-- dump date 20120504_153216 -- class Genbank::CDS -- table cds -- table main -- field 1 id -- field 2 GI -- field 3 GeneID -- field 4 chrom_position -- field 5 chromosome -- field 6 codon_start -- field 7 contig -- field 8 description -- field 9 end_pos -- field 10 gene -- field 11 gene_id -- field 12 name -- field 13 organism -- field 14 product -- field 15 protein_id -- field 16 start_pos -- field 17 strand -- field 18 taxid -- field 19 type -- header -- id GI GeneID chrom_position chromosome codon_start contig description end_pos gene gene_id name organism product protein_id start_pos strand taxid type YP_424001.1 83319700 3828310 1..1353 1 NC_007633.1 binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.; chromosomal replication initiation protein 1353 dnaA 3828310 dnaA Mycoplasma capricolum subsp. capricolum ATCC 27343 chromosomal replication initiation protein YP_424001.1 1 D 340047 CDS YP_424002.1 83319869 3829107 1518..2645 1 NC_007633.1 identified by similarity to SP:P05649; match to protein family HMM PF00712; match to protein family HMM PF02767; match to protein family HMM PF02768; match to protein family HMM TIGR00663; DNA polymerase III subunit beta 2645 dnaN 3829107 dnaN Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA polymerase III subunit beta YP_424002.1 1518 D 340047 CDS YP_424003.1 83319973 3828721 2682..3224 1 NC_007633.1 identified by match to protein family HMM PF01751; match to protein family HMM TIGR00334; primase-like protein 3224 3828721 MCAP_0003 Mycoplasma capricolum subsp. capricolum ATCC 27343 primase-like protein YP_424003.1 2682 D 340047 CDS YP_424004.1 83319298 3828432 3214..4014 1 NC_007633.1 catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin; dimethyladenosine transferase 4014 ksgA 3828432 ksgA Mycoplasma capricolum subsp. capricolum ATCC 27343 dimethyladenosine transferase YP_424004.1 3214 D 340047 CDS YP_424005.1 83319509 3828561 4069..5163 1 NC_007633.1 MCAP_0005 has 3 membrane spanning regions; hypothetical protein 5163 3828561 MCAP_0005 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424005.1 4069 D 340047 CDS YP_424006.1 83319309 3828443 5328..5771 1 NC_007633.1 identified by match to protein family HMM PF00383; cytidine/deoxycytidylate deaminase zinc-binding domain-containing protein 5771 3828443 MCAP_0007 Mycoplasma capricolum subsp. capricolum ATCC 27343 cytidine/deoxycytidylate deaminase zinc-binding domain-containing protein YP_424006.1 5328 D 340047 CDS YP_424007.1 83320030 3828328 5851..7860 1 NC_007633.1 identified by similarity to SP:P09122; match to protein family HMM PF00004; match to protein family HMM TIGR02397; DNA polymerase III subunits gamma/tau 7860 dnaX 3828328 dnaX Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA polymerase III subunits gamma/tau YP_424007.1 5851 D 340047 CDS YP_424008.1 83319376 3829093 7862..8452 1 NC_007633.1 identified by similarity to SP:P24277; match to protein family HMM PF01751; DNA repair protein RecM 8452 recM 3829093 recM Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA repair protein RecM YP_424008.1 7862 D 340047 CDS YP_424009.1 83319417 3828798 8455..9096 1 NC_007633.1 identified by similarity to SP:P37537; match to protein family HMM PF02223; match to protein family HMM TIGR00041; thymidylate kinase 9096 tmk 3828798 tmk Mycoplasma capricolum subsp. capricolum ATCC 27343 thymidylate kinase YP_424009.1 8455 D 340047 CDS YP_424010.1 83319611 3829033 9074..9817 1 NC_007633.1 identified by similarity to SP:P37540; DNA polymerase III, delta prime subunit 9817 3829033 MCAP_0011 Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA polymerase III, delta prime subunit YP_424010.1 9074 D 340047 CDS YP_424011.1 83319521 3828574 9877..10539 1 NC_007633.1 N-6 adenine-specific DNA methylases 10539 3828574 MCAP_0012 Mycoplasma capricolum subsp. capricolum ATCC 27343 N-6 adenine-specific DNA methylases YP_424011.1 9877 D 340047 CDS YP_424012.1 83319854 3828948 10590..11411 1 NC_007633.1 This protein has some homology to RpiR family transcriptional regulators.; hypothetical protein 11411 3828948 MCAP_0013 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424012.1 10590 D 340047 CDS YP_424013.1 83319710 3828851 11416..12621 1 NC_007633.1 This family of proteins belongs to the PP-loop superfamily (MEDLINE:7731953) for which no biological role has been determined; identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432; hypothetical protein 12621 3828851 MCAP_0014 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424013.1 11416 D 340047 CDS YP_424014.1 83320027 3828325 complement(12618..13454) 1 NC_007633.1 hypothetical protein 13454 3828325 MCAP_0015 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424014.1 12618 R 340047 CDS YP_424015.1 83319940 3828957 13687..15639 1 NC_007633.1 identified by match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480; match to protein family HMM TIGR01241; ATP-dependent metalloprotease FtsH 15639 ftsH 3828957 ftsH Mycoplasma capricolum subsp. capricolum ATCC 27343 ATP-dependent metalloprotease FtsH YP_424015.1 13687 D 340047 CDS YP_424016.1 83319828 3828921 complement(16712..22105) 1 NC_007633.1 MCAP_0018 has 8 membrane spanning regions; MCAP_0018 has characteristics of an ABC transporter permease; however it is not near any ATPase; identified by match to protein family HMM PF02687; hypothetical protein 22105 3828921 MCAP_0018 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424016.1 16712 R 340047 CDS YP_424017.1 83320018 3828911 22249..25407 1 NC_007633.1 MCAP_0019 has 1 membrane spanning region, N-terminal; hypothetical protein 25407 3828911 MCAP_0019 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424017.1 22249 D 340047 CDS YP_424018.1 83319749 3828607 25583..26449 1 NC_007633.1 identified by match to protein family HMM PF01430; chaperonin HSP33 26449 hslO 3828607 hslO Mycoplasma capricolum subsp. capricolum ATCC 27343 chaperonin HSP33 YP_424018.1 25583 D 340047 CDS YP_424019.1 83319807 3828364 26497..27534 1 NC_007633.1 This gene is not part of any apparent ABC trasporter cassette. The start site confidence is low; identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 27534 3828364 MCAP_0021 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein YP_424019.1 26497 D 340047 CDS YP_424020.1 83319505 3828557 complement(27586..28185) 1 NC_007633.1 identified by similarity to SP:P41407; match to protein family HMM PF02525; azoreductase 28185 3828557 MCAP_0022 Mycoplasma capricolum subsp. capricolum ATCC 27343 azoreductase YP_424020.1 27586 R 340047 CDS YP_424021.1 83319695 3828305 28374..28580 1 NC_007633.1 identified by similarity to SP:P15277; match to protein family HMM PF00313; cold shock protein 28580 3828305 MCAP_0023 Mycoplasma capricolum subsp. capricolum ATCC 27343 cold shock protein YP_424021.1 28374 D 340047 CDS YP_424022.1 83319327 3828461 28783..29196 1 NC_007633.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 29196 rpsF 3828461 rpsF Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S6 YP_424022.1 28783 D 340047 CDS YP_424023.1 83319323 3828457 29212..29652 1 NC_007633.1 identified by similarity to SP:P37455; match to protein family HMM PF00436; match to protein family HMM PF01336; match to protein family HMM TIGR00621; single-strand DNA-binding protein 29652 ssb 3828457 ssb Mycoplasma capricolum subsp. capricolum ATCC 27343 single-strand DNA-binding protein YP_424023.1 29212 D 340047 CDS YP_424024.1 83319872 3829110 29671..29898 1 NC_007633.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit; 30S ribosomal protein S18 29898 rpsR 3829110 rpsR Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S18 YP_424024.1 29671 D 340047 CDS YP_424025.1 83319435 3828816 30594..31982 1 NC_007633.1 Similar genes in other organisms are annotated as ATP-dependent DNA helicase recG; however this gene has insufficient similarity to any characterized protein to make that annotation. The ortholog in M, mycoides SC is disrupted; identified by match to protein family HMM PF04326; hypothetical protein 31982 3828816 MCAP_0027 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424025.1 30594 D 340047 CDS YP_424026.1 83319352 3828486 32257..33810 1 NC_007633.1 The Bacillus stearothermophilus MtlA protein was characterized and is 38% identical to this gene; identified by similarity to SP:P50852; match to protein family HMM PF02302; PTS system mannitol-specific transporter subunit IIBC 33810 3828486 MCAP_0028 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system mannitol-specific transporter subunit IIBC YP_424026.1 32257 D 340047 CDS YP_424027.1 83320002 3828789 33810..34568 1 NC_007633.1 catalyzes the conversion of sorbitol 6-phosphate into fructose 6-phosphate; sorbitol-6-phosphate dehydrogenase 34568 3828789 MCAP_0029 Mycoplasma capricolum subsp. capricolum ATCC 27343 sorbitol-6-phosphate dehydrogenase YP_424027.1 33810 D 340047 CDS YP_424028.1 83319928 3828683 34568..34813 1 NC_007633.1 identified by similarity to SP:Q45420; PTS system mannitol-specific transporter subunit IIA 34813 3828683 MCAP_0030 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system mannitol-specific transporter subunit IIA YP_424028.1 34568 D 340047 CDS YP_424029.1 83319840 3828934 35027..35824 1 NC_007633.1 This is a weak hit to the rpiR transcriptional regulator family. The gene is adjacent to mannitol specific PTS system genes and genes for manitol metabolism; identified by similarity to SP:P37767; match to protein family HMM PF01380; RpiR family phosphosugar-binding transcriptional regulator 35824 3828934 MCAP_0031 Mycoplasma capricolum subsp. capricolum ATCC 27343 RpiR family phosphosugar-binding transcriptional regulator YP_424029.1 35027 D 340047 CDS YP_424030.1 83319746 3828604 35825..36829 1 NC_007633.1 identified by similarity to SP:P55800; match to protein family HMM PF01232; match to protein family HMM PF08125; mannitol-1-phosphate 5-dehydrogenase 36829 3828604 MCAP_0032 Mycoplasma capricolum subsp. capricolum ATCC 27343 mannitol-1-phosphate 5-dehydrogenase YP_424030.1 35825 D 340047 CDS YP_424031.1 83319296 3828430 complement(36866..38458) 1 NC_007633.1 lipoprotein LppA 38458 3828430 MCAP_0033 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein LppA YP_424031.1 36866 R 340047 CDS YP_424032.1 83319596 3829018 complement(38483..40042) 1 NC_007633.1 LppA family lipoprotein 40042 3829018 MCAP_0034 Mycoplasma capricolum subsp. capricolum ATCC 27343 LppA family lipoprotein YP_424032.1 38483 R 340047 CDS YP_424033.1 83320001 3828788 40240..41769 1 NC_007633.1 methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content; methionyl-tRNA synthetase 41769 metG 3828788 metG Mycoplasma capricolum subsp. capricolum ATCC 27343 methionyl-tRNA synthetase YP_424033.1 40240 D 340047 CDS YP_424034.1 83319838 3828932 43614..45221 1 NC_007633.1 This is part of a two permease, one ATPase ABC transporter cassette. Both permeases have significant HMM socres for PF02653: Branched-chain amino acid transport system / permease component. The best BLAST BER hits are two genes annotated as sugar transporters. Thus we cannot predict a substrate; identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 45221 3828932 MCAP_0037 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein YP_424034.1 43614 D 340047 CDS YP_424035.1 83319467 3828692 45211..47769 1 NC_007633.1 This is part of a two permease, one ATPase ABC transporter cassette. Both permeases have significant HMM socres for PF02653: Branched-chain amino acid transport system / permease. component. The best BLAST BER hits are two genes annotated as sugar transporters. Thus we cannot predict a substrate. This protein has a long COOH domain with no TMHs, and may serve as both permaease and substrante binding domain; identified by match to protein family HMM PF02653; ABC transporter permease 47769 3828692 MCAP_0038 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter permease YP_424035.1 45211 D 340047 CDS YP_424036.1 83319356 3828490 47772..48749 1 NC_007633.1 This is part of a two permease, one ATPase ABC transporter cassette. Both permeases have significant HMM socres for PF02653: Branched-chain amino acid transport system / permease component. The best BLAST BER hits are two genes annotated as sugar transporters. Thus we cannot predict a substrate; identified by match to protein family HMM PF02653; ABC transporter permease 48749 3828490 MCAP_0039 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter permease YP_424036.1 47772 D 340047 CDS YP_424037.1 83319625 3829049 complement(48817..51204) 1 NC_007633.1 identified by similarity to SP:P05653; match to protein family HMM PF00521; match to protein family HMM PF03989; match to protein family HMM TIGR01063; DNA gyrase subunit A 51204 gyrA 3829049 gyrA Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA gyrase subunit A YP_424037.1 48817 R 340047 CDS YP_424038.1 83319520 3828573 complement(51336..53240) 1 NC_007633.1 identified by similarity to SP:P05652; match to protein family HMM PF00204; match to protein family HMM PF00986; match to protein family HMM PF01751; match to protein family HMM PF02518; match to protein family HMM TIGR01059; DNA gyrase subunit B 53240 gyrB 3828573 gyrB Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA gyrase subunit B YP_424038.1 51336 R 340047 CDS YP_424039.1 83319266 3828743 complement(53640..55241) 1 NC_007633.1 lipoprotein 55241 3828743 MCAP_0042 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424039.1 53640 R 340047 CDS YP_424040.1 83319304 3828438 complement(55409..56182) 1 NC_007633.1 MCAP_0043 has 6 membrane spanning regions; The most N-terminal, signal peptide sequence is autoannotated as having a lipoptrotein motif, but it is atypical of many LPs. The orthologous gene of M. mycoides subsp mycoides SC is annotated as a membrane protein.; hypothetical protein 56182 3828438 MCAP_0043 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424040.1 55409 R 340047 CDS YP_424041.1 83319582 3829004 complement(56166..56888) 1 NC_007633.1 MCAP_0044 has 6 membrane spanning regions; hypothetical protein 56888 3829004 MCAP_0044 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424041.1 56166 R 340047 CDS YP_424042.1 83319511 3828563 complement(56998..59832) 1 NC_007633.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; in some organisms, there are paralogous proteins that have been found to be nonessential but do function in secretion of a subset of exported proteins; preprotein translocase subunit SecA 59832 secA 3828563 secA Mycoplasma capricolum subsp. capricolum ATCC 27343 preprotein translocase subunit SecA YP_424042.1 56998 R 340047 CDS YP_424043.1 83319813 3828370 59912..60487 1 NC_007633.1 identified by match to protein family HMM PF01205; hypothetical protein 60487 3828370 MCAP_0046 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424043.1 59912 D 340047 CDS YP_424044.1 83319696 3828306 60583..61497 1 NC_007633.1 identified by match to protein family HMM PF01367; match to protein family HMM PF02739; 5'-3' exonuclease 61497 3828306 MCAP_0047 Mycoplasma capricolum subsp. capricolum ATCC 27343 5'-3' exonuclease YP_424044.1 60583 D 340047 CDS YP_424045.1 83319983 3828731 61692..62708 1 NC_007633.1 Part of an apparent operon containing another adenine specific methlyase and a IIS restriction endonuclease; identified by similarity to SP:P14871; match to protein family HMM PF02086; adenine-specific DNA methylase 62708 3828731 MCAP_0048 Mycoplasma capricolum subsp. capricolum ATCC 27343 adenine-specific DNA methylase YP_424045.1 61692 D 340047 CDS YP_424046.1 83319264 3828741 62638..63615 1 NC_007633.1 Part of an apparent operon containing another adenine specific methlyase and a IIS restriction endonuclease; identified by similarity to SP:P00475; match to protein family HMM PF02086; DNA adenine methylase 63615 dam 3828741 dam Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA adenine methylase YP_424046.1 62638 D 340047 CDS YP_424047.1 83319365 3829082 63593..65170 1 NC_007633.1 There is high identity to a Helicobacter pylori IIS restriction endonuclease recently characterized. This is in an apparent operon with two likely adenine specific DNA methylases; identified by similarity to GB:BAD00171.1; restriction endonuclease 65170 3829082 MCAP_0050 Mycoplasma capricolum subsp. capricolum ATCC 27343 restriction endonuclease YP_424047.1 63593 D 340047 CDS YP_424048.1 83319665 3828700 66644..67114 1 NC_007633.1 hypothetical protein 67114 3828700 MCAP_0052 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424048.1 66644 D 340047 CDS YP_424049.1 83320006 3828793 67839..68114 1 NC_007633.1 hypothetical protein 68114 3828793 MCAP_0053 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424049.1 67839 D 340047 CDS YP_424050.1 83320013 3828906 68104..68670 1 NC_007633.1 identified by match to protein family HMM PF01121; match to protein family HMM TIGR00152; dephospho-CoA kinase 68670 3828906 MCAP_0054 Mycoplasma capricolum subsp. capricolum ATCC 27343 dephospho-CoA kinase YP_424050.1 68104 D 340047 CDS YP_424051.1 83319276 3828753 complement(68672..69481) 1 NC_007633.1 identified by similarity to SP:Q06803; match to protein family HMM PF01479; match to protein family HMM PF01728; hemolysin A 69481 3828753 MCAP_0055 Mycoplasma capricolum subsp. capricolum ATCC 27343 hemolysin A YP_424051.1 68672 R 340047 CDS YP_424052.1 83319277 3828754 complement(69481..69696) 1 NC_007633.1 hypothetical protein 69696 3828754 MCAP_0056 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424052.1 69481 R 340047 CDS YP_424053.1 83319530 3828583 complement(69689..71095) 1 NC_007633.1 identified by similarity to SP:P04994; match to protein family HMM PF01336; match to protein family HMM PF02601; match to protein family HMM TIGR00237; exodeoxyribonuclease VII large subunit 71095 xseA 3828583 xseA Mycoplasma capricolum subsp. capricolum ATCC 27343 exodeoxyribonuclease VII large subunit YP_424053.1 69689 R 340047 CDS YP_424054.1 83319650 3828497 complement(71097..71495) 1 NC_007633.1 identified by match to protein family HMM PF01029; match to protein family HMM TIGR01951; N utilization substance protein B 71495 3828497 MCAP_0058 Mycoplasma capricolum subsp. capricolum ATCC 27343 N utilization substance protein B YP_424054.1 71097 R 340047 CDS YP_424055.1 83319506 3828558 complement(71507..72577) 1 NC_007633.1 MCAP_0059 is a continuous ORF with high DNA similarity to a region in M. mycoides SC annotated as: [MSC_104 - (intergenic region) - MSC_103]; lipoprotein 72577 3828558 MCAP_0059 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424055.1 71507 R 340047 CDS YP_424056.1 83319329 3828463 complement(72604..73473) 1 NC_007633.1 Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues; endonuclease IV 73473 3828463 MCAP_0060 Mycoplasma capricolum subsp. capricolum ATCC 27343 endonuclease IV YP_424056.1 72604 R 340047 CDS YP_424057.1 83320034 3828332 complement(73466..74218) 1 NC_007633.1 Similar non-mycoplasma proteins have 65 amino acids at the NH2 end not present in this protein; identified by similarity to SP:P54575; match to protein family HMM PF01687; riboflavin kinase / FAD synthetase family protein 74218 3828332 MCAP_0061 Mycoplasma capricolum subsp. capricolum ATCC 27343 riboflavin kinase / FAD synthetase family protein YP_424057.1 73466 R 340047 CDS YP_424058.1 83319717 3828858 74775..76349 1 NC_007633.1 In the absence of evidence for cell wall or lipopolysccharide synthesis in mycoplasmas, or capsule synthesis in M. capricolum subsp capricolum Kid, the role category biosynthesis/degradation of surface polysaccharides and lipopolysaccharides is assigned to foster comparison with genes having possible capsule-associated functions in other organisms of the Mycoplasma mycoides phylogenetic cluster; identified by match to protein family HMM PF00535; glycosyl transferase family protein 76349 3828858 MCAP_0063 Mycoplasma capricolum subsp. capricolum ATCC 27343 glycosyl transferase family protein YP_424058.1 74775 D 340047 CDS YP_424059.1 83319439 3829137 76352..77230 1 NC_007633.1 identified by match to protein family HMM PF00483; UTP-glucose-1-phosphate uridylyltransferase 77230 3829137 MCAP_0064 Mycoplasma capricolum subsp. capricolum ATCC 27343 UTP-glucose-1-phosphate uridylyltransferase YP_424059.1 76352 D 340047 CDS YP_424060.1 83319927 3828682 77432..77860 1 NC_007633.1 binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 77860 rplK 3828682 rplK Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L11 YP_424060.1 77432 D 340047 CDS YP_424061.1 83319637 3828286 77860..78540 1 NC_007633.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA; 50S ribosomal protein L1 78540 rplA 3828286 rplA Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L1 YP_424061.1 77860 D 340047 CDS YP_424062.1 83319357 3828491 78769..79266 1 NC_007633.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 79266 rplJ 3828491 rplJ Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L10 YP_424062.1 78769 D 340047 CDS YP_424063.1 83319793 3828408 79342..79710 1 NC_007633.1 present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors; 50S ribosomal protein L7/L12 79710 rplL 3828408 rplL Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L7/L12 YP_424063.1 79342 D 340047 CDS YP_424064.1 83319531 3828584 79881..81053 1 NC_007633.1 hypothetical protein 81053 3828584 MCAP_0069 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424064.1 79881 D 340047 CDS YP_424065.1 83319487 3828896 81043..84906 1 NC_007633.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme; DNA-directed RNA polymerase subunit beta 84906 rpoB 3828896 rpoB Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-directed RNA polymerase subunit beta YP_424065.1 81043 D 340047 CDS YP_424066.1 83319423 3828804 84918..88685 1 NC_007633.1 identified by similarity to SP:P37871; match to protein family HMM PF00623; match to protein family HMM PF04983; match to protein family HMM PF04997; match to protein family HMM PF04998; match to protein family HMM PF05000; match to protein family HMM TIGR02386; DNA-directed RNA polymerase subunit beta' 88685 rpoC 3828804 rpoC Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-directed RNA polymerase subunit beta' YP_424066.1 84918 D 340047 CDS YP_424067.1 83319632 3828281 88775..90964 1 NC_007633.1 lipoprotein 90964 3828281 MCAP_0072 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424067.1 88775 D 340047 CDS YP_424068.1 83319742 3828395 complement(90971..91276) 1 NC_007633.1 identified by match to protein family HMM PF00581; hypothetical protein 91276 3828395 MCAP_0073 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424068.1 90971 R 340047 CDS YP_424069.1 83319834 3828928 91301..91798 1 NC_007633.1 identified by similarity to OMNI:NTL02MM0853; match to protein family HMM PF02502; match to protein family HMM TIGR00689; ribose 5-phosphate isomerase B 91798 3828928 MCAP_0074 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribose 5-phosphate isomerase B YP_424069.1 91301 D 340047 CDS YP_424070.1 83319931 3828829 91782..93023 1 NC_007633.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 93023 glyA 3828829 glyA Mycoplasma capricolum subsp. capricolum ATCC 27343 serine hydroxymethyltransferase YP_424070.1 91782 D 340047 CDS YP_424071.1 83319896 3828866 93125..93748 1 NC_007633.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase 93748 upp 3828866 upp Mycoplasma capricolum subsp. capricolum ATCC 27343 uracil phosphoribosyltransferase YP_424071.1 93125 D 340047 CDS YP_424072.1 83319999 3828786 93889..94287 1 NC_007633.1 MCAP_0464 has 4 membrane spanning regions; hypothetical protein 94287 3828786 MCAP_0077 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424072.1 93889 D 340047 CDS YP_424073.1 83319402 3828763 94287..95147 1 NC_007633.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; F0F1 ATP synthase subunit A 95147 atpB 3828763 atpB Mycoplasma capricolum subsp. capricolum ATCC 27343 F0F1 ATP synthase subunit A YP_424073.1 94287 D 340047 CDS YP_424074.1 83319513 3828566 95186..95491 1 NC_007633.1 identified by similarity to SP:O08310; match to protein family HMM PF00137; match to protein family HMM TIGR01260; ATP synthase F0 subunit C 95491 atpE 3828566 atpE Mycoplasma capricolum subsp. capricolum ATCC 27343 ATP synthase F0 subunit C YP_424074.1 95186 D 340047 CDS YP_424075.1 83319804 3828361 95519..96064 1 NC_007633.1 identified by similarity to SP:P37814; match to protein family HMM PF00430; match to protein family HMM TIGR01144; ATP synthase F0 subunit B 96064 atpF 3828361 atpF Mycoplasma capricolum subsp. capricolum ATCC 27343 ATP synthase F0 subunit B YP_424075.1 95519 D 340047 CDS YP_424076.1 83319489 3828898 96066..96611 1 NC_007633.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex; F0F1 ATP synthase subunit delta 96611 atpH 3828898 atpH Mycoplasma capricolum subsp. capricolum ATCC 27343 F0F1 ATP synthase subunit delta YP_424076.1 96066 D 340047 CDS YP_424077.1 83319474 3828697 96623..98200 1 NC_007633.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; F0F1 ATP synthase subunit alpha 98200 atpA1 3828697 atpA1 Mycoplasma capricolum subsp. capricolum ATCC 27343 F0F1 ATP synthase subunit alpha YP_424077.1 96623 D 340047 CDS YP_424078.1 83319574 3828996 98202..99044 1 NC_007633.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; F0F1 ATP synthase subunit gamma 99044 atpG 3828996 atpG Mycoplasma capricolum subsp. capricolum ATCC 27343 F0F1 ATP synthase subunit gamma YP_424078.1 98202 D 340047 CDS YP_424079.1 83319730 3828383 99053..100483 1 NC_007633.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta 100483 atpD1 3828383 atpD1 Mycoplasma capricolum subsp. capricolum ATCC 27343 F0F1 ATP synthase subunit beta YP_424079.1 99053 D 340047 CDS YP_424080.1 83320026 3828324 100483..100782 1 NC_007633.1 identified by similarity to PIR:S29042; match to protein family HMM PF02823; ATP synthase F1 subunit epsilon 100782 atpC 3828324 atpC Mycoplasma capricolum subsp. capricolum ATCC 27343 ATP synthase F1 subunit epsilon YP_424080.1 100483 D 340047 CDS YP_424081.1 83319904 3828874 complement(100840..102051) 1 NC_007633.1 MCAP_0086 has 5 membrane spanning regions; hypothetical protein 102051 3828874 MCAP_0086 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424081.1 100840 R 340047 CDS YP_424082.1 83319358 3828492 102390..105218 1 NC_007633.1 identified by similarity to SP:P39168; match to protein family HMM PF00122; match to protein family HMM PF00690; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01524; magnesium-translocating P-type ATPase 105218 mgtA 3828492 mgtA Mycoplasma capricolum subsp. capricolum ATCC 27343 magnesium-translocating P-type ATPase YP_424082.1 102390 D 340047 CDS YP_424083.1 83319328 3828462 complement(105679..105813) 1 NC_007633.1 MCAP_0088 has 1 membrane spanning region, N-terminal.; hypothetical protein 105813 3828462 MCAP_0088 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424083.1 105679 R 340047 CDS YP_424084.1 83319656 3828503 105998..107209 1 NC_007633.1 identified by similarity to SP:P16962; match to protein family HMM PF02274; arginine deiminase 107209 arcA 3828503 arcA Mycoplasma capricolum subsp. capricolum ATCC 27343 arginine deiminase YP_424084.1 105998 D 340047 CDS YP_424085.1 83319698 3828308 107227..108222 1 NC_007633.1 identified by match to protein family HMM PF00185; match to protein family HMM PF02729; match to protein family HMM TIGR00658; ornithine carbamoyltransferase, catabolic 108222 arcB 3828308 arcB Mycoplasma capricolum subsp. capricolum ATCC 27343 ornithine carbamoyltransferase, catabolic YP_424085.1 107227 D 340047 CDS YP_424086.1 83319593 3829015 108285..109754 1 NC_007633.1 Part of a likely operon including arginine deaminiase, and ornithine carbamoyltransferase. The match to the PFAM for C4-dicarboxylate anaerobic carrier and the presence of 13 membrane spanning regions support the annotation; identified by match to protein family HMM PF03606; transporter 109754 3829015 MCAP_0091 Mycoplasma capricolum subsp. capricolum ATCC 27343 transporter YP_424086.1 108285 D 340047 CDS YP_424087.1 83319262 3828739 complement(111276..112403) 1 NC_007633.1 identified by match to protein family HMM PF00144; beta-lactamase 112403 3828739 MCAP_0093 Mycoplasma capricolum subsp. capricolum ATCC 27343 beta-lactamase YP_424087.1 111276 R 340047 CDS YP_424088.1 83319967 3829130 complement(112508..114721) 1 NC_007633.1 identified by similarity to SP:P20166; match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; PTS system glucose-specific transporter subunit IIABC 114721 ptsG 3829130 ptsG Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system glucose-specific transporter subunit IIABC YP_424088.1 112508 R 340047 CDS YP_424089.1 83319512 3828564 complement(115141..115629) 1 NC_007633.1 MCAP_0095 has 1 membrane spanning region, N-terminal.; hypothetical protein 115629 3828564 MCAP_0095 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424089.1 115141 R 340047 CDS YP_424090.1 83319425 3828806 complement(115629..116075) 1 NC_007633.1 binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation; SsrA-binding protein 116075 smpB 3828806 smpB Mycoplasma capricolum subsp. capricolum ATCC 27343 SsrA-binding protein YP_424090.1 115629 R 340047 CDS YP_424091.1 83319777 3828841 complement(116085..118199) 1 NC_007633.1 identified by match to protein family HMM PF00575; match to protein family HMM PF00773; match to protein family HMM TIGR00358; 3'-5' exoribonuclease 118199 3828841 MCAP_0097 Mycoplasma capricolum subsp. capricolum ATCC 27343 3'-5' exoribonuclease YP_424091.1 116085 R 340047 CDS YP_424092.1 83319671 3829062 complement(118235..118591) 1 NC_007633.1 identified by match to protein family HMM TIGR00810; preprotein translocase subunit SecG 118591 secG 3829062 secG Mycoplasma capricolum subsp. capricolum ATCC 27343 preprotein translocase subunit SecG YP_424092.1 118235 R 340047 CDS YP_424093.1 83319806 3828363 118773..119792 1 NC_007633.1 B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE; ribonucleotide-diphosphate reductase subunit beta 119792 nrdF 3828363 nrdF Mycoplasma capricolum subsp. capricolum ATCC 27343 ribonucleotide-diphosphate reductase subunit beta YP_424093.1 118773 D 340047 CDS YP_424094.1 83319863 3829101 119802..120275 1 NC_007633.1 in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF; ribonucleotide reductase stimulatory protein 120275 nrdI 3829101 nrdI Mycoplasma capricolum subsp. capricolum ATCC 27343 ribonucleotide reductase stimulatory protein YP_424094.1 119802 D 340047 CDS YP_424095.1 83319418 3828799 120262..122424 1 NC_007633.1 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 122424 nrdE 3828799 nrdE Mycoplasma capricolum subsp. capricolum ATCC 27343 ribonucleotide-diphosphate reductase subunit alpha YP_424095.1 120262 D 340047 CDS YP_424096.1 83320003 3828790 122709..123743 1 NC_007633.1 identified by similarity to SP:P14193; match to protein family HMM PF00156; match to protein family HMM TIGR01251; phosphoribosylpyrophosphate synthase 123743 prs 3828790 prs Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphoribosylpyrophosphate synthase YP_424096.1 122709 D 340047 CDS YP_424097.1 83320028 3828326 124048..124608 1 NC_007633.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase 124608 pth 3828326 pth Mycoplasma capricolum subsp. capricolum ATCC 27343 peptidyl-tRNA hydrolase YP_424097.1 124048 D 340047 CDS YP_424098.1 83319898 3828868 124739..125182 1 NC_007633.