-- dump date   	20120504_153215
-- class       	Genbank::Feature
-- table       	feature
-- table       	main
-- field 1	id
-- field 2	type
-- field 3	name
-- field 4	contig
-- field 5	start_pos
-- field 6	end_pos
-- field 7	strand
-- field 8	description
-- field 9	chrom_position
-- field 10	organism
-- field 11	GeneID
-- header
-- id	type	name	contig	start_pos	end_pos	strand	description	chrom_position	organism	GeneID
340047000001	SEQ_END	SEQ_END	NC_007633.1	1010023	1010023	DR	NC_007633.1; contig end	1010023..1010023	Mycoplasma capricolum subsp. capricolum ATCC 27343	<NULL_VALUE>
YP_424001.1	CDS	dnaA	NC_007633.1	1	1353	D	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	1..1353	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828310
YP_424002.1	CDS	dnaN	NC_007633.1	1518	2645	D	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	1518..2645	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829107
YP_424003.1	CDS	MCAP_0003	NC_007633.1	2682	3224	D	identified by match to protein family HMM PF01751; match to protein family HMM TIGR00334; primase-like protein	2682..3224	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828721
YP_424004.1	CDS	ksgA	NC_007633.1	3214	4014	D	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	3214..4014	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828432
YP_424005.1	CDS	MCAP_0005	NC_007633.1	4069	5163	D	MCAP_0005 has 3 membrane spanning regions; hypothetical protein	4069..5163	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828561
YP_424006.1	CDS	MCAP_0007	NC_007633.1	5328	5771	D	identified by match to protein family HMM PF00383; cytidine/deoxycytidylate deaminase zinc-binding domain-containing protein	5328..5771	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828443
YP_424007.1	CDS	dnaX	NC_007633.1	5851	7860	D	identified by similarity to SP:P09122; match to protein family HMM PF00004; match to protein family HMM TIGR02397; DNA polymerase III subunits gamma/tau	5851..7860	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828328
YP_424008.1	CDS	recM	NC_007633.1	7862	8452	D	identified by similarity to SP:P24277; match to protein family HMM PF01751; DNA repair protein RecM	7862..8452	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829093
YP_424009.1	CDS	tmk	NC_007633.1	8455	9096	D	identified by similarity to SP:P37537; match to protein family HMM PF02223; match to protein family HMM TIGR00041; thymidylate kinase	8455..9096	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828798
YP_424010.1	CDS	MCAP_0011	NC_007633.1	9074	9817	D	identified by similarity to SP:P37540; DNA polymerase III, delta prime subunit	9074..9817	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829033
YP_424011.1	CDS	MCAP_0012	NC_007633.1	9877	10539	D	N-6 adenine-specific DNA methylases	9877..10539	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828574
YP_424012.1	CDS	MCAP_0013	NC_007633.1	10590	11411	D	This protein has some homology to RpiR family transcriptional regulators.; hypothetical protein	10590..11411	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828948
YP_424013.1	CDS	MCAP_0014	NC_007633.1	11416	12621	D	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	11416..12621	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828851
YP_424014.1	CDS	MCAP_0015	NC_007633.1	12618	13454	R	hypothetical protein	complement(12618..13454)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828325
YP_424015.1	CDS	ftsH	NC_007633.1	13687	15639	D	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	13687..15639	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828957
YP_424016.1	CDS	MCAP_0018	NC_007633.1	16712	22105	R	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	complement(16712..22105)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828921
YP_424017.1	CDS	MCAP_0019	NC_007633.1	22249	25407	D	MCAP_0019 has 1 membrane spanning region, N-terminal; hypothetical protein	22249..25407	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828911
YP_424018.1	CDS	hslO	NC_007633.1	25583	26449	D	identified by match to protein family HMM PF01430; chaperonin HSP33	25583..26449	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828607
YP_424019.1	CDS	MCAP_0021	NC_007633.1	26497	27534	D	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	26497..27534	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828364
YP_424020.1	CDS	MCAP_0022	NC_007633.1	27586	28185	R	identified by similarity to SP:P41407; match to protein family HMM PF02525; azoreductase	complement(27586..28185)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828557
YP_424021.1	CDS	MCAP_0023	NC_007633.1	28374	28580	D	identified by similarity to SP:P15277; match to protein family HMM PF00313; cold shock protein	28374..28580	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828305
YP_424022.1	CDS	rpsF	NC_007633.1	28783	29196	D	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6	28783..29196	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828461
YP_424023.1	CDS	ssb	NC_007633.1	29212	29652	D	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	29212..29652	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828457
YP_424024.1	CDS	rpsR	NC_007633.1	29671	29898	D	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	29671..29898	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829110
YP_424025.1	CDS	MCAP_0027	NC_007633.1	30594	31982	D	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	30594..31982	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828816
YP_424026.1	CDS	MCAP_0028	NC_007633.1	32257	33810	D	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	32257..33810	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828486
YP_424027.1	CDS	MCAP_0029	NC_007633.1	33810	34568	D	catalyzes the conversion of sorbitol 6-phosphate into fructose 6-phosphate; sorbitol-6-phosphate dehydrogenase	33810..34568	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828789
YP_424028.1	CDS	MCAP_0030	NC_007633.1	34568	34813	D	identified by similarity to SP:Q45420; PTS system mannitol-specific transporter subunit IIA	34568..34813	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828683
YP_424029.1	CDS	MCAP_0031	NC_007633.1	35027	35824	D	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	35027..35824	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828934
YP_424030.1	CDS	MCAP_0032	NC_007633.1	35825	36829	D	identified by similarity to SP:P55800; match to protein family HMM PF01232; match to protein family HMM PF08125; mannitol-1-phosphate 5-dehydrogenase	35825..36829	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828604
YP_424031.1	CDS	MCAP_0033	NC_007633.1	36866	38458	R	lipoprotein LppA	complement(36866..38458)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828430
YP_424032.1	CDS	MCAP_0034	NC_007633.1	38483	40042	R	LppA family lipoprotein	complement(38483..40042)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829018
YP_424033.1	CDS	metG	NC_007633.1	40240	41769	D	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	40240..41769	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828788
YP_424034.1	CDS	MCAP_0037	NC_007633.1	43614	45221	D	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	43614..45221	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828932
YP_424035.1	CDS	MCAP_0038	NC_007633.1	45211	47769	D	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	45211..47769	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828692
YP_424036.1	CDS	MCAP_0039	NC_007633.1	47772	48749	D	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	47772..48749	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828490
YP_424037.1	CDS	gyrA	NC_007633.1	48817	51204	R	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	complement(48817..51204)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829049
YP_424038.1	CDS	gyrB	NC_007633.1	51336	53240	R	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	complement(51336..53240)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828573
YP_424039.1	CDS	MCAP_0042	NC_007633.1	53640	55241	R	lipoprotein	complement(53640..55241)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828743
YP_424040.1	CDS	MCAP_0043	NC_007633.1	55409	56182	R	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	complement(55409..56182)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828438
YP_424041.1	CDS	MCAP_0044	NC_007633.1	56166	56888	R	MCAP_0044 has 6 membrane spanning regions; hypothetical protein	complement(56166..56888)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829004
YP_424042.1	CDS	secA	NC_007633.1	56998	59832	R	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	complement(56998..59832)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828563
YP_424043.1	CDS	MCAP_0046	NC_007633.1	59912	60487	D	identified by match to protein family HMM PF01205; hypothetical protein	59912..60487	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828370
YP_424044.1	CDS	MCAP_0047	NC_007633.1	60583	61497	D	identified by match to protein family HMM PF01367; match to protein family HMM PF02739; 5'-3' exonuclease	60583..61497	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828306
YP_424045.1	CDS	MCAP_0048	NC_007633.1	61692	62708	D	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	61692..62708	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828731
YP_424046.1	CDS	dam	NC_007633.1	62638	63615	D	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	62638..63615	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828741
YP_424047.1	CDS	MCAP_0050	NC_007633.1	63593	65170	D	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	63593..65170	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829082
YP_424048.1	CDS	MCAP_0052	NC_007633.1	66644	67114	D	hypothetical protein	66644..67114	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828700
YP_424049.1	CDS	MCAP_0053	NC_007633.1	67839	68114	D	hypothetical protein	67839..68114	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828793
YP_424050.1	CDS	MCAP_0054	NC_007633.1	68104	68670	D	identified by match to protein family HMM PF01121; match to protein family HMM TIGR00152; dephospho-CoA kinase	68104..68670	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828906
YP_424051.1	CDS	MCAP_0055	NC_007633.1	68672	69481	R	identified by similarity to SP:Q06803; match to protein family HMM PF01479; match to protein family HMM PF01728; hemolysin A	complement(68672..69481)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828753
YP_424052.1	CDS	MCAP_0056	NC_007633.1	69481	69696	R	hypothetical protein	complement(69481..69696)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828754
YP_424053.1	CDS	xseA	NC_007633.1	69689	71095	R	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	complement(69689..71095)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828583
YP_424054.1	CDS	MCAP_0058	NC_007633.1	71097	71495	R	identified by match to protein family HMM PF01029; match to protein family HMM TIGR01951; N utilization substance protein B	complement(71097..71495)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828497
YP_424055.1	CDS	MCAP_0059	NC_007633.1	71507	72577	R	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	complement(71507..72577)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828558
YP_424056.1	CDS	MCAP_0060	NC_007633.1	72604	73473	R	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	complement(72604..73473)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828463
YP_424057.1	CDS	MCAP_0061	NC_007633.1	73466	74218	R	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	complement(73466..74218)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828332
YP_424058.1	CDS	MCAP_0063	NC_007633.1	74775	76349	D	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	74775..76349	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828858
YP_424059.1	CDS	MCAP_0064	NC_007633.1	76352	77230	D	identified by match to protein family HMM PF00483; UTP-glucose-1-phosphate uridylyltransferase	76352..77230	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829137
YP_424060.1	CDS	rplK	NC_007633.1	77432	77860	D	binds directly to 23S ribosomal RNA; 50S ribosomal protein L11	77432..77860	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828682
YP_424061.1	CDS	rplA	NC_007633.1	77860	78540	D	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	77860..78540	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828286
YP_424062.1	CDS	rplJ	NC_007633.1	78769	79266	D	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10	78769..79266	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828491
YP_424063.1	CDS	rplL	NC_007633.1	79342	79710	D	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	79342..79710	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828408
YP_424064.1	CDS	MCAP_0069	NC_007633.1	79881	81053	D	hypothetical protein	79881..81053	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828584
YP_424065.1	CDS	rpoB	NC_007633.1	81043	84906	D	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	81043..84906	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828896
YP_424066.1	CDS	rpoC	NC_007633.1	84918	88685	D	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'	84918..88685	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828804
YP_424067.1	CDS	MCAP_0072	NC_007633.1	88775	90964	D	lipoprotein	88775..90964	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828281
YP_424068.1	CDS	MCAP_0073	NC_007633.1	90971	91276	R	identified by match to protein family HMM PF00581; hypothetical protein	complement(90971..91276)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828395
YP_424069.1	CDS	MCAP_0074	NC_007633.1	91301	91798	D	identified by similarity to OMNI:NTL02MM0853; match to protein family HMM PF02502; match to protein family HMM TIGR00689; ribose 5-phosphate isomerase B	91301..91798	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828928
YP_424070.1	CDS	glyA	NC_007633.1	91782	93023	D	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase	91782..93023	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828829
YP_424071.1	CDS	upp	NC_007633.1	93125	93748	D	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase	93125..93748	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828866
YP_424072.1	CDS	MCAP_0077	NC_007633.1	93889	94287	D	MCAP_0464 has 4 membrane spanning regions; hypothetical protein	93889..94287	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828786
YP_424073.1	CDS	atpB	NC_007633.1	94287	95147	D	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	94287..95147	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828763
YP_424074.1	CDS	atpE	NC_007633.1	95186	95491	D	identified by similarity to SP:O08310; match to protein family HMM PF00137; match to protein family HMM TIGR01260; ATP synthase F0 subunit C	95186..95491	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828566
YP_424075.1	CDS	atpF	NC_007633.1	95519	96064	D	identified by similarity to SP:P37814; match to protein family HMM PF00430; match to protein family HMM TIGR01144; ATP synthase F0 subunit B	95519..96064	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828361
YP_424076.1	CDS	atpH	NC_007633.1	96066	96611	D	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	96066..96611	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828898
YP_424077.1	CDS	atpA1	NC_007633.1	96623	98200	D	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	96623..98200	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828697
YP_424078.1	CDS	atpG	NC_007633.1	98202	99044	D	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	98202..99044	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828996
YP_424079.1	CDS	atpD1	NC_007633.1	99053	100483	D	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	99053..100483	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828383
YP_424080.1	CDS	atpC	NC_007633.1	100483	100782	D	identified by similarity to PIR:S29042; match to protein family HMM PF02823; ATP synthase F1 subunit epsilon	100483..100782	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828324
YP_424081.1	CDS	MCAP_0086	NC_007633.1	100840	102051	R	MCAP_0086 has 5 membrane spanning regions; hypothetical protein	complement(100840..102051)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828874
YP_424082.1	CDS	mgtA	NC_007633.1	102390	105218	D	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	102390..105218	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828492
YP_424083.1	CDS	MCAP_0088	NC_007633.1	105679	105813	R	MCAP_0088 has 1 membrane spanning region, N-terminal.; hypothetical protein	complement(105679..105813)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828462
YP_424084.1	CDS	arcA	NC_007633.1	105998	107209	D	identified by similarity to SP:P16962; match to protein family HMM PF02274; arginine deiminase	105998..107209	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828503
YP_424085.1	CDS	arcB	NC_007633.1	107227	108222	D	identified by match to protein family HMM PF00185; match to protein family HMM PF02729; match to protein family HMM TIGR00658; ornithine carbamoyltransferase, catabolic	107227..108222	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828308
YP_424086.1	CDS	MCAP_0091	NC_007633.1	108285	109754	D	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	108285..109754	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829015
YP_424087.1	CDS	MCAP_0093	NC_007633.1	111276	112403	R	identified by match to protein family HMM PF00144; beta-lactamase	complement(111276..112403)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828739
YP_424088.1	CDS	ptsG	NC_007633.1	112508	114721	R	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	complement(112508..114721)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829130
YP_424089.1	CDS	MCAP_0095	NC_007633.1	115141	115629	R	MCAP_0095 has 1 membrane spanning region, N-terminal.; hypothetical protein	complement(115141..115629)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828564
YP_424090.1	CDS	smpB	NC_007633.1	115629	116075	R	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	complement(115629..116075)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828806
YP_424091.1	CDS	MCAP_0097	NC_007633.1	116085	118199	R	identified by match to protein family HMM PF00575; match to protein family HMM PF00773; match to protein family HMM TIGR00358; 3'-5' exoribonuclease	complement(116085..118199)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828841
YP_424092.1	CDS	secG	NC_007633.1	118235	118591	R	identified by match to protein family HMM TIGR00810; preprotein translocase subunit SecG	complement(118235..118591)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829062
YP_424093.1	CDS	nrdF	NC_007633.1	118773	119792	D	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	118773..119792	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828363
YP_424094.1	CDS	nrdI	NC_007633.1	119802	120275	D	in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF; ribonucleotide reductase stimulatory protein	119802..120275	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829101
YP_424095.1	CDS	nrdE	NC_007633.1	120262	122424	D	Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha	120262..122424	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828799
YP_424096.1	CDS	prs	NC_007633.1	122709	123743	D	identified by similarity to SP:P14193; match to protein family HMM PF00156; match to protein family HMM TIGR01251; phosphoribosylpyrophosphate synthase	122709..123743	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828790
YP_424097.1	CDS	pth	NC_007633.1	124048	124608	D	Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase	124048..124608	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828326
YP_424098.1	CDS	rplI	NC_007633.1	124739	125182	D	in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9	124739..125182	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828868
YP_424099.1	CDS	dnaC	NC_007633.1	125184	126512	D	identified by match to protein family HMM PF00772; match to protein family HMM PF03796; match to protein family HMM TIGR00665; replicative DNA helicase	125184..126512	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828768
YP_424100.1	CDS	MCAP_0108	NC_007633.1	126601	127863	D	hypothetical protein	126601..127863	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828576
YP_424101.1	CDS	MCAP_0109	NC_007633.1	127990	128916	D	MCAP_0109 has 8 membrane spanning regions; hypothetical protein	127990..128916	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829046
YP_424102.1	CDS	cysS	NC_007633.1	128925	130250	D	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	128925..130250	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828384
YP_424103.1	CDS	MCAP_0111	NC_007633.1	130252	130986	D	identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186; RNA methyltransferase	130252..130986	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828348
YP_424104.1	CDS	rpmG	NC_007633.1	131047	131208	D	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	131047..131208	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828669
