Refseq_ID	Mycobrowser_Version	Feature	Start	Stop	Score	Strand	Frame	Locus	Name	Function	Product	Comments	UniProt_AC	Is_Pseudogene	Functional_Category	Orthologues M. leprae	Orthologues M. marinum	Orthologues M. smegmatis	Orthologues M. bovis	Orthologues M. lepromatosis	Orthologues M. tuberculosis	Orthologues M. abscessus	Orthologues M. haemophilum
NC_000962.3	Mycobrowser_v3	CDS	4174873	4178070	.	+	0	Rv3728	Rv3728	Unknown, but seems involved in efflux system (probably sugar or drug transport).	Probable conserved two-domain membrane protein	Rv3728, (MTV025.076), len: 1065 aa. Probable conserved transmembrane protein organised into two domains. Domain comprising the first ~510 aa residues is similar to various multidrug resistance and efflux proteins and contains sugar transport protein signature 1 (PS00216). Domain corresponding to the last 550 aa residues contains cyclic nucleotide-binding domain signature 2 (PS00889) and is very similar to Q50733|YP65_MYCTU|Rv2565|MT2641|MTCY9C4.03c hypothetical 62.1 kDa protein from Mycobacterium tuberculosis (31.0% identity in 546 aa overlap). Highly similar to O05884|Rv3239c|MTCY20B11.14c probable transmembrane transport protein from Mycobacterium tuberculosis (1048 aa) FASTA scores: opt: 4328, E(): 5e-201, (64.15% identity in 1046 aa overlap). N-terminal end similar to P71879|Rv2333c|MTCY3G12.01|MTCY98.02c (537 aa); P71836|Rv0783c|MTCY369.27c (540 aa); and O07753|Rv1877|MTCY180.41c (687 aa). Seems belong to the sugar transporter family. Possibly member of major facilitator superfamily (MFS).	O69695	No	cell wall and cell processes	ML2340	MMAR_2964		Mb3755				
NC_000962.3	Mycobrowser_v3	CDS	4178285	4180615	.	+	0	Rv3729	Rv3729	Function unknown; probably involved in cellular metabolism.	Possible transferase	Rv3729, (MTV025.077), len: 776 aa. Conserved hypothetical protein, possible transferase, similar to several hypothetical proteins and various transferases e.g. O26919|MTH831 molybdenum cofactor biosynthesis MOAA homolog from Methanobacterium thermoautotrophicum (497 aa), FASTA scores: opt: 697, E(): 4.8e-34, (30.7% identity in 492 aa overlap); Q58036|Y619_METJA|MJ0619 hypothetical protein from Methanococcus jannaschii (506 aa), FASTA scores: opt: 670, E(): 2e-32, (30.6% identity in 497 aa overlap); O27968|AF2316 conserved hypothetical protein from Archaeoglobus fulgidus (518 aa), FASTA scores: opt: 477, E(): 6.4e-21, (29.4% identity in 500 aa overlap); BAB60102|TVG0985801 molybdenum cofactor biosynthesis protein from Thermoplasma volcanium (606 aa), FASTA scores: opt: 402, E(): 2.1e-16, (28.1% identity in 509 aa overlap); etc. C-terminus similar to methyltransferases e.g. Q9S0N6|AVED C5-O-methyltransferase from Streptomyces avermitilis (283 aa), FASTA scores: opt: 298, E(): 1.9e-10, (31.5% identity in 292 aa overlap). Also similar to the Mycobacterium tuberculosis proteins P71673|YE05_MYCTU|Rv1405c|MT1449|MTCY21B4.22c (274 aa); and Q50584|Rv1523|MTCY19G5.05c.	O69696	No	intermediary metabolism and respiration				Mb3756				
NC_000962.3	Mycobrowser_v3	CDS	4180680	4181720	.	-	0	Rv3730c	Rv3730c	Function unknown	Conserved hypothetical protein	Rv3730c, (MTV025.078c), len: 346 aa. Conserved hypothetical protein, highly similar to Q9XAM1|SC4C6.19 hypothetical 38.5 KDA protein from Streptomyces coelicolor (341 aa), FASTA scores: opt: 1313, E(): 2.2e-75, (59.25% identity in 336 aa overlap); and similar to C-terminal end of putative ATP-dependent DNA ligases e.g. BAB49297|MLL2077 from Rhizobium loti (Mesorhizobium loti) (833 aa), FASTA scores: opt: 550, E(): 5.3e-27, (31.3% identity in 294 aa overlap); and BAB54816|MLL9625 from Rhizobium loti (Mesorhizobium loti) plasmid pMLb (883 aa) FASTA scores: opt: 492, E(): 2.5e-23, (33.7% identity in 291 aa overlap); etc. Also similar to the hypothetical proteins e.g. Q9ZC15|SC1E6.07 hypothetical 34.9 KDA protein from Streptomyces coelicolor (319 aa) FASTA scores: opt: 537, E(): 1.5e-26, (34.95% identity in 292 aa overlap); Q9XAF7|SC6G9.25 hypothetical 32.1 KDA protein from Streptomyces coelicolor (293 aa), FASTA scores: opt: 474, E(): 1.3e-22, (33.75% identity in 302 aa overlap); etc. Also highly similar to P95226|Rv0269c|MTCY06A4.13c hypothetical 44.0 KDA protein from Mycobacterium tuberculosis (397 aa), FASTA scores: opt: 940, E(): 7.7e-52, (50.3% identity in 312 aa overlap).	O69697	No	conserved hypotheticals	ML2342,ML2342c	MMAR_5265	MSMEG_6301	Mb3757c				
NC_000962.3	Mycobrowser_v3	CDS	4205538	4205840	.	+	0	Rv3760	Rv3760	Unknown	Possible conserved membrane protein	Rv3760, (MTV025.108), len: 100 aa. Possible conserved membrane protein, equivalent to Q50094|ML2366|MLCB12.11c putative membrane protein from Mycobacterium leprae (113 aa), FASTA scores: opt: 423, E(): 1.2e-20, (67.7% identity in 99 aa overlap). Also similar with Q9JST1|NMA2149 putative inner membrane hypothetical protein from Neisseria meningitidis (serogroup A) (104 aa), FASTA scores: opt: 113, E(): 0.95, (33.85% identity in 62 aa overlap); and showing similarity with Q9ZAX7 ABC transporter membrane protein subunit from Streptococcus mutans (498 aa), FASTA scores: opt: 108, E(): 6.7, (42.35% identity in 85 aa overlap) (similarity at C-terminus); and P33108|SECY_MICLU preprotein translocase SECY subunit from Micrococcus luteus (Micrococcus lysodeikticus) (436 aa), FASTA scores: opt: 106, E(): 8.2, (29.05% identity in 86 aa overlap). Equivalent to AAK48231 from Mycobacterium tuberculosis strain CDC1551 (117 aa) but shorter 17 aa.	O69726	No	cell wall and cell processes	ML2366,ML2366c	MMAR_5303	MSMEG_6336	Mb3786				
NC_000962.3	Mycobrowser_v3	CDS	4182934	4183992	.	+	0	Rv3732	Rv3732	Function unknown	Conserved protein	Rv3732, (MTV025.080), len: 352 aa. Conserved protein. The region between aa 175-352 is highly similar to the region between aa 72-257 of Q9KH39 hypothetical 55.5 KDA protein from Mycobacterium smegmatis (511 aa), FASTA scores: opt: 1122, E(): 7.3e-63, (98.85% identity in 176 aa overlap). Also shows some similarity with Q55304 hypotheticalk protein from Synechocystis sp. strain PCC 6803 (387 aa), FASTA scores: opt: 201, E(): 2.7e-05, (27.1% identity in 251 aa overlap); and P74254|SLR1173 hypothetical 52.5 KDA protein from Synechocystis sp. strain PCC 6803 (463 aa), FASTA scores: opt: 201, E(): 3.1e-05, (27.1% identity in 251 aa overlap). Also slightly similar to MTCY01B2_21 and DPO1_MYCTU DNA polymerase I.	O69699	No	conserved hypotheticals		MMAR_5269		Mb3759				
NC_000962.3	Mycobrowser_v3	CDS	4184012	4184512	.	-	0	Rv3733c	Rv3733c	Function unknown	Conserved hypothetical protein	Rv3733c, (MTV025.081c), len: 166 aa. Conserved hypothetical protein, highly similar to Q9FCB0|2SCG58.03 putative mutt-like protein from Streptomyces coelicolor (153 aa), FASTA scores: opt: 541, E(): 7.2e-29, (52.7% identity in 148 aa overlap); and BAB49143|MLR1881 hypothetical protein from Rhizobium loti (Mesorhizobium loti) (156 aa), FASTA scores: opt: 526, E(): 7.2e-28, (52.65% identity in 150 aa overlap).	O69700	No	conserved hypotheticals		MMAR_5270	MSMEG_3679	Mb3760c				
NC_000962.3	Mycobrowser_v3	CDS	4198205	4198597	.	-	0	Rv3750c	Rv3750c	Sequence excision.	Possible excisionase	Rv3750c, (MTV025.098c), len: 130 aa. Possible excisionase, similar to others e.g. Q9LCU5 putative excisionase from Arthrobacter sp. TM1 (174 aa) FASTA scores: opt: 297, E(): 1.2e-12, (40.35% identity in 114 aa overlap); O85865 putative excisionase from Sphingomonas aromaticivorans plasmid pNL1 (152 aa), FASTA scores: opt: 223, E(): 7.3e-08, (39.15% identity in 97 aa overlap); Q9XBH1|xis excisionase from Bacteroides fragilis (124 aa) FASTA scores: opt: 128, E(): 0.1, (30.7% identity in 88 aa overlap); etc. Also some similarity to transcriptional regulators. Also similar to Mycobacterium tuberculosis hypothetical proteins e.g. P71902|YN10_MYCTU|Rv2310|MT2372|MTCY3G12.24c (114 aa) FASTA scores: opt: 224, E(): 4.9e-08, (42.7% identity in 82 aa overlap). Contains helix-turn-helix motif at aa 55-76 (Score 1925,+5.74 SD). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O69717	No	insertion seqs and phages				Mb3776c				
NC_000962.3	Mycobrowser_v3	CDS	4198874	4199089	.	+	0	Rv3751	Rv3751	Sequence integration.	Probable integrase (fragment)	Rv3751, (MTV025.099), len: 71 aa. Probable integrase (fragment), similar to part of many e.g. Q48908 integrase (fragment) from Mycobacterium paratuberculosis (191 aa), FASTA scores: opt: 206, E(): 5.5e-08, (57.65% identity in 59 aa overlap); Q9ZWV7|int integrase from Corynephage 304L (395 aa), FASTA scores: opt: 156, E(): 0.00036, (45.75% identity in 59 aa overlap); Q9K722|BH3551 integrase (phage-related protein) from Bacillus halodurans (378 aa), FASTA scores: opt: 151, E(): 0.00079, (46.15% identity in 52 aa overlap); etc. Also similarity with various conjugative transposons. Also similar to Mycobacterium tuberculosis hypothetical proteins e.g. P71903|Rv2309c|MTCY3G12.25 (151 aa), FASTA scores: opt: 193, E(): 3.8e-07, (50.85% identity in 59 aa overlap); O53403|Rv1055|MTV017.08 (78 aa), FASTA scores: opt: 171, E(): 7.8e-06, (54.15% identity in 48 aa overlap); etc. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O69718	No	insertion seqs and phages				Mb3777				
NC_000962.3	Mycobrowser_v3	CDS	4187699	4189288	.	+	0	Rv3737	Rv3737	Unknown	Probable conserved transmembrane protein	Rv3737, (MTV025.085), len: 529 aa. Probable conserved transmembrane protein, similar to others and also some hypothetical proteins e.g. AAK61331|THRE threonine export carrier from Corynebacterium glutamicum (Brevibacterium flavum) (489 aa), FASTA scores: opt: 773, E(): 1.8e-36, (37.25% identity in 424 aa overlap); Q9X8J0|SCE9.17 putative membrane protein from Streptomyces coelicolor (578 aa), FASTA scores: opt: 642, E(): 5.4e-29, (31.6% identity in 481 aa overlap) (shorter 119 aa at N-terminus); Q9CJU6|PM1895 hypothetical protein from Pasteurella multocida (262 aa), FASTA scores: opt: 233, E(): 4.1e-06, (25.0% identity in 256 aa overlap); Q9S267|SCI30A.06 putative integral membrane protein from Streptomyces coelicolor (297 aa), FASTA scores: opt: 163, E(): 0.042, (29.65% identity in 263 aa overlap); etc. Also partially similar to O05435|Rv3910|MTCY15F10.01c|MTV028.01 hypothetical 123.6 KDA protein from Mycobacterium tuberculosis (1184 aa) (34.4% identity in 125 aa overlap).	O69704	No	cell wall and cell processes		MMAR_3034	MSMEG_3459	Mb3764				
NC_000962.3	Mycobrowser_v3	CDS	4189285	4190232	.	-	0	Rv3738c	PPE66	Function unknown	PPE family protein PPE66	Rv3738c, (MTV025.086c), len: 315 aa. PPE66, Member of the Mycobacterium tuberculosis PPE family, highly similar to many e.g. O53265|Rv3018c|MTV012.32c (434 aa), FASTA scores: opt: 464, E(): 2.2e-17, (47.05% identity in 338 aa overlap). Probably a continuation of the upstream ORF MTV025.87c|Rv3739c|PPE67. At position 97470-72 a stop codon is present which interrupts a possibly longer ORF, observed in related ORFs MTV012_32 or MTCY21B4_4. The sequence has been checked and no errors were detected. A similar situation, but with a frameshift separating the ORFs is found in MTV012_36/MTV012_35. Sequence similarity is also seen with MTCY251_15; MTCY261_19; MLCB2492_30 from Mycobacterium leprae; MTCY10G2_10; MTY21C12_9; MTCI125_26; MTCY164_36; MTCY6A4_1.	P9WHX1	No	PE/PPE		MMAR_3005,MMAR_3006		Mb3765c				
NC_000962.3	Mycobrowser_v3	tRNA	4199131	4199217	.	-	0	MTB000047	serX	-	tRNA-Ser (CGA)	serX, tRNA-Ser, anticodon cga, length = 87. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	4193391	4195373	.	-	0	Rv3743c	ctpJ	Cation-transporting ATPase; possibly catalyzes the transport of a undetermined cation (possibly cadmium) with hydrolyse of ATP [catalytic activity: ATP + H(2)O + undetermined cation(in) = ADP + phosphate + undetermined cation(out)].	Probable cation transporter P-type ATPase CtpJ	Rv3743c, (MTV025.091c), len: 660 aa. Probable ctpJ, cation-transporting P-type ATPase, transmembrane protein highly similar to others e.g. Q9ZBF3|SC9B5.27 putative cation-transporting ATPase from Streptomyces coelicolor (638 aa), FASTA scores: opt: 1635, E(): 2.5e-86, (62.25% identity in 63.95 aa overlap); Q59997|CADA|SLR0797 cadmium-transporting ATPase from Synechocystis sp. strain PCC 6803 (642 aa), FASTA scores: opt: 1474, E(): 4.3e-77, (42.4% identity in 604 aa overlap); P30336|CADA_BACFI probable cadmium-transporting ATPase from Bacillus firmus (723 aa), FASTA scores: opt: 1327, E(): 1.3e-68, (36.6% identity in 626 aa overlap); etc. Also highly similar to O53160|CTPD_MYCTU|Rv1469|MT1515|MTV007.16 probable cation-transporting P-type ATPase D from Mycobacterium tuberculosis (657 aa), FASTA scores: opt: 1845, E(): 2.3e-98, (55.85% identity in 650 aa overlap). Contains PS00154 E1-E2 ATPases phosphorylation site and PS01229 Hypothetical family signature 2. Belongs to the cation transport ATPases family (E1-E2 ATPases). Transcription is repressed by NmtR (See Cavet et al., 2002).	P9WPT7	No	cell wall and cell processes				Mb3769c				
NC_000962.3	Mycobrowser_v3	CDS	4190833	4192179	.	-	0	Rv3740c	Rv3740c	May be involved in synthesis of triacylglycerol	Possible triacylglycerol synthase (diacylglycerol acyltransferase)	Rv3740c, (MTV025.088c), len: 448 aa. Possible triacylglycerol synthase (See Daniel et al., 2004), highly similar to several other Mycobacterium tuberculosis hypothetical proteins e.g. O69701|Y1D4_MYCTU|Rv3734c|MT3839|MTV025.082c (454 aa) FASTA scores: opt: 1917, E(): 2.3e-112, (61.4% identity in 451 aa overlap); Q50680|YM85_MYCTU|Rv2285|MT2343|MTCY339.25c (445 aa) FASTA scores: opt: 858, E(): 3.4e-46, (37.4% identity in 460 aa overlap); Q10554|Y895_MYCTU|Rv0895|MT0919|MTCY31.23 (505 aa), FASTA scores: opt: 767, E(): 1.9e-40, (44.3% identity in 467 aa overlap); MTCY31_25; MTCY28_26; MTCY493_29; MTCY21B4_43; MTCY8D5_16; MTCY3A2_28; MTV013_8; MTY13E12_33; MTV013_9; MTY20B11_9; etc. Also similar to Q9RIU8|SCM11.13c hypothetical 47.1 KDA protein from Streptomyces coelicolor (446 aa), FASTA scores: opt: 319, E(): 1.7e-12, (30.9% identity in 453 aa overlap).	P9WKA5	No	lipid metabolism		MMAR_5278		Mb3766c				
NC_000962.3	Mycobrowser_v3	CDS	4192179	4192853	.	-	0	Rv3741c	Rv3741c	Function unknown; probably involved in cellular metabolism.	Possible oxidoreductase	Rv3741c, (MTV025.089c), len: 224 aa. Possible oxidoreductase, probably combines with product of upstream ORF MTV025.090c to form a functional monooxygenase, highly similar to C-terminal end of various oxidoreductases e.g. Q9APW3 aromatic-ring hyroxylase from Pseudomonas aeruginosa (508 aa), FASTA scores: opt: 549, E(): 5.9e-28, (56.1% identity in 155 aa overlap); Q9A588|CC2569 monooxygenase (flavin-binding family) from Caulobacter crescentus (498 aa), FASTA scores: opt: 487, E(): 5.6e-24, (39.55% identity in 225 aa overlap); Q9RZT0|DRB0033 arylesterase/monoxygenase from Deinococcus radiodurans (833 aa), FASTA scores: opt: 460, E(): 4.7e-22, (38.5% identity in 226 aa overlap); etc. Also similar to C-terminal end of Mycobacterium tuberculosis proteins (generally monooxygenases) e.g. P96223|Rv3854c|MTCY01A6.14 hypothetical 55.3 KDA protein (489 aa), FASTA scores: opt: 542, E(): 1.6e-27, (50.0% identity in 162 aa overlap); O53762|Rv0565c|MTV039.03c putative monoxygenase (486 aa), FASTA scores: opt: 462, E(): 2.2e-22, (37.15% identity in 226 aa overlap); O53300|Rv3083|MTV013.04 monoxygenase (495 aa), FASTA scores: opt: 462, E(): 2.2e-22, (45.65% identity in 173 aa overlap); etc. Note similarity to MTCY01A6.14 and MTV013.04 continue in upstream ORF (MTV025.090c) after a gap of ~100 aa.	O69708	No	intermediary metabolism and respiration				Mb3767c				
NC_000962.3	Mycobrowser_v3	CDS	4215881	4216063	.	-	0	Rv3770A	Rv3770A	Possibly required for the transposition of an insertion element.	Probable remnant of a transposase	Rv3770A, len: 60 aa. Probable remnant of a transposase, similar to many e.g. Rv2812|MTCY16B7.31c|Z81331_17 IS1604 putative transposase from Mycobacterium tuberculosis (469 aa), FASTA scores: opt: 204, E(): 1e-07, (80.5% identity in 41 aa overlap). Continuation of Rv3770B.	L7N6A0	No	insertion seqs and phages				Mb3797c				
NC_000962.3	Mycobrowser_v3	CDS	4201289	4201888	.	-	0	Rv3755c	Rv3755c	Function unknown	Conserved protein	Rv3755c, (MTV025.103c), len: 199 aa. Conserved protein showing similarity to CAC47343|SMC03980 conserved hypothetical protein from Rhizobium meliloti (Sinorhizobium meliloti) (196 aa) FASTA scores: opt: 244, E(): 4.1e-09, (30.9% identity in 191 aa overlap); Q9I2B5|PA1994 from Pseudomonas aeruginosa (187 aa), FASTA scores: opt: 226, E(): 6e-08, (29.9% identity in 194 aa overlap); and Q98N73|MLR0268 hypothetical protein (183 aa), FASTA scores: opt: 234, E(): 1.8e-08, (27.05% identity in 185 aa overlap).	O86358	No	conserved hypotheticals	ML2471	MMAR_5298	MSMEG_6329	Mb3781c				
NC_000962.3	Mycobrowser_v3	CDS	4202610	4203299	.	-	0	Rv3757c	proW	Thought to be involved in active transport of osmoprotectant (glycine betaine/carnitine/choline/L-proline) across the membrane (import). Responsible for the translocation of the substrate across the membrane.	Possible osmoprotectant (glycine betaine/carnitine/choline/L-proline) transport integral membrane protein ABC transporter ProW	Rv3757c, (MTV025.105c), len: 229 aa. Possible proW, osmoprotectant transport integral membrane protein ABC transporter (see citation below), similar to osmoprotection proteins (proW, proZ) involved in glycine betaine/L-proline/choline transport, e.g. BAB58607|Q99RI6|OPUCD|SA2234|SAV2445 OPUCD protein (probable glycine betaine/carnitine/choline ABC transporter) from Staphylococcus aureus (231 aa) FASTA scores: opt: 364, E(): 7.1e-15, (30.0% identity in 220 aa overlap); Q45461|OPBB_BACSU|OPUBB|prow choline transport system permease protein (mediate the uptake of choline for synthesis of the osmoprotectant glycine betaine) from Bacillus subtilis (217 aa), FASTA scores: opt: 348, E(): 6.2e-14, (31.05% identity in 206 aa overlap); O34878|OPCB_BACSU|OPUCB glycine betaine/carnitine/choline transport system permease protein from Bacillus subtilis (217 aa), FASTA scores: opt: 343, E(): 1.2e-13, (30.1% identity in 206 aa overlap); O34742|OPCD_BACSU|OPUCD glycine betaine/carnitine/choline transport system permease protein from Bacillus subtilis (229 aa) FASTA scores: opt: 337, E(): 2.9e-13, (31.1% identity in 193 aa overlap); etc. Could belong to the CYSTW subfamily.	O69723	No	virulence, detoxification, adaptation		MMAR_5300	MSMEG_6332	Mb3783c				
NC_000962.3	Mycobrowser_v3	CDS	4273739	4274593	.	+	0	Rv3810	pirG	Surface-exposed protein required for multiplication and intracellular growth. Seems to play a role in virulence.	Exported repetitive protein precursor PirG (cell surface protein) (EXP53)	Rv3810, (MTV026.15), len: 284 aa. PirG (alternate gene names: P36 or erp for Exported Repeated Protein), cell surface protein precursor (see citations below), equivalent to P19361|28KD_MYCLE|ML0091 28 KDA antigen precursor from Mycobacterium leprae (236 aa), FASTA scores: opt: 555, E(): 9.8e-18, (52.65% identity in 281 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WIQ7	No	cell wall and cell processes	ML0091,ML0091c	MMAR_5374	MSMEG_6405	Mb3840				
NC_000962.3	Mycobrowser_v3	CDS	4325074	4325478	.	+	0	Rv3852	hns	Function unknown	Possible histone-like protein Hns	Rv3852, (MTCY01A6.16c), len: 134 aa. Possible hns, histone-like protein, equivalent to Q9CDD1|HNS|ML0067 histone-like protein from Mycobacterium leprae (121 aa), FASTA scores: opt: 341, E(): 4.3e-09, (51.5% identity in 134 aa overlap). Shows some similarity with other histone-like proteins e.g. O65795|HIS1 histone H1 from Triticum aestivum (Wheat) (288 aa), FASTA scores: opt: 183, E(): 0.091, (34.85% identity in 109 aa overlap); etc.	I6YHB0	No	information pathways	ML0067,ML0067c	MMAR_5402		Mb3882				
NC_000962.3	Mycobrowser_v3	CDS	4204426	4205373	.	-	0	Rv3759c	proX	Thought to be involved in active transport of osmoprotectant (glycine betaine/carnitine/choline/L-proline) across the membrane (import).	Possible osmoprotectant (glycine betaine/carnitine/choline/L-proline) binding lipoprotein ProX	Rv3759c, (MTV025.107c), len: 315 aa. Possible proX, osmoprotectant-binding lipoprotein component of osmoprotectant transport system (see citation below), similar to osmoprotection proteins (proX) involved in glycine betaine/L-proline/choline transport, e.g. AAK79442|CAC1474 proline/glycine betaine ABC transport system periplasmic component from Clostridium acetobutylicum (303 aa), FASTA scores: opt: 308, E(): 1.2e-11, (27.4% identity in 314 aa overlap); Q9X4J2|PROXL|SCE19A.33 PROXL protein from Streptomyces coelicolor (322 aa), FASTA scores: opt: 302, E(): 3e-11, (27.2% identity in 327 aa overlap); O29280|AF0982 osmoprotection protein (PROX) from Archaeoglobus fulgidus (292 aa), FASTA scores: opt: 235, E(): 3.4e-07, (23.15% identity in 285 aa overlap); etc. Also similar to MTV006_16 hypothetical protein from Mycobacterium tuberculosis, and MLU15180_43 hypothetical protein from Mycobacterium leprae. Equivalent to AAK48230 from Mycobacterium tuberculosis strain CDC1551 (343 aa) but shorter 28 aa. Contains probable N-terminal signal sequence.	O69725	No	virulence, detoxification, adaptation	ML2367	MMAR_5302	MSMEG_6334	Mb3785c				
NC_000962.3	Mycobrowser_v3	CDS	4205862	4206917	.	-	0	Rv3761c	fadE36	Function unknown, but possibly involvement in lipid degradation.	Possible acyl-CoA dehydrogenase FadE36	Rv3761c, (MTV025.109c), len: 351 aa. Possible fadE36, acyl-CoA dehydrogenase, similar to many conserved hypothetical proteins and showing some similarity with few acyl-CoA dehydrogenases, e.g. Q9APX7|FADE36 FADE36 protein from Pseudomonas aeruginosa (360 aa), FASTA scores: opt: 147, E(): 0.046, (26.15% identity in 214 aa overlap); part of AAB52261.2|U97002 protein similar to acyl-CoA dehydrogenases and epoxide hydrolases from Caenorhabditis elegans (985 aa), FASTA score: (31.2% identity in 324 aa overlap). C-terminal part is highly similar to Q50095|U1740AK|MLU15183_45 hypothetical protein from Mycobacterium leprae cosmid B174 (122 aa), FASTA scores: opt: 341, E(): 7.3e-15, (57.6% identity in 99 aa overlap). Contains PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2.	O69727	No	lipid metabolism	ML2365	MMAR_5304	MSMEG_6337	Mb3787c				
NC_000962.3	Mycobrowser_v3	CDS	4216078	4216269	.	-	0	Rv3770B	Rv3770B	Possibly required for the transposition of an insertion element.	Probable remnant of a transposase	Rv3770B, len: 63 aa. Probable remnant of a transposase, similar to many e.g. Rv2812|MTCY16B7.31c|Z81331_17 IS1604 putative transposase from Mycobacterium tuberculosis (469 aa), FASTA scores: opt: 379, E(): 1.6e-21, (93.55% identity in 62 aa overlap). Continues as Rv3770A.	L7N679	No	insertion seqs and phages				Mb3798c				
NC_000962.3	Mycobrowser_v3	CDS	4288260	4291529	.	-	0	Rv3823c	mmpL8	Thought to be involved in the transport of lipids, it has been shown to be required in the production of a sulfated glycolipid, sulfolipid-1 (SL-1).	Conserved integral membrane transport protein MmpL8	Rv3823c, (MTCY409.07), len: 1089 aa. mmpL8, conserved integral membrane transport protein (see Tekaia et al., 1999), member of RND superfamily, equivalent to Q49619|MMLA_MYCLE|MMPL10|TP1|ML1231|B1170_C1_181 putative membrane protein from Mycobacterium leprae (1008 aa), FASTA scores: opt: 2718, E(): 7.3e-149, (56.25% identity in 1028 aa overlap). Also similar to others e.g. Q9XCF6|TMTPC from Mycobacterium avium (974 aa), FASTA scores: opt: 660, E(): 2.7e-30, (28.2% identity in 1050 aa overlap); Q9XCF5|TMTPB from Mycobacterium avium (963 aa), FASTA scores: opt: 653, E(): 6.7e-30, (27.0% identity in 1014 aa overlap); Q9KH53|TMTPC from Mycobacterium smegmatis (994 aa), FASTA scores: opt: 648, E(): 1.3e-29, (28.45% identity in 1013 aa overlap); etc. Also highly similar to other mmpL proteins from Mycobacterium tuberculosis; O50439|MMLA_MYCTU|MMPL10|RV1183|MT1220|MTV005.19 (1002 aa), FASTA scores: opt: 2777, E(): 2.9e-152, (58.25% identity in 996 aa overlap); Q50585|MMLC_MYCTU|MMPL12|Rv1522c|MT1573|MTCY19G5.06 (1146 aa), FASTA scores: opt: 2433, E(): 2.1e-132, (49.9% identity in 1050 aa overlap); and similar to others e.g. P95235|MML9_MYCTU|MMPL9|Rv2339|MT2402|MTCY98.08 (962 aa), FASTA scores: opt: 651, E(): 8.8e-30, (28.6% identity in 1038 aa overlap); etc. Belongs to the MmpL family.	P9WJU5	No	cell wall and cell processes			MSMEG_4741	Mb3853c				
NC_000962.3	Mycobrowser_v3	CDS	4356693	4357535	.	+	0	Rv3878	espJ	Function unknown	ESX-1 secretion-associated protein EspJ. Conserved alanine rich protein.	Rv3878, (MTV027.13), len: 280 aa. EspJ, ESX-1 secretion-associated protein, conserved ala-rich protein. Predicted to be an outer membrane protein (See Song et al., 2008).	P9WJC3	No	cell wall and cell processes	ML0046c	MMAR_5453		Mb3908				
NC_000962.3	Mycobrowser_v3	CDS	4209047	4209526	.	+	0	Rv3763	lpqH	Shown to inhibit gamma interferon regulated HLA-DR protein and mRNA expression in human macrophages	19 kDa lipoprotein antigen precursor LpqH	Rv3763, (MTV025.111), len: 159 aa. LpqH, conserved 19 KDa lipoprotein antigen precursor (see citations below), equivalent to P31502|19KD_MYCIT|MI22 19 KDA lipoprotein antigen precursor (MI22 antigen) from Mycobacterium intracellulare (162 aa), FASTA scores: opt: 773, E(): 6.2e-35, 75.95(% identity in 162 aa overlap); P46733|19KD_MYCAV 19 KDA lipoprotein antigen precursor from Mycobacterium avium (161 aa), FASTA scores: opt: 743, E(): 2.5e-33, (72.5% identity in 160 aa overlap); and Q9X7A5|LPQH|ML1966 possible lipoprotein from Mycobacterium leprae FASTA scores: opt: 371, E(): 2.2e-13, (42.6% identity in 162 aa overlap). Possibly attached to the membrane by a lipid anchor. Similar to other mycobacterium 19 KDA antigen. Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	P9WK61	No	cell wall and cell processes	ML1966	MMAR_5315	MSMEG_6316	Mb3789				
NC_000962.3	Mycobrowser_v3	CDS	4279230	4280015	.	-	0	Rv3814c	Rv3814c	Function unknown; probably involved in cellular metabolism.	Possible acyltransferase	Rv3814c, (MTCY409.16), len: 261 aa. Possible acyltransferase, highly similar to Q9CDC0|ML0087 putative acyltransferase from Mycobacterium leprae (257 aa), FASTA scores: opt: 753, E(): 7.7e-42, (46.75% identity in 246 aa overlap). Also highly similar to many acyltransferases and hypothetical proteins e.g. Q9K3R3|2SCG4.01 putative acyltransferase from Streptomyces coelicolor (242 aa), FASTA scores: opt: 587, E(): 4.6e-31, (41.95% identity in 243 aa overlap); Q9ZBS1|SC7A1.02 putative acyltransferase from Streptomyces coelicolor (264 aa), FASTA scores: opt: 293, E(): 6.6e-12, (29.2% identity in 267 aa overlap); Q9PNZ5|AAS|CJ0938 putative 2-acylglycerophosphoethanolamine acyltransferase / acyl-acyl carrier protein synthetase from Campylobacter jejuni (1170 aa), FASTA scores: opt: 274, E(): 3.9e-10, (29.1% identity in 219 aa overlap) (similarity only with middle section); Q9EY25 putative acetyl transferase from Xanthomonas oryzae pv. oryzae (249 aa), FASTA scores: opt: 238, E(): 2.4e-08, (29.2% identity in 209 aa overlap); etc. Also highly similar to downstream ORFs O07808|Rv3815c|MTCY409.15 putative acyltransferase from Mycobacterium tuberculosis (251 aa), FASTA scores: opt: 1069, E(): 2.1e-62, (60.4% identity in 245 aa overlap); and O07807|Rv3816c|MTCY409.14 putative acyltransferase from Mycobacterium tuberculosis (259 aa), FASTA scores: opt: 776, E(): 2.5e-43, (50.9% identity in 228 aa overlap). And similar to O53516|Rv2182c|MTV021.15c hypothetical 27.0 KDA protein from Mycobacterium tuberculosis (247 aa), FASTA scores: opt: 239, E(): 2e-08, (30.6% identity in 232 aa overlap).	O07809	No	intermediary metabolism and respiration		MMAR_5377		Mb3844c				
NC_000962.3	Mycobrowser_v3	CDS	4209582	4211009	.	-	0	Rv3764c	tcrY	Sensor part of a two component regulatory system.	Possible two component sensor kinase TcrY	Rv3764c, (MTV025.112c), len: 475 aa. Possible tcrY, histidine protein kinase, part of a two-component regulatory system, similar to others e.g. Q9ADN6|2SC10A7.25 putative two component system histidine kinase from Streptomyces coelicolor (524 aa), FASTA scores: opt: 1332, E(): 5.4e-70, (49.9% identity in 477 aa overlap); Q9L3C1|KB|CAC42479 putative histidine kinase from Amycolatopsis mediterranei (469 aa), FASTA scores: opt: 515, E(): 1.4e-22, (36.1% identity in 313 aa overlap); P72560 histidine protein kinase from Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) (438 aa), FASTA scores: opt: 480, E(): 1.4e-20, (40.1% identity in 232 aa overlap); P30847|P76401|BAES_ECOLI|B2078 sensor protein from Escherichia coli strain K12 (467 aa); etc. Also similar to others from Mycobacterium tuberculosis e.g. P96368|Rv1032c|MTCY10G2.17 (509 aa), FASTA scores: opt: 1007, E(): 4e-51, (43.5% identity in 416 aa overlap); and P71815|Rv0758|MTCY369.03 (485 aa), FASTA scores: opt: 738, E(): 1.6e-35, (28.6% identity in 438 aa overlap). Equivalent to AAK48235 from Mycobacterium tuberculosis strain CDC1551 (506 aa) but shorter 31 aa.	O69729	No	regulatory proteins	ML2362	MMAR_5316	MSMEG_4989	Mb3790c				
NC_000962.3	Mycobrowser_v3	CDS	4214615	4214887	.	+	0	Rv3769	Rv3769	Unknown	Hypothetical protein	Rv3769, (MTCY13D12.03), len: 90 aa. Hypothetical unknown protein, possible coiled-coil protein.	P72036	No	conserved hypotheticals		MMAR_4959		Mb3795				
NC_000962.3	Mycobrowser_v3	CDS	4214070	4214429	.	+	0	Rv3768	Rv3768	Unknown	Unknown protein	Rv3768, (MTCY13D12.02), len: 119 aa. Unknown protein.	P72035	No	conserved hypotheticals		MMAR_5324		Mb3794				
NC_000962.3	Mycobrowser_v3	CDS	4215200	4215775	.	-	0	Rv3770c	Rv3770c	Unknown	Hypothetical leucine rich protein	Rv3770c, (MTCY13D12.04c), len: 191 aa. Hypothetical unknown leu-rich protein.	P72037	No	conserved hypotheticals				Mb3796c				
NC_000962.3	Mycobrowser_v3	CDS	4218241	4218825	.	-	0	Rv3773c	Rv3773c	Function unknown	Conserved protein	Rv3773c, (MTCY13D12.07c), len: 194 aa. Conserved protein, highly similar to C-terminal end of O53773|Rv0576|MTV039.14 possible transcriptional regulator from Mycobacterium tuberculosis (434 aa), FASTA scores: opt: 575, E(): 8.3e-30, (47.4% identity in 192 aa overlap); and some similarity with other proteins from Mycobacterium tuberculosis e.g. P71985|Rv1727|MTCY04C12.12 (189 aa) FASTA scores: opt: 176, E(): 0.00022, (31.1% identity in 180 aa overlap).	P72040	No	conserved hypotheticals		MMAR_5328	MSMEG_6832	Mb3801c,Mb3802c				
NC_000962.3	Mycobrowser_v3	CDS	4218849	4219673	.	+	0	Rv3774	echA21	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Possible enoyl-CoA hydratase EchA21 (enoyl hydrase) (unsaturated acyl-CoA hydratase) (crotonase)	Rv3774, (MTCY13D12.08), len: 274 aa. Possible echA21, enoyl-CoA hydratase, equivalent to Q9CD94|ECHA1|ML0120 putative enoyl-CoA hydratase from Mycobacterium leprae (278 aa), FASTA scores: opt: 1593, E(): 2.2e-92, (88.3% identity in 274 aa overlap). Also similar to others e.g. Q9I2S4|PA1821 from Pseudomonas aeruginosa (270 aa), FASTA scores: opt: 761, E(): 2e-40, (42.3% identity in 267 aa overlap); Q9FHR8 from Arabidopsis thaliana (Mouse-ear cress) (278 aa) FASTA scores: opt: 638, E(): 9.9e-33, (39.4% identity in 269 aa overlap); Q9AB78|CC0353 from Caulobacter crescentus (286 aa), FASTA scores: opt: 601, E(): 2.1e-31, (39.25% identity in 266 aa overlap); etc.	P75019	No	lipid metabolism	ML0120,ML0120c	MMAR_5329	MSMEG_6353	Mb3803				
NC_000962.3	Mycobrowser_v3	CDS	4221089	4222648	.	+	0	Rv3776	Rv3776	Function unknown	Conserved hypothetical protein	Rv3776, (MTCY13D12.10), len: 519 aa. Conserved hypothetical protein, highly similar to Q10709|YL00_MYCTU|Rv2100|MTCY49.40 hypothetical 58.9 KDA protein from Mycobacterium tuberculosis (550 aa) FASTA scores: opt: 1646, E(): 1.2e-83, (77.85% identity in 510 aa overlap) (homology from potential start at 7744); and similar to other proteins from Mycobacterium tuberculosis (strains H37Rv and CDC1551) e.g. O33266|Rv0336|MTCY279.03 (503 aa) FASTA scores: opt: 682, E(): 2.2e-30, (41.65% identity in 497 aa overlap).	P72042	No	conserved hypotheticals			MSMEG_3957,MSMEG_5583	Mb3805				
NC_000962.3	Mycobrowser_v3	CDS	4224985	4226985	.	+	0	Rv3779	Rv3779	Unknown	Probable conserved transmembrane protein alanine and leucine rich	Rv3779, (MTCY13D12.13), len: 666 aa. Predicted to be in the GT-C superfamily of glycosyltransferases (See Liu and Mushegian, 2003). Probable conserved transmembrane ala-, leu-rich protein, equivalent to Q9CD98|ML0116 putative membrane protein from Mycobacterium leprae (654 aa), FASTA scores: opt: 1991, E(): 2e-112, (66.5% identity in 666 aa overlap). Shows some similarity with Q9RRU0|DR2395 putative NA+/H+ antiporter from Deinococcus radiodurans (458 aa), FASTA scores: opt: 138, E(): 0.69, (31.9% identity in 138 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P72045	No	cell wall and cell processes	ML0116,ML0116c	MMAR_5334		Mb3808				
NC_000962.3	Mycobrowser_v3	CDS	4226989	4227525	.	+	0	Rv3780	Rv3780	Function unknown	Conserved protein	Rv3780, (MTCY13D12.14), len: 178 aa. Conserved protein, equivalent to Q9CD99|ML0115 hypothetical 19.1 KDA protein from Mycobacterium leprae (174 aa), FASTA scores: opt: 903, E(): 2.3e-48, (82.95% identity in 170 aa overlap). Also highly similar to Q9XA56|SCGD3.23c hypothetical 19.5 KDA protein from Streptomyces coelicolor (179 aa), FASTA scores: opt: 692, E(): 1.8e-35, (65.9% identity in 170 aa overlap). Note that this putative protein is 4 aa longer at the N-terminus compared to previous annotation (in Nature 393: 537-544 (1998)).	P9WKX3	No	conserved hypotheticals	ML0115,ML0115c	MMAR_5335	MSMEG_6365	Mb3809				
NC_000962.3	Mycobrowser_v3	CDS	4283996	4284331	.	+	0	Rv3819	Rv3819	Unknown	Unknown protein	Rv3819, (MTCY409.11c), len: 111 aa. Unknown protein. Contains PS00012 Phosphopantetheine attachment site.	O07804	No	conserved hypotheticals	ML0084,ML0084c	MMAR_5382	MSMEG_6411	Mb3849				
NC_000962.3	Mycobrowser_v3	CDS	4228347	4229261	.	+	0	Rv3782	glfT1	Transfers galactofuranose in the initiation of cell wall galactan polymerization	UDP-galactofuranosyl transferase GlfT1	Rv3782, (MTCY13D12.16), len: 304 aa. GlfT1, UDP-galactofuranosyl transferase (See Mikusova et al., 2006; Belanova et al., 2008), equivalent to Q9CDA1|RFBE|ML0113 putative glycosyl transferase from Mycobacterium leprae (283 aa), FASTA scores: opt: 1583, E(): 9.3e-96, (81.6% identity in 277 aa overlap). Also some similarity with AAK68916|WCFN putative glycosyltransferase from Bacteroides fragilis (291 aa) FASTA scores: opt: 241, E(): 2.1e-08, (30.75% identity in 195 aa overlap); O58161|PH0424 hypothetical 40.5 KDA protein from Pyrococcus horikoshii (348 aa), FASTA scores: opt: 194, E(): 2.8e-05, (23.85% identity in 302 aa overlap); O26448|MTH348 rhamnosyl transferase from Methanothermobacter thermautotrophicus (313 aa), FASTA scores: opt: 177, E(): 0.00033, (28.2% identity in 333 aa overlap); O07868|CPS19BQ putative rhamnosyl transferase FASTA from Streptococcus pneumoniae (300 aa), FASTA scores: opt: 156, E(): 0.0074, (25.45% identity in 232 aa overlap); and other putative transferases. Note that C-terminal end shows some similarity with part of Q05161|RFB O-antigen biosynthesis protein B from Escherichia coli strain 0101. Note that previously known as rfbE.	P9WMX3	No	cell wall and cell processes	ML0113,ML0113c	MMAR_5337	MSMEG_6367	Mb3811				
NC_000962.3	Mycobrowser_v3	CDS	4229258	4230100	.	+	0	Rv3783	rfbD	May form an ATP-driven O-antigen/lipopolysaccharide export apparatus, in association with RFBE|Rv3781. Responsible for the translocation of the substrate across the membrane.	Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD	Rv3783, (MTCY13D12.17), len: 280 aa. Probable rfbD, polysaccharide-transport integral membrane protein ABC transporter (see Braibant et al., 2000), involved in O-antigen/lipopolysaccharides (LPS) transport, equivalent to Q9CDA2|ML0112 putative ABC transporter component from Mycobacterium leprae (276 aa), FASTA scores: opt: 1646, E(): 4e-102, (84.3% identity in 280 aa overlap). Also highly similar to Q9PAF1|XF2567 ABC transporter permease protein from Xylella fastidiosa (267 aa), FASTA scores: opt: 723, E(): 7.6e-41, (41.3% identity in 259 aa overlap); and similar to others e.g. Q56902|RFBD_YEREN O-antigen export system permease protein from Yersinia enterocolitica (259 aa) (see Zhang et al., 1993), FASTA scores: opt: 566, E(): 2e-30, (28.05% identity in 264 aa overlap); Q06955|RFBH RFBH protein (involved in the export of lipopolysaccharide) (alias Q9KVA3|VC0246) lipopolysaccharide/O-antigen transport protein from Vibrio cholerae (257 aa), FASTA scores: opt: 358, E(): 1.3e-16, (24.4% identity in 258 aa overlap); Q9HTB8|WZM|PA5451 membrane subunit of a-band LPS efflux transporter from Pseudomonas aeruginosa (265 aa), FASTA scores: opt: 263, E(): 2.7e-10, (25.45% identity in 263 aa overlap); etc. Belongs to the ABC-2 subfamily of integral membrane proteins.	P72049	No	cell wall and cell processes	ML0112,ML0112c	MMAR_5338	MSMEG_6369	Mb3812				
NC_000962.3	Mycobrowser_v3	CDS	4231320	4232393	.	+	0	Rv3785	Rv3785	Unknown	Hypothetical protein	Rv3785, (MTCY13D12.19), len: 357 aa. Hypothetical unknown protein. Note that this putative protein is equivalent to AAK48258|MT3893 NAD-dependent epimerase/dehydratase family protein from Mycobacterium tuberculosis strain CDC1551 (712 aa), but shorter 355 aa.	P9WKX1	No	conserved hypotheticals				Mb3814				
NC_000962.3	Mycobrowser_v3	CDS	4232374	4233597	.	-	0	Rv3786c	Rv3786c	Unknown	Unknown protein	Rv3786c, (MTCY13D12.20), len: 407 aa. Unknown protein. Segment between aa 265-300 (approximately) is highly similar to part of O03937|RORF1608 minor capsid protein from Bacteriophage phig1e (1608 aa), FASTA scores: opt: 242, E(): 8.4e-07, (26.85% identity in 272 aa overlap); Q9ETT9|ORF36 putative peptidase from Corynebacterium equii (Rhodococcus equi) plasmid pREAT701 (p33701) and Plasmid virulence (546 aa), FASTA scores: opt: 231, E(): 1.6e-06, (34.15% identity in 167 aa overlap); O69910|SC2E1.40c hypothetical 22.8 KDA protein. from Streptomyces coelicolor (226 aa) FASTA scores: opt: 218, E(): 4.6e-06, (34.15% identity in 164 aa overlap); and others.	P9WKW9	No	conserved hypotheticals		MMAR_5347		Mb3815c				
NC_000962.3	Mycobrowser_v3	CDS	4233610	4234536	.	-	0	Rv3787c	Rv3787c	Function unknown	Conserved hypothetical protein	Rv3787c, (MTCY13D12.21), len: 308 aa. Conserved hypothetical protein, highly similar to several mycobacterial hypothetical proteins e.g. P95074|Rv0726c|MTCY210.45c from Mycobacterium tuberculosis (367 aa), FASTA scores: opt: 1038, E(): 1.6e-58, (55.85% identity in 283 aa overlap); O53795|MBE50c|Rv0731c|MTV041.05c from Mycobacterium tuberculosis (318 aa), FASTA scores: opt: 1030, E(): 4.5e-58, (56.15% identity in 292 aa overlap); Q9CCZ4|ML2640 from Mycobacterium leprae (310 aa) FASTA scores: opt: 709, E(): 9.9e-38, (43.75% identity in 279 aa overlap); etc.	P9WFH3	No	conserved hypotheticals		MMAR_3534	MSMEG_1888	Mb3816c				
NC_000962.3	Mycobrowser_v3	CDS	4234780	4235265	.	+	0	Rv3788	Rv3788	Unknown	Hypothetical protein	Rv3788, (MTCY13D12.22), len: 161 aa. Hypothetical unknown protein.	P9WKW7	No	conserved hypotheticals	ML0111,ML0111c	MMAR_5350		Mb3817				
NC_000962.3	Mycobrowser_v3	CDS	4235374	4235739	.	+	0	Rv3789	Rv3789	Function unknown	GTRA family protein	Rv3789, (MTCY13D12.23), len: 121 aa. GtrA family protein; possible integral membrane protein, equivalent to Q9CDA3|ML0110 hypothetical 13.9 KDA protein from Mycobacterium leprae (123 aa) FASTA scores: opt: 587, E(): 7.3e-34, (72.95% identity in 122 aa overlap). Also equivalent to AAK48262 from Mycobacterium tuberculosis strain CDC1551 (142 aa) but shorter 21 aa.	P9WMS9	No	cell wall and cell processes	ML0110,ML0110c	MMAR_5351	MSMEG_6372	Mb3818				
NC_000962.3	Mycobrowser_v3	CDS	4322326	4323234	.	+	0	Rv3848	Rv3848	Unknown	Probable conserved transmembrane protein	Rv3848, (MTCY01A6.20c), len: 302 aa. Probable conserved transmembrane protein, similar to hypothetical (transmembrane) proteins e.g. Q9HVG2|PA4629 hypothetical protein from Pseudomonas aeruginosa (192 aa), FASTA scores: opt: 304, E(): 5.3e-11, (35.05% identity in 174 aa overlap); Q9A5S7|CC2370 hypothetical protein from Caulobacter crescentus (207 aa), FASTA scores: opt: 285, E(): 7.4e-10, (29.9% identity in 184 aa overlap); Q9KY43|SCC8A.05c putative integral membrane protein from Streptomyces coelicolor (193 aa), FASTA scores: opt: 245, E(): 1.6e-07, (32.8% identity in 195 aa overlap); etc.	P96229	No	cell wall and cell processes		MMAR_5398	MSMEG_5329	Mb3878				
NC_000962.3	Mycobrowser_v3	CDS	4239863	4243147	.	+	0	Rv3793	embC	Involved in the biosynthesis of the mycobacterial cell wall arabinan and resistance to ethambutol (EMB; dextro-2,2'-(ethylenediimino)-DI-1-butanol). Polymerizes arabinose into the arabinan of arabiogalactan [catalytic activity: UDP-L-arabinose + indol-3-ylacetyl-myo-inositol = UDP + indol-3-ylacetyl-myo-inositol L-arabinoside].	Integral membrane indolylacetylinositol arabinosyltransferase EmbC (arabinosylindolylacetylinositol synthase)	Rv3793, (MTCY13D12.27), len: 1094 aa. EmbC, integral membrane protein, indolylacetylinositol arabinosyltransferase (see citations below), equivalent to Q9CDA7|EMBC|ML0106 putative arabinosyl transferase from Mycobacterium leprae (1070 aa) FASTA scores: opt: 6078,E(): 0, (82.95% identity in 1072 aa overlap); Q50393|EMBC putative arabinosyl transferase from Mycobacterium smegmatis (1074 aa), FASTA scores: opt: 5523, E(): 0, (75.35% identity in 1072 aa overlap). Also similar to Q9CDA9|EMBB| ML0104 putative arabinosyl transferase from Mycobacterium leprae (1083 aa), FASTA scores: opt: 2789, E(): 1.9e-156, (44.0% identity in 1095 aa overlap); O30406|EMBB putative arabinosyl transferase from Mycobacterium smegmatis (1082 aa), FASTA scores: opt: 2746, E(): 6.4e-154, (44.6% identity in 1096 aa overlap); etc. Also similar to to P72030|EMBB|Rv3795|MTCY13D12.29 indolylacetylinositol arabinosyltransferase from Mycobacterium tuberculosis (1098 aa), FASTA scores: opt: 2276, E(): 3.1e-126, (44.45% identity in 1118 aa overlap); and P72060|EMBA|Rv3794|MTCY13D12.28 indolylacetylinositol arabinosyltransferase from Mycobacterium tuberculosis (1094 aa), FASTA scores: opt: 1974, E(): 1.9e-108, (41.0% identity in 1110 aa overlap). Contains PS00044 Bacterial regulatory proteins, lysR family signature; and PS00017 ATP/GTP-binding site motif A (P-loop). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WNL5	No	cell wall and cell processes	ML0106,ML0106c	MMAR_5355	MSMEG_6387	Mb3822				
NC_000962.3	Mycobrowser_v3	CDS	4246514	4249810	.	+	0	Rv3795	embB	Involved in the biosynthesis of the mycobacterial cell wall arabinan and resistance to ethambutol (EMB; dextro-2,2'-(ethylenediimino)-DI-1-butanol). Polymerizes arabinose into the arabinan of arabiogalactan [catalytic activity: UDP-L-arabinose + indol-3-ylacetyl-myo-inositol = UDP + indol-3-ylacetyl-myo-inositol L-arabinoside].	Integral membrane indolylacetylinositol arabinosyltransferase EmbB (arabinosylindolylacetylinositol synthase)	Rv3795, (MTCY13D12.29), len: 1098 aa. EmbB, integral membrane protein, indolylacetylinositol arabinosyltransferase (see citations below), equivalent to P71486|EMBB arabinosyl transferase from Mycobacterium avium (1065 aa), FASTA scores: opt: 4998, E(): 0, (83.25% identity in 1076 aa overlap); Q9CDA9|EMBB|ML0104 putative arabinosyl transferase from Mycobacterium leprae (1083 aa), FASTA scores: opt: 4706, E(): 0, (78.0% identity in 1101 aa overlap); O30406|EMBB (alias Q50395) putative arabinosyl transferase from Mycobacterium smegmatis (1082 aa), FASTA scores: opt: 4163, E(): 0, (68.4% identity in 1091 aa overlap); etc. Also similar to Q50393|EMBC putative arabinosyl transferase from Mycobacterium smegmatis (1074 aa), FASTA scores: opt: 2482, E(): 5e-135, (44.7% identity in 1101 aa overlap); Q9CDA7|EMBC|ML0106 putative arabinosyl transferase from Mycobacterium leprae (1070 aa), FASTA scores: opt: 2259, E(): 3.4e-122, (43.4% identity in 1104 aa overlap); etc. Also similar to P72059|EMBC|Rv3793|MTCY13D12.27 indolylacetylinositol arabinosyltransferase from Mycobacterium tuberculosis (1094 aa), FASTA scores: opt: 2276, E(): 3.6e-123, (44.45% identity in 1118 aa overlap); and P72060|EMBA|Rv3794|MTCY13D12.28 indolylacetylinositol arabinosyltransferase from Mycobacterium tuberculosis (1094 aa), FASTA scores: opt: 1288, E(): 2.5e-66, (42.35% identity in 1114 aa overlap). Supposedly regulated by embR|Rv1267c. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WNL7	No	cell wall and cell processes	ML0104,ML0104c	MMAR_5357	MSMEG_6389	Mb3824				
NC_000962.3	Mycobrowser_v3	CDS	4249878	4251005	.	+	0	Rv3796	Rv3796	Function unknown	Conserved protein	Rv3796, (MTV026.01-MTCY13D12.30), len: 375 aa. Conserved protein. C-terminal end similar in part to Q983J3|MLR8305 hypothetical protein from Rhizobium loti (Mesorhizobium loti) (227 aa), FASTA scores: opt: 288, E(): 4e-09, (38.95% identity in 154 aa overlap). Similar to P54548|YQJK_BACSU hypothetical protein (belongs to the ATSA/ELAC family) from Bacillus subtilis (307 aa) FASTA scores: opt: 263, E(): 1.3e-07, (26.1% identity in 295 aa overlap); and some similarity to other proteins e.g. AAK46775|MT2479 putative arylsulfatase from Mycobacterium tuberculosis strain CDC1551 (224 aa), FASTA scores: opt: 194, E(): 0.00072, (25.85% identity in 259 aa overlap). Equivalent to AAK48269 from Mycobacterium tuberculosis strain CDC1551 (338 aa) but longer 37 aa. Some similarity to the A. carrageenovora AtsA / E. coli ElaC family. Note that previously known as atsH. Predicted to be an outer membrane protein (See Song et al., 2008).	P72062	No	conserved hypotheticals		MMAR_5358		Mb3825				
NC_000962.3	Mycobrowser_v3	CDS	4252993	4254327	.	+	0	Rv3798	Rv3798	Required for the transposition of the insertion sequence element IS1557.	Probable transposase	Rv3798, (MTV026.03), len: 444 aa. Probable transposase for insertion sequence element IS1557, highly similar to Q60255 similar to transposase of ISAE1 from alcaligenes eutrophus H1-4 (fragment) from dibenzofuran-degrading bacterium DPO360 (163 aa) FASTA scores: opt: 767, E(): 3.2e-42, (67.25% identity in 168 aa overlap); and similar to P74920 transposase from Thiobacillus ferrooxidans (404 aa), FASTA scores: opt: 375, E(): 1.1e-16, (27.55% identity in 439 aa overlap); Q48349 transposase from Alcaligenes eutrophus (Ralstonia eutropha) (408 aa), FASTA scores: opt: 324, E(): 2e-13, (3.9% identity in 369 aa overlap); Q9FDC1|TNP transposase from Burkholderia mallei (Pseudomonas mallei) (386 aa) FASTA scores: opt: 282, E(): 9.8e-11, (25.85% identity in 391 aa overlap); etc. C-terminal end identical to O53804|Rv0741|MTV041.15 transposase from Mycobacterium tuberculosis (104 aa), FASTA scores: opt: 582, E(): 1.8e-30, (85.6% identity in 104 aa overlap). Belongs to the transposase family 12.	P9WKH7	No	insertion seqs and phages			MSMEG_6697	Mb3827,Mb3828				
NC_000962.3	Mycobrowser_v3	CDS	4255945	4261146	.	-	0	Rv3800c	pks13	Involved in the final steps of mycolic acid biosynthesis. Catalyses the condensation of two fatty acyl chains.	Polyketide synthase Pks13	Rv3800c, (MTV026.05c), len: 1733 aa. Probable pks13, polyketide synthase, equivalent to Q9CDB1|PKS13|ML0101 polyketide synthase from Mycobacterium leprae (1784 aa), FASTA scores: opt: 7454, E(): 0, (83.6% identity in 1748 aa overlap); and similar to Q9Z5K6|ML2357|MLCB12.02c putative polyketide synthase from Mycobacterium leprae (1871 aa), FASTA scores: opt: 1682, E(): 1.2e-85, (38.3% identity in 1096 aa overlap). Also similar in part to many e.g. Q9ADL6|SORA soraphen polyketide synthase a from Polyangium cellulosum (6315 aa) FASTA scores: opt: 1422, E(): 1e-70, (31.45% identity in 1616 aa overlap); AAK73501|AMPHI AMPHI protein (involved in amphotericin biosynthesis) from Streptomyces nodosus (9510 aa), FASTA scores: opt: 1441, E(): 1.2e-71, (30.45% identity in 1662 aa overlap); Q9RFL0|MTAB MTAB protein (involved in myxothiazol biosynthesis) from Stigmatella aurantiaca (4003 aa), FASTA scores: opt: 1429, E(): 2.8e-71, (33.8% identity in 1089 aa overlap); Q9L4X2|NYSJ from Streptomyces noursei (5435 aa), FASTA scores: opt: 1407, E(): 6.1e-70, (30.5% identity in 1764 aa overlap); CAC37876|SC1G7.01c from Streptomyces coelicolor (3489 aa) FASTA scores: opt: 1382, E(): 1e-68, (31.05% identity in 1489 aa overlap); etc. Also highly similar to Q10977|PPSA_MYCTU|Rv2931|MT3000|MTCY338.20 phenolpthiocerol synthesis polyketide synthase from Mycobacterium tuberculosis (1876 aa), FASTA scores: opt: 1728, E(): 3.4e-88, (36.95% identity in 1269 aa overlap); and P96203|PPSD|Rv2934|MTCY19H9.02. Contains PS00606 Beta-ketoacyl synthases active site.	I6X8D2	No	lipid metabolism	ML0101	MMAR_5364	MSMEG_6392	Mb3830c				
NC_000962.3	Mycobrowser_v3	CDS	4266953	4268836	.	-	0	Rv3805c	aftB	Involved in the biosynthesis of the mycobacterial cell wall arabinan	Possible arabinofuranosyltransferase AftB	Rv3805c, (MTV026.10c), len: 627 aa. Possible aftB, arabinofuranosyltransferase (See Seidel et al., 2007). Probable conserved transmembrane protein, equivalent, but shorter 19 aa, to Q9CDB4|ML0096 putative membrane protein from Mycobacterium leprae (649 aa), FASTA scores: opt: 3511, E(): 1.1e-204, (80.9% identity in 629 aa overlap). Equivalent to AAK48278 from Mycobacterium tuberculosis strain CDC1551 (641 aa) but shorter 14 aa. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O53582	No	cell wall and cell processes	ML0096		MSMEG_6400	Mb3835c				
NC_000962.3	Mycobrowser_v3	CDS	4263355	4264365	.	-	0	Rv3802c	Rv3802c	Shown to have phospholipase and thioesterase activity	Probable conserved membrane protein	Rv3802c, (MTV026.07c), len: 336 aa. Probable conserved membrane protein, with a N-terminal signal sequence followed by Pro-rich region. Equivalent to Q9CDB3|ML0099 hypothetical protein from Mycobacterium leprae (336 aa) FASTA scores: opt: 1759, E(): 1.1e-85, (75.5% identity in 335 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004). Predicted to be an outer membrane protein (See Song et al., 2008).	O53581	No	cell wall and cell processes	ML0099	MMAR_5366	MSMEG_6394	Mb3832c				
NC_000962.3	Mycobrowser_v3	CDS	4264563	4265462	.	-	0	Rv3803c	fbpD	Involved in cell wall mycoloylation. Proteins of the antigen 85 complex are responsible for the high affinity of mycobacteria to fibronectin. Possesses a mycolyltransferase activity required for the biogenesis of trehalose dimycolate (cord factor), a dominant structure necessary for maintaining cell wall integrity.	Secreted MPT51/MPB51 antigen protein FbpD (MPT51/MPB51 antigen 85 complex C) (AG58C) (mycolyl transferase 85C) (fibronectin-binding protein C) (85C)	Rv3803c, (MT3910, MTV026.08c), len: 299 aa. FbpD (alternate gene names: mpt51, mpb51, fbpC1), secreted MPB51/MPT51 antigen protein (fibronectin-binding protein C) (mycolyl transferase 85C) (see citations below), identical to Q48923|MPT51|MPB51 antigen precursor from Mycobacterium bovis (299 aa), FASTA scores: opt: 2093, E(): 1.5e-112, (100.0% identity in 299 aa overlap) (see Ohara et al., 1995); and highly similar to other Mycobacterial antigen precursors e.g. Q05868|MPT5_MYCLE|MPT51|ML0098 MPT51 antigen precursor from Mycobacterium leprae (301 aa), FASTA scores: opt: 1624, E(): 9.8e-86, (77.8% identity in 302 aa overlap); O52972|A85C_MYCAV|FBPC antigen 85-C precursor (fibronectin-binding protein C) from Mycobacterium avium (352 aa), FASTA scores: opt: 753, E(): 6.6e-36, (41.5% identity in 315 aa overlap); P21160|A85B_MYCKA antigen 85-B precursor (fibronectin-binding protein B) from Mycobacterium kansasii (325 aa), FASTA scores: opt: 574, E(): 1.1e-25, (37.55% identity in 309 aa overlap); P12942|A85B_MYCBO antigen 85-B precursor from Mycobacterium bovis (323 aa), FASTA scores: opt: 572, E(): 1.4e-25, (39.85% identity in 291 aa overlap); etc. Also similar to P31953|A85C_MYCTU|FBPC|MPT45|Rv0129c|MTCI5.03c|FBPC2 secreted antigen 85-C (mycolyl transferase 85C) (fibronectin-binding protein C) from Mycobacterium tuberculosis (340 aa), FASTA scores: opt: 751, E(): 8.4e-36, (40.65% identity in 310 aa overlap); P17944|A85A_MYCTU|FBPA|MPT44|Rv3804c|MT3911|MTV026.09c secreted antigen 85-a (mycolyl transferase 85A) (fibronectin-binding protein A) from Mycobacterium tuberculosis (338 aa), FASTA scores: opt: 592, E(): 1e-26, (39.05% identity in 302 aa overlap); etc. Contains PS00178 Aminoacyl-transfer RNA synthetases class-I signature. Note that the secreted protein MPB51 is one of the major proteins in the culture filtrate of Mycobacterium bovis BCG. Note that overexpression in an FbpC-deficient M. tuberculosis clinical isolate has no effect on the amount of cell wall-linked mycolates (See Puech et al., 2002).	P9WQN7	No	lipid metabolism	ML0098	MMAR_5367	MSMEG_6396	Mb3833c				
NC_000962.3	Mycobrowser_v3	CDS	4265642	4266658	.	-	0	Rv3804c	fbpA	Involved in cell wall mycoloylation. Proteins of the antigen 85 complex are responsible for the high affinity of mycobacteria to fibronectin. Possesses a mycolyltransferase activity required for the biogenesis of trehalose dimycolate (cord factor), a dominant structure necessary for maintaining cell wall integrity.	Secreted antigen 85-a FbpA (mycolyl transferase 85A) (fibronectin-binding protein A) (antigen 85 complex A)	Rv3804c, (MT3911, MTV026.09c), len: 338 aa. FbpA (alternate gene names: mpt44, 85A), precursor of the 85-a antigen (fibronectin-binding protein A) (mycolyl transferase 85A) (see citations below), identical to P17944|P17996|FBPA|MPT44 antigen 85-a precursor from Mycobacterium bovis (338 aa), FASTA scores: opt: 2341, E(): 1.2e-132, (100.0% identity in 338 aa overlap); and highly similar to other Mycobacterial antigen precursors e.g. O52956|A85A_MYCAV|FBPA antigen 85-a precursor (85A) from Mycobacterium avium (347 aa), FASTA scores: opt: 1987, E(): 1.7e-111, (82.55% identity in 338 aa overlap); Q05861|A85A_MYCLE|FBPA|ML0097 antigen 85-a precursor (85A) from Mycobacterium leprae (330 aa), FASTA scores: opt: 1936, E(): 1.9e-108, (83.0% identity in 329 aa overlap); O06052|A85A_MYCGO|FBPA antigen 85-a precursor (85A) from Mycobacterium gordonae (339 aa), FASTA scores: opt: 1932, E(): 3.3e-108, (80.45% identity in 338 aa overlap); etc. Also highly similar to P31952|A85B_MYCTU|FBPB|Rv1886c|MT1934|MTCY180.32 secreted antigen 85-B from Mycobacterium tuberculosis (325 aa), FASTA scores: opt: 1830, E(): 3.9e-102, (78.85% identity in 317 aa overlap); P31953|A85C_MYCTU|FBPC|MPT45|Rv0129c|MTCI5.03c|FBPC2 secreted antigen 85-C from Mycobacterium tuberculosis (340 aa), FASTA scores: opt: 1597, E(): 3.4e-88, (67.25% identity in 336 aa overlap). Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WQP3	No	lipid metabolism	ML0097	MMAR_5368	MSMEG_2078,MSMEG_6398	Mb3834c				
NC_000962.3	Mycobrowser_v3	CDS	4302786	4303397	.	-	0	Rv3828c	Rv3828c	Prevents the cointegration of foreign DNA before integration into the chromosome.	Possible resolvase	Rv3828c, (MTCY409.02), len: 203 aa. Possible resolvase within IS1537 element, similar to others e.g. Q97X40|SSO1915 first ORF in transposon ISC1913 from Sulfolobus solfataricus (213 aa), FASTA scores: opt: 275, E(): 1.6e-11, (30.6% identity in 196 aa overlap); Q9V1M0|PAB2076 resolvase related protein from Pyrococcus abyssi (212 aa), FASTA scores: opt: 254, E(): 4.2e-10, (29.95% identity in 197 aa overlap); Q9RMU7|ORFA putative transposase (belongs to the MerR family of transcriptional regulators) from Helicobacter pylori (Campylobacter pylori) (217 aa), FASTA scores: opt: 243, E(): 2.3e-09, (31.8% identity in 154 aa overlap); etc. Also highly similar to proteins from Mycobacterium tuberculosis e.g. O33334|Rv2792c|MTV002.57c resolvase (193 aa), FASTA scores: opt: 970, E(): 1.5e-58, (79.25% identity in 193 aa overlap); O07773|Rv0605|MTCY19H5.17c putative resolvase (202 aa), FASTA scores: opt: 964, E(): 4e-58, (76.25% identity in 202 aa overlap); P95116|Rv2979c|MTCY349.08 hypothetical 21.4 KDA protein (194 aa), FASTA scores: opt: 895, E(): 1.8e-53, (74.75% identity in 194 aa overlap); Q10831|YS86_MYCTU|Rv2886c|MT2954|MTCY274.17c hypothetical 31.9 KDA protein (295 aa), FASTA scores: opt: 826, E(): 1.1e-48, (66.2% identity in 204 aa overlap) (similarity only at C-terminus); etc. Contains PS00397 Site-specific recombinases active site. Possible helix-turn-helix motif from aa 11-32, Score 1305 (+3.63 SD).	O07795	No	insertion seqs and phages				Mb3858c				
NC_000962.3	Mycobrowser_v3	CDS	4269840	4270337	.	-	0	Rv3807c	Rv3807c	Unknown	Possible conserved transmembrane protein	Rv3807c, (MTV026.12), len: 165 aa. Possible conserved transmembrane protein, equivalent to Q9CDB6|ML0094 putative membrane protein from Mycobacterium leprae (192 aa), FASTA scores: opt: 714, E(): 2.4e-38, (72.85% identity in 151 aa overlap). Also highly similar to Q9KZA3|SC5G8.11 putative integral membrane protein from Streptomyces coelicolor (169 aa), FASTA scores: opt: 324, E(): 1.1e-13, (41.5% identity in 159 aa overlap); and similar in part to others e.g. Q9K3L3|SCG20A.27 putative integral membrane protein from Streptomyces coelicolor (230 aa), FASTA scores: opt: 277, E(): 1.3e-10, (41.65% identity in 168 aa overlap); P72269|ORF8 hypothetical protein from Rhodococcus erythropolis (487 aa) FASTA scores: opt: 229, E(): 2.7e-07, (36.25% identity in 149 aa overlap); O86625|SC3A7.24c putative integral membrane protein from Streptomyces coelicolor (201 aa) FASTA scores: opt: 200, E(): 9.1e-06, (34.95% identity in 146 aa overlap); Q9KYD7|SCD72A.19 putative integral membrane protein from Streptomyces coelicolor (238 aa) FASTA scores: opt: 178, E(): 0.00026, (35.7% identity in 112 aa overlap); etc. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WI53	No	cell wall and cell processes	ML0094	MMAR_5371	MSMEG_6402	Mb3837c				
NC_000962.3	Mycobrowser_v3	CDS	4270366	4272279	.	-	0	Rv3808c	glfT2	Converts UDP-galactofuranose in cell wall galactan polymerization. Has UDP-Galf:beta-D-(1->5) and UDP-Galf:beta-D-(1->6) galactofuranosyltransferase activities.	Bifunctional UDP-galactofuranosyl transferase GlfT2	Rv3808c, (MTV026.13c), len: 637 aa. GlfT2, bifunctional UDP-galactofuranosyl transferase (see citations below). Equivalent to Q9CDB7|ML0093 hypothetical protein from Mycobacterium leprae (643 aa), FASTA scores: opt: 3751, E(): 0, (85.4% identity in 643 aa overlap). Contains a beta-glycosyltransferase domain A. Note that previously known as glfT. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O53585	No	cell wall and cell processes	ML0093	MMAR_5372	MSMEG_6403	Mb3838c				
NC_000962.3	Mycobrowser_v3	CDS	4276571	4278085	.	+	0	Rv3812	PE_PGRS62	Function unknown. Thought to be involved in virulence.	PE-PGRS family protein PE_PGRS62	Rv3812, (MTV026.17, MTCY409.18c), len: 504 aa. PE_PGRS62, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citations below), similar to many e.g. P96828|Rv0151c|MTCI5.25c (588 aa), FASTA scores: opt: 389, E(): 6.2e-14, (29.2% identity in 473 aa overlap); MTCY7H7B_27; MTCY493_24; MTCY441_4; MTCY39_36; MTCY1A11_4; MTCY359_33; MTCY130_10; MTCY98_9; etc. The transcription of this CDS seems to be activated in macrophages (see Ramakrishnan et al., 2000).	L7N680	No	PE/PPE		MMAR_2458,MMAR_2459,MMAR_2460,MMAR_2973,MMAR_3494		Mb3842				
NC_000962.3	Mycobrowser_v3	CDS	4278394	4279215	.	-	0	Rv3813c	Rv3813c	Function unknown	Conserved protein	Rv3813c, (MTCY409.17), len: 273 aa. Conserved protein, equivalent to Q9CDB9|ML0089 hypothetical protein from Mycobacterium leprae (281 aa) FASTA scores: opt: 1479, E(): 9.6e-81, (80.45% identity in 271 aa overlap); and similar to Q98LI0|MLL1014 from (280 aa). Also similar to many hypothetical proteins from several organisms e.g. Q9ZBX2|SCD78.27c from Streptomyces coelicolor (280 aa), FASTA scores: opt: 597, E(): 2.2e-28, (43.25% identity in 266 aa overlap); Q9RXR7|DR0240 from Deinococcus radiodurans (284 aa), FASTA scores: opt: 543, E(): 3.5e-25, (38.65% identity in 264 aa overlap); Q99YH5|SPY1700 from Streptococcus pyogenes (274 aa) FASTA scores: opt: 373, E(): 4.3e-15, (30.75% identity in 270 aa overlap); P70947|YITU from Bacillus subtilis (270 aa) FASTA scores: opt: 353, E(): 6.5e-14, (30.0% identity in 280 aa overlap); etc.	O07810	No	conserved hypotheticals	ML0089	MMAR_5376	MSMEG_6407	Mb3843c				
NC_000962.3	Mycobrowser_v3	CDS	4286721	4287935	.	+	0	Rv3822	Rv3822	Function unknown	Conserved hypothetical protein	Rv3822, (MTCY409.08c), len: 404 aa. Conserved hypothetical protein, similar in part to hypothetical proteins from Mycobacterium leprae: Q9CC62|ML1232 (358 aa) FASTA scores: opt: 601, E(): 1.1e-25, (36.7% identity in 335 aa overlap); and Q49633|B1170_F3_112 (391 aa) FASTA scores: opt: 601, E(): 1.2e-25, (36.25% identity in 347 aa overlap). Also similar to P71862|Rv3539|MTCY03C7.17c PPE family protein from Mycobacterium tuberculosis (479 aa), FASTA scores: opt: 547, E(): 1.3e-22, (38.1% identity in 281 aa overlap); O50440|Rv1184c|MTV005.20c (359 aa); O06828|Rv1430|MTCY493.24c (528 aa); O53642|Rv0159c|MTV032.02c (468 aa); etc.	O07801	No	conserved hypotheticals				Mb3852				
NC_000962.3	Mycobrowser_v3	CDS	4309047	4310396	.	+	0	Rv3835	Rv3835	Unknown	Conserved membrane protein	Rv3835, (MTCY01A6.34c), len: 449 aa. Conserved membrane protein, equivalent to Q9CDC2|ML0081 putative membrane protein from Mycobacterium leprae (450 aa), FASTA scores: opt: 2079, E(): 1.8e-74, (69.35% identity in 457 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WKW5	No	cell wall and cell processes	ML0081,ML0081c	MMAR_5387	MSMEG_6414	Mb3865				
NC_000962.3	Mycobrowser_v3	CDS	4385373	4386308	.	-	0	Rv3900c	Rv3900c	Function unknown	Conserved hypothetical alanine rich protein	Rv3900c, (MTCY15F10.12), len: 311 aa. Conserved hypothetical ala-rich protein, highly similar to N-terminal end of Q10690|YK82_MYCTU|Rv2082|MTCY49.21 hypothetical 73.6 KDA protein from Mycobacterium tuberculosis (721 aa), FASTA scores: opt: 592, E(): 2.7e-22, (37.15% identity in 280 aa overlap). Note that MTCY15F10.12 and MTCY15F10.13 appear frameshifted with respect to MTCY49.21 although the sequence appears to be correct. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O05445	No	conserved hypotheticals				Mb3930c				
NC_000962.3	Mycobrowser_v3	CDS	4281647	4282402	.	+	0	Rv3817	Rv3817	Function unknown; probably involved in cellular metabolism [catalytic activity: ATP + substrate = ADP + substrate 3'-phosphate].	Possible phosphotransferase	Rv3817, (MTCY409.13c), len: 251 aa. Possible phosphotransferase, similar to many phosphotransferases e.g. O53023 kanamycin marker from Escherichia coli (264 aa), FASTA scores: opt: 232, E(): 7.5e-08, (32.4% identity in 247 aa overlap); BAA78209|NEO neomycine phosphotransferase from Drosophila melanogaster (Fruit fly) (264 aa), FASTA scores: opt: 227, E(): 1.6e-07, (32.0% identity in 247 aa overlap); AAG09774 aminoglycoside 3'-phosphotransferase from Vibrio cholerae (264 aa), FASTA scores: opt: 227, E(): 1.6e-07, (32.0% identity in 247 aa overlap); P00552|KKA2_KLEPN|NEO|KAN aminoglycoside 3'-phosphotransferase from Klebsiella pneumoniae (264 aa), FASTA scores: opt: 227, E(): 1.6e-07, (32.0% identity in 247 aa overlap); etc.	O07806	No	intermediary metabolism and respiration	ML0086,ML0086c	MMAR_5380		Mb3847				
NC_000962.3	Mycobrowser_v3	CDS	4282449	4283999	.	+	0	Rv3818	Rv3818	Unknown	Unknown protein	Rv3818, (MTCY409.12c), len: 516 aa. Unknown protein.	P9WH21	No	conserved hypotheticals	ML0085,ML0085c	MMAR_5381	MSMEG_6410	Mb3848				
NC_000962.3	Mycobrowser_v3	CDS	4284419	4285825	.	-	0	Rv3820c	papA2	Involved in sulfolipid-1 (SL-1) biosynthesis	Possible conserved polyketide synthase associated protein PapA2	Rv3820c, (MTCY409.10), len: 468 aa. Possible papA2, conserved polyketide synthase (PKS) associated protein, highly similar to Q49618|PAPA3|ML1230|B1170_C1_180 PKS-associated protein A3 from Mycobacterium leprae (471 aa), FASTA scores: opt: 1660, E(): 2.7e-102, (53.95% identity in 456 aa overlap). Also similar to Q9F2R3|SCD65.19c hypothetical 52.8 KDA protein from Streptomyces coelicolor (473 aa), FASTA scores: opt: 575, E(): 1.8e-30, (27.8% identity in 464 aa overlap); and weakly similar to part of other proteins. Also high similarity with other PKS-associated proteins from Mycobacterium tuberculosis; O50438|PAPA3|Rv1182|MTV005.18 (472 aa), FASTA scores: opt: 1694, E(): 1.5e-104, (53.8% identity in 461 aa overlap); and O07799|PAPA1|Rv3824c|MTCY409.06 (511 aa), FASTA scores: opt: 1664, E(): 1.6e-102, (53.9% identity in 462 aa overlap); and similar to C-terminal end of O53902|PAPA4|Rv1528c|MTV045.02 (165 aa), FASTA scores: opt: 186, E(): 4.1e-05, (37.9% identity in 66 aa overlap).	P9WIK7	No	lipid metabolism		MMAR_2343	MSMEG_4728	Mb3850c				
NC_000962.3	Mycobrowser_v3	CDS	4285973	4286686	.	+	0	Rv3821	Rv3821	Unknown	Probable conserved integral membrane protein	Rv3821, (MTCY409.09c), len: 237 aa. Probable conserved integral membrane protein, equivalent to Q49630|ML1233|B1170_F2_64 hypothetical 24.4 KDA protein/INTEGRAL MEMBRANE PROTEIN (POTENTIAL) from Mycobacterium leprae (230 aa), FASTA scores: opt: 619, E(): 2.4e-32, (46.65% identity in 240 aa overlap). Shows some similarity to P29466|I1BC_HUMAN|CASP1|IL1BC|IL1BCE (404 aa), FASTA scores: opt: 126, E(): 0.88, (29.05% identity in 155 aa overlap). Also highly similar to P71796|Rv1517|MTCY277.39 HYPOTHETICAL 26.9 KDA PROTEIN from Mycobacterium tuberculosis (254 aa), FASTA scores: opt: 284, E(): 5.4e-11, (36.35% identity in 256 aa overlap). Start site chosen on basis of similarity to LEPB1170_F2_64 and MTCY277.39, but may extend further upstream. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O07802	No	cell wall and cell processes	ML1233,ML1233c	MMAR_3658	MSMEG_0413	Mb3851				
NC_000962.3	Mycobrowser_v3	CDS	4323499	4323897	.	+	0	Rv3849	espR	Involved in transcriptional mechanism. Regulates transcription of genes required for ESX-1 system.	ESX-1 transcriptional regulatory protein EspR	Rv3849, (MTCY01A6.19c), len: 132 aa. EspR, ESX-1 secreted protein regulator (See Raghavan et al., 2008), equivalent to Q9CDC9|ML0069 hypothetical protein from Mycobacterium leprae (132 aa) FASTA scores: opt: 724, E(): 8.7e-41, (83.95% identity in 131 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WJB7	No	regulatory proteins	ML0069,ML0069c	MMAR_5399	MSMEG_6431	Mb3879				
NC_000962.3	Mycobrowser_v3	CDS	4293225	4299605	.	-	0	Rv3825c	pks2	Function unknown; supposedly involved in lipid metabolism.	Polyketide synthase Pks2	Rv3825c, (MTCY409.05), len: 2126 aa. pks2, polyketide synthase (see citation below), equivalent to Q9CD78|mas|ML0139 putative mycocerosic synthase from Mycobacterium leprae (2116 aa), FASTA scores: opt: 6828, E(): 0, (63.3% identity in 2128 aa overlap); and Q49624|PKS3|MASA|ML1229|B1170_C2_209 probable mycocerosic acid synthase from Mycobacterium leprae (2118 aa) FASTA scores: opt: 5220, E(): 0, (62.4% identity in 2130 aa overlap); or similar in part to others from Mycobacterium leprae e.g. Q9CB70|ML2354 polyketide synthase (1822 aa) FASTA scores: opt: 2787, E(): 2.1e-145, (34.7% identity in 2135 aa overlap). Also highly similar to Q02251|MCAS_MYCBO|mas mycocerosic acid synthase from Mycobacterium bovis (2110 aa), FASTA scores: opt: 3495, E(): 2.6e-184, (61.65% identity in 2130 aa overlap). Also highly similar to other polyketide synthases from Mycobacterium tuberculosis e.g. O53901|PKS5|Rv1527c|MTV045.01c|MTCY19G5.01 (2108 aa) FASTA scores: opt: 9576, E(): 0, (69.8% identity in 2124 aa overlap); P96291|mas|Rv2940c|MTCY24G1.09|MTCY19H9.08c (2111 aa), FASTA scores: opt: 3518, E(): 1.4e-185, (64.05% identity in 2126 aa overlap); O50437|PKS4|Rv1181|MTV005.17 (1582 aa), FASTA scores: opt: 3461, E(): 1.6e-182, (64.55% identity in 1609 aa overlap); etc. Contains PS00606 Beta-ketoacyl synthases active site and PS00012 Phosphopantetheine attachment site.	P9WQE9	No	lipid metabolism			MSMEG_4727	Mb3855c				
NC_000962.3	Mycobrowser_v3	CDS	4299812	4301566	.	+	0	Rv3826	fadD23	Function unknown, but involved in lipid degradation.	Probable fatty-acid-AMP ligase FadD23 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)	Rv3826, (MTCY409.04c), len: 584 aa. Probable fadD23, fatty-acid-AMP synthetase, highly similar to P71495 acyl-CoA synthase from Mycobacterium bovis (582 aa), FASTA scores: opt: 2571, E(): 4.4e-146, (66.15% identity in 576 aa overlap); Q9CD79|FADD28|ML0138 acyl-CoA synthetase from Mycobacterium leprae (579 aa) FASTA scores: opt: 2520, E(): 4.9e-143, (65.2% identity in 575 aa overlap); P54200|FD21_MYCLE putative fatty-acid--CoA ligase (acyl-CoA synthetase) from Mycobacterium leprae (579 aa), FASTA scores: opt: 2330, E(): 1.1e-131, (60.2% identity in 578 aa overlap); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. P96290|FADD28|Rv2941|MTCY24G1.08c (580 aa), FASTA scores: opt: 2587, E(): 4.9e-147, (66.5% identity in 576 aa overlap); O53903|FADD24|Rv1529|MTV045.03 (584 aa), FASTA scores: opt: 2457, E(): 2.9e-139, (63.35% identity in 584 aa overlap); Q50586|FADD25|Rv1521|MT1572|MTCY19G5.07 (583 aa) FASTA scores: opt: 2389, E(): 3.3e-135, (61.45% identity in 581 aa overlap); etc.	P9WQ47	No	lipid metabolism			MSMEG_4731	Mb3856				
NC_000962.3	Mycobrowser_v3	CDS	4306867	4307658	.	+	0	Rv3833	Rv3833	Involved in a transcriptional mechanism.	Transcriptional regulatory protein (probably AraC-family)	Rv3833, (MTCY01A6.36c), len: 263 aa. Probable transcriptional regulator belonging to araC family, similar to others e.g. Q9KYN4|SC9H11.05 putative AraC-family transcriptional regulator from Streptomyces coelicolor (289 aa), FASTA scores: opt: 754, E(): 1.2e-42, (50.45% identity in 232 aa overlap); Q9HXH2|PA3830 probable transcriptional regulator from Pseudomonas aeruginosa (270 aa), FASTA scores: opt: 501, E(): 6.2e-26, (34.85% identity in 238 aa overlap); Q9HX87|PA3927 probable transcriptional regulator from Pseudomonas aeruginosa (262 aa), FASTA scores: opt: 496, E(): 1.3e-25, (36.45% identity in 266 aa overlap); P76241|YEAM_ECOLI|B1790 hypothetical transcriptional regulator from Escherichia coli strain K12 (273 aa) FASTA scores: opt: 388, E(): 1.9e-18, (30.5% identity in 223 aa overlap); etc. Contains probable helix-turn-helix motif from aa 164-185, Score 2014 (+6.05 SD). Seems to belong to the AraC/XylS family of transcriptional regulators.	P96245	No	regulatory proteins				Mb3863				
NC_000962.3	Mycobrowser_v3	CDS	4325495	4325968	.	+	0	Rv3853	rraA	Binds to RNASE E and inhibits RNASE E endonucleolytic cleavages	Regulator of RNase E activity a RraA	Rv3853, (MTCY01A6.15c), len: 157 aa. RraA, regulator of RNase E activity A, equivalent to Q9CDD2|RRAA|ML0066 rraA, regulator of RNase E activity a from Mycobacterium leprae (157 aa) FASTA scores: opt: 896, E(): 1.3e-49, (87.1% identity in 155 aa overlap). Also similar to others e.g. P32165|RRAA_ECOLI|B3929|Z5476|ECS4856 from Escherichia coli strain K12 (161 aa), FASTA scores: opt: 428, E(): 3.7e-20, (45.65% identity in 149 aa overlap); etc. Previously known as menG.	P9WGY3	No	regulatory proteins	ML0066,ML0066c	MMAR_5403	MSMEG_6439	Mb3883				
NC_000962.3	Mycobrowser_v3	CDS	4303398	4305008	.	-	0	Rv3829c	Rv3829c	Function unknown; probably involved in cellular metabolism.	Probable dehydrogenase	Rv3829c, (MTCY409.01, MTCY01A6.40), len: 536 aa. Probable oxidoreductase dehydrogenase, similar to others e.g. Q9A3T1|CC3121 phytoene dehydrogenase-related protein from Caulobacter crescentus (543 aa), FASTA scores: opt: 607, E(): 9.2e-28, (28.25% identity in 552 aa overlap); Q98FP6|MLR3676 phytoene dehydrogenase from Rhizobium loti (Mesorhizobium loti) (521 aa), FASTA scores: opt: 605, E(): 1.2e-27, (28.2% identity in 546 aa overlap); Q97W24|SSO2422 phytoene dehydrogenase related protein from Sulfolobus solfataricus (518 aa), FASTA scores: opt: 388, E(): 4.4e-15, (27.35% identity in 530 aa overlap); Q98BS8|MLL5443 probable dehydrogenase from Rhizobium loti (Mesorhizobium loti) (524 aa), FASTA scores: opt: 374, E(): 2.9e-14, (24.35% identity in aa overlap); etc. Also similar to MTCY493.22c|Rv1432|MTCY493.22c hypothetical 50.5 KDA protein (probable dehydrogenase) from Mycobacterium tuberculosis (25.1% identity in 295 aa overlap).	O07794	No	intermediary metabolism and respiration		MMAR_5383	MSMEG_0664	Mb3859c				
NC_000962.3	Mycobrowser_v3	CDS	4305056	4305685	.	-	0	Rv3830c	Rv3830c	Involved in transcriptional mechanism.	Transcriptional regulatory protein (probably TetR-family)	Rv3830c, (MTCY01A6.39), len: 209 aa. Probable transcriptional regulator TetR family, similar to others e.g. P39885|TCMR_STRGA tetracenomycin C transcriptional repressor from Streptomyces glaucescens (226 aa) FASTA scores: opt: 255, E(): 6.1e-10, (33.65% identity in 202 aa overlap); Q9RDR0|SC4A7.02 putative transcriptional regulator from Streptomyces coelicolor (227 aa) FASTA scores: opt: 230, E(): 2.8e-08, (30.05% identity in 213 aa overlap); Q9EWU3|3SC5B7.06 putative regulatory protein from Streptomyces coelicolor (244 aa), FASTA scores: opt: 221, E(): 1.2e-07, (32.05% identity in 181 aa overlap); Q9AJ68|BUTR putative transcriptional repressor from Streptomyces cinnamonensis (268 aa), FASTA scores: opt: 216, E(): 2.7e-07, (37.8% identity in 119 aa overlap); etc. Contains possible helix-turn-helix motif from aa 33-54, Score 1699 (+4.97 SD). Seems to belong to the TetR/AcrR family of transcriptional regulators.	P96248	No	regulatory proteins		MMAR_5384		Mb3860c				
NC_000962.3	Mycobrowser_v3	CDS	4306236	4306811	.	-	0	Rv3832c	Rv3832c	Function unknown	Conserved protein	Rv3832c, (MTCY01A6.37), len: 191 aa. Conserved protein, similar in part to various proteins e.g. Q9XBC9|CZA382.22c putative rRNA methylase from Amycolatopsis orientalis (259 aa), FASTA scores: opt: 196, E(): 1.3e-05, (38.2% identity in 110 aa overlap); CAC48459|SMB20059 conserved hypothetical protein from Rhizobium meliloti (Sinorhizobium meliloti) plasmid pSymB (259 aa), FASTA scores: opt: 188, E(): 4.3e-05, (33.8% identity in 136 aa overlap); Q98FP8|MLL3672 methyl transferase-like protein from Rhizobium loti (Mesorhizobium loti) (264 aa), FASTA scores: opt: 180, E(): 0.00014, (32.05% identity in 156 aa overlap); etc.	P96246	No	conserved hypotheticals		MMAR_2358		Mb3862c				
NC_000962.3	Mycobrowser_v3	CDS	4321538	4322071	.	+	0	Rv3847	Rv3847	Unknown	Hypothetical protein	Rv3847, (MTCY01A6.21c), len: 177 aa. Conserved hypothetical protein, equivalent to Q9CDC7|ML0071 hypothetical protein from Mycobacterium leprae (177 aa) FASTA scores: opt: 1149, E(): 1.6e-64, (96.6% identity in 177 aa overlap); and Q9F9R0 hypothetical 18.5 KDA protein from Mycobacterium paratuberculosis (177 aa), FASTA scores: opt: 1139, E(): 6.8e-64, (96.6% identity in 177 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P96230	No	conserved hypotheticals	ML0071,ML0071c	MMAR_5397	MSMEG_6428	Mb3877				
NC_000962.3	Mycobrowser_v3	CDS	4386365	4386814	.	-	0	Rv3901c	Rv3901c	Unknown	Possible membrane protein	Rv3901c, (MTCY15F10.11), len: 149 aa. Possible membrane protein (hydrophobic stretch from ~30-52), showing some similarity with O53200|Rv2473|MTV008.29 hypothetical 25.1 KDA protein from Mycobacterium tuberculosis (238 aa), FASTA scores: opt: 147, E(): 0.036, (31.35% identity in 134 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O05444	No	cell wall and cell processes		MMAR_3063,MMAR_3065,MMAR_3073		Mb3931c				
NC_000962.3	Mycobrowser_v3	CDS	4310401	4310814	.	+	0	Rv3836	Rv3836	Function unknown	Conserved hypothetical protein	Rv3836, (MTCY01A6.33c), len: 137 aa. Conserved hypothetical protein, highly similar to Q9RKJ2|SCD25.30 hypothetical 13.1 KDA protein from Streptomyces coelicolor (116 aa), FASTA scores: opt: 395, E(): 3.3e-19, (54.4% identity in 114 aa overlap); and similar to CAC47753|SMC0379 conserved hypothetical protein from Rhizobium meliloti (Sinorhizobium meliloti) (144 aa) FASTA scores: opt: 194, E(): 6e-06, (33.05% identity in 109 aa overlap); and Q98E37|MLL4425 hypothetical protein from Rhizobium loti (Mesorhizobium loti) (201 aa), FASTA scores: opt: 184, E(): 3.7e-05, (29.75% identity in 121 aa overlap). Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature.	P96242	No	conserved hypotheticals	ML0080,ML0080c	MMAR_5388	MSMEG_6415	Mb3866				
NC_000962.3	Mycobrowser_v3	CDS	4311704	4312669	.	-	0	Rv3838c	pheA	Involved in L-phenylalanine biosynthesis [catalytic activity: prephenate = phenylpyruvate + H(2)O + CO(2)].	Prephenate dehydratase PheA	Rv3838c, (MTCY01A6.31), len: 321 aa. PheA, prephenate dehydratase (see citation below), equivalent to Q9CDC4|PHEA|ML0078 putative prephenate dehydratase from Mycobacterium leprae (322 aa), FASTA scores: opt: 1690, E(): 1.3e-93, (84.25% identity in 311 aa overlap). Also highly similar to others e.g. P10341|PHEA_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (315 aa), FASTA scores: opt: 843, E(): 4e-43, (45.8% identity in 308 aa overlap); Q9ZBX0|SCD78.29c from Streptomyces coelicolor (310 aa), FASTA scores: opt: 820, E(): 9.2e-42, (46.45% identity in 312 aa overlap); Q44104|PHEA_AMYME|PDT from Amycolatopsis methanolica (304 aa), FASTA scores: opt: 707, E(): 4.9e-35, (45.7% identity in 313 aa overlap); etc. Contains PS00858 Prephenate dehydratase signature 2.	P9WIC3	No	intermediary metabolism and respiration	ML0078	MMAR_5390	MSMEG_6418	Mb3868c				
NC_000962.3	Mycobrowser_v3	CDS	4312765	4313541	.	+	0	Rv3839	Rv3839	Function unknown	Conserved hypothetical protein	Rv3839, (MTCY01A6.30c), len: 258 aa. Conserved hypothetical protein, similar in part to Q9RD78|SCF43.10cfrom hypothetical 25.8 KDA protein Streptomyces coelicolor (241 aa), FASTA scores: opt: 270, E(): 3.2e-10, (33.45% identity in 272 aa overlap); and O00320|F25451_2 hypothetical protein from Homo sapiens (Human) (339 aa), FASTA scores: opt: 126, E(): 0.77, (28.75% identity in 240 aa overlap).	P96239	No	conserved hypotheticals	ML0077,ML0077c	MMAR_5391	MSMEG_6419	Mb3869				
NC_000962.3	Mycobrowser_v3	CDS	4342770	4343321	.	+	0	Rv3867	espH	Function unknown	ESX-1 secretion-associated protein EspH	Rv3867, (MTV027.02), len: 183 aa. EspH, ESX-1 secretion-associated protein, highly similar to the hypothetical proteins from Mycobacterium leprae: Q9CDD6|ML0056 (169 aa) FASTA scores: opt: 403, E(): 1.8e-18, (48.2% identity in 166 aa overlap); Q49730|ML0407|B1620_C3_264|MLCL383.03 (216 aa), FASTA scores: opt: 517, E(): 1.7e-25, (51.45% identity in 175 aa overlap); and O33090|MLCB628.19c (338 aa), FASTA scores: opt: 403, E(): 3.4e-18, (48.2% identity in 166 aa overlap). Also highly similar to O06269|Rv3614c|MTCY07H7B.08 hypothetical 19.8 KDA protein from Mycobacterium tuberculosis (184 aa), FASTA scores: opt: 559, E(): 3.4e-28, (54.35% identity in 173 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O69732	No	cell wall and cell processes	ML0056c	MMAR_5442	MSMEG_0058,MSMEG_0080	Mb3897				
NC_000962.3	Mycobrowser_v3	CDS	4314178	4314723	.	+	0	Rv3841	bfrB	Involved in iron storage; ferritin is an intracellular molecule that stores iron in a soluble, nontoxic, readily available form. The functional molecule, which is composed of 24 chains, is roughly spherical and contains a central cavity in which the polymeric ferric iron core is deposited.	Bacterioferritin BfrB	Rv3841, (MTCY01A6.28c), len: 181 aa. bfrB, bacterioferritin, similar to other ferritin or hypothetical proteins e.g. O26261|MTH158|RSGA ferritin like protein from Methanothermobacter thermautotrophicus (171 aa), FASTA scores: opt: 277, E(): 6.6e-11, (30.1% identity in 166 aa overlap); Q99SZ3|SA1709 hypothetical protein from Staphylococcus aureus subsp. aureus N315 (166 aa), FASTA scores: opt: 275, E(): 8.7e-11, (33.35% identity in 156 aa overlap); Q9X0L2|TM1128 ferritin from Thermotoga maritima (164 aa), FASTA scores: opt: 247, E(): 5.3e-09, (25.65% identity in 156 aa overlap); Q9KDT7|BH1124 ferritin from Bacillus halodurans (169 aa), FASTA scores: opt: 246, E(): 6.3e-09, (28.95% identity in 152 aa overlap); O29424|AF0834 putative ferritin from Archaeoglobus fulgidu (169 aa), FASTA scores: opt: 246, E(): 6.3e-09, (28.95% identity in 152 aa overlap); etc. Also shows similarity with Rv1876|MTCY180.42|BFRA probable bacterioferritin from Mycobacterium tuberculosis (159 aa). Seems belong to the bacterioferritin family.	P9WNE5	No	intermediary metabolism and respiration	ML0075,ML0075c	MMAR_5393	MSMEG_6422	Mb3871				
NC_000962.3	Mycobrowser_v3	CDS	4314738	4315562	.	-	0	Rv3842c	glpQ1	Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols [catalytic activity: a glycerophosphodiester + H(2)O = an alcohol + SN-glycerol 3-phosphate].	Probable glycerophosphoryl diester phosphodiesterase GlpQ1 (glycerophosphodiester phosphodiesterase)	Rv3842c, (MTCY01A6.27), len: 274 aa. Probable glpQ1, glycerophosphoryl diester phosphodiesterase, equivalent to Q9CDC5|GLPQ|ML0074 putative glycerophosphoryl diester phosphodiesterase from Mycobacterium leprae (271 aa), FASTA scores: opt: 1635, E(): 1.9e-100, (88.85% identity in 269 aa overlap). Also highly similar to others e.g. CAC44700|SCBAC25E3.13c putative phosphodiesterase from Streptomyces coelicolor (275 aa), FASTA scores: opt: 413, E(): 5.7e-20, (48.05% identity in 258 aa overlap); P37965|GLPQ_BACSU glycerophosphoryl diester phosphodiesterase from Bacillus subtilis (293 aa), FASTA scores: opt: 405, E(): 2e-19, (31.3% identity in 249 aa overlap); Q99VC9|GLPQ|SA0820 glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus subsp. aureus N315 (309 aa) FASTA scores: opt: 341, E(): 3.5e-15, (29.3% identity in 273 aa overlap); etc.	P9WMU3	No	intermediary metabolism and respiration	ML0074		MSMEG_6423	Mb3872c				
NC_000962.3	Mycobrowser_v3	CDS	4315568	4316596	.	-	0	Rv3843c	Rv3843c	Unknown	Probable conserved transmembrane protein	Rv3843c, (MTCY01A6.26), len: 342 aa. Probable conserved transmembrane protein, equivalent to Q9CDC6|ML0073 putative membrane protein from Mycobacterium leprae (344 aa), FASTA scores: opt: 1420, E(): 2.6e-68, (63.05% identity in 349 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P96235	No	cell wall and cell processes	ML0073	MMAR_5395	MSMEG_6424	Mb3873c				
NC_000962.3	Mycobrowser_v3	CDS	4320704	4321327	.	+	0	Rv3846	sodA	Destroys radicals which are normally produced within the cells and are toxic to biological systems [catalytic activity: 2 peroxide radical + 2 H(+) = O(2) + H(2)O(2)].	Superoxide dismutase [FE] SodA	Rv3846, (MTCY01A6.22c), len: 207 aa. SodA (alternate gene names: sodB, sod), superoxide dismutase (see citations below), equivalent to many e.g. P47201|SODM_MYCAV|soda|sod from Mycobacterium avium (206 aa), FASTA scores: opt: 1210, E(): 1.8e-73, (82.5% identity in 206 aa overlap); Q9F9R1|sod from Mycobacterium paratuberculosis (207 aa), FASTA scores: opt: 1207, E(): 2.9e-73, (81.65% identity in 207 aa overlap); O86165|SODM_MYCLP|soda|sod from Mycobacterium lepraemurium (206 aa), FASTA scores: opt: 1204, E(): 4.5e-73, (82.05% identity in 206 aa overlap); P13367|SODM_MYCLE|soda|ML0072 from Mycobacterium leprae (206 aa), FASTA scores: opt: 1169, E(): 9.6e-71, (80.5% identity in 205 aa overlap); etc. Contains PS00088 Manganese and iron superoxide dismutases signature. Belongs to the iron/manganese superoxide dismutase family. Although found extracellularly, no signal sequence is present. An alternative secretory pathway may be used.	P9WGE7	No	virulence, detoxification, adaptation	ML0072,ML0072c	MMAR_5396	MSMEG_6427,MSMEG_6636	Mb3876				
NC_000962.3	Mycobrowser_v3	CDS	4324015	4324671	.	+	0	Rv3850	Rv3850	Function unknown	Conserved protein	Rv3850, (MTCY01A6.18c), len: 218 aa. Conserved protein, equivalent to Q9CDD0|ML0068 hypothetical protein from Mycobacterium leprae (238 aa) FASTA scores: opt: 1071, E(): 7.2e-55, (78.35% identity in 217 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P96227	No	conserved hypotheticals	ML0068,ML0068c	MMAR_5400	MSMEG_6434	Mb3880				
