAA AGCGCCGTAA 601 AAAGCTATAA ATAGTATCCA GATATGGGGT GTCCAGATTG TGTTCACGTT 651 GCCCTTCAAT AAATAAAGCC TTGGAAATGC TTCGACTTCC AGAAGGTTGC 701 CTGAATGC

>gnl |PID|el24050 (X82620) alpha-acetolactate decarboxylase [Lactococcus lactis] Length = 236

Plus Strand HSPs:

[SEQ ID NO: ] score = 202 (92.9 bits). Expect = 5.1e-33, Sum P(3) = 5.1e-33 Identities = 34/77 (44%), Positives = 53/77 (68%), Frame = +2

Query: 182 TRLIDSARRQPEEKRQDIRGAIVGFFTPELFHGVGSAGFHIHFADDERAYGGHVLDFEVD 361

T+ ++ ++ QPE --^p-I+G IVG +TPE+FHGV AG+H+HF ++ +GGHVLDF +D Sbjct: 136 TKFVEVSQNQPEYTEENIKGTIVGIWTPEMFHGVSVAGYHLHFIΞEDFTFGGHVLDFIID 195

Query: 362 DVWEIQNFGNIPTTFP 412

+ VEI + +FP Sbjct: 196 NGTVEIGAIDQLNQSFP 212

[SEQ ID NO: ] score = 75 (34.5 bits). Expect = 5.1e-33, Sum P(3) = 5.1e-33 Identities = 15/38 (39%), Positives = 25/38 (65%), Frame = +2

Query: 50 LSQDDVFAQIKNEMLSENLFSAVKIYGTFKHMHVRMMP 163

+S ++ +I++ +NLF ++KI G F MHVRM+P Sbjct: 93 VSDKELEDRIEΞYFDGQNLFRΞIKITGKFPKMHVRMIP 130

[SEQ ID NO: ] score = 49 (22.5 bits), Expect = 5.1e-33, Sum P(3) = 5.1e-33 Identities = 10/33 (30%), Positives = 19/33 (57%), Frame = +3

Query: 387 LETFQQHFPVNNETFVKAKIDYKDVAEEIREAE 485

++ Q FPV + F+ A +D + + ++I AE Sbjct: .204 IDQLNQSFPVQDRKFLFADLDIEALKKDIDVAE 236

[SEQ ID NO: ] contig [0078 ] Length: 605 Check: 8053 ..

1 CCATGGATTT GTGGTATACA ACGCAACGTA TATGCATCTT GTACACGTAT

51 TTCTGCTTGT CGCGTCGTTA ATGTTGATCC TTCTAACCAA TCACGCATAC

101 GCGCTGCCAC ATTAATCTGT TCTTGAAAAT TACGAACAGA GTGCACATCA

151 TGTCGATATG CATCTATAAT GCCATTAAGA GACTGATGCG TTAATGCAGC

201 AATCCATTCA GATTGGTAAC CTAAATCTTC TGCTTCTATA TAACTAATGA

251 CACCTTGAGC TGTCATAGCT TGCGTACCAT TAATCAATGC TAAACCCTCT

301 TTAGCCTGAA GGTTCAAAGG TTGTCTATTT AATTCTCTTA AT CATCGTC 351 ACTATCCTTT TCTTCCCCTC TGTACAATAC TTCCCCTTCA CCAATTAATG

401 CTAATGCTAA ATGTGATAAT GGCGCTAAAT CTCCTGATGC ACCGAGAGAG

451 CCTTGTTGTG GGATTATCGG TATAATACGT TCATTTATAA AAAATTGTAA

501 TTGTCTCACT AATTCTAAAG TGGCACCTGA AATGACCTTT TAATAATGTA

551 TTCAATCGTA AAATCATCAT GACTAATGCT ACTTCTTTTG AAAATGGCTC

601 ACTAA

>sp|P10944|HUTH_BACΞU HIΞTIDINE AMMONIA-LYAΞE (HIΞTIDASE) . >pir||UFBSHS histidine ammonia-lyase (EC 4.3.1.3) - Bacillus subtilis >gi| 143076 (M20659) histidase [Bacillus subtilis] >gi| 603770 (D31856) histidase [Bacillus subtilis) Length = 508

Minus Strand HSPs:

[SEQ ID NO: ] score = 564 (259.4 bits). Expect = 4.8e-77, Sum P(2) = 4.8e-77 Identities = 112/179 (62%), Positives = 138/179 (77%), Frame = -1

Query: 539 KVISGATLELVRQLQFFINERIIPIIPQQGΞLGASGDLAPLΞHLALALIGEGEVLYRGEE 360

K SG EL+ QL F+N+R+ P+IPQQGSLGASGDLAPLSHLALALIG+GEV + GE Sbjct: 108 KGFSGVRAELIEQLLAFLNKRVHPVIPQQGSLGASGDLAPLSHLALALIGQGEVFFEGER 167

Query: 359 KDΞDDVLRELNRQPLNLQAKEGLALINGTQAMTAQGVISYIEAEDLGYQSEWIAALTHQS 180

+ L++ QP+ L i-KEGLALINGTQAMTA GV++YIEAE L YQ+E IA+LT + Sbjct: 168 MPAMTGLKKAGIQPVTLTSKEGLALINGTQAMTAMGWAYIEAEKLAYQTERIASLTIEG 227

Query: 179 LNGIIDAYRHDVHΞVRNFQEQINVAARMRDWLEGSTLTTRQAEIRVQDAYTLRCIPQIH 3

L GIIDA+ D+H R +QEQI+VA R+R +L S LTT Q E+RVQDAY+LRCIPQ+H Sbjct: 228 LQGIIDAFDEDIHLARGYQEQIDVAERIRFYLSDΞGLTTSQGΞLRVQDAYSLRCIPQVH 286

[SEQ ID NO: ] score = 58 (26.7 bits), Expect = 4.8e-77, Sum P(2) = 4.8e-77 Identities = 13/37 (35%), Positives = 20/37 (54%), Frame = -3

Query: 600 EPFSKEVALVMMILRLNTLLKGHFRCHFRISETITIF 490

+PF + V+ M++LR N LLKG + E + F Sbjct: 88 DPFPECVSRAMLLLRANALLKGFSGVRAELIEQLLAF 124

[SEQ ID NO: ] contig[0077] Length: 549 Check: 6153 ..

1 GCGACAAAAA ACGAGGAAAT ATTACGTAAA CCGGATTGGT TGAAAATAAA

51 ATTAAATACC AACGAAAACT ATACAGGACT TAAGAAGATG ATGAGGGAAA

101 AAAATCTTAA TACTGTATGT GAAGAAGCTA AATGTCCTAA TATACATGAA

151 TGTTGGGGTG CACGTCGTAC AGCGACATTT ATGATTTTAG GTGCCGTATG 201 TACAAGAGCT TGTCGTTTTT GTGCGGTTAA GACAGGTTTA CCTAATGAAC

251 TTGATTTAAA TGAGCCTGAA CGTGTAGCTG AATCAGTTGA ATTAATGAAT

301 TTGAAACACG TTGTTATCAC TGCTGTTGCG CGTGATGATT TAAGAGATGC

351 TGGTTCAAAT GTTTATGCTG AGACAGTACG TAAAGTTAGA GAAAGAAATC

401 CATTTACAAC GATTGAAATT TTACCATCAG ATATGGGCGG GGACTATGAT

451 GCGTTAGAAA CATTAATGGC GTCAAGACCT GACATTTTAA ACCATAATAT

501 TGAAACTGTT CGTCGCTTAA CACCGAGAGT TCGTGCGCGT GCGACTTAC

>sp|P44463 |LIPA_HAEIN LIPOIC ACID SYNTHETASE (LIP-SYN) . >pι | | G64043 lipoate biosynthesis protein A (lipA) homolog - Haemophilus influenzae (strain Rd KW20) >gi| 1572971 (U32688) lipoate biosynthesis protein A (lipA) [Haemophilus influenzae] Length = 320

Plus Strand HSPs:

[SEQ ID NO: ] score = 241 (110.6 bits) , Expect = 1.6e-61, Sum P(4) = 1.6e-61 Identities = 50/91 (54%) , Positives = 63/91 (69%) , Frame = +1

Query: 169 TATFMILGAVCTRACRFCAVKTGLPNELDLNEPERVAEΞVELMNLKHWITAVARDDLRD 348

TATFMILGA+CTR C FC V G P D EP+++AE+ + + M LK+WIT+V RDDL D Sbjct: 83 TATFMILGAICTRRCPFCDVAHGKPLPPDPEEPQKLAETIQDMKLKYWITSVDRDDLPD 142

Query: 349 AGSNVYAETVRKVRERNPFTTIEILPSDMGG 441

G+ -n-E V+ VRE NP IEIL D G Sbjct: 143 RGAGHFSECVKAVRELNPNIKIEILVPDFRG 173

[SEQ ID NO: ] score = 93 (42.7 bits) , Expect = 1.6e-61, Sum P(4) = 1.6e-61 Identities = 15/26 (57%) , Positives = 20/26 (76%) , Frame = +1

Query: 79 LKKMMREKNLNTVCEEAKCPNIHECW 156

+K MR L++VCEEA CPN+HEC+ Sbjct: ^• 54 IKNGMRRHGLHSVCΞEAΞCPNLHECF 79

[SEQ ID NO: ] score = 83 (38.1 bits) . Expect = 1.6e-61, Sum P(4) = 1.6e-61 Identities = 18/44 (40%), Positives = 24/44 (54%), Frame = +1

Query: 418 ILPSDMGGDYDALETLMASRPDILNHNIETVRRLTPRVRARATY 549

++P G ALE L + PD+ NHN+E V RL +R A Y

Sbjct: 167 LVPDFRGRITQALEKLKDNPPDVFNHNLENVPRLYKEIRPGADY 210

[SEQ ID NO: ] score = 63 (28.9 bits), Expect = 1.6e-61, Sum P(4) = 1.6e-61 Identities = 9/15 (60%), Positives = 15/15 (100%) , Frame = +1 Query: 10 NEEILRKPDWLKIKL 54

N+++L+KP+W+KIKL Sbjct: 30 NQDLLKKPEWMKIKL 44

[SEQ ID NO: ] contig[0076] Length: 765 Check: 4346 ..

1 CGGAATTTTT TTCTTTTTCA TAGATACTTC ACTCCAACCT ATTATTCAGA

51 TTCTTTCTCT ACATTTGTTT CAACTGAAAC ATCATTTACC TCTTCGGTTG

101 ATTCTGTTGT GTCAGCATCT TCTAAAGCAA TATCTTCTTC AGTTACTTTT

151 TCAGCTTCAA CTACTGGATA GATACCCGCT TCACGCGCAT CTGTTTCTGA

201 TTTAATATCA ATTTTCCAGC CGGTTAATTT AGCAGCTAGA CGTGCGTTTT

251 GTCCTCTTTT ACCAATCGCT AATGACAATT GATAATCAGG AACAACAACT

301 ACTGTAGATT GATTTGTTTC ATCAACAATA ACTTCTAAAA CTTGAGAAGG

351 GCTTAAAGCA T TTTTACAA ATACTTTTGG ATCTTCATTC CATTGAAACG

401 ATGTCGATTT TTCGCCACCT AGCTCTTCAA CAACAGCTTC AACACGTGCG

451 CCTTTAGCAC CAACACATGC ACCAACAGCA TCTATATCAT TGTTTTCAGA

501 GAAGACACTA ATTTTAGAGC GATCGCCAGC TTCACGTGCT ACTGATTTAA

551 CAATTACAGT ACCATCGTAA ATTTCTGGGA ACTTCTTGTT CAAATAAACG

601 TTTTAATAAA CCTGGGATGG CTACGAAAAA ACATAGATTT GAAGAACTTT

651 TGTCGTTTGT TCCACTTTGG TTAACATATA CTTTGATACG TTCGTTAGGA

701 ATATATTTTT CCGTTAGGAC TTCTTTCTGC TTCAGATAAA ACAGCTTCGA

751 ATACGAACTA AATTC

Minus Strand HSPs:

[ΞEQ ID NO: ] score = 518 (238.3 bits) , Expect = 9.0e-82, Ξum P(3) = 9.0e-82 Identities = 102/138 (73%) , Positives = 117/138 (84%) , Frame = -2

Query: 578 PEIYDGTVIVKSVAREAGDRSKISVFSENNDIDAVGACVGAKGARVEAWEELGGEKSTS 399

PEIYDGTV +KSVAREAGDRSKIΞV +++ D+D VG+CVG KG RV+A+V EL GEK Sbjct: 213 PEIYDGTVELKSVAREAGDRSKISVRTDDPDVDPVGSCVGPKGQRVQAIVNELKGEKIDI 272

Query: 398 FQWNEDPKVFVKNALSPSQVLEVIVDETNQSTWWPDYQLSLAIGKRGQNARLAAKLTG 219

W+ DP FV NALSPS+VL+VIV+E ++T V+VPDYQLSLAIGKRGQNARLAAKLTG Sbjct: 273 VNWSSDPVEFVANALSPΞKVLDVIVNEEEKATTVIVPDYQLSLAIGKRGQNARLAAKLTG 332

Query: 218 WKIDIKSETDAREAGIYP 165

WKIDIKSETDARE GIYP Sbjct: 333 WKIDIKSETDARELGIYP 350 [SEQ ID NO: ] score = 59 (27.1 bits), Expect = 9.0e-82, Sum P(3) = 9.0e-82 Identities = 12/13 (92%), Positives = 12/13 (92%), Frame = -1

Query: 615 PGLLKRLFEQEVP 577

PGLLKRLFE EVP Sbjct: 201 PGLLKRLFEIEVP 213

[SEQ ID NO: ] score = 54 (24.8 bits), Expect = 9.0e-82, Sum P(3) = 9.0e-82 Identities = 12/18 (66%), Positives = 14/18 (77%), Frame = -2

Query: 683 KYMLTKVEQTTKVLQIYV 630

K +TKVE+TTK QIYV Sbjct: 179 KVYITKVEKTTKGPQIYV 196

[SEQ ID NO: ] score = 49 (22.5 bits), Expect = 4.3e-81, Sum P(3) = 4.3e-81 Identities = 8/20 (40%), Positives = 15/20 (75%), Frame = -1

Query: 726 KEVLTEKYIPNERIKVYVNQ 667

+++ E Y P++RIKVY+ + Sbjct: 165 EQMPNESYKPHDRIKVYITK 184

[SEQ ID NO: ] contig[0075] Length: 617 check: 9313 ..

1 GAATTGGATA CACCGAAACA TTTAGACACG GATAGATTTT TTGAAAATAT

51 CGCTAAACTT GATAAAGCTA ATGTAGATGC GGTAACACTC GCAGATAATT

101 CATTGGCAAC TGTCAGAATT AGCAATATTG CTGCTGCTAG CTTAATTAAG

151 CAATATTACA ATATTGAACC ACTCGTACAT ATTACATGTC GAGACCGAAA

201 CTTAATCGGC TTGCAGTCCC ATTTACTTGG ATTATCGCTC ATTGGCGTTA

251 ACGAAATATT AGCCATAACT GGTGATCCTT CAAAAGTTGG TCACTTACCA

301 GGTGCAACCA ATGTCTATGA TGTTAATTCT AAAGGATTAA CTGAACTCGC

351 TCTAAGATTT AATCAAGGTA TTAACACTGA CGGTGATGCG CTGAAGAAAC

401 GTACACACTT CAACATCGCT GGCGCCTTTA ACCCTAATGT TCGTAAATTA

451 GATGGTGCCG TCGAAAGATT AGAGAAAAAG A AGAAAGCG GAATGTCTTA

501 TTTTATAACA CAACCCGTGT TACAGCAAAG AGAAAATCAT TGAAATTTAC

551 CATGCCACTA AGCACTTGAA CAAACCATTT TTCATAGGCA TTATGCCTAT

601 CGCAAGTTAC AAAAACG

>gi 11652804 (D90908) hypothetical protein [Synechocystis sp.) Length = 340

Plus Strand HSPs:

[SEQ ID NO: ] score = 177 (81.4 bits), Expect = 9.0e-25, Sum P(3) = 9.0e-25 Identities = 37/81 (45%), Positives = 50/81 (61%), Frame = +1

Query: 133 AAΞLIKQYYNIEPLVHITCRDRNLIGLQSHLLGLSLIGVNEILAITGDPSKVGHLPGATN 312

AA ++ Q IE + +TCRDRNLIGLQ+ L+G +G+ +LA+TGDP K G A Sbjct: 104 AACVLLQQRGIEAICQMTCRDRNLIGLQADLMGAYALGLRNVLALTGDPLKAGDHAKARP 163

Query: 313 VYDVNSKGLTELALRFNQGIN 375

VYD+ S L L NQG++ Sbjct: 164 VYDLESVRLLSLIRΞLNQGLD 184

[SEQ ID NO: ] score = 56 (25.8 bits), Expect = 9.0e-25, Sum P(3) = 9.0e-25 Identities = 12/30 (40%), Positives = 19/30 (63%), Frame = +1

Query: 64 KANVDAVTLADNΞLATVRISNIAAASLIKQ 153

+ V V + D S A +R+S+IAA L++Q Sbjct: 82 RGRVHGVNVTDGSRAVLRMΞSIAACVLLQQ 111

[SEQ ID NO: ] score = 51 (23.5 bits), Expect = 9.0e-25, Sum P(3) = 9.0e-25 Identities = 9/30 (30%), Positives = 17/30 (56%), Frame = +1

Query: 424 AFNPNVRKLDGAVERLEKKIEΞGMSYFITQ 513

A +P ++ G R E+K+ +G +F +Q Sbjct: 202 AVDPQLKSWSGLQSRFERKLTAGAQFFQSQ 231

>gi 11039454 (U36624) Lpb8p [Saccharomyces cerevisiae] Length = 657

Plus Strand HΞPs:

[SEQ ID NO: ] score = 77 (35.4 bits), Expect = 0.00015, Sum P(3) = 0.00015 Identities = 22/86 (25%), Positives = 37/86 (43%), Frame = +1

Query: 22 LDTDRFFENIAKLDKANVDAVTLADNSLATVRISNIAAAΞLIKQYYNIEPLVHITCRDRN 201

L T E + ++ + +T+ + T + ASL +Q NI +H+TC + Sbjct: 26 LGTRNLMERMHRMTALDPLFITVTWGAGGTTAEKTLTLASLAQQTLNIPVCMHLTCTNTE 85

Query: 202 LIGLQSHLLGLΞLIGVNEILAITGDP 279

+ L G+ ILA+ GDP Sbjct: 86 KAIIDDALDRCYNAGIRNILALRGDP 111

[SEQ ID NO: ] score = 43 (19.8 bits), Expect = 0.00015, Sum P(3) = 0.00015 Identities = 8/12 (66%), Positives = 9/12 (75%), Frame = +2 Query: 575 PFFIGIMPIASY 610

P F G+MPI SY Sbjct: 213 PLFPGLMPINSY 224

[SEQ ID NO: ] score = 41 (18.9 bits), Expect = 0.00015, Sum P(3) = 0.00015 Identities = 7/15 (46%), Positives = 12/15 (80%), Frame = +1

Query: 469 LEKKIESGMΞYFITQ 513

L++K+E+G + ITQ Sbjct: 175 LKEKVEAGADFVITQ 189

>sp|P42898|MTHR_HUMAN METHYLΞNETETRAHYDROFOLATE REDUCTASE. >gi| 945023 (U09806) methylenetetrahydrofolate reductase [Homo sapiens] Length = 416

Plus Strand HSPs:

[SEQ ID NO: ] score = 84 (38.6 bits), Expect = 0.00040, Sum P(2) = 0.00040 Identities = 17/53 (32%), Positives = 29/53 (54%), Frame = +1

Query: 121 SNIAAASLIKQYYNIEPLVHITCRDRNLIGLQSHLLGLSLIGVNEILAITGDP 279

S++ AS Y +E ++H+TC + L + HL +G+ I+A+ GDP Sbjct: 109 SSMMIASTAVNYCGLETILHMTCCRQRLEEITGHLHKAKQLGLKNIMALRGDP 161

[SEQ ID NO: ] score = 45 (20.7 bits). Expect = 0.00040, Sum P(2) = 0.00040 Identities = 7/28 (25%), Positives = 16/28 (57%), Frame = +1

Query: 430 NPNVRKLDGAVERLEKKIESGMSYFITQ 513

+P + ++ L++K+ ÷G + ITQ Sbjct: 202 HPEAGSFEADLKHLKEKVΞAGADFIITQ 229

[SEQ ID NO: ] contig[0073] Length: 1510 Check: 2912

1 GGGCTGCAGG AAATTCGGCA CGAGCTCGTG CCGCGACCAA TAACTTCGCA

51 TTGATGACCA TTTACATTTA CAAAGCTACC TTGCATTATG CGTAAATAGC

101 CATCTGCATA TCCAATAGGT AACAAAGCTA TTGTAGTTGG GTCAGTAGCT

151 GTATAAGTTG CACCATAACT TACAGACTCA CCCGCTTGTA GCGTCTTTGT

201 TTGAACTACA TTAGCAATTA ATTGCACACT TGGTTTAAGG TGTACTTTAA

251 CTTTTTGCTG TACATACTCT GATGGATAAT ATCCATAAAG GGAAATTCCT

301 GGTCTTATTG CATTACAGAA TTGGCAATCC ATTAATAGAG AGCCTGCTGA

351 GTTCTGACAA TGTATATATT CAGGTTTAAT TGCTTCATTG ACCATATCTT

401 TAAAACGTTG ATATTGTTCA GTTGTCATAT CTCCTGGTTC GTCAGCACAG

451 GCAAAGTGTG TAAACACGCC TTCAAATACA AGTTGCTCAT ATTGTTGAAT 98/23738

501 GATTTCAATC ACTTCTTGAT ACGTATTAGT ATCTTTAATA CCTAAACGTC

551 CCATTCCTGT TATCTAATTT AATGTGCAAC CATAACTTTT TCTCTTGCTC

601 ACCAGAAATG TTTTTAATTG CTTCTTTCAA CCACTGTTTA AACGGAACCG

651 TTAAGGCAAC TCTGTGTTGT ATCGCTTTAT CAATATCTTT AAGCTGGTAA

701 CACACCTAAG ACTAAAATTT TAGCAGTAAT CCCATGCATT CTAAGTTCTA

751 TCGCTTCATC TAACGTTGCT ACAGCAAAAA ATGTGGCGCC ATTTTCCATT

801 AAATGACGTG CTACTTTAAC ACTACCTAGT CCATAGGCAT TGGCTTTAAC

851 GACAGCCATC ACTGTTTTAT TTGGATGCAA TGTACTGAAT ACTTTGAAAT

901 TTGATGCAAC AGCGTTTAAA TCTACATTCA TATACGCAGA TCTATAATAT

951 TTATCCGACA TATTACTTCC TCCTGTAATT CCCACACGTT TTAAAACTAG

1001 ATCTTAATTA TCATTGTATA ACAAATTTAA AATGCTGACT TTTCTAAAAC

1051 AACTTGGCTC ATCGCATAAT GCTCAGTGTG TGAGATACTA ACATGTACGA

1101 TGAACCCTTC GTAATCAATC TTTGGTTTGC CAAGTTCGTC GTTGTAACAG

1151 TCTATATCGT TAAAAGCTAC ATGTTTTCCT AAGCCTGTGC CTAATGCTTT

1201 ACTGAACGCT TCTTTTGTAG CAAACCTGCC AGCTAAAAAT TCAATTTTAC

1251 GTTGCTCATG TGTGAAATTG TTGAATTTGT GCTGTTCATT TTTAGTTAAA

1301 ATCCGCTCAA CCAATTTTGG CTGCTTACTA TATAACACTT TTATTCGATC

1351 GATTTCGATT AAATCTACAC CAATTCCATG TATCATTGAT TATTCCTCAT

1401 TTTTATTGTT TTCTAAATGT CTCTCGTTAT TTAACCATCG TTTCAATCTA

1451 CGTGCTTCAC TTCTATCTAT TAATTCAATT TCAGCTTGAC CACCCGCTGT

1501 ATAAA

>sp|P10724|ALR_BACST ALANINE RACEMASE. >pir||A29984 alanine racemase (EC

5.1.1.1) - Bacillus stearothermophilus >gi|l42467 (M19142) alanine racemase (EC 5.1.1.1) [Bacillus stearothermophilus] Length = 386

Minus Strand HSPs:

[SEQ ID NO: ] score = 203 (93.4 bits). Expect = 6.2e-58, Sum P(6) = 6.2e-58 Identities = 43/97 (44%), Positives = 57/97 (58%), Frame = -3

Query: -377 KPEYIHCQNSAGΞLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANWQT 198

+P +HC NΞA SL + N +R GI++YG PS ++ + LK + L + +V Sbjct: 194 RPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHV 253

Query: 197 KTLQAGESVSYGATYTATDPTTIALLPIGYADGYLRI 87

K LQ GE VSYGATYTA I +PIGYADG R+ Sbjct: 254 KKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGVRRL 290

(SEQ ID NO: ] score = 119 (54.7 bits), Expect = 6.2e-58, Sum P(6) = 6.2e-58 Identities = 20/41 (48%), Positives =^' 30/41 (73%), Frame = -3

Query: 560 TGMGRLGIKDTNTYQEVIEIIQQYEQLVFEGVFTHFACADE 438 TGMGRLG+KD + ++ +I+++ V EG++THFA ADE Sbjct: 131 TGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADE 171

[SEQ ID NO: ] score = 83 (38.2 bits), Expect = 6.2e-58, Sum P(6) = 6.2e-58 Identities = 17/25 (68%), Positives = 20/25 (80%), Frame = -1

Query: 862 VMAWKANAYGLGSVKVARHLMENG 788

+MAWKANAYG G V+VAR +E G Sbjct: 34 IMAWKANAYGHGDVQVARTALERG 58

[SEQ ID NO: ] score = 70 (32.2 bits), Expect = 6.2e-58, Sum P(6) = 6.2e-58 Identities = 17/24 (70%), Positives = 18/24 (75%), Frame = -1

Query: 775 AVATLDEAIELRMHGITAKILVLG 704

AVA LDEA+ LR GI A ILVLG Sbjct: 62 AVAFLDEALALREKGIEAPILVLG 85

[SEQ ID NO: ] score = 55 (25.3 bits), Expect = 6.2e-58, Sum P(6) = 6.2e-58 Identities = 14/29 (48%), Positives = 16/29 (55%), Frame = -2

Query: 687 DIDKAIQHRVALTVPFKQWLKEAIKNISG 601

D A Q R+ALTV WL+EA SG Ξbj t: 91 DAALAAQQRIALTVFRSDWLEEASALYSG 119

[SEQ ID NO: ] score = 46 (21.2 bits). Expect = 6.2e-58, Sum P(6) = 6.2e-58 Identities = 10/34 (29%), Positives = 18/34 (52%), Frame = -1

Query: 949 YYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAW 848

++R + VDL+A+ N + L P+ T + V Sbjct: 4 FHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAV 37

[SEQ ID NO: ] contig[0068] Length: 990 Check: 5777 ..

