Sinorhizobium medicae WSM419 plasmid pSMED03, complete sequence NC_009622 GI_Number Pathogen_associated Gene_name Product Synonym Number_of_Genera COG_Number COG_Description COG_Category 150378342 Nonpathogen - hypothetical protein Smed_6428 1 None None None 150378356 Common - hypothetical protein Smed_6451 77 COG3293 COG3293, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378407 Common - response regulator receiver protein Smed_6520 22 COG0775 Pfs, Nucleoside phosphorylase Nucleotide transport and metabolism 150378400 Common - transposase IS3/IS911 family protein Smed_6511 26 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378410 Common - glycoside hydrolase family 24 Smed_6523 31 COG3772 COG3772, Phage-related lysozyme (muraminidase) General function prediction only 150378310 Common - Catalase Smed_6390 46 COG3546 COG3546, Mn-containing catalase Inorganic ion transport and metabolism 150378347 Common - polar amino acid ABC transporter, inner membrane subunit Smed_6439 184 COG0765 HisM, ABC-type amino acid transport system, permease component Amino acid transport and metabolism 150378397 Common - transposase IS3/IS911 family protein Smed_6507 53 None None None 150378287 Common - putative cytochrome c oxidase subunit III protein Smed_6356 19 COG1845 CyoC, Heme/copper-type cytochrome/quinol oxidase, subunit 3 Energy production and conversion 150378388 Nonpathogen - hypothetical protein Smed_6495 1 None None None 150378382 Common - transposase IS3/IS911 family protein Smed_6488 26 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378370 Common - amino acid adenylation domain Smed_6473 221 COG1020 EntF, Non-ribosomal peptide synthetase modules and related proteins Secondary metabolites biosynthesis, transport, and catabolism 150378275 Nonpathogen - hypothetical protein Smed_6343 1 None None None 150378295 Common - transposase IS3/IS911 family protein Smed_6366 25 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378412 Common - glycoside hydrolase family 25 Smed_6525 9 COG3757 Acm, Lyzozyme M1 (1,4-beta-N-acetylmuramidase) Cell envelope biogenesis, outer membrane 150378317 Common - P-type conjugative transfer protein VirB9 Smed_6399 53 COG3504 VirB9, Type IV secretory pathway, VirB9 components Intracellular trafficking and secretion 150378324 Common - type IV secretory pathway VirB3 family protein Smed_6406 13 COG3702 VirB3, Type IV secretory pathway, VirB3 components Intracellular trafficking and secretion 150378332 Common - hypothetical protein Smed_6414 2 None None None 150378306 Common - hypothetical protein Smed_6382 11 COG5271 MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain General function prediction only 150378368 Nonpathogen - hypothetical protein Smed_6471 8 COG1921 SelA, Selenocysteine synthase [seryl-tRNASer selenium transferase] Amino acid transport and metabolism 150378344 Common - hypothetical protein Smed_6430 5 None None None 150378312 Nonpathogen - hypothetical protein Smed_6393 1 None None None 150378283 Common - extracellular solute-binding protein family 3 Smed_6352 20 COG0834 HisJ, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain Amino acid transport and metabolism / Signal transduction mechanisms 150378319 Common - TrbL/VirB6 plasmid conjugal transfer protein Smed_6401 27 COG3704 VirB6, Type IV secretory pathway, VirB6 components Intracellular trafficking and secretion 150378386 Common - replication protein C Smed_6492 18 None None None 150378277 Common - transposase mutator type Smed_6345 64 COG3328 COG3328, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378285 Common - Cytochrome c oxidase subunit II Smed_6354 159 COG1622 CyoA, Heme/copper-type cytochrome/quinol oxidases, subunit 2 Energy production and conversion 150378405 Common - IstB domain protein ATP-binding protein Smed_6518 99 COG1484 DnaC, DNA replication protein DNA replication, recombination, and repair 150378304 Common - hypothetical protein Smed_6380 91 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 150378381 Common - IS66 Orf2 family protein Smed_6487 52 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378268 Nonpathogen - hypothetical protein Smed_6334 1 None None None 150378350 Common - hypothetical protein Smed_6445 2 None None None 150378349 Nonpathogen - hypothetical protein Smed_6442 1 None None None 150378395 Nonpathogen - hypothetical protein Smed_6505 1 None None None 150378330 Common - hypothetical protein Smed_6412 2 None None None 150378339 Nonpathogen - hypothetical protein Smed_6421 3 None None None 150378322 