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Supplemental Table 1.Predicted Enzymes of S. Oneidensis MR-1 and Their Closest Homolog by Darwin Analysis. the Microbial Genomes

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Supplemental Table 1.Predicted Enzymes of S. Oneidensis MR-1 and Their Closest Homolog by Darwin Analysis. the Microbial Genomes Supplemental Table 1.Predicted enzymes of S. oneidensis MR-1 and their closest homolog by Darwin analysis. The microbial genomes used for the comparion is listed at the end of this table. Gene ID Gene Name Enzyme name/partial information genbankID;organism of best match Pam value of best match PMID of experimentally verified function SO0003 trmE tRNA modification GTPase TrmE 26250447;Escherichia coli CFT073 31 SO0006 rnpA ribonuclease P protein component 50123362;Erwinia caratovora 63 SO0009 dnaN DNA polymerase III, beta subunit 24114989;Shigella flexneri 54 SO0010 recF DNA replication and repair protein RecF 28896787;Vibrio parahaemolyticus 80 SO0011 gyrB DNA gyrase, B subunit 9654406;Vibrio cholerae 31 SO0014 glyS glycyl-tRNA synthetase, beta subunit 50119046;Erwinia caratovora 38 SO0015 glyQ glycyl-tRNA synthetase, alpha subunit 50119045;Erwinia caratovora 17 SO0016 tag DNA-3-methyladenine glycosidase I 26250189;Escherichia coli CFT073 60 SO0017 none multimodular: protein with TolB and Tricorn protease domains (N-terminal); protein with metallo-dependent hydrolase domains 16124371;Caulobacter crescentus 91 SO0020 fadA fatty oxidation complex, beta subunit (2.3.1.16;3.1.2.4) 28896803;Vibrio parahaemolyticus 26 PMID:2191949 SO0021 fadB multimodular: 3-hydroxybutyryl-CoA epimerase, delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase, enoyl-CoA hydratase (N-terminal); 3-hydroxyacyl-CoA dehydrogenase (C-terminal) (1.3.99.12;4.2.1.17) 9949116;Pseudomonas aeruginosa 42 PMID:3286611,15137080 SO0022 pepQ prolidase 15981680;Yersinia pestis 72 SO0023 none protein with NAD/FAD-binding domain 12721882;Pasteurella multocida 80 SO0025 none protoporphyrinogen oxidase 12721884;Pasteurella multocida 80 SO0027 none protoporphyrinogen oxidase, putative 15981677;Yersinia pestis 94 SO0030 sun 16S rRNA m5C967 methyltransferase 9654437;Vibrio cholerae 66 SO0031 fmt methionyl-tRNA formyltransferase 9654438;Vibrio cholerae 39 SO0032 def-1 polypeptide deformylase 34499720;Chromobacterium violaceum 46 SO0034 none DNA processing protein DprA, putative 28867415;Pseudomonas syringae 75 SO0036 none topoisomerase DNA-binding C4 zinc finger domain protein 9654444;Vibrio cholerae 71 SO0038 hemF coproporphyrinogen III oxidase, aerobic 16420991;Salmonella typhimurium 31 SO0040 aroE shikimate 5-dehydrogenase 9945845;Pseudomonas aeruginosa 64 SO0042 none carbonic anhydrase, family 3 28899805;Vibrio parahaemolyticus 38 SO0047 none carboxyl-terminal protease, putative 51246408;Desulfotalea psychrophila 90 SO0048 none peptidase, M23/M37 family 15978176;Yersinia pestis 93 SO0049 gpmA phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (5.4.2.1) 15978177;Yersinia pestis 39 PMID:10437801 SO0050 none rhodanese domain protein 9657246;Vibrio cholerae 80 SO0053 gpsA glycerol-3-phosphate dehydrogenase (NAD(P)+) 28899606;Vibrio parahaemolyticus 31 SO0054 none oxidoreductase with NAD(P)binding Rossmann-fold and FAD/NAD(P)-binding domains 28896853;Vibrio parahaemolyticus 