NC_000962.3	Mycobrowser_v3	CDS	4327549	4328199	.	+	0	Rv3855	ethR	Regulates negatively the production of ETHA. Induced ETH resistance when overexpressed in Mycobacterium tuberculosis.	Transcriptional regulatory repressor protein (TetR-family) EthR	Rv3855, (MTCY01A6.13c), len: 216 aa. EthR (alternate gene names: aka, etaR), regulatory protein TetR family, involved in ethionamide sensitivity/resistance, negatively controls neighbouring ethA (Rv3854c, MTCY01A6.14; alternate gene names: aka etaA) (see citations below). Equivalent to Q9CDD3|ML0064 putative transcriptional regulator from Mycobacterium leprae (214 aa), FASTA scores: opt: 1017, E(): 7e-62, (77.0% identity in 213 aa overlap). Also similar to other transcriptional regulator e.g. Q9S1R1|SCJ9A.09 putative TetR-family transcriptional regulator from Streptomyces coelicolor (204 aa), FASTA scores: opt: 305, E(): 1.2e-13, (34.5% identity in 200 aa overlap); Q9KYT9|SCE22.24 putative TetR-family transcriptional regulator (fragment) from Streptomyces coelicolor (244 aa), FASTA scores: opt: 179, E(): 4.9e-05, (35.5% identity in 93 aa overlap); Q9RUK2|DR1384 transcriptional regulator (TetR family) from Deinococcus radiodurans (196 aa), FASTA scores: opt: 167, E(): 0.00026, (41.75% identity in 79 aa overlap); etc. Also similar to P95100|Rv3058c|MTCY22D7.23 hypothetical 23.8 KDA protein from Mycobacterium tuberculosis (216 aa) FASTA scores: opt: 261, E(): 1.2e-10, (31.65% identity in 221 aa overlap); and O08377|Rv1534|MTCY07A7A.03 hypothetical 24.5 KDA protein from Mycobacterium tuberculosis (225 aa), FASTA scores: opt: 164, E(): 0.00047, (25.5% identity in 248 aa overlap). Contains helix-turn-helix motif at aa 45-66, Score 1320 (+3.68 SD). Belongs to the TetR/AcrR family of transcriptional regulators.	P9WMC1	No	regulatory proteins	ML0064,ML0064c	MMAR_5405	MSMEG_6441	Mb3885				
NC_000962.3	Mycobrowser_v3	CDS	4328401	4329408	.	-	0	Rv3856c	Rv3856c	Function unknown	Conserved hypothetical protein	Rv3856c, (MTCY01A6.12), len: 335 aa. Conserved hypothetical protein, highly similar to various proteins from diverse organisms e.g. Q9EWR3|3SCF60.21 conserved hypothetical protein from Streptomyces coelicolor (372 aa) FASTA scores: opt: 1286, E(): 2.4e-73, (64.0% identity in 336 aa overlap); P72464|ORF1 from Streptomyces lividans (343 aa), FASTA scores: opt: 1275, E(): 1.1e-72, (60.1% identity in 336 aa overlap); Q9K899|BH3107 DNA-dependent DNA polymerase beta chain from Bacillus halodurans (571 aa), FASTA scores: opt: 592, E(): 1.2e-29, (39.15% identity in 240 aa overlap); etc. May be a DNA polymerase beta (gene name: yshC) (see citation below).	P96221	No	conserved hypotheticals	ML0063	MMAR_5407	MSMEG_6445	Mb3886c				
NC_000962.3	Mycobrowser_v3	CDS	4346481	4348724	.	+	0	Rv3870	eccCa1	Unknown	ESX conserved component EccCa1. ESX-1 type VII secretion system protein. Possible transmembrane protein.	Rv3870, (MTV027.05), len: 747 aa. EccCa1, esx conserved component, ESX-1 type VII secretion system protein, possible transmembrane protein, equivalent to O33087|ML0053|MLCB628.16c putative membrane protein from Mycobacterium leprae (744 aa), FASTA scores: opt: 4333, E(): 0, (85.4% identity in 746 aa overlap); and similar to N-terminal end of others e.g. Q9CD30|ML2535 hypothetical protein from Mycobacterium leprae (1329 aa), FASTA scores: opt: 1003, E(): 1e-52, (33.65% identity in 725 aa overlap); O86653|SC3C3.20c ATP/GTP binding protein from Streptomyces coelicolor (1321 aa), FASTA scores: opt: 1078, E(): 3e-57, (35.4% identity in 774 aa overlap); P71068|YUKA YUKA protein from Bacillus subtilis (1207 aa) FASTA scores: opt: 529, E(): 4.3e-24, (26.1% identity in 636 aa overlap); Q9KE81|BH0975 hypothetical protein from Bacillus halodurans (1489 aa), FASTA scores: opt: 455, E(): 1.5e-19, (27.1% identity in 734 aa overlap); etc. Also similar to N-terminal end of hypothetical proteins from Mycobacterium tuberculosis e.g. O53689|Rv0284|MTV035.12 (1330 aa), FASTA scores: opt: 982, E(): 1.9e-51, (33.8% identity in 719 aa overlap); O06264|Rv3447c|MTCY77.19c (1236 aa), FASTA scores: opt: 761, E(): 4.1e-38, (38.2% identity in 746 aa overlap); O53935|Rv1784|MTV049.06 (932 aa), FASTA scores: opt: 547, E(): 2.8e-25, (36.25% identity in 276 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop). Note some similarity (with hypothetical proteins from Mycobacterium tuberculosis and P71068|YUKA) continues in downstream ORF MTV027.06.	P9WNB3	No	cell wall and cell processes	ML0053c	MMAR_5445	MSMEG_0061	Mb3900				
NC_000962.3	Mycobrowser_v3	CDS	4351075	4352181	.	+	0	Rv3873	PPE68	Function unknown	PPE family protein PPE68	Rv3873, (MTV027.08), len: 368 aa. PPE68, Member of the Mycobacterium tuberculosis PPE family, highly similar to many e.g. O33085|ML0051|MLCB628.14c from Mycobacterium leprae (302 aa), FASTA scores: opt: 656, E(): 2.8e-24, (46.2% identity in 288 aa overlap); and O53691|Rv0286|MTV035.14 (513 aa), FASTA scores: opt: 566, E(): 7.8e-20, (35.25% identity in 363 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004). Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WHW9	No	PE/PPE	ML0051,ML0051c	MMAR_5448	MSMEG_0064	Mb3903				
NC_000962.3	Mycobrowser_v3	CDS	4383653	4383985	.	-	0	Rv3898c	Rv3898c	Function unknown	Conserved hypothetical protein	Rv3898c, (MTCY15F10.14), len: 110 aa. Conserved hypothetical protein. Highly similar, but in part, to Q10691|YK83_MYCTU|Rv2083|MT2145|MTCY49.22 hypothetical 30.8 KDA protein from Mycobacterium tuberculosis (314 aa) FASTA scores: opt: 204, E(): 0.00042, (50.6% identity in 81 aa overlap). Similarity suggests it should be in frame with next ORF and that the stop codon could be read through, the sequence appears to be correct. Homology lost upstream at 15138 gatc sequence may suggest discontinuity due to chimerism in cY15F10 or cY49.	O05447	No	conserved hypotheticals				Mb3927c				
NC_000962.3	Mycobrowser_v3	CDS	4337946	4338272	.	+	0	Rv3861	Rv3861	Unknown	Hypothetical protein	Rv3861, (MTCY01A6.07c), len: 108 aa. Hypothetical unknown protein. Overlaps in part next ORF Rv3862c|whiB6.	P96216	No	conserved hypotheticals				Mb3891				
NC_000962.3	Mycobrowser_v3	CDS	4331498	4336081	.	-	0	Rv3859c	gltB	Probably involved in glutamate biosynthesis [catalytic activity: 2 L-glutamate + NADP(+) = L-glutamine + 2-oxoglutarate + NADPH].	Probable ferredoxin-dependent glutamate synthase [NADPH] (large subunit) GltB (L-glutamate synthase) (L-glutamate synthetase) (NADH-glutamate synthase) (glutamate synthase (NADH))(NADPH-GOGAT)	Rv3859c, (MTCY01A6.09), len: 1527 aa. Probable gltB, ferredoxin-dependent glutamate synthase large subunit, equivalent to Q9CDD5|GLTB|ML0061 putative ferredoxin-dependent glutamate synthase from Mycobacterium leprae (1527 aa), FASTA scores: opt: 9277, E(): 0, (90.25% identity in 1527 aa overlap). Also highly similar to many e.g. Q9S2Y9|SC3A3.04c from Streptomyces coelicolor (1514 aa), FASTA scores: opt: 5939, E(): 0, (64.3% identity in 1544 aa overlap); Q9Z465|GLTB from Corynebacterium glutamicum (Brevibacterium flavum) (1510 aa), FASTA scores: opt: 5790, E(): 0, (63.25% identity in 1534 aa overlap); P39812|GLTB_BACSU|GLTA from Bacillus subtilis (1520 aa), FASTA scores: opt: 3445, E(): 2.8e-196, (52.25% identity in 1531 aa overlap); etc. Similar to other glutamate synthases.	P96218	No	intermediary metabolism and respiration	ML0061		MSMEG_6459	Mb3889c				
NC_000962.3	Mycobrowser_v3	CDS	4338171	4338521	.	-	0	Rv3862c	whiB6	Involved in transcriptional mechanism.	Possible transcriptional regulatory protein WhiB-like WhiB6	Rv3862c, (MTCY01A6.06), len: 116 aa. Possible whiB6 (alternate gene name: whmF), WhiB-like regulatory protein (see citation below), similar to WhiB paralogue of Streptomyces coelicolor, wblE gene product (85 aa). Shows similarity with Q49765|WHIB7|ML0639|B1937_F2_68 putative transcriptional regulator WHIB7 from Mycobacterium leprae (89 aa) FASTA scores: opt: 112, E(): 0.49, (41.2% identity in 51 aa overlap). Some similarity to Q9AD55|SCP1.95 putative regulatory protein from Streptomyces coelicolor (102 aa) FASTA scores: opt: 129, E(): 0.038, (32.95% identity in 85 aa overlap); AAK47632|MT3290.1 conserved hypothetical protein from Mycobacterium tuberculosis strain CDC1551 (96 aa), FASTA scores: opt: 126, E(): 0.058, (33.35% identity in 84 aa overlap); Q9FC80|SC4B10.07 conserved hypothetical protein from Streptomyces coelicolor (88 aa), FASTA scores: opt: 119, E(): 0.16, (44.65% identity in 70 aa overlap); Q9K4K8|SC5F8.16c regulatory protein from Streptomyces coelicolor (83 aa), FASTA scores: opt: 114, E(): 0.34, (37.05% identity in 54 aa overlap); etc.	P9WF37	No	regulatory proteins		MMAR_5437	MSMEG_0051	Mb3892c				
NC_000962.3	Mycobrowser_v3	CDS	4338849	4340027	.	+	0	Rv3863	Rv3863	Unknown	Unknown alanine rich protein	Rv3863, (MTCY01A6.05c), len: 392 aa. Unknown ala-rich protein.	P96214	No	conserved hypotheticals	ML0059,ML0059c	MMAR_5438		Mb3893				
NC_000962.3	Mycobrowser_v3	CDS	4363417	4364757	.	-	0	Rv3883c	mycP1	Has proteolytic activity. Cleaves ESPB|Rv3881c. Expressed during infection of macrophages.	Membrane-anchored mycosin MycP1 (serine protease) (subtilisin-like protease) (subtilase-like) (mycosin-1)	Rv3883c, (MTCY15F10.29), len: 446 aa. MycP1, membrane-anchored serine protease (mycosin) (see citations below), equivalent to O33076|ML0041|MLCB628.04 probable secreted protease from Mycobacterium leprae (446 aa), FASTA scores: opt: 2448, E(): 1.5e-124, (79.15% identity in 446 aa overlap); and highly similar, but in part, to several putative proteases from Mycobacterium leprae; Q9CBV3|ML1538 (567 aa) FASTA scores: opt: 902, E(): 3e-41, (37.25% identity in 556 aa overlap); and Q9CD36|ML2528 (475 aa), FASTA scores: opt: 873, E(): 9.4e-40, (42.7% identity in 459 aa overlap). Shows also similarity with several proteases from other organisms e.g. Q9PCD0|XF1851 serine protease from Xylella fastidiosa (1000 aa), FASTA scores: opt: 281, E(): 1.3e-07, (27.95% identity in 422 aa overlap); P42780|BPRX_BACNO extracellular subtilisin-like protease precursor from Bacteroides nodosus (Dichelobacter nodosus) (595 aa), FASTA scores: opt: 270, E(): 3.2e-07, (28.9% identity in 384 aa overlap); Q46541|APRV5 acidic protease V5 from Bacteroides nodosus (Dichelobacter nodosus) (595 aa), FASTA scores: opt: 264, E(): 6.8e-07, (28.65% identity in 384 aa overlap); etc. Also highly similar to various proteins from Mycobacterium tuberculosis e.g. O53695|Rv0291|MTV035.19 probable membrane-anchored mycosin MYCP3 (461 aa), FASTA scores: opt: 1168, E(): 1.2e-55, (44.6% identity in 453 aa overlap); O53945|Rv1796|MTV049.18 probable membrane-anchored mycosin MYCP5 (585 aa), FASTA scores: opt: 928, E(): 1.2e-42, (37.85% identity in 555 aa overlap) (note gap from aa 155-264); and downstream ORF O05458|Rv3886c|MTCY15F10.26 probable membrane-anchored mycosin MYCP2 (550 aa), FASTA scores: opt: 910, E(): 1.1e-41, (40.15% identity in 533 aa overlap) (note partial gap from aa 146-234); etc. Equivalent to AAK48366 from Mycobacterium tuberculosis strain CDC1551 (411 aa) but longer 35 aa. Has signal sequence with possible signal peptidase I cleavage site in residues 19-21 (ASA) and hydrophobic stretch at C-terminus, followed by short positively charged segment, that seems to act as a membrane anchor. Activated by Ca2+ (see Dave et al., 2002). Contains three serine protease, subtilase family active site motifs: a aspartic acid active site motif (PS00136); a histidine active site motif (PS00137); and a serine active site motif (PS00138). Belongs to peptidase family S8 (also known as the subtilase family), pyrolysin subfamily. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	O05461	No	intermediary metabolism and respiration	ML0041	MMAR_5459	MSMEG_0083	Mb3913c				
NC_000962.3	Mycobrowser_v3	CDS	4390437	4390709	.	-	0	Rv3904c	esxE	Unknown	Putative ESAT-6 like protein EsxE (hypothetical alanine rich protein) (ESAT-6 like protein 12)	Rv3904c, (MT4023, MTCY15F10.07), len: 90 aa. EsxE, ESAT-6 like protein, hypothetical unknown ala-rich protein. Belongs to the ESAT6 family (see citation below).	P9WNH9	No	cell wall and cell processes		MMAR_5465	MSMEG_1871	Mb3934c				
NC_000962.3	Mycobrowser_v3	CDS	4341566	4341877	.	+	0	Rv3865	espF	Function unknown	ESX-1 secretion-associated protein EspF	Rv3865, (MTCY01A6.03c), len: 103 aa. EspF, ESX-1 secretion-associated protein, showing some similarity to O06268|Rv3615c|MTCY07H7B.07 hypothetical 10.8 KDA protein from Mycobacterium tuberculosis (103 aa), FASTA scores: opt: 198, E(): 7.5e-07, (36.25% identity in 102 aa overlap); Q49723|ML0406|B1620_C2_214|MLCL383.02 hypothetical 11.1 KDA protein from Mycobacterium leprae (106 aa), FASTA scores: opt: 154, E(): 0.00071, (31.05% identity in 103 aa overlap).	P9WJD1	No	cell wall and cell processes		MMAR_5440		Mb3895				
NC_000962.3	Mycobrowser_v3	CDS	4343314	4345035	.	+	0	Rv3868	eccA1	Function unknown	ESX conserved component EccA1. ESX-1 type VII secretion system protein.	Rv3868, (MTV027.03), len: 573 aa. EccA1, esx conserved component, ESX-1 type VII secretion system protein. Member of the CbxX/CfqX family of hypothetical proteins; C-terminal end is highly similar to many e.g. P40118|CBXC_ALCEU|CBXXC|CFXXC CbxX protein (317 aa) FASTA scores: opt: 572, E(): 3e-24, (42.7% identity in 294 aa overlap); CAC48589 probable CBBX protein from Rhizobium meliloti (Sinorhizobium meliloti) plasmid pSymB (311 aa) FASTA scores: opt: 569, E(): 4.3e-24, (40.05% identity in 292 aa overlap); P95648|CBBX_RHOSH CBBX protein from Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides) (309 aa), FASTA scores: opt: 559, E(): 1.5e-23, (41.4% identity in 290 aa overlap); etc. Equivalent to O33089|Y2G8_MYCLE|ML0055|MLCB628.18c hypothetical 62.3 KDA protein from Mycobacterium leprae (573 aa), FASTA scores: opt: 3330, E(): 3.9e-175, (89.2% identity in 573 aa overlap); and similar to Q9CD28|Y282_MYCLE|ML2537 hypothetical 69.1 KDA protein from Mycobacterium leprae (640 aa), FASTA scores: opt: 943, E(): 2.4e-44, (37.5% identity in 571 aa overlap). Also similar to many proteins from Mycobacterium tuberculosis (strains H37Rv and CDC1551) e.g. O53687|Y282_MYCTU|Rv0282|MT0295|MTV035.10 hypothetical 68.1 KDA protein (631 aa), FASTA scores: opt: 936, E(): 5.8e-44, (39.05% identity in 568 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop).	P9WPH9	No	cell wall and cell processes	ML0055c	MMAR_5443	MSMEG_0059	Mb3898				
NC_000962.3	Mycobrowser_v3	CDS	4350745	4351044	.	+	0	Rv3872	PE35	Function unknown	PE family-related protein PE35	Rv3872, (MTV027.07), len: 99 aa. PE35, Some similarity to Mycobacterium tuberculosis conserved PE family proteins (see Brennan & Delogu 2002), e.g. O69713|Rv3746c|MTV025.094c (111 aa), FASTA scores: opt: 306, E(): 5.5e-13, (50.5% identity in 99 aa overlap). Equivalent to AAK48354 from Mycobacterium tuberculosis strain CDC1551 (112 aa) but shorter 14 aa.	P9WIG7	No	PE/PPE		MMAR_0185,MMAR_5286,MMAR_5447	MSMEG_0063	Mb3902				
NC_000962.3	Mycobrowser_v3	CDS	4352274	4352576	.	+	0	Rv3874	esxB	Unknown. Exported protein cotranscribed with Rv3875|MT3989|MTV027.10.	10 kDa culture filtrate antigen EsxB (LHP) (CFP10)	Rv3874, (MT3988, MTV027.09), len: 100 aa. EsxB, 10 KDA culture filtrate antigen (see citations below, especially first), highly similar to O33084|CF10_MYCLE|ML0050|MLCB628.13c 10 KDA culture filtrate antigen CFP10 homolog from Mycobacterium leprae (99 aa), FASTA scores: opt: 237, E(): 2.4e-08, (39.4% identity in 99 aa overlap). Also similar to O05440|ES6D_MYCTU|Rv3905c|MT4024|MTCY15F10.06 putative ESAT-6 like protein 13 from Mycobacterium tuberculosis (103 aa) FASTA scores: opt: 126, E(): 0.18, (23.1% identity in 91 aa overlap); and shows some similarity with other proteins from Mycobacterium tuberculosis. Contains probable coiled-coil from aa 49-93. Belongs to the ESAT6 family. Note that previously known as lhp (alternate gene name: cfp10). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WNK5	No	cell wall and cell processes	ML0050,ML0050c	MMAR_5449	MSMEG_0065	Mb3904				
NC_000962.3	Mycobrowser_v3	CDS	4352609	4352896	.	+	0	Rv3875	esxA	Unknown. Elicits high level of inf-gamma from memory effector cells during the first phase of a protective immune response. Exported protein cotranscribed with Rv3874|MT3988|MTV027.09|LHP|CFP10.	6 kDa early secretory antigenic target EsxA (ESAT-6)	Rv3875, (MT3989, MTV027.10), len: 95 aa. EsxA, early secretory antigenic target (see citations below), identical to Q57165|O84901|ESAT6 early secretory antigenic target from Mycobacterium bovis (94 aa), FASTA scores: opt: 596, E(): 4.6e-33, (100.0% identity in 94 aa overlap). Also similar to Q50206|ESA6_MYCLE|ESAT6|ESX|L45|ML0049|MLCB628.12c 6 KDA early secretory antigenic target homolog (ESAT-6-like protein) (L-ESAT) from Mycobacterium leprae (95 aa), FASTA scores: opt: 236, E(): 3.3e-09, (36.25% identity in 91 aa overlap); and weak similarity with others proteins ESAT-like from Mycobacterium leprae. Also some similarity with O53266|ES69_MYCTU|Rv3019c|MT3104|MTV012.33c putative secreted ESAT-6 like protein 9 from Mycobacterium tuberculosis (96 aa), FASTA scores: opt: 131, E(): 0.03, (26.15% identity in 88 aa overlap); and other ESAT-like protein. Contains probable coiled-coil from 56 to 92 aa. Belongs to the ESAT6 family. Note that previously known as esat-6. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004). Predicted possible vaccine candidate (See Zvi et al., 2008). EspD|Rv3614c expression but not secretion is required for EsxA|Rv3875 secretion (See Chen et al., 2012).	P9WNK7	No	cell wall and cell processes	ML0049,ML0049c	MMAR_0188,MMAR_5450	MSMEG_0066	Mb3905				
NC_000962.3	Mycobrowser_v3	CDS	4353010	4355010	.	+	0	Rv3876	espI	Function unknown	ESX-1 secretion-associated protein EspI. Conserved proline and alanine rich protein.	Rv3876, (MTV027.11), len: 666 aa. EspI, ESX-1 secretion-associated protein, conserved pro-, ala-rich protein, similar to several proteins from Mycobacterium leprae e.g. Q9CDD8|ML0048 hypothetical protein (586 aa), FASTA scores: opt: 1682, E(): 2.1e-45, (50.75% identity in 672 aa overlap); O33082|MLCB628.11c hypothetical 52.0 KDA protein (478 aa), FASTA scores: opt: 1588, E(): 1.5e-42, (53.5% identity in 542 aa overlap) (also has a proline rich N-terminus); etc. Also similar to other proteins from Mycobacterium tuberculosis, especially in C-terminus, e.g. O06396|Rv0530|MTCY25D10.09 (405 aa), FASTA scores: opt: 670, E(): 2.5e-14, (34.85% identity in 396 aa overlap) (also has Pro-rich N-terminus); etc. Note that N-terminus is repetitive and highly Proline rich.	P9WJC5	No	cell wall and cell processes	ML0048c	MMAR_5451		Mb3906				
NC_000962.3	Mycobrowser_v3	CDS	4372800	4373630	.	-	0	Rv3889c	espG2	Unknown	ESX-2 secretion-associated protein EspG2	Rv3889c, (MTCY15F10.23), len: 276 aa. EspG2, ESX-2 secretion-associated protein.	P9WJC9	No	cell wall and cell processes				Mb3918c				
NC_000962.3	Mycobrowser_v3	CDS	4355007	4356542	.	+	0	Rv3877	eccD1	Unknown	ESX conserved component EccD1. ESX-1 type VII secretion system protein. Probable transmembrane protein.	Rv3877, (MTV027.12), len: 511 aa. EccD1, esx conserved component, ESX-1 type VII secretion system protein, probable transmembrane protein, equivalent to Q9CDD9|ML0047 putative membrane protein from Mycobacterium leprae (512 aa), FASTA scores: opt: 2496, E(): 2.8e-140, (74.0% identity in 512 aa overlap); and highly similar, but longer 32 aa, to O33081|MLCB628.10c hypothetical 51.4 KDA protein from Mycobacterium leprae (480 aa), FASTA scores: opt: 2346, E(): 2e-131, (74.15% identity in 480 aa overlap). Shows also similarity with other membrane proteins from Mycobacterium leprae e.g. Q9CBV2|ML1539 probable membrane protein (503 aa), FASTA scores: opt: 318, E(): 2e-11, (22.7% identity in 520 aa overlap). Also similar to various proteins from Mycobacterium tuberculosis e.g. O53944|Rv1795|MTV049.17 putative membrane protein (503 aa), FASTA scores: opt: 391, E(): 9.4e-16, (24.45% identity in 523 aa overlap); O86362|Rv0290|MTV035.18 hypothetical 47.9 KDA protein (472 aa), FASTA scores: opt: 332, E(): 2.8e-12, (28.1% identity in 509 aa overlap); O05457|Rv3887c|MTCY15F10.25 hypothetical 53.2 KDA protein (509 aa), FASTA scores: opt: 167, E(): 0.017, (24.0% identity in 517 aa overlap); etc. Equivalent to AAK48359 from Mycobacterium tuberculosis strain CDC1551 (479 aa) but longer 32 aa. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WNQ7	No	cell wall and cell processes	ML0047c	MMAR_5452	MSMEG_0068	Mb3907				
NC_000962.3	Mycobrowser_v3	CDS	4357593	4359782	.	-	0	Rv3879c	espK	Unknown	ESX-1 secretion-associated protein EspK. Alanine and proline rich protein.	Rv3879c, (MTV027.14c), len: 729 aa. EspK, ESX-1 secretion-associated protein, ala- and pro-rich protein (N-terminal end is repetitive and highly Proline-rich). There may be an unknown protein Orf14 encoded in the opposite orientation, within rv3879c (See Ahmad et al., 1999; Daugelat et al., 2003).	P9WJC1	No	cell wall and cell processes	ML0045	MMAR_4351,MMAR_5455	MSMEG_0071	Mb3909c				
NC_000962.3	Mycobrowser_v3	CDS	4360199	4360546	.	-	0	Rv3880c	espL	Function unknown	ESX-1 secretion-associated protein EspL	Rv3880c, (MTV027.15c), len: 115 aa. EspL, ESX-1 secretion-associated protein, equivalent to O33080|ML0044|MLCB628.09 hypothetical 12.2 KDA protein from Mycobacterium leprae (113 aa), FASTA scores: opt: 397, E(): 2e-19, (56.35% identity in 110 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WJB9	No	cell wall and cell processes	ML0044	MMAR_5456	MSMEG_0081	Mb3910c				
NC_000962.3	Mycobrowser_v3	CDS	4374049	4374372	.	-	0	Rv3891c	esxD	Function unknown	Possible ESAT-6 like protein EsxD	Rv3891c, (MTCY15F10.21), len: 107 aa (first GTG taken). EsxD, ESAT-6 like protein, equivalent to Q9K547 hypothetical 10.3 KDA protein (fragment) from Mycobacterium paratuberculosis (100 aa), FASTA scores: opt: 498, E(): 1.7e-26, (77.25% identity in 101 aa overlap). Seems to belong to the ESAT6 family (see Gey Van Pittius et al., 2001).	O05453	No	cell wall and cell processes				Mb3920c				
NC_000962.3	Mycobrowser_v3	CDS	4390720	4391031	.	-	0	Rv3905c	esxF	Unknown	Putative ESAT-6 like protein EsxF (hypothetical alanine and glycine rich protein) (ESAT-6 like protein 13)	Rv3905c, (MT4024, MTCY15F10.06), len: 103 aa. EsxF, ESAT-6 like protein (see citation below), hypothetical unknown ala-, gly-rich protein, ESAT-6 like protein. Belongs to the ESAT6 family.	P9WNH7	No	cell wall and cell processes		MMAR_5466		Mb3935c				
NC_000962.3	Mycobrowser_v3	CDS	4366908	4368521	.	-	0	Rv3885c	eccE2	Unknown	ESX conserved component EccE2. ESX-2 type VII secretion system protein. Possible membrane protein.	Rv3885c, (MTCY15F10.27), len: 537 aa. eccE2, esx conserved component, ESX-2 type VII secretion system protein. possible membrane protein (has hydrophobic stretch near N-terminus), showing some similarity with O05462|Rv3882c|MTV027.17c|MTCY15F10.30 possible membrane protein from Mycobacterium tuberculosis (462 aa) FASTA scores: opt: 283, E(): 8.3e-10, (26.55% identity in 414 aa overlap); and O33077|ML0042|MLCB628.05 putative membrane protein from Mycobacterium leprae (467 aa), FASTA scores: opt: 260, E(): 2.1e-08, (28.0% identity in 382 aa overlap). Equivalent to AAK48368 from Mycobacterium tuberculosis strain CDC1551 (422 aa) but longer 115 aa.	P9WJE7	No	cell wall and cell processes	ML0038			Mb3915c				
NC_000962.3	Mycobrowser_v3	CDS	4370155	4371684	.	-	0	Rv3887c	eccD2	Unknown	ESX conserved component EccD2. ESX-2 type VII secretion system protein. Probable transmembrane protein.	Rv3887c, (MTCY15F10.25), len: 509 aa. eccD2, esx conserved component, ESX-2 type VII secretion system protein, probable transmembrane protein (has hydrophilic stretch from ~1-130 then very hydrophobic domain), similar to other membrane proteins and with weak similarity to known transporters, e.g. Q9CBV2|ML1539 probable membrane protein from Mycobacterium leprae (503 aa), FASTA scores: opt: 395, E(): 2.3e-16, (28.0% identity in 496 aa overlap); Q9CD35|ML2529 conserved membrane protein from Mycobacterium leprae (485 aa), FASTA scores: opt: 221, E(): 6.6e-06, (24.6% identity in 423 aa overlap); Q9ADP8|2SC10A7.11 putative integral membrane protein from Streptomyces coelicolor (430 aa), FASTA scores: opt: 171, E(): 0.0062, (26.55% identity in 358 aa overlap); CAC44275|SCBAC17F8.03 putative drug efflux protein from Streptomyces coelicolor (416 aa), FASTA scores: opt: 160, E(): 0.028, (27.85% identity in 323 aa overlap); etc. Also similar to others from Mycobacterium tuberculosis e.g. O53944|Rv1795|MTV049.17 putative membrane protein (503 aa), FASTA scores: opt: 360, E(): 2.9e-14, (26.65% identity in 514 aa overlap); etc. Equivalent to AAK48369 from Mycobacterium tuberculosis strain CDC1551 (469 aa) but longer 40 aa.	P9WNQ5	No	cell wall and cell processes	ML0036			Mb3917c				
NC_000962.3	Mycobrowser_v3	CDS	4371681	4372706	.	-	0	Rv3888c	Rv3888c	Unknown	Probable conserved membrane protein	Rv3888c, (MTCY15F10.24), len: 341 aa. Probable conserved membrane protein, showing similarity with hypothetical proteins from Mycobacterium leprae: O33082|MLCB628.11c (478 aa), FASTA scores: opt: 530, E(): 7.7e-26, (32.45% identity in 336 aa overlap); Q9CDD8|ML0048 (586 aa), FASTA scores: opt: 530, E(): 9.1e-26, (32.45% identity in 336 aa overlap); Q9CCI1|ML0798 (592 aa), FASTA scores: opt: 426, E(): 3e-19, (27.5% identity in 342 aa overlap) (similarity only at C-terminus). Also similar to proteins from Mycobacterium tuberculosis e.g. P96217|Rv3860|MTCY01A6.08c (390 aa), FASTA scores: opt: 603, E(): 1.7e-30, (35.2% identity in 284 aa overlap); O06396|Rv0530|MTCY25D10.09 (405 aa), FASTA scores: opt: 573, E(): 1.3e-28, (32.0% identity in 328 aa overlap); C-terminus of O69740|Rv3876|MTV027.1 (666 aa), FASTA scores: opt: 509, E(): 2.1e-24, (31.0% identity in 303 aa overlap); etc.	O05456	No	cell wall and cell processes	ML0035							
NC_000962.3	Mycobrowser_v3	CDS	4391097	4391606	.	-	0	Rv3906c	Rv3906c	Function unknown	Conserved hypothetical protein	Rv3906c, (MTCY15F10.05), len: 169 aa. Conserved hypothetical protein, strongly related to Q50578|AT9S (sod related in Escherichia coli) from Mycobacterium tuberculosis strain aoyama B (155 aa), but apparently different as flanking sequences differ and shorter 43 aa, FASTA scores: opt: 548, E(): 1.3e-26, (79.4% identity in 102 aa overlap). Selfmarch results suggest that Rv3906c is not related to any other hypothetical protein from Mycobacterium tuberculosis strain H37Rv except itself. Shows also similarity with Q9VFR2|CG9297 hypothetical protein from Drosophila melanogaster (Fruit fly) (930 aa), FASTA scores: opt: 221, E(): 4.9e-06, (36.95% identity in 157 aa overlap); Q9HQ55|CBP|VNG1320G calcium-binding protein homology from Halobacterium sp. strain NRC-1 (385 aa) FASTA scores: opt: 143, E(): 0.13, (35.65% identity in 160 aa overlap); Q24795 calcium-binding protein (fragment) from Echinococcus granulosus (338 aa), FASTA scores: opt: 140, E(): 0.17, (33.95% identity in 156 aa overlap).	O05439	No	conserved hypotheticals	ML0033	MMAR_5470	MSMEG_6925	Mb3936c				
NC_000962.3	Mycobrowser_v3	CDS	4376262	4380452	.	-	0	Rv3894c	eccC2	Unknown	ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein.	Rv3894c, (MTCY15F10.18), len: 1396 aa. EccC2, esx conserved component, ESX-2 type VII secretion system protein, possible membrane protein (possible transmembrane segments from aa ~37-85), similar to Q9CD30|ML2535 hypothetical protein from Mycobacterium leprae (1329 aa), FASTA scores: opt: 652, E(): 2.2e-30, (27.85% identity in 1425 aa overlap); Q9CDD7|ML0052 hypothetical protein from Mycobacterium leprae (597 aa), FASTA scores: opt: 537, E(): 6.6e-24, (27.5% identity in 585 aa overlap) (similarity only with C-terminal end); Q9Z5I2|ML1543|MLCB596.28 possible SPOIIIE-family membrane protein from Mycobacterium leprae (1345 aa), FASTA scores: opt: 523, E(): 8.6e-23, (31.65% identity in 1412 aa overlap). Also similar to various proteins e.g. O86653|SC3C3.20c ATP/GTP binding protein from Streptomyces coelicolor (1321 aa), FASTA scores: opt: 973, E(): 2.8e-49, (28.1% identity in 1409 aa); Q9L0T6|SCD35.15c putative cell division-related protein from Streptomyces coelicolor(1525 aa), FASTA scores: opt: 524, E(): 8.3e-23, (24.95% identity in 1450 aa overlap); Q9KE81|BH0975 hypothetical protein from Bacillus halodurans (1489 aa), FASTA scores: opt: 444, E(): 4.1e-18, (22.5% identity in 1346 aa overlap); etc. Also similar to AAK46103|MT1833 FTSK/SPOIIIE family protein from Mycobacterium tuberculosis strain CDC1551 (1391 aa), FASTA scores: opt: 769, E(): 2.9e-37, (30.6% identity in 1434 aa overlap); and other hypothetical proteins from Mycobacterium tuberculosis e.g. O53689|Rv0284|MTV035.12 (1330 aa), FASTA scores: opt: 634, E(): 2.5e-29, (28.2% identity in 1443 aa overlap); O06264|Rv3447c|MTCY77.19c (1236 aa), FASTA scores: opt: 632, E(): 3.1e-29, (28.75% identity in 1391 aa overlap); O69736|R3871|MTV027.06 (591 aa), FASTA scores: opt: 588, E(): 6.6e-27, (27.75% identity in 605 aa overlap) (similarity only with C-terminal end); etc. Contains two possible (PS00017) ATP/GTP-binding sites (P-loop) in central portion.	O05450	No	cell wall and cell processes				Mb3923c,Mb3924c				
NC_000962.3	Mycobrowser_v3	CDS	4381943	4382851	.	-	0	Rv3896c	Rv3896c	Function unknown	Conserved hypothetical protein	Rv3896c, (MTCY15F10.16), len: 302 aa (first GTG taken, although TBParse suggests TTG at 16079). Putative conserved ala-rich protein. C-terminus highly similar to C-terminal end of other proteins e.g. Q9XAS4|SC10A7.01 hypothetical 17.2 KDA protein from Streptomyces coelicolor (244 aa), FASTA scores: opt: 255, E(): 1.4e-08, (32.0% identity in 222 aa overlap); CAC44611|STBAC16H6.32 putative secreted protein from Streptomyces coelicolor (172 aa), FASTA scores: opt: 214, E(): 3.4e-06, (42.55% identity in 94 aa overlap); Q38352|ORF360 from Lactococcus delbrueckii bacteriophage ll-H (360 aa), FASTA scores: opt: 211, E(): 9.5e-06, (40.0% identity in 115 aa overlap); P54334|XKDO_BACSU|XKDO phage-like element PBSX protein from Bacillus subtilis (1332 aa), FASTA scores: opt: 209, E(): 3.6e-05, (38.35% identity in 86 aa overlap); etc. Also similar to P71594|P71594|Rv0024|MTCY10H4.24 hypothetical 30.3 KDA protein from Mycobacterium tuberculosis (281 aa), FASTA scores: opt: 265, E(): 3.9e-09, (29.25% identity in 287 aa overlap).	O05448	No	conserved hypotheticals		MMAR_5461		Mb3926c				
NC_000962.3	Mycobrowser_v3	CDS	4387892	4390432	.	-	0	Rv3903c	Rv3903c	Unknown	Hypothetical alanine and proline rich protein	Rv3903c, (MTCY15F10.08), len: 846 aa. Hypothetical unknown ala-, pro-rich protein.	O05442	No	conserved hypotheticals		MMAR_5464		Mb3933c				
NC_000962.3	Mycobrowser_v3	CDS	4393449	4394195	.	+	0	Rv3908	mutT4	Function unknown	Possible mutator protein MutT4	Rv3908, (MTCY15F10.03c), len: 248 aa. Possible mutT4, mutator protein, equivalent to Q50195|ML2698|L222-ORF6 hypothetical protein from Mycobacterium leprae (251 aa), FASTA scores: opt: 1270, E(): 3.4e-62, (79.05% identity in 248 aa overlap). Also similar to O66548|APFA|AQ_158 hydrolase from Aquifex aeolicus (134 aa), FASTA scores: opt: 300, E(): 1.1e-09, (37.3% identity in 142 aa overlap); and similarity with other various proteins e.g. O93721 diadenosine 5'5'''-P1,P4-tetraphosphate pyrophosphohydrolase from Pyrobaculum aerophilum (143 aa), FASTA scores: opt: 205, E(): 0.00017, (34.85% identity in 109 aa overlap); Q9HS29|APA|VNG0431G diadenosine tetraphosphate pyrophosphohydrolase from Halobacterium sp. strain NRC-1 (142 aa), FASTA scores: opt: 199, E(): 0.00036, (34.0% identity in 147 aa overlap); Q9YA58|APE2080 hypothetical 19.2 KDA protein from Aeropyrum pernix (175 aa) FASTA scores: opt: 191, E(): 0.0012, (36.9% identity in 141 aa overlap); etc. Also similar to P95110|MUTT1|Rv2985|MTCY349.02 hypothetical 34.7 KDA protein from Mycobacterium tuberculosis (317 aa) FASTA scores: opt: 224, E(): 3e-05, (34.05% identity in 144 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008). Seems to belong to the NUDIX hydrolase family.	P9WIX7	No	information pathways	ML2698	MMAR_5472	MSMEG_6927	Mb3938				
NC_000962.3	Mycobrowser_v3	CDS	4402732	4403082	.	+	0	Rv3914	trxC	Thioredoxin participates in various redox reactions through the reversible oxidation of its active center dithiol, to a disulfide, & catalyzes dithiol-disulfide exchange reactions. Forms together with thioredoxin reductase and NADPH a redox active system which donates electrons to a wide variety of different metabolic process. Seems regulated by sigh (Rv3223c product).	Thioredoxin TrxC (TRX) (MPT46)	Rv3914, (MT4033, MTV028.05), len: 116 aa. TrxC (alternate gene names: mpt46, trx, trxA *), thioredoxin (see citations below), equivalent to O30974|THIO_MYCSM|TRXA thioredoxin from Mycobacterium smegmatis (112 aa), FASTA scores: opt: 576, E(): 2.1e-32, (80.2% identity in 111 aa overlap); and also equivalent to C-terminal end of P46843|TRXB_MYCLE|TRXB/a|TRX|ML2703 bifunctional thioredoxin reductase/thioredoxin from Mycobacterium leprae (458 aa), FASTA scores: opt: 628, E(): E(): 2e-35, (82.9% identity in 117 aa overlap). Also highly similar to many e.g. P80579|THIO_ALIAC from Alicyclobacillus acidocaldarius (Bacillus acidocaldarius) (105 aa), FASTA scores: opt: 411, E(): 3e-21, (57.15% identity in 105 aa overlap); P00275|THI1_CORNE from Corynebacterium nephridii (105 aa), FASTA scores: opt: 394, E(): 4.3e-20, (56.7% identity in 97 aa overlap); P00274|THIO_ECOLI|TRXA|TSNC|FIPA|B3781 from Escherichia coli and Salmonella typhimurium strain K12 and LT2 respectively (108 aa), FASTA scores: opt: 364, E(): 4.7e-18, (54.45% identity in 101 aa overlap); etc. Also similar to O53162|TRXB|Rv1471|MTV007.18 thioredoxin from Mycobacterium tuberculosis (123 aa), FASTA scores: E(): 2.3e-15, (41.9% identity in 93 aa overlap). Contains PS00194 Thioredoxin family active site. Belongs to the thioredoxin family. The product of this CDS is supposedly secreted. In this case, this protein could exert its free radical scavenging activity inside macrophages. (*) Warning: note that Rv1470|MTV007.17 correspond also to trxA.	P9WG67	No	intermediary metabolism and respiration	ML2703	MMAR_5478	MSMEG_6934	Mb3945				
NC_000962.3	Mycobrowser_v3	CDS	4396597	4400151	.	+	0	Rv3910	Rv3910	Unknown	Probable conserved transmembrane protein	Rv3910, (MTCY15F10.01c.MTV028.01), len: 1184 aa. Probable conserved transmembrane protein (hydrophobic domain ~50-550), equivalent to Q9CCX9|ML2700 possible conserved membrane protein from Mycobacterium leprae (1206 aa), FASTA scores: opt: 5554, E(): 0, (75.15% identity in 1182 aa overlap); and highly similar, but shorter 380 aa, to Q50199|L222-ORF10 from Mycobacterium leprae (784 aa) FASTA scores: opt: 3297, E(): 5.5e-170, (68.8% identity in 769 aa overlap); and at the N-terminal end with Q50198|L222-ORF also from Mycobacterium leprae (379 aa) FASTA scores: opt: 1955, E(): 5.7e-98, (88.4% identity in 353 aa overlap) (ORFs 9 and 10 are adjacent on L222). Also similar in part (principally at the N-terminal end) to other membrane proteins e.g. Q9X8T0|SCH24.16c putative transmembrane protein from Streptomyces coelicolor (811 aa), FASTA scores: opt: 573, E(): 2.8e-23, (31.05% identity in 573 aa overlap); O05467|MVIN_RHITR integral membrane protein virulence factor MVIN homolog from Rhizobium tropici (533 aa), FASTA scores: opt: 468, E(): 9e-18, (27.1% identity in 524 aa overlap); P56882|MVIN_RHIME integral membrane protein virulence factor MVIN homolog from Rhizobium meliloti (Sinorhizobium meliloti) (535 aa), FASTA scores: opt: 453, E(): 5.8e-17, (26.2% identity in 557 aa overlap); etc.	P9WJK3	No	cell wall and cell processes	ML2700	MMAR_5474	MSMEG_6929	Mb3940				
NC_000962.3	Mycobrowser_v3	CDS	4401728	4402735	.	+	0	Rv3913	trxB2	Enzyme that catalyse the reduction of disulphides by pyridine nucleotides through an enzyme disulphide and a flavin. Seems regulated by sigh (Rv3223c product). [catalytic activity: NADPH + oxidized thioredoxin = NADP(+) + reduced thioredoxin].	Probable thioredoxin reductase TrxB2 (TRXR) (TR)	Rv3913, (MT4032, MTV028.04), len: 335 aa. Probable trxB2, thioredoxin reductase (see citation below), equivalent to O30973|TRXB_MYCSM thioredoxin reductase from Mycobacterium smegmatis (311 aa), FASTA scores: opt: 1575, E(): 1.8e-87, (78.35% identity in 305 aa overlap); and highly similar, but shorter at C-terminus, to P46843|TRXB_MYCLE|TRXB/a|TRX|ML2703 bifunctional thioredoxin reductase/thioredoxin from Mycobacterium leprae (458 aa), FASTA scores: opt: 1766, E(): 8.7e-99, (83.25% identity in 328 aa overlap). Also highly similar to many e.g. P52215|TRXB_STRCO|SCH24.12 from Streptomyces coelicolor (321 aa), FASTA scores: opt: 1249, E(): 7.2e-68, (60.4% identity in 313 aa overlap); Q9Z8M4|TRXB_CHLPN from Chlamydia pneumoniae (Chlamydophila pneumoniae) (311 aa), FASTA scores: opt: 978, E(): 1.3e-51, (49.85% identity in 307 aa overlap); P09625|TRXB_ECOLI|B0888 from Escherichia coli strain K12 (320 aa), FASTA scores: opt: 948, E(): 8.6e-50, (49.2% identity in 309 aa overlap); etc. Contains PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site. Belongs to the pyridine nucleotide-disulfide oxidoreductases class-II. Cofactor: FAD (by similarity).	P9WHH1	No	intermediary metabolism and respiration		MMAR_5477	MSMEG_6933	Mb3944				
NC_000962.3	Mycobrowser_v3	CDS	4406488	4407531	.	-	0	Rv3918c	parA	Involved in chromosome partition. Localize to both POLES of the predivisional cell following completion of DNA replication.	Probable chromosome partitioning protein ParA	Rv3918c, (MTV028.09c), len: 347 aa. Probable parA, chromosome partitioning protein, highly similar to Q9CCX7|para|ML2707 putative cell division protein from Mycobacterium leprae (351 aa), FASTA scores: opt: 1679, E(): 2.9e-93, (78.1% identity in 347 aa overlap). Also highly similar to others e.g. Q9RFM1|para para protein from Streptomyces coelicolor (357 aa), FASTA scores: opt: 1197, E(): 2e-64, (60.45% identity in 306 aa overlap); Q98DZ3|MLL4479|para chromosome partitioning protein from Rhizobium loti (Mesorhizobium loti) (266 aa), FASTA scores: opt: 835, E(): 7.2e-43, (50.95% identity in 257 aa overlap); O05189|PARA_CAUCR chromosome partitioning protein from Caulobacter crescentus (267 aa), FASTA scores: opt: 813, E(): 1.5e-41, (51.35% identity in 261 aa overlap) (has its N-terminus shorter); etc. Equivalent to AAK48403 from Mycobacterium tuberculosis strain CDC1551 (381 aa) but shorter 34 aa. Also similar to other Mycobacterium tuberculosis proteins: MTCI125.30, FASTA scores: E(): 4.3e-32, (35.2% identity in 327 aa overlap); and MTCY07D11.13, FASTA scores: E(): 3e-30, (39.9% identity in 263 aa overlap). Belongs to the para family. Possible alternative start site at aa 107. Note that previously known as parB.	Q1LVD4	No	cell wall and cell processes	ML2707,ML2707c	MMAR_5482	MSMEG_6939	Mb3949c				
NC_000962.3	Mycobrowser_v3	CDS	4404433	4405167	.	-	0	Rv3916c	Rv3916c	Function unknown	Conserved hypothetical protein	Rv3916c, (MTV028.07c), len: 244 aa. Conserved hypothetical protein, equivalent to Q50200|ML2705|L222-ORF1 hypothetical protein from Mycobacterium leprae (259 aa), FASTA scores: opt: 1266, E(): 2e-74, (76.4% identity in 250 aa overlap). Also highly similar (but with gaps) to Q9R3S2|STH24.10 hypothetical 22.6 KDA protein from Streptomyces coelicolor (205 aa), FASTA scores: opt: 387, E(): 7.5e-18, (40.25% identity in 231 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008).	O53594	No	conserved hypotheticals	ML2705,ML2705c	MMAR_5480	MSMEG_6936	Mb3947c				
NC_000962.3	Mycobrowser_v3	CDS	4407528	4408202	.	-	0	Rv3919c	gid	Unknown	Probable glucose-inhibited division protein B Gid	Rv3919c, (MT4038, MTV028.10c), len: 224 aa. Probable gid (alternate gene name: gidB), glucose-inhibited division protein B, equivalent, but shorter 20 aa, to Q9L7M3 putative GIDB (fragment) from Mycobacterium paratuberculosis (245 aa), FASTA scores: opt: 1018, E(): 4.8e-57, (73.95% identity in 211 aa overlap); and Q50203|GIDB_MYCLE|ML2708 glucose inhibited division protein B from Mycobacterium leprae (245 aa), FASTA scores: opt: 966, E(): 9.1e-54, (68.4% identity in 212 aa overlap). Also highly similar to many e.g. O54571|GIDB_STRCO|STH24.07 from Streptomyces coelicolor (239 aa), FASTA scores: opt: 654, E(): 3.9e-34, (47.95% identity in 221 aa overlap); Q9KNG5|VC2774 from Vibrio cholerae (210 aa), FASTA scores: opt: 300, E(): 6.9e-12, (38.15% identity in 139 aa overlap); P17113|GIDB_ECOLI|B3740|Z5240|ECS4682 from Escherichia coli (several strains) (207 aa), FASTA scores: opt: 287, E(): 4.5e-11, (34.8% identity in 138 aa overlap); etc. Contains PS00539 Pyrokinins signature. Belongs to the GIDB family. Nucleotide position 4407904 in the genome sequence has been corrected, G:A resulting in S100F.	P9WGW9	No	cell wall and cell processes	ML2708,ML2708c	MMAR_5483	MSMEG_6940	Mb3950c				
NC_000962.3	Mycobrowser_v3	CDS	4408334	4408897	.	-	0	Rv3920c	Rv3920c	Unknown	Conserved protein similar to jag protein	Rv3920c, (MTV028.11c), len: 187 aa. Conserved protein, similar to jag protein, equivalent to Q9L7M2 hypothetical 20.1 KDA protein from Mycobacterium paratuberculosis (183 aa), FASTA scores: opt: 1004, E(): 7.3e-52, (85.05% identity in 187 aa overlap); and Q50204|ML2709 hypothetical protein similar to jag protein SPOIIIJ associated protein in bacillus subtilis from Mycobacterium leprae (193 aa), FASTA scores: opt: 871, E(): 4.4e-44, (73.05% identity in 193 aa overlap). Also similar to other bacterial proteins e.g. O54595|STH24.06|jag jag-like protein from Streptomyces coelicolor (170 aa), FASTA scores: opt: 593, E(): 6.7e-28, (62.85% identity in 167 aa overlap); Q9RCA6|jag|BH4063 jag protein homolog from Bacillus halodurans (207 aa), FASTA scores: opt: 282, E(): 1.1e-09, (35.0% identity in 140 aa overlap); Q9X1H1|TM1460 putative jag protein, putative from Thermotoga maritima (221 aa), FASTA scores: opt: 258, E(): 3e-08, (31.9% identity in 138 aa overlap);Q01620|JAG_BACSU jag protein (SPOIIIJ associated protein) from Bacillus subtilis (208 aa), FASTA scores: opt: 196, E(): 0.00012, (28.05% identity in 139 aa overlap); etc.	O53598	No	conserved hypotheticals	ML2709,ML2709c	MMAR_5484	MSMEG_6941	Mb3951c				
NC_000962.3	Mycobrowser_v3	CDS	4410786	4410929	.	-	0	Rv3924c	rpmH	Involved in translation mechanism. This protein is one of the early assembly proteins of the 50S ribosomal subunit.	50S ribosomal protein L34 RpmH	Rv3924c, (MTV028.15), len: 47 aa. rpmH, 50s ribosomal protein l34 (see citations below), equivalent to many mycobacterial 50S ribosomal protein L34 e.g. P46386|RL34_MYCLE|RPMH|ML2713 from Mycobacterium leprae (47 aa), FASTA scores: opt: 287, E(): 8.5e-17, (91.5% identity in 47 aa overlap); and Q9L7L8|RL34_MYCPA|RPMH from Mycobacterium paratuberculosis (47 aa), FASTA scores: opt: 281, E(): 2.6e-16, (89.35% identity in 47 aa overlap). Also highly similar to other ribosomal proteins e.g. P27901|RL34_STRCO|RPMH|STH24.02 from Streptomyces coelicolor (45 aa), FASTA scores: opt: 234, E(): 1.4e-12, (79.05% identity in 43 aa overlap); and P05647|RL34_BACSU|RPMH from Bacillus subtilis (44 aa) FASTA scores: opt: 229, E(): 3.7e-12, (72.35% identity in 47 aa overlap); etc. Contains PS00784 Ribosomal protein L34 signature. Belongs to the L34P family of ribosomal proteins.	P9WH93	No	information pathways	ML2713,ML2713c			Mb3955c				
NC_000962.3	Mycobrowser_v3	CDS	3593369	3593852	.	+	0	Rv3216	Rv3216	Acetylation, substrate unknown	GCN5-related N-acetyltransferase, pseudogene	Rv3216, (MTCY07D11.10c), len: 160 aa. Acetyltransferase (2.3.1.-), contains GNAT domain (Gcn5-related N-acetyltransferase. See Vetting et al. 2005), probably pseudogene as appears frameshifted due to 1bp insertion at position 3593438. Frameshift present in all sequenced tubercle bacilli. Start changed since first submission, extended by 50aa. Similar to many acetyltransferases e.g. Q9AB32|CC0402 acetyltransferase (GNAT family) from Caulobacter crescentus (159 aa), FASTA scores: opt: 325, E(): 3.8e-17, (45.65% identity in 103 aa overlap); P79081|ATS1 putative acetyltransferase ATS1 from Schizosaccharomyces pombe (Fission yeast) (168 aa), FASTA scores: opt: 313, E(): 3.1e-16, (47.6% identity in 105 aa overlap).	O05850	Yes	intermediary metabolism and respiration	ML0807,ML0807c	MMAR_1341	MSMEG_1924	Mb3242				
NC_000962.3	Mycobrowser_v3	CDS	333160	333417	.	-	0	Rv0277A	vapB25	Unknown	Possible antitoxin VapB25	Rv0277A, len: 85 aa. Possible vapB25, antitoxin, part of toxin-antitoxin (TA) operon with Rv0277c, see Arcus et al. 2005. Has in-frame stop codon so may not be expressed. Very similar to others in Mycobacterium tuberculosis e.g. Rv0748 (85 aa). Fasta score E(): 4e-24; 88.2% identity in 85 aa overlap	P0CW33	Yes	virulence, detoxification, adaptation								
NC_000962.3	Mycobrowser_v3	CDS	2725571	2726087	.	-	0	Rv2427A	oxyR'		Transcriptional regulator OxyR', pseudogene	Rv2427A, Pseudogene oxyR', inactivated by multiple mutations; identical to sequence in u16243 (see Deretic et al., 1995).		Yes	virulence, detoxification, adaptation								
NC_000962.3	Mycobrowser_v3	CDS	4410053	4410415	.	-	0	Rv3922c	Rv3922c	Unknown	Possible hemolysin	Rv3922c, (MTV028.13c), len: 120 aa. Possible hemolysin, highly similar to Q9L7M0|YIDD_MYCPA hypothetical 12.4 KDA protein from Mycobacterium paratuberculosis (115 aa), FASTA scores: opt: 521, E(): 1.9e-29, (65.2% identity in 112 aa overlap). Also highly similar to Q44066|HLYA_AERHY putative alpha-hemolysin from Aeromonas hydrophila (85 aa), FASTA scores: opt: 276, E(): 1.5e-12, (51.45% identity in 70 aa overlap); and to many bacterial hypothetical proteins from bacterium e.g. P22847|YIDD_ECOLI|B3704.1 hypothetical protein from Escherichia coli strain K12 (85 aa), FASTA scores: opt: 276, E(): 1.5e-12, (51.45% identity in 70 aa overlap).	P9WFL9	No	virulence, detoxification, adaptation	ML2711,ML2711c	MMAR_5578		Mb3953c				
NC_000962.3	Mycobrowser_v3	ncRNA	759479	759610	.	+		MTB000115	ncRv10666	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	786021	786074	.	+		MTB000116	ncRv10685	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	80240	80440	.	+		MTB000100	ncRv10071	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	80254	80344	.	-		MTB000101	ncRv10071c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	156452	156567	.	+		MTB000102	ncRv10128	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	156521	156568	.	-		MTB000103	ncRv10128c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	177236	177285	.	-		MTB000104	ncRv10150c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	209683	209841	.	+		MTB000105	ncRv0179	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	218320	218379	.	-		MTB000106	ncRv0186c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	293603	293663	.	+		MTB000107	ncRv10243	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	530246	530353	.	-		MTB000108	ncRv0441c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	558815	558884	.	+		MTB000109	ncRv10467	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	579290	579408	.	+		MTB000110	ncRv0490	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	704185	704246	.	+		MTB000111	ncRv10609	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	733361	733459	.	+		MTB000112	ncRv10637	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	734118	734244	.	+		MTB000113	ncRv0638	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	736166	736284	.	+		MTB000114	ncRv0641	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	800242	800359	.	+		MTB000117	ncRv10699	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	815417	815685	.	+		MTB000118	ncRv0724	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	905075	905164	.	-		MTB000119	ncRv0810c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	958459	958509	.	+		MTB000120	ncRv10860	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1000719	1000826	.	+		MTB000121	ncRv0897	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1063969	1064101	.	+		MTB000122	ncRv0952	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1113606	1113664	.	+		MTB000123	ncRv10996	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1165548	1165613	.	-		MTB000124	ncRv11042c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1197082	1197179	.	+		MTB000125	ncRv1072	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1271918	1271961	.	-		MTB000126	ncRv11144c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1275610	1275674	.	-		MTB000127	ncRv11147c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1313343	1313452	.	-		MTB000128	ncRv11179c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1342888	1342941	.	+		MTB000129	ncRv11199	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1821646	1821753	.	-		MTB000138	ncRv1621c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1960667	1960774	.	+		MTB000139	ncRv11733	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2030986	2031038	.	+		MTB000140	ncRv11793	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2068863	2068962	.	+		MTB000141	ncRv1821	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2096766	2096867	.	+		MTB000142	ncRv11846	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2268164	2268231	.	+		MTB000143	ncRv12023	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2489205	2489252	.	+		MTB000144	ncRv12220	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2762409	2762484	.	+		MTB000145	ncRv12459	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2877751	2877808	.	+		MTB000146	ncRv12557	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2966410	2966450	.	+		MTB000147	ncRv12641	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3092761	3092886	.	-		MTB000148	ncRv12783c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3343113	3343216	.	-		MTB000149	ncRv2986c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3350950	3351074	.	-		MTB000150	ncRv2993c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3363029	3363152	.	-		MTB000151	ncRv13003c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3595951	3596059	.	+		MTB000152	ncRv3220	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3690941	3691059	.	+		MTB000153	ncRv13303	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3837346	3837458	.	-		MTB000155	ncRv13418cB	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3880231	3880294	.	-		MTB000156	ncRv3461c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	3956291	3956550	.	+		MTB000157	ncRv3520	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	4088267	4088350	.	-		MTB000158	ncRv3648c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	4099384	4099477	.	-		MTB000159	ncRv13660c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	4168192	4168281	.	-		MTB000160	ncRv13722c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	4265583	4265765	.	-		MTB000161	ncRv3804c	Unknown	Putative small regulatory RNA	Supported by sRNA-Seq in H37Rv (see DeJesus et al. 2017)		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	1446193	1446265	.	-	0	MTB000018	argV	-	tRNA-Arg (CCG)	argV, tRNA-Arg, anticodon ccg, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	1512728	1512811	.	+	0	MTB000022	leuW	-	tRNA-Leu (TAG)	leuW, tRNA-Leu, anticodon tag, length = 84		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	1828015	1828088	.	-	0	MTB000023	leuV	-	tRNA-Leu (CAA)	leuV, tRNA-Leu, anticodon caa, length = 74		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	1950632	1951051	.	-	0	Rv1724c	Rv1724c	Unknown	Hypothetical protein	Rv1724c, (MTCY04C12.09c), len: 139 aa. Hypothetical unknown protein.	P71982	No	conserved hypotheticals				Mb1753c				
NC_000962.3	Mycobrowser_v3	CDS	2006636	2006947	.	+	0	Rv1772	Rv1772	Unknown	Hypothetical protein	Rv1772, (MTCY28.38), len: 103 aa. Hypothetical unknown protein.	O06805	No	conserved hypotheticals				Mb1801				
NC_000962.3	Mycobrowser_v3	CDS	2012081	2012530	.	-	0	Rv1778c	Rv1778c	Unknown	Unknown protein	Rv1778c, (MTCY25C11.05c), len: 149 aa. Unknown protein.	O33181	No	conserved hypotheticals				Mb1807c				
NC_000962.3	Mycobrowser_v3	CDS	2159921	2160328	.	-	0	Rv1914c	Rv1914c	Unknown	Unknown protein	Rv1914c, (MTCY180.04), len: 135 aa. Unknown protein. Predicted to be an outer membrane protein (See Song et al., 2008).	O07719	No	conserved hypotheticals		MMAR_2820		Mb1949c				
NC_000962.3	Mycobrowser_v3	CDS	2202584	2203129	.	+	0	Rv1957	Rv1957	Unknown	Hypothetical protein	Rv1957, (MTCY09F9.07c), len: 181 aa. Hypothetical unknown protein.	P95257	No	conserved hypotheticals				Mb1992				
NC_000962.3	Mycobrowser_v3	CDS	2256084	2256428	.	-	0	Rv2007c	fdxA	Involved in electron transfer.	Ferredoxin FdxA	Rv2007c, (MTCY39.10), len: 114 aa. FdxA, ferredoxin, similar to many e.g. FER_MYCSM P00215 ferredoxin, Mycobacterium smegmatis (106 aa).	P9WNE7	No	intermediary metabolism and respiration		MMAR_2080,MMAR_2994	MSMEG_1124	Mb2030c				
NC_000962.3	Mycobrowser_v3	CDS	2280240	2281082	.	-	0	Rv2033c	Rv2033c	Unknown	Conserved hypothetical protein	Rv2033c, (MTV018.20), len: 280 aa. Conserved hypothetical protein, similar to many.	O53477	No	conserved hypotheticals	ML1422,ML1422c	MMAR_3007	MSMEG_3020	Mb2059c				
NC_000962.3	Mycobrowser_v3	CDS	2287884	2288681	.	-	0	Rv2042c	Rv2042c	Unknown	Conserved protein	Rv2042c, (MTV018.29c), len: 265 aa. Conserved protein, similar to many.	O53486	No	conserved hypotheticals	ML1431,ML1431c	MMAR_3015	MSMEG_3684	Mb2068c				
NC_000962.3	Mycobrowser_v3	CDS	2327491	2328225	.	-	0	Rv2070c	cobK	Involved in cobalamin biosynthesis.	Precorrin-6X reductase CobK	Rv2070c, (MTCY49.09c), len: 244 aa. CobK, precorrin-6x reductase, similar to many.	P9WP89	No	intermediary metabolism and respiration	ML1449,ML1449c	MMAR_3052	MSMEG_3875	Mb2096c				
NC_000962.3	Mycobrowser_v3	CDS	2402507	2402722	.	-	0	Rv2142A	parD2	Unknown	Possible antitoxin ParD2	Rv2142A, len: 71 aa. Possible parD2, antitoxin, part of toxin-antitoxin (TA) operon with Rv2142c (See Pandey and Gerdes, 2005).	P9WJ75	No	virulence, detoxification, adaptation								
NC_000962.3	Mycobrowser_v3	tRNA	2835494	2835566	.	+	0	MTB000034	lysU	-	tRNA-Lys (CTT)	lysU, tRNA-Lys, anticodon ctt, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2881252	2881320	.	+	0	MTB000068	mpr11	Unknown	Fragment of putative small regulatory RNA	mpr11, fragment of putative small regulatory RNA (See DiChiara et al., 2010), ends not mapped, 82-100 nt band detected by Northern blot in M. bovis BCG Pasteur.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	1138076	1138147	.	-	0	MTB000016	glnT	-	tRNA-Gln (TTG)	glnT, tRNA-Gln, anticodon ttg, length = 72		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	1177396	1177469	.	+	0	MTB000017	leuX	-	tRNA-Leu (TAA)	leuX, tRNA-Leu, anticodon taa, length = 74. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1220388	1220487	.	-	0	MTB000074	MTS0858	Unknown	Putative small regulatory RNA	MTS0858, putative small regulatory RNA (See Arnvig et al., 2011), ends not mapped, ~100 bp band detected by Northern blot.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	1535417	1535716	.	-	0	MTB000065	mcr15	Unknown	Putative small regulatory RNA	mcr15, putative small regulatory RNA (See DiChiara et al., 2010). 5'-end mapped by 5'RLM-RACE in M. bovis BGC Pasteur, 3'-end not mapped.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2882185	2882276	.	+	0	MTB000069	mpr12	Unknown	Fragment of putative small regulatory RNA	mpr12, fragment of putative small regulatory RNA (See DiChiara et al., 2010), ends not mapped, ~118 nt band detected by Northern blot in M. bovis BCG Pasteur.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	2765331	2765404	.	-	0	MTB000030	proU	-	tRNA-Pro (TGG)	proU, tRNA-Pro; anticodon tgg, length = 74		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	2926355	2926975	.	+	0	Rv2597	Rv2597	Unknown	Probable membrane protein	Rv2597, (MTCY227.04c), len: 206 aa. Probable membrane protein. Predicted to be an outer membrane protein (See Song et al., 2008).	P9WL73	No	cell wall and cell processes	ML0480,ML0480c	MMAR_2108		Mb2628				
NC_000962.3	Mycobrowser_v3	CDS	2962470	2962712	.	+	0	Rv2635	Rv2635	Unknown	Hypothetical protein	Rv2635, (MTCY441.05), len: 80 aa. Hypothetical unknown protein.	P9WL57	No	conserved hypotheticals				Mb2668				
NC_000962.3	Mycobrowser_v3	CDS	2976586	2976909	.	-	0	Rv2653c	Rv2653c	Unknown	Possible PhiRv2 prophage protein	Rv2653c, (MTCY441.22c), len: 107 aa. Hypothetical unknown protein, possibly phiRv2 phage protein (see citation below).	P9WJ13	No	insertion seqs and phages								
NC_000962.3	Mycobrowser_v3	CDS	2979326	2979688	.	-	0	Rv2658c	Rv2658c	Unknown	Possible prophage protein	Rv2658c, (MTCY441.27c), len: 120 aa. Hypothetical unknown protein, probably phage protein.	P9WL47	No	insertion seqs and phages								
NC_000962.3	Mycobrowser_v3	CDS	3020200	3020457	.	-	0	Rv2706c	Rv2706c	Unknown	Hypothetical protein	Rv2706c, (MTCY05A6.27c), len: 85 aa (unlikely ORF). Hypothetical unknown protein.	O07207	No	conserved hypotheticals	ML1019			Mb2725c				
NC_000962.3	Mycobrowser_v3	CDS	3042542	3043018	.	+	0	Rv2730	Rv2730	Unknown	Hypothetical protein	Rv2730, (MTCY174.10), len: 158 aa. Hypothetical unknown protein. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6Y1K4	No	conserved hypotheticals				Mb2749				
NC_000962.3	Mycobrowser_v3	CDS	3115408	3115719	.	+	0	Rv2809	Rv2809	Unknown	Hypothetical protein	Rv2809, (MTCY16B7.34c), len: 103 aa (questionable ORF). Hypothetical unknown protein. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6YEF3	No	conserved hypotheticals				Mb2832				
NC_000962.3	Mycobrowser_v3	CDS	3366644	3367267	.	+	0	Rv3008	Rv3008	Unknown	Hypothetical protein	Rv3008, (MTV012.22), len: 207 aa (start uncertain). Hypothetical unknown protein.	I6YEY1	No	conserved hypotheticals				Mb3033				
NC_000962.3	Mycobrowser_v3	CDS	3392812	3393201	.	+	0	Rv3032A	Rv3032A	Unknown	Conserved protein	Rv3032A, len: 129 aa. Conserved protein.	I6X630	No	conserved hypotheticals								
NC_000962.3	Mycobrowser_v3	CDS	3540882	3541364	.	-	0	Rv3172c	Rv3172c	Unknown	Hypothetical protein	Rv3172c, (MTV014.16c), len: 160 aa. Hypothetical unknown protein.	O53322	No	conserved hypotheticals	ML0645			Mb3197c				
NC_000962.3	Mycobrowser_v3	CDS	3611300	3611941	.	+	0	Rv3235	Rv3235	Unknown	Hypothetical alanine arginine proline rich protein	Rv3235, (MTCY20B11.10), len: 213 aa. Hypothetical unknown ala-, arg-, pro-rich protein.	O05880	No	conserved hypotheticals	ML0783,ML0783c	MMAR_1310	MSMEG_1880	Mb3263				
NC_000962.3	Mycobrowser_v3	CDS	3908072	3908236	.	+	0	Rv3489	Rv3489	Unknown	Unknown protein	Rv3489, (MTCY13E12.42), len: 54 aa. Unknown protein. No similarity with other proteins.	I6YC91	No	conserved hypotheticals		MMAR_4977	MSMEG_5890	Mb3519				
NC_000962.3	Mycobrowser_v3	CDS	3909890	3910468	.	+	0	Rv3491	Rv3491	Unknown	Unknown protein	Rv3491, (MTCY13E12.44), len: 192 aa. Unknown protein. No significant homology with other proteins.	I6XHD1	No	conserved hypotheticals	ML2255	MMAR_4979	MSMEG_4353	Mb3521				
NC_000962.3	Mycobrowser_v3	CDS	3963605	3964054	.	+	0	Rv3527	Rv3527	Unknown	Hypothetical protein	Rv3527, (MTCY03C7.29c), len: 149 aa. Hypothetical unknown protein.	I6XHG6	No	conserved hypotheticals		MMAR_5016	MSMEG_5927	Mb3557				
NC_000962.3	Mycobrowser_v3	CDS	4196724	4197107	.	+	0	Rv3747	Rv3747	Function unknown	Conserved protein	Rv3747, (MTV025.095), len: 127 aa. Conserved protein, highly similar to downstream ORF O69715|Rv3748|MTV025.096 conserved hypothetical protein (119 aa), FASTA scores: opt: 494, E(): 6e-27, (64.4% identity in 118 aa overlap).	O69714	No	conserved hypotheticals		MMAR_5287		Mb3773				
NC_000962.3	Mycobrowser_v3	tRNA	2765541	2765611	.	+	0	MTB000031	glyV	-	tRNA-Gly (TCC)	glyV, tRNA-Gly; anticodon tcc, length = 71		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	3174747	3174995	.	+	0	Rv2862A	vapB23	Unknown	Possible antitoxin VapB23	Rv2862A, len: 82 aa. Possible vapB23, antitoxin, part of toxin-antitoxin (TA) operon with Rv2863 (See Pandey and Gerdes, 2005).	P0CW32	No	virulence, detoxification, adaptation								
NC_000962.3	Mycobrowser_v3	CDS	4008167	4008433	.	-	0	Rv3566A	Rv3566A	Unknown	Hypothetical protein	Rv3566A, len: 88 aa. Hypothetical unknown protein.	I6YGI1	No	conserved hypotheticals				Mb3597c				
NC_000962.3	Mycobrowser_v3	CDS	4042952	4043035	.	-	0	Rv3599c	Rv3599c	Unknown	Hypothetical short protein	Rv3599c, (MTCY07H7B.23), len: 27 aa. Hypothetical unknown protein.	O06283	No	unknown								
NC_000962.3	Mycobrowser_v3	tRNA	4081365	4081437	.	-	0	MTB000044	thrU	-	tRNA-Thr (CGT)	thrU, tRNA-Thr, anticodon cgt, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	2772098	2772331	.	-	0	Rv2468A	Rv2468A	Unknown	Conserved protein	Rv2468A, len: 77 aa. Conserved protein.	I6YDH3	No	conserved hypotheticals								
NC_000962.3	Mycobrowser_v3	CDS	4053881	4054042	.	-	0	Rv3613c	Rv3613c	Unknown	Hypothetical protein	Rv3613c, (MTCY07H7B.09), len: 53 aa. Hypothetical unknown protein.	O06270	No	conserved hypotheticals				Mb3643c				
NC_000962.3	Mycobrowser_v3	ncRNA	4099386	4099478	.	-	0	MTB000058	B11	Unknown	Putative small regulatory RNA	B11, putative small regulatory RNA (See Arnvig and Young, 2009; DiChiara et al., 2010).		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	547344	547517	.	-	0	Rv0456B	mazE1	Unknown	Possible antitoxin MazE1	Rv0456B, len: 57 aa. Possible mazE1, antitoxin, part of toxin-antitoxin (TA) operon with Rv0456A (See Pandey and Gerdes, 2005; Zhu et al., 2006).	P0CL57	No	virulence, detoxification, adaptation								
NC_000962.3	Mycobrowser_v3	CDS	883451	884050	.	-	0	Rv0789c	Rv0789c	Unknown	Hypothetical protein	Rv0789c, (MTCY369.33c), len: 199 aa. Hypothetical unknown protein.	I6Y4U0	No	conserved hypotheticals	ML2218	MMAR_4896		Mb0813c				
NC_000962.3	Mycobrowser_v3	CDS	3533913	3534395	.	-	0	Rv3165c	Rv3165c	Unknown	Unknown protein	Rv3165c, (MTV014.09)c, len: 160 aa. Unknown protein.	O53315	No	conserved hypotheticals	ML0653	MMAR_1398	MSMEG_3868	Mb3190c				
NC_000962.3	Mycobrowser_v3	CDS	474940	475344	.	+	0	Rv0395	Rv0395	Unknown	Hypothetical protein	Rv0395, (MTCY04D9.07), len: 134 aa. Hypothetical unknown protein.	P95203	No	conserved hypotheticals				Mb0401				
NC_000962.3	Mycobrowser_v3	tRNA	658109	658189	.	+	0	MTB000005	tyrT	-	tRNA-Tyr (GTA)	tyrT, tRNA-Tyr, anticodon gta, length = 81		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	4013511	4014041	.	+	0	Rv3572	Rv3572	Unknown	Unknown protein	Rv3572, (MTCY06G11.19), len: 176 aa. Unknown protein. Predicted to be an outer membrane protein (See Song et al., 2008).	I6X7P2	No	conserved hypotheticals	ML0341,ML0341c	MMAR_5067	MSMEG_6040	Mb3603				
NC_000962.3	Mycobrowser_v3	tRNA	733524	733596	.	+	0	MTB000008	trpT	-	tRNA-Trp (CCA)	trpT, tRNA-Trp, anticodon cca, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	1113511	1113583	.	+	0	MTB000015	alaV	-	tRNA-Ala (CGC)	alaV, tRNA-Ala, anticodon cgc, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	376573	377055	.	-	0	Rv0307c	Rv0307c	Unknown	Unknown protein	Rv0307c, (MTCY63.12c), len: 160 aa. Unknown protein.	O07234	No	conserved hypotheticals	ML2524	MMAR_0557	MSMEG_0632	Mb0315c				
NC_000962.3	Mycobrowser_v3	CDS	665042	665383	.	-	0	Rv0572c	Rv0572c	Unknown	Hypothetical protein	Rv0572c, (MTV039.10c), len: 113 aa. Hypothetical unknown protein.	P9WM81	No	conserved hypotheticals				Mb0587c				
NC_000962.3	Mycobrowser_v3	CDS	1280843	1281484	.	-	0	Rv1154c	Rv1154c	Unknown	Hypothetical protein	Rv1154c, (MTCI65.21c), len: 213 aa. Hypothetical unknown protein, start uncertain.	O06552	No	conserved hypotheticals	ML1509	MMAR_4299	MSMEG_5172	Mb1185c				
NC_000962.3	Mycobrowser_v3	CDS	2075571	2075828	.	+	0	Rv1831	Rv1831	Unknown	Hypothetical protein	Rv1831, (MTCY1A11.12c), len: 85 aa. Hypothetical unknown protein.	P9WLR3	No	conserved hypotheticals				Mb1862				
NC_000962.3	Mycobrowser_v3	CDS	1735976	1736212	.	+	0	Rv1535	Rv1535	Unknown	Unknown protein	Rv1535, (MTCY07A7A.04), len: 78 aa. Unknown protein.	O06180	No	conserved hypotheticals		MMAR_2348		Mb1562				
NC_000962.3	Mycobrowser_v3	CDS	2314661	2314825	.	-	0	Rv2057c	rpmG1	Involved in translation	50S ribosomal protein L33 RpmG1	Rv2057c, (MTCY63A.03), len: 54 aa. rpmG1, 50S ribosomal protein L33, similar to many. Note that previously known as rpmG.	P9WH97	No	information pathways		MMAR_0291	MSMEG_6067	Mb2083c				
NC_000962.3	Mycobrowser_v3	CDS	1612256	1612393	.	+	0	Rv1434	Rv1434	Unknown	Hypothetical protein	Rv1434, (MTCY493.20c), len: 45 aa. Hypothetical unknown protein.	O06824	No	conserved hypotheticals				Mb1469				
NC_000962.3	Mycobrowser_v3	CDS	2201277	2201579	.	+	0	Rv1954A	Rv1954A	Unknown	Hypothetical protein	Rv1954A, len: 100 aa. Hypothetical unknown protein.	P0CV86	No	unknown								
NC_000962.3	Mycobrowser_v3	tRNA	1946613	1946686	.	+	0	MTB000024	proT	-	tRNA-Pro (GGG)	proT, tRNA-Pro, anticodon ggg, length = 74		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	2139419	2139656	.	+	0	MTB000056	AS1890	Unknown	Putative small regulatory RNA	AS1890, putative small regulatory RNA (See Arnvig and Young, 2009). Alternate 5'-ends at positions 2139466, 2139548, 2139594.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	2510598	2510669	.	-	0	MTB000027	valV	-	tRNA-Val (TAC)	valV, tRNA-Val, anticodon tac, length = 72		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	3082352	3082756	.	-	0	Rv2774c	Rv2774c	Unknown	Hypothetical protein	Rv2774c, (MTV002.39c), len: 134 aa. Hypothetical unknown protein.	O33316	No	conserved hypotheticals				Mb2796c				
NC_000962.3	Mycobrowser_v3	CDS	3502945	3503277	.	-	0	Rv3136A	Rv3136A	Unknown	Conserved protein	Rv3136A, len: 110 aa. Conserved protein.	I6Y2Q7	No	conserved hypotheticals								
NC_000962.3	Mycobrowser_v3	CDS	3556855	3557064	.	+	0	Rv3190A	Rv3190A	Unknown	Conserved protein	Rv3190A, len: 69 aa. Conserved protein.	I6XGJ1	No	conserved hypotheticals								
NC_000962.3	Mycobrowser_v3	CDS	3566696	3566896	.	-	0	Rv3196A	Rv3196A	Unknown	Unknown protein	Rv3196A, len: 66 aa. Unknown protein.	L7N668	No	conserved hypotheticals		MMAR_1367		Mb3219c				
NC_000962.3	Mycobrowser_v3	tRNA	4168345	4168430	.	+	0	MTB000046	serV	-	tRNA-Ser (GGA)	serV, tRNA-Ser, anticodon gga, length = 86		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	ncRNA	4317073	4317165	.	+	0	MTB000080	MTS2975	Unknown	Putative small regulatory RNA	MTS2975, putative small regulatory RNA (See Arnvig et al., 2011), ends not mapped, ~100 bp band detected by Northern blot.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	1774860	1775144	.	-	0	Rv1567c	Rv1567c	Unknown	Probable hypothetical membrane protein	Rv1567c, (MTCY336.36), len: 94 aa. Probable membrane protein.	O06623	No	cell wall and cell processes	ML1215,ML1215c	MMAR_2382		Mb1594c				
NC_000962.3	Mycobrowser_v3	CDS	1815253	1815693	.	+	0	Rv1615	Rv1615	Unknown	Probable membrane protein	Rv1615, (MTCY01B2.07), len: 146 aa. Probable membrane protein	O06132	No	cell wall and cell processes		MMAR_2417	MSMEG_3223	Mb1641				
NC_000962.3	Mycobrowser_v3	CDS	1786307	1786528	.	-	0	Rv1584c	Rv1584c	Unknown	Possible PhiRv1 phage protein	Rv1584c, (MTCY336.20), len: 73 aa. Possible phiRv1 phage protein (putative excisionase) (see citation below). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06606	No	insertion seqs and phages				Mb1610c				
NC_000962.3	Mycobrowser_v3	CDS	606149	606448	.	+	0	Rv0514	Rv0514	Unknown	Possible transmembrane protein	Rv0514, (MTCY20G10.04), len: 99 aa. Possible transmembrane protein.	O33359	No	cell wall and cell processes		MMAR_0847	MSMEG_0960	Mb0527				
NC_000962.3	Mycobrowser_v3	CDS	710345	710587	.	+	0	Rv0615	Rv0615	Unknown	Probable integral membrane protein	Rv0615, (MTCY19H5.06c), len: 80 aa. Probable integral membrane protein.	O07762	No	cell wall and cell processes		MMAR_0115		Mb0632				
NC_000962.3	Mycobrowser_v3	CDS	789157	789411	.	-	0	Rv0689c	Rv0689c	Unknown	Hypothetical protein	Rv0689c, (MTCY210.06c), len: 84 aa. Hypothetical unknown protein.	I6WZ39	No	conserved hypotheticals				Mb0708c				
NC_000962.3	Mycobrowser_v3	rRNA	1471846	1473382	.	+	0	MTB000019	rrs	-	Ribosomal RNA 16S	rrs, 16s rRNA gene (alternate gene name: rrnS).		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	386204	386274	.	-	0	MTB000004	glyU	-	tRNA-Gly (CCC)	glyU, tRNA-Gly, anticodon ccc, length = 71		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	2546839	2547087	.	-	0	Rv2274A	mazE8	Unknown	Possible antitoxin MazE8	Rv2274A, len: 82 aa. Possible mazE8, antitoxin, part of toxin-antitoxin (TA) operon with Rv2274c (See Pandey and Gerdes, 2005).	P0CL60	No	virulence, detoxification, adaptation								
NC_000962.3	Mycobrowser_v3	CDS	1003805	1003957	.	+	0	Rv0900	Rv0900	Unknown	Possible membrane protein	Rv0900, (MTCY31.28), len: 50 aa. Possible membrane protein, with hydrophobic domain from aa 4-26.	P9WJG7	No	cell wall and cell processes				Mb0924				
NC_000962.3	Mycobrowser_v3	CDS	2307293	2307517	.	-	0	Rv2049c	Rv2049c	Unknown	Conserved hypothetical protein	Rv2049c, (MTV018.36c), len: 74 aa. Conserved hypothetical protein.	O53491	No	conserved hypotheticals	ML1438,ML1438c		MSMEG_3857	Mb2075c				
NC_000962.3	Mycobrowser_v3	tRNA	850642	850713	.	-	0	MTB000009	thrV	-	tRNA-Thr (TGT)	thrV, tRNA-Thr, anticodon tgt, length = 72		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	3348547	3348619	.	-	0	MTB000039	gluU	-	tRNA-Glu (CTC)	gluU, tRNA-Glu; anticodon ctc, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	186495	186623	.	-	0	Rv0157A	Rv0157A	Unknown	Conserved protein	Rv0157A, len: 42 aa. Conserved protein, showing similarity to C-terminal part (aa 186-220) of O53976|Rv1975|MTV051.13 conserved hypothetical protein from Mycobacterium tuberculosis (221 aa), FASTA scores: opt: 173, E(): 3e-06, (62.5% identity in 40 aa overlap).	I6WXK8	No	conserved hypotheticals								
NC_000962.3	Mycobrowser_v3	CDS	28362	29207	.	+	0	Rv0024	Rv0024	Unknown. The P60 protein is a major extracellular protein may be involved in the invasion of host cells.	Putative secreted protein P60-related protein	Rv0024, (MTCY10H4.24), len: 281 aa. Putative secreted protein, p60 homologue, similar to many. Similar to Mycobacterium tuberculosis proteins Rv1477, Rv1478, Rv1566c, Rv2190c. Could belong to the E. coli NLPC / listeria P60 family.	P71594	No	virulence, detoxification, adaptation		MMAR_0043		Mb0024,Mb0025				
NC_000962.3	Mycobrowser_v3	CDS	1947416	1947643	.	-	0	Rv1721c	vapB12	Unknown	Possible antitoxin VapB12	Rv1721c, (MTCY04C12.06c), len: 75 aa. Possible vapB12, antitoxin, part of toxin-antitoxin (TA) operon with Rv1720c (See Arcus et al., 2005; Pandey and Gerdes, 2005). Similar to others from Mycobacterium tuberculosis e.g. Rv0300|MTCY63.05|O07227 conserved hypothetical protein (73 aa). Start changed since original submission.	P9WJ53	No	virulence, detoxification, adaptation				Mb1750c				
NC_000962.3	Mycobrowser_v3	CDS	4434	4997	.	+	0	Rv0004	Rv0004	Function unknown	Conserved hypothetical protein	Rv0004, (MTCY10H4.02), len: 187 aa. Conserved hypothetical protein (see Salazar et al., 1996). Belongs to superfamily DUF721; this family contains several actinomycete proteins of unknown function.	P9WFL1	No	conserved hypotheticals	ML0004	MMAR_0004	MSMEG_0004	Mb0004				
NC_000962.3	Mycobrowser_v3	CDS	2337306	2337869	.	+	0	Rv2080	lppJ	Unknown	Lipoprotein LppJ	Rv2080, (MTCY49.19), len: 187 aa. LppJ, lipoprotein; contains prokayotic lipoprotein modification site (PS00013) and signal sequence at N-terminus.	P9WK77	No	cell wall and cell processes		MMAR_5467						
NC_000962.3	Mycobrowser_v3	CDS	42433	43365	.	-	0	Rv0040c	mtc28	Unknown	Secreted proline rich protein Mtc28 (proline rich 28 kDa antigen)	Rv0040c, (MTCY21D4.03c), len: 310 aa. Mtc28, secreted proline rich 28 kDa antigen protein (has hydrophobic stretch at N-terminus) (see citation below). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WIM9	No	cell wall and cell processes	ML0031,ML0031c	MMAR_0056	MSMEG_6919	Mb0041c				
NC_000962.3	Mycobrowser_v3	CDS	31514	31819	.	+	0	Rv0028	Rv0028	Unknown	Conserved hypothetical protein	Rv0028, (MTCY10H4.28), len: 101 aa. Conserved hypothetical unknown protein.	P9WM97	No	conserved hypotheticals		MMAR_0047		Mb0029				
NC_000962.3	Mycobrowser_v3	ncRNA	1471619	1471742	.	+	0	MTB000064	mcr3	Unknown	Putative small regulatory RNA	mcr3, putative small regulatory RNA (See DiChiara et al., 2010). 5'-end mapped by 5'RLM-RACE in M. bovis BGC Pasteur, 3'-end not mapped.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	33224	33553	.	+	0	Rv0030	Rv0030	Unknown	Conserved hypothetical protein	Rv0030, (MTCY10H4.30), len: 109 aa. Conserved hypothetical unknown protein.	P9WM95	No	conserved hypotheticals		MMAR_0049		Mb0031				
NC_000962.3	Mycobrowser_v3	CDS	33582	33794	.	+	0	Rv0031	Rv0031	Normally, required for the transposition of an insertion element.	Possible remnant of a transposase	Rv0031, (MTCY10H4.31), len: 70 aa. Possible remnant of a transposase, showing partial similarity to mycobacterial transposases in a short overlap, e.g. Rv2791c|MTV002_57 (459 aa), FASTA score: (72.2% identity in 36 aa overlap); Rv2885c, Rv2978c, Rv3827c, etc.	P71601	No	insertion seqs and phages				Mb0032				
NC_000962.3	Mycobrowser_v3	CDS	51828	52697	.	-	0	Rv0048c	Rv0048c	Unknown	Possible membrane protein	Rv0048c, MTCY21D4.11c, len: 289 aa. Possible membrane protein.	P9WM87	No	cell wall and cell processes	ML2690	MMAR_0067	MSMEG_6902	Mb0049c				
NC_000962.3	Mycobrowser_v3	rRNA	1476899	1477013	.	+	0	MTB000021	rrf	-	Ribosomal RNA 5S	rrf, 5S rRNA gene. Identical to Em_ba:MT5SRR, D10035 M.tuberculosis 5S rRNA, len: 116.		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	86528	87133	.	+	0	Rv0078	Rv0078	Possibly involved in transcriptional mechanism.	Probable transcriptional regulatory protein	Rv0078, (MTV030.22), len: 201 aa. Probable transcriptional regulator. Contains probable helix-turn-helix motif from aa 35 to 56 (Score 1348, +3.78 SD).	O53623	No	regulatory proteins	ML2677	MMAR_0224		Mb0080				
NC_000962.3	Mycobrowser_v3	tRNA	10887	10960	.	+	0	MTB000001	ileT	-	tRNA-Ile (GAT)	ileT, tRNA-Ile, anticodon gat, length = 74		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	11112	11184	.	+	0	MTB000002	alaT	-	tRNA-Ala (TGC)	alaT, tRNA-Ala, anticodon tgc, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	2123174	2123611	.	+	0	Rv1873	Rv1873	Unknown	Conserved hypothetical protein	Rv1873, (MTCY180.45c), len: 145 aa. Conserved hypothetical protein. Some similarity to AL591783 hypothetical protein from Sinorhizobium meliloti.	O07756	No	conserved hypotheticals			MSMEG_3577	Mb1904				
NC_000962.3	Mycobrowser_v3	CDS	1160095	1160433	.	-	0	Rv1036c	Rv1036c	Possibly required for the transposition of the insertion element IS1560.	Probable IS1560 transposase (fragment)	Rv1036c, (MTCY10G2.13), len: 112 aa. Probable IS1560 transposase fragment, similar to part of Rv3386|E1202304|MTV004.44 (234 aa) (82.8% identity in 87 aa overlap).	P96365	No	insertion seqs and phages				Mb1065c				
NC_000962.3	Mycobrowser_v3	CDS	882524	882763	.	+	0	Rv0787A	Rv0787A	Function unknown	Conserved protein	Rv0787A, len: 79 aa. Conserved protein, equivalent to MLCB5.24 hypothetical protein from Mycobacterium leprae (79 aa), FASTA scores: opt: 434, (84.8% identity in 79 aa overlap). Also similar to P12049|YEXA_BACSU hypothetical 9.7 kDa protein from Bacillus subtilis (84 aa), FASTA scores: opt: 172, E(): 4e-06, (44.4% identity in 72 aa overlap). Belongs to the UPF0062 family.	I6Y8S6	No	conserved hypotheticals	ML2219A	MMAR_4898	MSMEG_5832	Mb0811				
NC_000962.3	Mycobrowser_v3	CDS	2338065	2338505	.	-	0	Rv2081c	Rv2081c	Unknown	Conserved transmembrane protein	Rv2081c, (MTCY49.20c), len: 146 aa. Conserved transmembrane protein, similar to many. Hydrophobic stretch from aa 32-54.	P9WLK5	No	cell wall and cell processes				Mb2107c				
NC_000962.3	Mycobrowser_v3	CDS	1779194	1779298	.	-	0	Rv1572c	Rv1572c	Unknown	Conserved hypothetical protein	Rv1572c, (MTCY336.31B), len: 34 aa. Partial ORF, part of REP13E12 repeat element; 3' end of Rv1587c (MTCY336.17) after phage-like element (see citation below). Similar to C-terminal ends of other REP13E12 repeat elements e.g. Rv1148, Rv1945, Rv3467, etc. Length extended since first submission (+7 aa). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06618	No	insertion seqs and phages								
NC_000962.3	Mycobrowser_v3	CDS	25913	26881	.	-	0	Rv0021c	Rv0021c	Function unknown	Conserved hypothetical protein	Rv0021c, (MTCY10H4.21c), len: 322 aa. Conserved hypothetical protein, similar to various proteins.	P71591	No	conserved hypotheticals		MMAR_1721		Mb0021c				
NC_000962.3	Mycobrowser_v3	CDS	476394	476642	.	+	0	Rv0397A	Rv0397A	Unknown	Conserved protein	Rv0397A, len: 82 aa. Conserved protein.	I6Y3N9	No	conserved hypotheticals								
NC_000962.3	Mycobrowser_v3	CDS	1492320	1494425	.	-	0	Rv1327c	glgE	Function unknown; probably involved in polysaccharides degradation.	M1P-dependent maltosyltransferase GlgE	Rv1327c, (MTCY130.12c), len: 701 aa. Probable glgE, glucanase, similar to AF172946|AF172946_2 putative glucanase GlgE from Mycobacterium smegmatis (697 aa), FASTA scores: opt: 3816, E(): 0, (78.5% identity in 692 aa overlap). Similar to putative alpha-amylases e.g. Q9L1K2 Streptomyces coelicolor (675 aa), FASTA scores: opt: 2243, E(): 7.4e-132, (54.2% identity in 684 aa overlap). Start changed since original submission (-36) based on similarity to GlgE of Mycobacterium smegmatis; previous start at position 1494531.	P9WQ17	No	intermediary metabolism and respiration	ML1161,ML1161c	MMAR_4071	MSMEG_4916	Mb1362c				
NC_000962.3	Mycobrowser_v3	CDS	1	1524	.	+	0	Rv0001	dnaA	Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (DNAA box): 5'-TTATC(C/A)A(C/A)A-3'. DNAA binds to ATP and to acidic phospholipids. DNAA protein binds the origin of replication (oriC), ATP and ADP, and exhibited weak ATPase activity.	Chromosomal replication initiator protein DnaA	Rv0001, (MT0001, MTV029.01, P49993), len: 507 aa. dnaA, chromosomal replication initiator protein (see citations below), equivalent to other Mycobacterial chromosomal replication initiator proteins. Also highly similar to others except in N-terminus e.g. Q9ZH75|DNAA_STRCH chromosomal replication initiator protein from Streptomyces chrysomallus (624 aa). Contains PS00017 ATP/GTP-binding site motif A (P-loop) and PS01008 DnaA protein signature. Belongs to the DnaA family. Note that the first base of this gene has been taken as base 1 of the Mycobacterium tuberculosis H37Rv genomic sequence.	P9WNW3	No	information pathways	ML0001	MMAR_0001	MSMEG_6947	Mb0001				
NC_000962.3	Mycobrowser_v3	CDS	2716395	2717138	.	-	0	Rv2418c	octT	Transfers octanoate to glucosylglycerate (GG) and diglucosylglycerate (DGG), the earliest intermediates in methylglucose lipopolysaccharides (MGLP) biosynthesis (see Maranha et al. 2015).	Sugar octanoyltransferase OctT	Enzymatic studies, synthetic chemistry, NMR spectroscopy and mass spectrometry approaches suggest that, in contrast to the prevailing consensus, octanoate is not esterified to the primary hydroxyl group of glycerate but instead to the C6 OH of the second glucose in DGG (see Maranha et al. 2015).	P71725	No	conserved hypotheticals		MMAR_3746	MSMEG_4578	Mb2441c				
NC_000962.3	Mycobrowser_v3	CDS	2052	3260	.	+	0	Rv0002	dnaN	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA [catalytic activity: N deoxynucleoside triphosphate = N diphosphate + {DNA}N].	DNA polymerase III (beta chain) DnaN (DNA nucleotidyltransferase)	Rv0002, (MTV029.02, MTCY10H4.0), len: 402 aa. DnaN, DNA polymerase III (beta chain) (see citations below), equivalent to other Mycobacterial DNA polymerases III beta chain. Also highly similar to others e.g. P27903|DP3B_STRCO DNA polymerase III beta chain from Streptomyces coelicolor (376 aa). Overlaps and extends CDS in neighbouring cosmid MTCY10H4.01.	P9WNU1	No	information pathways	ML0002	MMAR_0002	MSMEG_0001	Mb0002				
NC_000962.3	Mycobrowser_v3	CDS	3280	4437	.	+	0	Rv0003	recF	The RECF protein is involved in DNA metabolism and recombination; it is required for DNA replication and normal sos inducibility. RECF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP.	DNA replication and repair protein RecF (single-strand DNA binding protein)	Rv0003, (MTCY10H4.01), len: 385 aa. RecF, DNA replication and repair protein (see citations below), equivalent to other mycobacterial DNA replication and repair proteins. Also highly similar to many others. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00617 RecF protein signature 1, and PS00618 RecF protein signature 2. Belongs to the RecF family.	P9WHI9	No	information pathways	ML0003	MMAR_0003	MSMEG_0003	Mb0003				
NC_000962.3	Mycobrowser_v3	CDS	7302	9818	.	+	0	Rv0006	gyrA	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings [catalytic activity: ATP-dependent breakage, passage and rejoining of double-stranded DNA].	DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)	Rv0006, (MTCY10H4.04), len: 838 aa. GyrA, DNA gyrase subunit A (see citations below). Contains PS00018 EF-hand calcium-binding domain.	P9WG47	No	information pathways	ML0006	MMAR_0006	MSMEG_0006	Mb0006				
NC_000962.3	Mycobrowser_v3	CDS	9914	10828	.	+	0	Rv0007	Rv0007	Unknown	Possible conserved membrane protein	Rv0007, (MTCY10H4.05), len: 304 aa. Possible conserved membrane protein. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WMA7	No	cell wall and cell processes	ML0007	MMAR_0007	MSMEG_0007	Mb0007				
NC_000962.3	Mycobrowser_v3	CDS	11874	12311	.	-	0	Rv0008c	Rv0008c	Unknown	Possible membrane protein	Rv0008c, (MTCY10H4.07c), len: 145 aa. Possible membrane protein.	P9WJF3	No	cell wall and cell processes	ML0010,ML0010c	MMAR_0010	MSMEG_0023	Mb0008c				
NC_000962.3	Mycobrowser_v3	CDS	12468	13016	.	+	0	Rv0009	ppiA	PPIases accelerate the folding of proteins [catalytic activity: cis-trans isomerization of proline imidic peptide bonds in oligopeptides].	Probable iron-regulated peptidyl-prolyl cis-trans isomerase A PpiA (PPIase A) (rotamase A)	Rv0009, (MTCY10H4.08), len: 182 aa. Probable ppiA (alternate gene name: cfp22), iron-regulated peptidyl-prolyl cis-trans isomerase A. Belongs to the cyclophilin-type PPIase family. Alternative start codon has been suggested.	P9WHW3	No	information pathways	ML0011	MMAR_0011	MSMEG_0024	Mb0009				
NC_000962.3	Mycobrowser_v3	CDS	583375	583704	.	-	0	Rv0492A	Rv0492A	Unknown	Hypothetical protein	Rv0492A, len: 109 aa. Hypothetical unknown protein. GC plot suggests CDS.	Q6MX36	No	conserved hypotheticals		MMAR_0818		Mb0503c				
NC_000962.3	Mycobrowser_v3	CDS	13133	13558	.	-	0	Rv0010c	Rv0010c	Unknown	Probable conserved membrane protein	Rv0010c, (MTCY10H4.10c), len: 141 aa. Probable conserved membrane protein. Belongs to superfamily DUF2581, conserved in the Actinomycetales. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WMA3	No	cell wall and cell processes	ML0012,ML0012c	MMAR_0012	MSMEG_0025	Mb0010c				
NC_000962.3	Mycobrowser_v3	CDS	13714	13995	.	-	0	Rv0011c	Rv0011c	Unknown	Probable conserved transmembrane protein	Rv0011c, (MTCY10H4.11c), len: 93 aa. Probable conserved transmembrane protein. Belongs to uncharacterized protein family UPF0233. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WP57	No	cell wall and cell processes	ML0013,ML0013c	MMAR_0013	MSMEG_0026	Mb0011c				
NC_000962.3	Mycobrowser_v3	CDS	14089	14877	.	+	0	Rv0012	Rv0012	Unknown	Probable conserved membrane protein	Rv0012, (MTCY10H4.12), len: 262 aa. Probable conserved membrane protein. Belongs to superfamily DUF881. Contains probable N-terminal signal sequence.	L0T243	No	cell wall and cell processes	ML0014	MMAR_0014	MSMEG_0027	Mb0012				
NC_000962.3	Mycobrowser_v3	CDS	15590	17470	.	-	0	Rv0014c	pknB	Involved in signal transduction (via phosphorylation). Thought to regulate cell division/differentiation. Can phosphorylate the peptide substrate myelin basic protein (MBP) [catalytic activity: ATP + a protein = ADP + a phosphoprotein].	Transmembrane serine/threonine-protein kinase B PknB (protein kinase B) (STPK B)	Rv0014c, (MTCY10H4.14c), len: 626 aa. PknB, transmembrane serine/threonine-protein kinase (see citations below). Contains PS00107 Protein kinases ATP-binding region signature, and PS00108 Serine/Threonine protein kinases active-site signature. Contains Hank's kinase subdomain. Belongs to the Ser/Thr family of protein kinases. Experimental studies show evidence of auto-phosphorylation on serine/threonine residues. PknB has been shown to be a substrate for PstP and its kinase activity is affected by PstP-mediated dephosphorylation. PknB and PstP (Rv0018c) may act as a functional pair in vivo to control mycobacterial cell growth.	P9WI81	No	regulatory proteins	ML0016,ML0016c	MMAR_0016	MSMEG_0028	Mb0014c				