1 TGCAAATGGA TTATCAGATT GTTTCGTGTT TGATGAATTA TTGTACGAAT

51 TGTTTTGTCC TGATTGTTGA CCACCGAATC CTTGACCGTA ATCTTGGAAT

101 TCATTTTGTT GACGTTGGCC ACCATTTTGT TGCGCATTTT TAGGTTCAAG

151 GAATTGAACG CTATCACACA CAACTTCAGT AACAAACACA CGACGACCTT

201 CTTGATTTTC ATAATTACGG GATTGTAAGC GACCATCTAC ACCAGCTAAA

251 CTACCTTTAG ATAAATAGTT ATTTACATTA TCTGCTTGTC TTCTAAAAAC

301 AACACAGTTA ATAAAATCTG CTTCGCGCTC CCCTTGAGCA TTCGTGAACG

351 TACGATTTAC TGCAAGAGTG AATGTCGCTA CACTCACACC TGAGGGAGTG

401 GTTCTGTATT CCGGATCTTT CGTTAAACGA CCTACTAATA CAACTCTATT

451 TAGCATTTAA ACGCCCCCTC TAATTATTAC TTGTCTTCGT CTTCACGAAT

501 AACCATGTAA CGAATGATAT CGTCACTGAT TTTAGCTAGA CGATCTAATC 98/23738

551 AATATTACAC AGAAAGCCAT TGTTTGATGA GAATATGGTT AATAAATTAG

601 ATGATTACTA CTTCATTTAT GGTATTTGTA ATGAATACCC GGATCAAGAC

651 CGTTATCTTA AGCAGAGATA TTTAATACAT AAATTG ATT AAATAACTAG

701 GGTGGTACCA CGACGATCTC GTCCCTTGTA TAGGGGCGGG ATTTTTTGTT

751 TTTTTCAGAC ATAAATGTTT GTTGGTGTCA TATATTCCCT GTTTATTGTT

801 AATAGGTTTA ATGTTAAAAC GATGATTGTT GTTCAATTTT TTAACGAGTC

851 AGATAAAAGT ATTTATAAAG CAAATAGGAG GGTTTAACAT GGAACAAATT

901 AATATTCAAT TTCCAGATGG TAATAAAAAG GCGTTTGATA AAGGTACTAC

951 TACTGAAGAT ATAGCACAAT CAATTAGTCC TGGATTACGT

>sp|P37455|SSB_BACΞU SINGLE-STRAND BINDING PROTEIN (SSB) (HELIX-DESTABILIZING PROTEIN) . >gi|467374 (D26185) single strand DNA binding protein [Bacillus subtilis] Length = 172

Minus Strand HSPs:

[SEQ ID NO: ] score = 483 (222.2 bits) , Expect = 8.0e-62, P = 8.0e-62 Identities = 98/151 (64%) , Positives = 112/151 (74%) , Frame = -1

Query: 456 MLNRWLVGRLTKDPEYRTTPSGVSVATFTLAVNRTFTNAQGEREADFINCWFRRQADN 277

MLNRWLVGRLTKDPE R TP+G +VATFTLAVNRTFTN GEREADFINCV -^p-RRQA+N Sbjct: 1 MLNRWLVGRLTKDPELRYTPNGAAVATFTLAVNRTFTNQSGEREADFINCVTWRRQAEN 60

Query: 276 VNNYLSKGSLAGVDGRLQSRNYENQEGRRVFVTEWCDSVQFLEPKNAQQNGGQRQQNEF 97

V N+L KGSLAGVDGRLQ+RNYENQ÷G+RVFVTEV +SVQFLEPKN +G Sbjct: 61 VANFLKKGSLAGVDGRLQTRNYENQQGQRVFVTEVQAEΞVQFLEPKNGGGSGSGGYNEGN 120

Query: 96 QDYGQGFGGQQSGQNNSYNNΞSNTKQSDNPF 4

GQ FGG Q+ N ++ + N F

Sbjct: 121 SGGGQYFGGGQNDNPFGGNQNNQRRNQGNSF 151

>gi 1662792 (U12515) single-stranded DNA binding protein [unidentified eubacterium] >prf | | 2108276A ssDNA-binding protein [Rattus norvegicus] Length = 181

Minus Strand HSPs:

[SEQ ID NO: 1 score = 341 (156.9 bits) , Expect = 1.9e-40, P = 1.9e-40 Identities = 64/106 (60%) , Positives = 83/106 (78%) , Frame = -1

Query: 456 MLNRWLVGRLTKDPEYRTTPSGVSVATFTLAVNRTFTNAQGEREADFINCWFRRQADN 277 M+NRWL+GRLT+D E R T SG +V TF+LAVNR FTN GEREADFIN V+-P-R+ A+N Sbjct: 1 MINRWLIGRLTRDVELRYTQSGTAVGTFSLAVNRQFTNQAGEREADFINAVIWRKAAEN 60

Query: 276 VNNYLSKGSLAGVDGRLQSRNYENQEGRRVFVTEWCDΞVQFLEPK 139

N+ KG+L ++GRLQ+RNYEN +G+RV+VTEW D+ LE + Sbjct: 61 FANFTGKGALVAIΞGRLQTRNYENNQGQRVΎVTEVWDNFSLLESR 106

[SEQ ID NO: ] contig[0067] Length: 1278 Check: 6243

1 AGATTTCAAT CCATTATTAT CGCTCATTTC AATAATTGCA TCATACTGTG

51 CTTGTGACAT ACTTGCAATA GCCTGTTTTG CATTTTCTTG AAGGAAATAT

101 AAATTTTTCA ATTTAGGATG CTTATTTAAT GTACTTAATG TAATCGGCGT

151 AATGTCTTTC TCATAAGACA CTTCAATCAC TGTACTATTT GTTCTACCAG

201 GAATTGGTGG TTTTTCATGA ATATGCTTTG AAACTTCTCC AATTCCAACG

251 ACAGATTGAT TTTTCGTTCG ATTATAAAAA ATAATATTGT CGCCTTCTTC

301 TAACTGAGTA TAAAAATGAT AACCATTACG TTTAATACCG TTGTACGTGT

351 GCGTATAAAT CGTATATTGG TTTCCAGGTT CAAATTCTTC AGTTTCAGCT

401 AAAAAGAAAT AACGTGGTAT CTTAATTTCG CCTTTACCAA GACCACTTAT

451 TAAATCAAAC TCTTCTGCAG TGATTTGGTT GAACAATGTC TCTTTCATAT

501 TACTCATACG AAATTCCAAA GCTTCACTAC GCTTTAAATA ATCAGCTGTT

551 AATGGTTTCA ATTGTTCATT AAAACGAAAC TGTACACGTA TTTTATTTTG

601 TGCACCTGTT TCAACACTAA TAATTTCACC ACATCCAAGT AGTCCAGTAT

651 CCGTCTGAAC TTGATAAAAG ATGACTTGAT CTCCTACTTT AGCCTTTTTA

701 AACGCTCTAA ATCCTTGAGA TGGGTTAAAA TGTGCGCCTG ATTCAAATAA

751 AGCTGTTTGT CCTACTAACG GTTCATTATG ATTCCAACGG TTATATCCAC

801 AATTCAACCA AAAATAATTC GTTTCTGCTG TCATCTTAAT ACTCCTTAAC

851 CTGAATAAAT TTTAGAAACA CTATGAATTA CATTCTTTTA GTGTTTCTTA

901 TGCAGTTGGA CGCGTATGCG AACAACTGTA TACCCTTTGT TCACTGCGAT

951 TTTAATCGCA TTTCCTATAA CATTGTAGCG CCCAGGACAT TAATTTACGT

1001 CCCAGACCCT TATCGTTTTC ACTTCTAAGT AAGTCGAACT ATTTTGCTTT

1051 ACAACAAGTG CGACTCTAAA TACAGTTGGA CACACATACG AGCAACTGTA

1101 TACCTTTTAA TCAGTTTTCT ATATTTTATT TATTATATCT GTCTTAATGA

1151 TAAAAATTGT TACAAACAGT TTAACATATT TAGCTATCTA TTTTGCATAT

1201 AAAAAACATG CTTGCATACA CTATGCAATA AAAATTACAA ATTTATATAT

1251 GATACCACTA TGCTTGCTTA TCTCTATA

220578 (D00570) open reading frame [Mus musculus] Length = 250

Plus Strand HSPs:

[SEQ ID NO: ] score = 53 (24.4 bits). Expect = 3.8, Sum P(3) = 0.98 Identities = 11/32 (34%), Positives = 20/32 (62%), Frame = +1 Query: 1177 YLAIYFAYKKHACIHYAIKITNLYMIPLCLLI 1272

YL+IY +Y + 1+ + + +Y+ +CLLI Sbjct: 170 YLSIYLSYVCLΞSIYLSYAVYIIYLSYVCLLI 201

[SEQ ID NO: ] score = 40 (18.4 bits), Expect = 3.8, Sum P(3) = 0.98 Identities = 6/18 (33%), Positives = 12/18 (66%), Frame = +3

Query: 1095 TVYLLISFLYFIYYICLN 1148

++YL I ++ Y+CL+ Sbjct: 146 SIYLCIYLSIYLSYVCLS 163

[SEQ ID NO: ] score = 37 (17.0 bits), Expect = 3.8, Sum P(3) = 0.98 Identities = 5/14 (35%), Positives = 10/14 (71%), Frame = +1

Query: 37 CIILCL*HTCNSLF 78

C+ +CL + C S++ Sbjct: 122 CLΞICLSYVCLΞIY 135

[SEQ ID NO: ] contig [0166 ]

[SEQ ID NO: ] contig[0166] Length: 829 Check: 9816 ..

1 TTCCGCAGTA TAACCTTTAC GAAAATCTTT TCTTTCTAAC TTCTTACCGG

51 TAATTTCACT TAACGCATGA TAGACACCTG TCGACTCAAT TAAACTAACG

101 ATAGCTACAA TAAAGAACAC TAACGTCGAT GTCACATCAA AGCTAAATCC

151 TGAGAATCTA AACGGCACTG GGATGCCTAA CCAACCGGCA TGATTGACTT

201 GATTAATATC GACCATCCCA AGTAAGCCAG CACCTATCGT TCCTAAAACG

251 AGTCCAATTA ATATGGCAAT ACTCTTAATA AATCCAGTTG TGAATCTTTG

301 TAAAACAAGA ATAATGATTA ATGTCATTAA ACCTAACAAA ATGTTCTTAA

351 CATCTCCATA GTCCTTTGCA CCTTGACCTC CAGCTAAGTA ATTCATTGCT

401 ACTGGCATTA AATTGATACC AATGATAGTA ACAACACTAC CCGTTACTAC

451 TGGTGGGAAG AATTTTACAA GATGTGAAAA GAAAGGCGCG ATGATAATAA

501 CTAATATCCC TGATAAAAAT AGCGAACCGT AAAGTACATC TATTCCTTTC

551 GTTTGACCAA TTAAAATCAT GGGCGCAACA GCCGTGAATG TACATCCAAG

601 AACGATTGGT AATCCTGTTC CTGTTACTTT ATTGGCTTGT AAAAATGTGG

651 CAACCCCACA CATAAATATA TCTACTGTAA CTAAGTAAGC GATTTGTTCA

701 GGTGTAAACT TCAAACTTGT ACCAACAATG ATTGGAACTA AGATGGCACC

751 TGCGTACATA GCTAAAAGAT GTTGAACACT TAGGATTAAA TTTTTCATTA

801 TTCTTCTCCC ACCAATGTCA CTTTGTTTC

>sp|P42086|PBUX_BACΞU XANTHINE PERMEAΞE. >pir||S51310 xanthine permease -

Bacillus subtilis >gi| 633170 (X83878) xanthine permease [Bacillus subtilis) >gi 11256618 (L77 46) transport protein [Bacillus subtilis) Length = 438

Minus Strand HSPs:

[SEQ ID NO: ] score = 583 (268.2 bits). Expect = 6.7e-101, Sum P(2) = 6.7e-101 Identities = 117/212 (55%), Positives = 150/212 (70%), Frame = -2

Query: 636 ANKVTGTGLPIVLGCTFTAVAPMILIGQTKGIDVLYGSLFLSGILVIIIAPFFSHLVKFF 457

+N+ G GLP+VLGCTFTAV+PMI IG G+ +YGS+ SGILVI+I+ FF LV FF Sbjct: 62 SNRFFGIGLPWLGCTFTAVSPMIAIGSEYGVSTVYGSIIAΞGILVILISFFFGKLVΞFF 121

Query: 456 PPWTGSWTIIGINLMPVAMNYLAGGQGAKDYGDVKNILLGLMTLIIILVLQRFTTGFI 277

PPWTGSWTIIGI LMPVAMN +AGG+G+ D+GD+ N+ L L II++L RFT GFI Sbjct: 122 PPWTGSWTIIGITLMPVAMNNMAGGEGSADFGDLSNLALAFTVLSIIVLLYRFTKGFI 181

Query: 276 KΞIAILIGLVLGTIGAGLLGMVDINQVNHAGWLGIPVPFRFΞGFSFDvTSTLVFFIVAIV 97

KS++ILIG+++GT A +G V + V+ A + + PF F SF + IVAIV Sbjct: 182 KSVSILIGILIGTFIAYFMGKVQFDNVSDAAWQMIQPFYFGAPΞFHAAPIITMSIVAIV 241

Query: 96 SLIESTGVYHALSEITGKKLERKDFRKGYTAE 1

SL+ESTGVY AL ++T ++L D KGY AE Sbjct: 242 SLVESTGVYFALGDLTNRRLTEIDLSKGYRAE 273

[SEQ ID NO: ] score = 186 (85.6 bits). Expect = 6.7e-101, Sum P(2) = 6.7e-101 Identities = 35/53 (66%), Positives = 44/53 (83%), Frame = -2

Query: 795 KNLILSVQHLLAMYAGAILVPIIVGTΞLKFTPEQIAYLVTVDIFMCGVATFLQ 637

K L L +QH+LAMYAGAI+VP+IVG ++ T EQ+ YLV++DIFMCGVAT LQ Sbjct: 7 KTLSLGIQHVLAMYAGAIWPLIVGKAMGLTVEQLTYLVΞIDIFMCGVATLLQ 59

[SEQ ID NO: ] contig[0165]

[SEQ ID NO: ] contig [0165 ] Length: 1098 5:00 PM Check: 2020

1 TTTTAATACT AGCATTAATC GATTCACTGA TAGTGACATT TTCAGTATTC

51 GTAAGTTATT ACATTTTAGA ACCGTATTTC AAAACATATT CTGTCAAATT

101 ATTAATATTG GCAGCTA AT CACTATTCAT ATCGCATCAT ATTTCAGCAT

151 TTATTTTTAA TATGTATCAT CGAGCGTGGG AATATGCCAG TGTGAGTGAA

201 TTGATTTTAA TTGTTAAAGC TGTGACGACA TCTATCGTTA TTACGATGGT

251 GGTCGTGACA ATTGTTACAG GCAATAGACC GTTTTTTAGA TTGTATTTAA

301 TTACTTGGAT GATGCACTTG ATTTTAATAG GTGGCTCAAG GTTATTTTGG

351 CGTATTTATC GGAAATACCT TGGAGGTAAG TCATTTAATA AGAACCCAAC

401 TTTAGTTGTT GGTGCTGGTC AAGCAGGTTC AATGCTGATT AGACAAATGT 98/23738

451 TGAAAAGTGA CGAAATGAAA CTTGAACCGG TATTAGCAGT CGATGATGAC

501 GAACATAAAC GCAATATCAC AATTACTGAG GGTGTAAAAG TCCAAGGTAA

551 AATTGCGGAT ATTCCAGAAC TAGTGAGGAA ATATAAGATT AAAAAAATCA

601 TCATTGCAAT TCCAACTATT GGTCAAGAGC GTTTGAAAGA AATTAATAAT

651 ATTTGCCATA TGGATGGCGT TGAGTTATTG AAAATGCCAA ATATAGAAGA

701 CTCATGTCTG GTGAGTTAGA AGTGAATCAA CTGAAAAAAG TTGAAGTAGA

751 AGATTTACTA GGCAGAGATC CTGTTGAATT AGATATGGAT ATGATATCAA

801 ATGAATTGAC GAATAAAACT ATTTTAGTTA CGGGTGCAGG TGGTTCAATA

851 GGATCAGAAA TTTGTAGACA AGTTTGTAAT TTCTATCCAN AACGTATTAT

901 TCTACTTGGC CATGGTGAAA ACAGTATTTA TTTAATCAAT CGTGAATTGC

951 GAAATCGCTT CGGAAAAAAT GTTGATATCG TTCCTATTAT AGCGGATGTG

1001 CAAAATAGAG CGCGTATGTT TGAAATTATG GAAACGTATA AACCATACGC

1051 AGTTTATCAT GCAGCAGCAC ACAAGCACGT GCCGTTAATG GAAGACAA

>gi 11468939 (D86412) meso-2, 3-butanediol dehydrogenase (D-acetoin forming) [Klebsiella pneumoniae] Length = 256

Minus Strand HSPs:

[ΞEQ ID NO: ] score = 190 (87.4 bits) , Expect = 7.0e-18, P = 7.0e-18 Identities = 35/70 (50%), Positives = 50/70 (71%) , Frame = -3

Query: 565 QTPMRESIAEATAEEAGKPEAWGLGKFTSQIAMGRVSQPEDVSNWSFLAGKDSDYITGQ 386

+TPM I +E AGKP +G +F +1 +GR+S+PEDV+ VS+LA DSDY+TGQ

Sbjct: 186 KTPMWAEIDRQVΞEAAGKPLGYGTAEFAKRITLGRLSEPEDVAACVΞYLASPDΞDYMTGQ 245

Query: 385 TIIVDGGMRF 356 Sbjct: 246 SLLIDGGMVF 255

>gi 11616920 (D82061) a member of the short-chain alcohol dehydrogenase family [Homo sapiens] Length = 259

Minus Strand HSPs:

[SEQ ID NO: ] score = 121 (55.7 bits), Expect = 1.0e-07, P = 1.0e-07^' Identities = 23/43 (53%), Positives = 31/43 (72%), Frame = -3

Query: 490 KFTSQIAMGRVSQPEDVSNWΞFLAGKDSDYITGQTIIVDGGM 362

K T I MG + PEDV++W+FLA +DS YITG ++ V GG+ Sbjct: 215 KITEMIPMGHLGDPEDVADWAFLASEDSGYITGTSVEVTGGL 257 >pir||A48154 short-chain alcohol dehydrogenase family member Ke 6 - mouse Length = 260

Minus Strand HSPs:

[SEQ ID NO: ] score = 119 (54.7 bits). Expect = 2.0e-07, P = 2. Oe-07 Identities = 22/43 (51%), Positives = 32/43 (74%), Frame = -3

Query: 490 KFTΞQIAMGRVSQPEDVΞNWSFLAGKDSDYITGQTIIVDGGM 362

K T+ I +G + PEDV++W+FLA +DS YITG ++ V GG+ Sbjct: 216 KVTAMIPLGHMGDPEDVADWAFLASEDSGYITGASVEVSGGL 258

[SEQ ID NO: ] contig[0164]

[SEQ ID NO: ] contig[0164] Length: 567 4:54 PM Check: 7533

1 TTCCAAATCT TCCACTCATT TATACATTAA AAATATATCA TAAAAACATA

51 ATGTATTGTA AGCTTTTTAT CGAGATTTTT TATTTATAAA AATAAAATGA

101 GATAACTTTG TGAATTTTTA TTGAGATAAA TTASATAGTG GTGTTTTTGT

151 GATGTTTTAT AATATCTTGG GTGTGTTAAT ACTAGTAATG CTTTCAACTG

201 ATGCATTAGA CTGTGACATC ATAACTCATT TAAGAACTTC GCTTATTAAT

251 TTTCTACCAA TACAATCCCT TCTAAGTGCA CTAAAAAATC CTTACTGCTA

301 AGTGAT AAA CTTAACAATA AGGATTTATT TATCGCTAAT GCATGATTAT

351 TAACGGAATC TCATACCACC ATCTACAATA ATTGTTTGTC CAGTAATGTA

401 ATCAGAGTCT TTACCAGCTA AGAAGCTCAC TACATTTGAA ACATCTTCTG

451 GTTGAGAAAC TCTGCCCATA GCTATCTGAC TTGTAAATTT TCCCAACCCC

501 CATGCTTCAG GTTTACCTGC TTCTTCCGCT GTTGCCTCTG CGATACTTTC

551 CCTCATTGGT GTTTGAA

>gi|1468939 (D86412) meso-2, 3-butanediol dehydrogenase (D-acetoin forming) [Klebsiella pneumoniae] Length = ₂56

Minus Strand HSPs:

[SEQ ID NO: ] score = 190 (87.4 bits), Expect = 7.0e-18, P = 7.0e-18 Identities = 35/70 (50%), Positives = 50/70 (71%), Frame = -3

Query: 565 QTPMRESIAEATAEEAGKPEAWGLGKFTSQIAMGRVΞQPEDVSNWSFLAGKDSDYITGQ 386

+TPM I +E AGKP +G +F +1 +GR+S+PEDV+ VS+LA DSDY+TGQ

Sbjct: 186 KTPMWAEIDRQVSEAAGKPLGYGTAEFAKRITLGRLSEPEDVAACVSYLASPDSDYMTGQ 245 Query: 385 TIIVDGGMRF 356

++++DGGM F Sbjct: 246 SLLIDGGMVF 255

?gi 11616920 (D82061) a member of the short-chain alcohol dehydrogenase family [Homo sapiens] Length = 259

Minus Ξtrand HSPs:

[SEQ ID NO: ] score = 121 (55.7 bits). Expect = 1.0e-07, P = 1.0e-07 Identities = 23/43 (53%), Positives = 31/43 (72%), Frame = -3

Query: 490 KFTSQIAMGRVSQPEDVSNWΞFLAGKDSDYITGQTIIVDGGM 362

K T I MG + PEDV++W+FLA +DS YITG ++ V GG+ Sbjct: 215 KITEMIPMGHLGDPEDVADWAFLASEDSGYITGTΞVEVTGGL 257

>pir||A48154 short-chain alcohol dehydrogenase family member Ke 6 - mouse Length = 260

Minus Strand HSPs:

[SEQ ID NO: ) score = 119 (54.7 bits), Expect = 2.0e-07, P = 2.0e-07 Identities = 22/43 (51%), Positives = 32/43 (74%), Frame = -3

Query: 490 KFTSQIAMGRVSQPEDVΞNWSFLAGKDΞDYITGQTIIVDGGM 362

K T+ I +G + PEDV++W+FLA +DS YITG ++ V GG+ Sbjct: 216 KVTAMIPLGHMGDPEDVADWAFLASEDΞGYITGASVEVΞGGL 258

[SEQ ID NO: ] contig [0160] Length: 1155 Check: 379 ..

