Silicibacter sp. TM1040 mega plasmid, complete sequence NC_008043 GI_Number Pathogen_associated Gene_name Product Synonym Number_of_Genera COG_Number COG_Description COG_Category 99078221 Common - MCP methyltransferase, CheR-type TM1040_3243 150 COG1352 CheR, Methylase of chemotaxis methyl-accepting proteins Cell motility and secretion / Signal transduction mechanisms 99078526 Common - phage integrase TM1040_3553 20 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 99078587 Common - periplasmic solute binding protein TM1040_3616 131 COG4531 ZnuA, ABC-type Zn2+ transport system, periplasmic component/surface adhesin Inorganic ion transport and metabolism 99078617 Common - protein of unknown function DUF395, YeeE/YedE TM1040_3646 70 None None None 99078209 Common - periplasmic sensor hybrid histidine kinase TM1040_3231 208 COG4191 COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system Signal transduction mechanisms 99078176 Common - dihydrodipicolinate synthetase TM1040_3198 207 COG0329 DapA, Dihydrodipicolinate synthase/N-acetylneuraminate lyase Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane 99078478 Nonpathogen - hypothetical protein TM1040_3502 1 None None None 99078690 Common - Methyltransferase FkbM TM1040_3719 8 None None None 99078355 Common - transcriptional regulator, AraC family TM1040_3379 145 COG4977 COG4977, Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain Transcription 99078485 Nonpathogen - hypothetical protein TM1040_3509 1 None None None 99078463 Common - dihydroxy-acid dehydratase TM1040_3487 210 COG0129 IlvD, Dihydroxyacid dehydratase/phosphogluconate dehydratase Amino acid transport and metabolism / Carbohydrate transport and metabolism 99078300 Common - transcriptional regulator, GntR family TM1040_3324 136 COG1802 GntR, Transcriptional regulators Transcription 99078594 Common pheT phenylalanyl-tRNA synthetase subunit beta TM1040_3623 235 COG0072 PheT, Phenylalanyl-tRNA synthetase beta subunit Translation, ribosomal structure and biogenesis 99078346 Common - DNA photolyase-like protein TM1040_3370 131 COG0415 PhrB, Deoxyribodipyrimidine photolyase DNA replication, recombination, and repair 99078412 Common - binding-protein-dependent transport systems inner membrane component TM1040_3436 219 COG0601 DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078493 Common - malate dehydrogenase TM1040_3517 202 COG0039 Mdh, Malate/lactate dehydrogenases Energy production and conversion 99078648 Nonpathogen - hypothetical protein TM1040_3677 5 None None None 99078313 Common - NADH:flavin oxidoreductase/NADH oxidase TM1040_3337 178 COG1902 NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme family Energy production and conversion 99078172 Common - methyl-accepting chemotaxis sensory transducer TM1040_3194 148 COG0840 Tar, Methyl-accepting chemotaxis protein Cell motility and secretion / Signal transduction mechanisms 99078079 Common - ATPase TM1040_3101 24 COG0507 RecD, ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member DNA replication, recombination, and repair 99078531 Common - Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase TM1040_3558 89 COG0388 COG0388, Predicted amidohydrolase General function prediction only 99078216 Common - hypothetical protein TM1040_3238 2 None None None 99078543 Common - haloacid dehalogenase, type II TM1040_3570 66 COG1011 COG1011, Predicted hydrolase (HAD superfamily) General function prediction only 99078552 Nonpathogen - hypothetical protein TM1040_3579 1 None None None 99078722 Common - molybdopterin binding domain TM1040_3751 195 COG0303 MoeA, Molybdopterin biosynthesis enzyme Coenzyme metabolism 99078047 Common - protein of unknown function DUF179 TM1040_3069 131 COG1678 COG1678, Putative transcriptional regulator Transcription 99078670 Common phnK phosphonates transport ATP-binding protein TM1040_3699 249 COG4107 PhnK, ABC-type phosphonate transport system, ATPase component Inorganic ion transport and metabolism 99078467 Common - SMP-30/Gluconolaconase/LRE-like region TM1040_3491 74 COG3386 COG3386, Gluconolactonase Carbohydrate transport and metabolism 99078271 Common - transcriptional regulator, AraC family TM1040_3293 120 COG4977 COG4977, Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain Transcription 99078626 Common - NLPA lipoprotein TM1040_3655 99 COG0715 TauA, ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components Inorganic ion transport and metabolism 99078371 Common - Mandelate racemase/muconate lactonizing enzyme-like TM1040_3395 134 COG4948 COG4948, L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Cell envelope biogenesis, outer membrane / General function prediction only 99078449 Common - uracil-xanthine permease TM1040_3473 127 COG2233 UraA, Xanthine/uracil permeases Nucleotide transport and metabolism 99078429 Common - hypothetical protein TM1040_3453 30 None None None 99078108 Common - hypothetical protein TM1040_3130 16 COG3090 DctM, TRAP-type C4-dicarboxylate transport system, small permease component Carbohydrate transport and metabolism 99078187 Common - methyl-accepting chemotaxis sensory transducer TM1040_3209 150 COG0840 Tar, Methyl-accepting chemotaxis protein Cell motility and secretion / Signal transduction mechanisms 99078167 Nonpathogen - hypothetical protein TM1040_3189 1 COG5470 COG5470, Uncharacterized conserved protein Function unknown 99078409 Nonpathogen - hypothetical protein TM1040_3433 3 COG5628 COG5628, Predicted acetyltransferase General function prediction only 99078210 Common - two component transcriptional regulator, winged helix family TM1040_3232 215 COG0745 OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain Signal transduction mechanisms / Transcription 99078507 Common - Phytanoyl-CoA dioxygenase TM1040_3531 13 COG5285 COG5285, Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin Secondary metabolites biosynthesis, transport, and catabolism 99078566 Common - Auxin Efflux Carrier TM1040_3595 93 COG0679 COG0679, Predicted permeases General function prediction only 99078679 Common - Phosphonate-binding periplasmic protein TM1040_3708 88 COG3221 PhnD, ABC-type phosphate/phosphonate transport system, periplasmic component Inorganic ion transport and metabolism 99078163 Common - transcriptional regulator, LysR family TM1040_3185 192 COG0583 LysR, Transcriptional regulator Transcription 99078680 Common - Phosphonate ABC transporter PhnC, ATP-binding TM1040_3709 249 COG3638 COG3638, ABC-type phosphate/phosphonate transport system, ATPase component Inorganic ion transport and metabolism 99078500 Common - Phosphoglycerate mutase TM1040_3524 12 COG0406 GpmB, Fructose-2,6-bisphosphatase Carbohydrate transport and metabolism 99078139 Common - transcriptional regulator, AraC family TM1040_3161 137 COG3449 COG3449, DNA gyrase inhibitor DNA replication, recombination, and repair 99078686 Nonpathogen - hypothetical protein TM1040_3715 2 None None None 99078704 Common - Redoxin TM1040_3733 151 COG0526 TrxA, Thiol-disulfide isomerase and thioredoxins Posttranslational modification, protein turnover, chaperones / Energy production and conversion 99078023 Nonpathogen - hypothetical protein TM1040_3045 2 None None None 99078132 Common - binding-protein-dependent transport systems inner membrane component TM1040_3154 140 COG1175 UgpA, ABC-type sugar transport systems, permease components Carbohydrate transport and metabolism 99078145 Common - Mandelate racemase/muconate lactonizing enzyme-like TM1040_3167 130 COG4948 COG4948, L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Cell envelope biogenesis, outer membrane / General function prediction only 99078094 Common - succinyl-diaminopimelate desuccinylase TM1040_3116 203 COG0624 ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases Amino acid transport and metabolism 99078420 Nonpathogen - hypothetical protein TM1040_3444 1 None None None 99078480 Common - Dihydrolipoamide dehydrogenase TM1040_3504 245 COG1249 Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes Energy production and conversion 99078293 Common - TRAP dicarboxylate transporter- DctM subunit TM1040_3317 136 COG1593 DctQ, TRAP-type C4-dicarboxylate transport system, large permease component Carbohydrate transport and metabolism 99078514 Common - hypothetical protein TM1040_3539 4 None None None 99078124 Common - aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding TM1040_3146 98 COG1529 CoxL, Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs Energy production and conversion 99078718 Common - Glyoxalase/bleomycin resistance protein/dioxygenase TM1040_3747 9 COG0346 GloA, Lactoylglutathione lyase and related lyases Amino acid transport and metabolism 99078081 Nonpathogen - hypothetical protein TM1040_3103 1 None None None 99078570 Common - Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like TM1040_3599 249 COG1123 COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase General function prediction only 99078089 Common - transcriptional regulator, LysR family TM1040_3111 104 COG0583 LysR, Transcriptional regulator Transcription 99078553 Common - hypothetical protein TM1040_3580 30 COG4938 COG4938, Uncharacterized conserved protein Function unknown 99078577 Common - UDP-glucose/GDP-mannose dehydrogenase TM1040_3606 205 COG0677 WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase Cell envelope biogenesis, outer membrane 99078242 Common - ROK domain protein TM1040_3264 136 COG1940 NagC, Transcriptional regulator/sugar kinase Transcription / Carbohydrate transport and metabolism 99078232 Common - periplasmic sensory protein associated with the TorRS two-component regulatory system TM1040_3254 71 COG1879 RbsB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078539 Common - hypothetical protein TM1040_3566 21 None None None 99078654 Common - extracellular solute-binding protein, family 5 TM1040_3683 117 COG0747 DdpA, ABC-type dipeptide transport system, periplasmic component Amino acid transport and metabolism 99078035 Nonpathogen - hypothetical protein TM1040_3057 3 None None None 99078283 Common - extracellular solute-binding protein, family 1 TM1040_3307 36 COG1653 UgpB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078376 Common - transcriptional regulator, IclR family TM1040_3400 107 COG1414 IclR, Transcriptional regulator Transcription 99078457 Common - ABC transporter related TM1040_3481 249 COG3839 MalK, ABC-type sugar transport systems, ATPase components Carbohydrate transport and metabolism 99078631 Common - cobalt transport protein TM1040_3660 62 COG0619 CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters Inorganic ion transport and metabolism 99078192 Common - binding-protein-dependent transport systems inner membrane component TM1040_3214 148 COG0395 UgpE, ABC-type sugar transport system, permease component Carbohydrate transport and metabolism 99078665 Common - hypothetical protein TM1040_3694 5 None None None 99078196 Common - ferredoxin TM1040_3218 144 COG1018 Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 Energy production and conversion 99078735 Nonpathogen - hypothetical protein TM1040_3764 3 None None None 99078436 Common - hypothetical protein TM1040_3460 25 COG1196 Smc, Chromosome segregation ATPases Cell division and chromosome partitioning 99078268 Common - GCN5-related N-acetyltransferase TM1040_3290 29 COG0456 RimI, Acetyltransferases General function prediction only 99078487 Common kgd alpha-ketoglutarate decarboxylase TM1040_3511 148 COG0567 SucA, 2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, and related enzymes Energy production and conversion 99078306 Common - ABC transporter related TM1040_3330 249 COG3842 PotA, ABC-type spermidine/putrescine transport systems, ATPase components Amino acid transport and metabolism 99078692 Common - cytochrome P450 TM1040_3721 69 COG2124 CypX, Cytochrome P450 Secondary metabolites biosynthesis, transport, and catabolism 99078057 Common - protein of unknown function DUF558 TM1040_3079 198 COG1385 COG1385, Uncharacterized protein conserved in bacteria Function unknown 99078418 Common - Isopentenyl-diphosphate delta-isomerase, type 1 TM1040_3442 38 COG1443 Idi, Isopentenyldiphosphate isomerase Lipid metabolism 99078623 Common thiG thiazole synthase TM1040_3652 166 COG2022 ThiG, Uncharacterized enzyme of thiazole biosynthesis Nucleotide transport and metabolism 99078380 Common - putative integrase TM1040_3404 34 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 99078200 Common - TRAP C4-dicarboxylate transport system permease DctM subunit TM1040_3222 122 COG1593 DctQ, TRAP-type C4-dicarboxylate transport system, large permease component Carbohydrate transport and metabolism 99078011 Common - Excisionase/Xis, DNA-binding TM1040_3033 62 COG1910 COG1910, Periplasmic molybdate-binding protein/domain Inorganic ion transport and metabolism 99078519 Common - BRO-like TM1040_3546 12 COG3617 COG3617, Prophage antirepressor Transcription 99078152 Common - D-xylose ABC transporter, substrate-binding protein TM1040_3174 74 COG4213 XylF, ABC-type xylose transport system, periplasmic component Carbohydrate transport and metabolism 99078102 Common - hypothetical protein TM1040_3124 5 None None None 99078257 Common - hypothetical protein TM1040_3279 30 COG3126 COG3126, Uncharacterized protein conserved in bacteria Function unknown 99078656 Common - binding-protein-dependent transport systems inner membrane component TM1040_3685 220 COG1173 DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078361 