50 SO0065 mog molybdenum cofactor biosynthesis protein Mog 34557568;Wolinella succinogenes 26 SO0066 none conserved hypothetical protein 15980562;Yersinia pestis 108 SO0067 none multimodular: transglycosylase (N-terminal); transpeptidase (C-terminal) 12720919;Pasteurella multocida 97 SO0071 none hydrolase, alpha/beta hydrolase fold family 37519622;Gloeobacter violaceus 122 SO0075 none AMP-binding family protein 15978630;Yersinia pestis 63 SO0077 none protein with with thioesterase/thiol ester dehydrase-isomerase domain 45358130;Methanococcus maripaludis 87 SO0079 none protein with Acyl-CoA N-acyltransferase domain 19553760;Corynebacterium glutamicum 117 SO0080 none protein with thioesterase/thiol ester dehydrase-isomerase domain 9656475;Vibrio cholerae 49 SO0083 none carboxymuconolactone decarboxylase family protein (4.1.1.44) 27379688;Bradyrhizobium japonicum 45 SO0084 none hydrolase, haloacid dehalogenase-like family 28869251;Pseudomonas syringae 83 SO0092 deoD-1 purine nucleoside phosphorylase 9657436;Vibrio cholerae 54 SO0095 hutI imidazolonepropionase (3.5.2.7) 9655684;Vibrio cholerae 53 PMID:2858467 SO0097 hutU urocanate hydratase (4.2.1.49) 28898048;Vibrio parahaemolyticus 17 PMID:4899017 SO0098 hutH histidine ammonia-lyase (4.3.1.3) 9655681;Vibrio cholerae 29 PMID:4899017 SO0098.1 none formate dehydrogenase-N, nitrate-inducible, alpha subunit 12720659;Pasteurella multocida 56 SO0101 fdnG formate dehydrogenase, nitrate inducible, alpha subunit, selenocysteine-containing (1.2.1.2) 3868719;Escherichia coli K12 48 PMID:2168848 SO0102 fdnH formate dehydrogenase, nitrate-inducible, iron-sulfur subunit (1.2.1.2) 1572950;Haemophilus influenzae 63 PMID:2168848 SO0103 fdnI formate dehydrogenase, nitrate-inducible, cytochrome b556 subunit (1.2.1.2) 1572950;Shigella flexneri 89 PMID:2168848 SO0105 selA L-seryl-tRNA selenium transferase 16762626;Salmonella enterica 63 SO0123 none acyltransferase family protein 34498663;Chromobacterium violaceum 98 SO0130 none protease, putative 9657617;Vibrio cholerae 97 SO0131 none chorismate pyruvate lyase 12721237;Pasteurella multocida 114 SO0134 none methyltransferase with S-adenosyl-L-methionine-dependent methyltransferase domain 51245141;Desulfotalea psychrophila 72 SO0135 none hemolysin protein, putative 0 SO0137 moeB molybdopterin biosynthesis MoeB protein 9658030;Vibrio cholerae 49 SO0138 moeA molybdopterin biosynthesis MoeA protein 50121760;Erwinia caratovora 70 SO0142 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase 9658505;Vibrio cholerae 30 SO0144 ptrB protease II 9106503;Xylella fastidiosa 73 SO0145 none protein with GIY-YIG endonuclease domain 50119670;Erwinia caratovora 78 SO0151 none methyltransferase with S-adenosyl-L-methionine-dependent methyltransferase domain 9948503;Pseudomonas aeruginosa 123 SO0152 none protein with Zn-dependent exopeptidase domain 16124566;Caulobacter crescentus 86 SO0162 pckA phosphoenolpyruvate carboxykinase 9951497;Pseudomonas aeruginosa 41 SO0177 none hydrolase, haloacid dehalogenase-like family 15978246;Yersinia pestis 71 SO0180 none methyltransferase with S-adenosyl-L-methionine-dependent methyltransferase domain 0 SO0183 none acetyltransferase, GNAT family 13473742;Mesorhizobium loti 94 SO0188 none protein with quinoprotein amine dehydrogenase domain 37521410;Gloeobacter violaceus 115 SO0190 