1 ACATTAAAAT TATTTATTAA GCCTTTATGG CAATATCATT GTCGCTTTTA

51 TAAAGTTGAT CAACTAAGTG TACAATATCG TACATCATTT TTTATATATA

101 AAGAAGAAAC GAGTCGAATT GAACGTTTAC AATACTTGTC GATTAAATCT

151 AATCCAATTA GTAAAGTGCT TAATTTGTAT AAAGTTGGAT TTATGACTGC

201 AGGTCATACT ATTTATTTAC CGATGATGTC TCATGACGAT GTTAAAATAA

251 TCGAAGCGAG AACTATGTCG AATTTGAGAG GGGTTGAAAG TGATGTCTGA

301 ACCTCAAAAA TTACATCCGA TTTCATATTT TAATGGCATA ATCAATGCTA

351 TCAAACAAAA CATAGTCGTC TTTTTTATTT TCATTATCTT TCAATTGAAA

401 GATTTTGATT ATACGAATCC CGAATCATAT TTATGGATAG GTATTGTATT

451 TGTATTCTTT TTAATATCAT ACATTTCTCA AATTGTCGGA ATTATGAACA

501 CGCGATATTG GATTGAGGAT AATTATTTCA TTTTAACAAC AGGTATTTTT 551 AATAAAAAGC GTAAAGAATT AAATATAAAA CGTATTCAGT CCGTTGATAT

601 GACACAAGGG GTCGTCAATC AAATTATTGG TGGTGTGGAT TTACAAATCA

651 AAACACCAAG TGATGGTATT GTCTTAAGTG TTATTTCGAA AAAACAAGGT

701 GAATATCTTG AACGATATAT TGATCAATTG CAAACAGAGT TGAAGACAGA

751 AGTGGCGCAA AAGTCTAGTG CTGAGAAGAA TGACAACTGT AATCATGACA

801 TTGAAGGTAA TGTGGAAGAC ATCGCAGAAG GTCGCTTAGA TGAAGTGCAG

851 AACACTGATA GTATGCTTAA TCAGAAAAAT AAACGCATTC CTATATATCA

901 GATGAATTTT AAAGAATCAC TATTTATGGC AATGACCAGT GGCGCCATTG

951 GTGTAACGTT AGCAGCTTTA GTACCGATTT ACGGGGCTGT AAGAGAGTTG

1001 ATCCCATGGT CGAAGCTAAA TCATGAAATT AGTCAATGGG TTCAAATTGT

1051 AAGTATTTCA GTATTAATCA TCATTTTACT AGTATTAATA GTGGCATATA

1101 TTATTGGGAA CGATTATAAC AATGATAAGA TTTTATGGCT TTTCGGTGAT

1151 GCTTG

>gi 11171589 (X95275) frameshift [Plasmodium falciparum) Length = 960

Plus Strand HSPs:

[SEQ ID NO: ] score = 50 (23.0 bits). Expect = 0.47, Sum P(4) = 0.38 Identities = 11/29 (37%), Positives = 17/29 (58%), Frame = +1

Query: 94 IYKEETSRIERLQYLSIKSNPISKVLNLY 180

+YK + + I +Y IK+N 1+ LN Y Sbjct: 63 LYKNKINNIYNNKYYEIKNNYINVFLNNY 91

[SEQ ID NO: ] score = 48 (22.1 bits), Expect = 0.47, Sum P(4) = 0.38 Identities = 11/59 (18%), Positives = 29/59 (49%), Frame = +2

Query: 455 FFLISYISQIVGIMNTRYWIEDNYFILTTGIFNKKRKELNIKRIQSVDMTQGWNQIIG 631

++ + I++I GI+N + + N +F + ++ ++Q + -^p-G ++ I G Sbjct: 91 YYYLKVINKIQGILNNNLYNKINPIYSNLFLFFNNKIKIKYΞQLQQLIGYKGYISNIKG 149

[SEQ ID NO: ] score = 39 (17.9 bits). Expect = 0.47, Sum P(4) = 0.38 Identities = 7/21 (33%), Positives = 12/21 (57%), Frame = +1

Query: 1048 CKYFΞINHHFTSINΞGIYYWE 1110

C ++INH+ +N Y +E Sbjct: 753 CNKYNINHYKYKLNFYSYIFE 773

[SEQ ID NO: ] score = 39 (17.9 bits). Expect = 8.1, Sum P(3) = 1.0 Identities = 8/21 (38%), Positives = 12/21 (57%), Frame = +1

Query: 1042 SNCKYFSINHHFTSINSGIYY 1104 SN Y N+++ INS Y+ Sbjct: 503 SNYYYKIYNNNYNFINΞNYYF 523

[SEQ ID NO: ] score = 37 (17.0 bits). Expect = 0.47, Sum P(4) = 0.38 Identities = 8/18 (44%), Positives = 12/18 (66%), Frame = +3

Query: 870 IRKINAFLYIR*ILKNHY 923

I+K N FLY+ I K ++ Sbjct: 587 IKKYNNFLYLYEIFKYNW 604

[SEQ ID NO: ] score = 37 (17.0 bits). Expect = 0.83, Sum P(4) = 0.56 Identities = 7/19 (36%), Positives = 12/19 (63%), Frame = +1

Query: 1057 FSINHHFTSINSGIYYWER 1113

+S++ F SIN + Y+ R Sbjct: 783 YΞLHTEFYΞINKNLKYYFR 801

>sp|P44701|SRMB_HAEIN ATP-DEPENDENT RNA HELICASE SRMB HOMOLOG. >pir||H64066

ATP-dependent RNA helicase (srmB) homolog - Haemophilus influenzae

(strain Rd KW20) >gi| 1573394 (U32725) ATP-dependent RNA helicase

(srmB) [Haemophilus influenzae] Length = 439

Plus Strand HSPs:

[SEQ ID NO: ] score = 73 (33.6 bits), Expect = 2.3, P = 0.90 Identities = 17/54 (31%), Positives = 30/54 (55%), Frame = +2

Query: 620 QIIGGVDLQIKTPSDGIVLSVIΞKKQGEYLERYIDQLQTELKTEVAQKSSAEKN 781

+1+ G++ + K P DG V SV K++ E+ ++ +TE K +V + KN Sbjct: 374 RILAGLEPRTKPPKDGEVKSVSKKQKARIKEKREEKKKTEAKKKVKLRHKDTKN 427

[SEQ ID NO: ] contig[0159] Length: 1052 Check: 9581 ..

1 CCCGACAAAA TGTATTGTGC TATAGTATTT GCATACTTAA AATACTAACA

51 GCAAAGGAAT GACAGCAAGA TGAAAAAAAC TCTTACAGTG ACGGTTTCGT

101 CAGTGTTAGC TTTTTTAGCT TTAAATAATG CAGCACATGC ACAACAACAT

151 GGCACACAAG TAAAAACACC TGTTCAACAT AACTATGTNT CAAATGTTCA

201 AGCACAAACG CAATCACCGA CAACTTATAC AGTAGTTGCT GGCGATTCAT

251 TATATAAGAT TGCTTTAGAG CATCACTTAA CGTTGAATCA ATTATATTCA

301 TACAATCCTG GTGTAACACC TTTAATTTTT CCTGGTGACG TGATTTCACT

351 TGTGCCTCAA AATAAAGTGA AACAAACTAA AGCGGTTAAA TCACCAGTAA

401 GAAAAGCAAG CCAAGCTAAA AAGGTAGTAA AACAACCTGT ACAACAAGCG 451 TCTAAAAAAG TAGTAGTTAA GCAAGCACCT AAGCAAGCAG TAGCTAAGAC

501 AGTTAATGTA GCATATAAAC CTGCTCAAGT ACAAAAATCA GTACCAACTG

551 TACCTGTTGC ACATAACTAC AATAAATCAG TTGCTAACAG AGGAAACTTA

601 TATGCTTATG GAAACTGCAC ATATTATGCC TTCGATCGTC GTGCACAATT

651 AGGTAGAAGT ATAGGAAGTT TATGGGGCAA TGCAAATAAC TGGAAT ACG

701 CAGCAAAAGT TGCAGGATTT AAAGTAGATA AAACACCAGA AGTTGGCGCT

751 ATTTTCCAAA CAGCTGCTGG CCCATATGGA CATGTTGGTG TTGTTGAATC

801 TGTAAACCCT AATGGAACAA TTACTGTTTC GGAAATGAAC TATGCTGGAT

851 TTAATGTTAA ATCTTCAAGA ACAATTTTAA ATCCAGGAAA ATATAATTAC

901 ATCCACTAAG TAATATATCA AGACAAGACT ATCCTCTTAG CCTGTTTAAG

951 TAACAGGTTG AGAGGATTTT TTGGTATCAT TTAATCAGAG TTATATAAAG

1001 AAGATATTTA AATGATATTT AATTGATTGA TATGTAAAAA GAAAGTATA

gnl|PID|e244971 (X97985) ORF1 [Staphylococcus aureus] Length = 255

Plus Strand HSPs:

[SEQ ID NO: ] score = 210 (96.6 bits) . Expect = 1.9e-25, Sum P(2) = 1.9e-25 Identities = 39/66 (59%) , Positives = 48/66 (72%) , Frame = +1

Query: 646 QLGRSIGSLWGNANNWNYAAKVAGFKVDKTPEVGAIFQTAAGPYGHVGWESVNPNGTIT 825

++G IGS WGNA+NW AA +G+ V+ TP+VGAI QT G YGHV VE VN NG+ + Sbjct: 166 RVGGKIGSTWGNASNWANAAASSGYTVNNTPKVGAIMQTTQGYYGHVAYVEGVNΞNGSVR 225

Query: 826 VSEMNY 843

VΞEMNY Sbjct: 226 VSEMNY 231

[SEQ ID NO: ) score = 69 (31.7 bits) . Expect = 1.9e-25, Sum P(2) = 1.9e-25 Identities = 12/19 (63%) , Positives = 13/19 (68%), Frame = +1

Query: ^■ 583 ANRGNLYAYGNCTYYAFDR 639

A+ NLY G CTYY FDR Sbjct: 148 ASGSNLYTSGQCTYYVFDR 166

[SEQ ID NO: ] score = 46 (21.2 bits) , Expect = 5.2e-22, Sum P(2) = 5.2e-22 Identities = 8/24 (33%) , Positives = 13/24 (54%) , Frame = +1

Query: 565 NYNKSVANRGNLYAYGNCTYYAFD 636

N+N S + N Y Y N Y+++ Sbjct: 61 NWNPSQLTQNNTYYYNNYNTYSYN 84

[SEQ ID NO: ] score = 37 (17.0 bits). Expect = l.le-20. Sum P(2) = l.le-20 Identities = 6/13 (46%), Positives = 8/13 (61%) Frame = +1

Query 586 NRGNLYAYGNCTY 624

N N Y+Y N +Y Sbjct 76 NNYNTYΞYNNASY 88

>gι 1405566 (L19570) TraG protein shares sequence similarity with a 45 kDa secreted protein from Lactococcus lactis [Plasmid pSK41] >pr I |2004267H traG protein [Staphylococcus sp ] Length = 358

Plus Strand HSPs.

[SEQ ID NO ] score = 129 (59 3 bits) Expect = 3 0e-17 Sum P(3) = 3 Oe-17 Identities = 22/63 (34%) Positives = 33/63 (52%) Frame = +1

Query 592 GNLYAYGNCTYYAFDRRAQLGRSIGSLWGNANNWNYAAKVAGFKVDKTPEVGAIFQTAAG 771

G Y +G CT+Y RR ++G+ + WGN +W AK G++V P+ GA G Sbjct 244 GQSYPWGQCTWYVHQRRKEIGKPVPLTWGNGGDWGDNAKAQGWEVGSKPKAGAGAΞVKPG 303

Query 772 PYG 780

+G Sbjct 304 NFG 306

(SEQ ID NO ] score = 85 (39 1 bits) Expect = 3 Oe-17, Sum P(3) = 3 Oe-17 Identities = 19/36 (52%), Positives = 21/36 (58%), Frame = +1

Query 763 AAGPYGHVGWEΞVNPNGTITVSEMNYAGFNVKSSR 870

A PYGH+ VE V +G I VSE N G V SSR Sbjct 307 APPPYGHIMFVEKVKKDGGIWSEANVKGLGVISSR 342

[SEQ ID-NO ] score = 41 (18 9 bits) Expect = 3 0e-17, Sum P(3) = 3 Oe-17 Identities = 9/30 (30%), Positives = 18/30 (60%), Frame = +1

Query 1 PDKMYCAIVFAYLKY'QQRNDΞKMKKTLTV 90

P K++ AIV + ++ + N +K K L++ Sbjct 109 PPKLFIAIVASESEWGRGANATKQKNPLΞI 138

[SEQ ID NO: ] contig [0158 ] Length: 864 Check: 7402 ..

1 CCCAGGAATA AGTAATGCTG CTACTTTTTT ACGATTTTCT TTAGGTGTCG

51 TAGCATACAT TGCTAAAGCA ATACCTAAAC ATCCAAATAC TTTCCCCATT

101 TCCTTGAAGC ATAAAGCCAT AAGGGAATTG CTCTTTTAAT GGCTTAGTAC

151 TCTTAGCAAA CTCATTTAAA TGTTGTAACC ATTCAGCTTT CAAGCCATGA 201 TTGACTACTA CTGGTCCAAC TTCAATTGGT GCATAAATAA AGTGATGTAA

251 TCCTGTTGGT ATTAATACAC GTTCTAAGAA GTGGTACAGC CAAACACCGA

301 TATAGCCTGA AGCGATGATA AAGTGTTGCA TTGAACCAAT ACCGTGCTGA

351 ACAGTTGGCC AAATAACACA AGTAATTGCT GCTAATGGTA ACATCACAAA

401 AAATGAAATT GTAACCACAA ATGTTAAACC TTGGAATACA CCAACCATTT

451 CTGGTAATCG TTTACTGTAG TATCTATTGT GAATCCACGT AATAATAGCT

501 GAAATAATAA TACCACCTAG AATATTCGTA TCCAATGTGG CAATACCTGC

551 AATTGATTTT AAACCAGGTA CATTTTCAAC GCCTTTTTCT AAATTAGCGC

601 CAAATGTATG TGGCCATTGC GTTAAAATGG CATTTATAAA TGTATTAAAC

651 ATTAAGTAAC CCATCAATGC TGCAAGCGCT GCATGACCTG GTGCTTTTTT

701 AGCTAAAGAA AGTGGTAAAC CTACAACAAA TACAACTTCC ATATGCGTAA

751 AAATAACCCA GCCACCAGAT TCTATCACTG ACCAAAATTT AAACCAAAAC

801 GTATGTTGAT CTGCTAAACT CCCCATGATT GTAGGATTTT TAAATAATGT

851 CGCAAAGCCA

>gι 11486243 (D50543) unknown [Bacillus subtilis] Length = 527

Minus Strand HSPs:

[SEQ ID NO: ] score = 776 (357.0 bits) . Expect = 1.7e-114, Sum P(2) = 1.7e-114 Identities = 136/249 (54%) , Positives = 179/249 (71%) , Frame = -3

Query: 862 LGFATLFKNPTIMGSLADQHTFWFKFWSVIESGGWVIFTHMEWFWGLPLΞLAKKAPGH 683

+G +TLFKN T+MG LAD FW++ W +IE GGW +F M ++F +G+P++LAKKA Sbjct: 26 VGISTLFKNKTLMGPLADPDGFWYQCWYIIEQGGWTVFNQMPLLFAIGIPVALAKKAQAR 85

Query: 682 AALAALMGYLMFNTFINAILTQWPHTFGANLEKGVENVPGLKΞIAGIATLDTNILGGIII 503

A L AL YL FN F++AILT W FG ++ + V GL IAGI TLDTNI+G I I

Sbjct: 86 ACLEALTVYLTFNYFVSAILTVWGGAFGVDMNQEVGGTΞGLTMIAGIKTLDTNIIGAIFI 145

Query: 502 SAIITWIHNRYYSKRLPEMVGVFQGLTFWTISFFVMLPLAAITCVIWPTVQHGIGSMQH 323

S+I+ ++HNRY+ K+LP+ +G+FQG T++V IΞFF+M+P+A IWP VQ GIGS+Q

Sbjct: 146 SSIWFLHNRYFDKKLPDFLGIFQGSTYIVMISFFIMIPIALAVSYIWPMVQSGIGΞLQS 205

Query: 322 FIIAΞGYIGVWLYHFLERVLIPTGLHHFIYAPIEVGPVWNHGLKAEWLQHLNEFAKΞTK 143

F++ASG +GVW+Y FLER+LIPTGLHHFIY P GP V G+ W QHL E+++S K Sbjct: 206 FLVASGAVGVWIYTFLERILIPTGLHHFIYTPFIYGPAVAEGGIVTYWAQHLGEYSQSAK 265

Query: 142 PLKEQFPYG 116

PLKE FP G Ξbjct: 266 PLKELFPQG 274

[SEQ ID NO: ] score = 91 (41.9 bits) , Expect = 1.7e-114, Sum P(2) = 1.7e-114 Identities = 19/30 (63%), Positives = 21/30 (70%), Frame = -1

Query: 93 KVFGCLGIALAMYATTPKENRKKVAALLIP 4

K+FG GIALA Y T KE +K VA LLIP Sbjct: 283 KIFGIPGIALAFYVTAKKEKKKLVAGLLIP 312

>gi 1 90532 (L10328) similar to phosphotransferase system II permeases [Escherichia coli] Length = 455

Minus Strand HSPs:

[SEQ ID NO: ] score = 61C (280.6 bits), Expect = 1.2e-92, Sum P(2) = 1.2e-92 Identities = 114/235 (48%), Positives = 158/235 (67%), Frame = -3

Query: ^' 820 SLADQHTFWFKFWSVIESGGWVIFTHMEWFWGLPLSLAKKAPGHAALAALMGYLMFNT 641

S D ++ + + +IE GGW +F +M ++F VGLP+ LAK+A G A LA ++ +L +N Sbjct: 128 SLTDPNSLFAQIVHIIEEGGWTVFRNMPLIFAVGLPIGLAKQAQGRACLAVMVSFLTWNY 187

Query: 640 FINAILTQWPHTFGANLEKGVENVPGLKSIAGIATLDTNILGGIIISAIITWIHNRYYΞK 461

FINA+ W FG + + GL +AGI TLDT+I+G HIS I+T +HNR + K Sbjct: 188 FINAMGMTWGSYFGVDFTQDAVAGSGLTMMAGIKTLDTSIIGAIIISGIVTALHNRLFDK 247

Query: 460 RLPEMVGVFQGLTFWTISFFVMLPLAAITCVIWPTVQHGIGSMQHFIIAΞGYIGVWLYH 231

+LP +G+FQG ++W I+F VM+P A +T + WP VQ GI S+Q F+ ++G +GVW+Y Sbjct: 248 KLPVFLGIFQGTSYWIIAFLVMIPCAWLTLLGWPKVQMGIESLQAFLRSAGALGVWVYT 307

Query: 280 FLERVLIPTGLHHFIYAPIEVGPWVNHGLKAEWLQHLNEFAKSTKPLKEQFPYG 116

FLER+LIPTGLHHFIY GP V G++ W QHL EF+ S +PLK FP G Sbjct: 308 FLERILIPTGLHHFIYGQFIFGPAAVEGGIQMYWAQHLQEFSLSAEPLKSLFPEG 362

(SEQ ID. NO: ] score = 99 (45.5 bits). Expect = 1.2e-92, Sum P(2) = 1.2e-92 Identities = 20/30 (66%), Positives = 23/30 (76%), Frame = -1

Query: 93 KVFGCLGIALAMYATTPKENRKKVAALLIP 4

K+FG +GI+LAMY T ENR KVA LLIP Sbjct: 371 KIFGAVGISLAMYFTAAPENRVKVAGLLIP 400

[SEQ ID NO: ] contig[0157] Length: 805 Check: 2790 ..

1 CCCGTGTCCC TAGAAGGAGA GCTAAGCAAA AAGCATTAGA ACTTGTCGAA

51 CTCGTCGGTT TAAAAGGTAG AGAAAAGGCT TATCCATCAG AGTTATCAGG

101 TGGACAAAAG CAACGTGTTG GGATTGCACG AGCGTTAGCT AATGATCCAA 98/23738

151 CGGTCTTGCT TTGTGATGAG GCAACAAGTG CACTTGATCC GCAAACAACA

201 GATGAAATTT TAGATCTACT ACTAAAAATT AGAGAACAAC AAAATTTAAC

251 AATTGTACTA ATTACGCATG AAATGCATGT CATTCGTCGT ATTTGTGATG

301 AAGTTGCAGT TATGGAAAGT GGTAAAGTGA TAGAACATGG ACCGGTGACA

351 CAGGTTTTTG AAAATCCGCA ACACACTGTG ACAAAACGAT TTGTGAAAGA

401 AGATTTAAAT GATGATTTCG AAACATCTTT AACAGAATTA GAGCCATTAG

451 AAAAAGATGC TTATATCGTT AGATTAGTTT TCGCTGGTTC AACAACAACC

501 GAGCCTATTG TATCGAGTCT ATCAACTGCC TATGATATTA AAATTAATAT

551 TTTAGAAGCA AATATTAAAA ATACAAAAAA TGGAACAGTC GGCTTTTTAG

601 TTCTGCATAT TCCATATATT TCAAGTGTAG ATTTCGGAAA ATTCGAAAAA

651 GAGTTAATTG AGCGACAAGT TAAAATGGAG GTGTTAAGAC ATGGGTAAAT

701 CATTTAGTGA AATTATAAAT GAAATGATTA CAATGCCTAA TATTNCAGTG

751 GCCAGAAGTT TGGACTGCAA TAGTCGAAAC ACTATACATG ACAGTCGTCT

sp|P44785|ABC_HAEIN ATP-BINDING PROTEIN ABC. >pir| |C64082 ATP-binding protein

(abc) homolog - Haemophilus influenzae (strain Rd KW20) >gi| 1573615 (U32744) ATP-binding protein (abc) [Haemophilus influenzae] Length = 345

Plus Strand HSPs:

[SEQ ID NO: ] score = 372 (171.1 bits) . Expect = 1.4e-52, Sum P(2) = 1.4e-52 Identities = 70/129 (54%) , Positives = 97/129 (75%), Frame = +3

Query: 12 RRRAKQKALELVELVGLKGREKAYPSELΞGGQKQRVGIARALANDPTVLLCDEATSALDP 191

+ + ++K L++LVGL + AYPS LSGGQKQRV IARALA+DP VLLCDEATSALDP Sbjct: 114 KAKIQEKITALLDLVGLSEKRDAYPSNLSGGQKQRVAIARALASDPKVLLCDEATSALDP 173

Query: 192 QTTDEILDLLLKIREQQNLTIVLITHEMHVIRRICDEVAVMEΞGKVIEHGPVTQVFENPQ 371

TT IL LL +1 +TI+LITHEM V+++ICD+VAV++ G+++E G V ++F NP+

Sbjct: 174 ATTQSILKLLKEINRTLGITILLITHEMEWKQICDQVAVIDQGRLVEQGTVGEIFANPK 233

Query: 372 HTVTKRFVK 398

+ + F++ Sbjct: 234 TELAQEFIR 242

[SEQ ID NO: ] score = 69 (31.7 bits) , Expect = 1.4e-52, Sum P(2) = 1.4e-52 Identities = 15/69 (21%) , Positives = 33/69 (47%) , Frame = +3