YP_424105.1	CDS	secE	NC_007633.1	131208	131522	D	identified by match to protein family HMM TIGR00964; Preprotein translocase subunit SecE	131208..131522	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828904
YP_424106.1	CDS	nusG	NC_007633.1	131539	132183	D	identified by similarity to SP:P36264; match to protein family HMM PF00467; match to protein family HMM PF02357; transcription antitermination protein NusG	131539..132183	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829003
YP_424107.1	CDS	MCAP_0115	NC_007633.1	132631	138528	D	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	132631..138528	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828893
YP_424108.1	CDS	MCAP_0116	NC_007633.1	138537	141491	D	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	138537..141491	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828477
YP_424109.1	CDS	MCAP_0117	NC_007633.1	141491	142564	D	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	141491..142564	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829067
YP_424110.1	CDS	MCAP_0118	NC_007633.1	142566	143576	D	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	142566..143576	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828784
YP_424111.1	CDS	MCAP_0119	NC_007633.1	143655	145028	D	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	143655..145028	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828976
YP_424112.1	CDS	MCAP_0120	NC_007633.1	145104	146357	D	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	145104..146357	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828445
YP_424113.1	CDS	MCAP_0121	NC_007633.1	146389	146817	R	MCAP_0121 has 1 membrane spanning region; hypothetical protein	complement(146389..146817)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828950
YP_424114.1	CDS	MCAP_0122	NC_007633.1	146872	147651	D	MCAP_0122 has 6 membrane spanning regions; identified by match to protein family HMM PF02660; match to protein family HMM TIGR00023; membrane protein	146872..147651	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828876
YP_424115.1	CDS	MCAP_0123	NC_007633.1	147705	149243	D	This protein has two ATPase domains; identified by match to protein family HMM PF00005; ABC transporter ATP-binding protein	147705..149243	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828889
YP_424116.1	CDS	MCAP_0124	NC_007633.1	149275	150072	R	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010; TatD family hydrolase	complement(149275..150072)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828916
YP_424117.1	CDS	ilvA	NC_007633.1	150259	151485	D	identified by similarity to SP:P11954; match to protein family HMM PF00291; match to protein family HMM TIGR01127; threonine dehydratase	150259..151485	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828312
YP_424118.1	CDS	MCAP_0126	NC_007633.1	151701	153290	D	MCAP_0126 has 12 membrane spanning regions; hypothetical protein	151701..153290	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828539
YP_424119.1	CDS	MCAP_0127	NC_007633.1	153295	154158	D	MCAP_0127 has 1 membrane spanning region; hypothetical protein	153295..154158	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828567
YP_424120.2	CDS	nagB	NC_007633.1	154353	155120	D	catalyzes the reversible formation of fructose 6-phosphate from glucosamine 6-phosphate; glucosamine-6-phosphate deaminase	154353..155120	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828725
YP_424121.1	CDS	MCAP_0129	NC_007633.1	155124	156806	D	identified by match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system N-acetylglucosamine-specific transporter subunit IIBC	155124..156806	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828330
YP_424122.1	CDS	gltX	NC_007633.1	156937	158388	D	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase	156937..158388	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828322
YP_424123.1	CDS	MCAP_0132	NC_007633.1	159630	160067	D	DNA-directed RNA polymerase subunit delta	159630..160067	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829053
YP_424124.1	CDS	pyrG	NC_007633.1	160160	161758	D	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	160160..161758	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828399
YP_424125.1	CDS	MCAP_0134	NC_007633.1	162260	163033	D	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	162260..163033	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828301
YP_424126.1	CDS	MCAP_0135	NC_007633.1	163048	164022	D	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	163048..164022	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828678
YP_424127.1	CDS	fba	NC_007633.1	164174	165067	D	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	164174..165067	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829112
YP_424128.1	CDS	MCAP_0137	NC_007633.1	165285	166778	R	MCAP_0137 has 12 membrane spanning regions; hypothetical protein	complement(165285..166778)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828454
YP_424129.1	CDS	MCAP_0138	NC_007633.1	166983	168434	D	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	166983..168434	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828596
YP_424130.1	CDS	MCAP_0139	NC_007633.1	168519	169235	D	identified by match to protein family HMM PF03009; glycerophosphoryl diester phosphodiesterase family protein	168519..169235	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828391
YP_424131.1	CDS	rpmE	NC_007633.1	169372	169650	D	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	169372..169650	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828929
YP_424132.1	CDS	MCAP_0141	NC_007633.1	169725	171653	D	hypothetical protein	169725..171653	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828942
YP_424133.1	CDS	MCAP_0142	NC_007633.1	171663	172613	D	identified by match to protein family HMM PF01368; match to protein family HMM PF02272; DHH phosphoesterase family protein	171663..172613	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828594
YP_424134.1	CDS	tdk	NC_007633.1	172616	173245	D	catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase	172616..173245	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828506
YP_424135.1	CDS	prfA	NC_007633.1	173248	174339	D	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	173248..174339	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828470
YP_424136.1	CDS	MCAP_0145	NC_007633.1	174332	175144	D	identified by match to protein family HMM TIGR00536; HemK family modification methylase	174332..175144	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828317
YP_424137.1	CDS	MCAP_0146	NC_007633.1	175190	176662	D	MCAP_0146 has 8 membrane spanning regions; hypothetical protein	175190..176662	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828591
YP_424138.1	CDS	MCAP_0147	NC_007633.1	176671	177171	D	SUA5/yciO/yrdC family signature protein; hypothetical protein	176671..177171	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829141
YP_424139.1	CDS	MCAP_0148	NC_007633.1	177239	178192	D	hypothetical protein	177239..178192	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828744
YP_424140.1	CDS	MCAP_0149	NC_007633.1	178316	179023	D	MCAP_0149 has 2 membrane spanning regions; hypothetical protein	178316..179023	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828636
YP_424141.1	CDS	MCAP_0150	NC_007633.1	179023	180552	D	identified by similarity to SP:O66043; match to protein family HMM PF00614; cardiolipin synthetase	179023..180552	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828464
YP_424142.2	CDS	rpsL	NC_007633.1	180676	181095	D	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	180676..181095	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828412
YP_424143.1	CDS	rpsG	NC_007633.1	181185	181652	D	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7	181185..181652	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828828
YP_424144.1	CDS	fusA	NC_007633.1	181679	183748	D	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G	181679..183748	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828987
YP_424145.1	CDS	tuf	NC_007633.1	183880	185067	D	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	183880..185067	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829066
YP_424146.1	CDS	MCAP_0155	NC_007633.1	185190	187031	D	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	185190..187031	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828501
YP_424147.1	CDS	MCAP_0156	NC_007633.1	187015	189282	D	identified by similarity to SP:Q9F234; match to protein family HMM PF01055; isoglycosyl hydrolase family protein	187015..189282	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828327
YP_424148.1	CDS	pepA1	NC_007633.1	189469	190824	D	MCAP_0195 pepA2 is a paralog of MCAP_0157; identified by match to protein family HMM PF00883; cytosol aminopeptidase	189469..190824	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828696
YP_424149.1	CDS	alaS	NC_007633.1	192390	195080	R	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	complement(192390..195080)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828869
YP_424150.1	CDS	MCAP_0160	NC_007633.1	195149	195643	R	MCAP_0160 has 3 membrane spanning regions; hypothetical protein	complement(195149..195643)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828367
YP_424151.1	CDS	MCAP_0161	NC_007633.1	195862	197106	D	identified by similarity to SP:P24138; match to protein family HMM PF00528; oligopeptide ABC transporter permease	195862..197106	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828476
YP_424152.1	CDS	MCAP_0162	NC_007633.1	197122	198132	D	identified by similarity to SP:P24139; match to protein family HMM PF00528; oligopeptide ABC transporter permease	197122..198132	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828905
YP_424153.1	CDS	MCAP_0163	NC_007633.1	198146	199846	D	identified by similarity to SP:P24136; match to protein family HMM PF00005; match to protein family HMM TIGR01727; oligopeptide ABC transporter ATP-binding protein	198146..199846	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828380
YP_424154.1	CDS	MCAP_0164	NC_007633.1	199848	201725	D	identified by similarity to SP:P24137; match to protein family HMM PF00005; oligopeptide ABC transporter ATP-binding protein	199848..201725	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829000
YP_424155.1	CDS	MCAP_0165	NC_007633.1	201742	204849	D	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	201742..204849	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829139
YP_424156.1	CDS	MCAP_0166	NC_007633.1	204948	205049	D	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	204948..205049	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828955
YP_424157.1	CDS	MCAP_0167	NC_007633.1	205361	206965	D	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	205361..206965	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828331
YP_424158.1	CDS	MCAP_0168	NC_007633.1	207895	209073	D	MCAP_0168, encoded within Tra island II, has 1 membrane spanning region; hypothetical protein	207895..209073	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828716
YP_424159.1	CDS	MCAP_0169	NC_007633.1	209054	209689	D	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	209054..209689	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828734
YP_424160.1	CDS	MCAP_0170	NC_007633.1	209791	210543	D	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	209791..210543	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829073
YP_424161.1	CDS	MCAP_0171	NC_007633.1	210593	211243	D	MCAP_0171, encoded within Tra island II, has 4 membrane spanning regions; hypothetical protein	210593..211243	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828941
YP_424162.1	CDS	MCAP_0172	NC_007633.1	211364	212194	D	lipoprotein	211364..212194	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828288
YP_424163.1	CDS	MCAP_0173	NC_007633.1	212404	212691	D	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	212404..212691	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828293
YP_424164.1	CDS	MCAP_0175	NC_007633.1	213766	214179	D	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	213766..214179	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828770
YP_424165.1	CDS	MCAP_0176	NC_007633.1	214289	214405	R	hypothetical protein	complement(214289..214405)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828991
YP_424166.1	CDS	MCAP_0177	NC_007633.1	214527	214916	D	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	214527..214916	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829090
YP_424167.1	CDS	MCAP_0178	NC_007633.1	215059	216234	D	MCAP_0178, encoded within Tra Island II, has 6 membrane spanning regions; hypothetical protein	215059..216234	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828630
YP_424168.1	CDS	MCAP_0179	NC_007633.1	216319	219186	D	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	216319..219186	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828507
YP_424169.1	CDS	MCAP_0180	NC_007633.1	219507	219827	D	hypothetical protein	219507..219827	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828837
YP_424170.1	CDS	MCAP_0181	NC_007633.1	219869	220444	D	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	219869..220444	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829143
YP_424171.1	CDS	MCAP_0182	NC_007633.1	220472	221119	D	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	220472..221119	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828422
YP_424172.1	CDS	MCAP_0183	NC_007633.1	221144	221575	D	MCAP_0183, encoded within Tra Island II, has 90% amino acid sequence identity to MCAP_0298 encoded within Tra Island I.; hypothetical protein	221144..221575	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828530
YP_424173.1	CDS	MCAP_0184	NC_007633.1	221642	222379	D	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	221642..222379	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828913
YP_424174.1	CDS	MCAP_0185	NC_007633.1	222379	222585	D	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	222379..222585	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828883
YP_424175.1	CDS	MCAP_0186	NC_007633.1	222935	225676	D	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	222935..225676	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828737
YP_424176.1	CDS	MCAP_0187	NC_007633.1	226062	227186	D	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	226062..227186	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828862
YP_424177.1	CDS	MCAP_0189	NC_007633.1	228765	229850	D	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	228765..229850	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828309
YP_424178.1	CDS	MCAP_0190	NC_007633.1	229949	232246	D	identified by match to protein family HMM PF03632; match to protein family HMM PF03633; match to protein family HMM PF03636; maltose phosphorylase	229949..232246	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828912
YP_424179.1	CDS	MCAP_0191	NC_007633.1	232248	233852	D	identified by similarity to SP:P39795; match to protein family HMM PF00128; glycosyl hydrolase family protein	232248..233852	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829104
YP_424180.1	CDS	MCAP_0192	NC_007633.1	233874	234593	D	identified by match to protein family HMM PF00392; GntR family transcriptional regulator	233874..234593	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828778
YP_424181.1	CDS	MCAP_0193	NC_007633.1	234626	236419	R	identified by match to protein family HMM PF01432; match to protein family HMM TIGR00181; oligoendopeptidase F	complement(234626..236419)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828949
YP_424182.1	CDS	MCAP_0194	NC_007633.1	236419	237102	R	hypothetical protein	complement(236419..237102)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828861
YP_424183.1	CDS	pepA2	NC_007633.1	237118	238473	R	MCAP_0157 pepA1 is a paralog of MCAP_0195; identified by match to protein family HMM PF00883; cytosol aminopeptidase	complement(237118..238473)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828294
YP_424184.1	CDS	MCAP_0196	NC_007633.1	238589	239884	R	This protein has a Prosite motif for an ATP/GTP-binding site A (P-loop).; hypothetical protein	complement(238589..239884)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828590
YP_424185.1	CDS	MCAP_0197	NC_007633.1	240127	240747	D	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	240127..240747	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829026
YP_424186.1	CDS	MCAP_0198	NC_007633.1	240747	241424	D	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	240747..241424	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828340
YP_424187.1	CDS	MCAP_0200	NC_007633.1	242913	246038	R	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	complement(242913..246038)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828421
YP_424188.1	CDS	MCAP_0201	NC_007633.1	246023	247015	R	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	complement(246023..247015)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829126
YP_424189.1	CDS	MCAP_0202	NC_007633.1	247015	248070	R	identified by match to protein family HMM PF00005; spermidine/putrescine ABC transporter ATP-binding protein	complement(247015..248070)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828933
YP_424190.1	CDS	rplT	NC_007633.1	248432	248791	R	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20	complement(248432..248791)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828973
YP_424191.1	CDS	rpmI	NC_007633.1	248810	249001	R	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001; 50S ribosomal protein L35	complement(248810..249001)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828280
YP_424192.1	CDS	infC	NC_007633.1	249027	249572	R	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	complement(249027..249572)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828450
YP_424193.1	CDS	def	NC_007633.1	249761	250363	R	identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079; polypeptide deformylase	complement(249761..250363)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829109
YP_424194.1	CDS	MCAP_0207	NC_007633.1	250437	250994	D	identified by match to protein family HMM PF03602; methyltransferase	250437..250994	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828730
YP_424195.1	CDS	gmk	NC_007633.1	250997	251890	D	identified by match to protein family HMM PF00625; guanylate kinase	250997..251890	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828787
YP_424196.1	CDS	MCAP_0209	NC_007633.1	251853	253139	D	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)	251853..253139	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828366
YP_424197.1	CDS	typA	NC_007633.1	253143	254972	R	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	complement(253143..254972)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828411
YP_424198.1	CDS	MCAP_0211	NC_007633.1	255250	256059	D	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	255250..256059	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828909
YP_424199.1	CDS	MCAP_0212	NC_007633.1	256070	256867	D	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	256070..256867	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828802
YP_424200.1	CDS	eno	NC_007633.1	256990	258345	D	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase	256990..258345	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828581
YP_424201.1	CDS	MCAP_0214	NC_007633.1	258411	259232	D	identified by match to protein family HMM PF01569; PAP2 superfamily domain-containing protein	258411..259232	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828997
YP_424202.1	CDS	MCAP_0215	NC_007633.1	259234	259665	D	identified by match to protein family HMM PF03652; match to protein family HMM TIGR00250; holliday junction resolvase	259234..259665	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828860
YP_424203.1	CDS	hpt1	NC_007633.1	259671	260243	D	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	259671..260243	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828857
YP_424204.1	CDS	MCAP_0217	NC_007633.1	260290	261069	R	identified by match to protein family HMM PF00230; glycerol uptake facilitator protein	complement(260290..261069)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828571
YP_424205.1	CDS	glpK	NC_007633.1	261105	262622	R	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	complement(261105..262622)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828718
YP_424206.1	CDS	MCAP_0219	NC_007633.1	262639	263802	R	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	complement(262639..263802)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828473
YP_424207.1	CDS	pfkA	NC_007633.1	264143	265123	D	catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis; 6-phosphofructokinase	264143..265123	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829069
