Salmonella enterica subsp. enterica serovar Typhi str. CT18 plasmid pHCM1, complete sequence NC_003384 GI_Number Pathogen_associated Gene_name Product Synonym Number_of_Genera COG_Number COG_Description COG_Category 18466438 Pathogen - hypothetical protein HCM1.22c 1 None None None 18466630 Common mucA putative DNA-repair modulator HCM1.252 125 COG1974 LexA, SOS-response transcriptional repressors (RecA-mediated autopeptidases) Transcription / Signal transduction mechanisms 18466548 Pathogen - hypothetical protein HCM1.144 1 None None None 18466506 Common trhU plasmid transfer protein HCM1.100 26 None None None 18466609 Common - putative transposase HCM1.225 4 None None None 18466459 Pathogen - hypothetical protein HCM1.43a 1 None None None 18466482 Pathogen trhA putative pilin precursor HCM1.67 2 None None None 18466432 Pathogen - hypothetical protein HCM1.10c 1 None None None 18466450 Pathogen - hypothetical protein HCM1.34c 2 None None None 18466502 Pathogen htdK hypothetical protein HCM1.96 2 None None None 18466645 Pathogen - hypothetical protein HCM1.270 2 None None None 18466642 Pathogen - hypothetical protein HCM1.266c 2 None None None 18466654 Pathogen - hypothetical protein HCM1.279ac 1 None None None 18466467 Common - hypothetical protein HCM1.52 3 None None None 18466430 Common corA magnesium/nickel/cobalt transporter CorA HCM1.07c 149 COG0598 CorA, Mg2+ and Co2+ transporters Inorganic ion transport and metabolism 18466490 Common trhV putative plasmid transfer protein HCM1.76 3 None None None 18466517 Pathogen - hypothetical protein HCM1.112 1 None None None 18466569 Pathogen - hypothetical protein HCM1.176 1 None None None 18466636 Common - putative thiol:disulfide interchange protein HCM1.258c 61 COG1651 DsbG, Protein-disulfide isomerase Posttranslational modification, protein turnover, chaperones 18466564 Common int putative integrase HCM1.167 219 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 18466453 Pathogen - hypothetical protein HCM1.38c 2 None None None 18466656 Pathogen - hypothetical protein HCM1.280c 2 None None None 18466603 Common bla beta-lactamase HCM1.216 58 COG2367 PenP, Beta-lactamase class A Defense mechanisms 18466592 Pathogen - hypothetical protein HCM1.198c 1 None None None 32765051 Common - hypothetical protein HCM1.272 31 COG3451 VirB4, Type IV secretory pathway, VirB4 components Intracellular trafficking and secretion 18466528 Pathogen - hypothetical protein HCM1.124 2 None None None 18466478 Pathogen - hypothetical protein HCM1.61c 2 None None None 18466586 Pathogen - hypothetical protein HCM1.192 2 None None None 18466537 Common - putative recombinase HCM1.134c 4 None None None 18466519 Common - hypothetical protein HCM1.116 8 COG4547 CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) Coenzyme metabolism 18466551 Pathogen - hypothetical protein HCM1.149 1 None None None 18466658 Pathogen - hypothetical protein HCM1.282 1 None None None 18466449 Pathogen - hypothetical protein HCM1.33c 2 None None None 18466476 Common - putative DNA modification methylase HCM1.59 99 COG0338 Dam, Site-specific DNA methylase DNA replication, recombination, and repair 18466555 Common merC putative mercury transport protein HCM1.157 9 None None None 18466615 Common merP putative mercuric transport protein periplasmic binding protein HCM1.233c 69 COG2608 CopZ, Copper chaperone Inorganic ion transport and metabolism 18466535 Pathogen - hypothetical protein HCM1.132 2 None None None 18466627 Common - transposase HCM1.249c 19 None None None 32765046 Common - hypothetical protein HCM1.32c 28 COG0175 CysH, 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes Amino acid transport and metabolism / Coenzyme metabolism 18466504 Common trhF putative pilin maturation protein HCM1.98 20 COG4959 TraF, Type IV secretory pathway, protease TraF Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion 18466486 Pathogen - hypothetical protein HCM1.72 2 None None None 18466508 Common - hypothetical protein HCM1.102 4 COG4469 CoiA, Competence protein General function prediction only 18466594 Common - putative transposase HCM1.201 29 COG3415 COG3415, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466573 Pathogen - hypothetical protein HCM1.179c 1 None None None 32765048 Pathogen - hypothetical protein HCM1.142c 2 None None None 18466640 Common - putative pilus assembly protein HCM1.263c 24 