Query: 405 LNDDFETSLTELEPLEKDAYIVRLVFAGΞTTTEPIVSSLSTAYDIKINILEANIKNTKNG 584

L D++ +LT+ K I++ F G + P++S S + ++++IL + I

Sbjct: 249 LPDEYLENLTDTPKHSKAYPIIKFEFTGRSVDAPLLΞQAΞKKFGVELSILTSQIDYAGGV 308 Query: 585 TVGFLVLHI 611

G+ + + Sbjct: 309 KFGYTIAEV 317

[SEQ ID NO: ] contig[0156] Length: 1096 Check: 5331

1 TGTAGGGTGA TTGCAATGTC ATCTAAGCCA TTTACAAGTT TATTTTTCCA

51 AGTTTCATCA ATTTCAAAAT GGAAACGCTT GTCTGGTGAT GACACAGTTT

101 GATTTGGTAA ATCTATTTCA ATTTCCTCAT ATTGTGCAAG ATGTTCACGA

151 GCACTTTTTT CTAAAACGAT AGGCAACATC GCATTTTTAG TGCAATTCAT

201 ATAAAATATG TCACTGAAAC TTCCTGCAAT AATAATATGA AAACCATAGT

251 CCTTAAGAGC CCAAGCAGCA TGTTCACGAC TTGAACCACA TCCAAAATTA

301 TCTCCAGTAA TTAAAATAGA AGCCCCTTTA TATTGTGGTT TGTTAGGATT

351 GAAATCAGGA TTATCTGAAC CATCAGGTAA GTACCGCCAT TCATCAAAAG

401 CAAATGGACC AAAGCCACTT TTTGAAATAC GCTTTAAGTG TACCTTAGGA

451 ATGATTTGGT CTGTATCGAT ATTGTCGTTG AAGAGAGGGA CTATTTTACC

501 TTTATATGTT GTAATAGGTT TGATTGCTGC CATTTAAACA ACCACCTTTC

551 TTACGTCCAC AAATTTACCA TGAATAGCTG CTGCTGCTGC CATAGCAGGG

601 GATACTAAAT GTGTTCTTGC ACCTTTGCCT TGTCGTCCTT CAAAGTTTCG

651 ATTACTTGTA GATGCACAAT GTACGCCCTC AGGTACTTGG TCAGGATTCA

701 TGCCTAAACA CATTGAACAT CCTGGTTCAC GCCATTCAAA TCCTGCATTT

751 TTAAAGATAG TATCTAGACC TAATTTTTCT GCTTCTTTTT TTACTGTACG

801 AGAACCTGGT ACGACAATAG CTGTAATATT TGGATGAACT TTATTTCCTT

851 TAACAATATG ACTAGCTTCA ATCAAATCTG ATAGTCTAGC ATTTGTACAT

901 GAACCGAGAA AAACATACCC TAAGTCGATG TCTTCAGCTT TTTGACCTGG

951 TTCTAACCCC ATATAATCAT ACGCACGTTG ATCGTTGATA TCATTGATTT

1001 CAGGGAATGG TTCACTGAAA TTAACACCCA TTTCAGGATT AGTTCCCCCA

1051 TGTCACTTGT GGTTCTAATG TTGAAACATC AAGTTCAATT ACA

gi|1000692 (D67033) LeuA [Rhizomucor pusillus) Length = 755

Minus Strand HSPs:

[ΞEQ ID NO: ) score = 484 (222.6 bits), Expect = 1.3e-119, Sum P(6) = 1.3e-119 Identities = 92/146 (63%), Positives = 112/146 (76%), Frame = -3

Query: 980 QRAYDYMGLEPGQKAEDIDLGYVFLGSCTNARLSDLIEASHIVKGNKVHPNITAIWPGS 801

+RA DY+GL+P +++ + VF+GSCTN+R+ DL A+ I KG V + A+WPGS Sbjct: 326 ERALDYIGLKPNTPMQEVKIDKVFIGSCTNSRIEDLRAAAAIAKGRHVADWVYAMWPGS 385

Query: 800 RTVKKEAEKLGLDTIFKNAGFEWREPGCSMCLGMNPDQVPEGVHCASTSNRNFEGRQGKG 621 VKK+AE+ GLD IFK AGF+WRE GCΞMCLGMNPDQ+ G CASTSNRNFEGRQG G Sbjct: 386 GLVKKQAEQEGLDRIFKEAGFDWREAGCSMCLGMNPDQLKPGERCASTΞNRNFEGRQGAG 445

Query: 620 ARTHLVSPAMAAAAAIHGKFVDVRKV 543

RTHL+SPAMAAAAA+ G F DVRK+ Sbjct: 446 GRTHLMSPAMAAAAAVTGYFTDVRKL 471

[SEQ ID NO: ] score = 205 (94.3 bits). Expect = 1.3e-119, Sum P(6) = 1.3e-119 Identities = 39/78 (50%), Positives = 52/78 (66%), Frame = -3

Query: 341 KPQYKGAΞILITGDNFGCGSΞREHAAWALKDYGFHIIIAGSFΞDIFYMNCTKNAMLPIVL 162

+P + ++ TG NFGCGSSREHA WA D+G HA SF+DIF+ NC KN MLPI L Ξbjct: 592 EPYRQΞRILVCTGPNFGCGSΞREHAPWAFNDFGIRSIIAPSFADIFFNNCFKNGMLPITL 651

Query: 161 EKΞAREHLAQYEEIEIDL 108

+ E LA++ + + +L Ξbjct: 652 PQDKVEMLAEHAKQKAEL 669

(SEQ ID NO: ] score = 108 (49.7 bits), Expect = 1.3e-119, Ξum P(6) = 1.3e-119 Identities = 22/48 (45%), Positives = 30/48 (62%), Frame = -3

Query: 146 EHLAQYEEIEIDLPNQTVSSPDKRFHFEIDETWKNKLVNGLDDIAITL 3

EH Q E+E+DL NQ V P F+++ K+ LVNGLDDI +T+ Ξbjct: 661 EHAKQKAELEVDLVNQWRYPGGEVPFDVEPFRKHCLVNGLDDIGLTM 708

[SEQ ID NO: ] score = 94 (43.2 bits), Expect = 1.3e-119, Sum P(6) = 1.3e-119 Identities = 21/50 (42%), Positives = 27/50 (5 %) , Frame = -3

Query: 530 AAIKPITTYKGKIVPLFNDNIDTDQIIPKVHLKRISKΞGFGPFAFDEWRY 381

A + TT +G PL N+DTD IIPK LK I ++G G F R+ Ξbjct: 527 AGMPKFTTLRGYAAPLDIANVDTDMIIPKQFLKTIKRTGLGTALFYNIRF 576

[SEQ ID NO: ) score = 50 (23.0 bits). Expect = 1.3e-119, Ξum P(6) = 1.3e-119 Identities = 9/21 (42%), Positives = 14/21 (66%), Frame = -3

Query: 371 GSDNPDFNPNKPQYKGASILI 309

G +NPDF N+ Y+ + IL+ Sbjct: 581 GEENPDFVLNQEPYRQSRILV 601

[SEQ ID NO: ] score = 38 (17.5 bits), Expect = 1.3e-119, Sum P(6) = 1.3e-119 Identities = 5/13 (38%), Positives = 9/13 (69%), Frame = -2

Query: 1083 LDVSTLEPQVTWG 1045

+D + + P +TWG Sbjct: 285 IDAADIAPTLTWG 297 98/23738

[SEQ ID NO : ] contig [ 0155 ] Length : 933 Check : 7811 . .

1 CCCAACTTCT CCAACCAATT CTTCTGATCG TTCTGGCCCA TAAATATATG

51 CCGTATCTAA TAAATTAATA CCATGATTAA TGGCTTGACG AACAACATCT

101 TTTCCTTGTT CTTCATCTAA GTTCGGATAT AAATTATGCC CACCTACTGC

151 GTTCGTCCCA AGTGCGATTG GAAACACTTC AACATCAGAT TTACCTAAGT

201 TTACAAATTG CTTCATTAGA CCCAGCTCCT TATCTTTATA ACTTTTCCAC

251 TATCACACTA TCATGATTTA ATACAACTTC CAAATGTTAG AATTAGGGTT

301 TGAATTAAGG CGGTGTATTA GAAAAATGTT ATGTAGAACT CAGTTAAAAT

351 AAGTATGCTT AAGTTGATAT GCATATAGCG CGATTGCTCG TTGACCTTTA

401 AATTACATGT ACTTTTGAAT CAGAAATTGA AAAACATTTA AGAACGACAA

451 TATTAAAGCC ATTGCAAATT TAATTAGAAA TACTATAATG TTTTGATTTG

501 CATAACAAAG AAATTAAAAC TGTTAATATT AACATGGGAT ATCCATTATA

551 AAATATTCAT CTTTGTAGTT GATAATTCTA TATTTCGGAT TTTTATTCAT

601 TCTATCTATG AGTCAAATTT TTA ATTAAA TTTAATAATT TTAGATTTAA

651 AAAACTCATT TATTATTCAG CTTTTTTAAG AAGTATTACA TGAGCTTTTT

701 TAATGCCAAT GGGAACAATG TTTATAAAAA AGAAAAACAT AGTTACTGCA

751 CCCCAACAGA TAAATATAAT TATATTTTGA ACATCTATAG TTATCAGGGC

801 ATATAAAGTG AAAAATGAAA AACCACCGAA ATATAAATAT GCAAATATTA

851 TAAAGAAAAA ATGTTTTAAA TTAGGTAGTA ATATCATTTT CTGACTTTTT

901 TCTTTATTCA TAGTAAAAAC ACTTAATGCT

>sp | P4633 6 | YXBF_BACΞU HYPOTHETICAL 35 . 2 KD PROTEIN IN HTPG- IOLR INTERGENIC

REGION . >gi 1 904205 (D45242 ) similar to common tobacco auxin-induced protein : PIR Accession Number Ξ16390 [Bacillus subtilis ] Length = 310

Minus Ξtrand HΞPs :

( ΞEQ ID NO : ] score = 266 ( 122 .4 bi ts ) , Expect = 4 . 6e-28 , P = 4 . 6e-28 Identities = 49/65 (75% ) , Positives = 59/65 ( 90% ) , Frame = -1

Query: 198 LGKSDVEVFPIALGTNAVGGHNLYPNLDEEQGKDWRQAINHGINLLDTAYIYGPERSEE 19

LGKSD++VFPI LGTNAVGGHNLYPNL+EE GK++VR+AI +G+ +LDTAYIYG RSEE Ξbjct : 6 LGKSDLQVFPIGLGTNAVGGHNLYPNLNEETGKELVREAIRNGVTMLDTAYIYGIGRSEE 65

Query: 18 LVGEV 4

L+GEV Sbjct : 66 LIGEV 70

[SEQ ID NO: ] contig [0153] Length: 924 Check: 6397 98/23738

1 GGACCAGGTG CTACACAGTT CACTCTAATT CCTTTTGGTC CTAATTCTTC

51 TGAAAAACTT TTAGTTAATG AAATAATTGC TGCTTTTGAA GCGGCATAAT

101 CATGAAGAAT AGGACTAGGA TTATAACCTT GTACAGATGA TGTCGTTGTA

151 ATTGACGCAC CCGGTTTTAA ATATTCCAAT GCTTTTTGAA CTGTCCAAAA

201 TAGCGGATAG ACATTCGTTT CAAATGTTTC TGTAAATGCC TCAGTTGTAA

251 ATCCATGAAT ATCATCATGA TACTGTTGAT GTCCAGCAAC TAAAGTAACA

301 TTATCTAAGC CACCTAATTG TTGATATGCT TGTTCAACAA GGTCATAGTT

351 GAACTGCTCA TCTCTTATAT CACCAGGAAT TAACACTGCC TTTTGACCAC

401 TTTCTTCAAT TACTTGGCGT ACTTCTTGTG CATCTTGTTC TTCACTCGGA

451 AGATAGTTAA TCGCTACATC TGCACCTTCT TTAGCATACG CAATTGCTGC

501 TGCACGCCCT ATTGCTGAGT CACCACCTGT GACTAACATT TTATAGCCTT

551 GTAAGCGTTG ATGACCTTGG TAAGACGTTT CGCCACAATC AGGTGCTGGC

601 GTCATTTCAG ATTGTAAACC CGGTACCTCT TGTTCTTGTT TTTCATATTC

651 CGTTGTTTTA AATTTTGTTC TAGGATCTTG AGTTGCCATT TTTTAACATC

701 TCCTTATTCG CTTAATGGTT ATTATTTACC CAATCTTCCT AGGAACTTAA

751 TCATGATTAC ACTAAAAATT ACTTTCTTCT TTATAAAAAC AAGCTCGAAT

801 TACTCATGCA ATAGTCTCTT TACAAATTCA ACAAAATACT CAGGTACTTT

851 TTCCAGAATC CTTTCATCCG GTTTATATTG AGGGTGATGT AAATCATATT

901 CACTATGAGA ACCAATTAAC

>gi 1 882532 (U28377 ) ORF_o294 [Escherichia coli ) Length = 294

Minus Strand HSPs :

[ SEQ ID NO : ] score = 679 ( 312 . 3 bits ) , Expect = 3 . 4e-89 , P = 3 . 4e-89 Identi ties = 132/226 ( 58% ) , Positives = 171/226 (75% ) , Frame = -2

Query : 680 QDPRTKFKTTEYEKQEQEVPGLQΞEMTPAPDCGETSYQGHQRLQGYKMLVTGGDΞAIGRA 501

+DP T++ T EY KQ+Q PG+Q++MTP PDCGE +Y G RL+ K LVTGGDS IGRA Sbjct : 5 KDPTTQYYTGEYPKQKQPTPGIQAKMTPVPDCGEKTYVGΞGRLKDRKALVTGGDΞGIGRA 64

Query : . 500 AAIAYAKEGADVAINYLPSEEQDAQEVRQVIEESGQKAVLIPGDIRDEQFNYDLVEQAYQ 321

AAIAYA+EGADVAI+YLP EE+DAQ+V+++IEE G+KAVL+PGD+ DE+F LV +A++ Sbjct : 65 AAIAYAREGADVAISYLPVEEEDAQDVKKIIEECGRKAVLLPGDLΞDEKFARSLVHEAHK 124

Query : 320 QLGGLDNVTLVAGHQQYHDDIHGFTTEAFTETFETNVYPLFWTVQKALEYLKPGASITTT 141

LGGLD + LVAG Q DI T + E F +TF NV+ LFW Q+A+ L GASI TT

Sbj ct : 125 ALGGLDIMALVAGKQVAIPDIADLTSEQFQKTFAINVFALFWLTQEAIPLLPKGASIITT 184

Query : 140 ΞSVQGYNPSPILHDYAASKAAIISLTKSFΞEELGPKGIRVNCVAPG 3

SS+Q Y PSP L DYAA+KAAI++ ++ + + + + KGIRVN VAPG Sbj ct : 185 SSIQAYQPSPHLLDYAATKAAILNYΞRGLAKQVAEKGIRVNIVAPG 230 [ SEQ ID NO : ] contig [ 0152 ] Length : 874 Check : 3335 . .

1 CCCGTCGTTT CACTTGGTTT CGTAATTTCA CCACTCATAA TCTTGGCCAT

51 ATCATGTTTA ATTTGATCTG ATTTTGGACC AAAGATAGCT TGCATATTGT

101 TTCCAACTTC TAATACACCT GATGCGCCTA AAGCTTTAAT ACCTGCTACA

151 TCTACTTTTG ATTTATCAAC CACTTCTACG CGCAGACGTG TAATACATGC

201 ATCTAAATGT TTAATGTTTT CTTTTCCACC CATTGCATCT AAGACATCAA

251 ATGGTAATTT TGCGACACTA GAGTTACGAA TTTCAGTTTC TTCATCTTCA

301 CGACCTGGTG TTTTCAATTT AAACTTACGA ATTGCAAAGT CGAATAAGAA

351 GTAATACACG ATAGCATATA CAATACCGAC TGGAATAACT AATAATGCGT

401 GTGAACGATC CCAGTTTAAT AAACCATATA AAATATAATC TATGAAACCA

451 CCTGAGAATG TCATACCAAT TTTAACGCCT AATAAATGCA TTACTAAGAA

501 TGATGTACCA GCTAATAATA CGTGAATTCC A AAAGTACT GGTGCTACAA

551 ATAAGAATGA AAATTCTAAT GGCTCAGTGA TACCAGTTAA AAATGCAGTT

601 AATCCTGCTG ATAACATTAA ACCACCCACG ACTTTTTTGC GTTCTGGTCG

651 TGCATTTTTA TAAATAGCAA ATGCCGCCGC TGGTAAACCA AACATCATAA

701 ATGGATATTT ACCAGTAGTA AATGCACCAG CAGTAAATGG TACGCCATCT

751 TTCAATTGTG CCATCCAAAT ACGTTGGTCA CCACGAACTA ATTCACCTGC

801 GTGATTTGNA TAACTTCCGA ATTCAAACCA GAACGGTGAA TAGAAAATAT

851 GATGTAAACC AAATGGAATT AGGG

gi | 1072419 (X93360 ) glcB gene product [ Staphylococcus carnosus ] >prf | | 2209412B glcB gene [ Staphylococcus carnosus ] Length = 692

Minus Strand HSPs :

[SEQ ID NO : ] score = 1246 ( 573 . 1 bits ) . Expect = 4 . 4e-168 , P = 4 . 4e-168 Identities = 234 / 290 ( 80% ) , Posi tives = 261 /290 ( 90% ) , Frame = -3

Query : 872 LIPFGLHHIFYSPFWFEFGΞYXNHAGELVRGDQRIWMAQLKDGVPFTAGAFTTGKYPFMM 693

LIPFGLHHIFY+PFWFEFG Y N +G LVRGDQRIWMAQ +DGVPFTAGAFTTGKYPFMM Ξbj ct : 238 LIPFGLHHIFYAPFWFEFGHYVNEΞGNLVRGDQRIWMAQYQDGVPFTAGAFTTGKYPFMM 297

Query : 692 FGLPAAAFAIYKNARPERKKWGGLMLΞAGLTAFLTGITEPLEFSFLFVAPVLYGIHVLL 513

FGLPAAAFAIY A+PER+KWGGLMLΞA LT+FLTGITEPLEFΞFLFVAP+LY HV+L Ξbjct : 298 FGLPAAAFAIYPQAKPERRKWGGLMLΞAALTSFLTGITEPLEFSFLFVAPILYVAHVIL 357

Query : 512 AGTΞFLVMHLLGVKIGMTFSGGFIDYILYGLLNWDRSHALLVIPVGIVYAIVYYFLFDFA 333

AGTSFL+MHLL V+IGMTFΞGGFIDYILYGLL+WDRS+ALLVIPVGI YA++YYFLF F Sbj ct : 358 AGTSFLIMHLLHVQIGMTFΞGGFIDYILYGLLΞWDRSNALLVIPVGIAYALIYYFLFTFL 417

Query : 332 IRKFKLKTPGREDEETEIRNΞSVAKLPFDVLDAMGGKENIKHLDACITRLRVEWDKSKV 153 I+K LKTPGRED+E E ++ SV++LPF+VL+AMG K+NIKHLDACITRLRVEV DK V Ξbjct: 418 IKKLNLKTPGREDKEVESKDVSVSELPFEVLEAMGNKDNIKHLDACITRLRVEVRDKGLV 477

Query: 152 DVAGIKALGAΞGVLEVGNNMQAIFGPKSDQIKHDMAKIMSGEITKPΞETT 3

DV +K LGAΞGVLEVGNNMQAIFGPKSDQIKHDM +IM G+IT P+ETT Sbjct: 478 DVEKLKQLGASGVLEVGNNMQAIFGPKΞDQIKHDMQQIMDGKITSPAETT 527

[SEQ ID NO: ] contig[0150] Length: 877 Check: 4544 ..

1 CCCTCGAATT TATGATGATT AGCATAAAAA TACACCCCAT AAAGTTAGTT

51 TTTTAGTCTA ACTTTCGGGA TGCACATCTT AGTTCTAATG GAGATTGTCT

101 TT AAATAGG CTATGACATT TCTATTTCAG GCTAGATATA TTTGTATTTA

151 TAGTATAAAT ACAAAGAATG TAAAGACAAC TATGATATTA ATAGGTAGTA

201 ACGACAAACA TAACTCTTTA GCTTTTTCGC CATTTTTTCC CATCATAACT

251 TCATTATATC GATTCATATA CTTTTCGACA TCTTTAACAG TGACATCTAT

301 TTCCTGAGTT GCTCAATTTA CTTTTCATAA TTATTTTTGA TTTCGTATTG

351 TGATTATCCA CTACTTATCT ATAACGAGTT CGCAACTTTA GTACCATCAC

401 AGCATTCATA GTTAAAATAT GTTGGTGTCG TATTTTAAAC TTGAAAATGT

451 CACGTTTTCC ACAATATTTG TAAGTGTATA AGCCATGATC CTTTTCCTTA

501 TATCTTAGTC CATACTTGCT TTACCACTGT TCGATATTTT GTCGTTCACC

551 TTTAAAGTTA TTGCGCTTAT GATGTCTACG CGCTAATTCC GCCTCAATTT

601 CTGAAAAATC GACGCCTAGC GCATGCATCA AGACAAATAA ATGATAAAGT

651 TCATCTGCTA CTTCACTTAC AAATGCTTTT TTGTCACCTT TAATTGCTTC

701 AATTACGACT TCAAAAGCTT CTTCACCGTA TTTTTTTGTA ATCTTTTCTA

751 TACCTTCTGT TAATAAA AT TTTGTATATG ACTTTTCATT ATTGGATTGG

801 GCACTATCTT GAACTGTCTG CGCTAATGTT TGCACTGAAA ATGGAACTTC

851 TGTGTTGAAA CAACTTTGAC TGCCGGG

sp|Q02130|HIΞ2_LACLA PHOΞPHORIBOSYL-AMP CYCLOHYDROLASE / PHOSPHORIBOSYL-ATP PYROPHOSPHOHYDROLAΞE . >pir| |C47754 phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19) / phosphor ibosyl -ATP pyrophosphatase (EC 3.6.1.31) - Lactococcus lactis subsp. lactis >gi|149384 (M90760) HisIE [Lactococcus lactis] Length = 212

Minus Strand HΞPs:

[ΞEQ ID NO: ] score = 192 (88.3 bits), Expect = 1.0e-17, P = 1.0e-17 Identities = 39/79 (49%), Positives = 48/79 (60%), Frame = -1

Query: 787 EKSYTKYLLTEGIEKITKKYGEEAFEWIEAIKGDKKAFVSEVADELYHLFVLMHALGVD 608

EKSYT YLL EGI+K+ KK GEEA EV I + DK + E+ D LYHLFVLM+ G+ Sbjct: 126 EKSYTNYLLGEGIDKVLKKVGEEASEVTIAΞKNSDKGELLGEIDDLLYHLFVLMNQQGIΞ 185 Query: 607 FΞEIEAELARRHHKRNNFK 551

E+ + RH N K Ξbjct: 186 LEEVRQKAKERHQLEGNKK 204

[SEQ ID NO: ] contig[0149] Length: 990 Check: 5463

1 TTGAATTGAA ATTTTGGGGG GAGGTATTGT AATGACGTTT CTTACAGTCA

51 TGCAATTTAT AGTTAACATT ATCGTTGTAG GCTTCCTGCT TACGGTTATT

101 GTTATCGGGC TTATTTGGTT AATTAAAGAT AAAAGACAAT CACAACATAG

151 TGTATTAAGG AATTATCCTT TACTAGCACG TATTAGATAT ATTTCAGAAA

201 AAATGGGACC GGAATTACGT CAGTATTTAT TTTCTGGGGA TAATGAAGGG

251 AAACCTTTTT CACGTAATGA TTATAAAAAT ATCGTTTTGG CTGGAAAATA

301 TAACTCTCGT ATGACCAGCT TCGGTACTAC TAAAGATTAT CAAGACGGCT

351 TTTACATACA GAACACAATG TTTCCGATGC AACGTAATGA GATTTCAGTA

401 GATAATACAA CATTGTTATC AACATTCATT TATAAAATCG CGAATGAGCG

451 TTTATTTAGT CGTGAAGAAT ATCGTGTACC GACAAAGATT GATCCGTATT

501 ACTTAAGTGA TGACCATGCA ATAAAATTAG GTGAACATTT AAAACATCCA

551 TTTATTTTAA AACGTATCTA GGACAATCTG GTATGAGTTA TGGCGCTTTA

601 GAAAAAATGC CATTACAGCT TTATCTAAAG GTCTAGCAAA GCGGGCACTT

651 GGATGAATAC AGGTGAAGGT GGCTTATCAG AATATCATTT AAAAGGTAAT

701 GGGGATATCA TTTTCCAAAT TGGTCCCGGT TTATTTGGTG TTCGTGATAA

751 AGAAGGTAAT TTTAGTGAAG GTTTATTTAA AGAGGTCGCA CAGTTATCTA

801 ACGTACGCGC ATTTGAGCTG AAGTTGGCAC AAGGTGCTAA GACTCGTGGT

851 GGTCATATGG AAGCTGAAAA GGTAAACGAA GAAATTGCTA AAATCCGAAA

901 TGTTGAACCT TATAAAACAA TCAATTCACC TAACCGTTAC GAATTTATTC

951 ATAATGCTGA AGATTTGATT CGTTTCGTCG ATCAGTTGCA

gi 11591994 (U67575) glutamate synthase (NADPH) , subunit alpha [Methanococcus jannaschii] Length =.510

Plus Ξtrand HSPs:

[SEQ ID NO: ] score = 83 (38.2 bits) , Expect = 5.3e-08, Sum P(3) = 5.3e-08 Identities = 21/53 (39%) , Positives = 27/53 (50%) , Frame = +2

Query: 593 AL*KKCHYΞFI*RΞSKAGTWMNTGEGGLSEYHLKGNGDIIFQIGPGLFGVRDK 751

AL H SF + GT+M TGEGGL + II Q+ G FGV ++

Sbjct: 187 ALSLNAHLΞFAKAVKECGTFMGTGEGGLPKALYPYADHIITQVAΞGRFGVNEE 239

[SEQ ID NO: ] score = 71 (32.7 bits), Expect = 5.3e-08, Sum P(3) = 5.3e-08 Identities = 17/47 (36%), Positives = 24/47 (51%), Frame = +2

Query: 848 GGHMEAEKVNEEIAKIRNVEPYKTINSPNRYEFIHNAEDLIRFVDQL 988 GGH+ EKV EI+ R + SP + I++ EDL + V L Sbjct: 260 GGHLPGEKVTAEISATRMIPEGΞDAIΞPAPHHDIYSIEDLAQLVRSL 306

[SEQ ID NO: ] score = 38 (17.5 bits), Expect = 5.3e-08, Sum P(3) = 5.3e-08 Identities = 7/11 (63%), Positives = 9/11 (81%), Frame = +2

Query: 809 AFELKLAQGAK 841

A E+K+ QGAK Ξbjct: 246 AIEIKIGQGAK 256

>sp|Q06434|GLΞF_ANTΞP FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE (FD-GOGAT).