NC_000962.3	Mycobrowser_v3	CDS	18759	20234	.	-	0	Rv0016c	pbpA	Involved in peptidoglycan synthesis (at the final stages). Cell wall formation; PBPA is supposed to be responsible for the determination of the rod shape of the cell. It synthesizes cross-linked peptidoglycan from lipid intermediates.	Probable penicillin-binding protein PbpA	Rv0016c, (MTCY10H4.16c), len: 491 aa. Probable pbpA, penicillin-binding protein, similar to many.	P9WKD1	No	cell wall and cell processes	ML0018,ML0018c	MMAR_0018	MSMEG_0031	Mb0016c				
NC_000962.3	Mycobrowser_v3	CDS	21637	23181	.	-	0	Rv0018c	pstP	Involved in regulation (using dephosphorylation of a specific phosphorylated substrate).	Phosphoserine/threonine phosphatase PstP	Rv0018c, (MTCY10H4.18c), len: 514 aa. PstP, phosphoserine/threonine phosphatase. Experimental studies have shown that PstP specifically dephosporylates model phospho-Ser/Thr substrates and it is likely that PknB (Rv0014c) and PstP may act as a functional pair in vivo to control mycobacterial cell growth (See Boitel et al., 2003).	P9WHW5	No	regulatory proteins	ML0020,ML0020c	MMAR_0020	MSMEG_0033	Mb0018c				
NC_000962.3	Mycobrowser_v3	CDS	39877	41202	.	-	0	Rv0037c	Rv0037c	Unknown; possibly involved in transport of macrolide across the membrane.	Probable conserved integral membrane protein	Rv0037c, (MTCY10H4.37c), len: 441 aa. Probable conserved integral membrane protein, member of major facilitator superfamily (MFS) possibly involved in transport of macrolide.	P9WJY1	No	cell wall and cell processes	ML0027,ML0027c	MMAR_0052	MSMEG_6922	Mb0038c				
NC_000962.3	Mycobrowser_v3	CDS	375914	376585	.	+	0	Rv0306	Rv0306	Function unknown; probably involved in cellular metabolism.	Putative oxidoreductase	Rv0306, (MTCY63.11), len: 223 aa. Putative oxidoreductase, highly similar to H83485|9947208|AAG04663.1|AE004557_4|AE004557 conserved hypothetical protein from Pseudomonas aeruginosa strain PAO1 (218 aa); and to other putative oxidoreductases e.g. middle part of CAB76073.1|AL157953 putative nitroreductase from Streptomyces coelicolor (1212 aa); Q52685|BLUB protein involved in cobalamin (vitamin B12) synthesis from Rhodobacter capsulatus (206 aa), FASTA scores: opt: 318, E(): 2e-15, (35.6% identity in 191 aa overlap).	O07233	No	intermediary metabolism and respiration		MMAR_0555	MSMEG_6053	Mb0314				
NC_000962.3	Mycobrowser_v3	CDS	27595	28365	.	+	0	Rv0023	Rv0023	Possibly involved in transcriptional mechanism.	Possible transcriptional regulatory protein	Rv0023, (MTCY10H4.23), len: 256 aa. Possible transcriptional regulator. Contains probable helix-turn helix motif from aa 19 to 40 (Score 1615, +4.69 SD).	P9WMI3	No	regulatory proteins		MMAR_0042		Mb0023				
NC_000962.3	Mycobrowser_v3	CDS	29245	29607	.	+	0	Rv0025	Rv0025	Function unknown	Conserved hypothetical protein	Rv0025, (MTCY10H4.25), len: 120 aa. Conserved hypothetical protein, showing some similarity to other proteins from Mycobacterium tuberculosis e.g. Rv0739 (268 aa), FASTA score: (37.6% identity in 101 aa overlap), and Rv0026 FASTA score: (35.4% identity in 113 aa overlap); etc.	P9WMA1	No	conserved hypotheticals		MMAR_0044		Mb0026				
NC_000962.3	Mycobrowser_v3	CDS	29722	31068	.	+	0	Rv0026	Rv0026	Function unknown	Conserved hypothetical protein	Rv0026, (MTCY10H4.26), len: 448 aa. Conserved hypothetical protein, showing some similarity to other proteins from Mycobacterium tuberculosis: Rv0025 FASTA score: (35.4% identity in 113 aa overlap) and Rv0739 (268 aa), FASTA score: (32.4% identity in 142 aa overlap).	P9WMB1	No	conserved hypotheticals		MMAR_0045		Mb0027				
NC_000962.3	Mycobrowser_v3	CDS	31189	31506	.	+	0	Rv0027	Rv0027	Unknown	Conserved hypothetical protein	Rv0027, (MTCY10H4.27), len: 105 aa. Conserved hypothetical unknown protein.	P9WM99	No	conserved hypotheticals		MMAR_0046		Mb0028				
NC_000962.3	Mycobrowser_v3	CDS	32057	33154	.	+	0	Rv0029	Rv0029	Function unknown	Conserved hypothetical protein	Rv0029, (MTCY10H4.29), len: 365 aa. Conserved hypothetical protein, showing some similarity to other proteins from Mycobacterium tuberculosis e.g. C-terminal region of Rv2082; Rv3899c.	P71599	No	conserved hypotheticals		MMAR_0048		Mb0030				
NC_000962.3	Mycobrowser_v3	CDS	34295	36610	.	+	0	Rv0032	bioF2	Could be involved in biotin biosynthesis (at the first step) [catalytic activity: 6-carboxyhexanoyl-CoA + L-alanine = 8-amino-7-oxononanoate + CoA + CO2].	Possible 8-amino-7-oxononanoate synthase BioF2 (AONS) (8-amino-7-ketopelargonate synthase) (7-keto-8-amino-pelargonic acid synthetase) (7-KAP synthetase) (L-alanine--pimelyl CoA ligase)	Rv0032, (MTCY10H4.32), len: 771 aa. Probable bioF2, 8-amino-7-oxononanoate synthase, with its C-terminal similar to others. Contains PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site. Belongs to class-II of pyridoxal-phosphate-dependent aminotransferases.	P9WQ85	No	intermediary metabolism and respiration				Mb0033				
NC_000962.3	Mycobrowser_v3	CDS	36607	36870	.	+	0	Rv0033	acpA	Key component in de novo fatty acid biosynthesis. This protein is supposed to be the carrier of the growing fatty acid chain in fatty acid biosynthesis.	Probable acyl carrier protein AcpA (ACP)	Rv0033, (MTCY10H4.33), len: 87 aa. Probable acpA (alternate gene name: acpP), acyl carrier protein, similar to others. Also similar to proteins of Mycobacterium tuberculosis Rv1344 and Rv2244 (31.5% identity in 73 aa overlap).	I6WX95	No	lipid metabolism				Mb0034				
NC_000962.3	Mycobrowser_v3	CDS	36867	37262	.	+	0	Rv0034	Rv0034	Function unknown	Conserved hypothetical protein	Rv0034, (MTCY10H4.34), len: 131 aa. Conserved hypothetical protein, showing weak similarity to AE001980|AE001980_7 hypothetical protein from Deinococcus radiodurans (120 aa), FASTA scores: opt: 141, E(): 0.0028, (29.3% identity in 123 aa overlap).	P9WM93	No	conserved hypotheticals				Mb0035				
NC_000962.3	Mycobrowser_v3	CDS	41304	41912	.	+	0	Rv0038	Rv0038	Function unknown	Conserved protein	Rv0038, (MTCY10H4.38), len: 202 aa. Conserved protein, similar to many.	P9WFK5	No	conserved hypotheticals	ML0028	MMAR_0053	MSMEG_6921	Mb0039				
NC_000962.3	Mycobrowser_v3	CDS	42004	42351	.	-	0	Rv0039c	Rv0039c	Unknown	Possible conserved transmembrane protein	Rv0039c, (MTCY21D4.02c, MTCY10H4.39c), len: 115 aa. Possible conserved transmembrane protein. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WM89	No	cell wall and cell processes	ML0030,ML0030c	MMAR_0055	MSMEG_6920	Mb0040c				
NC_000962.3	Mycobrowser_v3	CDS	43562	46471	.	+	0	Rv0041	leuS	Involved in translation mechanism [catalytic activity: ATP + L-leucine + tRNA(LEU) = AMP + diphosphate + L-leucyl-tRNA(LEU)].	Probable leucyl-tRNA synthetase LeuS (leucine--tRNA ligase) (LEURS)	Rv0041, (MTCY21D4.04), len: 969 aa. Probable leucyl-tRNA synthetase, similar to many. Contains PS00178 Aminoacyl-transfer RNA synthetases class-I signature. Belongs to class-I aminoacyl-tRNA synthetase family.	P9WFV1	No	information pathways	ML0032	MMAR_0057	MSMEG_6917	Mb0042				
NC_000962.3	Mycobrowser_v3	CDS	51185	51727	.	-	0	Rv0047c	Rv0047c	Function unknown	Conserved protein	Rv0047c, (MTCY21D4.10c), len: 180 aa. Conserved protein, similar to many.	P71704	No	conserved hypotheticals	ML2691	MMAR_0066	MSMEG_6903	Mb0048c				
NC_000962.3	Mycobrowser_v3	CDS	418949	419608	.	+	0	Rv0349	Rv0349	Unknown	Hypothetical protein	Rv0349, (MTCY13E10.09), len: 219 aa. Hypothetical unknown protein. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06300	No	conserved hypotheticals				Mb0357				
NC_000962.3	Mycobrowser_v3	CDS	52831	53244	.	+	0	Rv0049	Rv0049	Function unknown	Conserved hypothetical protein	Rv0049, (MTCY21D4.12), len: 137 aa. Conserved hypothetical protein. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WM85	No	conserved hypotheticals	ML2689,ML2689c	MMAR_0068	MSMEG_6901	Mb0050				
NC_000962.3	Mycobrowser_v3	CDS	53663	55699	.	+	0	Rv0050	ponA1	Involved in peptidoglycan synthesis (at the final stages), cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits).	Probable bifunctional penicillin-binding protein 1A/1B PonA1 (murein polymerase) (PBP1): penicillin-insensitive transglycosylase (peptidoglycan TGASE) + penicillin-sensitive transpeptidase (DD-transpeptidase)	Rv0050, (MTCY21D4.13), len: 678 aa. Probable ponA1, penicillin-binding protein (class A), bienzymatic protein with transglycosylase and transpeptidase activities (see Graham & Clark-Curtiss 1999), highly similar to many (see Billman-Jacobe et al., 1999). Belongs to the transglycosylase family in the N-terminal section, and to the transpeptidase family in the C-terminal section.	P71707	No	cell wall and cell processes	ML2688,ML2688c	MMAR_0069	MSMEG_6900	Mb0051				
NC_000962.3	Mycobrowser_v3	CDS	58192	58482	.	+	0	Rv0053	rpsF	Binds together with S18 to 16S ribosomal RNA.	30S ribosomal protein S6 RpsF	Rv0053, (MTCY21D4.16), len: 96 aa. rpsF, 30S ribosomal protein S6, highly similar to many. Contains PS01048 Ribosomal protein S6 signature. Belongs to the S6P family of ribosomal proteins.	P9WH31	No	information pathways	ML2685,ML2685c	MMAR_0072	MSMEG_6897	Mb0054				
NC_000962.3	Mycobrowser_v3	CDS	63909	64967	.	+	0	Rv0060	Rv0060	Function unknown	Conserved hypothetical protein	Rv0060, (MTV030.03), len: 352 aa. Conserved hypothetical protein.	O53605	No	conserved hypotheticals				Mb0061				
NC_000962.3	Mycobrowser_v3	CDS	65012	65350	.	-	0	Rv0061c	Rv0061c	Unknown	Hypothetical protein	Rv0061c, len: 112 aa. Conserved hypothetical protein supported by RNA-seq data. Similar to MMAR_3839, 76% identity in 112 aa overlap. Replaces questionable ORF Rv0061 (MTV030.04).	I6X8E6	No	conserved hypotheticals				Mb0062				
NC_000962.3	Mycobrowser_v3	CDS	65552	66694	.	+	0	Rv0062	celA1	The biological conversion of cellulose to glucose generally requires three types of hydrolytic enzymes: (1) endoglucanases which cut internal beta-1,4-glucosidic bonds; (2) exocellobiohydrolases that cut the dissaccharide cellobiose from the nonreducing end of the cellulose polymer chain; (3) beta-1,4-glucosidases which hydrolyze the cellobiose and other short cello-oligosaccharides to glucose [catalytic activity:endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose].	Possible cellulase CelA1 (endoglucanase) (endo-1,4-beta-glucanase) (FI-cmcase) (carboxymethyl cellulase)	Rv0062, (MTV030.05), len: 380 aa. Possible celA1, cellulase, similar to many. Seems to belong to cellulase family B (family 6 of glycosyl hydrolases). Note that previously known as celA.	Q79G13	No	intermediary metabolism and respiration		MMAR_0107	MSMEG_6752	Mb0063				
NC_000962.3	Mycobrowser_v3	CDS	72274	74511	.	-	0	Rv0066c	icd2	Involved in the KREBS cycle [catalytic activity: isocitrate + NADP+ = 2-oxoglutarate + CO(2) + NADPH].	Probable isocitrate dehydrogenase [NADP] Icd2 (oxalosuccinate decarboxylase) (IDH) (NADP+-specific ICDH) (IDP)	Rv0066c, (MTV030.09c), len: 745 aa. Probable icd2, isocitrate dehydrogenase NADP-dependent. Belongs to the monomeric-type family of IDH. Note that in H37Rv, Rv0066c is named icd2 and Rv3339c is icd1 while in CDC1551 and Erdman strains, Rv0066c is icd1 and Rv3339c is icd2.	O53611	No	intermediary metabolism and respiration	ML2672,ML2672c	MMAR_0158	MSMEG_1654	Mb0067c				
NC_000962.3	Mycobrowser_v3	CDS	75301	76212	.	+	0	Rv0068	Rv0068	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase	Rv0068, (MTV030.11), len: 303 aa. Probable oxidoreductase, similar to many.	O53613	No	intermediary metabolism and respiration	ML0315,ML0315c		MSMEG_0876	Mb0069				
NC_000962.3	Mycobrowser_v3	CDS	76237	77622	.	-	0	Rv0069c	sdaA	Involved in gluconeogenesis from serine [catalytic activity: L-serine + H2O = pyruvate + NH3 + H2O].	Probable L-serine dehydratase SdaA (L-serine deaminase) (SDH) (L-SD)	Rv0069c, (MTV030.12c), len: 461 aa. Probable sdaA, L-serine dehydratase. Belongs to the iron-sulfur dependent L-serine dehydratase family. Cofactor: iron-sulfur (4FE-4S) (probable).	P9WGT5	No	intermediary metabolism and respiration	ML1755,ML1755c	MMAR_0207		Mb0070c				
NC_000962.3	Mycobrowser_v3	CDS	81676	82668	.	+	0	Rv0073	Rv0073	Thought to be involved in active transport of glutamine across the membrane (import). Responsible for the translocation of the substrate across the membrane.	Probable glutamine-transport ATP-binding protein ABC transporter	Rv0073, (MTV030.17), len: 330 aa. Probable glutamine-transport ATP-binding protein ABC-transporter (see citation below), similar to many ATP-binding proteins. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and PS00889 Cyclic nucleotide-binding domain signature 2. Belongs to the ATP-binding transport protein family (ABC transporters). Note that supposed act with near ORF Rv0072|MTV030.16 transmembrane ABC-transporter.	P9WQK5	No	cell wall and cell processes		MMAR_0216		Mb0074,Mb0075				
NC_000962.3	Mycobrowser_v3	CDS	85636	86466	.	-	0	Rv0077c	Rv0077c	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase	Rv0077c, (MTV030.21c), len: 276 aa. Possible oxidoreductase, weakly similar to others from Streptomyces. Also similar to MTCY05A6_35 and MTCY1A11_10 from Mycobacterium tuberculosis. And shows some similarity in part with AAL17935.1|AY054120 putative epoxide hydrolase from Mycobacterium smegmatis (203 aa).	O53622	No	intermediary metabolism and respiration	ML2676,ML2676c		MSMEG_6763	Mb0079c				
NC_000962.3	Mycobrowser_v3	CDS	87208	87801	.	-	0	Rv0078A	Rv0078A	Unknown	Hypothetical protein	Rv0078A, len: 197 aa. Hypothetical unknown protein. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	L7N686	No	conserved hypotheticals				Mb0081c				
NC_000962.3	Mycobrowser_v3	CDS	87798	88004	.	-	0	Rv0078B	Rv0078B	Unknown	Conserved protein	Rv0078B, len: 68 aa. Conserved protein.	I6X8G2	No	conserved hypotheticals								
NC_000962.3	Mycobrowser_v3	CDS	88204	89025	.	+	0	Rv0079	Rv0079	Unknown	Unknown protein	Rv0079, (MTV030.23), len: 273 aa. Unknown protein. Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WMA9	No	conserved hypotheticals		MMAR_3705	MSMEG_3935	Mb0082				
NC_000962.3	Mycobrowser_v3	CDS	89022	89480	.	+	0	Rv0080	Rv0080	Function unknown	Conserved hypothetical protein	Rv0080, (MTV030.24), len: 152 aa. Conserved hypothetical protein. Belongs to pyridoxine 5'-phosphate (PNP) oxidase-like (PNPOx-like) superfamily.	P9WMA5	No	conserved hypotheticals			MSMEG_5136	Mb0083				
NC_000962.3	Mycobrowser_v3	CDS	90400	92322	.	+	0	Rv0083	Rv0083	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase	Rv0083, (MTV030.27, MTCY251.01), len: 640 aa. Probable oxidoreductase, showing some similarity to other various oxidoreductases. Nucleotide position 91071 in the genome sequence has been corrected, T:C resulting in I224I.	P9WIW3	No	intermediary metabolism and respiration		MMAR_1655		Mb0086				
NC_000962.3	Mycobrowser_v3	CDS	1211560	1213863	.	+	0	Rv1087	PE_PGRS21	Function unknown	PE-PGRS family protein PE_PGRS21	Rv1087, (MTV017.40), len: 767 aa. PE_PGRS21, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citation below). Similar to Rv1090|AL021897|MTV017_43 Mycobacterium tuberculosis H37Rv (853 aa), FASTA scores: opt: 2819, E(): 0, (59.8% identity in 860 aa overlap). Contains PS00583 pfkB family of carbohydrate kinases signature 1 near C -terminus. Predicted to be an outer membrane protein (See Song et al., 2008).	Q79FT0	No	PE/PPE		MMAR_4224		Mb1116				
NC_000962.3	Mycobrowser_v3	CDS	98480	99250	.	+	0	Rv0090	Rv0090	Unknown	Possible membrane protein	Rv0090, (MTCY251.08), len: 256 aa. Possible membrane protein. Contains IPR014511 Protein of unknown function DUF2068, transmembrane, subgroup.	P9WM71	No	cell wall and cell processes	ML2653	MMAR_0246		Mb0093				
NC_000962.3	Mycobrowser_v3	CDS	99684	100451	.	+	0	Rv0091	mtn	Responsible for cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH) [catalytic activity 1: methylthioadenosine + H2O = adenine + 5-methylthio-D-ribose] [catalytic activity 2: S-adenosyl-L-homocysteine + H2O = adenine + S-D-ribosyl-L-homocysteine].	Probable bifunctional MTA/SAH nucleosidase Mtn: 5'-methylthioadenosine nucleosidase (methylthioadenosine methylthioribohydrolase) + S-adenosylhomocysteine nucleosidase (S-adenosyl-L-homocysteine homocysteinylribohydrolase)	Rv0091, (MTCY251.10), len: 255 aa. Probable mtn (alternate gene name: pfs), methylthioadenosine/S-Adenosylhomocysteine nucleosidase (MTA/SAH nucleosidase), including 5'-methylthioadenosine nucleosidase and S-adenosylhomocysteine nucleosidase, similar to others. Belongs to the MTN family.	P9WJM3	No	intermediary metabolism and respiration		MMAR_0251	MSMEG_1753	Mb0094				
NC_000962.3	Mycobrowser_v3	CDS	100583	102868	.	+	0	Rv0092	ctpA	Cation-transporting ATPase; possibly catalyzes the transport of a cation (possibly copper) with the hydrolyse of ATP [catalytic activity: ATP + H(2)O + cation(in) = ADP + phosphate + cation(out)].	Cation transporter P-type ATPase a CtpA	Rv0092, (MTCY251.11), len: 761 aa. CtpA, cation-transporting P-type ATPase a (transmembrane protein), highly similar to many. Contains PS01047 Heavy-metal-associated domain, and PS00154 E1-E2 ATPases phosphorylation site. Belongs to the cation transport ATPases family (E1-E2 ATPases), subfamily IB.	P9WPU1	No	cell wall and cell processes	ML1987	MMAR_0264		Mb0095				
NC_000962.3	Mycobrowser_v3	CDS	105324	106715	.	+	0	Rv0096	PPE1	Function unknown	PPE family protein PPE1	Rv0096, (MTCY251.15), len: 463 aa. PPE1, Member of the Mycobacterium tuberculosis PPE family, similar to many. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WI49	No	PE/PPE	ML1991	MMAR_0261		Mb0099				
NC_000962.3	Mycobrowser_v3	CDS	108156	109778	.	+	0	Rv0099	fadD10	Function unknown, but involvement in lipid degradation.	Possible fatty-acid-CoA ligase FadD10 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv0099, (MTCY251.18), len: 540 aa. Possible fadD10, fatty-acid-CoA synthetase, similar to many. Contains PS00455 putative AMP-binding domain signature. Contains IPR000873 AMP-dependent synthetase/ligase domain. Belongs to the ATP-dependent AMP-binding enzyme family.	P9WQ55	No	lipid metabolism	ML1994	MMAR_0258		Mb0102				
NC_000962.3	Mycobrowser_v3	CDS	110001	117539	.	+	0	Rv0101	nrp	Involved in lipid metabolism.	Probable peptide synthetase Nrp (peptide synthase)	Rv0101, (MTCY251.20), len: 2512 aa. Probable nrp, peptide synthetase, similar to others e.g. AAD44234.1|AF143772_40|PstB peptide synthetase from Mycobacterium avium (2552 aa); 7476034|S77657 cyclic peptide synthetase from Mycobacterium leprae (1401 aa), FASTA scores: opt: 4268, E(): 0, (65.7% identity in 1091 aa overlap); part of CAB55600.1|AJ238027 peptide synthetase from Mycobacterium smegmatis (5990). Also similar to e.g. AAD56240.1|AF184977_1|AF184977 DhbF protein from Bacillus subtilis (2378 aa); SRF1_BACSU|P27206 surfactin synthetase subunit 1 (3587 aa), FASTA scores: opt: 1708, E(): 0, (30.6% identity in 1633 aa overlap): etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), 2 x PS00455 Putative AMP-binding domain signature, and PS00012 Phosphopantetheine attachment site. Belongs to the ATP-dependent AMP-binding enzyme family. Thought to be not involved in mycobactin biosynthesis (see citation below).	Q10896	No	lipid metabolism	ML1996			Mb0104				
NC_000962.3	Mycobrowser_v3	CDS	117714	119699	.	+	0	Rv0102	Rv0102	Unknown	Probable conserved integral membrane protein	Rv0102, (MTCY251.21), len: 661 aa. Probable conserved integral membrane protein, highly similar to P53525|Y102_MYCLE|ML1998|NP_302349.1|NC_002677 possible membrane protein from Mycobacterium leprae (659 aa), FASTA scores: opt: 3107, E(): 0, (70.2% identity in 662 aa overlap). Also similar to others e.g. CAC01497.1|AL391017 putative integral membrane protein from Streptomyces coelicolor (316 aa); etc. Contains PS00343 Gram-positive cocci surface proteins 'anchoring' hexapeptide.	P9WM63	No	cell wall and cell processes	ML1998	MMAR_0267	MSMEG_4702	Mb0105				
NC_000962.3	Mycobrowser_v3	CDS	124374	125570	.	+	0	Rv0106	Rv0106	Function unknown	Conserved hypothetical protein	Rv0106, (MTCY251.25), len: 398 aa. Conserved hypothetical protein, similar to others e.g. AL049841|SCE9_33 from Streptomyces coelicolor (370 aa), FASTA scores: opt: 282, E(): 2.5e-11, (32.0% identity in 381 aa overlap); etc. Some similarity to P94400 homologue to nitrile hydratase region from Bacillus subtilis (397 aa), FASTA scores: opt: 226, E(): 5.4e-08, (26.4% identity in 405 aa overlap). Also similar to COBW_PSEDE|P29937 FASTA score: (25.3% identity in 186 aa overlap); and P47K_PSECL|P31521 47 kDa protein (p47k) (419 aa), FASTA score: (25.9% identity in 401 aa overlap).	P9WPI5	No	conserved hypotheticals			MSMEG_6069	Mb0109				
NC_000962.3	Mycobrowser_v3	CDS	131382	132872	.	+	0	Rv0109	PE_PGRS1	Function unknown	PE-PGRS family protein PE_PGRS1	Rv0109, (MTV031.03c), len: 496 aa. PE_PGRS1, Member of the M. tuberculosis PE family, PGRS subfamily of gly-rich proteins (see Brennan and Delogu, 2002), highly similar to many e.g. Q50615|Y0DP_MYCTU hypothetical glycine-rich 40.8 kDa protein from Mycobacterium tuberculosis (498 aa), FASTA scores: opt: 1772, E(): 0, (57.3% identity in 513 aa overlap); etc.	L0T2H7	No	PE/PPE		MMAR_0299		Mb0113				
NC_000962.3	Mycobrowser_v3	CDS	137319	137909	.	+	0	Rv0113	gmhA	Involved in biosynthesis of nucleotide-activated glycero-manno-heptose: synthesis of glyceromannoheptose 7-phosphate (inner core lipopolysaccharide biosynthesis) [catalytic activity: D-sedoheptulose 7-phosphate = D-glycero-alpha,beta-D-manno-heptose 7-phosphate].	Probable sedoheptulose-7-phosphate isomerase GmhA (phosphoheptose isomerase)	Rv0113, (MTV031.07), len: 196 aa. Probable gmhA (alternate gene name: lpcA), sedoheptulose-7-phosphate isomerase (see citation below), similar to many e.g. AE0005|HPAE000596_11 from Helicobacter pylori (192 aa), FASTA scores: opt: 451, E(): 1.9e-24, (45.1% identity in 162 aa overlap). Belongs to the sis family, LPCA subfamily. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WGG1	No	cell wall and cell processes				Mb0117				
NC_000962.3	Mycobrowser_v3	CDS	137941	138513	.	+	0	Rv0114	gmhB	Involved in biosynthesis of nucleotide-activated glycero-manno-heptose. Involved in two pathways, D-alpha-D pathway [catalytic activity: D-glycero-alpha-D-manno-heptose 1,7-biphosphate = D-glycero-alpha-D-manno-heptose 1-phosphate] and L-beta-D pathway [catalytic activity: D-glycero-beta-D-manno-heptose 1,7-biphosphate = D-glycero-beta-D-manno-heptose 1-phosphate].	Possible D-alpha,beta-D-heptose-1,7-biphosphate phosphatase GmhB (D-glycero-D-manno-heptose 7-phosphate kinase)	Rv0114, (MTV031.08), len: 190 aa. Possible gmhB, D-alpha,beta-D-heptose-1,7-biphosphate phosphatase (see citation below), similar to several hypothetical proteins and phosphatases e.g. HIS7_ECOLI|P06987 imidazoleglycerol-phosphate dehydratase (355 aa), FASTA scores: opt: 250, E(): 3.6e-11, (34.0 % identity in 141 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WMV3	No	cell wall and cell processes				Mb0118				
NC_000962.3	Mycobrowser_v3	CDS	142128	143876	.	-	0	Rv0118c	oxcA	Involved in catabolism of oxalic acid [catalytic activity: oxalyl-CoA = formyl-CoA + CO2].	Probable oxalyl-CoA decarboxylase OxcA	Rv0118c, (MTV031.12c), Len: 582 aa. Probable oxcA, oxalyl-CoA decarboxylase, highly similar to many e.g. P78093|OXC_ECOLI|7449483|B65011|YFDU|B2373|Z3637|ECS325 probable oxalyl-CoA decarboxylase from Escherichia coli (564 aa); M77128|OXAOXA_1 oxalyl-CoA decarboxylase from Oxalobacter formigenes (568 aa), FASTA scores: opt: 2124, E():0, (55.6% identity in 568 aa overlap). Also similar to mycobacterial IlvB proteins e.g. MLCB1788.46c unknown TPP-requiring enzyme from Mycobacterium leprae (548 aa); and AL0086|MLCB1788_19 from Mycobacterium leprae (548 aa), FASTA scores: opt: 831, E(): 0, (33.9% identity in 567 aa overlap).	O53639	No	intermediary metabolism and respiration	ML2662	MMAR_0318	MSMEG_0157,MSMEG_5297	Mb0122c				
NC_000962.3	Mycobrowser_v3	CDS	151148	152215	.	+	0	Rv0125	pepA	Function unknown; possibly hydrolyzes peptides and/or proteins (seems to cleave preferentially after serine residues).	Probable serine protease PepA (serine proteinase) (MTB32A)	Rv0125, (MTCI418B.07, MTB32A), len: 355 aa. Probable pepA (alternate gene name: mtb32a), serine protease (see Skeiky et al., 1999), highly similar to other proteases e.g. HHOB_ECOLI|P31137 protease hhob precursor (355 aa), FASTA scores: opt: 400, E(): 3.8e-14, (32.4% identity in 346 aa overlap). Also similar to Q50320 34 kDa protein precursor from Mycobacterium tuberculosis (361 aa), FASTA scores: opt: 1689, E(): 0, (70.7% identity in 362 aa overlap). Contains PS00135 Serine proteases, trypsin family, serine active site. Has a putative signal sequence at the N-terminus. Belongs to the serine protease family. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	O07175	No	intermediary metabolism and respiration	ML2659,ML2659c	MMAR_0324		Mb0130				
NC_000962.3	Mycobrowser_v3	CDS	152324	154129	.	+	0	Rv0126	treS	Involved in trehalose biosynthesis (protective effect). Converts maltose to trehalose. Mycobacteria can produce trehalose from glucose 6-phosphate and UDP-glucose (the OtsA-OtsB pathway) from glycogen-like alpha(1-->4)-linked glucose polymers (the TreY-TreZ pathway) and from maltose (the TreS pathway).	Trehalose synthase TreS	Rv0126, (MTCI418B.08), len: 601 aa. TreS, trehalose synthase (see citation below), highly similar to others e.g. CAA04601.2|AJ001205 putative trehalose synthase from Streptomyces coelicolor (566 aa); S71450|1536814|BAA11303.1|D78198 trehalose synthase maltose-specific from Pimelobacter sp. strain R48 (573 aa). Also similar to MAL1_DROME|P07191 possible maltase precursor (508 aa), FASTA scores: opt: 807, E(): 0, (33.7% identity in 504 aa overlap); and similar to proteins associated with amino-acid transport e.g. Q64319 rat protein which stimulates transport of cystine and dibasic and neutral amino acids (683 aa), FASTA scores: opt: 839, E(): 0, (32.0% identity in 531 aa overlap). Also similar to several other Mycobacterium tuberculosis proteins e.g. Rv2471 FASTA score: (31.7% identity in 164 aa overlap).	P9WQ19	No	virulence, detoxification, adaptation	ML2658,ML2658c	MMAR_0325	MSMEG_6515	Mb0131				
NC_000962.3	Mycobrowser_v3	CDS	166910	167290	.	+	0	Rv0140	Rv0140	Function unknown	Conserved protein	Rv0140, (MTCI5.14), len: 126 aa. Conserved protein, similar to others e.g. P74567|D90916_48 hypothetical 20.8 KDP protein from Synechocystis sp. (180 aa), FASTA scores: opt: 229, E(): 4.7e-10, (36.1% identity in 108 aa overlap). Also similar to Rv1056 and Rv1670 from Mycobacterium tuberculosis.	P96817	No	conserved hypotheticals		MMAR_0350	MSMEG_6469	Mb0145				
NC_000962.3	Mycobrowser_v3	CDS	156578	157600	.	-	0	Rv0129c	fbpC	Proteins of the antigen 85 complex are responsible for the high affinity of mycobacteria to fibronectin. Possesses a mycolyltransferase activity required for the biogenesis of trehalose dimycolate (cord factor), a dominant structure necessary for maintaining cell wall integrity.	Secreted antigen 85-C FbpC (85C) (antigen 85 complex C) (AG58C) (mycolyl transferase 85C) (fibronectin-binding protein C)	Rv0129c, (MT0137, MTCI5.03c), len: 340 aa. FbpC (alternate gene names: mpt45, 85C, fbpC2), secreted antigen 85c (fibronectin-binding protein C) (mycolyl transferase 85C) (see citations below), also highly similar to other Mycobacterial antigen precursors e.g. A85C_MYCLE|Q05862 antigen 85-c precursor (85c) from Mycobacterium leprae (333 aa), FASTA scores: opt: 1937, E(): 0, (81.4% identity in 333 aa overlap); etc.	P9WQN9	No	lipid metabolism	ML2655	MMAR_0328	MSMEG_3580	Mb0134c				
NC_000962.3	Mycobrowser_v3	CDS	162644	163249	.	-	0	Rv0135c	Rv0135c	Could be involved in transcriptional mechanism.	Possible transcriptional regulatory protein	Rv0135c, (MTCI5.09c), len: 201 aa. Possible transcriptional regulator, weakly similar to others e.g. P32398|YHGD_BACSU hypothetical transcriptional regulator from Bacillus subtilis (191 aa), FASTA scores: opt: 145, E(): 0.0012, (21.0% identity in 162 aa overlap).	P96812	No	regulatory proteins		MMAR_0345	MSMEG_6480	Mb0140c				
NC_000962.3	Mycobrowser_v3	CDS	163366	164691	.	+	0	Rv0136	cyp138	Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	Probable cytochrome P450 138 Cyp138	Rv0136, (MT0144, MTCI5.10), len: 441 aa. Probable cyp138, cytochrome P450 138, similar to others e.g. SLR0574|Q59990 from synechocystis SP. (444 aa), FASTA scores: opt: 315, E(): 1e-13, (25.7% identity in 416 aa overlap); etc. Also similar to MTV039_6 from Mycobacterium tuberculosis (472 aa), FASTA score: (38.2% identity in 442 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop); and PS00086 Cytochrome P450 cysteine heme-iron ligand signature. Belongs to the cytochrome P450 family.	P9WPM3	No	intermediary metabolism and respiration	ML2648,ML2648c	MMAR_0346	MSMEG_6478	Mb0141				
NC_000962.3	Mycobrowser_v3	CDS	164712	165260	.	-	0	Rv0137c	msrA	Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine [catalytic activity: protein L-methionine + oxidized thioredoxin + H2O = protein-L-methionine-(S)-S-oxide + reduced thioredoxin].	Probable peptide methionine sulfoxide reductase MsrA (protein-methionine-S-oxide reductase) (peptide met(O) reductase)	Rv0137c, (MTCI5.11c), len: 182 aa. Probable msrA, peptide methionine sulfoxide reductase (See St. John et al., 2001), equivalent to CAC32179.1|AL583926 putative peptide methionine sulfoxide from Mycobacterium leprae (177 aa). Highly similar to others e.g. CAC18703.1|AL451182 putative peptide methionine sulfoxide reductase from Streptomyces coelicolor (172 aa); PMSR_SCHPO|Q09859 putative peptide methionine sulfoxide reductase from Streptomyces (187 aa), FASTA scores: opt: 468, E(): 9.9e-26, (45.6% identity in 158 aa overlap); etc. Belongs to the MsrA family.	P9WJM5	No	intermediary metabolism and respiration	ML2647	MMAR_0347	MSMEG_6477	Mb0142c				
NC_000962.3	Mycobrowser_v3	CDS	167711	168637	.	+	0	Rv0142	Rv0142	Function unknown	Conserved hypothetical protein	Rv0142, (MTCI5.16), len: 308 aa. Conserved hypothetical protein, similar, except in N-terminus, to AB88922.1|AL353862 hypothetical protein SCE34.20 from Streptomyces coelicolor (326 aa).	P96819	No	conserved hypotheticals		MMAR_0352	MSMEG_6468	Mb0147				
NC_000962.3	Mycobrowser_v3	CDS	168704	170182	.	-	0	Rv0143c	Rv0143c	Unknown; possibly ion channel involved in transport of chloride across the membrane.	Probable conserved transmembrane protein	Rv0143c, (MTCI5.17c), len: 492 aa. Probable conserved transmembrane protein, CIC family possibly involved in transport of chloride, similar to others and hypothetical proteins e.g. O28857 putative chloride channel from Archaeoglobus fulgidus (589 aa), FASTA scores: opt: 966, E(): 0, (37.7% identity in 453 aa overlap); YADQ_ECOLI|P37019 hypothetical 46.0 kDa protein (436 aa), FASTA scores: opt: 452, E(): 2.4e-20, (28.0% identity in 460 aa overlap).	P96820	No	cell wall and cell processes	ML2643	MMAR_0353	MSMEG_6465	Mb0148c				
NC_000962.3	Mycobrowser_v3	CDS	173238	174758	.	+	0	Rv0147	Rv0147	Function unknown; probably involved in cellular metabolism [catalytic activity: an aldehyde + NAD+ + H2O = an acid + NADH].	Probable aldehyde dehydrogenase (NAD+) dependent	Rv0147, (MTCI5.21), len: 506 aa. Probable aldehyde dehydrogenase (NAD+) dependent, similar to others e.g. DHAP_RAT|P11883 aldehyde dehydrogenase (dimeric NADP-preferring) (452 aa), FASTA scores: opt: 1291, E(): 0, (43.9% identity in 453 aa overlap). Also similar to several Mycobacterium tuberculosis aldehyde dehydrogenases e.g. Rv0768, Rv2858c, etc. Contains PS00687 aldehyde dehydrogenases glutamic acid active site, and PS00070 aldehyde dehydrogenases cysteine active site. Belongs to the aldehyde dehydrogenases family.	P96824	No	intermediary metabolism and respiration	ML2639,ML2639c	MMAR_0359		Mb0152				
NC_000962.3	Mycobrowser_v3	CDS	177543	179309	.	-	0	Rv0151c	PE1	Function unknown	PE family protein PE1	Rv0151c, (MTCI5.25c), len: 588 aa. PE1, Member of the Mycobacterium tuberculosis PE family (see citation below), with N-terminal region similar to others e.g. MTV032_2 PE_PGRS family from Mycobacterium tuberculosis (468 aa), FASTA scores: opt: 1125, E(): 0, (46.3% identity in 456 aa overlap); MTCY493_24 from Mycobacterium tuberculosis FASTA score: (42.5% identity in 558 aa overlap). Also similar to upstream ORF MTCI5.26c FASTA score: (54.7% identity in 464 aa overlap). Also shows similarity to C-terminal part of some PPE family proteins e.g. MTV049_21 from Mycobacterium tuberculosis FASTA score: (41.5% identity in 591 aa overlap).	Q79G06	No	PE/PPE		MMAR_0372		Mb0156c				
NC_000962.3	Mycobrowser_v3	CDS	179319	180896	.	-	0	Rv0152c	PE2	Function unknown	PE family protein PE2	Rv0152c, (MTCI5.26c), len: 525 aa. PE2, Member of the Mycobacterium tuberculosis PE family (see citation below), similar to ORF downstream Z92770|MTCI5_25 (588 aa), FASTA scores: opt: 1492, E(): 0, (54.7% identity in 464 aa overlap); and to many other PE family type members. Predicted to be an outer membrane protein (See Song et al., 2008).	Q79G05	No	PE/PPE				Mb0157c				
NC_000962.3	Mycobrowser_v3	CDS	181155	181985	.	-	0	Rv0153c	ptbB	Involved in signal transduction (via dephosphorylation). Can dephosphorylate in vitro the phosphotyrosine residue of myelin basic protein (MBP) at pH 7.0. Could be involved in virulence by interfering with phosphotyrosine-mediated signals in macrophages. Also able to dephosphorylate phosphoserine/threonine peptides and phosphoinositide substrates. [catalytic activity: protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate]	Phosphotyrosine protein phosphatase PTPB (protein-tyrosine-phosphatase) (PTPase)	Rv0153c, (MTCI5.27c), len: 276 aa. PtbB (alternate gene name: MPtpB), protein-tyrosine-phosphatase (see citation below), showing some similarity to several protein-tyrosine phosphatases, polyketide synthase and aminotransferase e.g. Q05918|IPHP_NOSCO|IPH protein-tyrosine-phosphatase precursor from Nostoc commune (294 aa), FASTA scores: opt: 150, E(): 0.0096, (26.8% identity in 269 aa overlap); etc. Supposedly a secreted protein. Potent and selective inhibitor is an isoxazole compound (See Seollner et al., 2007).	I6WXK4	No	regulatory proteins		MMAR_0373	MSMEG_0100	Mb0158c				
NC_000962.3	Mycobrowser_v3	CDS	185052	186479	.	+	0	Rv0157	pntB	The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane [catalytic activity: NADPH + NAD+ = NADP+ + NADH].	Probable NAD(P) transhydrogenase (subunit beta) PntB [integral membrane protein] (pyridine nucleotide transhydrogenase subunit beta) (nicotinamide nucleotide transhydrogenase subunit beta)	Rv0157, (MTCI5.31), len: 475 aa. Probable pntB, pyridine nucleotide transhydrogenase (nicotinamide nucleotide transhydrogenase) subunit beta, integral membrane protein, similar to others e.g. Q59763 proton-translocating nicotinamide nucleotide transhydrogenase subunit beta from hodospirillum rubrum (464 aa), FASTA scores: opt: 1344, E(): 0, (46.4% identity in 472 aa overlap); P07002|PNTB_ECOLI|P76890|PNTB|B1602|Z2597|ECS2308 NAD(P) transhydrogenase subunit beta from Escherichia coli strains K12 and O157:H7 (462 aa).	P96834	No	intermediary metabolism and respiration	ML2634,ML2634c	MMAR_0379	MSMEG_0150	Mb0162				
NC_000962.3	Mycobrowser_v3	CDS	190607	191956	.	+	0	Rv0161	Rv0161	Function unknown; probably involved in cellular metabolism.	Possible oxidoreductase	Rv0161, (MTCI28.01, MTV032.04), len: 449 aa. Possible oxidoreductase, similar to hypothetical proteins and various oxidoreductases e.g. AIP2_YEAST|P46681 actin interacting protein 2 (530 aa), FASTA scores: opt: 356, E (): 0, (33.3% identity in 357 aa overlap); DLD1_YEAST|P32891 d-lactate dehydrogenase (cytochrome) (587 aa), FASTA scores: opt: 311, E(): 2.5e-20, (27.9% identity in 366 aa overlap). Also similar to other Mycobacteria proteins e.g. MTCY339.30c from Mycobacterium tuberculosis FASTA score: (29.4% identity in 357 aa overlap); MLCL622.30c from Mycobacterium tuberculosis (449 aa).	O07406	No	intermediary metabolism and respiration	ML2631,ML2631c	MMAR_0388	MSMEG_5045	Mb0166				
NC_000962.3	Mycobrowser_v3	CDS	194993	196657	.	+	0	Rv0166	fadD5	Function unknown, but involved in lipid degradation.	Probable fatty-acid-CoA ligase FadD5 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv0166, (MTCI28.06), len: 554 aa. Probable fadD5, fatty-acid-CoA synthetase, similar to many eg LCFA_ECOLI|P29212 long-chain-fatty-acid--CoA ligase (561 aa), FASTA scores: opt: 612, E(): 0, (29.4% identity in 534 aa overlap). Also similar to many other fatty-acid-CoA ligases from Mycobacterium tuberculosis e.g. MTCY07A7.11c FASTA score: (35.3% identity in 487 aa overlap), MTV013_10, MTY25D10_30, etc. Contains PS00455 putative AMP-binding domain signature.	O07411	No	lipid metabolism	ML2586	MMAR_0409	MSMEG_0131	Mb0172				
NC_000962.3	Mycobrowser_v3	CDS	198534	199898	.	+	0	Rv0169	mce1A	Unknown, but thought to be involved in host cell invasion (entry and survival inside macrophages).	Mce-family protein Mce1A	Rv0169, (MTCI28.09), len: 454 aa. Mce1A; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07789|MCE2|Rv0589|MTCY19H5.33c|mce2A (404 aa); O53967|MCE3|Rv1966|MTV051.04|mce3A (425 aa); etc. Also highly similar to others e.g. AAD52105.1|AF113402_1|AF113402 mycobacterial cell entry protein from Mycobacterium bovis BCG (454 aa); NP_302656.1|NC_002677 putative cell invasion protein from Mycobacterium leprae (441 aa); AAA92845.1|U26018 mce gene product from Mycobacterium avium (88 aa) (similarity on C-terminus); CAC12798.1|AL445327 putative secreted protein from Streptomyces coelicolor (418 aa); etc. Note that equivalent, but longer 22 aa, to P72013|CAA50257.1|X70901 Mcep protein from Mycobacterium tuberculosis (432 aa). Contains a very hydrophobic region around residues 20-35. Note that previously known as mce1. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004). Predicted to be an outer membrane protein (See Song et al., 2008).	Q79FZ9	No	virulence, detoxification, adaptation	ML2589			Mb0175				
NC_000962.3	Mycobrowser_v3	CDS	200932	202479	.	+	0	Rv0171	mce1C	Unknown, but thought to be involved in host cell invasion.	Mce-family protein Mce1C	Rv0171, (MTCI28.11), len: 515 aa. Mce1C; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07787|Rv0591|MTCY19H5.31|mce2C (481 aa); O53969|Rv1968|MTV051.06|mce3C (410 aa); etc. Also highly similar to others e.g. NP_302658.1|NC_002677 putative secreted protein from Mycobacterium leprae (519 aa); CAC12796.1|AL445327 putative secreted protein from Streptomyces coelicolor (351 aa); etc. Weakly similar to downstream ORF Rv0172|MTCI28.12|mce1D (530 aa), FASTA score: (24.6% identity in 552 aa overlap). Contains possible signal sequence and highly proline-rich C-terminus. Predicted to be an outer membrane protein (See Song et al., 2008).	O07415	No	virulence, detoxification, adaptation	ML2591	MMAR_0414	MSMEG_0136	Mb0177				
NC_000962.3	Mycobrowser_v3	CDS	205231	206778	.	+	0	Rv0174	mce1F	Unknown, but thought involved in host cell invasion.	Mce-family protein Mce1F	Rv0174, (MTCI28.14), len: 515 aa. Mce1F; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), similar to Mycobacterium tuberculosis proteins O07784|Rv0594|MTCY19H5.28c|mce2F (516 aa); O53972|Rv1971|MTV051.09|mce3F (437 aa); etc. Also highly similar to others e.g. NP_302661.1|NC_002677 putative secreted protein from Mycobacterium leprae (516 aa); AAF74993.1|AF143400_1|AF143400|996A027a protein from Mycobacterium avium (80 aa) (similarity on C-terminus); CAC12793.1|AL445327 putative secreted protein from Streptomyces coelicolor (433 aa); etc. Has hydrophobic stretch, possibly a signal peptide at the N-terminus. Predicted to be an outer membrane protein (See Song et al., 2008).	L0T2W6	No	virulence, detoxification, adaptation	ML2594	MMAR_0417	MSMEG_0139	Mb0180				
NC_000962.3	Mycobrowser_v3	CDS	208938	209672	.	+	0	Rv0178	Rv0178	Unknown	Probable conserved Mce associated membrane protein	Rv0178, (MTCI28.18), len: 244 aa. Probable conserved Mce-associated membrane protein, highly similar in C-terminus to CAC32130.1|AL583926 putative secreted protein from Mycobacterium leprae (184 aa). Also similar to mce-associated proteins from Mycobacterium tuberculosis e.g. Rv1363c, Rv0177, Rv1973, etc. Note that there is a 10 aa overlap with the upstream ORF. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O07422	No	cell wall and cell processes	ML2598	MMAR_0421		Mb0184				
NC_000962.3	Mycobrowser_v3	CDS	215715	216224	.	+	0	Rv0185	Rv0185	Function unknown; probably involved in a cellular metabolism.	Conserved hypothetical protein	Rv0185, (MTCI28.25a), len: 169 aa. Conserved hypothetical protein, equivalent to CAB08794.1|Z95398|MLCL622_2 from Mycobacterium leprae (168 aa), FASTA scores: opt: 861, E(): 0, (76.4% identity in 165 aa overlap). Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O07429	No	conserved hypotheticals	ML2605	MMAR_0429	MSMEG_0223	Mb0191				
NC_000962.3	Mycobrowser_v3	CDS	237206	237895	.	+	0	Rv0200	Rv0200	Unknown	Possible conserved transmembrane protein	Rv0200, (MTV033.08), len: 229 aa. Possible conserved transmembrane protein, equivalent to Z95398|MLCL622.14 from Mycobacterium leprae (229 aa), FASTA scores: opt: 1147, E(): 0, (74.7% identity in 229 aa overlap). Also some similarity to Rv1973 from Mycobacterium tuberculosis (160 aa); and Rv1362c|Z75555|MTCY02B10_26 (220 aa), FASTA scores: opt: 134, E(): 0.063, (25.8% identity in 159 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O53651	No	cell wall and cell processes	ML2615	MMAR_0440	MSMEG_0236	Mb0206				
NC_000962.3	Mycobrowser_v3	CDS	219996	221723	.	-	0	Rv0189c	ilvD	Involved in valine and isoleucine biosynthesis (at the fourth step) [catalytic activity: 2,3-dihydroxy-3-methylbutanoate = 3-methyl-2- oxobutanoate + H(2)O].	Probable dihydroxy-acid dehydratase IlvD (dad)	Rv0189c, (MTCI28.28c), len: 575 aa. Probable ilvD, dihydroxy-acid dehydratase, similar to many e.g. ILVD_LACLA|Q02139 dihydroxy-acid dehydratase (dad) from Lactococcus lactis (subsp. lactis) (Streptococcus lactis) (570 aa), FASTA scores: opt: 1605, E(): 0, (46.0% identity in 561 aa overlap). Also similar to ML2608|MLCL622.06c|O06069|ILVD_MYCLE dihydroxy-acid dehydratase from Mycobacterium leprae (564 aa). Contains PS00886 Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. Belongs to the ILVD / EDD family. Cofactor: binds 1 4FE-4S cluster (potential).	P9WKJ5	No	intermediary metabolism and respiration	ML2608,ML2608c	MMAR_0432	MSMEG_0229	Mb0195c				
NC_000962.3	Mycobrowser_v3	CDS	230899	231534	.	+	0	Rv0195	Rv0195	Possibly sensor part of a two component regulatory system.	Possible two component transcriptional regulatory protein (probably LuxR-family)	Rv0195, (MTV033.03), len: 211 aa. Possible two-component response regulator, luxR family, similar to many e.g. U00008|ECOHU49_15 regulatory protein narP from Escherichia coli strain K12 (225 aa), FASTA scores: opt: 232, E(): 7.3e-09, (29.2% identity in 219 aa overlap). Start chosen by similarity. Contains probable helix-turn-helix motif at aa 166-187 (Score 1164, +3.15 SD).	O53646	No	regulatory proteins				Mb0201				
NC_000962.3	Mycobrowser_v3	CDS	232231	234519	.	+	0	Rv0197	Rv0197	Function unknown; probably involved in cellular metabolism.	Possible oxidoreductase	Rv0197, (MTV033.05), len: 762 aa. Possible oxidoreductase, similar to others e.g. 9948789|AAG06102.1|AE004699_7|B83307 probable molybdopterin oxidoreductase from Pseudomonas aeruginosa strain PAO1 (769 aa); 5441785|CAB46809.1|AL096811|T36812 probable dehydrogenase from Streptomyces coelicolor (747 aa), FASTA scores: opt: 617, E(): 9.8e-30, (29.9% identity in 762 aa overlap); BAB04334.1|AP001509 assimilatory nitrate reductase (catalytic subunit) from Bacillus halodurans (743 aa); etc.	L0T2Z1	No	intermediary metabolism and respiration	ML2612	MMAR_0437	MSMEG_3521	Mb0203				
NC_000962.3	Mycobrowser_v3	CDS	454421	455386	.	+	0	Rv0377	Rv0377	Possibly involved in transcriptional mechanism.	Probable transcriptional regulatory protein (probably LysR-family)	Rv0377, (MTV036.12), len: 321 aa. Probable transcription regulator, lysR family, showing similarity with many hypothetical transcriptional regulators lysR homolog e.g. P32484|YEIE_ECOLI|M89774 hypothetical transcriptional regulator from Escherichia coli (293 aa), FASTA scores: opt: 265, E(): 4.9e-11, (28.6% identity in 266 aa overlap). Also similar to Rv2282c from Mycobacterium tuberculosis. Contains PS00044 bacterial regulatory protein lysR family signature. Seems to belong to the LysR family of transcriptional regulators.	P9WMF7	No	regulatory proteins	ML2484	MMAR_0653	MSMEG_0742	Mb0384				
NC_000962.3	Mycobrowser_v3	CDS	238392	241292	.	-	0	Rv0202c	mmpL11	Unknown. Thought to be involved in fatty acid transport.	Probable conserved transmembrane transport protein MmpL11	Rv0202c, (MTV033.10c), len: 966 aa. Probable mmpL11, conserved transmembrane transport protein (see citation below), equivalent to Z95398|MLCL622.16c from Mycobacterium leprae (1014 aa), FASTA scores: opt: 4076, E(): 0, (72.8% identity in 1017 aa overlap). Member of RND superfamily, similar to several putative transport proteins e.g. P96687 from Bacillus subtilis (724 aa), FASTA scores: opt: 594, E(): 9.1e-29, (26.9% identity in 717 aa overlap); etc. Belongs to the MmpL family.	P9WJT9	No	cell wall and cell processes	ML2617,ML2617c	MMAR_0442	MSMEG_0241	Mb0208c				
NC_000962.3	Mycobrowser_v3	CDS	250120	251598	.	+	0	Rv0210	Rv0210	Unknown	Hypothetical protein	Rv0210, (MTCY08D5.05), len: 492 aa. Hypothetical unknown protein. Possibly membrane protein; has hydrophobic stretches around aa 333 - 381.	P96392	No	conserved hypotheticals	ML2623	MMAR_0450	MSMEG_0254	Mb0216				
NC_000962.3	Mycobrowser_v3	CDS	251782	253602	.	+	0	Rv0211	pckA	Rate-limiting gluconeogenic enzyme [catalytic activity: GTP + oxaloacetate = GDP + phosphoenolpyruvate + CO2].	Probable iron-regulated phosphoenolpyruvate carboxykinase [GTP] PckA (phosphoenolpyruvate carboxylase) (PEPCK)(pep carboxykinase)	Rv0211, (MTCY08D5.06), len: 606 aa. Probable pckA (alternate gene names: pckG and pck1), iron-regulated phosphoenolpyruvate carboxykinase [GTP], equivalent to Z95398|MLCL622_21 probable phosphoenolpyruvate carboxykinase from Mycobacterium leprae (609 aa), FASTA score: (86.1% identity in 605 aa overlap). Also highly similar to others e.g. PPCK_NEOFR|P22130 phosphoenolpyruvate carboxykinase [GTP] (608 aa), FASTA scores: opt: 2287, E(): 0, (55.9% identity in 598 aa overlap). Contains PS00505 Phosphoenolpyruvate carboxykinase (GTP) signature. Belongs to the phosphoenolpyruvate carboxykinase [GTP] family.	P9WIH3	No	intermediary metabolism and respiration	ML2624	MMAR_0451	MSMEG_0255	Mb0217				
NC_000962.3	Mycobrowser_v3	CDS	296005	296493	.	+	0	Rv0245	Rv0245	Function unknown; probably involved in cellular metabolism.	Possible oxidoreductase	Rv0245, (MTV034.11), len: 162 aa. Possible oxidoreductase, equivalent to AL022486|MLCB1883_17|T44882 probable oxidoreductase from Mycobacterium leprae (162 aa), FASTA scores: opt: 860, E(): 0, (83.4% identity in 157 aa overlap). Also similar to several hypothetical proteins and various oxidoreductases e.g. AAK24246.1|AE005898 NADH:riboflavin 5'-phosphate oxidoreductase from Caulobacter crescentus (174 aa); Q02058|DIM6_STRCO|CAA45048.1 actinorhodin polyketide dimerase from streptomyces coelicolor (177 aa), FASTA scores: opt: 308, E(): 3. 2e-15, (37.8% identity in 143 aa overlap). Also similar to Z84498|Rv1939|MTCY09F9.25c from Mycobacterium tuberculosis (171 aa), FASTA scores: opt: 517, E(): 3.5e-30, (49.4% identity in 158 aa overlap).	O53667	No	intermediary metabolism and respiration	ML2561,ML2561c	MMAR_0506	MSMEG_0415	Mb0251				
NC_000962.3	Mycobrowser_v3	CDS	256064	257677	.	+	0	Rv0214	fadD4	Function unknown, but involved in lipid degradation.	Probable fatty-acid-CoA ligase FadD4 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv0214, (MTCY08D5.09), len: 537 aa. Probable fadD4, fatty-acid-CoA synthetase, similar to many e.g. 4CL_PINTA|P41636 4-coumarate--CoA ligase (537 aa), FASTA scores: opt: 622, E(): 1e-31, (30.0% identity in 514 aa overlap). Also similar to others from Mycobacterium tuberculosis e.g. MTCY6A4.14 FASTA score: (30.7% identity in 501 aa overlap); MTCY493_27, MTCY07A7_11, MTCI28_6. Contains PS00455 putative AMP-binding domain signature.	P96396	No	lipid metabolism	ML2625	MMAR_0452	MSMEG_0257	Mb0220				
NC_000962.3	Mycobrowser_v3	CDS	262812	264023	.	+	0	Rv0220	lipC	Function unknown; lipolytic enzyme probably involved in cellular metabolism.	Probable esterase LipC	Rv0220, (MTCY08D5.15), len: 403 aa. Probable esterase, similar to others proteins and esterases from various organisms and Mycobacterium tuberculosis e.g. Q50681 (431 aa), FASTA scores: opt: 841, E(): 0, (38.2% identity in 408 aa overlap); Rv1426c, Rv1399c, etc. Contains PS00122 Carboxylesterases type-B serine active site.	P96402	No	intermediary metabolism and respiration		MMAR_0463	MSMEG_0289	Mb0226				
NC_000962.3	Mycobrowser_v3	CDS	266301	267764	.	-	0	Rv0223c	Rv0223c	Thought to oxidize a wide variety of aliphatic and aromatic aldehydes.	Probable aldehyde dehydrogenase	Rv0223c, (MTCY08D5.18), len: 487 aa. Probable aldehyde dehydrogenase, similar to others e.g. A75608|6460525|AAF12231.1|AE001862_57 aldehyde dehydrogenase from Deinococcus radiodurans strain R1 (495 aa); Q47943 L-sorbosone dehydrogenase NAD(P) dependent from Gluconobacter oxydans (498 aa), FASTA scores: opt: 1157, E (): 0, (42.1% identity in 482 aa overlap); etc. Also similar to Rv0768, Rv2858c, etc from Mycobacterium tuberculosis. Contains PS00687 Aldehyde dehydrogenases glutamic acid active site; and PS00070 Aldehyde dehydrogenases cysteine active site. Belongs to the aldehyde dehydrogenases family.	I6X8S7	No	intermediary metabolism and respiration	ML2585	MMAR_0472	MSMEG_0309	Mb0228c				
NC_000962.3	Mycobrowser_v3	CDS	269834	271564	.	-	0	Rv0226c	Rv0226c	Unknown	Probable conserved transmembrane protein	Rv0226c, (MTCY08D5.21c), len: 576 aa. Probable conserved transmembrane protein, equivalent, except in N-terminal part, to AC32114.1|AL583926 conserved membrane protein from Mycobacterium leprae (600 aa), FASTA scores: opt: 2086, E(): 0, (70.3% identity in 579 aa overlap). Also similar to AL021411|SC7H1_20 from Streptomyces coelicolor (483 aa), FASTA scores: opt: 180, E(): 0.00028, (26.5 identity in 388 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P96408	No	cell wall and cell processes	ML2582	MMAR_0475	MSMEG_0315	Mb0231c				
NC_000962.3	Mycobrowser_v3	CDS	276058	277764	.	+	0	Rv0231	fadE4	Function unknown, but involved in lipid degradation.	Probable acyl-CoA dehydrogenase FadE4	Rv0231, (MTCY08D5.27), len: 568 aa. Probable fadE4, acyl-CoA dehydrogenase, similar to many e.g. O29752 acyl-CoA dehydrogenase (ACD-3) from Archaeoglobus fulgidus (576 aa), FASTA scores: opt: 1788, E(): 0, (51.0% identity in 577 aa overlap); ACDB_BACSU|P45857 acyl-CoA dehydrogenase from Bacillus subtilis (379 aa), FASTA scores: opt: 232, E(): 2.2e- 08, (21.6% identity in 291 aa overlap).	P96414	No	lipid metabolism	ML2578,ML2578c	MMAR_0488		Mb0236				
NC_000962.3	Mycobrowser_v3	CDS	279605	281140	.	-	0	Rv0234c	gabD1	Involved in 4-aminobutyrate (GABA) degradation pathway [catalytic activity: succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H].	Succinate-semialdehyde dehydrogenase [NADP+] dependent (SSDH) GabD1	Rv0234c, (MTCY08D5.30c), len: 511 aa. gabD1, succinate-semialdehyde dehydrogenase [NADP+] dependent, equivalent to AL022486|MLCB1883_6 probable aldehyde dehydrogenase from Mycobacterium leprae (457 aa), FASTA scores: opt: 2617, E(): 0, (85.7% identity in 455 aa overlap). Also highly similar to Q55585|GABD|SLR0370 probable succinate-semialdehyde dehydrogenase from Synechocystis sp. strain PCC 6803 (454 aa), FASTA scores: opt: 1676, E(): 0, (55.8% identity in 455 aa overlap); and similar to others e.g. GABD_ECOLI|P25526 succinate-semialdehyde dehydrogenase from Escherichia coli (482 aa), FASTA scores: opt: 929, E(): 0, (36.5% identity in 452 aa overlap); etc. Note that similar to other cytosolic aldehyde dehydrogenases with EC number: 1.2.1.3. Also similar to Rv0768|aldA semialdehyde dehydrogenase from Mycobacterium tuberculosis (489 aa); and gabD2|Rv1731|MTCY04C12.16 possible succinate-semialdehyde dehydrogenase [NADP+] dependent from Mycobacterium tuberculosis (518 aa). Contains PS00070 aldehyde dehydrogenases cysteine active site. Belongs to the aldehyde dehydrogenases family. Could start at different site by homology. Note that previously known as gabD2.	P9WNX9	No	intermediary metabolism and respiration	ML2573	MMAR_0490		Mb0239c				
NC_000962.3	Mycobrowser_v3	CDS	298116	298862	.	-	0	Rv0247c	Rv0247c	Involved in interconversion of fumarate and succinate (aerobic respiration) [catalytic activity: succinate + acceptor = fumarate + reduced acceptor].	Probable succinate dehydrogenase [iron-sulfur subunit] (succinic dehydrogenase)	Rv0247c, (MTV034.13c), len: 248 aa. Probable succinate dehydrogenase, iron-sulfur subunit, highly similar to CAC44313.1|AL596043 putative succinate dehydrogenase iron-sulfur subunit from Streptomyces coelicolor (259 aa); and similar to iron-sulphur protein subunits of fumarate reductase or succinate dehydrogenases from many bacteria e.g. NP_147618.1|7521083|B72691 fumarate reductase iron-sulfur protein from Aeropyrum pernix (305 aa); NP_069516.1|2649932|AAB90556.1|AE001057 succinate dehydrogenase iron-sulfur subunit B (sdhB) from Archaeoglobus fulgidus (236 aa); etc. Also similar to Q10761|FRDB_MYCTU|7431693|F70762 fumarate reductase iron-sulfur protein from Mycobacterium tuberculosis (247 aa), FASTA scores: opt: 358, E():1e-16, (31.3% identity in 214 aa overlap). Contains PS00197 2Fe-2S ferredoxins, iron-sulfur binding region signature. Note that succinate dehydrogenase forms generally part of an enzyme complex containing four subunits: a flavoprotein (Rv0248c ?), an iron-sulfur (Rv0247c ?), and two hydrophobic anchor proteins (Rv0249c ?).	O53669	No	intermediary metabolism and respiration	ML2560	MMAR_0510	MSMEG_0417	Mb0253c				
NC_000962.3	Mycobrowser_v3	CDS	1547832	1549151	.	+	0	Rv1375	Rv1375	Function unknown	Conserved hypothetical protein	Rv1375, (MTCY02B12.09), len: 439 aa. Conserved hypothetical protein, similar to hypothetical proteins from several organisms e.g. Q52871|U39409 Rhizobium leguminosarum (420 aa), FASTA scores: E(): 2e-30, (34.4% identity in 378 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008).	P9WF27	No	conserved hypotheticals	ML1354,ML1354c	MMAR_2494		Mb1410				
NC_000962.3	Mycobrowser_v3	CDS	287186	288352	.	+	0	Rv0237	lpqI	Unknown	Probable conserved lipoprotein LpqI	Rv0237, (MTV034.03), len: 388 aa. Probable lpQI, conserved lipoprotein, equivalent to AL022486|MLCB1883_8|T44873 probable secreted hydrolase from Mycobacterium leprae (387 aa), FASTA scores: opt: 1831, E(): 0, (73.3% identity in 390 aa overlap). Also similar to other lipoproteins and various hydrolases e.g. P40406|2126897|YBBD_BACSU|I39839 hypothetical 70.6 KDA lipoprotein from Bacillus subtilis (642 aa); P48823|HEXA_ALTSO beta-hexosaminidase a precursor from alteromonas SP. (598 aa), FASTA scores: opt: 415, E(): 5.8e-17, (31.2% identity in 343 aa overlap); PCC6803|P74340 beta-glucosidase from Synechocystis sp. (538 aa), FASTA scores: opt: 414, E(): 6.1e-17, (30.6 identity in 320 aa overlap). Contains signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	L7N6B0	No	cell wall and cell processes	ML2569,ML2569c	MMAR_0499	MSMEG_0361	Mb0243				
NC_000962.3	Mycobrowser_v3	CDS	290665	292029	.	-	0	Rv0242c	fabG4	Involved in the fatty acid biosynthesis pathway (first reduction step) [catalytic activity: (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = 3-oxoacyl-[acyl-carrier protein] + NADPH].	Probable 3-oxoacyl-[acyl-carrier protein] reductase FabG4 (3-ketoacyl-acyl carrier protein reductase)	Rv0242c, (MTV034.08c), len: 454 aa. Probable fabG4, 3-oxoacyl-[acyl-carrier protein] reductase, equivalent to 3063883|CAA18568.1|AL022486|MLCB1883_13|T44878 3-oxoacyl-[acyl-carrier protein] reductase homolog from Mycobacterium leprae (454 aa), FASTA scores: opt: 2486, E(): 0, (84.8% identity in 454 aa overlap). C-terminal part highly similar to many FabG proteins e.g. U39441|VHU3944 1_2 from Vibrio harveyi (244 aa), FASTA scores: opt: 562, E(): 3.4e-28, (40.2% identity in 241 aa overlap); U91631|PAU91631_3 from Pseudomonas aeruginosa (247 aa), FASTA scores: opt: 584, E(): 1.5e-29, (44.4% identity in 241 aa overlap). Has N-terminal extension of ~200 aa and C-terminal part contains PS00061 Short-chain dehydrogenases/reductases family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	I6Y778	No	lipid metabolism	ML2565	MMAR_0503	MSMEG_0372	Mb0248c				
NC_000962.3	Mycobrowser_v3	CDS	293798	295633	.	-	0	Rv0244c	fadE5	Function unknown, but involved in lipid degradation.	Probable acyl-CoA dehydrogenase FadE5	Rv0244c, (MTV034.10c), len: 611 aa. Probable fadE5, acyl-CoA dehydrogenase, equivalent to AL022486|MLCB1883_15 from Mycobacterium leprae (611 aa), FASTA scores: opt: 3598, E(): 0, (89.4% identity in 611 aa overlap). Also highly similar to AL0211|MTV007.14 from Mycobacterium tuberculosis (609 aa), FASTA scores: opt: 2576, E(): 0, (64.6% identity in 611 aa overlap); and to various other bacterial proteins described as putative acyl-CoA dehydrogenases e.g. AE0010|AE001025_6 from Archaeoglobus fulgidus (387 aa), FASTA scores: opt: 229, E(): 6.8e-08, (29.8% identity in 409 aa overlap); etc.	O53666	No	lipid metabolism	ML2563	MMAR_0505	MSMEG_0406	Mb0250c				
NC_000962.3	Mycobrowser_v3	CDS	306374	307858	.	-	0	Rv0255c	cobQ1	Involved in cobalamin biosynthesis	Probable cobyric acid synthase CobQ1	Rv0255c, (MTV034.21c), len: 494 aa. Probable cobQ1, cobyric acid synthase, similar to many e.g. Z46611|RCBLUGNS_8 cobyric acid synthase from R.capsulatus (483 aa), FASTA scores: opt: 1239, E(): 0, (47.1% identity in 493 aa overlap); P29932|COBQ_PSEDE cobyric acid synthase from Pseudomonas denitrificans (484 aa), FASTA scores: opt: 1168, E():0, (44.9% identity in 490 aa overlap); etc. Belongs to the COBB/COBQ family, COBQ subfamily. Note that previously known as cobQ.	P9WP95	No	intermediary metabolism and respiration	ML1827,ML1827c	MMAR_3838	MSMEG_2588	Mb0261c				
NC_000962.3	Mycobrowser_v3	CDS	612255	612605	.	+	0	Rv0520	Rv0520	Could cause methylation.	Possible methyltransferase/methylase (fragment)	Rv0520, (MTCY20G10.10), len: 116 aa. Possible fragment of methyltransferase (possibly first part), highly similar to part of several methyltransferases e.g. Q43445|U43683 S-adenosyl-L-methionine:DELTA24-sterol-C-methyltransferase from Glycine max (Soybean)(367 aa), FASTA scores: opt: 190, E(): 2.3e-12, (39.2% identity in 74 aa overlap). Also some similarity to MTCY19G5_5 from Mycobacterium tuberculosis. Possibly continues as Rv0521 but we can find no frameshift to account for this.	O33365	No	intermediary metabolism and respiration				Mb0533				
NC_000962.3	Mycobrowser_v3	CDS	312759	314168	.	-	0	Rv0261c	narK3	Involved in excretion of nitrite produced by the dissimilatory reduction of nitrate. Responsible for the translocation of the substrate across the membrane.	Probable integral membrane nitrite extrusion protein NarK3 (nitrite facilitator)	Rv0261c, (MTCY06A4.05c), len: 469 aa. Probable nirK3, nitrite extrusion protein, integral membrane protein possibly member of major facilitator superfamily (MFS), equivalent to AAB41700.1|U72744 nitrite extrusion protein from Mycobacterium fortuitum (471 aa); and 2342627|CAB11406.1|Z98741|T44908 nitrite extrusion protein homolog from Mycobacterium leprae (517 aa; longer in N-terminus). Also similar to other nitrite extrusion proteins e.g. NARK_ECOLI|P10903|B1223 nitrite extrusion protein 1 from Escherichia coli strain K12 (463 aa), FASTA scores: opt: 755, E(): 0, (35.0% identity in 466 aa overlap). Belongs to the nark/NASA family of transporters.	P95218	No	cell wall and cell processes	ML2552	MMAR_0521	MSMEG_0433	Mb0267c				
NC_000962.3	Mycobrowser_v3	CDS	316511	317503	.	-	0	Rv0265c	Rv0265c	Thought to be involved in iron transport across the membrane (import).	Probable periplasmic iron-transport lipoprotein	Rv0265c, (MTCY06A4.09c), len: 330 aa. Probable iron-transport lipoprotein, most similar to T36412|5763945|CAB53324.1|AL109974 probable iron-siderophore binding lipoprotein from Streptomyces coelicolor (350 aa); and (N-terminus may be incorrect) to T14166|3560508|AAC82551.1|AF027770 fxuD protein from Mycobacterium smegmatis (420 aa), FASTA scores: opt: 385, E(): 1.5e-16, (32.3% identity in 232 aa overlap). Also similar to AAB97475.1|U02617 DtxR/iron regulated lipoprotein precursor from Corynebacterium diphtheriae (355 aa); FECB_ECOLI|P15028 iron(III) dicitrate-binding periplasmic protein (300 aa), FASTA scores: opt: 191, E(): 2.3e-05, (26.5% identity in 196 aa overlap). Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Note that previously known as fecB2.	L7N6B2	No	cell wall and cell processes	ML2548	MMAR_0525	MSMEG_0438	Mb0271c				
NC_000962.3	Mycobrowser_v3	CDS	321331	322722	.	+	0	Rv0267	narU	Involved in excretion of nitrite produced by the dissimilatory reduction of nitrate. Responsible for the translocation of the substrate across the membrane.	Probable integral membrane nitrite extrusion protein NarU (nitrite facilitator)	Rv0267, (MTCY06A4.11), len: 463 aa. Probable narU, nitrite extrusion protein, integral membrane protein possibly member of major facilitator superfamily (MFS), similar to other nitrite extrusion proteins e.g. NARU_ECOLI|P37758 nitrite extrusion protein 2 from Escherichia coli (462 aa), FASTA scores: opt: 630, E(): 4.4e-33, (38.9% identity in 463 aa overlap); and NARK_ECOLI|P10903|B1223 nitrite extrusion protein 1 from Escherichia coli strain K12 (463 aa), FASTA scores: opt: 607, E(): 1.3e-31, (42.0% identity in 457 aa overlap). Also similar to Rv0261c, Rv2329c, Rv1737c, and to MLCB22_25 from Mycobacterium leprae (517 aa), FASTA score: (35.1 identity in 459 aa overlap). Belongs to the nark/NASA family of transporters.	P95224	No	cell wall and cell processes		MMAR_0526		Mb0273				
NC_000962.3	Mycobrowser_v3	CDS	366150	372764	.	-	0	Rv0304c	PPE5	Function unknown	PPE family protein PPE5	Rv0304c, (MTCY63.9c), len: 2204 aa. PPE5, Member of the Mycobacterium tuberculosis PE family (PPE, MPTR), similar to others e.g. Z95324|MTY13E10_16 from Mycobacterium tuberculosis (1443 aa), FASTA scores: E(): 0, (50.6% identity in 1403 aa overlap); Y04H_MYCTU|Q10778 from Mycobacterium tuberculosis (734 aa), FASTA scores: opt: 989, E(): 0, (42.3% identity in 522 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	Q6MX49	No	PE/PPE				Mb0312c,Mb0313c				
NC_000962.3	Mycobrowser_v3	CDS	330422	331003	.	+	0	Rv0274	Rv0274	Function unknown	Conserved protein	Rv0274, (MTV035.02), len: 193 aa. Conserved protein, highly similar to AAK25058.1|AE005973 conserved hypothetical protein from Caulobacter crescentus (174 aa). Shows also some similarity to others hypothetical proteins e.g. AJ002571|BSAJ2571_7 from Bacillus subtilis (316 aa), FASTA scores: opt: 138, E(): 0.033, (27.1% identity in 133 aa overlap). Previous hits with Q56415|M85195 fosfomycin-resistance protein from serratia marcescens (141 aa), FASTA scores: opt: 82, E(): 1.1e -08, (29.1% identity in 151 aa overlap). Contains PS00082 Extradiol ring-cleavage dioxygenases signature near C-terminus. May belong to the vicinal-oxygen-chelate (VOC) superfamily of metalloenzymes (See Rawat et al., 2003).	O53680	No	conserved hypotheticals	ML2542,ML2542c		MSMEG_0608	Mb0280				
NC_000962.3	Mycobrowser_v3	CDS	333437	336310	.	-	0	Rv0278c	PE_PGRS3	Function unknown	PE-PGRS family protein PE_PGRS3	Rv0278c, (MTV035.06c), len: 957 aa. PE_PGRS3, Member of the Mycobacterium tuberculosis PE family (see citation below), PGRS subfamily of gly-rich proteins, similar to many e.g. Z95890|MTCY28_25|Rv1759c from Mycobacterium tuberculosis (914 aa), FASTA scores: opt: 3849, E(): 0, (67.8% identity in 903 aa overlap). Contains PS00583 pfkB family of carbohydrate kinases signature 1.	P9WIG3	No	PE/PPE				Mb0284c,Mb0285c,Mb0286c				
NC_000962.3	Mycobrowser_v3	CDS	340998	341906	.	+	0	Rv0281	Rv0281	Possible methyltransferase	Possible S-adenosylmethionine-dependent methyltransferase	Rv0281, (MTV035.09), len: 302 aa. Possible S-adenosylmethionine-dependent methyltransferase (see Grana et al., 2007), member of Mycobacterium tuberculosis protein family that includes Rv0726c, Rv0731c, Rv3399, Rv1729c, etc. MTCY31_23 (325 aa), FASTA scores: opt: 1386, E(): 0, (69. 1% identity in 301 aa overlap). Contains possible N-terminal signal sequence.	P9WFI9	No	lipid metabolism	ML2539,ML2539c	MMAR_0539	MSMEG_0614	Mb0289				
NC_000962.3	Mycobrowser_v3	CDS	342130	344025	.	+	0	Rv0282	eccA3	Function unknown	ESX conserved component EccA3. ESX-3 type VII secretion system protein.	Rv0282, (MTV035.10), len: 631 aa. eccA3, esx conserved component, ESX-3 type VII secretion system protein, similar to Y14967|MLCB628.18c hypothetical protein from Mycobacterium leprae (573 aa), FASTA scores: opt: 916, E(): 0, (38.7% identity in 568 aa overlap). Also similar to Mycobacterium tuberculosis proteins e.g. Z94121|MTY15F10.26 (619 aa), FASTA scores: opt: 743, E(): 0, (29.9% identity in 612 aa overlap). Member of CFXQ, CBXP family - 9 members in Mycobacterium tuberculosis. Contains PS00017 ATP/GTP-binding site motif A (P-loop).	P9WPI3	No	cell wall and cell processes	ML2537c	MMAR_0541	MSMEG_0615	Mb0290				
NC_000962.3	Mycobrowser_v3	CDS	364044	364469	.	+	0	Rv0301	vapC2	Unknown	Possible toxin VapC2	Rv0301, (MTCY63.06), len: 141 aa. Possible vapC2, toxin, part of toxin-antitoxin (TA) operon with Rv0300, contains PIN domain (See Arcus et al., 2005; Pandey and Gerdes, 2005). Similar to others in Mycobacterium tuberculosis e.g. Rv2757c, Rv0229c, Rv2546, etc. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WFB9	No	virulence, detoxification, adaptation				Mb0309				
NC_000962.3	Mycobrowser_v3	CDS	372820	375711	.	-	0	Rv0305c	PPE6	Function unknown	PPE family protein PPE6	Rv0305c, (MTCY63.10c), len: 963 aa. PPE6, Member of the Mycobacterium tuberculosis PE family (PPE, MPTR), similar to others e.g. Y04H_MYCTU|Q10778 from Mycobacterium tuberculosis (734 aa), FASTA scores: opt: 1340, E(): 0, (40.9% identity in 815 aa overlap).	Q6MX48	No	PE/PPE				Mb0313c				
NC_000962.3	Mycobrowser_v3	CDS	352149	353036	.	+	0	Rv0289	espG3	Function unknown	ESX-3 secretion-associated protein EspG3	Rv0289, (MTV035.17), len: 295 aa. EspG3, ESX-3 secretion-associated protein, equivalent to CAC32061.1|AL583926 possible DNA-binding protein from Mycobacterium leprae (289 aa); and showing some similarity to Rv3866|G70656|CAB06238.1|Z94121|MTCY15F10.23 from Mycobacterium tuberculosis (276 aa), FASTA scores: opt: 149, E(): 0.0035, (27.7% identity in 289 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WJC7	No	cell wall and cell processes	ML2530c	MMAR_0548	MSMEG_0622	Mb0297				
NC_000962.3	Mycobrowser_v3	CDS	364605	365237	.	+	0	Rv0302	Rv0302	Involved in transcriptional mechanism.	Probable transcriptional regulatory protein (probably TetR/AcrR-family)	Rv0302, (MTCY63.07), len: 210 aa. Probable transcription regulatory protein, TetR family (see citation below), with its N-terminus similar to N-terminus of several repressors and regulatory proteins of TetR/AcrR family e.g. ACRR_ECOLI|P34000 potential acraB operon repressor from Escherichia coli (215 aa), FASTA scores: opt: 172, E(): 3.1e-05, (22.7% identity in 194 aa overlap). Also similar in N-terminus to N-terminus of MTCY07A7.24 hypothetical regulator from Mycobacterium tuberculosis FASTA score: (38.7% identity in 62 aa overlap). Contains probable helix-turn helix motif from aa 35-56 (Score 1728, +5.07 SD). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07229	No	regulatory proteins		MMAR_1504		Mb0310				
NC_000962.3	Mycobrowser_v3	CDS	354498	355883	.	+	0	Rv0291	mycP3	Thought to have proteolytic activity.	Probable membrane-anchored mycosin MycP3 (serine protease) (subtilisin-like protease) (subtilase-like) (mycosin-3)	Rv0291, (MTV035.19), len: 461 aa. Probable mycP3, membrane-anchored serine protease (mycosin) (see Brown et al., 2000), similar to several others in mycobacteria e.g. Z94121|MTY15F10_28|Rv1796 from Mycobacterium tuberculosis (446 aa), FASTA scores: opt: 1168, E(): 0, (44.6% identity in 453 aa overlap); Rv3886c; Rv3883c; Rv3449; and Y14967|MLCB628_4|MLCB628.04 from Mycobacterium leprae (446 aa), FASTA scores: opt: 1159, E(): 0, (43.5 identity in 446 aa overlap). Has signal sequence and hydrophobic stretch at C-terminus, followed by short positively charged segment, that seems to act as a membrane anchor. Contains PS00137 Serine proteases, subtilase family, histidine active site signature. Belongs to peptidase family S8 (also known as the subtilase family), pyrolysin subfamily. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	O53695	No	intermediary metabolism and respiration	ML2528,ML2528c	MMAR_0550	MSMEG_0624	Mb0299				
NC_000962.3	Mycobrowser_v3	CDS	359758	361155	.	-	0	Rv0296c	Rv0296c	Function unknown; probably involved in cellular metabolism.	Probable sulfatase	Rv0296c, (MTCY63.01c, MTV035.24c), len: 465 aa. Probable sulfatase, possibly an aryl-/steryl-sulfatase or a sulfamidase (sulfohydrolase) (sulphamidase). Similar to various hydrolases e.g. AAG41945.1|AF304053_1|AF304053 heparan N-sulfatase from Mus musculus (502 aa); NP_061292.1|6851181|AAF29460.1|AF153827_1|AF153827 N-sulfoglucosamine sulfohydrolase (sulfamidase) (sulphamidase) from Mus musculus (502 aa); AAG17206.1|AF217203_1|AF217203 heparan sulfate sulfamidase from Canis familiaris (507 aa); P08842|STS_HUMAN|1360652 steryl-sulfatase precursor (steroid sulfatase) (steryl-sulfate sulfohydrolase) (arylsulfatase C) (ASC) from Homo sapiens (583 aa); ARSB_FELCA|P33727 arylsulfatase B precursor (535 aa), FASTA scores: opt: 231, E(): 1.7e-08, (30.3% identity in 261 aa overlap). Also similarity with 4 others sulfatases in Mycobacterium tuberculosis. Contains sulfatases signature 1 (PS00523). Note that previously known as atsG.	Q6MX51	No	intermediary metabolism and respiration	ML2525	MMAR_0554		Mb0304c				
NC_000962.3	Mycobrowser_v3	CDS	361334	363109	.	+	0	Rv0297	PE_PGRS5	Function unknown	PE-PGRS family protein PE_PGRS5	Rv0297, (MTCY63.02), len: 591 aa. PE_PGRS5, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citation below), highly similar to others e.g. Y03A_MYCTU|Q10637 from Mycobacterium tuberculosis (603 aa), FASTA scores: opt: 1884, E(): 0, (53.7% identity in 635 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	Q6MX50	No	PE/PPE		MMAR_4149		Mb0305				
NC_000962.3	Mycobrowser_v3	CDS	385173	385943	.	-	0	Rv0317c	glpQ2	Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols [catalytic activity: a glycerophosphodiester + H(2)O = an alcohol + SN-glycerol 3-phosphate].	Possible glycerophosphoryl diester phosphodiesterase GlpQ2 (glycerophosphodiester phosphodiesterase)	Rv0317c, (MTCY63.22c), len: 256 aa (start uncertain, chosen by homology). Possible glpQ2, glycerophosphoryl diester phosphodiesterase, similar to others e.g. E75317|6459876|AAF11631.1|AE002044_4 glycerophosphoryl diester phosphodiesterase from Deinococcus radiodurans (285 aa); P10908|UGPQ_ECOLI from Escherichia coli (247 aa), FASTA scores: opt: 220, E(): 5.2e-07, (28.0% identity in 250 aa overlap). Also similar to MTCY01A6.27 from Mycobacterium tuberculosis FASTA score: (27.5% identity in 247 aa overlap).	O07244	No	intermediary metabolism and respiration		MMAR_0494		Mb0325c				
NC_000962.3	Mycobrowser_v3	CDS	391352	392032	.	+	0	Rv0324	Rv0324	Possibly involved in transcriptional mechanism.	Possible transcriptional regulatory protein (possibly ArsR-family)	Rv0324, (MTCY63.29), len: 226 aa. Possible transcriptional regulator, arsR family, with its N-terminus similar to the N-terminus of other DNA-binding proteins e.g. P30346|MERR_STRLI probable mercury resistance operon from Streptomyces lividans (125 aa), FASTA scores: opt: 154, E(): 0.002, (32.2% identity in 90 aa overlap), and its C-terminal part similar to hypothetical bacterial proteins e.g. P54510|YQHL_BACSU hypothetical 14.6 kDa protein from Bacillus subtilis (126 aa), FASTA scores: opt: 159, E(): 0.00097, (35.5% identity in 76 aa overlap). Most similar to AJ005575|SPE005575_2 ORF1 required for antibiotic production from Streptomyces peucetius (226 aa), FASTA scores: opt: 816, E(): 0, (60.7% identity in 211 aa overlap). Also similar in C-terminus to MTCY164.26 molybdopterin biosynthesis moeb protein from Mycobacterium tuberculosis FASTA score: (36.8% identity in 114 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O08446	No	regulatory proteins				Mb0332				
NC_000962.3	Mycobrowser_v3	CDS	396201	397367	.	+	0	Rv0331	Rv0331	Function unknown; probably involved in cellular metabolism.	Possible dehydrogenase/reductase	Rv0331, (MTCY63.36), len: 388 aa. Possible dehydrogenase/reductase, similar to various dehydrogenases/reductases e.g. NP_103779.1|14022957|BAB49565.1|AP002999 flavoprotein reductase from Mesorhizobium loti (377 aa); NP_147681.1 predicted NAD(FAD)-dependent dehydrogenase from Aeropyrum pernix (381 aa); DHSU_CHRVI|Q06530 sulfide dehydrogenase (431 aa), FASTA scores: opt: 347, E(): 6.8e-15, (25.6% identity in 348 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07255	No	intermediary metabolism and respiration				Mb0338				
NC_000962.3	Mycobrowser_v3	CDS	398658	399524	.	+	0	Rv0334	rmlA	dTDP-L-rhamnose biosynthesis within the O antigen biosynthesis pathway of lipopolysaccharide biosynthesis [catalytic activity: dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose].	Alpha-D-glucose-1-phosphate thymidylyltransferase RmlA (dTDP-glucose synthase) (dTDP-glucose pyrophosphorylase)	Rv0334, (MTCY279.01), len: 288 aa. RmlA (alternate gene name: rfbA), alpha-D-glucose-1-phosphate thymidylyl-transferase (see citations below), equivalent to CAC32020.1|AL583925 glucose-1-phosphate thymidyltransferase from Mycobacterium leprae (288 aa). Also highly similar to others e.g. AAG29804.1|AF235050 glucose-1-phosphate thymidylyltransferase from Streptomyces rishiriensis (296 aa); RBA1_ECOLI|P37744 glucose-1-phosphate thymidylyltransferase from Escherichia coli strain K12 (293 aa), FASTA scores: opt: 1199, E(): 0, (62.0% identity in 284 aa overlap). Belongs to the glucose-1-phosphate thymidylyltransferase family.	P9WH13	No	intermediary metabolism and respiration	ML2503,ML2503c	MMAR_0606	MSMEG_0384	Mb0341				
NC_000962.3	Mycobrowser_v3	CDS	403193	405841	.	-	0	Rv0338c	Rv0338c	Function unknown; probably involved in cellular metabolism.	Probable iron-sulfur-binding reductase	Rv0338c, (MTCY279.05c), len: 882 aa. Probable iron-sulphur-binding reductase, possibly membrane-bound, equivalent to CAC32018.1|AL583925 probable iron-sulphur-binding reductase from Mycobacterium leprae (880 aa). Also highly similar to others e.g. T36608|5019323|CAB44376.1|AL078610 probable iron-sulfur-binding reductase from Streptomyces coelicolor (760 aa), FASTA scores: opt: 1658, E(): 0, (49.9% identity in 772 aa overlap); BAB07521.1|AP001520 iron-sulphur-binding reductase from Bacillus halodurans (700 aa). Contains PS00070 Aldehyde dehydrogenases cysteine active site and two of PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature. First of several possible start sites chosen.	O33268	No	intermediary metabolism and respiration	ML2501	MMAR_0611	MSMEG_0690	Mb0345c				
NC_000962.3	Mycobrowser_v3	CDS	405950	408448	.	-	0	Rv0339c	Rv0339c	Could be involved in transcriptional mechanism.	Possible transcriptional regulatory protein	Rv0339c, (MTCY279.06c), len: 832 aa. Possible transcriptional regulator, showing very weak similarity with parts of others. Contains PS00017 ATP/GTP-binding site motif A (P-loop); and probable helix-turn helix motif from aa 778-799 (Score 1041, +2.73 SD).	O33269	No	regulatory proteins		MMAR_0612	MSMEG_0691	Mb0346c				
NC_000962.3	Mycobrowser_v3	CDS	409362	410801	.	+	0	Rv0341	iniB	Unknown	Isoniazid inductible gene protein IniB	Rv0341, (MTCY13E10.01), len: 479 aa. IniB, isoniazid-inducible gene, (see citations below). Protein very Gly-, Ala-rich, similar to cell wall proteins e.g. P27483|GRP_ARATH glycine-rich cell wall structural protein from A.thaliana (338 aa), FASTA scores: opt: 532, E(): 5.2e-13, (39.3% identity in 321 aa overlap). MEME-mast analysis shows similarity to product of upstream gene, Rv0340.	P9WJ97	No	cell wall and cell processes				Mb0348				
NC_000962.3	Mycobrowser_v3	CDS	412757	414238	.	+	0	Rv0343	iniC	Unknown	Isoniazid inductible gene protein IniC	Rv0343, (MTCY13E10.03), len: 493 aa. IniC, isoniazid-inducible gene, (see citations below). Shows slight similarity to P40983|YOR6_THER8 hypothetical protein (402 aa), FASTA scores: opt: 196, E(): 2.6e-05, (25.9% identity in 228 aa overlap). Also some similarity to upstream ORF Rv0342|iniA. Contains (PS00017) ATP/GTP-binding site motif A (P-loop). Note that the iniA gene is also induced by the antibiotic ethambutol, an agent that inhibits cell wall biosynthesis by a mechanism that is distinct from isoniazid.	P9WJ95	No	cell wall and cell processes		MMAR_0616	MSMEG_0698	Mb0350				
NC_000962.3	Mycobrowser_v3	CDS	415502	416965	.	-	0	Rv0346c	ansP2	Thought to be involved in transport of L-asparagine across the membrane. Responsible for the translocation of the substrate across the membrane.	Possible L-asparagine permease AnsP2 (L-asparagine transport protein)	Rv0346c, (MTCY13E10.06c), len: 487 aa. Possible ansP2, L-asparagine permease, integral membrane protein belonging to family containing many amino acid permeases, highly similar to G467030|B2126_F2_85|NP_301937.1|NC_002677 probable L-asparagine permease from Mycobacterium leprae (498 aa); and NP_301938.1|NC_002677 probable L-asparagine permease from Mycobacterium leprae (505 aa). Also highly similar to others e.g. P77610|ANSP_ECOLI L-asparagine permease from Escherichia coli strain K-12 (499 aa). Also highly similar to ANSP1|Rv2127|MT2186|MTCY261_22|O33261 probable L-asparagine permease from Mycobacterium tuberculosis (489 aa), FASTA score: (72.1% identity in 473 aa overlap). And shows some similarity to MTCY3G12.14 from Mycobacterium tuberculosis. Belongs to the amino acid permease family (APC family). Note that previously known as aroP2.	P9WQM7	No	cell wall and cell processes	ML1304c,ML1305c	MMAR_0627		Mb0354c				
NC_000962.3	Mycobrowser_v3	CDS	422452	423639	.	+	0	Rv0352	dnaJ1	Acts as a co-chaperone. Stimulates, jointly with GRPE|Rv0351, the ATPase activity of DNAK|Rv0350. Seems to be regulated negatively by HSPR (Rv0353 product).	Probable chaperone protein DnaJ1	Rv0352, (MTCY13E10.12), len: 395 aa. Probable dnaJ1, chaperone protein, equivalent to AAA25363.1|M95576 DNA J heatshock protein from Mycobacterium leprae (389 aa). Also highly similar to others. Contains both DnaJ signatures (PS00636, and PS00637). Belongs to the DNAJ family. Cofactor: binds two zinc ions per monomer. Note that sequence differs from DNAJ_MYCTU|P07881 due to a frameshift at the N-terminus. Note that previously known as dnaJ.	P9WNV9	No	virulence, detoxification, adaptation	ML2494,ML2494c	MMAR_0639	MSMEG_0711	Mb0360				
NC_000962.3	Mycobrowser_v3	CDS	435471	436769	.	-	0	Rv0357c	purA	Involved in AMP biosynthesis (first committed step). Plays an important role in the de novo pathway of purine nucleotide biosynthesis [catalytic activity: GTP + imp + L-aspartate = GDP + phosphate + adenylosuccinate].	Probable adenylosuccinate synthetase PurA (imp--aspartate ligase) (ADSS) (ampsase)	Rv0357c, (MTCY13E10.19c), len: 432 aa. Probable purA, adenylosuccinate synthase, equivalent to AL023514|MLCB4_13 from adenylosuccinate synthetase Mycobacterium leprae (432 aa), FASTA scores: opt: 2555, E(): 0, (87.9% identity in 431 aa overlap). Also highly similar to many bacterial adenylosuccinates synthetases e.g. P12283|PURA_ECOLI adenylosuccinates synthetase from Escherichia coli (431 aa), FASTA scores: E(): 0, (51.1% identity in 425 aa overlap); etc. Belongs to the adenylosuccinate synthetase family.	P9WHN3	No	intermediary metabolism and respiration	ML0280,ML0280c	MMAR_0680	MSMEG_0759	Mb0364c				
NC_000962.3	Mycobrowser_v3	CDS	453230	454372	.	-	0	Rv0376c	Rv0376c	Function unknown	Conserved hypothetical protein	Rv0376c, (MTV036.11c), len: 380 aa. Conserved hypothetical protein, highly similar to T35481|4008539|CAA22508.1|AL034492|SC6C5.10 hypothetical protein from Streptomyces coelicolor (395 aa); and AAK64260.1|AF373840_20 ORF377 hypothetical CoxI from Arthrobacter nicotinovorans (377 aa). And similar to other conserved hypothetical proteins e.g. NP_101963.1|14021136|BAB47749.1|AP002994 hypothetical protein from Mesorhizobium loti (245 aa). Note that C-terminus shows similarity with C-termini of CAB76248.1|X82447|COXF CoxF protein from Pseudomonas/Oligotropha carboxidovorans (280 aa); CAB76250.1|X82447|COXI CoxI protein from Pseudomonas/Oligotropha carboxidovorans (330 aa); and AJ224684|BJAJ4684_6 cooxS from Bradyrhizobium japonicum (176 aa), FASTA scores: E(): 1.9e-17, (47.1% identity in 138 aa overlap). Also some partial similarity with AJ224684|BJAJ4684_5 cooxS from Bradyrhizobium japonicum (107 aa), FASTA scores: opt: 321, E(): 4.2e-14, (53.3% identity in 92 aa overlap); E1184330|Z99120|YURF YURF protein from Bacillus subtilis (330 aa), FASTA scores: opt: 170, E(): 2.9e- 16, (27.5% identity in 345 aa overlap). Also similar to downstream ORF Rv0372c from Mycobacterium tuberculosis (251 aa), FASTA scores: E(): 2.1e-06, (30.7% identity in 277 aa overlap).	O53711	No	conserved hypotheticals		MMAR_0654	MSMEG_0743	Mb0383c				
NC_000962.3	Mycobrowser_v3	CDS	439871	441253	.	+	0	Rv0362	mgtE	Thought to be involved in Mg2+ transport. Responsible for the translocation of the substrate across the membrane.	Possible Mg2+ transport transmembrane protein MgtE	Rv0362, (MTCY13E10.24), len: 460 aa. Possible mgtE, magnesium (Mg2+) transport transmembrane protein; C-terminal region is highly similar to MGTE|G780283 putative Mg2+ transporter from Providencia stuarti (314 aa), FASTA scores: E(): 0, (47.2% identity in 307 aa overlap) (N-terminus extends approx. 150 aa further upstream compared to P. stuarti ORF). Also similar in part to others e.g. AAK20879.1|AF334760_1|AF334760 putative Mg2+ transporter from Aeromonas hydrophila (455 aa); NP_231292.1|NC_002505 magnesium transporter from Vibrio cholerae (451 aa); NP_102305.1|NC_002678 Mg2+ transport protein from Mesorhizobium loti (454 aa); etc. Also similar to Rv1232c|MTV006.04c from Mycobacterium tuberculosis (435 aa). Extended hydrophobic segment spanning last 130 residues. Belongs to the MgtE family.	O06312	No	cell wall and cell processes		MMAR_0670	MSMEG_6269	Mb0369				
NC_000962.3	Mycobrowser_v3	CDS	444844	445233	.	-	0	Rv0367c	Rv0367c	Unknown	Hypothetical protein	Rv0367c, (MTV036.02c), len: 129 aa. Hypothetical unknown protein.	O53702	No	conserved hypotheticals			MSMEG_3435	Mb0374c				
NC_000962.3	Mycobrowser_v3	CDS	445314	446525	.	-	0	Rv0368c	Rv0368c	Function unknown	Conserved hypothetical protein	Rv0368c, (MTV036.03c), len: 403 aa. Conserved hypothetical protein, showing some similarity to AJ224684|BJAJ4684_4 cooxS protein from Bradyrhizobium japonicum (422 aa), FASTA scores: opt: 341, E(): 4.3e-13, (27.4% identity in 387 aa overlap); Rv2425c|MTCY428_22 hypothetical protein from Mycobacterium tuberculosis FASTA score: (30.7% identity in 238 aa overlap). Contains PS00213 Lipocalin signature.	O53703	No	conserved hypotheticals	ML2479,ML2479c	MMAR_0662	MSMEG_0751	Mb0375c				