Nonpathogen - hypothetical protein TM1040_3385 5 None None None 99078350 Common - Hemolysin-type calcium-binding region TM1040_3374 88 COG2931 COG2931, RTX toxins and related Ca2+-binding proteins Secondary metabolites biosynthesis, transport, and catabolism 99078399 Common - DegT/DnrJ/EryC1/StrS aminotransferase TM1040_3423 194 COG0399 WecE, Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis Cell envelope biogenesis, outer membrane 99078214 Common - Phosphonate uptake transporter TM1040_3236 145 COG3639 COG3639, ABC-type phosphate/phosphonate transport system, permease component Inorganic ion transport and metabolism 99078110 Common - diguanylate cyclase/phosphodiesterase TM1040_3132 171 COG5001 COG5001, Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain Signal transduction mechanisms 99078596 Common - hypothetical protein TM1040_3625 77 COG1670 RimL, Acetyltransferases, including N-acetylases of ribosomal proteins Translation, ribosomal structure and biogenesis 99078364 Common - transcriptional regulator, LysR family TM1040_3388 179 COG0583 LysR, Transcriptional regulator Transcription 99078255 Common - periplasmic sensor hybrid histidine kinase TM1040_3277 225 COG0642 BaeS, Signal transduction histidine kinase Signal transduction mechanisms 99078696 Common - phenylacetic acid degradation B TM1040_3725 37 COG3460 COG3460, Uncharacterized enzyme of phenylacetate metabolism Secondary metabolites biosynthesis, transport, and catabolism 99078159 Common - transcriptional regulator, LuxR family TM1040_3181 2 COG2197 CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain Signal transduction mechanisms / Transcription 99078039 Common - phage SPO1 DNA polymerase-related protein TM1040_3061 155 COG1573 COG1573, Uracil-DNA glycosylase DNA replication, recombination, and repair 99078442 Common - Aromatic-L-amino-acid decarboxylase TM1040_3466 90 COG0076 GadB, Glutamate decarboxylase and related PLP-dependent proteins Amino acid transport and metabolism 99078414 Common panB 3-methyl-2-oxobutanoate hydroxymethyltransferase TM1040_3438 195 COG0413 PanB, Ketopantoate hydroxymethyltransferase Coenzyme metabolism 99078545 Common - Spermidine/putrescine-binding periplasmic protein-like TM1040_3572 21 COG0687 PotD, Spermidine/putrescine-binding periplasmic protein Amino acid transport and metabolism 99078104 Common - Integrase, catalytic region TM1040_3126 133 COG2801 Tra5, Transposase and inactivated derivatives DNA replication, recombination, and repair 99078278 Nonpathogen - hypothetical protein TM1040_3302 1 None None None 99078062 Common - phosphatidylserine decarboxylase TM1040_3084 94 COG0688 Psd, Phosphatidylserine decarboxylase Lipid metabolism 99078223 Common - CheW protein TM1040_3245 107 COG0835 CheW, Chemotaxis signal transduction protein Cell motility and secretion / Signal transduction mechanisms 99078589 Common - 5-methyltetrahydrofolate--homocysteine methyltransferase TM1040_3618 168 COG1410 MetH, Methionine synthase I, cobalamin-binding domain Amino acid transport and metabolism 99078116 Common - transcriptional regulator, TetR family TM1040_3138 27 COG1309 AcrR, Transcriptional regulator Transcription 99078615 Nonpathogen - hypothetical protein TM1040_3644 1 None None None 99078597 Nonpathogen - hypothetical protein TM1040_3626 2 None None None 99078465 Common - 2-keto-3-deoxy-galactonokinase TM1040_3489 39 COG3734 DgoK, 2-keto-3-deoxy-galactonokinase Carbohydrate transport and metabolism 99078725 Common mobA molybdopterin-guanine dinucleotide biosynthesis protein A TM1040_3754 73 COG0746 MobA, Molybdopterin-guanine dinucleotide biosynthesis protein A Coenzyme metabolism 99078142 Common - Glyoxalase/bleomycin resistance protein/dioxygenase TM1040_3164 2 COG3324 COG3324, Predicted enzyme related to lactoylglutathione lyase General function prediction only 99078573 Common - binding-protein-dependent transport systems inner membrane component TM1040_3602 219 COG0601 DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078027 Common - Twin-arginine translocation pathway signal TM1040_3049 159 COG0747 DdpA, ABC-type dipeptide transport system, periplasmic component Amino acid transport and metabolism 99078564 Common - TatD-related deoxyribonuclease TM1040_3593 238 COG0084 TatD, Mg-dependent DNase DNA replication, recombination, and repair 99078165 Common - metal dependent phosphohydrolase TM1040_3187 16 COG4341 COG4341, Predicted HD phosphohydrolase General function prediction only 99078393 Common - Na(+)-translocating NADH-quinone reductase subunit A TM1040_3417 39 COG1726 NqrA, Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA Energy production and conversion 99078185 Common - response regulator receiver protein TM1040_3207 225 COG2204 AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Signal transduction mechanisms 99078672 Common - phosphonate metabolism TM1040_3701 45 COG3626 PhnI, Uncharacterized enzyme of phosphonate metabolism Inorganic ion transport and metabolism 99078537 Nonpathogen - hypothetical protein TM1040_3564 2 None None None 99078266 Common - phage Tail Collar TM1040_3288 33 COG4675 MdpB, Microcystin-dependent protein Function unknown 99078251 Common - transcriptional regulator, LuxR family TM1040_3273 105 COG2197 CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain Signal transduction mechanisms / Transcription 99078049 Nonpathogen - hypothetical protein TM1040_3071 2 None None None 99078592 Common - Aldehyde dehydrogenase (NAD+) TM1040_3621 220 COG1012 PutA, NAD-dependent aldehyde dehydrogenases Energy production and conversion 99078337 Common - aldo/keto reductase TM1040_3361 179 COG4989 COG4989, Predicted oxidoreductase General function prediction only 99078590 Common - putative thiol-disulphide oxidoreductase DCC TM1040_3619 24 COG3011 COG3011, Uncharacterized protein conserved in bacteria Function unknown 99078161 Nonpathogen - hypothetical protein TM1040_3183 1 None None None 99078040 Common - metallophosphoesterase TM1040_3062 42 COG2129 COG2129, Predicted phosphoesterases, related to the Icc protein General function prediction only 99078476 Common - phospholipid/glycerol acyltransferase TM1040_3500 149 COG0204 PlsC, 1-acyl-sn-glycerol-3-phosphate acyltransferase Lipid metabolism 99078724 Common - molybdopterin-guanine dinucleotide biosynthesis protein B TM1040_3753 105 COG1763 MobB, Molybdopterin-guanine dinucleotide biosynthesis protein Coenzyme metabolism 99078572 Common - binding-protein-dependent transport systems inner membrane component TM1040_3601 220 COG1173 DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078230 Common - inner-membrane translocator TM1040_3252 110 COG1172 AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components Carbohydrate transport and metabolism 99078555 Nonpathogen - hypothetical protein TM1040_3582 2 None None None 99078319 Common - periplasmic binding protein/LacI transcriptional regulator TM1040_3343 51 COG1879 RbsB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078122 Common - extracellular solute-binding protein, family 5 TM1040_3144 204 COG0747 DdpA, ABC-type dipeptide transport system, periplasmic component Amino acid transport and metabolism 99078579 Common - amino acid carrier protein TM1040_3608 114 COG1115 AlsT, Na+/alanine symporter Amino acid transport and metabolism 99078033 Common - Endoribonuclease L-PSP TM1040_3055 24 COG0251 TdcF, Putative translation initiation inhibitor, yjgF family Translation, ribosomal structure and biogenesis 99078411 Common - binding-protein-dependent transport systems inner membrane component TM1040_3435 219 COG1173 DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078097 Nonpathogen - hypothetical protein TM1040_3119 1 COG2410 COG2410, Uncharacterized conserved protein Function unknown 99078440 Common - 2-oxo-hepta-3-ene-1,7-dioic acid hydratase TM1040_3464 66 COG3971 COG3971, 2-keto-4-pentenoate hydratase Secondary metabolites biosynthesis, transport, and catabolism 99078170 Common - transcriptional regulator, LysR family TM1040_3192 171 COG0583 LysR, Transcriptional regulator Transcription 99078087 Common - hypothetical protein TM1040_3109 41 COG3665 COG3665, Uncharacterized conserved protein Function unknown 99078652 Common - transcriptional regulator, TetR family TM1040_3681 32 COG1309 AcrR, Transcriptional regulator Transcription 99078727 Common - formate dehydrogenase family accessory protein FdhD TM1040_3756 136 COG1526 FdhD, Uncharacterized protein required for formate dehydrogenase activity Energy production and conversion 99078608 Common - binding-protein-dependent transport systems inner membrane component TM1040_3637 171 COG1176 PotB, ABC-type spermidine/putrescine transport system, permease component I Amino acid transport and metabolism 99078147 Common - Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B TM1040_3169 86 COG3384 COG3384, Uncharacterized conserved protein Function unknown 99078702 Nonpathogen - lipoprotein, putative TM1040_3731 1 None None None 99078140 Common - Lysine exporter protein (LYSE/YGGA) TM1040_3162 80 COG1280 RhtB, Putative threonine efflux protein Amino acid transport and metabolism 99078491 Nonpathogen - hypothetical protein TM1040_3515 1 None None None 99078684 Common - Betaine-aldehyde dehydrogenase TM1040_3713 220 COG1012 PutA, NAD-dependent aldehyde dehydrogenases Energy production and conversion 99078029 Common - FAD linked oxidase-like TM1040_3051 91 COG0277 GlcD, FAD/FMN-containing dehydrogenases Energy production and conversion 99078386 Common - NmrA-like TM1040_3410 53 COG0702 COG0702, Predicted nucleoside-diphosphate-sugar epimerases Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism 99078227 Common - transposase orfB TM1040_3249 34 None None None 99078349 Common - two component transcriptional regulator, winged helix family TM1040_3373 224 COG0745 OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain Signal transduction mechanisms / Transcription 99078527 Common - protein of unknown function DUF329 TM1040_3554 31 COG3024 COG3024, Uncharacterized protein conserved in bacteria Function unknown 99078061 Nonpathogen - hypothetical protein TM1040_3083 1 COG4994 COG4994, Uncharacterized protein conserved in bacteria Function unknown 99078068 Nonpathogen - Haem oxygenase TM1040_3090 1 COG3230 HemO, Heme oxygenase Inorganic ion transport and metabolism 99078129 Common - ATPase, BadF/BadG/BcrA/BcrD type TM1040_3151 55 COG2971 COG2971, Predicted N-acetylglucosamine kinase Carbohydrate transport and metabolism 99078295 Common - TRAP dicarboxylate transporter, DctP subunit TM1040_3319 100 COG1638 DctP, TRAP-type C4-dicarboxylate transport system, periplasmic component Carbohydrate transport and metabolism 99078073 Common - ABC transporter related TM1040_3095 249 COG3845 COG3845, ABC-type uncharacterized transport systems, ATPase components General function prediction only 99078520 Nonpathogen - hypothetical protein TM1040_3547 1 None None None 99078516 Common - N-6 DNA methylase TM1040_3541 155 COG0286 HsdM, Type I restriction-modification system methyltransferase subunit Defense mechanisms 99078498 Common - hypothetical protein TM1040_3522 17 COG5515 COG5515, Uncharacterized conserved small protein Function unknown 99078646 Common - 5-carboxymethyl-2-hydroxymuconate delta-isomerase TM1040_3675 183 COG0179 MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) Secondary metabolites biosynthesis, transport, and catabolism 99078202 Nonpathogen - hypothetical protein TM1040_3224 1 None None None 99078154 Common - ABC transporter related TM1040_3176 249 COG1129 MglA, ABC-type sugar transport system, ATPase component Carbohydrate transport and metabolism 99078403 Common - hypothetical protein TM1040_3427 120 COG1044 LpxD, UDP-3-O- 3-hydroxymyristoyl 99078628 Common - ABC transporter related TM1040_3657 249 COG1116 TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component Inorganic ion transport and metabolism 99078732 Common - protein of unknown function DUF6, transmembrane TM1040_3761 87 COG0697 RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only 99078190 Common - putative transcriptional regulator, TetR family TM1040_3212 82 COG3226 COG3226, Uncharacterized protein conserved in bacteria Function unknown 99078054 Common - glutamate--cysteine ligase TM1040_3076 58 COG3572 GshA, Gamma-glutamylcysteine synthetase Coenzyme metabolism 99078374 Common - binding-protein-dependent transport systems inner membrane component TM1040_3398 144 COG1175 UgpA, ABC-type sugar transport systems, permease components Carbohydrate transport and metabolism 99078459 Common - extracellular solute-binding protein, family 1 TM1040_3483 73 COG1653 UgpB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078323 Common - oxidoreductase-like TM1040_3347 131 COG0673 MviM, Predicted dehydrogenases and related proteins General function prediction only 99078281 Common - binding-protein-dependent transport systems inner membrane component TM1040_3305 152 COG0395 UgpE, ABC-type sugar transport system, permease component Carbohydrate transport and metabolism 99078228 Common - putative signal-transduction protein with CBS domains TM1040_3250 167 COG2905 COG2905, Predicted signal-transduction protein containing cAMP-binding and CBS domains Signal transduction mechanisms 99078633 Common - Molybdate ABC transporter, ATP-binding protein TM1040_3662 249 COG4148 ModC, ABC-type molybdate transport system, ATPase component Inorganic ion transport and metabolism 