>pir||S39510 glutamate synthase (ferredoxin) (EC 1.4.7.1) - red alga (Antithamnion sp.) chloroplast >gi| 14400 (Z21705) ferredoxin [Antithamnion sp.) Length = 1536

Plus Ξtrand HSPs:

[ΞEQ ID NO: ] score = 80 (36.8 bits), Expect = 0.00013, Ξum P(3) = 0.00013 Identities = 17/47 (36%), Positives = 29/47 (61%), Frame = +2

Query: 848 GGHMEAEKVNEEIAKIRNVEPYKTINΞPNRYEFIHNAEDLIRFVDQL 988

GG + +KV+ IA++RN +P T+ SP + I++ EDL + + L Sbjct: 997 GGQLPGKKVSPYIAELRNCKPGVTLISPPPHHDIYΞIΞDLAQLIFDL 1043

[ΞEQ ID NO: ] score = 48 (22.1 bits). Expect = 0.00013, Ξum P(3) = 0.00013 Identities = 10/20 (50%), Positives = 13/20 (65%), Frame = +2

Query: 794 LΞNVRAFELKLAQGAKTRGG 853

L N + E+K+AQGAK G Sbjct: 978 LVNAKQLEIKIAQGAKPGEG 997

[SEQ ID NO: 1 score = ^'47 (₂1.6 bits). Expect = 0.00013, Sum P(3) = 0.00013 Identities = 12/39 (30%), Positives = 19/39 (48%), Frame = +2

Query: 593 AL*KKCHYSFI*RΞΞKAGTWMNTGEGGLΞEYHLKGNGDI 709

AL ++ H + R ++ G N+GEGG K D+ Sbjct: 900 ALSRETHETLAIRMNRIGGKSNSGEGGEDSTRFKSIQDL 938

>gi|1100774 (D78371) ferredoxin-dependent glutamate synthase [Synechocystis sp.) >gi 11653782 (D90916) ferredoxin-dependent glutamate synthase (Synechocystis sp . ] Length = 1556

[SEQ ID NO: ] contig[0148] Length: 784 Check: 455 ..

1 CCCGTCTCCA TTAAAAATAC TAGAATATAA TGAAATGCCA TTATAATGAT

51 ATATAAATGG TGAATTTAAT GCATAGTCTG ACATATAATC AATGCGATTA

101 AATGGGCCTG TTGCATTTTG ATTTATCTTT TTTATAAGCT GGTTTACATA

151 GTTACTATGG TAATCATGTT GTTTCAAACG TTGATAATGA TTGTTGATAA

201 GGTTTGATTG CCATATTTTT GTTGTTATCT AAAATGACGA TTTGTTGAAT

251 CATAACGATT AATACTAATA TTGCAACGGT TAATTTTTTA TAACGCCATA

301 AACTAAATTT TAAAATAACG GCAAGCACCA TTAGCAGGAT AATACCTACT

351 ATAAGTGCAA GTGGGTGTGT CGGTGATAGT AATACATAAA GTAATGCGAT

401 GATACTTACT GGTATTGTTC TGATTAAATA ATATTTCATA TTTAATGTTG

451 ATAAATGTTG AATAAACAAT CCGCAAAGAG CGCTTGATGA TAGTGCTAAG

501 ATATACACCC AACGCCTTTC TGGAAATGAA AAACCATTAA AAGCACTGTC

551 GAAATACTGT GATAATGAAC CAATAAATAA TATCCATGTT ACTATTGCGA

601 AAAGTCTATA AAAGTAAAAA CGATACAGTT TGAATGACAA TAATGCAACG

651 ATAGTAAGAA TTGAAATCGT AATATAAAAT CCATCGCTAA AGAAAAAATA

701 ATGATAATCA AGTGGTGTCA AAAACGGTAT ATCAACATTG GGATTTTGCT

751 TTCTGTCATT TTCCAAAAAC GCAGAAATGC CGGG

>sp|P43993 |Y392_HAEIN HYPOTHETICAL PROTEIN HI0392. >pir||B64007 hypothetical protein HI0392 - Haemophilus influenzae (strain Rd KW20) >gi 11573364 (U32723) H. influenzae predicted coding region HI0392 [Haemophilus influenzae) Length = 245

Minus Strand HSPs:

[SEQ ID NO: ] score = 64 (29.4 bits). Expect = 1.0, Sum P(₂) = 0.65 Identities = 18/52 (34%), Positives = 26/52 (50%), Frame = -1

Query: 697 FFFΞDGFYITISILTIVALLΞFKLYRFYFYRLFAIVTWILFIGΞLΞQYFDΞA 542

FF GF IT I+T + SF L +FY R+ I + + +L + SA

Sbjct: 4 FFVISGFLITGIIITEIQQNSFSLKQFYTRRIKRIYPAFITVMALVΞFIASA 55

[SEQ ID NO: ] score = 40 (18.4 bits), Expect = 1.0, Sum P(2) = 0.65 Identities = 11/45 (24%), Positives = 24/45 (53%), Frame = -1

Query: 355 LIVGIILLMVLAVILKFSLWRYKKLTVAILVLIVMIQQIVILDNN 221

L+VG +L + + K L + +AIL + + + + +++NN

Sbjct: 172 LLVGSLLAIYHNLSNKVQLSKQVNNILAILSTLLLFSCLFLMNNN 216 >sp|P24873|NU6M_ASCΞU NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 6. >pir||S26014 NADH dehydrogenase (ubiquinone) (EC 1.6.5.3) chain 6 - pig roundworm mitochondrion (SGC4) >gi|559488 (X54253) ND6 protein [Ascaris suum) Length = 144

Minus Strand HSPs:

(SEQ ID NO: ] score = 51 (23.5 bits). Expect = 2.3, Sum P(2) = 0.90 Identities = 10/31 (32%), Positives = 16/31 (51%), Frame = -1

Query: 619 FYFYRLFAIVTWILFIGSLΞQYFDΞAFNGFΞ 527

FYF + ++ W++F+ F Ξ F FΞ Sbjct: 108 FYFΞVYWMLLVWVIFVLIFFMNFTΞYFLNFΞ 138

[ΞEQ ID NO: ] score = 47 (21.6 bits). Expect = 2.3, Sum P(2) = 0.90 Identities = 8/24 (33%) , Positives = 17/24 (70%) , Frame = -1

Query: 679 FYITISILTIVALLSFKLYRFYFY 608

F++ S+L ++ L+SF L+ ++ Y Sbjct: 27 FFLIFΞLLMVMPLIΞFFLHVWFSY 50

>gi I 581306 (X75323) histidin kinase [Lactobacillus plantarum) >gnl | PID| e217592 (X94434) histidine protein kinase PlnB [Lactobacillus plantarum) Length = 442

Minus Strand HSPs:

[SEQ ID NO: ] score = 54 (24.8 bits), Expect = 4.5, Sum P(2) = 0.99 Identities = 12/51 (23%), Positives = 26/51 (50%), Frame = -2

Query: .153 NYVNQLIKKINQNATGPFNRIDYMΞDYALNSPFIYHYNGISLYSSIFNGDG 1

N + Q K ++ T FN ID ++ A+++P +N ++ + ++ G Sbjct: 351 NAIEQAQKMTDKIVTVAFNEIDNTAEIAISNPIDΞDFNQHQIFΞTGYSTKG 401

[ΞEQ ID NO: ) score = 48 (22.1 bits). Expect = 4.5, Ξum P(2) = 0.99 Identities = 11/39 (28%), Positives = 22/39 (56%), Frame = -1

Query: 451 ΞTLNMKYYLIRTIPVΞIIALLYVLLΞPTHPLALIVGIIL 335

S N+K + I + +++L+ +L T L L++G 1+ Ξbjct: 29 ΞNTNIKRIIYΞLILLLVLSLVGAILDDTTSLILVLGAII 67 [SEQ ID NO : ] contig [ 0145 ] Length : 792 Check : 9423 . .

1 CCCTCTCATG GTGCATATGT CGTTGCCATC ACAAATTTCG AAGGTAGTAA

51 ACTTACAGAT TGTGCAGATT TAGTACTTTT AACAACGGAT CAATCGCGTA

101 ATACCGACCA TCAATTTATC AACACACAAA TTGCGACACT CTTTTTAATC

151 GATATCGTGA GTTATCATTT ATTAGNAAAA TACAAATCTG AGTCAAACTT

201 ATCAACATAC TAAATCTATT ATCCTAGACA ACAAATAACT AGTAGTATAT

251 TCAAATCCAC CTGCAACTGT AGACAATCAT CGTGATTGTC CTAACGAGTT

301 GCTAGGTGCT TTTTTAATTT CAATACCAAA TACTTTTTTA CATTTTTGAG

351 ATCTATACGT TCAACCGTCT TCAATTTAAT ATGCCCGTGG CACACTGTTG

401 GTTGATATAG TTTAGATTGG TCCTAGATAG AGTGTGATGT GTGGAACTAA

451 CAACAGCTCT CATCTCTCGT AACGGTTTCA AATTCTATTT TAGAATGACT

501 CCTTCTTTCA ACTATCATTG CAAACAGCCA TATAATGCTG CATCATTTTT

551 ACTCTTAGTC GTTTGTATTG GTGCATAAAC ATAGTCTTTT GGTAAATAGT

601 GTGCAACTTT CGGCTCGATA TATTTAATGA GATTGTCTCC TTGTTCAGAT

651 ATACCGCCAC CAATTAATAT AAGCCCTGGA TCATACATGA CTTGTATTTG

701 GGCAATCCCT TCTGCTACAT CTTCTGCCCA CTCATTCAAT ATTTGTTTTG

751 CAATATCATC ACCTTCTTCA GCTGCTTCAA ACAATACTGG CA

sp | P 0184 | GLK_ΞTRCO GLUCOKINASE (GLUCOSE KINASE) . >pir | | Ξ26208 glucose kinase - Ξtreptomyces coelicolor >gi | 46851 (X65932 ) glucose kinase [Ξtreptomyces coelicolor) >gnl | PID | e248582 (X98363 ) glucose kinase [Plasmid pIJ2581) Length = 317

Minus Ξtrand HΞPs :

(ΞEQ ID NO: ] score = 92 (42 . 3 bits) , Expect = 0 .0028 , P = 0 .0027 Identities = 18/ 61 (29%) , Positives = 32/ 61 (52%) , Frame = -3

Query: 775 AAEEGDDIAKQILNEWAEDVAEGIAQIQVMYDPGLILIGGGIΞEQGDNLIKYIEPKVAHY 596

AA +G +A E A G+A + ++DP ++GGG+S ++GD ++ I +

Ξbjct : 221 AARQGCPVAVDΞYRELARWAGAGLADLAΞLFDPSAFIVGGGLSDEGDLVLDPIRKSYKRW 280

Query: 595 L 593

L Sbjct : 281 L 281

[SEQ ID NO: ] contig[0144] Length: 843 Check: 7606 ..

1 GGCTTGGCAT TCTAACAGCA ACTGATGATA AACCTCCAGA AACTTTTCGA

51 CATAGATAGC CTGGCTTTAG CGGCAATATA AACGAAATAG GGCCCGGCCA

101 GAATGCCTGC ATTAACTTTT CTACGCGTGG ATCCAAAGTA TATGTAAAAT

151 CTTTTAATTG AACTTTACTG TGTATATGAA CAATAAGCGG ATTGTCAGAT

201 GGACGGCCTT TAGCTTCATA TATTTTAGCT ACAGCTTCTT CATCTGTCGC 251 ATTTGCTGCA AGTCCATAAA CTGTTTCAGT TGGTAAACCT ATTAAACCAC

301 CGTTTAAAAC AATGTCTTTT ATTTCATTAA TTTTAGGATA TTGCTGTAAA

351 TCTTCATTAT ATTCTCTAAC ATCCCAAATT TTAGTATCCA ACTTAATCAC

401 GCCTTTCTTA TTTATCATAA TATAAAGCAA AAAGCTATGC ACTTAACTAA

451 TCATAGCAAA GGCATAACTT CTAATTACCA TTTAAATGAG ACGATTCGAT

501 CGTGGCCATT TATATCTTTA ATAATGTCGA TTTTTTTGTC AGGAAATTTA

551 TTTAAAATTA TTGATTTAAG TGCCTCACCT TGATTGTAAC CAATTTCAAA

601 AACAACTGGG CTGCCTTTTT CCATAACGTG AGGTAAATCT CCAATGNTNG

651 ATTCATAAAT AGCATATCCC ATGGTTATCT GCAAACAATG CCTGATGTGG

701 TTCGAATNTC GTAACCGTTG GAGACATCGT AACCATATCT TTTTCATCTA

751 TATATGGTGG ATTAGATATC AAGCCGTTCA ACTTGATACC TTCTTTAATT

801 AAGGGCTTTA ATGCATCCCC TGTTAAAAAT TGTATTTGTG ATT

>sp|P45873 |HEMK_BACΞU POΞΞIBLE PROTOPORPHYRINOGEN OXIDASE. >pιr||Ξ55438 ywkE protein - Bacillus subtilis >gι| 853777 (Z49782) product similar to E.coli PRFA2 protein [Bacillus subtilis] Length = 288

Minus Strand HSPs:

[SEQ ID NO: ] score = 135 (62.1 bits). Expect = 4.5e-22, Ξum P(2) = 4.5e-22 Identities = 26/60 (43%), Positives = 39/60 (65%), Frame = -1

Query: 669 GYAIYEΞXIGDLPHVMEKGΞPWFEIGYNQGEALKΞIILNKFPDKKIDIIKDINGHDRIV 490

G Y+ + D+P VM+ WFEIG+ QG A+K +IL F +++++KDING DR +

Ξbjct: 221 GLKFYKRFMEDIPLVMKDKVFWFEIGWKQGAAVKDLILKAFKGAEVEVLKDINGKDRTI 280

[ΞEQ ID NO: J score = 120 (55.2 bits), Expect = 4.5e-22, Sum P(2) = 4.5e-22 Identities = 24/59 (40%), Positives = 35/59 (59%), Frame = -3

Query: 841 ΞQIQFLTGDALKPLIKEGIKLNGLISNPPYIDEKDMVTMSPTVTXFEPHQALFADNHGI 665

+ ++F GD L+P IK G K + ++SNPPYI E++M +Ξ V EP AL G+

Ξbjct. 164 ANVRFYQGDLLEPFIKAGKKADIIVΞNPPYISEEEMADLSEIVRFHEPLHALTDGGDGL 222

>sp|P4583l|YRFE_MYCLE HYPOTHETICAL 22.7 KD PROTEIN IN RFE-HEMK INTERGENIC REGION. >gι 1699330 (U15186) yeast ΞUA5 protein [Mycobacterium leprae] Length = 220

Minus Ξtrand HSPs:

[SEQ ID NO: ] score = 159 (73.1 bits), Expect = 6.3e-13, P = 6.3e-13 Identi ties = 32 / 80 ( 40% ) , Posi tives = 49 / 80 ( 61% ) , Frame = -3

Query : 301 GGLIGLPTETVYGLAANATDEEAVAKIYEAKGRPΞDNPLIVHIHSKVQLKDFTYTLDPRV 122

G L+ +PT+TVYG+ A+A D AVA + AKGR D P+ V + S ++ YT+ Ξbj ct : 30 GRLWMPTDTVYGIGADAFDRAAVAALLSAKGRGRDMPVGVLVGSWHTIEGLVYTMPDGA 89

Query : 121 EKLMQAFWPGPISFILPLKP 62

+L++AFWPG +Ξ ++ P Ξbj ct : 90 RELIRAFWPGALΞLVWHAP 109

[SEQ ID NO: ] contig[0143] Length: 765 Check: 1293

1 GCAACGTTCA TACCAGCATT GATTAATTTC TCAATCATTT CTTCTGATTC

51 TGAAGCTGGT CCAATTGTAC ATACAATTTT AGTTTTTCTC ATTTTATAAT

101 TCCTCCTGAA ATCTTATATA GATAACTTGT TAGCAAGTTC ATATAGACTA

151 TAATCAAATT TATGATCTTT ACCATCAAAA ATTTCATCAA AAGATGTTGC

201 TACAATTTTA TTGTTCTTAA TTCCAACACC CTTAGCTGTT TCACCTTGCA

251 TTAATAAGTC TACCGCATAT CCACCTAAAC GTGATGCTAA AACTCTATCC

301 GCACCTGTTG GGCTACCACC ACGTTGAACG TGACCTAACA CAGACACTCT

351 ATTATCAACA TTGATGTATT GTGATAATTC TTTTTGACAA TCTTGCGCAG

401 TCATGCAACC TTCTGCTACA AGAACGATTG AGTGTTTCTT ACCACGTTTA

451 ATACCTTGTT CAATTTTATC AGCTATTTCT TTAATATCTG TTTTCACTTC

501 TGGAACTACA ATTGTCTCAG CACCAACTGA TAATCCAGCC CATAATGCTA

551 GATCTCCACA ATCACGGCCC ATTGCTTCAA TGATAAATGT TCGTGCGTGA

601 CTTGACGCAG TATCTCTAAT TTTGTCGACT AAGCCAATAA TCGTATTTAA

651 AGCTGTGTCA AATCCAATTG TAAAATCAGT ACCATTGATA TCATTGTCAA

701 TCGTACCAGG AATACCGATA GTTTGAATTT CTTTGCATTC CTCACTGATG

751 CGTTGTGCAC CGCGA

>sp|P49620|KDGG_RAT DIACYLGLYCEROL KINAΞE, GAMMA (DIGLYCERIDE KINAΞE) (DGK) (88 KD DIACYLGLYCEROL KINASE) . >gi|784935 (D38448) 88kDa-diacylglycerol kinase (DGK-III) [Rattus norvegicus) Length = 788

Minus Strand HSPs:

[SEQ ID NO: ] score = 46 (21.2 bits), Expect = 0.19, Sum P(2) = 0.18 Identities = 8/20 (40%), Positives = 12/20 (60%), Frame = -2

Query: 106 PPCN'EIVYKNKRRSVCAPP 47

PPC +1 +KN+ + PP Ξbjct: 753 PPCMIKITHKNQAPMMMGPP 772 [SEQ ID NO: ] score = 36 (16.6 bits). Expect = 0.19, Sum P(2) = 0.18 Identities = 7/12 (58%), Positives = 9/12 (75%), Frame = -1

Query: 137 IRNNFFSHGVΞΞ 102

I NN+FΞ GV + Ξbjct: 575 IMNNYFΞIGVDA 586

[ SEQ ID NO : ] contig [ 0142 ] Length : 1111 Check : 2472 . .

1 TCATAACTGG ACCCACGCGG TGGCGGCCGC TCTAGAATAG TGGATCCCCC

51 TGGCCAAGTA TGATGTCGTC CCTTCAGATA ACAAATTTTC GGGATAGATA

101 TTTTAAGCCA TCGTATGACC CATCCATTGC ATCTTGACCA TAACCACCAT

151 GAATATGTAT ATCAATAAAA CCTGGTAATA CATGATGACC TTTAGCATCA

201 ATCACTTGAA TTTTATTTGT CGTATCATTA TCAATTGCTG CTTTATCATC 251 CCCTTCTCCA ATTGCAACAA TCTGTCCATC TTTCACATGA ATGTAACCAT

301 TATCGATTTT GCCATCTTCA GTATAAACTT TGCCGTTATA TATAATTAAT 351 TCTGACACGT ATAAACCCTT CTTTATTTAT AAATTTTCAC TTTAAGACAC 401 TCATATTTTA CTATATCTGC TTCGTTTGGC ATAACTTTTT GCAAAATATT 451 AAAAAAGTCT ATACATTTGT GGTGTCTATT TCTTCATTCA TTTATCTAAA 501 AATAAAAACA CCTTCATATC AATTCATAAA AACTGAATTA ATAGAAAGTG 551 TTTTTACAGC TTTGGTATAA GCTACCGTTA ACACGATGTA TAAAACTAAC 601 ATATATTCAT TGAACTTACA ACTTAATATG AAGCTCTTTG CTAACAATCA 651 TTTTACATCA TTAAAACTAC TCGTCCATTG ATTTTGAAGC TTCGATTTCT 701 GTTTCAGTTA ACTTTGGTTT AATAAGTCCA TAAATTAATG CTGAAACTAA 751 TGTACCAACT AGAAGTGCAA TAAGAGTTTG AAGTAAGTGT GCACCATCAG 801 TACCAACAAT TACAATAATA CCACCATGTG GCGCAGTAAT TCGAGAACCT 851 AAGCCTAAAG CAATTGCGCC ACCTATACCT GAACCAATCA TCATTGAAGG 901 AATAACACGT AATGGATCGG CAGCTGCAAA TGGAATCGCA CCTTCTGTAA 951 TAAAGGACAT ACCCATCACA TAGTTAGGGA TAATTGAACC ACGTTGTTCT

1001 TTTGTAAATT TACGTCTGAA AATTAACATC GCTGTCGCAA TTGCTAACGG 1051 TGGAATCATA CCACCAATCA TTGCAGCTGT AATTGGTGCT GCATTACCTT 1101 CAATCAACGC A

>sp | P49620 | DGG_RAT DIACYLGLYCEROL KINAΞE, GAMMA (DIGLYCERIDE KINASE) (DGK) ( 88 KD DIACYLGLYCEROL KINAΞE) . >gi | 784935 (D38448 ) 88kDa-diacylglycerol kinase (DGK-III ) [ Rattus norvegicus ] Length = 788

Minus Strand HSPs :

[SEQ ID NO: ] score = 46 (21 .2 bits) , Expect = 0 .19 , Sum P ( 2) = 0 .18 Identities = 8/20 (40% ) , Positives = 12/20 ( 60% ) , Frame = -2

Query: 106 PPCN*EIVYKNKRRSVCAPP 47 PPC +1 +KN+ + PP Ξbjct: 753 PPCMIKITHKNQAPMMMGPP 772

[ΞEQ ID NO: ] score = 36 (16.6 bits), Expect = 0.19, Ξum P(2) = 0.18 Identities = 7/12 (58%), Positives = 9/12 (75%), Frame = -1

Query: 137 IRNNFFΞHGVSS 102

I NN+FΞ GV + Sbjct: 575 IMNNYFSIGVDA 586

[SEQ ID NO: ] contig[0141] Length: 152 Check: 395 ..