NC_000962.3	Mycobrowser_v3	CDS	448040	448633	.	-	0	Rv0371c	Rv0371c	Function unknown	Conserved hypothetical protein	Rv0371c, (MTV036.06c), len: 197 aa. Conserved hypothetical protein, similar to other hypothetical proteins e.g. AL132824|SCAH10.09c|CAB60163.1|AL132824 hypothetical protein from Streptomyces coelicolor (207 aa), FASTA scores: opt: 247, E(): 4.5e-09, (32.3% identity in 195 aa overlap). Also weak similarity with YURE|D70017|Z99120|BSUB0017_134 hypothetical protein yurE from Bacillus subtilis (197 aa), FASTA scores: opt: 217, E(): 2.5e-08, (27.0% identity in 174 aa overlap).	I6WY86	No	conserved hypotheticals	ML2482,ML2482c	MMAR_0659		Mb0378c				
NC_000962.3	Mycobrowser_v3	CDS	448630	449385	.	-	0	Rv0372c	Rv0372c	Function unknown	Conserved hypothetical protein	Rv0372c, (MTV036.07c), len: 251 aa. Conserved hypothetical protein, showing some similarity with CAB76248.1|X82447|COXF CoxF protein from Pseudomonas/Oligotropha carboxidovorans (280 aa); AJ224684|BJAJ4684_6 cooxS from Bradyrhizobium japonicum (176 aa), FASTA scores: opt: 186, E(): 1.6e-05, (41.1% identity in 95 aa overlap). Also similar to upstream ORF Rv0376c from Mycobacterium tuberculosis (380 aa), FASTA scores: E(): 6.8e-07, (31.0% identity in 277 aa overlap).	O53707	No	conserved hypotheticals	ML2483,ML2483c	MMAR_0658	MSMEG_0747	Mb0379c				
NC_000962.3	Mycobrowser_v3	CDS	449404	451803	.	-	0	Rv0373c	Rv0373c	Function unknown; probably involved in cellular metabolism [catalytic activity: CO + H(2)O + acceptor = CO(2) + reduced acceptor].	Probable carbon monoxyde dehydrogenase (large chain)	Rv0373c, (MTV036.08c), len: 799 aa. Probable carbon monoxide dehydrogenase, large chain, highly similar to others e.g. AAD00363.1| U80806|CUTL carbon monoxide dehydrogenase large subunit CutL protein from Hydrogenophaga pseudoflava (803 aa); S49124|509391|CAA54902.1|X77931|1094915|2107180C|CUTA carbon-monoxide dehydrogenase large chain (cut operon) from Pseudomonas thermocarboxydovorans (842 aa); C56279|809566|CAA57829.1|X82447|OCCOXMSL4_3|COXL carbon-monoxide dehydrogenase large chain (cluster coxMSL) from Pseudomonas/Oligotropha carboxydovorans (809 aa), FASTA scores: opt: 2484, E(): 0, (56.0% identity in 804 aa overlap); etc.	O53708	No	intermediary metabolism and respiration		MMAR_0657	MSMEG_0746	Mb0380c				
NC_000962.3	Mycobrowser_v3	CDS	612598	612903	.	+	0	Rv0521	Rv0521	Could cause methylation	Possible methyltransferase/methylase (fragment)	Rv0521, (replaces MTCY20G10.11), len: 101 aa. Possible fragment of methyltransferase (possibly second part), highly similar to C-terminus of several methyltransferases e.g. AAF87203.1|AF216282 sarcosine-dimethylglycine methyltransferase from Halorhodospira halochloris (279 aa). Possibly continuation of Rv0520 but we can find no frameshift to account for this.	L7N6C0	No	intermediary metabolism and respiration				Mb0534				
NC_000962.3	Mycobrowser_v3	CDS	457841	458380	.	-	0	Rv0382c	pyrE	Involved in pyrimidine biosynthesis (at the fifth step) [catalytic activity: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate].	Probable orotate phosphoribosyltransferase PyrE (OPRT) (oprtase)	Rv0382c, (MTV036.17c), len: 179 aa. Probable pyrE, orotate phosphoribosyltransferase, equivalent to CAC32004.1|AL583925 probable purine/pyrimidine phosphoribosyltransferase from Mycobacterium leprae (179 aa). Also highly similar to many others e.g. T36540|4753874|CAB42037.1|AL049754|SCH10.28c probable orotate phosphoribosyltransferase from Streptomyces coelicolor (182 aa); H69115|2622996|AAB86326.1|AE000938_10|MTH1860 probable orotate phosphoribosyltransferase from Methanobacterium thermoautotrophicum (180 aa), FASTA scores: opt: 389, E(): 2.7e-20, (40.7% identity in 172 aa overlap); O08359|PYRE_SULAC|2065444|CAA73352.1|Y12822 orotate phosphoribosyltransferase from Sulfolobus acidocaldarius (197 aa); etc. Note that also similar to other puridine 5'-monophosphate synthases (umpA genes; UMP synthases), generally in N-terminus that corresponds to orotate phosphoribosyltransferase activity. Contains PS00589 PTS HPR component serine phosphorylation site signature. Belongs to the purine/pyrimidine phosphoribosyltransferase family. Note that previously known as umpA. Nucleotide position 458282 in the genome sequence has been corrected, A:G resulting in Y33Y.	P9WHK9	No	intermediary metabolism and respiration	ML2487,ML2487c	MMAR_0649		Mb0389c				
NC_000962.3	Mycobrowser_v3	CDS	459456	462002	.	-	0	Rv0384c	clpB	Thought to be an ATPase subunit of an intracellular ATP-dependent protease. Seems to be regulated positively by sigh (Rv3223c product) and negatively by HSPR (Rv0353 product).	Probable endopeptidase ATP binding protein (chain B) ClpB (ClpB protein) (heat shock protein F84.1)	Rv0384c, (MTV036.19c), len: 848 aa. Probable clpB (alternate gene name: htpM), endopeptidase ATP-binding protein, chain B, equivalent to AC32007.1|AL583925 heat shock protein from Mycobacterium leprae (848 aa). Also highly similar to others e.g. P53532|CLPB_CORGL|1163118|AAB49540.1|U43536|CGU43536_1 CLPB protein (heat-inducible expression) from Corynebacterium glutamicum (852 aa), FASTA scores: opt: 4113, E(): 0, (74.5% identity in 846 aa overlap); T36551|4753885|CAB42048.1|AL049754|clpB|SCOEDB|SCH10.39c probable ATP-dependent proteinase ATP-binding chain from Streptomyces coelicolor (853 aa); P03815|CLPB_ECOLI|1788943|AAC75641.1|AE000345 CLPB protein (heat shock protein F84.1) from Escherichia coli strains K12 and O157:H7 (857 aa); etc. Also similar to Rv3596c|ClpC from Mycobacterium tuberculosis. Contains PS00870 and PS00871 Chaperonins clpA/B signatures and two PS000017 ATP/GTP-binding site motives a (P-loop). Belongs to the CLPA/CLPB family. Contains probable coiled-coil domain from aa 411-503. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P9WPD1	No	virulence, detoxification, adaptation	ML2490,ML2490c	MMAR_0645	MSMEG_0732	Mb0391c				
NC_000962.3	Mycobrowser_v3	CDS	468335	469594	.	+	0	Rv0389	purT	Involved in third step (first of two transformylation reactions) in de novo purine biosynthesis. This is an alternative enzyme to the PURN|Rv0956 gar transformylase (5'-phosphoribosylglycinamide formyltransferase). Catalyzes two reactions: the first one is the production of beta-formyl glycinamide ribonucleotide (gar) from formate, ATP and beta gar; the second, a side reaction, is the production of acetyl phosphate and ADP from acetate and ATP [catalytic activity: formate + ATP + 5'-phospho-ribosylglycinamide = 5'-phosphoribosyl-N-formylglycinamide + ADP + pyrophosphate].	Probable phosphoribosylglycinamide formyltransferase 2 PurT (GART 2) (gar transformylase 2) (5'-phosphoribosylglycinamide transformylase 2) (formate-dependent gar transformylase)	Rv0389, (MTCY04D9.01, MTV036.24), len: 419 aa. Probable purT, phosphoribosylglycinamide formyltransferase 2, similar to others e.g. P33221|PURT_ECOLI|B1849 phosphoribosylglycinamide formyltransferase 2 from Escherichia coli strain K-12 (391 aa), FASTA scores: opt: 481, E(): 1.3e-22, (40.1% identity in 379 aa overlap); etc. Belongs to the PurK / PurT family. Cofactor: magnesium.	P95197	No	intermediary metabolism and respiration		MMAR_0686	MSMEG_0766	Mb0395				
NC_000962.3	Mycobrowser_v3	CDS	483977	485734	.	+	0	Rv0404	fadD30	Function unknown, but involved in lipid degradation.	Fatty-acid-AMP ligase FadD30 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)	Rv0404, (MTCY04D9.17-MTCY22G10.00), len: 585 aa. fadD30, fatty-acid-AMP synthetase, similar to many e.g. MBU75685_1|AAB52538.1|U75685 acyl-CoA synthase from Mycobacterium bovis (582 aa); MASC_MYCLE|P54200 masc protein from Mycobacterium leprae (372 aa), FASTA scores: opt: 888, E(): 0, (44.2% identity in 342 aa overlap). Also similar to Y06J_MYCTU|Q10976 hypothetical 67.9 kDa protein (626 aa), FASTA scores: opt: 1463, E(): 0, (42.4% identity in 568 aa overlap).	P9WQ57	No	lipid metabolism		MMAR_0706		Mb0411				
NC_000962.3	Mycobrowser_v3	CDS	472781	474106	.	+	0	Rv0393	Rv0393	Function unknown	Conserved 13E12 repeat family protein	Rv0393, (MTCY04D9.05), len: 441 aa. Member of Mycobacterium tuberculosis 13E12 repeat family of conserved proteins, similar to many e.g. Rv1148c, Rv1945, Rv3467, Rv0336|MTCY279_3 (503 aa), FASTA scores: E(): 0, (61.1% identity in 347 aa overlap).	P95201	No	insertion seqs and phages		MMAR_1213,MMAR_2226		Mb0399				
NC_000962.3	Mycobrowser_v3	tRNA	924110	924183	.	+	0	MTB000012	aspT	-	tRNA-Asp (GTC)	aspT, tRNA-Asp, anticodon gtc, length = 74		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	tRNA	1025321	1025393	.	-	0	MTB000014	argT	-	tRNA-Arg (CCT)	argT, tRNA-Arg, anticodon cct, length = 73		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	478566	479753	.	-	0	Rv0400c	fadE7	Function unknown, but involved in lipid degradation.	Acyl-CoA dehydrogenase FadE7	Rv0400c, (MTCY04D9.12c), len: 395 aa. Probable fadE7, acyl-CoA dehydrogenase, similar to many e.g. CAC12923.1|AL445403 putative acyl CoA dehydrogenase from Streptomyces coelicolor (397 aa); G624219 glutaryl-CoA dehydrogenase precursor (438 aa), FASTA scores: opt: 1161, E(): 0, (48.1% identity in 391 aa overlap); etc.	P95208	No	lipid metabolism	ML0273			Mb0406c				
NC_000962.3	Mycobrowser_v3	CDS	1896475	1896867	.	+	0	Rv1671	Rv1671	Unknown	Probable membrane protein	Rv1671, (MTV047.06), len: 130 aa. Probable membrane protein. Weak similarity to mercuric transport proteins.	O53918	No	cell wall and cell processes				Mb1698				
NC_000962.3	Mycobrowser_v3	CDS	490783	491793	.	+	0	Rv0407	fgd1	Catalyzes oxidation of glucose-6-phosphate to 6-phosphogluconolactone using coenzyme F420 (an *-hydroxy-5-deazaflavin derivative) as the electron acceptor.	F420-dependent glucose-6-phosphate dehydrogenase Fgd1	Rv0407, (MTCY22G10.03), len: 336 aa. fgd1, F420-dependent glucose-6-phosphate dehydrogenase, equivalent to others from Mycobacteria e.g. AAD38165.1|AF152394_3 from Mycobacterium avium (336 aa), FASTA scores: opt: 2082, E(): 0, (89.9% identity in 336 aa overlap); AL023514|MLCB 4_7 from Mycobacterium leprae (336 aa), FASTA scores: opt: 2069, E(): 0, (89.0% identity in 336 aa overlap). Also similar to other dehydrogenases e.g. CAA77276.1|Y18730 F420-dependent alcohol dehydrogenase from Methanofollis liminatans (330 aa). Also similar to many proteins from Mycobacterium tuberculosis e.g. Rv0953c, Rv0791c, etc. Note that previously known as fgd.	P9WNE1	No	intermediary metabolism and respiration	ML0269,ML0269c	MMAR_0709	MSMEG_0777	Mb0415				
NC_000962.3	Mycobrowser_v3	CDS	491786	493858	.	+	0	Rv0408	pta	Involved at the last step (of two) in the conversion of acetate to acetyl-CoA [catalytic activity: acetyl-CoA + phosphate = CoA + acetyl phosphate].	Probable phosphate acetyltransferase Pta (phosphotransacetylase)	Rv0408, (MTCY22G10.04), len: 690 aa. Probable pta, phosphate acetyltransferase, highly similar to others e.g. PTA_ECOLI|P39184|11279789|JX0357|B2297 phosphate acetyltransferase from Escherichia coli strain K12 (713 aa), FASTA scores: opt: 1303, E(): 0, (38.0% identity in 718 aa overlap); etc. Belongs to the phosphate acetyltransferase and butyryltransferase family.	P9WHP1	No	intermediary metabolism and respiration	ML0268,ML0268c	MMAR_0710	MSMEG_0783	Mb0416				
NC_000962.3	Mycobrowser_v3	CDS	499713	500366	.	+	0	Rv0413	mutT3	Possibly involved in the go system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite DA and DC residues of template DNA with almost equal efficiency thus leading to A.T to G.C transversions. MutT specifically degrades 8-oxo-dGTP to the monophosphate [catalytic activity: 8-oxo-dGTP + H2O = 8-oxo-dGMP + pyrophosphate].	Possible mutator protein MutT3 (7,8-dihydro-8-oxoguanine-triphosphatase) (8-oxo-dGTPase) (dGTP pyrophosphohydrolase)	Rv0413, (MTCY22G10.10), len: 217 aa. Possible mutT3, mutator protein (see citation below), showing some similarity with e.g. MUTT_PROVU|P32090 mutator mutt protein from Proteus vulgaris (112 aa), FASTA scores: opt: 151, E(): 0.0008, (40.7% identity in 59 aa overlap). Seems to belong to the NUDIX hydrolase family.	P9WIX9	No	information pathways	ML0301,ML0301c	MMAR_0716	MSMEG_0790	Mb0421				
NC_000962.3	Mycobrowser_v3	CDS	500350	501018	.	-	0	Rv0414c	thiE	Involved in thiamine biosynthesis. Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate (THZ-P) and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-pp) to form thiamine monophosphate (TMP) [catalytic activity: 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-4-methyl-5-(2-phosphonooxyethyl)-thiazole = diphosphate + thiamine monophosphate].	Thiamine-phosphate pyrophosphorylase ThiE (TMP pyrophosphorylase) (TMP-PPASE) (thiamine-phosphate synthase)	Rv0414c, (MTCY22G10.11c), len: 222 aa. thiE, thiamin phosphate pyrophosphorylase, equivalent to Q9ZBL5|AL035159|MLCB1450_17 probable thiamine-phosphate pyrophosphorylase from Mycobacterium leprae (235 aa), FASTA scores: opt: 1095, E(): 0, (78.0% identity in 223 aa overlap). Also similar to others e.g. T34974|5689976|CAB52013.1|AL109663 probable thiamin phosphate pyrophosphorylase from Streptomyces coelicolor (223 aa); THIE_ECOLI|P30137 thie protein from Escherichia coli strain K12 (211 aa), FASTA scores: opt: 275, E(): 7.8e-12, (37.8% identity in 196 aa overlap); etc. Belongs to the TMP-PPASE family.	P9WG75	No	intermediary metabolism and respiration	ML0300	MMAR_0717	MSMEG_0789	Mb0422c				
NC_000962.3	Mycobrowser_v3	CDS	502366	503124	.	+	0	Rv0417	thiG	Involved in thiamine biosynthesis. Required for the synthesis of the thiazole moiety of thiamine.	Probable thiamin biosynthesis protein ThiG (thiazole biosynthesis protein)	Rv0417, (MTCY22G10.14), len: 252 aa. Probable thiG, thiamin biosynthesis protein, equivalent to AL035159|MLCB1450_20|T44741|THIG probable thiamin biosynthesis protein from Mycobacterium leprae (261 aa), FASTA scores: opt: 1380, E(): 0, (86.8% identity in 250 aa overlap). Also highly similar to others e.g. SCOEDB|SC6E10.03|T35490|THIG probable thiazole biosynthesis protein from Streptomyces coelicolor (264 aa); F82761|9105679|AAF83593.1|AE003919_4|XF0783|THIG thiamin biosynthesis protein thiG from Xylella fastidiosa (275 aa); P30139|THIG_ECOLI|7448315|B65206|409790|AAC43089.1|U00006 THIG protein thiamin biosynthesis protein from Escherichia coli strain K-12 (281 aa); etc. Belongs to the THIG family.	P9WG73	No	intermediary metabolism and respiration	ML0297,ML0297c	MMAR_0720	MSMEG_0793	Mb0425				
NC_000962.3	Mycobrowser_v3	CDS	503496	504998	.	+	0	Rv0418	lpqL	Function unknown; hydrolyzes peptides and/or proteins.	Probable lipoprotein aminopeptidase LpqL	Rv0418, (MTCCY22G10.15), len: 500 aa. Probable lpqL, lipoprotein aminopeptidase, similar to others e.g. B83278|9949035|AAG06327.1|AE004720_3|AE004720|PA2939 probable aminopeptidase from Pseudomonas aeruginosa (536 aa); P80561|APX_STRGR|SGAP|S66427 aminopeptidase from Streptomyces griseus (284 aa) (homology only with C-terminus of Rv0418); P37302|APE3_YEAST|1077010|A54134 aminopeptidase Y from Saccharomyces cerevisiae (537 aa); etc. Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	P96264	No	cell wall and cell processes		MMAR_0726	MSMEG_0806	Mb0426				
NC_000962.3	Mycobrowser_v3	CDS	508582	510225	.	-	0	Rv0423c	thiC	Involved in thiamine biosynthesis. Required for the synthesis of the hydromethylpyrimidine (HMP) moiety of thiamine (4-amino-2-methyl-5-hydroxymethylpyrimidine).	Probable thiamine biosynthesis protein ThiC	Rv0423c, (MTCY22G10.20c), len: 547 aa. Probable thiC, thiamin biosynthesis protein, equivalent to Q9ZBL0|THIC_MYCLE|11279601|T44743|AL035159|MLCB1450_22 thiamine biosynthesis protein from Mycobacterium leprae (547 aa), FASTA scores: opt: 3283, E(): 0, (90.1% identity in 547 aa overlap). Also highly similar to others e.g. P45740|THIC_BACSU thiamin biosynthesis protein from Bacillus subtilis (590 aa), FASTA scores: opt: 2295, E(): 0, (65.2% identity in 580 aa overlap); P30136|THIC_ECOLI THIC protein from Escherichia coli strain K12 (631 aa), FASTA scores: opt: 2141, E(): 0, (62.1% identity in 568 aa overlap); etc. Belongs to the ThiC family.	P9WG79	No	intermediary metabolism and respiration	ML0294	MMAR_0735	MSMEG_0826	Mb0431c				
NC_000962.3	Mycobrowser_v3	CDS	510702	515321	.	-	0	Rv0425c	ctpH	Metal cation-transporting ATPase; possibly catalyzes the transport of an undetermined metal cation with the hydrolysis of ATP [catalytic activity: ATP + H(2)O + undetermined metal cation(in) = ADP + phosphate + undetermined metal cation(out)].	Possible metal cation transporting P-type ATPase CtpH	Rv0425c, (MTCY22G10.22c), len: 1539 aa. Possible ctpH, metal cation-transporting P-type ATPase (transmembrane protein), showing some similarity with CAA17934.1|AL022118|13093871|CAC32203.1|AL583926 putative cation-transporting ATPase from Mycobacterium leprae (1609 aa). Also similar to others ATPases e.g. AE000873_1 cation-transporting P-ATPase from Methanobacterium thermoautotrop (844 aa), FASTA score: (30.5% identity in 827 aa overlap); AB69720.1|AL137166 putative transport ATPase from Streptomyces coelicolor (1472 aa); etc. C-terminal region similar to other ATPases from Mycobacterium tuberculosis e.g. Y05Q_MYCTU|Q10900 putative cation-transporting ATPase C (855 aa), FASTA scores: opt: 770, E(): 5.3e-32, (44.9% identity in 820 aa overlap). Nucleotide position 511518 in the genome sequence has been corrected, T:G resulting in I1268I.	P96271	No	cell wall and cell processes	ML1933	MMAR_0740		Mb0433c				
NC_000962.3	Mycobrowser_v3	CDS	516017	516892	.	-	0	Rv0427c	xthA	Involved in base excision repair. Apurinic-apyrimidinic endonuclease. Supposed to remove the damaged DNA at cytosines and guanines by cleaving at the 3' side of the AP site by a beta-elimination reaction. Possibly exhibites 3'-5'-exonuclease, 3'-phosphomonoesterase, 3'-repair diesterase and ribonuclease H activities [catalytic activity: degradation of double-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing 5'-phosphomononucleotides].	Probable exodeoxyribonuclease III protein XthA (exonuclease III) (EXO III) (AP endonuclease VI)	Rv0427c, (MTCY22G10.24c), len: 291 aa. Probable xthA (alternate gene name: xth), exodeoxyribonuclease III protein (see citation below), similar to others e.g. EX3_ECOLI|P09030 exodeoxyribonuclease III from Escherichia Coli strain K12 (268 aa), FASTA scores: opt: 360, E(): 1.2e-17, (29.3% identity in 270 aa overlap); etc. Belongs to the AP/EXOA family of DNA repair enzymes.	P96273	No	information pathways	ML1931	MMAR_0742	MSMEG_0829	Mb0435c				
NC_000962.3	Mycobrowser_v3	CDS	516895	517803	.	-	0	Rv0428c	Rv0428c	Acetylation, substrate unknown	GCN5-related N-acetyltransferase	Rv0428c, (MTCY22G10.25c), len: 302 aa. Probable acetyltransferase. Contains GNAT (Gcn5-related N-acetyltransferase) domain in C-terminal part. See Vetting et al. 2005.	P96274	No	intermediary metabolism and respiration	ML1930			Mb0436c				
NC_000962.3	Mycobrowser_v3	CDS	520324	521454	.	+	0	Rv0433	Rv0433	Function unknown	Conserved hypothetical protein	Rv0433, (MTCY22G10.30), len: 376 aa. Conserved hypothetical protein, similar to other hypothetical proteins e.g. P77213|YBDK_ECOLI hypothetical 41.7 KD protein from Escherichia coli strain K12 (372 aa), FASTA scores: opt: 555, E(): 2e-30, (28.2% identity in 365 aa overlap).	P9WPK9	No	conserved hypotheticals	ML1924,ML1924c	MMAR_0748	MSMEG_0836	Mb0441				
NC_000962.3	Mycobrowser_v3	CDS	521514	522167	.	+	0	Rv0434	Rv0434	Function unknown	Conserved hypothetical protein	Rv0434, (MTCY22G10.31), len: 217 aa. Conserved hypothetical protein, similar to AE002052_2 from Deinococcus radiodurans (213 aa), FASTA scores: opt: 258, E(): 4e-10, (31.9% identity in 213 aa overlap); SYCSLRB_122|Q55701 hypothetical 24.5 kDa protein from Synechocystis (214 aa), FASTA scores: opt: 156, E(): 0.00041, (28.4% identity in 204 aa overlap); MXABSGA_1|LON2_MYXXA|P36774 ATP-dependent protease la 2 from Myxococcus xanthus (826 aa), FASTA scores: opt: 160, E(): 0.00068, (28.4% identity in 197 aa overlap); etc.	P96280	No	conserved hypotheticals	ML0307			Mb0442				
NC_000962.3	Mycobrowser_v3	CDS	522347	524533	.	-	0	Rv0435c	Rv0435c	ATPase; possibly catalyzes the transport of undetermined substrate with hydrolyse of ATP [catalytic activity: ATP + H(2)O + undetermined substrate(in) = ADP + phosphate + undetermined substrate(out)].	Putative conserved ATPase	Rv0435c, (MTCY22G10.32c), len: 728 aa. Putative conserved ATPase, similar to others e.g. SAV_SULAC|Q07590 sav protein involved in cell division from sulfolobus acidocaldarius (780 aa), FASTA scores: opt: 897, E(): 0, (34.5% identity in 693 aa overlap); NP_148637.1|7435761|B72479 transitional endoplasmic reticulum ATPase from Aeropyrum pernix (699 aa); etc. Also similar to Rv3610c and Rv2115c from Mycobacterium tuberculosis. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00674 AAA-protein family signature.	P96281	No	cell wall and cell processes	ML0309,ML0309c	MMAR_0752	MSMEG_0858	Mb0443c				
NC_000962.3	Mycobrowser_v3	CDS	525387	526082	.	-	0	Rv0437c	psd	Function unknown, but involved in lipid metabolism [catalytic activity: phosphatidyl-L-serine = phosphatidylethanolamine + CO(2)].	Possible phosphatidylserine decarboxylase Psd (PS decarboxylase)	Rv0437c, (MTV037.01c), len: 231 aa (start uncertain). Possible psd, phosphatidylserine decarboxylase , equivalent to CAC29819.1|AL583918 conserved hypothetical protein from Mycobacterium leprae (243 aa); and highly similar to MLCB1450.11|T44729|4154044|CAA22695.1|AL035159 hypothetical protein from Mycobacterium leprae (202 aa), FASTA score: (74.6% identity in 197 aa overlap). Also similar to other phosphatidylserine decarboxylases e.g. NP_108058.1|14027249|BAB54203.1|AP003012 phosphatidylserine decarboxylase from Mesorhizobium loti (232 aa); AAK86872|g15156090|AGR_C_1963 phosphatidylserine decarboxylase from Agrobacterium tumefaciens (244 aa); AAG12422.1|AY005137|Psd phosphatidylserine decarboxylase from Chlorobium tepidum (216 aa); etc.	P9WHQ5	No	lipid metabolism	ML0311,ML0311c	MMAR_0754	MSMEG_0861	Mb0445c				
NC_000962.3	Mycobrowser_v3	CDS	527379	528314	.	-	0	Rv0439c	Rv0439c	Function unknown; possibly involved in cellular metabolism.	Probable dehydrogenase/reductase	Rv0439c, (MTV037.03c), len: 311 aa. Probable dehydrogenase/reductase, equivalent to AL035159|MLCB1450_6|T44727 probable oxidoreductase from Mycobacterium leprae (304 aa), FASTA scores: opt: 1360, E(): 0, (69.2% identity in 302 aa overlap). Also highly similar to various oxidoreductases, generally dehydrogenases/reductases e.g. PA5031|C83017|9951320|AAG08416.1|AE004916_5|AE004916 probable short chain dehydrogenase from Pseudomonas aeruginosa (309 aa); Q03326|OXIR_STRAT probable oxidoreductase from Streptomyces antibioticus (298 aa), FASTA scores: opt: 400, E(): 1.2e-18, (34.6% identity in 298 aa overlap); etc.	O53726	No	intermediary metabolism and respiration	ML0313,ML0313c			Mb0447c				
NC_000962.3	Mycobrowser_v3	CDS	528608	530230	.	+	0	Rv0440	groEL2	Prevents misfolding and promotes the refolding and proper assembly of unfolded polypeptides generated under stress conditions.	60 kDa chaperonin 2 GroEL2 (protein CPN60-2) (GroEL protein 2) (65 kDa antigen) (heat shock protein 65) (cell wall protein A) (antigen A)	Rv0440, (MTV037.04), len: 540 aa. GroEL2 (alternate gene names: groL2, groEL-2, hsp65, hsp60), 60 kDa chaperonin 2 (see Shinnick 1987). Purified 65 kDa antigen can elicit a strong delayed-type hypersensitivity reaction in experimental animals infected with M. tuberculosis. This protein is one of the major immunoreactive proteins of the mycobacteria. This antigen contains epitopes that are common to various species of mycobacteria. Contains PS00296 Chaperonins cpn60 signature. Belongs to the chaperonin (HSP60) family. Phosphorylated in vitro by PknJ|Rv2088 (See Arora et al., 2010).	P9WPE7	No	virulence, detoxification, adaptation	ML0317	MMAR_0759		Mb0448				
NC_000962.3	Mycobrowser_v3	CDS	533833	534396	.	-	0	Rv0445c	sigK	Involved in transcription mechanism. The sigma factor is an initiation factor that promotes attachment of the RNA polymerase to specific initiation sites and then is released.	Alternative RNA polymerase sigma factor SigK	Rv0445c, (MTV037.09c), len: 187 aa. sigK, alternative RNA polymerase sigma factor (see citations below), highly similar to others e.g. 5531433|CAB50938.1|AL096849|T36745 probable RNA polymerase sigma factor from Streptomyces coelicolor (185 aa); NP_105607.1|14024791|BAB51393.1|AP003005 RNA polymerase sigma factor from Mesorhizobium loti (179 aa); 1654108|AAB17906.1|U11283|A58883 probable transcription initiation factor sigma E from Rhodobacter phaeroides (168 aa), FASTA scores: opt: 299, E(): 2e-14, (32.7% identity in 168 aa overlap); Q45585|SIGW_BACSU RNA polymerase sigma factor SIGW from Bacillus subtilis (187 aa), FASTA scores: opt: 213, E(): 2.9e-08, (26.8% identity in 179 aa overlap); etc.	P9WGH7	No	information pathways	ML2370,ML2370c	MMAR_0766		Mb0453c				
NC_000962.3	Mycobrowser_v3	CDS	535224	536507	.	-	0	Rv0447c	ufaA1	Transfers a methylene group from S-adenosyl-L-methionine to the cis double bond of an unsaturated fatty acid chain resulting in the replacement of the double bond with a methylene bridge [catalytic activity: S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid].	Probable cyclopropane-fatty-acyl-phospholipid synthase UfaA1 (cyclopropane fatty acid synthase) (CFA synthase)	Rv0447c, (MTV037.11c), len: 427 aa (start uncertain). Probable ufaA1, cyclopropane-fatty-acyl-phospholipid synthase, similar to others e.g. NP_102178.1|14021351|BAB47964.1|AP002994 cyclopropane-fatty-acyl-phospholipid synthase from Mesorhizobium loti (378 aa); B82240|9655593|AAF94281.1|AE004192 cyclopropane-fatty-acyl-phospholipid synthase from Vibrio cholerae (432 aa); P30010|CFA_ECOLI cyclopropane-fatty-acyl-phospholipid synthase from Escherichia coli strain K-12 (382 aa); X55704|PPLPD_3 LPD-3 from P.putida (394 aa), FASTA scores: opt: 556, E(): 2.8e-30, (33.3% identity in 387 aa overlap); AE0005|HPAE000557_9 from Helicobacter pylori (389 aa), FASTA scores: opt: 539, E(): 3.9e-29, (34.3% identity in 382 aa overlap).	O53732	No	lipid metabolism	ML2372,ML2372c			Mb0455c				
NC_000962.3	Mycobrowser_v3	CDS	538588	541491	.	-	0	Rv0450c	mmpL4	Unknown. Thought to be involved in fatty acid transport.	Probable conserved transmembrane transport protein MmpL4	Rv0450c, (MTV037.14c), len: 967 aa. Probable mmpL4, conserved transmembrane transport protein (see citations below), member of RND superfamily, equivalent to U1740V|P54881|YV34_MYCLE hypothetical 105.2 kDa protein from Mycobacterium leprae (959 aa), FASTA scores: opt: 5051, E(): 0, (78.4% identity in 962 aa overlap). Also highly similar to other proteins from Mycobacterium tuberculosis e.g. Z83860|MTCY98.08 (962 aa), FASTA scores: opt: 3917, E(): 0, (61.3% identity in 950 aa overlap), MTCY20G9.34, etc. Contains PS00211 ABC transporters family signature. Belongs to the MmpL family.	P9WJV3	No	cell wall and cell processes	ML2378	MMAR_0771	MSMEG_0382	Mb0458c				
NC_000962.3	Mycobrowser_v3	CDS	545375	545821	.	-	0	Rv0455c	Rv0455c	Function unknown	Conserved protein	Rv0455c, (MTV037.19c), len: 148 aa. Conserved protein, equivalent to CAC31896.1|AL583925 possible secreted protein from Mycobacterium leprae (153 aa). Has hydrophobic stretch at N-terminus. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004). Predicted to be an outer membrane protein (See Song et al., 2008).	O53740	No	conserved hypotheticals	ML2380,ML2380c		MSMEG_3494	Mb0463c				
NC_000962.3	Mycobrowser_v3	CDS	554882	556306	.	-	0	Rv0465c	Rv0465c	Possibly involved in transcriptional mechanism.	Probable transcriptional regulatory protein	Rv0465c, (MTV038.09c), len: 474 aa. Probable transcriptional regulator, highly similar to AC44331.1|AL596102 putative DNA-binding protein from Streptomyces coelicolor (489 aa); and similar to several hypothetical proteins and others transcriptional regulators. Some similarity in N-terminal region (1-100 aa) with repressors e.g. P06153|RPC_BPPH1 immunity repressor protein (144 aa), FASTA scores: opt: 130, E(): 0.084,(27.0% identity in 100 aa overlap). Very similar to Rv1129c|Z95585|MTCY22G8.18c from Mycobacterium tuberculosis (486 aa), FASTA scores: opt: 1475, E(): 0, (47.4% identity in 468 aa overlap). Contains probable helix-turn-helix motif at aa 19-40 (1827, +5.41 SD).	P9WMI1	No	regulatory proteins	ML2464	MMAR_0790	MSMEG_0906	Mb0474c				
NC_000962.3	Mycobrowser_v3	CDS	557527	558813	.	+	0	Rv0467	icl1	Involved in glyoxylate bypass (at the first step), an alternative to the tricarboxylic acid cycle (in bacteria, plants, and fungi) [catalytic activity: isocitrate = succinate + glyoxylate]. Involved in the persistence in the host.	Isocitrate lyase Icl (isocitrase) (isocitratase)	Rv0467, (MTV038.11), len: 428 aa. Icl1, isocitrate lyase (see citations below), highly similar to many, closest to Z29367|RFISCILY_1 from R. fascians (429 aa), FASTA scores: opt: 2359, E(): 0, (80.7% identity in 429 aa overlap). Belongs to the isocitrate lyase family. Has 2-methyl-isocitrate lyase (MCL) activity in M. tuberculosis Erdman (See Munoz-Elias et al., 2006; Gould et al., 2006). Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WKK7	No	intermediary metabolism and respiration	ML2462,ML2462c	MMAR_0792	MSMEG_0911	Mb0476				
NC_000962.3	Mycobrowser_v3	CDS	560848	561711	.	-	0	Rv0470c	pcaA	Involved in the mycolic acid modification or synthesis; essential for the cyclopropanation function. Required for cording and mycolic acid cyclopropane ring synthesis in the cell wall.	Mycolic acid synthase PcaA (cyclopropane synthase)	Rv0470c, (MTV038.14), len: 287 aa. PcaA (previously known as umaA2), mycolic acid synthase (cyclopropane synthase) (see citations below), equivalent to CAC31976.1|AL583925 Mycolic acid synthase from Mycobacterium leprae (295 aa); and highly similar to S72886|B2168_F3_130|467038|AAA17222.1|U00018 hypothetical protein from Mycobacterium leprae (308 aa); Q11195|CFA1_MYCTU cyclopropane-fatty-acyl-phospholipid synthase 1 (cyclopropane mycolic acid synthase 1) (287 aa) (see Glickman et al., 2000); U27357|MTU27357_1 cyclopropane mycolic acid synthase from Mycobacterium tuberculosis (287 aa), FASTA scores: opt: 1415, E(): 0, (72.8% identity in 287 aa overlap); and related enzymes e.g. MTCY20H10.25c|Z92772|MTY20H10_26 (287 aa), FASTA scores: opt: 1387, E(): 0, (72.5% identity in 287 aa overlap).	P9WPB3	No	lipid metabolism	ML2459	MMAR_0796		Mb0479c				
NC_000962.3	Mycobrowser_v3	CDS	562723	563427	.	-	0	Rv0472c	Rv0472c	Possibly involved in transcriptional mechanism.	Probable transcriptional regulatory protein (possibly TetR-family)	Rv0472c, (MTV038.16c), len: 234 aa. Probable regulatory protein, possibly TetR family, equivalent to CAC31974.1|AL583925 possible TetR-family transcriptional regulator from Mycobacterium leprae (233 aa). Also similar to CAC01492.1|AL391017 putative transcriptional regulatory protein from Streptomyces coelicolor (218 aa); and CAC01371.1|AL390975 putative TetR-family transcriptional regulator from Streptomyces coelicolor (228 aa). Also similar to AL0212|MTV012_65 from Mycobacterium tuberculosis (246 aa), FASTA scores: opt: 327, E(): 1.8e-15, (31.0% identity in 232 aa overlap); and Z95120|MTCY07D11.18c (228 aa), FASTA scores: opt: 190, E(): 4.4e-06, (23.1% identity in 186 aa overlap). Contains probable helix-turn-helix doimain at aa 45-66 (Score 1429, +4.05 SD).	P9WMD9	No	regulatory proteins	ML2457	MMAR_0797	MSMEG_0916	Mb0482c				
NC_000962.3	Mycobrowser_v3	CDS	565797	566396	.	+	0	Rv0475	hbhA	Required for extrapulmonary dissemination. Mediates adherence to epithelial cells by binding to sulfated glycoconjugates present at the surface of these cells; binds heparin, dextran sulfate, fucoidan and chondroitin sulfate. Promotes hemagglutination of erythrocytes of certain host species. Induces mycobacterial aggregation.	Iron-regulated heparin binding hemagglutinin HbhA (adhesin)	Rv0475, hbhA (MTCY20G9.01), len: 199 aa. HbhA, iron-regulated heparin-binding hemagglutinin (see citations below), equivalent to CAC31971.1|AL583925 possible hemagglutinin from Mycobacterium leprae (188 aa). Contains possible N-terminal signal sequence and K-a-rich region at C-terminus: subcellular location: surface associated. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WIP9	No	cell wall and cell processes	ML2454,ML2454c	MMAR_0800	MSMEG_0919	Mb0485				
NC_000962.3	Mycobrowser_v3	CDS	568964	569806	.	-	0	Rv0480c	Rv0480c	Function unknown; hydrolytic enzyme probably involved in cellular metabolism.	Possible amidohydrolase	Rv0480c, (MTCY20G9.06c), len: 280 aa. Possible amidohydrolase, highly similar to NP_302587.1|NC_002677|CAC31966.1|AL583925 putative hydrolase from Mycobacterium leprae (271 aa). Also similar to other hydrolases and hypothetical proteins e.g. NP_601985.1|NC_003450 Predicted amidohydrolase from Corynebacterium glutamicum (266 aa); NP_459623.1|NC_003197 putative hydrolase from Salmonella typhimurium LT2 (262 aa); AL096822|SCGD3_8|NP_627996.1|NC_003888 probable hydrolase from Streptomyces coelicolor (264 aa), FASTA scores: opt: 368, E(): 6.1e-15, (34.2% identity in 272 aa overlap); YAUB_SCHPO|Q10166 hypothetical 35.7 kDa protein c26a3.11 from S. pombe (322 aa), FASTA scores: opt: 338, E():1.4e-13, (30.3% identity in 277 aa overlap); etc. Start changed since first submission (-60 aa).	P9WJ01	No	intermediary metabolism and respiration	ML2449	MMAR_0805	MSMEG_0924	Mb0490c				
NC_000962.3	Mycobrowser_v3	CDS	570539	571648	.	+	0	Rv0482	murB	Involved in cell wall formation; peptidoglycan biosynthesis [catalytic activity: UDP-N-acetylmuramate + NADP+ = UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine + NADPH].	Probable UDP-N-acetylenolpyruvoylglucosamine reductase MurB (UDP-N-acetylmuramate dehydrogenase)	Rv0482, (MTCY20G9.08), len: 369 aa. Probable murB, UDP-N-acetylenolpyruvoylglucosamine reductase (see citation below), equivalent to CAC31964.1|AL583925 UDP-N-acetylenolpyruvoylglucosamine reductase from Mycobacterium leprae (367 aa). Also highly similar to others e.g. MURB_ECOLI|P08373 UDP-N-acetylenolpyruvoylglucosamine reductase from Escherichia coli (342 aa), FASTA scores: opt: 292, E(): 6.3e-12, (33.5% identity in 355 aa overlap); etc. Belongs to the MurB family. Cofactor: FAD.	P9WJL9	No	cell wall and cell processes	ML2447,ML2447c	MMAR_0808	MSMEG_0928	Mb0492				
NC_000962.3	Mycobrowser_v3	CDS	575348	576790	.	+	0	Rv0486	mshA	Involved in the first step of mycothiol biosynthesis	Glycosyltransferase MshA	Rv0486, (MTCY20G9.12), len: 480 aa. MshA, glycosyltransferase (see citations below), highly similar to P54138|Y486_MYCLE|ML2443 possible glycosyl transferase from Mycobacterium leprae (428 aa); and S72892|B2168_C2_201 probable hexosyltransferase from Mycobacterium leprae (409 aa), FASTA scores: opt: 2375, E(): 0, (86.4% identity in 413 aa overlap). Also highly similar to CAC04040.1|AL391406 putative transferase from Streptomyces coelicolor (496 aa); and similar to various transferases e.g. NP_437172.1|NC_003078 putative membrane-anchored glycosyltransferase protein from Sinorhizobium meliloti (416 aa); O26550|U67601_1 LPS biosynthesis related protein from Methanococcus jannaschii (411 aa), FASTA score: (25.3% identity in 387 aa overlap); etc. Also similar to CAC87824.1|AJ316594 putative sucrose-phosphate synthase from Nostoc punctiforme (422 aa). Contains a match to Pfam entry PF00534 glycosyl_transf_1 - Glycosyl transferases group 1.	P9WMY7	No	intermediary metabolism and respiration	ML2443,ML2443c	MMAR_0812	MSMEG_0933	Mb0496				
NC_000962.3	Mycobrowser_v3	CDS	577664	578269	.	+	0	Rv0488	Rv0488	Unknown; possibly involved in transport of lysine across the membrane.	Probable conserved integral membrane protein	Rv0488, (MTCY20G9.14), len: 201 aa. Probable conserved integral membrane protein, LysE family possibly involved in transport of Lysine, similar to others and conserved hypothetical proteins e.g. AB93746.1|AL357613 putative membrane transport protein from Streptomyces coelicolor (204 aa); D83100|PA4365 probable transporter from Pseudomonas aeruginosa (200 aa); YGGA_ECOLI|P11667 hypothetical 21.7 kDa protein from Escherichia coli (197 aa), FASTA scores: opt: 382, E(): 1.1e-19, (39.1% identity in 179 aa overlap); CGLYSEG_2 C|P94633 lysine exporter protein (236 aa), FASTA scores: E(): 2.3e-07, (33.3% identity in 219 aa overlap). Also similar to Rv1986 from Mycobacterium tuberculosis.	P9WK33	No	cell wall and cell processes				Mb0498				
NC_000962.3	Mycobrowser_v3	CDS	579349	580581	.	+	0	Rv0490	senX3	Sensor part of a two component regulatory system. Probably forms part of a two-component regulatory system SENX3/REGX3; phosphorylates REGX3.	Putative two component sensor histidine kinase SenX3	Rv0490, (MTCY20G9.16), len: 410 aa. Putative senX3, two-component sensor histidine kinase, transmembrane protein (see citations below), equivalent to O07129|SEX3_MYCBO sensor-like histidine kinase SENX3 from Mycobacterium bovis BCG (410 aa), FASTA scores: E(): 0, (99.5% identity in 410 aa overlap); and highly similar to P54883|SEX3_MYCLE|SENX3 sensor-like histidine kinase from Mycobacterium leprae (443 aa), FASTA score: (83.8% identity in 408 aa overlap). Also highly similar, except in N-terminus, to CAC31957.1|AL583925 probable two-component system sensor histidine kinase from Mycobacterium leprae (441 aa). Also highly similar to sensor kinase proteins from other organisms e.g. CAB77323.1|AL160331 putative sensor kinase protein from Streptomyces coelicolor (426 aa).	P9WGK5	No	regulatory proteins	ML2440,ML2440c	MMAR_0815	MSMEG_0936	Mb0500				
NC_000962.3	Mycobrowser_v3	CDS	581489	583378	.	-	0	Rv0492c	Rv0492c	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase GMC-type	Rv0492c, (MT0511/MT0512, MTCY20G9.18c), len: 629 aa. Probable oxidoreductase GMC type, similar to others except in N-terminus e.g. P55582|AE000087_5|Y4NJ_RHISN hypothetical GMC-type oxidoreductase from Rhizobium sp. (505 aa), FASTA scores: opt: 873, E():0, (34.3% identity in 502 aa overlap); YTH2_RHOER|P46371 hypothetical 53.0 kDa GMC-type oxidoreductase from Rhodococcus erythropolis (493 aa), FASTA score: (25.7% identity in 521 aa overlap); YTH2_RHOSO|P46371 hypothetical 53.0 kDa gmc-type oxidoreductase from Rhodococcus erythropolis (493 aa), FASTA score: (25.7% identity in 521 aa overlap); NP_085596.1|NC_002679 probable oxidoreductase from Mesorhizobium loti (507 aa); NP_285451.1|NC_001264 GMC oxidoreductase from Deinococcus radiodurans (722 aa); NP_249055.1|NC_002516 probable oxidoreductase from Pseudomonas aeruginosa (531 aa); etc. Contains PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature, and PS00624 GMC oxidoreductases signature 2. Belongs to the GMC oxidoreductases family. Cofactor: FAD (by similarity). Note that start changed since first submission (previously 684 aa).	P9WMV7	No	intermediary metabolism and respiration	ML2438	MMAR_0817	MSMEG_5967	Mb0502c				
NC_000962.3	Mycobrowser_v3	CDS	591111	591347	.	+	0	Rv0500A	Rv0500A	Function unknown	Conserved protein	Rv0500A, len: 78 aa. Conserved protein, similar to proteins from Mycobacterium leprae and Streptomyces coelicolor e.g. U00018_25 from Mycobacterium leprae cosmid B2168 (86 aa), FASTA scores: opt: 428, E(): 1.3e-27, (82.6% identity in 86 aa overlap); AL079345|SCE68_26 from Streptomyces coelicolor cosmid E6 (70 aa), FASTA scores: opt: 252, E(): 1.2 e-13, (72.2 identity in 54 aa overlap).	P9WKT7	No	conserved hypotheticals	ML2429,ML2429c			Mb0512				
NC_000962.3	Mycobrowser_v3	CDS	591654	592784	.	+	0	Rv0501	galE2	Involved in galactose metabolism [catalytic activity: UDP-glucose = UDP-galactose].	Possible UDP-glucose 4-epimerase GalE2 (galactowaldenase) (UDP-galactose 4-epimerase) (uridine diphosphate galactose 4-epimerase) (uridine diphospho-galactose 4-epimerase)	Rv0501, (MTCY20G9.28), len: 376 aa. Possible galE2, UDP-glucose 4-epimerase, highly similar (except in N-terminus) to CAC31944.1|AL583925 possible glucose epimerase/dehydratase from Mycobacterium leprae (364 aa). N-terminus highly similar to S72923|B2168_C1_174|467075|AAA17259.1|U00018 hypothetical protein from Mycobacterium leprae (180 aa), FASTA scores: opt: 934, E(): 0, (89.6% identity in 164 aa overlap); and C-terminus highly similar to S72898|467050|AAA17234.1|U00018 hypothetical protein from Mycobacterium leprae (168 aa), FASTA scores: opt: 928, E(): 0, (82.7% identity in 168 aa overlap). Also highly similar to T36274|5123671|CAB45360.1|AL079345 probable epimerase from Streptomyces coelicolor (353 aa); and similar in part to other epimerases e.g. GALE_ECOLI|P09147 UDP-glucose 4-epimerase from Escherichia coli (338 aa), FASTA scores: opt: 241, E(): 6.7e-09, (28.2% identity in 294 aa overlap); etc. Belongs to the sugar epimerase family. Cofactor: NAD. Note that previously known as galE1.	P9WKT3	No	intermediary metabolism and respiration	ML2428,ML2428c	MMAR_0829	MSMEG_0946	Mb0513				
NC_000962.3	Mycobrowser_v3	CDS	593871	594779	.	-	0	Rv0503c	cmaA2	Essential for the cyclopropanation function. Transfers a methylene group from S-adenosyl-L-methionine to the cis double bond of an unsaturated fatty acid chain resulting in the replacement of the double bond with a methylene bridge. Mycolic acids, which represent the major constituent of mycobacterial cell wall complex, act as substrates [catalytic activity: S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid].	Cyclopropane-fatty-acyl-phospholipid synthase 2 CmaA2 (cyclopropane fatty acid synthase) (CFA synthase) (cyclopropane mycolic acid synthase 2) (mycolic acid trans-cyclopropane synthetase)	Rv0503c, (MTCY20G9.30c), len: 302 aa. CmaA2 (alternate gene name: cma2), cyclopropane-fatty-acyl-phospholipid synthase 2 (mycolic acid trans-cyclopropane synthetase) (see citations below). Note that this protein has 302 aa and not 322 aa: we have chosen a different initiation codon on the basis of homology. Equivalent to S72886|B2168_F3_130 hypothetical protein from Mycobacterium leprae (308 aa), FASTA score: (78.9% identity in 303 aa overlap); and highly similar to other proteins from Mycobacterium leprae. Also similar to other proteins from Mycobacterium tuberculosis and Mycobacterium bovis BCG e.g. MTV038_14|UMAA2|Rv0470c|MTV038.14 putative mycolic acid synthesis/modification protein (287 aa) (57.2% identity in 297 aa overlap).	P9WPB5	No	lipid metabolism	ML2426	MMAR_0831	MSMEG_1205	Mb0515c				
NC_000962.3	Mycobrowser_v3	CDS	595464	596585	.	-	0	Rv0505c	serB1	Removes a phosphate from phosphoserine [catalytic activity: phosphoserine + H2O = serine + phosphate].	Possible phosphoserine phosphatase SerB1 (PSP) (O-phosphoserine phosphohydrolase) (pspase)	Rv0505c, (MTCY20G9.32c), len: 373 aa. Possible serB1, phosphoserine phosphatase, equivalent (but longer ~70 aa in N-terminus) to S72914|serB phosphoserine phosphatase from Mycobacterium leprae (300 aa), FASTA scores: opt: 1570, E(): 0, (83.0% identity in 306 aa overlap). C-terminus highly similar to CAB55344.1|AJ010584 phosphoserine phosphatase from Streptomyces coelicolor (266 aa). Low similarity to SERB_ECOLI|P06862 phosphoserine phosphatase from Escherichia coli strains K12 and O157:H7 (322 aa), FASTA scores: opt: 148, E(): 0.043, (24.0% identity in 150 aa overlap). C-terminus is also similar to O33611|AB004855_1|IMD_STRCN protein involved in inhibition of morphological differentiation from Streptomyces cyaneus (277 aa), FASTA score: (37.7% identity in 252 aa overlap). Seems to belong to the SERB family. Note that previously known as serB.	P9WGJ3	No	intermediary metabolism and respiration	ML2424	MMAR_0833	MSMEG_0949	Mb0517c				
NC_000962.3	Mycobrowser_v3	CDS	613038	614342	.	+	0	Rv0522	gabP	Involved in 4-aminobutyrate (GABA) degradation pathway. Transporter for GABA. Responsible for the translocation of the substrate across the membrane.	Probable GABA permease GabP (4-amino butyrate transport carrier) (GAMA-aminobutyrate permease)	Rv0522, (MTCY20G10.12), len: 434 aa. Probable gabP, GABA permease (gamma-aminobutyrate permease), integral membrane protein, highly similar to others e.g. GABP_ECOLI|P25527 gaba permease from Escherichia coli (466 aa), FASTA scores: opt: 1218, E(): 0, (44.3% identity in 424 aa overlap); etc. Also similar to other M. tuberculosis permeases e.g. MTCY13E10.06c FASTA score: (34.4% identity in 407 aa overlap). Contains PS00218 Amino acid permeases signature. Overlaps and extends Rv0523c|MTCY25D10.01 from overlapping cosmid. Belongs to the amino acid permease family (APC family).	L7N6B9	No	cell wall and cell processes	ML2416,ML2416c	MMAR_0862		Mb0535				
NC_000962.3	Mycobrowser_v3	CDS	3004035	3004748	.	-	0	Rv2687c	Rv2687c	Thought to be involved in active transport of unidentified antibiotic across the membrane (export): antibiotic resistance by an export mechanism. Responsible for the translocation of the substrate across the membrane.	Antibiotic-transport integral membrane leucine and valine rich protein ABC transporter	Rv2687c, (MTCY05A6.08c), len: 237 aa. Antibiotic-transport integral membrane leu-, val-rich protein ABC transporter (see citation below), showing some similarity with two other hypothetical proteins, BAB59668|TVG0517148 from Thermoplasma volcanium (241 aa), FASTA scores: opt: 136, E(): 0.32, (23.1% identity in 208 aa overlap); and Q97U55|SSO3168 from Sulfolobus solfataricus (249 aa), FASTA scores: opt: 136, E(): 0.33, (25.15% identity in 195 aa overlap). Has some hydrophobic stretches and contains bacterial regulatory proteins, araC family signature (PS00041).	P9WJB1	No	cell wall and cell processes	ML1034	MMAR_2027	MSMEG_1503	Mb2706c				
NC_000962.3	Mycobrowser_v3	CDS	601857	602786	.	+	0	Rv0510	hemC	Involved in porphyrin biosynthesis by the C5 pathway (at the fourth step). Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane preuroporphyrinogen in several discrete steps [catalytic activity: 4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3].	Probable porphobilinogen deaminase HemC (PBG) (hydroxymethylbilane synthase) (HMBS) (pre-uroporphyrinogen synthase)	Rv0510, (MTCY21C8.01-MTCY20G9.37), len: 309 aa. Probable hemC, hydroxymethylbilane synthase (porphobilinogen deaminase), equivalent to HEM3B|Q49808|HEM3_MYCLE porphobilinogen deaminase from Mycobacterium leprae (315 aa), FASTA scores: opt: 889, E(): 0, (88.1% identity in 159 aa overlap). Also highly similar to others e.g. Q9WX16|HE31_STRCO probable porphobilinogen deaminase from Streptomyces coelicolor (319 aa); Q9L6Q2|HEM3_SALTY porphobilinogen deaminase from Salmonella typhimurium (313 aa); etc. Belongs to the HMBS family. Cofactor: covalently binds a dipyrromethane cofactor to which the porphobilinogen subunits are ADDED.	P9WMP3	No	intermediary metabolism and respiration	ML2421,ML2421c	MMAR_0843	MSMEG_0953	Mb0523				
NC_000962.3	Mycobrowser_v3	CDS	602819	604516	.	+	0	Rv0511	hemD	Possibly involved in the biosynthesis of siroheme and cobalamin [catalytic activity: 2 S-adenosyl-L-methionine + uroporphyrin III = 2 S-adenosyl-L-homocysteine + sirohydrochlorin].	Probable uroporphyrin-III C-methyltransferase HemD (uroporphyrinogen III methylase) (urogen III methylase) (SUMT) (urogen III methylase) (UROM)	Rv0511, (MTCY21C8.02), len: 565 aa. Probable hemD (alternate gene name: cysG), uroporphyrin-III C-methyltransferase, highly similar to others e.g. CAC31936.1|AL583925 possible uroporphyrin-III C-methyltransferase from Mycobacterium leprae (563 aa); and S72909|CYSG from Mycobacterium leprae (472 aa), FASTA scores: opt: 1946, E(): 0, (83.3% identity in 472 aa overlap); T36265|5123662|CAB45351.1|AL079345 probable uroporphyrin-III C-methyltransferase from Streptomyces coelicolor (565 aa); and similar to others e.g. AAK00606.1|AF221100_3|AF221100 from Selenomonas ruminantium subsp. ruminantium (505 aa); etc. Also similar to Rv2071c and Rv2847c from Mycobacterium tuberculosis. Note that previously known as cysG.	Q6MX34	No	intermediary metabolism and respiration	ML2420,ML2420c			Mb0524				
NC_000962.3	Mycobrowser_v3	CDS	614835	616223	.	+	0	Rv0524	hemL	Involved in porphyrin biosynthesis by the C5 pathway (at the second step) [catalytic activity: (S)-4-amino-5-oxopentanoate = 5-aminolevulinate].	Probable glutamate-1-semialdehyde 2,1-aminomutase HemL (GSA) (glutamate-1-semialdehyde aminotransferase) (GSA-at)	Rv0524, (MTCY25D10.03), len: 462 aa. Probable hemL, glutamate-1-semialdehyde 2,1-aminomutase, equivalent to P46716|GSA_MYCLE glutamate-1-semialdehyde 2,1-aminomutase from Mycobacterium leprae (446 aa), FASTA scores: opt: 1532, E(): 0, (82.6% identity in 460 aa overlap). Also highly similar to others e.g. Q9F2S0|GSA_STRCO from Streptomyces coelicolor (438 aa); Q06774|GSA_PROFR from Propionibacterium freudenreichii (441 aa); etc. Contains PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site. Belongs to class-III of pyridoxal-phosphate-dependent aminotransferases. Cofactor: pyridoxal phosphate.	P9WMN9	No	intermediary metabolism and respiration	ML2414,ML2414c	MMAR_0870	MSMEG_0969	Mb0537				
NC_000962.3	Mycobrowser_v3	CDS	617493	618272	.	+	0	Rv0527	ccdA	Possibly involved in cytochrome C synthesis. Might transfer reducing equivalents across the cytoplasmic membrane, promoting efficient disulfide bond isomerization of proteins localized on the outer surface of the membrane.	Possible cytochrome C-type biogenesis protein CcdA	Rv0527, (MTCY25D10.06), len: 259 aa. Possible ccdA, cytochrome C-type biogenesis protein, integral membrane protein, equivalent to Q49810|B2168_C1_192|S72890 hypothetical protein from Mycobacterium leprae (262 aa), FASTA scores: opt: 1341, E(): 0, (79.0% identity in 262 aa overlap). Also highly similar to others e.g. CAC08380.1 (253 aa); CCDA_BACSU|P45706 cytochrome C-type biogenesis protein from Bacillus subtilis (235 aa), FASTA scores: opt: 307, E(): 7.4e-13, (30.4% identity in 237 aa overlap); etc. Seems to belong to the DSBD subfamily. Note that previously known as ccsA.	L7N671	No	intermediary metabolism and respiration	ML2411,ML2411c	MMAR_0873	MSMEG_0972	Mb0540				
NC_000962.3	Mycobrowser_v3	CDS	622329	622646	.	+	0	Rv0531	Rv0531	Unknown	Possible conserved membrane protein	Rv0531, (MTCY25D10.10), len: 105 aa. Possible conserved membrane protein, highly similar to Y13803|MLB1306_1|CAA74131.1 hypothetical protein from Mycobacterium leprae (86 aa), FASTA scores: E(): 2.1e-24, (74.4% identity in 86 aa overlap); and NP_302557.1|NC_002677 putative membrane protein from Mycobacterium leprae (111 aa). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O06397	No	cell wall and cell processes	ML2407,ML2407c	MMAR_0878	MSMEG_0977	Mb0544				
NC_000962.3	Mycobrowser_v3	CDS	624473	625480	.	-	0	Rv0533c	fabH	Involved in fatty acid biosynthesis. Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. KAS III catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities [catalytic activity: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]].	3-oxoacyl-[acyl-carrier-protein] synthase III FabH (beta-ketoacyl-ACP synthase III) (KAS III)	Rv0533c, (MTCY25D10.12c), len: 335 aa. FabH (alternate gene name: mtFabH), 3-oxoacyl-[acyl-carrier protein] synthase III (see citations below), highly similar to others e.g. Q54206|FABH from streptomyces glaucescens (333 aa), FASTA scores: opt: 1109, E(): 0, (51.4% identity in 333 aa overlap); FABH_ECOLI|P24249 3-oxoacyl-[acyl-carrier-protein] synthase III (317 aa), FASTA scores: opt: 666, E(): 0, (37.1% identity in 318 aa overlap); etc. Belongs to the FabH family.	P9WNG3	No	lipid metabolism		MMAR_0879		Mb0547c				
NC_000962.3	Mycobrowser_v3	CDS	626457	627251	.	+	0	Rv0535	pnp	Phosphorylates 5'-methylthioadenosin [catalytic activity: 5'-methylthioadenosine + phosphate = adenine + 5-methylthio-D-ribose 1-phosphate].	Probable 5'-methylthioadenosine phosphorylase Pnp (MTA phosphorylase)	Rv0535, (MTCY25D10.14c), len: 264 aa. Probable pnp, 5'-methylthioadenosine phosphorylase, highly similar to others e.g. CAB90972.1|AL355832 putative methylthioadenosine phosphorylase from Streptomyces coelicolor (280 aa); etc. Also similar to Rv3307|deoD probable purine nucleoside phosphorylase from Mycobacterium tuberculosis (268 aa). Belongs to the PNP/MTAP family 2 of phosphorylases. Gene name could be inappropriate.	O06401	No	intermediary metabolism and respiration	ML2405,ML2405c	MMAR_0881	MSMEG_0990	Mb0549				
NC_000962.3	Mycobrowser_v3	CDS	627248	628288	.	+	0	Rv0536	galE3	Possibly involved in galactose metabolism [catalytic activity: UDP-glucose = UDP-galactose].	Probable UDP-glucose 4-epimerase GalE3 (galactowaldenase) (UDP-galactose 4-epimerase) (uridine diphosphate galactose 4-epimerase) (uridine diphospho-galactose 4-epimerase)	Rv0536, (MTCY25D10.15), len: 346 aa. Possible galE3, UDP-glucose 4-epimerase, highly similar to CAB76986.1|AL159178 putative epimerase from Streptomyces coelicolor (334 aa); and similar to other epimerases e.g. NP_436775.1|NC_003078 putative NDP-glucose dehydrataseepimerase protein from Sinorhizobium meliloti (368 aa); AF143772|AF143772_7 GepiA from Mycobacterium avium strain 2151 (353 aa), FASTA scores: opt: 577, E(): 3.9e-29, (36.6% identity in 352 aa overlap); GALE_METJA|Q57664 putative UDP-glucose 4-epimerase (305 aa), FASTA scores: opt: 300, E(): 1.6e-12, (30.9% identity in 343 aa overlap); etc. Also similar to Mycobacterium tuberculosis proteins e.g. Rv3634c, Rv3784, etc. Seems to belong to the sugar epimerase family. Note that previously known as galE2.	L7N670	No	intermediary metabolism and respiration	ML2404,ML2404c	MMAR_0882	MSMEG_0991	Mb0550				
NC_000962.3	Mycobrowser_v3	CDS	710782	711009	.	+	0	Rv0616A	vapB29	Unknown	Possible antitoxin VapB29	Rv0616A, len: 75 aa. Possible vapB29, antitoxin, part of toxin-antitoxin (TA) operon with Rv0617, see Arcus et al. 2005. Similar to many others in M. tuberculosis e.g. Rv2530A (74 aa) 35.9% identity in 78 aa overlap	P9WJ37	No	virulence, detoxification, adaptation								
NC_000962.3	Mycobrowser_v3	CDS	630040	631686	.	+	0	Rv0538	Rv0538	Unknown	Possible conserved membrane protein	Rv0538, (MTCY25D10.17), len: 548 aa. Possible conserved membrane protein. Middle region highly similar to AAB63811.1|AF009829|MBE4863a|O32850 unknown protein from Mycobacterium bovis (295 aa) possible transmembrane protein with a repetitive proline, threonine-rich region at C-terminus.	O06404	No	cell wall and cell processes	ML0306	MMAR_0884	MSMEG_1188	Mb0552				
NC_000962.3	Mycobrowser_v3	CDS	634416	635504	.	-	0	Rv0542c	menE	Involved in menaquinone biosynthesis. O-succinylbenzoic acid (OSB) to O-succinylbenzoyl-CoA (OSB-CoA) [catalytic activity: ATP + O-succinylbenzoate + CoA = AMP + diphosphate + O-succinylbenzoyl-CoA].	Possible O-succinylbenzoic acid--CoA ligase MenE (OSB-CoA synthetase) (O-succinylbenzoate-CoA synthase)	Rv0542c, (MTCY25D10.21c), len: 362 aa. Possible menE, O-succinylbenzoic acid-CoA ligase, highly similar to Q50170|AAA63145.1|U15187|XCLB 4-Coumarate--CoA ligase from Mycobacterium leprae (352 aa), FASTA scores: opt: 1815, E(): 0, (78.9% identity in 351 aa overlap). Also similar to N-terminus of acid-CoA ligases e.g. NP_471116.1|NC_003212 O-succinylbenzoic acid-CoA ligase from Listeria innocua (469 aa); NP_390957.1|NC_000964 O-succinylbenzoic acid-CoA ligase from Bacillus subtilis (486 aa); MENE_HAEIN|P44565 O-succinylbenzoic acid-CoA ligase from Haemophilus influenzae (452 aa), FASTA scores: opt: 307, E(): 4.6e-12, (25.4% identity in 339 aa overlap); etc. Also some similarity with fadD proteins from Mycobacterium tuberculosis. Contains PS00455 Putative AMP-binding domain signature. Belongs to the ATP-dependent AMP-binding enzyme family.	P9WQ39	No	intermediary metabolism and respiration	ML2257,ML2257c	MMAR_0888	MSMEG_1062	Mb0556c				
NC_000962.3	Mycobrowser_v3	CDS	635935	636213	.	-	0	Rv0544c	Rv0544c	Unknown	Possible conserved transmembrane protein	Rv0544c, (MTCY25D10.23c), len: 92 aa. Possible conserved transmembrane protein, equivalent to NP_302470.1|NC_002677 possible membrane protein from Mycobacterium leprae (96 aa); and shows some similarity to MLU15187_33|Q50172|U296V from Mycobacterium leprae (36 aa), FASTA scores: opt: 151, E(): 2.1e-05, (71.4% identity in 35 aa overlap). Also some similarity with VATL_NEPNO|Q26250 vacuolar ATP synthase 16 kDa proteolipid from Nephrops norvegicus (159 aa), FASTA scores: opt: 80, E(): 11, (26.1% identity in 88 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O06410	No	cell wall and cell processes	ML2259,ML2259c	MMAR_0890	MSMEG_1065	Mb0558c				
NC_000962.3	Mycobrowser_v3	CDS	636210	637463	.	-	0	Rv0545c	pitA	Involved in low-affinity inorganic phosphate transport across the membrane. Responsible for the translocation of the substrate across the membrane.	Probable low-affinity inorganic phosphate transporter integral membrane protein PitA	Rv0545c, (MTCY25D10.24c), len: 417 aa. Probable pitA, low-affinity inorganic phosphate transporter, integral membrane protein, equivalent to Q50173|NP_302471.1 pitA from Mycobacterium leprae (414 aa), FASTA scores: opt: 2035, E(): 0, (76.3% identity in 418 aa overlap). Also highly similar to others e.g. CAB59461.1|AL132644 putative low-affinity phosphate transport protein from Streptomyces coelicolor (423 aa); PITA_ECOLI|P37308 low-affinity inorganic phosphate transporter from Escherichia coli (499 aa), FASTA scores: opt: 304, E(): 6.9e-10, (32.5 % identity in 234 aa overlap); etc. Belongs to the PHO-4 family of transporters, pit subfamily.	P9WIA7	No	cell wall and cell processes	ML2260,ML2260c	MMAR_0891	MSMEG_1064	Mb0559c				
NC_000962.3	Mycobrowser_v3	CDS	641096	642811	.	-	0	Rv0551c	fadD8	Function unknown, but involved in lipid degradation.	Probable fatty-acid-CoA ligase FadD8 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv0551c, (MTCY25D10.30c), len: 571 aa. Probable fadD8, fatty-acid-CoA synthetase, similar to many e.g. LCFA_ECOLI|P29212 long-chain-fatty-acid--CoA ligase (561 aa), FASTA scores: opt: 585, E(): 9.5e-30, (28.7% identity in 536 aa overlap); etc. Contains PS00455 Putative AMP-binding domain signature. Note other possible start sites exist downstream of this start.	O06417	No	lipid metabolism	ML2266,ML2266c	MMAR_0897	MSMEG_1098	Mb0566c				
NC_000962.3	Mycobrowser_v3	CDS	646298	647962	.	+	0	Rv0555	menD	Involved in menaquinone biosynthesis (at the first step) [catalytic activity 1: isochorismate + 2-ketoglutarate = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate + pyruvate + CO(2)] [catalytic activity 2: 2-oxoglutarate = succinate semialdehyde + CO(2)].	Probable bifunctional menaquinone biosynthesis protein MenD : 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (SHCHC synthase) + 2-oxoglutarate decarboxylase (alpha- ketoglutarate decarboxylase) (KDC)	Rv0555, (MTCY25D10.34), len: 554 aa. Probable menD, menaquinone biosynthesis protein, including 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase and 2-oxoglutarate decarboxylase activities. Equivalent to NP_302478.1|NC_002677 putative 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / 2-oxoglutarate decarboxylase from Mycobacterium leprae (556 aa). Also similar to others e.g. MEND_BACSU|P23970 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase from Bacillus subtilis (548 aa), FASTA scores: opt: 488, E(): 2.3e-21, (34.3% identity in 545 aa overlap); etc. Cofactor: thiamine pyrophosphate.	P9WK11	No	intermediary metabolism and respiration	ML2270	MMAR_0901	MSMEG_1109	Mb0570				
NC_000962.3	Mycobrowser_v3	CDS	649689	650393	.	+	0	Rv0558	menH	Involved in menaquinone biosynthesis (at the last step) converts DMKH2 into MKH2 [catalytic activity: S-adenosyl-L-methionine + demethylmenaquinol = S-adenosyl-L-homocysteine + menaquinol].	Probable ubiquinone/menaquinone biosynthesis methyltransferase MenH (2-heptaprenyl-1,4-naphthoquinone methyltransferase)	Rv0558, (MTCY25D10.37), len: 234 aa. Probable menH (alternate gene name: menG), ubiquinone/menaquinone biosynthesis methlytransferase (2-heptaprenyl-1,4-naphthoquinone methyltransferase), equivalent to NP_302480.1|NC_002677 putative ubiquinone/menaquinone biosynthesis methyltransferase from Mycobacterium leprae (238 aa). Also highly similar to others e.g. CAB44537.1|AL078618|T34630 from Streptomyces coelicolor (231 aa); UBIE_ECOLI|P27851 from Escherichia coli strain K12 (251 aa), FASTA scores: opt: 421, E(): 1.2e-21, (43.2% identity in 227 aa overlap); GRC2_BACSU|P31113 from Bacillus subtilis (233 aa), FASTA scores: opt: 345, E(): 1.4e-16, (34.6% identity in 231 aa overlap); etc. Belongs to the UbiE family. Note that previously known as ubiE.	P9WFR3	No	intermediary metabolism and respiration	ML2273	MMAR_0907	MSMEG_1115	Mb0573				
NC_000962.3	Mycobrowser_v3	CDS	650407	650745	.	-	0	Rv0559c	Rv0559c	Unknown	Possible conserved secreted protein	Rv0559c, (MTCY25D10.38c), len: 112 aa. Possible conserved secreted protein, similar to NP_302481.1|NC_002677 putative secreted protein from Mycobacterium leprae (112 aa). Also similar to Y08B_MYCTU|Q11048 hypothetical 11.6 kDa protein FASTA scores: opt: 111, E(): 011, (25.4% identity in 114 aa overlap). Contains possible N-terminal signal sequence. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WKL3	No	cell wall and cell processes	ML2274,ML2274c	MMAR_0908	MSMEG_3493	Mb0574c				
NC_000962.3	Mycobrowser_v3	CDS	653879	654739	.	+	0	Rv0563	htpX	Possibly involved in adaptation. Hydrolizes specific peptides and/or proteins.	Probable protease transmembrane protein heat shock protein HtpX	Rv0563, (MTV039.01, MTCY25D10.42), len: 286 aa. (alternative start at position 654006). Probable htpX, protease heat shock protein X (transmembrane protein), equivalent to NP_302484.1|NC_002677 putative peptidase from Mycobacterium leprae (287 aa). Also highly similar to others e.g. CAC08262.1|AL392146 putative peptidase from Streptomyces coelicolor (287 aa); NP_387431.1|NC_003047 putative protease transmembrane protein from Sinorhizobium meliloti (319 aa); NP_105051.1|NC_002678 heat shock protein (htpX) from Mesorhizobium loti (336 aa); NP_248692.1|NC_000909|U67608|MJU67608_8 heat shock protein HtpX, possibly protease (htpX) from Methanococcus jannaschii (284 aa), FASTA scores: opt: 660, E(): 0, (46.5 identity in 245 aa overlap). Continuation of MTCY25D10.42. Belongs to peptidase family M48 (zinc metalloprotease). Cofactor: Zinc. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P9WHS5	No	virulence, detoxification, adaptation	ML2278	MMAR_0912	MSMEG_1134	Mb0578				
NC_000962.3	Mycobrowser_v3	CDS	1265472	1266488	.	-	0	Rv1138c	Rv1138c	Function unknown; probably involved in cellular metabolism.	Possible oxidoreductase	Rv1138c, (MTCI65.05c), len: 338 aa. Possible oxidoreductase, similar to Q9EWQ8 putative oxidoreductase from Streptomyces coelicolor (343 aa). Also similar to many Mycobacterium tuberculosis hypothetical proteins e.g. Rv1751|P72008|MTCY04C12.35 (412 aa), fasta scores: opt: 89, E(): 4.5e-09, (24.6% identity in 358 aa overlap).	O06538	No	intermediary metabolism and respiration	ML0965,ML0965c	MMAR_4315	MSMEG_0811	Mb1170c				
NC_000962.3	Mycobrowser_v3	CDS	659450	660868	.	+	0	Rv0568	cyp135B1	Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	Possible cytochrome P450 135B1 Cyp135B1	Rv0568, (MT0594, MTV039.06), len: 472 aa. Possible cyp135B1, cytochrome P450, similar to putative cytochrome P-450 monoxygenases and other cytochrome P-450 related enzymes e.g. P29980|CPXN_ANASP probable cytochrome P450 from Anabaena sp. strain PCC 7120 (459 aa), FASTA scores: opt: 525, E(): 7.2e-27, (31.9% identity in 417 aa overlap); etc. Also similar to others from Mycobacterium tuberculosis e.g. Rv0327c|NP_214841.1|NC_000962|CYP135A1|MT0342|MTCY63.32c putative cytochrome P450 (449 aa), FASTA scores: opt: 1080, E(): 0, (40.5% identity in 444 aa overlap); Rv3685c|NP_218202.1|NC_000962 putative cytochrome P450 (476 aa); Rv0136|NP_214650.1|NC_000962 putative cytochrome P450 (441 aa); etc. Contains cytochrome P450 cysteine heme-iron ligand signature (PS00086).	P9WPM9	No	intermediary metabolism and respiration		MMAR_0938	MSMEG_1213	Mb0583				
NC_000962.3	Mycobrowser_v3	CDS	661295	663373	.	+	0	Rv0570	nrdZ	Involved in the DNA replication pathway (at the first reaction). Provides the precursors necessary for DNA synthesis [catalytic activity: 2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H2O = ribonucleoside diphosphate + reduced thioredoxin].	Probable ribonucleoside-diphosphate reductase (large subunit) NrdZ (ribonucleotide reductase)	Rv0570, (MTV039.08), len: 692 aa. Probable nrdZ, ribonucleoside-diphosphate reductase, large subunit, highly similar to others e.g. NP_070492.1|NC_000917|NRD|AE000988_11 ribonucleotide reductase from Archaeoglobus fulgidus (752 aa), FASTA scores: opt: 2001, E(): 0, (52.5% identity in 562 aa overlap) (N-terminus shorter); U73619|TAU73619_1|T37459 ribonucleotide reductase from Thermoplasma acidophilum (857 aa), FASTA scores: opt: 1678, E(): 0, (43.7% identity in 723 aa overlap); etc. Belongs to the ribonucleoside diphosphate reductase large chain family.	P9WH77	No	information pathways	ML2099,ML2099c			Mb0585				
NC_000962.3	Mycobrowser_v3	CDS	665851	667242	.	-	0	Rv0573c	pncB2	Involved in NAD salvage. Phosphoribosylation of nicotinic acid. [catalytic activity: nicotinate + 5-phosphoribosyl 1-pyrophosphate = nicotinate mononucleotide + diphosphate]	Nicotinic acid phosphoribosyltransferase PncB2	Rv0573c, (MTV039.11c), len: 463 aa. PncB2, nicotinic acid phosphoribosyltransferase (See Boshoff et al., 2008). Similar to e.g. NP_213718.1|NC_000918 hypothetical protein from Aquifex aeolicus (426 aa); AL109962|T36953|SCJ1.20 conserved hypothetical protein from Streptomyces coelicolor (438 aa), FASTA scores: opt: 1089, E(): 0, (49.4% identity in 385 aa overlap); P_391053.1|Z99120|BSUB0017_57|NC_000964 protein similar to nicotinate phosphoribosyltransferase from Bacillus subtilis (490 aa), FASTA scores: opt: 955, E():0, (43.5% identity in 356 aa overlap); etc. Also similar to Q10641|Y03F_MYCTU|MTCY130.15c|Rv1330c conserved hypothetical protein from Mycobacterium tuberculosis (509 aa), FASTA scores: opt: 761, E(): 0, (38.4% identity in 437 aa overlap).	P9WJI7	No	intermediary metabolism and respiration				Mb0588c				
NC_000962.3	Mycobrowser_v3	CDS	838451	840856	.	+	0	Rv0747	PE_PGRS10	Function unknown	PE-PGRS family protein PE_PGRS10	Rv0747, (MTV041.21), len: 801 aa. PE_PGRS10, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citation below), highly similar to part of MTCY28.25c|Rv1759c|Z95890 antigen wag22 from M. tuberculosis (914 aa), FASTA scores: opt: 2772, E(): 0, (60.9% identity in 941 aa overlap). Also similar to other PE-PGRS family proteins e.g. Z95844|MTCY493_2 FASTA score: (50.2% identity in 815 aa overlap). Contains PS00012 Phosphopantetheine attachment site. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WIG1	No	PE/PPE				Mb0768				
NC_000962.3	Mycobrowser_v3	CDS	671996	675916	.	-	0	Rv0578c	PE_PGRS7	Function unknown	PE-PGRS family protein PE_PGRS7	Rv0578c, (MTV039.16c), len: 1306 aa. PE_PGRS7, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citation below), highly similar to many other PGRS proteins e.g. MTCY493.04|Z95844 from Mycobacterium tuberculosis (1329 aa), FASTA scores: opt: 3994, E(): 0, (54.6% identity in 1375 aa overlap). Contains two PS00583 pfkB family of carbohydrate kinases signatures possibly fortuitously.	Q6MX28	No	PE/PPE		MMAR_0943		Mb0593c				
NC_000962.3	Mycobrowser_v3	CDS	678389	679075	.	-	0	Rv0583c	lpqN	Unknown	Probable conserved lipoprotein LpqN	Rv0583c, (MTV039.21c), len: 228 aa. Probable lpqN, conserved lipoprotein, equivalent to AAA90989.1|U20446|MK35|U20446|MKU20446_1 lipoprotein precursor from Mycobacterium kansasii (225 aa), FASTA scores: opt: 945, E(): 0, (62.7% identity in 228 aa overlap); and similar to others from Mycobacteria e.g. Rv0040c and Rv1016c from Mycobacterium tuberculosis. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	O53780	No	cell wall and cell processes	ML1914	MMAR_0950	MSMEG_5456	Mb0598c				
NC_000962.3	Mycobrowser_v3	CDS	681885	684272	.	-	0	Rv0585c	Rv0585c	Unknown	Probable conserved integral membrane protein	Rv0585c, (MTV039.23c, MTCY19H5.37), len: 795 aa. Probable conserved integral membrane protein. C-terminus similar to CAB88984.1|AL353864 putative integral membrane protein from Streptomyces coelicolor (299 aa); and C-terminal region of CAC01311.1|AL390968 putative integral membrane protein from Streptomyces coelicolor (925 aa). Also some similarity with Rv0204 from Mycobacterium tuberculosis.	O53781	No	cell wall and cell processes		MMAR_0953	MSMEG_1199	Mb0600c				
NC_000962.3	Mycobrowser_v3	CDS	685928	686815	.	+	0	Rv0588	yrbE2B	Unknown	Conserved hypothetical integral membrane protein YrbE2B	Rv0588, (MTCY19H5.34c), len: 295 aa. YrbE2B, hypothetical unknown integral membrane protein, part of mce2 operon and member of YrbE family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07413|Rv0168|MTCI28.08|yrbE1B (289 aa); O53966|Rv1965|MTV051.03|yrbE3B (271 aa); etc. Also highly similar to conserved hypothetical integral membrane proteins of the yrbEB type, e.g. P45392|YRBE_ECOLI hypothetical 27.9 kDa protein from Escherichia coli (260 aa), FASTA scores: opt: 232, E(): 8.4e-08, (22.1 % identity in 267 aa overlap); P45030|YRBE_HAEIN|HI1086 hypothetical protein from Haemophilus influenzae (261 aa), FASTA scores: opt: 234, E(): 6.3e-08, (24.2% identity in 215 aa overlap); NP_302655.1|NC_002677 conserved membrane protein from Mycobacterium leprae (289 aa); etc.	O07790	No	virulence, detoxification, adaptation			MSMEG_0133	Mb0603				
NC_000962.3	Mycobrowser_v3	CDS	686821	688035	.	+	0	Rv0589	mce2A	Unknown, but thought to be involved in host cell invasion.	Mce-family protein Mce2A	Rv0589, (MTCY19H5.33c), len: 404 aa. Mce2A; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins P72013|MCE1|Rv0169|MTCI28.09|mce1A (454 aa); O53967|MCE3|Rv1966|MTV051.04|mce3A (425 aa); etc. Also highly similar to others e.g. AAD52105.1|AF113402_1|AF113402 mycobacterial cell entry protein from Mycobacterium bovis BCG (454 aa); NP_302656.1|NC_002677 putative cell invasion protein from Mycobacterium leprae (441 aa); CAC12798.1|AL445327 putative secreted protein from Streptomyces coelicolor (418 aa); etc. Also highly similar, but longer 21 aa, to P72013|CAA50257.1|X70901|MTCI28.08 Mcep protein from Mycobacterium tuberculosis (432 aa), FASTA scores: opt: 1324, E(): 0, (62.6% identity in 436 aa overlap). Contains a possible N-terminal signal or anchor sequence. Predicted to be an outer membrane protein (See Song et al., 2008). Note that previously known as mce2.	Q79FY7	No	virulence, detoxification, adaptation		MMAR_4883	MSMEG_0134,MSMEG_5818,MSMEG_6540	Mb0604				
NC_000962.3	Mycobrowser_v3	CDS	688032	688859	.	+	0	Rv0590	mce2B	Unknown, but thought to be involved in host cell invasion.	Mce-family protein Mce2B	Rv0590, (MTCY19H5.32c), len: 275 aa. Mce2B; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07414|Rv0170|MTCI28.10|mce1B (346 aa); O53968|Rv1967|MTV051.05|mce3B (342 aa); etc. Also highly similar to others e.g. NP_302657.1|NC_002677 putative secreted protein from Mycobacterium leprae (346 aa); P45391|YRBD_ECOLI hypothetical 19.6 kDa protein from Escherichia coli (183 aa), FASTA scores: opt: 160, E(): 0.00099, (28.3% identity in 166 aa overlap); P45029|YRBD_HAEIN|HI1085 hypothetical protein from Haemophilus influenzae (167 aa), FASTA scores: opt: 135, E():0.035, (25.9% identity in 143 aa overlap); etc. Contains possible N-terminal signal or anchor sequence. Predicted to be an outer membrane protein (See Song et al., 2008).	O07788	No	virulence, detoxification, adaptation				Mb0605				
NC_000962.3	Mycobrowser_v3	CDS	688808	689062	.	+	0	Rv0590A	Rv0590A	Unknown, but could be involved in host cell invasion.	Mce-family related protein	Rv0590A, len: 84 aa. Probable continuation of mce2B|Rv0590. Can find no frameshift to account for this. Possible nucleotide G missing at 688793 as there are 5 in Mycobacterium bovis but only 4 in CDC1551. Strong similarity to C-terminus of other Mce proteins e.g. AL583926|AL583926_38 from Mycobacterium leprae strain tn (346 aa), FASTA scores: E(): 1.2e-20, (67.85% identity in 84 aa overlap).	I6X9D2	No	virulence, detoxification, adaptation				Mb0605				
NC_000962.3	Mycobrowser_v3	CDS	689059	690504	.	+	0	Rv0591	mce2C	Unknown, but thought to be involved in host cell invasion.	Mce-family protein Mce2C	Rv0591, (MTCY19H5.31c), len: 481 aa. Mce2C; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07415|R0171|MTCI28.11|mce1C (515 aa); O53969|Rv1968|MTV051.06|mce3C (410 aa); etc. Also highly similar to others e.g. NP_302658.1|NC_002677 putative secreted protein from Mycobacterium leprae (519 aa); CAC12796.1|AL445327 putative secreted protein from Streptomyces coelicolor (351 aa); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and may contain N-terminal signal or anchor sequence. Has highly Pro-rich C-terminus.	O07787	No	virulence, detoxification, adaptation				Mb0606				
NC_000962.3	Mycobrowser_v3	CDS	690501	692027	.	+	0	Rv0592	mce2D	Unknown, but thought to be involved in host cell invasion.	Mce-family protein Mce2D	Rv0592, (MTCY19H5.30c), len: 508 aa. Mce2D; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07416|Rv0172|MTCI28.12|mce1D (530 aa); O53970|Rv1969|MTV051.07|mce3D (423 aa); etc. Also highly similar to others e.g. NP_302659.1|NC_002677 putative secreted protein from Mycobacterium leprae (531 aa); CAC12795.1|AL445327 putative secreted protein from Streptomyces coelicolor (337 aa); etc. Has highly Pro-rich C-terminus and may contain N-terminal signal or anchor sequence. Predicted to be an outer membrane protein (See Song et al., 2008).	I6WYT7	No	virulence, detoxification, adaptation			MSMEG_0137	Mb0607,Mb0608				
NC_000962.3	Mycobrowser_v3	CDS	692024	693232	.	+	0	Rv0593	lprL	Unknown, but thought to be involved in host cell invasion.	Possible Mce-family lipoprotein LprL (Mce-family lipoprotein Mce2E)	Rv0593, (MTCY19H5.29c), len: 402 aa. Possible lprL (alternate gene name: mce2E), lipoprotein which belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07417|LPRK|Rv0173|MTCI28.13|mce1E (390 aa); O53971|LPRM|Rv1970|MTV051.08|mce3E (377 aa); etc. Also highly similar to others e.g. NP_302660.1|NC_002677 putative lipoprotein from Mycobacterium leprae (392 aa); CAC12794.1|AL445327 putative secreted protein from Streptomyces coelicolor (413 aa); etc. Contains possible signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	I6Y461	No	cell wall and cell processes			MSMEG_0138	Mb0609				
NC_000962.3	Mycobrowser_v3	CDS	693237	694787	.	+	0	Rv0594	mce2F	Unknown, but thought involved in host cell invasion.	Mce-family protein Mce2F	Rv0594, (MTCY19H5.28c), len: 516 aa. Mce2F; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), similar to Mycobacterium tuberculosis proteins O07418|Rv0174|MTCI28.14|mce1F (515 aa); O53972|Rv1971|MTV051.09|mce3F (437 aa); etc. Also highly similar to others e.g. NP_302661.1|NC_002677 putative secreted protein from Mycobacterium leprae (516 aa); AAF74993.1|AF143400_1|AF143400|996A027a protein from Mycobacterium avium (80 aa) (similarity on C-terminus); CAC12793.1|AL445327 putative secreted protein from Streptomyces coelicolor (433 aa); etc. Contains possible N-terminal signal or anchor sequence. Predicted to be an outer membrane protein (See Song et al., 2008).	O07784	No	virulence, detoxification, adaptation				Mb0610				
NC_000962.3	Mycobrowser_v3	CDS	694839	695231	.	-	0	Rv0595c	vapC4	Unknown	Possible toxin VapC4	Rv0595c, (MTCY19H5.27), len: 130 aa. Possible vapC4, toxin, part of toxin-antitoxin (TA) operon with Rv0596c, contains PIN domain (See Arcus et al., 2005; Pandey and Gerdes, 2005). Similar to other conserved hypothetical proteins e.g. Rv0627 (135 aa) and Rv0665 (112 aa) from Mycobacterium tuberculosis; and STBB_PSESM|Q52562 plasmid stability protein from Pseudomonas syringae (139 aa), FASTA scores: opt: 131, E(): 0.0035, (35.2% identity in 88 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07783	No	virulence, detoxification, adaptation				Mb0611c				
NC_000962.3	Mycobrowser_v3	CDS	695228	695485	.	-	0	Rv0596c	vapB4	Unknown	Possible antitoxin VapB4	Rv0596c, (MTCY19H5.26), len: 85 aa. Possible vapB4, antitoxin, part of toxin-antitoxin (TA) operon with Rv0595c (See Arcus et al., 2005; Pandey and Gerdes, 2005). Highly similar in part to other M. tuberculosis hypothetical proteins e.g. Rv0626, Rv3181c, Rv3385c, Rv3407, etc. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WF21	No	virulence, detoxification, adaptation				Mb0612c				
NC_000962.3	Mycobrowser_v3	CDS	695668	696903	.	-	0	Rv0597c	Rv0597c	Function unknown	Conserved hypothetical protein	Rv0597c, (MTCY19H5.25), len: 411 aa. Conserved hypothetical protein, highly similar to Rv3179 conserved hypothetical protein from Mycobacterium tuberculosis (429 aa). Also similar to AAF76191.1|AF271296_1|AF271296 putative ATP/GTP binding protein from Mycobacterium smegmatis (428 aa); Rv2008c|YW09_MYCTU|Q10849 conserved hypothetical protein from Mycobacterium tuberculosis (441 aa), FASTA scores: opt: 270, E(): 3.6e-11, (30.5% identity in 416 aa overlap) (N-terminus longer). Also similar to other hypothetical proteins e.g. NP_085874.1|NC_002679 hypothetical protein from Mesorhizobium loti (435 aa) (N-terminus longer). Contains PS00017 ATP/GTP-binding site motif A (P-loop). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6WYU2	No	conserved hypotheticals				Mb0613c				
NC_000962.3	Mycobrowser_v3	CDS	697564	697800	.	-	0	Rv0599c	vapB27	Unknown	Possible antitoxin VapB27	Rv0599c, (MTCY19H5.23), len: 78 aa. Possible vapB27, antitoxin, part of toxin-antitoxin (TA) operon with Rv0598c, see Arcus et al. 2005. Similar to others e.g. Rv2595|Y0B6_MYCTU|Q50626 conserved hypothetical protein from Mycobacterium tuberculosis (81 aa), FASTA scores: opt: 160, E(): 6.2e-07, (35.8% identity in 81 aa overlap). N-terminus shows stong similarity with N-terminus of NP_104908.1|NC_002678 hypothetical protein from Mesorhizobium loti (89 aa). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07779	No	virulence, detoxification, adaptation				Mb0615c				
NC_000962.3	Mycobrowser_v3	CDS	697904	698410	.	-	0	Rv0600c	Rv0600c	Sensor part of a two component regulatory system.	Two component sensor kinase [second part]	Rv0600c, (MTCY19H5.22), len: 168 aa (probable partial CDS). Two-component sensor kinase (second part), similar to part (C-termini) of many others e.g. Q04943|AFQ2_STRCO sensor protein afsq2 from Streptomyces coelicolor (535 aa), FASTA scores: opt: 347, E(): 1.9e-12, (33.0% identity in 206 aa overlap); etc. Note that sequence was checked and no errors were detected, which would allow this and the upstream ORF to be joined. Start changed since first submission (- 39 aa). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07778	No	regulatory proteins				Mb0616c				
NC_000962.3	Mycobrowser_v3	CDS	699856	700167	.	+	0	Rv0603	Rv0603	Unknown	Possible exported protein	Rv0603, (MTCY19H5.19c), len: 103 aa. Possible exported protein with hydrophobic stretch at aa 7-29. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07775	No	cell wall and cell processes				Mb0619				
NC_000962.3	Mycobrowser_v3	CDS	700239	701189	.	+	0	Rv0604	lpqO	Unknown	Probable conserved lipoprotein LpqO	Rv0604, (MTCY19H5.18c), len: 316 aa. Probable lpqO, conserved lipoprotein, highly similar to Rv2999|lppY putative lipoprotein from Mycobacterium tuberculosis (321 aa), FASTA scores: opt: 1153, E(): 0, (53.2% identity in 312 aa overlap). Contains probable N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6X9E2	No	cell wall and cell processes				Mb0620				
NC_000962.3	Mycobrowser_v3	CDS	701406	702014	.	+	0	Rv0605	Rv0605	Prevents the cointegration of foreign DNA before integration into the chromosome.	Possible resolvase	Rv0605, (MTCY19H5.17c), len: 202 aa. Possible resolvase for IS_Y349 element, similar to several Mycobacterial hypothetical proteins and weakly similar to Q52563 resolvase from Pseudomonas syringae (210 aa), FASTA scores: opt: 99, E(): 3.1, (35.7% identity in 98 aa overlap). Contains PS00397 Site-specific recombinases active site and probable helix-turn helix motif from aa 9-30 (Score 1815, +5.37 SD). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6Y890	No	insertion seqs and phages				Mb0621				
NC_000962.3	Mycobrowser_v3	CDS	702016	702759	.	+	0	Rv0606	Rv0606	Thought to be required for the transposition of the insertion element IS_1536.	Possible transposase (fragment)	Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to N-terminus of other transposases from Mycobacterium tuberculosis e.g. YX16_MYCTU|Q10809|Rv2885c|MT2953|MTCY274.16c putative transposase from Mycobacterium tuberculosis (460 aa), FASTA scores: opt: 1368, E(): 0, (83.5% identity in 237 aa overlap); Rv2978c, Rv0922, Rv3827c, etc. Also similar to N-terminus of MTV002_57|Rv2792 resolvase from M. tuberculosis (193 aa), FASTA score: (87.4% identity in 238 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07772	No	insertion seqs and phages				Mb0622				
NC_000962.3	Mycobrowser_v3	CDS	703486	703887	.	+	0	Rv0609	vapC28	Unknown	Possible toxin VapC28. Contains PIN domain.	Rv0609, (MTCY19H5.13c), len: 133 aa. Possible vapC28, toxin, part of toxin-antitoxin (TA) operon with Rv0608, contains PIN domain, see Arcus et al. 2005. Similar to several Mycobacterium tuberculosis hypothetical proteins e.g. YW37_MYCTU|Q10874|Rv1982c|MT2034|MTCY39.37 conserved hypothetical protein (139 aa), FASTA scores: opt: 262, E(): 8.1e-12, (39.1% identity in 128 aa overlap); MTCY20H10.05|Rv0624|MT0652|MTCY20H10.05 conserved hypothetical protein (131 aa), FASTA score: (42.9% identity in 126 aa overlap), Rv0565c, Rv3854c, etc. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WF81	No	virulence, detoxification, adaptation				Mb0625				
NC_000962.3	Mycobrowser_v3	CDS	706324	706929	.	+	0	Rv0612	Rv0612	Function unknown	Conserved hypothetical protein	Rv0612, (MTCY19H5.09c), len: 201 aa. Conserved hypothetical protein, highly similar, but in part, to downstream ORF Rv0609A conserved hypothetical protein from Mycobacterium tuberculosis (75 aa); and showing weak similarity with other hypothetical proteins from Mycobacterium tuberculosis. Note that first start has been taken although this overlaps slightly with the upstream ORF. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6X9E8	No	conserved hypotheticals				Mb0629				
NC_000962.3	Mycobrowser_v3	CDS	706948	709515	.	-	0	Rv0613c	Rv0613c	Unknown	Unknown protein	Rv0613c, (MTCY19H5.08), len: 855 aa. Unknown protein. Contains a very short region with strong similarity to several preprotein translocases e.g. P47847|SECA_LISMO preprotein translocase seca subunit (836 aa), FASTA scores: opt: 138, E(): 0.18, (38.6% identity in 70 aa overlap, and 72.7% identity in 22 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6Y897	No	conserved hypotheticals			MSMEG_1285	Mb0630c				
NC_000962.3	Mycobrowser_v3	CDS	709356	710348	.	+	0	Rv0614	Rv0614	Function unknown	Conserved hypothetical protein	Rv0614, (MTCY19H5.07c), len: 330 aa. Conserved hypothetical protein, similar in part to Mycobacterium tuberculosis hypothetical proteins e.g. YY16_MYCTU|Q10685|Rv2077c|MT2137|MTCY49.16c conserved hypothetical protein (323 aa), FASTA scores: opt: 200, E(): 0.00016, (28.3% identity in 269 aa overlap); MTCY9F9_15 FASTA score: (40.3% identity in 144 aa overlap), Rv1949c, Rv2542, etc. Several start sites are possible; first start has been chosen. Note that this ORF overlaps with the upstream ORF. Predicted to be an outer membrane protein (See Song et al., 2008). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O07763	No	conserved hypotheticals		MMAR_0116		Mb0631				