99078489 Common - glycosyl transferase, family 25 TM1040_3513 21 COG3306 COG3306, Glycosyltransferase involved in LPS biosynthesis Cell envelope biogenesis, outer membrane 99078603 Common - molybdopterin converting factor, subunit 1 TM1040_3632 67 COG1977 MoaD, Molybdopterin converting factor, small subunit Coenzyme metabolism 99078612 Common - Twin-arginine translocation pathway signal TM1040_3641 81 COG4663 FcbT1, TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component Secondary metabolites biosynthesis, transport, and catabolism 99078719 Common - transcription elongation factor GreA TM1040_3748 204 COG0782 GreA, Transcription elongation factor Transcription 99078304 Common - Mammalian cell entry related TM1040_3328 61 COG3008 PqiB, Paraquat-inducible protein B General function prediction only 99078179 Common - proline racemase TM1040_3201 47 COG3938 COG3938, Proline racemase Amino acid transport and metabolism 99078275 Common - multi-sensor signal transduction histidine kinase TM1040_3299 218 COG4251 COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) Signal transduction mechanisms 99078569 Common - Gamma-glutamyltransferase TM1040_3598 148 COG0405 Ggt, Gamma-glutamyltransferase Amino acid transport and metabolism 99078118 Common - Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like TM1040_3140 249 COG0444 DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078620 Common - Phosphomethylpyrimidine kinase type-2 TM1040_3649 218 COG0351 ThiD, Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase Coenzyme metabolism 99078292 Common - metallophosphoesterase TM1040_3316 95 COG1409 Icc, Predicted phosphohydrolases General function prediction only 99078497 Common - NnrU TM1040_3521 33 COG4094 COG4094, Predicted membrane protein Function unknown 99078109 Common - TRAP dicarboxylate transporter- DctP subunit TM1040_3131 91 COG1638 DctP, TRAP-type C4-dicarboxylate transport system, periplasmic component Carbohydrate transport and metabolism 99078417 Common - hypothetical protein TM1040_3441 70 COG0654 UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases Coenzyme metabolism / Energy production and conversion 99078299 Common - Malate/L-lactate dehydrogenase TM1040_3323 67 COG2055 COG2055, Malate/L-lactate dehydrogenases Energy production and conversion 99078547 Nonpathogen - hypothetical protein TM1040_3574 2 None None None 99078070 Common - peptidase M22, glycoprotease TM1040_3092 197 COG1214 COG1214, Inactive homolog of metal-dependent proteases, putative molecular chaperone Posttranslational modification, protein turnover, chaperones 99078674 Common - phosphonate metabolism PhnG TM1040_3703 31 COG3624 PhnG, Uncharacterized enzyme of phosphonate metabolism Inorganic ion transport and metabolism 99078562 Common - Thymidylate kinase TM1040_3591 227 COG0125 Tmk, Thymidylate kinase Nucleotide transport and metabolism 99078426 Common - Auxin Efflux Carrier TM1040_3450 118 COG0679 COG0679, Predicted permeases General function prediction only 99078112 Common - flagellin-like TM1040_3134 100 COG1344 FlgL, Flagellin and related hook-associated proteins Cell motility and secretion 99078473 Nonpathogen - Zinc finger/thioredoxin putative TM1040_3497 6 None None None 99078576 Common - aminotransferase, class I and II TM1040_3605 238 COG0436 COG0436, Aspartate/tyrosine/aromatic aminotransferase Amino acid transport and metabolism 99078638 Common - cyclic nucleotide-binding protein TM1040_3667 171 COG2905 COG2905, Predicted signal-transduction protein containing cAMP-binding and CBS domains Signal transduction mechanisms 99078390 Common - Na(+)-translocating NADH-quinone reductase subunit D TM1040_3414 76 COG1347 NqrD, Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD Energy production and conversion 99078490 Common sucC succinyl-CoA synthetase subunit beta TM1040_3514 206 COG0045 SucC, Succinyl-CoA synthetase, beta subunit Energy production and conversion 99078366 Common - aldo/keto reductase TM1040_3390 180 COG0667 Tas, Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) Energy production and conversion 99078160 Nonpathogen - hypothetical protein TM1040_3182 2 None None None 99078432 Nonpathogen - hypothetical protein TM1040_3456 5 None None None 99078318 Common - inner-membrane translocator TM1040_3342 138 COG1172 AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components Carbohydrate transport and metabolism 99078335 Common - Tripartite ATP-independent periplasmic transporter, DctQ component TM1040_3359 21 COG3090 DctM, TRAP-type C4-dicarboxylate transport system, small permease component Carbohydrate transport and metabolism 99078203 Common - von Willebrand factor, type A TM1040_3225 21 COG1240 ChlD, Mg-chelatase subunit ChlD Coenzyme metabolism 99078618 Common - beta-lactamase-like TM1040_3647 193 COG0491 GloB, Zn-dependent hydrolases, including glyoxylases General function prediction only 99078311 Common - two component transcriptional regulator, winged helix family TM1040_3335 225 COG0745 OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain Signal transduction mechanisms / Transcription 99078540 Common - 3-oxoadipate enol-lactonase TM1040_3567 162 COG0596 MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) General function prediction only 99078613 Common - transcriptional regulator, GntR family TM1040_3642 106 COG2188 PhnF, Transcriptional regulators Transcription 99078733 Common - 3-isopropylmalate dehydrogenase TM1040_3762 222 COG0473 LeuB, Isocitrate/isopropylmalate dehydrogenase Amino acid transport and metabolism 99078599 Common - alanine dehydrogenase TM1040_3628 167 COG0686 Ald, Alanine dehydrogenase Amino acid transport and metabolism 99078356 Common - transcriptional regulator, LysR family TM1040_3380 184 COG0583 LysR, Transcriptional regulator Transcription 99078075 Common - inner-membrane translocator TM1040_3097 119 COG1079 COG1079, Uncharacterized ABC-type transport system, permease component General function prediction only 99078535 Common - hypothetical protein TM1040_3562 31 COG5328 COG5328, Uncharacterized protein conserved in bacteria Function unknown 99078661 Common - glycosyl transferase, group 1 TM1040_3690 144 COG0438 RfaG, Glycosyltransferase Cell envelope biogenesis, outer membrane 99078444 Common - 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase TM1040_3468 220 COG1012 PutA, NAD-dependent aldehyde dehydrogenases Energy production and conversion 99078111 Common - sulfatase TM1040_3133 88 COG3119 AslA, Arylsulfatase A and related enzymes Inorganic ion transport and metabolism 99078183 Common - CheW protein TM1040_3205 132 COG0835 CheW, Chemotaxis signal transduction protein Cell motility and secretion / Signal transduction mechanisms 99078119 Common - binding-protein-dependent transport systems inner membrane component TM1040_3141 220 COG1173 DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078521 Common - protein of unknown function DUF45 TM1040_3548 150 COG1451 COG1451, Predicted metal-dependent hydrolase General function prediction only 99078343 Common - MltA-interacting MipA TM1040_3367 26 COG3713 OmpV, Outer membrane protein V Cell envelope biogenesis, outer membrane 99078017 Common - Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine TM1040_3039 177 COG0765 HisM, ABC-type amino acid transport system, permease component Amino acid transport and metabolism 99078506 Common sdhB succinate dehydrogenase iron-sulfur subunit TM1040_3530 196 COG0479 FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit Energy production and conversion 99078501 Common - succinate dehydrogenase, cytochrome b subunit TM1040_3525 39 COG2009 SdhC, Succinate dehydrogenase/fumarate reductase, cytochrome b subunit Energy production and conversion 99078239 Common - transcriptional regulator, XRE family with cupin sensor TM1040_3261 114 COG1396 HipB, Predicted transcriptional regulators Transcription 99078453 Common - transcriptional regulator, LysR family TM1040_3477 146 COG0583 LysR, Transcriptional regulator Transcription 99078263 Common - Outer membrane autotransporter barrel TM1040_3285 48 None None None 99078439 Common - 2-dehydro-3-deoxyglucarate aldolase TM1040_3463 74 COG3836 HpcH, 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase Carbohydrate transport and metabolism 99078458 Common - transcriptional regulator, IclR family TM1040_3482 122 COG1414 IclR, Transcriptional regulator Transcription 99078482 Common - inner membrane protein TM1040_3506 14 COG3686 COG3686, Predicted membrane protein Function unknown 99078321 Common - oxidoreductase-like TM1040_3345 172 COG0673 MviM, Predicted dehydrogenases and related proteins General function prediction only 99078051 Common - protein of unknown function DUF205 TM1040_3073 158 COG0344 COG0344, Predicted membrane protein Function unknown 99078246 Common - hypothetical protein TM1040_3268 13 COG3457 COG3457, Predicted amino acid racemase Amino acid transport and metabolism 99078328 Common - Myo-inositol 2-dehydrogenase TM1040_3352 184 COG0673 MviM, Predicted dehydrogenases and related proteins General function prediction only 99078451 Common - polysaccharide deacetylase TM1040_3475 68 COG3195 COG3195, Uncharacterized protein conserved in bacteria Function unknown 99078683 Common - hypothetical protein TM1040_3712 29 COG5441 COG5441, Uncharacterized conserved protein Function unknown 99078090 Common - extracellular solute-binding protein, family 5 TM1040_3112 191 COG0747 DdpA, ABC-type dipeptide transport system, periplasmic component Amino acid transport and metabolism 99078636 Common - hypothetical protein TM1040_3665 54 COG4327 COG4327, Predicted membrane protein Function unknown 99078584 Common - ABC-3 TM1040_3613 177 COG1108 ZnuB, ABC-type Mn2+/Zn2+ transport systems, permease components Inorganic ion transport and metabolism 99078204 Nonpathogen - hypothetical protein TM1040_3226 1 None None None 99078038 Common - Sua5/YciO/YrdC/YwlC TM1040_3060 223 COG0009 SUA5, Putative translation factor (SUA5) Translation, ribosomal structure and biogenesis 99078542 Common - alpha/beta hydrolase fold TM1040_3569 145 COG0596 MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) General function prediction only 99078601 Common - protein of unknown function DUF344 TM1040_3630 127 COG2326 COG2326, Uncharacterized conserved protein Function unknown 99078303 Common - Paraquat-inducible protein A TM1040_3327 54 COG2995 PqiA, Uncharacterized paraquat-inducible protein A Function unknown 99078434 Common - hypothetical protein TM1040_3458 14 None None None 99078643 Common - Alcohol dehydrogenase, zinc-binding TM1040_3672 208 COG1062 AdhC, Zn-dependent alcohol dehydrogenases, class III Energy production and conversion 99078377 Common - amidohydrolase 2 TM1040_3401 50 COG3618 COG3618, Predicted metal-dependent hydrolase of the TIM-barrel fold General function prediction only 99078580 Common - transcriptional regulator, RpiR family TM1040_3609 54 COG1737 RpiR, Transcriptional regulators Transcription 99078607 Common - ABC transporter related TM1040_3636 249 COG3842 PotA, ABC-type spermidine/putrescine transport systems, ATPase components Amino acid transport and metabolism 99078469 Common - metallophosphoesterase TM1040_3493 89 COG0420 SbcD, DNA repair exonuclease DNA replication, recombination, and repair 99078099 Nonpathogen - hypothetical protein TM1040_3121 1 None None None 99078495 Nonpathogen - hypothetical protein TM1040_3519 7 None None None 99078708 Common - transcriptional regulator, LysR family TM1040_3737 166 COG0583 LysR, Transcriptional regulator Transcription 99078020 Common - PfkB TM1040_3042 122 COG0524 RbsK, Sugar kinases, ribokinase family Carbohydrate transport and metabolism 99078127 Common - Glutamine-fructose-6-phosphate transaminase (isomerizing) TM1040_3149 234 COG2222 AgaS, Predicted phosphosugar isomerases Cell envelope biogenesis, outer membrane 99078015 Common - transcriptional regulator, GntR family TM1040_3037 58 COG1802 GntR, Transcriptional regulators Transcription 99078155 Common - methyl-accepting chemotaxis sensory transducer TM1040_3177 149 COG0840 Tar, Methyl-accepting chemotaxis protein Cell motility and secretion / Signal transduction mechanisms 99078327 Common - ketose-bisphosphate aldolase, class-II TM1040_3351 147 COG0191 Fba, Fructose/tagatose bisphosphate aldolase Carbohydrate transport and metabolism 99078225 Common - Integrase, catalytic region TM1040_3247 133 COG2801 Tra5, Transposase and inactivated derivatives DNA replication, recombination, and repair 99078290 Common - binding-protein-dependent transport systems inner membrane component TM1040_3314 176 COG1177 PotC, ABC-type spermidine/putrescine transport system, permease component II Amino acid transport and metabolism 99078063 Common - CDP-diacylglycerol--serine O-phosphatidyltransferase TM1040_3085 146 COG1183 PssA, Phosphatidylserine synthase Lipid metabolism 99078713 Common - Farnesyltranstransferase TM1040_3742 243 COG0142 IspA, Geranylgeranyl pyrophosphate synthase Coenzyme metabolism 99078143 Common - Citryl-CoA lyase TM1040_3165 113 COG2301 CitE, Citrate lyase beta subunit Carbohydrate transport and metabolism 99078567 Common - Redoxin TM1040_3596 89 COG0678 AHP1, Peroxiredoxin Posttranslational modification, protein turnover, chaperones 99078574 Common - extracellular solute-binding protein, family 5 TM1040_3603 207 COG0747 DdpA, ABC-type dipeptide transport system, periplasmic component Amino acid transport and metabolism 99078085 Common - histone-like nucleoid-structuring protein H-NS TM1040_3107 27 COG2916 Hns, DNA-binding protein H-NS General function prediction only 99078644 Common - Mandelate racemase/muconate lactonizing enzyme-like TM1040_3673 116 COG4948 COG4948, L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Cell envelope biogenesis, outer membrane / General function prediction only 99078424 Common - Carboxylesterase TM1040_3448 93 COG0627 COG0627, Predicted esterase General function prediction only 99078120 Common - binding-protein-dependent transport systems inner membrane component TM1040_3142 219 COG0601 DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078277 Common - Endoribonuclease L-PSP TM1040_3301 73 COG0251 TdcF, Putative translation initiation inhibitor, yjgF family Translation, ribosomal structure and biogenesis 99078297 Common - aldehyde dehydrogenase TM1040_3321 222 COG1012 PutA, NAD-dependent aldehyde dehydrogenases Energy production and conversion 99078389 Common - Na(+)-translocating NADH-quinone reductase subunit E TM1040_3413 76 COG2209 NqrE, Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrE Energy production and conversion 99078658 Common - MscS Mechanosensitive ion channel TM1040_3687 123 COG0668 MscS, Small-conductance mechanosensitive channel Cell envelope biogenesis, outer membrane 99078695 Common - Phenylacetate-CoA oxygenase, PaaG subunit TM1040_3724 46 COG3396 COG3396, Uncharacterized conserved protein Function unknown 99078052 Common - hypothetical protein TM1040_3074 19 COG3350 COG3350, Uncharacterized conserved protein Function unknown 99078136 Common - putative transcriptional regulator, TetR family TM1040_3158 65 COG3226 COG3226, Uncharacterized protein conserved in bacteria Function unknown 99078430 Common - NLP/P60 TM1040_3454 59 COG0791 Spr, Cell wall-associated hydrolases (invasion-associated proteins) Cell envelope biogenesis, outer membrane 99078333 Common - TRAP dicarboxylate transporter- DctP subunit TM1040_3357 97 COG1638 DctP, TRAP-type C4-dicarboxylate transport system, periplasmic component Carbohydrate transport and metabolism 99078611 Common - Tripartite ATP-independent periplasmic transporter, DctQ component TM1040_3640 70 COG4665 FcbT2, TRAP-type mannitol/chloroaromatic compound transport system, small permease component Secondary metabolites biosynthesis, transport, and catabolism 99078212 Common - Phosphonate ABC transporter PhnC, ATP-binding TM1040_3234 249 COG3638 COG3638, ABC-type phosphate/phosphonate transport system, ATPase component Inorganic ion transport and metabolism 99078397 Common - secretion protein HlyD TM1040_3421 126 COG0845 AcrA, Membrane-fusion protein Cell envelope biogenesis, outer membrane 99078169 Common - NADH dehydrogenase (quinone) TM1040_3191 161 COG1894 NuoF, NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit Energy production and conversion 99078392 Common - Na(+)-translocating NADH-quinone reductase subunit B TM1040_3416 76 COG1805 NqrB, Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrB Energy production and conversion 99078316 Common - hypothetical protein TM1040_3340 31 COG3777 COG3777, Uncharacterized conserved protein Function unknown 99078367 Common - Mandelate racemase/muconate lactonizing enzyme-like TM1040_3391 98 COG4948 COG4948, L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Cell envelope biogenesis, outer membrane / General function prediction only 99078045 Common - NUDIX hydrolase TM1040_3067 13 COG1051 COG1051, ADP-ribose pyrophosphatase Nucleotide transport and metabolism 99078273 Common - protein of unknown function DUF849 TM1040_3295 62 COG3246 COG3246, Uncharacterized conserved protein Function unknown 99078219 Nonpathogen - hypothetical protein TM1040_3241 1 None None None 99078236 Common - hypothetical protein TM1040_3258 136 COG0511 AccB, Biotin carboxyl carrier protein Lipid metabolism 99078382 Common - Cobyrinic acid a,c-diamide synthase TM1040_3406 203 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 99078676 Common - transferase hexapeptide repeat TM1040_3705 66 COG0110 WbbJ, Acetyltransferase (isoleucine patch superfamily) General function prediction only 99078511 Common - Integrase, catalytic region TM1040_3535 133 COG2801 Tra5, Transposase and inactivated derivatives DNA replication, recombination, and repair 99078093 Common - Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like TM1040_3115 249 COG0444 DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078261 Common - transcriptional regulator, LysR family TM1040_3283 169 COG0583 LysR, Transcriptional regulator Transcription 99078560 Nonpathogen - Sporulation related TM1040_3589 5 COG3087 FtsN, Cell division protein Cell division and chromosome partitioning 99078699 Common - ferredoxin TM1040_3728 144 COG1018 Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 Energy production and conversion 99078401 Common - hypothetical protein TM1040_3425 8 None None None 99078058 Common ubiA prenyltransferase TM1040_3080 184 COG0382 UbiA, 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases Coenzyme metabolism 99078113 Common - Cytochrome-c peroxidase TM1040_3135 95 COG1858 MauG, Cytochrome c peroxidase Inorganic ion transport and metabolism 99078315 Common - transcriptional regulator, LysR family TM1040_3339 191 COG0583 LysR, Transcriptional regulator Transcription 99078351 Common - sarcosine oxidase, beta subunit family TM1040_3375 83 COG0665 DadA, Glycine/D-amino acid oxidases (deaminating) Amino acid transport and metabolism 99078533 Common - hypothetical protein TM1040_3560 17 COG3631 COG3631, Ketosteroid isomerase-related protein General function prediction only 99078549 Nonpathogen - hypothetical protein TM1040_3576 3 None None None 99078720 Nonpathogen - hypothetical protein TM1040_3749 6 None None None 99078593 Common - putative GAF sensor protein TM1040_3622 75 COG3284 AcoR, Transcriptional activator of acetoin/glycerol metabolism Secondary metabolites biosynthesis, transport, and catabolism / Transcription 99078504 Nonpathogen - hypothetical protein TM1040_3528 2 None None None 99078181 Common - response regulator receiver protein TM1040_3203 187 COG3706 PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain Signal transduction mechanisms 99078177 Common - proline racemase TM1040_3199 46 COG3938 COG3938, Proline racemase Amino acid transport and metabolism 99078259 Common - 4-oxalocrotonate tautomerase family enzyme TM1040_3281 37 COG1942 COG1942, Uncharacterized protein, 4-oxalocrotonate tautomerase homolog General function prediction only 99078437 Nonpathogen - hypothetical protein TM1040_3461 1 None None None 99078461 Common - binding-protein-dependent transport systems inner membrane component TM1040_3485 161 COG0395 UgpE, ABC-type sugar transport system, permease component Carbohydrate transport and metabolism 99078668 Common - Phosphonate metabolism, 1,5-bisphosphokinase (PRPP-forming) PhnN TM1040_3697 129 COG3709 COG3709, Uncharacterized component of phosphonate metabolism Inorganic ion transport and metabolism 99078622 Common - thiamine biosynthesis protein ThiS TM1040_3651 9 COG2104 ThiS, Sulfur transfer protein involved in thiamine biosynthesis Coenzyme metabolism 99078024 Nonpathogen - hypothetical protein TM1040_3046 1 None None None 99078419 Common - cytochrome c, class I TM1040_3443 41 COG3474 COG3474, Cytochrome c2 Energy production and conversion 99078066 Common lipB lipoyltransferase TM1040_3088 169 COG0321 LipB, Lipoate-protein ligase B Coenzyme metabolism 99078716 Common - Electron-transferring-flavoprotein dehydrogenase TM1040_3745 110 COG0644 FixC, Dehydrogenases (flavoproteins) Energy production and conversion 99078157 Common - methyl-accepting chemotaxis sensory transducer TM1040_3179 148 COG0840 Tar, Methyl-accepting chemotaxis protein Cell motility and secretion / Signal transduction mechanisms 99078175 Common - TRAP dicarboxylate transporter- DctM subunit TM1040_3197 132 COG1593 DctQ, TRAP-type C4-dicarboxylate transport system, large permease component Carbohydrate transport and metabolism 99078206 Common - transcriptional regulator, AraC family TM1040_3228 126 COG2207 AraC, AraC-type DNA-binding domain-containing proteins Transcription 99078586 Common - putative ferric uptake regulator, Fur family TM1040_3615 95 COG0735 Fur, Fe2+/Zn2+ uptake regulation proteins Inorganic ion transport and metabolism 99078330 Common - Di-haem cytochrome c peroxidase TM1040_3354 94 COG1858 MauG, Cytochrome c peroxidase Inorganic ion transport and metabolism 99078605 Common - transcriptional regulator, LysR family TM1040_3634 182 COG0583 LysR, Transcriptional regulator Transcription 99078339 Common - transcriptional regulator, GntR family TM1040_3363 126 COG2188 PhnF, Transcriptional regulators Transcription 99078407 Common - multi-sensor hybrid histidine kinase TM1040_3431 224 COG0642 BaeS, Signal transduction histidine kinase Signal transduction mechanisms 99078641 Common - alpha/beta hydrolase fold TM1040_3670 149 COG0596 MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) General function prediction only 99078240 Common - 4-aminobutyrate aminotransferase TM1040_3262 237 COG0160 GabT, 4-aminobutyrate aminotransferase and related aminotransferases Amino acid transport and metabolism 99078582 Common - Phosphonate-binding periplasmic protein TM1040_3611 58 COG3221 PhnD, ABC-type phosphate/phosphonate transport system, periplasmic component Inorganic ion transport and metabolism 99078150 Common - ASPIC/UnbV TM1040_3172 19 None None None 99078358 Common - peptidase M19, renal dipeptidase TM1040_3382 100 COG2355 COG2355, Zn-dependent dipeptidase, microsomal dipeptidase homolog Amino acid transport and metabolism 99078471 Common - diaminopimelate decarboxylase TM1040_3495 216 COG0019 LysA, Diaminopimelate decarboxylase Amino acid transport and metabolism 99078194 Common - extracellular solute-binding protein, family 1 TM1040_3216 113 COG1653 UgpB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078134 Common - oxidoreductase-like TM1040_3156 166 COG0673 MviM, Predicted dehydrogenases and related proteins General function prediction only 99078198 Common - TRAP dicarboxylate transporter- DctP subunit TM1040_3220 56 COG1638 DctP, TRAP-type C4-dicarboxylate transport system, periplasmic component Carbohydrate transport and metabolism 99078308 Common - Sulfate ABC transporter, permease protein CysT TM1040_3332 213 COG0555 CysU, ABC-type sulfate transport system, permease component Posttranslational modification, protein turnover, chaperones 99078249 Common - AMP-dependent synthetase and ligase TM1040_3271 223 COG0318 CaiC, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism 99078484 Nonpathogen - hypothetical protein TM1040_3508 1 None None None 99078455 Common - guanine deaminase TM1040_3479 133 COG0402 SsnA, Cytosine deaminase and related metal-dependent hydrolases Nucleotide transport and metabolism / General function prediction only 99078422 Common - protein of unknown function DUF188 TM1040_3446 95 COG1671 COG1671, Uncharacterized protein conserved in bacteria Function unknown 99078517 Common - phage integrase TM1040_3542 9 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 99078083 Common - phospholipid/glycerol acyltransferase TM1040_3105 48 COG2937 PlsB, Glycerol-3-phosphate O-acyltransferase Lipid metabolism 99078344 Common - 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1 7-dioic acid hydratase (catechol pathway)-like TM1040_3368 8 COG0179 MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) Secondary metabolites biosynthesis, transport, and catabolism 99078558 Common - phage integrase TM1040_3585 172 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 99078125 Common - (2Fe-2S)-binding TM1040_3147 122 COG2080 CoxS, Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs Energy production and conversion 99078681 Common - Ribulose-phosphate 3-epimerase TM1040_3710 216 COG0036 Rpe, Pentose-5-phosphate-3-epimerase Carbohydrate transport and metabolism 99078688 Common - transcriptional regulator, IclR family TM1040_3717 108 COG1414 IclR, Transcriptional regulator Transcription 99078234 Common - Allophanate hydrolase subunit 1 TM1040_3256 103 COG2049 DUR1, Allophanate hydrolase subunit 1 Amino acid transport and metabolism 99078387 Nonpathogen - hypothetical protein TM1040_3411 3 None None None 99078036 Common - beta-lactamase-like TM1040_3058 51 COG0491 GloB, Zn-dependent hydrolases, including glyoxylases General function prediction only 99078100 Common - hypothetical protein TM1040_3122 7 None None None 99078404 Common - Tetratricopeptide TPR_2 TM1040_3428 52 COG3914 Spy, Predicted O-linked N-acetylglucosamine transferase, SPINDLY family Posttranslational modification, protein turnover, chaperones 99078043 Common - secretion protein HlyD TM1040_3065 94 COG1566 EmrA, Multidrug resistance efflux pump Defense mechanisms 99078325 Common - PfkB TM1040_3349 196 COG0524 RbsK, Sugar kinases, ribokinase family Carbohydrate transport and metabolism 99078524 Common - type I restriction-modification system, M subunit TM1040_3551 162 COG0286 HsdM, Type I restriction-modification system methyltransferase subunit Defense mechanisms 99078651 Common - 2-oxoacid ferredoxin oxidoreductase TM1040_3680 93 COG4231 COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits Energy production and conversion 99078076 Common - protein of unknown function DUF81 TM1040_3098 66 COG0730 COG0730, Predicted permeases General function prediction only 99078013 