1 GCTAGTGCTC AGAACTATTT AGCATTAATT AAAGCTTATG AGTAAGCGGG 51 GGAGCACAAA CGCTTCTCCG CTTATTTTTA TATACAATTT CCTAATTACA 101 AGGAGGAAAC ACCATGGCTA AAAAAATTGT TTCTGATTTA TATCTTAAAG 151 GT

>sp|P49620 I KDGG_RAT DIACYLGLYCEROL KINAΞE, GAMMA (DIGLYCERIDE KINAΞE) (DGK) (88 KD DIACYLGLYCEROL KINAΞE) . >gi|784935 (D38448) 88kDa-diacylglycerol kinase (DGK-III) [Rattus norvegicus] Length = 788

Minus Strand HSPs:

[ΞEQ ID NO: ] score = 46 (21.2 bits), Expect = 0.19, Sum P(2) = 0.18 Identities = 8/20 (40%) , Positives = 12/20 (60%) , Frame = -2

Query: 106 PPCN*EIVYKNKRRSVCAPP 47

PPC +1 +KN+ + PP Ξbjct: 753 PPCMIKITHKNQAPMMMGPP 772

[SEQ ID NO: ] score = 36 (16.6 bits) , Expect = 0.19, Ξum P(2) = 0.18 Identities = 7/12 (58%) , Positives = 9/12 (75%) , Frame = -1

Query: 137 IRNNFFΞHGVΞΞ 102

I NN+FS GV + Ξbjct: 575 IMNNYFΞIGVDA 586

[SEQ ID NO: ] contig[0140] Length: 732 check: 4454 ..

1 AATGGTTGAT ATTCAGGCTC GTCATCTGCT GTATTAATAT AGTAATTGAT

51 ACTACGTTGT AACGTTGAAC GTAGCATTGC ATCTACAACT TGAGAGCTGT

101 CTTCTTCATC AATAATACTA TTTCTTTCGT TATAGATAAT TTCACGTTGT

151 TTACGTAATA CTTCATCGTA TTCTAAGATA CGTTTACGCG CGTCGAAGTT

201 ATTACCTTCT ACACGTTTTT GTGCTGATTC TACAGCTCTT GATACCATTT 251 TTGATTCAAT TGGTGTAGAG TCATCTAAAC CTAGTCGGCT CATCATTT9C

301 TGTAAACGTT CAGAACCAAA ACGAATCATT AATTCATCTT GTAATGATAA

351 ATAGAAGCGA CTATCCCCTT TATCACCTTG ACGTCCAGAA CGACACGTAA

401 CTGGTCATCA ATACGACGAG ATTCATGTCG TTCTGTACCT ATTACTGCTA

451 AACCGCCTAA TTCCTCTACG CCTTCACCTA ATTTGATATC TGTACCACGA

501 CCAGCCATGT TAGTGGCAAT AGTAACGGCA CCTTTTTGTC CAGCGCCTGC

551 AACAATTTCA GCTTCACGTT CATGATTTTT CGCATTTAAC ACATCATGAC

601 GGATACCACG TTTTTTAAGT AAATTTGAAA TATATTCAGA AGTCTCAACT

651 GCAACAGTAC CTAATAGCAC TGGTTGCCCT GCCTTGTGTT TTTCAACAAC

701 ATCTTCTACT ACTGCATCAA ATTTACCTTT TT

Minus Strand HΞPs:

[ΞEQ ID NO: J score = 538 (247.5 bits) , Expect = 2.8e-139, Ξum P(2) = 2.8e-139 Identities = 105/130 (80%) , Positives = 118/130 (90%) , Frame = -2

Query: 392 RΞGRQGDKGDSRFYLΞLQDELMIRFGΞERLQKMMΞRLGLDDΞTPIESKMVΞRAVESAQKR 213

RSGRQGD+G+SRFYLΞLQDELM+RFGSERLQKMM RLG+DDSTPIEΞKMVΞRAVEΞAQKR Ξbjct: 531 RΞGRQGDRGEΞRFYLSLQDELMVRFGSERLQKMMGRLGMDDΞTPIEΞKMVΞRAVESAQKR 590

Query: 212 VEGNNFDARKRILEYDEVLRKQREIIYNERNSIIDEEDΞSQWDAMLRΞTLQRSINYYIN 33

VEGNNFDARKRILEYDEVLRKQREIIY ERN+IID E SΞ++V M+RSTL R+I+YY-N Sbjct: 591 VEGNNFDARKRILEYDEVLRKQREIIYGERNNIIDSEΞΞΞELVITMIRSTLDRAI3YYVN 650

Query: 32 TADDEPEYQP 3

+E +Y P Sbjct: 651 EELEEIDYAP 660

[SEQ ID NO: ] score = 535 (246.1 bits) , Expect = 2.8e-139, Sum P(2) = 2.8e-139 Identities = 106/112 (94%) , Positives = 109/112 (97%) , Frame = -3

Query: 730 KGKFDAWEDWEKHKAGQPVLLGTVAVETSEYIΞNLLKKRGIRHDVLNAKNHEREAEIV 551

KGKFDAWEDWEKHK GQP+LLGTVAVETΞEYIΞ LLKKRG+RHDVLNAKNHEREAEIV Ξbjct: 418 KGKFDAWEDWEKHKKGQPILLGTVAVETΞEYIΞQLLKKRGVRHDVLNAKNHEREAEIV 477

Query: 550 AGAGQKGAVTIATNMAGRGTDIKLGEGVEELGGLAVIGTERHEΞRRIDDQLR 395

+ AGQKGAVTIATNMAGRGTDIKLGEGVEELGGLAVIGTERHEΞRRIDDQLR Sbjct: 478 STAGQKGAVTIATNMAGRGTDIKLGEGVEELGGLAVIGTERHEΞRRIDDQLR 529 [SEQ ID NO: ] contig[0139] Length: 767 Check: 1851 ..

1 TGTCATAGTT TTTTCTTAAG TAAGTTGGCA ATTGTCGCAG CGCACTTGAA

51 CCAATACCAT TAAAGCGATA TGATTTATCC ACTTCAATAG CAGCAATGTT

101 CATGCGTTCA CCAATCTGCT CCAATGCGAT AAAGCCAACC TTTTGGCCAT

151 CAATCATTAA ATTAATGATA TGTACATTGG TCACTTCTGA ACGACTTTCT

201 TCTTCAAGCT TTAATGACGA AACATGTTTG AATCTAAGTC CAAGTAATAT

251 AGTCGTTCTT TGCCAATTGG TCCTTCTTCT TTAGTCGCTG TATGCATGAA

301 TCCAGCACGT TCGTATAGGT TCCAAGCATT GTCATTTTCC GCATCTACTA

351 CTAGATATAG ATGATTAAAA TCAGGAAATA CACCTTGAAC ATATTGCGGC

401 AATGACATCA TTATTTTCGT GCCATATCCA AAACCTTGAT ATTTTTCATT

451 AATCGATAAT GAACGAATAT AAACGACATT TTCAGGTGTA TCATAACCTT

501 CATGCTGATA GTAACGATGT AATACAAAAA AGCCCACCAC TTCATTTTTA

551 TCGTTTATTG CTACGTTAGC AATCCTATCA ACATCATTAA TTGCATCATC

601 AATAACTTCT TTAGGTAAAG ATGAATATAT TTGTTGTCTT TCATTCAAGT

651 CAAAATCATT AATTGCTGAA CGATATTGTT CATCAAATGC TTTTAAAGTG

701 ATACCTTCAA AACAAAGTTC TTTAGCCATA TATTTAACCC CTATCTTTTT

751 ATATATGAAG CATGAAT

gi 11303698 (D84432) BltD [Bacillus subtilis] Length = 152

Minus Ξtrand HΞPs:

[ΞEQ ID NO: ] score = 64 (29.4 bits), Expect = 3.3e-06, Sum P(3) = 3.3e-06 Identities = 13/51 (25%) , Positives = 27/51 (52%) , Frame = -3

Query: 528 FVLHRYYQHEGYDTPENWYIRSLSINEKYQGFGYGTKIMMSLPQYVQGVF 376

F ++ t- D V++ I+E+YQG G G K++ +L Q++ + +

Sbjct: 59 FAMYGLFPEYDEDNKNGRVWLDRFFIDERYQGKGLGKKMLKALIQHLAELY 109

[SEQ ID NO: ] score = 52 (23.9 bits) , Expect = 3.3e-06, Sum P(3) = 3.3e-06 Identities = 12/37 (32%) , Positives = 20/37 (54%) , Frame = -3

Query: 702 ITLKAFDEQYRSAINDFDLNERQQIYΞSLPKEVIDDA 592

I +KA -► R+AI D + + + Q Y K ++DA

Sbjct: 3 INIKAVTDDNRAAILDLHVSQNQLSYIESTKVCLEDA 39

[ΞEQ ID NO: ] score = 43 (19.8 bits). Expect = 3.3e-06, Sum P(3) = 3.3e-06 Identities = 9/21 (42%), Positives = 13/21 (61%) , Frame = -3

Query: 360 LYLWDAENDNAWNLYERAGF 298

+YL + N +A LY+R GF Sbjct: 114 IYLSIFΞNNIHAIRLYQRFGF 134 (SEQ ID NO: ] score = 42 (19.3 bits), Expect = 9.1, Ξum P(2) = 1.0 Identities = 8/26 (30%), Positives = 15/26 (57%), Frame = -2

Query: 82 VDKΞYRFNGIGΞΞALRQLPTYLRKNY 5

+D+ Y+ G+G L+ L +L + Y Ξbjct: 84 IDERYQGKGLGKKMLKALIQHLAELY 109

>sp|P39909|BLTD_BACSU TRANΞACETYLAΞE BLTD. >gi | 600711 (L32599) putative [Bacillus subtilis] Length = 152

Minus Ξtrand HΞPs:

[ΞEQ ID NO: ] score = 60 (27.6 bits). Expect = 1.4e-05, Sum P(3) = 1.4e-05 Identities ^'= 13/51 (25%), Positives = 26/51 (50%), Frame = -3

Query: 528 FVLHRYYQHEGYDTPENWYIRSLSINEKYQGFGYGTKIMMΞLPQYVQGVF 376

F ++ + D V++ I E+YQG G G K++ +L Q++ ♦+ Ξbjct: 59 FAMYGLFPEYDEDNKNGRVWLDRFFIIERYQGKGLGKKMLKALIQHLAELY 109

[SEQ ID NO: ] score = 52 (23.9 bits), Expect = 1.4e-05, Sum P(3) = 1.4e-05 Identities = 12/37 (32%), Positives = 20/37 (54%), Frame = -3

Query: 702 ITLKAFDEQYRΞAINDFDLNERQQIYΞΞLPKEVIDDA 592

I +KA + R+AI D +++ Q Y K ++DA Sbjct: 3 INIKAVTDDNRAAILDLHVSQNQLSYIEΞTKVCLEDA 39

[SEQ ID NO: ] score = 43 (19.8 bits). Expect = 1.4e-05, Ξum P(3) = 1.4e-05 Identities = 9/21 (42%), Positives = 13/21 (61%), Frame = -3

Query: ^' 360 LYLWDAENDNAWNLYERAGF 298

+YL + N +A LY+R GF Sbjct: 114 IYLSIFENNIHAIRLYQRFGF 134

[SEQ ID NO: ] contig[0138] Length: 596 Check: 4710 ..

1 CAGATCATCA AGCCGTTGAA CAACGTGGTA ACTTCATCAA TGCTGATACT

51 GATAAACAAA CTGCTTATAA TACAGCGGTA AATGAAGCAG CAGCAATGAT

101 TAACAAACAA ACTGGTCAAA ATGCGAACCA AACAGAAGTA GAACAAGCTA

151 TTACTAAAGT TCAAACAACA CTTCAAGCGT TAAATGGAGA TCATAATTTA

201 CAAGTTGCTA AAACAAATGC GACGCAAGCA ATTGATGATT TAACAAGCTT

251 AAATGATCCT CAAAAAACAG CATTAAAAGA CCAAGTTACA GCTGCAACTT 301 TAGTAACTGC AGTTCATCAA ATTGAACAAA ATGCGAATAC GCTTAACCAA

351 GCAATGCATG GTTTAAGACA GAGCATTCAA GATAACGCAG CAACTAAAGC

401 AAATAGCAAA TATATCAACG AAGATCAACC AGAGCAACAA AACTATGATC

451 AAGCTGTTCA AGCCGCAAAT AATATTATCA ATGAACAAAC TGCAACATTA

501 GATAATAATG CGATTAATCA AG AGCGGCA ACTGTGAATA CAACGAAAGC

551 AGCATTACAT GGTGATGTGA AATTACCAAA TGATAAAGAT CATGCT

>gi 11136210 (Z68329) unknown [Ξaccharomyces cerevisiae] >gi| 1226031 (Z70202) unknown [Ξaccharomyces cerevisiae] Length = 421

Plus Ξtrand HΞPs :

[SEQ ID NO: ] score = 65 (29.9 bits) . Expect = 0.0058, Sum P(3) = 0.0058 Identities = 18/40 (45%) , Positives = 23/40 (57%) , Frame = +1

Query: 106 NKLVKMRTKQK*NKLLLKFKQHFKR*MEIIIYKLLKQMRR 225

NK ++ + NKL K KQ FKR E+II KL K R+

Sbjct: 48 NKHIQEΞKPEVYNKLΞDKEKQKFKRKRELIIEKLSKΞQRQ 87

[ΞEQ ID NO: ] score = 42 (18.5 bits) . Expect = 0.0058, Ξum P(3) = 0.0058 Identities = 12/27 (44%) , Positives = 15/27 (55%) , Frame = +3

Query: 513 INQVAATVNTTKAALHGDVKLPNDKDH 593

I ++A TTK L DVKLP+ H

Ξbjct: 328 IRELAHVDWTTKDELPFDVKLPDFLTH 354

[ΞEQ ID NO: ] score = 39 (17.9 bits), Expect = 0.0058, Ξum P(3) = 0.0058 Identities = 7/26 (26%) , Positives = 15/26 (57%) , Frame = +1

Query: 382 ITQQLKQIANIΞTKINQΞNKTMIKLF 459

+ +Q+K ++ S + N+S +K F

Sbjct: ^" 92 VKKQIKYVSQQSNRFNKSTLNKLKEF 117

[SEQ ID NO: ] score = 37 (17.0 bits) . Expect = 0.011, Sum P(3) = 0.011 Identities = 8/22 (36%) , Positives = 13/22 (59%), Frame = -"-1

Query: 397 KQIANISTKINQΞNKTMIKLFK 462

KQI +S + N+ NK+ + K Sbjct: 94 KQIKYVSQQΞNRFNKΞTLNKLK 115

[SEQ ID NO: ] contig[0136] Length: 768 Check: 4081 ..

1 GGTGGCAAAG CAAGTTATCC ATCAACGGTT CTAATGACAG CGACTTTAGC 51 ACAAGTAGCG GGTGTAGAAA ATATTGTTGT TGTGACACCA CCTCAACCTA

101 ACGGAGTATC CCAAGAGGTA TTAGCTGCAT GTTATATTAC GCAAGTTAAT

151 CAAGTGTTTC AAGTTGGTGG TGCTCAAAGT ATTGCTGCAT TGACTTATGG

201 AACAGAAACG ATACCTAAAG TTGATAAGAT TGTAGGTCCA GGTAACCAAT

251 TTGTTGCATA TGCCAAAAAA TATTTATTTG GACAGGTAGG TATTGATCAA

301 ATTGCAGGAC CAACAGAAAT AGCACTGATT ATTGACGACA CCGCAGATTT

351 AGATGCCATC GTATATGATG TATTTGCGCA AGCAGAACAT GATGAATTAG

401 CACGTACATA TGTCATTGGT GAAGATGCGC AAGTCCTTAA AGATTTAGAA

451 TCACGTATTG CTAAAGCATT GCCTAATGTG GACAGATACG ACATTGTTTC

501 TAAAAGTATC GCTAATCAAC ACTACCTTAT CCATGCTAGT AATTTTGATG

551 AAGCATGCCA TGTCATGAAT ACAATCGCGC CTGAACATGC GTCGATTCAA

601 ACAGTAAATC CTCAACCATA TATTGAAAAA GTGAAATATG TGGGTGCATT

651 GTTTATTGGA CATTATTCGC CAGAGGTCAT AGGAGATTAC GTTGCAGGTC

701 CAAGTCATGT ATTACCTACG GGGGATCCAT AGTTCTAGAG CGGCCGCCAC

751 CGCGTGGGTC CAGTTTGA

Plus Strand HSPs.

(SEQ ID NO ] score = 491 (225 9 bits) Expect = 1 4e-73, Sum P(2) = 1 4e-73 Identities = 95/219 (43%) , Positives = 140/219 (63%) , Frame = +1

Query 67 ENIVWTPPQPNGVSQEVLAACYITQVNQVFQVGGAQΞIAALTYGTETIPKVDKIVGPGN 246

E I++ V+ +LAA + + +++VGGAQ +AA+ YGTE+IPKVDKIVGPGN

Sbjct 155 EIIMITPVKADGKVNPNILAAAEVCGIETIYKVGGAQGVAAVAYGTEΞIPKVDKIVGPGN 214

Query 247 QFVAYAKKYLFGQVGIDQIAGPTEIALIIDDTADLDAIVYDVFAQAEHDELARTYVIGED 426

FVA AKK +G V ID IAGP + E+ +1 D TA I D+ AQAEHD+LA + +

Ξbjct ^" 215 IFVATAKKICYGWDIDMIAGPΞEVLVIADKTAKPKYIAADLMAQAEHDKLASAILVTTS 274

Query 427 AQVLKDLESRIAKALPNVDRYDIVSKΞIANQHYLIHAΞNFDEACHVMNTIAPEHAΞIQTV 606

++++ ++ + + + N++R +1+ ΞI N I N D+A V N +APEH + T

Sbjct 275 EKLVQQVDEELNRQVQNLERREIIEΞΞIRNYGGAIWKNIDDAFDVΞNQLAPEHLEVLTS 334

Query 607 NPQPYIEKVKYVGALFIGHYΞPEVIGDYVAGPSHVLPTG 723

P + K+K G++FIG Y+PE +GDY++G +HVLPTG Sbjct 335 ΞPLTQLPKIKNAGSIFIGEYTPEPLGDYMSGΞNHVLPTG 373

[ΞEQ ID NO ] score = 97 (44 6 bits) Expect = 1 4e-73, Sum P(2) = 1 4e-73 Identities = 18/35 (51%) , Positives = 27/35 (77%) , Frame = +1 Query: 1 GGKAΞYPΞTVLMTATLAQVAGVENIVWTPPQPNG 105

GG A+YPΞTV+M A A +AGV+ I+++TP + +G Sbjct: 132 GGTAAYPΞTVIMNAVPALLAGVKEIIMITPVKADG 166

[ΞEQ ID NO: ] score = 40 (18.4 bits). Expect = 6.7e-05, Sum P(2) = 6.7e-05 Identities = 8/14 (57%), Positives = 9/14 (64%), Frame = +1

Query: 685 DYVAGPΞHVLPTGD 726

D +AGPS VL D Sbjct: 231 DMIAGPSEVLVIAD 244

[SEQ ID NO: ] contig[0135] Length: 542 Check: 369 ..

1 GTTTTAATTG TGAAGTTTGA AATAATTTGT AATGATTTTA ATTATTAGTA

51 GGGGAGTGGA CATCGTTGGA AGAACGATTA AATCGCGTTA AGCAACAATT

101 ACAACAATCA TCATATAAGC TAACGCCACA ACGCGAAGCT ACTGTTAGAG

151 TTCTAATTGA AAATGAAAAA GATCATCTAA GTGCTGAAGA CGTATATCTG

201 AAAGTAAAAG ACAAAGCGCC TGAAATTGGC TTGGCGACAG TATACAGAAC

251 GTTAGAGTTG TTAGCTGAAC TAAAAGTTGT CGACAAAATT AACTTTGGTG

301 ATGGCGTCGC TCGTTTTGAT TTAAGAAAAG AAGGCGCAAA ACATTTCCAC

351 CATCATTTAG TATGTATGGA ATGTGGTCGT GTAGATGAAA TCGATGAAGA

401 TTTGTTACCA GAAGTTGAAA ATCGAGTTGA AAATGAGTTC AATTTTAAAA

451 TTTTAGATCA TCGTTTAACT TTCCATGGTG TGTGTGAAAC ATGCCAAGCT

501 AAAGGTAAAG GATAGTAAAT TGCGTAGGTT AAATTAACCT TC

gi|1303993 (D84432) YqkL [Bacillus subtilis] Length = 149

Plus Ξtrand HΞPs:

[SEQ ID NO: ) score = 593 (272.8 bits). Expect = 5.4e-77, P = 5.4e-77 Identities = 110/146 (75%) , Positives = 127/146 (86%), Frame = +3

Query: 66 LEERLNRVKQQLQQSSYKLTPQREATVRVLIENEKDHLΞAEDVYLKVKDKAPEIGLATVY 245

+E R++R+K+QL ΞΞYKLTPQREATVRVL+ENE+DHLSAEDVYL VK+K+PEIGLATVY Sbjct: 1 MENRIDRIKKQLHSΞΞYKLTPQREATVRVLLENEEDHLSAEDVYLLVKEKSPEIGLATVY 60

Query: 246 RTLELLAELKWDKINFGDGVARFDLRKEGAKHFHHHLVCMECGRVDEIDEDLLPEVENR 425

RTLELL ELKWDKINFGDGV+R+DLRKEGA HFHHHLVCME G VDEI+ DLL +VE Ξbjct: 61 RTLELLTELKWDKINFGDGVΞRYDLRKEGAAHFHHHLVCMEFGAVDEIEGDLLEDVEEI 120

Query: 426 VENEFNFKILDHRLTFHGVCETCQAK 503

+E ++ FKI DHRLTFHG+C C K Ξbjct: 121 IERDWKFKIKDHRLTFHGICHRCNGK 146

>gi 1433299 (U01151) Fur protein [Neisseria meningitidis] >gi| 437629 (L19777) ferric uptake regulator [Neisseria meningitidis] Length = 144

Plus Strand HSPs:

[SEQ ID NO: ] score = 139 (63.9 bits), Expect = 3.0e-30, Sum P(2) = 3.0e-30 Identities = 22/54 (40%), Positives = 35/54 (64%), Frame = +3

Query: 348 HHHLVCMECGRVDEIDEDLLPEVENRVENEFNFKILDHRLTFHGVCETCQAKGK 509

H H+VC++CG V E + +++++ E ++I+DH L +GVC CQAKGK Ξbjct: 90 HDHIVCVKCGEVTEFHNPEIEALQDKIAEENGYRIVDHALYMYGVCΞDCQAKGK 143

[SEQ ID NO: ] score = 120 (55.2 bits), Expect = 3.0e-30, Sum P(2) = 3.0e-3O Identities =^'27/78 (34%), Positives = 46/78 (58%), Frame = +3

Query: 96 QLQQΞΞYKLTPQREATVRVLIENEKDHLSAEDVYLKVKDKAPEIGLATVYRTLELLAELK 275

QL-p- S K+T R + + + ++HLSAEDVY + ++ EIG_*AT+YR L + Ξbjct: 9 QLKDSGLKVTGPRLKILDLFETHAEEHLSAEDVYRILLEEGVEIGVATIYRVLTQFEQAG 68

Query: 276 WDKINFGDGVARFDLRK 329

++ + +F G A ++L K Ξbjct: 69 ILQRHHFETGKAVYELDK 86

[SEQ ID NO: ] contig[0134] Length: 525 Check: 4413

1 GAACATAAAT GCAACAAGTG TACCTGCTGA AATTAATTGT GCTAAAAATG 51 CGAATGGGAA CATAGAACCA ATTAAAACAC CAATAATAGT AAGTATAACT 101 AGTGCGCGAT TAGGTAAATG TTTGTCGTTT AAATGGCTTA ACCATGAAGG 151 TAATAAGCCG TCACGTCCAA ATGAATAAAG TAAACGTGAG CCTGCTAACA 201 TCATACCAAT TAATGCTGTA AACATACCGA TAACAGAGAT AGCTTGAACA 251 ATAGCTGCTA CAACACCATG ACCACTTTGA CGTAAAGCCC AACCAACAGG 301 TTCAGCATTG TTTGCGTATT GTGAGTAATG GAACATACCA ACTAACACAA 351 GTGCTACAGC AATAAATAAT ACGATAGCAA CACTTAAAGA ACCAAGAATA 401 CCTCTAGGCA TTGTCTTTTG AGGGTCAAGT GCTTCTGCTG AGTTTGCTGC 451 GATAGAATCG AAACCGATAT ACGCTAAGAA AATCATTGAA ACACCAGCAT 501 ATATGCCTTG CCATCCACCA AAGTC>gnl |PID|e264157 (Z79702) unknown [Mycobacterium tuberculosis] Length = 476

Minus Strand HSPs: [ΞEQ ID NO: ] score = 126 (58.0 bits). Expect = 4.5e-25, Ξum P(3) = 4.5e-25 Identities = 25/68 (36%), Positives = 39/68 (57%), Frame = -1

Query: 516 GWQGIYAGVSMIFLAYIGFDΞIAANSAEALDPQKTMPRGILGSLSVAIVLFIAVALVLVG 337

G GI + IF +YIG D+++ E DPQKTMPR ++ +L V +++ VAL +G Ξbjct: 226 GVAGIGΞAAGTIFFΞYIGLDAVSTAGDEVKDPQKTMPRALIAALVWTGVYVLVALAALG 285

Query: 336 MFHYΞQYA 313

+ +A Ξbjct: 286 TQPWQDFA 293

[SEQ ID NO: ] score = 84 (38.6 bits). Expect = 4.5e-25, Sum P(3) = 4.5e-25 Identities = 16/46 (34%), Positives = 30/46 (65%), Frame = -1

Query: 258 AAIVQAISVIGMFTALIGMMLAGSRLLYΞFGRDGLLPSWLΞHLNDK 121

+ 1+ A +V+ +FT ^'+ M +R+L++ GRDGLLP+ + +N + Ξbjct: 314 ΞTILAAGAWΞIFTVTLVTMYGQTRILFAMGRDGLLPARFAKVNPR 359

[ΞEQ ID NO: ] score = 58 (26.7 bits), Expect = 4.5e-25, Sum P(3) = 4.5e-25 Identities = 13/36 (36%), Positives = 18/36 (50%), Frame = -1

Query: 114 PNRALVILTIIGVLIGΞMFPFAFLAQLIΞAGTLVAF 7

P VI+ I + + P LA ++Ξ GTL AF Sbjct: 363 PVHNTVIVAIFASTLAAFIPLDSLADMVSIGTLTAF 398

[SEQ ID NO: ] contig [0133] Length: 521 Check: 9665 ..