None None None 18466469 Common repA replication initiation protein HCM1.54 6 None None None 18466605 Common - putative replication protein HCM1.221 10 None None None 18466488 Pathogen - hypothetical protein HCM1.74 2 None None None 18466543 Common insB putative IS1 transposase HCM1.139 20 COG1662 InsB, Transposase and inactivated derivatives, IS1 family DNA replication, recombination, and repair 18466566 Common tnpA transposase HCM1.169 55 COG4644 COG4644, Transposase and inactivated derivatives, TnpA family DNA replication, recombination, and repair 18466589 Common - hypothetical protein HCM1.195 5 None None None 18466514 Pathogen - hypothetical protein HCM1.109 2 None None None 18466530 Pathogen - hypothetical protein HCM1.126 2 None None None 18466475 Common - putative DNA-binding protein HCM1.58c 7 None None None 18466553 Common merT putative mercuric transport protein HCM1.152 20 None None None 18466526 Pathogen - hypothetical protein HCM1.122 2 None None None 18466447 Pathogen - hypothetical protein HCM1.31c 1 None None None 18466618 Common - putative transposase HCM1.236 76 COG3547 COG3547, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466617 Common merR putative mercuric resistance operon regulatory protein HCM1.235 133 COG0789 SoxR, Predicted transcriptional regulators Transcription 18466625 Common - hypothetical protein HCM1.246c 37 COG2329 COG2329, Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides General function prediction only 32765049 Common - hypothetical protein HCM1.177 5 None None None 18466549 Pathogen - hypothetical protein HCM1.145 2 None None None 18466513 Pathogen - hypothetical protein HCM1.108 2 None None None 18466635 Pathogen - puatative periplasmic protein HCM1.257c 2 None None None 18466544 Common - hypothetical protein HCM1.141 6 None None None 18466622 Common tetR tetracycline repressor protein HCM1.243 36 COG1309 AcrR, Transcriptional regulator Transcription 18466454 Common - hypothetical protein HCM1.39c 13 COG3549 HigB, Plasmid maintenance system killer protein General function prediction only 18466612 Common merD putative mercuric resistance operon coregulator HCM1.230c 10 COG0789 SoxR, Predicted transcriptional regulators Transcription 18466510 Common - hypothetical protein HCM1.104c 2 None None None 18466473 Pathogen - hypothetical protein HCM1.56ac 1 None None None 18466441 Pathogen - hypothetical protein HCM1.25c 1 None None None 18466649 Common - hypothetical protein HCM1.275 5 None None None 18466429 Common insA putative IS1 transposase HCM1.05c 14 COG3677 COG3677, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466556 Common merA putative mercuric reductase HCM1.158 243 COG1249 Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes Energy production and conversion 18466444 Pathogen - hypothetical protein HCM1.28c 2 None None None 18466524 Pathogen - hypothetical protein HCM1.120 2 None None None 18466499 Pathogen - hypothetical protein HCM1.93 2 None None None 18466495 Pathogen - putative lipoprotein HCM1.89c 2 None None None 18466463 Pathogen - hypothetical protein HCM1.48c 1 None None None 18466583 Pathogen - hypothetical protein HCM1.189 2 None None None 18466652 Pathogen - hypothetical protein HCM1.278c 2 None None None 18466568 Common - putative DNA-binding protein HCM1.175 3 None None None 18466632 Common - putative outer membrane protein HCM1.254c 65 COG1651 DsbG, Protein-disulfide isomerase Posttranslational modification, protein turnover, chaperones 18466639 Common - hypothetical protein HCM1.262 6 COG4694 COG4694, Uncharacterized protein conserved in bacteria Function unknown 18466457 Pathogen - hypothetical protein HCM1.42 2 None None None 18466578 Pathogen - hypothetical protein HCM1.184c 2 None None None 18466487 Common trhB putative plasmid transfer protein HCM1.73 25 None None None 18466608 Common strB streptomycin phosphotransferase HCM1.224 23 COG3570 StrB, Streptomycin 6-kinase Defense mechanisms 18466597 Common insA putative IS1 transposase HCM1.205c 14 COG3677 COG3677, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466599 Common - hypothetical protein HCM1.207c 29 COG0456 RimI, Acetyltransferases General function prediction only 18466452 Common - hypothetical protein HCM1.36c 3 None None None 18466620 Common insA putative IS1 transposase HCM1.239c 14 COG3677 COG3677, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466534 