Common - ABC transporter related TM1040_3035 249 COG1116 TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component Inorganic ion transport and metabolism 99078288 Common - putative periplasmic solute-binding protein TM1040_3312 81 COG1840 AfuA, ABC-type Fe3+ transport system, periplasmic component Inorganic ion transport and metabolism 99078667 Common - protein of unknown function DUF1045 TM1040_3696 27 None None None 99078065 Common - hypothetical protein TM1040_3087 37 None None None 99078706 Common - acetyl-CoA acetyltransferase TM1040_3735 167 COG0183 PaaJ, Acetyl-CoA acetyltransferase Lipid metabolism 99078528 Common - ribonuclease, Rne/Rng family TM1040_3555 167 COG1530 CafA, Ribonucleases G and E Translation, ribosomal structure and biogenesis 99078294 Common - Tripartite ATP-independent periplasmic transporter, DctQ component TM1040_3318 39 COG3090 DctM, TRAP-type C4-dicarboxylate transport system, small permease component Carbohydrate transport and metabolism 99078233 Common - Urea carboxylase TM1040_3255 114 COG1984 DUR1, Allophanate hydrolase subunit 2 Amino acid transport and metabolism 99078088 Common - Ornithine decarboxylase TM1040_3110 211 COG0019 LysA, Diaminopimelate decarboxylase Amino acid transport and metabolism 99078067 Common - multi-sensor signal transduction histidine kinase TM1040_3089 214 COG4251 COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) Signal transduction mechanisms 99078687 Common - Uncharacterized protein UPF0065 TM1040_3716 45 COG3181 COG3181, Uncharacterized protein conserved in bacteria Function unknown 99078554 Nonpathogen - hypothetical protein TM1040_3581 4 None None None 99078717 Common - transcriptional regulator, MerR family TM1040_3746 122 COG0789 SoxR, Predicted transcriptional regulators Transcription 99078146 Common - aminotransferase, class IV TM1040_3168 194 COG0115 IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase Amino acid transport and metabolism / Coenzyme metabolism 99078060 Nonpathogen - hypothetical protein TM1040_3082 6 None None None 99078095 Common - Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation)-like TM1040_3117 55 COG2843 PgsA, Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation) Cell envelope biogenesis, outer membrane 99078578 Common - Asparaginase TM1040_3607 148 COG0252 AnsB, L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D Amino acid transport and metabolism / Translation, ribosomal structure and biogenesis 99078195 Common - ABC transporter related TM1040_3217 249 COG3839 MalK, ABC-type sugar transport systems, ATPase components Carbohydrate transport and metabolism 99078022 Nonpathogen - protein of unknown function DUF1625 TM1040_3044 4 None None None 99078448 Common - hypothetical protein TM1040_3472 33 COG3257 GlxB, Uncharacterized protein, possibly involved in glyoxylate utilization General function prediction only 99078421 Nonpathogen - hypothetical protein TM1040_3445 1 None None None 99078286 Common - riboflavin synthase subunit beta TM1040_3310 192 COG0054 RibH, Riboflavin synthase beta-chain Coenzyme metabolism 99078655 Common - binding-protein-dependent transport systems inner membrane component TM1040_3684 219 COG0601 DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078034 Nonpathogen - hypothetical protein TM1040_3056 1 None None None 99078072 Common - basic membrane lipoprotein TM1040_3094 107 COG1744 Med, Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein General function prediction only 99078726 Nonpathogen - hypothetical protein TM1040_3755 1 None None None 99078241 Common - succinic semialdehyde dehydrogenase TM1040_3263 220 COG1012 PutA, NAD-dependent aldehyde dehydrogenases Energy production and conversion 99078158 Common - hypothetical protein TM1040_3180 17 COG0645 COG0645, Predicted kinase General function prediction only 99078614 Common - transcriptional regulator, Crp/Fnr family TM1040_3643 127 COG0664 Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases Signal transduction mechanisms 99078101 Nonpathogen - hypothetical protein TM1040_3123 1 None None None 99078666 Common - Phosphonate metabolism PhnM TM1040_3695 52 COG3454 COG3454, Metal-dependent hydrolase involved in phosphonate metabolism Inorganic ion transport and metabolism 99078173 Common - TRAP dicarboxylate transporter- DctP subunit TM1040_3195 77 COG1638 DctP, TRAP-type C4-dicarboxylate transport system, periplasmic component Carbohydrate transport and metabolism 99078486 Common - dihydrolipoamide acetyltransferase TM1040_3510 195 COG0508 AceF, Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes Energy production and conversion 99078307 Common - Sulfate ABC transporter, permease protein CysW TM1040_3331 212 COG4208 CysW, ABC-type sulfate transport system, permease component Inorganic ion transport and metabolism 99078260 Common - hypothetical protein TM1040_3282 8 None None None 99078301 Common - aldehyde dehydrogenase TM1040_3325 102 COG1012 PutA, NAD-dependent aldehyde dehydrogenases Energy production and conversion 99078721 Common - GCN5-related N-acetyltransferase TM1040_3750 8 COG0456 RimI, Acetyltransferases General function prediction only 99078413 Common - extracellular solute-binding protein, family 5 TM1040_3437 204 COG0747 DdpA, ABC-type dipeptide transport system, periplasmic component Amino acid transport and metabolism 99078080 Common - transcriptional regulator, LuxR family TM1040_3102 49 COG2197 CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain Signal transduction mechanisms / Transcription 99078218 Common - transcriptional regulator, LysR family TM1040_3240 172 COG0583 LysR, Transcriptional regulator Transcription 99078375 Common - extracellular solute-binding protein, family 1 TM1040_3399 72 COG1653 UgpB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078492 Nonpathogen - hypothetical protein TM1040_3516 3 COG1442 RfaJ, Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases Cell envelope biogenesis, outer membrane 99078657 Common - L-carnitine dehydratase/bile acid-inducible protein F TM1040_3686 112 COG1804 CaiB, Predicted acyl-CoA transferases/carnitine dehydratase Energy production and conversion 99078248 Common - short-chain dehydrogenase/reductase SDR TM1040_3270 237 COG1028 FabG, Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only 99078133 Common - binding-protein-dependent transport systems inner membrane component TM1040_3155 170 COG0395 UgpE, ABC-type sugar transport system, permease component Carbohydrate transport and metabolism 99078462 Common - glycoside hydrolase, clan GH-D TM1040_3486 44 COG3345 GalA, Alpha-galactosidase Carbohydrate transport and metabolism 99078736 Common - binding-protein-dependent transport systems inner membrane component TM1040_3765 63 COG4662 TupA, ABC-type tungstate transport system, periplasmic component Coenzyme metabolism 99078055 Nonpathogen - hypothetical protein TM1040_3077 6 None None None 99078571 Common - Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like TM1040_3600 249 COG0444 DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078191 Common - hypothetical protein TM1040_3213 221 COG0028 IlvB, Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] Amino acid transport and metabolism / Coenzyme metabolism 99078385 Common - transcriptional regulator, AraC family TM1040_3409 83 COG2207 AraC, AraC-type DNA-binding domain-containing proteins Transcription 99078010 Common - sulfate/tungstate uptake family ABC transporter, periplasmic substrate-binding protein TM1040_3032 62 COG2998 TupB, ABC-type tungstate transport system, permease component Coenzyme metabolism 99078456 Common - response regulator receiver protein TM1040_3480 14 COG2204 AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Signal transduction mechanisms 99078630 Common - BioY protein TM1040_3659 13 COG1268 BioY, Uncharacterized conserved protein General function prediction only 99078208 Common - Twin-arginine translocation pathway signal TM1040_3230 111 COG1529 CoxL, Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs Energy production and conversion 99078256 Nonpathogen - hypothetical protein TM1040_3278 2 None None None 99078691 Common - Glutamate--ammonia ligase TM1040_3720 224 COG0174 GlnA, Glutamine synthetase Amino acid transport and metabolism 99078352 Common - Sarcosine oxidase, delta subunit, heterotetrameric TM1040_3376 27 COG4311 SoxD, Sarcosine oxidase delta subunit Amino acid transport and metabolism 99078078 Common - short-chain dehydrogenase/reductase SDR TM1040_3100 237 COG4221 COG4221, Short-chain alcohol dehydrogenase of unknown specificity General function prediction only 99078220 Common - methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor TM1040_3242 174 COG0840 Tar, Methyl-accepting chemotaxis protein Cell motility and secretion / Signal transduction mechanisms 99078625 Common - UBA/THIF-type NAD/FAD binding fold TM1040_3654 197 COG0476 ThiF, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 Coenzyme metabolism 99078588 Common - 5-methyltetrahydrofolate--homocysteine S-methyltransferase TM1040_3617 163 COG0646 MetH, Methionine synthase I (cobalamin-dependent), methyltransferase domain Amino acid transport and metabolism 99078532 Common - hypothetical protein TM1040_3559 19 None None None 99078523 Common - restriction modification system DNA specificity domain TM1040_3550 106 COG0732 HsdS, Restriction endonuclease S subunits Defense mechanisms 99078151 Common - ROK domain protein TM1040_3173 166 COG1940 NagC, Transcriptional regulator/sugar kinase Transcription / Carbohydrate transport and metabolism 99078649 Common - ThiJ/PfpI TM1040_3678 36 COG4977 COG4977, Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain Transcription 99078632 Common - ABC transporter related TM1040_3661 249 COG1122 CbiO, ABC-type cobalt transport system, ATPase component Inorganic ion transport and metabolism 99078171 Common - hypothetical protein TM1040_3193 11 None None None 99078056 Common - GCN5-related N-acetyltransferase TM1040_3078 3 COG3393 COG3393, Predicted acetyltransferase General function prediction only 99078671 Common - phosphonate metabolism PhnJ TM1040_3700 45 COG3627 PhnJ, Uncharacterized enzyme of phosphonate metabolism Inorganic ion transport and metabolism 99078544 Common - peptidylprolyl isomerase, FKBP-type TM1040_3571 156 COG1047 SlpA, FKBP-type peptidyl-prolyl cis-trans isomerases 2 Posttranslational modification, protein turnover, chaperones 99078312 Common - periplasmic sensor signal transduction histidine kinase TM1040_3336 221 COG0642 BaeS, Signal transduction histidine kinase Signal transduction mechanisms 99078595 Common - hypothetical protein TM1040_3624 13 None None None 99078479 Common - Ethyl tert-butyl ether degradation EthD TM1040_3503 18 None None None 99078105 Common - transposase IS3/IS911 TM1040_3127 62 None None None 99078372 Common - ABC transporter related TM1040_3396 249 COG3839 MalK, ABC-type sugar transport systems, ATPase components Carbohydrate transport and metabolism 99078115 Common - NADH:flavin oxidoreductase/NADH oxidase TM1040_3137 191 COG1902 NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme family Energy production and conversion 99078446 Common - transcriptional regulator, MarR family TM1040_3470 92 COG1846 MarR, Transcriptional regulators Transcription 99078243 Common - peptidase M20 TM1040_3265 184 COG0624 ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases Amino acid transport and metabolism 99078551 Common - Reductive dehalogenase TM1040_3578 106 COG1018 Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 Energy production and conversion 99078698 Common - Phenylacetate-CoA oxygenase, PaaJ subunit TM1040_3727 88 COG2151 PaaD, Predicted metal-sulfur cluster biosynthetic enzyme General function prediction only 99078046 Common - Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis-like TM1040_3068 56 COG4233 COG4233, Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis Posttranslational modification, protein turnover, chaperones / Energy production and conversion 99078565 Common - beta-lactamase-like TM1040_3594 85 COG1235 PhnP, Metal-dependent hydrolases of the beta-lactamase superfamily I General function prediction only 99078184 Common - CheA signal transduction histidine kinases TM1040_3206 164 COG0643 CheA, Chemotaxis protein histidine kinase and related kinases Cell motility and secretion / Signal transduction mechanisms 99078272 Common - acetyl-CoA synthetase TM1040_3294 204 COG0365 Acs, Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases Lipid metabolism 99078211 Common - Phosphonate-binding periplasmic protein TM1040_3233 85 COG3221 PhnD, ABC-type phosphate/phosphonate transport system, periplasmic component Inorganic ion transport and metabolism 99078164 Common - transcriptional regulator, LysR family TM1040_3186 46 COG0583 LysR, Transcriptional regulator Transcription 99078508 Common - transcriptional regulator, LacI family TM1040_3532 41 COG1879 RbsB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078086 Common - purine nucleoside phosphorylase TM1040_3108 95 COG0813 DeoD, Purine-nucleoside phosphorylase Nucleotide transport and metabolism 99078207 Common - (2Fe-2S)-binding TM1040_3229 122 COG2080 CoxS, Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs Energy production and conversion 99078188 Common - CheB methylesterase TM1040_3210 149 COG2201 CheB, Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain Cell motility and secretion / Signal transduction