Common - Lytic transglycosylase catalytic Smed_6404 174 COG0741 MltE, Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) Cell envelope biogenesis, outer membrane 150378376 Common - hypothetical protein Smed_6480 2 COG5489 COG5489, Uncharacterized conserved protein Function unknown 150378293 Common - transposase IS66 Smed_6364 61 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378390 Common - prevent-host-death family protein Smed_6498 11 None None None 150378308 Common - protein of unknown function DUF1486 Smed_6384 28 COG5485 COG5485, Predicted ester cyclase General function prediction only 150378315 Common - P-type DNA transfer ATPase VirB11 Smed_6397 224 COG4962 CpaF, Flp pilus assembly protein, ATPase CpaF Intracellular trafficking and secretion 150378267 Nonpathogen - hypothetical protein Smed_6333 1 None None None 150378375 Common - Transposase and inactivated derivatives-like protein Smed_6478 75 COG3293 COG3293, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378365 Common - 4'-phosphopantetheinyl transferase Smed_6467 53 COG2091 Sfp, Phosphopantetheinyl transferase Coenzyme metabolism 150378361 Common - transposase IS3/IS911 family protein Smed_6460 13 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378402 Common - transposase IS66 Smed_6513 65 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378366 Common - hypothetical protein Smed_6468 52 COG0778 NfnB, Nitroreductase Energy production and conversion 150378335 Common - hypothetical protein Smed_6417 6 COG1647 COG1647, Esterase/lipase General function prediction only 150378321 Common - conjugal transfer protein Smed_6403 4 None None None 150378352 Common - calcium/proton exchanger Smed_6447 47 COG0387 ChaA, Ca2+/H+ antiporter Inorganic ion transport and metabolism 150378291 Nonpathogen - hypothetical protein Smed_6362 1 None None None 150378298 Common - transcriptional regulator, MucR family Smed_6371 34 COG4957 COG4957, Predicted transcriptional regulator Transcription 150378313 Common - protein of unknown function DUF1214 Smed_6394 38 COG5361 COG5361, Uncharacterized conserved protein Function unknown 150378337 Nonpathogen - hypothetical protein Smed_6419 1 None None None 150378282 Common - Pyrrolo-quinoline quinone Smed_6351 63 COG4993 Gcd, Glucose dehydrogenase Carbohydrate transport and metabolism 150378271 Common - IS66 Orf2 family protein Smed_6339 51 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378392 Common - restriction endonuclease Smed_6502 4 COG1715 Mrr, Restriction endonuclease Defense mechanisms 150378265 Nonpathogen - hypothetical protein Smed_6331 1 None None None 150378396 Common - Integrase catalytic region Smed_6506 110 COG2801 Tra5, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378358 Common - feruloyl esterase Smed_6453 49 COG3415 COG3415, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378340 Common - Integrase catalytic region Smed_6422 26 None None None 150378363 Common - phage integrase family protein Smed_6462 178 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 150378328 Common - succinoglycan biosynthesis protein ExoI-like protein Smed_6410 6 COG1525 COG1525, Micrococcal nuclease (thermonuclease) homologs DNA replication, recombination, and repair 150378326 Common - Lytic transglycosylase catalytic Smed_6408 138 COG0741 MltE, Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) Cell envelope biogenesis, outer membrane 150378372 Common - transcriptional regulator, LysR family Smed_6475 174 COG0583 LysR, Transcriptional regulator Transcription 150378301 Nonpathogen - hypothetical protein Smed_6376 1 None None None 150378280 Common - MgtC/SapB transporter Smed_6348 4 COG1285 SapB, Uncharacterized membrane protein Function unknown 150378289 Common - hypothetical protein Smed_6358 18 COG3336 COG3336, Predicted membrane protein Function unknown 150378409 Common - hypothetical protein Smed_6522 5 None None None 150378273 Common - putative PAS/PAC sensor protein Smed_6341 154 COG1352 CheR, Methylase of chemotaxis methyl-accepting proteins Cell motility and secretion / Signal transduction mechanisms 150378399 Nonpathogen - hypothetical protein Smed_6509 1 None None None 150378385 Common - parB-like partition protein Smed_6491 131 COG1475 Spo0J, Predicted transcriptional regulators Transcription 150378379 Common - hypothetical protein Smed_6485 5 None None None 150378346 Common - polar amino acid ABC transporter, inner membrane subunit Smed_6438 172 COG4597 BatB, ABC-type amino acid transport system, permease component Amino