Common - putative DNA replication terminus site-binding protein HCM1.131 4 None None None 18466542 Common insA putative IS1 transposase HCM1.138 14 COG3677 COG3677, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466619 Common insB putative IS1 transposase HCM1.238c 21 COG1662 InsB, Transposase and inactivated derivatives, IS1 family DNA replication, recombination, and repair 18466637 Common - hypothetical protein HCM1.259 23 None None None 18466539 Common insA putative IS1 transposase HCM1.136 14 COG3677 COG3677, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466646 Common - hypothetical protein HCM1.271 22 COG3481 COG3481, Predicted HD-superfamily hydrolase General function prediction only 18466576 Pathogen - hypothetical protein HCM1.182 2 None None None 18466460 Pathogen - hypothetical protein HCM1.44 1 None None None 18466493 Common - putative plasmid partition protein HCM1.87 11 None None None 18466437 Pathogen - hypothetical protein HCM1.21c 3 None None None 18466522 Pathogen - hypothetical protein HCM1.118 2 None None None 18466497 Pathogen - hypothetical protein HCM1.91c 2 COG0388 COG0388, Predicted amidohydrolase General function prediction only 18466660 Pathogen - hypothetical protein HCM1.284c 1 None None None 18466442 Pathogen - hypothetical protein HCM1.26c 3 None None None 18466427 Pathogen - hypothetical protein HCM1.03c 2 None None None 18466588 Common - transposase HCM1.194 19 None None None 18466613 Common merA putative mercuric reductase HCM1.231c 243 COG1249 Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes Energy production and conversion 18466590 Pathogen - hypothetical protein HCM1.196 2 None None None 18466465 Common - putative periplasmic protein HCM1.50 4 None None None 18466581 Common - DNA cytosine methylase HCM1.187c 116 COG0270 Dcm, Site-specific DNA methylase DNA replication, recombination, and repair 18466650 Common - putative peptidase HCM1.276 183 COG0616 SppA, Periplasmic serine proteases (ClpP class) Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion 18466529 Pathogen - hypothetical protein HCM1.125 2 None None None 18466484 Common trhE putative pilus assembly protein HCM1.70 7 None None None 18466435 Pathogen - hypothetical protein HCM1.17c 1 None None None 18466558 Common - hypothetical protein HCM1.160 11 None None None 18466515 Pathogen - hypothetical protein HCM1.110 2 None None None 18466443 Common - hypothetical protein HCM1.27c 10 None None None 18466518 Common - hypothetical protein HCM1.114 5 None None None 18466565 Common tnpR resolvase HCM1.168 121 COG1961 PinR, Site-specific recombinases, DNA invertase Pin homologs DNA replication, recombination, and repair 18466657 Pathogen - hypothetical protein HCM1.281c 2 None None None 18466580 Common - hypothetical protein HCM1.186c 2 None None None 18466466 Common - hypothetical protein HCM1.51 4 None None None 18466559 Common - hypothetical protein HCM1.161 9 None None None 18466604 Common - putative transposase HCM1.219 48 COG3316 COG3316, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466470 Pathogen - putative periplasmic protein HCM1.55c 1 None None None 18466574 Common - hypothetical protein HCM1.180c 2 None None None 18466643 Pathogen - hypothetical protein HCM1.268c 2 None None None 18466532 Pathogen - hypothetical protein HCM1.128 2 None None None 32765045 Pathogen - hypothetical protein HCM1.15c.1N 1 None None None 32765050 Common - putative transposase HCM1.211c.2N 48 COG3316 COG3316, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466662 Pathogen - hypothetical protein HCM1.288 1 None None None 18466479 Pathogen - hypothetical protein HCM1.62c 1 None None None 18466629 Pathogen - hypothetical protein HCM1.251c 1 None None None 18466552 Common merR putative mercuric resistance operon regulatory protein HCM1.151c 135 COG0789 SoxR, Predicted transcriptional regulators Transcription 18466527 Pathogen - hypothetical protein HCM1.123 2 None None None 18466545 Pathogen - hypothetical protein HCM1.141ac 1 None None None 18466616 Common merT putative mercuric transport protein HCM1.234c 22 None None None 18466540 Common insB putative IS1 transposase HCM1.136a 21 COG1662 InsB, Transposase and inactivated derivatives, IS1 family DNA replication, recombination, and repair 18466631 Common mucB putative DNA-repair modulator HCM1.253 177 COG0389 DinP, Nucleotidyltransferase/DNA polymerase