YP_424208.1	CDS	pyk	NC_007633.1	265192	266628	D	catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate kinase	265192..266628	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828599
YP_424209.1	CDS	thrS	NC_007633.1	266899	268818	D	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	266899..268818	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828379
YP_424210.1	CDS	MCAP_0223	NC_007633.1	269448	270812	D	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	269448..270812	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828429
YP_424211.1	CDS	MCAP_0224	NC_007633.1	270824	271828	D	identified by similarity to SP:P32099; match to protein family HMM PF03099; match to protein family HMM TIGR00545; lipoate-protein ligase	270824..271828	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828543
YP_424212.1	CDS	pdhA	NC_007633.1	271863	272975	D	identified by similarity to SP:P21881; match to protein family HMM PF00676; pyruvate dehydrogenase complex, EI component subunit alpha	271863..272975	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828691
YP_424213.1	CDS	pdhB	NC_007633.1	272975	273964	D	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	272975..273964	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828875
YP_424214.1	CDS	pdhC	NC_007633.1	273993	275309	D	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	273993..275309	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828394
YP_424215.1	CDS	pdhD	NC_007633.1	275328	277217	D	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	275328..277217	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829042
YP_424216.1	CDS	pta	NC_007633.1	277239	278207	D	identified by similarity to SP:P39646; match to protein family HMM PF01515; match to protein family HMM TIGR00651; phosphate acetyltransferase	277239..278207	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828892
YP_424217.1	CDS	ackA	NC_007633.1	278221	279402	D	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	278221..279402	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828773
YP_424218.1	CDS	MCAP_0231	NC_007633.1	279470	281437	D	identified by match to protein family HMM PF01732; lipoprotein	279470..281437	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828347
YP_424219.1	CDS	coaD	NC_007633.1	281447	281869	D	catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-CoA; phosphopantetheine adenylyltransferase	281447..281869	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828952
YP_424220.1	CDS	ptsI	NC_007633.1	281962	283683	D	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	281962..283683	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828981
YP_424221.1	CDS	crr	NC_007633.1	283765	284229	D	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	283765..284229	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828900
YP_424222.1	CDS	MCAP_0235	NC_007633.1	284721	285347	D	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	284721..285347	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829115
YP_424223.1	CDS	MCAP_0236	NC_007633.1	285355	285744	D	identified by match to protein family HMM PF03610; match to protein family HMM TIGR02364; PTS system mannnose-specific transporter subunit IIA	285355..285744	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829133
YP_424224.1	CDS	rpsD	NC_007633.1	285801	286427	R	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	complement(285801..286427)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828736
YP_424225.1	CDS	MCAP_0238	NC_007633.1	286682	288469	D	MCAP_0238 has 1 membrane spanning region, N-terminal; hypothetical protein	286682..288469	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828512
YP_424226.1	CDS	thiI	NC_007633.1	288478	289665	D	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	288478..289665	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828407
YP_424227.1	CDS	MCAP_0240	NC_007633.1	289797	291767	D	MCAP_0240 has 2 membrane spanning regions and a likely C-terminal peptidase domain; identified by match to protein family HMM PF03572; hypothetical protein	289797..291767	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828495
YP_424228.1	CDS	MCAP_0241	NC_007633.1	291884	293554	D	MCAP_0241 has one membrane spanning region; hypothetical protein	291884..293554	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828990
YP_424229.1	CDS	MCAP_0242	NC_007633.1	293564	295852	D	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	293564..295852	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828761
YP_424230.1	CDS	MCAP_0243	NC_007633.1	296087	298150	D	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	296087..298150	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828487
YP_424231.1	CDS	MCAP_0244	NC_007633.1	298176	301091	R	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	complement(298176..301091)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829055
YP_424232.1	CDS	engB	NC_007633.1	301100	301690	R	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	complement(301100..301690)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828378
YP_424233.1	CDS	MCAP_0246	NC_007633.1	301684	302244	R	MCAP_0246 has 3 membrane spanning regions; hypothetical protein	complement(301684..302244)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828927
YP_424234.1	CDS	MCAP_0247	NC_007633.1	302246	302824	R	MCAP_0247 has 1 membrane spanning region, N-terminal; hypothetical protein	complement(302246..302824)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828404
YP_424235.1	CDS	MCAP_0248	NC_007633.1	302827	303516	R	hypothetical protein	complement(302827..303516)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829102
YP_424236.1	CDS	MCAP_0249	NC_007633.1	303598	304293	D	hypothetical protein	303598..304293	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828439
YP_424237.1	CDS	MCAP_0250	NC_007633.1	304294	305016	R	identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase family oxidoreductase	complement(304294..305016)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828988
YP_424238.1	CDS	greA	NC_007633.1	305075	305548	R	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	complement(305075..305548)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828680
YP_424239.1	CDS	uvrC	NC_007633.1	305640	307394	R	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	complement(305640..307394)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828962
YP_424240.1	CDS	MCAP_0253	NC_007633.1	307403	308479	R	MCAP_0253 has 6 membrane spanning regions; hypothetical protein	complement(307403..308479)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828314
YP_424241.1	CDS	MCAP_0255	NC_007633.1	310275	312026	R	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	complement(310275..312026)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828747
YP_424242.1	CDS	MCAP_0256	NC_007633.1	312145	312864	R	identified by match to protein family HMM PF00106; short chain dehydrogenase/reductase family oxidoreductase	complement(312145..312864)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829094
YP_424243.1	CDS	MCAP_0257	NC_007633.1	312876	313673	R	identified by match to protein family HMM PF01513; inorganic polyphosphate/ATP-NAD kinase	complement(312876..313673)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828780
YP_424244.1	CDS	valS	NC_007633.1	313797	316415	R	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	complement(313797..316415)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828894
YP_424245.1	CDS	MCAP_0259	NC_007633.1	316500	317126	R	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	complement(316500..317126)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828362
YP_424246.1	CDS	rpe	NC_007633.1	317116	317793	R	identified by match to protein family HMM PF00834; ribulose-phosphate 3-epimerase	complement(317116..317793)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829002
YP_424247.1	CDS	rsgA	NC_007633.1	317795	318697	R	identified by match to protein family HMM PF03193; match to protein family HMM TIGR00157; ribosome small subunit-dependent GTPase A	complement(317795..318697)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828972
YP_424248.1	CDS	MCAP_0262	NC_007633.1	318707	319822	R	identified by similarity to GB:AAL58474.1; match to protein family HMM PF00069; serine/threonine protein kinase	complement(318707..319822)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829134
YP_424249.1	CDS	MCAP_0263	NC_007633.1	319822	320085	R	hypothetical protein	complement(319822..320085)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828824
YP_424250.1	CDS	MCAP_0264	NC_007633.1	320054	320581	R	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	complement(320054..320581)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828792
YP_424251.1	CDS	MCAP_0265	NC_007633.1	320611	322023	R	MCAP_0265 has 1 membrane spanning region; hypothetical protein	complement(320611..322023)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828609
YP_424252.1	CDS	MCAP_0266	NC_007633.1	322126	322542	D	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	322126..322542	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828623
YP_424253.1	CDS	MCAP_0267	NC_007633.1	322544	323107	D	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	322544..323107	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828612
YP_424254.1	CDS	MCAP_0268	NC_007633.1	323167	324522	R	This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM TIGR02167; lipoprotein	complement(323167..324522)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828373
YP_424255.1	CDS	MCAP_0269	NC_007633.1	324791	326143	R	This ORF encodes tandem sequences containing the lppQ-Variable-Repeat-Peptide motif; identified by match to protein family HMM TIGR02167; lipoprotein	complement(324791..326143)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828695
YP_424256.1	CDS	MCAP_0270	NC_007633.1	326350	331656	R	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	complement(326350..331656)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829028
YP_424257.1	CDS	MCAP_0271	NC_007633.1	331924	335061	D	MCAP_0271 has 1 membrane spanning region, N-terminal.; hypothetical protein	331924..335061	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829024
YP_424258.1	CDS	MCAP_0272	NC_007633.1	335085	335603	D	lipoprotein	335085..335603	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828621
YP_424259.1	CDS	MCAP_0273	NC_007633.1	335689	336228	D	lipoprotein	335689..336228	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829059
YP_424260.1	CDS	MCAP_0274	NC_007633.1	336621	337358	D	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	336621..337358	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828349
YP_424261.1	CDS	MCAP_0275	NC_007633.1	338352	338984	D	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	338352..338984	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828939
YP_424262.1	CDS	MCAP_0276	NC_007633.1	339294	339815	D	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	339294..339815	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829064
YP_424263.1	CDS	MCAP_0277	NC_007633.1	339845	340249	D	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	339845..340249	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828311
YP_424264.1	CDS	MCAP_0278	NC_007633.1	340321	340929	D	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	340321..340929	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828279
YP_424265.1	CDS	MCAP_0279	NC_007633.1	340973	341833	D	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	340973..341833	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828569
YP_424266.1	CDS	MCAP_0280	NC_007633.1	342147	342296	D	Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein	342147..342296	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828809
YP_424267.1	CDS	MCAP_0281	NC_007633.1	342461	342769	D	Tra Island I encoded ORF; identified by similarity to GP:1763709; match to protein family HMM PF00436; single-strand binding protein family	342461..342769	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828814
YP_424268.1	CDS	MCAP_0282	NC_007633.1	342820	343560	D	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	342820..343560	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828884
YP_424269.1	CDS	MCAP_0283	NC_007633.1	343562	343777	D	Hypothetical protein encoded within Tra Island I. Paralogous MCAP_0185 (45% amino acid identity) encoded within Tra Island II; identified by Glimmer2; hypothetical protein	343562..343777	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828984
YP_424270.1	CDS	MCAP_0284	NC_007633.1	343855	344736	D	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	343855..344736	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829088
YP_424271.1	CDS	MCAP_0285	NC_007633.1	344834	345322	D	Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein	344834..345322	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828823
YP_424272.1	CDS	MCAP_0286	NC_007633.1	345374	345943	D	Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein	345374..345943	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829084
YP_424273.1	CDS	MCAP_0287	NC_007633.1	346021	346839	D	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	346021..346839	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829099
YP_424274.1	CDS	MCAP_0288	NC_007633.1	346886	347458	D	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	346886..347458	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829129
YP_424275.1	CDS	MCAP_0289	NC_007633.1	347716	348396	D	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	347716..348396	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828393
YP_424276.1	CDS	MCAP_0290	NC_007633.1	348460	348876	D	Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein	348460..348876	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828406
YP_424277.1	CDS	MCAP_0291	NC_007633.1	348951	349499	D	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	348951..349499	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828455
YP_424278.1	CDS	MCAP_0292	NC_007633.1	349555	350307	D	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	349555..350307	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828285
YP_424279.1	CDS	MCAP_0293	NC_007633.1	350364	351119	D	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	350364..351119	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828769
YP_424280.1	CDS	MCAP_0294	NC_007633.1	351168	351779	D	Tra Island I encoded ORF; identified by Glimmer2; hypothetical protein	351168..351779	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828386
YP_424281.1	CDS	MCAP_0295	NC_007633.1	351830	352243	D	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	351830..352243	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828701
YP_424282.1	CDS	MCAP_0296	NC_007633.1	352322	353125	D	This Tra Island I encodede ORF has strong homology to MSC_0201 in M. mycoides SC; hypothetical protein	352322..353125	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829007
YP_424283.1	CDS	MCAP_0297	NC_007633.1	353126	353794	D	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	353126..353794	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828750
YP_424284.1	CDS	MCAP_0298	NC_007633.1	353798	354178	D	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	353798..354178	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829080
YP_424285.1	CDS	MCAP_0299	NC_007633.1	354758	359698	D	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	354758..359698	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829103
YP_424286.1	CDS	MCAP_0300	NC_007633.1	360401	361894	R	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	complement(360401..361894)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828706
YP_424287.1	CDS	MCAP_0301	NC_007633.1	362143	364599	R	Tra Island I encoded ORF exhibits homology to multiple ORFs annotated as TraE/TrsE family NTPases.; hypothetical protein	complement(362143..364599)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828853
YP_424288.1	CDS	MCAP_0302	NC_007633.1	364659	365339	R	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	complement(364659..365339)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828375
YP_424289.1	CDS	MCAP_0303	NC_007633.1	366143	366730	R	MCAP_0303, resident within Tra Island I, contains 2 membrane spanning regions; hypothetical protein	complement(366143..366730)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828568
YP_424290.1	CDS	MCAP_0304	NC_007633.1	366730	368646	R	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	complement(366730..368646)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828471
YP_424291.1	CDS	MCAP_0305	NC_007633.1	368903	370393	R	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	complement(368903..370393)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828335
YP_424292.1	CDS	MCAP_0306	NC_007633.1	370524	370844	R	MCAP_0306, encoded within Tra Island I, has 2 membrane spanning regions; hypothetical protein	complement(370524..370844)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828674
YP_424293.1	CDS	MCAP_0307	NC_007633.1	371320	372405	R	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	complement(371320..372405)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828579
YP_424294.1	CDS	MCAP_0308	NC_007633.1	372470	373015	R	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	complement(372470..373015)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829075
YP_424295.1	CDS	MCAP_0309	NC_007633.1	373077	374006	R	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	complement(373077..374006)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828440
YP_424296.1	CDS	MCAP_0310	NC_007633.1	374061	374963	R	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	complement(374061..374963)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828699
YP_424297.1	CDS	MCAP_0311	NC_007633.1	375026	375997	R	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	complement(375026..375997)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828995
YP_424298.1	CDS	MCAP_0312	NC_007633.1	376060	377175	R	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	complement(376060..377175)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828947
YP_424299.1	CDS	hupB	NC_007633.1	377232	377510	R	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	complement(377232..377510)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828535
YP_424300.1	CDS	MCAP_0314	NC_007633.1	377579	378211	R	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	complement(377579..378211)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828638
YP_424301.1	CDS	MCAP_0315	NC_007633.1	378592	379707	D	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	378592..379707	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828854
YP_424302.1	CDS	MCAP_0317	NC_007633.1	380492	381184	D	hypothetical protein	380492..381184	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828416
YP_424303.2	CDS	proS	NC_007633.1	381165	382589	D	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase	381165..382589	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828890
YP_424304.1	CDS	MCAP_0319	NC_007633.1	382602	383222	D	identified by match to protein family HMM PF00075; ribonuclease H1	382602..383222	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829009
YP_424305.1	CDS	MCAP_0320	NC_007633.1	383224	384123	D	hypothetical protein	383224..384123	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828805
YP_424306.1	CDS	lepA	NC_007633.1	384137	385939	D	binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA	384137..385939	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828815
YP_424307.1	CDS	MCAP_0322	NC_007633.1	385973	386776	D	hypothetical protein	385973..386776	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829011
YP_424308.1	CDS	aspS	NC_007633.1	386797	388524	R	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	complement(386797..388524)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829065
YP_424309.1	CDS	hisS	NC_007633.1	388533	389777	R	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	complement(388533..389777)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828446
YP_424310.1	CDS	rbfA	NC_007633.1	389949	390302	D	identified by similarity to SP:P09170; match to protein family HMM PF02033; match to protein family HMM TIGR00082; ribosome-binding factor A	389949..390302	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828472
YP_424311.1	CDS	MCAP_0326	NC_007633.1	390352	391230	D	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	390352..391230	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829091
YP_424312.1	CDS	MCAP_0327	NC_007633.1	391217	391771	D	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	391217..391771	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828958
YP_424313.1	CDS	MCAP_0328	NC_007633.1	391784	393832	R	MCAP_0328 has 1 membrane spanning region; identified by match to protein family HMM PF03572; hypothetical protein	complement(391784..393832)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828720