1 AATTCCTTGT TTCATTATTT TCAGCTCCTT TGCCCTGAAC CATCTGGAAC 51 AGAGTTATTT GTGAGTTTTT ACCCAATACT GTGTAATTAT AAAGGTAATT 101 AATTCAAAAC GCAAGCCCCT ATATAATGTT TATTAAATTA TAGGTCGACC 151 CGTTTTAGTA CTTTCTTCTG CAGACTTTTG TAGCTGCTTG AAGAAATCTT 2Θ1 CATTATTCTT AGACCTTTTA AGTTTGCGAA TAAATCTTTC AGTAAAGTCA 251 GTTGAGTCAG TGAATAGATT TCTTAATTGC CATAATGTGT CTAATTCAGA 301 TTTACTTATT AACAATTCTT CTTTACGCGT TGAACTTCTG CCAATATCAA 351 TTGCAGGGGA AGATACGACG TTCAGACAAT TTACGATCTA AATGTAACTC 401 CATGTTACCT GTTCCTTTAA ATTCTTCGTA AATCATATCG TCCATACGTG 451 AACCCGTATC AACTAATGCA GTTGCAAGTA TTGTTAAACT TCCACCCGCT 501 TCAATATTTC TCGCTGCACC G >pir| |A47051 transcriptional terminator Rho - Bacillus subtilis >gi|143434 (M97678) Rho Factor [Bacillus subtilis] Length = 427

Minus Strand HSPs: [SEQ ID NO: ] score = 260 (119.6 bits), Expect = 1.8e-52, Sum P(2) = 1.8e-52 Identities = 51/55 (92%), Positives = 53/55 (96%), Frame = -2

Query: 520 GAARNIEAGGSLTILATALVDTGΞRMDDMIYEEFKGTGNMELHLDRKLSERRIFP 356

GAARNIE GGΞLTILATALVDTGSRMDD+IYEEFKGTGNMELHLDR L+ERRIFP Sbjct: 301 GAARNIEEGGΞLTILATALVDTGΞRMDDVIYEEFKGTGNMELHLDRΞLAERRIFP 355

[SEQ ID NO: ] score = 187 (86.0 bits), Expect = 1.8e-52, Sum P(2) = 1.8e-52 Identities = 34/66 (51%), Positives = 48/66 (72%), Frame = -3

Query: 357 PAIDIGRSSTRKEELLISKSELDTLWQLRNLFTDΞTDFTERFIRKLKRΞKNNEDFFKQLQ 178

PAIDI RΞ TRKEELL+ K LD LW +R +DS DF E+F+RK+K++K N++FF L Ξbjct: 355 PAIDIRRΞGTRKEELLVPKEHLDRLWΞIRKTMSDSPDFAEKFMRKMKKTKTNQEFFDILN 414

Query: 177 KSAEEΞ 160

Sbjct: 415 QEWKQA 420

[SEQ ID NO: ] contig[0132] Length: 524 Check: 4142

1 GTAAAAATAG CTTTACTAGT GGGTTGTTGG CTGAAGATTT TTCAGAAATA

51 GAAAATCACT ATGTAGGACC AACACCACCT GATAAAGATC ATCAATATGA

101 ATTAACAGTT TATGCGTTAG ATCATTCTTT AAATTTGAAG AATGGGTTCT

151 ACTTGAATGA ATTTTTAAAA GAAGTAAATC AACATAAAAT TGATCAAACA

201 AGTATTAACC TTATAGGAAG AAAAATTTAA TGCTAAATAT CTCATCAATA

251 TAAAATTGTT CAATTAAAAG TACAAAGAAA CAAGAGATTT AATTTATATA

301 TTAGGTACGG CGTTCGCTAT AATGCAAAGA AGTAATTAAA TTTAAGAAAT

351 GTAAACTTAG TTATTGTAAT GTGAATTTAT TTGAAAAAAT AGAAAGTATT

401 AACAATTATA GCTTTTACAT TAATTAAAAT TTATTTTTAA AAACAAGTAA

451 ACAATTTACA TACTTATAAT TTTTGAAACT TTTAGATTTG TGTTATATTG

501 ATTTTGTAAG ATACTT AAC TCAC

>gi 11151158 (U43145) repeat organellar protein [Plasmodium chabaudi] Length = 1939

Plus Strand HSPs:

(SEQ ID NO: ] score = 46 (21.2 bits). Expect = 5.8, Sum P(4) = 1.0 Identities = 12/32 (37%), Positives = 18/32 (56%), Frame = +2

Query: 371 VNLFEKIESINNYΞFYIN'NLFLKTΞKQFTYL 466

VNLFEKI+ I YI + + + F++L Sbjct: 1638 VNLFEKIDKILWKQMYIPTEIRILFLRYFSFL 1669 [ΞEQ ID NO: ) score = 37 (17.0 bits), Expect = 5.8, Sum P(4) = 1.0 Identities = 11/26 (42%), Positives = 14/26 (53%), Frame = +1

Query: 220 EKFNAKYLINIKLFN'KYKETRDLIY 297

EK N +N KL N K ET++ Y Sbjct: 1150 EKENEIKKLNKKLΞNYKVFETKENTY 1175

(ΞEQ ID NO: ] score = 36 (16.6 bits), Expect = 5.8, Ξum P(4) = 1.0 Identities = 7/17 (41%), Positives = 12/17 (70%), Frame = +3

Query: 156 NEFLKEVNQHKIDQTΞI 206

NE+ +E+N+ KI Q + Ξbjct: 1124 NEYNEEINKLKIVQNΞM 1140

[ΞEQ ID NO: ] score = 36 (16.6 bits), Expect = 5.8, Ξum P(4) = 1.0 Identities = 7/25 (28%), Positives = 13/25 (52%), Frame = +3

Query: 33 EDFSEIENHYVGPTPPDKDHQYELT 107

E ++IE+ Y+ + YE+T Sbjct: 165 EKLNDIEΞEYIEKNKEKEKLNYEVT 189

[SEQ ID NO: ] contig[0131] Length: 745 Check: 2466 ..

1 TAACAATTCT TGGGACCGAA ACCTGTAAAG ACAGAAGCGC CAACTTTAAC

51 GGAATCGCTA TCGTTTGATA GTTCTACCTC TAAGTAGTTA CTAAAACCTG

101 TCTCTGCTTT ATTATTTTCA ATATTTAATG TCACTTGTTG TTGATTTAAC

151 AACATTAGAG CATTGATAAT ATTGACTTCA GGACCAAGAT CATCTTTTAA

201 AATATGAGTA ATAATTGTAC GTGTTAATAA ACTACTATCA ATAGAGGCTA

251 AGTCGCCACC GTACGTAATT TTAATAGAGC TTGGTGCATT GTACATTAAT

301 TGAATAGCTA ATTCACCAAC TGTTTGGCTT AAATTGATGA ATGATTTTAC

351 AGTATCATCT ATATTGCTTA AGTCCATTTT AGGTGCATTC ACTGCATGCG

401 TTACAGTACC ATCAATTAAA ATTTCGATGA TTTCATTTGA AACAGAAATT

451 GCCACTTTTT CTTGAGCTTC GACTGTTGAT GCACCCAAAT GAGGTGTAAC

501 AATAATTTTA TCATGTGCAA CAAGAGGCGA ATCAGTTGCA GGTTCATGTT

551 CAAACACATC GATAGCTGCC CGACTAATTT GTCCTTCGTC TAATGCTTTT

601 ATTAGCGCCT TTTCATCAAT AATACCACCA CGTGCCACAT TGAATATTTG

651 CAAACTAGGT TTTGCTTTGG CAAAAAAGTC AGCATTAATT AAGCCTTTTG

701 TTTTAGGTGT TAGTGGTGTA TGTAATGTAA CGAAATCAGA ATGTT

>pir| |Ξ45534 phosphoglycerate dehydrogenase (EC 1.1.1.95) - Bacillus subtilis (fragment) >gi| 410116 (L09228) phosphoglycerate dehydrogenase [Bacillus subtilis] Length = 419 Minus Strand HSPs:

[SEQ ID NO: ] score = 319 (144.2 bits), Expect = 2.4e-52, Sum P(2) = 2.4e-52 Identities = 63/122 (51%), Positives = 84/122 (68%), Frame = -3

Query: 740 SDFVTLHTPLTPKTKGLINADFFAKAKPSLQIFN^PVARGGIIDEKALIKALDEGQIΞRAAI 561

+D +T+HTPLT +TKGL+N + AK K +++ N ARGGIIDE AL++AL+ G ++ AA+ Ξbjct: 87 ADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALLEALENGHVAGAAL 146

Query: 560 DVFEHEPATDSPLVAHDKIIVTPHLGASTVEAQEKVAIΞVΞNEIIEILIDGTVTHAVNAP 381

DVFE EP D+ LV H +1 TPHLGAΞT EAQ VA VΞ E+++ V A+N P Sbjct: 147 DVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVΞEEVLQFAKGLPVMSAINLP 206

Query: 380 KM 375

M Ξbjct: 207 AM 208

[ΞEQ ID NO: ] score = 132 (59.7 bits), Expect = 2.4e-52, Ξum P(2) = 2.4e-52 Identities = 26/114 (22%), Positives = 61/114 (53%), Frame = -3

Query: 350 VKΞFINLΞQTVGELAIQLMYNAPSSIKITYGGDLASIDSSLLTRTIITHILKDDLGPEVN 171

+K + ++ +G L Q M + I Y G +A +++Ξ +T+ +++ LK + VN Sbjct: 216 IKPYHQIAGKIGSLVΞQCMKEPVQDVAIQYEGTIAKLETΞFITKALLΞGFLKPRVDΞTVN 275

Query: 170 IINALMLLNQQQVTLNIENNKAETGFSNYLEVELSNDΞDSVKVGASVFTGFGPK 9

+NA + ++ ++ + + + +E+G+ N + V+++ D + V A+ FG + Sbjct: 276 EVNAGGVAKERGIΞFSEKISSSESGYDNCIΞVKVTGDRΞTFTVTATYIPHFGΞR 329

[SEQ ID NO: ] contig[0130] Length: 659 Check: 487 ..

•1 CGCTAATGAT GTATAGTTTG GTATTGCAAC TGTGAAACCT TTATAATCCA

51 TAGTCTTTGC CGTTGCTTTA TAAATATCAC GCTCAACTAT AATTGGTACT

101 TCAACCTCTG CTAACTTCAA TCGCAATTGA AGTTCTTCTG CTCGTGTACC

151 TGTCACGATG ATAGCTTCAA TTTGTTGCTT AGATAATTTT TCAAAATCTG

201 CATCATAAAT CCATGAAGTA TCTCGACCAT CTGCAGCGTT ATCATTTAGC

251 GAAATAACAT ACACTTTTTC GCCTTCTAAT TGTTCACCAA CTGATAAACT

301 TGCATTCATT CCTGCAGGAT TTTTAGCTAA ATTGATCATC GCTTCTTTTC

351 GTTCTTTTTT AAAGTACTGC ATACGACCAT TGTCTGATGT ATACGTTTCA

401 AAGCCATTTT TAATTGTTTG TTCATTTAAC CCTAGCTCTC TTAAAACAGT

451 ATATGCTGCT AACGCGTTAT AAGCGTTAAA GTCACCTGCA ATTTTCATAT

501 CATATTTTTC ATCATTGATA TTTAAATATA AAAACGGTGC CACATCAAAA

551 CTTGATATTT CATATTTTGC TTGCTCTCGT TTGAAACCAC ACTGACAGTG 601 ATAATGACAA TTTGATTATA ATGAATATAA TCGTATTGCA ATAAGCGACC 651 ACAGTTTGG

>gι 11653484 (D90914) hypothetical protein (Synechocystis sp.] Length = 459

Minus Strand HSPs:

[ΞEQ ID NO: ] score = 123 (56.6 bits). Expect = 6.4e-14, Ξum P(2) = 6.4e-14 Identities = 26/81 (32%), Positives = 43/81 (53%), Frame = -3

Query: 516 NDEKYDMKIAGDFNAYNALAAYTVLRELGLNEQTIKNGFETYTΞDNGRMQYFKKERKEAM 337

+ K+ + G +N YN LAA V ++LG+N + I N ++ + GR + E K Ξbjct: 256 HSΞKWPQILIGVYNKYNTLAAGLVAQQLGVNTENIFNNIRSFKAAFGRAEELNVEGKHVR 315

Query: 336 INLAKNPAGMNASLSVGEQLE 274

I L+KNP G+N ++ L+ Sbjct: 316 ILLSKNPVGLNETIRAVNDLK 336

[SEQ ID NO: ) score = 76 (35.0 bits). Expect = 6.4e-14, Ξum P(2) = 6.4e-14 Identities = 14/25 (56%), Positives = 17/25 (68%), Frame = -3

Query: 258 VIΞLNDNAADGRDTΞWIYDADFEKL 184

1-+ LND ADG D ΞWI+D D E L Ξbjct: 345 LLVLNDRIADGTDVSWIWDVDTEPL 369

>sp|P40087|YEX3_YEAΞT HYPOTHETICAL 47.4 KD PROTEIN IN MAG1-UBP5 INTERGENIC REGION. >pιr||S50646 hypothetical protein YER143w - yeast (Saccharomyces cerevisiae) >gι| 603383 (U18917) Yerl43p [Ξaccharomyces cerevisiae) Length = 428

Minus Strand HSPs:

[SEQ ID NO: ] score = 62 (28.5 bits), Expect = 5.1, Sum P(2) = 0.99 Identities = 15/57 (26%), Positives = 24/57 (42%), Frame = -3

Query: 579 REQAKYEISSFDVAPFLYLNINDEKYDMKIAGDFNAYNALAAYTVLRELGLNEQTIK 409

R +Y F P LY+NI Y +K D A + + + ++ GL+ K Sbjct: 188 RNAIEYTPEMFTQVPMLYINIΞINNYPVKAFVDTGAQTTIMΞTRLAKKTGLΞRMIDK 244

[SEQ ID NO: ] score = 38 (17.5 bits), Expect = 5.1, Sum P(2) = 0.99 Identities = 8/19 (42%), Positives = 13/19 (68%), Frame = -3 Query: 120 LKLAEVEVPIIVERDIYKA 64

L++AEVE + E +1 K+ Ξbjct: 308 LRIAEVETΞFLSEAEIPKS 326

[SEQ ID NO: ] contig[0129] Length: 1459 Check: 6212

1 TTAAAACAAT GAAGTGGAGA AAATATAAGG AGGAATAAGC TTATGAAAAA

51 TATTTCAGAA TTCTCAGCCC AACTTGATCA AACTTTTGAT CAAGGGGAAG

101 CCGTCTCTAT GGAGTGGTTA TTCCGTCCGT TGCTAAAAAT GCTGGCGGAG

151 GGCGATCCAG TCCCCGTTGA GGACATCGCG GCGGAGACCG GGAAGCCCGT

201 CGAGGAAGTT AAGCAAGTCC TACAGACTCT ACCTAGTGTG GAACTTGATG

251 AGCAGGGCCG TGTCGTCGGT TATGGCCTCA CACTGTTCCC TACCCCCCAT

301 CGCTTCGAGG TTGATGGGAA GCAACTATAT GCATGGTGCC CCTTGACACA

351 CTTATGTTCC CAGCACTCAT CGGCCGGACG GTCCACATCG CTTCGCCTTG

401 TCACGGCACC GGTAAGTCCG TCCGGTTGAC GGTGGAACCG GACCGCGTTG

451 TAAGCGTCGA GCCTTCAACA GCCGTTGTCT CGATTGTTAC ACCAGATGAA

501 ATGGCCTCGG TTCGGTCGGC CTTCTGTAAC GACGTTCACT TTTTCAGTTC

551 ACCGAGTGCA GCCCAAGACT GGCTTAACCA ACACCCTGAG TCGAGCGTTT

601 TGCCCGTTGA AGATGCCTTT GAACTGGGTC GCCATTTGGG AGCGCGTTAT

651 GAGGAGTCAG GACCTACTAA TGGGTCCTGT TGTAACATTT AATCTTAGGC

701 AATAACGCCT GCGTCAATCT TGGCCTTACG ATGATGTCCT GTAACCGAAG

751 CTCTATCTAG TGAAACCAAT TTTATGGGAA ACCAAATAAA TAAAAAGATC

801 AATTGCTTGT GCCTATATCG GGGAGTTAAT AAAGCGAGAA AGTGGATTCT

851 TGAATATAGG AGTAAA AAG GTGCCAAAAT GGCACCTTAT TTAAAATATG

901 TAACGCCAAG GTCTGCCGTA TTATATTGCA TTGGAAAAAG AAAACCTTCT

951 GTATAAGGAG ATGTTATATG ATATTTGGTA AACTGTTCGG CAGTTTGGGC

1001 GTAGAAAGCT TTTGCTCCTT GAACATCACG TTTGCCAGTT ACAATGTCAT

1051 TTAACAAGTT TAAAGATAAA AAATTCATCG CTTCCTCATG ACACTTTGCT

1101 GATGCCTCAC CTGTAGTTCG ATCTAAGTAG ACACTTCCAT CAAAAGCGGC

1151 AATCGCATCA TATAAGTGTT CGGGCACTTT ATAATCGATG GTCTGCTTAA

1201 GGAAATCAAG GTGAGGGGTA GGGAAGTTAT GAGGGACTGG ATCCTTATAT

1251 ACTATCGTGC GTTTCCATGG CCCGCTATTG TACCAAATTA ATCGACTCAT

1301 TGTTGCTTCC TGGGGATATC CATACTTACT AATTATGGTT TTTGCCCCTT

1351 CCAACGGTGG TCCCTGCCAA TAGGACAAAA TGTGATTTAA ATGACTATCC

1401 ATTGCCATAC CTCCTAAACA TTTGCCTAAA AGCATTGTAT GCCCAATAAA

1451 TGAATTTTA

>sp|P08653|MERB_ΞTAAU ALKYLMERCURY LYASE (ORGANOMERCURIAL LYASE). >pir||F29504 alkylmercury lyase (EC 4.99.1.2) - Staphylococcus aureus plasmid PI258 >gi 1459908 (L29436) organomercurial lyase [Plasmid pI258] Length = 216

Plus Strand HΞPs: [ΞEQ ID NO: ] score = 611 (281.1 bits). Expect = 7.8e-151, Ξum P(2) = 7.8e-151 Identities = 116/116 (100%), Positives = 116/116 (100%), Frame = +3

Query: 342 LDTLMFPALIGRTVHIASPCHGTGKSVRLTVEPDRWSVEPSTAWSIVTPDEMASVRΞA 521

LDTLMFPALIGRTVHIAΞPCHGTGKΞVRLTVEPDRWΞVEPΞTAWSIVTPDEMAΞVRSA Sbjct: 101 LDTLMFPALIGRTVHIASPCHGTGKSVRLTVEPDRWSVEPSTAWSIVTPDEMASVRSA 160

Query: 522 FCNDVHFFΞΞPSAAQDWLNQHPEΞSVLPVEDAFELGRHLGARYEESGPTNGΞCCNI 689

FCNDVHFFSΞPSAAQDWLNQHPEΞΞVLPVEDAFELGRHLGARYEEΞGPTNGΞCCNI Ξbjct: 161 FCNDVHFFΞΞPSAAQDWLNQHPESΞVLPVEDAFELGRHLGARYEEΞGPTNGΞCCNI 216

[SEQ ID NO: ) score = 522 (240.1 bits), Expect = 7.8e-151, Ξum P(2) = 7.8e-151 Identities = 101/104 (97%), Positives = 101/104 (97%), Frame = +1

Query: 43 MKNIΞEFΞAQLDQTFDQGEAVΞMEWLFRPLLKMLAEGDPVPVEDIAAETGKPVEEVKQVL 222

MKNIΞEFSAQLDQTFDQGEAVSMEWLFRPLLKMLAEGDPVPVEDIAAETGKPVEEVKQVL Sbjct: 1 MKNIΞEFΞAQLDQTFDQGEAVΞMEWLFRPLLKMLAEGDPVPVEDIAAETGKPVEEVKQVL 60

Query: 223 QTLPΞVELDEQGRWGYGLTLFPTPHRFEVDGKQLYAWCPLTHL 354

QTLPΞVELDEQGRWGYGLTLFPTPHRFEVDGKQLYAWC L L Sbjct: 61 QTLPΞVELDEQGRWGYGLTLFPTPHRFEVDGKQLYAWCALDTL 104

[SEQ ID NO: ] contig[0128] Length: 396 Check: 5695 ..