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 125182 rplI 3828868 rplI Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L9 YP_424098.1 124739 D 340047 CDS YP_424099.1 83319407 3828768 125184..126512 1 NC_007633.1 identified by match to protein family HMM PF00772; match to protein family HMM PF03796; match to protein family HMM TIGR00665; replicative DNA helicase 126512 dnaC 3828768 dnaC Mycoplasma capricolum subsp. capricolum ATCC 27343 replicative DNA helicase YP_424099.1 125184 D 340047 CDS YP_424100.1 83319523 3828576 126601..127863 1 NC_007633.1 hypothetical protein 127863 3828576 MCAP_0108 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424100.1 126601 D 340047 CDS YP_424101.1 83319622 3829046 127990..128916 1 NC_007633.1 MCAP_0109 has 8 membrane spanning regions; hypothetical protein 128916 3829046 MCAP_0109 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424101.1 127990 D 340047 CDS YP_424102.1 83319731 3828384 128925..130250 1 NC_007633.1 catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA; cysteinyl-tRNA synthetase 130250 cysS 3828384 cysS Mycoplasma capricolum subsp. capricolum ATCC 27343 cysteinyl-tRNA synthetase YP_424102.1 128925 D 340047 CDS YP_424103.1 83319473 3828348 130252..130986 1 NC_007633.1 identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186; RNA methyltransferase 130986 3828348 MCAP_0111 Mycoplasma capricolum subsp. capricolum ATCC 27343 RNA methyltransferase YP_424103.1 130252 D 340047 CDS YP_424104.1 83319914 3828669 131047..131208 1 NC_007633.1 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group have the CXXC motif; 50S ribosomal protein L33 131208 rpmG 3828669 rpmG Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L33 YP_424104.1 131047 D 340047 CDS YP_424105.1 83320011 3828904 131208..131522 1 NC_007633.1 identified by match to protein family HMM TIGR00964; Preprotein translocase subunit SecE 131522 secE 3828904 secE Mycoplasma capricolum subsp. capricolum ATCC 27343 Preprotein translocase subunit SecE YP_424105.1 131208 D 340047 CDS YP_424106.1 83319581 3829003 131539..132183 1 NC_007633.1 identified by similarity to SP:P36264; match to protein family HMM PF00467; match to protein family HMM PF02357; transcription antitermination protein NusG 132183 nusG 3829003 nusG Mycoplasma capricolum subsp. capricolum ATCC 27343 transcription antitermination protein NusG YP_424106.1 131539 D 340047 CDS YP_424107.1 83319484 3828893 132631..138528 1 NC_007633.1 MCAP_0115 has a lipocalin Prosite signiture. The lipocalins transport small hydrophobic molecules such as steroids, bilins,retinoids, and lipid. They share limited regions of sequence homology and a common tertiary structure architecture. The protein also has a neutral zinc metallopeptidases, zinc-binding region Prosite signature. MCAP_0115 has 1 membrane spanning region, N-terminal.; hypothetical protein 138528 3828893 MCAP_0115 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424107.1 132631 D 340047 CDS YP_424108.1 83319343 3828477 138537..141491 1 NC_007633.1 MCAP_0116 is part of a 5 gene ABC transporter cassette. It has one transmembrane region; identified by match to protein family HMM PF00496; oligopeptide ABC transporter oligopeptide-binding protein 141491 3828477 MCAP_0116 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter oligopeptide-binding protein YP_424108.1 138537 D 340047 CDS YP_424109.1 83319676 3829067 141491..142564 1 NC_007633.1 This is part of a 5 gene ABC transporter cassette. It is a good match for B. subtilis oligopeptide transporter permease OppB. Like other genes in this operon it is larger at the NH2 end than orthologs; identified by similarity to SP:P24138; match to protein family HMM PF00528; oligopeptide ABC transporter permease 142564 3829067 MCAP_0117 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter permease YP_424109.1 141491 D 340047 CDS YP_424110.1 83319997 3828784 142566..143576 1 NC_007633.1 This is part of a 5 gene ABC transporter cassette; identified by similarity to OMNI:SMT1571; match to protein family HMM PF00528; oligopeptide ABC transporter permease 143576 3828784 MCAP_0118 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter permease YP_424110.1 142566 D 340047 CDS YP_424111.1 83319554 3828976 143655..145028 1 NC_007633.1 This is part of a 5 gene ABC transporter cassette.. This gene is a good match (41% identity) for the B. subtilis OppD protein. The start site makes this gene longer than orthologs in other bacteria. Other start sites look to be worse given that there is a potential RBS at the current start site location but not at other sites farther into the gene; identified by similarity to SP:P24136; match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide ABC transporter ATP-binding protein 145028 3828976 MCAP_0119 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter ATP-binding protein YP_424111.1 143655 D 340047 CDS YP_424112.1 83319311 3828445 145104..146357 1 NC_007633.1 This is part of a 5 gene ABC transporter cassette; identified by similarity to SP:P24137; match to protein family HMM PF00005; oligopeptide ABC transporter ATP-binding protein 146357 3828445 MCAP_0120 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter ATP-binding protein YP_424112.1 145104 D 340047 CDS YP_424113.1 83319856 3828950 complement(146389..146817) 1 NC_007633.1 MCAP_0121 has 1 membrane spanning region; hypothetical protein 146817 3828950 MCAP_0121 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424113.1 146389 R 340047 CDS YP_424114.1 83319906 3828876 146872..147651 1 NC_007633.1 MCAP_0122 has 6 membrane spanning regions; identified by match to protein family HMM PF02660; match to protein family HMM TIGR00023; membrane protein 147651 3828876 MCAP_0122 Mycoplasma capricolum subsp. capricolum ATCC 27343 membrane protein YP_424114.1 146872 D 340047 CDS YP_424115.1 83319480 3828889 147705..149243 1 NC_007633.1 This protein has two ATPase domains; identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 149243 3828889 MCAP_0123 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein YP_424115.1 147705 D 340047 CDS YP_424116.1 83319824 3828916 complement(149275..150072) 1 NC_007633.1 identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010; TatD family hydrolase 150072 3828916 MCAP_0124 Mycoplasma capricolum subsp. capricolum ATCC 27343 TatD family hydrolase YP_424116.1 149275 R 340047 CDS YP_424117.1 83319702 3828312 150259..151485 1 NC_007633.1 identified by similarity to SP:P11954; match to protein family HMM PF00291; match to protein family HMM TIGR01127; threonine dehydratase 151485 ilvA 3828312 ilvA Mycoplasma capricolum subsp. capricolum ATCC 27343 threonine dehydratase YP_424117.1 150259 D 340047 CDS YP_424118.1 83319391 3828539 151701..153290 1 NC_007633.1 MCAP_0126 has 12 membrane spanning regions; hypothetical protein 153290 3828539 MCAP_0126 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424118.1 151701 D 340047 CDS YP_424119.1 83319514 3828567 153295..154158 1 NC_007633.1 MCAP_0127 has 1 membrane spanning region; hypothetical protein 154158 3828567 MCAP_0127 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424119.1 153295 D 340047 CDS YP_424120.2 162316927 3828725 154353..155120 1 NC_007633.1 catalyzes the reversible formation of fructose 6-phosphate from glucosamine 6-phosphate; glucosamine-6-phosphate deaminase 155120 nagB 3828725 nagB Mycoplasma capricolum subsp. capricolum ATCC 27343 glucosamine-6-phosphate deaminase YP_424120.2 154353 D 340047 CDS YP_424121.1 83320032 3828330 155124..156806 1 NC_007633.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system N-acetylglucosamine-specific transporter subunit IIBC 156806 3828330 MCAP_0129 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system N-acetylglucosamine-specific transporter subunit IIBC YP_424121.1 155124 D 340047 CDS YP_424122.1 83320024 3828322 156937..158388 1 NC_007633.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 158388 gltX 3828322 gltX Mycoplasma capricolum subsp. capricolum ATCC 27343 glutamyl-tRNA synthetase YP_424122.1 156937 D 340047 CDS YP_424123.1 83319457 3829053 159630..160067 1 NC_007633.1 DNA-directed RNA polymerase subunit delta 160067 3829053 MCAP_0132 Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-directed RNA polymerase subunit delta YP_424123.1 159630 D 340047 CDS YP_424124.1 83319784 3828399 160160..161758 1 NC_007633.1 CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer; CTP synthetase 161758 pyrG 3828399 pyrG Mycoplasma capricolum subsp. capricolum ATCC 27343 CTP synthetase YP_424124.1 160160 D 340047 CDS YP_424125.1 83319691 3828301 162260..163033 1 NC_007633.1 MCAP_0134 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0134 has 1 membrane spanning region; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 163033 3828301 MCAP_0134 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424125.1 162260 D 340047 CDS YP_424126.1 83319923 3828678 163048..164022 1 NC_007633.1 MCAP_0135 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0135 has 2 membrane spanning regions; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 164022 3828678 MCAP_0135 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424126.1 163048 D 340047 CDS YP_424127.1 83319873 3829112 164174..165067 1 NC_007633.1 identified by similarity to SP:P75089; match to protein family HMM PF01116; match to protein family HMM TIGR00167; match to protein family HMM TIGR01859; fructose-1,6-bisphosphate aldolase 165067 fba 3829112 fba Mycoplasma capricolum subsp. capricolum ATCC 27343 fructose-1,6-bisphosphate aldolase YP_424127.1 164174 D 340047 CDS YP_424128.1 83319320 3828454 complement(165285..166778) 1 NC_007633.1 MCAP_0137 has 12 membrane spanning regions; hypothetical protein 166778 3828454 MCAP_0137 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424128.1 165285 R 340047 CDS YP_424129.1 83319449 3828596 166983..168434 1 NC_007633.1 MCAP_0138, which has 11 transmembrane regions, is conserved in all the mycoplasmas except Ureaplasma parvum,M. arthritidis, and Phytoplasma asteris. All orthologs have 10-11 transmembrane helices.; hypothetical protein 168434 3828596 MCAP_0138 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424129.1 166983 D 340047 CDS YP_424130.1 83319738 3828391 168519..169235 1 NC_007633.1 identified by match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase family protein 169235 3828391 MCAP_0139 Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerophosphoryl diester phosphodiesterase family protein YP_424130.1 168519 D 340047 CDS YP_424131.1 83319835 3828929 169372..169650 1 NC_007633.1 RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome; 50S ribosomal protein L31 169650 rpmE 3828929 rpmE Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L31 YP_424131.1 169372 D 340047 CDS YP_424132.1 83319848 3828942 169725..171653 1 NC_007633.1 hypothetical protein 171653 3828942 MCAP_0141 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424132.1 169725 D 340047 CDS YP_424133.1 83319541 3828594 171663..172613 1 NC_007633.1 identified by match to protein family HMM PF01368; match to protein family HMM PF02272; DHH phosphoesterase family protein 172613 3828594 MCAP_0142 Mycoplasma capricolum subsp. capricolum ATCC 27343 DHH phosphoesterase family protein YP_424133.1 171663 D 340047 CDS YP_424134.1 83319659 3828506 172616..173245 1 NC_007633.1 catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 173245 tdk 3828506 tdk Mycoplasma capricolum subsp. capricolum ATCC 27343 thymidine kinase YP_424134.1 172616 D 340047 CDS YP_424135.1 83319336 3828470 173248..174339 1 NC_007633.1 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2; peptide chain release factor 1 174339 prfA 3828470 prfA Mycoplasma capricolum subsp. capricolum ATCC 27343 peptide chain release factor 1 YP_424135.1 173248 D 340047 CDS YP_424136.1 83319283 3828317 174332..175144 1 NC_007633.1 identified by match to protein family HMM TIGR00536; HemK family modification methylase 175144 3828317 MCAP_0145 Mycoplasma capricolum subsp. capricolum ATCC 27343 HemK family modification methylase YP_424136.1 174332 D 340047 CDS YP_424137.1 83319538 3828591 175190..176662 1 NC_007633.1 MCAP_0146 has 8 membrane spanning regions; hypothetical protein 176662 3828591 MCAP_0146 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424137.1 175190 D 340047 CDS YP_424138.1 83319443 3829141 176671..177171 1 NC_007633.1 SUA5/yciO/yrdC family signature protein; hypothetical protein 177171 3829141 MCAP_0147 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424138.1 176671 D 340047 CDS YP_424139.1 83319267 3828744 177239..178192 1 NC_007633.1 hypothetical protein 178192 3828744 MCAP_0148 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424139.1 177239 D 340047 CDS YP_424140.1 83320063 3828636 178316..179023 1 NC_007633.1 MCAP_0149 has 2 membrane spanning regions; hypothetical protein 179023 3828636 MCAP_0149 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424140.1 178316 D 340047 CDS YP_424141.1 83319330 3828464 179023..180552 1 NC_007633.1 identified by similarity to SP:O66043; match to protein family HMM PF00614; cardiolipin synthetase 180552 3828464 MCAP_0150 Mycoplasma capricolum subsp. capricolum ATCC 27343 cardiolipin synthetase YP_424141.1 179023 D 340047 CDS YP_424142.2 162316928 3828412 180676..181095 1 NC_007633.1 interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance; 30S ribosomal protein S12 181095 rpsL 3828412 rpsL Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S12 YP_424142.2 180676 D 340047 CDS YP_424143.1 83319930 3828828 181185..181652 1 NC_007633.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 181652 rpsG 3828828 rpsG Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S7 YP_424143.1 181185 D 340047 CDS YP_424144.1 83319565 3828987 181679..183748 1 NC_007633.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 183748 fusA 3828987 fusA Mycoplasma capricolum subsp. capricolum ATCC 27343 elongation factor G YP_424144.1 181679 D 340047 CDS YP_424145.1 83319675 3829066 183880..185067 1 NC_007633.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 185067 tuf 3829066 tuf Mycoplasma capricolum subsp. capricolum ATCC 27343 elongation factor Tu YP_424145.1 183880 D 340047 CDS YP_424146.1 83319654 3828501 185190..187031 1 NC_007633.1 although this probably tranports a hexose, one cannot be certain it is glucose; identified by similarity to SP:P19642; match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system transporter subunit IIBC 187031 3828501 MCAP_0155 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system transporter subunit IIBC YP_424146.1 185190 D 340047 CDS YP_424147.1 83320029 3828327 187015..189282 1 NC_007633.1 identified by similarity to SP:Q9F234; match to protein family HMM PF01055; isoglycosyl hydrolase family protein 189282 3828327 MCAP_0156 Mycoplasma capricolum subsp. capricolum ATCC 27343 isoglycosyl hydrolase family protein YP_424147.1 187015 D 340047 CDS YP_424148.1 83319471 3828696 189469..190824 1 NC_007633.1 MCAP_0195 pepA2 is a paralog of MCAP_0157; identified by match to protein family HMM PF00883; cytosol aminopeptidase 190824 pepA1 3828696 pepA1 Mycoplasma capricolum subsp. capricolum ATCC 27343 cytosol aminopeptidase YP_424148.1 189469 D 340047 CDS YP_424149.1 83319899 3828869 complement(192390..195080) 1 NC_007633.1 Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; alanyl-tRNA synthetase 195080 alaS 3828869 alaS Mycoplasma capricolum subsp. capricolum ATCC 27343 alanyl-tRNA synthetase YP_424149.1 192390 R 340047 CDS YP_424150.1 83319810 3828367 complement(195149..195643) 1 NC_007633.1 MCAP_0160 has 3 membrane spanning regions; hypothetical protein 195643 3828367 MCAP_0160 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424150.1 195149 R 340047 CDS YP_424151.1 83319342 3828476 195862..197106 1 NC_007633.1 identified by similarity to SP:P24138; match to protein family HMM PF00528; oligopeptide ABC transporter permease 197106 3828476 MCAP_0161 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter permease YP_424151.1 195862 D 340047 CDS YP_424152.1 83320012 3828905 197122..198132 1 NC_007633.1 identified by similarity to SP:P24139; match to protein family HMM PF00528; oligopeptide ABC transporter permease 198132 3828905 MCAP_0162 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter permease YP_424152.1 197122 D 340047 CDS YP_424153.1 83319727 3828380 198146..199846 1 NC_007633.1 identified by similarity to SP:P24136; match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide ABC transporter ATP-binding protein 199846 3828380 MCAP_0163 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter ATP-binding protein YP_424153.1 198146 D 340047 CDS YP_424154.1 83319578 3829000 199848..201725 1 NC_007633.1 identified by similarity to SP:P24137; match to protein family HMM PF00005; oligopeptide ABC transporter ATP-binding protein 201725 3829000 MCAP_0164 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter ATP-binding protein YP_424154.1 199848 D 340047 CDS YP_424155.1 83319441 3829139 201742..204849 1 NC_007633.1 This is part of a ABC transporter cassette for oligopeptides. It is a hit for the characterized Streptococcus pyogenes OppF; identified by similarity to SP:P35592; match to protein family HMM PF00496; oligopeptide ABC transporter oligopeptide-binding protein 204849 3829139 MCAP_0165 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligopeptide ABC transporter oligopeptide-binding protein YP_424155.1 201742 D 340047 CDS YP_424156.1 83319938 3828955 204948..205049 1 NC_007633.1 A large integrated element (designated Tra island II) is integrated into MCAP_0166; As a consequence of this event MCAP_0166 represents the N-terminal portion of a larger ORF. The C-terminal portion is represented in MCAP_0188. The last 9 amino acids of MCAP_0166 are derived by read through into the element. Nondisrupted orthologs of MCAP_0188/0166 have been sequenced for 3 additional M. capricolum subsp. capricolum isolates. 205021 is first nt of TraI2 element. MCAP_0166 contains 1 membrane spanning region, N-terminal. The C-terminal portion of the disrupted ORF (MCAP_0188) contains 2 membrane spanning regions and encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif.; truncated membrane protein 205049 3828955 MCAP_0166 Mycoplasma capricolum subsp. capricolum ATCC 27343 truncated membrane protein YP_424156.1 204948 D 340047 CDS YP_424157.1 83320033 3828331 205361..206965 1 NC_007633.1 First ORF in integrated element (designated Tra island II). This island spans nucleotides 205021-227425 and encodes ORFs MCAP_0167-MCAP_0187. Weak homology to DnaC helicases; identified by Glimmer2; hypothetical protein 206965 3828331 MCAP_0167 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424157.1 205361 D 340047 CDS YP_424158.1 83319892 3828716 207895..209073 1 NC_007633.1 MCAP_0168, encoded within Tra island II, has 1 membrane spanning region; hypothetical protein 209073 3828716 MCAP_0168 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424158.1 207895 D 340047 CDS YP_424159.1 83319986 3828734 209054..209689 1 NC_007633.1 MCAP_0275, MCAP_0314 and MCAP_0169 form a highly paralagous family (>92% amino acid sequence identity)of hypothetical proteins of unknown function. MCAP_0275 and MCAP_0314 are encoded in Tra island I. MCAP_0169 is encoded in Tra island II; hypothetical protein 209689 3828734 MCAP_0169 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424159.1 209054 D 340047 CDS YP_424160.1 83319682 3829073 209791..210543 1 NC_007633.1 This ORF, resident within Tra island II, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 210543 3829073 MCAP_0170 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424160.1 209791 D 340047 CDS YP_424161.1 83319847 3828941 210593..211243 1 NC_007633.1 MCAP_0171, encoded within Tra island II, has 4 membrane spanning regions; hypothetical protein 211243 3828941 MCAP_0171 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424161.1 210593 D 340047 CDS YP_424162.1 83319639 3828288 211364..212194 1 NC_007633.1 lipoprotein 212194 3828288 MCAP_0172 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424162.1 211364 D 340047 CDS YP_424163.1 83319644 3828293 212404..212691 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. The reading frame is open for 87 codons 5' to the Met codon and overlaps upstream MCAP_0172. MCAP_0172 and MCAP_0173 may constitute a single gene with a frameshift mutation; identified by Glimmer2; hypothetical protein 212691 3828293 MCAP_0173 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424163.1 212404 D 340047 CDS YP_424164.1 83319409 3828770 213766..214179 1 NC_007633.1 MCAP_0175, resident within Tra Island II, exhibits high amino acid sequence identity to Tra Island I encoded MCAP_0295 (88% amino acid identity).; hypothetical protein 214179 3828770 MCAP_0175 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424164.1 213766 D 340047 CDS YP_424165.1 83319569 3828991 complement(214289..214405) 1 NC_007633.1 hypothetical protein 214405 3828991 MCAP_0176 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424165.1 214289 R 340047 CDS YP_424166.1 83319373 3829090 214527..214916 1 NC_007633.1 This ORF, resident within Tra Island II, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM TIGR02167; hypothetical protein 214916 3829090 MCAP_0177 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424166.1 214527 D 340047 CDS YP_424167.1 83320057 3828630 215059..216234 1 NC_007633.1 MCAP_0178, encoded within Tra Island II, has 6 membrane spanning regions; hypothetical protein 216234 3828630 MCAP_0178 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424167.1 215059 D 340047 CDS YP_424168.1 83319660 3828507 216319..219186 1 NC_007633.1 MCAP_0179, encoded within Tra Island II, has homology to TraE/TrsE orthologs encoded within mobile DNAs. Contains two membrane spanning regions; membrane bound ATPase 219186 3828507 MCAP_0179 Mycoplasma capricolum subsp. capricolum ATCC 27343 membrane bound ATPase YP_424168.1 216319 D 340047 CDS YP_424169.1 83319774 3828837 219507..219827 1 NC_007633.1 hypothetical protein 219827 3828837 MCAP_0180 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424169.1 219507 D 340047 CDS YP_424170.1 83319445 3829143 219869..220444 1 NC_007633.1 MCAP_0181, encoded by Tra Island II, exhibits weak homology to ICEF ORF11, an ORF of unknown function encoded by an Integrative Conjugal Element of Mycoplasma fermentans. Tra Island I encoded ORFs MCAP_0278 and MCAP_0279 also exhibit similar low homology to ICEF ORF11; identified by Glimmer2; hypothetical protein 220444 3829143 MCAP_0181 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424170.1 219869 D 340047 CDS YP_424171.1 83319288 3828422 220472..221119 1 NC_007633.1 MCAP_0182, encoded within Tra Island II, is >93% identical to MCAP_0297 encoded within Tra Island I; identified by match to protein family HMM PF02086; adenine-specific DNA methylase 221119 3828422 MCAP_0182 Mycoplasma capricolum subsp. capricolum ATCC 27343 adenine-specific DNA methylase YP_424171.1 220472 D 340047 CDS YP_424172.1 83319382 3828530 221144..221575 1 NC_007633.1 MCAP_0183, encoded within Tra Island II, has 90% amino acid sequence identity to MCAP_0298 encoded within Tra Island I.; hypothetical protein 221575 3828530 MCAP_0183 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424172.1 221144 D 340047 CDS YP_424173.1 83319821 3828913 221642..222379 1 NC_007633.1 Homology in amino-terminus to ParA family of DNA partitioning proteins. Paralog encoded by MCAP_0282 is resident within Tra Island I; identified by Glimmer2; hypothetical protein 222379 3828913 MCAP_0184 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424173.1 221642 D 340047 CDS YP_424174.1 83319913 3828883 222379..222585 1 NC_007633.1 Hypothetical protein encoded by Tra Island II. Paralogous MCAP_0283(45% amino acid sequence identity) encoded within Tra Island I; identified by Glimmer2; hypothetical protein 222585 3828883 MCAP_0185 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424174.1 222379 D 340047 CDS YP_424175.1 83319629 3828737 222935..225676 1 NC_007633.1 MCAP_0186, resident in Tra Island II, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0186 has two membrane spanning regions; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 225676 3828737 MCAP_0186 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424175.1 222935 D 340047 CDS YP_424176.1 83319721 3828862 226062..227186 1 NC_007633.1 Homology to IS3 family transposases. Last gene of Tra Island II. This island spans nucleotides 205021-227425 and encodes ORFs MCAP_0167-MCAP_0187; identified by match to protein family HMM PF00665; IS3 family transposase 227186 3828862 MCAP_0187 Mycoplasma capricolum subsp. capricolum ATCC 27343 IS3 family transposase YP_424176.1 226062 D 340047 CDS YP_424177.1 83319699 3828309 228765..229850 1 NC_007633.1 This looks like an ATP binding protein for a sugar ABC transporter; however there are no other ABC transporter components in the region; identified by similarity to SP:Q00752; match to protein family HMM PF00005; multiple sugar ABC transporter ATP-binding protein 229850 3828309 MCAP_0189 Mycoplasma capricolum subsp. capricolum ATCC 27343 multiple sugar ABC transporter ATP-binding protein YP_424177.1 228765 D 340047 CDS YP_424178.1 83320019 3828912 229949..232246 1 NC_007633.1 identified by match to protein family HMM PF03632; match to protein family HMM PF03633; match to protein family HMM PF03636; maltose phosphorylase 232246 3828912 MCAP_0190 Mycoplasma capricolum subsp. capricolum ATCC 27343 maltose phosphorylase YP_424178.1 229949 D 340047 CDS YP_424179.1 83319866 3829104 232248..233852 1 NC_007633.1 identified by similarity to SP:P39795; match to protein family HMM PF00128; glycosyl hydrolase family protein 233852 3829104 MCAP_0191 Mycoplasma capricolum subsp. capricolum ATCC 27343 glycosyl hydrolase family protein YP_424179.1 232248 D 340047 CDS YP_424180.1 83319991 3828778 233874..234593 1 NC_007633.1 identified by match to protein family HMM PF00392; GntR family transcriptional regulator 234593 3828778 MCAP_0192 Mycoplasma capricolum subsp. capricolum ATCC 27343 GntR family transcriptional regulator YP_424180.1 233874 D 340047 CDS YP_424181.1 83319855 3828949 complement(234626..236419) 1 NC_007633.1 identified by match to protein family HMM PF01432; match to protein family HMM TIGR00181; oligoendopeptidase F 236419 3828949 MCAP_0193 Mycoplasma capricolum subsp. capricolum ATCC 27343 oligoendopeptidase F YP_424181.1 234626 R 340047 CDS YP_424182.1 83319720 3828861 complement(236419..237102) 1 NC_007633.1 hypothetical protein 237102 3828861 MCAP_0194 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424182.1 236419 R 340047 CDS YP_424183.1 83319645 3828294 complement(237118..238473) 1 NC_007633.1 MCAP_0157 pepA1 is a paralog of MCAP_0195; identified by match to protein family HMM PF00883; cytosol aminopeptidase 238473 pepA2 3828294 pepA2 Mycoplasma capricolum subsp. capricolum ATCC 27343 cytosol aminopeptidase YP_424183.1 237118 R 340047 CDS YP_424184.1 83319537 3828590 complement(238589..239884) 1 NC_007633.1 This protein has a Prosite motif for an ATP/GTP-binding site A (P-loop).; hypothetical protein 239884 3828590 MCAP_0196 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424184.1 238589 R 340047 CDS YP_424185.1 83319604 3829026 240127..240747 1 NC_007633.1 This protein and the one encoded by the adjacent both have significant hits to the chromate ion transporter (CHR) family HMM(PF02417). Combined the two proteins have the proper size and requisite 10 transmembrane alpha-helical spanners. In B. subtilis and other Gram positives the transporter is comprised to two genes like here. These tranporters are characterized chromate efflux pumps of P. aeruginosa and A. eutrophus; identified by similarity to SP:P17551; match to protein family HMM PF02417; chromate transporter 240747 3829026 MCAP_0197 Mycoplasma capricolum subsp. capricolum ATCC 27343 chromate transporter YP_424185.1 240127 D 340047 CDS YP_424186.1 83320041 3828340 240747..241424 1 NC_007633.1 This protein and the one encoded by the adjacent both have significant hits to the chromate ion transporter (CHR) family HMM(PF02417). Combined the two proteins have the proper size and requisite 10 transmembrane alpha-helical spanners. In B. subtilis and other Gram positives the transporter is comprised to two genes like here. These tranporters are characterized chromate efflux pumps of P. aeruginosa and A. eutrophus.; chromate transporter 241424 3828340 MCAP_0198 Mycoplasma capricolum subsp. capricolum ATCC 27343 chromate transporter YP_424186.1 240747 D 340047 CDS YP_424187.1 83319667 3828421 complement(242913..246038) 1 NC_007633.1 This large protein has 7 transmembrate helices at at the NH2 end plus a signal peptide. Also there is no likely indendent substrate binding protein in the region; identified by match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease and spermidine/putrescine-binding protein 246038 3828421 MCAP_0200 Mycoplasma capricolum subsp. capricolum ATCC 27343 spermidine/putrescine ABC transporter permease and spermidine/putrescine-binding protein YP_424187.1 242913 R 340047 CDS YP_424188.1 83319963 3829126 complement(246023..247015) 1 NC_007633.1 This and other orthologous mycoplasma spermidine/putrescine ABC transporter permeases have 45 amino acids at the NH2 end not present in otherwise very similar proteins in other bacteria; identified by similarity to SP:P23860; match to protein family HMM PF00528; spermidine/putrescine ABC transporter permease 247015 3829126 MCAP_0201 Mycoplasma capricolum subsp. capricolum ATCC 27343 spermidine/putrescine ABC transporter permease YP_424188.1 246023 R 340047 CDS YP_424189.1 83319839 3828933 complement(247015..248070) 1 NC_007633.1 identified by match to protein family HMM PF00005; spermidine/putrescine ABC transporter ATP-binding protein 248070 3828933 MCAP_0202 Mycoplasma capricolum subsp. capricolum ATCC 27343 spermidine/putrescine ABC transporter ATP-binding protein YP_424189.1 247015 R 340047 CDS YP_424190.1 83319552 3828973 complement(248432..248791) 1 NC_007633.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 248791 rplT 3828973 rplT Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L20 YP_424190.1 248432 R 340047 CDS YP_424191.1 83319631 3828280 complement(248810..249001) 1 NC_007633.1 identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001; 50S ribosomal protein L35 249001 rpmI 3828280 rpmI Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L35 YP_424191.1 248810 R 340047 CDS YP_424192.1 83319316 3828450 complement(249027..249572) 1 NC_007633.1 IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits; translation initiation factor IF-3 249572 infC 3828450 infC Mycoplasma capricolum subsp. capricolum ATCC 27343 translation initiation factor IF-3 YP_424192.1 249027 R 340047 CDS YP_424193.1 83319871 3829109 complement(249761..250363) 1 NC_007633.1 identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; polypeptide deformylase 250363 def 3829109 def Mycoplasma capricolum subsp. capricolum ATCC 27343 polypeptide deformylase YP_424193.1 249761 R 340047 CDS YP_424194.1 83319982 3828730 250437..250994 1 NC_007633.1 identified by match to protein family HMM PF03602; methyltransferase 250994 3828730 MCAP_0207 Mycoplasma capricolum subsp. capricolum ATCC 27343 methyltransferase YP_424194.1 250437 D 340047 CDS YP_424195.1 83320000 3828787 250997..251890 1 NC_007633.1 identified by match to protein family HMM PF00625; guanylate kinase 251890 gmk 3828787 gmk Mycoplasma capricolum subsp. capricolum ATCC 27343 guanylate kinase YP_424195.1 250997 D 340047 CDS YP_424196.1 83319809 3828366 251853..253139 1 NC_007633.1 Although the TIGRFAM score is above the trusted cutoff, there is no characterised sun protein with >35% identity, The E. coli gene is only 28% identical; identified by match to protein family HMM PF01029; match to protein family HMM PF01189; match to protein family HMM TIGR00563; rRNA methyltransferase RsmB (sun protein) 253139 3828366 MCAP_0209 Mycoplasma capricolum subsp. capricolum ATCC 27343 rRNA methyltransferase RsmB (sun protein) YP_424196.1 251853 D 340047 CDS YP_424197.1 83319795 3828411 complement(253143..254972) 1 NC_007633.1 identified by similarity to SP:Q9EXN7; match to protein family HMM PF00009; match to protein family HMM PF00679; match to protein family HMM PF03144; match to protein family HMM TIGR00231; GTP-binding protein TypA/BipA 254972 typA 3828411 typA Mycoplasma capricolum subsp. capricolum ATCC 27343 GTP-binding protein TypA/BipA YP_424197.1 253143 R 340047 CDS YP_424198.1 83320016 3828909 255250..256059 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 256059 3828909 MCAP_0211 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424198.1 255250 D 340047 CDS YP_424199.1 83319421 3828802 256070..256867 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 256867 3828802 MCAP_0212 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424199.1 256070 D 340047 CDS YP_424200.1 83319528 3828581 256990..258345 1 NC_007633.