none nudix hydrolase (MutT/nudix family) 9657319;Vibrio cholerae 46 SO0191 cysQ-1 cysQ protein 9657320;Vibrio cholerae 55 SO0192 none acetyltransferase, GNAT family 34496363;Chromobacterium violaceum 88 SO0194 none acyltransferase family protein 28897711;Vibrio parahaemolyticus 72 SO0195 ybbB selenophosphate-dependent tRNA 2-selenouridine synthase 28868022;Pseudomonas syringae 78 SO0196 selD selenide, water dikinase 1573160;Haemophilus influenzae 40 SO0197 none fatty acid desaturase, family 1 6321383;Saccharomyces cerevisiae 85 SO0206 trmA tRNA (uracil-5-)-methyltransferase 28899713;Vibrio parahaemolyticus 40 SO0213 murB UDP-N-acetylenolpyruvoylglucosamine reductase 1573234;Haemophilus influenzae 76 SO0215 panK pantothenate kinase 12722163;Pasteurella multocida 50 SO0224 rpoB DNA-directed RNA polymerase, beta subunit 9654742;Vibrio cholerae 22 SO0225 rpoC DNA-directed RNA polymerase, beta' subunit 26250759;Escherichia coli CFT073 20 SO0207 murI glutamate racemase 28899710;Vibrio parahaemolyticus 62 SO0256 rpoA DNA-directed RNA polymerase, alpha subunit 12721765;Pasteurella multocida 13 SO0259 ccmE cytochrome c biogenesis protein CcmE 9656598;Vibrio cholerae 49 SO0266 ccmF-1 cytochrome c-type biogenesis protein CcmF 30248772;Nitrosomonas europaea 65 SO0267 dsbE thiol:disulfide interchange protein DsbE 50120818;Erwinia caratovora 77 SO0274 ppc phosphoenolpyruvate carboxylase (4.1.1.31;1.1.1.38) 28899535;Vibrio parahaemolyticus 57 PMID:6368527 SO0275 argC N-acetyl-gamma-glutamyl-phosphate reductase 9657235;Vibrio cholerae 59 SO0276 argB acetylglutamate kinase 9657234;Vibrio cholerae 75 SO0277 argF ornithine carbamoyltransferase 3257134;Pyrococcus horikoshii 78 SO0278 argG argininosuccinate synthase 28899531;Vibrio parahaemolyticus 28 SO0279 argH argininosuccinate lyase 9657232;Vibrio cholerae 41 SO0280 mrcA multimodular penicillin-binding protein 1a: transglycosylase (N-terminal); transpeptidase (C-terminal) 9657226;Vibrio cholerae 65 SO0286 aroK shikimate kinase 9657219;Vibrio cholerae 19 SO0287 aroB 3-dehydroquinate synthase 9657218;Vibrio cholerae 41 SO0289 dam DNA adenine methylase 28899516;Vibrio parahaemolyticus 48 SO0292 rpe ribulose-phosphate 3-epimerase (5.1.3.1) 16422041;Salmonella typhimurium 14 PMID:7603433 SO0293 gph phosphoglycolate phosphatase 9657214;Vibrio cholerae 79 SO0294 trpS tryptophanyl-tRNA synthetase 15978262;Yersinia pestis 29 SO0298 gmhA phosphoheptose isomerase 9950658;Pseudomonas aeruginosa 36 SO0301 none protein with cobalt precorrin-4 methyltransferase domain 28897224;Vibrio parahaemolyticus 41 SO0314 speF ornithine decarboxylase, inducible 9658508;Vibrio cholerae 17 SO0325 none dsrE-related protein 26247544;Escherichia coli CFT073 52 SO0332 none protein with protein kinase-like (PK-like) domain 9654428;Vibrio cholerae 58 SO0333 dsbA thiol:disulfide interchange protein DsbA 28899828;Vibrio parahaemolyticus 96 SO0340 ilvE branched-chain amino acid aminotransferase (2.6.1.42) 14246322;Staphylococcus aureus 91 PMID:3069843 SO0343 acnA 2-methylcitrate dehydratase, Fe-S dependent (4.2.1.79;4.2.1.3) 33593359;Bordetella pertussis 19 PMID:14702315 SO0344 prpC methylcitrate synthase (2.3.3.5) 28869488;Pseudomonas syringae 32 PMID:9579066 SO0345 prpB methylisocitrate lyase (4.1.3.30) 7225654;Neisseria meningitidis
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