NC_000962.3	Mycobrowser_v3	CDS	712716	713807	.	+	0	Rv0620	galK	Involved in galactose metabolism (leloir pathway) (at the first reaction) [catalytic activity: ATP + D-galactose = ADP + D-galactose 1-phosphate].	Probable galactokinase GalK (galactose kinase)	Rv0620, (MTCY19H5.01c, MTCY20H10.01), len: 363 aa. Probable galK, galactokinase, similar to others e.g. P13227|GAL1_STRLI galactokinase from Streptomyces lividans (397 aa); P06976|GAL1_ECOLI galactokinase from Escherichia coli (381 aa), FASTA scores: opt: 669, E(): 0, (35.9% identity in 365 aa overlap); etc. Contains PS00106 Galactokinase signature and PS00560 Serine carboxypeptidases, histidine active site. Belongs to the GHMP kinase family. GALK subfamily.	P9WN63	No	intermediary metabolism and respiration		MMAR_0941	MSMEG_3692	Mb0636				
NC_000962.3	Mycobrowser_v3	CDS	720005	721732	.	-	0	Rv0629c	recD	Involved in homologous recombination.	Probable exonuclease V (alpha chain) RecD (exodeoxyribonuclease V alpha chain) (exodeoxyribonuclease V polypeptide)	Rv0629c, (MTCY20H10.10c), len: 575 aa. Probable recD, exonuclease V, alpha chain (exodeoxyribonuclease V, alpha chain) (see citation below), highly similar to other exonucleases e.g. AF157643_3|AAD46809.1|recD Escherichia coli RecD protein homolog from Mycobacterium smegmatis (554 aa); P04993|EX5A_ECOLI|B2819 exodeoxyribonuclease V 67kd polypeptide (exonuclease V alpha chain) from Escherichia coli strain K12 (608 aa), FASTA scores: opt: 512, E(): 1.9e-24, (36.9% identity in 582 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Consists of three subunits; RECB|Rv0630c, RECC|Rv0631c and RECD.	P9WHJ1	No	information pathways		MMAR_0956	MSMEG_1325	Mb0645c				
NC_000962.3	Mycobrowser_v3	CDS	725013	728306	.	-	0	Rv0631c	recC	Involved in homologous recombination.	Probable exonuclease V (gamma chain) RecC (exodeoxyribonuclease V gamma chain)(exodeoxyribonuclease V polypeptide)	Rv0631c, (MTCY20H10.12c), len: 1097 aa. Probable recC, exonuclease V, gamma chain (exodeoxyribonuclease V, gamma chain) (see Mizrahi & Andersen 1998), highly similar to other exonucleases e.g. AF157643_1|RecC|AAD46807.1 Escherichia coli RecC protein homolog from Mycobacterium smegmatis (1085 aa); P07648|EX5C_ECOLI|B2822 exodeoxyribonuclease V 125 kDa polypeptide (exonuclease V gamma chain) from Escherichia coli strain K12 (1122 aa), FASTA scores: opt: 954, E(): 0, (29.2% identity in 1109 aa overlap); etc. Consists of three subunits; RECB|Rv0630c, RECC and recd|Rv0629c. The transcription of this CDS seems to be activated specifically in host granulomas (see Ramakrishnan et al., 2000).	P9WIQ5	No	information pathways		MMAR_0958	MSMEG_1328	Mb0648c				
NC_000962.3	Mycobrowser_v3	CDS	728583	729278	.	-	0	Rv0632c	echA3	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Probable enoyl-CoA hydratase EchA3 (enoyl hydrase) (unsaturated acyl-CoA hydratase) (crotonase)	Rv0632c, (MTCY20H10.13c), len: 231 aa. Probable echA3, enoyl-CoA hydratase, almost identical to the MTU88877_1 enoyl-CoA hydratase of Mycobacterium tuberculosis field isolate NTI64719, FASTA score: (92.4% identity in 184 aa overlap). Also similar to others e.g. P24162|ECHH_RHOCA enoyl-CoA hydratase from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (257 aa), FASTA scores: opt: 206, E(): 6.3e-07, (31.5% identity in 232 aa overlap); etc.	I6Y8B5	No	lipid metabolism	ML1913	MMAR_0962	MSMEG_1331	Mb0649c				
NC_000962.3	Mycobrowser_v3	CDS	730320	731033	.	-	0	Rv0634c	Rv0634c	Thought to be involved in glyoxal pathway. Thiolesterase that catalyses the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid [catalytic activity: (S)-(2-hydroxyacyl)glutathione + H2O = glutathione + a 2-hydroxy acid anion].	Possible glyoxalase II (hydroxyacylglutathione hydrolase) (GLX II)	Rv0634c, (MTCY20H10.15c), len: 237 aa. Possible glyoxalase II, equivalent to NP_302290.1|NC_002677 putative glyoxylase II from Mycobacterium leprae (238 aa); and similar to U00011_3|Y0BK_MYCLE|Q49649 hypothetical 23.9 kDa protein from Mycobacterium leprae (218 aa), FASTA scores: opt: 281, E(): 3.9e-12, (31.8% identity in 201 aa overlap). Also similar to other glyoxalases and metallo-beta-lactamase family proteins e.g. NP_386770.1|NC_003047 putative hydroxyacylglutathione hydrolase from Sinorhizobium meliloti (256 aa); etc. Also similar to other putative glyoxylases from Mycobacterium tuberculosis e.g. Rv1637c. Belongs to the glyoxalase II family. Cofactor: binds two zinc ions.	I6Y4A5	No	virulence, detoxification, adaptation	ML1912	MMAR_0965	MSMEG_1334	Mb0651c				
NC_000962.3	Mycobrowser_v3	CDS	731113	731364	.	+	0	Rv0634A	Rv0634A	Unknown	Unknown protein	Rv0634A, len: 83 aa. Unknown protein. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WKS5	No	conserved hypotheticals	ML1911A	MMAR_0966,MMAR_0967	MSMEG_1339	Mb0652				
NC_000962.3	Mycobrowser_v3	CDS	732825	733325	.	+	0	Rv0637	hadC	Involved in fatty acid synthesis type II (fas-II)	(3R)-hydroxyacyl-ACP dehydratase subunit HadC	Rv0637, (MTCY20H10.18), len: 166 aa. HadC, (3R)-hydroxyacyl-ACP dehydratase subunit, equivalent to NP_302285.1|NC_002677|YV31_MYCLE|P54879 conserved hypothetical protein from Mycobacterium leprae (166 aa), FASTA scores: opt: 352, E(): 4e-19, (39.2% identity in 148 aa overlap); and highly similar to others from Mycobacterium leprae e.g. NP_302287.1|NC_002677 conserved hypothetical protein (159 aa). Also highly similar to CAB77410.1|AL160431|SCD82.07 hypothetical protein from Streptomyces coelicolor (150 aa); Rv0635|NP_215149.1|NC_000962|MTY20H10_17 conserved hypothetical protein (two ORFs upstream) from Mycobacterium tuberculosis (158 aa), FASTA score: (49.3% identity in 150 aa overlap); and Rv0504c|NP_215018.1|NC_000962|YV31_MYCTU|Q11168 hypothetical protein from Mycobacterium tuberculosis (166 aa), FASTA scores: opt: 380, E(): 3.8e-21, (43.1% identity in 137 aa overlap).	P9WFJ9	No	intermediary metabolism and respiration	ML1908,ML1908c	MMAR_0970	MSMEG_1342	Mb0656				
NC_000962.3	Mycobrowser_v3	CDS	735517	736224	.	+	0	Rv0641	rplA	This protein binds directly to 23S ribosomal RNA and is located in the neighborhood of the site where elongation factor TU is bound to the ribosome.	50S ribosomal protein L1 RplA	Rv0641, (MTCY20H10.22), len: 235 aa. rplA, 50S ribosomal protein L1, equivalent to NP_302281.1|NC_002677 50S ribosomal protein L1 from Mycobacterium leprae (235 aa). Also highly similar to others e.g. P3625|RL1_STRGR 50s ribosomal protein L1 from Streptomyces griseus (240 aa), FASTA scores: opt: 1081, E(): 0, (72.2% identity in 230 aa overlap); etc. Belongs to the L1P family of ribosomal proteins.	P9WHC7	No	information pathways	ML1904,ML1904c	MMAR_0974	MSMEG_1347	Mb0660				
NC_000962.3	Mycobrowser_v3	CDS	1894224	1895342	.	-	0	Rv1668c	Rv1668c	Thought to be involved in active transport of macrolide across the membrane (export). Macrolide antibiotics resistance by an export mechanism. Responsible for energy coupling to the transport system.	Probable first part of macrolide-transport ATP-binding protein ABC transporter	Rv1668c, (MTV047.04c), len: 372 aa. Probable first part of macrolide-transport ATP-binding protein ABC transporter (see citation below), similar to many ATP-binding proteins ABC transporter e.g. X80735|SEABCT_1|Q54072 Saccharopolyspora erythraea ertX gene (481 aa), FASTA scores: opt: 938, E(): 0, (45.6% identity in 353 aa overlap); etc. Similarity to other NBD components of ABC transporters suggests that Rv1667c and Rv1668c should be contiguous. However, sequence has been checked and no error found, also same sequence in Mycobacterium tuberculosis CSU93 and Mycobacterium bovis. Contains PS00211 ABC transporters family signature and two times PS00017 ATP/GTP-binding site motif A. Belongs to the ATP-binding transport protein family (ABC transporters).	O53916	No	cell wall and cell processes	ML1240,ML1240c		MSMEG_3768	Mb1695c				
NC_000962.3	Mycobrowser_v3	CDS	736298	737203	.	-	0	Rv0642c	mmaA4	Involved in mycolic acids modification. Catalyzes unusual S-adenosyl-methionine-dependent transformation of a cis-olefin mycolic acid into a secondary alcohol. Catalyzes introduction of a hydroxyl group at the distal position on mycolic acid chains to produce the hydroxyl mycolate. Mycolic acids represent a major constituent of the mycobacterial cell wall complex. Methyl transfer results in formation of a secondary hydroxy group with an adjacent methyl branch; olefinic mycolic acid methyl transferase.	Methoxy mycolic acid synthase 4 MmaA4 (methyl mycolic acid synthase 4) (MMA4) (hydroxy mycolic acid synthase)	Rv0642c, (MTCY20H10.23c), len: 301 aa. MmaA4, methoxy mycolic acid synthase 4 (methyltransferase) (see citations below). Equivalent to AAC44876|AAC44876.1|cmaA methyl transferase (mycolic acid modification protein) from Mycobacterium bovis BCG strain Pasteur (298 aa); NP_302280.1|NC_002677 methyl mycolic acid synthase 4 from Mycobacterium leprae (298 aa); and highly similar to others from Mycobacteria e.g. downstream ORF P72027|mmaA3|Rv0643c|MTCY20H10.24c putative methoxy mycolic acid synthase 3 from Mycobacterium tuberculosis (293 aa). Phosphorylated in vitro by PknJ|Rv2088 (See Jang et al., 2010).	Q79FX8	No	lipid metabolism	ML1903			Mb0661c				
NC_000962.3	Mycobrowser_v3	CDS	739327	740187	.	-	0	Rv0645c	mmaA1	Involved in mycolic acids modification. Catalyzes unusual S-adenosyl-methionine-dependent transformation of a cis-olefin mycolic acid into a secondary alcohol. Catalyzes introduction of a hydroxyl group at the distal position on mycolic acid chains to produce the hydroxyl mycolate. Mycolic acids represent a major constituent of the mycobacterial cell wall complex. Methyl transfer results in formation of a secondary hydroxy group with an adjacent methyl branch; olefinic mycolic acid methyl transferase.	Methoxy mycolic acid synthase 1 MmaA1 (methyl mycolic acid synthase 1) (MMA1) (hydroxy mycolic acid synthase)	Rv0645c, (MTCY20H10.26c), len: 286 aa. MmaA1, methoxy mycolic acid synthase 1 (methyltransferase) (see citations below). Equivalent to NP_302279.1|NC_002677 methyl mycolic acid synthase 1 from Mycobacterium leprae (286 aa); and highly similar to others from Mycobacteria e.g. upstream ORF P72028|mmaA4|Rv0642c|MTCY20H10.23c putative methoxy mycolic acid synthase 4 from Mycobacterium tuberculosis (301 aa).	P9WPB1	No	lipid metabolism	ML1900	MMAR_0980	MSMEG_1203	Mb0664c				
NC_000962.3	Mycobrowser_v3	CDS	742719	746366	.	+	0	Rv0648	Rv0648	Alpha-mannosidase activity: hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides.	Alpha-mannosidase	Rv0648, (MTCY20H10.29), len: 1215 aa. Alpha-mannosidase (see citation below), showing some similarity to hypothetical proteins and various sugar hydrolases e.g. SYCSLRA_6|Q55528 hypothetical 1 20.4 kDa protein from Synechocystis (1042 aa), FASTA scores: opt: 260, E(): 3.6e-08, (23.4% identity in 602 aa overlap); etc. Contains PS00659 Glycosyl hydrolases family 5 signature.	P96937	No	intermediary metabolism and respiration		MMAR_0985	MSMEG_1361	Mb0667				
NC_000962.3	Mycobrowser_v3	CDS	786149	786946	.	+	0	Rv0686	Rv0686	Unknown	Probable membrane protein	Rv0686, (MTCY210.03), len: 265 aa. Probable membrane protein, with hydrophobic N-terminus.	I6XVZ6	No	cell wall and cell processes	ML1876,ML1876c	MMAR_1015	MSMEG_1406	Mb0705				
NC_000962.3	Mycobrowser_v3	CDS	749234	749929	.	-	0	Rv0653c	Rv0653c	Involved in transcriptional mechanism.	Possible transcriptional regulatory protein (probably TetR-family)	Rv0653c, (MTCI376.23, MTCY20H10.34c), len: 231 aa. Possible transcriptional regulator, TetR family, similar in N-terminus to others e.g. CAC03642.1|AL391338 putative TetR-family transcriptional regulator from Streptomyces coelicolor (190 aa); Q51597 cam repressor from Pseudomonas putida (186 aa), FASTA scores: opt: 150, E(): 0.00085, (27.8% identity in 97 aa overlap); etc. Also some similarity to Mycobacterium tuberculosis hypothetical transcriptional regulators Rv0681 and Rv1816. Contains probable helix-turn helix motif from aa 27-48 (Score 1156, +3.12 SD).	P96941	No	regulatory proteins	ML1894			Mb0672c				
NC_000962.3	Mycobrowser_v3	CDS	750000	751505	.	+	0	Rv0654	Rv0654	Function unknown; probably involved in cellular metabolism.	Probable dioxygenase	Rv0654, (MTCI376.22), len: 501 aa. Probable dioxygenase, highly similar to others eg AAK06796.1|AF324838_15|AF324838|SimC5 putative dioxygenase (involved in tetraene formation) from Streptomyces antibioticus (456 aa); CAB56138.1| AL117669 putative dioxygenase from Streptomyces coelicolor (503 aa); T51734 neoxanthin cleavage enzyme (9-cis-epoxy-carotenoid dioxygenase) from Arabidopsis thaliana (538 aa); Q53353 lignostilbene-alpha,beta-dioxygenase from Pseudomonas paucimobilis (Sphingomonas paucimobilis), FASTA scores: opt: 280, E(): 2.3e-11, (28.5% identity in 523 aa overlap); etc. Also some similarity with Rv0913c|MTCY21C12.07c possible dioxygenase from Mycobacterium tuberculosis (501 aa), FASTA score: (29.5% identity in 522 aa overlap).	P9WPR5	No	intermediary metabolism and respiration	ML1893,ML1893c	MMAR_0993		Mb0673				
NC_000962.3	Mycobrowser_v3	CDS	753693	754409	.	-	0	Rv0658c	Rv0658c	Unknown. Supposedly involved in stationary-phase survival.	Probable conserved integral membrane protein	Rv0658c, (MTCI376.18), len: 238 aa. Probable conserved integral membrane protein, equivalent to a predicted homologous protein from Mycobacterium smegmatis (see citation below), and showing some similarity with P33774|YPRB_ECOLI hypothetical 24.3 kDa protein from Escherichia coli (217 aa), FASTA scores: opt: 174, E(): 5.3e-05, (25.6% identity in 223 aa overlap). Also similar to Rv1863c and Rv0804 from Mycobacterium tuberculosis. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06781	No	cell wall and cell processes		MMAR_0147	MSMEG_3474	Mb0677c				
NC_000962.3	Mycobrowser_v3	CDS	756137	758500	.	+	0	Rv0663	atsD	Thought to play an important role in the mineralization of sulfates [catalytic activity: a phenol sulfate + H2O = a phenol + sulfate].	Possible arylsulfatase AtsD (aryl-sulfate sulphohydrolase) (arylsulphatase)	Rv0663, (MTCI376.13c), len: 787 aa. Possible atsD, arylsulfatase, similar to others e.g. P5169|ARS_PSEAE arylsulfatase from Pseudomonas aeruginosa (532 aa), FASTA scores: opt: 653, E(): 0, (33.1% identity in 544 aa overlap); etc. Also similar to P95059|MTCY210.30|ATSA|Rv0711|MTCY210.30 from Mycobacterium tuberculosis (787 aa), FASTA score: (38.9% identity in 769 aa overlap); and other arylsulfatases from Mycobacterium tuberculosis e.g. Rv3299c|ATSB (970 aa), Rv0711, etc. Contains PS00523 Sulfatases signature 1. Belongs to the sulfatase family. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6XVW9	No	intermediary metabolism and respiration	ML0795,ML0795c	MMAR_4950		Mb0682				
NC_000962.3	Mycobrowser_v3	CDS	787099	787926	.	+	0	Rv0687	Rv0687	Function unknown; possibly involved in cellular metabolism.	Probable short-chain type dehydrogenase/reductase	Rv0687, (MTCY210.04), len: 275 aa. Probable short-chain dehydrogenase/reductase, highly similar to various dehydrogenases (generally SDR family) e.g. U17129|RSU17129_7 short-chain dehydrogenase from Rhodococcus erythropolis (275 aa), FASTA scores: opt: 1112, E(): 0, (61.2% identity in 268 aa overlap); MMU34072_2 steroid dehydrogenase from Musmus culus (260 aa), FASTA scores: opt: 390, E(): 2.2e-17, (34.1% identity in 267 aa overlap); etc. Also similar to MTV002_16|O33292|Rv2750 dehydrogenase from Mycobacterium tuberculosis (272 aa). Contains PS00061 Short-chain alcohol dehydrogenase family signature.	P9WGS7	No	intermediary metabolism and respiration	ML1875,ML1875c	MMAR_1016	MSMEG_1410	Mb0706				
NC_000962.3	Mycobrowser_v3	CDS	763370	767320	.	+	0	Rv0668	rpoC	Catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates [catalytic activity: N nucleoside triphosphate = N diphosphate + {RNA}(N)].	DNA-directed RNA polymerase (beta' chain) RpoC (transcriptase beta' chain) (RNA polymerase beta' subunit).	Rv0668, (MTCI376.07c), len: 1316 aa. RpoC, DNA-directed RNA polymerase, beta' chain (see Miller et al., 1994), equivalent to P30761|RPOC_MYCLE|ML1890|S31146 DNA-directed RNA polymerase beta' chain from Mycobacterium leprae (1316 aa), FASTA scores: opt: 8295, E(): 0, (95.6% identity in 1316 aa overlap). Also highly similar to others e.g. CAB77429.1|AL160431 DNA-directed RNA polymerase beta' chain (fragment) from Streptomyces coelicolor (1059 aa); P37871|RPOC_BACSU from Bacillus subtilis (1199 aa), FASTA scores: opt: 2367, E(): 0, (52.9 identity in 1317 aa overlap); etc. Belongs to the RNA polymerase beta' chain family.	P9WGY7	No	information pathways	ML1890,ML1890c	MMAR_0996	MSMEG_1368	Mb0687				
NC_000962.3	Mycobrowser_v3	CDS	767684	769597	.	-	0	Rv0669c	Rv0669c	Function unknown; hydrolytic enzyme probably involved in cellular metabolism.	Possible hydrolase	Rv0669c, (MTCI376.05), len: 637 aa. Possible hydrolase, highly similar to various hydrolases (N-terminus shorter) e.g. BAA88409.1|AB028646 alkaline ceramidase from Pseudomonas aeruginosa (670 aa,) FASTA scores: opt: 1490, E(): 0, (41.2% identity in 651 aa overlap); NP_063946.1|NM_019893 mitochondrial ceramidase from Homo sapiens (761 aa); P_446098.1|NM_053646 N-acylsphingosine amidohydrolase 2 from Rattus norvegicus (761 aa); BAB09641.1|AB016885 neutral ceramidase from Arabidopsis thaliana (705 aa); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop).	O06769	No	intermediary metabolism and respiration		MMAR_0997		Mb0688c				
NC_000962.3	Mycobrowser_v3	CDS	770582	771424	.	+	0	Rv0671	lpqP	Unknown	Possible conserved lipoprotein LpqP	Rv0671, (MTCI376.03c), len: 280 aa. Possible lpqP, conserved lipoprotein, similar to U00012|B1308_F2_43|Q49658 from Mycobacterium leprae (302 aa), FASTA scores: opt: 449, E(): 2.4e-22, (37.6% identity in 242 aa overlap). Also highly similar to lpqC|Rv3298c|MTCY71.38c putative lipoprotein from Mycobacterium tuberculosis (304 aa). Also similar to a large variety of proteins including various esterases and poly(3-hydroxyalkanoate) depolymerases, e.g. NP_249234.1|NC_002516 hypothetical protein from Pseudomonas aeruginosa (322 aa); C-terminus of AAD45376.1|AF164516_1|AF164516 cinnamoyl ester hydrolase EstA from Piromyces equi (536 aa); part of P52090|PHA1_PSELE poly(3-hydroxyalkanoate) depolymerase C precursor from Pseudomonas lemoignei (414 aa); CAC10310.1|AL442629 putative secreted protein from Streptomyces coelicolor (348 aa); etc. Has a 17 aa signal sequence and contains appropriately positioned (PS00013) Prokaryotic membrane lipoprotein lipid attachment site.	I6XVY0	No	cell wall and cell processes		MMAR_1000		Mb0690				
NC_000962.3	Mycobrowser_v3	CDS	771484	773112	.	+	0	Rv0672	fadE8	Function unknown, but involved in lipid degradation.	Probable acyl-CoA dehydrogenase FadE8	Rv0672, (MTCI376.02c), len: 542 aa. Probable fadE8, acyl-CoA dehydrogenase, highly similar to many e.g. CAC33951.1|AL589708 putative acyl-CoA dehydrogenase from Streptomyces coelicolor (557 aa); P33224|AIDB_ECOLI|B4187 aidb protein (acyl-CoA dehydrogenases family) from Escherichia coli strain K12 (546 aa), FASTA scores: opt: 1369, E(): 0, (44.1% identity in 524 aa overlap); etc. Also similar to several other M. tuberculosis proteins e.g. Rv0154c|MTCI5.28c FASTA score: (26.3% identity in 342 aa overlap); etc. Contains acyl-CoA dehydrogenases signature 2 (PS00073). Belongs to the acyl-CoA dehydrogenases family.	I6X9J0	No	lipid metabolism	ML1888,ML1888c	MMAR_1001	MSMEG_1387	Mb0691				
NC_000962.3	Mycobrowser_v3	CDS	774783	775574	.	+	0	Rv0675	echA5	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Probable enoyl-CoA hydratase EchA5 (enoyl hydrase) (unsaturated acyl-CoA hydratase) (crotonase)	Rv0675, (MTV040.03), len: 263 aa. Probable echA5, enoyl-CoA hydratase, similar to several e.g. NP_252116.1|NC_002516 probable enoyl CoA-hydratase/isomerase from Pseudomonas aeruginosa (256 aa); Q20376 protein similar to enoyl-CoA hydratase from Caenorhabditis elegans (258 aa), FASTA scores: opt: 697, E(): 0, (47.3% identity in 245 aa overlap); etc. Also similar to others from Mycobacterium tuberculosis e.g. Z92669|MTCY8D5_17 (262 aa), FASTA scores: opt: 493, E(): 3.6e-25, (39.1% identity in 243 aa overlap); etc.	I6Y4E8	No	lipid metabolism	ML1885,ML1885c	MMAR_1004	MSMEG_1390	Mb0694				
NC_000962.3	Mycobrowser_v3	CDS	781560	781934	.	+	0	Rv0682	rpsL	Protein S12 is involved in the translation initiation step.	30S ribosomal protein S12 RpsL	Rv0682, (MTV040.10), len: 124 aa. rpsL, 30S ribosomal protein S12 (see citations below), equivalent to others from Mycobacteria e.g. P41195|RS12_MYCSM 30S ribosomal protein S12 from Mycobacterium smegmatis (124 aa); P51999|RS12_MYCAV 30S ribosomal protein S12 from Mycobacterium avium (124 aa); etc. Also highly similar to others from other organisms e.g. P97222|RS12_STRCO 30S ribosomal protein S12 from Streptomyces roseosporus, lividans and coelicolor (123 aa); etc. Contains PS00055 Ribosomal protein S12 signature. Belongs to the S12P family of ribosomal proteins. Nucleotide position 781922 in the genome sequence has been corrected, A:G resulting in K121K.	P9WH63	No	information pathways	ML1880,ML1880c	MMAR_1011	MSMEG_1398	Mb0701				
NC_000962.3	Mycobrowser_v3	CDS	787940	789160	.	+	0	Rv0688	Rv0688	Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.	Putative ferredoxin reductase	Rv0688, (MTCY210.05), len: 406 aa. Putative ferredoxin reductase, highly similar to others e.g. BAB55881.1|AB054975 ferredoxin reductase from Terrabacter sp. DBF63 (410 aa); CAC04223.1|AL391515 putative ferredoxin reductase from Streptomyces coelicolor (420 aa); PPU24215_8|Q51973 P-cumate dioxygenase ferredoxin reductase subunit from Pseudomonas putida (402 aa), FASTA scores: opt: 738, E(): 0, (38.8% identity in 330 aa overlap); etc. Also similar to Rv0253 and Rv1869c from Mycobacterium tuberculosis. Could belong to the bacterial type ferredoxin family.	P95034	No	intermediary metabolism and respiration	ML1874,ML1874c	MMAR_1017	MSMEG_1416	Mb0707				
NC_000962.3	Mycobrowser_v3	CDS	791070	791666	.	-	0	Rv0691c	Rv0691c	Involved in transcriptional mechanism	Probable transcriptional regulatory protein	Rv0691c, (MTCY210.08c), len: 198 aa. Probable transcriptional regulator, highly similar to AAC77476.1|U17129 unknown protein from Rhodococcus erythropolis (185 aa); and showing similarity with putative regulatory proteins eg STMTCREP_1|TCMR_STRGA|P39885 tetracenomycin c transcriptional repressor from Streptomyces glaucescens (226 aa), FASTA scores: opt: 178, E(): 8.5e-06, (27.9% identity in 201 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop) and probable helix-turn helix motifs from aa 34-55 (Score 1100, +2.93 SD) and 151-172 (Score 1124, +3.02 SD).	P9WMB7	No	regulatory proteins	ML1872	MMAR_1019	MSMEG_1420	Mb0710c				
NC_000962.3	Mycobrowser_v3	CDS	793335	794525	.	+	0	Rv0694	lldD1	Involved in respiration; catalyzes conversion of lactate into pyruvate [catalytic activity: (S)-lactate + 2 ferricytochrome C = pyruvate + 2 ferrocytochrome C].	Possible L-lactate dehydrogenase (cytochrome) LldD1	Rv0694, (MTCY210.11), len: 396 aa. Possible lldD1, L-lactate dehydrogenase (cytochrome), similar to NP_302368.1|NC_002677 L-lactate dehydrogenase from Mycobacterium leprae (414 aa). Also similar to others e.g. NP_384560.1|NC_003047 putative L-lactate dehydrogenase (cytochrome) protein from Sinorhizobium meliloti (403 aa); NP_251072.1|NC_002516 L-lactate dehydrogenase from Pseudomonas aeruginosa (383 aa); P33232|LLDD_ECOLI L-lactate dehydrogenase (cytochrome) from Escherichia coli strain K12 (396 aa), FASTA scores: opt: 697, E(): 0, (34.5 identity in 380 aa overlap); etc; and also similar to other oxidoreductases. Note that also highly similar to RSU17129_5|AAC77479.1|U17129 unknown protein from Rhodococcus erythropolis (392 aa), FASTA scores: opt: 2006, E(): 0, (74.1% identity in 386 aa overlap). Also similar to lldD2|Rv1872c|MTCY180.46|MTCY359.01 possible L-lactate dehydrogenase (cytochrome) from Mycobacterium tuberculosis (414 aa). Belongs to the FMN-dependent alpha-hydroxy acid dehydrogenases family.	P9WND7	No	intermediary metabolism and respiration	ML1869,ML1869c	MMAR_1022	MSMEG_1424	Mb0713				
NC_000962.3	Mycobrowser_v3	CDS	795519	796931	.	+	0	Rv0696	Rv0696	Function unknown; probably involved in cellular metabolism.	Probable membrane sugar transferase	Rv0696, (MTCY210.13), len: 470 aa. Probable membrane sugar transferase, similar (except in N-terminus) to NP_069157.1|NC_000917 glycosyl transferase from Archaeoglobus fulgidus (324 aa); NP_279985.1|NC_002607 rhamnosyl transferase from Halobacterium sp. NRC-1 (299 aa); NP_059113.1|NM_017417 polypeptide N-acetylgalactosaminyltransferase 8 from (637 aa). Note that also highly similar to P46370|YTH1_RHOER hypothetical 55.3 KDA protein from Rhodococcus erythropolis (513 aa), FASTA scores: opt: 1514, E(): 0, (51.8% identity in 469 aa overlap).	P9WMX1	No	intermediary metabolism and respiration	ML1867,ML1867c	MMAR_1024	MSMEG_1426	Mb0715				
NC_000962.3	Mycobrowser_v3	CDS	803411	803692	.	+	0	Rv0705	rpsS	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.	30S ribosomal protein S19 RpsS	Rv0705, (MTCY210.24), len: 93 aa. rpsS, 30S ribosomal protein S19, equivalent to S36895 ribosomal protein S19 from Mycobacterium bovis (93 aa), FASTA scores: opt: 623, E(): 0, (98.9% identity in 93 aa overlap); and NP_302261.1|NC_002677 30S ribosomal protein S19 from Mycobacterium leprae (93 aa). Also highly similar to others e.g. CAB82074.1|AL161803 30S ribosomal protein S19 from Streptomyces coelicolor (93 aa); etc. Contains PS00323 Ribosomal protein S19 signature. Belongs to the S19P family of ribosomal proteins.	P9WH45	No	information pathways	ML1859,ML1859c	MMAR_1035	MSMEG_1440	Mb0725				
NC_000962.3	Mycobrowser_v3	CDS	803689	804282	.	+	0	Rv0706	rplV	This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, E.G., L4, L17, and L20. It is important during the early stages of 50S reconstitution.	50S ribosomal protein L22 RplV	Rv0706, (MTCY210.25), len: 197 aa. rplV, 50S ribosomal protein L22, equivalent to O06115|RL22_MYCSM 50S ribosomal protein L22 from Mycobacterium smegmatis (153 aa); MBS10OPER_7 50S ribosomal protein L22 from Mycobacterium bovis BCG; and MLCB2492_7 50S ribosomal protein L22 from Mycobacterium leprae (175 aa). Also highly similar to others e.g. CAB82075.1|AL161803 50S ribosomal protein L22 from Streptomyces coelicolor (125 aa); P42060|RL22_BACSU 50s ribosomal protein L22 from Bacillus subtilis (113 aa), FASTA scores: opt: 368, E(): 2.4e-13, (52.8% identity in 108 aa overlap); etc. Contains PS00464 Ribosomal protein L22 signature, and contains repetitive sequence at C-terminus. Belongs to the L22P family of ribosomal proteins.	P9WHC1	No	information pathways	ML1858,ML1858c	MMAR_1036	MSMEG_1441	Mb0726				
NC_000962.3	Mycobrowser_v3	CDS	806335	808698	.	+	0	Rv0711	atsA	Thought to play an important role in the mineralization of sulfates [catalytic activity: a phenol sulfate + H2O = a phenol + sulfate].	Possible arylsulfatase AtsA (aryl-sulfate sulphohydrolase) (arylsulphatase)	Rv0711, (MTCY210.30), len: 787 aa. Possible atsA, arylsulfatase, similar to others e.g. P51691|ARS_PSEAE arylsulfatase from Pseudomonas aeruginosa (532 aa), FASTA scores: opt: 439, E(): 2.9e-21, (30.8% identity in 552 aa overlap); etc. Also similar to other hypothetical arylsulfatases from Mycobacterium tuberculosis e.g. Rv3299c, Rv0663, etc. Contains PS00523 Sulfatases signature 1, and PS00149 Sulfatases signature 2. Belongs to the sulfatase family.	P95059	No	intermediary metabolism and respiration	ML1853,ML1853c	MMAR_1041	MSMEG_1451	Mb0731,Mb0732				
NC_000962.3	Mycobrowser_v3	CDS	812976	813374	.	+	0	Rv0718	rpsH	Binds directly to the central domain of 16S ribosomal RNA.	30S ribosomal protein S8 RpsH	Rv0718, (MTCY210.37), len: 132 aa. rpsH, 30S ribosomal protein S8, equivalent to O32997|MLCB2492_18 30S ribosomal protein S8 from Mycobacterium leprae (132 aa). Also highly similar to others e.g. CAB82084.1|AL161803 30S ribosomal protein S8 from Streptomyces coelicolor (132 aa); P33106|RS8_MICLU 30s ribosomal protein S8 from Micrococcus luteus (132 aa), FASTA scores: opt: 669, E(): 0, (77.3% identity in 132 aa overlap); etc. Contains PS00053 Ribosomal protein S8 signature. Belongs to the S8P family of ribosomal proteins.	P9WH27	No	information pathways	ML1845,ML1845c	MMAR_1049	MSMEG_1469	Mb0739				
NC_000962.3	Mycobrowser_v3	CDS	822866	823594	.	+	0	Rv0730	Rv0730	Acetylation, substrate unknown	GCN5-related N-acetyltransferase	Rv0730, (MTV041.04), len: 242 aa. Probable acetyltransferase. Contains GNAT (Gcn5-related N-acetyltransferase) domain in C-terminal part. See Vetting et al. 2005. Equivalent to Z98756|MLCB2492_26 hypothetical protein from Mycobacterium leprae (227 aa), FASTA scores: opt: 1180, E(): 0, (83.5% identity in 218 aa overlap).	I6XW38	No	intermediary metabolism and respiration	ML1835,ML1835c	MMAR_1067	MSMEG_6565	Mb0751				
NC_000962.3	Mycobrowser_v3	CDS	814328	814990	.	+	0	Rv0721	rpsE	Protein S5 is important in the assembly and function of the 30S ribosomal subunit.	30S ribosomal protein S5 RpsE	Rv0721, (MTCY210.40), len: 220 aa. rpsE, 30S ribosomal protein S5, equivalent to MLCB2492_21 ribosomal protein S5 from Mycobacterium leprae (217 aa). Also highly similar to others e.g. P46790|RS5_STRCO 30s ribosomal protein S5 from Streptomyces coelicolor (167 aa), FASTA scores: opt: 889, E(): 0, (82.1% identity in 162 aa overlap); etc. Note N-terminus is extented compared to other rpsE genes. Contains PS00585 Ribosomal protein S5 signature, PTS HPr component phosphorylation sites signature. Belongs to the S5P family of ribosomal proteins.	P9WH33	No	information pathways	ML1842,ML1842c	MMAR_1052	MSMEG_1472	Mb0742				
NC_000962.3	Mycobrowser_v3	CDS	815663	817534	.	+	0	Rv0724	sppA	Involved in digestion of the cleaved signal peptides. This activity is necessary to maintain proper secretion of mature proteins across the membrane.	Possible protease IV SppA (endopeptidase IV) (signal peptide peptidase)	Rv0724, (MTCY210.43), len: 623 aa. Possible sppA, protease IV (endopeptidase IV), equivalent (but longer 23 aa) to MLCB2492_24|O33003 endopeptidase IV from Mycobacterium leprae (602 aa). Also similar to others e.g. NP_419743.1|NC_002696 signal peptide peptidase SppA from Caulobacter crescentus (594 aa); P08395|SPPA_ECOLI|B1766 protease IV (endopeptidase) from Escherichia coli strain K-12 (618 aa), FASTA scores: opt: 582, E(): 8.9e-27, (34.1% identity in 525 aa overlap); etc. Belongs to peptidase family S49. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P95072	No	cell wall and cell processes	ML1839,ML1839c	MMAR_1056	MSMEG_1476	Mb0745				
NC_000962.3	Mycobrowser_v3	CDS	821507	822853	.	+	0	Rv0729	xylB	Phosphorylates D-xylulose [catalytic activity: ATP + D-xylulose = ADP + D-xylulose 5-phosphate].	Possible D-xylulose kinase XylB (xylulokinase) (xylulose kinase)	Rv0729, (MTV041.03), len: 448 aa. Possible xylB, D-xylulose-kinase (xylulokinase). C-terminus highly similar to AAD09880.1|U77912 unknown protein from Mycobacterium bovis (102 aa); and N-terminus highly similar to T45387|Z98756|MLCB2492_25 hypothetical protein from Mycobacterium leprae (110 aa), FASTA scores: opt: 427, E(): 1.1e-19, (60.9% identity in 110 aa overlap). Also similar to xylA/xylB genes from various bacterial species e.g. AAC26499.1|AF045245 D-xylulose-kinase from Klebsiella pneumoniae (487 aa); NP_418021.1|NC_000913 xylulokinase from Escherichia coli strain K12 (484 aa), FASTA scores: opt: 260, E(): 7.5e-09, (25.9% identity in 478 aa overlap); etc. Also similar to Rv3696c|glpK probable glycerol kinase from Mycobacterium tuberculosis (517 aa). Belongs to the fucokinase / gluconokinase / glycerokinase / xylulokinase family.	I6Y4K0	No	intermediary metabolism and respiration	ML1836,ML1836c	MMAR_1066	MSMEG_3113,MSMEG_3263	Mb0750				
NC_000962.3	Mycobrowser_v3	CDS	824800	826125	.	+	0	Rv0732	secY	Essential for protein export. Interacts with SECA|Rv3240c and SECE|Rv0638 to allow the translocation of proteins across the plasma membrane, by forming part of a channel.	Probable preprotein translocase SecY	Rv0732, (MTV041.06), len: 441 aa. Probable SecY, preprotein translocase (integral membrane protein) (see citation below), equivalent to NP_302243.1|NC_002677 SecY subunit of preprotein translocase from Mycobacterium leprae (438 aa); AAC04389.1|AF047021 preprotein translocase subunit from Mycobacterium smegmatis (438 aa); and U77912|MBU77912_1 preprotein translocase subunit from Mycobacterium bovis (441 aa), FASTA scores: opt: 2802, E(): 0, (99.8% identity in 441 aa overlap). Also highly similar to others e.g. P46785|SECY_STRCO preprotein translocase SECY subunit from Streptomyces coelicolor (437 aa); etc. Contains PS00755 and PS00756 protein secY signatures 1 and 2. Belongs to the SECE/SEC61-alpha family. Part of the prokaryotic protein translocation apparatus which comprise SECA|Rv3240c, SECD|Rv2587c, SECE|Rv0638, SECF|Rv2586c, SECG|Rv1440 and SECY.	P9WGN3	No	cell wall and cell processes	ML1833,ML1833c	MMAR_1070	MSMEG_1483	Mb0753				
NC_000962.3	Mycobrowser_v3	CDS	831776	832303	.	+	0	Rv0740	Rv0740	Function unknown	Conserved hypothetical protein	Rv0740, (MTV041.14), len: 175 aa. Conserved hypothetical protein; C-terminus (possibly part of truncated IS1557) shows nearly perfect identity to Rv0750|MTV041_24 (81 aa), FASTA score: (92.6% identity in 81 aa overlap). Also shows weak similarity to MTV007_5 hypothetical protein from Mycobacterium tuberculosis (313 aa), FASTA score: (34.5% identity in 110 aa overlap); and MLCL536_27 hypothetical protein from Mycobacterium leprae (315 aa), FASTA score: (34.5% identity in 84 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O53803	No	conserved hypotheticals				Mb0761				
NC_000962.3	Mycobrowser_v3	CDS	834440	834946	.	-	0	Rv0744c	Rv0744c	Thought to be involved in transcriptional mechanism.	Possible transcriptional regulatory protein	Rv0744c, (MTV041.18c), len: 168 aa. Possible transcriptional regulator, showing weak similarity with O86661|SC4A2.05 putative two-component sensor from Streptomyces coelicolor (436 aa), FASTA scores: opt: 117, E(): 0.88, (37.25% identity in 94 aa overlap); and some putative excisionases or transposases. Also weakly similar to P71902|YN10_MYCTU|Rv2310|MT2372|MTCY3G12.24c conserved hypothetical protein from Mycobacterium tuberculosis (114 aa); and Q11144|Y477_MYCTU|Rv0477|MT0495|MTCY20G9.03 conserved hypothetical protein from Mycobacterium tuberculosis (148 aa). Equivalent to AAK45006 from Mycobacterium tuberculosis strain CDC1551 (179 aa) but shorter 11 aa. Contains probable helix-turn helix motif from aa 5-26 (Score 1350, +3.78 SD). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O53807	No	regulatory proteins				Mb0765c				
NC_000962.3	Mycobrowser_v3	CDS	842347	843231	.	-	0	Rv0751c	mmsB	Catalyzes the NAD-dependent, reversible oxidation of 3-hydroxbutyrate to methylmalonate [catalytic activity: 3-hydroxy-2-methylpropanoate + NAD+ = 2-methyl-3-oxopropanoate + NADH].	Probable 3-hydroxyisobutyrate dehydrogenase MmsB (hibadh)	Rv0751c, (MTV041.25c), len: 294 aa. Probable mmsB, 3-hydroxyisobutyrate dehydrogenase, highly similar to others e.g. NP_102847.1|NC_002678 3-hydroxyisobutyrate dehydrogenase from Mesorhizobium loti (294 aa); NP_420167.1|NC_002696 3-hydroxyisobutyrate dehydrogenase from Caulobacter crescentus (298 aa); A32867 3-hydroxyisobutyrate dehydrogenase from Rattus norvegicus (346 aa); etc. Also similar to methylmalonate semialdehyde dehydrogenases e.g. M84911|PSE MMSRAB_3 methylmalonate semialdehyde dehydrogenase from Pseudomonas aeruginosa (298 aa), FASTA scores: opt: 786, E(): 0, (45.8% identity in 297 aa overlap). Also similar to 6-phosphogluconate dehydrogenases from Mycobacterium tuberculosis e.g. Rv1122 and Rv1844c. Contains PS00895 3-hydroxyisobutyrate dehydrogenase signature. Belongs to the 3-hydroxyisobutyrate dehydrogenase family.	P9WNY5	No	intermediary metabolism and respiration		MMAR_1077	MSMEG_1496	Mb0773c				
NC_000962.3	Mycobrowser_v3	CDS	844421	845953	.	-	0	Rv0753c	mmsA	Plays a role in valine and pyrimidine metabolism. Binds fatty acyl-CoA [catalytic activity: 2-methyl-3-oxopropanoate + CoA + NAD+ = propanoyl-CoA + CO2 + NADH].	Probable methylmalonate-semialdehyde dehydrogenase MmsA (methylmalonic acid semialdehyde dehydrogenase) (MMSDH)	Rv0753c, (MTV041.27c), len: 510 aa. Probable mmsA, methylmalonic acid semialdehyde dehydrogenase, highly similar to others e.g. NP_420115.1|NC_002696 putative methylmalonate-semialdehyde dehydrogenase from Caulobacter crescentus (499 aa); L48550|STMMSDA_1|CAB75315.1|AL139164 methylmalonic acid semialdehyde dehydrogenase from Streptomyces coelicolor (500 aa), FASTA score: (51.6% identity in 498 aa overlap); M84911|PSEMMSRAB_2|NP_252260.1|NC_002516 methylmalonate-semialdehyde dehydrogenase from Pseudomonas aeruginosa (497 aa), FASTA scores: opt: 1127, E(): 0, (47.9% identity in 507 aa overlap); etc. Note that also highly similar to malonic semialdehyde oxidative decarboxylases e.g. NP_104968.1|NC_002678 malonic semialdehyde oxidative decarboxylase from Mesorhizobium loti (498 aa); NP_384832.1|NC_003047 putative malonic semialdehyde oxidative decarboxylase protein from Sinorhizobium meliloti (498 aa); etc. Contains PS00070 Aldehyde dehydrogenases cysteine active site. Belongs to the aldehyde dehydrogenases family.	O53816	No	intermediary metabolism and respiration		MMAR_1079	MSMEG_1498	Mb0775c				
NC_000962.3	Mycobrowser_v3	CDS	851608	852351	.	+	0	Rv0757	phoP	Involved in transcriptional mechanism. Part of the two component regulatory system PHOP/PHOQ. This protein is thought to be a positive regulator for the phosphate regulon, required for intracellular growth. Transcription of this operon is positively regulated by PHOB and PHOR|Rv0758 when phosphate is limited.	Possible two component system response transcriptional positive regulator PhoP	Rv0757, (MTCY369.02), len: 247 aa. Possible phoP, two component system response phosphate regulon transcriptional regulator (see citations below), highly similar to various transcriptional regulators e.g. CAC32360.1|AL583945 putative two component system response regulator from Streptomyces coelicolor (271 aa); T45446 probable two-component response regulator from Mycobacterium leprae (253 aa); and similar to phoP proteins e.g. P13792|PHOP_BACSU alkaline phosphatase synthesis transcription regulatory protein from Bacillus subtilis (240 aa), FASTA scores: opt: 594, E(): 2.3e-33, (41.0% identity in 234 aa overlap); etc. Also highly similar to Rv3765c from Mycobacterium tuberculosis (234 aa), Rv1033c (257 aa), RV0903c|MTCY31.31c|Q10531 (236 aa), FASTA score: (45.4% identity in 229 aa overlap); MTCY10G2_16 and MTU88959_1.	P71814	No	regulatory proteins	ML2239,ML2239c	MMAR_4942	MSMEG_5872	Mb0780				
NC_000962.3	Mycobrowser_v3	CDS	852396	853853	.	+	0	Rv0758	phoR	Sensor part of a two component regulatory system. This protein is thought to be a sensor kinase for the phosphate regulon. Transcription of this operon is positively regulated by PHOB|Rv0757 and PHOR when phosphate is limited.	Possible two component system response sensor kinase membrane associated PhoR	Rv0758, (MTCY369.03), len: 485 aa. Possible phoR, two component system response phosphate sensor kinase membrane-associated, highly similar to various sensor kinases e.g. CAC32361.1|AL583945 putative two component system histidine kinase from Streptomyces coelicolor (524 aa); NP_349365.1|NC_003030 Membrane-associated sensory histidine kinase with HAMP domain from Clostridium acetobutylicum (482 aa); and similar to phoP proteins e.g. NP_372216.1|NC_002758 alkaline phosphatase synthesis sensor protein from Staphylococcus aureus (554 aa); P23545|PHOR_BACSU alkaline phosphatase synthesis sensor from Bacillus subtilis (579 aa), FASTA scores: opt: 515, E(): 1.9e-25, (40.0% identity in 230 aa overlap); etc. Also similar to proteins from Mycobacterium tuberculosis e.g. MTCY20G9.16 FASTA scores: (34.5% identity in 264 aa overlap), MTU88959_2 (509 aa), MTCY10G2_17, etc.	P71815	No	regulatory proteins	ML2238,ML2238c	MMAR_4941	MSMEG_5870	Mb0781				
NC_000962.3	Mycobrowser_v3	CDS	902111	903694	.	+	0	Rv0808	purF	Involved in de novo purine biosynthesis (at the first step) [catalytic activity: 5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H2O].	Amidophosphoribosyltransferase PurF (glutamine phosphoribosylpyrophosphate amidotransferase) (ATASE) (gpatase)	Rv0808, (MTCY07H7A.01c), len: 527 aa. PurF, amidophosphoribosyltransferase, equivalent to MLCB5_32|Q50028|PURF from Mycobacterium leprae (556 aa), FASTA scores: (91.3% identity in 518 aa overlap); and CAB96578.1|AJ278609 phosphoribosyl pyrophosphate amidotransferase from Mycobacterium smegmatis (511 aa)(see citation below). Also highly similar to others e.g. BAA89439.1|AB003158 amidophosphoribosyl transferase from Corynebacterium ammoniagenes (490 aa); P00497|PUR1_BACSU amidophosphoribosyltransferase precursor from Bacillus subtilis (476 aa), FASTA scores: opt: 1412, E(): 0, (46.2% identity in 470 aa overlap); etc. Contains PS00103 Purine/pyrimidine phosphoribosyl transferases signature. Belongs to the purine/pyrimidine phosphoribosyltransferase family.	P9WHQ7	No	intermediary metabolism and respiration	ML2206,ML2206c	MMAR_4881	MSMEG_5800	Mb0831				
NC_000962.3	Mycobrowser_v3	CDS	854699	855826	.	-	0	Rv0761c	adhB	Thought to catalyze the reversible oxidation of ethanol to acetaldehyde with the concomitant reduction of NAD. Probably acts on primary or secondary alcohols or hemiacetals [catalytic activity: an alcohol + NAD+ = an aldehyde or ketone + NADH].	Possible zinc-containing alcohol dehydrogenase NAD dependent AdhB	Rv0761c, (MTCY369.06c), len: 375 aa. Possible adhB, zinc-containing alcohol dehydrogenase NAD-dependent, similar to others e.g. AAC15839.1|AF060871_4 hypothetical alcohol dehydrogenase from Rhodococcus rhodochrous (370 aa), FASTA scores: opt: 1234, E(): 0, (46.8% identity in 370 aa overlap); P80468|ADH2_STRCA alcohol dehydrogenase II from Struthio camelus (Ostrich) (379 aa); Q03505|ADH1_RABIT alcohol dehydrogenase alpha chain from Oryctolagus cuniculus (Rabbit) (374 aa), FASTA scores: opt: 872, E(): 0, (39.1% identity in 379 aa overlap); etc. Also similar to adhD alcohol dehydrogenase from Mycobacterium tuberculosis (368 aa). Contains PS00059 Zinc-containing alcohol dehydrogenases signature. Belongs to the zinc-containing alcohol dehydrogenase family.	P9WQC7	No	intermediary metabolism and respiration		MMAR_4935	MSMEG_5866	Mb0784c				
NC_000962.3	Mycobrowser_v3	CDS	856682	858037	.	-	0	Rv0764c	cyp51	Involved in sterol biosynthesis. Its precise biological substrate is not known. Catalyzes C14-demethylation of lanosterol, 24,25-dihydrolanosterol and obtusifoliol which is critical for ergosterol biosynthesis. It transforms lanosterol into 4,4'-dimethyl cholesta-8,14,24-triene-3-beta-ol.	Cytochrome P450 51 Cyp51 (CYPL1) (P450-L1A1) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (P450-14DM)	Rv0764c, (MT0788, MTCY369.09c), len: 451 aa. Cyp51, cytochrome P450 51 (sterol 14-alpha demethylase), similar to others e.g. Q16850|CP51_HUMAN cytochrome P450 51 (CYPL1) (P450L1) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) from Homo sapiens (509 aa), FASTA scores: opt: 848, E(): 0, (33.9% identity in 439 aa overlap); NP_172633.1|NC_003070 putative obtusifoliol 14-alpha demethylase from Arabidopsis thaliana (488 aa); P93596|CP51_WHEAT cytochrome P450 51 (CYPL1) (P450-L1A1) (obtusifoliol 14-alpha demethylase) from Triticum aestivum (453 aa); etc. Also similar to many other Mycobacterium tuberculosis cytochromes P450 e.g. Rv1394c, FASTA score: (22.5% identity in 444 aa overlap). Contains PS00086 Cytochrome P450 cysteine heme-iron ligand signature. Belongs to the cytochrome P450 family.	P9WPP9	No	intermediary metabolism and respiration		MMAR_4932	MSMEG_5863	Mb0787c				
NC_000962.3	Mycobrowser_v3	CDS	860912	862381	.	+	0	Rv0768	aldA	Oxidizes a variety of aldehydes [catalytic activity: an aldehyde + NAD+ + H2O = an acid + NADH].	Probable aldehyde dehydrogenase NAD dependent AldA (aldehyde dehydrogenase [NAD+])	Rv0768, (MTCY369.13), len: 489 aa. Probable aldA, NAD-dependent aldehyde dehydrogenase, highly similar to others e.g. AAL14238.1|AY052630 6-oxolauric acid dehydrogenase from Rhodococcus ruber (474 aa); NP_285450.1|NC_001264 aldehyde dehydrogenase from Deinococcus radiodurans (495 aa); NP_241405.1|NC_002570 NADP-dependent aldehyde dehydrogenase from Bacillus halodurans (498 aa); P42757|DHAB_ATRHO betaine-aldehyde dehydrogenase precursor from Atriplex hortensis (Mountain spinach) (502 aa), FASTA scores: opt: 1001, E(): 0, (35.6% identity in 486 aa overlap); etc. Also highly similar to Rv0223c aldehyde dehydrogenase from Mycobacterium tuberculosis (487 aa). Contains PS00687 Aldehyde dehydrogenases glutamic acid active site. Belongs to the aldehyde dehydrogenases family.	I6X9R9	No	intermediary metabolism and respiration		MMAR_4928	MSMEG_5859	Mb0791				
NC_000962.3	Mycobrowser_v3	CDS	862412	863158	.	+	0	Rv0769	Rv0769	Function unknown; probably involved in cellular metabolism.	Probable dehydrogenase/reductase	Rv0769, (MTCY369.14), len: 248 aa. Probable dehydrogenase/reductase, similar to others, especially short-chain type dehydrogenases/reductases and 3-oxoacyl-(acyl-carrier protein) reductases e.g. NP_106890.1|NC_002678 probable short-chain type dehydrogenase/reductase from Mesorhizobium loti (374 aa); NP_243357.1|NC_002570 3-oxoacyl-(acyl-carrier protein) reductase from Bacillus halodurans (246 aa); P28643|FABG_CUPLA 3-oxoacyl-[acyl-carrier protein] reductase from Cuphea lanceolata (320 aa); P25529|HDHA_ECOLI 7-alpha-hydroxysteroid dehydrogenase from Escherichia coli (255 aa), FASTA scores: opt: 536, E(): 6.5e-27, (37.7% identity in 247 aa overlap); etc. Also similar to others from Mycobacterium tuberculosis e.g. MTCY02B10.14, FASTA score: (33.7% identity in 249 aa overlap); etc.	P9WGQ9	No	intermediary metabolism and respiration		MMAR_4927	MSMEG_5858	Mb0792				
NC_000962.3	Mycobrowser_v3	CDS	864586	865854	.	+	0	Rv0772	purD	Involved in de novo purine biosynthesis (at the second step) [catalytic activity: ATP + 5-phosphoribosylamine + glycine = ADP + phosphate + 5'-phosphoribosylglycinamide].	Probable phosphoribosylamine--glycine ligase PurD (GARS) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase) (5'-phosphoribosylglycinamide synthetase)	Rv0772, (MTCY369.17), len: 422 aa. Probable purD, phosphoribosylamine--glycine ligase, equivalent to Q50144|PURD|PUR2_MYCLE|ML2235|MLCB5.08 phosphoribosylamine--glycine ligase from Mycobacterium leprae (422 aa), FASTA scores: opt: 2272, E(): 0, (81.8% identity in 422 aa overlap). Also highly similar to others e.g. CAB56348.1|AL118514 phosphoribosylamine-glycine ligase from Streptomyces coelicolor (416 aa); P1564|PUR2_ECOLI phosphoribosylamine--glycine ligase from Escherichia coli (429 aa), FASTA scores: opt: 1039, E(): 0, (42.7% identity in 431 aa overlap); etc. Belongs to the GarS family.	P9WHM9	No	intermediary metabolism and respiration	ML2235,ML2235c	MMAR_4924	MSMEG_5852	Mb0795				
NC_000962.3	Mycobrowser_v3	CDS	996524	997705	.	+	0	Rv0894	Rv0894	Thought to be involved in transcriptional mechanism.	Possible transcriptional regulatory protein (possibly LuxR-family)	Rv0894, (MTCY31.22), len: 393 aa. Possible regulatory protein, LuxR family, highly similar in part to NP_302202.1|NC_002677 possible transcriptional regulator from Mycobacterium leprae (1106 aa). Also similar to others e.g. CAB95788.1|AL359949 putative multi-domain regulatory protein from Streptomyces coelicolor (780 aa); NP_107293.1|NC_002678 transcriptional regulator from Mesorhizobium loti (903 aa); etc. Also similar to other regulatory proteins from Mycobacterium tuberculosis e.g. Rv2488c|MTV008_44 (1137 aa), FASTA score: (53.2% identity in 363 aa overlap); Rv1358|MTCY02B10_22 (1159 aa), FASTA score: (52.3% identity in 365 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WKP9	No	regulatory proteins				Mb0918				
NC_000962.3	Mycobrowser_v3	CDS	870008	871426	.	+	0	Rv0777	purB	Involved in de novo purine biosynthesis (at the eight step) [catalytic activity: 1-(5-phosphoribosyl)-4-(N-succino-carboxamide) -5-aminoimidazole = fumarate + 5'-phosphoribosyl-5-amino-4-imidazolecarboxamide (also catalyzes: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP)].	Probable adenylosuccinate lyase PurB (adenylosuccinase) (ASL) (ASASE)	Rv0777, (MTCY369.21b), len: 472 aa. Probable purB, adenylosuccinate lyase, equivalent (but shorter 15 aa) to MLCB5.13|Z95151|g2076607|PURB adenylosuccinate lyase from Mycobacterium leprae (487 aa), FASTA scores: opt: 2640, E(): 0, (86.7% identity in 472 aa overlap). More similar to eukaryotic adenylosuccinate lyases than to prokaryotic adenylosuccinate lyases e.g. P54822|PUR8_MOUSE adenylosuccinate lyase from Mus musculus (484 aa), FASTA scores: opt: 762, E(): 0, (32.4% identity in 445 aa overlap); CAB99134.1|AL390188 putative adenylosuccino lyase (fragment) from Streptomyces coelicolor (362 aa); etc. Contains PS00163 Fumarate lyases signature. Belongs to the lyase 1 family, adenylossucinate lyase subfamily.	I6XWA1	No	intermediary metabolism and respiration	ML2230,ML2230c	MMAR_4916	MSMEG_5847	Mb0800				
NC_000962.3	Mycobrowser_v3	CDS	873343	874236	.	+	0	Rv0780	purC	Involved in de novo purine biosynthesis (at the seventh step) [catalytic activity: ATP + 1-(5-phosphoribosyl)-4-carboxy-5-aminoimidazole + L-aspartate = ADP + phosphate + 1-(5-phosphoribosyl)-4-(N-succino-carboxamide)-5-aminoimidazole].	Phosphoribosylaminoimidazole- succinocarboxamide synthase PurC (SAICAR synthetase)	Rv0780, (MTCY369.24), len: 297 aa. PurC, phosphoribosylaminoimidazole- succinocarboxamide synthase (see citations below), equivalent to MTU34957_1|PURC phosphoribosylaminoimidazole-succinocarboxamide synthase from Mycobacterium leprae (297 aa), FASTA scores: opt: 1986, E(): 0, (99.3% identity in 297 aa overlap). Also similar to others e.g. CAB56351.1|AL118514 phosphoribosylaminoimidazole-succinocarboxamide synthase from Streptomyces coelicolor (299 aa); etc. Contains PS01058 SAICAR synthetase signature 2. Belongs to the SAICAR synthetase family.	P9WHN1	No	intermediary metabolism and respiration	ML2227,ML2227c	MMAR_4909	MSMEG_5841	Mb0803				
NC_000962.3	Mycobrowser_v3	CDS	874233	874943	.	+	0	Rv0781	ptrBa	Cleaves peptide bonds on the C-terminal side of lysyl and argininyl residues [catalytic activity: hydrolysis of ARG-|-XAA and LYS-|-XAA bonds in oligopeptides, even when P1' residue is proline].	Probable protease II PtrBa [first part] (oligopeptidase B)	Rv0781, (MTCY369.25), len: 236 aa. Probable ptrBa, first part of protease II, equivalent to N-terminus of NP_302455.1|NC_002677 protease II from Mycobacterium leprae (724 aa). Also highly similar to N-termini of many proteases II e.g. P24555|PTRB_ECOLI|TLP|B1845 protease II from Escherichia coli strains K12 and HB101 (707 aa), FASTA scores: opt: 204, E(): 7.4e-07, (29.6% identity in 230 aa overlap); etc. ORFs Rv0782 and Rv0781 appear to be a frameshifted homologues of protease II, but we can find no error in the cosmid sequence to account for this. Belongs to peptidase family S9A; also known as the prolyl oligopeptidase family. Note that previously known as ptrBb. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P71835	No	intermediary metabolism and respiration				Mb0804				
NC_000962.3	Mycobrowser_v3	CDS	876818	878440	.	-	0	Rv0783c	emrB	Translocase that confers resistance to substances of high hydrophobicity. Involved in transport of multidrug across the membrane (export): multidrug resistance by an export mechanism. Responsible for the translocation of the substrate across the membrane.	Possible multidrug resistance integral membrane efflux protein EmrB	Rv0783c, (MTCY369.27c), len: 540 aa. Possible emrB, integral membrane drug efflux protein, member of major facilitator superfamily (MFS), equivalent to AAL16083.1|AF421382_1|AF421382 EmrB efflux protein from Mycobacterium avium (538 aa). Also similar to other membrane proteins e.g. CAB61606.1|AL133210 putative export protein from Streptomyces coelicolor (496 aa); NP_108371.1|NC_002678 efflux pump protein FarB from Mesorhizobium loti (511 aa); P44927|EMRB_HAEINHI0897| multidrug resistance protein b homologue from Haemophilus influenzae (510 aa), FASTA scores: opt: 706, E(): 1.3e-36, (30.4% identity in 408 aa overlap); etc. Also similar to Rv2333c|MTCY3G12.01 from Mycobacterium tuberculosis (537 aa), FASTA score: (28.2% identity in 408 aa overlap); and Rv1410c|MTCY21B4.27c from Mycobacterium tuberculosis (518 aa), FASTA score: (26.8% identity in 496 aa overlap). Belongs to the major facilitator family; also known as the drug resistance translocase family.	P9WG89	No	cell wall and cell processes	ML2224	MMAR_4905		Mb0805c				
NC_000962.3	Mycobrowser_v3	CDS	879340	881040	.	+	0	Rv0785	Rv0785	Function unknown	Conserved protein	Rv0785, (MTCY369.29), len: 566 aa. Conserved protein, highly similar to other conserved hypothetical proteins e.g. NP_105777.1| NC_002678 hypothetical protein from Mesorhizobium loti (552 aa); SC5F8.14|CAB93742.1|AL357613 conserved hypothetical protein from Streptomyces coelicolor (557 aa); AE001863|AE001863_31 from Deinococcus radiodurans (554 aa), FASTA scores: opt: 2243, E(): 0, (61.1% identity in 550 aa overlap); YEF7_YEAST|P32614 hypothetical 50.8 kd protein (470 aa), FASTA scores: opt: 169, E(): 0.0014, (23.8% identity in 542 aa overlap); etc. Also similar to Rv1817|MTCY1A11.26c from Mycobacterium tuberculosis (487 aa), FASTA score: (26.7% identity in 587 aa overlap). And shows similarity with other dehydrogenases.	P71838	No	conserved hypotheticals	ML2222,ML2222c	MMAR_4632	MSMEG_5835	Mb0807,Mb0808				
NC_000962.3	Mycobrowser_v3	CDS	887137	888636	.	-	0	Rv0794c	Rv0794c	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase	Rv0794c, (MTV042.04c), len: 499 aa. Probable oxidoreductase, possibly dihydrolipoamide dehydrogenase or mercuric reductase. Highly similar to CAB62675.1|AL133422 probable oxidoreductase from Streptomyces coelicolor (477 aa); and similar to various oxidoreductases e.g. P08663|MERA_STAAU mercuric reductase (HG(II) reductase) from Staphylococcus aureus (547 aa); AAK70920.1|AC087551_19|AC087551 putative lipoamide dehydrogenase from Oryza sativa (563 aa); NP_437349.1|NC_003078 putative FAD-dependent pyridine nucleotide-disulphide oxidoreductase, similar to mercuric reductases protein from Sinorhizobium meliloti (473 aa); Q04829|DLDH_HALVO dihydrolipoamide dehydrogenase from Haloferax volcanii (475 aa); P08332|MERA_SHIFL mercuric reductase (564 aa), FASTA scores: opt: 522, E(): 3.7e-26, (31.7% identity in 467 aa overlap); P72740|DLDH_SYNY3|Q53395|LPDA|PDHD|SLR1096 dihydrolipoamide dehydrogenase from Synechocystis sp. strain PCC 6803 (474 aa), FASTA scores: opt: 602, E(): 2.3e-31, (31.0% identity in 493 aa overlap); etc. Note that previously known as lpdB.	I6Y4U4	No	intermediary metabolism and respiration	ML2216,ML2216c	MMAR_4894	MSMEG_4023	Mb0818c,Mb0819c				
NC_000962.3	Mycobrowser_v3	CDS	889347	890333	.	+	0	Rv0796	Rv0796	Required for the transposition of the insertion element IS6110.	Putative transposase for insertion sequence element IS6110	Rv0796, (MTV042.06), len: 328 aa. Putative transposase for IS6110. Identical to many other M. tuberculosis IS6110 transposase subunits. The transposase described here may be made by a frame shifting mechanism during translation that fuses Rv0795 and Rv0796, the sequence UUUUAAAG (directly upstream of Rv0796) maybe responsible for such a frameshifting event (see McAdam et al., 1990). Start changed since first submission (+ 50 aa).	P9WKH9	No	insertion seqs and phages								
NC_000962.3	Mycobrowser_v3	CDS	892266	893273	.	-	0	Rv0799c	Rv0799c	Function unknown	Conserved protein	Rv0799c, (MTCY07H7A.10, MTCI429B.01), len: 335 aa. Conserved protein, similar to Q50021|U2266C from Mycobacterium leprae (146 aa), FASTA scores: opt: 147, E(): 0.0016, (33.3% identity in 117 aa overlap); Q50020|U2266B from Mycobacterium leprae (27 aa), FASTA scores: opt: 94, E(): 1.3, (56.5% identity in 23 aa overlap). Also highly similar to others e.g. CAC01593.1|AL391041 conserved hypothetical protein from Streptomyces coelicolor (316 aa); AF088897|AF088897_9 hypothetical protein from Zymomonas mobilis (322 aa), FASTA scores: opt: 1132, E(): 0, (56.1% identity in 303 aa overlap); P76536|ECAE000330_8 hypothetical protein from Escherichia coli strain K-12 (308 aa), FASTA scores: E(): 2.2e-30, (37.4% identity in 297 aa overlap); etc. Also similar to some tyrA proteins. Predicted to be an outer membrane protein (See Song et al., 2008).	I6Y4U9	No	conserved hypotheticals	ML2214	MMAR_4892	MSMEG_5829	Mb0822c				
NC_000962.3	Mycobrowser_v3	CDS	895820	898084	.	+	0	Rv0803	purL	Involved in de novo purine biosynthesis (at the fourth step) [catalytic activity: ATP + 5'-phosphoribosylformylglycinamide + L-glutamine + H(2)O = ADP + phosphate + 5'-phosphoribosylformylglycinamidine + L-glutamate].	Phosphoribosylformylglycinamidine synthase II PurL (FGAM synthase II)	Rv0803, (MTCY07H7A.06c), len: 754 aa. PurL, phosphoribosylformylglycinamidine synthase II (see citations below), equivalent to NP_302451.1|NC_002677 phosphoribosylformylglycinamidine synthase II from Mycobacterium leprae (754 aa). Also highly similar to others e.g. Q9RKK5|PURL_STRCO from Streptomyces coelicolor (752 aa); P12042|PURL_BACSU from Bacillus subtilis (742 aa), FASTA score: (44.7% identity in 716 aa); etc. Start was chosen by similarity. Belongs to the FGAMS family.	P9WHL7	No	intermediary metabolism and respiration	ML2211,ML2211c	MMAR_4888	MSMEG_5824	Mb0826				
NC_000962.3	Mycobrowser_v3	CDS	899732	901330	.	-	0	Rv0806c	cpsY	Thought to be involved in exopolysaccharide and/or lipopolysaccharide biosynthetic pathway [catalytic activity: UDP-glucose = UDP-galactose].	Possible UDP-glucose-4-epimerase CpsY (galactowaldenase) (UDP-galactose-4-epimerase) (uridine diphosphate galactose-4-epimerase) (uridine diphospho-galactose-4-epimerase)	Rv0806c, (MTCY07H7A.03), len: 532 aa. Possible cpsY, UDP-glucose-4-epimerase, equivalent to Q50025|CPSY probable UDP-glucose-4-epimerase from Mycobacterium leprae (542 aa), FASTA scores: opt: 2964, E(): 0, (82.3% identity in 530 aa overlap). Also similar to AAC38286.1|AF019760|SACB CpsY homolog (involved in meningococcal capsule biosynthesis) from Neisseria meningitidis serogroup a (545 aa); Q51151 capsule gene complex UPD-glucose-4-epimerase (gale) from Neisseria meningitidis (373 aa), FASTA scores: opt: 496, E(): 9.5e-27, (29.3% identity in 358 aa overlap); C-terminus of CAB75373.1|AL139298 putative transferase from Streptomyces coelicolor (942 aa); and many hypothetical proteins from Streptomyces coelicolor. Seems to belong to the sugar epimerase family.	P9WGD1	No	cell wall and cell processes	ML2209	MMAR_4885		Mb0829c				
NC_000962.3	Mycobrowser_v3	CDS	1024684	1025184	.	+	0	Rv0919	Rv0919	Acetylation, substrate unknown	GCN5-related N-acetyltransferase	Rv0919, (MTCY21C12.13), len: 166 aa. Probable acetyltransferase. Contains GNAT (Gcn5-related N-acetyltransferase) domain. See Vetting et al. 2005. Some similarity to Q50115 hypothetical protein from Mycobacterium leprae (90 aa), FASTA scores: opt: 243, E(): 5.3e-11, (56.5% identity in 85 aa overlap). Alternative nucleotide at position 1025106 (T->C; F141F) has been observed.	I6XA42	No	intermediary metabolism and respiration	ML2107,ML2107c			Mb0943				
NC_000962.3	Mycobrowser_v3	CDS	908485	909318	.	-	0	Rv0815c	cysA2	May be a sulfotransferase involved in the formation of thiosulfate [catalytic activity: thiosulfate + cyanide = sulfite + thiocyanate].	Probable thiosulfate sulfurtransferase CysA2 (rhodanese-like protein) (thiosulfate cyanide transsulfurase) (thiosulfate thiotransferase)	Rv0815c, (MTV043.07c, MT0837, O05793), len: 277 aa. Probable cysA2 (alternate gene name: sseC4), thiosulfate sulfurtransferase (see Wooff et al., 2002), equivalent to Q50036|CYSA|CYSA3|ML2198|THTR_MYCLE putative sulfurtransferase thiosulfate from Mycobacterium leprae (277 aa). Also highly similar to other putative thiosulfate sulfurtransferases e.g. P16385|THTR_SACER putative thiosulfate sulfurtransferase from Saccharopolyspora erythraea (Streptomyces erythraeus) (281 aa); NP_293941.1|NC_001263 thiosulfate sulfurtransferase from Deinococcus radiodurans (286 aa); etc. Identical second copy present as Rv3117|MTCY164.27|MT3199|O05793|cysA3 (277 aa) (100.0% identity in 277 aa overlap). Contains PS00683 Rhodanese C-terminal signature at C-terminus. Belongs to the rhodanese family.	P9WHF9	No	intermediary metabolism and respiration	ML2198	MMAR_4868	MSMEG_5789	Mb0838c				
NC_000962.3	Mycobrowser_v3	CDS	909611	910033	.	-	0	Rv0816c	thiX	Thioredoxin participates in various redox reactions through the reversible oxidation of its active center dithiol, to a disulfide, & catalyzes dithiol-disulfide exchange reactions.	Probable thioredoxin ThiX	Rv0816c, (MTV043.08c), len: 140 aa. Probable thiX, thioredoxin, equivalent to ThiX|U15182|MLU15182_21 thioredoxin from Mycobacterium leprae (172 aa), FASTA scores: opt: 556, E(): 8.8e-31, (63.8% identity in 141 aa overlap); and similar to AAL08576.1|AF418548_2|AF418548 thioredoxin from Mycobacterium avium subsp. paratuberculosis (117 aa). Also similar to other bacterial thioredoxins e.g. CAB95303.1|AL359779 putative thioredoxin from Streptomyces coelicolor (126 aa); P33791|THIO_STRAU|TRX|TRXA thioredoxin from Streptomyces aureofaciens (106 aa); etc. And similar to Rv3914|MT4033|MTV028.05|NP_218431.1|NC_000962|trxC thioredoxin (TRX) (MPT46) from Mycobacterium tuberculosis (116 aa). Has hydrophobic stretch at N-terminus. Seems to belong to the thioredoxin family.	I6Y8V2	No	intermediary metabolism and respiration	ML2196	MMAR_3647	MSMEG_5786	Mb0839c				
NC_000962.3	Mycobrowser_v3	CDS	913558	914199	.	-	0	Rv0821c	phoY2	Involved in transcriptional regulation of active transport of inorganic phosphate across the membrane.	Probable phosphate-transport system transcriptional regulatory protein PhoY2	Rv0821c, (MTV043.13c), len: 213 aa. Probable phoY2, phosphate-transport system regulatory protein, highly similar to PhoY|MLU15182_29|U15182 phosphate transport system regulator from Mycobacterium leprae (222 aa), FASTA scores: opt: 1268, E(): 0, (93.0% identity in 213 aa overlap). Also similar to others e.g. NP_384620.1|NC_003047 probable phosphate transport system transcriptional regulator protein from Sinorhizobium meliloti (237 aa); etc. Also highly similar to MTCI418A.03c|Z96070|PhoY1 probable phosphate transport system transcriptional regulator protein from Mycobacterium tuberculosis (221 aa), FASTA scores: opt: 937, E(): 0, (63.4% identity in 213 aa overlap). Belongs to the PhoU family.	P9WI95	No	cell wall and cell processes	ML2188	MMAR_4859	MSMEG_5776	Mb0844c				
NC_000962.3	Mycobrowser_v3	CDS	914257	916311	.	-	0	Rv0822c	Rv0822c	Function unknown	Conserved protein	Rv0822c, (MTV043.14c), len: 684 aa. Conserved protein, highly similar in the region between aa 370 - 580 to U2266O|U15182|MLU15182_30 hypothetical protein from Mycobacterium leprae (222 aa), FASTA scores: opt: 819, E(): 0, (60.6% identity in 221 aa overlap). More extended similarity to Rv3267|Z92771|MTCY71_7 from Mycobacterium tuberculosis (498 aa), FASTA scores: opt: 434, E(): 2.2e-17, (26.6% identity in 541 aa overlap), and Rv3484. Also similar to various proteins, preferiously putative membrane proteins and membrane-bound regulatory proteins e.g. CAC44512.1|AL596138 putative membrane protein from Streptomyces coelicolor (524 aa); U56901|BSU56901_1 regulatory protein from Bacillus subtilis (391 aa), FASTA scores: opt: 225, E(): 1.3e-05, (24.7% identity in 340 aa overlap). Contains hydrophobic stretch (aa ~ 160-195) and PS00041 Bacterial regulatory proteins, araC family signature.	I6WZI4	No	conserved hypotheticals	ML2187	MMAR_4858	MSMEG_5775	Mb0845c				
NC_000962.3	Mycobrowser_v3	CDS	925361	927610	.	+	0	Rv0833	PE_PGRS13	Function unknown	PE-PGRS family protein PE_PGRS13	Rv0833, (MTV043.25), len: 749 aa. PE_PGRS13, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see Brennan and Delogu, 2002), but lacking N-terminal domain (present in preceding ORF), possibly due to frameshift. Similar in part to many others e.g. MTCY28_25|Z95890 (914 aa), FASTA scores: opt: 2726, E(): 0, (60.1% identity in 776 aa overlap); etc.	Q79FV7	No	PE/PPE				Mb0856				
NC_000962.3	Mycobrowser_v3	CDS	927837	930485	.	-	0	Rv0834c	PE_PGRS14	Function unknown	PE-PGRS family protein PE_PGRS14	Rv0834c, (MTV043.26c), len: 882 aa. PE_PGRS14, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see Brennan & Delogu 2002), highly similar to many others e.g. MTCY493_4|Z95844 (1329 aa), FASTA scores: opt: 2577, E(): 0, (52.0% identity in 950 aa overlap); etc. Thought to be differentially expressed within host cells (see Triccas et al., 1999).	Q79FV6	No	PE/PPE		MMAR_0492		Mb0857c				
NC_000962.3	Mycobrowser_v3	CDS	930953	931597	.	+	0	Rv0835	lpqQ	Unknown	Possible lipoprotein LpqQ	Rv0835, (MTV043.27), len: 214 aa. Possible lpqQ, lipoprotein. Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	O53846	No	cell wall and cell processes		MMAR_1362		Mb0858				
NC_000962.3	Mycobrowser_v3	CDS	932279	932932	.	-	0	Rv0836c	Rv0836c	Unknown	Hypothetical protein	Rv0836c, (MTV043.29c), len: 217 aa (start uncertain). Hypothetical unknown protein. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O53848	No	conserved hypotheticals				Mb0859c				
NC_000962.3	Mycobrowser_v3	CDS	940456	941106	.	-	0	Rv0844c	narL	Involved in transcriptional mechanism and regulates nitrate/nitrite.	Possible nitrate/nitrite response transcriptional regulatory protein NarL	Rv0844c, (MTV043.37c), len: 216 aa. Possible narL, nitrate/nitrite response regulator protein, similar to many e.g. CAB44989.1|AJ131854 NarL protein from Pseudomonas stutzeri (218 aa); CAA75536.1|Y15252 nitrate/nitrite regulatory protein from Pseudomonas aeruginosa (216 aa); PCC6803|D64005|SYCSLRG_24 NarL protein from Synechocystis sp. (209 aa), FASTA scores: opt: 438, E(): 1.5e-23, (34.6% identity in 208 aa overlap); etc. Also similar to unidentified regulator e.g. CAB76009.1|AL157916 putative two-component system response regulator from Streptomyces coelicolor (224 aa); etc. Contains probable helix-turn helix motif from aa 170-191 (Score 1124, +3.02 SD).	P9WGM5	No	regulatory proteins		MMAR_4782	MSMEG_0105	Mb0867c				
NC_000962.3	Mycobrowser_v3	CDS	941190	942467	.	+	0	Rv0845	Rv0845	Possible sensor part of a two component regulatory system.	Possible two component sensor kinase	Rv0845, (MTV043.38), len: 425 aa. Possible two-component sensor kinase, with its C-terminus similar to C-terminal part of others e.g. NP_294951.1|NC_001263 two-component sensor histidine kinase from Deinococcus radiodurans (469 aa); CAC32293.1|AL583943 putative two component system histidine kinase from Streptomyces coelicolor (404 aa); NP_464546.1|NC_003210 protein similar to two-component sensor histidine kinase from Listeria monocytogenes (352 aa); BSUB0017_193|Z9912 two-component sensor kinase from Bacillus subtilis (360 aa), FASTA scores: opt: 275, E(): 1.6e-11, (30.3% identity in 234 aa overlap); etc.	O53857	No	regulatory proteins		MMAR_4781	MSMEG_0106	Mb0868				
NC_000962.3	Mycobrowser_v3	CDS	944938	946056	.	+	0	Rv0848	cysK2	Thought to be involved in cysteine biosynthesis [catalytic activity: O3-acetyl-L-serine + H(2)S = L-cysteine + acetate].	Possible cysteine synthase a CysK2 (O-acetylserine sulfhydrylase) (O-acetylserine (thiol)-lyase) (CSASE)	Rv0848, (MTV043.41), len: 372 aa. Possible cysK2, cysteine synthase A, but could be also a cysteine synthase B cysM2-product, similar to many e.g. NP_109408.1|NC_002682 cysteine synthase from Mesorhizobium loti (357 aa); Q44004|CYSM_ALCEU cysteine synthase from Alcaligenes eutrophus strain CH34 (Ralstonia eutropha) (339 aa), FASTA scores: opt: 511, E(): 1.7e-25, (35.0% identity in 314 aa overlap); etc. Belongs to the cysteine synthase/cystathionine beta-synthase family. Cofactor: pyridoxal phosphate. Note that previously known as cysM3.	Q79FV4	No	intermediary metabolism and respiration		MMAR_4768		Mb0871				
NC_000962.3	Mycobrowser_v3	CDS	947641	948468	.	-	0	Rv0851c	Rv0851c	Function unknown; possibly involved in cellular metabolism.	Probable short-chain type dehydrogenase/reductase	Rv0851c, (MTV043.44c), len: 275 aa. Probable short-chain dehydrogenase/reductase, similar to many e.g. Q01198|LIGD_PSEPA C alpha-dehydrogenase (SDR family) from Pseudomonas paucimobilis (Sphingomonas paucimobilis) (305 aa); D11473|PSELIG_1 C alpha-dehydrogenase from P. paucimobilis (305 aa), FASTA scores: opt: 468, E(): 4.9e-23, (30.8% identity in 279 aa overlap); NP_421969.1|NC_002696 short chain dehydrogenase family protein from Caulobacter crescentus (278 aa); etc. Contains PS00061 Short-chain dehydrogenases/reductases family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	O53863	No	intermediary metabolism and respiration		MMAR_4755		Mb0874c				
NC_000962.3	Mycobrowser_v3	CDS	1025497	1026816	.	-	0	Rv0920c	Rv0920c	Required for the transposition of the insertion element IS1554.	Probable transposase	Rv0920c, (MTCY21C12.14c), len: 439 aa. Probable transposase for IS1554, highly similar to others e.g. MTCY441.35|Q45111 transposase from Mycobacterium tuberculosis (419 aa), FASTA scores: opt: 1113, E(): 0, (43.9% identity in 378 aa overlap); etc. Contains transposases mutator family signature (PS01007).	I6Y941	No	insertion seqs and phages				Mb0944c				
NC_000962.3	Mycobrowser_v3	CDS	951632	952711	.	+	0	Rv0855	far	Function unknown, but involvement in lipid degradation (racemization).	Probable fatty-acid-CoA racemase Far	Rv0855, (MTV043.48), len: 359 aa. Probable far, fatty acid-CoA racemase, highly similar to CAB08122.1|Z94723 unknown protein from Mycobacterium leprae (253 aa) (C-terminus shorter). Also similar to many eukaryotic and bacteria racemases e.g. T35425 probable fatty acid CoA racemase from Streptomyces coelicolor (387 aa); P70473|AMAC_RAT alpha-methylacyl-CoA racemase (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase) from Rattus norvegicus (Rat) (382 aa); NP_103687.1|NC_002678 probable fatty acid Co-a racemase from Mesorhizobium loti (389 aa); etc. Also similar to proteins from Mycobacterium tuberculosis e.g. Rv1143|MTCI65.10|MCR from Mycobacterium tuberculosis (360 aa), FASTA scores: opt: 1373, E(): 0, (56.8% identity in 359 aa overlap), Rv1866|MTCY359.07 (C-terminal half) (778 aa), Rv3272 (360 aa).	I6Y8Y0	No	lipid metabolism	ML2165,ML2165c	MMAR_4681	MSMEG_5734	Mb0878				
NC_000962.3	Mycobrowser_v3	CDS	955077	956288	.	+	0	Rv0859	fadA	Function unknown, but involvement in lipid degradation.	Possible acyl-CoA thiolase FadA	Rv0859, (MTV043.52), len: 403 aa. Possible fadA, acyl-CoA thiolase, equivalent to NP_302423.1|NC_002677 putative beta-ketoadipyl CoA thiolase from Mycobacterium leprae (403 aa). Also highly similar to acyl/acetyl-CoA thiolases and beta-ketoadipyl CoA thiolases, e.g. T35428 probable acetyl CoA acetyltransferase (thiolase) from Streptomyces coelicolor (404 aa); NP_250427.1|NC_002516 probable acyl-CoA thiolase from Pseudomonas aeruginosa (401 aa); NP_106253.1|NC_002678 probable acyl-CoA thiolase from Mesorhizobium loti (402 aa); NP_248919.1|NC_002516|PcaF beta-ketoadipyl CoA thiolase PcaF from Pseudomonas aeruginosa (401 aa); etc. Contains PS00098 Thiolases acyl-enzyme intermediate signature, PS00737 Thiolases signature 2 and PS00099 Thiolases active site.	O53871	No	lipid metabolism	ML2162,ML2162c	MMAR_4677	MSMEG_5721	Mb0882				
NC_000962.3	Mycobrowser_v3	CDS	956293	958455	.	+	0	Rv0860	fadB	Involved in fatty acid degradation (probably in fatty acid beta-oxidation cycle).	Probable fatty oxidation protein FadB	Rv0860, (MTV043.53), len: 720 aa. Probable fadB, fatty oxidation protein, equivalent to NP_302422.1|NC_002677 putative fatty oxidation complex alpha subunit from Mycobacterium leprae (714 aa). Also highly similar to others and various proteins involved in fatty acid metabolism, e.g. T35429 probable fatty oxidation protein from Streptomyces coelicolor (733 aa); NP_250428.1|NC_002516 probable 3-hydroxyacyl-CoA dehydrogenase from Pseudomonas aeruginosa (714 aa); NP_418895.1|NC_002696 fatty oxidation complex alpha subunit from Caulobacter crescentus (709 aa); P40939|ECHA_HUMAN trifunctional enzyme alpha subunit [includes: long-chain enoyl-CoA hydratase ; long chain 3-hydroxyacyl-CoA dehydrogenase ] from Homo sapiens (763 aa), FASTA scores: opt: 1176, E(): 0, (32.4% identity in 722 aa overlap); P21177|FADB_ECOLI fatty oxidation complex alpha subunit [includes: enoyl-CoA hydratase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; 3-hydroxyacyl-CoA dehydrogenase; 3- hydroxybutyryl-CoA epimerase] from Escherichia coli strain K12 (729 aa), FASTA scores: opt: 873, E(): 0, (33.6% identity in 693 aa overlap); etc.	O53872	No	lipid metabolism	ML2161,ML2161c	MMAR_4676	MSMEG_5720	Mb0883				
NC_000962.3	Mycobrowser_v3	CDS	958523	960151	.	-	0	Rv0861c	ercc3	Involved in nucleotide excision repair. Has ATP-dependent 3' -> 5'helicase activity: acts by opening DNA either around the RNA transcription start site or the DNA damage.	DNA helicase Ercc3	Rv0861c, (MTV043.54c), len: 542 aa. Ercc3, DNA helicase (see citation below), equivalent to NP_302420.1|NC_002677 probable DNA helicase from Mycobacterium leprae (549 aa). Also highly similar to others (shorter than several eukaryotic enzymes) e.g. NP_218820.1|NC_000919|AE001217|AE0 01217_6 putative DNA repair helicase from Treponema pallidum (606 aa), FASTA scores: opt: 1275, E(): 0, (47.5% identity in 592 aa overlap); Q00578|RA25_YEAST DNA repair helicase from Saccharomyces cerevisiae (843 aa), FASTA scores: opt: 777, E(): 0, (30.4% identity in 605 aa overlap); P49135|XPB_MOUSE DNA-repair protein complementing XP-B cells from Mus musculus (Mouse) (783 aa), FASTA scores: opt: 761, E(): 0, (36.3% identity in 375 aa overlap); etc. Seems to belong to the helicase family. Alternative nucleotide at position 958922 (C->a; A410A) has been observed.	O53873	No	information pathways	ML2157	MMAR_4671	MSMEG_5706	Mb0884c				
NC_000962.3	Mycobrowser_v3	CDS	962890	963393	.	+	0	Rv0864	moaC2	Involved in the biosynthesis of molybdopterin.	Probable molybdenum cofactor biosynthesis protein C 2 MoaC2	Rv0864, (MTV043.57), len: 167 aa. Probable moaC2, molybdopterin cofactor biosynthesis protein, highly similar to others e.g. CAB59676.1|AL132674 molybdenum cofactor biosynthesis protein from Streptomyces coelicolor (170 aa); NP_418834.1|NC_002696 molybdenum cofactor biosynthesis protein C from Caulobacter crescentus (186 aa); Y10817|ANY10817_3|T44852 molybdopterin co-factor synthesis protein moaC from Arthrobacter nicotinovorans plasmid pAO1 (169 aa), FASTA scores: opt: 491, E(): 2.4e-29, (51.0% identity in 151 aa overlap); etc. Also highly similar to O05788|MOAC1|Rv3111|MTCY164.21 putative molybdenum cofactor biosynthesis protein C from Mycobacterium tuberculosis (170 aa), FASTA scores: opt: 491, E(): 2.4e-29, (54.9% identity in 153 aa overlap); and O53376|Rv3324c|MOAC3|MTV016.24c putative molybdenum cofactor biosynthesis protein C3 (177 aa).	P9WJR7	No	intermediary metabolism and respiration	ML2154,ML2154c	MMAR_4668	MSMEG_5703	Mb0887,Mb0888				
NC_000962.3	Mycobrowser_v3	CDS	963390	963872	.	+	0	Rv0865	mog	Involved in molybdopterin biosynthesis; involved in the biosynthesis of a demolybdo-cofactor (molybdopterin), necessary for molybdo-enzymes.	Probable molybdopterin biosynthesis Mog protein	Rv0865, (MTV043.58), len: 160 aa. Probable mog, molybdopterin biosynthesis MOG protein, highly similar or similar to other molybdenum cofactor biosynthesis proteins e.g. CAB59675.1|AL132674 molybdenum cofactor biosynthesis protein from Streptomyces coelicolor (179 aa); NP_301253.1|NC_002677 putative molybdenum cofactor biosynthesis protein from Mycobacterium leprae (181 aa); CAC39235.1|AJ312124 Mog protein from Eubacterium acidaminophilum (162 aa); P44645|MOG_HAEIN|MOGA|HI0336 molybdopterin biosynthesis MOG protein from Haemophilus influenzae (197 aa), FASTA scores: opt: 306, E(): 9e-13, (39.6% identity in 139 aa overlap); P28694|MOG_ECOLI molybdopterin biosynthesis MOG protein from Escherichia coli (195 aa), FASTA scores: opt: 265, E(): 3.6e-10, (34.2 identity in 146 aa overlap); etc. Also highly similar to Rv0984|MTV044.12|MOAB2 possible pterin-4-alpha-carbinolamine dehydratase from Mycobacterium tuberculosis (181 aa).	I6Y8Y8	No	intermediary metabolism and respiration	ML2153,ML2153c	MMAR_4667	MSMEG_5702	Mb0889				
NC_000962.3	Mycobrowser_v3	CDS	963869	964294	.	+	0	Rv0866	moaE2	Possibly a molybdenum biosynthesis cofactor. Conversion of molybdopterin precursor Z into molybdopterin requires transfer of two sulfur atoms to precursor Z (to generate the dithiolene group). This is catalyzed by the converting factor composed of a small and large subunit.	Probable molybdenum cofactor biosynthesis protein E2 MoaE2 (molybdopterin converting factor large subunit) (molybdopterin [MPT] converting factor, subunit 2)	Rv0866, (MTV043.59), len: 141 aa. Probable moaE2, molybdopterin converting factor E (molybdopterin converting factor (subunit 2)), similar to others e.g. Y10817|ANY10817_4|T44853 molybdopterin biosynthesis protein E chain from Arthrobacter nicotinovorans plasmid pAO1 (155 aa), FASTA scores: opt: 460, E(): 3.5e-27, (49.3 identity in 146 aa overlap); CAC01331.1|AL390968 moaE-like protein from Streptomyces coelicolor (152 aa); NP_389313.1|NC_000964 molybdopterin converting factor (subunit 2) from Bacillus subtilis (157 aa); etc. Also highly similar to Rv3119|MOAE1|Z95150|MTCY164_30 putative molybdenum cofactor biosynthesis protein E from Mycobacterium tuberculosis (147 aa), FASTA scores: opt: 321, E(): 5.9e-17, (40.9% identity in 132 aa overlap); and O53375|GPHA|Rv3323c|MTV016.23c MOAD-MOAE fusion protein from Mycobacterium tuberculosis (221 aa).	P9WJR1	No	intermediary metabolism and respiration	ML2152,ML2152c	MMAR_4666	MSMEG_5701	Mb0890				
NC_000962.3	Mycobrowser_v3	CDS	966265	967347	.	-	0	Rv0869c	moaA2	Involved in molybdenum cofactor biosynthesis; involved in the biosynthesis of molybdopterin precursor Z from guanosine.	Probable molybdenum cofactor biosynthesis protein A2 MoaA2	Rv0869c, (MTV043.62c), len: 360 aa. Probable moaA2, molybdenum cofactor biosynthesis protein, highly similar to others e.g. CAB59437.1|AL132644|SCI8_6 molybdenum cofactor biosynthesis protein A from Streptomyces coelicolor (341 aa), FASTA scores: opt: 1336, E(): 0, (61.7% identity in 332 aa overlap); S57490|X78980|ANMOAA_1 molybdopterin cofactor synthesis protein from Arthrobacter nicotinovorans (fragment) (374 aa), FASTA scores: opt: 1059, E(): 0, (49.9% identity in 369 aa overlap); Q44118|MOAA_ARTNI probable molybdopterin cofactor synthesis protein A from Arthrobacter nicotinovorans plasmid pAO1 (355 aa); etc. Also similar to Rv3109|MTCY164.19|Z95150|MOAA1 putative molybdenum cofactor biosynthesis protein A from Mycobacterium tuberculosis (359 aa), FASTA scores: opt: 657, E(): 0, (36.6% identity in 309 aa overlap). Belongs to the MoaA / NifB / PqqE family.	P9WJS1	No	intermediary metabolism and respiration	ML2149	MMAR_4663	MSMEG_5698	Mb0893c				
NC_000962.3	Mycobrowser_v3	CDS	976872	978203	.	-	0	Rv0878c	PPE13	Function unknown	PPE family protein PPE13	Rv0878c, (MTCY31.06c), len: 443 aa. PPE13, Member of the Mycobacterium tuberculosis PPE family, highly similar to many e.g. P4261|YHS6_MYCTU (517 aa), FASTA scores: opt: 1044, E(): 0, (47.4% identity in 397 aa overlap); MTV014_3, MTCI65_2, MTCY98_24, MTCY3C7_23, MTCY48_17, MTV004_5, MTV004_3, etc. Predicted to be an outer membrane protein (See Song et al., 2008).	P9WI35	No	PE/PPE		MMAR_4319		Mb0902c				
NC_000962.3	Mycobrowser_v3	CDS	979362	980228	.	+	0	Rv0881	Rv0881	Causes methylation	Possible rRNA methyltransferase (rRNA methylase)	Rv0881, (MTCY31.09), len: 288 aa. Possible rRNA methyltransferase, highly similar to others and hypothetical proteins e.g. CAB76071.1|AL157953 putative rRNA methylase from Streptomyces coelicolor (272 aa); NP_421117.1|NC_002696 spoU rRNA methylase family protein from Caulobacter crescentus (268 aa); D90913_93|P74261 rRNA methylase from Synechocystis sp. (274 aa), FASTA scores: E(): 1.1e-13, (26.3% identity in 278 aa overlap); P18644|TSNR_STRCN rRNA methyltransferase from Streptomyces cyaneus (Streptomyces curacoi) (269 aa), FASTA scores: E(): 3.7e-08, (23.9% identity in 268 aa overlap); etc. Equivalent to AAK45146.1 from Mycobacterium tuberculosis strain CDC1551 (242 aa) but longer 46 aa.	P9WFY3	No	intermediary metabolism and respiration	ML2139,ML2139c	MMAR_4651	MSMEG_5687	Mb0905				
NC_000962.3	Mycobrowser_v3	CDS	981424	982554	.	-	0	Rv0884c	serC	Catalyzes the reversible interconversion of phosphoserine and 2-oxoglutarate to 3-phosphonooxypyruvate and glutamate. Require both in the major phosphorylated pathway of serine biosynthesis and in pyridoxine biosynthesis [catalytic activity: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate].	Possible phosphoserine aminotransferase SerC (PSAT)	Rv0884c, (MTCY31.12c), len: 376 aa. Possible serC, phosphoserine aminotransferase, equivalent to MLCB57_17 putative phosphoserine aminotransferase from Mycobacterium leprae (376 aa), FASTA scores: E(): 0, (87.5 identity in 376 aa overlap). Also highly similar to CAC08322.1|AL392149 putative aminotransferase from Streptomyces coelicolor (363 aa); and similar to other phosphoserine aminotransferases e.g. NP_386837.1|NC_003047 putative phosphoserine aminotransferase protein from Sinorhizobium meliloti (392 aa); P52878|SERC_METBA phosphoserine aminotransferase from Methanosarcina barkeri (370 aa); P10658|SERC_RABIT|RABEPIP_1 phosphoserine aminotransferase from Rabbit (370 aa), FASTA scores: opt: 271, E(): 3.5e-11, (24.5% identity in 368 aa overlap); etc. Belongs to class-V of pyridoxal-phosphate-dependent aminotransferases. Cofactor: pyridoxal phosphate.	P9WQ73	No	intermediary metabolism and respiration	ML2136	MMAR_4648	MSMEG_5684	Mb0908c				
NC_000962.3	Mycobrowser_v3	CDS	988740	989861	.	-	0	Rv0889c	citA	Involved in tricarboxylic acid cycle (KREBS cycle) [catalytic activity: citrate + CoA = acetyl-CoA + H2O + oxaloacetate].	Probable citrate synthase II CitA	Rv0889c, (MTCY31.17c), len: 373 aa. Probable citA (alternate gene name: gltA), citrate synthase 2, highly similar to others e.g. CAB95899.1|AL359988 putative citrate synthase from Streptomyces coelicolor (387 aa); P39119|CISY_BACSU citrate synthase II from Bacillus subtilis (366 aa), FASTA scores: opt: 586, E(): 5.8e-30, (33.8% identity in 367 aa overlap); etc. Also similar to Rv0896|MTCY31.24 from Mycobacterium tuberculosis (29.2% identity in 274 aa overlap) and Rv1131. Contains PS00480 Citrate synthase signature. Belongs to the citrate synthase family.	P9WPD3	No	intermediary metabolism and respiration	ML2132	MMAR_4643	MSMEG_5676	Mb0913c				
NC_000962.3	Mycobrowser_v3	CDS	1002812	1003792	.	+	0	Rv0899	ompA	The protein behaved as a porin of low specific activity. Structural protein that may protect the integrity of the bacterium.	Outer membrane protein A OmpA	Rv0899, (MTCY31.27), len: 326 aa. OmpA, outer membrane protein A (See Senaratne et al., 1998). C-terminal region similar to C-terminus of many members of the OmpA family of outer membrane proteins, e.g. NP_458280.1|NC_003198 putative outer membrane protein from Salmonella enterica subsp. enterica serovar Typhi (220); NP_418008.1|NC_000913 putative outer membrane protein from Escherichia coli strain K12 (219 aa), FASTA scores: opt: 296, E(): 2.2e-11, (45.3% identity in 117 aa overlap); NP_231844.1|NC_002505 outer membrane protein OmpA from Vibrio cholerae (321 aa); Q05146|OMPA_BORAV outer membrane protein A precursor from Bordetella avium (194 aa); etc. A signal peptide sequence probably exists at the N-terminus. N-terminal domain is necessary and sufficient for membrane translocation (See Alahari et al., 2007). Contains PS00044 Bacterial regulatory proteins, lysR family signature. Belongs to the OmpA family. Pore-forming activity is pH-dependent.	P9WIU5	No	cell wall and cell processes	ML2126,ML2126c	MMAR_4637		Mb0923				