1 TACCAGTTAA TTTCATGCAT ATTGAGCAAA TTCCTATTAC TATTAATGGG

51 AAATTAGATA AGAAGGCATT GCCTATCATG GACTATGTCG ATACGGATGC

101 CTATGTAGCA CCGAGTACAG ATACCGAACA CTTGCTATGC CAAATTTTTG

151 CAGATATTTT ACATGTGAAT CAAGTAGGTA TTCATGATAA TTTCTTTGAA

201 TTAGGTGGCC ATTCATTAAA AGCAACGTTA GTGGTGAATC GGATAGAGGC

251 ATCTACTGGG AAACGATTAC AAATTGGTGA TTTATTACAA AAGCCAACTG

301 TATTTGAACT AGCACAAGCG ATTGCTAAGG TTCAAGAACA AAACTATGAA

351 GTGATTCCAG AAGCTATAGT TAAAGATGAT TATGTGCTGA GCTCTG

>gnl|PID|e280810 (Z82015) yukK [Bacillus subtilis] Length = 472

Plus Ξtrand HΞPs:

[SEQ ID NO: ] score = 248 (113.7 bits), Expect = 3.6e-27, P = 3.6e-27 Identities = 48/114 (42%), Positives = 72/114 (63%), Frame = +3

Query: 3 PVNFMHIEQIPITINGKLDKKALPIMDYVDTDAYVAPSTDTEHLLCQIFADILHVNQVGI 182 p F+ ++++P+T NGKLD+KALP D+ P T E +LC +F ++LH+ +VGI Ξbjct 95 PAAFVTMKELPLTPNGKLDRKALPAPDFAAAVTGRGPRTPQEEILCDLFMEVLHLPRVGI 154

Query 183 HDNFFELGGHSLKATLWNRIEASTGKRLQIGDLLQKPTVFELAQAIAKVQEQN 344

D FF+LGGHΞL A +++RI + G L IG+L + PTV LA+ + Q+ Sbjct 155 DDRFFDLGGHSLLAVQLMSRIREALGVELSIGNLFEAPTVAGLAERLEMGΞΞQS 208

>gι 1899317 (Z28338) peptide synthetase module [Microcystis aeruginosa) Length = 993

Plus Strand HSPs:

[SEQ ID NO ) score = 201 (92 1 bits), Expect = 9 le-26 Sum P(2) = 9 le-26 Identities = 42/111 (37%) Positives = 63/111 (56%) Frame = +3

Query 60 KKALPIMDYVDTDAYVAPΞTDTEHLLCQIFADILHVNQVGIHDNFFELGGHΞLKATLWN 239

K +P + AY+AP + E LL QI+ D+L V+++G+ DNFFELGGHSLKA +V+ Ξbjct 551 KLPIPDETΞIIEΞAYIAPRNEKESLLAQIWEDVLQVΞKIGVΞDNFFELGGHΞLKAIΞLVΞ 610

Query 240 RIEAΞTGKRLQIGDLLQKPTVFELAQAIAKVQEQNYEVIPEAIVKDDYVLΞ 392

+1+ G+ L I + PT+ E A ++ V IP ++ Y S Sbjct 611 KIQEKLGQSLPIKQVFAHPTIAEQAALLΞTVTPLTVATIPLVSAQETYETS 661

[SEQ ID NO ] score = 62 (28 4 bits), Expect = 9 le-26, Ξum P(2) = 9 le-26 Identities = 12/27 (44%), Positives = 17/27 (62%), Frame = +3

Query 3 PVNFMHIEQIPITINGKLDKKALPIMD 83

P F+ + P+ NGK+D+K LPI D Ξbjct 530 PΞAFVLLΞAΞPLNNNGKIDRKKLPIPD 556

>prf I I 2208293A peptide synthetase (Microcystis aeruginosa] Length = 997

Plus Strand HSPs

[SEQ ID NO ] score = 201 (92 1 bits). Expect = 9 le-26, Sum P(2) = 9 le-26 Identities = 42/111 (37%), Positives = 63/111 (56%), Frame = +3

Query 60 KKALPIMDYVDTDAYVAPΞTDTEHLLCQIFADILHVNQVGIHDNFFELGGHSLKATLWN 239

K +P + AY+AP + E LL QI+ D+L V+++G+ DNFFELGGHSLKA +V+ Sbjct 551 KLPIPDETSIIESAYIAPRNEKEΞLLAQIWEDVLQVΞKIGVΞDNFFELGGHSLKAIΞLVΞ 610

Query 240 RIEASTGKRLQIGDLLQKPTVFELAQAIAKVQEQNYEVIPEAIVKDDYVLS 392 +1+ G+ L I + PT+ E A ++ V IP ++ Y S Ξbjct: 611 KIQEKLGQΞLPIKQVFAHPTIAEQAALLΞTVTPLTVATIPLVSAQETYETS 661

[SEQ ID NO: ] score = 62 (28.4 bits), Expect = 9. le-26, Ξum P(2) = 9. le-26 Identities = 12/27 (44%), Positives = 17/27 (62%), Frame = +3

Query: 3 PVNFMHIEQIPITINGKLDKKALPIMD 83

P F+ + P+ NGK+D+K LPI D Ξbjct: 530 PΞAFVLLSAΞPLNNNGKIDRKKLPIPD 556

[SEQ ID NO: ] contig[0126] Length: 1079

1 TCGTTACTTG CGTTGCTGCA TTTGTAACAT CTGATGGTGT TAACGTTGGT

51 GTTGGTGTAC CACTAACGAT ATGTTCTGCA GCTGTCACTT TTTCATCATA

101 TGCTTGGCGT TTATTCGCAT CAGCATTGAC ATAATTACCA CTAGCTTTTG

151 TGTCAGCTTT ATCAGCAATG GCACGTTTTA AAGCTGTCAT CGCASTATTT

201 AATTCAGTCG CAGTATGTTC AACACCATTT GCTGCAGATA CGCGTCCTGC

251 ACTTGTTACT TGTGCTTTCA ATGCTTCTTT TTGTTTTGTA TTTAAGTCCG

301 AAGCATTTGT AATCGCTGTG TTCGCAGCCT GTTTCGCACG TTCTAAGGTT

351 TTGAATACCG TTTAATGCAG TATTGGCTTG TGTAACAGCT TGCATTGCTC

401 TTTCGACATC TGCTTTAGGT GTATTTCCTC CAGCTGTTTT ATTTAAAATA

451 GTTGCTGCTG CATTTACTGC TTGAGAATAA GCCGTTCGTT TAGCATCATC

501 AGCATCTTGA TAATTTTGAC TTTGTAACGT CGTGTCTTTA TCACGAATTG

551 ATGTTTCTAA TTGACCCATA GCACCATCTA ATTGTTGCGC TTTGGCTTTA

601 ACTGTATTAA CACCTTCAAC ATTTGTTGCT TGTGTAATTT CATTATCTAA

651 CGCATTACGT TGTGCATTAT TAATGTGTGT TAATGTACCT AACGTTTGTT

701 TCGCAGCAGC TTTAGCTTCA TTTAATTTCG CATCACCGTT CAACGCCGTC

751 TTCGTACTGT TCACATTTTG TAATGCTTGT TCAACTGCTG CTTTGTCTAC

801 ATTTTGACCA CTAGCTTTTG TTAAAATTGC TTTTGCTGCA TTTACTGCTT

851 GATCATAAGC TGATTTCTTA CTTGGCTCAG CATCTAGGTA TTTCTGAGTT

901 TGTTTTGTTT GTGTCTCATC ATTGATACCA TTTTGTAAAC TGTGCATTGC

951 GTTATTTAAT TCTGTTGCTT TTGCAGTTTC TTGATTTACA CCAGCTACTG

1001 TAGTTGCACC ATCCAATGTT ACGCGTTAAC GCATCTTTTT GTGCATTGTT

1051 AATTGATGTT AAGTTATTCA AGTTTTTTT

>pir||Ξ54157 extensin-like protein - cowpea (fragment) Length = 279

Plus Strand HSPs:

[ΞEQ ID NO: ] score = 52 (23.9 bits), Expect = 2.9e-05, Ξum P(5) = 2.9e-05 Identities = 15/48 (31%), Positives = 22/48 (45%), Frame = +2 Query: 719 HLIΞHHRSTPΞΞYCΞHFVMLVQLLLCLHFDH*LLLKLLLLHLLLDHKL 862

HL+ HH +Ξ+ ++L L +C+ H LL L L H L Sbjct: 141 HLLHHHLPMΞTΞHPLLHLLLHHLHMCIΞHHHHHLLHLRLPTFTΞPHLL 188

[SEQ ID NO: ] score = 42 (19.3 bits). Expect = 9.6, Sum P(3) = 1.0 Identities = 8/18 (44%), Positives = 9/18 (50%), Frame = +1

Query: 88 LFHHMLGVYSHQH*HNYH 141

L HH+ SH H H H Ξbjct: 159 LLHHLHMCISHHHHHLLH 176

[ΞEQ ID NO: ] score = 42 (19.3 bits). Expect = 9.6, Ξum P(3) = 1.0 Identities = 9/28 (32%), Positives = 12/28 (42%), Frame = +2

Query: 494 HHQHLDNFDFVTΞCLYHELMFLIDP*HH 577

HH H+ L+H L+ P HH

Sbjct: 241 HHLHMCISRHHHHLLHHHLLMΞTΞPHHH 268

[SEQ ID NO: ] score = 42 (19.3 bits), Expect = 9.6, Sum P(3) = 1.0 Identities = 13/39 (33%), Positives = 19/39 (48%), Frame = +1

Query: 244 VLHLLLVLSMLLFVLYLΞPKHL*ΞLCSQPVSHVLRF*IP 360

+LHL L +L+L P HL S + H+L +P Ξbjct: 174 LLHLRLPTFTSPHLLHLLPHHLPMFTSLHLLHLLPHHLP 212

(SEQ ID NO: ] score = 41 (18.9 bits), Expect = 2.9e-05, Sum P(5) = 2.9e-05 Identities = 7/18 (38%), Positives = 12/18 (66%), Frame = +2

Query: 617 QHLLLV*FHYLTHYWHY 670

+HLL+ H+L H + H+ Sbjct: 102 RHLLMFTSHHLLHLLPHH 119

[SEQ ID NO: ] score = 40 (18.4 bits), Expect = 2.9e-05, Sum P(5) = 2.9e-05 Identities = 12/39 (30%), Positives = 20/39 (51%), Frame = +1

Query: 244 VLHLLLVLSMLLFVLYLSPKHL*ΞLCSQPVΞHVLRF*IP 360

+LH L++ +L+L P HL S + H+L +P Sbjct: 51 LLHHHLLMFTSHHLLHLLPHHLPMFTΞLHLLHLLPHHLP 89

(ΞEQ ID NO: ] score = 40 (18.4 bits). Expect = 0.022, Ξum P(4) = 0.022 Identities = 7/17 (41%), Positives = 11/17 (64%), Frame = +2

Query: 620 HLLLV*FHYLTHYWHY 670 HLL+ H+L H + H+ Ξbjct: 55 HLLMFTSHHLLHLLPHH 71

Example 1

Isolation of DNA coding for a Novel Protein from S. Aureus WCUH 29

The polynucleotide having the DNA sequence given herein can be obtained from a library of clones of chromosomal DNA of S.aureus WCUH 29 in E.coli. Libraries may be prepared by routine methods, for example: Methods 1 and 2.

Total cellular DNA is isolated from Staphylococcus aureus strain WCUH29 (NCIMB 40771) according to standard procedures and size-fractionated by either of two methods. Method I.

Total cellular DNA is mechanically sheared by passage through a needle in order to size-fractionate according to standard procedures. DNA fragments of up to 1 lkbp in size are rendered blunt by treatment with exonuclease and DNA polymerase, and EcoRl linkers added. Fragments are ligated into the vector Lambda ZapII that has been cut with £cøRI, the library packaged by standard procedures and E.coli infected with the packaged library. The library is amplified by standard procedures. Method 2.

Total cellular DNA is partially hydrolysed with a combination of four restriction enzymes (Rsal, Pall, Alul and Bsh 12351) and size-fractionated according to standard procedures. £cσRI linkers are ligated to the DNA and the fragments then ligated into the vector Lambda ZapII that have been cut with £coRI, the library packaged by standard procedures, and E.coli infected with the packaged library. The library is amplified by standard procedures.

Example 2

The determination of expression during infection of a gene from Staphylococcus aureus WCUH29

Necrotic fatty tissue from a four day groin infection of Staphylococcus aureus WCUH29 in the mouse is efficiently disrupted and processed in the presence of chaotropic agents and RNAase inhibitor to provide a mixture of animal and bacterial RNA. The optimal conditions for disruption and processing to give stable preparations and high yields of bacterial RNA are followed by the use of hybridisation to a radiolabelled oligonucleotide specific to Staphylococcus aureus 16S RNA on Northern blots. The RNase free, DNase free, DNA and protein free preparations of RNA obtained are suitable for Reverse Transcription PCR (RT-PCR) using unique primer pairs designed from the sequence of each gene of Staphylococcus aureus WCUH29. a) Isolation of tissue infected with Staphylococcal aureus WCUH29 from a mouse animal model of infection

10 ml. volumes of sterile nutrient broth (No.2 Oxoid) are seeded with isolated, individual colonies of Staphylococcus aureus WCUH29 from an agar culture plate.

The cultures are incubated aerobically (static culture) at 37 degrees C for 16-20 hours . 4 week old mice (female, 18g-22g, strain MF1) are each infected by subcutaneous injection of 0.5ml. of this broth culture of Staphylococcus aureus WCUH29 (diluted in broth to approximately 108 cfu/ml.) into the anterior , right lower quadrant (groin area). Mice should be monitored regularly during the first 24 hours after infection, then daily until termination of study. Animals with signs of systemic infection, i.e. lethargy, ruffled appearance, isolation from group, should be monitored closely and if signs progress to moribundancy, the animal should be culled immediately.

Visible external signs of lesion development will be seen 24-48h after infection. Examination of the abdomen of the animal will show the raised outline of the abscess beneath the skin. The localised lesion should remain in the right lower quadrant, but may occasionally spread to the left lower quadrant, and superiorly to the thorax. On occasions, the abscess may rupture through the overlying skin layers. The affected animal should be culled immediately and the tissues sampled if possible. Failure to cull the animal may result in the necrotic skin tissue overlying the abscess being sloughed off, exposing the abdominal muscle wall.

Approximately 96h after infection, animals are killed using carbon dioxide asphyxiation. To minimise delay between death and tissue processing /storage, mice should be killed individually rather than in groups.The dead animal is placed onto its back and the fur swabbed liberally with 70% alcohol. An initial incision using scissors is made through the skin of the abdominal left lower quadrant, travelling superiorly up to, then across the thorax. The incision is completed by cutting inferiorly to the abdominal lower right quadrant. Care should be taken not to penetrate the abdominal wall. Holding the skin flap with forceps, the skin is gently pulled way from the abdomen. The exposed abscess, which covers the peritoneal wall but generally does not penetrate the muscle sheet completely, is excised, taking care not to puncture the viscera.

The abscess/muscle sheet and other infected tissue, such as the necrotic pads of fatty tissue in the abdominal lower right and left quadrants may require cutting in sections, prior to flash-freezing in liquid nitrogen, thereby allowing easier storage in plastic collecting vials. b) Isolation of Staphylococcus aureus WCUH29 RNA from infected tissue samples

4-6 infected tissue samples(each approx 0.5-0.7g) in 2ml screw-cap tubes are removed from -80°C.storage into a dry ice ethanol bath In a microbiological safety cabinet the samples are disrupted individually whilst the remaining samples are kept cold in the dry ice ethanol bath. To disrupt the bacteria within the tissue sample 1ml of TRIzol Reagent (Gibco BRL, Life Technologies) is added followed by enough 0.1mm zirconia silica beads to almost fill the tube,the lid is replaced taking care not to get any beads into the screw thread so as to ensure a good seal and eliminate aerosol generation. The sample is then homogenised in a Mini-BeadBeater Type BX-4 (Biospec Products) Necrotic fatty tissue is treated for 100 seconds at 5000 φm in order to achieve bacterial lysis. In vivo grown bacteria require longer treatment than in vitro grown S.aureus WCUH29 which are disrupted by a 30 second bead-beat.

After bead-beating the tubes are chilled on ice before opening in a fume-hood as heat generated during disruption may degrade the TRIzol and release cyanide.

200 microlitres of chloroform is then added and the tubes shaken by hand for 15 seconds to ensure complete mixing. After 2-3 minutes at room temperature the tubes are spun down at 12,000 x g, 4 °C for 15minutes and RNA extraction is then continued according to the method given by the manufacturers of TRIzol Reagent i.e.:- The aqueous phase, approx 0.6 ml, is transferred to a sterile eppendorf tube and 0.5 ml of isopropanol is added. After 10 minutes at room temperature the samples are spun at 12,000 x g, 4"C for 10 minutes. The supernatant is removed and discarded then the RNA pellet is washed with 1 ml 75% ethanol. A brief vortex is used to mix the sample before centrifuging at 7,500 x g, 4 "C for 5 minutes. The ethanol is removed and the RNA pellet dried under vacuum for no more than 5 minutes. Samples are then resuspended by repeated pipetting in 100 microlitres of DEPC treated water, followed by 5-10 minutes at 55^λ'C .Finally, after at least 1 minute on ice, 200 units of Rnasin (Promega) is added

RNA preparations are stored at -80 "C for up to one month. For longer term storage the RNA precipitate can be stored at the wash stage of the protocol in 75% ethanol for at least one year at -20 °C.

Quality of the RNA isolated is assessed by running samples on 1% agarose gels. 1 x TBE gels stained with ethidium bromide are used to visualise total RNA yields. To demonstrate the isolation of bacterial RNA from the infected tissue 1 x MOPS, 2.2M formaldehyde gels are run and vacuum blotted to Hybond-N (Amersham). The blot is then hybridised with a " P labelled oligonucleotide probe specific to 16s rRNA of S.aureus ( K. Greisen, et al., J. Clin. Microbiol. 32 335-351(1994)). An oligonucleotide selected from the group consisting of the polynucleotides of Table 1 is used as a probe. The size of the hybridising band is compared to that of control RNA isolated from in vitro grown S.aureus WCUH29. Correct sized bacterial 16s rRNA bands can be detected in total RNA samples which show extensive degradation of the mammalian RNA when visualised on TBE gels. c) The removal of DNA from Staphylococcus aureus WCUH29 derived RNA

DNA was removed from 73 microlitre samples of RNA by a 15 minute treatment on ice with 3 units of DNasel, amplification grade (Gibco BRL, Life Technologies) in the buffer supplied with the addition of 200 units of Rnasin (Promega) in a final volume of 90 microlitres.

The DNase was inactivated and removed by treatment with TRIzol LS Reagent (Gibco BRL, Life Technologies) according to the manufacturers protocol. DNase treated RNA was resuspended in 73 microlitres of DEPC treated water with the addition -of Rnasin as described in Method 1. d) The preparation of cDNA from RNA samples derived from infected tissue

10 microlitre samples of DNase treated RNA are reverse transcribed using a Superscript Preamplification System for First Strand cDNA Synthesis kit (Gibco BRL, Life Technologies) according to the manufacturers instructions. 1 nanogram of random hexamers is used to prime each reaction. Controls without the addition of SuperScriptll reverse transcriptase are also run. Both +/-RT samples are treated with RNaseH before proceeding to the PCR reaction e) The use of PCR to determine the presence of a bacterial cDNA species PCR reactions are set up on ice in 0.2ml tubes by adding the following components:

45 microlitres PCR SUPERMIX (Gibco BRL, Life Technologies). 1 microlitre 50mM MgCl, , to adjust final concentration to 2.5mM.

1 microlitre PCR primers(optimally 18-25 basepairs designed to possess similar annealing temperatures), each primer at lOmM initial concentration.

2 microlitres cDNA.

PCR reactions are run on a Perkin Elmer GeneAmp PCR System 9600 as follows: 5 minutes at 95 "C, then 50 cycles of 30 seconds each at 94 °C, 42 "C and 72 °C followed by 3 minutes at 72 "C and then a hold temperature of 4"C. 10 microlitre aliquots are then run out on 1 % 1 x TBE gels stained with ethidium bromide with PCR product sizes estimated by comparison to a 100 bp DNA Ladder (Gibco BRL, Life Technologies). RT/PCR controls may include +/- reverse transcriptase reactions, 16s rRNA primers or DNA specific primer pairs designed to produce PCR products from non-transcribed S.aureus WCUH29 genomic sequences.

To test the efficiency of the primer pairs they are used in DNA PCR with WCUH29 total DNA. PCR reactions are set up and run as described above using approx. 1 microgram of DNA in place of the cDNA and 35 cycles of PCR rather than 50.

Primer pairs which fail to give the predicted sized product in either DNA PCR or RT PCR (approx 20%) are PCR failures and as such are uninformative. Of those which give the correct size product with DNA PCR three classes are distinguished in RT/PCR:

1. Genes which are not expressed in vivo reproducibly fail to give a product in RT PCR.

2. Genes which are expressed in vivo reproducibly give the correct size product in RT/PCR and show a stronger signal in the +RT samples than in the -RT controls.

3. Genes which may be expressed in vivo give similar amounts of product in both +/-RT samples.

Claims

What is claimed is:

I . An isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of:

(a) a polynucleotide having at least a 70% identity to a polynucleotide encoding a polypeptide comprising an amino acid sequence of Table 1 ;

(b) a polynucleotide having at least a 70% identity to a polynucleotide encoding a mature polypeptide expressed by the gene contained in the 5. aureus of the deposited strain that was sequenced to obtain a polynucleotide sequence of Table 1;

(c) a polynucleotide encoding a polypeptide comprising an amino acid sequence which is at least 70% identical to an amino acid sequence of Table 1;

(d) a polynucleotide which is complementary to the polynucleotide of (a), (b) or (c); and

(e) a polynucleotide comprising at least 15 sequential bases of the polynucleotide of (a), (b), (c) or (d).

2. The polynucleotide of Claim 1 wherein the polynucleotide is DNA.

3. The polynucleotide of Claim 1 wherein the polynucleotide is RNA.

4. The polynucleotide of Claim 2 comprising the nucleic acid sequence selected from the group consisting of the nucleic acid sequences set forth in Table 1.

5. The polynucleotide of Claim 2 which encodes a polypeptide comprising an amino acid sequence sequence selected from the group consisting of the amino acid sequences set forth in Table 1.

6. A vector comprising the polynucleotide of Claim 1.

7. A host cell comprising the vector of Claim 6.

8. A process for producing a polypeptide comprising: expressing from the host cell of Claim 7 a polypeptide encoded by said DNA.

9. A process for producing a polypeptide or fragment comprising culturing a host of claim 7 under conditions sufficient for the production of said polypeptide or fragment.

10. A polypeptide comprising an amino acid sequence which is at least 70% identical to an amino acid sequence selected from the group consisting of the amino acid sequences set forth in Table 1.

I I. A polypeptide comprising an amino acid sequence selected from the group consisting of the amino acid sequences set forth in Table 1.

12. An antibody against the polypeptide of claim 10.

13. An antagonist or agonist of the activity or expression of the polypeptide of claim 10.

14. A method for the treatment or prevention of disease of an individual comprising: administering to the individual a therapeutically effective amount of the polypeptide of claim 10.

15. A method for the treatment of an individual having need to inhibit a bacterial polypeptide comprising: administering to the individual a therapeutically effective amount of the antagonist of Claim 13.

16. A process for diagnosing a disease related to expression or activity of the polypeptide of claim 10 in an individual comprising:

(a) determining a nucleic acid sequence encoding said polypeptide, and/or

(b) analyzing for the presence or amount of said polypeptide in a sample derived from the individual.

17. A method for identifying compounds which interact with and inhibit or activate an activity of the polypeptide of claim 10 comprising: contacting a composition comprising the polypeptide with the compound to be screened under conditions to permit interaction between the compound and the polypeptide to assess the interaction of a compound, such interaction being associated with a second component capable of providing a detectable signal in response to the interaction of the polypeptide with the compound; and determining whether the compound interacts with and activates or inhibits an activity of the polypeptide by detecting the presence or absence of a signal generated from the interaction of the compound with the polypeptide.

18. A method for inducing an immunological response in a mammal which comprises inoculating the mammal with the polypeptide of claim 10, or a fragment or variant thereof, adequate to produce antibody and/or T cell immune response to protect said animal from disease.

19. A method of inducing immunological response in a mammal which comprises delivering a nucleic acid vector to direct expression of a polypeptide of claim 10, or fragment or a variant thereof, for expressing said polypeptide, or a fragment or a variant thereof in vivo in order to induce an immunological response to produce antibody and/ or T cell immune response to protect said animal from disease.

20. A polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1, 52, 95, 184, 127, 128, 153, 212, 215 and 227.

21. A polypeptide comprising a polypeptide encoded by the polynculeotide of claim 20.

22. The isolated polynucleotide of claim 1 wherein said nucleotide is selected from the group consisting of: (a) a polynucleotide having at least a 90% identity to a polynucleotide encoding a polypeptide comprising the amino acid sequence of Table 1;

(b) a polynucleotide having at least a 90% identity to a polynucleotide encoding the same mature polypeptide expressed by the gene contained in the S. aureus of the deposited strain that was sequenced to obtain a polynucleotide sequence of Table 1; (c) a polynucleotide encoding a polypeptide comprising an amino acid sequence which is at least 90% identical to the amino acid sequence of Table 1;

23. The isolated polynucleotide of claim 1 selected from the group consisting of:

(a) a polynucleotide having at least a 95% identity to a polynucleotide encoding a polypeptide comprising the amino acid sequence of Table 1;

(b) a polynucleotide having at least a 95% identity to a polynucleotide encoding the same mature polypeptide expressed by the gene contained in the S. aureus of the deposited strain that was sequenced to obtain a polynucleotide sequence of Table 1;

(c) a polynucleotide encoding a polypeptide comprising an amino acid sequence which is at least 95% identical to the amino acid sequence of Table 1;

24. An isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of: (a) a polynucleotide having at least a 50% identity to a polynucleotide encoding a polypeptide comprising the amino acid sequence of Table 1 and obtained from a prokaryotic species other than S. aureus; (b) a polynucleotide encoding a polypeptide comprising an amino acid sequence which is at least 50% identical to the amino acid sequence of Table 1 and obtained from a prokaryotic species other than S. aureus; and

(c) a polynucleotide which is complementary to the polynucleotide of (a) or (b).

25. An isolated Streptococcal polypeptide having one of the amino acid sequences given in Table 1.

26. An isolated nucleic acid encoding one of the amino acid sequences of

Claim 1 and nucleic acid sequences capable of hybridizing therewith under stringent conditions.

27. Recombinant vectors comprising the nucleic acid sequences of

Claim 26 and host cells transformed or transfected therewith.

28. A method of identifying an antimicrobial compound comprising contacting candidate compounds with a polypeptide of Claim 1 and selecting those compounds capable of inhibiting the bioactivity of said polypeptide.

29. Antimicrobial compounds identified by the method of Claim 28.