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 258345 eno 3828581 eno Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphopyruvate hydratase YP_424200.1 256990 D 340047 CDS YP_424201.1 83319575 3828997 258411..259232 1 NC_007633.1 identified by match to protein family HMM PF01569; PAP2 superfamily domain-containing protein 259232 3828997 MCAP_0214 Mycoplasma capricolum subsp. capricolum ATCC 27343 PAP2 superfamily domain-containing protein YP_424201.1 258411 D 340047 CDS YP_424202.1 83319719 3828860 259234..259665 1 NC_007633.1 identified by match to protein family HMM PF03652; match to protein family HMM TIGR00250; holliday junction resolvase 259665 3828860 MCAP_0215 Mycoplasma capricolum subsp. capricolum ATCC 27343 holliday junction resolvase YP_424202.1 259234 D 340047 CDS YP_424203.1 83319716 3828857 259671..260243 1 NC_007633.1 MCAP_0765 (hpt2) is a paralog of MCAP_0216; identified by similarity to SP:Q02522; match to protein family HMM PF00156; match to protein family HMM TIGR01203; hypoxanthine phosphoribosyltransferase 260243 hpt1 3828857 hpt1 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypoxanthine phosphoribosyltransferase YP_424203.1 259671 D 340047 CDS YP_424204.1 83319518 3828571 complement(260290..261069) 1 NC_007633.1 identified by match to protein family HMM PF00230; glycerol uptake facilitator protein 261069 3828571 MCAP_0217 Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol uptake facilitator protein YP_424204.1 260290 R 340047 CDS YP_424205.1 83319894 3828718 complement(261105..262622) 1 NC_007633.1 identified by similarity to SP:P08859; match to protein family HMM PF00370; match to protein family HMM PF02782; match to protein family HMM TIGR01311; glycerol kinase 262622 glpK 3828718 glpK Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol kinase YP_424205.1 261105 R 340047 CDS YP_424206.1 83319339 3828473 complement(262639..263802) 1 NC_007633.1 While the annotation of MCAP_0129 is , M. capricolum does have glycerol-3-phosphate dehyrogenase activity; identified by similarity to GP:26454097; match to protein family HMM PF01266; glycerol-3-phosphate dehydrogenase 263802 3828473 MCAP_0219 Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol-3-phosphate dehydrogenase YP_424206.1 262639 R 340047 CDS YP_424207.1 83319678 3829069 264143..265123 1 NC_007633.1 catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis; 6-phosphofructokinase 265123 pfkA 3829069 pfkA Mycoplasma capricolum subsp. capricolum ATCC 27343 6-phosphofructokinase YP_424207.1 264143 D 340047 CDS YP_424208.1 83319452 3828599 265192..266628 1 NC_007633.1 catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate kinase 266628 pyk 3828599 pyk Mycoplasma capricolum subsp. capricolum ATCC 27343 pyruvate kinase YP_424208.1 265192 D 340047 CDS YP_424209.1 83319726 3828379 266899..268818 1 NC_007633.1 identified by similarity to SP:P18255; match to protein family HMM PF00587; match to protein family HMM PF02824; match to protein family HMM PF03129; match to protein family HMM TIGR00418; threonyl-tRNA synthetase 268818 thrS 3828379 thrS Mycoplasma capricolum subsp. capricolum ATCC 27343 threonyl-tRNA synthetase YP_424209.1 266899 D 340047 CDS YP_424210.1 83319295 3828429 269448..270812 1 NC_007633.1 MCAP_0223 is a paralog of MCAP_0858; identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM PF07992; NADH oxidase 270812 3828429 MCAP_0223 Mycoplasma capricolum subsp. capricolum ATCC 27343 NADH oxidase YP_424210.1 269448 D 340047 CDS YP_424211.1 83319395 3828543 270824..271828 1 NC_007633.1 identified by similarity to SP:P32099; match to protein family HMM PF03099; match to protein family HMM TIGR00545; lipoate-protein ligase 271828 3828543 MCAP_0224 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoate-protein ligase YP_424211.1 270824 D 340047 CDS YP_424212.1 83319466 3828691 271863..272975 1 NC_007633.1 identified by similarity to SP:P21881; match to protein family HMM PF00676; pyruvate dehydrogenase complex, EI component subunit alpha 272975 pdhA 3828691 pdhA Mycoplasma capricolum subsp. capricolum ATCC 27343 pyruvate dehydrogenase complex, EI component subunit alpha YP_424212.1 271863 D 340047 CDS YP_424213.1 83319905 3828875 272975..273964 1 NC_007633.1 identified by similarity to SP:P21882; match to protein family HMM PF02779; match to protein family HMM PF02780; pyruvate dehydrogenase complex, E1 component subunit beta 273964 pdhB 3828875 pdhB Mycoplasma capricolum subsp. capricolum ATCC 27343 pyruvate dehydrogenase complex, E1 component subunit beta YP_424213.1 272975 D 340047 CDS YP_424214.1 83319741 3828394 273993..275309 1 NC_007633.1 identified by match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM PF02817; branched-chain alpha-keto acid dehydrogenase subunit E2 275309 pdhC 3828394 pdhC Mycoplasma capricolum subsp. capricolum ATCC 27343 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_424214.1 273993 D 340047 CDS YP_424215.1 83319618 3829042 275328..277217 1 NC_007633.1 identified by similarity to GB:AAA21748.1; match to protein family HMM PF00070; match to protein family HMM PF00364; match to protein family HMM PF01134; match to protein family HMM PF02852; match to protein family HMM PF07992; match to protein family HMM TIGR01350; dihydrolipoamide dehydrogenase 277217 pdhD 3829042 pdhD Mycoplasma capricolum subsp. capricolum ATCC 27343 dihydrolipoamide dehydrogenase YP_424215.1 275328 D 340047 CDS YP_424216.1 83319483 3828892 277239..278207 1 NC_007633.1 identified by similarity to SP:P39646; match to protein family HMM PF01515; match to protein family HMM TIGR00651; phosphate acetyltransferase 278207 pta 3828892 pta Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphate acetyltransferase YP_424216.1 277239 D 340047 CDS YP_424217.1 83319412 3828773 278221..279402 1 NC_007633.1 AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA; acetate kinase 279402 ackA 3828773 ackA Mycoplasma capricolum subsp. capricolum ATCC 27343 acetate kinase YP_424217.1 278221 D 340047 CDS YP_424218.1 83319472 3828347 279470..281437 1 NC_007633.1 identified by match to protein family HMM PF01732; lipoprotein 281437 3828347 MCAP_0231 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424218.1 279470 D 340047 CDS YP_424219.1 83319935 3828952 281447..281869 1 NC_007633.1 catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-CoA; phosphopantetheine adenylyltransferase 281869 coaD 3828952 coaD Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphopantetheine adenylyltransferase YP_424219.1 281447 D 340047 CDS YP_424220.1 83319559 3828981 281962..283683 1 NC_007633.1 The M. capricolum phosphoenolpyruvate-protein phosphotransferase (ptsI) was cloned, expressed and characterized in Zhu,P.P., Reizer,J. and Peterkofsky,A. 1994.Unique dicistronic operon (ptsI-crr) in Mycoplasma capricolum encoding enzyme I and the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system: cloning, sequencing, promoter analysis, and protein characterization. Protein Sci. 3 (11), 2115-2128; identified by similarity to SP:P45617; match to protein family HMM PF00391; match to protein family HMM PF02896; match to protein family HMM PF05524; match to protein family HMM TIGR01417; phosphoenolpyruvate-protein phosphotransferase 283683 ptsI 3828981 ptsI Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphoenolpyruvate-protein phosphotransferase YP_424220.1 281962 D 340047 CDS YP_424221.1 83319491 3828900 283765..284229 1 NC_007633.1 This M. capricolum protein was characterized in: Zhu,P.P., Reizer,J. and Peterkofsky,A.. 1994.Unique dicistronic operon (ptsI-crr) in Mycoplasma capricolum encoding enzyme I and the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system: cloning, sequencing, promoter analysis, and protein characterization. Protein Sci. 3 (11), 2115-2128 (1994); identified by similarity to SP:P45618; match to protein family HMM PF00358; match to protein family HMM TIGR00830; PTS system glucose-specific transporter subunit IIA 284229 crr 3828900 crr Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system glucose-specific transporter subunit IIA YP_424221.1 283765 D 340047 CDS YP_424222.1 83319954 3829115 284721..285347 1 NC_007633.1 In E. coli dihydroxyacetone kinase is encoded by two proteins. MCAP_0235 corresponds to the C-=terminal part. M. capricolum likely uses dihydroxyacetone kinase under anaerobic conditions along with triosephosphate isomerase to catalyzes the transformation of dihydroxyacetone to glyceraldehyde-3-phosphate. This then feeds into glycolysis; identified by similarity to SP:P76014; match to protein family HMM PF02734; match to protein family HMM TIGR02365; dihydroxyacetone kinase family protein 285347 3829115 MCAP_0235 Mycoplasma capricolum subsp. capricolum ATCC 27343 dihydroxyacetone kinase family protein YP_424222.1 284721 D 340047 CDS YP_424223.1 83319970 3829133 285355..285744 1 NC_007633.1 identified by match to protein family HMM PF03610; match to protein family HMM TIGR02364; PTS system mannnose-specific transporter subunit IIA 285744 3829133 MCAP_0236 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system mannnose-specific transporter subunit IIA YP_424223.1 285355 D 340047 CDS YP_424224.1 83319988 3828736 complement(285801..286427) 1 NC_007633.1 primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination; 30S ribosomal protein S4 286427 rpsD 3828736 rpsD Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S4 YP_424224.1 285801 R 340047 CDS YP_424225.1 83319932 3828512 286682..288469 1 NC_007633.1 MCAP_0238 has 1 membrane spanning region, N-terminal; hypothetical protein 288469 3828512 MCAP_0238 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424225.1 286682 D 340047 CDS YP_424226.1 83319792 3828407 288478..289665 1 NC_007633.1 The characterized E. coli ThiI has a COOH terminal rhodanese domain (3-mercaptopyruvate sulfotransferase) not found in the mycpolasma ThiI proteins; identified by similarity to SP:Q8FKB7; match to protein family HMM PF02568; match to protein family HMM PF02926; match to protein family HMM TIGR00342; thiamine biosynthesis protein ThiI 289665 thiI 3828407 thiI Mycoplasma capricolum subsp. capricolum ATCC 27343 thiamine biosynthesis protein ThiI YP_424226.1 288478 D 340047 CDS YP_424227.1 83319648 3828495 289797..291767 1 NC_007633.1 MCAP_0240 has 2 membrane spanning regions and a likely C-terminal peptidase domain; identified by match to protein family HMM PF03572; hypothetical protein 291767 3828495 MCAP_0240 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424227.1 289797 D 340047 CDS YP_424228.1 83319568 3828990 291884..293554 1 NC_007633.1 MCAP_0241 has one membrane spanning region; hypothetical protein 293554 3828990 MCAP_0241 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424228.1 291884 D 340047 CDS YP_424229.1 83319400 3828761 293564..295852 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. Strong coiled-coil prediction in region 1-525 of this ORF. QVRP motifs extend from that region to the C-terminus; identified by match to protein family HMM TIGR02167; lipoprotein 295852 3828761 MCAP_0242 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424229.1 293564 D 340047 CDS YP_424230.1 83319353 3828487 296087..298150 1 NC_007633.1 MCAP_0243 has 9 transmembrane regions. The Clostridium perfringens PfoR protein was shown to regulate the downstream bperfringolysin O gene. The deduced amino acid sequence of the C. perfringens pfoR possesses several motifs that are characteristic of DNA-binding proteins. When a region coding for a helix-turn-helix, one of the most important motifs of DNA-binding proteins, was deleted within pfoR, stimulation was completely abolished; identified by similarity to PIR:A43577; regulatory protein PfoR 298150 3828487 MCAP_0243 Mycoplasma capricolum subsp. capricolum ATCC 27343 regulatory protein PfoR YP_424230.1 296087 D 340047 CDS YP_424231.1 83319459 3829055 complement(298176..301091) 1 NC_007633.1 identified by match to protein family HMM PF00122; match to protein family HMM PF00690; match to protein family HMM PF00702; match to protein family HMM TIGR01494; cation transporter E1-E2 family ATPase 301091 3829055 MCAP_0244 Mycoplasma capricolum subsp. capricolum ATCC 27343 cation transporter E1-E2 family ATPase YP_424231.1 298176 R 340047 CDS YP_424232.1 83319725 3828378 complement(301100..301690) 1 NC_007633.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential; ribosome biogenesis GTP-binding protein YsxC 301690 engB 3828378 engB Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosome biogenesis GTP-binding protein YsxC YP_424232.1 301100 R 340047 CDS YP_424233.1 83319833 3828927 complement(301684..302244) 1 NC_007633.1 MCAP_0246 has 3 membrane spanning regions; hypothetical protein 302244 3828927 MCAP_0246 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424233.1 301684 R 340047 CDS YP_424234.1 83319789 3828404 complement(302246..302824) 1 NC_007633.1 MCAP_0247 has 1 membrane spanning region, N-terminal; hypothetical protein 302824 3828404 MCAP_0247 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424234.1 302246 R 340047 CDS YP_424235.1 83319864 3829102 complement(302827..303516) 1 NC_007633.1 hypothetical protein 303516 3829102 MCAP_0248 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424235.1 302827 R 340047 CDS YP_424236.1 83319305 3828439 303598..304293 1 NC_007633.1 hypothetical protein 304293 3828439 MCAP_0249 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424236.1 303598 D 340047 CDS YP_424237.1 83319566 3828988 complement(304294..305016) 1 NC_007633.1 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase family oxidoreductase 305016 3828988 MCAP_0250 Mycoplasma capricolum subsp. capricolum ATCC 27343 short chain dehydrogenase/reductase family oxidoreductase YP_424237.1 304294 R 340047 CDS YP_424238.1 83319925 3828680 complement(305075..305548) 1 NC_007633.1 necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus; transcription elongation factor GreA 305548 greA 3828680 greA Mycoplasma capricolum subsp. capricolum ATCC 27343 transcription elongation factor GreA YP_424238.1 305075 R 340047 CDS YP_424239.1 83319764 3828962 complement(305640..307394) 1 NC_007633.1 identified by similarity to SP:P14951; match to protein family HMM PF01541; match to protein family HMM PF02151; match to protein family HMM TIGR00194; excinuclease ABC subunit C 307394 uvrC 3828962 uvrC Mycoplasma capricolum subsp. capricolum ATCC 27343 excinuclease ABC subunit C YP_424239.1 305640 R 340047 CDS YP_424240.1 83319704 3828314 complement(307403..308479) 1 NC_007633.1 MCAP_0253 has 6 membrane spanning regions; hypothetical protein 308479 3828314 MCAP_0253 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424240.1 307403 R 340047 CDS YP_424241.1 83319270 3828747 complement(310275..312026) 1 NC_007633.1 Contains an ATP-binding domain at the N-terminal end of the protein. Possibly part of a superfamily of beta-lactmases; identified by match to protein family HMM PF00753; hypothetical protein 312026 3828747 MCAP_0255 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424241.1 310275 R 340047 CDS YP_424242.1 83319377 3829094 complement(312145..312864) 1 NC_007633.1 identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase family oxidoreductase 312864 3829094 MCAP_0256 Mycoplasma capricolum subsp. capricolum ATCC 27343 short chain dehydrogenase/reductase family oxidoreductase YP_424242.1 312145 R 340047 CDS YP_424243.1 83319993 3828780 complement(312876..313673) 1 NC_007633.1 identified by match to protein family HMM PF01513; inorganic polyphosphate/ATP-NAD kinase 313673 3828780 MCAP_0257 Mycoplasma capricolum subsp. capricolum ATCC 27343 inorganic polyphosphate/ATP-NAD kinase YP_424243.1 312876 R 340047 CDS YP_424244.1 83319485 3828894 complement(313797..316415) 1 NC_007633.1 valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain; valyl-tRNA synthetase 316415 valS 3828894 valS Mycoplasma capricolum subsp. capricolum ATCC 27343 valyl-tRNA synthetase YP_424244.1 313797 R 340047 CDS YP_424245.1 83319805 3828362 complement(316500..317126) 1 NC_007633.1 This protein has a thiamin pyrophosphokinase, catalytic domain (EC# 2.7.6.2); identified by match to protein family HMM PF04263; match to protein family HMM TIGR01378; hypothetical protein 317126 3828362 MCAP_0259 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424245.1 316500 R 340047 CDS YP_424246.1 83319580 3829002 complement(317116..317793) 1 NC_007633.1 identified by match to protein family HMM PF00834; ribulose-phosphate 3-epimerase 317793 rpe 3829002 rpe Mycoplasma capricolum subsp. capricolum ATCC 27343 ribulose-phosphate 3-epimerase YP_424246.1 317116 R 340047 CDS YP_424247.1 83319551 3828972 complement(317795..318697) 1 NC_007633.1 identified by match to protein family HMM PF03193; match to protein family HMM TIGR00157; ribosome small subunit-dependent GTPase A 318697 rsgA 3828972 rsgA Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosome small subunit-dependent GTPase A YP_424247.1 317795 R 340047 CDS YP_424248.1 83319436 3829134 complement(318707..319822) 1 NC_007633.1 identified by similarity to GB:AAL58474.1; match to protein family HMM PF00069; serine/threonine protein kinase 319822 3829134 MCAP_0262 Mycoplasma capricolum subsp. capricolum ATCC 27343 serine/threonine protein kinase YP_424248.1 318707 R 340047 CDS YP_424249.1 83319668 3828824 complement(319822..320085) 1 NC_007633.1 hypothetical protein 320085 3828824 MCAP_0263 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424249.1 319822 R 340047 CDS YP_424250.1 83320005 3828792 complement(320054..320581) 1 NC_007633.1 The orthologous genes in other organisms are annotated as serine/threonine phosphatase; however no clear case can be made for this gene having that enzymatic activity based on sequence homology to known serine/threonine phosphatases.; hypothetical protein 320581 3828792 MCAP_0264 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424250.1 320054 R 340047 CDS YP_424251.1 83319751 3828609 complement(320611..322023) 1 NC_007633.1 MCAP_0265 has 1 membrane spanning region; hypothetical protein 322023 3828609 MCAP_0265 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424251.1 320611 R 340047 CDS YP_424252.1 83320050 3828623 322126..322542 1 NC_007633.1 Thiw protein contains a P-loop and a nucleotide-binding motif GXXGXGKT characteristic of the TIGR00150 proteins; identified by match to protein family HMM PF02367; match to protein family HMM TIGR00150; hypothetical protein 322542 3828623 MCAP_0266 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424252.1 322126 D 340047 CDS YP_424253.1 83319754 3828612 322544..323107 1 NC_007633.1 This has a ProDom Peptidase M22, glycoprotease signature. This is a member of COG1214 Inactive homologs of metal-dependent proteases, molecular chaperones. Is is conserved in all mycoplasma genomes except Phytoplasma asteris. The gene cannot be disrupted in M. genitalium; identified by match to protein family HMM PF00814; metalloendopeptidase 323107 3828612 MCAP_0267 Mycoplasma capricolum subsp. capricolum ATCC 27343 metalloendopeptidase YP_424253.1 322544 D 340047 CDS YP_424254.1 83319816 3828373 complement(323167..324522) 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM TIGR02167; lipoprotein 324522 3828373 MCAP_0268 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424254.1 323167 R 340047 CDS YP_424255.1 83319470 3828695 complement(324791..326143) 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM TIGR02167; lipoprotein 326143 3828695 MCAP_0269 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424255.1 324791 R 340047 CDS YP_424256.1 83319606 3829028 complement(326350..331656) 1 NC_007633.1 This appears to be an ABC transporter permease or possibly a permease/substrate bindng protein; however there is no ATPase in the vicinity. There are similar genes in other mycoplasmas also without nearby ATPases; identified by match to protein family HMM PF02687; ABC transporter permease 331656 3829028 MCAP_0270 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter permease YP_424256.1 326350 R 340047 CDS YP_424257.1 83319602 3829024 331924..335061 1 NC_007633.1 MCAP_0271 has 1 membrane spanning region, N-terminal.; hypothetical protein 335061 3829024 MCAP_0271 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424257.1 331924 D 340047 CDS YP_424258.1 83320048 3828621 335085..335603 1 NC_007633.1 lipoprotein 335603 3828621 MCAP_0272 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424258.1 335085 D 340047 CDS YP_424259.1 83320023 3829059 335689..336228 1 NC_007633.1 lipoprotein 336228 3829059 MCAP_0273 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424259.1 335689 D 340047 CDS YP_424260.1 83319945 3828349 336621..337358 1 NC_007633.1 First ORF of Tra Island I. Element starts at nucleotide 336353 and encodes MCAP_0274-MCAP_0315. The last nucleotide of the element is 379887; identified by Glimmer2; hypothetical protein 337358 3828349 MCAP_0274 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424260.1 336621 D 340047 CDS YP_424261.1 83319845 3828939 338352..338984 1 NC_007633.1 MCAP_0275, MCAP_0314 and MCAP_0169 form a highly paralagous family (>92% amino acid sequence identity)of hypothetical proteins of unknown function. MCAP_0275 and MCAP_0314 are encoded in Tra Island I. MCAP_0169 is encoded in Tra Island II; hypothetical protein 338984 3828939 MCAP_0275 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424261.1 338352 D 340047 CDS YP_424262.1 83319673 3829064 339294..339815 1 NC_007633.1 MCAP_0276, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. The annotated start site is in a repeat motif. In-frame sequence extends nearly 90 amino acid residues 5' from the start, but no alternative start codon occurs in the extension. The extended region also has good homology with orthologous ORFs in M. mycoides SC: MSC_0203 and MSC_0209; identified by match to protein family HMM TIGR02167; hypothetical protein 339815 3829064 MCAP_0276 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424262.1 339294 D 340047 CDS YP_424263.1 83319701 3828311 339845..340249 1 NC_007633.1 MCAP_0277 is truncated in size compared to the Helicobacter pylori and M. mycoides plasmid homologs. However, homologs from M. capricolum subspecies capripneumoniae strain F38 and Mycoplasma bovine group 7 are also shorter, suggesting that a deletion has not occurred in MCAP_0277 (unpublished findings); identified by similarity to GP:150185; plasmid replication-initiation protein 340249 3828311 MCAP_0277 Mycoplasma capricolum subsp. capricolum ATCC 27343 plasmid replication-initiation protein YP_424263.1 339845 D 340047 CDS YP_424264.1 83319630 3828279 340321..340929 1 NC_007633.1 Tra Island I encoded ORF with weak homology to ICEF ORF11, an ORF of unknown function encoded by an Integrative Conjugal Element of Mycoplasma fermentans. Tra Island I encoded MCAP_0279 and Tra Island II encoded MCAP_0181 also exhibit similar low homology to ICEF ORF11.; hypothetical protein 340929 3828279 MCAP_0278 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424264.1 340321 D 340047 CDS YP_424265.1 83319516 3828569 340973..341833 1 NC_007633.1 Tra Island I encoded ORF with weak homology to ICEF ORF11, an ORF of unknown function encoded by an Integrative Conjugal Element of Mycoplasma fermentans. Tra Island I encoded MCAP_0278 and Tra Island II encoded MCAP_0181 also exhibit similar low homology to ICEF ORF11; identified by Glimmer2; hypothetical protein 341833 3828569 MCAP_0279 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424265.1 340973 D 340047 CDS YP_424266.1 83319428 3828809 342147..342296 1 NC_007633.1 Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein 342296 3828809 MCAP_0280 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424266.1 342147 D 340047 CDS YP_424267.1 83319433 3828814 342461..342769 1 NC_007633.1 Tra Island I encoded ORF; identified by similarity to GP:1763709; match to protein family HMM PF00436; single-strand binding protein family 342769 3828814 MCAP_0281 Mycoplasma capricolum subsp. capricolum ATCC 27343 single-strand binding protein family YP_424267.1 342461 D 340047 CDS YP_424268.1 83319475 3828884 342820..343560 1 NC_007633.1 Homology to ParA family proteins involved in partitioning of mobile elements. Paralogs are within Tra Island II (MCAP_0184) and Integrative Conjugal Element (ICEC) MCAP_0570; identified by Glimmer2; hypothetical protein 343560 3828884 MCAP_0282 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424268.1 342820 D 340047 CDS YP_424269.1 83319562 3828984 343562..343777 1 NC_007633.1 Hypothetical protein encoded within Tra Island I. Paralogous MCAP_0185 (45% amino acid identity) encoded within Tra Island II; identified by Glimmer2; hypothetical protein 343777 3828984 MCAP_0283 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424269.1 343562 D 340047 CDS YP_424270.1 83319371 3829088 343855..344736 1 NC_007633.1 MCAP_0284, resident within Tra Island I, has 5 membrane spanning regions; The C-terminal 94 amino acid residue region exhibits homology to MCAP_0086 and M. mycoides SC ORF MSC_0882.; hypothetical protein 344736 3829088 MCAP_0284 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424270.1 343855 D 340047 CDS YP_424271.1 83319257 3828823 344834..345322 1 NC_007633.1 Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein 345322 3828823 MCAP_0285 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424271.1 344834 D 340047 CDS YP_424272.1 83319367 3829084 345374..345943 1 NC_007633.1 Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein 345943 3829084 MCAP_0286 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424272.1 345374 D 340047 CDS YP_424273.1 83319861 3829099 346021..346839 1 NC_007633.1 This Tra Island I resident ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 346839 3829099 MCAP_0287 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424273.1 346021 D 340047 CDS YP_424274.1 83319966 3829129 346886..347458 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 347458 3829129 MCAP_0288 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424274.1 346886 D 340047 CDS YP_424275.1 83319740 3828393 347716..348396 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 348396 3828393 MCAP_0289 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424275.1 347716 D 340047 CDS YP_424276.1 83319791 3828406 348460..348876 1 NC_007633.1 Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein 348876 3828406 MCAP_0290 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424276.1 348460 D 340047 CDS YP_424277.1 83319321 3828455 348951..349499 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 349499 3828455 MCAP_0291 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424277.1 348951 D 340047 CDS YP_424278.1 83319636 3828285 349555..350307 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 350307 3828285 MCAP_0292 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424278.1 349555 D 340047 CDS YP_424279.1 83319408 3828769 350364..351119 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 351119 3828769 MCAP_0293 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424279.1 350364 D 340047 CDS YP_424280.1 83319733 3828386 351168..351779 1 NC_007633.1 Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein 351779 3828386 MCAP_0294 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424280.1 351168 D 340047 CDS YP_424281.1 83319820 3828701 351830..352243 1 NC_007633.1 MCAP_0295, resident within Tra Island I, exhibits high amino acid sequence identity to Tra Island II encoded MCAP_0175 (88% amino acid identity).; hypothetical protein 352243 3828701 MCAP_0295 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424281.1 351830 D 340047 CDS YP_424282.1 83319585 3829007 352322..353125 1 NC_007633.1 This Tra Island I encodede ORF has strong homology to MSC_0201 in M. mycoides SC; hypothetical protein 353125 3829007 MCAP_0296 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424282.1 352322 D 340047 CDS YP_424283.1 83319273 3828750 353126..353794 1 NC_007633.1 MCAP_0297, resident within Tra Island I, exhibits strong homology to MCAP_0182 encoded within Tra Island II; identified by match to protein family HMM PF02086; adenine-specific DNA methylase 353794 3828750 MCAP_0297 Mycoplasma capricolum subsp. capricolum ATCC 27343 adenine-specific DNA methylase YP_424283.1 353126 D 340047 CDS YP_424284.1 83319363 3829080 353798..354178 1 NC_007633.1 MCAP_0298, resident within Tra Island I, has high sequence identity (90% amino acid level) to MCAP_0183, encoded within Tra Island II.; hypothetical protein 354178 3829080 MCAP_0298 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424284.1 353798 D 340047 CDS YP_424285.1 83319865 3829103 354758..359698 1 NC_007633.1 MCAP_0299, resident within Tra Island I, has 2 membrane spanning regions; MCAP_0299 corresponds to an orthologous region in M. mycoides SC PG1 annotated to encode four contiguous ORFS (MSC_0198, MSC_0197, MSC_0196 and MSC_0195), which may be separated by interspersed frameshifts relative to MCAP_0299.; hypothetical protein 359698 3829103 MCAP_0299 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424285.1 354758 D 340047 CDS YP_424286.1 83319882 3828706 complement(360401..361894) 1 NC_007633.1 Tra Island I resident ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 361894 3828706 MCAP_0300 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424286.1 360401 R 340047 CDS YP_424287.1 83319712 3828853 complement(362143..364599) 1 NC_007633.1 Tra Island I encoded ORF exhibits homology to multiple ORFs annotated as TraE/TrsE family NTPases.; hypothetical protein 364599 3828853 MCAP_0301 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424287.1 362143 R 340047 CDS YP_424288.1 83319818 3828375 complement(364659..365339) 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 365339 3828375 MCAP_0302 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424288.1 364659 R 340047 CDS YP_424289.1 83319515 3828568 complement(366143..366730) 1 NC_007633.1 MCAP_0303, resident within Tra Island I, contains 2 membrane spanning regions; hypothetical protein 366730 3828568 MCAP_0303 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424289.1 366143 R 340047 CDS YP_424290.1 83319337 3828471 complement(366730..368646) 1 NC_007633.1 MCAP_0304 is encoded within Tra Island I. There are two of these genes in M. mycoides SC; however both genes are divided into two parts. The HN2 domain of the M. capricolum gene with the 5 transmembrane helices is one SC ORF and the e3 binding domain is the other. The e3 binding domain is a small domain of the E2 subunit of 2-oxo-acid dehydrogenases that is responsible for the binding of the E3 subunit. Proteins containing the e3 binding domain include the branched-chain -keto acid dehydrogenase complex of bacteria, which catalyses the overall conversion of -keto acids to acyl-CoA and carbon dioxide; identified by match to protein family HMM PF02817; E3 binding domain-containing protein 368646 3828471 MCAP_0304 Mycoplasma capricolum subsp. capricolum ATCC 27343 E3 binding domain-containing protein YP_424290.1 366730 R 340047 CDS YP_424291.1 83320036 3828335 complement(368903..370393) 1 NC_007633.1 MCAP_0305, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0305 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 370393 3828335 MCAP_0305 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424291.1 368903 R 340047 CDS YP_424292.1 83319919 3828674 complement(370524..370844) 1 NC_007633.1 MCAP_0306, encoded within Tra Island I, has 2 membrane spanning regions; hypothetical protein 370844 3828674 MCAP_0306 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424292.1 370524 R 340047 CDS YP_424293.1 83319526 3828579 complement(371320..372405) 1 NC_007633.1 MCAP_0307, encoded within Tra Island I, has 2 membrane spanning regions; There is a DnaJ domain; identified by match to protein family HMM PF00226; hypothetical protein 372405 3828579 MCAP_0307 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424293.1 371320 R 340047 CDS YP_424294.1 83319684 3829075 complement(372470..373015) 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 373015 3829075 MCAP_0308 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424294.1 372470 R 340047 CDS YP_424295.1 83319306 3828440 complement(373077..374006) 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 374006 3828440 MCAP_0309 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424295.1 373077 R 340047 CDS YP_424296.1 83319628 3828699 complement(374061..374963) 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 374963 3828699 MCAP_0310 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424296.1 374061 R 340047 CDS YP_424297.1 83319573 3828995 complement(375026..375997) 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 375997 3828995 MCAP_0311 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424297.1 375026 R 340047 CDS YP_424298.1 83319853 3828947 complement(376060..377175) 1 NC_007633.1 This ORF, resident within Tra Island I, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 377175 3828947 MCAP_0312 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424298.1 376060 R 340047 CDS YP_424299.1 83319387 3828535 complement(377232..377510) 1 NC_007633.1 MCAP_0313 is one of three M. capricolum ORFs with homology to multiple HU-like DNA binding proteins. MCAP_0575 is identical to the single HU-like protein of M. mycoides SC (MSC_0410) and is most likely therefore the chromosomal equivalent of HU. MCAP_0313 is a Tra Island I encoded paralog. MCAP_0813 also exhibits homology to HU proteins; identified by similarity to SP:P02346; match to protein family HMM PF00216; DNA-binding protein, HU 377510 hupB 3828535 hupB Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-binding protein, HU YP_424299.1 377232 R 340047 CDS YP_424300.1 83320065 3828638 complement(377579..378211) 1 NC_007633.1 MCAP_0275, MCAP_0314 and MCAP_0169 form a highly paralagous family (>92% amino acid sequence identity)of hypothetical proteins of unknown function. MCAP_0275 and MCAP_0314 are encoded in Tra Island I. MCAP_0169 is encoded in Tra Island II; hypothetical protein 378211 3828638 MCAP_0314 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424300.1 377579 R 340047 CDS YP_424301.1 83319713 3828854 378592..379707 1 NC_007633.1 Terminal ORF of Tra island I. Element starts at nucleotide 336353 and encodes MCAP_0274-MCAP_0315. The last nucleotide of the element is 379887; identified by match to protein family HMM PF00665; IS3 family transposase 379707 3828854 MCAP_0315 Mycoplasma capricolum subsp. capricolum ATCC 27343 IS3 family transposase YP_424301.1 378592 D 340047 CDS YP_424302.1 83319763 3828416 380492..381184 1 NC_007633.1 hypothetical protein 381184 3828416 MCAP_0317 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424302.1 380492 D 340047 CDS YP_424303.2 162316930 3828890 381165..382589 1 NC_007633.