YP_424314.1	CDS	MCAP_0329	NC_007633.1	393844	395682	R	identified by match to protein family HMM PF03572; lipoprotein	complement(393844..395682)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829061
YP_424315.1	CDS	rpsO	NC_007633.1	395895	396161	D	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	395895..396161	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828414
YP_424316.1	CDS	MCAP_0332	NC_007633.1	396385	397035	D	There are 4 membrane spanning regions in MCAP_0332.; hypothetical protein	396385..397035	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829052
YP_424317.1	CDS	infB	NC_007633.1	397049	398911	R	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	complement(397049..398911)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829005
YP_424318.1	CDS	MCAP_0334	NC_007633.1	398931	399230	R	identified by match to protein family HMM PF01248; ribosomal protein L7A family protein	complement(398931..399230)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828776
YP_424319.1	CDS	MCAP_0335	NC_007633.1	399217	399504	R	identified by match to protein family HMM PF04296; hypothetical protein	complement(399217..399504)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828759
YP_424320.1	CDS	nusA	NC_007633.1	399479	401155	R	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA	complement(399479..401155)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828290
YP_424321.1	CDS	MCAP_0337	NC_007633.1	401164	401658	R	hypothetical protein	complement(401164..401658)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828299
YP_424322.1	CDS	MCAP_0338	NC_007633.1	401771	402394	R	identified by match to protein family HMM PF00881; nitroreductase family protein	complement(401771..402394)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828880
YP_424323.1	CDS	polC	NC_007633.1	402434	406873	R	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	complement(402434..406873)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828732
YP_424324.1	CDS	cdsA	NC_007633.1	406882	407910	R	identified by match to protein family HMM PF01148; phosphatidate cytidylyltransferase	complement(406882..407910)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828481
YP_424325.1	CDS	MCAP_0341	NC_007633.1	408108	409184	R	identified by match to protein family HMM PF00557; Xaa-Pro peptidase	complement(408108..409184)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829034
YP_424326.1	CDS	trpS	NC_007633.1	409342	410352	D	identified by match to protein family HMM PF00579; match to protein family HMM TIGR00233; tryptophanyl-tRNA synthetase	409342..410352	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828377
YP_424327.1	CDS	MCAP_0343	NC_007633.1	410382	411272	R	MCAP_0343 has 1 membrane spanning region; hypothetical protein	complement(410382..411272)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828964
YP_424328.1	CDS	MCAP_0344	NC_007633.1	411606	412175	D	identified by match to protein family HMM PF02661; Fic family protein	411606..412175	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828710
YP_424329.1	CDS	MCAP_0345	NC_007633.1	412795	415050	D	MCAP_0345 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein	412795..415050	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828345
YP_424330.1	CDS	MCAP_0346	NC_007633.1	415071	417659	D	lipoprotein	415071..417659	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828740
YP_424331.1	CDS	MCAP_0347	NC_007633.1	417869	420121	D	MCAP_0347 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein	417869..420121	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828967
YP_424332.1	CDS	MCAP_0348	NC_007633.1	420139	422718	D	lipoprotein	420139..422718	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829050
YP_424333.1	CDS	MCAP_0349	NC_007633.1	422903	425152	D	MCAP_0349 has 1 membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein	422903..425152	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829117
YP_424334.1	CDS	MCAP_0350	NC_007633.1	425172	427751	D	lipoprotein	425172..427751	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829072
YP_424335.1	CDS	MCAP_0351	NC_007633.1	428011	430263	D	MCAP_0351 has one membrane spanning region, N-terminal; identified by match to protein family HMM TIGR02184; hypothetical protein	428011..430263	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828459
YP_424336.1	CDS	MCAP_0352	NC_007633.1	430287	432854	D	lipoprotein	430287..432854	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828353
YP_424337.1	CDS	MCAP_0353	NC_007633.1	432889	434352	D	MCAP_0353 has 12 membrane spanning regions; hypothetical protein	432889..434352	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828551
YP_424338.1	CDS	MCAP_0354	NC_007633.1	434327	434821	D	hypothetical protein	434327..434821	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828673
YP_424339.1	CDS	MCAP_0355	NC_007633.1	434823	435734	D	hypothetical protein	434823..435734	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829071
YP_424340.1	CDS	MCAP_0356	NC_007633.1	435734	436177	D	hypothetical protein	435734..436177	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828442
YP_424341.1	CDS	MCAP_0357	NC_007633.1	436179	438446	D	There are 3 membrane spanning regions in MCAP_0357.; hypothetical protein	436179..438446	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828865
YP_424342.1	CDS	atpA2	NC_007633.1	438451	439998	D	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	438451..439998	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828320
YP_424343.1	CDS	atpD2	NC_007633.1	439998	441377	D	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	439998..441377	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828797
YP_424344.1	CDS	MCAP_0360	NC_007633.1	441432	443936	R	hypothetical protein	complement(441432..443936)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828484
YP_424345.1	CDS	MCAP_0361	NC_007633.1	444199	446745	R	hypothetical protein	complement(444199..446745)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829029
YP_424346.1	CDS	MCAP_0362	NC_007633.1	446899	449406	R	hypothetical protein	complement(446899..449406)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828844
YP_424347.1	CDS	MCAP_0363	NC_007633.1	449586	450185	D	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	449586..450185	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828319
YP_424348.1	CDS	MCAP_0364	NC_007633.1	450199	450744	D	identified by match to protein family HMM PF00588; RNA methyltransferase	450199..450744	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828526
YP_424349.1	CDS	MCAP_0365	NC_007633.1	450744	451610	D	identified by match to protein family HMM TIGR00099; match to protein family HMM TIGR01484; HAD superfamily hydrolase	450744..451610	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829136
YP_424350.1	CDS	MCAP_0366	NC_007633.1	451775	453916	D	identified by match to protein family HMM PF00004; match to protein family HMM PF07724; ATP-dependent Clp protease, ATP-binding subunit ClpB	451775..453916	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828675
YP_424351.1	CDS	hrcA	NC_007633.1	453921	454943	D	identified by match to protein family HMM PF01628; match to protein family HMM TIGR00331; heat-inducible transcription repressor HrcA	453921..454943	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828723
YP_424352.1	CDS	grpE	NC_007633.1	454927	455547	D	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	454927..455547	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828825
YP_424353.1	CDS	dnaK	NC_007633.1	455607	457382	D	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	455607..457382	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828296
YP_424354.1	CDS	dnaJ	NC_007633.1	457447	458565	D	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	457447..458565	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828575
YP_424355.1	CDS	rpsB	NC_007633.1	458769	459644	D	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	458769..459644	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828690
YP_424356.1	CDS	tsf	NC_007633.1	459656	460543	D	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	459656..460543	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829125
YP_424357.1	CDS	MCAP_0373	NC_007633.1	460546	461151	D	There are 3 membrane spanning regions in MCAP_0373.; hypothetical protein	460546..461151	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828822
YP_424358.1	CDS	pyrH	NC_007633.1	461283	461996	D	identified by match to protein family HMM PF00696; match to protein family HMM TIGR02075; uridylate kinase	461283..461996	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828536
YP_424359.1	CDS	frr	NC_007633.1	462007	462555	D	identified by match to protein family HMM PF01765; match to protein family HMM TIGR00496; ribosome recycling factor	462007..462555	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828505
YP_424360.1	CDS	argS	NC_007633.1	462557	464221	D	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	462557..464221	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828392
YP_424361.1	CDS	MCAP_0381	NC_007633.1	469387	473832	D	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	469387..473832	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829127
YP_424362.1	CDS	MCAP_0382	NC_007633.1	473844	474452	D	hypothetical protein	473844..474452	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829132
YP_424363.1	CDS	pheS	NC_007633.1	474483	475535	D	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	474483..475535	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829087
YP_424364.1	CDS	pheT	NC_007633.1	475544	477928	D	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	475544..477928	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828897
YP_424365.1	CDS	MCAP_0385	NC_007633.1	477928	478443	D	hypothetical protein	477928..478443	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828616
YP_424366.1	CDS	rpmF	NC_007633.1	478458	478637	D	some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32	478458..478637	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828545
YP_424367.1	CDS	MCAP_0387	NC_007633.1	478742	479140	D	MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ	478742..479140	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828873
YP_424368.1	CDS	mraW	NC_007633.1	479149	480078	D	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	479149..480078	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829025
YP_424369.1	CDS	MCAP_0389	NC_007633.1	480087	481244	D	hypothetical protein	480087..481244	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828757
YP_424370.1	CDS	ftsZ	NC_007633.1	481359	482498	D	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	481359..482498	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828608
YP_424371.1	CDS	MCAP_0391	NC_007633.1	482511	482954	D	hypothetical protein	482511..482954	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828686
YP_424372.1	CDS	MCAP_0392	NC_007633.1	482987	483976	D	hypothetical protein	482987..483976	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828426
YP_424373.1	CDS	ileS	NC_007633.1	484559	487285	D	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	484559..487285	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828544
YP_424374.1	CDS	lspA	NC_007633.1	487294	487902	D	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase	487294..487902	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828943
YP_424375.1	CDS	MCAP_0395	NC_007633.1	487883	488851	D	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	487883..488851	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828419
YP_424376.1	CDS	MCAP_0396	NC_007633.1	488835	490145	D	MCAP_0396 has 7 membrane spanning regions; hypothetical protein	488835..490145	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828919
YP_424377.1	CDS	MCAP_0397	NC_007633.1	490172	490633	D	identified by similarity to SP:P16006; match to protein family HMM PF00383; deoxycytidylate deaminase	490172..490633	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828970
YP_424378.1	CDS	MCAP_0398	NC_007633.1	490673	491827	D	MCAP_0398 has two membrane spanning regions; hypothetical protein	490673..491827	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828724
YP_424379.1	CDS	MCAP_0399	NC_007633.1	491908	493293	D	MCAP_0399 has 2 membrane spanning regions; hypothetical protein	491908..493293	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828945
YP_424380.1	CDS	MCAP_0400	NC_007633.1	493313	493645	D	identified by match to protein family HMM PF01648; match to protein family HMM TIGR00556; holo-(acyl-carrier-protein) synthase	493313..493645	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828458
YP_424381.1	CDS	MCAP_0401	NC_007633.1	493687	494838	D	MCAP_0401 has 2 membrane spanning regions; hypothetical protein	493687..494838	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828907
YP_424382.1	CDS	MCAP_0402	NC_007633.1	494973	495926	D	identified by match to protein family HMM PF01553; 1-acyl-sn-glycerol-3-phosphate acyltransferase	494973..495926	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828848
YP_424383.1	CDS	MCAP_0403	NC_007633.1	495977	496594	D	hypothetical protein	495977..496594	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828282
YP_424384.1	CDS	MCAP_0409	NC_007633.1	497250	498314	R	lipoprotein	complement(497250..498314)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828953
YP_424385.1	CDS	MCAP_0410	NC_007633.1	498691	499581	D	identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096; hypothetical protein	498691..499581	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828694
YP_424386.1	CDS	MCAP_0411	NC_007633.1	499603	500004	D	hypothetical protein	499603..500004	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828504
YP_424387.1	CDS	rplU	NC_007633.1	500149	500451	D	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061; 50S ribosomal protein L21	500149..500451	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828722
YP_424388.1	CDS	MCAP_0413	NC_007633.1	500454	500768	D	identified by match to protein family HMM PF04327; hypothetical protein	500454..500768	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828337
YP_424389.1	CDS	rpmA	NC_007633.1	500770	501051	D	involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27	500770..501051	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829016
YP_424390.1	CDS	nanA	NC_007633.1	501245	502132	D	catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid; N-acetylneuraminate lyase	501245..502132	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828601
YP_424391.1	CDS	MCAP_0416	NC_007633.1	502136	503848	D	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	502136..503848	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829030
YP_424392.1	CDS	MCAP_0417	NC_007633.1	503857	504306	D	identified by match to protein family HMM PF04074; match to protein family HMM TIGR00022; hypothetical protein	503857..504306	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828447
YP_424393.1	CDS	MCAP_0418	NC_007633.1	504299	505174	D	identified by match to protein family HMM PF00480; ROK family protein	504299..505174	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828689
YP_424394.1	CDS	MCAP_0419	NC_007633.1	505254	505934	D	Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate; N-acetylmannosamine-6-phosphate 2-epimerase	505254..505934	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828617
YP_424395.1	CDS	MCAP_0420	NC_007633.1	506088	507437	D	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	506088..507437	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828960
YP_424396.1	CDS	MCAP_0421	NC_007633.1	507518	507952	D	There are 4 membrane spanning regions in MCAP_0421.; hypothetical protein	507518..507952	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828728
YP_424397.1	CDS	udk	NC_007633.1	507977	508600	D	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	507977..508600	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828360
YP_424398.1	CDS	MCAP_0423	NC_007633.1	508728	509954	D	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	508728..509954	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828493
YP_424399.1	CDS	MCAP_0424	NC_007633.1	509967	511070	R	identified by match to protein family HMM PF01926; hypothetical protein	complement(509967..511070)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828483
YP_424400.1	CDS	MCAP_0425	NC_007633.1	511079	511999	R	hypothetical protein	complement(511079..511999)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828771
YP_424401.1	CDS	MCAP_0426	NC_007633.1	512075	512890	D	hypothetical protein	512075..512890	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828808
YP_424402.1	CDS	MCAP_0427	NC_007633.1	512935	514296	R	Catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase	complement(512935..514296)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828448
YP_424403.1	CDS	ruvA	NC_007633.1	515351	515911	R	identified by similarity to SP:P75243; Holliday junction DNA helicase ruvA	complement(515351..515911)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828485
YP_424404.2	CDS	rpsU	NC_007633.1	516022	516186	R	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	complement(516022..516186)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829047
YP_424405.1	CDS	MCAP_0431	NC_007633.1	516454	517083	D	lipoprotein	516454..517083	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829081
YP_424406.1	CDS	MCAP_0432	NC_007633.1	517320	518039	D	lipoprotein	517320..518039	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828777
YP_424407.1	CDS	MCAP_0433	NC_007633.1	518278	518916	D	lipoprotein	518278..518916	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828846
YP_424408.1	CDS	MCAP_0434	NC_007633.1	518964	520697	R	hypothetical protein	complement(518964..520697)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828300
YP_424409.1	CDS	MCAP_0435	NC_007633.1	520850	522502	D	There are 2 membrane spanning regions in MCAP_0435.; hypothetical protein	520850..522502	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828339
YP_424410.1	CDS	MCAP_0436	NC_007633.1	522507	523106	D	There are 4 membrane spanning regions in MCAP_0436.; hypothetical protein	522507..523106	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828546
YP_424411.1	CDS	MCAP_0437	NC_007633.1	523118	523927	R	MCAP_0437 has 6 membrane spanning regions; hypothetical protein	complement(523118..523927)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828840
YP_424412.1	CDS	nagA	NC_007633.1	524021	525178	D	identified by similarity to SP:O34450; match to protein family HMM PF01979; match to protein family HMM TIGR00221; N-acetylglucosamine-6-phosphate deacetylase	524021..525178	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828297
YP_424413.1	CDS	ldh	NC_007633.1	525231	526184	D	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	525231..526184	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829124
YP_424414.1	CDS	MCAP_0440	NC_007633.1	526250	526912	R	MCAP_0440 has 6 membrane spanning regions; identified by match to protein family HMM PF01061; hypothetical protein	complement(526250..526912)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828796
YP_424415.1	CDS	MCAP_0441	NC_007633.1	527269	527469	R	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	complement(527269..527469)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828482
YP_424416.1	CDS	MCAP_0442	NC_007633.1	527481	528965	R	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	complement(527481..528965)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828749
YP_424417.1	CDS	MCAP_0443	NC_007633.1	529220	529492	D	hypothetical protein	529220..529492	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828549
YP_424418.1	CDS	MCAP_0444	NC_007633.1	529607	530716	D	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	529607..530716	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829114
YP_424419.1	CDS	MCAP_0445	NC_007633.1	530742	531539	R	MCAP_0446 is a paralog of this triacylglycerol lipase gene; identified by match to protein family HMM PF00561; triacylglycerol lipase	complement(530742..531539)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828628
YP_424420.1	CDS	MCAP_0446	NC_007633.1	531553	532341	R	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	complement(531553..532341)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828413
YP_424421.1	CDS	MCAP_0447	NC_007633.1	532528	532872	D	glycine cleavage system H protein	532528..532872	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828871
YP_424422.1	CDS	MCAP_0448	NC_007633.1	532879	533730	D	hypothetical protein	532879..533730	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828830
YP_424423.1	CDS	MCAP_0449	NC_007633.1	533708	534745	D	identified by match to protein family HMM PF03099; match to protein family HMM TIGR00545; lipoate-protein ligase	533708..534745	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828918