NC_000962.3	Mycobrowser_v3	CDS	1004501	1005841	.	-	0	Rv0902c	prrB	Sensor part of the two component regulatory system PRRA/PRRB. Thought to be involved in the environmental adaptation, specifically in an early phase of the intracellular growth.	Two component sensor histidine kinase PrrB	Rv0902c, (MTCY31.30c), len: 446 aa. PrrB, two-component sensor histidine kinase (see citations below), transmembrane protein, equivalent to MLCB57_26|NP_302403.1|NC_002677 sensor histidine kinase from Mycobacterium leprae (446 aa); and similar at C-termini to NP_301251.1|NC_002677 putative two-component system sensor kinase from Mycobacterium leprae (519 aa). C-terminus also similar to the C-termini of many sensor-like histidine kinase proteins e.g. P08336|CPXA_ECOLI|ECFB|SSD|EUP|B3911|Z5456|ECS4837 sensor protein from Escherichia coli strain K12 (457 aa), FASTA scores: opt: 364, E(): 1.7e-15, (27.1% identity in 398 aa overlap); CAB89748.1|AL354616 putative two-component histidine kinase from Streptomyces coelicolor (483 aa); CAB82845.1|AJ277081 putative histidine kinase from Amycolatopsis mediterranei (472 aa); etc. Also similar in part to Mycobacterium tuberculosis proteins Rv3764c (475 aa); and Rv0982 (504 aa). Thought to be induced at phagocytosis (see Graham & Clark-Curtiss 1999).	P9WGK7	No	regulatory proteins	ML2124	MMAR_4634	MSMEG_5663	Mb0926c				
NC_000962.3	Mycobrowser_v3	CDS	1006693	1008180	.	-	0	Rv0904c	accD3	This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA [catalytic activity ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA].	Putative acetyl-coenzyme A carboxylase carboxyl transferase (subunit beta) AccD3 (accase beta chain)	Rv0904c, (MTCY31.32c, MT0927), len: 495 aa. Putative accD3, acetyl-CoA carboxylase carboxyl transferase, beta subunit (carboxyltransferase subunit of acetyl-CoA carboxylase), highly similar in part to AAA63045.1|U15184 zinc finger protein from Mycobacterium leprae (201 aa). Also highly similar to others e.g. CAC42827.1|Y17592 putative carboxyltransferase subunit of acetyl-CoA carboxylase from Corynebacterium glutamicum (491 aa); CAB86110.1|AL163003 putative acetyl CoA carboxylase (alpha and beta subunits) from Streptomyces coelicolor (458 aa); Q54776|ACCD_SYNP7 acetyl-coenzyme A carboxylase carboxyl transferase subunit beta from Synechococcus sp. (305 aa); P12217|ACCD_MARPO acetyl-coenzyme A carboxylase carboxyl transferase subunit beta from Marchantia polymorpha (316 aa), FASTA scores: opt: 519, E():1.6e-24, (40.2% identity in 219 aa overlap); etc. Also similar to Rv3280, Rv2502c, etc from Mycobacterium tuberculosis. Belongs to the ACCD/PCCB family.	P9WQH9	No	lipid metabolism	ML2119	MMAR_4626	MSMEG_5642	Mb0928c				
NC_000962.3	Mycobrowser_v3	CDS	1011731	1014124	.	+	0	Rv0908	ctpE	Metal cation-transporting ATPase; possibly catalyzes the transport of an undetermined metal cation with the hydrolysis of ATP [catalytic activity: ATP + H(2)O + undetermined metal cation(in) = ADP + phosphate + undetermined metal cation(out)].	Probable metal cation transporter ATPase P-type CtpE	Rv0908, (MTCY21C12.02), len: 797 aa. Probable ctpE, metal cation-transporting ATPase P-type, transmembrane protein, E1-E2 family, highly similar to many e.g. AB93406.1|AL357524 putative integral membrane ATPase from Streptomyces coelicolor (802 aa); NP_346063.1|NC_003028 cation-transporting ATPase (E1-E2 family) from Streptococcus pneumoniae (778 aa); P37278|ATCL_SYNP7|PACL cation-transporting atpase from Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) (926 aa), FASTA scores: opt: 257, E(): 4.8e-33, (27.7% identity in 905 aa overlap); etc. Contains E1-E2 ATPases phosphorylation site (PS00154). Belongs to the cation transport ATPases family (E1-E2 ATPases).	P9WPT1	No	cell wall and cell processes	ML2115,ML2115c	MMAR_4622	MSMEG_5636	Mb0932				
NC_000962.3	Mycobrowser_v3	CDS	1018727	1019965	.	-	0	Rv0914c	Rv0914c	Thought to be involved in degradative pathways such as fatty acid BETA_OXIDATION.	Possible lipid carrier protein or keto acyl-CoA thiolase	Rv0914c, (MTCY21C12.08c), len: 412 aa. Possible lipid carrier protein or keto acyl-CoA thiolase, highly similar to NP_421905.1|NC_002696 thiolase family protein from Caulobacter crescentus (407 aa); and similar to others e.g. NP_107896.1|NC_002678 3-ketoacyl-CoA thiolase from Mesorhizobium loti (392 aa); NP_385796.1|NC_003047 putative 3-ketoacyl-CoA thiolase protein from Sinorhizobium meliloti (389 aa); NP_275932.1|NC_000916 lipid-transfer protein (sterol or nonspecific) from Methanothermobacter thermautotrophicus (383 aa); AB55378.1|AL117263 possible 3-ketoacyl-CoA thiolase from Leishmania major (441 aa), FASTA scores: opt: 547, E(): 3.1e-26, (31.0% identity in 435 aa overlap); etc. Also similar to Rv2790c, Rv1627c, Rv0244, etc from Mycobacterium tuberculosis. Could belong to the thiolase family.	I6XWJ8	No	lipid metabolism	ML2109	MMAR_4613	MSMEG_5608	Mb0938c				
NC_000962.3	Mycobrowser_v3	CDS	1022087	1023868	.	+	0	Rv0917	betP	High-affinity uptake of glycine betaine. Supposedly responsible for the translocation of the substrate across the membrane.	Possible glycine betaine transport integral membrane protein BetP	Rv0917, (MTCY21C12.11), len: 593 aa. Possible betP, glycine betaine transporter, integral membrane protein, highly similar to many transporters, mainly glycine betaine transporters, e.g. P54582|BETP_CORGL glycine betaine transporter from Corynebacterium glutamicum (Brevibacterium flavum) (595 aa), FASTA scores: opt: 1367, E(): 0, (42.7% identity in 504 aa overlap); T35264 probable BccT family transporter from Streptomyces coelicolor (578 aa); NP_243511.1|NC_002570 glycine betaine transporter from Bacillus halodurans (504 aa); NP_439848.1|NC_000907 high-affinity choline transport protein (betT) from Haemophilus influenzae (669 aa); etc. Seems to belong to the BCCT (TC 2.33) family of transporters.	P9WPR7	No	cell wall and cell processes		MMAR_2913		Mb0941				
NC_000962.3	Mycobrowser_v3	CDS	1030578	1031864	.	-	0	Rv0924c	mntH	H(+)-stimulated, highly selective, divalent cation uptake system. Responsible for the translocation of the divalent metal across the membrane.	Divalent cation-transport integral membrane protein MntH (BRAMP) (MRAMP)	Rv0924c, (MTCY21C12.18c), len: 428 aa. MntH (alternative gene name: Nramp, Mramp), H+-dependent divalent cation-transport integral membrane protein (see citations below), equivalent to O69443|MNTH_MYCBO probable manganese transport protein MNTH (BRAMP) from Mycobacterium bovis (415 aa); and NP_302396.1|NC_002677 probable manganese transport protein from Mycobacterium leprae (426 aa). Also similar (but longer 51 aa in N-terminus) to AAA63075.1|U15184 SMF2 protein from Mycobacterium leprae (377 aa), FASTA scores: opt: 1780, E(): 0, (74.5% identity in 376 aa overlap). Also similar to many orthologues of the eukaryotic Nramp (natural resistance-associated macrophage protein), also known as mntH, e.g. NP_456951.1|NC_003198 manganese transport protein MntH from Salmonella enterica subsp. enterica serovar Typhi (413 aa); etc. Belongs to the NRAMP family.	P9WIZ5	No	cell wall and cell processes	ML2098	MMAR_4584	MSMEG_5589	Mb0948c				
NC_000962.3	Mycobrowser_v3	CDS	1036028	1037002	.	+	0	Rv0929	pstC2	Involved in active transport of inorganic phosphate across the membrane (import); responsible for the translocation of the substrate across the membrane. This is one of the proteins required for binding-protein-mediated phosphate transport.	Phosphate-transport integral membrane ABC transporter PstC2	Rv0929, (MTCY21C12.23), len: 324 aa. PstC2, phosphate-transport integral membrane ABC transporter (see citations below), highly similar to others e.g. NP_302394.1|NC_002677 membrane-bound component of phosphate transport from Mycobacterium leprae (319 aa); CAB88474.1|AL353816 phosphate ABC transport system permease protein from Streptomyces coelicolor (336 aa); NP_290359.1| NC_002655 high-affinity phosphate-specific transport system (cytoplasmic membrane component) from Escherichia coli strain O157:H7 (319 aa); etc. Also similar to Rv935|MTCY08D9.04c|PSTC1 probable transmembrane ABC transporter component of phosphate uptake system from Mycobacterium tuberculosis (338 aa). Contains binding-protein-dependent transport systems inner membrane component signature (PS00402).	P9WG05	No	cell wall and cell processes	ML2094,ML2094c	MMAR_4579		Mb0952				
NC_000962.3	Mycobrowser_v3	CDS	1039936	1041048	.	-	0	Rv0932c	pstS2	Involved in active transport of inorganic phosphate across the membrane (import). This is one of the proteins required for binding-protein-mediated phosphate transport.	Periplasmic phosphate-binding lipoprotein PstS2 (PBP-2) (PstS2)	Rv0932c, (MTCY08D9.07), len: 370 aa. PstS2, phosphate-binding lipoprotein component of inorganic phosphate transport system (see citations below), highly similar to AAF74819.1|AF137360_1|AF137360 periplasmic phosphate permease from Mycobacterium avium (369 aa); Rv0928|MTCY21C12.22|pstS3 phosphate-binding periplasmic lipoprotein from Mycobacterium tuberculosis (370 aa), FASTA scores: opt: 1601, E(): 0, (64.5% identity in 372 aa overlap); and Rv0934|MTCY08D9.05c|pstS1 phosphate-binding periplasmic lipoprotein from Mycobacterium tuberculosis (374 aa) (Mycobacterium tuberculosis seems to have three PstS-like proteins, others being Rv0928 and Rv0934c). Also highly similar to MTCY08D9.05c|P15712|PAB_MYCTU protein antigen B precursor from Mycobacterium tuberculosis (374 aa), FASTA scores: opt: 460, E(): 2.7e-20, (31.2% identity in 375 aa overlap). Contains prokaryotic membrane lipoprotein lipid attachment site (PS00013) at N-terminus so the leader peptide of 22 aa is probably removed. Belongs to family of phosphate receptors for bacterial ABC-type lipoprotein transporters. Appears to be co-transcribed with Rv0931c|pknD|mbk.	P9WGT9	No	cell wall and cell processes	ML0742	MMAR_4576		Mb0956c				
NC_000962.3	Mycobrowser_v3	CDS	1042115	1043239	.	+	0	Rv0934	pstS1	Involved in active transport of inorganic phosphate across the membrane (import). This is one of the proteins required for binding-protein-mediated phosphate transport.	Periplasmic phosphate-binding lipoprotein PstS1 (PBP-1) (PstS1)	Rv0934, (MTCY08D9.05c), len: 374 aa. PstS1 (previously known as phoS1 or phoS), phosphate-binding lipoprotein component of inorganic phosphate transport system (see citations below), highly similar to Rv0932c|MTCY08D9.07|pstS2 phosphate-binding periplasmic lipoprotein from Mycobacterium tuberculosis (370 aa), FASTA scores: opt: 460, E(): 5.9e-19, (31.2% identity in 375 aa overlap); and Rv0928|MTCY21C12.22|pstS3 phosphate-binding periplasmic lipoprotein from Mycobacterium tuberculosis (374 aa), FASTA scores: opt: 435, E():1.1e-17, (30.0% identity in 380 aa overlap) (Mycobacterium tuberculosis seems to have three PstS-like proteins, others being Rv0932c and Rv0928c). Also highly similar to MTCY08D9.05c|P15712|PAB_MYCTU protein antigen B precursor from Mycobacterium tuberculosis (374 aa), FASTA scores: opt: 2459, E(): 0, (100% identity in 374 aa overlap). Contains a prokaryotic membrane lipoprotein lipid attachment site (PS00013) at the N-terminus so the 23 aa leader peptide sequence is probably removed. Belongs to family of phosphate receptors for bacterial ABC-type lipoprotein transporters.	P9WGU1	No	cell wall and cell processes	ML0740,ML0740c			Mb0959				
NC_000962.3	Mycobrowser_v3	CDS	1046136	1048415	.	+	0	Rv0938	ligD	Involved in DNA double-strand break repair, by nonhomologous end joining (NHEJ). Interacts with KU (Rv0937c) [catalytic activity:ATP + {deoxyribonucleotide}(N) + {deoxyribonucleotide}(M) = AMP + diphosphate + {deoxyribonucleotide}(N+M)].	ATP dependent DNA ligase LigD (ATP dependent polydeoxyribonucleotide synthase) (thermostable DNA ligase) (ATP dependent polynucleotide ligase) (sealase) (DNA repair enzyme) (DNA joinase)	Rv0938, (MTCY08D9.01c, MTCY10D7.36c), len: 759 aa. ligD, ATP-dependent DNA ligase, with its C-terminus similar to N-terminal parts of many ATP-dependent DNA ligases e.g. NP_250828.1|NC_002516 probable ATP-dependent DNA ligase from Pseudomonas aeruginosa (840 aa); NP_105436.1|NC_002678 ATP-dependent DNA ligase from Mesorhizobium loti (829 aa); CAB92891.1|AL356932 probable ATP-dependent DNA ligase from Streptomyces coelicolor (326 aa); etc. The N-terminal half shows similarity with hypothetical proteins from Mycobacterium tuberculosis Rv0269c and Rv3730c; and the C-terminal half with the DNA ligases Rv3731 and Rv3062.	P9WNV3	No	information pathways	ML2090,ML2090c	MMAR_4573	MSMEG_5570	Mb0963				
NC_000962.3	Mycobrowser_v3	CDS	1054247	1055008	.	+	0	Rv0945	Rv0945	Function unknown; possibly involved in cellular metabolism.	Probable short-chain type dehydrogenase/reductase	Rv0945, (MTCY10D7.29c), len: 253 aa. Probable short-chain dehydrogenase/reductase, similar to various dehydrogenases/reductases e.g. NP_346338.1|NC_003028 oxidoreductase (short chain dehydrogenase/reductase family) from Streptococcus pneumoniae (253 aa); AAB70845.1|AF019986|PksB from Dictyostelium discoideum (260 aa); AAF86624.1|U87786 clavaldehyde dehydrogenase from Streptomyces clavuligerus (247 aa); P37440|UCPA_ECOLI oxidoreductase from Escherichia coli (285 aa), FASTA scores: opt: 275, E(): 1.1e-12, (33.8% identity in 201 aa overlap); etc. Contains PS00061 Short-chain dehydrogenases/reductases family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	P9WGR7	No	intermediary metabolism and respiration	ML0149	MMAR_4558	MSMEG_5544	Mb0970				
NC_000962.3	Mycobrowser_v3	CDS	1055024	1056685	.	-	0	Rv0946c	pgi	Involved in glycolysis and in gluconeogenesis [catalytic activity: D-glucose 6-phosphate = D-fructose 6-phosphate].	Probable glucose-6-phosphate isomerase Pgi (GPI) (phosphoglucose isomerase) (phosphohexose isomerase) (phi)	Rv0946c, (MTCY10D7.28), len: 553 aa. Probable pgi, glucose-6-phosphate isomerase, equivalent to NP_301236.1|NC_002677 glucose-6-phosphate isomerase from Mycobacterium leprae (554 aa); and P96803|G6PI_MYCSM glucose-6-phosphate isomerase from Mycobacterium smegmatis (442 aa). Also highly similar to others e.g. T36015 glucose-6-phosphate isomerase from Streptomyces coelicolor (551 aa); P11537|G6PI_ECOLI|GPI glucose-6-phosphate isomerase from Escherichia coli strains K12 and O157:H7 (549 aa), FASTA scores: opt: 1779, E(): 0, (51.4% identity in 554 aa overlap); etc. Contains PS00765 Phosphoglucose isomerase signature 1, and PS00174 Phosphoglucose isomerase signature 2. Belongs to the GPI family.	P9WN69	No	intermediary metabolism and respiration	ML0150,ML0150c	MMAR_4557	MSMEG_5541	Mb0971c				
NC_000962.3	Mycobrowser_v3	CDS	1058260	1060575	.	+	0	Rv0949	uvrD1	Involved in nucleotide excision repair. Has a 3'-5' helicase activity in presence of ATP. Preferred substrate being one with both single and double stranded regions of DNA.	Probable ATP-dependent DNA helicase II UvrD1	Rv0949, (MTCY10D7.25c), len: 771 aa. Probable uvrD1, ATP dependent DNA helicase II (see citation below), equivalent to P_301239.1|NC_002677 putative ATP-dependent DNA helicase from Mycobacterium leprae (778 aa). Also highly similar to others e.g. CAB92660.1|AL356832 from Streptomyces coelicolor (831 aa) (N-terminus longer); P56255|PCRA_BACST from Bacillus stearothermophilus (724 aa); Q10213|YAY5_SCHPO from Schizosaccharomyces pombe (Fission yeast) (887 aa), FASTA scores: opt: 927, E(): 0, (33.5% identity in 659 aa overlap); etc. Also similar to several other UvrD-like proteins in Mycobacterium tuberculosis e.g. Rv3201c, Rv3198c, Rv3202c. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the UVRD subfamily of helicases. Note that previously known as uvrD.	P9WMQ1	No	information pathways	ML0153	MMAR_4553	MSMEG_5534	Mb0974				
NC_000962.3	Mycobrowser_v3	CDS	1061964	1063127	.	+	0	Rv0951	sucC	Involved in tricarboxylic acid cycle [catalytic activity: ATP + succinate + CoA = ADP + succinyl-CoA + phosphate].	Probable succinyl-CoA synthetase (beta chain) SucC (SCS-beta)	Rv0951, (MTCY10D7.23c), len: 387 aa. Probable sucC, succinyl-CoA synthetase, beta chain, equivalent to AL035500|MLCL373_3|NP_301241.1|NC_002677 succinyl-CoA synthase [beta] chain from Mycobacterium leprae (393 aa), FASTA score: (86.7% identity in 391 aa overlap). Also highly similar to others e.g. AB92671.1|AL356832 succinyl-CoA synthetase beta chain from Streptomyces coelicolor (394 aa); P25126|SUCC_THEFL succinyl-CoA synthetase beta chain from Thermus aquaticus (378 aa); P07460|SUCC_ECOLI succinyl-CoA synthetase beta chain from Escherichia coli (388 aa), FASTA scores: opt: 933, E(): 0, (41.0% identity in 390 aa overlap); etc.	P9WGC5	No	intermediary metabolism and respiration	ML0155	MMAR_4550	MSMEG_5525	Mb0976				
NC_000962.3	Mycobrowser_v3	CDS	1067561	1068208	.	+	0	Rv0956	purN	Involved in de novo purine biosynthesis (at the third step) [catalytic activity: 10-formyltetrahydrofolate + 5'-phosphoribosylglycinamide = tetrahydrofolate + 5'-phosphoribosyl-N-formylglycinamide].	Probable 5'-phosphoribosylglycinamide formyltransferase PurN (GART) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)	Rv0956, (MTCY10D7.18c), len: 215 aa. Probable purN, 5'-phosphoribosylglycinamide formyltransferase, equivalent to AAF05726.1|AF191543_1|AF191543|PurN phosphoribosylglycinamide formyltransferase from Mycobacterium avium subsp. paratuberculosis (209 aa); and AL035500|MLCL373_7 from Mycobacterium leprae (215 aa), FASTA score: (79.4% identity in 214 aa overlap). Also highly similar to others e.g. BAA89443.1|AB003159 from Corynebacterium ammoniagenes (199 aa); NP_241498.1|NC_002570 from Bacillus halodurans (188 aa); P08179|PUR3_ECOLI|B2500 from Escherichia coli strain K12 (212 aa), FASTA scores: opt: 380, E(): 2.4e-18, (36.6% identity in 183 aa overlap); C-terminus of P16340|PUR2_DROPS trifunctional purine biosynthetic protein adenosine-3 from Drosophila pseudoobscura (Fruit fly) (1364 aa); etc.	P9WHM5	No	intermediary metabolism and respiration	ML0160	MMAR_4543	MSMEG_5516	Mb0981				
NC_000962.3	Mycobrowser_v3	CDS	1068205	1069776	.	+	0	Rv0957	purH	Involved in de novo purine biosynthesis (at the ninth and tenth steps) [catalytic activity 1: 10-formyltetrahydrofolate + 5'-phosphoribosyl-5-amino-4-imidazolecarboxamide = tetrahydrofolate + 5'-phosphoribosyl-5-formamido-4-imidazolecarboxamide] [catalytic activity 2: imp + H2O = 5-formamido-1-(5-phosphoribosyl)imidazole-4-carboxamide].	Probable bifunctional purine biosynthesis protein PurH: phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase) (5'-phosphoribosyl-5-aminoimidazole-4-carboxamide formyltransferase) + inosinemonophosphate cyclohydrolase (imp cyclohydrolase) (inosinicase) (imp synthetase) (ATIC)	Rv0957, (MTCY10D7.17c), len: 523 aa. Probable purH, bifunctional purine biosynthesis protein including 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide formyltransferase and inosine-monophosphate (imp) cyclohydrolase, equivalent to AL035500|MLCL373_8 putative phosphoribosylaminoimidazolecarboxamide formyltransferase from Mycobacterium leprae (527 aa), FASTA score: (88.1% identity in 520 aa overlap); and AF05727.1|AF191543_2|AF191543|PurH from Mycobacterium avium subsp. paratuberculosis (527 aa). Also highly similar to others e.g. CAB92677.1|AL356832 bifunctional purine biosynthesis protein from Streptomyces coelicolor (523 aa); NP_388534.1|NC_000964 phosphoribosylaminoimidazole carboxy formyl formyltransferase + inosine-monophosphate cyclohydrolase from Bacillus subtilis (512 aa); P15639|PUR9_ECOLI phosphoribosylaminoimidazolecarboxamide formyltransferase from Escherichia coli (529 aa), FASTA scores: opt: 1147, E(): 0, (44.8% identity in 533 aa overlap); etc. Belongs to the PurH family.	P9WHM7	No	intermediary metabolism and respiration	ML0161	MMAR_4542	MSMEG_5515	Mb0982				
NC_000962.3	Mycobrowser_v3	CDS	1606386	1607972	.	+	0	Rv1430	PE16	Function unknown	PE family protein PE16	Rv1430, (MTCY493.24c), len: 528 aa. PE16, Member of the Mycobacterium tuberculosis PE family of proteins (see citation below), e.g. Y0D4_MYCTU|Q50594 (55.9% identity in 127 aa overlap). The C-terminus shows similarity to Q49633|LEPB1170_F3_112 hypothetical Mycobacterium leprae protein (391 aa), FASTA scores: opt: 342, E(): 1.2e-13, (29.8% identity in 292 aa overlap). Possible TMhelix aa 500-522.	L7N697	No	PE/PPE		MMAR_2235		Mb1465				
NC_000962.3	Mycobrowser_v3	CDS	1078743	1081055	.	+	0	Rv0969	ctpV	Metal cation-transporting ATPase; possibly catalyzes the transport of an undetermined metal cation with the hydrolysis of ATP [catalytic activity: ATP + H(2)O + undetermined metal cation(in) = ADP + phosphate + undetermined metal cation(out)].	Probable metal cation transporter P-type ATPase CtpV	Rv0969, (MTCY10D7.05c), len: 770 aa. Probable ctpV, metal cation transporter P-type ATPase (transmembrane protein) (see citation below), part of cso operon, highly similar (except in N-terminus) to others e.g. NP_391230.1|NC_000964 similar to heavy metal-transporting ATPase from Bacillus subtilis (803 aa); P37279|ATCS_SYNP7|PACS cation-transporting ATPase from Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) (747 aa), FASTA scores: opt: 1851, E(): 0, (52.1% identity in 664 aa overlap); etc. Equivalent to AAK45246.1 from Mycobacterium tuberculosis strain CDC1551 (792 aa) but shorter 22 aa. Contains PS00154 E1-E2 ATPases phosphorylation site. Belongs to the cation transport ATPases family (E1-E2 ATPases).	P9WPS3	No	cell wall and cell processes		MMAR_1431	MSMEG_5014	Mb0994				
NC_000962.3	Mycobrowser_v3	CDS	1179396	1180577	.	+	0	Rv1057	Rv1057	Function unknown	Conserved hypothetical protein	Rv1057, (MTV017.10), len: 393 aa. Conserved hypothetical protein, some similarity to X84710|MMSAG_1 surface antigen of Methanosarcina mazeii (491 aa), FASTA scores: opt: 363, E():6.2e-15, (31.3% identity in 294 aa overlap). Regulated by MprA (Rv0981) under physiological conditions and environmental stress (SDS and Triton X-100) (See He et al., 2006).	O53405	No	conserved hypotheticals				Mb1086				
NC_000962.3	Mycobrowser_v3	CDS	1083747	1085750	.	-	0	Rv0973c	accA2	This protein carries two functions: biotin carboxyl carrier protein and biotin carboxyltransferase. Involved in the first step of long-chain fatty acid synthesis [catalytic activity: ATP + biotin-carboxyl-carrier protein + CO(2) = ADP + phosphate + carboxybiotin-carboxyl-carrier protein].	Probable acetyl-/propionyl-coenzyme A carboxylase alpha chain (alpha subunit) AccA2: biotin carboxylase + biotin carboxyl carrier protein (BCCP)	Rv0973c, (MTV044.01c, MTCY10D7.01), len: 667 aa. Probable accA2 (alternate gene name: bccA), acetyl-/propionyl-coenzyme A carboxylase (alpha subunit) [includes: biotin carboxylase ; biotin carboxyl carrier protein (BCCP)], highly similar to others e.g. CAB95892.1|AL359988 putative acetyl/propionyl CoA carboxylase alpha subunit from Streptomyces coelicolor (614 aa); NP_250702.1|NC_002516 probable acyl-CoA carboxylase alpha chain from Pseudomonas aeruginosa (655 aa); NP_420971.1|NC_002696 acetyl/propionyl-CoA carboxylase alpha subunit from Caulobacter crescentus ( 654 aa); NP_251581.1|NC_002516 probable biotin carboxylase/biotin carboxyl carrier protein from Pseudomonas aeruginosa (661 aa); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. Rv2501c|P46401|MTCY07A7.07c|BCCA_MYCTU|ACCA1 probable acetyl-/propionyl-coenzyme A carboxylase alpha chain (alpha subunit) (654 aa), FASTA scores, opt: 250, E(): 4e-09, (28.6% identity in 182 aa overlap); and Rv3285|MTCY71.25|ACCA3 (600 aa); Z83018|MTCY349_20 (1127 aa), FASTA scores: opt: 838, E(): 0, (40.2% identity in 500 aa overlap). Contains PS00867 Carbamoyl-phosphate synthase subdomain signature 2 and PS00188 Biotin-requiring enzymes attachment site.	P71538	No	lipid metabolism	ML0166	MMAR_4534	MSMEG_5493					
NC_000962.3	Mycobrowser_v3	CDS	1087348	1088496	.	-	0	Rv0975c	fadE13	Function unknown, but involved in lipid degradation.	Probable acyl-CoA dehydrogenase FadE13	Rv0975c, (MTV044.03c), len: 382 aa. Probable fadE13, acyl-CoA dehydrogenase, highly similar to many e.g. T35427 probable acyl-CoA dehydrogenase from Streptomyces coelicolor (382 aa); M74096|HUMACADL_1 Human long chain acyl-CoA dehydrogenase from Homo sapiens (430 aa), FASTA scores: opt: 819, E(): 0, (37.0% identity in 376 aa overlap); etc. Also similar to others from Mycobacterium tuberculosis e.g. fadE20|Z98209|MTCY154_4 (386 aa), FASTA scores: (40.3% identity in 375 aa overlap). Contains PS00073 Acyl-CoA dehydrogenases signature 2. Belongs to the acyl-CoA dehydrogenases family.	O86319	No	lipid metabolism	ML0164	MMAR_4532	MSMEG_5491	Mb1000c				
NC_000962.3	Mycobrowser_v3	CDS	1090373	1093144	.	+	0	Rv0977	PE_PGRS16	Function unknown	PE-PGRS family protein PE_PGRS16	Rv0977, (MTV044.05), len: 923 aa. PE_PGRS16, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citation below), highly similar to other PGRS-type sequences e.g. AL0091|MTV004_1 from Mycobacterium tuberculosis (1125 aa), FASTA score: (45.4% identity in 959 aa overlap); Z80225|MTCY441_4 from Mycobacterium tuberculosis (778 aa), FASTA score: (51.5% identity in 750 aa overlap); etc.	Q79FU3	No	PE/PPE				Mb1002				
NC_000962.3	Mycobrowser_v3	CDS	1096822	1097508	.	+	0	Rv0981	mprA	Regulator part of a two component regulatory system (MPRAB system)	Mycobacterial persistence regulator MRPA (two component response transcriptional regulatory protein)	Rv0981, (MTV044.09), len: 228 aa. MprA, mycobacterial persistence regulator, a two-component response regulator whose expression is required for entrance into and maintenance of persistent infection (see citation below), equivalent to NP_301250.1|NC_002677 putative two-component response regulator from Mycobacterium leprae (228 aa); and highly similar to others from Mycobacterium leprae. Also highly similar to others e.g. AAG36759.1|AF119221_1|AF119221 response regulator from Corynebacterium glutamicum (232 aa); CAB88489.1|AL353816 putative two-component system response regulator from Streptomyces coelicolor (248 aa); BJY09666_1 two-component response regulator (ragA, ragB and rpoH3) from B.japonicum (226 aa), FASTA score: (43.8% identity in 224 aa overlap); BSAJ2571_44 two-component response regulator from Bacillus subtilis (228 aa), FASTA score: (46.4% identity in 224 aa overlap); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. Rv1033c (257 aa); Rv0903c (236 aa), FASTA score: (50.7 identity in 225 aa overlap); etc. Contains PS00217 Sugar transport proteins signature 2. Start changed since first submission (-2 aa). MprAB is involved in the regulation of genes in response to environmental stress (See He et al., 2006).	P9WGM9	No	regulatory proteins	ML0174	MMAR_4529	MSMEG_5488	Mb1007				
NC_000962.3	Mycobrowser_v3	CDS	1097508	1099022	.	+	0	Rv0982	mprB	Sensor part of a two component regulatory system (MPRAB system)	Two component sensor kinase MprB	Rv0982, (MTV044.10), len: 504 aa. MprB, two component sensor kinase, probable transmembrane protein (see citation below), equivalent to AL035500|MLCL373_16|NP_301251.1|NC_002677 putative two-component system sensor kinase from Mycobacterium leprae (519 aa), FASTA score: (81.0% identity in 521 aa overlap). Also highly similar to others (especially in C-terminal part) e.g. AAG36760.1|AF119221_2|AF119221 sensor kinase from Corynebacterium glutamicum (455 aa); CAB89748.1|AL354616 putative two-component histidine kinase from Streptomyces coelicolor (481 aa); X58793|SLCUTRS_2 sensor kinase from S.lividans (414 aa), FASTA scores: opt: 451, E(): 4.2e-21, (36.0% identity in 303 aa overlap); P30847|BAES_ECOLI sensor protein from Escherichia coli (467 aa), FASTA scores: opt: 412, E(): 1.3e-18, (30.4% identity in 336 aa overlap); etc. Also similar in C-terminal region to C-terminus of Rv0902c|Z73101|MTCY31_33 from Mycobacterium tuberculosis (446 aa), FASTA scores: opt: 423, E(): 2.6e-19, (28.4 identity in 462 aa overlap). MprAB is involved in the regulation of genes in response to environmental stress (See He et al., 2006).	P9WGL1	No	regulatory proteins	ML0175	MMAR_4528	MSMEG_5487	Mb1008				
NC_000962.3	Mycobrowser_v3	CDS	1101025	1101480	.	-	0	Rv0985c	mscL	Ion channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell.	Possible large-conductance ion mechanosensitive channel MscL	Rv0985c, (MTV044.13c), len: 151 aa. Possible mscL, large conductance mechanosensitive ion channel (integral membrane protein) (see citations below, equivalent to AL035500|MLCL373_19|NP_301254.1|NC_002677 putative mechanosensitive channel protein from Mycobacterium leprae (154 aa), FASTA score: (71.0% identity in 155 aa overlap). Also highly similar to others e.g. NP_268999.1|NC_002737 putative large conductance mechanosensitive channel from Streptococcus pyogenes (120 aa); CAB90974.1|AL355832 putative mechanosensitive channel from Streptomyces coelicolor (156 aa); Q9X722|MSCL_CLOHI large-conductance mechanosensitive channel from Clostridium histolyticum (133 aa); Z83337|BSZ83337_6 large conductance mechanosensitive channel from Bacillus subtilis (130 aa), FASTA scores: opt: 248, E(): 8.4e-10, (39.0% identity in 136 aa overlap); U08371|ECU08371_1 large conductance mechanosensitive channel from Escherichia coli strain K-12 (136 aa), FASTA score: (36.6% identity in 134 aa overlap); etc. Belongs to the MscL family.	P9WJN5	No	cell wall and cell processes	ML0178,ML0178c	MMAR_4525	MSMEG_5482	Mb1011c				
NC_000962.3	Mycobrowser_v3	CDS	1101803	1102549	.	+	0	Rv0986	Rv0986	Thought to be involved in active transport of adhesion component across the membrane: involved in attachment and virulence. Responsible for energy coupling to the transport system.	Probable adhesion component transport ATP-binding protein ABC transporter	Rv0986, (MTV044.14), len: 248 aa. Probable ATP-binding protein ABC transporter supposedly involved in transport of adhesion component (see citation below), highly similar to many ATP-binding proteins e.g. AE0010|AE001033_8 ABC transporter ATP-binding protein from Archaeoglobus fulgidus (228 aa), FASTA scores: opt: 669, E(): 0, (45.7% identity in 219 aa overlap); CAB81857.1|AL161691 putative ABC-transporter ATP-binding protein from Streptomyces coelicolor (246 aa); X84019|ZMDNAGRP_4 glutamate uptake regulatory protein (grp) from Z.mobilis (232 aa), FASTA score: (44.4% identity in 225 aa overlap); Z99111|BSUB0008_108 from Bacillus subtilis (230 aa), FASTA score: (38.7% identity in 222 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters). Believed to have been acquired by horizontal gene transfer (See Rosas-Magallanes et el., 2006; Becq et al., 2007).	P9WQK1	No	cell wall and cell processes				Mb1012				
NC_000962.3	Mycobrowser_v3	CDS	1106405	1107382	.	-	0	Rv0989c	grcC2	Possible supplier of polyprenyl diphosphate.	Probable polyprenyl-diphosphate synthase GrcC2 (polyprenyl pyrophosphate synthetase)	Rv0989c, (MTCI237.03c), len: 325 aa. Probable grcC2, polyprenyl diphosphate synthetase, highly similar to NP_302483.1|NC_002677 polyprenyl diphosphate synthase component from Mycobacterium leprae (330 aa). Also similar to others (generally hepta or hexaprenyl e.g. NP_471378.1|NC_003212 protein similar to heptaprenyl diphosphate synthase component II (menaquinone biosynthesis) from Listeria innocua (321 aa); NP_371994.1|NC_002758 heptaprenyl diphosphate syntase component II from Staphylococcus aureus subsp. aureus Mu50 (319 aa); P55785|HEP2_BACST heptaprenyl diphosphate synthase component from Bacillus subtilis (323 aa), FASTA scores: opt: 496, E(): 1.4e-24, (31.4% identity in 306 aa overlap); etc. Also highly similar to Mycobacterium tuberculosis proteins e.g. Rv0562|grcC1|NP_215076.1|MTCY25D10.41 probable polyprenyl-diphosphate synthase (335 aa); Rv3383, Rv3398c, Rv2173, etc. Seems to belong to the FPP/GGPP synthetases family. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O05572	No	intermediary metabolism and respiration				Mb1016c				
NC_000962.3	Mycobrowser_v3	CDS	1109272	1110192	.	+	0	Rv0993	galU	May play a role in stationary phase survival [catalytic activity: UTP + alpha-D-glucose 1-phosphate = diphosphate + UDP-glucose].	UTP--glucose-1-phosphate uridylyltransferase GalU (UDP-glucose pyrophosphorylase) (UDPGP) (alpha-D-glucosyl-1-phosphate uridylyltransferase) (uridine diphosphoglucose pyrophosphorylase)	Rv0993, (MTCI237.07), len: 306 aa. GalU, UTP--glucose-1-phosphate uridylyltransferase, equivalent to AL035500|MLCL373_22 putative UTP-glucose-1-phosphate uridylyltransferase from Mycobacterium leprae (306 aa), FASTA score: (89.7% identity in 302 aa overlap). Also highly similar to others e.g. AB59678.1|AL132674 UTP-glucose-1-phosphate uridylyltransferase from Streptomyces coelicolor (303 aa); NP_244519.1|NC_002570 UTP-glucose-1-phosphate uridylyltransferase from Bacillus halodurans (297 aa); P25520|GALU_ECOLI|B1236|Z2012|ECS17 UTP--glucose-1-phosphate uridylyltransferase from Escherichia coli strains K12 and O157:H7 (301 aa), FASTA scores: opt: 624, E(): 2.4e-33, (38.8% identity in 299 aa overlap); etc. Belongs to the prokaryotic UDPGP family.	O05576	No	intermediary metabolism and respiration	ML0182	MMAR_4521	MSMEG_5471	Mb1020				
NC_000962.3	Mycobrowser_v3	CDS	1125444	1127003	.	-	0	Rv1007c	metS	It is probably essential for cell survival, being required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation [catalytic activity: ATP + L-methionine + tRNA(met) = AMP + diphosphate + L-methionyl-tRNA(met)]	Methionyl-tRNA synthetase MetS (MetRS) (methionine--tRNA ligase)	Rv1007c, (MTCI237.24), len: 519 aa. metS (MetG), methionyl-tRNA synthetase, similar to many e.g. SYM_BACSU|P37465 methionyl-tRNA synthetase from Bacillus subtilus (664 aa), FASTA scores: opt: 1506, E(): 0, (44.9% identity in 492 aa overlap); similar to other Mycobacterium tuberculosis tRNA synthases e.g. Rv2448c, Rv1536, Rv0041. Contains PS00178 Aminoacyl-transfer RNA synthetases class-I signature. Belongs to class-I aminoacyl-tRNA synthetase family. Strong, to cysteinyl-tRNA synthetase.	P9WFU5	No	information pathways	ML0238,ML0238c	MMAR_4481	MSMEG_5441	Mb1034c				
NC_000962.3	Mycobrowser_v3	CDS	1114748	1115749	.	+	0	Rv0998	Rv0998	Unknown	Conserved hypothetical protein	Rv0998, (MTCI237.12), len: 333 aa. Conserved hypothetical protein, with cyclic nucleotide-binding domain in N-terminal part and GNAT (Gcn5-related N-acetyltransferase) domain in C-terminal part. See Vetting et al. 2005. Possibly cyclic nucleotide-dependent protein kinase, highly similar to NP_301261.1|NC_002677 conserved hypothetical protein from Mycobacterium leprae (353 aa); and AL035500|MLCL373.38|T45457 hypothetical protein from Mycobacterium leprae (143 aa), FASTA score: (61.5% identity in 143 aa overlap). Also similar to many hypothetical proteins and cyclic-NMP-dependent protein kinases (generally at C-terminus) e.g. N-terminus of SC9B10.09|T35878 hypothetical protein from Streptomyces coelicolor (1039 aa); P05987|KAPR_DICDI camp-dependent protein kinase regulatory chain from Dictyostelium discoideum (327 aa), FASTA scores: opt: 177, E(): 0.00036, (32.0% identity in 122 aa overlap); NP_104403.1|NC_002678 hypothetical protein (contains similarity to cAMP-dependent protein kinase regulatory subunit) from Mesorhizobium loti (151 aa); etc. Contains PS00889 Cyclic nucleotide-binding domain signature 2. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O05581	No	conserved hypotheticals	ML0187	MMAR_4496	MSMEG_5458	Mb1025				
NC_000962.3	Mycobrowser_v3	CDS	1115767	1116525	.	+	0	Rv0999	Rv0999	Unknown	Unknown protein	Rv0999, (MTCI237.13), len: 252 aa. Unknown protein. Predicted to be an outer membrane protein (See Song et al., 2008).	O05582	No	conserved hypotheticals	ML0189	MMAR_4494	MSMEG_5452	Mb1026				
NC_000962.3	Mycobrowser_v3	CDS	1131625	1133259	.	+	0	Rv1013	pks16	Potentially involved in some intermediate steps for the synthesis of a polyketide molecule which may be involved in secondary metabolism.	Putative polyketide synthase Pks16	Rv1013, (MTCI237.30-MTCY10G2.36c), len: 544 aa. Putative pks16, polyketide synthase, similar to many e.g. N-terminus of Q50857|U24657 saframycin MX1 synthetase B (1770 aa), FASTA scores: opt: 526, E(): 1.4e-25, (29.3% identity in 542 aa overlap); etc. Contains PS00455 Putative AMP-binding domain signature. Belongs to the ATP-dependent AMP-binding enzyme family.	O05598	No	lipid metabolism	ML0243	MMAR_4476	MSMEG_5435	Mb1041				
NC_000962.3	Mycobrowser_v3	CDS	1134785	1135465	.	-	0	Rv1016c	lpqT	Unknown	Probable conserved lipoprotein LpqT	Rv1016c, (MTCY10G2.33), len: 226 aa. Probable lpqT, conserved lipoprotein. Similar to several Mycobacterium tuberculosis hypothetical proteins e.g. Rv0040c|Y0H3_MYCTU|P71697 Proline rich 28 kDA antigen (310 aa), FASTA scores: opt: 329, E(): 2e-17, (32.3% identity in 229 aa overlap); Rv0583c. Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WK59	No	cell wall and cell processes	ML0246,ML0246c	MMAR_4470	MSMEG_5429	Mb1044c				
NC_000962.3	Mycobrowser_v3	CDS	1146561	1147028	.	+	0	Rv1025	Rv1025	Function unknown	Conserved protein	Rv1025, (MTCY10G2.24c), len: 155 aa. Conserved protein, similar to hypothetical protein AE001768|AE001768_4 Thermotoga maritima (170 aa) FASTA scores: opt: 254, E(): 9.5e-10, (35.7% identity in 143 aa overlap).	P96375	No	conserved hypotheticals	ML0257	MMAR_4460		Mb1053				
NC_000962.3	Mycobrowser_v3	CDS	1147019	1147978	.	+	0	Rv1026	Rv1026	Unknown. Could be involved in an adaptive process that allows bacteria to respond to amino acid starvation.	Conserved protein	Rv1026, (MTCY10G2.23c), len: 319 aa. Conserved protein. Similar to GPPA_ECOLI|P25552 guanosine-5'-triphosphate,3'-diphosphate pyrophoshatase from Escherichia coli (494 aa), FASTA scores: opt: 281, E(): 3.2e-11, (30.6% identity in 291 aa overlap). Equivalent to AL023514|MLCB4.02 hypothetical protein from Mycobacterium leprae (317 aa) (77.9% identity in 321 aa overlap).	P96374	No	virulence, detoxification, adaptation	ML0258	MMAR_4459	MSMEG_5413	Mb1054				
NC_000962.3	Mycobrowser_v3	CDS	1152012	1153727	.	+	0	Rv1029	kdpA	One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions [catalytic activity: ATP + H(2)O + K(+)(out) = ADP + phosphate + K(+)(in)].	Probable potassium-transporting ATPase a chain KdpA (potassium-translocating ATPase a chain) (ATP phosphohydrolase [potassium-transporting] a chain) (potassium binding and translocating subunit A)	Rv1029, (MTCY10G2.20c), len: 571 aa. Probable kdpA, potassium-transporting ATPase a chain (transmembrane protein), similar to others e.g. ATKA_ECOLI|P03959|KDPA|B0698 potassium-transporting ATPase A chain from Escherichia coli strain K12 (557 aa), FASTA scores: opt: 1763, E(): 0, (50.4% identity in 569 aa overlap); etc. Belongs to the KdpA family.	P9WKF3	No	cell wall and cell processes		MMAR_0631	MSMEG_5392	Mb1058				
NC_000962.3	Mycobrowser_v3	CDS	1153724	1155853	.	+	0	Rv1030	kdpB	One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions [catalytic activity:ATP + H(2)O + K(+)(out) = ADP + phosphate + K(+)(in)].	Probable potassium-transporting P-type ATPase B chain KdpB (potassium-translocating ATPase B chain) (ATP phosphohydrolase [potassium-transporting] B chain) (potassium binding and translocating subunit B)	Rv1030, (MTCY10G2.19c), len: 709 aa. Probable kdpB, potassium-transporting P-type ATPase B chain (transmembrane protein), similar to others e.g. ATKB_ECOLI|P03960 potassium-transporting ATPase B chain from Escherichia coli strain K12 (682 aa), FASTA scores: opt: 1481, E(): 0, (63.4% identity in 686 aa overlap); etc. Very similar to AL078610|SCH35.47 H+/K+-exchanging ATPase chain B from Streptomyces coelicolor (707 aa), FASTA scores: opt: 2731, E(): 0, (71.6% identity in 676 aa overlap). Contains PS00154 E1-E2 ATPases phosphorylation site.	P9WPU3	No	cell wall and cell processes		MMAR_0632	MSMEG_5393	Mb1059				
NC_000962.3	Mycobrowser_v3	CDS	1157963	1158736	.	-	0	Rv1033c	trcR	Sensor part of the two component regulatory system TRCS/TRCR. Involved in transcriptional autoactivation: TRCR activates its own expression by interacting with the at-rich sequence of the TRCR promoter.	Two component transcriptional regulator TrcR	Rv1033c, (MTCY10G2.16), len: 257 aa. TrcR, two-component regulatory protein (see citations below), similar to Q50825 two component response regulator from Mycobacterium tuberculosis (234 aa), FASTA scores: opt: 628, E(): 0, (46.0% identity in 226 aa overlap). Note that in vitro autophosphorylation of TrcS requires the presence of Mn2+or Ca2+as a divalent cation cofactor and subsequent transphosphorylation of TrcR is evident in the presence of TrcS-phosphate and Ca2+.	L7N689	No	regulatory proteins	ML0261,ML0261c		MSMEG_2916	Mb1062c				
NC_000962.3	Mycobrowser_v3	CDS	1176011	1176286	.	-	0	Rv1053c	Rv1053c	Unknown	Hypothetical protein	Rv1053c, (MTV017.06c), len: 91 aa. Hypothetical unknown protein. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O53401	No	conserved hypotheticals				Mb1082c				
NC_000962.3	Mycobrowser_v3	CDS	1176928	1177242	.	+	0	Rv1054	Rv1054	Use for sequence integration. Integrase is necessary for integration of a phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome.	Probable integrase (fragment)	Rv1054, (MTV017.07), len: 104 aa. Probable integrase (fragment), similar to Rv2309c|MTCY3G12_25|Z79702 hypothetical protein (shows similarity to integrases) from Mycobacterium tuberculosis (151 aa), FASTA scores: opt: 273, E(): 8.8e-13, (64.7% identity in 68 aa overlap); and to L39071|MSGINT_1 integrase from Mycobacterium paratuberculosis (191 aa), FASTA scores: opt: 105, E(): 0.9, (31.8% identity in 85 aaoverlap). This ORF continues in another frame as Rv1055|MTV017.08 but no error can be found to account for frameshift. Length extended since first submission (+36 aa). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O53402	No	insertion seqs and phages				Mb1083				
NC_000962.3	Mycobrowser_v3	CDS	1185741	1186823	.	-	0	Rv1063c	Rv1063c	Function unknown	Conserved hypothetical protein	Rv1063c, (MTV017.16c), len: 360 aa. Conserved hypothetical protein, similar to P37053|YCHK_ECOLI hypothetical protein from Escherichia coli (314 aa), FASTA scores: opt: 487, E(): 7.2e-23, (32.7% identity in 321 aa overlap). Also partially similar to Rv3239c|MTCY20B11.14c. Belongs to the UPF0028 (SWS) family.	P9WIY9	No	conserved hypotheticals		MMAR_4403	MSMEG_5284	Mb1092c				
NC_000962.3	Mycobrowser_v3	CDS	1188421	1190424	.	-	0	Rv1067c	PE_PGRS19	Function unknown	PE-PGRS family protein PE_PGRS19	Rv1067c, (MTV017.20c), len: 667 aa. PE_PGRS19, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see Brennan & Delogu 2002). Similar to Rv3388|MTV004.46 M. tuberculosis (731 aa), FASTA scores: opt: 2227, E(): 0, (55.6% identity in 710 aa overlap). Contains PS00583 pfkB family of carbohydrate kinases signature 1, probably fortuitous. Predicted to be an outer membrane protein (See Song et al., 2008).	Q79FT3	No	PE/PPE		MMAR_2097,MMAR_4735		Mb1096c				
NC_000962.3	Mycobrowser_v3	CDS	1195055	1196092	.	-	0	Rv1071c	echA9	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Possible enoyl-CoA hydratase EchA9 (enoyl hydrase) (unsaturated acyl-CoA hydratase) (crotonase)	Rv1071c, (MTV017.24c), len: 345 aa. Possible echA9, enoyl-CoA hydratase, equivalent to Y13803|B1306.06c putative enoyl-CoA hydratase/isomerase from Mycobacterium leprae (345 aa), FASTA scores: opt: 1799, E(): 0, (77.7% identity in 345 aa overlap). Also similar to many eukaryotic and prokaryotic enoyl-CoA hydratases e.g. NP_437984.1|NC_003078 putative enoyl-CoA hydratase protein from Sinorhizobium meliloti (356 aa); NP_420165.1|NC_002696 enoyl-CoA hydratase/isomerase family protein from Caulobacter crescentus (350 aa); Q19278 protein similar to enoyl-CoA hydratases from Caenorhabditis elegans (386), FASTA scores: opt: 787, E(): 0, (38.5% identity in 348 aa overlap); etc.	O53419	No	lipid metabolism	ML2401	MMAR_4395	MSMEG_5276	Mb1100c				
NC_000962.3	Mycobrowser_v3	CDS	1210595	1211383	.	+	0	Rv1086	Rv1086	Catalyzes the first committed step in the synthesis of decaprenyl diphosphate, a molecule which has a central role in the biosynthesis of most features of the mycobacterial cell wall. Adds one isoprene unit to omega,E-geranyl diphosphate. The product, omega,E, Z-farnesyl diphosphate, is the putative substrate of Rv2361c product [catalytic activity: geranyl diphosphate + isopentenyl diphosphate = diphosphate + trans,trans-farnesyl diphosphate].	Short (C15) chain Z-isoprenyl diphosphate synthase (Z-FPP synthase) (Z-farnesyl diphosphate synthase) (Z-FPP synthetase) (Z-farnesyl diphosphate synthetase) (geranyltranstransferase) (farnesyl pyrophosphate synthetase)	Rv1086, (MTV017.39), len: 262 aa. Short (C15) chain Z-isoprenyl diphosphate synthase (see citations below), equivalent to NP_302598.1|NC_002677 possible undecaprenyl pyrophosphate synthetase from Mycobacterium leprae (262 aa), similar to many hypothetical proteins and several potential members of the upp synthase family e.g. NP_296167.1|NC_001263 undecaprenyl diphosphate synthase from Deinococcus radiodurans (339 aa); P20182|YT14_STRFR Hypothetical protein from Streptomyces fradiae (259 aa), FASTA scores: opt: 840, E(): 0, (51.0% identity in 259 aa overlap); and P38118|YARF_CORGL Hypothetical protein from Corynebacterium glutamicicum (234 aa), FASTA scores: opt: 729, E(): 0, (56.0% identity in 209 aa overlap); etc. Also similar to Rv2361c|MTCY27.19 (296 aa) (35.6% identity in 233 aa overlap). Contains PS01066 Uncharacterized protein family UPF0015 signature. Seems to belong to the UPP synthetase family.	P9WFF5	No	cell wall and cell processes	ML2467	MMAR_4380	MSMEG_5256	Mb1115				
NC_000962.3	Mycobrowser_v3	CDS	1197231	1198082	.	+	0	Rv1073	Rv1073	Function unknown	Conserved hypothetical protein	Rv1073, (MTV017.26), len: 283 aa. Conserved hypothetical protein, similar to several hypothetical mycobacterial proteins e.g. Rv1482c|Z79701|MTCY277.03 Mycobacterium tuberculosis (339 aa), FASTA scores: opt: 810, E(): 0, (47.4% identity in 272 aa overlap); Rv3555c|Z92774|MTCY6G11_2 Mycobacterium tuberculosis (289 aa), FASTA scores: opt: 704, E(): 0, (44.4% identity in 259 aa overlap); and Rv3517, etc., and GIR10|AF002133_10 Mycobacterium avium strain GIR10 (346 aa), FASTA scores: opt: 802, E(): 0, (48.1% identity in 270 aa overlap).	O53421	No	conserved hypotheticals				Mb1102				
NC_000962.3	Mycobrowser_v3	CDS	1198156	1199373	.	-	0	Rv1074c	fadA3	Function unknown, but supposedly involved in lipid degradation (beta oxidation).	Probable beta-ketoacyl CoA thiolase FadA3	Rv1074c, (MTV017.27c), len: 405 aa. Probable fadA3, beta-ketoacyl CoA thiolase, highly similar to many involved in beta-oxidation e.g. CAB89028.1|AL353870 beta-ketoadipyl-CoA thiolase from Streptomyces coelicolor (395 aa); P77525|PAAJ_ECOLI probable beta-ketoadipyl CoA thiolase from Escherichia coli (401 aa), FASTA scores: opt: 1034, E(): 5.4e-56, (43.5% identity in 416 aa overlap) and X97452 acetyl-CoA acetyltransferase (thiolase) from Escherichia coli (401 aa), FASTA scores: opt: 1043, E(): 0, (43.4% identity in 415 aa overlap); Q43935|CATF_ACICA beta-ketoadipyl CoA thiolase from Acinetobacter calcoaceticus (401 aa), FASTA scores: opt: 992, E(): 0, (41.5% identity in 415 aa overlap); etc. Contains PS00737 Thiolases signature 2, and PS00445 FGGY family of carbohydrate kinases signature 2, although this is probably fortuitous. Belongs to the thiolase family.	O53422	No	lipid metabolism	ML2399	MMAR_4393	MSMEG_5273	Mb1103c				
NC_000962.3	Mycobrowser_v3	CDS	1201717	1203111	.	+	0	Rv1077	cbs	Thought to be involved in homocysteine transulfuration [catalytic activity: L-serine + L-homocysteine = cystathionine + H2O]	Probable cystathionine beta-synthase Cbs (serine sulfhydrase) (beta-thionase) (hemoprotein H-450)	Rv1077, (MTV017.30), len: 464 aa. Probable cbs (previously cysM2), cystathionine beta-synthase, similar throughout its length to many eukaryotic cystathionine beta-synthases e.g. P32232|CBS_RAT cystathionine beta-synthase (560 aa), FASTA scores: opt: 951, E(): 0, (40.2% identity in 450 aa overlap); also similar in N-terminal domain (aa 1 - 330) to Rv2334|MTCY98.03 CysK Mycobacterium tuberculosis (310 aa), FASTA scores: opt: 855, E(): 0, (46.8% identity in 314 overlap); and other cysteine synthase proteins e.g. Rv1336, Rv0848, etc. Contains PS00217 Sugar transport proteins signature 2 probably spurious. Belongs to the cysteine synthase/cystathionine beta-synthase family.	P9WP51	No	intermediary metabolism and respiration	ML2396,ML2396c	MMAR_4390	MSMEG_5270	Mb1106				
NC_000962.3	Mycobrowser_v3	CDS	1206520	1207386	.	+	0	Rv1082	mca	Mycothiol-dependent detoxification enzyme, involved in mycothiol biosynthesis.	Mycothiol conjugate amidase Mca (mycothiol S-conjugate amidase)	Rv1082, (MTV017.35), len: 288 aa. Mca, mycothiol conjugate amidase (see citation below), equivalent to NP_302547.1|NC_002677 conserved hypothetical protein from Mycobacterium leprae (290 aa), FASTA scores: opt: 1737, E(): 0, (86.4% identity in 287 aa overlap); and similar to Q54358|X79146 lmbE protein from Streptomyces lincolnensis (270 aa). Also similar to Rv1170|MTV005.06|MSHB GlcNAc-Ins deacetylase from Mycobacterium tuberculosis (303 aa), FASTA scores: opt: 411, E(): 9.4e-20, (35.8% identity in 299 aa overlap).	P9WJN1	No	virulence, detoxification, adaptation	ML2391,ML2391c	MMAR_4385	MSMEG_5261	Mb1111				
NC_000962.3	Mycobrowser_v3	CDS	1221959	1222786	.	+	0	Rv1094	desA2	Thought to catalyze the principal conversion of saturated fatty acids to unsaturated fatty acids. Thought to convert stearoyl-ACP to oleoyl-ACP by introduction of a cis double bond between carbons delta-9 and delta-10 of the acyl chain [catalytic activity: stearoyl-[acyl-carrier protein] + AH2 + O2 = oleoyl-[acyl-carrier protein] + a + 2 H2O].	Possible acyl-[acyl-carrier protein] desaturase DesA2 (acyl-[ACP] desaturase) (stearoyl-ACP desaturase)	Rv1094, (MTV017.47), len: 275 aa. Possible desA2, acyl-[acyl-carrier protein] desaturase (stearoyl-ACP desaturase), equivalent to AL049491|MLCB1222_15 from Mycobacterium leprae (275 aa), FASTA score: (78.1% identity in 274 aa overlap). Also weakly similar to plant stearoyl-acyl carrier protein desaturases, and very similar to U49839|MTV043.16C|Rv0824c enzyme desA1 from Mycobacterium tuberculosis (338 aa), FASTA scores: opt: 525, E(): 8.5e-30, (32.2% identity in 270 aa overlap); and to U15182|MLU15182_32 acyl-carrier protein desaturase precursor from Mycobacterium leprae (338 aa), FASTA scores: opt: 506, E(): 1.9e-28, (34.1% identity in 261 aa overlap).	P9WNZ5	No	lipid metabolism	ML1952,ML1952c	MMAR_4374	MSMEG_5248	Mb1124				
NC_000962.3	Mycobrowser_v3	CDS	1225263	1226144	.	-	0	Rv1097c	Rv1097c	Unknown	Probable membrane glycine and proline rich protein	Rv1097c, (MTV017.50c), len: 293 aa. Probable membrane Gly-, Pro-rich protein, similar to Mycobacterium tuberculosis Rv2507|MTCY07A7. 13|Z95556 (273 aa), FASTA scores: opt: 219, E(): 0.023, (30.5% identity in 266 aa overlap); and Rv2507. Contains potential membrane spanning region (aa ~68-92).	O53445	No	cell wall and cell processes		MMAR_4369		Mb1127c				
NC_000962.3	Mycobrowser_v3	CDS	1247127	1248077	.	+	0	Rv1124	ephC	Thought to be involved in detoxification reactions following oxidative damage to lipids [catalytic activity: an epoxide + H(2)O = a glycol].	Probable epoxide hydrolase EphC (epoxide hydratase)	Rv1124, (MTCY22G8.13), len: 316 aa. Probable ephC, epoxide hydrolase (see citation below), similar to Q42566 epoxide hydrolase from Arabidopsis thaliana (321 aa), FASTA scores: opt: 298, E(): 8.2e-13, (27.6% identity in 333 aa overlap). Similar to other M. tuberculosis epoxide hydrolases and non-heme bromoperoxidases e.g. Rv1938, Rv3617, Rv3670, Rv3473c, etc.	O06576	No	virulence, detoxification, adaptation	ML0951	MMAR_4334	MSMEG_1998	Mb1155				
NC_000962.3	Mycobrowser_v3	CDS	1226141	1227565	.	-	0	Rv1098c	fum	Involved in the tricarboxylic acid cycle. Catalyzes the reversible hydration of fumarate to L-malate [catalytic activity: (S)-malate = fumarate + H2O]	Probable fumarase Fum (fumarate hydratase)	Rv1098c, (MTV017.51c), len: 474 aa. Probable fum, fumarase. Equivalent to AL049491|MLCB1222_11 Mycobacterium leprae (474 aa) (89.5 % identity in 467 aa overlap). Similar to many e.g. P14408|FUMH_RAT fumarate hydratase, mitochondrial precursor from Rattus norvegicus (507 aa), FASTA scores: opt: 1427, E(): 0, (52.3% identity in 461 aa overlap); and P05042|FUMC_ECOLI Fumarate hydratase class II from Escherichia coli (467 aa), FASTA scores: opt: 1355, E(): 0, (50.2% identity in 444 aa overlap). Contains PS00163 Fumarate lyases signature.	P9WN93	No	intermediary metabolism and respiration	ML1947	MMAR_4368	MSMEG_5240	Mb1128c				
NC_000962.3	Mycobrowser_v3	CDS	1232844	1233956	.	-	0	Rv1106c	Rv1106c	Oxidizes 3-beta-hydroxysterols using NAD+ as cofactor	3-beta-hydroxysteroid dehydrogenase	Rv1106c, (MTV017.59c), len: 370 aa. 3-beta-hydroxysteroid dehydrogenase (see Yang et al., 2007). Equivalent to AL049491|MLCB1222_7 Mycobacterium leprae (376 aa) (75.5% identity in 375 aa overlap). Highly similar to Q03704 NAD(P)-dependent cholesterol dehydrogenase from Nocardia sp. (364 aa), FASTA scores: opt: 1789, E(): 0, (74.5% identity in 361 aa overlap). Also similar to U32426|MCU32426_1 3-beta-hydroxy-Delta5-steroid dehydrogenase from Molluscum contagiosum virus (354 aa), FASTA scores: opt: 432, E(): 1.7e-22, (34.6% identity in 347 aa overlap). Also similar to series of Mycobacterium tuberculosis hypothetical proteins described as sugar epimerases or dehydratases e.g. Rv3634c, Rv3784, Rv3464, etc. The transcription of this CDS seems to be activated specifically in host granulomas (see Ramakrishnan et al., 2000).	P9WQP7	No	intermediary metabolism and respiration	ML1942	MMAR_4359	MSMEG_5228	Mb1136c				
NC_000962.3	Mycobrowser_v3	CDS	1357293	1357625	.	-	0	Rv1214c	PE14	Function unknown	PE family protein PE14	Rv1214c, (MTCI364.26c), len: 110 aa. PE14, Member of Mycobacterium tuberculosis PE family (see citation below), appears to be frameshifted but sequence appears to be correct. The 5'-end is atypical as first 9 aa appear to be missing.	L7N6A7	No	PE/PPE		MMAR_0625		Mb1246c				
NC_000962.3	Mycobrowser_v3	CDS	1236185	1237192	.	+	0	Rv1110	lytB2	Unknown. In other organisms, LYTB product is involved in penicillin tolerance and control of the stringent response.	Probable LYTB-related protein LytB2	Rv1110, (MTV017.63), len: 335 aa. Probable lytB2, LytB-related protein, equivalent to AL049491|MLCB1222_3 from Mycobacterium leprae (335 aa), FASTA score: (82.9% identity in 333 aa overlap). Also similar to LytB proteins from many bacteria (appears to have N-terminal extension) e.g. P22565|LYTB_ECOLI|B0029|Z0034|ECS0032 LYTB protein from Escherichia coli strains K12 and O157:H7 (316 aa), FASTA scores: opt: 1041, E():0, (52.4% identity in 309 aa overlap); etc. Also very similar to another LytB-related protein from Mycobacterium tuberculosis: LytB1|Rv3382c|MTV004.40c (329 aa), FASTA scores: opt: 975, E(): 0, (51.3% identity in 312 aa overlap). Belongs to the LytB family.	P9WKG1	No	cell wall and cell processes	ML1938,ML1938c	MMAR_4355	MSMEG_5224	Mb1140				
NC_000962.3	Mycobrowser_v3	CDS	1249932	1251404	.	-	0	Rv1127c	ppdK	Catalyzes the reversible phosphorylation of pyruvate and phosphate [catalytic activity: ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate]	Probable pyruvate, phosphate dikinase PpdK	Rv1127c, (MTCY22G8.16c), len: 490 aa. Probable ppdK, Pyruvate, phosphate dikinase. Equivalent (but shorter) to Z94723|MLCB33_16 ppdK from Mycobacterium leprae (601 aa) (71.8% identity in 478 aa overlap). Highly similar to N-terminus of PODK_CLOSY|P22983 pyruvate, phosphate dikinase from Clostridium symbiosum (873 aa), FASTA scores: opt: 786, E(): 0, (37.4% identity in 514 aa overlap).	O06579	No	intermediary metabolism and respiration	ML0955,ML0955c	MMAR_4331		Mb1158c				
NC_000962.3	Mycobrowser_v3	CDS	1256132	1257313	.	+	0	Rv1131	prpC	Involved in methyl citrate cycle [catalytic activity: propionyl-CoA + oxaloacetate + H2O = 2-methylcitrate + CoA]	Probable methylcitrate synthase PrpC	Rv1131, (MTCY22G8.20), len: 393 aa. Probable prpC, methylcitrate synthase (MCS) (previously known as gltA1) , highly similar to CISY_MYCSM|P26491 citrate synthase from Mycobacterium smegmatis (375 aa), FASTA scores: opt:1942, E(): 0, (80.0% identity in 375 aa overlap). Also similar to two other M. tuberculosis citrate synthases, Rv0896c|MTCY31.24|gltA2 (431 aa), FASTA score: (33.1% identity in 381 aa overlap) and Rv0889|MTCY31.17c|citA (373 aa), FASTA score: (31.8% identity in 371 aa overlap). Contains PS00480 Citrate synthase signature. Belongs to the citrate synthase family.	I6Y9Q3	No	intermediary metabolism and respiration		MMAR_1381	MSMEG_6647	Mb1162				
NC_000962.3	Mycobrowser_v3	CDS	1259067	1261346	.	-	0	Rv1133c	metE	Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation (pathway: terminal step in the de novo biosynthesis of methionine) [catalytic activity: 5-methyltetrahydropteroyltri-L-glutamate + L- homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine.]	Probable 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE (methionine synthase, vitamin-B12 independent isozyme)	Rv1133c, (MTC22G8.22), len: 759 aa (start site chosen by homology). Probable metE, 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase, highly similar to others e.g. METE_ECOLI|P25665 Escherichia coli (752 aa), FASTA scores: opt: 2251, E(): 0, (48.1% identity in 756 aa overlap). Equivalent to Z94723|MLCB33_14 metE from M. leprae (760 aa) (85.3% identity in 755 aa overlap). Belongs to the vitamin-B12 independent methionine synthase family.	P9WK07	No	intermediary metabolism and respiration	ML0961,ML0961c	MMAR_4328	MSMEG_6638	Mb1164c				
NC_000962.3	Mycobrowser_v3	CDS	1269152	1269958	.	-	0	Rv1142c	echA10	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Probable enoyl-CoA hydratase EchA10 (enoyl hydrase) (unsaturated acyl-CoA hydratase) (crotonase)	Rv1142c, (MTCI65.09c), len: 268 aa. Probable echA10, enoyl-CoA hydratase, similar to others e.g. CAA66096.1|X97452 enoyl-CoA isomerase from Escherichia coli (262 aa), FASTA scores: opt: 525, E(): 1.3e-26, (35.1% identity in 251 aa overlap); NP_420658.1|NC_002696 enoyl-CoA hydratase/isomerase family protein from Caulobacter crescentus (267 aa); NP_438092.1|NC_003078 putative enoyl-CoA hydratase protein from Sinorhizobium meliloti (263 aa); etc. Also similarity with naphthoate synthases. Also highly similar to upstream ORF Rv1141c|MTCI65.08c|echA11 probable enoyl-CoA hydratase from Mycobacterium tuberculosis (268 aa), FASTA score: opt: 1225, E(): 0, (72.3% identity in 267 aa overlap).	O06542	No	lipid metabolism		MMAR_4309		Mb1174c				
NC_000962.3	Mycobrowser_v3	CDS	1273355	1274767	.	+	0	Rv1146	mmpL13b	Unknown. Thought to be involved in fatty acid transport.	Probable conserved transmembrane transport protein MmpL13b	Rv1146, (MTCI65.13), len: 470 aa. Probable mmpL13b, conserved transmembrane transport protein (see citation below), member of RND superfamily, showing some similarity to putative Mycobacterial and Streptomyces membrane proteins e.g. Q53902|C40046 antibiotic transport-associated protein from Streptomyces coelicolor (711 aa), FASTA scores: opt: 193, E(): 2.1e-05, (28.9% identity in 394 aa overlap); etc. Could be in frame with previous ORF mmpL13A|Rv1145, but no sequence error apparent to account for this; sequence is identical in M. tuberculosis strain CDC1551, and Mycobacterium bovis strain AF2122/97. Belongs to the MmpL family.	O06546	No	cell wall and cell processes	ML0972			Mb1177				
NC_000962.3	Mycobrowser_v3	CDS	1937313	1938149	.	+	0	Rv1709	scpA	Involved in chromosome structure and partitioning	Possible segregation and condensation protein ScpA	Rv1709, (MTCI125.31), len: 278 aa. Possible scpA, segregation and condensation protein, similar to e.g. P35154|YPUG_BACSU from Bacillus subtilis (251 aa), FASTA scores: opt: 271, E(): 8.2e-10, (27.0% identity in 248 aa overlap); Q9S230|SCI51.10C|AL109848 from Streptomyces coelicolor (264 aa), FASTA scores: opt: 855, E(): 0, (56.8% identity in 257 aa overlap). Equivalent to Q49888|MLC1351.05C|Z95117 from Mycobacterium leprae (268 aa), FASTA scores: (78.9% identity in 251 aa overlap).	O33208	No	cell wall and cell processes	ML1368	MMAR_2524	MSMEG_3742	Mb1736				
NC_000962.3	Mycobrowser_v3	CDS	1284179	1284862	.	-	0	Rv1158c	Rv1158c	Function unknown	Conserved hypothetical ala-, pro-rich protein	Rv1158c, (MTCI65.25c), len: 227 aa. Conserved hypothetical Ala-, Pro-rich protein, similar to other proline rich proteins and extensins e.g. MMSAP62|g633250 house mouse (485 aa), FASTA scores: opt: 367, E(): 1.2e-08, (36.3% identity in 212 aa overlap). Has hydrophobic stretch at N-terminus suggestive of secretion signal. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O06556	No	conserved hypotheticals	ML1505	MMAR_4293	MSMEG_5151	Mb1189c				
NC_000962.3	Mycobrowser_v3	CDS	1284992	1286287	.	+	0	Rv1159	pimE	Polyprenol-phosphate-mannose dependent mannosyltransferase involved in phosphatidylinositol mannoside synthesis	Mannosyltransferase PimE	Rv1159, (MTCI65.26), len: 431 aa. PimE, mannosyltransferase (see Morita et al., 2006) Conserved transmembrane protein, similar to others in Mycobacterium tuberculosis e.g. Rv2181|MTCY21D4.13 (560 aa), FASTA scores: opt: 172; E(): 0.00035, (25.0% identity in 332 aa overlap). Belongs to the GT-C superfamily of glycosyltransferases (See Liu and Mushegian, 2003).	P9WN01	No	cell wall and cell processes	ML1504,ML1504c		MSMEG_5149	Mb1190				
NC_000962.3	Mycobrowser_v3	CDS	1291065	1292741	.	+	0	Rv1162	narH	Nitrate reduction [catalytic activity: nitrite + acceptor = nitrate + reduced acceptor].	Probable respiratory nitrate reductase (beta chain) NarH	Rv1162, (MTCI65.29), len: 558 aa. Probable narH, respiratory nitrate reductase beta chain. Similar to others e.g. NARH_BACSU|P42176 nitrate reductase beta chain from Bacillus subtilis (487 aa), FASTA scores: opt: 2049, E(): 0, (56.8% identity in 488 aa overlap); etc. Contains PS00190 cytochrome c family heme-binding site signature.	O06560	No	intermediary metabolism and respiration	ML1501,ML1501c		MSMEG_5139	Mb1194				
NC_000962.3	Mycobrowser_v3	CDS	1293406	1294146	.	+	0	Rv1164	narI	Nitrate reduction [catalytic activity: nitrite + acceptor = nitrate + reduced acceptor].	Probable respiratory nitrate reductase (gamma chain) NarI	Rv1164, (MTCI65.31), len: 246 aa. Probable narI, respiratory nitrate reductase gamma chain. Similar to others e.g. NARI_BACSU|P42177 nitrate reductase gamma chain from Bacillus subtilis (223 aa), FASTA scores: opt: 652, E(): 0; (41.6% identity in 221 aa overlap); etc. Highly similar to C-terminal part of Rv1736c|MTCY04C12.21c|NARX probable nitrate reductase (gamma chain) from Mycobacterium tuberculosis (68.6% identity in 239 aa overlap).	O06562	No	intermediary metabolism and respiration	ML1499,ML1499c		MSMEG_5137	Mb1196				
NC_000962.3	Mycobrowser_v3	CDS	1370920	1371477	.	+	0	Rv1228	lpqX	Unknown	Probable lipoprotein LpqX	Rv1228, (MTCI61.11), len: 185 aa. Probable lipoprotein LpqX. Contains possible signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	O33224	No	cell wall and cell processes				Mb1260				
NC_000962.3	Mycobrowser_v3	CDS	1294168	1296054	.	+	0	Rv1165	typA	Unknown; probably interacts with the ribosomes in a GTP dependent manner	Possible GTP-binding translation elongation factor TypA (tyrosine phosphorylated protein A) (GTP-binding protein)	Rv1165, (MTV005.01-MTCI65.32), len: 628 aa. Possible typA (alternate gene name: bipA), GTP-binding translation elongation factor, similar to several e.g. P32132|TYPA_ECOLI|BIPA|B387 Escherichia coli (591 aa); YIHK_SYNY3|P72749 gtp-binding protein TYPA/BIPA homolog from synechocystis sp. (597 aa), FASTA scores: E(): 0, (46.9% identity in 610 aa overlap); and to elongation factor EF-G from many organims e.g. EFG_MICLU|P09952 micrococcus luteus (701 aa), FASTA scores: E(): 3e-24, (29.8% identity in 500 aa overlap). Belongs to the GTP-binding elongation factor family, TYPA subfamily.	O06563	No	information pathways	ML1498,ML1498c	MMAR_4289	MSMEG_5132	Mb1197				
NC_000962.3	Mycobrowser_v3	CDS	1300304	1301215	.	+	0	Rv1170	mshB	Involved in mycothiol biosynthesis. 1-D-myo-inosityl-2-acetamido-2-deoxy-alpha-D-glucopyranoside (GlcNAc-Ins) is converted to 1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside (GlcN-Ins) by this enzyme. Seems to possess weak mycothiol conjugate amidase activity but SHOWS substantial deacetylation activity with 1-D-myo-inosityl-2-acetamido-2-deoxy-alpha-D-glucopyranoside (GlcNAc-Ins), a hypothetical mycothiol biosynthetic precursor. GlcNAc-Ins is an intermediate in MSH biosynthesis.	N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase MshB (GlcNAc-Ins deacetylase)	Rv1170, (MTV005.06), len: 303 aa. MshB, N-Acetyl-1-D-myo-Inosityl-2-Amino-2-Deoxy-alpha-D-Glucopyranoside Deacetylase (GlcNAc-Ins deacetylase) (see citation below), similar to Q54358|X79146 lmbE gene from Streptomyces lincolnensis (270 aa), FASTA scores: opt: 308, E(): 1.2e-15, (32.0% identity in 278 aa overlap). Also similar to Rv1082|MCA Mycothiol conjugate amidase from Mycobacterium tuberculosis (288 aa).	P9WJN3	No	intermediary metabolism and respiration	ML1495,ML1495c	MMAR_4283	MSMEG_5129	Mb1203				
NC_000962.3	Mycobrowser_v3	CDS	1302931	1305501	.	+	0	Rv1173	fbiC	Essential for coenzyme F420 production: participates in a portion of the F420 biosynthetic pathway between pyrimidinedione and FO (biosynthesis intermediate), before the deazaflavin ring is formed.	Probable F420 biosynthesis protein FbiC	Rv1173, (MTV005.09), len: 856 aa. Probable fbiC, F420 biosynthesis protein, equivalent to AAL91922|FBIC F420 biosynthesis protein fbiC from Mycobacterium bovis BCG (856 aa) (see citation below). The N-terminus (aa 80-420) is similar to Y446_METJA|Q57888 hypothetical protein mj0446 from methanococcus jannaschii (361 aa), FASTA scores: opt: 801, E(): 0, (41.2% identity in 337 aa overlap); and the C-terminus region (aa 530-856) is similar to e.g. YE31_METJA|Q58826 hypothetical protein mj1431 from methanococcus jannaschii (359 aa), FASTA scores: opt: 1089, E(): 0, (48.7% identity in 337 aa overlap).	P9WP77	No	intermediary metabolism and respiration	ML1492,ML1492c	MMAR_4279	MSMEG_5126	Mb1206				
NC_000962.3	Mycobrowser_v3	CDS	1394179	1395918	.	+	0	Rv1250	Rv1250	Thought to be involved in transport of drug across the membrane (export): drug resistance by an export mechanism (conferes resistance to toxic compounds by removing them for the cells). Responsible for the translocation of the substrate across the membrane.	Probable drug-transport integral membrane protein	Rv1250, (MTV006.22), len: 579 aa. Probable drug-transport integral membrane protein, member of major facilitator superfamily (MFS), highly similar to several including P39886|TCMA_STRGA tetracenomycin C resistance protein from Streptomyces glaucescens (538 aa), FASTA scores: opt: 847, E(): 0, (32.9% identity in 517 aa overlap); etc. Also similar to MTCY20B11.14c|Rv3239C from Mycobacterium tuberculosis (1048 aa), FASTA scores: opt: 629, E(): 6.7e-13, (31.9% identity in 423 aa overlap).	P9WG87	No	cell wall and cell processes	ML1097	MMAR_4192		Mb1282				
NC_000962.3	Mycobrowser_v3	CDS	1309364	1310452	.	+	0	Rv1178	Rv1178	Function unknown; probably involved in cellular metabolism.	Probable aminotransferase	Rv1178, (MTV005.14), len: 362 aa. Probable aminotransferase, weak similarity to many aspartate aminotransferases e.g. Q55679|D64000 SLL0006 aspartate aminotransferase from Synechocystis sp. (394 aa), FASTA scores: opt: 218, E(): 1.3e-25, (32.5% identity in 379 aa overlap). Contains PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site. Also similar to Mycobacterium tuberculosis aminotransferases Rv2294, Rv0075, etc.	O50434	No	intermediary metabolism and respiration	ML1488,ML1488c	MMAR_4273	MSMEG_5121	Mb1211				
NC_000962.3	Mycobrowser_v3	CDS	1310480	1313299	.	-	0	Rv1179c	Rv1179c	Unknown	Unknown protein	Rv1179c, MTV005.15c, len: 939 aa. Unknown protein.	O50435	No	conserved hypotheticals				Mb1212c				
NC_000962.3	Mycobrowser_v3	CDS	1321520	1324528	.	+	0	Rv1183	mmpL10	Unknown. Thought to be involved in fatty acid transport.	Probable conserved transmembrane transport protein MmpL10	Rv1183, (MTV005.19), len: 1002 aa. Probable mmpL10, conserved transmembrane transport protein (see Tekaia et al., 1999), member of RND superfamily, similar to many Mycobacterial hypothetical membrane proteins e.g. Q49619|U00010 from Mycobacterium leprae (1008 aa), FASTA scores: opt: 4545, E(): 0, (70.6% identity in 978 aa overlap); etc. Belongs to the MmpL family.	P9WJU1	No	cell wall and cell processes	ML1231		MSMEG_0410	Mb1215				
NC_000962.3	Mycobrowser_v3	CDS	1329390	1331021	.	+	0	Rv1187	rocA	Involved in the arginase pathway [catalytic activity: 1-pyrroline-5-carboxylate + NAD(+) + H(2)O = L-glutamate + NADH]	Probable pyrroline-5-carboxylate dehydrogenase RocA	Rv1187, (MTV005.23), len: 543 aa. Probable rocA, pyrroline-5-carboxylate dehydrogenase, similar to many e.g. PUT2_HUMAN|P30038 human delta-1-pyrroline-5-carboxylate dehydrogenase (563 aa), FASTA scores: opt: 1596, E():0, (46.0% identity in 531 aa overlap). Also similar to other Mycobacterium tuberculosis hypothetical dehydrogenases e.g. Rv0768, Rv2858c, etc. Contains PS00687 Aldehyde dehydrogenases glutamic acid active site and PS00070 Aldehyde dehydrogenases cysteine active site.	O50443	No	intermediary metabolism and respiration		MMAR_4253	MSMEG_5119	Mb1219				
NC_000962.3	Mycobrowser_v3	CDS	1335794	1337215	.	+	0	Rv1193	fadD36	Function unknown, but supposedly involved in lipid degradation.	Probable fatty-acid-CoA ligase FadD36 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv1193, (MTCI364.05), len: 473 aa. Probable fadD36, fatty-acid-CoA synthetase, highly similar to Q50017|U15181 4-coumarate-CoA ligase from Mycobacterium leprae (476 aa), FASTA scores: opt: 2594, E(): 0, (81.3% identity in 476 aa overlap). Also highly similar to others e.g. CAB86109.1|AL163003 putative fatty acid synthase from Streptomyces coelicolor (485 aa); LCFA_ECOLI|P29212 long-chain-fatty-acid--CoA ligase from Escherichia coli (561 aa), FASTA scores: opt: 605, E(): 8.4e-30, (33.0% identity in 364 aa overlap); etc. Contains PS00455 Putative AMP-binding domain signature. Belongs to the ATP-dependent AMP-binding enzyme family.	O05295	No	lipid metabolism	ML1051	MMAR_4243	MSMEG_5114	Mb1225				
NC_000962.3	Mycobrowser_v3	CDS	1341358	1342605	.	-	0	Rv1199c	Rv1199c	Possibly required for the transposition of the insertion element IS1081.	Possible transposase	Rv1199c, (MTCI364.11c), len: 415 aa. Possible transposase for IS1081, identical to TRA1_MYCBO|P35882 transposase for insertion sequence element (415 aa); region identical to MTCY441.35 (100.0% identity in 261 aa overlap); and almost identical to MTCY10G2.02c (415 aa) (99.8% identity in 415 aa overlap). Contains PS01007 Transposases, Mutator family, signature, PS00435 Peroxidases proximal heme-ligand signature.	P60230	No	insertion seqs and phages				Mb1231c				
NC_000962.3	Mycobrowser_v3	CDS	1345260	1346324	.	+	0	Rv1202	dapE	Involved in biosynthesis of diaminopimelate and lysine from aspartate semialdehyde (at the fifth step) [catalytic activity: N-succinyl-ll-2,6-diaminoheptanedioate + H2O = succinate + ll-2,6-diaminoheptanedioate]	Probable succinyl-diaminopimelate desuccinylase DapE	Rv1202, (MTCI364.14), len: 354 aa. Probable dapE, succinyl-diaminopimelate desuccinylase, similar to DAPE_CORGL|Q59284 succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum (369 aa), FASTA scores: opt: 1301, E(): 0, (55.7% identity in 359 aa overlap), highly similar to Q49949|U1756G (400 aa), FASTA scores: opt: 2045, E(): 0, (87.0% identity in 354 aa overlap).	P9WHS9	No	intermediary metabolism and respiration	ML1059	MMAR_4235	MSMEG_5103	Mb1234				
NC_000962.3	Mycobrowser_v3	CDS	1349332	1351125	.	+	0	Rv1206	fadD6	Function unknown, but supposed involvement in lipid degradation.	Probable fatty-acid-CoA ligase FadD6 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv1206, (MTCI364.18), len: 597 aa. Probable fadD6, fatty-acid-CoA synthetase, highly similar to several e.g. NP_251583.1|NC_002516 probable very-long-chain acyl-CoA synthetase from Pseudomonas aeruginosa (608 aa); Q60714 mouse fatty acid transport protein fatp (646 aa), FASTA scores: opt:712, E(): 0, (36.8% identity in 600 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00455 Putative AMP-binding domain signature. Belongs to the ATP-dependent AMP-binding enzyme family.	O05307	No	lipid metabolism	ML1062	MMAR_4232	MSMEG_5086	Mb1238				
NC_000962.3	Mycobrowser_v3	CDS	1355836	1357050	.	+	0	Rv1213	glgC	Involved in glycogen biosynthesis (first step) [catalytic activity:ATP + alpha-D-glucose 1-phosphate = diphosphate + ADP-glucose].	Glucose-1-phosphate adenylyltransferase GlgC (ADP-glucose synthase) (ADP-glucose pyrophosphorylase)	Rv1213, (MTCI364.25), len: 404 aa. glgC, glucose-1-phosphate adenylyltransferase, similar to many e.g. GLGC_ECOLI|P00584 Escherichia coli (430 aa), FASTA scores: opt: 1075, E(): 0, (40.3% identity in 407 aa overlap); highly similar to Q49961 GLGC from Mycobacterium leprae (419 aa), FASTA scores: opt: 2532, E(): 0, (92.6% identity in 404 aa overlap). Belongs to the bacterial and plants glucose-1-phosphate adenylyltransferase family.	P9WN43	No	intermediary metabolism and respiration	ML1069	MMAR_4225	MSMEG_5078	Mb1245				
NC_000962.3	Mycobrowser_v3	CDS	1360155	1361801	.	-	0	Rv1217c	Rv1217c	Thought to be involved in active transport of tetronasin across the membrane (export): tetronasin resistance by an export mechanism. Responsible for the translocation of the substrate across the membrane.	Probable tetronasin-transport integral membrane protein ABC transporter	Rv1217c, (MTCI364.29c), len: 548 aa. Probable tetronasin-transport integral membrane ABC transporter (see citation below), similar to many e.g. AL049754|SCH10_12 probable ABC-type transport system membrane-spanning protein from Streptomyces coelicolor (539 aa), FASTA scores: opt: 1309, E(): 0, (40.9% identity in 550 aa overlap); Q54407|X73633 TnrB3 protein from Streptomyces longisporoflavus (337 aa), FASTA scores: opt: 692, E(): 0, (39.5% identity in 324 aa overlap); etc. Also has regions similar to Mycobacterium leprae proteins Q49964|U1756Q (109 aa), FASTA scores: opt: 431, E(): 3.1e-20, (64.8% identity in 105 aa overlap) and Q49965|U1756R (82 aa), FASTA scores: opt:154, E(): 0.0028, (61.0% identity in 41 aa overlap).	O05318	No	cell wall and cell processes	ML1072,ML1072c	MMAR_4221		Mb1249c				
NC_000962.3	Mycobrowser_v3	CDS	1364413	1365186	.	+	0	Rv1221	sigE	The sigma factor is an initiation factor that promotes attachment of the RNA polymerase to specific initiation sites and then is released. Seems to be regulated by sigh (Rv3223c product). Seems to regulate the heat-shock response.	Alternative RNA polymerase sigma factor SigE	Rv1221, (MTCI61.04), len: 257 aa. SigE, alternative sigma factor of extracytoplasmic function (ECF) family (see citations below). Similar to many e.g. RPOE_HAEIN|P44790 RNA polymerase sigma-e factor from Haemophilus influenzae (189 aa), FASTA scores: opt: 247, E(): 3.4e-06, (28.5% identity in 186 aa overlap); etc. Also similar to MTCY07D11.03 rpoE from Mycobacterium tuberculosis (35.2% identity in 159 aa overlap). Belongs to the sigma-70 factor family, ECF subfamily. Three promoters and three translational start codons have been detected (See Dona et al., 2008). Fourth transcriptional start point has been identified (See Pang et al., 2007). Note that in Mycobacterium bovis BCG, the sigE gene is transcribed from two promoters, P1 and P2, and that these promoters were expressed at temperatures from 30-50 degrees Celsius.	P9WGG7	No	information pathways	ML1076	MMAR_4216	MSMEG_5072	Mb1253				
NC_000962.3	Mycobrowser_v3	CDS	1365875	1367461	.	+	0	Rv1223	htrA	Possibly hydrolyzes peptides and/or proteins (seems to cleave preferentially after serine residue).	Probable serine protease HtrA (DEGP protein)	Rv1223, (MTCI61.06), len: 528 aa. Probable htrA (alternate gene name: degP), serine protease precursor (see citations below), equivalent to U15180|MLU15180_31|Q49972|ML1078|HTRA possible serine protease from Mycobacterium leprae (533 aa), FASTA scores: opt: 2777, E(): 4.1e-141, (81.6% identity in 533 aa overlap). Also similar to many others e.g. HTRA_ECOLI|P09376 protease do precursor from Escherichia coli (474 aa), FASTA scores: opt: 581, E(): 9.1e-27, (36.3% identity in 278 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Start changed since first submission (-21 aa). Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	O06291	No	intermediary metabolism and respiration	ML1078	MMAR_4214	MSMEG_5070	Mb1255				
NC_000962.3	Mycobrowser_v3	CDS	1367891	1368721	.	-	0	Rv1225c	Rv1225c	Function unknown	Conserved hypothetical protein	Rv1225c, (MTCI61.08c), len: 276 aa. Conserved hypothetical protein, some similarity to other hypothetical proteins e.g. AE001078|AE001078_2 Archaeoglobus fulgidus (265 aa), FASTA scores: opt: 339, E(): 5.1e-15, (27.1% identity in 262 aa overlap), and to NAGD_ECOLI|P15302 nagd protein from Escherichia coli (250 aa), FASTA scores: opt: 167, E(): 6.4e-12, (24.8% identity in 258 aa overlap). Also weakly similar to Mycobacterium tuberculosis hypothetical protein Rv3400|MTCY78.28c (29.1% identity in 251 aa overlap).	O33221	No	conserved hypotheticals			MSMEG_0867	Mb1257c				
NC_000962.3	Mycobrowser_v3	CDS	1374861	1376168	.	-	0	Rv1232c	Rv1232c	Function unknown	Conserved protein	Rv1232c, (MTV006.04c), len: 435 aa. Conserved protein, similar to other hypothetical proteins e.g. AB013374|AB013374_2 Bacillus halodurans C-125 mamX (449 aa), FASTA scores: opt: 381, E(): 1e-16, (29.9% identity in 251 aa overlap). Some similarity in N-terminus to U15180|MLU1518033 hypothetical Mycobacterium leprae protein u1756u (329 aa), FASTA scores: opt: 300, E(): 4.1e-12, (69.3% identity in 75 aa overlap).	O86315	No	conserved hypotheticals	ML1083,ML1083c	MMAR_4209	MSMEG_5065	Mb1264c				
NC_000962.3	Mycobrowser_v3	CDS	1377524	1378930	.	+	0	Rv1235	lpqY	Thought to be involved in active transport of sugar across the membrane (import).	Probable sugar-binding lipoprotein LpqY	Rv1235, (MTV006.07), len: 468 aa. Probable lpqY, sugar-binding lipoprotein component of sugar transport system (see citation below), equivalent to MLU1518034 protein u1756v from Mycobacterium leprae (469 aa), FASTA scores: opt: 2442, E(): 0, (77.4% identity in 470 aa overlap). Also similar to P18815|MALE_ENTAE maltose-binding periplasmic protein from Enterobacter aerogenes (396 aa), FASTA scores: opt: 193, E(): 2.3e-05, (24.2% identity in 297 aa overlap). Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	P9WGU9	No	cell wall and cell processes	ML1086	MMAR_4206	MSMEG_5061	Mb1267				
NC_000962.3	Mycobrowser_v3	CDS	1380684	1381865	.	+	0	Rv1238	sugC	Involved in active transport of sugar across the membrane (import). Responsible for energy coupling to the transport system.	Probable sugar-transport ATP-binding protein ABC transporter SugC	Rv1238, (MTV006.10), len: 393 aa. Probable sugC, sugar-transport ATP-binding protein ABC transporter (see citation below). Highly similar to U15180 protein ugpC from Mycobacterium leprae (392 aa), FASTA score: opt: 2007, E(): 0, (79.9% identity in 389 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop) and PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters).	P9WQI3	No	cell wall and cell processes	ML1089	MMAR_4203	MSMEG_5058	Mb1270				
NC_000962.3	Mycobrowser_v3	CDS	1484279	1484959	.	+	0	Rv1321	Rv1321	Function unknown	Conserved hypothetical protein	Rv1321, (MTCY130.06), len: 226 aa. Conserved hypothetical protein. Equivalent to P53524|YD21_MYCLE hypothetical protein from Mycobacterium leprae (201 aa), FASTA scores: opt: 1144, E(): 0, (87.6% identity in 193 aa overlap). Some similarity to hypothetical proteins from other organisms e.g. Y225_METJA|Q57678 Methanococcus jannaschii (263 aa), FASTA scores: E(): 6.5e-05, (25.0% identity in 212 aa overlap).	P9WIY5	No	conserved hypotheticals	ML1155	MMAR_4077	MSMEG_4923	Mb1355				
NC_000962.3	Mycobrowser_v3	CDS	1387798	1388628	.	-	0	Rv1245c	Rv1245c	Function unknown; supposedly involved in cellular metabolism.	Probable short-chain type dehydrogenase/reductase	Rv1245c, (MTV006.17c), len: 276 aa. Probable short-chain dehydrogenase/reductase, equivalent to NP_301801.1|NC_002677 short chain alcohol dehydrogenase from Mycobacterium leprae (277 aa). Also highly similar to various dehydrogenases and oxidoreductases e.g. NP_250228.1|NC_002516 probable short-chain dehydrogenase from Pseudomonas aeruginosa (295 aa); NP_421969.1|NC_002696 short chain dehydrogenase family protein from Caulobacter crescentus (278 aa); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. Rv3085|MTV013.06 probable short-chain type dehydrogenase/reductase (276 aa), FASTA scores: opt: 368, E(): 1.2e-16, (35.3% identity in 224 aa overlap); Rv3057c|MTCY22D7.24 putative short chain alcohol dehydrogenase/reductase (287 aa), FASTA scores: opt: 471, E(): 1.3e-21, (32.4% identity in 281 aa overlap); etc. Contains PS00061 Short-chain dehydrogenases/reductases family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	O50460	No	intermediary metabolism and respiration	ML1094,ML1094c	MMAR_4195	MSMEG_5053	Mb1277c				
NC_000962.3	Mycobrowser_v3	CDS	1389357	1393052	.	-	0	Rv1248c	Rv1248c	Involved in cellular metabolism. Has alpha-ketoglutarate dehydrogenase (KDH) [catalytic activity: 2-oxoglutarate + lipoamide = S-succinyldihydrolipoamide + CO2], alpha-ketoglutarate decarboxylase (KGD) [catalytic activity: 2-oxoglutarate = succinate semialdehyde + CO2], and 2-hydroxy-3-oxoadipate (HOA) synthase [catalytic activity: 2-oxoglutarate + glyoxylate + H+ = 2-hydroxy-3-oxoadipate + CO2] activities.	Multifunctional alpha-ketoglutarate metabolic enzyme	Rv1248c, (MTV006.20c), len: 1231 aa. Multifunctional alpha-ketoglutarate metabolic enzyme, highly similar to D84102 Corynebacterium glutamicum (1257 aa), FASTA scores: opt: 4418, E(): 0, (59.4% identity in 1223 aa overlap). Cofactor: thiamine diphosphate. Start changed since first submission (+17 aa).	P9WIS5	No	intermediary metabolism and respiration	ML1095,ML1095c	MMAR_4194	MSMEG_5049	Mb1280c				
NC_000962.3	Mycobrowser_v3	CDS	1406081	1407340	.	-	0	Rv1258c	Rv1258c	Thought to be involved in transport of undetermined substrate (possibly macrolide) across the membrane (export). Responsible for the translocation of the undetermined substrate across the membrane.	Probable conserved integral membrane transport protein	Rv1258c, MTCY50.24, len: 419 aa. Probable conserved integral membrane transport (efflux) protein, possibly member of major facilitator superfamily (MFS), highly similar to O32859|tap protein multidrug-resistance efflux pump from Mycobacterium fortuitum (409 aa), FASTA scores: E(): 0, (68.4% identity in 408 aa overlap). Contains PS00216 Sugar transport proteins signature 1.	P9WJX9	No	cell wall and cell processes	ML1104,ML1104c	MMAR_4182		Mb1288c				
NC_000962.3	Mycobrowser_v3	CDS	1408240	1409358	.	+	0	Rv1260	Rv1260	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase	Rv1260, (MTCY50.22c), len: 372 aa. Probable oxidoreductase, highly similar to E1245747|AL021411 putative oxidoreductase SC7H1.18 from Streptomyces coelicolor (397 aa), FASTA scores: E(): 1.4e-29, (45.9% identity in 355 aa overlap); also some similarity to G912582 FAD binding protein homologue from Pseudomonas aeruginosa (286 aa), FASTA scores: opt: 245, E(): 2e-09, (27.5% identity in 251 aa overlap); PCPB_FLASP|P42535 pentachlorophenol 4-monooxygenase (537 aa), FASTA scores: opt: 219, E(): 1.7e-07, (23.3% identity in 360 aa overlap); TETX_BACFR|Q01911 tetracycline resistance protein (388 aa), FASTA scores: opt: 183, E(): 3e-05, (22.8% identity in 373 aa overlap). Also similar to Mycobacterium tuberculosis hypothetical proteins Rv0575c and Rv1751.	P9WM51	No	intermediary metabolism and respiration		MMAR_4180		Mb1290,Mb1291				
