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. 2007 Sep 21;73(22):7199–7209. doi: 10.1128/AEM.01629-07

TABLE 2.

S. xylosus S04002-, S04009-, and 00-1747-specific sequences with significant protein matches in the GenBank database

Function group and predicted encoded protein Fragment E value % Identity Organism Accession no. Homology found
S04002 S04009 00-1747
Metabolism
    Biotin metabolism
        Biotin synthase BioB E5 2.00E-44 85 Staphylococcus aureus COL ER935916 +
E129 2.00E-34 80 S. aureus COL ER935940 +
        Adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA BioD E5 1.00E-17 62 S. aureus Mu50 ER935916 +
D128 6.00E-125 82 S. aureus COL ER935891 +
D128 4.00E-26 63 Staphylococcus epidermidis RP62A ER935891 +
    Myo-inositol catabolism
        IolA Mb262 5.00E-133 74 Bacillus licheniformis ATCC 14580 ER935857 + +
D76 6.00E-40 65 Geobacillus kaustophilus HTA426 ER935886 +
        IolB Mb11 1.00E-61 52 B. licheniformis ATCC 14580 ER935832 + +
        IolC Mb11 7.00E-59 63 Bacillus halodurans C-125 ER935832 + +
        IolC (putative) M141 1.00E-30 66 B. licheniformis ATCC 14580 ER935866 + +
        IolD M141 8.00E-71 70 B. halodurans C-125 ER935866 + +
        IolG E126 2.00E-64 50 Bacillus cereus E33L ER935938 +
        IolE Mb118 2.00E-79 63 Clostridium tetani E88 ER935843 + +
    Pentose and glucuronate interconversion
        d-Arabino-3-hexulose-6-phosphate formaldehyde lyase E51 2.00E-14 95 Staphylococcus saprophyticus ATCC 15305 ER935923 + +
        Putative hexulose-6-phosphate synthase E28 4.00E-75 95 S. saprophyticus ATCC 15305 ER935918 + +
        Putative 6-phospho-3-hexuloisomerase E28 9.00E-77 83 S. saprophyticus ATCC 15305 ER935918 + +
        UTP-glucose-1-phosphate uridyltransferase E36 7.00E-75 90 S. saprophyticus ATCC 15305 ER935921 +
        2-dehydro-3-deoxyphosphogluconate aldolase Mb275 3.00E-78 63 Bacillus thuringiensis serovar Israelensis ATCC 35646 ER935858 + +
        2-dehydro-3-deoxygluconokinase PfkB D151 5.00E-63 55 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 ER935896 +
D242 6.00E-29 49 Bacillus weihenstephanensis KBAB4 ER935906 + +
        Alpha/beta hydrolase fold family protein Mb59 3.00E-27 52 Flavobacteriales bacterium HTCC2170 ER935840 +
    Fructose and mannose metabolism
        Phosphomannomutase E127 4.00E-83 65 S. epidermidis RP62A ER935939 +
        Hexitol dehydrogenase Mb27 4.00E-94 69 S. aureus COL ER935835 + +
M139 1.00E-14 72 S. aureus COL ER935864 + +
        Sorbitol dehydrogenase M139 3.00E-10 62 S. aureus COL ER935864 + +
    Fermentative metabolism
        Acetoin (diacetyl) reductase ButA E129 9.00E-57 81 S. epidermidis ATCC 12228 ER935940 +
        α-Acetolactate synthase AlsS E190 0.0 97 S. saprophyticus ATCC 15305 ER935953 +
    Amino acid metabolism
        Saccharopine dehydrogenase-related protein D85 2.00E-04 54 Lactococcus lactis subsp. cremoris SK11 ER935887 +
D218 2.00E-35 64 L. lactis subsp. cremoris SK11 ER935905 +
        Sarcosine oxidase alpha subunit D129 5.00E-77 51 B. thuringiensis serovar Konkukian 97-27 ER935892 +
        Sarcosine oxidase beta subunit D298 4.00E-45 41 B. cereus ATCC 14579 ER935912 +
        Betaine aldehyde dehydrogenase D298 9.00E-25 63 B. weihenstephanensis KBAB4 ER935912 +
        Dihydrodipicolinate synthase D176 2.00E-06 42 Rickettsia felis URRWXCal2 ER935899 +
    Other
        Lipase E179 4.00E-92 92 S. saprophyticus ER935951 +
        Putative lipase D218 2.00E-88 83 S. saprophyticus ATCC 15305 ER935905 +
        UDP-glucose 4-epimerase D44 2.00E-20 59 G. kaustophilus ER935881 +
        Dihydroorotase D23 1.00E-71 56 B. cereus G9241 ER935879 + +