mechanisms 99078394 Common - ApbE-like lipoprotein TM1040_3418 138 COG1477 ApbE, Membrane-associated lipoprotein involved in thiamine biosynthesis Coenzyme metabolism 99078168 Common - formate dehydrogenase, alpha subunit TM1040_3190 216 COG3383 COG3383, Uncharacterized anaerobic dehydrogenase General function prediction only 99078338 Common - Alkanesulfonate monooxygenase TM1040_3362 78 COG2141 COG2141, Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases Energy production and conversion 99078703 Common - argininosuccinate lyase TM1040_3732 232 COG0165 ArgH, Argininosuccinate lyase Amino acid transport and metabolism 99078252 Nonpathogen - hypothetical protein TM1040_3274 1 None None None 99078466 Common - 2-dehydro-3-deoxy-6-phosphogalactonate aldolase TM1040_3490 126 COG0800 Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase Carbohydrate transport and metabolism 99078591 Common - Saccharopine dehydrogenase TM1040_3620 16 COG1748 LYS9, Saccharopine dehydrogenase and related proteins Amino acid transport and metabolism 99078348 Common - response regulator receiver protein TM1040_3372 27 COG2204 AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Signal transduction mechanisms 99078031 Common - Creatininase TM1040_3053 88 COG1402 COG1402, Uncharacterized protein, putative amidase General function prediction only 99078322 Common - Xylose isomerase-like TIM barrel TM1040_3346 65 COG1082 IolE, Sugar phosphate isomerases/epimerases Carbohydrate transport and metabolism 99078032 Common - glutamine amidotransferase TM1040_3054 109 COG0518 GuaA, GMP synthase - Glutamine amidotransferase domain Nucleotide transport and metabolism 99078642 Common - Helix-turn-helix, type 11 TM1040_3671 87 COG2378 COG2378, Predicted transcriptional regulator Transcription 99078728 Common - AzlC-like TM1040_3757 108 COG1296 AzlC, Predicted branched-chain amino acid permease (azaleucine resistance) Amino acid transport and metabolism 99078410 Common - ABC transporter related TM1040_3434 249 COG1123 COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase General function prediction only 99078653 Common - Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like TM1040_3682 249 COG1123 COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase General function prediction only 99078515 Common - restriction modification system DNA specificity domain TM1040_3540 102 COG0732 HsdS, Restriction endonuclease S subunits Defense mechanisms 99078053 Nonpathogen - hypothetical protein TM1040_3075 1 None None None 99078329 Common - conserved hypothetical protein 698 TM1040_3353 117 COG2855 COG2855, Predicted membrane protein Function unknown 99078341 Common - protein of unknown function DUF125, transmembrane TM1040_3365 64 COG1814 COG1814, Uncharacterized membrane protein Function unknown 99078362 Common - Malate/L-lactate dehydrogenase TM1040_3386 68 COG2055 COG2055, Malate/L-lactate dehydrogenases Energy production and conversion 99078701 Common - UspA TM1040_3730 26 COG0589 UspA, Universal stress protein UspA and related nucleotide-binding proteins Signal transduction mechanisms 99078383 Common - initiator RepB protein TM1040_3407 19 None None None 99078226 Common - transposase and inactivated derivative TM1040_3248 25 None None None 99078138 Common - acetyl-CoA carboxylase carboxyltransferase subunit alpha TM1040_3160 176 COG0825 AccA, Acetyl-CoA carboxylase alpha subunit Lipid metabolism 99078435 Common - aspartate-semialdehyde dehydrogenase TM1040_3459 236 COG0136 Asd, Aspartate-semialdehyde dehydrogenase Amino acid transport and metabolism 99078019 Common - Hemolysin-type calcium-binding region TM1040_3041 97 COG2931 COG2931, RTX toxins and related Ca2+-binding proteins Secondary metabolites biosynthesis, transport, and catabolism 99078069 Common - nitrogen-fixing NifU-like TM1040_3091 104 COG0694 COG0694, Thioredoxin-like proteins and domains Posttranslational modification, protein turnover, chaperones 99078296 Common - 6-phosphogluconate dehydrogenase, NAD-binding TM1040_3320 164 COG2084 MmsB, 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases Lipid metabolism 99078685 Common - protein of unknown function DUF112, transmembrane TM1040_3714 75 COG3333 COG3333, Uncharacterized protein conserved in bacteria Function unknown 99078131 Common - extracellular solute-binding protein, family 1 TM1040_3153 63 COG1653 UgpB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078731 Nonpathogen - hypothetical protein TM1040_3760 2 None None None 99078711 Common - methyltransferase small TM1040_3740 57 COG4123 COG4123, Predicted O-methyltransferase General function prediction only 99078664 Common - hypothetical protein TM1040_3693 10 None None None 99078402 Common - hypothetical protein TM1040_3426 13 COG0404 GcvT, Glycine cleavage system T protein (aminomethyltransferase) Amino acid transport and metabolism 99078700 Common - aminotransferase TM1040_3729 171 COG0115 IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase Amino acid transport and metabolism / Coenzyme metabolism 99078201 Common - putative ABC transporter, periplasmic substrate-binding TM1040_3223 13 COG0834 HisJ, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain Amino acid transport and metabolism / Signal transduction mechanisms 99078629 Common - binding-protein-dependent transport systems inner membrane component TM1040_3658 192 COG0600 TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component Inorganic ion transport and metabolism 99078475 Common - protein of unknown function DUF214 TM1040_3499 34 COG2177 FtsX, Cell division protein Cell division and chromosome partitioning 99078123 Common - hypothetical protein TM1040_3145 13 None None None 99078499 Common - hypothetical protein TM1040_3523 57 COG2030 MaoC, Acyl dehydratase Lipid metabolism 99078284 Common - transcriptional regulator, LacI family TM1040_3308 126 COG1609 PurR, Transcriptional regulators Transcription 99078021 Nonpathogen - hypothetical protein TM1040_3043 1 None None None 99078602 Common - CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase TM1040_3631 200 COG0558 PgsA, Phosphatidylglycerophosphate synthase Lipid metabolism 99078645 Common - transcriptional regulator, ArsR family TM1040_3674 89 COG0640 ArsR, Predicted transcriptional regulators Transcription 99078103 Nonpathogen - hypothetical protein TM1040_3125 1 None None None 99078267 Common - hypothetical protein TM1040_3289 3 None None None 99078488 Common - succinyl-CoA synthetase, alpha subunit TM1040_3512 206 COG0074 SucD, Succinyl-CoA synthetase, alpha subunit Energy production and conversion 99078710 Common - protein of unknown function DUF465 TM1040_3739 14 COG5570 COG5570, Uncharacterized small protein Function unknown 99078481 Common - hypothetical protein TM1040_3505 41 COG3034 COG3034, Uncharacterized protein conserved in bacteria Function unknown 99078305 Nonpathogen - protein of unknown function DUF330 TM1040_3329 5 COG3009 COG3009, Uncharacterized protein conserved in bacteria Function unknown 99078231 Common - ABC transporter related TM1040_3253 249 COG1129 MglA, ABC-type sugar transport system, ATPase component Carbohydrate transport and metabolism 99078153 Common - inner-membrane translocator TM1040_3175 112 COG4214 XylH, ABC-type xylose transport system, permease component Carbohydrate transport and metabolism 99078373 Common - binding-protein-dependent transport systems inner membrane component TM1040_3397 209 COG0395 UgpE, ABC-type sugar transport system, permease component Carbohydrate transport and metabolism 99078229 Nonpathogen - hypothetical protein TM1040_3251 1 None None None 99078634 Common modB molybdate ABC transporter permease protein TM1040_3663 227 COG4149 ModC, ABC-type molybdate transport system, permease component Inorganic ion transport and metabolism 99078477 Common - pyridoxamine 5'-phosphate oxidase-related, FMN-binding TM1040_3501 36 COG3576 COG3576, Predicted flavin-nucleotide-binding protein structurally related to pyridoxine 5'-phosphate oxidase General function prediction only 99078530 Common infA translation initiation factor IF-1 TM1040_3557 214 COG0361 InfA, Translation initiation factor 1 (IF-1) Translation, ribosomal structure and biogenesis 99078663 Common - hypothetical protein TM1040_3692 18 COG4671 COG4671, Predicted glycosyl transferase General function prediction only 99078546 Common - Lytic murein transglycosylase TM1040_3573 106 COG2951 MltB, Membrane-bound lytic murein transglycosylase B Cell envelope biogenesis, outer membrane 99078464 Common - short-chain dehydrogenase/reductase SDR TM1040_3488 238 COG1028 FabG, Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only 99078415 Common - pantoate--beta-alanine ligase TM1040_3439 182 COG0414 PanC, Panthothenate synthetase Coenzyme metabolism 99078379 Common - protein of unknown function DUF1403 TM1040_3403 9 None None None 99078697 Common - Phenylacetate-CoA oxygenase, PaaI subunit TM1040_3726 42 COG3396 COG3396, Uncharacterized conserved protein Function unknown 99078117 Common - Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like TM1040_3139 249 COG4608 AppF, ABC-type oligopeptide transport system, ATPase component Amino acid transport and metabolism 99078141 Common - transcriptional regulator, AsnC family TM1040_3163 145 COG1522 Lrp, Transcriptional regulators Transcription 99078396 Common - Hydrophobe/amphiphile efflux-1 HAE1 TM1040_3420 176 COG0841 AcrB, Cation/multidrug efflux pump Defense mechanisms 99078254 Common - transposase orfB TM1040_3276 15 None None None 99078215 Common - DSBA oxidoreductase TM1040_3237 8 COG2761 FrnE, Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis Secondary metabolites biosynthesis, transport, and catabolism 99078525 Common - BRO-like TM1040_3552 12 COG3617 COG3617, Prophage antirepressor Transcription 99078148 Common - protein of unknown function DUF1244 TM1040_3170 38 COG3492 COG3492, Uncharacterized protein conserved in bacteria Function unknown 99078647 Common - cyclic nucleotide-binding protein TM1040_3676 182 COG1132 MdlB, ABC-type multidrug transport system, ATPase and permease components Defense mechanisms 99078598 Common - MscS Mechanosensitive ion channel TM1040_3627 176 COG0668 MscS, Small-conductance mechanosensitive channel Cell envelope biogenesis, outer membrane 99078443 Common - 3,4-dihydroxyphenylacetate 2,3-dioxygenase HpaD TM1040_3467 41 COG2514 COG2514, Predicted ring-cleavage extradiol dioxygenase General function prediction only 99078222 Common - CheD, stimulates methylation of MCP proteins TM1040_3244 3 COG1871 CheD, Chemotaxis protein; stimulates methylation of MCP proteins Cell motility and secretion / Signal transduction mechanisms 99078563 Common - DNA polymerase III subunit delta' TM1040_3592 215 COG0470 HolB, ATPase involved in DNA replication DNA replication, recombination, and repair 99078028 Common - Taurine catabolism dioxygenase TauD/TfdA TM1040_3050 47 COG2175 TauD, Probable taurine catabolism dioxygenase Secondary metabolites biosynthesis, transport, and catabolism 99078107 Common - TRAP C4-dicarboxylate transport system permease DctM subunit TM1040_3129 122 COG1593 DctQ, TRAP-type C4-dicarboxylate transport system, large permease component Carbohydrate transport and metabolism 99078162 Common - protein of unknown function DUF6, transmembrane TM1040_3184 105 COG5006 COG5006, Predicted permease, DMT superfamily General function prediction only 99078279 Common - ABC transporter related TM1040_3303 249 COG3839 MalK, ABC-type sugar transport systems, ATPase components Carbohydrate transport and metabolism 99078369 Common - short-chain dehydrogenase/reductase SDR TM1040_3393 238 COG1028 FabG, Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only 99078505 Common - hypothetical protein TM1040_3529 2 None None None 99078166 Common - transcriptional regulator, LysR family TM1040_3188 87 COG0583 LysR, Transcriptional regulator Transcription 99078091 Common - binding-protein-dependent transport systems inner membrane component TM1040_3113 219 COG0601 DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078468 Common - Beta-galactosidase TM1040_3492 40 COG1874 LacA, Beta-galactosidase Carbohydrate transport and metabolism 99078217 Common - putative glutathione S-transferase TM1040_3239 79 COG0435 ECM4, Predicted glutathione S-transferase Posttranslational modification, protein turnover, chaperones 99078250 Common - acetyl-CoA acetyltransferase TM1040_3272 117 COG0183 PaaJ, Acetyl-CoA acetyltransferase Lipid metabolism 99078336 Common - flavin reductase-like, FMN-binding TM1040_3360 112 COG1853 COG1853, Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family General function prediction only 99078244 Common - periplasmic binding protein/LacI transcriptional regulator TM1040_3266 30 COG1879 RbsB, ABC-type sugar transport system, periplasmic component Carbohydrate transport and metabolism 99078408 Common - nicotinate phosphoribosyltransferase TM1040_3432 77 COG1488 PncB, Nicotinic acid phosphoribosyltransferase Coenzyme metabolism 99078270 Nonpathogen - hypothetical protein TM1040_3292 1 None None None 99078370 Common - protein of unknown function DUF718 TM1040_3394 40 COG3254 COG3254, Uncharacterized conserved protein Function unknown 99078723 Nonpathogen - hypothetical protein TM1040_3752 10 None None None 99078354 Common - sarcosine oxidase, gamma subunit family TM1040_3378 6 COG4583 COG4583, Sarcosine oxidase gamma subunit Amino acid transport and metabolism 99078538 Common - UDP-N-acetylglucosamine 1-carboxyvinyltransferase TM1040_3565 208 COG0766 MurA, UDP-N-acetylglucosamine enolpyruvyl transferase Cell envelope biogenesis, outer membrane 99078441 Common - 5-carboxymethyl-2-hydroxymuconate delta-isomerase TM1040_3465 172 COG0179 MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) Secondary metabolites biosynthesis, transport, and catabolism 99078513 Common - protein of unknown function DUF1524 RloF TM1040_3538 64 COG1479 COG1479, Uncharacterized conserved protein Function unknown 99078186 Nonpathogen - hypothetical protein TM1040_3208 1 COG1366 SpoIIAA, Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) Signal transduction mechanisms 99078627 Common - transcriptional activator, TenA family TM1040_3656 74 COG0819 TenA, Putative transcription activator Transcription 99078428 Common - transcriptional regulator, ArsR family TM1040_3452 37 COG0640 ArsR, Predicted transcriptional regulators Transcription 99078265 Common - phage Tail Collar TM1040_3287 38 COG4675 MdpB, Microcystin-dependent protein Function unknown 99078673 Common phnH carbon-phosphorus lyase complex subunit TM1040_3702 40 COG3625 PhnH, Uncharacterized enzyme of phosphonate metabolism Inorganic ion transport and metabolism 99078048 Common pyrB aspartate carbamoyltransferase catalytic subunit TM1040_3070 240 COG0540 PyrB, Aspartate carbamoyltransferase, catalytic chain Nucleotide transport and metabolism 99078264 Common - phage Tail Collar TM1040_3286 38 COG4675 MdpB, Microcystin-dependent protein Function unknown 99078050 Common - dihydroorotase, multifunctional complex type TM1040_3072 211 COG0044 PyrC, Dihydroorotase and related cyclic amidohydrolases Nucleotide transport and metabolism 99078452 Common - Transthyretin TM1040_3476 63 COG2351 COG2351, Transthyretin-like protein General function prediction only 99078635 Common - molybdenum ABC transporter, periplasmic molybdate-binding protein TM1040_3664 155 COG0725 ModA, ABC-type molybdate transport system, periplasmic component Inorganic ion transport and metabolism 99078320 Common - transcriptional regulator, LacI family TM1040_3344 129 COG1609 PurR, Transcriptional regulators Transcription 99078503 Common sdhA succinate dehydrogenase flavoprotein subunit TM1040_3527 226 COG1053 SdhA, Succinate dehydrogenase/fumarate reductase, flavoprotein subunit Energy production and conversion 99078707 Common - Acetoacetyl-CoA reductase TM1040_3736 238 COG1028 FabG, Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only 99078059 Common - OmpA/MotB TM1040_3081 160 COG2885 OmpA, Outer membrane protein and related peptidoglycan-associated (lipo)proteins Cell envelope biogenesis, outer membrane 99078541 Common - Pyridoxal-5'-phosphate-dependent enzyme, beta subunit TM1040_3568 202 COG1171 IlvA, Threonine dehydratase Amino acid transport and metabolism 99078583 Common - periplasmic sensor hybrid histidine kinase TM1040_3612 225 COG0642 BaeS, Signal transduction histidine kinase Signal transduction mechanisms 99078662 Common - Phosphoglycerate mutase TM1040_3691 88 COG0406 GpmB, Fructose-2,6-bisphosphatase Carbohydrate transport and metabolism 99078450 Common - ureidoglycolate hydrolase TM1040_3474 35 COG3194 DAL3, Ureidoglycolate hydrolase Nucleotide transport and metabolism 99078096 Common - phage integrase TM1040_3118 45 COG4973 XerC, Site-specific recombinase XerC DNA replication, recombination, and repair 99078037 Common - acyl-CoA dehydrogenase-like TM1040_3059 153 COG1960 CaiA, Acyl-CoA dehydrogenases Lipid metabolism 99078121 Common - extracellular solute-binding protein, family 5 TM1040_3143 205 COG0747 DdpA, ABC-type dipeptide transport system, periplasmic component Amino acid transport and metabolism 99078224 Common - transposase IS3/IS911 TM1040_3246 61 None None None 99078606 Common - extracellular solute-binding protein, family 1 TM1040_3635 125 COG0687 PotD, Spermidine/putrescine-binding periplasmic protein Amino acid transport and metabolism 99078600 Common - transcriptional regulator, AsnC family TM1040_3629 163 COG1522 Lrp, Transcriptional regulators Transcription 99078395 Common - hypothetical protein TM1040_3419 14 COG2991 COG2991, Uncharacterized protein conserved in bacteria Function unknown 99078237 Common - hypothetical protein TM1040_3259 100 COG1540 COG1540, Uncharacterized proteins, homologs of lactam utilization protein B General function prediction only 99078650 Common - transcriptional regulator, AsnC family TM1040_3679 150 COG1522 Lrp, Transcriptional regulators Transcription 99078518 Nonpathogen - putative transcriptional regulator TM1040_3544 2 COG3311 AlpA, Predicted transcriptional regulator Transcription 99078712 Common - hypothetical protein TM1040_3741 18 None None None 99078064 Common - Phosphatidylethanolamine N-methyltransferase TM1040_3086 174 COG2226 UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis Coenzyme metabolism 99078568 Common - hypothetical protein TM1040_3597 105 COG0624 ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases Amino acid transport and metabolism 99078609 Common - binding-protein-dependent transport systems inner membrane component TM1040_3638 144 COG1177 PotC, ABC-type spermidine/putrescine transport system, permease component II Amino acid transport and metabolism 99078326 Common - myo-inositol catabolism IolB protein TM1040_3350 51 COG3718 IolB, Uncharacterized enzyme involved in inositol metabolism Carbohydrate transport and metabolism 99078298 Nonpathogen - hypothetical protein TM1040_3322 1 None None None 99078659 Common - hypothetical protein TM1040_3688 18 COG4671 COG4671, Predicted glycosyl transferase General function prediction only 99078675 Common - transcriptional regulator, GntR family TM1040_3704 136 COG2188 PhnF, Transcriptional regulators Transcription 99078130 Common murQ N-acetylmuramic acid-6-phosphate etherase TM1040_3152 89 COG2103 COG2103, Predicted sugar phosphate isomerase General function prediction only 99078561 Common - Serine-type D-Ala-D-Ala carboxypeptidase TM1040_3590 153 COG1686 DacC, D-alanyl-D-alanine carboxypeptidase Cell envelope biogenesis, outer membrane 99078144 Common - protein of unknown function DUF1611 TM1040_3166 38 COG3367 COG3367, Uncharacterized conserved protein Function unknown 99078317 Common - ABC transporter related TM1040_3341 249 COG1129 MglA, ABC-type sugar transport system, ATPase component Carbohydrate transport and metabolism 99078360 Common - hypothetical protein TM1040_3384 12 None None None 99078137 Common - hypothetical protein TM1040_3159 16 None None None 99078694 Common - transcriptional regulator, GntR family TM1040_3723 103 COG1802 GntR, Transcriptional regulators Transcription 99078245 Common - inner-membrane translocator TM1040_3267 111 COG1172 AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components Carbohydrate transport and metabolism 99078425 Common - protein of unknown function DUF861, cupin_3 TM1040_3449 31 COG3450 COG3450, Predicted enzyme of the cupin superfamily General function prediction only 99078128 Common - transcriptional regulator, GntR family TM1040_3150 131 COG2188 PhnF, Transcriptional regulators Transcription 99078030 Common - amidohydrolase TM1040_3052 61 COG0402 SsnA, Cytosine deaminase and related metal-dependent hydrolases Nucleotide transport and metabolism / General function prediction only 99078084 Common - methylmalonyl-CoA mutase TM1040_3106 109 COG1884 Sbm, Methylmalonyl-CoA mutase, N-terminal domain/subunit Lipid metabolism 99078345 Common - ABC-1 TM1040_3369 185 COG0661 AarF, Predicted unusual protein kinase General function prediction only 99078282 Common - binding-protein-dependent transport systems inner membrane component TM1040_3306 152 COG1175 UgpA, ABC-type sugar transport systems, permease components Carbohydrate transport and metabolism 99078557 Nonpathogen - hypothetical protein TM1040_3584 2 None None None 99078610 Common - TRAP C4-dicarboxylate transport system permease DctM subunit TM1040_3639 135 COG4664 FcbT3, TRAP-type mannitol/chloroaromatic compound transport system, large permease component Secondary metabolites biosynthesis, transport, and catabolism 99078398 Common - WxcM-like TM1040_3422 24 None None None 99078510 Common - transposase IS3/IS911 TM1040_3534 62 None None None 99078427 Common - transcriptional regulator, TetR family TM1040_3451 114 COG1309 AcrR, Transcriptional regulator Transcription 99078529 Common - maf protein TM1040_3556 196 COG0424 Maf, Nucleotide-binding protein implicated in inhibition of septum formation Cell division and chromosome partitioning 99078474 Common - ABC transporter related TM1040_3498 249 COG2884 FtsE, Predicted ATPase involved in cell division Cell division and chromosome partitioning 99078276 Common - response regulator receiver sensor signal transduction histidine kinase TM1040_3300 221 COG4251 COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) Signal transduction mechanisms 99078042 Common - Molybdenum cofactor biosynthesis protein B TM1040_3064 184 COG0521 MoaB, Molybdopterin biosynthesis enzymes Coenzyme metabolism 99078291 Common - ABC transporter related TM1040_3315 249 COG3842 PotA, ABC-type spermidine/putrescine transport systems, ATPase components Amino acid transport and metabolism 99078496 Common - Citryl-CoA lyase TM1040_3520 111 COG2301 CitE, Citrate lyase beta subunit Carbohydrate transport and metabolism 99078384 Common - malonyl-CoA synthase TM1040_3408 223 COG0318 CaiC, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism 99078619 Common - sulfate permease TM1040_3648 159 COG0659 SUL1, Sulfate permease and related transporters (MFS superfamily) Inorganic ion transport and metabolism 99078289 Common - binding-protein-dependent transport systems inner membrane component TM1040_3313 172 COG0555 CysU, ABC-type sulfate transport system, permease component Posttranslational modification, protein turnover, chaperones 99078310 Nonpathogen - hypothetical protein TM1040_3334 7 None None None 99078575 Common - transcriptional regulator, IclR family TM1040_3604 114 COG1414 IclR, Transcriptional regulator Transcription 99078114 Common - diguanylate cyclase/phosphodiesterase TM1040_3136 178 COG5001 COG5001, Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain Signal transduction mechanisms 99078018 Common - ABC transporter related TM1040_3040 249 COG1126 GlnQ, ABC-type polar amino acid transport system, ATPase component Amino acid transport and metabolism 99078262 Common - NADPH-dependent FMN reductase TM1040_3284 118 COG0655 WrbA, Multimeric flavodoxin WrbA General function prediction only 99078149 Common - K+-dependent Na+/Ca+ exchanger related-protein TM1040_3171 104 COG0530 ECM27, Ca2+/Na+ antiporter Inorganic ion transport and metabolism 99078334 Common - TRAP dicarboxylate transporter- DctM subunit TM1040_3358 134 COG1593 DctQ, TRAP-type C4-dicarboxylate transport system, large permease component Carbohydrate transport and metabolism 99078433 Common - Carbonate dehydratase TM1040_3457 148 COG0288 CynT, Carbonic anhydrase Inorganic ion transport and metabolism 99078074 Common - inner-membrane translocator TM1040_3096 116 COG4603 COG4603, ABC-type uncharacterized transport system, permease component General function prediction only 99078522 Common - type I site-specific deoxyribonuclease, HsdR family TM1040_3549 135 COG0610 COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases Defense mechanisms 99078734 Common - Endonuclease/exonuclease/phosphatase TM1040_3763 21 COG3568 ElsH, Metal-dependent hydrolase General function prediction only 99078536 Common hisD histidinol dehydrogenase TM1040_3563 214 COG0141 HisD, Histidinol dehydrogenase Amino acid transport and metabolism 99078098 Nonpathogen - hypothetical protein TM1040_3120 1 None None None 99078548 Nonpathogen - hypothetical protein TM1040_3575 5 None None None 99078041 Common - Lysine exporter protein (LYSE/YGGA) TM1040_3063 88 COG1280 RhtB, Putative threonine efflux protein Amino acid transport and metabolism 99078199 Nonpathogen - Tripartite ATP-independent periplasmic transporter, DctQ component TM1040_3221 3 COG4665 FcbT2, TRAP-type mannitol/chloroaromatic compound transport system, small permease component Secondary metabolites biosynthesis, transport, and catabolism 99078026 Nonpathogen - hypothetical protein TM1040_3048 2 None None None 99078340 Common - oxidoreductase-like TM1040_3364 113 COG0673 MviM, Predicted dehydrogenases and related proteins General function prediction only 99078445 Common - 5-carboxymethyl-2-hydroxymuconate isomerase TM1040_3469 24 COG3232 HpaF, 5-carboxymethyl-2-hydroxymuconate isomerase Amino acid transport and metabolism 99078640 Common - DNA polymerase III, epsilon subunit TM1040_3669 195 COG2176 PolC, DNA polymerase III, alpha subunit (gram-positive type) DNA replication, recombination, and repair 99078556 Common - hypothetical protein TM1040_3583 19 None None None 99078357 Common - aldehyde dehydrogenase TM1040_3381 222 COG1012 PutA, NAD-dependent aldehyde dehydrogenases Energy production and conversion 99078363 Common - hypothetical protein TM1040_3387 236 COG0160 GabT, 4-aminobutyrate aminotransferase and related aminotransferases Amino acid transport and metabolism 99078406 Common - Nicotinamidase TM1040_3430 127 COG1335 PncA, Amidases related to nicotinamidase Secondary metabolites biosynthesis, transport, and catabolism 99078302 Common - Paraquat-inducible protein A TM1040_3326 54 COG2995 PqiA, Uncharacterized paraquat-inducible protein A