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 382589 proS 3828890 proS Mycoplasma capricolum subsp. capricolum ATCC 27343 prolyl-tRNA synthetase YP_424303.2 381165 D 340047 CDS YP_424304.1 83319587 3829009 382602..383222 1 NC_007633.1 identified by match to protein family HMM PF00075; ribonuclease H1 383222 3829009 MCAP_0319 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribonuclease H1 YP_424304.1 382602 D 340047 CDS YP_424305.1 83319424 3828805 383224..384123 1 NC_007633.1 hypothetical protein 384123 3828805 MCAP_0320 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424305.1 383224 D 340047 CDS YP_424306.1 83319434 3828815 384137..385939 1 NC_007633.1 binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 385939 lepA 3828815 lepA Mycoplasma capricolum subsp. capricolum ATCC 27343 GTP-binding protein LepA YP_424306.1 384137 D 340047 CDS YP_424307.1 83319589 3829011 385973..386776 1 NC_007633.1 hypothetical protein 386776 3829011 MCAP_0322 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424307.1 385973 D 340047 CDS YP_424308.1 83319674 3829065 complement(386797..388524) 1 NC_007633.1 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes; aspartyl-tRNA synthetase 388524 aspS 3829065 aspS Mycoplasma capricolum subsp. capricolum ATCC 27343 aspartyl-tRNA synthetase YP_424308.1 386797 R 340047 CDS YP_424309.1 83319312 3828446 complement(388533..389777) 1 NC_007633.1 catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG; histidyl-tRNA synthetase 389777 hisS 3828446 hisS Mycoplasma capricolum subsp. capricolum ATCC 27343 histidyl-tRNA synthetase YP_424309.1 388533 R 340047 CDS YP_424310.1 83319338 3828472 389949..390302 1 NC_007633.1 identified by similarity to SP:P09170; match to protein family HMM PF02033; match to protein family HMM TIGR00082; ribosome-binding factor A 390302 rbfA 3828472 rbfA Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosome-binding factor A YP_424310.1 389949 D 340047 CDS YP_424311.1 83319374 3829091 390352..391230 1 NC_007633.1 This gene has good similariy to the characterized 286 amino acid E. coli TruB protein for the first 2215 amino acids, after that there is no similarity. This also true for other mycoplasma tRNA pseudouridine synthases; identified by similarity to SP:P32732; match to protein family HMM PF01509; match to protein family HMM TIGR00431; tRNA pseudouridine synthase B 391230 3829091 MCAP_0326 Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA pseudouridine synthase B YP_424311.1 390352 D 340047 CDS YP_424312.1 83319941 3828958 391217..391771 1 NC_007633.1 Similar non-mycoplasma proteins have and additional 120 amino acids at the COOH end; identified by similarity to SP:P54575; match to protein family HMM PF06574; riboflavin kinase domain-containing protein 391771 3828958 MCAP_0327 Mycoplasma capricolum subsp. capricolum ATCC 27343 riboflavin kinase domain-containing protein YP_424312.1 391217 D 340047 CDS YP_424313.1 83319972 3828720 complement(391784..393832) 1 NC_007633.1 MCAP_0328 has 1 membrane spanning region; identified by match to protein family HMM PF03572; hypothetical protein 393832 3828720 MCAP_0328 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424313.1 391784 R 340047 CDS YP_424314.1 83319670 3829061 complement(393844..395682) 1 NC_007633.1 identified by match to protein family HMM PF03572; lipoprotein 395682 3829061 MCAP_0329 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424314.1 393844 R 340047 CDS YP_424315.1 83319798 3828414 395895..396161 1 NC_007633.1 primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence; 30S ribosomal protein S15 396161 rpsO 3828414 rpsO Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S15 YP_424315.1 395895 D 340047 CDS YP_424316.1 83319456 3829052 396385..397035 1 NC_007633.1 There are 4 membrane spanning regions in MCAP_0332.; hypothetical protein 397035 3829052 MCAP_0332 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424316.1 396385 D 340047 CDS YP_424317.1 83319583 3829005 complement(397049..398911) 1 NC_007633.1 Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex; translation initiation factor IF-2 398911 infB 3829005 infB Mycoplasma capricolum subsp. capricolum ATCC 27343 translation initiation factor IF-2 YP_424317.1 397049 R 340047 CDS YP_424318.1 83319415 3828776 complement(398931..399230) 1 NC_007633.1 identified by match to protein family HMM PF01248; ribosomal protein L7A family protein 399230 3828776 MCAP_0334 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosomal protein L7A family protein YP_424318.1 398931 R 340047 CDS YP_424319.1 83319398 3828759 complement(399217..399504) 1 NC_007633.1 identified by match to protein family HMM PF04296; hypothetical protein 399504 3828759 MCAP_0335 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424319.1 399217 R 340047 CDS YP_424320.1 83319641 3828290 complement(399479..401155) 1 NC_007633.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 401155 nusA 3828290 nusA Mycoplasma capricolum subsp. capricolum ATCC 27343 transcription elongation factor NusA YP_424320.1 399479 R 340047 CDS YP_424321.1 83319689 3828299 complement(401164..401658) 1 NC_007633.1 hypothetical protein 401658 3828299 MCAP_0337 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424321.1 401164 R 340047 CDS YP_424322.1 83319910 3828880 complement(401771..402394) 1 NC_007633.1 identified by match to protein family HMM PF00881; nitroreductase family protein 402394 3828880 MCAP_0338 Mycoplasma capricolum subsp. capricolum ATCC 27343 nitroreductase family protein YP_424322.1 401771 R 340047 CDS YP_424323.1 83319984 3828732 complement(402434..406873) 1 NC_007633.1 identified by similarity to SP:P13267; match to protein family HMM PF00929; match to protein family HMM PF01336; match to protein family HMM PF02231; match to protein family HMM PF02811; match to protein family HMM PF07733; match to protein family HMM TIGR00573; match to protein family HMM TIGR01405; DNA polymerase III subunit alpha 406873 polC 3828732 polC Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA polymerase III subunit alpha YP_424323.1 402434 R 340047 CDS YP_424324.1 83319347 3828481 complement(406882..407910) 1 NC_007633.1 identified by match to protein family HMM PF01148; phosphatidate cytidylyltransferase 407910 cdsA 3828481 cdsA Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphatidate cytidylyltransferase YP_424324.1 406882 R 340047 CDS YP_424325.1 83319612 3829034 complement(408108..409184) 1 NC_007633.1 identified by match to protein family HMM PF00557; Xaa-Pro peptidase 409184 3829034 MCAP_0341 Mycoplasma capricolum subsp. capricolum ATCC 27343 Xaa-Pro peptidase YP_424325.1 408108 R 340047 CDS YP_424326.1 83319724 3828377 409342..410352 1 NC_007633.1 identified by match to protein family HMM PF00579; match to protein family HMM TIGR00233; tryptophanyl-tRNA synthetase 410352 trpS 3828377 trpS Mycoplasma capricolum subsp. capricolum ATCC 27343 tryptophanyl-tRNA synthetase YP_424326.1 409342 D 340047 CDS YP_424327.1 83319766 3828964 complement(410382..411272) 1 NC_007633.1 MCAP_0343 has 1 membrane spanning region; hypothetical protein 411272 3828964 MCAP_0343 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424327.1 410382 R 340047 CDS YP_424328.1 83319886 3828710 411606..412175 1 NC_007633.1 identified by match to protein family HMM PF02661; Fic family protein 412175 3828710 MCAP_0344 Mycoplasma capricolum subsp. capricolum ATCC 27343 Fic family protein YP_424328.1 411606 D 340047 CDS YP_424329.1 83320046 3828345 412795..415050 1 NC_007633.1 MCAP_0345 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein 415050 3828345 MCAP_0345 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424329.1 412795 D 340047 CDS YP_424330.1 83319263 3828740 415071..417659 1 NC_007633.1 lipoprotein 417659 3828740 MCAP_0346 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424330.1 415071 D 340047 CDS YP_424331.1 83319546 3828967 417869..420121 1 NC_007633.1 MCAP_0347 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein 420121 3828967 MCAP_0347 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424331.1 417869 D 340047 CDS YP_424332.1 83319626 3829050 420139..422718 1 NC_007633.1 lipoprotein 422718 3829050 MCAP_0348 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424332.1 420139 D 340047 CDS YP_424333.1 83319956 3829117 422903..425152 1 NC_007633.1 MCAP_0349 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein 425152 3829117 MCAP_0349 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424333.1 422903 D 340047 CDS YP_424334.1 83319681 3829072 425172..427751 1 NC_007633.1 lipoprotein 427751 3829072 MCAP_0350 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424334.1 425172 D 340047 CDS YP_424335.1 83319325 3828459 428011..430263 1 NC_007633.1 MCAP_0351 has one membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein 430263 3828459 MCAP_0351 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424335.1 428011 D 340047 CDS YP_424336.1 83319949 3828353 430287..432854 1 NC_007633.1 lipoprotein 432854 3828353 MCAP_0352 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424336.1 430287 D 340047 CDS YP_424337.1 83319499 3828551 432889..434352 1 NC_007633.1 MCAP_0353 has 12 membrane spanning regions; hypothetical protein 434352 3828551 MCAP_0353 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424337.1 432889 D 340047 CDS YP_424338.1 83319918 3828673 434327..434821 1 NC_007633.1 hypothetical protein 434821 3828673 MCAP_0354 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424338.1 434327 D 340047 CDS YP_424339.1 83319680 3829071 434823..435734 1 NC_007633.1 hypothetical protein 435734 3829071 MCAP_0355 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424339.1 434823 D 340047 CDS YP_424340.1 83319308 3828442 435734..436177 1 NC_007633.1 hypothetical protein 436177 3828442 MCAP_0356 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424340.1 435734 D 340047 CDS YP_424341.1 83319895 3828865 436179..438446 1 NC_007633.1 There are 3 membrane spanning regions in MCAP_0357.; hypothetical protein 438446 3828865 MCAP_0357 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424341.1 436179 D 340047 CDS YP_424342.1 83319286 3828320 438451..439998 1 NC_007633.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a catalytic subunit; F0F1 ATP synthase subunit alpha 439998 atpA2 3828320 atpA2 Mycoplasma capricolum subsp. capricolum ATCC 27343 F0F1 ATP synthase subunit alpha YP_424342.1 438451 D 340047 CDS YP_424343.1 83319416 3828797 439998..441377 1 NC_007633.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta 441377 atpD2 3828797 atpD2 Mycoplasma capricolum subsp. capricolum ATCC 27343 F0F1 ATP synthase subunit beta YP_424343.1 439998 D 340047 CDS YP_424344.1 83319350 3828484 complement(441432..443936) 1 NC_007633.1 hypothetical protein 443936 3828484 MCAP_0360 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424344.1 441432 R 340047 CDS YP_424345.1 83319607 3829029 complement(444199..446745) 1 NC_007633.1 hypothetical protein 446745 3829029 MCAP_0361 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424345.1 444199 R 340047 CDS YP_424346.1 83319780 3828844 complement(446899..449406) 1 NC_007633.1 hypothetical protein 449406 3828844 MCAP_0362 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424346.1 446899 R 340047 CDS YP_424347.1 83319285 3828319 449586..450185 1 NC_007633.1 This proteins is 31% identical to the characterized E. coli RdgB, which is a pyrophosphatases active against non-standard purines NTPs. E. coli RdgB appears to act by intercepting non-canonical deoxyribonucleotide triphosphates from replication precursor pools; identified by similarity to SP:P94558; match to protein family HMM PF01725; match to protein family HMM TIGR00042; RdgB/HAM1 family non-canonical purine NTP pyrophosphatase 450185 3828319 MCAP_0363 Mycoplasma capricolum subsp. capricolum ATCC 27343 RdgB/HAM1 family non-canonical purine NTP pyrophosphatase YP_424347.1 449586 D 340047 CDS YP_424348.1 83319378 3828526 450199..450744 1 NC_007633.1 identified by match to protein family HMM PF00588; RNA methyltransferase 450744 3828526 MCAP_0364 Mycoplasma capricolum subsp. capricolum ATCC 27343 RNA methyltransferase YP_424348.1 450199 D 340047 CDS YP_424349.1 83319438 3829136 450744..451610 1 NC_007633.1 identified by match to protein family HMM TIGR00099; match to protein family HMM TIGR01484; HAD superfamily hydrolase 451610 3829136 MCAP_0365 Mycoplasma capricolum subsp. capricolum ATCC 27343 HAD superfamily hydrolase YP_424349.1 450744 D 340047 CDS YP_424350.1 83319920 3828675 451775..453916 1 NC_007633.1 identified by match to protein family HMM PF00004; match to protein family HMM PF07724; ATP-dependent Clp protease, ATP-binding subunit ClpB 453916 3828675 MCAP_0366 Mycoplasma capricolum subsp. capricolum ATCC 27343 ATP-dependent Clp protease, ATP-binding subunit ClpB YP_424350.1 451775 D 340047 CDS YP_424351.1 83319975 3828723 453921..454943 1 NC_007633.1 identified by match to protein family HMM PF01628; match to protein family HMM TIGR00331; heat-inducible transcription repressor HrcA 454943 hrcA 3828723 hrcA Mycoplasma capricolum subsp. capricolum ATCC 27343 heat-inducible transcription repressor HrcA YP_424351.1 453921 D 340047 CDS YP_424352.1 83319669 3828825 454927..455547 1 NC_007633.1 Start site prediction for grpE is uncertain. No ribosome binding site is predicted. We elect to make the largest ORF possible and have the gene start similar to the one choosen for the ortholog in Mycoplasma mycoides SC; identified by match to protein family HMM PF01025; co-chaperone GrpE 455547 grpE 3828825 grpE Mycoplasma capricolum subsp. capricolum ATCC 27343 co-chaperone GrpE YP_424352.1 454927 D 340047 CDS YP_424353.1 83319686 3828296 455607..457382 1 NC_007633.1 HSP70; heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria; molecular chaperone DnaK 457382 dnaK 3828296 dnaK Mycoplasma capricolum subsp. capricolum ATCC 27343 molecular chaperone DnaK YP_424353.1 455607 D 340047 CDS YP_424354.1 83319522 3828575 457447..458565 1 NC_007633.1 HSP40; chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion; chaperone protein DnaJ 458565 dnaJ 3828575 dnaJ Mycoplasma capricolum subsp. capricolum ATCC 27343 chaperone protein DnaJ YP_424354.1 457447 D 340047 CDS YP_424355.1 83319465 3828690 458769..459644 1 NC_007633.1 one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit; 30S ribosomal protein S2 459644 rpsB 3828690 rpsB Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S2 YP_424355.1 458769 D 340047 CDS YP_424356.1 83319962 3829125 459656..460543 1 NC_007633.1 EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu; elongation factor Ts 460543 tsf 3829125 tsf Mycoplasma capricolum subsp. capricolum ATCC 27343 elongation factor Ts YP_424356.1 459656 D 340047 CDS YP_424357.1 83319256 3828822 460546..461151 1 NC_007633.1 There are 3 membrane spanning regions in MCAP_0373.; hypothetical protein 461151 3828822 MCAP_0373 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424357.1 460546 D 340047 CDS YP_424358.1 83319388 3828536 461283..461996 1 NC_007633.1 identified by match to protein family HMM PF00696; match to protein family HMM TIGR02075; uridylate kinase 461996 pyrH 3828536 pyrH Mycoplasma capricolum subsp. capricolum ATCC 27343 uridylate kinase YP_424358.1 461283 D 340047 CDS YP_424359.1 83319658 3828505 462007..462555 1 NC_007633.1 identified by match to protein family HMM PF01765; match to protein family HMM TIGR00496; ribosome recycling factor 462555 frr 3828505 frr Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosome recycling factor YP_424359.1 462007 D 340047 CDS YP_424360.1 83319739 3828392 462557..464221 1 NC_007633.1 catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase; arginyl-tRNA synthetase 464221 argS 3828392 argS Mycoplasma capricolum subsp. capricolum ATCC 27343 arginyl-tRNA synthetase YP_424360.1 462557 D 340047 CDS YP_424361.1 83319964 3829127 469387..473832 1 NC_007633.1 MCAP_0381 has 8 membrane spanning regions; This protein characteristics of an ABC transporter permease; however it is not near any ATPase; identified by match to protein family HMM PF02687; hypothetical protein 473832 3829127 MCAP_0381 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424361.1 469387 D 340047 CDS YP_424362.1 83319969 3829132 473844..474452 1 NC_007633.1 hypothetical protein 474452 3829132 MCAP_0382 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424362.1 473844 D 340047 CDS YP_424363.1 83319370 3829087 474483..475535 1 NC_007633.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily; phenylalanyl-tRNA synthetase subunit alpha 475535 pheS 3829087 pheS Mycoplasma capricolum subsp. capricolum ATCC 27343 phenylalanyl-tRNA synthetase subunit alpha YP_424363.1 474483 D 340047 CDS YP_424364.1 83319488 3828897 475544..477928 1 NC_007633.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily; phenylalanyl-tRNA synthetase subunit beta 477928 pheT 3828897 pheT Mycoplasma capricolum subsp. capricolum ATCC 27343 phenylalanyl-tRNA synthetase subunit beta YP_424364.1 475544 D 340047 CDS YP_424365.1 83319758 3828616 477928..478443 1 NC_007633.1 hypothetical protein 478443 3828616 MCAP_0385 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424365.1 477928 D 340047 CDS YP_424366.1 83319397 3828545 478458..478637 1 NC_007633.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 478637 rpmF 3828545 rpmF Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L32 YP_424366.1 478458 D 340047 CDS YP_424367.1 83319903 3828873 478742..479140 1 NC_007633.1 MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 479140 3828873 MCAP_0387 Mycoplasma capricolum subsp. capricolum ATCC 27343 cell division protein MraZ YP_424367.1 478742 D 340047 CDS YP_424368.1 83319603 3829025 479149..480078 1 NC_007633.1 This protein has 41% identity to the characterized E. coli MraW; identified by similarity to OMNI:SA1192; match to protein family HMM PF01795; match to protein family HMM TIGR00006; S-adenosyl-methyltransferase MraW 480078 mraW 3829025 mraW Mycoplasma capricolum subsp. capricolum ATCC 27343 S-adenosyl-methyltransferase MraW YP_424368.1 479149 D 340047 CDS YP_424369.1 83319280 3828757 480087..481244 1 NC_007633.1 hypothetical protein 481244 3828757 MCAP_0389 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424369.1 480087 D 340047 CDS YP_424370.1 83319750 3828608 481359..482498 1 NC_007633.1 GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function; cell division protein FtsZ 482498 ftsZ 3828608 ftsZ Mycoplasma capricolum subsp. capricolum ATCC 27343 cell division protein FtsZ YP_424370.1 481359 D 340047 CDS YP_424371.1 83319461 3828686 482511..482954 1 NC_007633.1 hypothetical protein 482954 3828686 MCAP_0391 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424371.1 482511 D 340047 CDS YP_424372.1 83319292 3828426 482987..483976 1 NC_007633.1 hypothetical protein 483976 3828426 MCAP_0392 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424372.1 482987 D 340047 CDS YP_424373.1 83319396 3828544 484559..487285 1 NC_007633.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme; isoleucyl-tRNA synthetase 487285 ileS 3828544 ileS Mycoplasma capricolum subsp. capricolum ATCC 27343 isoleucyl-tRNA synthetase YP_424373.1 484559 D 340047 CDS YP_424374.1 83319849 3828943 487294..487902 1 NC_007633.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 487902 lspA 3828943 lspA Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein signal peptidase YP_424374.1 487294 D 340047 CDS YP_424375.1 83319260 3828419 487883..488851 1 NC_007633.1 This protein is 33% identical to the characterized E. coli pseudouridine synthase (PMID: 9814761); identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005; ribosomal large subunit pseudouridine synthase A 488851 3828419 MCAP_0395 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosomal large subunit pseudouridine synthase A YP_424375.1 487883 D 340047 CDS YP_424376.1 83319827 3828919 488835..490145 1 NC_007633.1 MCAP_0396 has 7 membrane spanning regions; hypothetical protein 490145 3828919 MCAP_0396 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424376.1 488835 D 340047 CDS YP_424377.1 83319549 3828970 490172..490633 1 NC_007633.1 identified by similarity to SP:P16006; match to protein family HMM PF00383; deoxycytidylate deaminase 490633 3828970 MCAP_0397 Mycoplasma capricolum subsp. capricolum ATCC 27343 deoxycytidylate deaminase YP_424377.1 490172 D 340047 CDS YP_424378.1 83319976 3828724 490673..491827 1 NC_007633.1 MCAP_0398 has two membrane spanning regions; hypothetical protein 491827 3828724 MCAP_0398 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424378.1 490673 D 340047 CDS YP_424379.1 83319851 3828945 491908..493293 1 NC_007633.1 MCAP_0399 has 2 membrane spanning regions; hypothetical protein 493293 3828945 MCAP_0399 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424379.1 491908 D 340047 CDS YP_424380.1 83319324 3828458 493313..493645 1 NC_007633.1 identified by match to protein family HMM PF01648; match to protein family HMM TIGR00556; holo-(acyl-carrier-protein) synthase 493645 3828458 MCAP_0400 Mycoplasma capricolum subsp. capricolum ATCC 27343 holo-(acyl-carrier-protein) synthase YP_424380.1 493313 D 340047 CDS YP_424381.1 83320014 3828907 493687..494838 1 NC_007633.1 MCAP_0401 has 2 membrane spanning regions; hypothetical protein 494838 3828907 MCAP_0401 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424381.1 493687 D 340047 CDS YP_424382.1 83319707 3828848 494973..495926 1 NC_007633.1 identified by match to protein family HMM PF01553; 1-acyl-sn-glycerol-3-phosphate acyltransferase 495926 3828848 MCAP_0402 Mycoplasma capricolum subsp. capricolum ATCC 27343 1-acyl-sn-glycerol-3-phosphate acyltransferase YP_424382.1 494973 D 340047 CDS YP_424383.1 83319633 3828282 495977..496594 1 NC_007633.1 hypothetical protein 496594 3828282 MCAP_0403 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424383.1 495977 D 340047 CDS YP_424384.1 83319936 3828953 complement(497250..498314) 1 NC_007633.1 lipoprotein 498314 3828953 MCAP_0409 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424384.1 497250 R 340047 CDS YP_424385.1 83319469 3828694 498691..499581 1 NC_007633.1 identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096; hypothetical protein 499581 3828694 MCAP_0410 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424385.1 498691 D 340047 CDS YP_424386.1 83319657 3828504 499603..500004 1 NC_007633.1 hypothetical protein 500004 3828504 MCAP_0411 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424386.1 499603 D 340047 CDS YP_424387.1 83319974 3828722 500149..500451 1 NC_007633.1 identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061; 50S ribosomal protein L21 500451 rplU 3828722 rplU Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L21 YP_424387.1 500149 D 340047 CDS YP_424388.1 83320038 3828337 500454..500768 1 NC_007633.1 identified by match to protein family HMM PF04327; hypothetical protein 500768 3828337 MCAP_0413 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424388.1 500454 D 340047 CDS YP_424389.1 83319594 3829016 500770..501051 1 NC_007633.1 involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 501051 rpmA 3829016 rpmA Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L27 YP_424389.1 500770 D 340047 CDS YP_424390.1 83319454 3828601 501245..502132 1 NC_007633.1 catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid; N-acetylneuraminate lyase 502132 nanA 3828601 nanA Mycoplasma capricolum subsp. capricolum ATCC 27343 N-acetylneuraminate lyase YP_424390.1 501245 D 340047 CDS YP_424391.1 83319608 3829030 502136..503848 1 NC_007633.1 This protein has the 13 TMH characteristic of bacterial sodium:solute symporters. It is not clear what solute is transported in addition to sodium; identified by match to protein family HMM PF00474; sodium/solute symporter family protein 503848 3829030 MCAP_0416 Mycoplasma capricolum subsp. capricolum ATCC 27343 sodium/solute symporter family protein YP_424391.1 502136 D 340047 CDS YP_424392.1 83319313 3828447 503857..504306 1 NC_007633.1 identified by match to protein family HMM PF04074; match to protein family HMM TIGR00022; hypothetical protein 504306 3828447 MCAP_0417 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424392.1 503857 D 340047 CDS YP_424393.1 83319464 3828689 504299..505174 1 NC_007633.1 identified by match to protein family HMM PF00480; ROK family protein 505174 3828689 MCAP_0418 Mycoplasma capricolum subsp. capricolum ATCC 27343 ROK family protein YP_424393.1 504299 D 340047 CDS YP_424394.1 83319759 3828617 505254..505934 1 NC_007633.1 Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate; N-acetylmannosamine-6-phosphate 2-epimerase 505934 3828617 MCAP_0419 Mycoplasma capricolum subsp. capricolum ATCC 27343 N-acetylmannosamine-6-phosphate 2-epimerase YP_424394.1 505254 D 340047 CDS YP_424395.1 83319943 3828960 506088..507437 1 NC_007633.1 This tart site is uncertain. There is no clear ribosome binding site. The start could be at the L or V just upstream; identified by match to protein family HMM PF01546; match to protein family HMM TIGR01887; dipeptidase 507437 3828960 MCAP_0420 Mycoplasma capricolum subsp. capricolum ATCC 27343 dipeptidase YP_424395.1 506088 D 340047 CDS YP_424396.1 83319980 3828728 507518..507952 1 NC_007633.1 There are 4 membrane spanning regions in MCAP_0421.; hypothetical protein 507952 3828728 MCAP_0421 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424396.1 507518 D 340047 CDS YP_424397.1 83319803 3828360 507977..508600 1 NC_007633.1 functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor; uridine kinase 508600 udk 3828360 udk Mycoplasma capricolum subsp. capricolum ATCC 27343 uridine kinase YP_424397.1 507977 D 340047 CDS YP_424398.1 83319646 3828493 508728..509954 1 NC_007633.1 Similar genes are annotated as DNA polymerase IV (EC 2.7.7.7) or damage inducible repair proteins (dinB); identified by match to protein family HMM PF00817; ImpB/MucB/SamB family protein 509954 3828493 MCAP_0423 Mycoplasma capricolum subsp. capricolum ATCC 27343 ImpB/MucB/SamB family protein YP_424398.1 508728 D 340047 CDS YP_424399.1 83319349 3828483 complement(509967..511070) 1 NC_007633.1 identified by match to protein family HMM PF01926; hypothetical protein 511070 3828483 MCAP_0424 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424399.1 509967 R 340047 CDS YP_424400.1 83319410 3828771 complement(511079..511999) 1 NC_007633.1 hypothetical protein 511999 3828771 MCAP_0425 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424400.1 511079 R 340047 CDS YP_424401.1 83319427 3828808 512075..512890 1 NC_007633.1 hypothetical protein 512890 3828808 MCAP_0426 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424401.1 512075 D 340047 CDS YP_424402.1 83319314 3828448 complement(512935..514296) 1 NC_007633.