acid transport and metabolism 150378274 Common - CheB methylesterase Smed_6342 147 COG2201 CheB, Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain Cell motility and secretion / Signal transduction mechanisms 150378380 Common - transposase IS66 Smed_6486 65 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378286 Common - Cytochrome c oxidase subunit I type Smed_6355 174 COG0843 CyoB, Heme/copper-type cytochrome/quinol oxidases, subunit 1 Energy production and conversion 150378338 Common - Integrase catalytic region Smed_6420 65 COG2826 Tra8, Transposase and inactivated derivatives, IS30 family DNA replication, recombination, and repair 150378389 Nonpathogen - hypothetical protein Smed_6497 1 None None None 150378383 Common - autoinducer synthesis protein Smed_6489 22 COG3916 LasI, N-acyl-L-homoserine lactone synthetase Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism 150378325 Common - VIRB2 type IV secretion fmaily protein Smed_6407 18 COG3838 VirB2, Type IV secretory pathway, VirB2 components (pilins) Intracellular trafficking and secretion 150378394 Common - hypothetical protein Smed_6504 16 None None None 150378296 Common - polysaccharide biosynthesis protein Smed_6369 13 COG2244 RfbX, Membrane protein involved in the export of O-antigen and teichoic acid General function prediction only 150378378 Common - addiction module toxin, RelE/StbE family Smed_6483 23 COG3668 ParE, Plasmid stabilization system protein General function prediction only 150378355 Common - transcriptional regulator, CopG family Smed_6450 11 COG3905 COG3905, Predicted transcriptional regulator Transcription 150378371 Nonpathogen - hypothetical protein Smed_6474 1 None None None 150378333 Nonpathogen - hypothetical protein Smed_6415 1 None None None 150378343 Common - Monophenol monooxygenase Smed_6429 19 None None None 150378357 Common - transposase IS116/IS110/IS902 family protein Smed_6452 80 COG3547 COG3547, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378401 Common - IS66 Orf2 family protein Smed_6512 52 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378411 Nonpathogen - hypothetical protein Smed_6524 1 None None None 150378369 Common - amino acid adenylation domain Smed_6472 218 COG1020 EntF, Non-ribosomal peptide synthetase modules and related proteins Secondary metabolites biosynthesis, transport, and catabolism 150378276 Common - putative reverse transcriptase Smed_6344 72 COG3344 COG3344, Retron-type reverse transcriptase DNA replication, recombination, and repair 150378336 Common - putative transmembrane protein Smed_6418 3 None None None 150378303 Common - hypothetical protein Smed_6379 3 None None None 150378404 Common - hypothetical protein Smed_6515 42 COG2801 Tra5, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378387 Nonpathogen - hypothetical protein Smed_6494 4 None None None 150378348 Common - ABC transporter related Smed_6440 249 COG1126 GlnQ, ABC-type polar amino acid transport system, ATPase component Amino acid transport and metabolism 150378331 Common - hypothetical protein Smed_6413 5 None None None 150378269 Common - homocysteine S-methyltransferase Smed_6335 44 COG2040 MHT1, Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) Amino acid transport and metabolism 150378323 Common - type IV secretion/conjugal transfer ATPase, VirB4 family Smed_6405 61 COG3451 VirB4, Type IV secretory pathway, VirB4 components Intracellular trafficking and secretion 150378294 Common - IS66 Orf2 family protein Smed_6365 47 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378377 Common - putative transcriptional regulators, CopG/Arc/MetJ family Smed_6482 20 COG3609 COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain Transcription 150378406 Common - Integrase catalytic region Smed_6519 83 COG4584 COG4584, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378345 Common - multicopper oxidase type 2 Smed_6431 73 COG2132 SufI, Putative multicopper oxidases Secondary metabolites biosynthesis, transport, and catabolism 150378311 Common - hypothetical protein Smed_6392 81 COG0657 Aes, Esterase/lipase Lipid metabolism 150378278 Common - protein of unknown function DUF1452 Smed_6346 26 COG5478 COG5478, Predicted small integral membrane protein Function unknown 150378318 Common - VirB8 family protein Smed_6400 41 COG3736 VirB8, Type IV secretory pathway, component VirB8 Intracellular trafficking and secretion 150378367 Common - hypothetical protein Smed_6469 6 None None None 150378305 Common - mobilisation protein Smed_6381 6 None None None 