NC_000962.3	Mycobrowser_v3	CDS	1411894	1413087	.	+	0	Rv1264	Rv1264	Possibly involved in cAMP synthesis [catalytic activity: ATP = 3',5'-cyclic AMP + diphosphate]. Activity is PH-dependent. Inhibited by polyphosphates.	Adenylyl cyclase (ATP pyrophosphate-lyase) (adenylate cyclase)	Rv1264, (MTCY50.18c), len: 397 aa. Adenylate cyclase (function proven experimentally: see Linder et al., 2002), showing some similarity to other adenylate cyclases e.g. CYAA_BRELI|P27580 (403 aa), FASTA scores, opt: 270, E(): 1.3e-10, (29.3% identity in 317 aa overlap); etc. Similar to other putative cyclases in M. tuberculosis e.g. Rv2212, Rv1647. The C terminus seems to code for a catalytic domain belonging to a subfamily of adenylyl cyclase isozymes (mostly found in Gram-positive bacteria). The N terminus seems to be a potential novel regulator of adenylyl cyclase activity (autoinhibitory domain). Belongs to the adenylyl cyclase class-4/guanylyl cyclase family.	P9WMU9	No	intermediary metabolism and respiration	ML1111	MMAR_4173	MSMEG_5018	Mb1295				
NC_000962.3	Mycobrowser_v3	CDS	1484982	1485278	.	+	0	Rv1322	Rv1322	Function unknown	Conserved hypothetical protein	Rv1322, (MTCY130.07), len: 98 aa. Conserved hypothetical protein.	P9WM27	No	conserved hypotheticals	ML1156		MSMEG_4922	Mb1356				
NC_000962.3	Mycobrowser_v3	CDS	1422302	1424050	.	-	0	Rv1273c	Rv1273c	Thought to be involved in active transport of drugs across the membrane (export): multidrugs resistance by an export mechanism. Responsible for energy coupling to the transport system and for the translocation of the substrate across the membrane.	Probable drugs-transport transmembrane ATP-binding protein ABC transporter	Rv1273c, (MTCY50.09), len: 582 aa. Probable drugs-transport transmembrane ATP-binding protein ABC transporter (see citation below), similar to e.g. YWJA_BACSU|P45861 hypothetical abc transporter from B. subtilis (575 aa), FASTA scores: opt: 810, E(): 0, (27.0% identity in 578 aa overlap); etc. Contains PS00136 Serine proteases, subtilase family, aspartic acid active site; 2 x PS00211 ABC transporters family signature; and PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the ATP-binding transport protein family (ABC transporters), MSBA subfamily.	P9WQJ1	No	cell wall and cell processes	ML1114,ML1114c	MMAR_4147	MSMEG_5008	Mb1304c				
NC_000962.3	Mycobrowser_v3	CDS	1431665	1433440	.	-	0	Rv1280c	oppA	Involved in active transport of oligopeptide across the membrane (import). This protein is a component of the oligopeptide permease, a binding protein-dependent transport system; it binds peptides up to five amino acids long with high affinity.	Probable periplasmic oligopeptide-binding lipoprotein OppA	Rv1280c, (MTCY50.02), len: 591 aa. Probable oppA, oligopeptide-binding lipoprotein component of peptide transport system (see citation below), sharing some similarity to other periplasmic solute binding proteins e.g. OPPA_SALTY|P06202 periplasmic oligopeptide-binding protein from Salmonella typhimurium (542 aa), FASTA scores: E(): 5.1e-05, (22.1% identity in 458 aa overlap); etc. Also similar to Rv1166 and Rv2585c from Mycobacterium tuberculosis. Has possible N-terminal signal sequence and prokaryotic lipoprotein lipid attachment site (PS00013). Belongs to the bacterial extracellular solute-binding protein family 5.	P9WGU5	No	cell wall and cell processes	ML1121,ML1121c	MMAR_4139	MSMEG_4999	Mb1311c				
NC_000962.3	Mycobrowser_v3	CDS	1437909	1438907	.	+	0	Rv1285	cysD	Involved in sulfate activation pathway. First step in the sulfate activation pathway. This reaction occurs early in the reductive branch of the cysteine biosynthetic pathway [catalytic activity:ATP + sulfate = diphosphate + adenylylsulfate]	Probable sulfate adenylyltransferase subunit 2 CysD	Rv1285, (MTCY373.04), len: 332 aa. Probable cysD, sulfate adenylyltransferase subunit 2 (see Wooff et al., 2002), homology suggests start site at aa 24 or 28, similar to e.g. CYSD_ECOLI|P21156 sulfate adenylate transferase subunit 2 from Escherichia coli (302 aa), FASTA score: opt: 973, E():0, (52.5% identity in 303 aa overlap). Also similar to Mycobacterium tuberculosis Rv2392, 3'-phosphoadenylylsulfate reductase. Belongs to the PAPS reductase family. CYSD subfamily. Thought to be differentially expressed within host cells (see Triccas et al., 1999).	P9WIK1	No	intermediary metabolism and respiration		MMAR_4133	MSMEG_4979	Mb1316				
NC_000962.3	Mycobrowser_v3	CDS	2413348	2414922	.	-	0	Rv2154c	ftsW	Unknown	FtsW-like protein FtsW	Rv2154c, (MTCY270.14), len: 524 aa. Probable ftsW, cell division protein, related to MTCY10H4.17c, 3.2e-17. FASTA best: SP5E_BACSU P07373 stage V sporulation protein E (366 aa) opt: 755, E(): 1.6e-33; (38.4% identity in 357 aa overlap). FtsW|Rv2154c interacts with PbpB|Rv2163c and FtsZ|RvRv2150c (See Datta et al., 2006).	P9WN97	No	cell wall and cell processes	ML0913	MMAR_3194	MSMEG_4228	Mb2178c				
NC_000962.3	Mycobrowser_v3	CDS	1449375	1450700	.	+	0	Rv1294	thrA	Involved in the conversion of L-aspartate to homoserine (third step). Homoserine participates in the biosynthesis of threonine and then isoleucine and in the biosynthesis of methionine [catalytic activity: L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H.]	Probable homoserine dehydrogenase ThrA	Rv1294, (MTCY373.14), len: 441 aa. Probable thrA (hom), homoserine dehydrogenase, highly similar to DHOM_MYCLE|P46806 from Mycobacterium leprae (441 aa), FASTA scores: opt: 2437, E():0, (89.5% identity in 438 aa overlap). Contains PS00017 ATP/GTP-binding site motif A; PS01042 Homoserine dehydrogenase signature. Belongs to the homoserine dehydrogenase family.	P9WPX1	No	intermediary metabolism and respiration	ML1129	MMAR_4103	MSMEG_4957	Mb1326				
NC_000962.3	Mycobrowser_v3	CDS	1453204	1455012	.	+	0	Rv1297	rho	Facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho'S RNA-dependent ATPase activity, and release of the mRNA from the DNA template	Probable transcription termination factor Rho homolog	Rv1297, (MTCY373.17), len: 602 aa. Probable rho, transcription termination factor homolog, highly similar to many e.g. RHO_MYCLE|P45835 Mycobacterium leprae (610 aa), FASTA scores: (81.5% identity in 612 aa overlap). Contains 1 RNA recognition motif (RRM). Nucleotide position 1453608 in the genome sequence has been corrected, T:C resulting in G135G.	P9WHF3	No	information pathways	ML1132	MMAR_4100	MSMEG_4954	Mb1329				
NC_000962.3	Mycobrowser_v3	CDS	1458295	1459509	.	+	0	Rv1302	rfe	Thought to be involved in AG biosynthesis. May be the tunicamycin sensitive transferase that catalyzes the synthesis of GlcNAc-pyrophosphorylundecaprenol (lipid I), the first lipid-linked intermediate involved in ECA synthesis.	Probable undecapaprenyl-phosphate alpha-N-acetylglucosaminyltransferase Rfe (UDP-GlcNAc transferase)	Rv1302, (MTCY373.22), len: 404 aa. Probable rfe (alternate gene name: wecA), undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase (see citation below), equivalent to RFE_MYCLE|P45830 Mycobacterium leprae (398 aa), FASTA scores, opt: 2285, E(): 0, (89.2% identity in 398 aa overlap).	P9WMW5	No	cell wall and cell processes	ML1137	MMAR_4095	MSMEG_4947	Mb1334				
NC_000962.3	Mycobrowser_v3	CDS	1461843	1463183	.	+	0	Rv1307	atpH	This protein seems to be part of the stalk that LINKS cf(0) to cf(1). It either transmits conformational changes from cf(0) into cf(1) or is implicated in proton conduction [catalytic activity: ATP + H(2)O + H(+)(in) = ADP + phosphate + H(+)(out)]	Probable ATP synthase delta chain AtpH	Rv1307, (MTCY373.27), len: 446 aa. Probable atpH, ATP synthase delta chain. This protein is much longer than that of other bacterial delta chains, the C-terminal region is homologous to delta chains while the N-terminal region is similar to B/B' subunits e.g. ATPD_STRLI|P50008 ATP synthase delta chain from Streptomyces lividans (273 aa), FASTA scores: opt: 505, E(): 5.4e-23, (35.0% identity in 277 aa overlap); and ATPF_HAEIN|P43720 ATP synthase B chain from Haemophilus influenzae (156 aa), FASTA scores: opt: 216, E(): 1.2e-06, (26.1% identity in 153 aa overlap). subunit: F-type ATPases have 2 components, cf(1) - the catalytic core - and cf(0) - the membrane proton channel. cf(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). cf(0) has three main subunits: A, B and C. Belongs to the ATPase delta chain family.	P9WPV3	No	intermediary metabolism and respiration	ML1142	MMAR_4090	MSMEG_4939	Mb1339				
NC_000962.3	Mycobrowser_v3	CDS	1463228	1464877	.	+	0	Rv1308	atpA	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit [catalytic activity:ATP + H(2)O + H(+)(in) = ADP + phosphate + H(+)(out)]	Probable ATP synthase alpha chain AtpA	Rv1308, (MTCY373.28), len: 549 aa. Probable atpA, ATP synthase alpha chain, highly similar to ATPA_MYCLE|P45825 from Mycobacterium leprae (558 aa), FASTA scores: opt: 3233, E(): 0, (90.3% identity in 547 aa overlap). Contains PS00017 ATP/GTP-binding site motif A, PS00152 ATP synthase alpha and beta subunits signature. subunit: F-type ATPases have 2 components, cf(1) - the catalytic core - and cf(0) - the membrane proton channel. cf(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). cf(0) has three main subunits: A, B and C. Belongs to the ATPase alpha/beta chains family.	P9WPU7	No	intermediary metabolism and respiration	ML1143		MSMEG_4938	Mb1340				
NC_000962.3	Mycobrowser_v3	CDS	1468171	1469505	.	-	0	Rv1313c	Rv1313c	Possibly required for the transposition of the insertion element IS1557.	Possible transposase	Rv1313c, (MTCY373.33c), len: 444 aa. Possible IS1557 transposase, similar to several transposases e.g. U57649|DBU57649 ORF1 from dibenzofuran-degrading bacterium DPO360 (163 aa), FASTA scores: opt: 767, E(): 0, (67.3% identity in 168 aa overlap); TNPA_BORPA|Q06126 transposase for insertion sequence element IS1001 from Bordetella parapertussis (406 aa), FASTA scores: opt: 254, E(): 3.3e-10, (24.9% identity in 402 aa overlap). Also similar to putative Mycobacterium tuberculosis transposases, Rv3798 and Rv0741.	P9WKH7	No	insertion seqs and phages				Mb1345c,Mb1346c				
NC_000962.3	Mycobrowser_v3	CDS	1477628	1479118	.	-	0	Rv1317c	alkA	Involved in the adaptive response to alkylation damage in DNA caused by alkylating agents. Repairs the SP diastereomer of DNA methylphosphotriester lesions by a direct and irreversible transfer of the methyl group to one of its own cysteine residues. The methylated ALKA protein acts as a positive regulator of its own synthesis, as well as that of other proteins.	Probable bifunctional regulatory protein and DNA repair enzyme AlkA (regulatory protein of adaptative response) (methylphosphotriester-DNA--protein-cysteine S-methyltransferase)	Rv1317c, (MTCY130.02c), len: 496 aa. Probable alkA (alternate gene name: ada), bifunctional regulatory protein (see citation below) and DNA repair enzyme, similar to 3MG2_ECOLI|P04395 dna-3-methyladenine glycosidase II from Escherichia coli (282 aa), FASTA scores, opt: 437, E(): 8.6e-22, (32.8% identity in 293 aa overlap), also similar to other ada proteins e.g. ADA_SALTY|P26189 Salmonella typhimurium (352 aa), FASTA scores: E(): 5.3e-08, (35.9% identity in 156 aa overlap). Contains PS00041 Bacterial regulatory proteins, araC family signature.	P9WJW3	No	information pathways	ML1152,ML1152c	MMAR_4081	MSMEG_4925					
NC_000962.3	Mycobrowser_v3	CDS	1480894	1482501	.	-	0	Rv1319c	Rv1319c	Thought to play an essential role in regulation of cellular metabolism by catalysing the synthesis of a second messenger, camp [catalytic activity: ATP = 3',5'-cyclic AMP + pyrophosphate].	Possible adenylate cyclase (ATP pyrophosphate-lyase) (adenylyl cyclase)	Rv1319c, (MTCY130.04c), len: 535 aa. Possible adenylate cyclase. Some similarity at the C-terminus to CYAA_RHIME|P19485 adenylate cyclase from Rhizobium meliloti (193 aa), FASTA scores: opt: 254, E(): 2.4e-10, (33.3% identity in 144 aa overlap); similar to other mycbacterium tuberculosis putative adenylate cyclases e.g. Rv1318c|MTCY130.03c (541 aa), FASTA scores: opt: 2505, E(): 0, (71.0% identity in 534 aa overlap); Rv1320c|MTCY130.05c (567 aa), FASTA scores: opt: 2354, E(): 0, (66.3% identity in 534 aa overlap). N-terminus is hydrophobic. Belongs to adenylyl cyclase class-3 family.	P9WQ31	No	intermediary metabolism and respiration			MSMEG_4924	Mb1353c				
NC_000962.3	Mycobrowser_v3	CDS	1488154	1489965	.	-	0	Rv1325c	PE_PGRS24	Function unknown	PE-PGRS family protein PE_PGRS24	Rv1325c, (MTCY130.10c), len: 603 aa. PE_PGRS24, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of ala-, gly-rich proteins (see Brennan & Delogu 2002), similar to many e.g. YQ04_MYCTU|P71933 hypothetical 63.1 kDa glycine-rich protein (778 aa), FASTA scores: E(): 0, (52.3% identity in 724 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008).	P9WIF7	No	PE/PPE				Mb1360c				
NC_000962.3	Mycobrowser_v3	CDS	1499213	1500559	.	-	0	Rv1330c	pncB1	Involved in NAD salvage. Phosphoribosylation of nicotinic acid. [catalytic activity: nicotinate + 5-phosphoribosyl 1-pyrophosphate = nicotinate mononucleotide + diphosphate]	Nicotinic acid phosphoribosyltransferase PncB1	Rv1330c, (MTCY130.15c), len: 448 aa. PncB1, nicotinic acid phosphoribosyltransferase (See Boshoff et al., 2008). Similar to e.g. O32090 YUEK protein from Bacillus subtilis (490 aa), FASTA scores: E(): 8.6e-22, (37.9% identity in 369 aa overlap). Also similar to Mycobacterium tuberculosis Rv0573c|MTV039.11c (38.0% identity in 437 aa overlap). Start changed since original submission based on similarity; previous start at position 1500740 (-61 aa).	P9WJI9	No	intermediary metabolism and respiration	ML1164,ML1164c	MMAR_4068	MSMEG_4911	Mb1365c				
NC_000962.3	Mycobrowser_v3	CDS	1509281	1510846	.	+	0	Rv1345	mbtM	Thought to be involved in the biogenesis of the hydroxyphenyloxazoline-containing siderophore mycobactins	Probable fatty acyl-AMP ligase MbtM	Rv1345, (MTCY02B10.09), len: 521 aa. Probable mbtM, fatty acyl-AMP ligase. Similar to N-terminus of T34918 polyketide synthase from Streptomyces coelicolor (2297 aa); and PKSJ_BACSU|P40806 putative polyketide biosynthesis protein from Bacillus subtilis (557 aa), FASTA scores: opt: 537, E(): 8.2e-27, (27.1% identity in 468 aa overlap). Also similar to other proteins from Mycobacterium tuberculosis eg Rv1013|MTCI237.30|MTCY10G2.36c|pks16 putative polyketide synthase (544 aa); etc. Note that previously known as fadD33.	P9WQ41	No	lipid metabolism			MSMEG_2131	Mb1380				
NC_000962.3	Mycobrowser_v3	CDS	1513047	1515626	.	+	0	Rv1348	irtA	Involved in iron homeostasis. Responsible for energy coupling to the transport system and for the translocation of the substrate across the membrane.	Iron-regulated transporter IrtA	Rv1348, (MTCY02B10.12), len: 859 aa. IrtA, iron-regulated transporter. Probable transmembrane protein, similar to HMT1_SCHPO|Q02592 heavy metal tolerance protein precursor from Schizosaccharomyces pombe (830 aa), FASTA scores: opt: 806, E(): 5.1e-39, (32.9% identity in 504 aa overlap); etc. Also similar to MTCY02B10.13 from Mycobacterium tuberculosis, FASTA score: (31.9% identity in 576 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters). Cofactor: FAD	P9WQJ9	No	cell wall and cell processes		MMAR_4037	MSMEG_6554	Mb1383				
NC_000962.3	Mycobrowser_v3	CDS	1515623	1517362	.	+	0	Rv1349	irtB	Involved in iron homeostasis. Responsible for energy coupling to the transport system and for the translocation of the substrate across the membrane.	Iron-regulated transporter IrtB	Rv1349, (MTCY02B10.13), len: 579 aa. IrtB, iron-regulated transporter. Probable transmembrane protein, most similar to YWJA_BACSU|P45861 hypothetical ABC transporter from Bacillus subtilis (575 aa), FASTA scores: opt: 721, E(): 1.8e-35, (28.9% identity in 567 aa overlap); etc. Also similar to MTCY02B10.12 from Mycobacterium tuberculosis, FASTA score: (31.9% identity in 576 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters). Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WQJ7	No	cell wall and cell processes		MMAR_4036	MSMEG_6553	Mb1384				
NC_000962.3	Mycobrowser_v3	CDS	1520005	1521876	.	-	0	Rv1354c	Rv1354c	Function unknown	Conserved hypothetical protein	Rv1354c, (MTCY02B10.18c), len: 623 aa. Conserved hypothetical protein, similar to many hypothetical proteins e.g. the C-terminus of G1001455 Synechocystis sp. (1244 aa), FASTA scores: opt: 933, E(): 0, (36.8% identity in 462 aa overlap); also similar to Rv1357c|MTCY02B10.21c (34.0% identity in 253 aa overlap).	P9WM13	No	conserved hypotheticals	ML1750,ML1750c		MSMEG_2196	Mb1389c				
NC_000962.3	Mycobrowser_v3	CDS	1526612	1530091	.	+	0	Rv1358	Rv1358	Involved in transcriptional mechanism	Probable transcriptional regulatory protein	Rv1358, (MTCY02B10.22), len: 1159 aa. Probable transcriptional regulatory protein, some similarity to AFSR_STRCO|P25941 regulatory protein afsr from Streptomyces coelicolor (993 aa), FASTA scores: opt: 210, E(): 5.5e-06, (27.5% identity in 739 aa overlap). Similar also to Rv0890C|MTCY31.18c (65.5% identity in 884 aa overlap) and to Rv1359|MTCY02B10.23 (43.7% identity in 197 aa overlap). Contains PS00017 ATP/GTP-binding site motif A, PS00622 Bacterial regulatory proteins, luxR family signature. Helix turn helix motif present at aa 1116-1137, (Score 1291, +3.59 SD).	Q11028	No	regulatory proteins	ML1753,ML1753c			Mb1393				
NC_000962.3	Mycobrowser_v3	CDS	1541020	1541805	.	+	0	Rv1368	lprF	Unknown	Probable conserved lipoprotein LprF	Rv1368, (MTCY02B12.02), len: 261 aa. Probable lprF, conserved lipoprotein; similar to Mycobacterium tuberculosis hypothetical lipoproteins e.g. Rv1270c|Y08C_MYCTU|Q11049 hypothetical 26.4 kDa protein cy50.12. (257 aa), FASTA scores: opt: 286, E(): 5.3e-11, (26.3% identity in 270 aa overlap), also Rv1411c|MTCY21B4.28c, (32.8% identity in 253 aa overlap) and Rv2945c. Contains possible N-terminal signal sequence and appropriately positioned prokaryotic lipoprotein lipid attachment site (PS00013). Belongs to the LPPX/lprafg family of lipoproteins.	P9WK47	No	cell wall and cell processes		MMAR_2188		Mb1403				
NC_000962.3	Mycobrowser_v3	CDS	1550579	1551217	.	-	0	Rv1377c	Rv1377c	Function unknown; probably involved in cellular metabolism	Putative transferase	Rv1377c, (MTCY02B12.11c), len: 212 aa. Putative transferase, similar to YQEM_BACSU|P54458 hypothetical 28.3 kDa protein from Bacillus subtilis (247 aa), FASTA scores: opt: 221, E(): 7.6e-08, (30.6% identity in 144 aa overlap); some similarity to methyltransferases, also similar to Mycobacterium tuberculosis hypothetical proteins Rv0560c, Rv3699, and Rv2675c (~ 39.1% identity in 197 aa overlap).	P71805	No	intermediary metabolism and respiration	ML0529,ML0529c		MSMEG_3041	Mb1412c				
NC_000962.3	Mycobrowser_v3	CDS	1551228	1552655	.	-	0	Rv1378c	Rv1378c	Function unknown	Conserved hypothetical protein	Rv1378c, (MTCY02B12.12c), len: 475 aa. Conserved hypothetical protein, similar to other Mycobacterium tuberculosis hypothetical proteins e.g. Rv3074|MTCY22D7.07C (424 aa), FASTA scores: E(): 0, (73.0% identity in 429 aa overlap).	P71806	No	conserved hypotheticals	ML0530,ML0530c		MSMEG_6025	Mb1413c				
NC_000962.3	Mycobrowser_v3	CDS	1553232	1554191	.	+	0	Rv1380	pyrB	Involved in pyrimidine biosynthesis (second step) [catalytic activity: carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate]	Probable aspartate carbamoyltransferase PyrB (ATCase) (aspartate transcarbamylase)	Rv1380, (MTCY02B12.14), len: 319 aa. Probable pyrB, aspartate carbamoyltransferase, similar to many e.g. PYRB_BACCL|P41008 aspartate carbamoyltransferase from Bacillus caldolyticus (308 aa), FASTA scores, opt: 639, E(): 7.3e-36, (39.5% identity in 311 aa overlap). Contains PS00097 Aspartate and ornithine carbamoyltransferases signature. Belongs to the ATCases/OTCases family.	P9WIT7	No	intermediary metabolism and respiration	ML0532	MMAR_2195	MSMEG_3043	Mb1415				
NC_000962.3	Mycobrowser_v3	CDS	1555971	1557101	.	+	0	Rv1383	carA	Involved in both arginine and pyrimidine biosynthesis [catalytic activity: 2 ATP + L-glutamine + CO(2) + H(2)O = 2 ADP + phosphate + glutamate + carbamoyl phosphate]	Probable carbamoyl-phosphate synthase small chain CarA (carbamoyl-phosphate synthetase glutamine chain)	Rv1383, (MTCY02B12.17), len: 376 aa. Probable carA, Carbamoyl-phosphate synthase small chain, similar to many e.g. CARA_ECOLI|P00907 carbamoyl-phosphate synthase small chain from Escherichia coli (382 aa), FASTA scores: opt: 796, E(): 0, (45.5% identity in 382 aa overlap). Contains PS00442 Glutamine amidotransferases class-I active site. The gatase domain belongs to type-1 glutamine amidotransferases. subunit: composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate.	P9WPK5	No	intermediary metabolism and respiration	ML0535	MMAR_2198	MSMEG_3046	Mb1418				
NC_000962.3	Mycobrowser_v3	CDS	1557101	1560448	.	+	0	Rv1384	carB	Involved in both arginine and pyrimidine biosynthesis [catalytic activity: 2 ATP + L-glutamine + CO(2) + H(2)O = 2 ADP + phosphate + glutamate + carbamoyl phosphate.]	Probable carbamoyl-phosphate synthase large chain CarB (carbamoyl-phosphate synthetase ammonia chain)	Rv1384, (MTCY02B12.18-MTCY21B4.01), len: 1115 aa. Probable carB, Carbamoyl-phosphate synthase large chain , similar to many e.g. CARB_ECOLI|P00968 E. coli (1072 aa), FASTA scores: E(): 0, (52.3% identity in 1118 aa overlap). Contains two PS00867 Carbamoyl-phosphate synthase subdomain signature 2 and PS00866 Carbamoyl-phosphatesynthase subdomain signature 1. subunit: composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate.	P9WPK3	No	intermediary metabolism and respiration	ML0536	MMAR_2199	MSMEG_3047	Mb1419				
NC_000962.3	Mycobrowser_v3	CDS	1561769	1563388	.	+	0	Rv1387	PPE20	Function unknown	PPE family protein PPE20	Rv1387, (MTCY21B4.04), len: 539 aa. PPE20, Member of Mycobacterium tuberculosis PPE family of proteins, similar to many e.g. Y05F_MYCTU|Q10892 hypothetical 46.9 kd protein cy251.15 (463 aa), FASTA scores: E(): 4.2e-26, (37.7% identity in 531 aa overlap); similar also to MTCY274.23c (37.5% identity in 168 aa overlap). Contains PS00343 Gram-positive cocci surface proteins 'anchoring' hexapeptide. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WI23	No	PE/PPE	ML0539			Mb1422				
NC_000962.3	Mycobrowser_v3	CDS	1565441	1566697	.	+	0	Rv1391	dfp	Flavoprotein affecting synthesis of DNA and pantothenate metabolism	Probable DNA/pantothenate metabolism flavoprotein homolog Dfp	Rv1391, (MTCY21B4.08), len: 418 aa. Probable dfp, DNA/pantothenate metabolism flavoprotein homolog, similar to many e.g. DFP_ECOLI|P24285 Escherichia coli (430 aa), FASTA scores: opt: 763, E(): 0, (40.2% identity in 408 aa overlap).	P9WNZ1	No	intermediary metabolism and respiration	ML0543	MMAR_2204	MSMEG_3054	Mb1426				
NC_000962.3	Mycobrowser_v3	CDS	1566825	1568036	.	+	0	Rv1392	metK	Involved in the activated methyl cycle. Catalyzes the formation of S-adenosylmethionine from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. [catalytic activity : ATP + L-methionine + H(2)O = phosphate + diphosphate + S-adenosyl-L-methionine]	Probable S-adenosylmethionine synthetase MetK (mat) (AdoMet synthetase) (methionine adenosyltransferase)	Rv1392, (MTCY21B4.09), len: 403 aa. Probable metK, S-adenosylmethionine synthetase, similar to many e.g. METK_STAAU|P50307 Staphylococcus aureus (397 aa), FASTA scores: opt: 1484, E(): 0, (58.0% identity in 400 aa overlap). Contains PS00376 S-adenosylmethionine synthetase signature 1, PS00377 S-adenosylmethionine synthetase signature 2. Belongs to the adomet synthetase family.	P9WGV1	No	intermediary metabolism and respiration	ML0544	MMAR_2205	MSMEG_3055	Mb1427				
NC_000962.3	Mycobrowser_v3	CDS	1571047	1572081	.	+	0	Rv1395	Rv1395	Involved in transcriptional mechanism	Transcriptional regulatory protein	Rv1395, (MTCY21B4.12), len: 344 aa. Transcriptional regulatory protein (see citation below), similar to many e.g. URER_PROMI|Q02458 urease operon transcriptional activator from Proteus mirabilis (293 aa), FASTA scores: E():1.5e-08, (41.7% identity in 84 aa overlap); YHIX_ECOLI|P37639 hypothetical transcriptional regulatory protein from Escherichia coli (274 aa), FASTA scores: opt: 238, E(): 3.5e-09, (27.3% identity in 249 aa overlap); and G296916|X68281 possible virulence-regulating protein from Mycobacterium tuberculosis (339 aa), FASTA scores: opt: 228, E(): 1.9e-08, (27.0% identity in 278 aa overlap). Helix turn helix motif present, aa 261-282 (+4.68 SD). Belongs to the AraC/XylS family of transcriptional regulators. 3' part corrected since first submission (-14 aa). Experimentally shown to induce the expression of the cytochrome P450 gene (Rv1394c) and represses its own transcription.	P9WMJ1	No	regulatory proteins				Mb1430				
NC_000962.3	Mycobrowser_v3	CDS	2752848	2752994	.	-	0	Rv2452c	Rv2452c	Unknown	Hypothetical protein	Rv2452c, (MTV008.08c), len: 48 aa. Hypothetical unknown protein (see citation below).	O53179	No	conserved hypotheticals				Mb2479c				
NC_000962.3	Mycobrowser_v3	CDS	1579598	1580422	.	-	0	Rv1403c	Rv1403c	Causes methylation	Putative methyltransferase	Rv1403c, (MTCY21B4.20c), len: 274 aa. Putative methyltransferase, similar to PMTA_RHOSH|Q05197 phosphatidylethanolamine m-methyltransferase (203 aa), FASTA scores: opt: 217, E(): 1.1e-07, (37.1% identity in 105 aa overlap); similar to Rv1405c|MTCY21B4.22c (59.3% identity in 273 aa overlap) and to Rv1523, Rv2952, etc.	P9WLY9	No	intermediary metabolism and respiration	ML0549,ML0549c	MMAR_2212		Mb1438c				
NC_000962.3	Mycobrowser_v3	CDS	1582166	1583104	.	+	0	Rv1406	fmt	Modify the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by:(I) promoting its recognition by IF2 and (II) impairing its binding to EFTU-GTP. [catalytic activity: 10-formyltetrahydrofolate + L-methionyl-tRNA + H(2)O = tetrahydrofolate + N-formylmethionyl-tRNA]	Probable methionyl-tRNA formyltransferase Fmt	Rv1406, (MTCY21B4.23), len: 312 aa. Probable fmt, methionyl-tRNA formyltransferase, similar to many e.g. FMT_ECOLI|P23882 Escherichia coli (314 aa), FASTA scores: opt: 616, E(): 6.7e-31, (39.3% identity in 303 aa overlap). Belongs to the FMT family.	P9WND3	No	information pathways	ML0552	MMAR_2215	MSMEG_3064	Mb1441				
NC_000962.3	Mycobrowser_v3	CDS	1585194	1586213	.	+	0	Rv1409	ribG	Involved in riboflavin biosynthesis (at the second and third steps). Converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate [catalytic activity 1: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5-phosphoribosylamino)uracil + NH(3)] [catalytic activity 2: 5-amino-6-(5-phosphoribitylamino)uracil + NADP(+) = 5-amino-6-(5-phosphoribosylamino)uracil + NADPH].	Probable bifunctional riboflavin biosynthesis protein RibG : diaminohydroxyphosphoribosylaminopyrimidine deaminase (riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino) uracil reductase (HTP reductase)	Rv1409, (MTCY21B4.26), len: 339 aa. Probable ribG (alternate gene name: ribD), bifunctional riboflavin biosynthesis protein, including diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase, similar to many e.g. RIBD_ECOLI|P25539 riboflavin-specific deaminase from Escherichia coli (367 aa), FASTA scores: E(): 0, (39.8% identity in 364 aa overlap); etc. Contains PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature. In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminases family. In the C-terminal section; belongs to the HTP reductase family.	P9WPH1	No	intermediary metabolism and respiration	ML0555	MMAR_2218	MSMEG_3067	Mb1444				
NC_000962.3	Mycobrowser_v3	CDS	1587772	1588482	.	-	0	Rv1411c	lprG	Unknown	Conserved lipoprotein LprG	Rv1411c, (MTCY21B4.28c), len: 236 aa. lprG (alternate gene name: P27), conserved lipoprotein, similar to Mycobacterium tuberculosis hypothetical lipoproteins e.g. Rv1270c|MTCY50.12 (35.1% identity in 245 aa overlap); Rv1368, Rv2945c. Contains N-terminal signal sequence and appropriately positioned prokaryotic lipoprotein lipid attachment site (PS00013). Note that the Rv1410c-Rv1411c operon seems transcribed from two promoters in Mycobacterium bovis BCG (see Bigi et al., 2000). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WK45	No	cell wall and cell processes	ML0557,ML0557c	MMAR_2220	MSMEG_3070	Mb1446c				
NC_000962.3	Mycobrowser_v3	CDS	1591671	1592153	.	+	0	Rv1416	ribH	Riboflavin synthase is a bifunctional enzyme complex involved in riboflavin synthesis. Riboflavin synthase catalyzes the formation of riboflavin from 5-amino-6-(1'-D)- ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2- butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl- amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone- 4-phosphate yielding 6,7-dimethyl-8-lumazine.	Probable riboflavin synthase beta chain RibH (6,7-dimethyl-8-ribityllumazine synthase) (DMRL synthase) (lumazine synthase)	Rv1416, (MTCY21B4.34), len: 160 aa. Probable ribH, riboflavin synthase beta chain, similar to many e.g. RISB_ECOLI|P25540 Escherichia coli (156 aa), FASTA scores: opt: 330, E(): 1.8e-15, (44.1% identity in 145 aa overlap). Note alternative GTG start possible overlapping the stop codon of Rv1415|MTCY21B4.33. Belongs to the DMRL synthase family. N-terminus extended since first submission (previously 154 aa).	P9WHE9	No	intermediary metabolism and respiration	ML0560	MMAR_2223	MSMEG_3073	Mb1451				
NC_000962.3	Mycobrowser_v3	CDS	1594042	1595982	.	+	0	Rv1420	uvrC	Involved in nucleotide excision repair. The ABC excision nuclease is a DNA repair enzyme that catalyzes the excision reaction of UV-damaged nucleotide segments producing oligomers having the modified base(S). Attaches to the UVRA-UVRB complex, displacing UVRA, and the damaged DNA strand is nicked on both sides of the damaged site	Probable excinuclease ABC (subunit C - nuclease) UvrC	Rv1420, (MTCY21B4.38), len: 646 aa. Probable uvrC, excinuclease ABC, subunit C; nuclease (see citations below), similar to many e.g. UVRC_PSEFL|P32966 Pseudomonas fluorescens (607 aa), fasta scores: opt: 738, E(): 8.4e-39, (36.6% identity in 629 aa overlap). Belongs to the UvrC family.	P9WFC5	No	information pathways	ML0562	MMAR_2227	MSMEG_3078	Mb1455				
NC_000962.3	Mycobrowser_v3	CDS	1597906	1598883	.	+	0	Rv1423	whiA	Involved in transcriptional mechanism	Probable transcriptional regulatory protein WhiA	Rv1423, (MTCY21B4.41-MTCY493.31c), len: 325 aa. Putative whiA, transcriptional regulator, probably equivalent to AL035591|SCC54.10 whiA protein from Streptomyces coelicolor (328 aa), FASTA scores: opt: 1505, E(): 0, (70.4% identity in 324 aa overlap). Also some similarity to O06975|YVCL hypothetical protein from Bacillus subtilis (316 aa), FASTA scores: E(): 1.8e-0 8, (25.7% identity in 304 aa overlap).	P9WF45	No	regulatory proteins	ML0565		MSMEG_3081	Mb1458				
NC_000962.3	Mycobrowser_v3	CDS	1612342	1612950	.	-	0	Rv1435c	Rv1435c	Unknown	Probable conserved proline, glycine, valine-rich secreted protein	Rv1435c, (MTCY493.19), len: 202 aa. Probable conserved Pro-, Gly-, Val-rich secreted protein (see citation below) with a N-terminal signal sequence. Similar at C-terminus to AF017099|AF017099_1 Mycobacterium tuberculosis pGB1 (87 aa), FASTA scores: opt: 550, E(): 2.3e-17, (97.7% identity in 86 aa overlap). Shows some similarity to N-terminus of CPN_DROME|Q02910 calphotin. Drosophila melanogaster (865 aa), FASTA scores: opt: 266, E(): 2.5e-05, (37.2% identity in 191 aa overlap). Contains at least five 7 aa imperfect repeats. Also shows similarity to other Mycobacterium tuberculosis proteins e.g. MTCI237.20c (34.7% identity in 193 aa overlap), MTCI65.25c (36.9% identity in 160 aa overlap) and MTCI65.24c (34.2% identity in 196 aa overlap).	O06823	No	cell wall and cell processes		MMAR_2238	MSMEG_0673	Mb1470c				
NC_000962.3	Mycobrowser_v3	CDS	1613307	1614326	.	+	0	Rv1436	gap	Involved in second phase of glycolysis (first step) [catalytic activity: D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH.]	Probable glyceraldehyde 3-phosphate dehydrogenase Gap (GAPDH)	Rv1436, (MTCY493.18c), len: 339 aa. Probable gap, Glyceraldehyde 3-phosphate dehydrogenase, highly similar to many e.g. G3P_MYCLE|P46713 Mycobacterium leprae (339 aa), FASTA scores: opt: 1933, E():0, (89.1% identity in 339 aa overlap). Contains PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. Belongs to the glyceraldehyde 3-phosphate dehydrogenase family.	P9WN83	No	intermediary metabolism and respiration	ML0570	MMAR_2239	MSMEG_3084	Mb1471				
NC_000962.3	Mycobrowser_v3	CDS	2894893	2895960	.	-	0	Rv2571c	Rv2571c	Unknown	Probable transmembrane alanine and valine and leucine rich protein	Rv2571c, (MTCY227.30), len: 355 aa. Probable transmembrane ala-, val-, leu-rich protein, showing some similarity with other membrane proteins e.g. Q99340|YFDA_CORGL hypothetical integral membrane protein from Corynebacterium glutamicum (Brevibacterium flavum) (359 aa), FASTA scores: opt: 338, E(): 2.5e-13, (29.4% identity in 255 aa overlap); Q9RD86|SCF43.02 putative integral membrane protein from Streptomyces coelicolor (379 aa), FASTA scores: opt: 208, E(): 2.1e-05, (26.05% identity in 303 aa overlap); Q9RD81|SCF43.07 putative integral membrane protein from Streptomyces coelicolor (419 aa), FASTA scores: opt: 205, E(): 3.5e-05, (25.15% identity in 362 aa overlap); etc.	P9WL89	No	cell wall and cell processes		MMAR_2160		Mb2601c				
NC_000962.3	Mycobrowser_v3	CDS	1625418	1626962	.	-	0	Rv1447c	zwf2	Involved in pentose phosphate pathway [catalytic activity: D-glucose 6-phosphate + NADP(+) = D-glucono- 1,5-lactone 6-phosphate + NADPH]	Probable glucose-6-phosphate 1-dehydrogenase Zwf2 (G6PD)	Rv1447c, (MTCY493.07), len: 514 aa. Probable zwf2 (ZWF), Glucose-6-phosphate 1-dehydrogenase, highly similar to many e.g. G6PD_SYNY3|P73411 Synechocystis sp. (509 aa), FASTA scores: opt: 1578, E(): 0, (46.8% identity in 509 aa overlap). Also similar to M. tuberculosis Rv1121, zwf glucose-6-phosphate 1-dehydrogenase. Contains PS00069 Glucose-6-phosphate dehydrogenase active site. Mycobacterium tuberculosis has two genes for ZWF. This one looks like a classical ZWF. Belongs to the glucose-6-phosphate dehydrogenase family.	P9WN73	No	intermediary metabolism and respiration	ML0581,ML0581c	MMAR_2252	MSMEG_3101	Mb1482c				
NC_000962.3	Mycobrowser_v3	CDS	1628097	1630199	.	-	0	Rv1449c	tkt	This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. It catalyzes the reversible transfer of a two-carbon KETOL unit from xylulose 5-phosphate to an aldose receptor [catalytic activity: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate]	Transketolase Tkt (TK)	Rv1449c, (MTCY493.05), len: 700 aa. tkt, transketolase. Highly similar to several e.g. TKT_MYCLE|P46708 transketolase (tk) from Mycobacterium leprae (699 aa), FASTA scores: opt: 4216, E(): 0, (89.1% identity in 700 aa overlap). Start site chosen by homology. Contains PS00801 Transketolase signature 1. Belongs to the transketolase family. Thought to be differentially expressed within host cells (see Triccas et al., 1999).	P9WG25	No	intermediary metabolism and respiration	ML0583,ML0583c	MMAR_2254		Mb1484c				
NC_000962.3	Mycobrowser_v3	CDS	1636004	1638229	.	-	0	Rv1452c	PE_PGRS28	Function unknown	PE-PGRS family protein PE_PGRS28	Rv1452c, (MTCY493.02), len: 741 aa. PE_PGRS28, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see Brennan and Delogu, 2002), similar to Y03A_MYCTU|Q10637 hypothetical glycine-rich 49.6 kDa protein (603 aa), fasta scores: opt: 2090, E(): 0, (56.3% identity in 641 aa overlap).	Q79FP1	No	PE/PPE				Mb1487c				
NC_000962.3	Mycobrowser_v3	CDS	1644363	1646138	.	-	0	Rv1459c	Rv1459c	Unknown	Possible conserved integral membrane protein	Rv1459c, (MTV007.06c), len: 591 aa. Predicted to be in the GT-C superfamily of glycosyltransferases (See Liu and Mushegian, 2003). Possible conserved integral membrane protein, equivalent to MLCL536.30|Z99125 hypothetical protein from Mycobacterium leprae (593 aa), FASTA scores: opt: 1670, E(): 0, (78.6% identity in 585 aa overlap). Also similar to M. tuberculosis protein Rv2174|MTV021.07 (33.1% identity in 523 aa overlap).	O53150	No	cell wall and cell processes	ML0591,ML0591c	MMAR_2264	MSMEG_3120	Mb1494c				
NC_000962.3	Mycobrowser_v3	CDS	1646989	1649529	.	+	0	Rv1461	Rv1461	Function unknown	Conserved protein	Rv1461, (MTV007.08), len: 846 aa. Conserved protein. Equivalent of spliced protein from Mycobacterium leprae MLCL536.28c len: 869. Residues 1-253 represent N-extein, and 613-846 the C-extein. The intein present from residues 254 - 612 is different in sequence and site of the insertion from the one present in MLCL536.28c. FASTA scores: Z99125|MLCL536_23 Mycobacterium leprae cosmid L536 (869 aa), opt: 1498 E(): 0, (54.1% identity in 917 aa overlap). The mature protein is similar to Z99120|BSUB0017_150 hypothetical Bacillus subtilis protein (465 aa), FASTA scores: opt:1053, E(): 0, (34.8% identity in 821 aa overlap). The intein shows some similarity to inteins from U67548|MJU67548_6 Methanococcus jannaschii (895 aa), FASTA scores: opt: 181, E(): 0.00023, (25.2% identity in 274 aa overlap).	P9WFP7	No	conserved hypotheticals	ML0593			Mb1496				
NC_000962.3	Mycobrowser_v3	CDS	1651518	1652771	.	+	0	Rv1464	csd	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine	Probable cysteine desulfurase Csd	Rv1464, (MTV007.11), len: 417 aa. Probable csd, cysteine desulfurase. Equivalent to Q49690|MLCL536.25C cysteine desulfurase from Mycobacterium leprae (418 aa), FASTA scores: opt: 2333, E(): 0, (85.4% identity in 417 aa overlap); and similar to cysteine desulfurase from other organisms. Also similar to M. tuberculosis proteins Rv3025c|ISCS and Rv3778c. Contains PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site. Belongs to class-V of pyridoxal-phosphate-dependent aminotransferases. CSD subfamily.	P9WQ69	No	intermediary metabolism and respiration	ML0596	MMAR_2269	MSMEG_3125	Mb1499				
NC_000962.3	Mycobrowser_v3	CDS	1653673	1655502	.	-	0	Rv1467c	fadE15	Function unknown, but involvement in lipid degradation.	Probable acyl-CoA dehydrogenase FadE15	Rv1467c, (MTV007.14c), len: 609 aa. Probable fadE15, acyl-CoA dehydrogenase, highly similar to NP_302639.1|NC_002677 acyl-CoA dehydrogenase from Mycobacterium leprae (611 aa). Also highly similar to many e.g. T36481 probable acyl-CoA dehydrogenase (fragment) from Streptomyces coelicolor (491 aa) (has its N-terminus very shorter); NP_384640.1|NC_003047 putative acyl-CoA dehydrogenase protein from Sinorhizobium meliloti (598 aa); ACDS_MEGEL|Q06319 acyl-CoA dehydrogenase (short-chain specific) from Megasphaera elsdenii (383 aa), FASTA scores: E(): 2e-12, (25.4% identity in 410 aa overlap); etc. Also highly similar to fadE5|Rv0244c|MTV034.10c acyl-CoA dehydrogenase from Mycobacterium tuberculosis (611 aa); and similar to other proteins from Mycobacterium tuberculosis.	O53158	No	lipid metabolism	ML0599,ML0599c	MMAR_2273		Mb1502c				
NC_000962.3	Mycobrowser_v3	CDS	1679322	1680629	.	+	0	Rv1490	Rv1490	Unknown	Probable membrane protein	Rv1490, (MTCY277.12), len: 435 aa. Probable membrane protein.	P9WLX1	No	cell wall and cell processes				Mb1527				
NC_000962.3	Mycobrowser_v3	CDS	1656963	1658936	.	+	0	Rv1469	ctpD	Cation-transporting ATPase; possibly catalyzes the transport of a cation (possibly cadmium) with the hydrolyse of ATP [catalytic activity: ATP + H(2)O + cation(in) = ADP + phosphate + cation(out)].	Probable cation transporter P-type ATPase D CtpD	Rv1469, (MTV007.16), len: 657 aa. Probable ctpD, cation-transporting P-type ATPase D (transmembrane protein), highly similar to others e.g. T35947 probable cation-transporting ATPase from Streptomyces coelicolor (638 aa); NP_442633.1|NC_000911 cation-transporting ATPase (E1-E2 ATPase) from Synechocystis sp. strain PCC 6803 (642 aa), FASTA scores: opt: 1438, E(): 0, (41.9% identity in 592 aa overlap); NP_389268.1|NC_000964 protein similar to heavy metal-transporting ATPase from Bacillus subtilis (637 aa); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. Rv3743c|MTV025.091c|CTPJ (660 aa). Contains PS00154 E1-E2 ATPases phosphorylation site. Belongs to the cation transport ATPases family (E1-E2 ATPases), subfamily IB.	P9WPT3	No	cell wall and cell processes	ML1819,ML1819c	MMAR_2275	MSMEG_5403	Mb1504				
NC_000962.3	Mycobrowser_v3	CDS	1659370	1659741	.	+	0	Rv1471	trxB1	Thioredoxin participates in various redox reactions through the reversible oxidation of its active center dithiol, to a disulfide, & catalyzes dithiol-disulfide exchange reactions.	Probable thioredoxin TrxB1	Rv1471, (MTV007.18), len: 123 aa. Probable trxB1, thioredoxin, similar to many bacterial thioredoxins e.g. P33636|THI2_ECOLI from Escherichia coli (139 aa), FASTA scores: opt: 290, E(): 1.8e-13, (44.3% identity in 97 aa overlap); etc. Highly similar to Rv1470|TrxA probable thioredoxin from Mycobacterium tuberculosis (124 aa), FASTA scores: opt: 402, E(): 1.2e-32, (54.4% identity in 114 aa overlap). Contains PS00194 Thioredoxin family active site. Belongs to the thioredoxin family. Note that previously known as trxB.	L7N664	No	intermediary metabolism and respiration	ML1818,ML1818c	MMAR_2277	MSMEG_3138	Mb1506				
NC_000962.3	Mycobrowser_v3	CDS	1659763	1660620	.	+	0	Rv1472	echA12	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Possible enoyl-CoA hydratase EchA12 (enoyl hydrase) (unsaturated acyl-CoA hydratase) (crotonase)	Rv1472, (MTV007.19), len: 285 aa. Possible echA12, enoyl-CoA hydratase, highly similar to P53526|ECHH_MYCLE|NP_301896.1|NC_002677 possible enoyl-CoA hydratase/isomerase from Mycobacterium leprae (294 aa), FASTA scores: opt: 1265, E(): 0, (72.0% identity in 271 aa overlap). Also similar to others e.g. CAA66096.1|X97452 enoyl-CoA isomerase from Escherichia coli strain K12 (262 aa); CAC44593.1|AL596162 putative enoyl-CoA hydratase from Streptomyces coelicolor (275 aa); etc. Also similar to others from Mycobacterium tuberculosis e.g. ECHA16|Rv2831|MTCY16B7.11c (249 aa), FASTA scores: opt: 232, E(): 1.3e-15, (33.8% identity in 204 aa overlap); etc.	P9WNN7	No	lipid metabolism	ML1241,ML1817c	MMAR_2278	MSMEG_3139	Mb1507				
NC_000962.3	Mycobrowser_v3	CDS	1662641	1663204	.	-	0	Rv1474c	Rv1474c	Involved in transcriptional mechanism	Probable transcriptional regulatory protein	Rv1474c, (MTV007.21c), len: 187 aa. Probable transcription regulator, equivalent to AF0021|AF002133_1 transcriptional regulator from Mycobacterium avium strain GIR10 (82 aa), FASTA scores: opt: 490, E(): 6.7e-26, (92.5% identity in 80 aa overlap). Also similar to Q59431|UIDR_ECOLI UID operon repressor (GUS operon) from Escherichia coli (196 aa), FASTA scores: opt: 192, E(): 5.8e-06, (28.5% identity in 172 aa overlap). Belongs to the TetR/AcrR family of transcriptional regulators. Helix turn helix motif predicted at aa 33-54 (+3.40 SD).	O53165	No	regulatory proteins	ML1815	MMAR_2281	MSMEG_3142	Mb1510c				
NC_000962.3	Mycobrowser_v3	CDS	1666990	1668408	.	+	0	Rv1477	ripA	Unknown, but supposed involvement in virulence.	Peptidoglycan hydrolase	Rv1477, (MTV007.24), len: 472 aa. RipA, peptidoglycan hydrolase (see Hett et al., 2007). Secreted, cell-associated protein. The last 277 residues are nearly identical to those of AF0060|AF006054_1 hypothetical invasion protein INV1 from Mycobacterium tuberculosis (277 aa), FASTA scores: opt: 1833, E(): 0, (98.2% identity in 277 aa overlap); also very similar to AF0021|AF002133_4 invasin 1 protein from Mycobacterium avium (273 aa), FASTA scores: opt: 1452, E(): 0, (78.1% identity in 279 aa overlap). Similar to Rv1566c|MTCY336.37|Z95586 Mycobacterium tuberculosis cosmid (230 aa), FASTA scores: opt: 528, E(): 4.4e-20, (52.0% identity in 150 aa overlap); and weakly similar to p60 proteins of Listeria spp throughout its length e.g. M80351|LISIAPB_1 Listeria monocytogenes iap-related protein (478 aa), FASTA scores: opt: 251, E(): 8e-06, (24.4% identity in 487 aa overlap). C-terminal domain highly similar to next orf Rv1478|MTV007.25. Interacts with RpfB and RpfE (see Hett et al., 2007). Predicted to be an outer membrane protein (See Song et al., 2008).	O53168	No	virulence, detoxification, adaptation	ML1812,ML1812c	MMAR_2284	MSMEG_3145	Mb1513				
NC_000962.3	Mycobrowser_v3	CDS	1678552	1678908	.	+	0	Rv1489	Rv1489	Function unknown	Conserved protein	Rv1489, len: 118 aa. Conserved protein, similar to hypothetical proteins from Mycobacterium avium subsp. paratuberculosis and Streptomyces coelicolor e.g. AJ250017_1 insertion sequence IS900, Locus 3, putative invasion protein from M. paratuberculosis (138 aa), FASTA scores: opt: 120, E(): 0.26, (34.375% identity in 96 aa overlap); SCD6.11c|AL353815_11 possible integral membrane protein from Streptomyces coelicolor (136 aa), FASTA scores: opt: 106, E(): 2.2, (35.9% identity in 103 aa overlap). ORF predicted by GC plot. Replaces previous Rv1489c on other strand.	L7N692	No	conserved hypotheticals		MMAR_2295	MSMEG_3156	Mb1525				
NC_000962.3	Mycobrowser_v3	CDS	1672457	1673299	.	-	0	Rv1482c	Rv1482c	Function unknown	Conserved hypothetical protein	Rv1482c, (MTCY277.03c), len: 280 aa. Conserved hypothetical protein, highly similar to O07396|AF002133 Mycobacterium avium protein MAV346 (346 aa), FASTA scores: E(): 0, (65.2% identity in 342 aa overlap); slight similarity to GRPE_ECOLI|P09372 heat shock protein from E. coli (197 aa), FASTA scores: opt: 139, E(): 0.012, (28.3% identity in 159 aa overlap). Similar to Mycobacterium tuberculosis hypothetical proteins Rv3517, Rv3555c, Rv3714c, Rv1073, etc. Start changed since first submission (-59 aa).	P71763	No	conserved hypotheticals			MSMEG_5643	Mb1518c				
NC_000962.3	Mycobrowser_v3	CDS	1674202	1675011	.	+	0	Rv1484	inhA	This isozyme is involved in mycolic acid biosynthesis. Second reductive step in fatty acid biosynthesis. Involved in the resistance against the antituberculosis drugs isoniazid and ethionamide [catalytic activity: acyl-[acyl-carrier protein] + NAD(+) = trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH].	NADH-dependent enoyl-[acyl-carrier-protein] reductase InhA (NADH-dependent enoyl-ACP reductase)	Rv1484, (MTCY277.05), len: 269 aa. InhA, NADH-dependent enoyl-[acyl-carrier-protein] reductase (see citations below). Identical to INHA_MYCTU|P46533 enoyl-[acyl-carrier-protein] reductase from Mycobacterium tuberculosis and G1155270 Mycobacterium bovis enoyl acp reductase. Some similarity to the short-chain dehydrogenases/reductases (SDR) family.	P9WGR1	No	lipid metabolism	ML1806,ML1806c	MMAR_2290	MSMEG_3151	Mb1520				
NC_000962.3	Mycobrowser_v3	CDS	1677397	1678542	.	+	0	Rv1488	Rv1488	Function unknown	Possible exported conserved protein	Rv1488, (MTCY277.09), len: 381 aa. Possible exported conserved protein; contains possible N-terminal signal sequence. Similar to YBBK_ECOLI|P77367 hypothetical protein ybbK from Escherichia coli (305 aa), FASTA scores: opt: 716, E(): 0, (37.1% identity in 307 aa overlap). Similar to stomatin-like proteins e.g. AF065260|AF065260_1 Clostridium difficile (320 aa), FASTA scores: opt: 767, E(): 0, (42.3% identity in 307 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008).	P9WPR9	No	cell wall and cell processes	ML1802,ML1802c	MMAR_2294	MSMEG_3155	Mb1524				
NC_000962.3	Mycobrowser_v3	CDS	1681208	1681966	.	-	0	Rv1491c	Rv1491c	Unknown	Conserved membrane protein	Rv1491c, (MTCY277.13c), len: 252 aa. Conserved membrane protein. Similar to hypothetical proteins from many organisms e.g. YDJZ_ECOLI|P76221 Escherichia coli (235 aa), FASTA scores: opt: 223, E():6.7 e-07, (31.7% identity in 145 aa overlap); AL133252|SCE46.15 Streptomyces coelicolor (249 aa), FASTA scores: opt: 378, E(): 1.5e-17, (39.1% identity in 169 aa overlap). Also similar to Mycobacterium tuberculosis hypothetical protein Rv0625c.	P9WFS3	No	cell wall and cell processes	ML1801	MMAR_2301	MSMEG_3157	Mb1528c				
NC_000962.3	Mycobrowser_v3	CDS	1682157	1684004	.	+	0	Rv1492	mutA	Involved in propionic acid fermentation. Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates [catalytic activity: (R)-2-methyl-3-oxopropanoyl-CoA = succinyl- CoA]	Probable methylmalonyl-CoA mutase small subunit MutA (MCM)	Rv1492, (MTCY277.14), len: 615 aa. Probable mutA, Methylmalonyl-CoA mutase small-subunit, strong similarity to e.g. MUTA_STRCM|Q05064 methylmalonyl-CoA mutase beta-subunit from Streptomyces cinnamonensis (616 aa), FASTA scores: opt: 1512, E(): 0, (45.9% identity in 628 aa overlap). Contains PS00213 Lipocalin signature, PS00544 Methylmalonyl-CoA mutase signature. Belongs to the methylmalonyl-CoA mutase family.	P9WJK7	No	lipid metabolism	ML1800,ML1800c	MMAR_2302	MSMEG_3158	Mb1529				
NC_000962.3	Mycobrowser_v3	CDS	1690407	1690805	.	+	0	Rv1499	Rv1499	Unknown	Hypothetical protein	Rv1499, (MTCY277.21), len: 132 aa. Hypothetical unknown protein; was initially longer but has been shortened (-24 aa) owing to overlap with Rv1498A. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P71780	No	conserved hypotheticals				Mb1537				
NC_000962.3	Mycobrowser_v3	CDS	1690850	1691878	.	+	0	Rv1500	Rv1500	Function unknown	Probable glycosyltransferase	Rv1500, (MTCY277.22), len: 342 aa. Probable glycosyltransferase, hydrophobic domain near C-terminus. Some similarity to putative glycosyl-transferases from Bacillus subtilis e.g. O34319|YKCC_BACSU (323 aa), opt: 490, E(): 6.1e-25, (28.85% identity in 312 aa overlap) and to N-acetyl glucosamine transferases. Also similar to G1001347 hypothetical 36.7 kDa protein (318 aa), FASTA scores: opt: 523, E(): 7.2e-26, (30.6% identity in 307 aa overlap).	P9WMX5	No	intermediary metabolism and respiration		MMAR_2313		Mb1538				
NC_000962.3	Mycobrowser_v3	CDS	1703074	1704096	.	+	0	Rv1511	gmdA	Unknown, probably involved in nucleotide-sugar metabolism	GDP-D-mannose dehydratase GmdA (GDP-mannose 4,6 dehydratase) (GMD)	Rv1511, (MTCY277.33), len: 340 aa. Probable gmdA, GDP-D-mannose dehydratase, equivalent to AF125999|AF125999_13 Mycobacterium avium enzyme (343 aa), FASTA scores: opt: 2085, E(): 0, (89.1% identity in 338 aa overlap); similar to G755218 pseudomonas aeruginosa GDP-D-mannose dehydratase (GCA) (323 aa), FASTA scores: opt: 1073, E(): 0, (51.9% identity in 320 aa overlap); and to S74433 GDP-D-mannose dehydratase rfbD - Syn (362 aa), FASTA scores: opt: 1405, E(): 0, (63.9% identity in 327 aa overlap).	P71790	No	intermediary metabolism and respiration								
NC_000962.3	Mycobrowser_v3	CDS	1704093	1705061	.	+	0	Rv1512	epiA	Unknown, probably involved in nucleotide-sugar metabolism	Probable nucleotide-sugar epimerase EpiA	Rv1512, (MTCY277.34), len: 322 aa. Probable epiA, nucleotide sugar epimerase, equivalent to AJ223832|MAS223832_4 from Mycobacterium avium silvaticum (339 aa), FASTA scores: opt: 1821, E(): 0, (84.6% identity in 318 aa overlap); and similar to WCAG_ECOLI|P32055 colanic acid biosynthesis protein wcaG (321 aa), FASTA scores: opt: 835, E(): 0, (53.5% identity in 316 aa overlap).	P71791	No	intermediary metabolism and respiration								
NC_000962.3	Mycobrowser_v3	CDS	1712302	1714053	.	+	0	Rv1521	fadD25	Function unknown, but involvement in lipid degradation.	Probable fatty-acid-AMP ligase FadD25 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)	Rv1521, (MTCY19G5.07), len: 583 aa. Probable fadD25, fatty-acid-AMP synthetase, highly similar to many e.g. P71495|U75685 acyl-CoA synthase from Mycobacterium bovis (582 aa), FASTA scores: opt: 2486, E(): 0, (63.4% identity in 584 aa overlap); NP_301232.1|NC_002677 acyl-CoA synthetase from Mycobacterium leprae (579 aa); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. fadD24 (584 aa); fadD28 (580 aa); etc.	P9WQ45	No	lipid metabolism		MMAR_2341	MSMEG_4731	Mb1548				
NC_000962.3	Mycobrowser_v3	CDS	1714172	1717612	.	-	0	Rv1522c	mmpL12	Unknown. Thought to be involved in fatty acid transport.	Probable conserved transmembrane transport protein MmpL12	Rv1522c, (MTCY19G5.06), len: 1146 aa. Probable mmpL12, conserved transmembrane transport protein (see Tekaia et al., 1999), member of RND superfamily. Strong similarity to many Mycobacterial membrane proteins e.g. Q49619|G466786 putative transport protein B1170_C1_181 from Mycobacterium leprae (1008 aa), FASTA scores: opt: 2418, E(): 0, (51.0% identity in 1006 aa overlap); etc. Also highly similar to MmpL8|MTCY48.08c|Rv3823c probable conserved transmembrane transport protein from Mycobacterium tuberculosis, FASTA score: (34.3% identity in 376 aa overlap); and some similarity to MmpL10|MTCY20G9|Rv1183 probable conserved transmembrane transport protein, FASTA score: (27.2% identity in 1011 aa overlap). Belongs to the MmpL family.	P9WJT7	No	cell wall and cell processes		MMAR_2342	MSMEG_4741	Mb1549c				
NC_000962.3	Mycobrowser_v3	CDS	1720780	1722060	.	-	0	Rv1526c	Rv1526c	Unknown; thought to be involved in cellular metabolism.	Probable glycosyltransferase	Rv1526c, (MTCY19G5.02), len: 426 aa. Probable glycosyltransferase, highly similar to G467196 Protein L518_C2_147 from Mycobacterium leprae (421 aa), FASTA scores, opt: 1497, E(): 0, (55.0% identity in 424 aa overlap); similar to G452504 rhamnosyltransferase (24.7% identity in 433 aa overlap); and P96565|U84350 glycosyltransferase GTFE from Amycolatopsis orientalis (408 aa), E(): 3.4e-24, (28.4% identity in 429 aa overlap), also high similarity to Rv1524|MTCY19G5.04c (58.7 % identity in 416 aa overlap).	P9WLV1	No	intermediary metabolism and respiration								
NC_000962.3	Mycobrowser_v3	CDS	1753716	1755431	.	+	0	Rv1550	fadD11	Function unknown, but involvement in lipid degradation.	Probable fatty-acid-CoA ligase FadD11 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv1550, (MTCY48.15c), len: 571 aa. Probable fadD11, fatty-acid-CoA synthetase, similar, except in N-terminus, to many e.g. SC6A5.39|T35430 probable long-chain-fatty-acid--CoA ligase from Streptomyces coelicolor (612 aa); NP_301672.1|NC_002677 putative long-chain-fatty-acid-CoA ligase from Mycobacterium leprae (600 aa); P44446|LCFH_HAEIN putative long-chain-fatty-acid-CoA ligase from Haemophilus influenzae (607 aa), FASTA scores: opt: 762, E(): 2.3e-38, (34.4% identity in 436 aa overlap); etc. Contains PS00455 Putative AMP-binding domain signature. Belongs to the ATP-dependent AMP-binding enzyme family. Possible frameshift with respect to previous ORF Rv1549|MTCY48.16c but we can find no sequence error to account for this.	P9WQ53	No	lipid metabolism		MMAR_2370	MSMEG_3131	Mb1576				
NC_000962.3	Mycobrowser_v3	CDS	1739856	1741247	.	+	0	Rv1537	dinX	Involved in DNA metabolism [catalytic activity: N deoxynucleoside triphosphate = N diphosphate + {DNA}N].	Probable DNA polymerase IV DinX (pol IV 1) (DNA nucleotidyltransferase (DNA-directed))	Rv1537, (MTCY48.28c, MT1589), len: 463 aa. Probable dinX (alternate gene name: dinB1), DNA polymerase IV. Similar to umuC, mucB, samb, and impb (UV protection and mutation) e.g. IMPB_SALTY|P18642 impb protein from Salmonella typhimurium (424 aa), FASTA scores: opt: 386, E(): 1.7e-17, (27.5% identity in 415 aa overlap); etc. Also similar to Mycobacterium tuberculosis Rv3056|dinP. Belongs to the DNA polymerase type-Y family.	P9WNT3	No	information pathways	ML1197	MMAR_2359	MSMEG_3172	Mb1564				
NC_000962.3	Mycobrowser_v3	CDS	1751297	1753333	.	-	0	Rv1548c	PPE21	Function unknown	PPE family protein PPE21	Rv1548c, (MTCY48.17), len: 678 aa. PPE21, Member of the Mycobacterium tuberculosis PPE family, similar to several e.g. YHS6_MYCTU|P42611 hypothetical 50.6 kDa protein in hsp65 3' region (517 aa), FASTA scores: opt:1142, E(): 0, (40.6% identity in 616 aa overlap); also similar to MTCY31.06c (54.9% identity in 381 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008).	P9WI21	No	PE/PPE				Mb1575c				
NC_000962.3	Mycobrowser_v3	CDS	1757681	1759432	.	+	0	Rv1552	frdA	Involved in interconversion of fumarate and succinate (anaerobic respiration) [catalytic activity: succinate + acceptor = fumarate + reduced acceptor].	Probable fumarate reductase [flavoprotein subunit] FrdA (fumarate dehydrogenase) (fumaric hydrogenase)	Rv1552, (MTCY48.13c), len: 583 aa. Probable frdA, fumarate reductase, flavoprotein subunit, highly similar to others e.g. P00363|FRDA_ECOLI fumarate reductase flavoprotein subunit from Escherichia coli strain K12 (601 aa), FASTA scores: opt: 2102, E(): 0, (54.7% identity in 585 aa overlap); NP_232284.1|NC_002505 fumarate reductase, flavoprotein subunit from Vibrio cholerae (602 aa); frdA|NP_438995.1|NC_000907 fumarate reductase, flavoprotein subunit from Haemophilus influenzae (599 aa); etc. Contains PS00504 Fumarate reductase / succinate dehydrogenase FAD-binding site. Note that fumarate reductase forms part of an enzyme complex containing four subunits: a flavoprotein (Rv1552|frdA), an iron-sulfur (Rv1553|frdB), and two hydrophobic anchor proteins (Rv1554|frdC and Rv1555|frdD).	P9WN91	No	intermediary metabolism and respiration				Mb1578				
NC_000962.3	Mycobrowser_v3	CDS	1761744	1762937	.	+	0	Rv1557	mmpL6	Unknown. Thought to be involved in fatty acid transport.	Probable conserved transmembrane transport protein MmpL6	Rv1557, (MTCY48.08c), len: 397 aa. Probable mmpL6, conserved transmembrane transport protein (see citations below). Member of RND superfamily, with strong similarity to C-terminal part of members of large Mycobacterial membrane protein family belonging to RND superfamily including: mmpL1, mmpL2, mmpL3, etc. Probably truncated (see Brosch et al., 2002). Belongs to the MmpL family.	P9WJU9	No	cell wall and cell processes				Mb1583				
NC_000962.3	Mycobrowser_v3	CDS	1765400	1767142	.	-	0	Rv1562c	treZ	Involved in trehalose biosynthesis (protective effect). Mycobacteria can produce trehalose from glucose 6-phosphate and UDP-glucose (the OTSA-OTSB pathway) from glycogen-like alpha(1-->4)-linked glucose polymers (the trey-TREZ pathway) and from maltose (the TRES pathway). Seems to have additional alpha-glucosidase activity.	Maltooligosyltrehalose trehalohydrolase TreZ	Rv1562c, (MTCY48.03), len: 580 aa. TreZ (previously called glgZ), Maltooligosyltrehalose trehalohydrolase, confirmed biochemically (see citation below). Similar to Q44316|D63343 TREZ maltooligosyl trehalose trehalohydrolase from arthrobacter SP (598 aa), FASTA scores: opt: 2071, E(): 0, (52.2% identity in 582 aa overlap); also similar to 1,4-alpha-glucan branching enzymes e.g. GLGB_BACST|P30538 (639 aa), FASTA scores: opt: 313, E(): 3.8e-13, (27.5% identity in 462 aa overlap). Also similar to Mycobacterium tuberculosis proteins Rv1326c|glgB, and Rv1563c treY (previously glgY).	P9WQ23	No	virulence, detoxification, adaptation		MMAR_2377	MSMEG_3184	Mb1588c				
NC_000962.3	Mycobrowser_v3	CDS	1769436	1771601	.	-	0	Rv1564c	treX	Possibly involved in trehalose biosynthesis (protective effect). Mycobacteria can produce trehalose from glucose 6-phosphate and UDP-glucose (the OtsA-OtsB pathway) from glycogen-like alpha(1-->4)-linked glucose polymers (the TreY-TreZ pathway) and from maltose (the TreS pathway).	Probable maltooligosyltrehalose synthase TreX	Rv1564c, (MTCY48.01), len: 721 aa. Probable treX (previously called glgX), Maltooligosyltrehalose synthase. Strong similarity to D83245|g1890053 treX, glycogen debranching enzyme (glgX) from Sulfolobus acidocaldarius (713 aa), FASTA score: opt: 2396, E(): 0, (48.4% identity in 709 aa overlap); similar to GLGX_HAEIN|P45178 glycogen operon protein glgx (659 aa), FASTA scores: opt: 1512, E(): 0, (42.3% identity in 645 aa overlap).	P9WQ25	No	virulence, detoxification, adaptation	ML1212,ML1212c	MMAR_2379	MSMEG_3186	Mb1591c				
NC_000962.3	Mycobrowser_v3	CDS	1771640	1773829	.	-	0	Rv1565c	Rv1565c	Unknown	Conserved hypothetical membrane protein	Rv1565c, (MTCY336.38), len: 729 aa. Conserved hypothetical membrane protein, some similarity to O05402 hypothetical 72.2 kDa protein from Bacillus subtilis (634 aa), FASTA results: opt: 384, E(): 4.8e-17, (29.1% identity in 378 aa overlap); and to Y392_HAEIN|P43993 hypothetical protein hi0392 from H. influenzae (245 aa), FASTA results: opt: 265, E(): 5.5e-10, (28.3% identity in 247 aa overlap). C-terminal half equivalent to AL049478|MLCL458_19 (274 aa) (78.5% identity in 274 aa overlap). Also similar to Mycobacterium tuberculosis hypothetical proteins Rv0111, Rv0228, Rv1254, Rv0517. N-terminal half hydrophobic.	O06625	No	cell wall and cell processes	ML1213,ML1213c	MMAR_2380	MSMEG_3187	Mb1592c				
NC_000962.3	Mycobrowser_v3	CDS	1775392	1776705	.	+	0	Rv1568	bioA	Involved in bioconversion of pimelate into dethiobiotin [catalytic activity: S-adenosyl-L-methionine + 8-amino-7- oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8- diaminononanoate]. Supposedly involved in stationary-phase survival.	Adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA	Rv1568, (MTCY336.35c), len: 437 aa. bioA, adenosylmethionine-8-amino-7-oxononanoate aminotransferase , equivalent to a predicted homologous protein from Mycobacterium smegmatis (see citation below). Highly similar to BIOA_MYCLE|P4548 from Mycobacterium leprae (436 aa), FASTA results: opt: 2534, E(): 0, (85.1% identity in 436 aa overlap). Also similar to other Mycobacterium tuberculosis proteins e.g. MTCY227.12c (449 aa), FASTA score: E(): 3.5e-16, (29.5% identity in 421 aa overlap). Contains aminotransferases class-III pyridoxal-phosphate attachment site (PS00600). Belongs to class-III of pyridoxal-phosphate-dependent aminotransferases.	P9WQ81	No	intermediary metabolism and respiration	ML1216	MMAR_2383	MSMEG_3188	Mb1595				
NC_000962.3	Mycobrowser_v3	CDS	1780643	1782064	.	-	0	Rv1576c	Rv1576c	Unknown	Probable PhiRv1 phage protein	Rv1576c, (MTCY336.28), len: 473 aa. Probable phiRV1 phage protein (capsid subunit) (see citation below). Highly similar to hypothetical Mycobacterium tuberculosis protein Rv2650c|MTCY441.19 phiRV2 phage related protein, FASTA scores: opt: 2782, E(): 0, (89.1% identity in 468 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06614	No	insertion seqs and phages				Mb1602c				
NC_000962.3	Mycobrowser_v3	CDS	1783309	1783623	.	-	0	Rv1579c	Rv1579c	Unknown	Probable PhiRv1 phage protein	Rv1579c, (MTCY336.25), len: 104 aa. Probable phiRv1 phage protein (see citation below). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06611	No	insertion seqs and phages				Mb1605c				
NC_000962.3	Mycobrowser_v3	CDS	1783620	1783892	.	-	0	Rv1580c	Rv1580c	Unknown	Probable PhiRv1 phage protein	Rv1580c, (MTCY336.24), len: 90 aa. Probable phiRv1 phage protein (see citation below). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06610	No	insertion seqs and phages				Mb1606c				
NC_000962.3	Mycobrowser_v3	CDS	1784497	1785912	.	-	0	Rv1582c	Rv1582c	Unknown	Probable PhiRv1 phage protein	Rv1582c, (MTCY336.22), len: 471 aa. Probable phiRv1 phage protein (see citation below). N-terminus is similar to C-terminus of Q38030 ORF9 Bacteriophage phi-C31 (519 aa), FASTA scores: opt: 331, E(): 6.5e-15, (28.5% identity in 235 aa overlap); and C-terminus to whole of Q38031 ORF10 of Bacteriophage phi-C31 (202 aa), FASTA scores: opt: 353, E(): 1e-16, (31.1% identity in 190 aa overlap). Also similar to part of AB016282|AB016282_42 Bacteriophage phi-105 (806 aa), FASTA scores: opt: 790, E(): 0, (32.7% identity in 459 aa overlap). Similarity to other phage proteins described as putative DNA-polymerase or DNA-primase. Also slightly similar to MTCY441.24c, FASTA scores: E(): 0.0055, (36.0% identity in 75 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06608	No	insertion seqs and phages				Mb1608c				
NC_000962.3	Mycobrowser_v3	CDS	1787096	1788505	.	-	0	Rv1586c	Rv1586c	Integration of phiRv1 into chromosome.	Probable PhiRv1 integrase	Rv1586c, (MTCY336.18), len: 469 aa. Probable phiRv1 integrase, possibly member of the serine family of recombinases (see citation below), similar to several bacteriophage integrases e.g. Q37839 ORF469 protein from Bacteriophage R4 (469 aa), FASTA scores: opt: 623, E(): 1.6e-29, (31.1% identity in 482 aa overlap); and Bacteriophage TP901-1. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O06604	No	insertion seqs and phages				Mb1612c				
NC_000962.3	Mycobrowser_v3	CDS	1802035	1802667	.	+	0	Rv1601	hisB	Histidine biosynthesis (seventh step) [catalytic activity: D-erythro-1-(imidazol-4-YL)glycerol 3- phosphate = 3-(imidazol-4-YL)-2-oxopropyl phosphate + H(2)O]	Probable imidazole glycerol-phosphate dehydratase HisB	Rv1601, (MTCY336.03c), len: 210 aa. Probable hisB, imidazole glycerol-phosphate dehydratase. Similar to many e.g. HIS7_STRCO|P16247 from Streptomyces coelicolor (197 aa),FASTA results: opt: 763, E(): 0, (57.4% identity in 202 aa overlap). Belongs to the imidazoleglycerol-phosphate dehydratase family.	P9WML9	No	intermediary metabolism and respiration	ML1259	MMAR_2397	MSMEG_3207	Mb1627				
NC_000962.3	Mycobrowser_v3	CDS	1793997	1794707	.	-	0	Rv1593c	Rv1593c	Function unknown	Conserved protein	Rv1593c, (MTCY336.11), len: 236 aa. Conserved protein, highly similar to Q49628|B1170_F1_44 from Mycobacterium leprae (286 aa), FASTA scores: opt: 1304, E (): 0, (85.4% identity in 233 aa overlap); similar to several putative DNA hydrolases e.g. Q9S233|SCI51.07C from Streptomyces coelicolor (239 aa), FASTA scores: opt: 415, E(): 4.6e-20, (34.8% identity in 221 aa overlap); also similar to P74291|SLR1690 hypothetical protein from synechocystis (261 aa), FASTA scores: opt: 228, E(): 1.4e-17, (31.5% identity in 213 aa overlap).	O06597	No	conserved hypotheticals	ML1224,ML1224c	MMAR_2390	MSMEG_3198	Mb1619c				
NC_000962.3	Mycobrowser_v3	CDS	1795805	1797388	.	+	0	Rv1595	nadB	Quinolinate biosynthesis. Catalyzes the oxidation of L-aspartate to iminoaspartate which is condensed with dihydroxyacetone phosphate to quinolinate under the action of quinolinate synthase a [catalytic activity: L-aspartate + H(2)O + O(2) = oxaloacetate + NH(3) + H(2)O(2)]	Probable L-aspartate oxidase NadB	Rv1595, (MTCY336.09c), len: 527 aa. Probable nadB, L-aspartate oxidase. Similar to many e.g. Q49617 L-aspartate oxidase (quinolinate synthetase) from Mycobacterium leprae (424 aa), FASTA results: opt: 2152, E(): 0, (82.0% identity in 400 aa overlap). Also shows some similarity to Rv1552 frdA from Mycobacterium tuberculosis (583 aa), FASTA results: E(): 1e-10, (35.3% identity in 566 aa overlap). Heterodimer. The quinolinate synthetase complex consists of the two enzymes quinolinate synthetase a and B.	P9WJJ9	No	intermediary metabolism and respiration	ML1226	MMAR_2392	MSMEG_3200	Mb1621				
NC_000962.3	Mycobrowser_v3	CDS	1800896	1802038	.	+	0	Rv1600	hisC1	Histidine biosynthesis (eighth step) [catalytic activity: L-histidinol-phosphate + 2-oxoglutarate = 3-(imidazol-4-YL)-2-oxopropyl phosphate + L-glutamate]	Probable histidinol-phosphate aminotransferase HisC1	Rv1600, (MTCY336.04c), len: 380 aa. Probable hisC1, histidinol-phosphate aminotransferase O06591. Similar to many e.g. HIS8_STRCO|P16246 from Streptomyces coelicolor (369 aa), FASTA results: opt: 1353, E(): 0, (59.0% identity in 356 aa overlap). Some similarity to other Mycobacterium tuberculosis aminotransferases e.g. Rv3772|MTCY13D12.06, FASTA results: E(): 7.4e-25, (33.7% identity in 365 aa overlap). Contains aminotransferases class-II pyridoxal-phosphate attachment site (PS00599). Belongs to class-II of pyridoxal-phosphate-dependent aminotransferases. Note that previously known as hisC.	P9WML7	No	intermediary metabolism and respiration	ML1258	MMAR_2396	MSMEG_3206	Mb1626				
NC_000962.3	Mycobrowser_v3	CDS	1892270	1893562	.	-	0	Rv1666c	cyp139	Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	Probable cytochrome P450 139 Cyp139	Rv1666c, (MT1706, MTV047.02c), len: 430 aa. Probable cyp139, cytochrome P450, similar to many e.g. U38537|APU38537_7 from Anabaena sp. (459 aa), FASTA scores: opt: 516, E(): 1.7e-26, (25.8% identity in 418 aa overlap). Contains PS00086 Cytochrome P450 cysteine heme-iron ligand signature. Belongs to the cytochrome P450 family.	P9WPM1	No	intermediary metabolism and respiration	ML1238,ML1238c	MMAR_2475		Mb1694c				
NC_000962.3	Mycobrowser_v3	CDS	1805653	1806000	.	+	0	Rv1606	hisI	Involved in histidine biosynthesis pathway (at the third step) [catalytic activity: 5-phosphoribosyl-AMP + H(2)O = 5-(5-phospho-D-ribosylaminoformimino)-1-(5-phospho-ribosyl) imidazole-4- carboxamide.]	Probable phosphoribosyl-AMP 1,6 cyclohydrolase HisI	Rv1606, (MTV046.04), len: 115 aa. Probable hisI, phosphoribosyl-AMP 1,6 cyclohydrolase, similar to several e.g. X82010|RSHISI_2 HISI from Rhodobacter sphaeroides (119 aa), FASTA scores: opt: 378, E(): 2.8e-21, (52.3% identity in 109 aa overlap); etc.	P9WMM7	No	intermediary metabolism and respiration	ML1264	MMAR_2402	MSMEG_3212	Mb1632				
NC_000962.3	Mycobrowser_v3	CDS	1806181	1807263	.	+	0	Rv1607	chaA	Involved in transport of ions (presumably calcium) across the membrane. Responsible for the translocation of the substrate across the membrane.	Probable ionic transporter integral membrane protein ChaA	Rv1607, (MTV046.05), len: 360 aa. Probable chaA, ionic transporter integral membrane protein, putative calcium/proton antiporter, similar to many e.g. P31801|CHAA_ECOLI calcium/proton antiporter from Escherichia coli (366 aa), FASTA scores: opt: 736, E(): 0, (35.9% identity in 351 aa overlap). Equivalent to Mycobacterium leprae AL049913|MLCB1610_21 (77.7% identity in 364 aa overlap). Seems to belong to the CaCA family.	O53910	No	cell wall and cell processes	ML1267	MMAR_2409		Mb1633				
NC_000962.3	Mycobrowser_v3	CDS	1807903	1809453	.	+	0	Rv1609	trpE	Involved in tryptophan biosynthesis pathway (at the first step). Supposed tetramer of two components I and two components II: component I (Rv1609|trpE) catalyzes the formation of anthranilate using ammonia rather than glutamine, whereas component II (Rv0013|trpG) provides glutamine amidotransferase activity [catalytic activity: chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate].	Anthranilate synthase component I TrpE (glutamine amidotransferase)	Rv1609, (MTCY01B2.01, MTV046.07), len: 516 aa. trpE, anthranilate synthase component I. FASTA best: TRPE_CLOTM|P14953 anthranilate synthase component I from Clostridium thermocellum (494 aa), E(): 0, (42.6% identity in 498 aa overlap). Some similarity to Rv2386c|MTCY253.35, E(): 6.3e-17; and Rv3215|MTCY07D11.11c, E(): 5.7e-15. Belongs to the anthranilate synthase component I family.	P9WFX3	No	intermediary metabolism and respiration	ML1269	MMAR_2411	MSMEG_3217	Mb1635				
NC_000962.3	Mycobrowser_v3	CDS	1811127	1812359	.	+	0	Rv1612	trpB	Tryptophan biosynthesis pathway (fifth last step). The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. [catalytic activity: L-serine + 1-(indol-3-YL)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H(2)O]	Tryptophan synthase, beta subunit TrpB	Rv1612, (MTCY01B2.04), len: 410 aa. TrpB, tryptophan synthase beta chain. Equivalent to AL049913|MLCB1610_25 from Mycobacterium leprae (340 aa) (88.5% identity in 331 aa overlap). Similar to others e.g. TRPB_CAUCR|P12290 tryptophan synthase beta chain from Caulobacter crescentus (406 aa), FASTA scores: opt: 1662, E(): 0, (60.6% identity in 404 aa overlap). Belongs to the TrpB family. Tetramer of two alpha and two beta chains.	P9WFX9	No	intermediary metabolism and respiration	ML1272	MMAR_2414	MSMEG_3220	Mb1638				
NC_000962.3	Mycobrowser_v3	CDS	1819963	1821693	.	-	0	Rv1620c	cydC	Involved in active transport across the membrane of component linked with the assembly of cytochrome: involved in cytochrome biogenesis (aerobic respiration). Responsible for energy coupling to the transport system and for the translocation of the substrate across the membrane.	Probable 'component linked with the assembly of cytochrome' transport transmembrane ATP-binding protein ABC transporter CydC	Rv1620c, (MTCY01B2.12c), len: 576 aa. Probable cydC, transmembrane ATP-binding protein ABC transporter involved in transport of component linked with the assembly of cytochrome (see citation below), similar to others e.g. CYDC_ECOLI|P23886 transport ATP-binding protein from Escherichia coli (573 aa), FASTA scores: opt: 631, E(): 1.6e-30, (28.5% identity in 569 aa overlap); C-terminal part of AL034355|SCD78_14 from Streptomyces coelicolor (1172 aa), FASTA scores: opt: 956, E(): 0, (38.8% identity in 554 aa overlap); etc. Contains (PS00211) ABC transporters family signature, and (PS00017) ATP/GTP-binding site motif A (P-loop). Belongs to the ATP-binding transport protein family (ABC transporters).	O06137	No	intermediary metabolism and respiration	ML1281,ML1281c	MMAR_2423		Mb1646c				
NC_000962.3	Mycobrowser_v3	CDS	1824430	1825887	.	-	0	Rv1623c	cydA	Involved in the respiratory chain (at the terminal step): aerobic respiration. Cytochrome D terminal oxidase complex is the component of the aerobic respiratory chain that is supposedly predominant when cells are grown at low aeration [catalytic activity: ubiquinol-8 + O(2) = ubiquinone-8 + H(2)O].	Probable integral membrane cytochrome D ubiquinol oxidase (subunit I) CydA (cytochrome BD-I oxidase subunit I)	Rv1623c, (MTCY01B2.15c), len: 485 aa. Probable cydA (previously known as appC, but renamed cydA to conform with Mycobacterium smegmatis nomenclature), cytochrome D ubiquinol oxidase subunit I, integral membrane protein, similar to others e.g. P26459|APPC_ECOLI|CYXA|CBDA|B0978 cytochrome BD-II oxidase subunit I from Escherichia coli strain K12 (514 aa), FASTA scores: opt: 870, E(): 0, (35.9% identity in 485 aa overlap); AL034355|SCD78_12 from Streptomyces coelicolor (501 aa), FASTA scores: opt: 1099, E(): 0, (48.6% identity in 510 aa overlap); etc.	L7N662	No	intermediary metabolism and respiration	ML1284,ML1284c	MMAR_2426	MSMEG_3233	Mb1649c				
NC_000962.3	Mycobrowser_v3	CDS	1826614	1827945	.	-	0	Rv1625c	cya	Involved in cAMP synthesis [catalytic activity: ATP = 3',5'-cyclic AMP + diphosphate]. Inhibited by polyphosphates.	Membrane-anchored adenylyl cyclase Cya (ATP pyrophosphate-lyase) (adenylate cyclase)	Rv1625c, (MT1661, MTCY01B2.17c), len: 443 aa. Cya, membrane-anchored adenylyl cyclase (see citations below). C-terminal half is similar to region in numerous eukaryotic adenylate and guanylate cyclases. N-terminal half hydrophobic. FASTA score: CYG2_RAT|P22717 guanylate cyclase soluble, beta-2 chain (682 aa), FASTA scores: opt: 552, E(): 2.7e-26, (40.3% identity in 226 aa overlap). Some similarity to Rv2435c|MTCY428.11 from Mycobacterium tuberculosis (730 aa), E(): 7e-19. Start changed since first submission (+25 aa). Belongs to adenylyl cyclase class-4/guanylyl cyclase family.	P9WQ35	No	intermediary metabolism and respiration	ML1285,ML1285c	MMAR_2428		Mb1651c				
NC_000962.3	Mycobrowser_v3	CDS	1830665	1833379	.	+	0	Rv1629	polA	Involved in post-incision events. In addition to DNA polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity [catalytic activity: N deoxynucleoside triphosphate = N diphosphate + {DNA}(N)].	Probable DNA polymerase I PolA	Rv1629, (MTCY01B2.21), len: 904 aa. Probable polA, DNA polymerase I (see citations below). Has DNA polymerase family a signature (PS00447) at C-terminal end. FASTA best: DPO1_MYCTU|Q07700 DNA polymerase I from Mycobacterium tuberculosis (904 aa). Some similarity to Rv2090|MTCY49.30 (393 aa), E(): 2.2e-18, (38.7% identity in 292 aa overlap). Belongs to DNA polymerase type-a family.	P9WNU5	No	information pathways	ML1381,ML1381c	MMAR_2432	MSMEG_3839	Mb1655				
NC_000962.3	Mycobrowser_v3	CDS	1833542	1834987	.	+	0	Rv1630	rpsA	Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short shine-dalgarno (SD) purine-rich sequence.	30S ribosomal protein S1 RpsA	Rv1630, (MTCY01B2.22), len: 481 aa. rpsA, 30S ribosomal protein S1. FASTA best: RS1_MYCLE|P46836 30s ribosomal protein S1 from Mycobacterium leprae (482 aa), opt: 2655, E(): 0, (87.2% identity in 483 aa overlap).	P9WH43	No	information pathways	ML1382	MMAR_2433	MSMEG_3833	Mb1656				
NC_000962.3	Mycobrowser_v3	CDS	1837075	1839171	.	+	0	Rv1633	uvrB	Involved in nucleotide excision repair. The ABC excision nuclease is a DNA repair enzyme that catalyzes the excision reaction of UV-damaged nucleotide segments producing oligomers having the modified base(S). UVRB stimulates the ATPase activity of UVRA in the presence of UV-irradiated double-stranded DNA. It also enhances the ability of UVRA to bind to UV-irradiated duplex DNA	Probable excinuclease ABC (subunit B - helicase) UvrB	Rv1633, (MTCY01B2.25), len: 698 aa. Probable uvrB, excinuclease ABC, subunit B; helicase (see Mizrahi & Andersen 1998; Sancar 1994); has ATP/GTP-binding site motif A (P-loop; PS00017) near N-terminus (see citation below). FASTA best: UVRB_MICLU|P10125 from Micrococcus luteus (709 aa), opt: 3268, E(): 0, (71.3% identity in 704 aa overlap). Also similar to Mycobacterium tuberculosis Rv2973c (recG); and Rv1020 (mfd). Belongs to the UVRB family.	P9WFC7	No	information pathways	ML1387	MMAR_2437	MSMEG_3816	Mb1659				
NC_000962.3	Mycobrowser_v3	CDS	1852273	1852878	.	+	0	Rv1641	infC	If-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins.	Probable initiation factor if-3 InfC	Rv1641, (MTCY06H11.05), len: 201 aa. Probable infC, initiation factor if-3, similar to many e.g. IF3_BACST|P03000 initiation factor if-3 from Bacillus stearothermophilus (171 aa), FASTA scores: opt: 560, E(): 1.9e-27, (50.6% identity in 166 aa overlap). Note that an AUC initiation codon has been used, the Bacillus (IF3_BACSU) and Escherichia coli (IF3_ECOLI) proteins use an AUU initiation codon, and the Myxococcus xanthus (DSG_MYXXA) homolog uses a AUC. Belongs to the if-3 family.	P9WKJ9	No	information pathways	ML1394	MMAR_2448	MSMEG_3793	Mb1668				
NC_000962.3	Mycobrowser_v3	CDS	1859758	1862253	.	+	0	Rv1650	pheT	Charging PHE-tRNA [catalytic activity: ATP + L-phenylalanine + tRNA(PHE) = AMP + diphosphate + L-phenylalanyl-tRNA(PHE)]	Probable phenylalanyl-tRNA synthetase, beta chain PheT	Rv1650, (MTCY06H11.15), len: 831 aa. Probable pheT, Phenylalanyl-tRNA synthetase beta chain, similar to several e.g. SYFB_ECOLI|P07395 from Escherichia coli (795 aa), FASTA scores: opt: 995, E(): 0, (31.8% identity in 847 aa overlap). Belongs to the phenylalanyl-tRNA synthetase beta chain family - subfamily 1.	P9WFU1	No	information pathways	ML1402	MMAR_2457	MSMEG_3777	Mb1677,Mb1678				
NC_000962.3	Mycobrowser_v3	CDS	1862347	1865382	.	-	0	Rv1651c	PE_PGRS30	Function unknown. Thought to be involved in virulence.	PE-PGRS family protein PE_PGRS30	Rv1651c, (MTCY06H11.16c), len: 1011 aa. PE_PGRS30, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citations below), similar to many e.g. Q10637|Y03A_MYCTU hypothetical glycine-rich 49.6 kd protein (603 aa), FASTA scores: opt: 1757, E(): 0, (50.8% identity in 714aa overlap). The transcription of this CDS seems to be activated in macrophages (see Ramakrishnan et al., 2000).	Q79FL8	No	PE/PPE	ML1403			Mb1679c				
NC_000962.3	Mycobrowser_v3	CDS	1870842	1871354	.	+	0	Rv1657	argR	Regulates arginine biosynthesis genes	Probable arginine repressor ArgR (AHRC)	Rv1657, (MTCY06H11.22), len: 170 aa. Probable argR, Arginine repressor (alternate gene name: ahrC). Similar to AHRC_BACSU|P17893 arginine hydroximate resistance protein from Bacillus subtilis (149 aa), FASTA scores: opt: 283, E(): 1.8e-11, (34.5% identity in 142 aa overlap); and ARGR_ECOLI|P15282 arginine repressor from Escherichia coli (156 aa), FASTA scores: opt: 194, E(): 6.4e-06, (30.8% identity in 146 aa overlap). Belongs to the ArgR family.	P9WPY9	No	regulatory proteins	ML1411	MMAR_2467	MSMEG_3771	Mb1685				
NC_000962.3	Mycobrowser_v3	CDS	1886512	1888020	.	+	0	Rv1663	pks17	Potentially involved in some intermediate steps for the synthesis of a polyketide molecule which may be involved in secondary metabolism	Probable polyketide synthase Pks17	Rv1663, (MTCY275.02), len: 502 aa. Probable pks17, polyketide synthase, similar to other polyketide synthases e g. ERY2_SACER|Q03132 erythronolide synthase, modules 3 and 4 (3567 aa) from Saccharopolyspora erythraea (Streptomyces erythraeus), FASTA scores: opt: 1207, E(): 0, (43.9% identity in 531 aa overlap). Also similar to other Mycobacterium tuberculosis probable polyketide synthases e.g. pks7 and pks1. Note that the similarity extends into the upstream ORF Rv1662 (MTCY275.01) and this could be accounted for by a frameshift, although the sequence has been checked and no discrepancy was found. Contains PS00012 Phosphopantetheine attachment site.	O06585	No	lipid metabolism				Mb1691				
NC_000962.3	Mycobrowser_v3	CDS	1891226	1892287	.	+	0	Rv1665	pks11	Possibly involved in the biosynthesis of secondary metabolites [catalytic activity: 3 malonyl-CoA + 4-coumaroyl-CoA = 4 CoA + naringenin chalcone + 3 CO2]	Chalcone synthase Pks11	Rv1665, (MTCY275.04-MTV047.01), len: 353 aa. pks11, chalcone synthase, some similarity to BCSA_BACSU|P54157 putative chalcone synthase from Bacillus subtilis (365 aa), FASTA scores: opt: 615, E(): 6.2e-32, (33.4% identity in 308 aa overlap); and to many plant chalcone synthases e.g. CHS_VIGUN|P51089 chalcone synthase (388 aa), FASTA scores: opt: 391, E(): 7.8e-18, (27.2% identity in 349 aa overlap). Highly similar to upstream ORF Rv1660|MTCY06H11.25 pks10 (72.7% identity in 308 aa overlap); and Rv1372 pks18.	P9WPF3	No	lipid metabolism	ML1236	MMAR_2474		Mb1693				
NC_000962.3	Mycobrowser_v3	CDS	1896876	1898207	.	-	0	Rv1672c	Rv1672c	Thought to be involved in transport across the membrane. Responsible for the translocation of undetermined substrate across the membrane.	Probable conserved integral membrane transport protein	Rv1672c, (MTV047.07c), len: 443 aa. Probable conserved integral membrane transport protein, major facilitator superfamily, similar to several phthalate transporters or tartrate transporters e.g. U25634|AVU25634_2 Agrobacterium vitis plasmid pTrAB (433 aa), FASTA scores: opt: 914, E(): 0, (37.1% identity in 426 aa overlap); etc.	O53919	No	cell wall and cell processes		MMAR_0596		Mb1699c				
NC_000962.3	Mycobrowser_v3	CDS	1903299	1904420	.	+	0	Rv1679	fadE16	Function unknown, but involvement in lipid degradation.	Possible acyl-CoA dehydrogenase FadE16	Rv1679, (MTV047.14, MTCI125.01), len: 373 aa. Possible fadE16, acyl-CoA dehydrogenase, similar to acyl/butyryl-CoA dehydrogenases e.g. NP_244665.1|NC_002570 acyl-CoA dehydrogenase from Bacillus halodurans (380 aa); NP_000008.1|NM_000017 acyl-Coenzyme A dehydrogenase from Homo sapiens (412 aa); Z99113|BSUB0010_119 from Bacillus subtilis (380 aa), FASTA scores: opt: 439, E(): 3.4e-20, (29.6% identity in 287 aa overlap); etc. Weakly similar to many dehydrogenases and to P31571|CAIA_ECOLI probable carnitine operon oxidoreductase from Escherichia coli (380 aa), FASTA scores: opt: 109, E(): 0.0066, (28.6% identity in 98 aa overlap).	O53926	No	lipid metabolism				Mb1706				
NC_000962.3	Mycobrowser_v3	CDS	1907594	1910593	.	+	0	Rv1683	Rv1683	Supposed involvement in lipid biosynthesis and degradation	Possible bifunctional enzyme; long-chain acyl-CoA synthase and lipase.	Rv1683, (MTCI125.05), len: 999 aa. Possible bifunctional long-chain acyl-CoA synthase and lipase. Equivalent to Z95117|MLCB1351_21 possible long-chain acyl-CoA synthase from Mycobacterium leprae (1002 aa) (85.6% identity in 1002 aa overlap). Weakly similar to FATP_MOUSE|Q60714 long-chain fatty acid transport protein (646 aa), fasta scores: opt: 331, E(): 5e-08, (24.8% identity in 630 aa overlap). Also similar to O35488|AF033031 Mouse very-long-chain acyl-CoA synthetase (620 aa), fasta scores: opt: 435, E(): 2.2e-12, (24.8% identity in 545 aa overlap). Weakly similar to Mycobacterium tuberculosis protein MTCI364.18 (27.4% identity in 583 aa overlap). Contains PS00120 Lipases, serine active site.	O33185	No	lipid metabolism	ML1346	MMAR_2478	MSMEG_3767	Mb1710				