YP_424424.1	CDS	MCAP_0450	NC_007633.1	534745	535923	D	identified by similarity to OMNI:SA0392; match to protein family HMM PF00724; NADH:flavin oxidoreductase/NADH oxidase family protein	534745..535923	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828478
YP_424425.1	CDS	MCAP_0451	NC_007633.1	536187	538070	R	identified by match to protein family HMM PF03202; lipoprotein LppB	complement(536187..538070)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828727
YP_424426.1	CDS	gtsC	NC_007633.1	538184	538987	R	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	complement(538184..538987)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829113
YP_424427.1	CDS	gtsB	NC_007633.1	538965	539969	R	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	complement(538965..539969)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828965
YP_424428.1	CDS	gtsA	NC_007633.1	539962	541173	R	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	complement(539962..541173)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828510
YP_424429.1	CDS	MCAP_0455	NC_007633.1	541179	543374	R	recombinase D	complement(541179..543374)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829036
YP_424430.1	CDS	parC	NC_007633.1	543485	546184	R	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	complement(543485..546184)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828405
YP_424431.1	CDS	parE	NC_007633.1	546186	548117	R	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	complement(546186..548117)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829140
YP_424432.1	CDS	MCAP_0458	NC_007633.1	548347	549924	D	identified by similarity to SP:P00550; match to protein family HMM PF02302; PTS system mannitol-specific transporter subunit IIBC	548347..549924	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828735
YP_424433.1	CDS	MCAP_0459	NC_007633.1	549927	550367	D	identified by similarity to SP:P27547; match to protein family HMM PF00359; PTS system mannitol-specific transporter subunit IIA	549927..550367	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829001
YP_424434.1	CDS	MCAP_0460	NC_007633.1	550367	551266	D	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	550367..551266	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829144
YP_424435.1	CDS	MCAP_0461	NC_007633.1	551321	552736	R	identified by match to protein family HMM PF00171; aldehyde dehydrogenase (NAD) family protein	complement(551321..552736)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828843
YP_424436.1	CDS	MCAP_0462	NC_007633.1	552903	553670	R	identified by similarity to OMNI:NTL01LP1288; match to protein family HMM PF00588; match to protein family HMM PF08032; RNA methyltransferase	complement(552903..553670)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828600
YP_424437.1	CDS	MCAP_0463	NC_007633.1	553687	554190	R	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	complement(553687..554190)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828511
YP_424438.1	CDS	MCAP_0464	NC_007633.1	554231	554677	R	MCAP_0464 has 3 membrane spanning regions; hypothetical protein	complement(554231..554677)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828836
YP_424439.1	CDS	pgi	NC_007633.1	554703	555986	R	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	complement(554703..555986)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828818
YP_424440.1	CDS	pepO	NC_007633.1	556207	558102	R	identified by similarity to GB:AAD40473.1; match to protein family HMM PF01431; match to protein family HMM PF05649; endopeptidase O	complement(556207..558102)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828548
YP_424441.1	CDS	MCAP_0467	NC_007633.1	558116	558685	R	identified by match to protein family HMM PF01812; 5-formyltetrahydrofolate cyclo-ligase	complement(558116..558685)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828831
YP_424442.1	CDS	MCAP_0468	NC_007633.1	558678	559115	R	hypothetical protein	complement(558678..559115)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828329
YP_424443.1	CDS	MCAP_0469	NC_007633.1	559119	560357	R	identified by match to protein family HMM PF00266; class V aminotransferase	complement(559119..560357)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828961
YP_424444.1	CDS	MCAP_0470	NC_007633.1	560551	563544	D	lipoprotein	560551..563544	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828812
YP_424445.1	CDS	MCAP_0471	NC_007633.1	563566	565737	D	lipoprotein	563566..565737	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828738
YP_424446.1	CDS	MCAP_0472	NC_007633.1	565740	566135	D	identified by similarity to SP:O07513; match to protein family HMM PF01230; HIT family protein	565740..566135	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828992
YP_424447.1	CDS	MCAP_0473	NC_007633.1	566171	567151	R	identified by match to protein family HMM PF01336; match to protein family HMM PF01966; hypothetical protein	complement(566171..567151)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829097
YP_424448.1	CDS	ung	NC_007633.1	567220	567876	R	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	complement(567220..567876)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828733
YP_424449.1	CDS	pmi	NC_007633.1	567869	568798	R	identified by similarity to SP:P39841; match to protein family HMM PF01238; phosphomannose isomerase type I	complement(567869..568798)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828313
YP_424450.1	CDS	gid	NC_007633.1	568919	570235	R	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	complement(568919..570235)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828914
YP_424451.1	CDS	MCAP_0477	NC_007633.1	570228	570911	R	identified by similarity to SP:P46719; match to protein family HMM PF03932; copper homeostasis protein CutC	complement(570228..570911)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828586
YP_424452.1	CDS	metK	NC_007633.1	570902	572065	R	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase	complement(570902..572065)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828502
YP_424453.1	CDS	MCAP_0479	NC_007633.1	572276	573049	R	identified by match to protein family HMM PF00149; match to protein family HMM TIGR00282; hypothetical protein	complement(572276..573049)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828417
YP_424454.1	CDS	p13	NC_007633.1	573037	573378	R	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	complement(573037..573378)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828532
YP_424455.1	CDS	ftsY	NC_007633.1	573362	574636	R	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	complement(573362..574636)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828606
YP_424456.1	CDS	MCAP_0482	NC_007633.1	574705	575376	R	identified by match to protein family HMM PF01895; match to protein family HMM TIGR02135; phosphate transport system regulatory protein PhoU	complement(574705..575376)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828401
YP_424457.1	CDS	pstB	NC_007633.1	575385	576194	R	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	complement(575385..576194)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828595
YP_424458.1	CDS	MCAP_0484	NC_007633.1	576187	578277	R	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	complement(576187..578277)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828289
YP_424459.1	CDS	MCAP_0485	NC_007633.1	578281	579492	R	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	complement(578281..579492)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828303
YP_424460.1	CDS	MCAP_0486	NC_007633.1	579583	580017	R	hypothetical protein	complement(579583..580017)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828531
YP_424461.1	CDS	rpmB	NC_007633.1	580246	580443	R	required for 70S ribosome assembly; 50S ribosomal protein L28	complement(580246..580443)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828513
YP_424462.1	CDS	MCAP_0489	NC_007633.1	580603	580932	D	hypothetical protein	580603..580932	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828977
YP_424463.1	CDS	MCAP_0490	NC_007633.1	580962	582605	D	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	580962..582605	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828316
YP_424464.1	CDS	plsX	NC_007633.1	582637	583641	D	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	582637..583641	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828888
YP_424465.1	CDS	MCAP_0492	NC_007633.1	583631	584329	D	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	583631..584329	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829010
YP_424466.1	CDS	MCAP_0493	NC_007633.1	584513	584908	D	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	584513..584908	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829070
YP_424467.1	CDS	MCAP_0494	NC_007633.1	584911	585297	D	hypothetical protein	584911..585297	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828357
YP_424468.1	CDS	MCAP_0495	NC_007633.1	585624	588590	D	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	585624..588590	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828382
YP_424469.1	CDS	MCAP_0496	NC_007633.1	588629	590893	R	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	complement(588629..590893)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828372
YP_424470.1	CDS	apt	NC_007633.1	590953	591465	R	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase	complement(590953..591465)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829135
YP_424471.1	CDS	MCAP_0498	NC_007633.1	591477	595691	R	MCAP_0498 has 12 membrane spanning regions; hypothetical protein	complement(591477..595691)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829116
YP_424472.1	CDS	MCAP_0499	NC_007633.1	595793	597304	R	MCAP_0499 has 6 membrane spanning regions; identified by match to protein family HMM PF02588; hypothetical protein	complement(595793..597304)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829032
YP_424473.1	CDS	MCAP_0500	NC_007633.1	597343	598704	R	identified by similarity to OMNI:SA1615; match to protein family HMM PF00270; match to protein family HMM PF00271; DEAD/DEAH box helicase	complement(597343..598704)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828427
YP_424474.1	CDS	MCAP_0501	NC_007633.1	598713	599489	R	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	complement(598713..599489)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828850
YP_424475.1	CDS	MCAP_0502	NC_007633.1	599476	600153	R	identified by match to protein family HMM PF04816; hypothetical protein	complement(599476..600153)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828374
YP_424476.1	CDS	rpoD	NC_007633.1	600156	601673	R	identified by similarity to SP:Q59753; match to protein family HMM PF04539; match to protein family HMM PF04542; RNA polymerase sigma factor RpoD	complement(600156..601673)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829106
YP_424477.1	CDS	dnaG	NC_007633.1	601676	603490	R	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	complement(601676..603490)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828350
YP_424478.1	CDS	glyS	NC_007633.1	603527	604897	R	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	complement(603527..604897)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829100
YP_424479.1	CDS	MCAP_0506	NC_007633.1	604961	605710	R	identified by similarity to SP:P42095; match to protein family HMM PF02565; match to protein family HMM TIGR00613; DNA repair protein RecO	complement(604961..605710)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828460
YP_424480.1	CDS	era	NC_007633.1	605710	606615	R	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	complement(605710..606615)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828766
YP_424481.1	CDS	MCAP_0508	NC_007633.1	606618	607112	R	identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043; hypothetical protein	complement(606618..607112)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828782
YP_424482.1	CDS	MCAP_0509	NC_007633.1	607118	609007	R	identified by match to protein family HMM PF03412; peptidase C39 family protein	complement(607118..609007)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828702
YP_424483.1	CDS	MCAP_0510	NC_007633.1	609000	609548	R	identified by match to protein family HMM PF01965; match to protein family HMM TIGR01383; DJ-1 family protein	complement(609000..609548)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829085
YP_424484.1	CDS	MCAP_0511	NC_007633.1	609596	614857	R	MCAP_0511 has 8 membrane spanning regions; MCAP_0511 may be a transporter permease; identified by match to protein family HMM PF02687; hypothetical protein	complement(609596..614857)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828456
YP_424485.1	CDS	MCAP_0513	NC_007633.1	617508	619751	D	lipoprotein	617508..619751	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828767
YP_424486.1	CDS	MCAP_0514	NC_007633.1	619809	622079	D	lipoprotein	619809..622079	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828704
YP_424487.1	CDS	MCAP_0515	NC_007633.1	622111	623349	R	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	complement(622111..623349)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829128
YP_424488.1	CDS	lon	NC_007633.1	623462	625801	R	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	complement(623462..625801)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828715
YP_424489.1	CDS	tig	NC_007633.1	625920	627206	R	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	complement(625920..627206)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828864
YP_424490.1	CDS	MCAP_0518	NC_007633.1	627223	627525	R	hypothetical protein	complement(627223..627525)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828409
YP_424491.1	CDS	efp	NC_007633.1	627543	628097	R	identified by match to protein family HMM PF01132; match to protein family HMM TIGR00038; translation elongation factor P	complement(627543..628097)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828603
YP_424492.1	CDS	fmt	NC_007633.1	628187	629140	R	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	complement(628187..629140)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828998
YP_424493.1	CDS	MCAP_0521	NC_007633.1	629130	631274	R	hypothetical protein	complement(629130..631274)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828688
YP_424494.1	CDS	MCAP_0522	NC_007633.1	631351	631968	R	MCAP_0522 has 1 membrane spanning region, N-terminal.; hypothetical protein	complement(631351..631968)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828356
YP_424495.1	CDS	mnmA	NC_007633.1	632010	633137	R	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA	complement(632010..633137)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829039
YP_424496.1	CDS	MCAP_0524	NC_007633.1	633233	634117	R	lipoprotein	complement(633233..634117)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828627
YP_424497.1	CDS	MCAP_0525	NC_007633.1	634769	635542	R	lipoprotein	complement(634769..635542)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828625
YP_424498.1	CDS	MCAP_0526	NC_007633.1	635564	636367	R	lipoprotein	complement(635564..636367)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828810
YP_424499.1	CDS	MCAP_0527	NC_007633.1	636581	637225	R	hypothetical protein	complement(636581..637225)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828488
YP_424500.1	CDS	MCAP_0528	NC_007633.1	637250	637885	R	identified by similarity to SP:O32028; match to protein family HMM PF01048; match to protein family HMM TIGR01704; MTA/SAH nucleosidase	complement(637250..637885)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829022
YP_424501.1	CDS	nadD	NC_007633.1	637908	639011	R	catalyzes the reversible adenylation of nicotinate mononucleotide to nicotinic acid adenine dinucleotide; nicotinate-nucleotide adenylyltransferase	complement(637908..639011)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829138
YP_424502.1	CDS	MCAP_0530	NC_007633.1	639029	639274	R	MCAP_0530 has 1 membrane spanning region; hypothetical protein	complement(639029..639274)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828403
YP_424503.1	CDS	MCAP_0531	NC_007633.1	639292	640053	R	identified by similarity to SP:P08164; match to protein family HMM PF02540; match to protein family HMM TIGR00552; NH3-dependent NAD+ synthetase	complement(639292..640053)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828755
YP_424504.1	CDS	obgE	NC_007633.1	640031	641332	R	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE	complement(640031..641332)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828287
YP_424505.1	CDS	MCAP_0533	NC_007633.1	641403	641711	R	hypothetical protein	complement(641403..641711)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828527
YP_424506.1	CDS	MCAP_0534	NC_007633.1	641701	642453	R	hypothetical protein	complement(641701..642453)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828441
YP_424507.1	CDS	MCAP_0536	NC_007633.1	642641	644245	R	There are very similar proteins in M mycoides (93% amino acid identity) and Mesoplasma florum (32% identit).; hypothetical protein	complement(642641..644245)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828719
YP_424508.1	CDS	MCAP_0537	NC_007633.1	644285	646138	R	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	complement(644285..646138)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828817
YP_424509.1	CDS	MCAP_0538	NC_007633.1	646156	648027	R	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	complement(646156..648027)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828677
YP_424510.1	CDS	MCAP_0539	NC_007633.1	648243	648548	R	identified by match to protein family HMM PF00436; single-strand binding protein family	complement(648243..648548)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828499
YP_424511.1	CDS	MCAP_0540	NC_007633.1	648710	649948	D	MCAP_0540 has 11 transmembrane regions; identified by similarity to SP:P31064; match to protein family HMM PF04143; YeeE/YedE family protein	648710..649948	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828397
YP_424512.1	CDS	MCAP_0541	NC_007633.1	649951	651747	D	identified by match to protein family HMM PF00581; match to protein family HMM PF02852; match to protein family HMM PF07992; hypothetical protein	649951..651747	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828956
YP_424513.1	CDS	MCAP_0542	NC_007633.1	651769	652392	R	identified by match to protein family HMM PF01351; ribonuclease HII	complement(651769..652392)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828937
YP_424514.1	CDS	MCAP_0543	NC_007633.1	652386	653336	R	identified by match to protein family HMM PF01926; match to protein family HMM TIGR00650; GTPase family protein	complement(652386..653336)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828480
YP_424515.1	CDS	rplS	NC_007633.1	653429	653821	R	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	complement(653429..653821)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828343
YP_424516.1	CDS	trmD	NC_007633.1	653823	654545	R	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase	complement(653823..654545)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828550
YP_424517.1	CDS	MCAP_0546	NC_007633.1	654547	655041	R	identified by match to protein family HMM TIGR02273; 16S rRNA processing protein RimM	complement(654547..655041)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828540
YP_424518.1	CDS	rpsP	NC_007633.1	655059	655385	R	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	complement(655059..655385)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828402
YP_424519.1	CDS	MCAP_0548	NC_007633.1	655474	655941	R	identified by match to protein family HMM PF02590; hypothetical protein	complement(655474..655941)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828390
YP_424520.1	CDS	ffh	NC_007633.1	655947	657290	R	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	complement(655947..657290)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828729
YP_424521.1	CDS	MCAP_0550	NC_007633.1	657320	658849	R	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP; phosphodiesterase	complement(657320..658849)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828845
YP_424522.1	CDS	recA	NC_007633.1	659001	659987	R	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	complement(659001..659987)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828554
YP_424523.1	CDS	MCAP_0552	NC_007633.1	660079	660627	R	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	complement(660079..660627)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828433
YP_424524.1	CDS	MCAP_0554	NC_007633.1	661194	662042	D	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	661194..662042	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828632
YP_424525.1	CDS	MCAP_0556	NC_007633.1	663622	664455	D	MCAP_0556 is encoded within ICEC element; identified by similarity to GP:21538805; C-5 cytosine-specific DNA methylase	663622..664455	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828371