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase 514296 3828448 MCAP_0427 Mycoplasma capricolum subsp. capricolum ATCC 27343 dihydrolipoamide dehydrogenase YP_424402.1 512935 R 340047 CDS YP_424403.1 83319351 3828485 complement(515351..515911) 1 NC_007633.1 identified by similarity to SP:P75243; Holliday junction DNA helicase ruvA 515911 ruvA 3828485 ruvA Mycoplasma capricolum subsp. capricolum ATCC 27343 Holliday junction DNA helicase ruvA YP_424403.1 515351 R 340047 CDS YP_424404.2 162316929 3829047 complement(516022..516186) 1 NC_007633.1 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA; 30S ribosomal protein S21 516186 rpsU 3829047 rpsU Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S21 YP_424404.2 516022 R 340047 CDS YP_424405.1 83319364 3829081 516454..517083 1 NC_007633.1 lipoprotein 517083 3829081 MCAP_0431 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424405.1 516454 D 340047 CDS YP_424406.1 83319990 3828777 517320..518039 1 NC_007633.1 lipoprotein 518039 3828777 MCAP_0432 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424406.1 517320 D 340047 CDS YP_424407.1 83319705 3828846 518278..518916 1 NC_007633.1 lipoprotein 518916 3828846 MCAP_0433 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424407.1 518278 D 340047 CDS YP_424408.1 83319690 3828300 complement(518964..520697) 1 NC_007633.1 hypothetical protein 520697 3828300 MCAP_0434 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424408.1 518964 R 340047 CDS YP_424409.1 83320040 3828339 520850..522502 1 NC_007633.1 There are 2 membrane spanning regions in MCAP_0435.; hypothetical protein 522502 3828339 MCAP_0435 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424409.1 520850 D 340047 CDS YP_424410.1 83319494 3828546 522507..523106 1 NC_007633.1 There are 4 membrane spanning regions in MCAP_0436.; hypothetical protein 523106 3828546 MCAP_0436 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424410.1 522507 D 340047 CDS YP_424411.1 83319776 3828840 complement(523118..523927) 1 NC_007633.1 MCAP_0437 has 6 membrane spanning regions; hypothetical protein 523927 3828840 MCAP_0437 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424411.1 523118 R 340047 CDS YP_424412.1 83319687 3828297 524021..525178 1 NC_007633.1 identified by similarity to SP:O34450; match to protein family HMM PF01979; match to protein family HMM TIGR00221; N-acetylglucosamine-6-phosphate deacetylase 525178 nagA 3828297 nagA Mycoplasma capricolum subsp. capricolum ATCC 27343 N-acetylglucosamine-6-phosphate deacetylase YP_424412.1 524021 D 340047 CDS YP_424413.1 83319961 3829124 525231..526184 1 NC_007633.1 identified by similarity to SP:P13714; match to protein family HMM PF00056; match to protein family HMM PF02866; match to protein family HMM TIGR01771; lactate dehydrogenase 526184 ldh 3829124 ldh Mycoplasma capricolum subsp. capricolum ATCC 27343 lactate dehydrogenase YP_424413.1 525231 D 340047 CDS YP_424414.1 83320009 3828796 complement(526250..526912) 1 NC_007633.1 MCAP_0440 has 6 membrane spanning regions; identified by match to protein family HMM PF01061; hypothetical protein 526912 3828796 MCAP_0440 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424414.1 526250 R 340047 CDS YP_424415.1 83319348 3828482 complement(527269..527469) 1 NC_007633.1 MCAP_0441 is encoded within a truncated form of the Integrative Conjugal Element of M. capricolum (ICEC). A complete element encodes the paralog MCAP_0562 (100% identity); identified by Glimmer2; hypothetical protein 527469 3828482 MCAP_0441 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424415.1 527269 R 340047 CDS YP_424416.1 83319272 3828749 complement(527481..528965) 1 NC_007633.1 MCAP_0442 and MCAP_0561 are paralogs (88% amino acid identity). MCAP_0561 is encoded by Integrative Conjugal Element of M. capricolum (ICEC). MCAP_0442 may be encoded within a remnant of ICEC.; lipoprotein 528965 3828749 MCAP_0442 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424416.1 527481 R 340047 CDS YP_424417.1 83319497 3828549 529220..529492 1 NC_007633.1 hypothetical protein 529492 3828549 MCAP_0443 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424417.1 529220 D 340047 CDS YP_424418.1 83319953 3829114 529607..530716 1 NC_007633.1 MCAP_0444 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. There are 2 membrane spanning regions in MCAP_0444; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 530716 3829114 MCAP_0444 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424418.1 529607 D 340047 CDS YP_424419.1 83320055 3828628 complement(530742..531539) 1 NC_007633.1 MCAP_0446 is a paralog of this triacylglycerol lipase gene; identified by match to protein family HMM PF00561; triacylglycerol lipase 531539 3828628 MCAP_0445 Mycoplasma capricolum subsp. capricolum ATCC 27343 triacylglycerol lipase YP_424419.1 530742 R 340047 CDS YP_424420.1 83319797 3828413 complement(531553..532341) 1 NC_007633.1 There are multiple orthologs of this protein in Mycoplasma mycoides SC. This protien is frame shifted relative to one but not others. In M. capricolum the next gene, MCAP_0445, is a paralog of this likely triacylglycerol lipase gene; identified by match to protein family HMM PF00561; triacylglycerol lipase 532341 3828413 MCAP_0446 Mycoplasma capricolum subsp. capricolum ATCC 27343 triacylglycerol lipase YP_424420.1 531553 R 340047 CDS YP_424421.1 83319901 3828871 532528..532872 1 NC_007633.1 glycine cleavage system H protein 532872 3828871 MCAP_0447 Mycoplasma capricolum subsp. capricolum ATCC 27343 glycine cleavage system H protein YP_424421.1 532528 D 340047 CDS YP_424422.1 83319543 3828830 532879..533730 1 NC_007633.1 hypothetical protein 533730 3828830 MCAP_0448 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424422.1 532879 D 340047 CDS YP_424423.1 83319826 3828918 533708..534745 1 NC_007633.1 identified by match to protein family HMM PF03099; match to protein family HMM TIGR00545; lipoate-protein ligase 534745 3828918 MCAP_0449 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoate-protein ligase YP_424423.1 533708 D 340047 CDS YP_424424.1 83319344 3828478 534745..535923 1 NC_007633.1 identified by similarity to OMNI:SA0392; match to protein family HMM PF00724; NADH:flavin oxidoreductase/NADH oxidase family protein 535923 3828478 MCAP_0450 Mycoplasma capricolum subsp. capricolum ATCC 27343 NADH:flavin oxidoreductase/NADH oxidase family protein YP_424424.1 534745 D 340047 CDS YP_424425.1 83319979 3828727 complement(536187..538070) 1 NC_007633.1 identified by match to protein family HMM PF03202; lipoprotein LppB 538070 3828727 MCAP_0451 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein LppB YP_424425.1 536187 R 340047 CDS YP_424426.1 83319874 3829113 complement(538184..538987) 1 NC_007633.1 The M. mycoides glycerol ABC transporter that is nearly identical to this M. capricolum ABC transporter cassette was biochemically characterized: Vilei EM, Frey J. 2001. Genetic and biochemical characterization of glycerol uptake in mycoplasma mycoides subsp. mycoides SC: its impact on H(2)O(2) production and virulence. Clinical Diagn Lab Immunol. 8(1):85-92; identified by similarity to GP:11934746; match to protein family HMM PF00528; glycerol ABC transporter permease 538987 gtsC 3829113 gtsC Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol ABC transporter permease YP_424426.1 538184 R 340047 CDS YP_424427.1 83319767 3828965 complement(538965..539969) 1 NC_007633.1 The M. mycoides glycerol ABC transporter that is nearly identical to this M. capricolum ABC transporter cassette was biochemically characterized: Vilei EM, Frey J. 2001. Genetic and biochemical characterization of glycerol uptake in mycoplasma mycoides subsp. mycoides SC: its impact on H(2)O(2) production and virulence. Clin Diagn Lab Immunol. 8(1):85-92; identified by similarity to GP:11934745; glycerol ABC transporter permease 539969 gtsB 3828965 gtsB Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol ABC transporter permease YP_424427.1 538965 R 340047 CDS YP_424428.1 83319663 3828510 complement(539962..541173) 1 NC_007633.1 The M. mycoides glycerol ABC transporter that is nearly identical to this M. capricolum ABC transporter cassette was biochemically characterized: Vilei EM, Frey J. 2001. Genetic and biochemical characterization of glycerol uptake in mycoplasma mycoides subsp. mycoides SC: its impact on H(2)O(2) production and virulence. Clinical Diagn Lab Immunol. 8(1):85-92; identified by similarity to GP:11934744; match to protein family HMM PF00005; glycerol ABC transporter ATP-binding protein 541173 gtsA 3828510 gtsA Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol ABC transporter ATP-binding protein YP_424428.1 539962 R 340047 CDS YP_424429.1 83319614 3829036 complement(541179..543374) 1 NC_007633.1 recombinase D 543374 3829036 MCAP_0455 Mycoplasma capricolum subsp. capricolum ATCC 27343 recombinase D YP_424429.1 541179 R 340047 CDS YP_424430.1 83319790 3828405 complement(543485..546184) 1 NC_007633.1 identified by similarity to SP:P72525; match to protein family HMM PF00521; match to protein family HMM PF03989; match to protein family HMM TIGR01061; DNA topoisomerase IV subunit A 546184 parC 3828405 parC Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA topoisomerase IV subunit A YP_424430.1 543485 R 340047 CDS YP_424431.1 83319442 3829140 complement(546186..548117) 1 NC_007633.1 identified by similarity to SP:Q59192; match to protein family HMM PF00204; match to protein family HMM PF00986; match to protein family HMM PF01751; match to protein family HMM PF02518; match to protein family HMM TIGR01058; DNA topoisomerase IV subunit B 548117 parE 3829140 parE Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA topoisomerase IV subunit B YP_424431.1 546186 R 340047 CDS YP_424432.1 83319987 3828735 548347..549924 1 NC_007633.1 identified by similarity to SP:P00550; match to protein family HMM PF02302; PTS system mannitol-specific transporter subunit IIBC 549924 3828735 MCAP_0458 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system mannitol-specific transporter subunit IIBC YP_424432.1 548347 D 340047 CDS YP_424433.1 83319579 3829001 549927..550367 1 NC_007633.1 identified by similarity to SP:P27547; match to protein family HMM PF00359; PTS system mannitol-specific transporter subunit IIA 550367 3829001 MCAP_0459 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system mannitol-specific transporter subunit IIA YP_424433.1 549927 D 340047 CDS YP_424434.1 83319446 3829144 550367..551266 1 NC_007633.1 similar to full-length Gnd, these proteins seems to have a truncated C-terminal 6PGD domainin; in Methylobacillus flagellatus this gene is essential for NAD+-dependent oxidation of 6-phosphogluconate; 6-phosphogluconate dehydrogenase 551266 3829144 MCAP_0460 Mycoplasma capricolum subsp. capricolum ATCC 27343 6-phosphogluconate dehydrogenase YP_424434.1 550367 D 340047 CDS YP_424435.1 83319779 3828843 complement(551321..552736) 1 NC_007633.1 identified by match to protein family HMM PF00171; aldehyde dehydrogenase (NAD) family protein 552736 3828843 MCAP_0461 Mycoplasma capricolum subsp. capricolum ATCC 27343 aldehyde dehydrogenase (NAD) family protein YP_424435.1 551321 R 340047 CDS YP_424436.1 83319453 3828600 complement(552903..553670) 1 NC_007633.1 identified by similarity to OMNI:NTL01LP1288; match to protein family HMM PF00588; match to protein family HMM PF08032; RNA methyltransferase 553670 3828600 MCAP_0462 Mycoplasma capricolum subsp. capricolum ATCC 27343 RNA methyltransferase YP_424436.1 552903 R 340047 CDS YP_424437.1 83319664 3828511 complement(553687..554190) 1 NC_007633.1 The gene is conserved in the sprioplasma/mycoides group and the hominus group of the mycoplasmas but not in any of the pneumoniae group species.; hypothetical protein 554190 3828511 MCAP_0463 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424437.1 553687 R 340047 CDS YP_424438.1 83319773 3828836 complement(554231..554677) 1 NC_007633.1 MCAP_0464 has 3 membrane spanning regions; hypothetical protein 554677 3828836 MCAP_0464 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424438.1 554231 R 340047 CDS YP_424439.1 83319876 3828818 complement(554703..555986) 1 NC_007633.1 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family; glucose-6-phosphate isomerase 555986 pgi 3828818 pgi Mycoplasma capricolum subsp. capricolum ATCC 27343 glucose-6-phosphate isomerase YP_424439.1 554703 R 340047 CDS YP_424440.1 83319496 3828548 complement(556207..558102) 1 NC_007633.1 identified by similarity to GB:AAD40473.1; match to protein family HMM PF01431; match to protein family HMM PF05649; endopeptidase O 558102 pepO 3828548 pepO Mycoplasma capricolum subsp. capricolum ATCC 27343 endopeptidase O YP_424440.1 556207 R 340047 CDS YP_424441.1 83319768 3828831 complement(558116..558685) 1 NC_007633.1 identified by match to protein family HMM PF01812; 5-formyltetrahydrofolate cyclo-ligase 558685 3828831 MCAP_0467 Mycoplasma capricolum subsp. capricolum ATCC 27343 5-formyltetrahydrofolate cyclo-ligase YP_424441.1 558116 R 340047 CDS YP_424442.1 83320031 3828329 complement(558678..559115) 1 NC_007633.1 hypothetical protein 559115 3828329 MCAP_0468 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424442.1 558678 R 340047 CDS YP_424443.1 83319944 3828961 complement(559119..560357) 1 NC_007633.1 identified by match to protein family HMM PF00266; class V aminotransferase 560357 3828961 MCAP_0469 Mycoplasma capricolum subsp. capricolum ATCC 27343 class V aminotransferase YP_424443.1 559119 R 340047 CDS YP_424444.1 83319431 3828812 560551..563544 1 NC_007633.1 lipoprotein 563544 3828812 MCAP_0470 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424444.1 560551 D 340047 CDS YP_424445.1 83319261 3828738 563566..565737 1 NC_007633.1 lipoprotein 565737 3828738 MCAP_0471 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424445.1 563566 D 340047 CDS YP_424446.1 83319570 3828992 565740..566135 1 NC_007633.1 identified by similarity to SP:O07513; match to protein family HMM PF01230; HIT family protein 566135 3828992 MCAP_0472 Mycoplasma capricolum subsp. capricolum ATCC 27343 HIT family protein YP_424446.1 565740 D 340047 CDS YP_424447.1 83319859 3829097 complement(566171..567151) 1 NC_007633.1 identified by match to protein family HMM PF01336; match to protein family HMM PF01966; hypothetical protein 567151 3829097 MCAP_0473 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424447.1 566171 R 340047 CDS YP_424448.1 83319985 3828733 complement(567220..567876) 1 NC_007633.1 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine; uracil-DNA glycosylase 567876 ung 3828733 ung Mycoplasma capricolum subsp. capricolum ATCC 27343 uracil-DNA glycosylase YP_424448.1 567220 R 340047 CDS YP_424449.1 83319703 3828313 complement(567869..568798) 1 NC_007633.1 identified by similarity to SP:P39841; match to protein family HMM PF01238; phosphomannose isomerase type I 568798 pmi 3828313 pmi Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphomannose isomerase type I YP_424449.1 567869 R 340047 CDS YP_424450.1 83319822 3828914 complement(568919..570235) 1 NC_007633.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine; tRNA (uracil-5-)-methyltransferase Gid 570235 gid 3828914 gid Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA (uracil-5-)-methyltransferase Gid YP_424450.1 568919 R 340047 CDS YP_424451.1 83319533 3828586 complement(570228..570911) 1 NC_007633.1 identified by similarity to SP:P46719; match to protein family HMM PF03932; copper homeostasis protein CutC 570911 3828586 MCAP_0477 Mycoplasma capricolum subsp. capricolum ATCC 27343 copper homeostasis protein CutC YP_424451.1 570228 R 340047 CDS YP_424452.1 83319655 3828502 complement(570902..572065) 1 NC_007633.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 572065 metK 3828502 metK Mycoplasma capricolum subsp. capricolum ATCC 27343 S-adenosylmethionine synthetase YP_424452.1 570902 R 340047 CDS YP_424453.1 83319258 3828417 complement(572276..573049) 1 NC_007633.1 identified by match to protein family HMM PF00149; match to protein family HMM TIGR00282; hypothetical protein 573049 3828417 MCAP_0479 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424453.1 572276 R 340047 CDS YP_424454.1 83319384 3828532 complement(573037..573378) 1 NC_007633.1 The p13 protein is encoded by the same operon as a protein homologous to the 54 kDa subunit of SRP, suggesting a functional relationship between the p13 protein and the SRP pathway. The helix-turn-helix motif, suggests the p13 proteins have a regulatory function; identified by similarity to SP:O05290; match to protein family HMM PF04297; DNA-binding protein 573378 p13 3828532 p13 Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-binding protein YP_424454.1 573037 R 340047 CDS YP_424455.1 83319748 3828606 complement(573362..574636) 1 NC_007633.1 identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM TIGR00064; signal recognition particle-docking protein FtsY 574636 ftsY 3828606 ftsY Mycoplasma capricolum subsp. capricolum ATCC 27343 signal recognition particle-docking protein FtsY YP_424455.1 573362 R 340047 CDS YP_424456.1 83319786 3828401 complement(574705..575376) 1 NC_007633.1 identified by match to protein family HMM PF01895; match to protein family HMM TIGR02135; phosphate transport system regulatory protein PhoU 575376 3828401 MCAP_0482 Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphate transport system regulatory protein PhoU YP_424456.1 574705 R 340047 CDS YP_424457.1 83319542 3828595 complement(575385..576194) 1 NC_007633.1 Part of a 3 transporter gene operon; identified by similarity to SP:P46341; match to protein family HMM PF00005; match to protein family HMM TIGR00972; phosphate ABC transporter ATP-binding protein 576194 pstB 3828595 pstB Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphate ABC transporter ATP-binding protein YP_424457.1 575385 R 340047 CDS YP_424458.1 83319640 3828289 complement(576187..578277) 1 NC_007633.1 This gene has 30% identity to the characterized E. coli PstA. Part of a 3 transporter gene operon; identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974; match to protein family HMM TIGR02138; phosphate ABC transporter permease 578277 3828289 MCAP_0484 Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphate ABC transporter permease YP_424458.1 576187 R 340047 CDS YP_424459.1 83319693 3828303 complement(578281..579492) 1 NC_007633.1 The start site of this protein makes it 25-30 amino acids longer than ortholgous genes. There are no other viable start sites that look better. Part of a 3 transporter gene operon.; phosphate ABC transporter substrate-binding protein 579492 3828303 MCAP_0485 Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphate ABC transporter substrate-binding protein YP_424459.1 578281 R 340047 CDS YP_424460.1 83319383 3828531 complement(579583..580017) 1 NC_007633.1 hypothetical protein 580017 3828531 MCAP_0486 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424460.1 579583 R 340047 CDS YP_424461.1 83319933 3828513 complement(580246..580443) 1 NC_007633.1 required for 70S ribosome assembly; 50S ribosomal protein L28 580443 rpmB 3828513 rpmB Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L28 YP_424461.1 580246 R 340047 CDS YP_424462.1 83319555 3828977 580603..580932 1 NC_007633.1 hypothetical protein 580932 3828977 MCAP_0489 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424462.1 580603 D 340047 CDS YP_424463.1 83319282 3828316 580962..582605 1 NC_007633.1 This protein contains the predicted phosphatase domain of the dihydroxyacetone kinase family; identified by match to protein family HMM PF02734; dihydroxyacetone kinase 2 domain-containing protein 582605 3828316 MCAP_0490 Mycoplasma capricolum subsp. capricolum ATCC 27343 dihydroxyacetone kinase 2 domain-containing protein YP_424463.1 580962 D 340047 CDS YP_424464.1 83319479 3828888 582637..583641 1 NC_007633.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; glycerol-3-phosphate acyltransferase PlsX 583641 plsX 3828888 plsX Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol-3-phosphate acyltransferase PlsX YP_424464.1 582637 D 340047 CDS YP_424465.1 83319588 3829010 583631..584329 1 NC_007633.1 identified by similarity to SP:P51833; match to protein family HMM PF00035; match to protein family HMM PF00636; match to protein family HMM TIGR02191; ribonuclease III 584329 3829010 MCAP_0492 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribonuclease III YP_424465.1 583631 D 340047 CDS YP_424466.1 83319679 3829070 584513..584908 1 NC_007633.1 Among the mycoplasmas this has similar genes in Ureaplasma parvum and M. mycoides. It is in COG3600 (uncharacterized phage associated proteins); identified by Glimmer2; hypothetical protein 584908 3829070 MCAP_0493 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424466.1 584513 D 340047 CDS YP_424467.1 83319800 3828357 584911..585297 1 NC_007633.1 hypothetical protein 585297 3828357 MCAP_0494 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424467.1 584911 D 340047 CDS YP_424468.1 83319729 3828382 585624..588590 1 NC_007633.1 identified by match to protein family HMM PF02463; match to protein family HMM PF02483; match to protein family HMM PF06470; match to protein family HMM TIGR00650; match to protein family HMM TIGR02168; structural maintenance of chromosomes (SMC) superfamily protein 588590 3828382 MCAP_0495 Mycoplasma capricolum subsp. capricolum ATCC 27343 structural maintenance of chromosomes (SMC) superfamily protein YP_424468.1 585624 D 340047 CDS YP_424469.1 83319815 3828372 complement(588629..590893) 1 NC_007633.1 identified by similarity to SP:O34098; match to protein family HMM PF01842; match to protein family HMM PF01966; match to protein family HMM PF02824; match to protein family HMM PF04607; match to protein family HMM TIGR00691; RelA/SpoT family protein 590893 3828372 MCAP_0496 Mycoplasma capricolum subsp. capricolum ATCC 27343 RelA/SpoT family protein YP_424469.1 588629 R 340047 CDS YP_424470.1 83319437 3829135 complement(590953..591465) 1 NC_007633.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 591465 apt 3829135 apt Mycoplasma capricolum subsp. capricolum ATCC 27343 adenine phosphoribosyltransferase YP_424470.1 590953 R 340047 CDS YP_424471.1 83319955 3829116 complement(591477..595691) 1 NC_007633.1 MCAP_0498 has 12 membrane spanning regions; hypothetical protein 595691 3829116 MCAP_0498 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424471.1 591477 R 340047 CDS YP_424472.1 83319610 3829032 complement(595793..597304) 1 NC_007633.1 MCAP_0499 has 6 membrane spanning regions; identified by match to protein family HMM PF02588; hypothetical protein 597304 3829032 MCAP_0499 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424472.1 595793 R 340047 CDS YP_424473.1 83319293 3828427 complement(597343..598704) 1 NC_007633.1 identified by similarity to OMNI:SA1615; match to protein family HMM PF00270; match to protein family HMM PF00271; DEAD/DEAH box helicase 598704 3828427 MCAP_0500 Mycoplasma capricolum subsp. capricolum ATCC 27343 DEAD/DEAH box helicase YP_424473.1 597343 R 340047 CDS YP_424474.1 83319709 3828850 complement(598713..599489) 1 NC_007633.1 There is significant homology to an uncharacterized family of proteins. One member of this family NIF3 (NGG1p interacting factor 3) interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex the exact function of this interaction is unknown; identified by match to protein family HMM PF01784; hypothetical protein 599489 3828850 MCAP_0501 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424474.1 598713 R 340047 CDS YP_424475.1 83319817 3828374 complement(599476..600153) 1 NC_007633.1 identified by match to protein family HMM PF04816; hypothetical protein 600153 3828374 MCAP_0502 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424475.1 599476 R 340047 CDS YP_424476.1 83319868 3829106 complement(600156..601673) 1 NC_007633.1 identified by similarity to SP:Q59753; match to protein family HMM PF04539; match to protein family HMM PF04542; RNA polymerase sigma factor RpoD 601673 rpoD 3829106 rpoD Mycoplasma capricolum subsp. capricolum ATCC 27343 RNA polymerase sigma factor RpoD YP_424476.1 600156 R 340047 CDS YP_424477.1 83319946 3828350 complement(601676..603490) 1 NC_007633.1 identified by similarity to SP:P05096; match to protein family HMM PF01751; match to protein family HMM PF01807; match to protein family HMM TIGR01391; DNA primase 603490 dnaG 3828350 dnaG Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA primase YP_424477.1 601676 R 340047 CDS YP_424478.1 83319862 3829100 complement(603527..604897) 1 NC_007633.1 Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase 604897 glyS 3829100 glyS Mycoplasma capricolum subsp. capricolum ATCC 27343 glycyl-tRNA synthetase YP_424478.1 603527 R 340047 CDS YP_424479.1 83319326 3828460 complement(604961..605710) 1 NC_007633.1 identified by similarity to SP:P42095; match to protein family HMM PF02565; match to protein family HMM TIGR00613; DNA repair protein RecO 605710 3828460 MCAP_0506 Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA repair protein RecO YP_424479.1 604961 R 340047 CDS YP_424480.1 83319405 3828766 complement(605710..606615) 1 NC_007633.1 Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome; GTP-binding protein Era 606615 era 3828766 era Mycoplasma capricolum subsp. capricolum ATCC 27343 GTP-binding protein Era YP_424480.1 605710 R 340047 CDS YP_424481.1 83319995 3828782 complement(606618..607112) 1 NC_007633.1 identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043; hypothetical protein 607112 3828782 MCAP_0508 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424481.1 606618 R 340047 CDS YP_424482.1 83319878 3828702 complement(607118..609007) 1 NC_007633.1 identified by match to protein family HMM PF03412; peptidase C39 family protein 609007 3828702 MCAP_0509 Mycoplasma capricolum subsp. capricolum ATCC 27343 peptidase C39 family protein YP_424482.1 607118 R 340047 CDS YP_424483.1 83319368 3829085 complement(609000..609548) 1 NC_007633.1 identified by match to protein family HMM PF01965; match to protein family HMM TIGR01383; DJ-1 family protein 609548 3829085 MCAP_0510 Mycoplasma capricolum subsp. capricolum ATCC 27343 DJ-1 family protein YP_424483.1 609000 R 340047 CDS YP_424484.1 83319322 3828456 complement(609596..614857) 1 NC_007633.1 MCAP_0511 has 8 membrane spanning regions; MCAP_0511 may be a transporter permease; identified by match to protein family HMM PF02687; hypothetical protein 614857 3828456 MCAP_0511 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424484.1 609596 R 340047 CDS YP_424485.1 83319406 3828767 617508..619751 1 NC_007633.1 lipoprotein 619751 3828767 MCAP_0513 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424485.1 617508 D 340047 CDS YP_424486.1 83319880 3828704 619809..622079 1 NC_007633.1 lipoprotein 622079 3828704 MCAP_0514 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424486.1 619809 D 340047 CDS YP_424487.1 83319965 3829128 complement(622111..623349) 1 NC_007633.1 AAA ATPases are often associated with chaparonins. This gene is adjacent to the ATP-dependent protease La and trigger factor genes; identified by match to protein family HMM PF00004; recombination factor protein RarA 623349 3829128 MCAP_0515 Mycoplasma capricolum subsp. capricolum ATCC 27343 recombination factor protein RarA YP_424487.1 622111 R 340047 CDS YP_424488.1 83319891 3828715 complement(623462..625801) 1 NC_007633.1 identified by match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM TIGR00763; ATP-dependent protease La 625801 lon 3828715 lon Mycoplasma capricolum subsp. capricolum ATCC 27343 ATP-dependent protease La YP_424488.1 623462 R 340047 CDS YP_424489.1 83319723 3828864 complement(625920..627206) 1 NC_007633.1 identified by match to protein family HMM PF00254; match to protein family HMM PF05697; match to protein family HMM PF05698; match to protein family HMM TIGR00115; trigger factor 627206 tig 3828864 tig Mycoplasma capricolum subsp. capricolum ATCC 27343 trigger factor YP_424489.1 625920 R 340047 CDS YP_424490.1 83319794 3828409 complement(627223..627525) 1 NC_007633.1 hypothetical protein 627525 3828409 MCAP_0518 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424490.1 627223 R 340047 CDS YP_424491.1 83319745 3828603 complement(627543..628097) 1 NC_007633.1 identified by match to protein family HMM PF01132; match to protein family HMM TIGR00038; translation elongation factor P 628097 efp 3828603 efp Mycoplasma capricolum subsp. capricolum ATCC 27343 translation elongation factor P YP_424491.1 627543 R 340047 CDS YP_424492.1 83319576 3828998 complement(628187..629140) 1 NC_007633.1 identified by similarity to SP:P23882; match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460; methionyl-tRNA formyltransferase 629140 fmt 3828998 fmt Mycoplasma capricolum subsp. capricolum ATCC 27343 methionyl-tRNA formyltransferase YP_424492.1 628187 R 340047 CDS YP_424493.1 83319463 3828688 complement(629130..631274) 1 NC_007633.1 hypothetical protein 631274 3828688 MCAP_0521 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424493.1 629130 R 340047 CDS YP_424494.1 83319952 3828356 complement(631351..631968) 1 NC_007633.1 MCAP_0522 has 1 membrane spanning region, N-terminal.; hypothetical protein 631968 3828356 MCAP_0522 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424494.1 631351 R 340047 CDS YP_424495.1 83319617 3829039 complement(632010..633137) 1 NC_007633.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 633137 mnmA 3829039 mnmA Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA-specific 2-thiouridylase MnmA YP_424495.1 632010 R 340047 CDS YP_424496.1 83320054 3828627 complement(633233..634117) 1 NC_007633.1 lipoprotein 634117 3828627 MCAP_0524 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424496.1 633233 R 340047 CDS YP_424497.1 83320052 3828625 complement(634769..635542) 1 NC_007633.1 lipoprotein 635542 3828625 MCAP_0525 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424497.1 634769 R 340047 CDS YP_424498.1 83319429 3828810 complement(635564..636367) 1 NC_007633.1 lipoprotein 636367 3828810 MCAP_0526 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424498.1 635564 R 340047 CDS YP_424499.1 83319354 3828488 complement(636581..637225) 1 NC_007633.1 hypothetical protein 637225 3828488 MCAP_0527 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424499.1 636581 R 340047 CDS YP_424500.1 83319600 3829022 complement(637250..637885) 1 NC_007633.1 identified by similarity to SP:O32028; match to protein family HMM PF01048; match to protein family HMM TIGR01704; MTA/SAH nucleosidase 637885 3829022 MCAP_0528 Mycoplasma capricolum subsp. capricolum ATCC 27343 MTA/SAH nucleosidase YP_424500.1 637250 R 340047 CDS YP_424501.1 83319440 3829138 complement(637908..639011) 1 NC_007633.1 catalyzes the reversible adenylation of nicotinate mononucleotide to nicotinic acid adenine dinucleotide; nicotinate-nucleotide adenylyltransferase 639011 nadD 3829138 nadD Mycoplasma capricolum subsp. capricolum ATCC 27343 nicotinate-nucleotide adenylyltransferase YP_424501.1 637908 R 340047 CDS YP_424502.1 83319788 3828403 complement(639029..639274) 1 NC_007633.1 MCAP_0530 has 1 membrane spanning region; hypothetical protein 639274 3828403 MCAP_0530 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424502.1 639029 R 340047 CDS YP_424503.1 83319278 3828755 complement(639292..640053) 1 NC_007633.1 identified by similarity to SP:P08164; match to protein family HMM PF02540; match to protein family HMM TIGR00552; NH3-dependent NAD+ synthetase 640053 3828755 MCAP_0531 Mycoplasma capricolum subsp. capricolum ATCC 27343 NH3-dependent NAD+ synthetase YP_424503.1 639292 R 340047 CDS YP_424504.1 83319638 3828287 complement(640031..641332) 1 NC_007633.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 641332 obgE 3828287 obgE Mycoplasma capricolum subsp. capricolum ATCC 27343 GTPase ObgE YP_424504.1 640031 R 340047 CDS YP_424505.1 83319379 3828527 complement(641403..641711) 1 NC_007633.1 hypothetical protein 641711 3828527 MCAP_0533 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424505.1 641403 R 340047 CDS YP_424506.1 83319307 3828441 complement(641701..642453) 1 NC_007633.1 hypothetical protein 642453 3828441 MCAP_0534 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424506.1 641701 R 340047 CDS YP_424507.1 83319971 3828719 complement(642641..644245) 1 NC_007633.1 There are very similar proteins in M mycoides (93% amino acid identity) and Mesoplasma florum (32% identit).; hypothetical protein 644245 3828719 MCAP_0536 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424507.1 642641 R 340047 CDS YP_424508.1 83319875 3828817 complement(644285..646138) 1 NC_007633.1 The next gene upstream is also an ABC transporter ATP-binding protein/permease. No substrate can be predicted for either element of the cassette; identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease 646138 3828817 MCAP_0537 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein/permease YP_424508.1 644285 R 340047 CDS YP_424509.1 83319922 3828677 complement(646156..648027) 1 NC_007633.1 The next gene downstream is also an ABC transporter ATP-binding protein/permease. No substrate can be predicted for either element of the cassette; identified by match to protein family HMM PF00005; match to protein family HMM PF00664; ABC transporter ATP-binding protein/permease 648027 3828677 MCAP_0538 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein/permease YP_424509.1 646156 R 340047 CDS YP_424510.1 83319652 3828499 complement(648243..648548) 1 NC_007633.1 identified by match to protein family HMM PF00436; single-strand binding protein family 648548 3828499 MCAP_0539 Mycoplasma capricolum subsp. capricolum ATCC 27343 single-strand binding protein family YP_424510.1 648243 R 340047 CDS YP_424511.1 83319782 3828397 648710..649948 1 NC_007633.1 MCAP_0540 has 11 transmembrane regions; identified by similarity to SP:P31064; match to protein family HMM PF04143; YeeE/YedE family protein 649948 3828397 MCAP_0540 Mycoplasma capricolum subsp. capricolum ATCC 27343 YeeE/YedE family protein YP_424511.1 648710 D 340047 CDS YP_424512.1 83319939 3828956 649951..651747 1 NC_007633.1 identified by match to protein family HMM PF00581; match to protein family HMM PF02852; match to protein family HMM PF07992; hypothetical protein 651747 3828956 MCAP_0541 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424512.1 649951 D 340047 CDS YP_424513.1 83319843 3828937 complement(651769..652392) 1 NC_007633.1 identified by match to protein family HMM PF01351; ribonuclease HII 652392 3828937 MCAP_0542 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribonuclease HII YP_424513.1 651769 R 340047 CDS YP_424514.1 83319346 3828480 complement(652386..653336) 1 NC_007633.1 identified by match to protein family HMM PF01926; match to protein family HMM TIGR00650; GTPase family protein 653336 3828480 MCAP_0543 Mycoplasma capricolum subsp. capricolum ATCC 27343 GTPase family protein YP_424514.1 652386 R 340047 CDS YP_424515.1 83320044 3828343 complement(653429..653821) 1 NC_007633.1 this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site; 50S ribosomal protein L19 653821 rplS 3828343 rplS Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L19 YP_424515.1 653429 R 340047 CDS YP_424516.1 83319498 3828550 complement(653823..654545) 1 NC_007633.