150378284 Common - cytochrome c class I Smed_6353 19 COG2010 CccA, Cytochrome c, mono- and diheme variants Energy production and conversion 150378351 Nonpathogen - hypothetical protein Smed_6446 1 None None None 150378329 Common - nuclease (SNase domain protein) Smed_6411 10 COG1525 COG1525, Micrococcal nuclease (thermonuclease) homologs DNA replication, recombination, and repair 150378292 Common - yecA family protein Smed_6363 11 COG3318 COG3318, Predicted metal-binding protein related to the C-terminal domain of SecA General function prediction only 150378299 Common - hypothetical protein Smed_6374 3 None None None 150378384 Common - Cobyrinic acid ac-diamide synthase Smed_6490 227 COG1192 Soj, ATPases involved in chromosome partitioning Cell division and chromosome partitioning 150378281 Common - hypothetical protein Smed_6350 37 COG3652 COG3652, Predicted outer membrane protein Function unknown 150378266 Common - glycoside hydrolase family 25 Smed_6332 10 COG3757 Acm, Lyzozyme M1 (1,4-beta-N-acetylmuramidase) Cell envelope biogenesis, outer membrane 150378393 Nonpathogen - TIR protein Smed_6503 9 None None None 150378270 Common - transposase IS3/IS911 family protein Smed_6338 18 COG2963 COG2963, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378279 Nonpathogen - hypothetical protein Smed_6347 1 None None None 150378374 Common - feruloyl esterase Smed_6477 51 COG3415 COG3415, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378398 Common - hypothetical protein Smed_6508 12 None None None 150378314 Common - TRAG family protein Smed_6396 80 COG3505 VirD4, Type IV secretory pathway, VirD4 components Intracellular trafficking and secretion 150378302 Common - transcriptional regulator, XRE family Smed_6378 4 COG1396 HipB, Predicted transcriptional regulators Transcription 150378309 Common - beta-lactamase domain protein Smed_6386 17 COG0491 GloB, Zn-dependent hydrolases, including glyoxylases General function prediction only 150378360 Common - putative transcriptional regulator, AsnC family Smed_6457 139 COG1522 Lrp, Transcriptional regulators Transcription 150378334 Nonpathogen - hypothetical protein Smed_6416 1 None None None 150378403 Common - hypothetical protein Smed_6514 5 None None None 150378290 Nonpathogen - hypothetical protein Smed_6361 1 None None None 150378327 Common - hypothetical protein Smed_6409 3 None None None 150378272 Common - transposase IS66 Smed_6340 60 COG3436 COG3436, Transposase and inactivated derivatives DNA replication, recombination, and repair 150378320 Nonpathogen - hypothetical protein Smed_6402 1 None None None 150378297 Common - K potassium transporter Smed_6370 88 COG3158 Kup, K+ transporter Inorganic ion transport and metabolism 150378300 Common - transcriptional regulator, XRE family Smed_6375 4 COG1396 HipB, Predicted transcriptional regulators Transcription 150378364 Common - IstB domain protein ATP-binding protein Smed_6464 96 COG1484 DnaC, DNA replication protein DNA replication, recombination, and repair 150378373 Common - cytochrome P-450 Smed_6476 9 COG2124 CypX, Cytochrome P450 Secondary metabolites biosynthesis, transport, and catabolism 150378288 Nonpathogen - hypothetical protein Smed_6357 1 None None None 150378408 Common - response regulator receiver protein Smed_6521 4 COG2204 AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Signal transduction mechanisms 150378353 Nonpathogen - hypothetical protein Smed_6448 2 None None None 150378391 Common - PilT protein domain protein Smed_6500 14 COG4113 COG4113, Predicted nucleic acid-binding protein, contains PIN domain General function prediction only 150378307 Nonpathogen - hypothetical protein Smed_6383 1 None None None 150378316 Common - conjugation TrbI family protein Smed_6398 59 COG2948 VirB10, Type IV secretory pathway, VirB10 components Intracellular trafficking and secretion 150378264 Nonpathogen - hypothetical protein Smed_6330 2 None None None 150378354 Common - plasmid stabilization system Smed_6449 12 COG3668 ParE, Plasmid stabilization system protein General function prediction only 150378359 Common - 1-aminocyclopropane-1-carboxylate deaminase Smed_6456 97 COG2515 Acd, 1-aminocyclopropane-1-carboxylate deaminase Amino acid transport and metabolism 150378362 Common - phage integrase family protein Smed_6461 211 COG4974 XerD, Site-specific recombinase XerD DNA replication, recombination, and repair 150378341 Nonpathogen - hypothetical protein Smed_6427 1 COG0270 Dcm, Site-specific DNA methylase DNA replication, recombination, and repair