        Putative nucleoside diphosphate-sugar epimerase DTDP-D-glucose 4,6-dehydratase D46 1.00E-55 82 S. saprophyticus ATCC 15305 ER935882 + +
        COG1670, putative acetyltransferase D96 5.00E-45 54 S. saprophyticus ATCC 15305 ER935888 + +
        Aldehyde dehydrogenase AldA D106 4.00E-55 69 Bacillus sp. B14905 ER935889 +
        Riboflavin kinase RibR D213 9.00E-10 40 B. subtilis subsp. subtilis 168 ER935904 + + +
        COG2936, putative peptidase S9, prolyl oligopeptidase precursor D273 5.00E-50 81 S. aureus RF122 ER935909 +
        Similar to oxidoreductase Mb127 8.00E-16 36 S. aureus Mu50 ER935844 + +
        COG0655, putative iron-sulfur flavoprotein (hypothetical protein SAS0063) E184 1.00E-16 53 S. aureus MSSA476 ER935952 +
        Short-chain alcohol dehydrogenase E139 9.00E-73 98 S. saprophyticus ATCC 15305 ER935942 +
        COG4221, putative short-chain alcohol dehydrogenase of unknown specificity E51 2.00E-42 100 S. saprophyticus ATCC 15305 ER935923 +
        COG1063, alcohol dehydrogenase M65 2.00E-141 97 S. saprophyticus ATCC 15305 ER935860 + +
    Regulatory
        Putative regulator of HxlAB (hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase) E111 1.00E-35 98 S. saprophyticus ATCC 15305 ER935932 +
        Transcriptional regulator, LysR family probable AlsR regulator E173 4.00E-37 33 Bacillus clausii KSM-K16 ER935950 +
        Putative regulator of sorbitol operon D7 4.00E-18 28 Clostridium beijerincki NCIMB 8052 ER935875 +
        Sorbitol operon activator D254 2.00E-24 39 C. beijerincki KSM-K16 ER935908 +
        Transcriptional regulator putative hydrogen peroxide-inducible genes activator E85 3.00E-81 99 S. saprophyticus ATCC 15305 ER935928 + +
        PTS multidomain regulator BglG Mb48 6.00E-41 44 S. aureus MSSA476 ER935839 +
D63 2.00E-16 45 S. aureus COL ER935884 + +
        Putative PTS multidomain regulator EIIA putative fructose/mannitol specific Mb147 6.00E-45 45 S. aureus MSSA476 ER935850 + +
        PTS system enzyme II B component putative sorbitol specific M149 6.00E-35 87 S. aureus Mu50 ER935867 + +
D53 2.00E-36 84 S. aureus Mu50 ER935883 + +
        PTS transport system IIA component putative galactitol specific D53 1.00E-07 44 S. aureus MRSA252 ER935883 + +
        Accessory gene regulator C agrC E154 5.00E-110 83 S. saprophyticus ATCC 15305 ER935944 +
        Protein SSP2020 putative ebsC transcription regulation protein M160 6.00E-40 61 S. saprophyticus ATCC 15305 ER935868 + +
        NmrA-like transcriptional regulator D11 8.00E-22 38 Salinispora tropica CNB-440 ER935876 +
        Transcriptional regulator, LysR family domain protein E184 4.00E-56 66 S. aureus MSSA476 ER935952 +
E116 8.00E-13 46 S. aureus USA300 ER935933 +
        Transcriptional regulator, GntR family/aminotransferase, class I E3 1.00E-53 57 S. aureus COL ER935914 + +
Mb46 1.00E-49 59 S. aureus COL ER935838 +
Mb145 9.00E-20 81 S. aureus COL ER935849 +
        COG1167, putative transcriptional regulator, GntR family E100 2.00E-165 98 S. saprophyticus ATCC 15305 ER935929 +
        Transcriptional regulator, AraC/XylS family D141 2.00E-43 58 Oceanobacillus iheyensis HTE831 ER935895 + +
        COG1733, putative transcriptional regulator E139 3.00E-17 93 S. saprophyticus ATCC 15305 ER935942 + +
    Cell membrane/surface structure
        Putative autolysin (mannosyl-glycoprotein endo-β-N-acetylglucosamidase) E73 3.00E-55 99 S. saprophyticus ATCC 15305 ER935926 + + +
E130 2.00E-178 97 S. saprophyticus ATCC 15305 ER935941 +
        Autolysin (mannosyl-glycoprotein endo-β-N-acetylglucosamidase) D294 5.00E-07 66 S. epidermidis ATCC 12228 ER935911 + + +
        67-kDa myosin-cross-reactive streptococcal antigen-like protein E110 3.00E-26 94 S. epidermidis ER935931 +