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase 654545 trmD 3828550 trmD Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA (guanine-N(1)-)-methyltransferase YP_424516.1 653823 R 340047 CDS YP_424517.1 83319392 3828540 complement(654547..655041) 1 NC_007633.1 identified by match to protein family HMM TIGR02273; 16S rRNA processing protein RimM 655041 3828540 MCAP_0546 Mycoplasma capricolum subsp. capricolum ATCC 27343 16S rRNA processing protein RimM YP_424517.1 654547 R 340047 CDS YP_424518.1 83319787 3828402 complement(655059..655385) 1 NC_007633.1 binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity; 30S ribosomal protein S16 655385 rpsP 3828402 rpsP Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S16 YP_424518.1 655059 R 340047 CDS YP_424519.1 83319737 3828390 complement(655474..655941) 1 NC_007633.1 identified by match to protein family HMM PF02590; hypothetical protein 655941 3828390 MCAP_0548 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424519.1 655474 R 340047 CDS YP_424520.1 83319981 3828729 complement(655947..657290) 1 NC_007633.1 identified by similarity to SP:P37105; match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM PF02978; match to protein family HMM TIGR00959; signal recognition particle protein 657290 ffh 3828729 ffh Mycoplasma capricolum subsp. capricolum ATCC 27343 signal recognition particle protein YP_424520.1 655947 R 340047 CDS YP_424521.1 83319781 3828845 complement(657320..658849) 1 NC_007633.1 protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP; phosphodiesterase 658849 3828845 MCAP_0550 Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphodiesterase YP_424521.1 657320 R 340047 CDS YP_424522.1 83319502 3828554 complement(659001..659987) 1 NC_007633.1 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs; recombinase A 659987 recA 3828554 recA Mycoplasma capricolum subsp. capricolum ATCC 27343 recombinase A YP_424522.1 659001 R 340047 CDS YP_424523.1 83319299 3828433 complement(660079..660627) 1 NC_007633.1 identified by similarity to SP:P46323; match to protein family HMM PF02464; match to protein family HMM TIGR00199; similar to competence/damage-inducible protein CinA; hypothetical protein 660627 3828433 MCAP_0552 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424523.1 660079 R 340047 CDS YP_424524.1 83320059 3828632 661194..662042 1 NC_007633.1 MCAP_0554 is the first ORF of an Integrative Conjugal Element (ICE) of M. capricolum strain Kid (designated ICEC); Exhibits modest similarity to first ORF of the related element ICEF of Mycoplasma fermentans. MCAP_0554 has 1 membrane spanning region; ICEC is located between nucleotides 661011 and 685387 and encodes ORFs MCAP_0554-MCAP_0571.; hypothetical protein 662042 3828632 MCAP_0554 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424524.1 661194 D 340047 CDS YP_424525.1 83319814 3828371 663622..664455 1 NC_007633.1 MCAP_0556 is encoded within ICEC element; identified by similarity to GP:21538805; C-5 cytosine-specific DNA methylase 664455 3828371 MCAP_0556 Mycoplasma capricolum subsp. capricolum ATCC 27343 C-5 cytosine-specific DNA methylase YP_424525.1 663622 D 340047 CDS YP_424526.1 83319592 3829014 664567..665148 1 NC_007633.1 MCAP_0557, resident within ICEC element, encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_055 has 1 membrane spanning region; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 665148 3829014 MCAP_0557 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424526.1 664567 D 340047 CDS YP_424527.1 83319482 3828891 665588..665737 1 NC_007633.1 MCAP_0558 is encoded within ICEC element; identified by Glimmer2; hypothetical protein 665737 3828891 MCAP_0558 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424527.1 665588 D 340047 CDS YP_424528.1 83319401 3828762 666111..668111 1 NC_007633.1 MCAP_0559 is encoded within ICEC element and exhibits homology to multiple members of the TraG/TraD family of proteins, associated with conjugal plasmids or elements. MACP0559 has 2 membrane spanning regions; identified by match to protein family HMM PF02534; TraG/TraD family membrane protein 668111 3828762 MCAP_0559 Mycoplasma capricolum subsp. capricolum ATCC 27343 TraG/TraD family membrane protein YP_424528.1 666111 D 340047 CDS YP_424529.1 83319529 3828582 668143..669558 1 NC_007633.1 MCAP_0560, encoded within ICEC, exhibits homology to LtrC-like proteins encoded by plasmids and mobile DNAs.; hypothetical protein 669558 3828582 MCAP_0560 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424529.1 668143 D 340047 CDS YP_424530.1 83320007 3828794 669691..671172 1 NC_007633.1 MCAP_0561 is encoded within Integrative Conjugal Element of M. capricolum (ICEC). MCAP_0561 and MCAP_0442 are paralogs (88% amino acid identity). MCAP_0422 occurs at a second genomic locus, that probably represents a truncated remnant of ICEC; lipoprotein 671172 3828794 MCAP_0561 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424530.1 669691 D 340047 CDS YP_424531.1 83319885 3828709 671184..671384 1 NC_007633.1 MCAP_0562 is resident on the Integrative Conjugal Element of M. capricolum (ICEC). A truncated form of this element encodes the paralog MCAP_0441 (100% identity); identified by Glimmer2; hypothetical protein 671384 3828709 MCAP_0562 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424531.1 671184 D 340047 CDS YP_424532.1 83319411 3828772 671489..671815 1 NC_007633.1 MCAP_0563, resident within ICEC, has 2 membrane spanning regions; hypothetical protein 671815 3828772 MCAP_0563 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424532.1 671489 D 340047 CDS YP_424533.1 83319294 3828428 671819..673462 1 NC_007633.1 MCAP_0564 has 8 membrane spanning regions; MCAP_0564 is encoded within the Integtaive Conjugal Element of M. capricolum (ICEC). Weak homology to ICEF ORF16 in Mycoplasma fermentans.; hypothetical protein 673462 3828428 MCAP_0564 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424533.1 671819 D 340047 CDS YP_424534.1 83319829 3828922 673465..676302 1 NC_007633.1 MCAP_0565 is encoded within ICEC and is a NTPase which exhibits homology to multiple TraE/TrsE proteins encoded with conjugative plasmids and elements. MCAP_0565 has 2 membrane spanning regions; hypothetical protein 676302 3828922 MCAP_0565 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424534.1 673465 D 340047 CDS YP_424535.1 83319718 3828859 676321..676944 1 NC_007633.1 MCAP_0566 is encoded by the Integrative Conjugal Element of M. capricolum (ICEC) and exhibits modest homology to ORF18 encoded by ICEF of M. fermentans; identified by Glimmer2; hypothetical protein 676944 3828859 MCAP_0566 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424535.1 676321 D 340047 CDS YP_424536.1 83319635 3828284 676937..680959 1 NC_007633.1 MCAP_0567 is encoded within Integrative Conjugal Element of M. capricolum (ICEC) and exhibits homology to ORF19 of ICEF of M. fermentans. MCAP_0567 has one membrane spanning region (C-terminal), and a possible signal peptide.; hypothetical protein 680959 3828284 MCAP_0567 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424536.1 676937 D 340047 CDS YP_424537.1 83319534 3828587 681011..681991 1 NC_007633.1 Hypothetical protein encoded within Integrative Conjugal Element of M. capricolum (ICEC). The sequence of the small stable RNA mcs4a starts 10nt upstream of MCAP_0568 start codon and extends 110 nt into the MCAP_0568 coding sequence; identified by Glimmer2; hypothetical protein 681991 3828587 MCAP_0568 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424537.1 681011 D 340047 CDS YP_424538.1 83320043 3828342 682175..682540 1 NC_007633.1 Hypothetical ORF encoded within Integrative Conjugal Element of M. capricolum (ICEC); identified by Glimmer2; hypothetical protein 682540 3828342 MCAP_0569 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424538.1 682175 D 340047 CDS YP_424539.1 83319850 3828944 682755..683672 1 NC_007633.1 This protein has a CobQ/CobB/MinD/ParA nucleotide binding domain, which is characteristic of a family of various cobyrinic acid a,c-diamide synthases. ParA family proteins are involved in partitioning of mobile elements. Three ParA family members are present in M. capricolum Kid. MCAP_0570 is encoded within ICEC, MCAP_0184 within Tra Island II and MCAP_0282 by Tra Island I; identified by match to protein family HMM PF01656; hypothetical protein 683672 3828944 MCAP_0570 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424539.1 682755 D 340047 CDS YP_424540.1 83319924 3828679 683782..685014 1 NC_007633.1 MCAP_0571 is the last ORF of an Integrative Conjugal Element (ICE) of M. capricolum strain Kid (designated ICEC); Exhibits modest similarity to ORF22 of the related element ICEF of Mycoplasma fermentans. ICEC is located between nucleotides 661011 and 685387 and encodes ORFs MCAP_0554-MCAP_0571; identified by Glimmer2; hypothetical protein 685014 3828679 MCAP_0571 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424540.1 683782 D 340047 CDS YP_424541.1 83319477 3828886 complement(685488..685865) 1 NC_007633.1 The M. mycoides ortholog is longer at the NH2 end.; hypothetical protein 685865 3828886 MCAP_0572 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424541.1 685488 R 340047 CDS YP_424542.1 83319747 3828605 685929..686438 1 NC_007633.1 identified by similarity to SP:P39792; match to protein family HMM PF03838; recombination protein U 686438 3828605 MCAP_0573 Mycoplasma capricolum subsp. capricolum ATCC 27343 recombination protein U YP_424542.1 685929 D 340047 CDS YP_424543.1 83319254 3828820 complement(686410..686946) 1 NC_007633.1 hypothetical protein 686946 3828820 MCAP_0574 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424543.1 686410 R 340047 CDS YP_424544.1 83320061 3828634 complement(687004..687276) 1 NC_007633.1 MCAP_0575 is one of three M. capricolum ORFs with homology to multiple HU-like DNA binding proteins. MCAP_0575 is identical to the single HU-like protein of M. mycoides SC (MSC_0410) and is most likely therefore the chromosomal equivalent of HU. MCAP_0313 is a Tra Island I encoded paralog. MCAP_0813 also exhibits homology to HU-like proteins; identified by similarity to SP:P08821; match to protein family HMM PF00216; DNA-binding protein HU 1 687276 hupA 3828634 hupA Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-binding protein HU 1 YP_424544.1 687004 R 340047 CDS YP_424545.1 83319366 3829083 complement(687308..688306) 1 NC_007633.1 identified by similarity to SP:P46919; match to protein family HMM PF01210; match to protein family HMM PF07479; glycerol-3-phosphate dehydrogenase (NAD(P)+) 688306 gpsA 3829083 gpsA Mycoplasma capricolum subsp. capricolum ATCC 27343 glycerol-3-phosphate dehydrogenase (NAD(P)+) YP_424545.1 687308 R 340047 CDS YP_424546.1 83319844 3828938 complement(688308..689615) 1 NC_007633.1 EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains; GTP-binding protein EngA 689615 engA 3828938 engA Mycoplasma capricolum subsp. capricolum ATCC 27343 GTP-binding protein EngA YP_424546.1 688308 R 340047 CDS YP_424547.1 83320058 3828631 complement(689615..690283) 1 NC_007633.1 identified by similarity to SP:P38493; match to protein family HMM PF02224; match to protein family HMM TIGR00017; cytidylate kinase 690283 cmk 3828631 cmk Mycoplasma capricolum subsp. capricolum ATCC 27343 cytidylate kinase YP_424547.1 689615 R 340047 CDS YP_424548.1 83319419 3828800 complement(690292..690987) 1 NC_007633.1 MCAP_0579 has 1 membrane spanning region; hypothetical protein 690987 3828800 MCAP_0579 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424548.1 690292 R 340047 CDS YP_424549.1 83319289 3828423 complement(691056..691943) 1 NC_007633.1 MCAP_0580 has 5 membrane spanning regions; hypothetical protein 691943 3828423 MCAP_0580 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424549.1 691056 R 340047 CDS YP_424550.1 83319598 3829020 692084..692644 1 NC_007633.1 identified by similarity to SP:P19514; match to protein family HMM PF00719; inorganic pyrophosphatase 692644 ppa 3829020 ppa Mycoplasma capricolum subsp. capricolum ATCC 27343 inorganic pyrophosphatase YP_424550.1 692084 D 340047 CDS YP_424551.1 83319490 3828899 complement(692752..693453) 1 NC_007633.1 hypothetical protein 693453 3828899 MCAP_0582 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424551.1 692752 R 340047 CDS YP_424552.1 83319399 3828760 complement(693511..695775) 1 NC_007633.1 MCAP_0583 encodes tandem 9-residue repeats near the predicted C-terminus. The same tandem repeat occurs at the C-terminus of MCAP_0585. These repeats are not encoded by the M. mycoides SC ortholog MSC_0402). The tandem repeat aligns with an 8-residue repeat of S. aureus protein A, but only if gapped, and the alignment is imperfect. Unlike some other repeat-containing lipoprotein ORFs, MCAP_0585 shows no evidence of a flanking 5' repetitive nt tract that might confer variable gene expression.; lipoprotein 695775 3828760 MCAP_0583 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424552.1 693511 R 340047 CDS YP_424553.1 83319957 3829118 complement(695820..695942) 1 NC_007633.1 MCAP_0584 encodes the signal peptide of a prolipoprotein and a very short sequence of a mature lipoprotein. No apparent frameshift or point mutation explains the short product that is predicted by this ORF.; lipoprotein 695942 3829118 MCAP_0584 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424553.1 695820 R 340047 CDS YP_424554.1 83319661 3828508 complement(696234..696569) 1 NC_007633.1 MCAP_0585 encodes tandem 9-residue repeats near the predicted C-terminus. The same tandem repeat occurs at the C-terminus of MCAP_0583. These repeats are not encoded by the M. mycoides SC ortholog MSC_0402). The tandem repeat aligns with an 8-residue repeat of S. aureus protein A, but only if gapped, and the alignment is imperfect. Unlike some other repeat-containing lipoprotein ORFs, MCAP_0585 shows no evidence of a flanking 5' repetitive nt tract that might confer variable gene expression.; lipoprotein 696569 3828508 MCAP_0585 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424554.1 696234 R 340047 CDS YP_424555.1 83320021 3829057 complement(696604..698397) 1 NC_007633.1 This is adjacent ot a ABC transporter ATP-binding protein whose substrate is unknown. The similar protein in Mesplasma florum is 59% identical.In M. mycoides SC, the similar protein is encoded by two ORFs.; ABC transporter permease 698397 3829057 MCAP_0586 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter permease YP_424555.1 696604 R 340047 CDS YP_424556.1 83319333 3828467 complement(698444..700279) 1 NC_007633.1 The adjacent gene is a possible membrane permease. It has multiple transmembrane regions. There is no hint of what this tranporter might transport; identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 700279 3828467 MCAP_0587 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein YP_424556.1 698444 R 340047 CDS YP_424557.1 83319620 3829044 complement(701486..702133) 1 NC_007633.1 identified by similarity to GB:CAE77029.1; match to protein family HMM PF00834; ribulose-phosphate 3-epimerase 702133 3829044 MCAP_0589 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribulose-phosphate 3-epimerase YP_424557.1 701486 R 340047 CDS YP_424558.1 83319837 3828931 complement(702133..703941) 1 NC_007633.1 identified by match to protein family HMM PF02302; match to protein family HMM PF04215; PTS system ascorbate-specific transporter subunits IICB 703941 3828931 MCAP_0590 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system ascorbate-specific transporter subunits IICB YP_424558.1 702133 R 340047 CDS YP_424559.1 83319770 3828833 complement(703953..704402) 1 NC_007633.1 identified by match to protein family HMM PF00359; PTS system transporter subunit IIA 704402 3828833 MCAP_0591 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system transporter subunit IIA YP_424559.1 703953 R 340047 CDS YP_424560.1 83319860 3829098 complement(704691..704795) 1 NC_007633.1 hypothetical protein 704795 3829098 MCAP_0592 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424560.1 704691 R 340047 CDS YP_424561.1 83319331 3828465 complement(704901..705830) 1 NC_007633.1 Expressed translation product is identified in Triton X114 phase of detergent fractionated organisms, by peptide mass mapping using mass spectrometry. This is consistent with a lipoprotein encoding an otherwise hydrophilic sequence. Tandem repeat sequence occurs in the ORF. Tandem nucleotide repeats of TA occur 5' of the ORF in a promoter region; this tract is possibly subject to dinucleotide indels governing phase variable expression of the gene.; lipoprotein VmcD 705830 3828465 MCAP_0593 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein VmcD YP_424561.1 704901 R 340047 CDS YP_424562.1 83319662 3828509 complement(706228..706662) 1 NC_007633.1 Expressed translation product is identified in Triton X114 phase of detergent fractionated organisms, by peptide mass mapping using mass spectrometry. This is consistent with a lipoprotein encoding an otherwise hydrophilic sequence. Tandem repeat sequence occurs in the ORF. Tandem nucleotide repeats of TA occur 5' of the ORF in a promoter region; this tract is possibly subject to dinucleotide indels governing phase variable expression of the gene.; lipoprotein VmcC 706662 3828509 MCAP_0594 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein VmcC YP_424562.1 706228 R 340047 CDS YP_424563.1 83319605 3829027 complement(707728..708435) 1 NC_007633.1 Expression of translation product is demonstrated by specific antibody to a synthetic peptide encoded by the ORF. Product partitions in Triton X-114 phase of detergent fractionated organisms, consistent with a cell-associated lipoprotein encoding an otherwise hydrophilic sequence. Product is identified on surface of organism by colony immunostaining. Product is also defined by peptide mass mapping using mass spectrometry. Tandem repeat sequence occurs in the ORF. Tandem nucleotide repeats of TA occur 5' of the ORF in a promoter region; this tract is possibly subject to dinucleotide indels governing phase variable expression of the gene.; lipoprotein VmcB 708435 3829027 MCAP_0595 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein VmcB YP_424563.1 707728 R 340047 CDS YP_424564.1 83319732 3828385 complement(709888..711366) 1 NC_007633.1 Expression of the translation product is demonstrated by specific antibody to a synthetic peptide encoded by the ORF. Product partitions in Triton X-114 phase of detergent fractionated organisms, consistent with a cell-associated lipoprotein encoding an otherwise hydrophilic sequence. Product is also defined by peptide mass mapping using mass spectrometry. Tandem repeat sequence occurs in the ORF. Tandem nucleotide repeats of TA occur 5' of the ORF in a promoter region; this tract is possibly subject to dinucleotide indels governing phase variable expression of the gene. The vmcA gene is located in the same genomic position relative to upstream conserved adjacent housekeeping genes as the vmm gene in M. mycoides SC; lipoprotein VmcA 711366 3828385 MCAP_0596 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein VmcA YP_424564.1 709888 R 340047 CDS YP_424565.1 83319842 3828936 complement(711633..712460) 1 NC_007633.1 MCAP_0597 has 3 membrane spanning regions; hypothetical protein 712460 3828936 MCAP_0597 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424565.1 711633 R 340047 CDS YP_424566.1 83319369 3829086 complement(712560..713273) 1 NC_007633.1 identified by match to protein family HMM PF01709; hypothetical protein 713273 3829086 MCAP_0598 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424566.1 712560 R 340047 CDS YP_424567.1 83319375 3829092 complement(713285..713902) 1 NC_007633.1 identified by similarity to SP:Q59484; match to protein family HMM PF01712; nucleoside kinase 713902 3829092 MCAP_0599 Mycoplasma capricolum subsp. capricolum ATCC 27343 nucleoside kinase YP_424567.1 713285 R 340047 CDS YP_424568.1 83319317 3828451 complement(713913..714671) 1 NC_007633.1 identified by similarity to SP:P35159; match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093; ribosomal large subunit pseudouridine synthase B 714671 3828451 MCAP_0600 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosomal large subunit pseudouridine synthase B YP_424568.1 713913 R 340047 CDS YP_424569.1 83320037 3828336 complement(714745..715374) 1 NC_007633.1 This gene is adjacent to the scpA gene; identified by similarity to SP:P35155; match to protein family HMM PF04079; match to protein family HMM TIGR00281; chromosomal segregation and condensation protein B 715374 scpB 3828336 scpB Mycoplasma capricolum subsp. capricolum ATCC 27343 chromosomal segregation and condensation protein B YP_424569.1 714745 R 340047 CDS YP_424570.1 83319619 3829043 complement(715358..716194) 1 NC_007633.1 This gene is adjacent to the scpB gene; identified by similarity to SP:P35154; match to protein family HMM PF02616; chromosomal segregation and condensation protein A 716194 scpA 3829043 scpA Mycoplasma capricolum subsp. capricolum ATCC 27343 chromosomal segregation and condensation protein A YP_424570.1 715358 R 340047 CDS YP_424571.1 83319888 3828712 complement(716204..716965) 1 NC_007633.1 MCAP_0603 has 1 membrane spanning region; hypothetical protein 716965 3828712 MCAP_0603 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424571.1 716204 R 340047 CDS YP_424572.1 83320008 3828795 complement(716977..718476) 1 NC_007633.1 MCAP_0604 has 13 membrane spanning regions; hypothetical protein 718476 3828795 MCAP_0604 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424572.1 716977 R 340047 CDS YP_424573.1 83319413 3828774 complement(718785..719183) 1 NC_007633.1 lipoprotein 719183 3828774 MCAP_0605 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424573.1 718785 R 340047 CDS YP_424574.1 83319715 3828856 complement(719333..720127) 1 NC_007633.1 identified by match to protein family HMM PF00561; alpha/beta fold family hydrolase 720127 3828856 MCAP_0606 Mycoplasma capricolum subsp. capricolum ATCC 27343 alpha/beta fold family hydrolase YP_424574.1 719333 R 340047 CDS YP_424575.1 83319651 3828498 complement(720139..722595) 1 NC_007633.1 lipoprotein 722595 3828498 MCAP_0607 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424575.1 720139 R 340047 CDS YP_424576.1 83319889 3828713 complement(722695..724239) 1 NC_007633.1 hypothetical protein 724239 3828713 MCAP_0608 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424576.1 722695 R 340047 CDS YP_424577.1 83319560 3828982 complement(724303..724548) 1 NC_007633.1 ORF00812 has one transmembrane region. ORF00812 a member of a family of bacterial proteins of unknown function. There is good identity with membrane proteins in many mycoplasmas; identified by match to protein family HMM PF03672; hypothetical protein 724548 3828982 MCAP_0609 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424577.1 724303 R 340047 CDS YP_424578.1 83319912 3828882 complement(724564..726534) 1 NC_007633.1 identified by similarity to SP:P45694; match to protein family HMM PF00456; match to protein family HMM PF02779; match to protein family HMM PF02780; match to protein family HMM TIGR00232; transketolase 726534 tkt 3828882 tkt Mycoplasma capricolum subsp. capricolum ATCC 27343 transketolase YP_424578.1 724564 R 340047 CDS YP_424579.1 83319422 3828803 complement(726575..726736) 1 NC_007633.1 identified by similarity to GB:CAE77008.1; hypothetical protein 726736 3828803 MCAP_0611 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424579.1 726575 R 340047 CDS YP_424580.1 83319755 3828613 complement(726871..727611) 1 NC_007633.1 MCAP_0612 has 6 membrane spanning regions; hypothetical protein 727611 3828613 MCAP_0612 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424580.1 726871 R 340047 CDS YP_424581.1 83319831 3828924 complement(727710..728981) 1 NC_007633.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine; tRNA (uracil-5-)-methyltransferase Gid 728981 3828924 MCAP_0613 Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA (uracil-5-)-methyltransferase Gid YP_424581.1 727710 R 340047 CDS YP_424582.1 83319734 3828387 729282..730358 1 NC_007633.1 MCAP_0614 is similar to the RmuC protein family. This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures. MCAP_0614 has 1 membrane spanning region, N-terminal.; hypothetical protein 730358 3828387 MCAP_0614 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424582.1 729282 D 340047 CDS YP_424583.1 83319846 3828940 complement(730500..730739) 1 NC_007633.1 The amino terminal 42 amino acids of this protein are 86% identical to the M. mycoides SC hypothetical protein MSC_0648. The carboxyl terminal 42 amino acids are 86% identical to M. mycoides SC hypothetical protein MSC_0638.; hypothetical protein 730739 3828940 MCAP_0615 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424583.1 730500 R 340047 CDS YP_424584.1 83319504 3828556 complement(730932..731777) 1 NC_007633.1 identified by match to protein family HMM PF01116; match to protein family HMM TIGR00167; fructose/tagatose bisphosphate aldolase, class II 731777 3828556 MCAP_0616 Mycoplasma capricolum subsp. capricolum ATCC 27343 fructose/tagatose bisphosphate aldolase, class II YP_424584.1 730932 R 340047 CDS YP_424585.1 83319550 3828971 731978..732712 1 NC_007633.1 identified by match to protein family HMM PF00455; DeoR family transcriptional regulator 732712 3828971 MCAP_0617 Mycoplasma capricolum subsp. capricolum ATCC 27343 DeoR family transcriptional regulator YP_424585.1 731978 D 340047 CDS YP_424586.1 83319908 3828878 732721..734607 1 NC_007633.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system transporter subunit IIBC 734607 3828878 MCAP_0618 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system transporter subunit IIBC YP_424586.1 732721 D 340047 CDS YP_424587.1 83319290 3828424 734620..735561 1 NC_007633.1 identified by similarity to SP:O31714; match to protein family HMM PF00294; 1-phosphofructokinase 735561 3828424 MCAP_0619 Mycoplasma capricolum subsp. capricolum ATCC 27343 1-phosphofructokinase YP_424587.1 734620 D 340047 CDS YP_424588.1 83319735 3828388 complement(735640..737490) 1 NC_007633.1 There are 2 membrane spanning regions in MCAP_0620.; hypothetical protein 737490 3828388 MCAP_0620 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424588.1 735640 R 340047 CDS YP_424589.1 83319917 3828672 complement(738045..738590) 1 NC_007633.1 MCAP_0621 has 1 membrane spanning region, N-terminal.; hypothetical protein 738590 3828672 MCAP_0621 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424589.1 738045 R 340047 CDS YP_424590.1 83319884 3828708 740123..741652 1 NC_007633.1 MCAP_0622 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0622 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 741652 3828708 MCAP_0622 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424590.1 740123 D 340047 CDS YP_424591.1 83319447 3829145 741987..743822 1 NC_007633.1 identified by match to protein family HMM PF00753; match to protein family HMM PF07521; metallo-beta-lactamase superfamily protein 743822 3829145 MCAP_0623 Mycoplasma capricolum subsp. capricolum ATCC 27343 metallo-beta-lactamase superfamily protein YP_424591.1 741987 D 340047 CDS YP_424592.1 83319571 3828993 743900..744853 1 NC_007633.1 MCAP_0624 has 7 membrane spanning regions; hypothetical protein 744853 3828993 MCAP_0624 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424592.1 743900 D 340047 CDS YP_424593.1 83319341 3828475 745896..747140 1 NC_007633.1 MCAP_0625 has 7 membrane spanning regions; hypothetical protein 747140 3828475 MCAP_0625 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424593.1 745896 D 340047 CDS YP_424594.1 83319444 3829142 747406..748809 1 NC_007633.1 MCAP_0626 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. There is 1 membrane spanning region in MCAP_0626; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 748809 3829142 MCAP_0626 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424594.1 747406 D 340047 CDS YP_424595.1 83320017 3828910 749130..750881 1 NC_007633.1 MCAP_0627 has 2 membrane spanning regions; hypothetical protein 750881 3828910 MCAP_0627 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424595.1 749130 D 340047 CDS YP_424596.1 83319458 3829054 750894..751562 1 NC_007633.1 MCAP_0628 has 1 membrane spanning region; hypothetical protein 751562 3829054 MCAP_0628 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424596.1 750894 D 340047 CDS YP_424597.1 83319937 3828954 751744..752391 1 NC_007633.1 Expression of translation product is demonstrated by specific antibody to a synthetic peptide encoded by the ORF. Product partitions in Triton X-114 phase of detergent fractionated organisms, consistent with a cell-associated lipoprotein encoding an otherwise hydrophilic sequence. Product is identified on surface of organism by colony immunostaining. Product is also defined by peptide mass mapping using mass spectrometry. Tandem repeat sequence occurs in the ORF. Tandem nucleotide repeats of TA occur 5' of the ORF in a promoter region; this tract is possibly subject to dinucleotide indels governing phase variable expression of the gene.; lipoprotein VmcE 752391 3828954 MCAP_0629 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein VmcE YP_424597.1 751744 D 340047 CDS YP_424598.1 83319556 3828978 753218..753748 1 NC_007633.1 Expression of translation product is demonstrated by specific antibody to a synthetic peptide encoded by the ORF. Product partitions in Triton X-114 phase of detergent fractionated organisms, consistent with a cell-associated lipoprotein encoding an otherwise hydrophilic sequence. Product is identified on surface of organism by colony immunostaining. Product is also defined by peptide mass mapping using mass spectrometry. Tandem repeat sequence occurs in the ORF. Tandem nucleotide repeats of TA occur 5' of the ORF in a promoter region; this tract is possibly subject to dinucleotide indels governing phase variable expression of the gene.; lipoprotein VmcF 753748 3828978 MCAP_0630 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein VmcF YP_424598.1 753218 D 340047 CDS YP_424599.1 83319915 3828670 complement(753818..755032) 1 NC_007633.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 755032 pgk 3828670 pgk Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphoglycerate kinase YP_424599.1 753818 R 340047 CDS YP_424600.1 83320051 3828624 complement(755160..756176) 1 NC_007633.1 identified by similarity to SP:Q59309; match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534; glyceraldehyde-3-phosphate dehydrogenase 756176 gap 3828624 gap Mycoplasma capricolum subsp. capricolum ATCC 27343 glyceraldehyde-3-phosphate dehydrogenase YP_424600.1 755160 R 340047 CDS YP_424601.1 83319318 3828452 complement(756269..757204) 1 NC_007633.1 This protein is similar to the B. subtilis DnaI primasomal protein (31% amino acid identity); hypothetical protein 757204 3828452 MCAP_0633 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424601.1 756269 R 340047 CDS YP_424602.1 83319403 3828764 complement(757214..758398) 1 NC_007633.1 identified by match to protein family HMM PF07261; hypothetical protein 758398 3828764 MCAP_0634 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424602.1 757214 R 340047 CDS YP_424603.1 83319527 3828580 complement(758556..759380) 1 NC_007633.1 identified by similarity to SP:P42371; match to protein family HMM PF01149; match to protein family HMM PF06831; match to protein family HMM TIGR00577; formamidopyrimidine-DNA glycosylase 759380 mutM 3828580 mutM Mycoplasma capricolum subsp. capricolum ATCC 27343 formamidopyrimidine-DNA glycosylase YP_424603.1 758556 R 340047 CDS YP_424604.1 83319510 3828562 complement(759391..762126) 1 NC_007633.1 identified by similarity to SP:Q04957; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593; DNA polymerase I 762126 polA 3828562 polA Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA polymerase I YP_424604.1 759391 R 340047 CDS YP_424605.1 83319615 3829037 complement(762135..765095) 1 NC_007633.1 identified by match to protein family HMM PF01336; match to protein family HMM PF02231; match to protein family HMM PF07733; match to protein family HMM TIGR00594; DNA-directed DNA polymerase III (polc) 765095 dnaE 3829037 dnaE Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-directed DNA polymerase III (polc) YP_424605.1 762135 R 340047 CDS YP_424606.1 83319315 3828449 765267..767921 1 NC_007633.1 MCAP_0638 has 2 membrane spanning regions; hypothetical protein 767921 3828449 MCAP_0638 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424606.1 765267 D 340047 CDS YP_424607.1 83319274 3828751 complement(768010..769254) 1 NC_007633.1 identified by similarity to SP:P22326; match to protein family HMM PF00579; match to protein family HMM PF01479; match to protein family HMM TIGR00234; tyrosyl-tRNA synthetase 769254 tyrS 3828751 tyrS Mycoplasma capricolum subsp. capricolum ATCC 27343 tyrosyl-tRNA synthetase YP_424607.1 768010 R 340047 CDS YP_424608.1 83319385 3828533 complement(769262..770323) 1 NC_007633.