YP_424526.1	CDS	MCAP_0557	NC_007633.1	664567	665148	D	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	664567..665148	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829014
YP_424527.1	CDS	MCAP_0558	NC_007633.1	665588	665737	D	MCAP_0558 is encoded within ICEC element; identified by Glimmer2; hypothetical protein	665588..665737	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828891
YP_424528.1	CDS	MCAP_0559	NC_007633.1	666111	668111	D	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	666111..668111	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828762
YP_424529.1	CDS	MCAP_0560	NC_007633.1	668143	669558	D	MCAP_0560, encoded within ICEC, exhibits homology to LtrC-like proteins encoded by plasmids and mobile DNAs.; hypothetical protein	668143..669558	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828582
YP_424530.1	CDS	MCAP_0561	NC_007633.1	669691	671172	D	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	669691..671172	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828794
YP_424531.1	CDS	MCAP_0562	NC_007633.1	671184	671384	D	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	671184..671384	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828709
YP_424532.1	CDS	MCAP_0563	NC_007633.1	671489	671815	D	MCAP_0563, resident within ICEC, has 2 membrane spanning regions; hypothetical protein	671489..671815	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828772
YP_424533.1	CDS	MCAP_0564	NC_007633.1	671819	673462	D	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	671819..673462	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828428
YP_424534.1	CDS	MCAP_0565	NC_007633.1	673465	676302	D	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	673465..676302	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828922
YP_424535.1	CDS	MCAP_0566	NC_007633.1	676321	676944	D	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	676321..676944	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828859
YP_424536.1	CDS	MCAP_0567	NC_007633.1	676937	680959	D	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	676937..680959	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828284
YP_424537.1	CDS	MCAP_0568	NC_007633.1	681011	681991	D	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	681011..681991	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828587
YP_424538.1	CDS	MCAP_0569	NC_007633.1	682175	682540	D	Hypothetical ORF encoded within Integrative Conjugal Element of M. capricolum (ICEC); identified by Glimmer2; hypothetical protein	682175..682540	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828342
YP_424539.1	CDS	MCAP_0570	NC_007633.1	682755	683672	D	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	682755..683672	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828944
YP_424540.1	CDS	MCAP_0571	NC_007633.1	683782	685014	D	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	683782..685014	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828679
YP_424541.1	CDS	MCAP_0572	NC_007633.1	685488	685865	R	The M. mycoides ortholog is longer at the NH2 end.; hypothetical protein	complement(685488..685865)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828886
YP_424542.1	CDS	MCAP_0573	NC_007633.1	685929	686438	D	identified by similarity to SP:P39792; match to protein family HMM PF03838; recombination protein U	685929..686438	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828605
YP_424543.1	CDS	MCAP_0574	NC_007633.1	686410	686946	R	hypothetical protein	complement(686410..686946)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828820
YP_424544.1	CDS	hupA	NC_007633.1	687004	687276	R	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	complement(687004..687276)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828634
YP_424545.1	CDS	gpsA	NC_007633.1	687308	688306	R	identified by similarity to SP:P46919; match to protein family HMM PF01210; match to protein family HMM PF07479; glycerol-3-phosphate dehydrogenase (NAD(P)+)	complement(687308..688306)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829083
YP_424546.1	CDS	engA	NC_007633.1	688308	689615	R	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	complement(688308..689615)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828938
YP_424547.1	CDS	cmk	NC_007633.1	689615	690283	R	identified by similarity to SP:P38493; match to protein family HMM PF02224; match to protein family HMM TIGR00017; cytidylate kinase	complement(689615..690283)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828631
YP_424548.1	CDS	MCAP_0579	NC_007633.1	690292	690987	R	MCAP_0579 has 1 membrane spanning region; hypothetical protein	complement(690292..690987)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828800
YP_424549.1	CDS	MCAP_0580	NC_007633.1	691056	691943	R	MCAP_0580 has 5 membrane spanning regions; hypothetical protein	complement(691056..691943)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828423
YP_424550.1	CDS	ppa	NC_007633.1	692084	692644	D	identified by similarity to SP:P19514; match to protein family HMM PF00719; inorganic pyrophosphatase	692084..692644	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829020
YP_424551.1	CDS	MCAP_0582	NC_007633.1	692752	693453	R	hypothetical protein	complement(692752..693453)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828899
YP_424552.1	CDS	MCAP_0583	NC_007633.1	693511	695775	R	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	complement(693511..695775)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828760
YP_424553.1	CDS	MCAP_0584	NC_007633.1	695820	695942	R	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	complement(695820..695942)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829118
YP_424554.1	CDS	MCAP_0585	NC_007633.1	696234	696569	R	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	complement(696234..696569)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828508
YP_424555.1	CDS	MCAP_0586	NC_007633.1	696604	698397	R	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	complement(696604..698397)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829057
YP_424556.1	CDS	MCAP_0587	NC_007633.1	698444	700279	R	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	complement(698444..700279)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828467
YP_424557.1	CDS	MCAP_0589	NC_007633.1	701486	702133	R	identified by similarity to GB:CAE77029.1; match to protein family HMM PF00834; ribulose-phosphate 3-epimerase	complement(701486..702133)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829044
YP_424558.1	CDS	MCAP_0590	NC_007633.1	702133	703941	R	identified by match to protein family HMM PF02302; match to protein family HMM PF04215; PTS system ascorbate-specific transporter subunits IICB	complement(702133..703941)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828931
YP_424559.1	CDS	MCAP_0591	NC_007633.1	703953	704402	R	identified by match to protein family HMM PF00359; PTS system transporter subunit IIA	complement(703953..704402)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828833
YP_424560.1	CDS	MCAP_0592	NC_007633.1	704691	704795	R	hypothetical protein	complement(704691..704795)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829098
YP_424561.1	CDS	MCAP_0593	NC_007633.1	704901	705830	R	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	complement(704901..705830)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828465
YP_424562.1	CDS	MCAP_0594	NC_007633.1	706228	706662	R	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	complement(706228..706662)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828509
YP_424563.1	CDS	MCAP_0595	NC_007633.1	707728	708435	R	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	complement(707728..708435)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829027
YP_424564.1	CDS	MCAP_0596	NC_007633.1	709888	711366	R	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	complement(709888..711366)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828385
YP_424565.1	CDS	MCAP_0597	NC_007633.1	711633	712460	R	MCAP_0597 has 3 membrane spanning regions; hypothetical protein	complement(711633..712460)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828936
YP_424566.1	CDS	MCAP_0598	NC_007633.1	712560	713273	R	identified by match to protein family HMM PF01709; hypothetical protein	complement(712560..713273)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829086
YP_424567.1	CDS	MCAP_0599	NC_007633.1	713285	713902	R	identified by similarity to SP:Q59484; match to protein family HMM PF01712; nucleoside kinase	complement(713285..713902)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829092
YP_424568.1	CDS	MCAP_0600	NC_007633.1	713913	714671	R	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	complement(713913..714671)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828451
YP_424569.1	CDS	scpB	NC_007633.1	714745	715374	R	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	complement(714745..715374)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828336
YP_424570.1	CDS	scpA	NC_007633.1	715358	716194	R	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	complement(715358..716194)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829043
YP_424571.1	CDS	MCAP_0603	NC_007633.1	716204	716965	R	MCAP_0603 has 1 membrane spanning region; hypothetical protein	complement(716204..716965)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828712
YP_424572.1	CDS	MCAP_0604	NC_007633.1	716977	718476	R	MCAP_0604 has 13 membrane spanning regions; hypothetical protein	complement(716977..718476)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828795
YP_424573.1	CDS	MCAP_0605	NC_007633.1	718785	719183	R	lipoprotein	complement(718785..719183)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828774
YP_424574.1	CDS	MCAP_0606	NC_007633.1	719333	720127	R	identified by match to protein family HMM PF00561; alpha/beta fold family hydrolase	complement(719333..720127)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828856
YP_424575.1	CDS	MCAP_0607	NC_007633.1	720139	722595	R	lipoprotein	complement(720139..722595)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828498
YP_424576.1	CDS	MCAP_0608	NC_007633.1	722695	724239	R	hypothetical protein	complement(722695..724239)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828713
YP_424577.1	CDS	MCAP_0609	NC_007633.1	724303	724548	R	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	complement(724303..724548)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828982
YP_424578.1	CDS	tkt	NC_007633.1	724564	726534	R	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	complement(724564..726534)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828882
YP_424579.1	CDS	MCAP_0611	NC_007633.1	726575	726736	R	identified by similarity to GB:CAE77008.1; hypothetical protein	complement(726575..726736)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828803
YP_424580.1	CDS	MCAP_0612	NC_007633.1	726871	727611	R	MCAP_0612 has 6 membrane spanning regions; hypothetical protein	complement(726871..727611)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828613
YP_424581.1	CDS	MCAP_0613	NC_007633.1	727710	728981	R	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	complement(727710..728981)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828924
YP_424582.1	CDS	MCAP_0614	NC_007633.1	729282	730358	D	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	729282..730358	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828387
YP_424583.1	CDS	MCAP_0615	NC_007633.1	730500	730739	R	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	complement(730500..730739)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828940
YP_424584.1	CDS	MCAP_0616	NC_007633.1	730932	731777	R	identified by match to protein family HMM PF01116; match to protein family HMM TIGR00167; fructose/tagatose bisphosphate aldolase, class II	complement(730932..731777)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828556
YP_424585.1	CDS	MCAP_0617	NC_007633.1	731978	732712	D	identified by match to protein family HMM PF00455; DeoR family transcriptional regulator	731978..732712	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828971
YP_424586.1	CDS	MCAP_0618	NC_007633.1	732721	734607	D	identified by match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system transporter subunit IIBC	732721..734607	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828878
YP_424587.1	CDS	MCAP_0619	NC_007633.1	734620	735561	D	identified by similarity to SP:O31714; match to protein family HMM PF00294; 1-phosphofructokinase	734620..735561	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828424
YP_424588.1	CDS	MCAP_0620	NC_007633.1	735640	737490	R	There are 2 membrane spanning regions in MCAP_0620.; hypothetical protein	complement(735640..737490)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828388
YP_424589.1	CDS	MCAP_0621	NC_007633.1	738045	738590	R	MCAP_0621 has 1 membrane spanning region, N-terminal.; hypothetical protein	complement(738045..738590)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828672
YP_424590.1	CDS	MCAP_0622	NC_007633.1	740123	741652	D	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	740123..741652	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828708
YP_424591.1	CDS	MCAP_0623	NC_007633.1	741987	743822	D	identified by match to protein family HMM PF00753; match to protein family HMM PF07521; metallo-beta-lactamase superfamily protein	741987..743822	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829145
YP_424592.1	CDS	MCAP_0624	NC_007633.1	743900	744853	D	MCAP_0624 has 7 membrane spanning regions; hypothetical protein	743900..744853	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828993
YP_424593.1	CDS	MCAP_0625	NC_007633.1	745896	747140	D	MCAP_0625 has 7 membrane spanning regions; hypothetical protein	745896..747140	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828475
YP_424594.1	CDS	MCAP_0626	NC_007633.1	747406	748809	D	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	747406..748809	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829142
YP_424595.1	CDS	MCAP_0627	NC_007633.1	749130	750881	D	MCAP_0627 has 2 membrane spanning regions; hypothetical protein	749130..750881	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828910
YP_424596.1	CDS	MCAP_0628	NC_007633.1	750894	751562	D	MCAP_0628 has 1 membrane spanning region; hypothetical protein	750894..751562	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829054
YP_424597.1	CDS	MCAP_0629	NC_007633.1	751744	752391	D	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	751744..752391	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828954
YP_424598.1	CDS	MCAP_0630	NC_007633.1	753218	753748	D	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	753218..753748	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828978
YP_424599.1	CDS	pgk	NC_007633.1	753818	755032	R	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase	complement(753818..755032)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828670
YP_424600.1	CDS	gap	NC_007633.1	755160	756176	R	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	complement(755160..756176)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828624
YP_424601.1	CDS	MCAP_0633	NC_007633.1	756269	757204	R	This protein is similar to the B. subtilis DnaI primasomal protein (31% amino acid identity); hypothetical protein	complement(756269..757204)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828452
YP_424602.1	CDS	MCAP_0634	NC_007633.1	757214	758398	R	identified by match to protein family HMM PF07261; hypothetical protein	complement(757214..758398)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828764
YP_424603.1	CDS	mutM	NC_007633.1	758556	759380	R	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	complement(758556..759380)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828580
YP_424604.1	CDS	polA	NC_007633.1	759391	762126	R	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	complement(759391..762126)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828562
YP_424605.1	CDS	dnaE	NC_007633.1	762135	765095	R	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)	complement(762135..765095)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829037
YP_424606.1	CDS	MCAP_0638	NC_007633.1	765267	767921	D	MCAP_0638 has 2 membrane spanning regions; hypothetical protein	765267..767921	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828449
YP_424607.1	CDS	tyrS	NC_007633.1	768010	769254	R	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	complement(768010..769254)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828751
YP_424608.1	CDS	MCAP_0640	NC_007633.1	769262	770323	R	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase	complement(769262..770323)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828533
YP_424609.1	CDS	MCAP_0641	NC_007633.1	770301	770933	R	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	complement(770301..770933)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828355
YP_424610.1	CDS	MCAP_0642	NC_007633.1	770984	771823	D	identified by match to protein family HMM PF02645; hypothetical protein	770984..771823	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828622
YP_424611.1	CDS	MCAP_0643	NC_007633.1	771834	772685	D	identified by match to protein family HMM PF02645; degV family protein	771834..772685	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829012
YP_424612.1	CDS	MCAP_0646	NC_007633.1	772982	773449	R	identified by similarity to SP:P71086; match to protein family HMM PF01475; FUR family transcriptional regulator	complement(772982..773449)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828930
YP_424613.1	CDS	MCAP_0647	NC_007633.1	773451	773672	R	identified by match to protein family HMM PF00550; acyl carrier protein	complement(773451..773672)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828572
YP_424614.1	CDS	MCAP_0648	NC_007633.1	773693	774061	R	lipoprotein	complement(773693..774061)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828418
YP_424615.1	CDS	MCAP_0649	NC_007633.1	774048	775115	R	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	complement(774048..775115)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828885
YP_424616.1	CDS	arcC	NC_007633.1	775419	776351	R	catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP; carbamate kinase	complement(775419..776351)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828577
YP_424617.1	CDS	MCAP_0652	NC_007633.1	776470	777564	R	catalyzes the formation of carbamoylputrescine from agmatine in the arginine decarboxylase pathway of putrescine biosynthesis; agmatine deiminase	complement(776470..777564)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828849
YP_424618.1	CDS	MCAP_0653	NC_007633.1	777571	778989	R	identified by similarity to SP:P39183; match to protein family HMM PF00324; amino acid permease family protein	complement(777571..778989)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829079
YP_424619.1	CDS	argF	NC_007633.1	779011	780108	R	catalyzes the formation of putrescine from carbamoyl-putrescine during agmatine degradation; putrescine carbamoyltransferase	complement(779011..780108)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828588
YP_424620.1	CDS	MCAP_0655	NC_007633.1	780339	781226	D	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	780339..781226	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828852
YP_424621.1	CDS	MCAP_0656	NC_007633.1	781228	781992	D	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	781228..781992	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828923
YP_424622.1	CDS	MCAP_0657	NC_007633.1	782026	782505	R	MCAP_0657 has 2 membrane spanning regions; hypothetical protein	complement(782026..782505)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828681
YP_424623.1	CDS	MCAP_0658	NC_007633.1	782589	784154	R	MCAP_0658 has 8 membrane spanning regions; hypothetical protein	complement(782589..784154)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828785
YP_424624.1	CDS	leuS	NC_007633.1	784221	786635	R	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	complement(784221..786635)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828466
YP_424625.1	CDS	MCAP_0661	NC_007633.1	786903	789746	R	lipoprotein	complement(786903..789746)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828292
YP_424626.1	CDS	rpsI	NC_007633.1	789908	790306	R	forms a direct contact with the tRNA during translation; 30S ribosomal protein S9	complement(789908..790306)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828985
YP_424627.1	CDS	rplM	NC_007633.1	790306	790761	R	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13	complement(790306..790761)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828494
YP_424628.1	CDS	MCAP_0664	NC_007633.1	790881	795026	R	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	complement(790881..795026)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828560