        smart00255, putative Toll-interleukin receptor D157 1.00E-35 69 S. aureus MSSA476 ER935897 +
        Glycosyl transferase, family 2, CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase E121 1.00E-32 40 Clostridium phytofermentans ISDg ER935935 +
        Lipopolysaccharide modification acyltransferase Mb127 8.00E-19 78 S. epidermidis ATCC 1228 ER935844 + +
        Biofilm-associated protein Bap D137 1.00E-18 28 Staphylococcus hyicus ER935894 +
        LPXTG cell wall surface anchor family protein, hypothetical protein SSPP105 E25 1.00E-27 98 S. saprophyticus ATCC 15305 ER935917 +
        Cell wall surface anchor family protein, hypothetical protein SSPP105 E34 2.00E-114 98 S. saprophyticus ATCC 15305 ER935920 +
        Putative membrane protein of unknown function D157 3.00E-05 36 S. saprophyticus ATCC 15305 ER935897 +
        COG3152, predicted membrane protein D158 0.056 31 Staphylococcus haemolyticus ER935898 +
        COG3949, SSP0396 uncharacterized membrane protein D294 9.00E-24 39 S. saprophyticus ATCC 15305 + + +
    Resistance
        Methicillin resistance protein MecA1 Mb201 4.00E-38 52 Staphylococcus sciuri ER935854 +
        MecR1, methicillin resistance regulatory protein M116 5.00E-73 58 S. aureus ER935862 +
        Metallothiol transferase FosB (fosfomycin resistance protein) M130 3.00E-69 89 S. haemolyticus JCSC1435 ER935863 +
        MphBM macrolide 2′-phosphotransferase II M180 1.00E-92 86 S. aureus ER935869 + +
        Micrococcin P1 peptide synthetase Mb107 6.00E-123 58 Staphylococcus equorum ER935842 + +
        Putative tetronasin resistance transmembrane protein D178 3.00E-18 36 B. halodurans C-125 ER935901 + +
        Aminoglycoside adenyltransferase D121 7.00E-51 79 S. saprophyticus ATCC 15305 ER935890 +
        Arsenate reductase E125 3,00E-73 100 S. xylosus plasmid Psx267 ER935937 + + +
        Arsenic efflux pump protein E125 2.00E-61 100 S. aureus ER935937 + + +
        Arsenic efflux pump membrane protein D284 4.00E-19 100 S. xylosus(Psx267) ER935910 + + +
        Arsenic resistance operon repressor D284 4.00E-49 89 S. aureus N315 ER935910 + + +
        Membrane protein TerC, possibly involved in tellurium resistance D16 1.00E-11 78 S. saprophyticus ATCC 15305 ER935877 +
        Probable drug resistance transporter of EmrB/QacA family Mb12 4.00E-19 46 Listeria monocytogenes 4b F2365 ER935833 + +
        Putative drug exporter of RND superfamily E4 8.00E-91 74 S. saprophyticus ATCC 15305 ER935915 +
        COG2329, putative antibiotic biosynthesis monooxygenase M266 2.00E-27 55 S. aureus JH1 ER935873 + +
    Transport
        l-lactate permease E117 2.00E-47 92 S. saprophyticus ATCC 15305 ER935934 +
        Na+:myo-inositol cotransporter Mb42 1,00E-56 70 Bacillus clausii KSM-K16 ER935837 + +
        Amino acid permease-associated region lysine-specific permease precursor D132 4.00E-58 53 Pseudomonas fluorescens PfO-1 ER935893 +
        PTS enzyme IIC component putative galactitol specific I M283 9.00E-34 57 Salmonella enterica serovar Typhimurium LT2 ER935874 +
        Ferrous iron transport protein B Mb142 8.00E-42 76 S. epidermidis RP62A ER935848 + +
        ATPase copper transport E158 4.00E-62 86 S. aureus USA300 ER935947 +
D182 4.00E-110 85 S. aureus USA300 ER935902 +
        Putative permease, putative role in amino acid adenylation E157 2.00E-51 81 S. aureus USA300 ER935946 + +
        Putative permease of drug and metabolite transporter superfamily E38 6.00E-122 98 S. saprophyticus ATCC 15305 ER935922 + +
        Putative transporter, EamA family E77 8.00E-50 53 S. aureus Mu50 ER935927 +