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 770323 3828533 MCAP_0640 Mycoplasma capricolum subsp. capricolum ATCC 27343 nicotinate phosphoribosyltransferase YP_424608.1 769262 R 340047 CDS YP_424609.1 83319951 3828355 complement(770301..770933) 1 NC_007633.1 This protein has a tRNA binding domain, but does not look like a phenylalanine tRNA synthetase as similar genes are annotated in some instances. The tRNA synthetase domain is found in prokaryotic methionyl-tRNA synthetases and phenylalanyl tRNA synthetases; identified by match to protein family HMM PF01588; methionyl/phenylalanyl tRNA synthetase domain-containing protein 770933 3828355 MCAP_0641 Mycoplasma capricolum subsp. capricolum ATCC 27343 methionyl/phenylalanyl tRNA synthetase domain-containing protein YP_424609.1 770301 R 340047 CDS YP_424610.1 83320049 3828622 770984..771823 1 NC_007633.1 identified by match to protein family HMM PF02645; hypothetical protein 771823 3828622 MCAP_0642 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424610.1 770984 D 340047 CDS YP_424611.1 83319590 3829012 771834..772685 1 NC_007633.1 identified by match to protein family HMM PF02645; degV family protein 772685 3829012 MCAP_0643 Mycoplasma capricolum subsp. capricolum ATCC 27343 degV family protein YP_424611.1 771834 D 340047 CDS YP_424612.1 83319836 3828930 complement(772982..773449) 1 NC_007633.1 identified by similarity to SP:P71086; match to protein family HMM PF01475; FUR family transcriptional regulator 773449 3828930 MCAP_0646 Mycoplasma capricolum subsp. capricolum ATCC 27343 FUR family transcriptional regulator YP_424612.1 772982 R 340047 CDS YP_424613.1 83319519 3828572 complement(773451..773672) 1 NC_007633.1 identified by match to protein family HMM PF00550; acyl carrier protein 773672 3828572 MCAP_0647 Mycoplasma capricolum subsp. capricolum ATCC 27343 acyl carrier protein YP_424613.1 773451 R 340047 CDS YP_424614.1 83319259 3828418 complement(773693..774061) 1 NC_007633.1 lipoprotein 774061 3828418 MCAP_0648 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424614.1 773693 R 340047 CDS YP_424615.1 83319476 3828885 complement(774048..775115) 1 NC_007633.1 The amino terminal 86 amino acids are 77% identical to the M. mycoides SC hypothetical protein MSC_0695. The carboxyl terminal 45 amino acids are 78% identical to the M. mycoides SC hypothetical protein MSC_0694. There is no clear BLASTp match for any of the middle part of the the protein.; hypothetical protein 775115 3828885 MCAP_0649 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424615.1 774048 R 340047 CDS YP_424616.1 83319524 3828577 complement(775419..776351) 1 NC_007633.1 catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP; carbamate kinase 776351 arcC 3828577 arcC Mycoplasma capricolum subsp. capricolum ATCC 27343 carbamate kinase YP_424616.1 775419 R 340047 CDS YP_424617.1 83319708 3828849 complement(776470..777564) 1 NC_007633.1 catalyzes the formation of carbamoylputrescine from agmatine in the arginine decarboxylase pathway of putrescine biosynthesis; agmatine deiminase 777564 3828849 MCAP_0652 Mycoplasma capricolum subsp. capricolum ATCC 27343 agmatine deiminase YP_424617.1 776470 R 340047 CDS YP_424618.1 83319362 3829079 complement(777571..778989) 1 NC_007633.1 identified by similarity to SP:P39183; match to protein family HMM PF00324; amino acid permease family protein 778989 3829079 MCAP_0653 Mycoplasma capricolum subsp. capricolum ATCC 27343 amino acid permease family protein YP_424618.1 777571 R 340047 CDS YP_424619.1 83319535 3828588 complement(779011..780108) 1 NC_007633.1 catalyzes the formation of putrescine from carbamoyl-putrescine during agmatine degradation; putrescine carbamoyltransferase 780108 argF 3828588 argF Mycoplasma capricolum subsp. capricolum ATCC 27343 putrescine carbamoyltransferase YP_424619.1 779011 R 340047 CDS YP_424620.1 83319711 3828852 780339..781226 1 NC_007633.1 This is adjacent to a possible permease that may comprise the rest of this ABC transporter cassette. There is no hint about what the substrate is for this transporter; identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 781226 3828852 MCAP_0655 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein YP_424620.1 780339 D 340047 CDS YP_424621.1 83319830 3828923 781228..781992 1 NC_007633.1 This gene has 6 transmembrane regions and is adjacent to an ATP binding protein of a likely ABC transporter cassette. Thus we annotate it as a ABC transporter permease.; ABC transporter permease 781992 3828923 MCAP_0656 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter permease YP_424621.1 781228 D 340047 CDS YP_424622.1 83319926 3828681 complement(782026..782505) 1 NC_007633.1 MCAP_0657 has 2 membrane spanning regions; hypothetical protein 782505 3828681 MCAP_0657 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424622.1 782026 R 340047 CDS YP_424623.1 83319998 3828785 complement(782589..784154) 1 NC_007633.1 MCAP_0658 has 8 membrane spanning regions; hypothetical protein 784154 3828785 MCAP_0658 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424623.1 782589 R 340047 CDS YP_424624.1 83319332 3828466 complement(784221..786635) 1 NC_007633.1 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase; leucyl-tRNA synthetase 786635 leuS 3828466 leuS Mycoplasma capricolum subsp. capricolum ATCC 27343 leucyl-tRNA synthetase YP_424624.1 784221 R 340047 CDS YP_424625.1 83319643 3828292 complement(786903..789746) 1 NC_007633.1 lipoprotein 789746 3828292 MCAP_0661 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424625.1 786903 R 340047 CDS YP_424626.1 83319563 3828985 complement(789908..790306) 1 NC_007633.1 forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 790306 rpsI 3828985 rpsI Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S9 YP_424626.1 789908 R 340047 CDS YP_424627.1 83319647 3828494 complement(790306..790761) 1 NC_007633.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 790761 rplM 3828494 rplM Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L13 YP_424627.1 790306 R 340047 CDS YP_424628.1 83319508 3828560 complement(790881..795026) 1 NC_007633.1 MCAP_0664 has 8 membrane spanning regions; MCAP_0664 has characteristics of an ABC transporter permease; however it is not near any ATPase; identified by match to protein family HMM PF02687; hypothetical protein 795026 3828560 MCAP_0664 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424628.1 790881 R 340047 CDS YP_424629.1 83320035 3828334 complement(795151..795900) 1 NC_007633.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 795900 truA 3828334 truA Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA pseudouridine synthase A YP_424629.1 795151 R 340047 CDS YP_424630.1 83319897 3828867 complement(795902..796912) 1 NC_007633.1 Part of a 3 gene ABC transporter cassette. There is no substrate binding protein evident; identified by match to protein family HMM PF02361; cobalt ABC transporter permease 796912 3828867 MCAP_0666 Mycoplasma capricolum subsp. capricolum ATCC 27343 cobalt ABC transporter permease YP_424630.1 795902 R 340047 CDS YP_424631.1 83319301 3828435 complement(796925..797794) 1 NC_007633.1 with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene; cobalt transporter ATP-binding subunit 797794 cbiO 3828435 cbiO Mycoplasma capricolum subsp. capricolum ATCC 27343 cobalt transporter ATP-binding subunit YP_424631.1 796925 R 340047 CDS YP_424632.1 83319389 3828537 complement(797821..799047) 1 NC_007633.1 with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene; cobalt transporter ATP-binding subunit 799047 cbiO 3828537 cbiO Mycoplasma capricolum subsp. capricolum ATCC 27343 cobalt transporter ATP-binding subunit YP_424632.1 797821 R 340047 CDS YP_424633.1 83319893 3828717 complement(799158..799517) 1 NC_007633.1 is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 799517 rplQ 3828717 rplQ Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L17 YP_424633.1 799158 R 340047 CDS YP_424634.1 83319728 3828381 complement(799537..800490) 1 NC_007633.1 catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme; DNA-directed RNA polymerase subunit alpha 800490 rpoA 3828381 rpoA Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-directed RNA polymerase subunit alpha YP_424634.1 799537 R 340047 CDS YP_424635.1 83319613 3829035 complement(800494..800883) 1 NC_007633.1 located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3; 30S ribosomal protein S11 800883 rpsK 3829035 rpsK Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S11 YP_424635.1 800494 R 340047 CDS YP_424636.1 83319525 3828578 complement(800909..801274) 1 NC_007633.1 located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA; 30S ribosomal protein S13 801274 rpsM 3828578 rpsM Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S13 YP_424636.1 800909 R 340047 CDS YP_424637.1 83319430 3828811 complement(801312..801425) 1 NC_007633.1 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif; 50S ribosomal protein L36 801425 rpmJ 3828811 rpmJ Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L36 YP_424637.1 801312 R 340047 CDS YP_424638.1 83319271 3828748 complement(801495..801719) 1 NC_007633.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 801719 infA 3828748 infA Mycoplasma capricolum subsp. capricolum ATCC 27343 translation initiation factor IF-1 YP_424638.1 801495 R 340047 CDS YP_424639.1 83319870 3829108 complement(801731..802486) 1 NC_007633.1 identified by similarity to SP:P19994; match to protein family HMM PF00557; match to protein family HMM TIGR00500; methionine aminopeptidase 802486 map 3829108 map Mycoplasma capricolum subsp. capricolum ATCC 27343 methionine aminopeptidase YP_424639.1 801731 R 340047 CDS YP_424640.1 83319545 3828966 complement(802486..803127) 1 NC_007633.1 identified by similarity to SP:P16304; match to protein family HMM PF00406; match to protein family HMM PF05191; match to protein family HMM TIGR01351; adenylate kinase 803127 adk 3828966 adk Mycoplasma capricolum subsp. capricolum ATCC 27343 adenylate kinase YP_424640.1 802486 R 340047 CDS YP_424641.1 83319677 3829068 complement(803256..804704) 1 NC_007633.1 forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase; preprotein translocase subunit SecY 804704 secY 3829068 secY Mycoplasma capricolum subsp. capricolum ATCC 27343 preprotein translocase subunit SecY YP_424641.1 803256 R 340047 CDS YP_424642.1 83319799 3828415 complement(804704..805141) 1 NC_007633.1 late assembly protein; 50S ribosomal protein L15 805141 rplO 3828415 rplO Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L15 YP_424642.1 804704 R 340047 CDS YP_424643.1 83319769 3828832 complement(805161..805925) 1 NC_007633.1 located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance; 30S ribosomal protein S5 805925 rpsE 3828832 rpsE Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S5 YP_424643.1 805161 R 340047 CDS YP_424644.1 83319958 3829120 complement(805944..806294) 1 NC_007633.1 binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 806294 rplR 3829120 rplR Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L18 YP_424644.1 805944 R 340047 CDS YP_424645.1 83319736 3828389 complement(806320..806862) 1 NC_007633.1 ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance; 50S ribosomal protein L6 806862 rplF 3828389 rplF Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L6 YP_424645.1 806320 R 340047 CDS YP_424646.1 83319832 3828925 complement(806876..807265) 1 NC_007633.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 807265 rpsH 3828925 rpsH Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S8 YP_424646.1 806876 R 340047 CDS YP_424647.1 83319468 3828693 complement(807287..807472) 1 NC_007633.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group appear to contain the zinc-binding motif; 30S ribosomal protein S14 807472 rpsN 3828693 rpsN Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S14 YP_424647.1 807287 R 340047 CDS YP_424648.1 83319577 3828999 complement(807491..808033) 1 NC_007633.1 part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13; 50S ribosomal protein L5 808033 rplE 3828999 rplE Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L5 YP_424648.1 807491 R 340047 CDS YP_424649.1 83320060 3828633 complement(808052..808378) 1 NC_007633.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 808378 rplX 3828633 rplX Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L24 YP_424649.1 808052 R 340047 CDS YP_424650.1 83319597 3829019 complement(808392..808760) 1 NC_007633.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 808760 rplN 3829019 rplN Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L14 YP_424650.1 808392 R 340047 CDS YP_424651.1 83319386 3828534 complement(808776..809033) 1 NC_007633.1 primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 809033 rpsQ 3828534 rpsQ Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S17 YP_424651.1 808776 R 340047 CDS YP_424652.1 83319500 3828552 complement(809033..809449) 1 NC_007633.1 one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 809449 rpmC 3828552 rpmC Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L29 YP_424652.1 809033 R 340047 CDS YP_424653.1 83319564 3828986 complement(809449..809862) 1 NC_007633.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 809862 rplP 3828986 rplP Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L16 YP_424653.1 809449 R 340047 CDS YP_424654.1 83319775 3828839 complement(809865..810566) 1 NC_007633.1 forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation; 30S ribosomal protein S3 810566 rpsC 3828839 rpsC Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S3 YP_424654.1 809865 R 340047 CDS YP_424655.1 83319685 3828295 complement(810584..810919) 1 NC_007633.1 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center; 50S ribosomal protein L22 810919 rplV 3828295 rplV Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L22 YP_424655.1 810584 R 340047 CDS YP_424656.1 83319959 3829121 complement(810943..811209) 1 NC_007633.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 811209 rpsS 3829121 rpsS Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S19 YP_424656.1 810943 R 340047 CDS YP_424657.1 83319372 3829089 complement(811231..812076) 1 NC_007633.1 one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation; 50S ribosomal protein L2 812076 rplB 3829089 rplB Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L2 YP_424657.1 811231 R 340047 CDS YP_424658.1 83319653 3828500 complement(812129..812413) 1 NC_007633.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 812413 rplW 3828500 rplW Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L23 YP_424658.1 812129 R 340047 CDS YP_424659.1 83319335 3828469 complement(812413..813039) 1 NC_007633.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA; 50S ribosomal protein L4 813039 rplD 3828469 rplD Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L4 YP_424659.1 812413 R 340047 CDS YP_424660.1 83319916 3828671 complement(813052..813723) 1 NC_007633.1 binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin; 50S ribosomal protein L3 813723 rplC 3828671 rplC Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L3 YP_424660.1 813052 R 340047 CDS YP_424661.1 83320025 3828323 complement(813798..814106) 1 NC_007633.1 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex; 30S ribosomal protein S10 814106 rpsJ 3828323 rpsJ Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S10 YP_424661.1 813798 R 340047 CDS YP_424662.1 83319762 3828620 complement(814402..815400) 1 NC_007633.1 with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase; dihydroxyacetone kinase subunit DhaK 815400 3828620 MCAP_0698 Mycoplasma capricolum subsp. capricolum ATCC 27343 dihydroxyacetone kinase subunit DhaK YP_424662.1 814402 R 340047 CDS YP_424663.1 83319823 3828915 815710..816549 1 NC_007633.1 MCAP_0699 has 6 membrane spanning regions; hypothetical protein 816549 3828915 MCAP_0699 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424663.1 815710 D 340047 CDS YP_424664.1 83319591 3829013 complement(817226..818425) 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 818425 3829013 MCAP_0704 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424664.1 817226 R 340047 CDS YP_424665.1 83319621 3829045 complement(818538..819233) 1 NC_007633.1 MCAP_0705 has 3 membrane spanning regions; hypothetical protein 819233 3829045 MCAP_0705 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424665.1 818538 R 340047 CDS YP_424666.1 83319359 3829076 complement(819238..820092) 1 NC_007633.1 MCAP_0706 has 50% identity to characterized E. coli folD protein. Also has EC number of 3.5.4.9 for methenyltetrahydrofolate cyclohydrolase activity; identified by match to protein family HMM PF00763; match to protein family HMM PF02882; methylene-tetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase 820092 folD 3829076 folD Mycoplasma capricolum subsp. capricolum ATCC 27343 methylene-tetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase YP_424666.1 819238 R 340047 CDS YP_424667.1 83319907 3828877 complement(820101..821702) 1 NC_007633.1 This gene and the one downstream are both likely potassium ion transporters of the Trk transporter family. The are on opposite strands; identified by similarity to PIR:B70007; match to protein family HMM PF02386; TrkH family potassium uptake protein 821702 3828877 MCAP_0707 Mycoplasma capricolum subsp. capricolum ATCC 27343 TrkH family potassium uptake protein YP_424667.1 820101 R 340047 CDS YP_424668.1 83319706 3828847 821781..822509 1 NC_007633.1 This gene and the one upstream are both likely cation transporters of the Trk transporter family. The are on opposite strands; identified by similarity to SP:P39760; match to protein family HMM PF02080; match to protein family HMM PF02254; TrkA family potassium uptake protein 822509 3828847 MCAP_0708 Mycoplasma capricolum subsp. capricolum ATCC 27343 TrkA family potassium uptake protein YP_424668.1 821781 D 340047 CDS YP_424669.1 83319771 3828834 complement(822546..823985) 1 NC_007633.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit B 823985 gatB 3828834 gatB Mycoplasma capricolum subsp. capricolum ATCC 27343 aspartyl/glutamyl-tRNA amidotransferase subunit B YP_424669.1 822546 R 340047 CDS YP_424670.1 83320039 3828338 complement(823987..825444) 1 NC_007633.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit A 825444 gatA 3828338 gatA Mycoplasma capricolum subsp. capricolum ATCC 27343 aspartyl/glutamyl-tRNA amidotransferase subunit A YP_424670.1 823987 R 340047 CDS YP_424671.1 83319319 3828453 complement(825444..825740) 1 NC_007633.1 identified by similarity to GP:2465557; match to protein family HMM PF02686; match to protein family HMM TIGR00135; glutamyl-tRNA(Gln) amidotransferase subunit C 825740 gatC 3828453 gatC Mycoplasma capricolum subsp. capricolum ATCC 27343 glutamyl-tRNA(Gln) amidotransferase subunit C YP_424671.1 825444 R 340047 CDS YP_424672.1 83319601 3829023 complement(825742..827748) 1 NC_007633.1 identified by similarity to SP:P49421; match to protein family HMM PF00533; match to protein family HMM PF00633; match to protein family HMM PF01653; match to protein family HMM PF03119; match to protein family HMM PF03120; match to protein family HMM TIGR00575; NAD-dependent DNA ligase 827748 ligA 3829023 ligA Mycoplasma capricolum subsp. capricolum ATCC 27343 NAD-dependent DNA ligase YP_424672.1 825742 R 340047 CDS YP_424673.1 83319495 3828547 complement(827752..829752) 1 NC_007633.1 MCAP_0713 has 14 membrane spanning regions; hypothetical protein 829752 3828547 MCAP_0713 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424673.1 827752 R 340047 CDS YP_424674.1 83319852 3828946 complement(829755..830663) 1 NC_007633.1 identified by match to protein family HMM PF00849; match to protein family HMM PF01479; ribosomal large subunit pseudouridine synthase A 830663 3828946 MCAP_0714 Mycoplasma capricolum subsp. capricolum ATCC 27343 ribosomal large subunit pseudouridine synthase A YP_424674.1 829755 R 340047 CDS YP_424675.1 83319757 3828615 complement(830666..831676) 1 NC_007633.1 MCAP_0715 has 9 transmembrane regions; identified by match to protein family HMM PF02517; CAAX amino terminal protease family protein 831676 3828615 MCAP_0715 Mycoplasma capricolum subsp. capricolum ATCC 27343 CAAX amino terminal protease family protein YP_424675.1 830666 R 340047 CDS YP_424676.1 83319942 3828959 complement(831735..832004) 1 NC_007633.1 The M. capricolum Hpr protein was characterized in: Zhu PP, Reizer J, Reizer A, Peterkofsky A. 1993. 'Unique monocistronic operon (ptsH) in Mycoplasma capricolum encoding the phosphocarrier protein, HPr, of the phosphoenolpyruvate:sugar phosphotransferase system. Cloning, sequencing, and characterization of ptsH'. Unique monocistronic operon (ptsH) in Mycoplasma capricolum encoding the phosphocarrier protein, HPr, of the phosphoenolpyruvate:sugar phosphotransferase system. Cloning, sequencing, and characterization of ptsH. J Biol Chem. 268(35):26531-40; identified by similarity to SP:P45611; match to protein family HMM PF00381; match to protein family HMM TIGR01003; phosphocarrier protein HPr 832004 ptsH 3828959 ptsH Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphocarrier protein HPr YP_424676.1 831735 R 340047 CDS YP_424677.1 83319825 3828917 complement(832070..834238) 1 NC_007633.1 identified by similarity to SP:P56255; match to protein family HMM PF00580; ATP-dependent DNA helicase pcrA 834238 pcrA 3828917 pcrA Mycoplasma capricolum subsp. capricolum ATCC 27343 ATP-dependent DNA helicase pcrA YP_424677.1 832070 R 340047 CDS YP_424678.1 83319753 3828611 complement(834250..834996) 1 NC_007633.1 MCAP_0718 has 4 membrane spanning regions; identified by match to protein family HMM PF06271; hypothetical protein 834996 3828611 MCAP_0718 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424678.1 834250 R 340047 CDS YP_424679.1 83320045 3828344 complement(834996..835952) 1 NC_007633.1 In the absence of evidence for cell wall or lipopolysccharide synthesis in mycoplasmas, or capsule synthesis in M. capricolum subsp capricolum Kid, the role category 'biosynthesis/degradation of surface polysaccharides and lipopolysaccharides' is assigned to foster comparison with genes having possible capsule-associated functions in other organisms of the Mycoplasma mycoides phylogenetic cluster; identified by match to protein family HMM PF00535; glycosyl transferase family protein 835952 3828344 MCAP_0719 Mycoplasma capricolum subsp. capricolum ATCC 27343 glycosyl transferase family protein YP_424679.1 834996 R 340047 CDS YP_424680.1 83319595 3829017 complement(836066..837283) 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 837283 3829017 MCAP_0720 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424680.1 836066 R 340047 CDS YP_424681.1 83319462 3828687 complement(837411..838655) 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 838655 3828687 MCAP_0721 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424681.1 837411 R 340047 CDS YP_424682.1 83319765 3828963 complement(838759..839688) 1 NC_007633.1 N-terminal section belongs to the msrA Met sulfoxide reductase family, and the C-terminal section belongs to the msrB Met sulfoxide reductase family; identified by similarity to SP:P35593; match to protein family HMM PF01625; match to protein family HMM PF01641; match to protein family HMM TIGR00357; match to protein family HMM TIGR00401; peptide methionine sulfoxide reductase msrA/msrB 839688 3828963 MCAP_0722 Mycoplasma capricolum subsp. capricolum ATCC 27343 peptide methionine sulfoxide reductase msrA/msrB YP_424682.1 838759 R 340047 CDS YP_424683.1 83319879 3828703 complement(839804..842017) 1 NC_007633.1 lipoprotein 842017 3828703 MCAP_0723 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424683.1 839804 R 340047 CDS YP_424684.1 83319996 3828783 complement(842026..842931) 1 NC_007633.1 MCAP_0724 has 7 membrane spanning regions; hypothetical protein 842931 3828783 MCAP_0724 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424684.1 842026 R 340047 CDS YP_424685.1 83319544 3828684 complement(843048..844337) 1 NC_007633.1 This protein is similar to Ureaplasma parvum proteins UU527 and UU090. They all fall into COG1479, which is described as 'uncharacterized ACR'; identified by match to protein family HMM PF07510; hypothetical protein 844337 3828684 MCAP_0725 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424685.1 843048 R 340047 CDS YP_424686.1 83319624 3829048 complement(844625..845593) 1 NC_007633.1 The amino terminal 190 amino acids of this protein are 32 identical to M. mycoides SC hypothetical protein MSC_0779 and the carboxyl end is similar to the adjacent M. mcyoides SC protein MSC_0780.; hypothetical protein 845593 3829048 MCAP_0726 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424686.1 844625 R 340047 CDS YP_424687.1 83320053 3828626 complement(845783..848155) 1 NC_007633.1 lipoprotein 848155 3828626 MCAP_0727 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424687.1 845783 R 340047 CDS YP_424688.1 83319752 3828610 complement(848167..849066) 1 NC_007633.1 MCAP_0728 has 6 membrane spanning regions; hypothetical protein 849066 3828610 MCAP_0728 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424688.1 848167 R 340047 CDS YP_424689.1 83319380 3828528 complement(849165..850913) 1 NC_007633.1 Adjacent to likely ATPase and substrate binding proteins; identified by similarity to SP:P15362; match to protein family HMM PF00528; ABC transporter permease p69 850913 3828528 MCAP_0729 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter permease p69 YP_424689.1 849165 R 340047 CDS YP_424690.1 83319557 3828979 complement(850877..851626) 1 NC_007633.1 Similar to ATP-binding protein p29 of Mycoplasma hyorhinis; identified by similarity to SP:P15361; match to protein family HMM PF00005; ABC transporter ATP-binding protein 851626 3828979 MCAP_0730 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein YP_424690.1 850877 R 340047 CDS YP_424691.1 83319275 3828752 complement(851627..853087) 1 NC_007633.1 Adjacent to likely permease and ATP binding proteins; identified by similarity to SP:P15363; ABC transporter substrate-binding protein 853087 3828752 MCAP_0731 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter substrate-binding protein YP_424691.1 851627 R 340047 CDS YP_424692.1 83319627 3828698 complement(853320..854183) 1 NC_007633.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484; cof family hydrolase 854183 3828698 MCAP_0732 Mycoplasma capricolum subsp. capricolum ATCC 27343 cof family hydrolase YP_424692.1 853320 R 340047 CDS YP_424693.1 83319553 3828974 854317..855510 1 NC_007633.1 identified by similarity to SP:Q08432; match to protein family HMM PF00155; aminotransferase, classes I and II 855510 3828974 MCAP_0733 Mycoplasma capricolum subsp. capricolum ATCC 27343 aminotransferase, classes I and II YP_424693.1 854317 D 340047 CDS YP_424694.1 83320015 3828908 855520..855921 1 NC_007633.1 identified by match to protein family HMM PF01042; match to protein family HMM TIGR00004; endoribonuclease L-PSP 855921 3828908 MCAP_0734 Mycoplasma capricolum subsp. capricolum ATCC 27343 endoribonuclease L-PSP YP_424694.1 855520 D 340047 CDS YP_424695.1 83319300 3828434 complement(855962..857209) 1 NC_007633.1 MCAP_0735 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0735 has 1 membrane spanning region (C-terminal)and one region scored only as a signal peptide (N-terminal). In this regard, it may have 2 membrane spanning regions, similar to closely related paralogs MCAP_0738, MCAP_0737, MCAP_0736; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 857209 3828434 MCAP_0735 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424695.1 855962 R 340047 CDS YP_424696.1 83319772 3828835 complement(857413..858684) 1 NC_007633.1 MCAP_0736 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. There are 2 membrane spanning regions in MCAP_0736; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 858684 3828835 MCAP_0736 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424696.1 857413 R 340047 CDS YP_424697.1 83319902 3828872 complement(858892..860133) 1 NC_007633.1 MCAP_0737 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. There are 2 membrane spanning regions in MCAP_0737; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 860133 3828872 MCAP_0737 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424697.1 858892 R 340047 CDS YP_424698.1 83319778 3828842 complement(860356..861696) 1 NC_007633.1 MCAP_0738 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0738 has 1 membrane spanning region (C-terminal)and one region scored only as a signal peptide (N-terminal). In this regard, it may have 2 membrane spanning regions, similar to closely related paralogs MCAP_0737, MCAP_0736, MCAP_0735; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 861696 3828842 MCAP_0738 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424698.1 860356 R 340047 CDS YP_424699.1 83319760 3828618 861836..862984 1 NC_007633.1 hypothetical protein 862984 3828618 MCAP_0739 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424699.1 861836 D 340047 CDS YP_424700.1 83319404 3828765 864129..864857 1 NC_007633.1 MCAP_0128 nagB2 is a paralog of MCAP_0749; identified by similarity to SP:O35000; match to protein family HMM PF01182; match to protein family HMM TIGR00502; glucosamine-6-phosphate isomerase 864857 nagB1 3828765 nagB1 Mycoplasma capricolum subsp. capricolum ATCC 27343 glucosamine-6-phosphate isomerase YP_424700.1 864129 D 340047 CDS YP_424701.1 83319507 3828559 864962..865708 1 NC_007633.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate; triosephosphate isomerase 865708 tpiA 3828559 tpiA Mycoplasma capricolum subsp. capricolum ATCC 27343 triosephosphate isomerase YP_424701.1 864962 D 340047 CDS YP_424702.1 83319355 3828489 865701..866537 1 NC_007633.1 identified by match to protein family HMM TIGR01484; HAD family hydrolase 866537 3828489 MCAP_0751 Mycoplasma capricolum subsp. capricolum ATCC 27343 HAD family hydrolase YP_424702.1 865701 D 340047 CDS YP_424703.1 83320056 3828629 866540..868135 1 NC_007633.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 868135 gpmI 3828629 gpmI Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphoglyceromutase YP_424703.1 866540 D 340047 CDS YP_424704.1 83319808 3828365 868232..868831 1 NC_007633.1 hypothetical protein 868831 3828365 MCAP_0753 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424704.1 868232 D 340047 CDS YP_424705.1 83319672 3829063 868833..869831 1 NC_007633.1 hypothetical protein 869831 3829063 MCAP_0754 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424705.1 868833 D 340047 CDS YP_424706.1 83320004 3828791 complement(869897..870565) 1 NC_007633.