involved in DNA repair DNA replication, recombination, and repair 18466538 Common - putative regulatory protein HCM1.135 12 None None None 18466500 Pathogen htdA transfer repressor HCM1.94 2 None None None 18466458 Pathogen - hypothetical protein HCM1.43 2 None None None 18466501 Pathogen htdF putative periplasmic protein HCM1.95 2 None None None 18466505 Common trhW plasmid transfer protein HCM1.99 21 None None None 18466626 Common - putative transcriptional regulator HCM1.248 20 COG0583 LysR, Transcriptional regulator Transcription 18466433 Pathogen - hypothetical protein HCM1.13c 1 None None None 18466579 Common - hypothetical protein HCM1.185c 15 None None None 18466439 Pathogen - hypothetical protein HCM1.23c 2 None None None 18466644 Common - hypothetical protein HCM1.269 3 None None None 18466606 Common - dihydropteroate synthase HCM1.222 218 COG0294 FolP, Dihydropteroate synthase and related enzymes Coenzyme metabolism 18466489 Common - putative plasmid transfer protein HCM1.75 4 COG1651 DsbG, Protein-disulfide isomerase Posttranslational modification, protein turnover, chaperones 18466593 Pathogen - hypothetical protein HCM1.199c 1 None None None 32765047 Common trhI putative DNA helicase HCM1.107 224 COG0210 UvrD, Superfamily I DNA and RNA helicases DNA replication, recombination, and repair 18466641 Common - putative pilus assembly protein HCM1.264c 20 None None None 18466503 Common - putative periplasmic protein HCM1.97 3 None None None 18466610 Common - hypothetical protein HCM1.227c 156 COG2200 Rtn, FOG: EAL domain Signal transduction mechanisms 18466655 Common - hypothetical protein HCM1.279bc 4 None None None 18466468 Pathogen - hypothetical protein HCM1.53 2 None None None 18466567 Pathogen - putative periplasmic protein HCM1.174 1 None None None 18466431 Common - hypothetical protein HCM1.08 4 COG3698 COG3698, Predicted periplasmic protein Function unknown 18466648 Pathogen - hypothetical protein HCM1.273 2 None None None 18466577 Common - hypothetical protein HCM1.183 157 COG1196 Smc, Chromosome segregation ATPases Cell division and chromosome partitioning 18466477 Pathogen - hypothetical protein HCM1.60c 2 None None None 18466554 Common merP putative mercuric transport protein periplasmic binding protein HCM1.153 101 COG2608 CopZ, Copper chaperone Inorganic ion transport and metabolism 18466480 Pathogen - hypothetical protein HCM1.63c 4 None None None 18466572 Common - putative DNA-binding protein HCM1.178ac 33 COG2916 Hns, DNA-binding protein H-NS General function prediction only 18466446 Pathogen - hypothetical protein HCM1.30c 1 None None None 32765052 Pathogen - hypothetical protein HCM1.288N 1 None None None 18466483 Pathogen trhL putative plasmid transfer protein HCM1.69 2 None None None 18466595 Pathogen - hypothetical protein HCM1.203 2 None None None 18466536 Pathogen - hypothetical protein HCM1.133 1 None None None 18466624 Pathogen - hypothetical protein HCM1.245c 4 COG4747 COG4747, ACT domain-containing protein General function prediction only 18466456 Pathogen - hypothetical protein HCM1.41 1 None None None 18466525 Pathogen - hypothetical protein HCM1.121 2 None None None 18466511 Pathogen - putative lipoprotein HCM1.106c 2 None None None 18466600 Common - putative transposase HCM1.209c 76 COG3547 COG3547, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466451 Pathogen - hypothetical protein HCM1.35c 1 None None None 18466633 Pathogen - putative lipoprotein HCM1.255 2 None None None 18466507 Common trhN mating pair stabilization protein HCM1.101 18 None None None 18466498 Common - putative plasmid stability/partition protein HCM1.92 13 None None None 18466557 Common merD putative mercuric resistance operon coregulator HCM1.159 11 COG0789 SoxR, Predicted transcriptional regulators Transcription 18466440 Pathogen - hypothetical protein HCM1.24c 1 None None None 18466523 Pathogen - hypothetical protein HCM1.119 2 None None None 18466562 Common dhfR putative dihydrofolate reductase HCM1.165c 143 COG0262 FolA, Dihydrofolate reductase Coenzyme metabolism 18466587 Common - hypothetical protein HCM1.193c 2 None None None 18466462 Pathogen - hypothetical protein HCM1.46 1 None None None 18466653 Pathogen - hypothetical protein HCM1.279c 2 None None None 18466474 Common - hypothetical protein HCM1.57c 8 COG4123 COG4123, Predicted O-methyltransferase General function prediction