        Putative ABC-type nitrate sulfonate taurine bicarbonate transport system ATPase component M237 3.00E-65 89 S. saprophyticus ATCC 15305 ER935871 + +
        TRAP-T family transporter, putative tripartite tricarboxylate transporter D177 2.00E-17 49 Rhodobacter sphaeroides 2.4.1 ER935900 + +
        ABC transporter, ATP-binding/permease protein D19 6.00E-18 73 S. aureus COL ER935878 +
        Putative ABC transporter permease E61 1.00E-10 89 S. saprophyticus ATCC 15305 ER935925 +
        Major facilitator family transporter E142 3.00E-32 54 Listeria innocua Clip11262 ER935943 + +
        Putative permease of the major facilitator superfamily D301 4.00E-20 96 S. saprophyticus ATCC 15305 ER935913 +
    Phage-related and IS elements
        IS605/IS200-like transposase Mb168 3.00E-86 89 S. epidermidis ATCC 1228 ER935851 + +
        Recombinase Sin E110 3.00E-75 94 S. epidermidis ATCC 12228 ER935931 +
        Integrase Mb194 7.00E-66 64 S. aureus RF122 ER935852 +
        Phage infection protein E168 0.0 99 S. epidermidis RP62A ER935949 + +
        Phage terminase large subunit, 77ORF003 Mb33 5.00E-68 62 Bacteriophage 77 ER935836 +
        ORF001 Mb66 3.00E-11 60 Bacteriophage 2638A ER935841 +
        ORF094 Mb66 7.00E-13 79 Bacteriophage 2638A ER935841 +
        ORF028 Mb66 3.00E-06 77 Bacteriophage 2638A ER935841 +
        Conserved phage protein probable ORF029 of bacteriophage 37 Mb131 1.00E-16 56 S. haemolyticus JCSC1435 ER935845 +
        phiPVL ORF050-like protein Mb133 3.00E-06 36 S. aureus USA300 ER935846 +
        ORF025 Mb137 3.00E-08 51 Bacteriophage EW ER935847 +
        ORF60 Mb215 2.00E-06 46 S. phage 187 ER935856 +
        ORF077 Mb215 0.012 41 Bacteriophage EW ER935856 +
        Capsid protein, 77ORF006 M85 7.00E-55 80 Bacteriophage 77 ER935861 +
        77ORF042 M85 1.00E-12 47 Bacteriophage 77 ER935861 +
        ORF001 M256 3.00E-59 59 Bacteriophage 2638A ER935872 +
        Phage helicase, C terminal M200 2.00E-22 31 Clostridium thermocellum ATCC 27405 ER935870 +
        Integrase, ORF010 D65 2.00E-30 56 Bacteriophage 52A ER935885 +
        Hypothetical protein SSPP103, phage infection protein E160 3.00E-11 S. saprophyticus ATCC 15305 ER935948 + + +
        Hypothetical protein SAR0381, probable phage protein Mb279 5.00E-09 38 S. aureus MRSA252 ER935859 +
    Unknown function
        COG3877, unnamed protein product E31 7.00E-37 79 S. haemolyticus JCSC1435 ER935919 +
        Hypothetical protein SSP0169 E55 2.00E-09 85 S. saprophyticus ATCC 15305 ER935924 +
        Similar to unknown protein SH2317 E108 7.00E-09 60 S. haemolyticus ER935930 +
        Hypothetical protein SE2200 E123 3.00E-09 89 S. epidermidis ATCC 12228 ER935936 + +
        Hypothetical protein SH0055 E156 1.00E-34 70 S. haemolyticus JCSC1435 ER935945 +
        COG1284, uncharacterized conserved protein SSP1949 Mb26 2.00E-36 84 S. saprophyticus ATCC 15305 ER935834 + +
        Hypothetical protein cn33 Mb198 2.00E-19 37 S. epidermidis bacteriophage CNPH82 ER935853 +
        Hypothetical protein SH1793 Mb215 0.001 54 S. haemolyticus JCSC1435 ER935856 +
        Hypothetical protein, no similarity found Mb213 ER935855 +
        Hypothetical protein SAB0188 M139 7.00E-07 64 S. aureus RF122 ER935864 + +
        Hypothetical protein Mbar_A2529 M266 2.00E-12 30 Methanosarcina barkeri strain Fusaro ER935873 + +
        Hypothetical protein D39 8.00E-12 45 S. aureus Mu50 ER935880 +
        Truncated hypothetical protein D121 1.00E-10 83 S. saprophyticus ATCC 15305 ER935890 +
        Hypothetical protein SSP2368 D197 4.00E-05 49 S. saprophyticus ATCC 15305 ER935903 + +
        No significant similarity found M140 ER935865 +
        No significant similarity found D246 ER935907 +
HHS Vulnerability Disclosure