YP_424629.1	CDS	truA	NC_007633.1	795151	795900	R	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A	complement(795151..795900)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828334
YP_424630.1	CDS	MCAP_0666	NC_007633.1	795902	796912	R	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	complement(795902..796912)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828867
YP_424631.1	CDS	cbiO	NC_007633.1	796925	797794	R	with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene; cobalt transporter ATP-binding subunit	complement(796925..797794)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828435
YP_424632.1	CDS	cbiO	NC_007633.1	797821	799047	R	with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene; cobalt transporter ATP-binding subunit	complement(797821..799047)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828537
YP_424633.1	CDS	rplQ	NC_007633.1	799158	799517	R	is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17	complement(799158..799517)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828717
YP_424634.1	CDS	rpoA	NC_007633.1	799537	800490	R	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	complement(799537..800490)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828381
YP_424635.1	CDS	rpsK	NC_007633.1	800494	800883	R	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	complement(800494..800883)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829035
YP_424636.1	CDS	rpsM	NC_007633.1	800909	801274	R	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	complement(800909..801274)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828578
YP_424637.1	CDS	rpmJ	NC_007633.1	801312	801425	R	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	complement(801312..801425)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828811
YP_424638.1	CDS	infA	NC_007633.1	801495	801719	R	stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1	complement(801495..801719)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828748
YP_424639.1	CDS	map	NC_007633.1	801731	802486	R	identified by similarity to SP:P19994; match to protein family HMM PF00557; match to protein family HMM TIGR00500; methionine aminopeptidase	complement(801731..802486)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829108
YP_424640.1	CDS	adk	NC_007633.1	802486	803127	R	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	complement(802486..803127)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828966
YP_424641.1	CDS	secY	NC_007633.1	803256	804704	R	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	complement(803256..804704)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829068
YP_424642.1	CDS	rplO	NC_007633.1	804704	805141	R	late assembly protein; 50S ribosomal protein L15	complement(804704..805141)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828415
YP_424643.1	CDS	rpsE	NC_007633.1	805161	805925	R	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	complement(805161..805925)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828832
YP_424644.1	CDS	rplR	NC_007633.1	805944	806294	R	binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18	complement(805944..806294)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829120
YP_424645.1	CDS	rplF	NC_007633.1	806320	806862	R	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	complement(806320..806862)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828389
YP_424646.1	CDS	rpsH	NC_007633.1	806876	807265	R	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8	complement(806876..807265)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828925
YP_424647.1	CDS	rpsN	NC_007633.1	807287	807472	R	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	complement(807287..807472)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828693
YP_424648.1	CDS	rplE	NC_007633.1	807491	808033	R	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	complement(807491..808033)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828999
YP_424649.1	CDS	rplX	NC_007633.1	808052	808378	R	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24	complement(808052..808378)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828633
YP_424650.1	CDS	rplN	NC_007633.1	808392	808760	R	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14	complement(808392..808760)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829019
YP_424651.1	CDS	rpsQ	NC_007633.1	808776	809033	R	primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17	complement(808776..809033)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828534
YP_424652.1	CDS	rpmC	NC_007633.1	809033	809449	R	one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29	complement(809033..809449)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828552
YP_424653.1	CDS	rplP	NC_007633.1	809449	809862	R	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16	complement(809449..809862)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828986
YP_424654.1	CDS	rpsC	NC_007633.1	809865	810566	R	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	complement(809865..810566)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828839
YP_424655.1	CDS	rplV	NC_007633.1	810584	810919	R	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	complement(810584..810919)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828295
YP_424656.1	CDS	rpsS	NC_007633.1	810943	811209	R	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19	complement(810943..811209)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829121
YP_424657.1	CDS	rplB	NC_007633.1	811231	812076	R	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	complement(811231..812076)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829089
YP_424658.1	CDS	rplW	NC_007633.1	812129	812413	R	binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23	complement(812129..812413)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828500
YP_424659.1	CDS	rplD	NC_007633.1	812413	813039	R	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	complement(812413..813039)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828469
YP_424660.1	CDS	rplC	NC_007633.1	813052	813723	R	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	complement(813052..813723)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828671
YP_424661.1	CDS	rpsJ	NC_007633.1	813798	814106	R	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	complement(813798..814106)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828323
YP_424662.1	CDS	MCAP_0698	NC_007633.1	814402	815400	R	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	complement(814402..815400)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828620
YP_424663.1	CDS	MCAP_0699	NC_007633.1	815710	816549	D	MCAP_0699 has 6 membrane spanning regions; hypothetical protein	815710..816549	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828915
YP_424664.1	CDS	MCAP_0704	NC_007633.1	817226	818425	R	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	complement(817226..818425)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829013
YP_424665.1	CDS	MCAP_0705	NC_007633.1	818538	819233	R	MCAP_0705 has 3 membrane spanning regions; hypothetical protein	complement(818538..819233)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829045
YP_424666.1	CDS	folD	NC_007633.1	819238	820092	R	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	complement(819238..820092)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829076
YP_424667.1	CDS	MCAP_0707	NC_007633.1	820101	821702	R	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	complement(820101..821702)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828877
YP_424668.1	CDS	MCAP_0708	NC_007633.1	821781	822509	D	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	821781..822509	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828847
YP_424669.1	CDS	gatB	NC_007633.1	822546	823985	R	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	complement(822546..823985)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828834
YP_424670.1	CDS	gatA	NC_007633.1	823987	825444	R	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	complement(823987..825444)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828338
YP_424671.1	CDS	gatC	NC_007633.1	825444	825740	R	identified by similarity to GP:2465557; match to protein family HMM PF02686; match to protein family HMM TIGR00135; glutamyl-tRNA(Gln) amidotransferase subunit C	complement(825444..825740)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828453
YP_424672.1	CDS	ligA	NC_007633.1	825742	827748	R	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	complement(825742..827748)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829023
YP_424673.1	CDS	MCAP_0713	NC_007633.1	827752	829752	R	MCAP_0713 has 14 membrane spanning regions; hypothetical protein	complement(827752..829752)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828547
YP_424674.1	CDS	MCAP_0714	NC_007633.1	829755	830663	R	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; ribosomal large subunit pseudouridine synthase A	complement(829755..830663)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828946
YP_424675.1	CDS	MCAP_0715	NC_007633.1	830666	831676	R	MCAP_0715 has 9 transmembrane regions; identified by match to protein family HMM PF02517; CAAX amino terminal protease family protein	complement(830666..831676)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828615
YP_424676.1	CDS	ptsH	NC_007633.1	831735	832004	R	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	complement(831735..832004)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828959
YP_424677.1	CDS	pcrA	NC_007633.1	832070	834238	R	identified by similarity to SP:P56255; match to protein family HMM PF00580; ATP-dependent DNA helicase pcrA	complement(832070..834238)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828917
YP_424678.1	CDS	MCAP_0718	NC_007633.1	834250	834996	R	MCAP_0718 has 4 membrane spanning regions; identified by match to protein family HMM PF06271; hypothetical protein	complement(834250..834996)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828611
YP_424679.1	CDS	MCAP_0719	NC_007633.1	834996	835952	R	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	complement(834996..835952)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828344
YP_424680.1	CDS	MCAP_0720	NC_007633.1	836066	837283	R	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	complement(836066..837283)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829017
YP_424681.1	CDS	MCAP_0721	NC_007633.1	837411	838655	R	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	complement(837411..838655)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828687
YP_424682.1	CDS	MCAP_0722	NC_007633.1	838759	839688	R	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	complement(838759..839688)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828963
YP_424683.1	CDS	MCAP_0723	NC_007633.1	839804	842017	R	lipoprotein	complement(839804..842017)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828703
YP_424684.1	CDS	MCAP_0724	NC_007633.1	842026	842931	R	MCAP_0724 has 7 membrane spanning regions; hypothetical protein	complement(842026..842931)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828783
YP_424685.1	CDS	MCAP_0725	NC_007633.1	843048	844337	R	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	complement(843048..844337)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828684
YP_424686.1	CDS	MCAP_0726	NC_007633.1	844625	845593	R	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	complement(844625..845593)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829048
YP_424687.1	CDS	MCAP_0727	NC_007633.1	845783	848155	R	lipoprotein	complement(845783..848155)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828626
YP_424688.1	CDS	MCAP_0728	NC_007633.1	848167	849066	R	MCAP_0728 has 6 membrane spanning regions; hypothetical protein	complement(848167..849066)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828610
YP_424689.1	CDS	MCAP_0729	NC_007633.1	849165	850913	R	Adjacent to likely ATPase and substrate binding proteins; identified by similarity to SP:P15362; match to protein family HMM PF00528; ABC transporter permease p69	complement(849165..850913)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828528
YP_424690.1	CDS	MCAP_0730	NC_007633.1	850877	851626	R	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	complement(850877..851626)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828979
YP_424691.1	CDS	MCAP_0731	NC_007633.1	851627	853087	R	Adjacent to likely permease and ATP binding proteins; identified by similarity to SP:P15363; ABC transporter substrate-binding protein	complement(851627..853087)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828752
YP_424692.1	CDS	MCAP_0732	NC_007633.1	853320	854183	R	identified by match to protein family HMM PF00702; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484; cof family hydrolase	complement(853320..854183)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828698
YP_424693.1	CDS	MCAP_0733	NC_007633.1	854317	855510	D	identified by similarity to SP:Q08432; match to protein family HMM PF00155; aminotransferase, classes I and II	854317..855510	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828974
YP_424694.1	CDS	MCAP_0734	NC_007633.1	855520	855921	D	identified by match to protein family HMM PF01042; match to protein family HMM TIGR00004; endoribonuclease L-PSP	855520..855921	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828908
YP_424695.1	CDS	MCAP_0735	NC_007633.1	855962	857209	R	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	complement(855962..857209)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828434
YP_424696.1	CDS	MCAP_0736	NC_007633.1	857413	858684	R	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	complement(857413..858684)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828835
YP_424697.1	CDS	MCAP_0737	NC_007633.1	858892	860133	R	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	complement(858892..860133)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828872
YP_424698.1	CDS	MCAP_0738	NC_007633.1	860356	861696	R	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	complement(860356..861696)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828842
YP_424699.1	CDS	MCAP_0739	NC_007633.1	861836	862984	D	hypothetical protein	861836..862984	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828618
YP_424700.1	CDS	nagB1	NC_007633.1	864129	864857	D	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	864129..864857	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828765
YP_424701.1	CDS	tpiA	NC_007633.1	864962	865708	D	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate; triosephosphate isomerase	864962..865708	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828559
YP_424702.1	CDS	MCAP_0751	NC_007633.1	865701	866537	D	identified by match to protein family HMM TIGR01484; HAD family hydrolase	865701..866537	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828489
YP_424703.1	CDS	gpmI	NC_007633.1	866540	868135	D	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase	866540..868135	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828629
YP_424704.1	CDS	MCAP_0753	NC_007633.1	868232	868831	D	hypothetical protein	868232..868831	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828365
YP_424705.1	CDS	MCAP_0754	NC_007633.1	868833	869831	D	hypothetical protein	868833..869831	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829063
YP_424706.1	CDS	deoC	NC_007633.1	869897	870565	R	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate; deoxyribose-phosphate aldolase	complement(869897..870565)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828791
YP_424707.1	CDS	MCAP_0756	NC_007633.1	870577	872259	R	identified by match to protein family HMM PF00408; match to protein family HMM PF02878; match to protein family HMM PF02879; phosphoglucomutase/phosphomannomutase	complement(870577..872259)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828827
YP_424708.1	CDS	deoA	NC_007633.1	872424	873737	D	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	872424..873737	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828903
YP_424709.1	CDS	MCAP_0758	NC_007633.1	873824	875980	R	lipoprotein	complement(873824..875980)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828318
YP_424710.1	CDS	mgtE	NC_007633.1	876647	878050	D	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	876647..878050	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828542
YP_424711.1	CDS	trmB	NC_007633.1	878052	878714	D	identified by match to protein family HMM PF02390; match to protein family HMM TIGR00091; tRNA (guanine-N(7)-)-methyltransferase	878052..878714	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828895
YP_424712.1	CDS	MCAP_0762	NC_007633.1	879090	879680	R	MCAP_0762 has 2 membrane spanning regions; hypothetical protein	complement(879090..879680)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828585
YP_424713.1	CDS	MCAP_0763	NC_007633.1	879834	880520	R	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	complement(879834..880520)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828589
YP_424714.1	CDS	MCAP_0764	NC_007633.1	880855	880977	R	hypothetical protein	complement(880855..880977)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829038
YP_424715.1	CDS	hpt2	NC_007633.1	881281	881832	R	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	complement(881281..881832)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829123
YP_424716.1	CDS	purB	NC_007633.1	881855	883153	R	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase	complement(881855..883153)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828321
YP_424717.1	CDS	purA	NC_007633.1	883146	884444	R	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase	complement(883146..884444)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829074
YP_424718.1	CDS	MCAP_0768	NC_007633.1	884729	885529	R	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010; TatD family deoxyribonuclease	complement(884729..885529)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828711
YP_424719.1	CDS	MCAP_0770	NC_007633.1	885990	887348	D	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	885990..887348	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828592
YP_424720.1	CDS	MCAP_0771	NC_007633.1	887434	888903	R	MCAP_0771 has 4 membrane spanning regions; hypothetical protein	complement(887434..888903)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828745
YP_424721.1	CDS	MCAP_0772	NC_007633.1	888906	889856	R	identified by match to protein family HMM TIGR01128; hypothetical protein	complement(888906..889856)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828781
YP_424722.1	CDS	uvrB	NC_007633.1	890143	892140	D	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	890143..892140	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828351
YP_424723.1	CDS	uvrA	NC_007633.1	892149	894989	D	identified by similarity to SP:O34863; match to protein family HMM PF00005; match to protein family HMM TIGR00630; excinuclease ABC subunit A	892149..894989	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828420
YP_424724.1	CDS	folC	NC_007633.1	894982	896091	D	identified by similarity to GP:12724120; match to protein family HMM TIGR01499; folate synthetase-polyglutamyl folate synthetase	894982..896091	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828593
YP_424725.1	CDS	MCAP_0776	NC_007633.1	896119	896793	D	MCAP_0776 has 6 membrane spanning regions; hypothetical protein	896119..896793	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828935
YP_424726.1	CDS	MCAP_0777	NC_007633.1	896874	897815	D	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system; HPr kinase/phosphorylase	896874..897815	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828431
YP_424727.1	CDS	lgt1	NC_007633.1	897826	899406	D	MCAP_0780 (lgt2) is a paralog of MCAP_0778; identified by match to protein family HMM PF01790; prolipoprotein diacylglyceryl transferase	897826..899406	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828291
YP_424728.1	CDS	trxB	NC_007633.1	899390	900322	D	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	899390..900322	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828468
YP_424729.1	CDS	lgt2	NC_007633.1	900331	901761	D	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	900331..901761	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828358
YP_424730.1	CDS	MCAP_0781	NC_007633.1	901773	902702	D	identified by match to protein family HMM PF02650; match to protein family HMM TIGR00647; hypothetical protein	901773..902702	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828705
YP_424731.1	CDS	MCAP_0782	NC_007633.1	903025	904158	R	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	complement(903025..904158)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828637
YP_424732.1	CDS	MCAP_0783	NC_007633.1	904220	905842	R	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	complement(904220..905842)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828813