only 18466584 Common - hypothetical protein HCM1.190 9 COG1502 Cls, Phosphatidylserine/phosphatidylglycerophosphate/cardioli pin synthases and related enzymes Lipid metabolism 18466550 Pathogen - hypothetical protein HCM1.146 1 None None None 18466638 Common - hypothetical protein HCM1.261 5 None None None 18466560 Common - putative transposase HCM1.162c 47 COG3316 COG3316, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466596 Common insB putative IS1 transposase HCM1.204c 21 COG1662 InsB, Transposase and inactivated derivatives, IS1 family DNA replication, recombination, and repair 18466575 Common - hypothetical protein HCM1.181 3 None None None 18466533 Pathogen - hypothetical protein HCM1.130 1 None None None 18466509 Common - putative DNA helicase HCM1.103 230 COG0210 UvrD, Superfamily I DNA and RNA helicases DNA replication, recombination, and repair 18466520 Pathogen - hypothetical protein HCM1.116a 2 None None None 18466481 Common repA2 replication initiation protein HCM1.64 6 None None None 18466541 Common rep putative replication initiation protein HCM1.137 26 COG5527 COG5527, Protein involved in initiation of plasmid replication DNA replication, recombination, and repair 18466494 Pathogen - putative periplasmic protein HCM1.88c 2 None None None 18466611 Common - hypothetical protein HCM1.229c 10 None None None 18466428 Common insB putative IS1 transposase HCM1.04c 19 COG1662 InsB, Transposase and inactivated derivatives, IS1 family DNA replication, recombination, and repair 32456053 Pathogen - hypothetical protein HCM1.01c 2 None None None 18466472 Common - putative periplasmic protein HCM1.56c 5 None None None 18466436 Common - hypothetical protein HCM1.20c 6 None None None 18466623 Common - putative transcriptional regulator HCM1.244c 44 COG0640 ArsR, Predicted transcriptional regulators Transcription 18466492 Common - putative plasmid partition protein HCM1.86 30 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 18466426 Pathogen - hypothetical protein HCM1.02c 1 None None None 18466661 Pathogen - putative DNA-binding protein HCM1.286c 4 None None None 18466607 Common strA streptomycin phosphotransferase HCM1.223 18 COG3231 Aph, Aminoglycoside phosphotransferase Translation, ribosomal structure and biogenesis 18466614 Common merC putative mercury transport protein HCM1.232c 9 None None None 18466516 Common - hypothetical protein HCM1.111 63 COG0714 COG0714, MoxR-like ATPases General function prediction only 18466521 Common - hypothetical protein HCM1.117 24 None None None 18466547 Pathogen - hypothetical protein HCM1.143 1 None None None 18466445 Common - hypothetical protein HCM1.29c 14 None None None 18466496 Pathogen - putative periplasmic protein HCM1.90c 2 None None None 18466602 Common - putative transposase HCM1.213c 48 COG3316 COG3316, Transposase and inactivated derivatives DNA replication, recombination, and repair 18466491 Common trhC plasmid transfer protein HCM1.77 30 COG3451 VirB4, Type IV secretory pathway, VirB4 components Intracellular trafficking and secretion 18466464 Common - putative periplasmic protein HCM1.49c 5 None None None 18466485 Common - putative periplasmic protein HCM1.71 5 None None None 18466651 Common - putative periplasmic protein HCM1.277 26 None None None 18466582 Common - putative nuclease HCM1.188 87 COG1525 COG1525, Micrococcal nuclease (thermonuclease) homologs DNA replication, recombination, and repair 18466471 Pathogen - hypothetical protein HCM1.55ac 1 None None None 18466598 Common cat chloramphenicol acetyltransferase HCM1.206 20 COG4845 COG4845, Chloramphenicol O-acetyltransferase Defense mechanisms 18466455 Pathogen - hypothetical protein HCM1.40c 2 COG0484 DnaJ, DnaJ-class molecular chaperone with C-terminal Zn finger domain Posttranslational modification, protein turnover, chaperones 18466591 Pathogen - hypothetical protein HCM1.197c 1 None None None 18466663 Common - small toxic polypeptide HCM1.290c 3 None None None 18466634 Pathogen - hypothetical protein HCM1.256c 2 None None None 18466531 Pathogen - hypothetical protein HCM1.127 2 None None None 18466621 Common tetA tetracycline resistance protein HCM1.241c 185 COG2814 AraJ, Arabinose efflux permease Carbohydrate transport and metabolism 18466461 Pathogen - hypothetical protein HCM1.45 2 None None None 18466628 Pathogen - putative periplasmic protein HCM1.250c 1 None None None