Function unknown 99078247 Common - ABC transporter related TM1040_3269 249 COG1129 MglA, ABC-type sugar transport system, ATPase component Carbohydrate transport and metabolism 99078581 Common - PEP-utilising enzyme, mobile region TM1040_3610 112 COG0574 PpsA, Phosphoenolpyruvate synthase/pyruvate phosphate dikinase Carbohydrate transport and metabolism 99078180 Nonpathogen - hypothetical protein TM1040_3202 1 None None None 99078604 Common - molybdopterin biosynthesis MoaE TM1040_3633 118 COG0314 MoaE, Molybdopterin converting factor, large subunit Coenzyme metabolism 99078693 Common - glutamine amidotransferase class-I TM1040_3722 83 COG0518 GuaA, GMP synthase - Glutamine amidotransferase domain Nucleotide transport and metabolism 99078205 Common - transcriptional regulator, LuxR family TM1040_3227 22 COG0596 MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) General function prediction only 99078585 Common - ABC transporter related TM1040_3614 249 COG1121 ZnuC, ABC-type Mn/Zn transport systems, ATPase component Inorganic ion transport and metabolism 99078669 Common - Phosphonate C-P lyase system, PhnL TM1040_3698 249 COG4778 PhnL, ABC-type phosphonate transport system, ATPase component Inorganic ion transport and metabolism 99078509 Nonpathogen - phage integrase TM1040_3533 7 COG4973 XerC, Site-specific recombinase XerC DNA replication, recombination, and repair 99078331 Common - Sel1-like repeat TM1040_3355 91 COG0790 COG0790, FOG: TPR repeat, SEL1 subfamily General function prediction only 99078502 Common - succinate dehydrogenase, hydrophobic membrane anchor protein TM1040_3526 15 COG2142 SdhD, Succinate dehydrogenase, hydrophobic anchor subunit Energy production and conversion 99078660 Common - glycosyl transferase, group 1 TM1040_3689 139 COG0438 RfaG, Glycosyltransferase Cell envelope biogenesis, outer membrane 99078012 Common - binding-protein-dependent transport systems inner membrane component TM1040_3034 170 COG0600 TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component Inorganic ion transport and metabolism 99078077 Common - hypothetical protein TM1040_3099 28 None None None 99078378 Common - putative transcriptional regulator TM1040_3402 134 COG1386 COG1386, Predicted transcriptional regulator containing the HTH domain Transcription 99078082 Common - Crotonyl-CoA reductase TM1040_3104 173 COG0604 Qor, NADPH:quinone reductase and related Zn-dependent oxidoreductases Energy production and conversion / General function prediction only 99078353 Common - sarcosine oxidase, alpha subunit family TM1040_3377 171 COG0404 GcvT, Glycine cleavage system T protein (aminomethyltransferase) Amino acid transport and metabolism 99078637 Common - Na+/solute symporter TM1040_3666 163 COG4147 DhlC, Predicted symporter General function prediction only 99078470 Common - hypothetical protein TM1040_3494 33 COG4717 COG4717, Uncharacterized conserved protein Function unknown 99078193 Common - binding-protein-dependent transport systems inner membrane component TM1040_3215 157 COG1175 UgpA, ABC-type sugar transport systems, permease components Carbohydrate transport and metabolism 99078197 Common - Rieske (2Fe-2S) region TM1040_3219 83 COG4638 HcaE, Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit Inorganic ion transport and metabolism / General function prediction only 99078730 Nonpathogen - lipoprotein, putative TM1040_3759 6 COG2060 KdpA, K+-transporting ATPase, A chain Inorganic ion transport and metabolism 99078534 Common - protein tyrosine phosphatase TM1040_3561 62 COG0394 Wzb, Protein-tyrosine-phosphatase Signal transduction mechanisms 99078135 Common - ABC transporter related TM1040_3157 249 COG3839 MalK, ABC-type sugar transport systems, ATPase components Carbohydrate transport and metabolism 99078388 Common - Na(+)-translocating NADH-quinone reductase subunit F TM1040_3412 163 COG2871 NqrF, Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF Energy production and conversion 99078274 Common - BCCT transporter TM1040_3298 95 COG1292 BetT, Choline-glycine betaine transporter Cell envelope biogenesis, outer membrane 99078106 Common - transcriptional regulator, LacI family TM1040_3128 127 COG1609 PurR, Transcriptional regulators Transcription 99078705 Common - diguanylate phosphodiesterase TM1040_3734 160 COG2200 Rtn, FOG: EAL domain Signal transduction mechanisms 99078423 Common - soluble pyridine nucleotide transhydrogenase TM1040_3447 244 COG1249 Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes Energy production and conversion 99078405 Common - Rhodanese-like TM1040_3429 107 COG1054 COG1054, Predicted sulfurtransferase General function prediction only 99078682 Nonpathogen - hypothetical protein TM1040_3711 3 COG2050 PaaI, Uncharacterized protein, possibly involved in aromatic compounds catabolism Secondary metabolites biosynthesis, transport, and catabolism 99078559 Common - phage integrase TM1040_3588 47 COG4973 XerC, Site-specific recombinase XerC DNA replication, recombination, and repair 99078156 Common - Extracellular ligand-binding receptor TM1040_3178 130 COG0683 LivK, ABC-type branched-chain amino acid transport systems, periplasmic component Amino acid transport and metabolism 99078454 Common - protein of unknown function DUF989 TM1040_3478 37 COG3748 COG3748, Predicted membrane protein Function unknown 99078347 Common - histidine kinase TM1040_3371 222 COG4191 COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system Signal transduction mechanisms 99078639 Common - hypothetical protein TM1040_3668 10 None None None 99078550 Common - FAD linked oxidase-like TM1040_3577 40 COG0277 GlcD, FAD/FMN-containing dehydrogenases Energy production and conversion 99078483 Nonpathogen - inner membrane protein TM1040_3507 9 COG3686 COG3686, Predicted membrane protein Function unknown 99078235 Common - acetyl-CoA carboxylase biotin carboxylase subunit TM1040_3257 222 COG4770 COG4770, Acetyl/propionyl-CoA carboxylase, alpha subunit Lipid metabolism 99078715 Common - Tetratricopeptide TPR_2 TM1040_3744 148 COG5010 TadD, Flp pilus assembly protein TadD, contains TPR repeats Intracellular trafficking and secretion 99078238 Common - transcriptional regulator, LysR family TM1040_3260 191 COG0583 LysR, Transcriptional regulator Transcription 99078624 Common thiE thiamine-phosphate pyrophosphorylase TM1040_3653 199 COG0352 ThiE, Thiamine monophosphate synthase Coenzyme metabolism 99078714 Common - 4-diphosphocytidyl-2C-methyl-D-erythritol kinase TM1040_3743 168 COG1947 IspE, 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase Lipid metabolism 99078324 Common - thiamine pyrophosphate enzyme, central region TM1040_3348 221 COG3962 COG3962, Acetolactate synthase Amino acid transport and metabolism 99078447 Common - Hydroxypyruvate reductase TM1040_3471 86 COG2379 GckA, Putative glycerate kinase Carbohydrate transport and metabolism 99078729 Nonpathogen - branched-chain amino acid transport TM1040_3758 7 COG4392 COG4392, Predicted membrane protein Function unknown 99078494 Nonpathogen - hypothetical protein TM1040_3518 1 None None None 99078709 Common - protein of unknown function DUF6, transmembrane TM1040_3738 24 COG2962 RarD, Predicted permeases General function prediction only 99078689 Common - hypothetical protein TM1040_3718 237 COG0161 BioA, Adenosylmethionine-8-amino-7-oxononanoate aminotransferase Coenzyme metabolism 99078280 Common - alpha amylase, catalytic region TM1040_3304 162 COG0366 AmyA, Glycosidases Carbohydrate transport and metabolism 99078189 Common - CheD, stimulates methylation of MCP proteins TM1040_3211 84 COG1871 CheD, Chemotaxis protein; stimulates methylation of MCP proteins Cell motility and secretion / Signal transduction mechanisms 99078677 Common - Phosphonate uptake transporter TM1040_3706 87 COG3639 COG3639, ABC-type phosphate/phosphonate transport system, permease component Inorganic ion transport and metabolism 99078253 Common - transposase orfB TM1040_3275 13 None None None 99078332 Common - Stress responsive alpha-beta barrel TM1040_3356 6 None None None 99078287 Common - transcriptional regulator, LacI family TM1040_3311 125 COG1609 PurR, Transcriptional regulators Transcription 99078213 Common - Phosphonate uptake transporter TM1040_3235 100 COG3639 COG3639, ABC-type phosphate/phosphonate transport system, permease component Inorganic ion transport and metabolism 99078391 Common - Na(+)-translocating NADH-quinone reductase subunit C TM1040_3415 46 COG2869 NqrC, Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC Energy production and conversion 99078016 Common - extracellular solute-binding protein, family 3 TM1040_3038 183 COG0834 HisJ, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain Amino acid transport and metabolism / Signal transduction mechanisms 99078092 Common - binding-protein-dependent transport systems inner membrane component TM1040_3114 220 COG1173 DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components Amino acid transport and metabolism / Inorganic ion transport and metabolism 99078365 Common - glucose-methanol-choline oxidoreductase TM1040_3389 90 COG2303 BetA, Choline dehydrogenase and related flavoproteins Amino acid transport and metabolism 99078285 Common - Beta-glucosidase TM1040_3309 103 COG2723 BglB, Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase Carbohydrate transport and metabolism 99078126 Common - N-acetylglucosamine-6-phosphate deacetylase TM1040_3148 118 COG1820 NagA, N-acetylglucosamine-6-phosphate deacetylase Carbohydrate transport and metabolism 99078431 Common - Leucyl aminopeptidase TM1040_3455 188 COG0260 PepB, Leucyl aminopeptidase Amino acid transport and metabolism 99078512 Common - type III restriction enzyme, res subunit TM1040_3537 119 COG4096 HsdR, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases Defense mechanisms 99078472 Common - hypothetical protein TM1040_3496 28 COG5271 MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain General function prediction only 99078737 Common - ABC transporter related TM1040_3766 249 COG1126 GlnQ, ABC-type polar amino acid transport system, ATPase component Amino acid transport and metabolism 99078368 Common - 5-carboxymethyl-2-hydroxymuconate delta-isomerase TM1040_3392 182 COG0179 MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) Secondary metabolites biosynthesis, transport, and catabolism 99078014 Common - sulfonate ABC transporter, periplamic sulfonate-binding protein TM1040_3036 35 COG0715 TauA, ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components Inorganic ion transport and metabolism 99078381 Common - ParB-like nuclease TM1040_3405 74 COG1475 Spo0J, Predicted transcriptional regulators Transcription 99078621 Common - Glycine oxidase ThiO TM1040_3650 84 COG0665 DadA, Glycine/D-amino acid oxidases (deaminating) Amino acid transport and metabolism 99078044 Common - acriflavin resistance protein TM1040_3066 176 COG0841 AcrB, Cation/multidrug efflux pump Defense mechanisms 99078269 Nonpathogen - hypothetical protein TM1040_3291 4 None None None 99078616 Common - protein of unknown function DUF395, YeeE/YedE TM1040_3645 62 COG2391 COG2391, Predicted transporter component General function prediction only 99078678 Common - Phosphonate uptake transporter TM1040_3707 103 COG3639 COG3639, ABC-type phosphate/phosphonate transport system, permease component Inorganic ion transport and metabolism 99078314 Common - transcriptional regulator, LysR family TM1040_3338 144 COG0583 LysR, Transcriptional regulator Transcription 99078182 Common - MCP methyltransferase, CheR-type TM1040_3204 151 COG1352 CheR, Methylase of chemotaxis methyl-accepting proteins Cell motility and secretion / Signal transduction mechanisms 99078342 Common - response regulator receiver protein TM1040_3366 16 COG3279 LytT, Response regulator of the LytR/AlgR family Transcription / Signal transduction mechanisms 99078309 Common - Thiosulphate-binding protein TM1040_3333 88 COG4150 CysP, ABC-type sulfate transport system, periplasmic component Inorganic ion transport and metabolism 99078400 Common - glycosyl transferase, family 2 TM1040_3424 130 COG0463 WcaA, Glycosyltransferases involved in cell wall biogenesis Cell envelope biogenesis, outer membrane 99078174 Nonpathogen - hypothetical protein TM1040_3196 1 COG3090 DctM, TRAP-type C4-dicarboxylate transport system, small permease component Carbohydrate transport and metabolism 99078359 Common - BCCT transporter TM1040_3383 95 COG1292 BetT, Choline-glycine betaine transporter Cell envelope biogenesis, outer membrane 99078071 Common - GCN5-related N-acetyltransferase TM1040_3093 147 COG0456 RimI, Acetyltransferases General function prediction only 99078025 Nonpathogen - hypothetical protein TM1040_3047 1 None None None 99078438 Common - Amidohydrolase 3 TM1040_3462 109 COG1574 COG1574, Predicted metal-dependent hydrolase with the TIM-barrel fold General function prediction only 99078460 Common - binding-protein-dependent transport systems inner membrane component TM1040_3484 154 COG1175 UgpA, ABC-type sugar transport systems, permease components Carbohydrate transport and metabolism 99078258 Common - protein of unknown function DUF6, transmembrane TM1040_3280 58 None None None 99078416 Common - glycerol kinase TM1040_3440 179 COG0554 GlpK, Glycerol kinase Energy production and conversion 99078178 Common - FAD dependent oxidoreductase TM1040_3200 124 COG0665 DadA, Glycine/D-amino acid oxidases (deaminating) Amino acid transport and metabolism