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate; deoxyribose-phosphate aldolase 870565 deoC 3828791 deoC Mycoplasma capricolum subsp. capricolum ATCC 27343 deoxyribose-phosphate aldolase YP_424706.1 869897 R 340047 CDS YP_424707.1 83319929 3828827 complement(870577..872259) 1 NC_007633.1 identified by match to protein family HMM PF00408; match to protein family HMM PF02878; match to protein family HMM PF02879; phosphoglucomutase/phosphomannomutase 872259 3828827 MCAP_0756 Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphoglucomutase/phosphomannomutase YP_424707.1 870577 R 340047 CDS YP_424708.1 83320010 3828903 872424..873737 1 NC_007633.1 identified by similarity to SP:P77836; match to protein family HMM PF00591; match to protein family HMM PF02885; match to protein family HMM PF07831; match to protein family HMM TIGR02644; pyrimidine-nucleoside phosphorylase 873737 deoA 3828903 deoA Mycoplasma capricolum subsp. capricolum ATCC 27343 pyrimidine-nucleoside phosphorylase YP_424708.1 872424 D 340047 CDS YP_424709.1 83319284 3828318 complement(873824..875980) 1 NC_007633.1 lipoprotein 875980 3828318 MCAP_0758 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424709.1 873824 R 340047 CDS YP_424710.1 83319394 3828542 876647..878050 1 NC_007633.1 identified by similarity to OMNI:SA1013; match to protein family HMM PF00571; match to protein family HMM PF03448; match to protein family HMM TIGR00400; magnesium transporter 878050 mgtE 3828542 mgtE Mycoplasma capricolum subsp. capricolum ATCC 27343 magnesium transporter YP_424710.1 876647 D 340047 CDS YP_424711.1 83319486 3828895 878052..878714 1 NC_007633.1 identified by match to protein family HMM PF02390; match to protein family HMM TIGR00091; tRNA (guanine-N(7)-)-methyltransferase 878714 trmB 3828895 trmB Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA (guanine-N(7)-)-methyltransferase YP_424711.1 878052 D 340047 CDS YP_424712.1 83319532 3828585 complement(879090..879680) 1 NC_007633.1 MCAP_0762 has 2 membrane spanning regions; hypothetical protein 879680 3828585 MCAP_0762 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424712.1 879090 R 340047 CDS YP_424713.1 83319536 3828589 complement(879834..880520) 1 NC_007633.1 MCAP_0763 encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif. MCAP_0763 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; hypothetical protein 880520 3828589 MCAP_0763 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424713.1 879834 R 340047 CDS YP_424714.1 83319616 3829038 complement(880855..880977) 1 NC_007633.1 hypothetical protein 880977 3829038 MCAP_0764 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424714.1 880855 R 340047 CDS YP_424715.1 83319960 3829123 complement(881281..881832) 1 NC_007633.1 MCAP_0216 (hpt1) is a paralog of MCAP_0765; identified by similarity to SP:Q02522; match to protein family HMM PF00156; match to protein family HMM TIGR01203; hypoxanthine phosphoribosyltransferase 881832 hpt2 3829123 hpt2 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypoxanthine phosphoribosyltransferase YP_424715.1 881281 R 340047 CDS YP_424716.1 83319287 3828321 complement(881855..883153) 1 NC_007633.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 883153 purB 3828321 purB Mycoplasma capricolum subsp. capricolum ATCC 27343 adenylosuccinate lyase YP_424716.1 881855 R 340047 CDS YP_424717.1 83319683 3829074 complement(883146..884444) 1 NC_007633.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 884444 purA 3829074 purA Mycoplasma capricolum subsp. capricolum ATCC 27343 adenylosuccinate synthetase YP_424717.1 883146 R 340047 CDS YP_424718.1 83319887 3828711 complement(884729..885529) 1 NC_007633.1 identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010; TatD family deoxyribonuclease 885529 3828711 MCAP_0768 Mycoplasma capricolum subsp. capricolum ATCC 27343 TatD family deoxyribonuclease YP_424718.1 884729 R 340047 CDS YP_424719.1 83319539 3828592 885990..887348 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 887348 3828592 MCAP_0770 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424719.1 885990 D 340047 CDS YP_424720.1 83319268 3828745 complement(887434..888903) 1 NC_007633.1 MCAP_0771 has 4 membrane spanning regions; hypothetical protein 888903 3828745 MCAP_0771 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424720.1 887434 R 340047 CDS YP_424721.1 83319994 3828781 complement(888906..889856) 1 NC_007633.1 identified by match to protein family HMM TIGR01128; hypothetical protein 889856 3828781 MCAP_0772 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424721.1 888906 R 340047 CDS YP_424722.1 83319947 3828351 890143..892140 1 NC_007633.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion; excinuclease ABC subunit B 892140 uvrB 3828351 uvrB Mycoplasma capricolum subsp. capricolum ATCC 27343 excinuclease ABC subunit B YP_424722.1 890143 D 340047 CDS YP_424723.1 83319666 3828420 892149..894989 1 NC_007633.1 identified by similarity to SP:O34863; match to protein family HMM PF00005; match to protein family HMM TIGR00630; excinuclease ABC subunit A 894989 uvrA 3828420 uvrA Mycoplasma capricolum subsp. capricolum ATCC 27343 excinuclease ABC subunit A YP_424723.1 892149 D 340047 CDS YP_424724.1 83319540 3828593 894982..896091 1 NC_007633.1 identified by similarity to GP:12724120; match to protein family HMM TIGR01499; folate synthetase-polyglutamyl folate synthetase 896091 folC 3828593 folC Mycoplasma capricolum subsp. capricolum ATCC 27343 folate synthetase-polyglutamyl folate synthetase YP_424724.1 894982 D 340047 CDS YP_424725.1 83319841 3828935 896119..896793 1 NC_007633.1 MCAP_0776 has 6 membrane spanning regions; hypothetical protein 896793 3828935 MCAP_0776 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424725.1 896119 D 340047 CDS YP_424726.1 83319297 3828431 896874..897815 1 NC_007633.1 catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system; HPr kinase/phosphorylase 897815 3828431 MCAP_0777 Mycoplasma capricolum subsp. capricolum ATCC 27343 HPr kinase/phosphorylase YP_424726.1 896874 D 340047 CDS YP_424727.1 83319642 3828291 897826..899406 1 NC_007633.1 MCAP_0780 (lgt2) is a paralog of MCAP_0778; identified by match to protein family HMM PF01790; prolipoprotein diacylglyceryl transferase 899406 lgt1 3828291 lgt1 Mycoplasma capricolum subsp. capricolum ATCC 27343 prolipoprotein diacylglyceryl transferase YP_424727.1 897826 D 340047 CDS YP_424728.1 83319334 3828468 899390..900322 1 NC_007633.1 identified by similarity to SP:P80880; match to protein family HMM PF00070; match to protein family HMM PF03486; match to protein family HMM PF07992; match to protein family HMM TIGR01292; thioredoxin reductase 900322 trxB 3828468 trxB Mycoplasma capricolum subsp. capricolum ATCC 27343 thioredoxin reductase YP_424728.1 899390 D 340047 CDS YP_424729.1 83319801 3828358 900331..901761 1 NC_007633.1 MCAP_0780 spans a region homologous to a region of M. mycoides SC (MSC) annotated as [ORF MSC_937-intergenic region - ORF MSC_936]. A deletion of a T residue in the MSC genome at nt 1063522-1063524 (three adjacent T residues)would cause a frameshift that would create a single long ORF in MSC corresponding to MCAP780. The corresponding locus of that frameshift in M. capricolum is at 900812-900813(two adjacent T residues). MCAP_0780 represents a second paralog of lgt in M. capricolum; although the HMM TIGR score is below trusted cutoff. MCAP_0778, the other M. capricolum lgt gene, has a better score. MCAP_0778 and MCAP_0780 are reciprocal and significant best hits by BLASTp. ORFs adjacent to MCAP_0778 and MCAP_0780 are not paralogous by BLASTp; identified by similarity to SP:O34752; match to protein family HMM PF01790; prolipoprotein diacylglyceryl transferase 901761 lgt2 3828358 lgt2 Mycoplasma capricolum subsp. capricolum ATCC 27343 prolipoprotein diacylglyceryl transferase YP_424729.1 900331 D 340047 CDS YP_424730.1 83319881 3828705 901773..902702 1 NC_007633.1 identified by match to protein family HMM PF02650; match to protein family HMM TIGR00647; hypothetical protein 902702 3828705 MCAP_0781 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424730.1 901773 D 340047 CDS YP_424731.1 83320064 3828637 complement(903025..904158) 1 NC_007633.1 This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM PF03382; match to protein family HMM TIGR02167; lipoprotein 904158 3828637 MCAP_0782 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424731.1 903025 R 340047 CDS YP_424732.1 83319432 3828813 complement(904220..905842) 1 NC_007633.1 identified by similarity to SP:P19642; match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; PTS system transporter subunit IIBC 905842 3828813 MCAP_0783 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system transporter subunit IIBC YP_424732.1 904220 R 340047 CDS YP_424733.1 83319303 3828437 complement(905894..906124) 1 NC_007633.1 MCAP_0784 has 2 membrane spanning regions; hypothetical protein 906124 3828437 MCAP_0784 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424733.1 905894 R 340047 CDS YP_424734.1 83319561 3828983 complement(906114..906833) 1 NC_007633.1 hypothetical protein 906833 3828983 MCAP_0785 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424734.1 906114 R 340047 CDS YP_424735.1 83319697 3828307 complement(906833..907342) 1 NC_007633.1 hypothetical protein 907342 3828307 MCAP_0786 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424735.1 906833 R 340047 CDS YP_424736.1 83319785 3828400 complement(907342..909021) 1 NC_007633.1 identified by similarity to SP:P20166; match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system transporter subunit IIBC 909021 3828400 MCAP_0787 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system transporter subunit IIBC YP_424736.1 907342 R 340047 CDS YP_424737.1 83320062 3828635 909644..909811 1 NC_007633.1 identified by similarity to SP:P44978; DeoR family transcriptional regulator 909811 3828635 MCAP_0788 Mycoplasma capricolum subsp. capricolum ATCC 27343 DeoR family transcriptional regulator YP_424737.1 909644 D 340047 CDS YP_424738.1 83319867 3829105 909935..910906 1 NC_007633.1 hypothetical protein 910906 3829105 MCAP_0789 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424738.1 909935 D 340047 CDS YP_424739.1 83319968 3829131 911127..912845 1 NC_007633.1 This protein has a low confidence match to the B domain of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.; hypothetical protein 912845 3829131 MCAP_0790 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424739.1 911127 D 340047 CDS YP_424740.1 83319448 3828826 complement(912884..913699) 1 NC_007633.1 hypothetical protein 913699 3828826 MCAP_0791 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424740.1 912884 R 340047 CDS YP_424741.1 83319302 3828436 913892..915823 1 NC_007633.1 identified by similarity to SP:P39814; match to protein family HMM PF01131; match to protein family HMM PF01396; match to protein family HMM PF01751; DNA topoisomerase I 915823 topA 3828436 topA Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA topoisomerase I YP_424741.1 913892 D 340047 CDS YP_424742.1 83319900 3828870 complement(916628..917509) 1 NC_007633.1 MCAP_0794 has 1 membrane spanning region, N-terminal.; hypothetical protein 917509 3828870 MCAP_0794 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424742.1 916628 R 340047 CDS YP_424743.1 83319811 3828368 complement(917496..918311) 1 NC_007633.1 MCAP_0795 has one membrane spanning region, N-terminal.; hypothetical protein 918311 3828368 MCAP_0795 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424743.1 917496 R 340047 CDS YP_424744.1 83319634 3828283 complement(918301..919653) 1 NC_007633.1 The single transmembrane region in this ORF may contain a lipoprotein signal motif. Ortholog in in M. mycoides SC is annotated as a prolipoprotein.; lipoprotein 919653 3828283 MCAP_0796 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424744.1 918301 R 340047 CDS YP_424745.1 83319478 3828887 complement(919631..920335) 1 NC_007633.1 The adjacent ORF is a likely permease, and also part of this apparant operon are several lipoproteins that could possibly be substrate binding proteins; identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein 920335 3828887 MCAP_0797 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter ATP-binding protein YP_424745.1 919631 R 340047 CDS YP_424746.1 83319360 3829077 complement(920337..922202) 1 NC_007633.1 This is part of a likely operon with an ABC transporter ATPase, and several lipoproteins that might be substrate binding proteins.; ABC transporter permease 922202 3829077 MCAP_0798 Mycoplasma capricolum subsp. capricolum ATCC 27343 ABC transporter permease YP_424746.1 920337 R 340047 CDS YP_424747.1 83319269 3828746 complement(922342..923238) 1 NC_007633.1 This lipoprotein is part of likely ABC transporter operon. The next two genes in the operon encode a likely permease and a clear ATPase.; lipoprotein 923238 3828746 MCAP_0799 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424747.1 922342 R 340047 CDS YP_424748.1 83319393 3828541 complement(923231..924070) 1 NC_007633.1 MCAP_0800 has 1 membrane spanning region, N-terminal.; hypothetical protein 924070 3828541 MCAP_0800 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424748.1 923231 R 340047 CDS YP_424749.1 83320022 3829058 complement(924057..925010) 1 NC_007633.1 lipoprotein 925010 3829058 MCAP_0801 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424749.1 924057 R 340047 CDS YP_424750.1 83319911 3828881 complement(925029..926867) 1 NC_007633.1 MCAP_0802 has 6 membrane spanning regions; hypothetical protein 926867 3828881 MCAP_0802 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424750.1 925029 R 340047 CDS YP_424751.1 83319426 3828807 complement(926975..928741) 1 NC_007633.1 These proteins are members of the C4-dicarboxylate Uptake C (DcuC) family. DcuC has 12 GES predicted transmembrane regions, is induced only under anaerobic conditions, and is not repressed by glucose. DcuC may therefore function as a succinate efflux system during anaerobic glucose fermentation; identified by match to protein family HMM PF03606; C4-dicarboxylate anaerobic carrier 928741 3828807 MCAP_0803 Mycoplasma capricolum subsp. capricolum ATCC 27343 C4-dicarboxylate anaerobic carrier YP_424751.1 926975 R 340047 CDS YP_424752.1 83319948 3828352 complement(928810..929499) 1 NC_007633.1 identified by match to protein family HMM PF01863; zinc metalloprotease 929499 3828352 MCAP_0804 Mycoplasma capricolum subsp. capricolum ATCC 27343 zinc metalloprotease YP_424752.1 928810 R 340047 CDS YP_424753.1 83319819 3828376 complement(929506..930600) 1 NC_007633.1 translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1; GTP-dependent nucleic acid-binding protein EngD 930600 engD 3828376 engD Mycoplasma capricolum subsp. capricolum ATCC 27343 GTP-dependent nucleic acid-binding protein EngD YP_424753.1 929506 R 340047 CDS YP_424754.1 83319609 3829031 complement(930636..930836) 1 NC_007633.1 hypothetical protein 930836 3829031 MCAP_0806 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424754.1 930636 R 340047 CDS YP_424755.1 83319743 3828396 complement(930838..931533) 1 NC_007633.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA; 16S rRNA methyltransferase GidB 931533 gidB 3828396 gidB Mycoplasma capricolum subsp. capricolum ATCC 27343 16S rRNA methyltransferase GidB YP_424755.1 930838 R 340047 CDS YP_424756.1 83319934 3828951 complement(931533..932129) 1 NC_007633.1 identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 932129 pgsA 3828951 pgsA Mycoplasma capricolum subsp. capricolum ATCC 27343 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase YP_424756.1 931533 R 340047 CDS YP_424757.1 83319992 3828779 complement(933920..934603) 1 NC_007633.1 MCAP_0810 has 6 membrane spanning regions; hypothetical protein 934603 3828779 MCAP_0810 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424757.1 933920 R 340047 CDS YP_424758.1 83319547 3828968 complement(934569..936116) 1 NC_007633.1 Orthologs of MCAP_0811 are often annotated as permeases for amino acid transport. There is no convincing wet science or sequence-based evidence for this. MCAP_0811 has 12 membrane spanning regions; identified by match to protein family HMM PF00324; hypothetical protein 936116 3828968 MCAP_0811 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424758.1 934569 R 340047 CDS YP_424759.1 83319694 3828304 complement(936175..938910) 1 NC_007633.1 identified by similarity to SP:P39168; match to protein family HMM PF00122; match to protein family HMM PF00702; match to protein family HMM TIGR01494; magnesium-transporting ATPase E1-E2 family protein 938910 3828304 MCAP_0812 Mycoplasma capricolum subsp. capricolum ATCC 27343 magnesium-transporting ATPase E1-E2 family protein YP_424759.1 936175 R 340047 CDS YP_424760.1 83319548 3828969 complement(938918..939544) 1 NC_007633.1 Start site prediction is difficult for this gene. The B. subtilis ortholog is much smaller, with 38% identity between amino acids 129-206 of this 208 amino acid protein. A start site with a good ribosome binding site was chosen; identified by similarity to SP:P08821; match to protein family HMM PF00216; DNA-binding protein HU 939544 hup 3828969 hup Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-binding protein HU YP_424760.1 938918 R 340047 CDS YP_424761.1 83319340 3828474 complement(940433..941860) 1 NC_007633.1 This protein has 12 membrane spanning regions and matches COG0477 (permeases of the major facilitator superfamily); identified by similarity to OMNI:NTL02MM0861; match to protein family HMM PF07672; match to protein family HMM PF07690; transporter protein 941860 3828474 MCAP_0814 Mycoplasma capricolum subsp. capricolum ATCC 27343 transporter protein YP_424761.1 940433 R 340047 CDS YP_424762.1 83319492 3828901 complement(942121..943695) 1 NC_007633.1 MCAP_0815 has 8 membrane spanning regions; hypothetical protein 943695 3828901 MCAP_0815 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424762.1 942121 R 340047 CDS YP_424763.1 83319921 3828676 complement(943860..944483) 1 NC_007633.1 This gene shares strong identity to two three gene clusters in Mycoplasma mycoides SC.; hypothetical protein 944483 3828676 MCAP_0816 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424763.1 943860 R 340047 CDS YP_424764.1 83319586 3829008 complement(944540..945520) 1 NC_007633.1 catalyzes the formation of asparagine from aspartate and ammonia; asparagine synthetase AsnA 945520 asnA 3829008 asnA Mycoplasma capricolum subsp. capricolum ATCC 27343 asparagine synthetase AsnA YP_424764.1 944540 R 340047 CDS YP_424765.1 83319493 3828902 945932..946177 1 NC_007633.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 946177 rpsT 3828902 rpsT Mycoplasma capricolum subsp. capricolum ATCC 27343 30S ribosomal protein S20 YP_424765.1 945932 D 340047 CDS YP_424766.1 83319722 3828863 complement(946228..947586) 1 NC_007633.1 in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE; tRNA modification GTPase TrmE 947586 trmE 3828863 trmE Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA modification GTPase TrmE YP_424766.1 946228 R 340047 CDS YP_424767.1 83320042 3828341 947790..948014 1 NC_007633.1 hypothetical protein 948014 3828341 MCAP_0820 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424767.1 947790 D 340047 CDS YP_424768.1 83319909 3828879 948123..949082 1 NC_007633.1 in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity; DNA-binding/iron metalloprotein/AP endonuclease 949082 3828879 MCAP_0821 Mycoplasma capricolum subsp. capricolum ATCC 27343 DNA-binding/iron metalloprotein/AP endonuclease YP_424768.1 948123 D 340047 CDS YP_424769.1 83319420 3828801 949106..950236 1 NC_007633.1 hypothetical protein 950236 3828801 MCAP_0822 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424769.1 949106 D 340047 CDS YP_424770.1 83319279 3828756 950247..951086 1 NC_007633.1 identified by match to protein family HMM TIGR00099; HAD superfamily hydrolase 951086 3828756 MCAP_0823 Mycoplasma capricolum subsp. capricolum ATCC 27343 HAD superfamily hydrolase YP_424770.1 950247 D 340047 CDS YP_424771.1 83319692 3828302 951095..952459 1 NC_007633.1 catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; asparaginyl-tRNA synthetase 952459 asnC 3828302 asnC Mycoplasma capricolum subsp. capricolum ATCC 27343 asparaginyl-tRNA synthetase YP_424771.1 951095 D 340047 CDS YP_424772.1 83319503 3828555 952728..954092 1 NC_007633.1 This is adjacent to two other phosphonate ABC transporter elements. The annotation is based on the gene being part of a likely ABC transporter operon and the presence of a lipoprotein attachment site and likely signal peptide.; phosphonate ABC transporter phosphonate-binding protein 954092 3828555 MCAP_0825 Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphonate ABC transporter phosphonate-binding protein YP_424772.1 952728 D 340047 CDS YP_424773.1 83319390 3828538 954106..954858 1 NC_007633.1 Part of a likely 3 gene ABC transporter cassette operon; identified by match to protein family HMM PF00005; match to protein family HMM TIGR02315; phosphonate ABC transporter ATP-binding protein 954858 3828538 MCAP_0826 Mycoplasma capricolum subsp. capricolum ATCC 27343 phosphonate ABC transporter ATP-binding protein YP_424773.1 954106 D 340047 CDS YP_424774.1 83320020 3829056 954862..957597 1 NC_007633.1 Member of Phosphonate Uptake Transporter (PhnT) Family. This is an element of a likely 3 gene ABC transporter cassette operon; identified by similarity to SP:P16683; match to protein family HMM PF00528; match to protein family HMM TIGR01097; alkylphosphonate ABC transporter permease 957597 3829056 MCAP_0827 Mycoplasma capricolum subsp. capricolum ATCC 27343 alkylphosphonate ABC transporter permease YP_424774.1 954862 D 340047 CDS YP_424775.1 83319950 3828354 complement(957622..959688) 1 NC_007633.1 This protein is similar to the characterized Bl subtilis DNA internalization-related competence protein ComEC/Rec2; however because M. capricolum is not competent we elected not to annotate the gene as a comEC related gene.; metallo-beta-lactamase superfamily protein 959688 3828354 MCAP_0828 Mycoplasma capricolum subsp. capricolum ATCC 27343 metallo-beta-lactamase superfamily protein YP_424775.1 957622 R 340047 CDS YP_424776.1 83319761 3828619 965268..966110 1 NC_007633.1 identified by match to protein family HMM TIGR01484; HAD superfamily hydrolase 966110 3828619 MCAP_0834 Mycoplasma capricolum subsp. capricolum ATCC 27343 HAD superfamily hydrolase YP_424776.1 965268 D 340047 CDS YP_424777.1 83319455 3829051 966122..966430 1 NC_007633.1 identified by similarity to SP:P14949; match to protein family HMM PF00085; match to protein family HMM TIGR01068; thioredoxin 966430 trxA 3829051 trxA Mycoplasma capricolum subsp. capricolum ATCC 27343 thioredoxin YP_424777.1 966122 D 340047 CDS YP_424778.1 83319783 3828398 complement(966562..968064) 1 NC_007633.1 class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1; lysyl-tRNA synthetase 968064 lysS 3828398 lysS Mycoplasma capricolum subsp. capricolum ATCC 27343 lysyl-tRNA synthetase YP_424778.1 966562 R 340047 CDS YP_424779.1 83320047 3828346 complement(968067..968993) 1 NC_007633.1 This protein has >40% identity to the E. coli tRNA-dihydrouridine synthase protein YhdG; identified by match to protein family HMM PF01207; match to protein family HMM TIGR00737; tRNA-dihydrouridine synthase 968993 dus 3828346 dus Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA-dihydrouridine synthase YP_424779.1 968067 R 340047 CDS YP_424780.1 83319857 3829095 complement(969043..969357) 1 NC_007633.1 hypothetical protein 969357 3829095 MCAP_0838 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424780.1 969043 R 340047 CDS YP_424781.1 83319858 3829096 complement(969451..970719) 1 NC_007633.1 catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; seryl-tRNA synthetase 970719 serS 3829096 serS Mycoplasma capricolum subsp. capricolum ATCC 27343 seryl-tRNA synthetase YP_424781.1 969451 R 340047 CDS YP_424782.1 83319688 3828298 complement(970800..971627) 1 NC_007633.1 MCAP_0840 has 6 membrane spanning regions; hypothetical protein 971627 3828298 MCAP_0840 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424782.1 970800 R 340047 CDS YP_424783.1 83319584 3829006 complement(971695..972279) 1 NC_007633.1 hypothetical protein 972279 3829006 MCAP_0841 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424783.1 971695 R 340047 CDS YP_424784.1 83319599 3829021 complement(972298..972588) 1 NC_007633.1 MCAP_0842 has 2 membrane spanning regions; hypothetical protein 972588 3829021 MCAP_0842 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424784.1 972298 R 340047 CDS YP_424785.1 83319501 3828553 972758..974992 1 NC_007633.1 lipoprotein 974992 3828553 MCAP_0843 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424785.1 972758 D 340047 CDS YP_424786.1 83319451 3828598 complement(975036..976778) 1 NC_007633.1 identified by similarity to SP:P20166; match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system glucose-specific IIBC component 976778 3828598 MCAP_0844 Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system glucose-specific IIBC component YP_424786.1 975036 R 340047 CDS YP_424787.1 83319345 3828479 976887..977321 1 NC_007633.1 identified by match to protein family HMM PF00578; bacterioferritin comigratory protein 977321 bcp 3828479 bcp Mycoplasma capricolum subsp. capricolum ATCC 27343 bacterioferritin comigratory protein YP_424787.1 976887 D 340047 CDS YP_424788.1 83319744 3828602 977485..979575 1 NC_007633.1 lipoprotein 979575 3828602 MCAP_0846 Mycoplasma capricolum subsp. capricolum ATCC 27343 lipoprotein YP_424788.1 977485 D 340047 CDS YP_424789.1 83319414 3828775 980325..981230 1 NC_007633.1 hypothetical protein 981230 3828775 MCAP_0847 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424789.1 980325 D 340047 CDS YP_424790.1 83319802 3828359 981284..981748 1 NC_007633.1 identified by similarity to GB:CAE77252.1; transposase IS1296EH (ORFA) 981748 3828359 MCAP_0848 Mycoplasma capricolum subsp. capricolum ATCC 27343 transposase IS1296EH (ORFA) YP_424790.1 981284 D 340047 CDS YP_424791.1 83319883 3828707 complement(981796..982449) 1 NC_007633.1 identified by similarity to SP:O34925; match to protein family HMM PF01048; purine nucleoside phosphorylase 982449 deoD 3828707 deoD Mycoplasma capricolum subsp. capricolum ATCC 27343 purine nucleoside phosphorylase YP_424791.1 981796 R 340047 CDS YP_424792.1 83319649 3828496 complement(982682..983662) 1 NC_007633.1 hypothetical protein 983662 3828496 MCAP_0850 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424792.1 982682 R 340047 CDS YP_424793.1 83319812 3828369 983814..984512 1 NC_007633.1 Gene is adjacent to fructose metabolism and transport genes; identified by match to protein family HMM PF00455; fructose operon transcriptional regulator 984512 3828369 MCAP_0851 Mycoplasma capricolum subsp. capricolum ATCC 27343 fructose operon transcriptional regulator YP_424793.1 983814 D 340047 CDS YP_424794.1 83319978 3828726 984512..985447 1 NC_007633.1 identified by similarity to SP:O31714; match to protein family HMM PF00294; 1-phosphofructokinase 985447 3828726 MCAP_0852 Mycoplasma capricolum subsp. capricolum ATCC 27343 1-phosphofructokinase YP_424794.1 984512 D 340047 CDS YP_424795.1 83319877 3828819 985450..987486 1 NC_007633.1 identified by similarity to SP:P47308; match to protein family HMM PF00359; match to protein family HMM PF02378; match to protein family HMM PF02379; match to protein family HMM TIGR00829; match to protein family HMM TIGR00848; match to protein family HMM TIGR01427; PTS system fructose-specific transporter subunit IIABC 987486 fruA 3828819 fruA Mycoplasma capricolum subsp. capricolum ATCC 27343 PTS system fructose-specific transporter subunit IIABC YP_424795.1 985450 D 340047 CDS YP_424796.1 83319361 3829078 988122..988697 1 NC_007633.1 hypothetical protein 988697 3829078 MCAP_0854 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424796.1 988122 D 340047 CDS YP_424797.1 83319310 3828444 988866..989453 1 NC_007633.1 hypothetical protein 989453 3828444 MCAP_0855 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424797.1 988866 D 340047 CDS YP_424798.1 83319255 3828821 complement(989799..991688) 1 NC_007633.1 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs; tRNA uridine 5-carboxymethylaminomethyl modification protein GidA 991688 gidA 3828821 gidA Mycoplasma capricolum subsp. capricolum ATCC 27343 tRNA uridine 5-carboxymethylaminomethyl modification protein GidA YP_424798.1 989799 R 340047 CDS YP_424799.1 83319265 3828742 complement(991832..993400) 1 NC_007633.1 identified by match to protein family HMM PF00375; proton/glutamate symporter family protein 993400 3828742 MCAP_0857 Mycoplasma capricolum subsp. capricolum ATCC 27343 proton/glutamate symporter family protein YP_424799.1 991832 R 340047 CDS YP_424800.1 83319381 3828529 complement(993422..994765) 1 NC_007633.1 MCAP_0858 is a paralog of MCAP_0223. This is a likely NADH oxidase; identified by similarity to SP:P37061; match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM PF07992; pyridine nucleotide-disulfide oxidoreductase 994765 3828529 MCAP_0858 Mycoplasma capricolum subsp. capricolum ATCC 27343 pyridine nucleotide-disulfide oxidoreductase YP_424800.1 993422 R 340047 CDS YP_424801.1 83319890 3828714 994986..995486 1 NC_007633.1 identified by similarity to SP:P21369; match to protein family HMM PF00857; pyrazinamidase/nicotinamidase 995486 pncA 3828714 pncA Mycoplasma capricolum subsp. capricolum ATCC 27343 pyrazinamidase/nicotinamidase YP_424801.1 994986 D 340047 CDS YP_424802.1 83319989 3829060 complement(995719..997977) 1 NC_007633.1 MCAP_0860 has 1 membrane spanning region, N-terminal; hypothetical protein 997977 3829060 MCAP_0860 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424802.1 995719 R 340047 CDS YP_424803.1 83319756 3828614 complement(997987..1000248) 1 NC_007633.1 MCAP_0861 has 1 transmembrane region.; hypothetical protein 1000248 3828614 MCAP_0861 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424803.1 997987 R 340047 CDS YP_424804.1 83319558 3828980 complement(1000520..1002772) 1 NC_007633.1 MCAP_0862 has 1 membrane spanning region, N-terminal. This protein has 9 copies of a KID repeat as found in Borrelia spirochete RepA / Rep+ proteins, and 5 copies of a Streptococcal M protein repeat.; hypothetical protein 1002772 3828980 MCAP_0862 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424804.1 1000520 R 340047 CDS YP_424805.1 83319460 3828685 complement(1002796..1003617) 1 NC_007633.1 hypothetical protein 1003617 3828685 MCAP_0863 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424805.1 1002796 R 340047 CDS YP_424806.1 83319281 3828315 complement(1003625..1005037) 1 NC_007633.1 There are 4 paralogous genes in M. capricolum; hypothetical protein 1005037 3828315 MCAP_0864 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424806.1 1003625 R 340047 CDS YP_424807.1 83319567 3828989 complement(1005242..1006399) 1 NC_007633.1 MCAP_0865 has 8 membrane spanning regions; hypothetical protein 1006399 3828989 MCAP_0865 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424807.1 1005242 R 340047 CDS YP_424808.1 83319714 3828855 complement(1006457..1007173) 1 NC_007633.1 hypothetical protein 1007173 3828855 MCAP_0866 Mycoplasma capricolum subsp. capricolum ATCC 27343 hypothetical protein YP_424808.1 1006457 R 340047 CDS YP_424809.1 83319291 3828425 complement(1007173..1007970) 1 NC_007633.1 identified by match to protein family HMM TIGR00099; match to protein family HMM TIGR01484; cof family hydrolase 1007970 3828425 MCAP_0867 Mycoplasma capricolum subsp. capricolum ATCC 27343 cof family hydrolase YP_424809.1 1007173 R 340047 CDS YP_424810.1 83319450 3828597 complement(1008050..1009216) 1 NC_007633.1 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria; inner membrane protein translocase component YidC 1009216 3828597 MCAP_0868 Mycoplasma capricolum subsp. capricolum ATCC 27343 inner membrane protein translocase component YidC YP_424810.1 1008050 R 340047 CDS YP_424811.1 83319517 3828570 complement(1009258..1009587) 1 NC_007633.1 identified by similarity to SP:P58031; match to protein family HMM PF00825; match to protein family HMM TIGR00188; ribonuclease P protein component 1009587 rnpA 3828570 rnpA Mycoplasma capricolum subsp. capricolum ATCC 27343 ribonuclease P protein component YP_424811.1 1009258 R 340047 CDS YP_424812.1 83319572 3828994 complement(1009594..1009728) 1 NC_007633.1 in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 1009728 rpmH 3828994 rpmH Mycoplasma capricolum subsp. capricolum ATCC 27343 50S ribosomal protein L34 YP_424812.1 1009594 R 340047 CDS