YP_424733.1	CDS	MCAP_0784	NC_007633.1	905894	906124	R	MCAP_0784 has 2 membrane spanning regions; hypothetical protein	complement(905894..906124)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828437
YP_424734.1	CDS	MCAP_0785	NC_007633.1	906114	906833	R	hypothetical protein	complement(906114..906833)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828983
YP_424735.1	CDS	MCAP_0786	NC_007633.1	906833	907342	R	hypothetical protein	complement(906833..907342)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828307
YP_424736.1	CDS	MCAP_0787	NC_007633.1	907342	909021	R	identified by similarity to SP:P20166; match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system transporter subunit IIBC	complement(907342..909021)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828400
YP_424737.1	CDS	MCAP_0788	NC_007633.1	909644	909811	D	identified by similarity to SP:P44978; DeoR family transcriptional regulator	909644..909811	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828635
YP_424738.1	CDS	MCAP_0789	NC_007633.1	909935	910906	D	hypothetical protein	909935..910906	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829105
YP_424739.1	CDS	MCAP_0790	NC_007633.1	911127	912845	D	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	911127..912845	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829131
YP_424740.1	CDS	MCAP_0791	NC_007633.1	912884	913699	R	hypothetical protein	complement(912884..913699)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828826
YP_424741.1	CDS	topA	NC_007633.1	913892	915823	D	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	913892..915823	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828436
YP_424742.1	CDS	MCAP_0794	NC_007633.1	916628	917509	R	MCAP_0794 has 1 membrane spanning region, N-terminal.; hypothetical protein	complement(916628..917509)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828870
YP_424743.1	CDS	MCAP_0795	NC_007633.1	917496	918311	R	MCAP_0795 has one membrane spanning region, N-terminal.; hypothetical protein	complement(917496..918311)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828368
YP_424744.1	CDS	MCAP_0796	NC_007633.1	918301	919653	R	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	complement(918301..919653)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828283
YP_424745.1	CDS	MCAP_0797	NC_007633.1	919631	920335	R	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	complement(919631..920335)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828887
YP_424746.1	CDS	MCAP_0798	NC_007633.1	920337	922202	R	This is part of a likely operon with an ABC transporter ATPase, and several  lipoproteins that might be substrate binding proteins.; ABC transporter permease	complement(920337..922202)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829077
YP_424747.1	CDS	MCAP_0799	NC_007633.1	922342	923238	R	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	complement(922342..923238)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828746
YP_424748.1	CDS	MCAP_0800	NC_007633.1	923231	924070	R	MCAP_0800 has 1 membrane spanning region, N-terminal.; hypothetical protein	complement(923231..924070)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828541
YP_424749.1	CDS	MCAP_0801	NC_007633.1	924057	925010	R	lipoprotein	complement(924057..925010)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829058
YP_424750.1	CDS	MCAP_0802	NC_007633.1	925029	926867	R	MCAP_0802 has 6 membrane spanning regions; hypothetical protein	complement(925029..926867)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828881
YP_424751.1	CDS	MCAP_0803	NC_007633.1	926975	928741	R	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	complement(926975..928741)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828807
YP_424752.1	CDS	MCAP_0804	NC_007633.1	928810	929499	R	identified by match to protein family HMM PF01863; zinc metalloprotease	complement(928810..929499)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828352
YP_424753.1	CDS	engD	NC_007633.1	929506	930600	R	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	complement(929506..930600)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828376
YP_424754.1	CDS	MCAP_0806	NC_007633.1	930636	930836	R	hypothetical protein	complement(930636..930836)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829031
YP_424755.1	CDS	gidB	NC_007633.1	930838	931533	R	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA; 16S rRNA methyltransferase GidB	complement(930838..931533)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828396
YP_424756.1	CDS	pgsA	NC_007633.1	931533	932129	R	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	complement(931533..932129)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828951
YP_424757.1	CDS	MCAP_0810	NC_007633.1	933920	934603	R	MCAP_0810 has 6 membrane spanning regions; hypothetical protein	complement(933920..934603)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828779
YP_424758.1	CDS	MCAP_0811	NC_007633.1	934569	936116	R	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	complement(934569..936116)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828968
YP_424759.1	CDS	MCAP_0812	NC_007633.1	936175	938910	R	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	complement(936175..938910)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828304
YP_424760.1	CDS	hup	NC_007633.1	938918	939544	R	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	complement(938918..939544)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828969
YP_424761.1	CDS	MCAP_0814	NC_007633.1	940433	941860	R	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	complement(940433..941860)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828474
YP_424762.1	CDS	MCAP_0815	NC_007633.1	942121	943695	R	MCAP_0815 has 8 membrane spanning regions; hypothetical protein	complement(942121..943695)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828901
YP_424763.1	CDS	MCAP_0816	NC_007633.1	943860	944483	R	This gene shares strong identity to two three gene clusters in Mycoplasma mycoides SC.; hypothetical protein	complement(943860..944483)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828676
YP_424764.1	CDS	asnA	NC_007633.1	944540	945520	R	catalyzes the formation of asparagine from aspartate and ammonia; asparagine synthetase AsnA	complement(944540..945520)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829008
YP_424765.1	CDS	rpsT	NC_007633.1	945932	946177	D	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20	945932..946177	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828902
YP_424766.1	CDS	trmE	NC_007633.1	946228	947586	R	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	complement(946228..947586)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828863
YP_424767.1	CDS	MCAP_0820	NC_007633.1	947790	948014	D	hypothetical protein	947790..948014	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828341
YP_424768.1	CDS	MCAP_0821	NC_007633.1	948123	949082	D	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	948123..949082	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828879
YP_424769.1	CDS	MCAP_0822	NC_007633.1	949106	950236	D	hypothetical protein	949106..950236	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828801
YP_424770.1	CDS	MCAP_0823	NC_007633.1	950247	951086	D	identified by match to protein family HMM TIGR00099; HAD superfamily hydrolase	950247..951086	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828756
YP_424771.1	CDS	asnC	NC_007633.1	951095	952459	D	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	951095..952459	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828302
YP_424772.1	CDS	MCAP_0825	NC_007633.1	952728	954092	D	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	952728..954092	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828555
YP_424773.1	CDS	MCAP_0826	NC_007633.1	954106	954858	D	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	954106..954858	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828538
YP_424774.1	CDS	MCAP_0827	NC_007633.1	954862	957597	D	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	954862..957597	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829056
YP_424775.1	CDS	MCAP_0828	NC_007633.1	957622	959688	R	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	complement(957622..959688)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828354
YP_424776.1	CDS	MCAP_0834	NC_007633.1	965268	966110	D	identified by match to protein family HMM TIGR01484; HAD superfamily hydrolase	965268..966110	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828619
YP_424777.1	CDS	trxA	NC_007633.1	966122	966430	D	identified by similarity to SP:P14949; match to protein family HMM PF00085; match to protein family HMM TIGR01068; thioredoxin	966122..966430	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829051
YP_424778.1	CDS	lysS	NC_007633.1	966562	968064	R	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	complement(966562..968064)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828398
YP_424779.1	CDS	dus	NC_007633.1	968067	968993	R	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	complement(968067..968993)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828346
YP_424780.1	CDS	MCAP_0838	NC_007633.1	969043	969357	R	hypothetical protein	complement(969043..969357)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829095
YP_424781.1	CDS	serS	NC_007633.1	969451	970719	R	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	complement(969451..970719)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829096
YP_424782.1	CDS	MCAP_0840	NC_007633.1	970800	971627	R	MCAP_0840 has 6 membrane spanning regions; hypothetical protein	complement(970800..971627)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828298
YP_424783.1	CDS	MCAP_0841	NC_007633.1	971695	972279	R	hypothetical protein	complement(971695..972279)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829006
YP_424784.1	CDS	MCAP_0842	NC_007633.1	972298	972588	R	MCAP_0842 has 2 membrane spanning regions; hypothetical protein	complement(972298..972588)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829021
YP_424785.1	CDS	MCAP_0843	NC_007633.1	972758	974992	D	lipoprotein	972758..974992	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828553
YP_424786.1	CDS	MCAP_0844	NC_007633.1	975036	976778	R	identified by similarity to SP:P20166; match to protein family HMM PF00367; match to protein family HMM PF02378; PTS system glucose-specific IIBC component	complement(975036..976778)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828598
YP_424787.1	CDS	bcp	NC_007633.1	976887	977321	D	identified by match to protein family HMM PF00578; bacterioferritin comigratory protein	976887..977321	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828479
YP_424788.1	CDS	MCAP_0846	NC_007633.1	977485	979575	D	lipoprotein	977485..979575	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828602
YP_424789.1	CDS	MCAP_0847	NC_007633.1	980325	981230	D	hypothetical protein	980325..981230	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828775
YP_424790.1	CDS	MCAP_0848	NC_007633.1	981284	981748	D	identified by similarity to GB:CAE77252.1; transposase IS1296EH (ORFA)	981284..981748	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828359
YP_424791.1	CDS	deoD	NC_007633.1	981796	982449	R	identified by similarity to SP:O34925; match to protein family HMM PF01048; purine nucleoside phosphorylase	complement(981796..982449)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828707
YP_424792.1	CDS	MCAP_0850	NC_007633.1	982682	983662	R	hypothetical protein	complement(982682..983662)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828496
YP_424793.1	CDS	MCAP_0851	NC_007633.1	983814	984512	D	Gene is adjacent to fructose metabolism and transport genes; identified by match to protein family HMM PF00455; fructose operon transcriptional regulator	983814..984512	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828369
YP_424794.1	CDS	MCAP_0852	NC_007633.1	984512	985447	D	identified by similarity to SP:O31714; match to protein family HMM PF00294; 1-phosphofructokinase	984512..985447	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828726
YP_424795.1	CDS	fruA	NC_007633.1	985450	987486	D	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	985450..987486	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828819
YP_424796.1	CDS	MCAP_0854	NC_007633.1	988122	988697	D	hypothetical protein	988122..988697	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829078
YP_424797.1	CDS	MCAP_0855	NC_007633.1	988866	989453	D	hypothetical protein	988866..989453	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828444
YP_424798.1	CDS	gidA	NC_007633.1	989799	991688	R	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	complement(989799..991688)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828821
YP_424799.1	CDS	MCAP_0857	NC_007633.1	991832	993400	R	identified by match to protein family HMM PF00375; proton/glutamate symporter family protein	complement(991832..993400)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828742
YP_424800.1	CDS	MCAP_0858	NC_007633.1	993422	994765	R	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	complement(993422..994765)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828529
YP_424801.1	CDS	pncA	NC_007633.1	994986	995486	D	identified by similarity to SP:P21369; match to protein family HMM PF00857; pyrazinamidase/nicotinamidase	994986..995486	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828714
YP_424802.1	CDS	MCAP_0860	NC_007633.1	995719	997977	R	MCAP_0860 has 1 membrane spanning region, N-terminal; hypothetical protein	complement(995719..997977)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3829060
YP_424803.1	CDS	MCAP_0861	NC_007633.1	997987	1000248	R	MCAP_0861 has 1 transmembrane region.; hypothetical protein	complement(997987..1000248)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828614
YP_424804.1	CDS	MCAP_0862	NC_007633.1	1000520	1002772	R	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	complement(1000520..1002772)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828980
YP_424805.1	CDS	MCAP_0863	NC_007633.1	1002796	1003617	R	hypothetical protein	complement(1002796..1003617)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828685
YP_424806.1	CDS	MCAP_0864	NC_007633.1	1003625	1005037	R	There are 4 paralogous genes in M. capricolum; hypothetical protein	complement(1003625..1005037)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828315
YP_424807.1	CDS	MCAP_0865	NC_007633.1	1005242	1006399	R	MCAP_0865 has 8 membrane spanning regions; hypothetical protein	complement(1005242..1006399)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828989
YP_424808.1	CDS	MCAP_0866	NC_007633.1	1006457	1007173	R	hypothetical protein	complement(1006457..1007173)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828855
YP_424809.1	CDS	MCAP_0867	NC_007633.1	1007173	1007970	R	identified by match to protein family HMM TIGR00099; match to protein family HMM TIGR01484; cof family hydrolase	complement(1007173..1007970)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828425
YP_424810.1	CDS	MCAP_0868	NC_007633.1	1008050	1009216	R	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	complement(1008050..1009216)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828597
YP_424811.1	CDS	rnpA	NC_007633.1	1009258	1009587	R	identified by similarity to SP:P58031; match to protein family HMM PF00825; match to protein family HMM TIGR00188; ribonuclease P protein component	complement(1009258..1009587)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828570
YP_424812.1	CDS	rpmH	NC_007633.1	1009594	1009728	R	in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34	complement(1009594..1009728)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828994
MCAP_0062	tRNA	MCAP_0062	NC_007633.1	74293	74368	R	tRNA-Lys	complement(74293..74368)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828662
MCAP_0316	tRNA	MCAP_0316	NC_007633.1	380276	380365	D	tRNA-Ser	380276..380365	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828519
MCAP_0331	tRNA	MCAP_0331	NC_007633.1	396221	396294	D	tRNA-Gly	396221..396294	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828656
MCAP_0404	tRNA	MCAP_0404	NC_007633.1	496721	496796	D	tRNA-Thr	496721..496796	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828522
MCAP_0405	tRNA	MCAP_0405	NC_007633.1	496803	496886	D	tRNA-Tyr	496803..496886	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828524
MCAP_0406	tRNA	MCAP_0406	NC_007633.1	496894	496968	D	tRNA-Gln	496894..496968	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828653
MCAP_0407	tRNA	MCAP_0407	NC_007633.1	496973	497048	D	tRNA-Lys	496973..497048	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828663
MCAP_0408	tRNA	MCAP_0408	NC_007633.1	497057	497145	D	tRNA-Leu	497057..497145	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828659
MCAP_0487	tRNA	MCAP_0487	NC_007633.1	580100	580184	R	tRNA-Leu	complement(580100..580184)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828660
MCAP_0535	tRNA	MCAP_0535	NC_007633.1	642510	642586	R	tRNA-Arg	complement(642510..642586)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828654
MCAP_0644	tRNA	MCAP_0644	NC_007633.1	772721	772795	R	tRNA-Trp	complement(772721..772795)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828523
MCAP_0645	tRNA	MCAP_0645	NC_007633.1	772833	772908	R	tRNA-Sec	complement(772833..772908)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828518
MCAP_0650	tRNA	MCAP_0650	NC_007633.1	775217	775292	R	tRNA-His	complement(775217..775292)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828657
MCAP_0660	tRNA	MCAP_0660	NC_007633.1	786769	786845	R	tRNA-Ile	complement(786769..786845)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828658
MCAP_0700	tRNA	MCAP_0700	NC_007633.1	816794	816869	R	tRNA-Thr	complement(816794..816869)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828521
MCAP_0701	tRNA	MCAP_0701	NC_007633.1	816882	816957	R	tRNA-Val	complement(816882..816957)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828525
MCAP_0702	tRNA	MCAP_0702	NC_007633.1	816965	817040	R	tRNA-Glu	complement(816965..817040)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828655
MCAP_0703	tRNA	MCAP_0703	NC_007633.1	817048	817123	R	tRNA-Asn	complement(817048..817123)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828667
MCAP_0740	tRNA	MCAP_0740	NC_007633.1	863181	863257	D	tRNA-Arg	863181..863257	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828666
MCAP_0741	tRNA	MCAP_0741	NC_007633.1	863305	863381	D	tRNA-Pro	863305..863381	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828517
MCAP_0742	tRNA	MCAP_0742	NC_007633.1	863392	863467	D	tRNA-Ala	863392..863467	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828652
MCAP_0743	tRNA	MCAP_0743	NC_007633.1	863473	863549	D	tRNA-Met	863473..863549	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828665
MCAP_0744	tRNA	MCAP_0744	NC_007633.1	863562	863638	D	tRNA-Met	863562..863638	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828514
MCAP_0745	tRNA	MCAP_0745	NC_007633.1	863680	863772	D	tRNA-Ser	863680..863772	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828520
MCAP_0746	tRNA	MCAP_0746	NC_007633.1	863795	863870	D	tRNA-Met	863795..863870	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828515
MCAP_0747	tRNA	MCAP_0747	NC_007633.1	863873	863949	D	tRNA-Asp	863873..863949	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828668
MCAP_0748	tRNA	MCAP_0748	NC_007633.1	863956	864031	D	tRNA-Phe	863956..864031	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828516
MCAP_0769	tRNA	MCAP_0769	NC_007633.1	885696	885770	R	tRNA-Cys	complement(885696..885770)	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828651
MCAP_0829	tRNA	MCAP_0829	NC_007633.1	959880	959955	D	tRNA-Lys	959880..959955	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828664
MCAP_0830	tRNA	MCAP_0830	NC_007633.1	959957	960040	D	tRNA-Leu	959957..960040	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828661
MCAP_0378	rRNA	rrs-1	NC_007633.1	464431	465954	D	16S ribosomal RNA	464431..465954	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828639
MCAP_0379	rRNA	rrl-1	NC_007633.1	466184	469077	D	23S ribosomal RNA	466184..469077	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828641
MCAP_0380	rRNA	rrf-1	NC_007633.1	469153	469261	D	5S ribosomal RNA	469153..469261	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828643
MCAP_0831	rRNA	rrs-2	NC_007633.1	960320	961843	D	16S ribosomal RNA	960320..961843	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828640
MCAP_0832	rRNA	rrl-2	NC_007633.1	962075	964968	D	23S ribosomal RNA	962075..964968	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828642
MCAP_0833	rRNA	rrf-2	NC_007633.1	965045	965153	D	5S ribosomal RNA	965045..965153	Mycoplasma capricolum subsp. capricolum ATCC 27343	3828644