NC_000962.3	Mycobrowser_v3	CDS	1912153	1912920	.	-	0	Rv1687c	Rv1687c	Thought to be involved in active transport of undetermined substrate (possibly drug) across the membrane. Responsible for energy coupling to the transport system.	Probable conserved ATP-binding protein ABC transporter	Rv1687c, (MTCI125.09c), len: 255 aa. Probable conserved ATP-binding protein ABC transporter (see citation below), similar to many ABC-type transporters e.g. P55476|NODI_RHISN nodulation ATP-binding protein I from Rhizobium sp. (343 aa), FASTA scores: opt: 479, E(): 3.7e-23, (34.6% identity in 243 aa overlap); etc. Also similar to many other Mycobacterium tuberculosis ABC-type transporters e.g. MTCY19H9.04 (34.5% identity in 238 aa overlap). Contains PS00211 ABC transporters family signature and PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the ATP-binding transport protein family (ABC transporters). Also contains PS00039 dead-box subfamily ATP-dependent helicases signature, though this may be spurious.	O33189	No	cell wall and cell processes	ML1350,ML1350c	MMAR_2486	MSMEG_3762	Mb1713c				
NC_000962.3	Mycobrowser_v3	CDS	1917940	1918746	.	+	0	Rv1694	tlyA	Methylates 16S and 23S rRNA. Also has contact-dependent haemolytic activity; possibly involved in virulence (pore formation).	2'-O-methyltransferase TlyA	Rv1694, (MTCI125.16), len: 268 aa. TlyA, 2'-O-methyltransferase; cytotoxin/haemolysin homologue (see citations below), almost identical to NP_301968.1|NC_002677 cytotoxin/haemolysin homologue TlyA from Mycobacterium leprae (269 aa). TlyA homologues were also identified by PCR in Mycobacterium avium, Mycobacterium bovis BCG, but appeared absent in M. smegmatis, M. vaccae, M. kansasii, M. chelonae and M. phlei (see Wren et al., 1998). Also highly similar to CAB83047.1|AJ271681 putative haemolysin from Mycobacterium ulcerans (281 aa); and similar to HLYA_TREHY|Q06803 pore-forming haemolysin/cytotoxin virulence determinant from Treponema hyodysenteriae (240 aa), FASTA scores: opt: 514, E():3e-30, (37.3% identity in 236 aa overlap).	P9WJ63	No	virulence, detoxification, adaptation	ML1358	MMAR_2499	MSMEG_3751	Mb1720				
NC_000962.3	Mycobrowser_v3	CDS	1929131	1929721	.	-	0	Rv1703c	Rv1703c	Catalyzes the O-methylation [catalytic activity: S-adenosyl-L-methionine + catechol = S-adenosyl-L-homocysteine + guaiacol]	Probable catechol-O-methyltransferase	Rv1703c, (MTCI125.25c), len: 196 aa. Probable catechol-o-methyltransferase, most similar to COMT_HUMAN|P21964 soluble form of mammalian catechol o-methyltransferase (271 aa), FASTA scores: opt: 405, E(): 7.8e-29, (38.9% identity in 190 aa overlap). Also similar to Mycobacterium tuberculosis hypothetical methyltransferases Rv0187, Rv1220c.	L0TAD5	No	intermediary metabolism and respiration	ML1366,ML1366c	MMAR_2507		Mb1729c				
NC_000962.3	Mycobrowser_v3	CDS	1929786	1931456	.	-	0	Rv1704c	cycA	Permease that is involved in the transport across the cytoplasmic membrane of D-alanine, D-serine and glycine	Probable D-serine/alanine/glycine transporter protein CycA	Rv1704c, (MTCI125.26c), len: 556 aa. Probable cycA, D-serine/D-alanine/glycine transporter, highly similar to P39312|CYCA_ECOLI d-serine/d-alanine/glycine transporter from Escherichia coli (470 aa), FASTA scores: opt: 1906, E(): 0, (59.3% identity in 459 aa overlap); etc. Also similar to other Mycobacterium tuberculosis amino-acid permeases e.g. Rv2127, Rv0346c, etc. Contains PS00218 amino acid permeases signature. Belongs to the amino acid permease family (APC family).	O33203	No	cell wall and cell processes		MMAR_1093	MSMEG_3587	Mb1730c				
NC_000962.3	Mycobrowser_v3	CDS	1934882	1936342	.	+	0	Rv1707	Rv1707	Unknown; possibly involved in transport of sulfate across the membrane.	Probable conserved transmembrane protein	Rv1707, (MTCI125.29), len: 486 aa. Probable conserved transmembrane protein, possibly involved in transport of sulfate, similar to several hypothetical proteins belonging to the sulfate permease family e.g. P40877|YCHM_ECOLI hypothetical 58.4 kDa protein in pth-prsa intergenic region from Escherichia coli (550 aa), FASTA scores: opt: 486, E(): 0, (33.1% identity in 492 aa overlap). Also similar to many other Mycobacterium tuberculosis membrane proteins e.g. Rv3273, Rv1739c. Seems to belong to the SulP family.	O33206	No	cell wall and cell processes				Mb1734				
NC_000962.3	Mycobrowser_v3	CDS	1942659	1943573	.	+	0	Rv1715	fadB3	Thought to be involved in fatty acid degradation. FADB and FADA are the alpha and beta subunits of the multifunctional enzyme complex of the fatty acid degradation cycle [catalytic activity: (S)-3-hydroxybutanoyl-CoA + NADP+ = 3-acetoacetyl-CoA + NADPH].	Probable 3-hydroxybutyryl-CoA dehydrogenase FadB3 (beta-hydroxybutyryl-CoA dehydrogenase) (BHBD)	Rv1715, (MTV048.02), len: 304 aa. Probable fadB3, 3-hydroxybutyryl-CoA dehydrogenase, highly similar to many e.g. NP_107236.1|NC_002678 3-hydroxybutyryl-CoA dehydrogenase from Mesorhizobium loti (309 aa); NP_250319.1|NC_002516 probable 3-hydroxyacyl-CoA dehydrogenase from Pseudomonas aeruginosa (509 aa); P45856|HBD_BACSU probable 3-hydroxybutyryl-CoA dehydrogenase from Bacillus subtilis (287 aa), FASTA scores: opt: 488, E(): 1.5e-24, (38.7% identity in 279 aa overlap); etc. Could belong to the 3-hydroxyacyl-CoA dehydrogenase family.	L7N688	No	lipid metabolism			MSMEG_6791	Mb1742,Mb1743				
NC_000962.3	Mycobrowser_v3	CDS	1947861	1949345	.	+	0	Rv1722	Rv1722	Function unknown, but supposed involvement in lipid metabolism	Possible carboxylase	Rv1722, (MTCY04C12.07), len: 494 aa. Possible carboxylases. Weak similarity to several e.g. ACCC_BACSU|P49787 biotin carboxylase from Bacillus subtilis (448 aa), fasta scores: opt: 171, E(): 0.00021, (22.8% identity in 237 aa overlap).	P71980	No	lipid metabolism		MMAR_3388		Mb1751				
NC_000962.3	Mycobrowser_v3	CDS	3004745	3005650	.	-	0	Rv2688c	Rv2688c	Thought to be involved in active transport of unidentified antibiotic across the membrane (export): antibiotic resistance by an export mechanism. Responsible for energy coupling to the transport system.	Antibiotic-transport ATP-binding protein ABC transporter	Rv2688c, (MTCY05A6.09c), len: 301 aa. Antibiotic-transport ATP-binding protein ABC transporter (see citation below), highly similar to AAK47077|MT2762 ABC transporter ATP-binding protein from Mycobacterium tuberculosis strain CDC1551 (317 aa), FASTA scores: opt: 1714, E(): 5.1e-93, (95.6% identity in 274 aa overlap). Also highly similar to other ATP-binding proteins ABC transporter e.g. Q9K639|BH3893 from Bacillus halodurans (282 aa), FASTA scores: opt: 644, E(): 1.4e-30, (38.% identity in 285 aa overlap); O58550|PH0820 from Pyrococcus horikoshii (312 aa), FASTA scores: opt: 574, E(): 1.8e-26, (39.1% identity in 307 aa overlap); Q9WYM0|TM0389 from Thermotoga maritima (301 aa), FASTA scores: opt: 536, E(): 2.9e-24, (36.1% identity in 291 aa overlap); etc. Has ATP/GTP-binding site motif A (P-loop) at N-terminus (PS00017). Belongs to the ATP-binding transport protein family (ABC transporters).	P9WQL7	No	cell wall and cell processes		MMAR_2026	MSMEG_1502	Mb2707c				
NC_000962.3	Mycobrowser_v3	CDS	1954631	1955569	.	-	0	Rv1729c	Rv1729c	Possible methyltransferase	Possible S-adenosylmethionine-dependent methyltransferase	Rv1729c, (MTCY04C12.14c), len: 312 aa. Possible S-adenosylmethionine-dependent methyltransferase (see Grana et al., 2007), similar to many Mycobacterium tuberculosis proteins e.g. Q50726|Rv3399|YX99_MYCTU (348 aa), FASTA scores: opt: 1019, E(): 0, (55.7% identity in 296 aa overlap); P95074|Rv0726c (367 aa), O53795|Rv0731c (318 aa), and O53841|Rv0830 (301 aa), etc.	P9WFH9	No	lipid metabolism		MMAR_1057		Mb1758c				
NC_000962.3	Mycobrowser_v3	CDS	1957677	1959233	.	+	0	Rv1731	gabD2	Involved in 4-aminobutyrate (GABA) degradation pathway [catalytic activity: succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H].	Possible succinate-semialdehyde dehydrogenase [NADP+] dependent (SSDH) GabD2	Rv1731, (MTCY04C12.16), len: 518 aa. Possible gabD2, succinate-semialdehyde dehydrogenase [NADP+] dependent, similar to others e.g. GABD_ECOLI|P25526 succinate-semialdehyde dehydrogenase from Escherichia coli (482 aa), FASTA scores: opt: 870, E(): 0, (34.7% identity in 449 aa overlap); etc. Also similar to gabD1|Rv0234c|MTCY08D5.30c probable succinate-semialdehyde dehydrogenase [NADP+] dependent from Mycobacterium tuberculosis (511 aa); and other semialdehyde dehydrogenases e.g. Rv0768|aldA (489 aa), Rv2858c|aldC (455 aa), etc. Contains PS00216 Sugar transport proteins signature 1, PS00687 Aldehyde dehydrogenases glutamic acid active site. Belongs to the aldehyde dehydrogenases family. Note that previously known as gabD1.	P9WNX7	No	intermediary metabolism and respiration		MMAR_2571	MSMEG_5912	Mb1760				
NC_000962.3	Mycobrowser_v3	CDS	1962228	1964186	.	-	0	Rv1736c	narX	Involved in nitrate reduction, and in the persistence in the host [catalytic activity: nitrite + acceptor = nitrate + reduced acceptor]	Probable nitrate reductase NarX	Rv1736c, (MTCY04C12.21c), len: 652 aa. Probable narX, nitrate reductase. Contains three domains: N-terminus (250 aa) is similar to e.g. N-terminus of NARG_ECOLI|P09152 respiratory nitrate reductase 1 alpha chain from Escherichia coli (1246 aa), FASTA scores: E(): 0, (58.6% identity in 251 aa overlap); and Rv1161|MTCI65.28|NARG probable respiratory nitrate reductase (alpha chain) from Mycobacterium tuberculosis (1232 aa). Central region (260-410 aa) is similar to Rv1163|O06561|NARJ probable respiratory nitrate reductase (delta chain) from Mycobacterium tuberculosis (201 aa), FASTA scores: E(): 0, (64.2% identity in 159 aa overlap). C-terminus (420 aa-) is similar to Rv1164|O06562|NARI probable respiratory nitrate reductase (gamma chain) from Mycobacterium tuberculosis (246 aa), FASTA scores: E(): 0, (68.6% identity in 239 aa overlap). Contains PS00551 Prokaryotic molybdopterin oxidoreductases signature 1.	P9WJQ1	No	intermediary metabolism and respiration				Mb1765c				
NC_000962.3	Mycobrowser_v3	CDS	1964183	1965370	.	-	0	Rv1737c	narK2	Involved in excretion of nitrite, produced by the dissimilatory reduction of nitrate, across the membrane. Responsible for the translocation of the substrate across the membrane.	Possible nitrate/nitrite transporter NarK2	Rv1737c, (MTCY04C12.22c), len: 395 aa. Possible narK2, nitrate/nitrite-transport integral membrane protein (see Hutter & Dick 2000), possibly member of major facilitator superfamily (MFS), similar to P46907|NARK_BACSU nitrite extrusion protein from Bacillus subtilis (395 aa), FASTA scores: opt: 742, E(): 0, (33.6% identity in 375 aa overlap); and to AL109989|SCJ12.23 hypothetical nitrate/nitrite transporter from Streptomyces coelicolor (412 aa), FASTA scores: opt: 1181, E(): 0, (49.4% identity in 389 aa overlap).	P9WJY7	No	cell wall and cell processes			MSMEG_5141	Mb1766c				
NC_000962.3	Mycobrowser_v3	CDS	1965955	1967637	.	-	0	Rv1739c	Rv1739c	Involved in sulphate transport across the membrane. Responsible for the translocation of the substrate across the membrane.	Probable sulphate-transport transmembrane protein ABC transporter	Rv1739c, (MTCY04C12.24c, MTCY28.01), len: 560 aa. Probable sulphate-transport transmembrane protein ABC transporter, similar to several e.g. P53392|G607186 high affinity sulphate transporter from Stylosanthes hamata (662 aa), FASTA scores: opt: 382, E(): 1.6e-16, (28.0% identity in 564 aa overlap); U59234.1|AAB88215.1 biotin carb. from Synechococcus sp. PCC 7942 (574 aa), FASTA scores: opt: 1838, E(): 0, (50.0% identity in 550 aa overlap); etc. Contains PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters), and seems to belong to the SULP family.	P9WGF7	No	cell wall and cell processes				Mb1768c				
NC_000962.3	Mycobrowser_v3	CDS	3034635	3034883	.	+	0	Rv2722	Rv2722	Function unknown	Conserved hypothetical protein	Rv2722, (MTCY154.02), len: 82 aa. Conserved hypothetical protein, similar to Q9CCB9|ML1001 hypothetical protein from Mycobacterium leprae (91 aa), FASTA scores: opt: 154, E(): 0.00053, (37.5% identity in 88 aa overlap). Equivalent to AAK47111 from Mycobacterium tuberculosis strain CDC1551 (94 aa) but shorter 12 aa. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O33227	No	conserved hypotheticals	ML1001,ML1001c			Mb2741				
NC_000962.3	Mycobrowser_v3	CDS	1969004	1970704	.	+	0	Rv1743	pknE	Involved in signal transduction (via phosphorylation). Thought to be involved in membrane transport [catalytic activity: ATP + a protein = ADP + a phosphoprotein].	Probable transmembrane serine/threonine-protein kinase E PknE (protein kinase E) (STPK E)	Rv1743, (MTCY28.05,MTCY04C12.28), len: 566 aa. Probable pknE, transmembrane serine/threonine protein kinase (see citation below), similar to PKN1_MYXXA|P33973 serine/threonine-protein kinase pkn1 (693 aa), fasta scores: opt: 542, E(): 1.1e-19, (35.8% identity in 302 aa overlap). Also highly similar to K08G_MYCTU|Q11053 probable serine/threonine-protein kinase (626 aa) (59.8% identity in 381 aa overlap). Contains PS00107 Protein kinases ATP-binding region signature. Contains Hank's kinase subdomain. Belongs to the Ser/Thr family of protein kinases.	P9WI77	No	regulatory proteins		MMAR_2581		Mb1772				
NC_000962.3	Mycobrowser_v3	CDS	1977969	1979567	.	-	0	Rv1750c	fadD1	Function unknown, but supposed involvement in lipid degradation.	Possible fatty-acid-CoA ligase FadD1 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv1750c, (MTCY28.13c, MTCY04C12.34), len: 532 aa. Possible fadD1, fatty-acid-CoA synthetase, similar in part to others e.g. O35488|VLCS_MOUSE very-long-chain acyl-CoA synthetase from Mus musculus (620 aa); NP_113924.1|NM_031736 solute carrier family 27 (fatty acid transporter) member 2 from Rattus norvegicus (620 aa); NP_459076.1|NC_003197 crotonobetaine/carnitine-CoA ligase from Salmonella typhimurium (517 aa); CAIC_ECOLI|P31552 probable crotonobetaine/carnitine-CoA ligase from Escherichia coli (522 aa), FASTA scores: opt: 448, E(): 1.9e-21, (25.1% identity in 502 aa overlap); etc. Also highly similar to fadD17|Rv3506|MTV023.13 probable fatty-acid-CoA ligase from Mycobacterium tuberculosis (502 aa); and similar to others from Mycobacterium tuberculosis e.g. fadD6|MTCI364.18|Rv1206|O05307 probable fatty-acid-CoA ligase (597 aa), FASTA score: (28.3% identity in 519 aa overlap); etc. Contains PS00455 Putative AMP-binding domain signature. Belongs to the ATP-dependent AMP-binding enzyme family.	P72007	No	lipid metabolism		MMAR_2625	MSMEG_4952	Mb1779c				
NC_000962.3	Mycobrowser_v3	CDS	1988680	1989006	.	-	0	Rv1757c	Rv1757c	Required for the transposition of the insertion element IS6110.	Putative transposase for insertion sequence element IS6110 (fragment)	Rv1757c, (MTCY28.23c), len: 108 aa. Putative Transposase for IS6110 (fragment), identical to many other Mycobacterium tuberculosis IS6110 transposase subunits e.g. Q50686|YIA4_MYCTU Insertion element IS6110 hypothetical 12.0 kDa protein (108 aa), fasta scores: E(): 1.4e-43, (100.00% identity in 108 aa overlap). The transposase described here may be made by a frame shifting mechanism during translation that fuses Rv1756c and Rv1757c, the sequence UUUUAAAG (directly upstream of Rv1756c) maybe responsible for such a frameshifting event (see McAdam et al., 1990).	P9WKH5	No	insertion seqs and phages								
NC_000962.3	Mycobrowser_v3	CDS	3430387	3430710	.	+	0	Rv3065	mmr	Involved in transport of multidrugs (tetraphenylphosphonium, erythromycin, ethidium bromide, acriflavine, safranin O, pyronin Y, etc) across the membrane (export): multidrugs resistance by an export mechanism (conferes resistance to toxic compounds by removing them for the cells). Responsible for the translocation of the substrate across the membrane.	Multidrugs-transport integral membrane protein Mmr	Rv3065, (MT3150.1, MTCY22D7.17c), len: 107 aa. Mmr, integral membrane multidrugs resistance transporter (see citation below), equivalent to Q9CBP1|ML1756 probable multidrug resistance protein from Mycobacterium leprae (107 aa), FASTA scores: opt: 534, E(): 3.3e-28, (77.55% identity in 107 aa overlap). Also highly similar to bacterial proteins involved in resistance to ethidium bromide or methyl viologen e.g. O87866|QACG_STASP quaternary ammonium compound-resistance protein QACG (quarternary ammonium determinant G) from Staphylococcus sp. strain ST94 (107 aa), FASTA scores: opt: 307, E(): 1.8e-13, (39.8% identity in 103 aa overlap); P96460|QAC quaternary ammonium compounds resistance protein QAC from Staphylococcus aureus (107 aa), FASTA scores: opt: 304, E(): 2.8e-13, (40.4% identity in 104 aa overlap); Q57225|QACE_ECOLI quaternary ammonium compound-resistance protein QACE (quarternary ammonium determinant E) from Escherichia coli (110 aa), FASTA scores: opt: 300, E(): 5.2e-13, (48.15% identity in 108 aa overlap); AAG55967|Z1870 methylviologen resistance protein encoded within prophage CP-933X from Escherichia coli strain O157:H7 EDL933 (110 aa); P23895|EMRE|MVRC|EB|B0543 EMRE protein from Escherichia coli (110 aa), FASTA scores: opt: 290, E(): 2.3e-12, (43.55% identity in 101 aa overlap); etc. Also similar to the SugE protein of enteric bacteria. Belongs to the small multidrug resistance (SMR) protein family. Note that previously known as emrE.	P9WGF1	No	cell wall and cell processes	ML1756	MMAR_1612		Mb3092				
NC_000962.3	Mycobrowser_v3	CDS	1989833	1992577	.	-	0	Rv1759c	wag22	Function unknown. Has fibronectin-binding activity (could thus mediate bacterial attachment to host cells). Thought to be expressed during infection.	PE-PGRS family protein Wag22	Rv1759c, (MT1807, MTCY28.25c), len: 914 aa. Wag22, antigen member (see citations below) of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins, highly similar to others e.g. MT1367|Q10637 hypothetical glycine-rich 49.6 kDa protein from Mycobacterium tuberculosis (603 aa), FASTA scores: opt: 2010, E(): 0, (53.0% identity in 724 aa overlap); etc.	P9WIG5	No	PE/PPE				Mb1789c,Mb1790c				
NC_000962.3	Mycobrowser_v3	CDS	1996427	1997413	.	+	0	Rv1764	Rv1764	Required for the transposition of the insertion element IS6110.	Putative transposase	Rv1764, (MTCY28.30), len: 328 aa. Putative Transposase for IS6110 insertion element. Identical to many other M. tuberculosis IS6110 transposase subunits. The transposase described here may be made by a frame shifting mechanism during translation that fuses Rv1763 and Rv1764, the sequence UUUUAAAG (directly upstream of Rv1764) maybe responsible for such a frameshifting event (see McAdam et al., 1990). Start changed since first submission (+ 34 aa)	P9WKH9	No	insertion seqs and phages		MMAR_2548	MSMEG_1721					
NC_000962.3	Mycobrowser_v3	CDS	2005161	2006447	.	+	0	Rv1771	Rv1771	Possibly involved in biosynthesis of L-ascorbic acid (vitamin C). Oxidizes L-gulono-1,4-lactone.	L-gulono-1,4-lactone dehydrogenase	Rv1771, (MTCY28.37), len: 428 aa. L-gulono-1,4-lactone dehydrogenase (See Wolucka and Communi, 2006), similar to e.g. GGLO_RAT|P10867 l-gulonolactone oxidase (439 aa), FASTA scores: opt: 862, E(): 0, (34.1% identity in 434 aa overlap). Also shows slight similarity to Mycobacterium tuberculosis oxidoreductase Rv1726|MTCY04C12.11 (22.9% identity in 441 aa overlap) and others e.g. Rv3107c, Rv1257c, Rv2251, etc. Contains PS00862 Oxygen oxidoreductases covalent FAD-binding site. Alternative nucleotide at position 2006032 (a->G; Q291R) has been observed.	P9WIT3	No	intermediary metabolism and respiration	ML1379	MMAR_2648		Mb1800				
NC_000962.3	Mycobrowser_v3	CDS	2010656	2011960	.	+	0	Rv1777	cyp144	Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	Probable cytochrome P450 144 Cyp144	Rv1777, (MT1827, MTCY25C11.04), len: 434 aa. Probable cyp144, cytochrome p450, similar to CPXM_BACME|Q06069 cytochrome p450 (meg) (410 aa), FASTA scores: opt: 435 E(): 2.3e-16, (28.8% identity in 372 aa overlap). Also similar to several other Mycobacterium tuberculosis p450 genes including Rv0766c, Rv2266, etc. Contains PS00086 Cytochrome P450 cysteine heme-iron ligand signature. Belongs to the cytochrome P450 family.	P9WPL1	No	intermediary metabolism and respiration		MMAR_2654	MSMEG_0675	Mb1806				
NC_000962.3	Mycobrowser_v3	CDS	2015302	2017476	.	-	0	Rv1781c	malQ	Transfers a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan	Probable 4-alpha-glucanotransferase MalQ (amylomaltase) (disproportionating enzyme) (D-enzyme)	Rv1781c, (MTV049.03c), len: 724 aa. Probable malQ, 4-alpha-glucanotransferase, similar to many, e.g. P15977|MALQ_ECOLI 4-alpha-glucanotransferase (694 aa), FASTA scores: opt: 964, E(): 0, (31.8% identity in 694 aa overlap). Belongs to the disproportionating enzyme family.	P9WK23	No	intermediary metabolism and respiration	ML1545	MMAR_2663	MSMEG_3673	Mb1810c				
NC_000962.3	Mycobrowser_v3	CDS	2028425	2029477	.	+	0	Rv1790	PPE27	Function unknown	PPE family protein PPE27	Rv1790, (MTV049.12), len: 350 aa. PPE27, Member of the Mycobacterium tuberculosis PPE family of glycine-rich protein, similar to Z74024|MTCY274.24 Mycobacterium tuberculosis cosmid (404 aa), FASTA scores: opt: 849, E(): 0, (50.0% identity in 406 aa overlap).	Q79FK5	No	PE/PPE				Mb1818				
NC_000962.3	Mycobrowser_v3	CDS	3709715	3710248	.	-	0	Rv3324c	moaC3	Thought to be involved in the biosynthesis of molybdopterin.	Probable molybdenum cofactor biosynthesis protein C 3 MoaC3	Rv3324c, (MTV016.24c), len: 177 aa. Probable moaC3, molybdopterin cofactor biosynthesis protein, highly similar to others e.g. Q9HX95|MOAC|PA3918 from Pseudomonas aeruginosa (160 aa), FASTA scores: opt: 567, E(): 7.5e-30, (58.35% identity in 156 aa overlap); Q9RKA8|MOAC from Streptomyces coelicolor (170 aa), FASTA scores: opt: 553, E(): 6.3e-29, (58.25% identity in 158 aa overlap); P30747|MOAC_ECOLI|CHLA3|B0783 from Escherichia coli strain K12 (160 aa), FASTA scores: opt: 516, E(): 1.5e-26, (55.95% identity in 159 aa overlap); etc. Also highly similar to O05788|MOAC1|Rv3111|MTCY164.21 putative molybdenum cofactor biosynthesis protein C from Mycobacterium tuberculosis (170 aa), FASTA scores: opt: 734, E(): 1.3e-40, (71.8% identity in 163 aa overlap); and Rv0864|MOAC2|MTV043.57 putative molybdenum cofactor biosynthesis protein (167 aa).	P9WJR5	No	intermediary metabolism and respiration				Mb3353c				
NC_000962.3	Mycobrowser_v3	CDS	2031066	2031968	.	+	0	Rv1794	Rv1794	Function unknown	Conserved protein	Rv1794, (MTV049.16), len: 300 aa. Conserved protein, slight similarity to Mycobacterium tuberculosis O53694|Rv0289|MTV035.17, (295 aa), FASTA scores: opt: 172, E(): 0.00083, (25.7% identity in 261 aa overlap). Equivalent to Mycobacterium leprae hypothetical protein Q9Z5I1|MLCB596.31|AL035472 (300 aa), (88.0% identity in 300 aa overlap). Contains PS00211 ABC transporters family signature. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O53943	No	conserved hypotheticals	ML1540,ML1540c	MMAR_2676		Mb1822				
NC_000962.3	Mycobrowser_v3	CDS	2033729	2035486	.	+	0	Rv1796	mycP5	Thought to have proteolytic activity.	Probable proline rich membrane-anchored mycosin MycP5 (serine protease) (subtilisin-like protease) (subtilase-like) (mycosin-5)	Rv1796, (MTV049.18), len: 585 aa. Probable mycP5, pro-rich membrane-anchored serine protease (mycosin) (see citations below). Member of family with four other Mycobacterium tuberculosis serine proteases: Rv3886c|O05458|MTCY15F10.26|Z94121 (550 aa), FASTA scores: opt: 1173, E(): 0, (47.9% identity in 578 aa overlap); Rv0291, Rv3883c, and Rv3449. Genes all linked to those of ESAT-6 family. Has possible N-terminal signal peptide and hydrophobic anchor-like stretch at C-terminus. Contains two serine protease, subtilase family active site motifs: a aspartic acid active site motif (PS00136); and a histidine active site motif (PS00137). Belongs to peptidase family S8 (also known as the subtilase family), pyrolysin subfamily. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	O53945	No	intermediary metabolism and respiration	ML1538,ML1538c	MMAR_2678		Mb1824				
NC_000962.3	Mycobrowser_v3	CDS	2035483	2036703	.	+	0	Rv1797	eccE5	Function unknown	ESX conserved component EccE5. ESX-5 type VII secretion system protein. Probable membrane protein.	Rv1797, (MTV049.19), len: 406 aa. eccE5, esx conserved component, ESX-5 type VII secretion system protein, probable membrane protein, some similarity to Mycobacterium tuberculosis O05462|Rv3882c|MTCY15F10.30|Z94121 (462 aa), FASTA scores: opt: 181, E(): 9.2e-05, (25.4% identity in 283 aa overlap). Has two hydrophobic stretch near N-terminus. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WJE3	No	cell wall and cell processes	ML1537c	MMAR_2679		Mb1825				
NC_000962.3	Mycobrowser_v3	CDS	2036700	2038532	.	+	0	Rv1798	eccA5	Function unknown	ESX conserved component EccA5. ESX-5 type VII secretion system protein.	Rv1798, (MTV049.20), len: 610 aa. eccA5, esx conserved component, ESX-5 type VII secretion system protein, similar to several mycobacterial proteins e.g. O05460|MTCY15F10.28|Rv3884c|Z94121 from M. tuberculosis (619 aa), FASTA scores: opt: 669, E(): 0, (31.0% identity in 549 aa overlap); and O33089|MLCB628.18c|Y14967 from Mycobacterium leprae (573 aa), FASTA scores: opt: 723, E(): 0, (32.4% identity in 568 aa overlap). Also very similar to Rv0282. May belong to the CbxX/CfqX family as last ~320 aa domain very similar to several family members. Contains ATP/GTP-binding site motif A (P-loop; PS00017).	P9WPI1	No	cell wall and cell processes	ML1536c	MMAR_2680		Mb1826				
NC_000962.3	Mycobrowser_v3	CDS	2044923	2046842	.	-	0	Rv1803c	PE_PGRS32	Function unknown	PE-PGRS family protein PE_PGRS32	Rv1803c, (MTV049.25c), len: 639 aa. PE_PGRS32, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citation below). Most similar to Rv1768|MTCY28.34|Z95890 (618 aa), FASTA scores: opt: 1827, E(): 0, (53.5% identity in 664 aa overlap). Contains two PS00583 pfkB family of carbohydrate kinases signatures 1. Predicted to be an outer membrane protein (See Song et al., 2008).	Q79FJ9	No	PE/PPE		MMAR_3008		Mb1831c,Mb1832c				
NC_000962.3	Mycobrowser_v3	CDS	2051282	2052688	.	+	0	Rv1809	PPE33	Function unknown	PPE family protein PPE33	Rv1809, (MTV049.31), len: 468 aa. PPE33, Member of the Mycobacterium tuberculosis PPE family of glycine-rich proteins, most similar to RV1802AL022021|MTV049.23 (463 aa), FASTA scores: opt: 1238, E(): 0, (51.2% identity in 471 aa overlap). Alternative nucleotide at position 2051746 (T->C; A155A) has been observed.	P9WI03	No	PE/PPE		MMAR_1460		Mb1838,Mb1839				
NC_000962.3	Mycobrowser_v3	CDS	2056521	2057423	.	+	0	Rv1814	erg3	Involved in lipid desaturation	Membrane-bound C-5 sterol desaturase Erg3 (sterol-C5-desaturase)	Rv1814, (MTCY1A11.29c), len: 300 aa. Erg3, transmembrane C-5 sterol desaturase (see *), weak similarity to several e.g. ERG3_YEAST|P32353 c-5 sterol desaturase (365 aa), FASTA scores: opt: 154, E(): 0.0011, (22.9% identity in 288 aa overlap). Belongs to the sterol desaturase family. [* Note: work of Jackson, C.J., Lamb, D.C., Kelly, D.E., Kelly, S.L., Characterization of a sterol delta 5,6-desaturase homolog in Mycobacterium bovis (BCG). Submitted (jun-2000) to the EMBL/GenBank/DDBJ databases].	P9WNZ9	No	lipid metabolism	ML0931	MMAR_2691	MSMEG_3666	Mb1844				
NC_000962.3	Mycobrowser_v3	CDS	2062809	2064728	.	-	0	Rv1819c	bacA	Thought to be involved in active transport of drugs across the membrane (export): multidrugs resistance by an export mechanism. Responsible for energy coupling to the transport system and for the translocation of the substrate across the membrane.	Probable drug-transport transmembrane ATP-binding protein ABC transporter BacA	Rv1819c, (MTCY1A11.24), len: 639 aa. Probable bacA, drug-transport transmembrane ATP-binding protein ABC transporter (see citation below), equivalent to AL008609|MLCB1788.47 hypothetical ABC transporter from Mycobacterium leprae (638 aa), (74.9% identity in 634 aa overlap). Also similar to other transmembrane ATP-binding proteins e.g. Q57335|Y036_HAEIN hypothetical ABC transporter ATP-binding protein from Haemophilus influenzae (592 aa), FASTA scores: opt: 1235, E(): 2.8e-61, (40.8% identity in 623 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters).	P9WQI9	No	cell wall and cell processes	ML2084	MMAR_2696	MSMEG_3655,MSMEG_4380	Mb1850c				
NC_000962.3	Mycobrowser_v3	CDS	3710433	3710759	.	+	0	Rv3325	Rv3325	Involved in the transposition of the insertion sequence element IS6110.	Probable transposase for insertion sequence element IS6110 (fragment)	Rv3325, (MTV016.25), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase subunits. The transposase described here may be made by a frame shifting mechanism during translation that fuses Rv3325 and Rv3326, the sequence UUUUAAAG (directly upstream of Rv3326) maybe responsible for such a frameshifting event (see McAdam et al., 1990). Belongs to the transposase family 8.	P9WKH5	No	insertion seqs and phages								
NC_000962.3	Mycobrowser_v3	CDS	2066457	2068883	.	+	0	Rv1821	secA2	Involved in protein export. May interact with the SECY/SECE subunits. SECA has a central role in coupling the hydrolysis of ATP to the transfer of PRE-secretory periplasmic and outer membrane proteins across the membrane.	Possible preprotein translocase ATPase SecA2	Rv1821, (MTCY1A11.22c), len: 808 aa. Possible secA2, preprotein translocase and ATPase, component of secretion apparatus (see Braunstein & Belisle 2000), similar to several preprotein translocases e.g. P28366|SECA_BACSU preprotein translocase secA subunit from Bacillus subtilis (841 aa), FASTA scores: opt: 1424, E(): 0, (35.9% identity in 786 aa overlap). Equivalent to AL008609|MLCB1788.45 Preprotein translocase SecA 2 from Mycobacterium leprae (778 aa) (87.1% identity in 780 aa overlap). Also similar to Rv3240c|MTCY20B11.15c secA preprotein translocase from Mycobacterium tuberculosis (949 aa). Could be part of the prokaryotic protein translocation apparatus which comprise SECA|Rv3240c, SECD|Rv2587c, SECE|Rv0638, SECF|Rv2586c, SECG|Rv1440 and SECY|Rv0732. Binds ATP.	P9WGP3	No	cell wall and cell processes	ML2082,ML2082c	MMAR_2698	MSMEG_3654	Mb1852				
NC_000962.3	Mycobrowser_v3	CDS	2071952	2072356	.	+	0	Rv1826	gcvH	The glycine cleavage system catalyses the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein	Probable glycine cleavage system H protein GcvH	Rv1826, (MTCY1A11.17c), len: 134 aa. Probable gcvH, glycine cleavage system H protein, highly similar to GCSH_ECOLI|P23884 glycine cleavage system H protein from Escherichia coli (129 aa), FASTA scores: opt: 428, E(): 2.2e-22, (47.8% identity in 134 aa overlap). Equivalent to MLCB1788.37c gcvH from Mycobacterium leprae (78.4% identity in 134 aa overlap). Contains PS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. Belongs to the GcvH family.	P9WN55	No	intermediary metabolism and respiration	ML2077,ML2077c	MMAR_2703	MSMEG_3648	Mb1857				
NC_000962.3	Mycobrowser_v3	CDS	2075877	2078702	.	+	0	Rv1832	gcvB	The glycine cleavage system catalyses the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein [catalytic activity: glycine + lipoylprotein = S- aminomethyldihydrolipoylprotein + CO(2)]	Probable glycine dehydrogenase GcvB (glycine decarboxylase) (glycine cleavage system P-protein)	Rv1832, (MTCY1A11.11c), len: 941 aa. Probable gcvB, glycine dehydrogenase [decarboxylating], highly similar to GCSP_ECOLI|P33195 glycine dehydrogenase (decarboxylating) from Escherichia coli (957 aa), FASTA scores: opt: 2194, E(): 0, (55.4% identity in 961 aa overlap). The glycine cleavage system is composed of four proteins: P, T, L, and H	P9WN53	No	intermediary metabolism and respiration	ML2072,ML2072c	MMAR_2708	MSMEG_3642	Mb1863				
NC_000962.3	Mycobrowser_v3	CDS	2082603	2084636	.	-	0	Rv1836c	Rv1836c	Function unknown	Conserved protein	Rv1836c, (MTCY1A11.07), len: 677 aa. Conserved protein. Equivalent to MLCB1788.28|AL008609 hypothetical protein from Mycobacterium leprae (710 aa), FASTA scores: opt: 2938, E(): 0, (66.0% identity in 714 aa overlap). Contains PS00036 bZIP transcription factors basic domain signature. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WLQ9	No	conserved hypotheticals	ML2070	MMAR_2712	MSMEG_3641	Mb1867c				
NC_000962.3	Mycobrowser_v3	CDS	2087971	2089518	.	-	0	Rv1840c	PE_PGRS34	Function unknown	PE-PGRS family protein PE_PGRS34	Rv1840c, (MTCY359.33), len: 515 aa. PE_PGRS34, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see citation below). Similar to many e.g. Y03A_MYCTU|Q10637 hypothetical glycine-rich 49.6 kDa protein (603 aa), FASTA scores: opt: 1693, E(): 0, (53.1% identity in 612 aa overlap); etc.	P9WIF3	No	PE/PPE		MMAR_2709		Mb1871c				
NC_000962.3	Mycobrowser_v3	CDS	2090718	2092085	.	-	0	Rv1842c	Rv1842c	Unknown	Conserved hypothetical membrane protein	Rv1842c, (MTCY359.31), len: 455 aa. Conserved hypothetical membrane protein. Similar to Z99109|0O7589 Potential integral membrane protein from Bacillus subtilis (461 aa), FASTA scores: opt: 723, E(): 0, (31.2% identity in 449 aa overlap). Similar to other Mycobacterium tuberculosis putative integral membrane proteins e.g. Rv2366c, Rv1841c.	P9WFP3	No	cell wall and cell processes	ML2067	MMAR_2716	MSMEG_3637	Mb1873c				
NC_000962.3	Mycobrowser_v3	CDS	2093731	2095188	.	-	0	Rv1844c	gnd1	Involved in hexose monophosphate shunt (pentose phosphate pathway) [catalytic activity: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH].	Probable 6-phosphogluconate dehydrogenase Gnd1	Rv1844c, (MTCY359.29), len: 485 aa. Probable gnd1, 6-phosphogluconate dehydrogenase. Similar to others e.g. 6PGD_ECOLI|P00350 from Escherichia coli (468 aa), FASTA scores: opt: 1661, E(): 0, (53.6% identity in 466 aa overlap); etc. Also similar to Rv1122|MTCY22G8.11|gnd2 probable 6-phosphogluconate dehydrogenase, decarboxylating from Mycobacterium tuberculosis (340 aa), FASTA score: (33.0% identity in 351 aa overlap). Note that Rv1844c is most similar to gnd's from Gram negative organisms, while Rv1122|MTCY22G8.11|gnd2 is most similar to gnd's from Gram positive organisms. Belongs to the 6-phosphogluconate dehydrogenase family.	Q79FJ2	No	intermediary metabolism and respiration	ML2065	MMAR_2718	MSMEG_3632	Mb1875c				
NC_000962.3	Mycobrowser_v3	CDS	2097961	2099694	.	+	0	Rv1850	ureC	Involved in the conversion of urea to NH3 [catalytic activity: urea + H2O = CO2 + 2 NH3]	Urease alpha subunit UreC (urea amidohydrolase)	Rv1850, (MTCY359.23c), len: 577 aa. UreC, urease alpha subunit. Similar to URE1_MYCTU|P50042 from Mycobacterium tuberculosis (577 aa), FASTA scores: opt: 3794, E(): 0, (98.3% identity in 577 aa overlap). Contains PS00145 Urease active site motif. Belongs to the urease family.	P9WFF1	No	intermediary metabolism and respiration		MMAR_2724	MSMEG_3625	Mb1881				
NC_000962.3	Mycobrowser_v3	CDS	2101651	2103042	.	-	0	Rv1854c	ndh	Transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Does not couple the redox reaction to proton translocation.	Probable NADH dehydrogenase Ndh	Rv1854c, (MTCY359.19), len: 463 aa. Probable ndh, NADH dehydrogenase (see citations below), similar to several e.g. S74826 NADH dehydrogenase from Synechocystis sp. (445 aa), FASTA score: opt: 1228, E(): 0, (46.3% identity in 432 aa overlap). Highly similar to Rv0392c|Z84725|g1817703 from Mycobacterium tuberculosis (470 aa), FASTA scores: opt: 1911, E(): 0, (64.7% identity in 459 aa overlap); and Rv1812c.	P95160	No	intermediary metabolism and respiration	ML2061	MMAR_2728	MSMEG_3621	Mb1885c				
NC_000962.3	Mycobrowser_v3	CDS	2105773	2106567	.	+	0	Rv1858	modB	Part of the binding-protein-dependent transport system modabc for molybdenum; responsible for the translocation of the substrate across the membrane.	Probable molybdenum-transport integral membrane protein ABC transporter ModB	Rv1858, (MTCY359.15c), len: 264 aa. Probable modB, molybdenum-transport integral membrane protein ABC transporter (see citation below), similar to others e.g. Y10817|ANY108175 ModB from Arthrobacter (239 aa), FASTA scores: opt: 937, E(): 0, (67.8% identity in 230 aa overlap); etc. Similar to other Mycobacterium tuberculosis transport proteins e.g. Rv2039c, Rv2316, etc.	P9WG13	No	cell wall and cell processes	ML2057,ML2057c	MMAR_2732	MSMEG_2015	Mb1889				
NC_000962.3	Mycobrowser_v3	CDS	2106574	2107683	.	+	0	Rv1859	modC	Part of the binding-protein-dependent transport system modabc for molybdenum; responsible for energy coupling to the transport system.	Probable molybdenum-transport ATP-binding protein ABC transporter ModC	Rv1859, (MTCY359.14c), len: 369 aa. Probable modC, molybdenum-transport ATP-binding protein ABC transporter (see citation below), similar to others e.g. Y10817|ANY108176 ModC from Arthrobacter (349 aa), FASTA scores: opt: 895, E(): 0, (46.0% identity in 361 aa overlap); etc. Shows similarity to other Mycobacterium tuberculosis ABC-transporter proteins e.g. Rv0073, Rv1238, Rv2564, etc. Contains both PS00017 ATP/GTP-binding site motif A (P-loop) and PS00211 ABC transporters family signatures involved in molybdate uptake. Belongs to the ATP-binding transport protein family (ABC transporters).	P9WQL3	No	cell wall and cell processes	ML2056,ML2056c	MMAR_2736	MSMEG_2014	Mb1890				
NC_000962.3	Mycobrowser_v3	CDS	3796448	3797437	.	-	0	Rv3382c	lytB1	Unknown. Possibly involved in drug/antibiotic tolerance. In other organisms, LYTB product is involved in penicillin tolerance and control of the stringent response.	Probable LYTB-related protein LytB1	Rv3382c, (MTV004.40c), len: 329 aa. Probable lytB1, lytB-related protein, highly similar to many e.g. Q9HVM7|LYTB_PSEAE|PA4557 from Pseudomonas aeruginosa (314 aa), FASTA scores: opt: 1048, E(): 2e-55, (53.2% identity in 314 aa overlap); Q9JR39|LYTB|NMA0624|NMB1831 from Neisseria meningitidis (serogroup a and B) (322 aa), FASTA scores: opt: 1041, E(): 5.4e-55, (52.25% identity in 312 aa overlap); P22565|LYTB_ECOLI|B0029 from Escherichia coli strain K12 (316 aa), FASTA scores: opt: 1013, E(): 2.5e-53, (51.45% identity in 311 aa overlap) (for more information about lytB protein, see citation below); Q9X781|LYTB_MYCLE|LYTB2|ML1938|MLCB1222.06c from Mycobacterium leprae (332 aa), FASTA scores: opt: 979, E(): 2.8e-51, (51.3% identity in 312 aa overlap); etc. Also similar to Q9PAS9|XF2416 drug tolerance protein from Xylella fastidiosa (316 aa), FASTA scores: opt: 1043, E(): 4.1e-55, (53.65% identity in 315 aa overlap). And similar to O53458|Rv1110|LYTB2|MTV017.63 from Mycobacterium tuberculosis (335 aa), FASTA scores: opt: 975, E(): 4.9e-51, (51.3% identity in 312 aa overlap). Belongs to the LytB family.	P9WKF9	No	cell wall and cell processes		MMAR_0277		Mb3414c				
NC_000962.3	Mycobrowser_v3	CDS	2113140	2115476	.	+	0	Rv1866	Rv1866	Function unknown, but supposed involvement in lipid degradation.	Conserved protein	Rv1866, (MTCY359.07c), len: 778 aa. Conserved protein, N-terminal region similar to fatty acyl-CoA racemases e.g. Rv0855, Rv1143, and C-terminal region (from aa 370) similar to L-carnitine dehydratases, racemases, and Rv3272|MTCY71.12 Mycobacterium tuberculosis (394 aa), FASTA score: opt: 472, E(): 2.1e-21, (29.9% identity in 388 aa overlap). Also similar to P31572|CAIB_ECOLI L-carnitine dehydratase (405 aa), FASTA score: opt: 306, E(): 2.1e-11, (23.3% identity in 424 aa overlap).	P95149	No	lipid metabolism		MMAR_2745	MSMEG_1903	Mb1897				
NC_000962.3	Mycobrowser_v3	CDS	2115764	2117248	.	+	0	Rv1867	Rv1867	Function unknown, but supposed involvement in lipid degradation.	Conserved protein	Rv1867, (MTCY359.06c), len: 494 aa. Conserved protein, some similarity to acetyl CoA synthase and to lipid carriers. FASTA best: E155295 acetyl CoA synthase (388 aa), opt: 213, E(): 4.5e-07, (23.2% identity in 423 aa overlap),	P95148	No	lipid metabolism		MMAR_2746	MSMEG_3608	Mb1898				
NC_000962.3	Mycobrowser_v3	CDS	2121907	2123151	.	-	0	Rv1872c	lldD2	Involved in respiration; catalyzes conversion of lactate into pyruvate [catalytic activity: (S)-lactate + 2 ferricytochrome C = pyruvate + 2 ferrocytochrome C].	Possible L-lactate dehydrogenase (cytochrome) LldD2	Rv1872c, (MTCY180.46, MTCY359.01), len: 414 aa (start uncertain). Possible lldD2, L-lactate dehydrogenase (cytochrome), similar to other lactate dehydrogenases and other oxidases e.g. LLDD_ECOLI|P33232 l-lactate dehydrogenase (cytochrome) from Escherichia coli strain K12 (396 aa), FASTA results: opt: 674, E(): 1.1e-37, (40.5% identity in 279 aa overlap); Q51135 lactate dehydrogenase from Neisseria meningitidis (390 aa), FASTA results: opt: 309, E(): 4.1e-15, (42.5% identity in 113 aa overlap); etc. Also shows similarity with Rv0694|lldD1|MTCY210.11 possible L-lactate dehydrogenase (cytochrome) from Mycobacterium tuberculosis (396 aa). Contains PS00557 FMN-dependent alpha-hydroxy acid dehydrogenases active site. Belongs to the FMN-dependent alpha-hydroxy acid dehydrogenases family. Phosphorylated in vitro by PknJ|Rv2088 (See Arora et al., 2010).	P9WND5	No	intermediary metabolism and respiration	ML2046	MMAR_2752		Mb1903c				
NC_000962.3	Mycobrowser_v3	CDS	2125340	2125819	.	+	0	Rv1876	bfrA	Involved in iron storage (may perform analogous functions in iron detoxification and storage as that of animal ferritins); ferritin is an intracellular molecule that stores iron in a soluble, nontoxic, readily available form. The functional molecule, which is composed of 24 chains, is roughly spherical and contains a central cavity in which the polymeric ferric iron core is deposited.	Probable bacterioferritin BfrA	Rv1876, (MTCY180.42c), len: 159 aa. Probable bfrA (alternate gene name: bfr), bacterioferritin (see citation below), similar to BFR_MYCLE|P43315 bacterioferritin (bfr) from Mycobacterium leprae (159 aa), FASTA results: opt: 958, E(): 0, (90.6% identity in 159 aa overlap). Also similar to Rv3841|MTCY01A6.28c|bfrB possible bacterioferritin from Mycobacterium tuberculosis (181 aa). Belongs to the bacterioferritin family.	P9WPQ9	No	intermediary metabolism and respiration	ML2038,ML2038c	MMAR_2761	MSMEG_3564	Mb1907				
NC_000962.3	Mycobrowser_v3	CDS	2125904	2127967	.	+	0	Rv1877	Rv1877	Unknown; possibly involved in transport of drug across the membrane.	Probable conserved integral membrane protein	Rv1877, (MTCY180.41c), len: 687 aa. Probable conserved integral membrane protein, part of major facilitator superfamily (MFS), similar to many antibiotic and drug efflux proteins. Similar to e.g. Q56175 TU22 dTDP-glucose dehydrtatase from Streptomyces violaceoruber (557 aa), FASTA scores: opt: 895, E(): 0, (34.7% identity in 528 aa overlap). Also similar to Mycobacterium tuberculosis relatives protein, include Rv3728, Rv3239c, Rv2846c, etc. Contains PS00217 Sugar transport proteins signature 2 (PS00217).	P9WG85	No	cell wall and cell processes		MMAR_3970	MSMEG_3563	Mb1908,Mb1909				
NC_000962.3	Mycobrowser_v3	CDS	2129377	2130513	.	+	0	Rv1879	Rv1879	Function unknown	Conserved hypothetical protein	Rv1879, (MTCY180.39c), len: 378 aa. Conserved hypothetical protein, similar to SCC22.14c|AL096839 hypothetical protein from Streptomyces coelicolor (368 aa), FASTA results: opt: 772, E(): 0 (40.3% identity in 372 aa overlap); and to N-terminal half of nodulin/glutamate-ammonia ligase-like protein. Some similarity to N-terminus of AL132958|ATT4D2_11 Arabidopsis thaliana (845 aa), FASTA results: opt: 354, E(): 3.1e-16, (29.2% identity in 383 aa overlap); and to P38094|FLUG_EMENI Flug protein of Emericella nidulans (865 aa), FASTA results: opt: 306, E(): 6.2e-13, (26.5% identity in 415 aa overlap). Note that the upstream ORF Rv1878|MTCY18 0.40c is similar to the C-terminus.	O07751	No	conserved hypotheticals	ML2036,ML2036c	MMAR_2764	MSMEG_0362	Mb1911				
NC_000962.3	Mycobrowser_v3	CDS	2130541	2131857	.	-	0	Rv1880c	cyp140	Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	Probable cytochrome P450 140 Cyp140	Rv1880c, (MT1929, MTCY180.38), len: 438 aa. Probable cyp140, cytochrome p450. Similar to Q00441|CPXJ_SACER 6-deoxyerythronolide beta hydroxylase (404 aa), FASTA scores: opt: 775, E(): 0, (44.2% identity in 319 aa overlap); and other members of the cytochrome P450 family. Related to Mycobacterium tuberculosis proteins include: Rv0766c, Rv2266, Rv0778, etc. Contains cytochrome P450 cysteine heme-iron ligand signature (PS00086). Belongs to the cytochrome P450 family.	P9WPL9	No	intermediary metabolism and respiration	ML2033	MMAR_2768	MSMEG_0681	Mb1912c				
NC_000962.3	Mycobrowser_v3	CDS	2132370	2133203	.	-	0	Rv1882c	Rv1882c	Function unknown; probably involved in cellular metabolism	Probable short-chain type dehydrogenase/reductase	Rv1882c, (MTCY180.36), len: 277 aa. Probable short-chain dehydrogenase/reductase, similar to various dehydrogenases/reductases, generally belonging to SDR family, e.g. NP_250789.1|NC_002516 probable short-chain dehydrogenase from Pseudomonas aeruginosa (251 aa); NP_421760.1|NC_002696 short chain dehydrogenase family protein from Caulobacter crescentus (270 aa); NP_107167.1|NC_002678 oxidoreductase (short chain dehydrogenase/reductase family) from Mesorhizobium loti (253 aa); P50197|LINC_PSEPA 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase from Pseudomonas paucimobilis (Sphingomonas paucimobilis) (250 aa), FASTA scores: opt: 301, E(): 2.3e-12, (30.0% identity in 223 aa overlap); etc. Also similar to proteins from Mycobacterium tuberculosis e.g. Rv3057c, Rv1245, etc. Contains possible helix-turn-helix motif at aa 246-267 (+4.32 SD). Contains PS00061 Short-chain alcohol dehydrogenase family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	O07749	No	intermediary metabolism and respiration		MMAR_2770		Mb1914c				
NC_000962.3	Mycobrowser_v3	CDS	2134890	2135867	.	-	0	Rv1886c	fbpB	Involved in cell wall mycoloylation. Proteins of the antigen 85 complex are responsible for the high affinity of mycobacteria to fibronectin. Possesses a mycolyltransferase activity required for the biogenesis of trehalose dimycolate (cord factor), a dominant structure necessary for maintaining cell wall integrity.	Secreted antigen 85-B FbpB (85B) (antigen 85 complex B) (mycolyl transferase 85B) (fibronectin-binding protein B) (extracellular alpha-antigen)	Rv1886c, (MT1934, MTCY180.32), len: 325 aa. FbpB (alternate gene names: mpt59, 85B), precursor of the 85-B antigen (fibronectin-binding protein B) (mycolyl transferase 85B) (see citations below), highly similar to other Mycobacterial antigen precursors e.g. P12942|A85B_MYCBO antigen 85-B precursor from Mycobacterium bovis (323 aa); P21160|A85B_MYCKA antigen 85-B precursor from Mycobacterium kansasii (325 aa); etc. Also highly similar to Mycobacterium tuberculosis antigen precursors: Rv3804c|fbpA (338 aa), Rv0129c|fbpC2 (340 aa), and Rv3803c|fbpC1 (299 aa). Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WQP1	No	lipid metabolism	ML2028	MMAR_2777	MSMEG_2078,MSMEG_6398	Mb1918c				
NC_000962.3	Mycobrowser_v3	CDS	2194644	2194973	.	-	0	Rv1942c	mazF5	Function unknown	Possible toxin MazF5	Rv1942c, (MTCY09F9.22), len: 109 aa. Possible mazF5, toxin, part of toxin-antitoxin (TA) operon with Rv1943c (See Pandey and Gerdes, 2005; Zhu et al., 2006), shows some similarity to Q10867|MTCY39.28|Rv1991 hypothetical 12.3 kDa protein (114 aa), FASTA scores: opt: 117, E(): 0.021, (24. 5% identity in 110 aa overlap) also P33645|CHPA_ECOLI pemk-like protein 1 (mazf protein) from Escherichia coli (111 aa), FASTA scores: opt: 104, E(): 0.18, (29.1% identity in 110 aa overlap). Also similar to Mycobacterium tuberculosis Rv0659c (102 aa) (32.7% identity in 101 aa overlap); Rv1102c (33.3% identity in 93 aa overlap) and Rv1495.	P95272	No	virulence, detoxification, adaptation	ML0329,ML0329c			Mb1977c				
NC_000962.3	Mycobrowser_v3	CDS	2140739	2141869	.	-	0	Rv1894c	Rv1894c	Function unknown	Conserved hypothetical protein	Rv1894c, (MTCY180.24), len: 376 aa. Conserved hypothetical protein, weak similarity to some oxidoreductases e.g. Q01284 2-nitropropane dioxygenase precursor (378 aa), FASTA results: opt: 204, E(): 5.8e-06, (34.3% identity in 140 aa overlap). Similar to hypothetical Mycobacterium tuberculosis proteins e.g. Rv3553|MTCY03C7.02c (355 aa), FASTA results: opt: 296, E(): 1.6e-10, (32.9% identity in 167 aa overlap); Rv1533 (375 aa) (48.1% identity in 376 aa overlap); Rv0021c, Rv2781c.	O07738	No	conserved hypotheticals	ML2021	MMAR_2787	MSMEG_3519	Mb1927c				
NC_000962.3	Mycobrowser_v3	CDS	2146245	2147633	.	-	0	Rv1900c	lipJ	Function unknown; probably involved in cellular metabolism	Probable lignin peroxidase LipJ	Rv1900c, (MTCY180.18), len: 462 aa. Probable lipJ, lignin peroxidase, with some similarity to esterases, hydrolases and hypothetical Mycobacterium tuberculosis proteins e.g. Q43936 beta-ketoadipate enol-lactone hydrolase from Acinetobacter calcoaceticus (267 aa), FASTA results: opt: 217, E(): 1.7e-07, (29.2% identity in 260 aa overlap). Also similar to other Mycobacterium tuberculosis hypothetical proteins e.g. Rv2212|Q10400|YM12_MYCTU (378 aa), FASTA results: opt: 216, E(): 6.7e-07, (27.7% identity in 285 aa overlap).	O07732	No	intermediary metabolism and respiration	ML2016	MMAR_0286	MSMEG_4477	Mb1935c				
NC_000962.3	Mycobrowser_v3	CDS	2153235	2153882	.	-	0	Rv1907c	Rv1907c	Unknown	Hypothetical protein	Rv1907c, (MTCY180.11), len: 215 aa. Hypothetical unknown protein. Similar to Q50763 Ethyl methane sulphonate resistance protein from Mycobacterium tuberculosis (168 aa), FASTA scores: opt: 638, E(): 0, (69.7% identity in 152 aa overlap). Downstream of a cloned katG gene (EMBL:mtkatg). Differences are due to frameshift errors in the EMBL sequence and the use of an earlier start codon. Alternative nucleotide at position 2153410 (a->G; V158A) has been observed.	L0TAY1	No	conserved hypotheticals	ML2007			Mb1942c				
NC_000962.3	Mycobrowser_v3	CDS	2153889	2156111	.	-	0	Rv1908c	katG	Multifunctional enzyme, exhibiting both a catalase, a broad-spectrum peroxidase, and a peroxynitritase activities. May play a role in the intracellular survival of mycobacteria within macrophages; protection against reactive oxygen and nitrogen intermediates produced by phagocytic cells. Seems regulated by SIGB|Rv2710 [catalytic activity: 2 H(2)O(2) = O(2) + 2 H(2)O].	Catalase-peroxidase-peroxynitritase T KatG	Rv1908c, (MTCY180.10), len: 740 aa. KatG, catalase-peroxidase-peroxynitritase T (see citations below), HPI. FASTA results: Q57215 catalase-peroxidase from Mycobacterium tuberculosis (740 aa) opt: 5081, E(): 0, (100% identity in 740 aa overlap). Contains peroxidases active site signature (PS00436) and ATP/GTP-binding site motif A (P-loop; PS00017). Cosmid sequence was corrected to agree with a sequencing read from the H37Rv genome. Deletions or defects in KATG gene cause isoniazid (INH) resistance. Belongs to the peroxidase family. Bacterial peroxidase/catalase subfamily. KATG transcription seems to be regulated by FURA|Rv1909c product. The catalase-peroxidase activity is associated with the amino-terminal domain but no definite function has been assigned to the carboxy-terminal domain. Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WIE5	No	virulence, detoxification, adaptation	ML2009		MSMEG_6384	Mb1943c				
NC_000962.3	Mycobrowser_v3	CDS	2158087	2159091	.	-	0	Rv1912c	fadB5	Thought to be involved in fatty acid degradation. FADB and FADA are the alpha and beta subunits of the multifunctional enzyme complex of the fatty acid degradation cycle.	Possible oxidoreductase FadB5	Rv1912c, (MTCY180.06), len: 334 aa. Possible fadB5, oxidoreductase, similar to various oxidoreductases: 3-hydroxyacyl-CoA dehydrogenase, quinone oxidoreductases, and polyketide synthases, e.g. NP_104067.1|NC_002678 probable oxidoreductase from Mesorhizobium loti (308 aa); NP_464140.1|NC_003210 protein similar to oxidoreductase from Listeria monocytogenes (313 aa); NP_193889.1|NC_003075 putative NADPH quinone oxidoreductase from Arabidopsis thaliana (325 aa); NP_001880.2|NM_001889 crystallin, zeta; quinone oxidoreductase; NADPH:quinone reductase from Homo sapiens (329 aa); part 2983 to 3197 of T17410 polyketide synthase type I from Streptomyces venezuelae (3739 aa); Q53927|SCBAC20F6.16 hydroxyacyl-CoA dehydrogenase from Streptomyces coelicolor (329 aa), FASTA scores: opt: 621, E(): 2e-30, (39.5% identity in 349 aa overlap); etc. Also similar to many hypothetical Mycobacterium tuberculosis proteins including: MTCY24G1.09, MTCY13D12.11, MTCY19H9.01, MTCY24G1.03, MTCY03A2.17c, etc. Contains quinone oxidoreductase/zeta-crystallin signature (PS01162).	O07721	No	lipid metabolism	ML2002	MMAR_2814		Mb1947c				
NC_000962.3	Mycobrowser_v3	CDS	2161566	2162762	.	+	0	Rv1916	aceAb	Involved in glyoxylate bypass, an alternative to the tricarboxylic acid cycle [catalytic activity: isocitrate = succinate + glyoxylate].	Probable isocitrate lyase AceAb [second part] (isocitrase) (isocitratase) (Icl)	Rv1916, (MTCY180.02c), len: 398 aa. Probable aceAb, isocitrate lyase (see citations below). Highly similar to the C-terminus of ACEA_MYCLE|P46831 isocitrate lyase from Mycobacterium leprae (606 aa), FASTA results: opt: 1635, E(): 0, (86.3% identity in 278 aa overlap). Although this ORF and the upstream ORF representing the N-terminal half of aceA could be joined by a frameshift no error is apparent in the cosmid, or in a seqencing read from the genome of H37Rv. As this ORF has a RBS and transcriptional start immediately following the stop of the upstream ORF, it is possible that they are expressed as two separate modules. In Mycobacterium tuberculosis strain CDC1551, aceA exists as a single gene, MT1966: the corresponding protein has been purified experimentally and seems have an active isocitrate lyase activity (see Honer et al., 1999). For Mycobacterium tuberculosis strain H37Rv, immunoblot assay didn't detect AceAa or AceAb products (see Honer et al., 1999) but mRNA of AceAa|Rv1915 has been detected (see Betts et al., 2002); so AceAb|Rv1916 could be a pseudogene. Icl2 has 2-methyl-isocitrate lyase (MCL) activity in M. tuberculosis Erdman (See Munoz-Elias et al., 2006).	O07717	No	intermediary metabolism and respiration	ML1985,ML1985c		MSMEG_3706	Mb1950				
NC_000962.3	Mycobrowser_v3	CDS	2171623	2172486	.	+	0	Rv1920	Rv1920	Unknown	Probable membrane protein	Rv1920, (MTV050.04), len: 287 aa. Probable membrane protein, similar to AL0215|SC10A5.04 putative membrane protein from Streptomyces coelicolor cosmid 10A5 (295 aa), FASTA scores: opt: 292, E(): 3.6e-13, (31.3% identity in 243 aa overlap). Also weakly similar to several Mycobacterial putative proteins with unknown function e.g. Rv0502, Rv1428c, U00018_22 Mycobacterium leprae cosmid B2168.	O53962	No	cell wall and cell processes		MMAR_2826		Mb1955				
NC_000962.3	Mycobrowser_v3	CDS	2174067	2175182	.	+	0	Rv1922	Rv1922	Unknown	Probable conserved lipoprotein	Rv1922, (MTCY09F9.42c), len: 371 aa. Probable conserved lipoprotein, possibly peptidase similar to many peptidases, e.g. P15555|DAC_STRSQ D-alanyl-D-alanine carboxypeptidase from Streptomyces sp. (406 aa), FASTA scores: opt: 382, E(): 3.1e-17, (28.0% identity in 379 aa overlap). Also similar to Mycobacterium tuberculosis hypothetical proteins Rv1497, Rv2463, Rv3775, etc. Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	P95291	No	cell wall and cell processes		MMAR_2827		Mb1957				
NC_000962.3	Mycobrowser_v3	CDS	2177087	2178949	.	+	0	Rv1925	fadD31	Function unknown, but involvement in lipid degradation.	Probable acyl-CoA ligase FadD31 (acyl-CoA synthetase) (acyl-CoA synthase)	Rv1925, (MTCY09F9.39c), len: 620 aa. Probable fadD31, acyl-CoA synthetase, highly similar to others from Mycobacterium leprae e.g. NP_301198.1|NC_002677 putative acyl-CoA synthetase (635 aa); NP_302537.1|NC_002677 probable acyl-CoA synthase (583 aa); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. fadD32 (637 aa); fadD21 (578 aa); fadD29 (619 aa); fadD26|FD26_MYCTU|Q10976 (626 aa), FASTA scores: opt: 945, E(): 0, (39.8% identity in 598 aa overlap); etc. Also similar to N-terminus of G1171128 saframycin MX1 synthetase B from Myxococcus xanthus (1770 aa), FASTA scores: opt: 845, E(): 0, (37.4% identity in 593 aa overlap); N-terminus of T34918 polyketide synthase from Streptomyces coelicolor (2297 aa); etc. Nucleotide position 2177654 in the genome sequence has been corrected, A:C resulting in M190L.	I6Y7V6	No	lipid metabolism	ML1980c	MMAR_2835	MSMEG_3465	Mb1960				
NC_000962.3	Mycobrowser_v3	CDS	2179673	2180446	.	+	0	Rv1927	Rv1927	Function unknown	Conserved hypothetical protein	Rv1927, (MTCY09F9.37c), len: 257 aa. Conserved hypothetical protein, similar to SCG11A.10c|AL133210 hypothetical protein from Streptomyces coelicolor (252 aa), FASTA scores: opt: 729, E(): 0, (48.3% identity in 238 aa overlap). Slight similarity with P54543|YQJF_BACSU hypothetical 23.9 kDa protein from Bacillus subtilis (209 aa), FASTA scores, opt: 230, E(): 2.8e-08, (28.0% identity in 164 aa overlap).	P95287	No	conserved hypotheticals		MMAR_2848		Mb1962				
NC_000962.3	Mycobrowser_v3	CDS	2180450	2181217	.	-	0	Rv1928c	Rv1928c	Function unknown; probably involved in cellular metabolism.	Probable short-chain type dehydrogenase/reductase	Rv1928c, (MTCY09F9.36), len: 255 aa. Probable short-chain dehydrogenase/reductase, highly similar to others e.g. NP_228109.1|NC_000853 oxidoreductase (short chain dehydrogenase/reductase family) from Thermotoga maritima (257 aa); T41116 short chain dehydrogenase from Schizosaccharomyces pombe (261 aa); P87219|SOU1_CANAL sorbitol utilization protein (SDR family) from Candida albicans (281 aa); P25529|HDHA_ECOLI 7-alpha-hydroxysteroid dehydrogenase from Escherichia coli (255 aa), FASTA scores: opt: 541, E(): 1.2e-27, (37.5% identity in 251 aa overlap); etc. Also similar to many mycobacterial tuberculosis proteins e.g. Rv1350, Rv0927c, Rv2002, Rv0769, Rv2766c, etc. Contains PS00061 Short-chain alcohol dehydrogenase family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	P95286	No	intermediary metabolism and respiration		MMAR_2849		Mb1963c				
NC_000962.3	Mycobrowser_v3	CDS	2184959	2186188	.	-	0	Rv1934c	fadE17	Function unknown, but supposed involvement in lipid degradation.	Probable acyl-CoA dehydrogenase FadE17	Rv1934c, (MTCY09F9.30), len: 409 aa. Probable fadE17, acyl-CoA dehydrogenase, highly similar to ACD_MYCLE|P46703 acyl-CoA dehydrogenase from Mycobacterium leprae (389 aa), FASTA scores: opt: 414, E(): 2.6e-19, (28.3% identity in 407 aa overlap). Also similar to many e.g. NP_249713.1|NC_002516 probable acyl-CoA dehydrogenase from Pseudomonas aeruginosa (381 aa); NP_420614.1|NC_002696 acyl-CoA dehydrogenase family protein from Caulobacter crescentus (355 aa); CAB61610.1|AL133210 putative acyl-CoA dehydrogenase from Streptomyces coelicolor (393 aa); etc. Also similar to others from Mycobacterium tuberculosis e.g. fadE30 (385 aa); fadE31 (377 aa); C-terminus of fadE34 (711 aa); etc. Could belong to the acyl-CoA dehydrogenases family.	P95280	No	lipid metabolism		MMAR_2862		Mb1969c				
NC_000962.3	Mycobrowser_v3	CDS	2188496	2191015	.	+	0	Rv1937	Rv1937	Function unknown; may be involved in electron transfer.	Possible oxygenase	Rv1937, (MTCY09F9.27c), len: 839 aa. Possible oxygenase, similar in N-terminus to N-terminal part (approx. 350 aa) of dioxygenases (including ring-hydroxylating dioxygenase electron transfer components) and monooxygenases, e.g. AAC34815.1|AF071556 anthranilate dioxygenase reductase from Acinetobacter sp. (343 aa); AAK52291.1|AY026914|AntC putative anthranilate dioxygenase reductase from Pseudomonas putida (340 aa); AAF63450.1|AF218267_7|AF218267 benzoate dioxygenase / ferredoxin reductase from Pseudomonas putida (336 aa); P23101|XYLZ_PSEPU toluate 1,2-dioxygenase electron transfer component [includes: ferredoxin; ferredoxin--NAD(+) reductase ] from Pseudomonas putida plasmid TOL pWW0 (336 aa), FASTA scores: opt: 700, E(): 0, (34.3% identity in 335 aa overlap); S23479 probable benzoate 1,2-dioxygenase reductase component benC from Acinetobacter calcoaceticus (338 aa); AAC45294.1|U81594 soluble methane monooxygenase protein C from Methylocystis sp. (343 aa); P22868|MEMC_METCA methane monooxygenase component C from Methylococcus capsulatus (348 aa); etc. Also similar in part to Mycobacterium tuberculosis hypothetical electron transfer proteins Rv3554, Rv3571, etc. Contains PS00197 2Fe-2S ferredoxins, iron-sulfur binding region signature.	P95277	No	intermediary metabolism and respiration		MMAR_2865		Mb1972				
NC_000962.3	Mycobrowser_v3	CDS	2192094	2192609	.	+	0	Rv1939	Rv1939	Function unknown; probably involved in cellular metabolism	Probable oxidoreductase	Rv1939, (MTCY09F9.25c), len: 171 aa. Probable oxidoreductase, similar to NP_302637.1|NC_002677 probable oxidoreductase from Mycobacterium leprae (162 aa) Also similar to NTAB_CHELE|P54990 nitrilotriacetate monooxygenase component from Chelatobacter heintzii (322 aa), fasta scores: opt: 269, E(): 5.3e-11, (33.1% identity in 151 aa overlap). And similar to Mycobacterium tuberculosis probable monooxygenase components Rv0246, Rv3567, and to a lesser extent, Rv3007c.	P95275	No	intermediary metabolism and respiration		MMAR_2867		Mb1974				
NC_000962.3	Mycobrowser_v3	CDS	2202138	2202587	.	+	0	Rv1956	higA	Possibly involved in transcriptional mechanism.	Possible antitoxin HigA	Rv1956, (MTCY09F9.08c), len: 149 aa. Possible higA, antitoxin, part of toxin-antitoxin (TA) operon with Rv1955 (See Pandey and Gerdes, 2005; Gupta, 2009). Possible transcriptional regulatory protein, contains probable helix-turn-helix motif at aa 52-73 (+4.78 SD). Upon expression in E.coli Rv1956 has been shown to function as a toxin inhibiting cell growth and colony formation that is neutralized by coexpression with Rv1955 (PubMed: 19016878); It is not clear if these conflicting results are due to expression in a heterologous system. The gene names higA and higB have been assigned to both Rv1955 and Rv1956; we have chosen to call Rv1956 higA after consulting the authors.	P9WJA7	No	virulence, detoxification, adaptation				Mb1991				
NC_000962.3	Mycobrowser_v3	CDS	2205582	2206802	.	-	0	Rv1963c	mce3R	Involved in transcriptional mechanism; repression of the MCE3 operon. Could also have a regulatory action on the MCE2 operon.	Probable transcriptional repressor (probably TetR-family) Mce3R	Rv1963c, (MTV051.01c-MTCY09F9.01), len: 406 aa. Probable mce3R, negative transcriptional regulatory protein, TetR family (see citation below); similar to several transcriptional regulator e.g. AL049485|SC6A5.30 Streptomyces coelicolor cosmid 6 a (404 aa), FASTA scores: opt: 319, E(): 6.4e-13, (29.5% identity in 373 aa overlap); and Z84498|MTCY9F9_1 (259 aa), FASTA scores: opt: 208, E(): 1.6e-07, (100.0% identity in 32 aa overlap). Contains probable helix-turn-helix at aa 36-57 (+4.23 SD) and two tet-R family signatures.	P95251	No	regulatory proteins		MMAR_2873		Mb1998c				
NC_000962.3	Mycobrowser_v3	CDS	2208507	2209322	.	+	0	Rv1965	yrbE3B	Unknown	Conserved hypothetical integral membrane protein YrbE3B	Rv1965, (MTV051.03), len: 271 aa. YrbE4B, hypothetical unknown integral membrane protein, part of mce3 operon and member of YrbE family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07413|Rv0168|MTCI28.08|yrbE1B (289 aa), FASTA scores: opt: 937, E(): 0, (54.3% identity in 254 aa overlap); O07790|Rv0588|MTCY19H5.34|yrbE2B (295 aa); etc. Also highly similar to conserved hypothetical integral membrane proteins of the yrbEB type, e.g. AAD24545.1|AF116213|YrbE1B from Mycobacterium leprae (106 aa); P45392|YRBE_ECOLI hypothetical 27.9 kDa protein from Escherichia coli (260 aa), FASTA scores: opt: 218, E(): 1.2e-07, (24.1% identity in 245 aa overlap); etc. The transcription of this CDS seems negatively regulated by the product of Rv1963c|mce3R (see Santangelo et al., 2002).	O53966	No	virulence, detoxification, adaptation		MMAR_2881	MSMEG_0345					
NC_000962.3	Mycobrowser_v3	CDS	2209327	2210604	.	+	0	Rv1966	mce3A	Unknown, but thought to be involved in host cell invasion.	Mce-family protein Mce3A	Rv1966, (MTV051.04), len: 425 aa. Mce3A; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins P72013|MCE1|Rv0169|MTCI28.09|mce1A (454 aa); O07789|MCE2|Rv0589|MTCY19H5.33c|mce2A (404 aa); etc. Also highly similar to others e.g. AAD52105.1|AF113402_1|AF113402 mycobacterial cell entry protein from Mycobacterium bovis BCG (454 aa); NP_302656.1|NC_002677 putative cell invasion protein from Mycobacterium leprae (441 aa); CAC12798.1|AL445327 putative secreted protein from Streptomyces coelicolor (418 aa); etc. Contains a possible N-terminal signal sequence or membrane anchor. Note that previously known as mce3. The transcription of this CDS seems negatively regulated by the product of Rv1963c|mce3R (see Santangelo et al., 2002). Predicted to be an outer membrane protein (See Song et al., 2008).	L7N698	No	virulence, detoxification, adaptation		MMAR_2882	MSMEG_0346					
NC_000962.3	Mycobrowser_v3	CDS	2211626	2212858	.	+	0	Rv1968	mce3C	Unknown, but thought to be involved in host cell invasion.	Mce-family protein Mce3C	Rv1968, (MTV051.06), len: 410 aa. Mce3C; belongs to 24-membered Mycobacterium tuberculosis Mce protein family (see citations below), highly similar to Mycobacterium tuberculosis proteins O07415|R0171|MTCI28.11|mce1C (515 aa); O07787|Rv0591|MTCY19H5.31|mce2C (481 aa); etc. Also similar to others e.g. CAC12796.1|AL445327 putative secreted protein from Streptomyces coelicolor (351 aa); NP_302658.1|NC_002677 putative secreted protein from Mycobacterium leprae (519 aa); etc. Contains a possible N-terminal signal sequence or membrane anchor. The transcription of this CDS seems negatively regulated by the product of Rv1963c|mce3R (see Santangelo et al., 2002). Predicted to be an outer membrane protein (See Song et al., 2008).	O53969	No	virulence, detoxification, adaptation			MSMEG_0348					
NC_000962.3	Mycobrowser_v3	CDS	2219754	2220800	.	+	0	Rv1977	Rv1977	Function unknown	Conserved protein	Rv1977, (MTV051.15), len: 348 aa. Conserved protein, similar to SCC123.20|AL136518 hypothetical protein from Streptomyces coelicolor (402 aa), blastp scores: Score = 311 bits (789), Expect = 5e-84 Identities = 156/316 (49%), Positives = 212/316 (66%); and PCC6803|D90907_31 Synechocystis sp. (303 aa), FASTA scores: opt: 533, E(): 4.7e- 29, (38.5% identity in 275 aa overlap). Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature. Alternative nucleotide at position 2219929 (T->C; L59P) has been observed.	O53978	No	conserved hypotheticals		MMAR_2906	MSMEG_3476					
NC_000962.3	Mycobrowser_v3	CDS	2234991	2237306	.	-	0	Rv1992c	ctpG	Metal cation-transporting ATPase; possibly catalyzes the transport of an undetermined metal cation with the hydrolysis of ATP [catalytic activity: ATP + H(2)O + undetermined metal cation(in) = ADP + phosphate + undetermined metal cation(out)].	Probable metal cation transporter P-type ATPase G CtpG	Rv1992c, (MTCY39.27), len: 771 aa. Probable ctpG, metal cation-transporting P-type ATPase G (transmembrane protein), similar to others, especially cadmium-transporting ATPases, e.g. NP_244904.1|NC_002570 cadmium-transporting ATPase from Bacillus halodurans (707 aa); P30336|CADA_BACFI probable cadmium-transporting ATPase from Bacillus firmus (723 aa); BAB47609.1|AB037671 cadmium resistance protein B from Staphylococcus aureus (804 aa); 3121832|Q60048|CADA_LISMO probable cadmium-transporting ATPase from Listeria monocytogenes (707 aa); etc. Also similar to others from Mycobacterium tuberculosis e.g. Rv0969|MTCY10D7.05c|ctpV putative cation transporter P-type ATPase V (770 aa); Rv1469; Rv0092; etc. Contains PS00435 Peroxidases proximal heme-ligand signature and PS00154 E1-E2 ATPases phosphorylation site. Belongs to the cation transport ATPases family (E1-E2 ATPases), subfamily IB.	P9WPS7	No	cell wall and cell processes		MMAR_2140		Mb2015c				
NC_000962.3	Mycobrowser_v3	CDS	2224220	2225188	.	-	0	Rv1981c	nrdF1	Involved in the DNA replication pathway. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides, precursors that are necessary for DNA synthesis [catalytic activity: 2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H(2)O = ribonucleoside diphosphate + reduced thioredoxin].	Ribonucleoside-diphosphate reductase (beta chain) NrdF1 (ribonucleotide reductase small subunit) (R2F protein)	Rv1981c, (MTCY39.38), len: 322 aa. NrdF1, ribonucleoside-diphosphate reductase, beta chain (see citation below), highly similar to others e.g. RIR4_SALTY|P17424 ribonucleoside-diphosphate reductase (319 aa), FASTA scores: opt: 1402, E(): 0, (66.0% identity in 315 aa overlap); etc. Also similar to Rv3048c|MTV012.63c from Mycobacterium tuberculosis. Contains PS00368 Ribonucleotide reductase small subunit signature. Belongs to the ribonucleoside diphosphate reductase small chain family. Cofactor: binds 2 iron ions (by similarity). Note that previously known as nrdF.	P9WH73	No	information pathways				Mb2003c				
NC_000962.3	Mycobrowser_v3	CDS	2226244	2227920	.	+	0	Rv1983	PE_PGRS35	Function unknown	PE-PGRS family protein PE_PGRS35	Rv1983, (MTCY39.36c), len: 558 aa. PE_PGRS35, Member of the Mycobacterium tuberculosis PE family, PGRS subfamily of gly-rich proteins (see Brennan & Delogu 2002). Similar to other PE proteins e.g. Rv0977, etc. Contains PS00141 Eukaryotic and viral aspartyl proteases active site.	P9WIF1	No	PE/PPE		MMAR_2933		Mb2005				
NC_000962.3	Mycobrowser_v3	CDS	2243816	2245138	.	-	0	Rv1999c	Rv1999c	Unknown. Possibly transporter involved in transport of undetermined substrate (possibly cationic amino acids) across the membrane: so responsible for the translocation of the substrate across the membrane.	Probable conserved integral membrane protein	Rv1999c, (MTCY39.19), len: 440 aa. Probable conserved integral membrane protein, possibly transporter of cationic amino acid, similar to many transporters, especially amino acid transporters, e.g. CAC08265.1|AL392146 putative amino acid transporter from Streptomyces coelicolor (414 aa); P39277|YJEH_ECOLI hypothetical 44.8 kDa protein from Escherichia coli (418 aa), FASTA scores, opt: 343, E(): 6.6e-15, (27.2% identity in 408 aa overlap); etc. Also similar to Rv1979c from Mycobacterium tuberculosis, FASTA score: (28.2% identity in 277 aa overlap); Rv2127, Rv0346c, Rv0522, etc. Seems to belong to the APC family.	P9WQM3	No	cell wall and cell processes			MSMEG_0812	Mb2022c				
NC_000962.3	Mycobrowser_v3	CDS	2263998	2265038	.	+	0	Rv2017	Rv2017	Thought to be involved in transcriptional mechanism.	Transcriptional regulatory protein	Rv2017, (MTV018.04), len: 346 aa. Transcriptional regulator. Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature in C-terminal half, may be fortuitous. Contains probable helix-turn-helix motif at aa 18-39 (Score 2243, +6.83 SD); IPR001387 Helix-turn-helix type 3.	O53463	No	regulatory proteins				Mb2040				
NC_000962.3	Mycobrowser_v3	CDS	2268693	2270240	.	-	0	Rv2024c	Rv2024c	Unknown	Conserved hypothetical protein	Rv2024c, (MTV018.11c), len: 515 aa. Conserved hypothetical protein. Identical to N-terminal part of much larger hypothetical protein, RvD1-Rv2024c' (1606 aa), from Mycobacterium bovis BCG: CAB44655.1|Y18605|13881753|AAK46361.1|AE007059 so probably truncated. Part of RvD1 chromosomal deletion region.	O53470	No	conserved hypotheticals				Mb2049c				
NC_000962.3	Mycobrowser_v3	CDS	2272787	2274508	.	-	0	Rv2027c	dosT	Sensor part of the two component regulatory system DEVR/DEVS/dost; O2, NO and CO are ligands, dost is inactive when bound to oxygen	Two component sensor histidine kinase DosT	Rv2027c, (MTV018.14c), len: 573 aa. DosT, Histidine kinase response regulator, highly similar to others.	P9WGK1	No	regulatory proteins			MSMEG_5241	Mb2052c				
NC_000962.3	Mycobrowser_v3	CDS	2289282	2289599	.	-	0	Rv2044c	Rv2044c	Unknown	Conserved hypothetical protein	Rv2044c, (MTV018.31c), len: 105 aa. Conserved hypothetical protein, similar to many.	O53487	No	conserved hypotheticals	ML1433,ML1433c			Mb2070c				
NC_000962.3	Mycobrowser_v3	CDS	3871084	3872496	.	-	0	Rv3450c	eccB4	Unknown	ESX conserved component EccB4. ESX-4 type VII secretion system protein. Probable membrane protein.	Rv3450c, (MTCY13E12.03c), len: 470 aa. EccB4, esx conserved component, ESX-4 type VII secretion system protein, probable membrane protein (possible membrane spanning region near N-terminus). Similar to hypothetical unknowns proteins from Mycobacterium leprae e.g. O33088|MLCB628.17C|ML0054 hypothetical 51.9 KDA protein (putative membrane protein)(481 aa), FASTA scores: opt: 708, E(): 6.4e-32, (32.9% identity in 480 aa overlap); Q9CD29|ML2536 (552 aa), FASTA scores: opt: 394, E(): 1.7e-14, (33.6% identity in 503 aa overlap); etc. Also similar to other proteins from Mycobacterium tuberculosis (strains H37Rv and CDC1551) e.g. O69734|Rv3869|MTV027.04 (480 aa), FASTA scores: opt: 717, E(): 2e-32, (32.55% identity in 479 aa overlap); O05449|Rv3895c|MTCY15F10.17 (495 aa), FASTA scores: opt: 670, E(): 8.3e-30, (36.4% identity in 475 aa overlap); O5368|Rv0283|MTV035.11 (538 aa), FASTA scores: opt: 467, E(): 1.5e-18, (36.3% identity in 493 aa overlap); etc.	P9WNR1	No	cell wall and cell processes		MMAR_1099	MSMEG_1534	Mb3480c				
NC_000962.3	Mycobrowser_v3	CDS	2279129	2280124	.	+	0	Rv2032	acg	Unknown. May have a role for bacteria within the host environment.	Conserved protein Acg	Rv2032, (MTV018.19), len: 331 aa. Acg (for acr-coregulated gene), conserved protein possibly member of a superfamily of classical nitroreductases (see Purkayastha et al., 2002), similar to Rv3127 and Rv3131. Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WIZ9	No	conserved hypotheticals			MSMEG_3943,MSMEG_5246	Mb2058				
NC_000962.3	Mycobrowser_v3	CDS	2308131	2310755	.	-	0	Rv2051c	ppm1	Transfers mannose from GDP-mannose to all endogenous polyprenol-phosphates.	Polyprenol-monophosphomannose synthase Ppm1	Rv2051c, (MTV018.38c), len: 874 aa. Ppm1, Polyprenol-monophosphomannose synthase. Transfers mannose from GDP-Mannose to all endogenous polyprenol-phosphates in Mycobacterium tuberculosis, proven experimentally (A. Baulard, Institut Pasteur de Lille: see citation below).	O53493	No	cell wall and cell processes	ML1440c,ML1441c	MMAR_3029		Mb2077c				
NC_000962.3	Mycobrowser_v3	CDS	2317169	2320753	.	-	0	Rv2062c	cobN	Required for cobalt insertion.	Cobalamin biosynthesis protein CobN	Rv2062c, (MTCY49.01c, MTV019.03), len: 1194 aa. cobN, cobalamin biosynthesis protein, similar to many.	O53498	No	intermediary metabolism and respiration	ML1447,ML1447c	MMAR_3037	MSMEG_3864	Mb2088c				
NC_000962.3	Mycobrowser_v3	CDS	2323175	2324701	.	+	0	Rv2066	cobI	Involved in cobalamin biosynthesis.	Probable bifunctional protein, CobI-COBJ fusion protein: S-adenosyl-L-methionine-precorrin-2 methyl transferase + precorrin-3 methylase	Rv2066, (MTCY49.05), len: 508 aa. Probable CobI-CobJ fusion protein, S-adenosyl-L-methionine-precorrin-2 methyl transferase and precorrin-3 methylase. Similar in N-terminal half (aa 1-240) to many S-adenosyl-L-methionine-precorrin-2 methyl transferase (244 aa), and in C-terminal half (aa 240-508) to precorrin-3 methylase (254 aa).	P9WGB3	No	intermediary metabolism and respiration		MMAR_3046	MSMEG_3873	Mb2092				
NC_000962.3	Mycobrowser_v3	CDS	2333037	2333288	.	-	0	Rv2076c	Rv2076c	Unknown	Conserved hypothetical protein	Rv2076c, (MTCY49.15c), len: 83 aa. Conserved hypothetical protein, similar to many.	P9WLL3	No	conserved hypotheticals		MMAR_5576		Mb2101c				
NC_000962.3	Mycobrowser_v3	CDS	2335355	2337325	.	+	0	Rv2079	Rv2079	Unknown	Conserved hypothetical protein	Rv2079, (MTCY49.18), len: 656 aa. Conserved hypothetical protein; part of Mycobacterium tuberculosis protein family with Rv2542, Rv2077c, Rv2797c, Rv0963c, Rv1949c. Contains PS00120 Lipases, serine active site	P9WLK7	No	conserved hypotheticals		MMAR_5468		Mb2105				
NC_000962.3	Mycobrowser_v3	CDS	2344411	2346180	.	+	0	Rv2088	pknJ	Involved in signal transduction (via phosphorylation). Can phosphorylate the peptide substrate myelin basic protein (MBP). [catalytic activity: ATP + a protein = ADP + a phosphoprotein].	Transmembrane serine/threonine-protein kinase J PknJ (protein kinase J) (STPK J)	Rv2088, (MTCY49.28), len: 589 aa. PknJ, transmembrane serine/threonine-protein kinase (see citation below). Contains PS00108 Serine/Threonine protein kinases active-site signature. Contains Hank's kinase subdomain. Belongs to the Ser/Thr family of protein kinases. Experimental studies show evidence of auto-phosphorylation. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007). Cofactor: requires divalent cations for activity.	P9WI67	No	regulatory proteins		MMAR_2408		Mb2115				
NC_000962.3	Mycobrowser_v3	CDS	2349334	2352054	.	-	0	Rv2092c	helY	DNA helicase activity.	ATP-dependent DNA helicase HelY	Rv2092c, (MTCY49.32c), len: 906 aa. HelY, ATP-dependent DNA helicase, similar to many; contains PS00017 ATP/GTP-binding site motif A, PS00402 Binding-protein-dependent transport systems inner membrane component signature. Belongs to the SKI2 subfamily of helicases.	P9WMR1	No	information pathways	ML1333	MMAR_3078	MSMEG_3885	Mb2119c				
NC_000962.3	Mycobrowser_v3	CDS	2358389	2360041	.	+	0	Rv2100	Rv2100	Unknown	Conserved hypothetical protein	Rv2100, (MTCY49.40), len: 550 aa. Conserved hypothetical protein. Member of Mycobacterium tuberculosis REP13E12 repeat family with Rv1148c, Rv1945, Rv3467, Rv0094c, Rv1128c, Rv1587c, Rv1702c, Rv3466, Rv1588c.	P9WLJ3	No	insertion seqs and phages	ML1327,ML1327c		MSMEG_3957,MSMEG_5583	Mb2126				
NC_000962.3	Mycobrowser_v3	CDS	2360240	2363281	.	+	0	Rv2101	helZ	Has helicase activity.	Probable helicase HelZ	Rv2101, (MTV020.01), len: 1013 aa. Probable helZ, helicase, similar to many. Nucleotide position 2361623 in the genome sequence has been corrected, A:C resulting in M462L.	I6YCF3	No	information pathways				Mb2127				
NC_000962.3	Mycobrowser_v3	CDS	2372630	2373823	.	+	0	Rv2113	Rv2113	Unknown	Probable integral membrane protein	Rv2113, (MTCY261.09), len: 397 aa. Probable integral membrane protein.	O33248	No	cell wall and cell processes	ML1318,ML1318c	MMAR_3089		Mb2137				
NC_000962.3	Mycobrowser_v3	CDS	2374461	2376290	.	-	0	Rv2115c	mpa	Involved in proteasomal protein degradation	Mycobacterial proteasome ATPase Mpa	Rv2115c, (MTCY261.11c), len: 609 aa. Mpa, mycobacterial proteasome ATPase, similar to many. Contains PS00674 AAA-protein family signature and PS00017 ATP/GTP-binding site motif A (P-loop). Identified as a substrate for proteasomal degradation (See Pearce et al., 2006). Pup|Rv2111c and Mpa|Rv2115c interact (See Pearce et al., 2008).	P9WQN5	No	cell wall and cell processes	ML1316	MMAR_3091	MSMEG_3902	Mb2139c				
NC_000962.3	Mycobrowser_v3	CDS	2382489	2386067	.	-	0	Rv2124c	metH	Involved in biosynthesis of methionine (at the terminal step) [catalytic activity: 5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine].	5-methyltetrahydrofolate--homocystein methyltransferase MetH (methionine synthase, vitamin-B12 dependent isozyme) (ms)	Rv2124c, (MTCY261.20c), len: 1192 aa. MetH, methionine synthase, similar to many. Contains PS00178 Aminoacyl-transfer RNA synthetases class-I signature. Belongs to the vitamin-B12 dependent methionine synthase family.	O33259	No	intermediary metabolism and respiration	ML1307		MSMEG_4185	Mb2148c				
NC_000962.3	Mycobrowser_v3	CDS	2388616	2390085	.	+	0	Rv2127	ansP1	Involved in L-asparagine transport.	L-asparagine permease AnsP1	Rv2127, (MTCY261.26), len: 489 aa. AnsP1, L-asparagine permease, integral membrane protein similar to many. Contains PS00218 Amino acid permeases signature. Seems to belong to the APC family.	P9WQM9	No	cell wall and cell processes		MMAR_4815		Mb2151				
NC_000962.3	Mycobrowser_v3	CDS	2390085	2390288	.	+	0	Rv2128	Rv2128	Unknown	Conserved transmembrane protein	Rv2128, (MTCY26.27), len: 67 aa. Conserved transmembrane protein, similar to many.	O33262	No	cell wall and cell processes		MMAR_4816		Mb2152				
NC_000962.3	Mycobrowser_v3	CDS	2409697	2410641	.	-	0	Rv2151c	ftsQ	This protein may be involved in septum formation.	Possible cell division protein FtsQ	Rv2151c, (MTCY270.17), len: 314 aa. Possible ftsQ, cell division protein, with some homology to FTSQ_STRGR|P45503 cell division protein ftsq homolog from Streptomyces griseus (208 aa), FASTA scores: opt: 204, E(): 4e-05; (30.6% identity in 193 aa overlap).	P9WNA1	No	cell wall and cell processes	ML0916	MMAR_3191	MSMEG_4225	Mb2175c				
NC_000962.3	Mycobrowser_v3	CDS	2392517	2393320	.	-	0	Rv2131c	cysQ	Can dephosphorylate a broad range of substrates. Likely involved in sulfur metabolism, controlling the pool of 3'-phosphoadenosine 5'-phosphate (pap) and 3'-phosphoadenoside 5'-phosphosulfate (PAPS) [catalytic activity: adenosine 3',5'-bisphosphate + H2O = adenosine 5'-phosphate + phosphate]. Has also been shown to have myo-inositol 1-phosphatase [catalytic activity: myo-inositol 1-phosphate + H(2)O = myo-inositol + phosphate] and fructose 1,6-bisphosphatase [catalytic activity: D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate] activities.	Monophosphatase CysQ	Rv2131c, (MTCY270.37), len: 267 aa. CysQ, monophosphatase, equivalent to CYSQ_MYCLE|P46726 cysQ protein homolog from Mycobacterium leprae (289 aa), FASTA scores: opt: 1374, E(): 0, (77.3% identity in 264 aa overlap). Contains inositol monophosphatase family signature 1 (PS00629), significance uncertain. Seems to belong to the inositol monophosphatase family. Cofactor: Mg2+. Inhibited by Li+; PAPase activity is inhibited by Na+ and K+, but IMPase activity is not (See Gu et al., 2006; Hatzios et al., 2008).	P9WKJ1	No	intermediary metabolism and respiration	ML1301	MMAR_3112	MSMEG_4190	Mb2155c				
NC_000962.3	Mycobrowser_v3	CDS	2396008	2396838	.	-	0	Rv2136c	Rv2136c	Unknown	Possible conserved transmembrane protein	Rv2136c, (MTCY270.32), len: 276 aa. Possible conserved transmembrane protein, very similar to hypothetical Mycobacterium leprae protein Q49783. FASTA best: Q49783 B2126_C2_190 opt: 1023, E(): 0; (82.4% identity in 187 aa over lap) similar to BACA_ECOLI P31054 bacitracin resistance protein (273 aa) opt: 477, E(): 7e-26, (35.6% identity in 267 aa overlap)	P9WFF9	No	cell wall and cell processes	ML1297	MMAR_3116	MSMEG_4194	Mb2160c				
NC_000962.3	Mycobrowser_v3	CDS	2400376	2401722	.	-	0	Rv2141c	Rv2141c	Unknown	Conserved protein	Rv2141c, (MTCY270.27), len: 448 aa. Conserved protein. Shows some similarity to conserved hypothetical proteins and to acetylornithine deacetylase and succinyl-diaminopimelate desuccinylase and contains ArgE/dapE/ACY1/CPG2/yscS family signature 1 (PS00758). FASTA best: CBPS_YEAST P27614 carboxypeptidases precursor (576 aa) opt: 234, E(): 4.3e-08; (24.3% identity in 412 aa overlap). Previously named dapE2. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	L7N684	No	intermediary metabolism and respiration	ML1288	MMAR_3123	MSMEG_4200	Mb2165c				
NC_000962.3	Mycobrowser_v3	CDS	2417472	2419004	.	-	0	Rv2157c	murF	Involved in cell wall formation; peptidoglycan biosynthesis.	Probable UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanyl ligase MurF	Rv2157c, (MTCY270.11), len: 510 aa. Probable murF, UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanyl ligase (UDP-murnac-pentapeptide synthetase) (see citation below), also related to other Mycobacterium tuberculosis mur gene products. FASTA best: MURF_ECOLI|P11880 (452 aa), opt: 515, E(): 2.6e-24, (31.9% identity in 511 aa overlap).	P9WJL1	No	cell wall and cell processes	ML0910	MMAR_3197	MSMEG_4231	Mb2181c				
NC_000962.3	Mycobrowser_v3	CDS	2425048	2427087	.	-	0	Rv2163c	pbpB	Involved in peptidoglycan biosynthesis	Probable penicillin-binding membrane protein PbpB	Rv2163c, (MTCY270.05), len: 679 aa. Probable pbpB, penicillin-binding membrane protein, similar to many bacterial PBP2 proteins e.g. P11882|PBP2_NEIME|PENA|NMA2072|NMB0413 penicillin-binding protein 2 (pbp-2) from Neisseria meningitidis (serogroups a and B) (581 aa), FASTA scores: opt: 665, E(): 1.6e-31, (33.2% identity in 591 aa overlap); etc. Also similar to Rv0016c and Rv2864c from Mycobacterium tuberculosis (2.8e-10). Contains PS00017 possible ATP/GTP-binding site motif A (P-loop) near C-terminus. FASTA best: PBP2_NEIME P11882 penicillin-binding protein 2 (pbp-2). (581 aa) opt: 665, E(): 1.6e-31; (33.2% identity in 591 aa overlap). FtsW|Rv2154c interacts with PbpB|Rv2163c and FtsZ|RvRv2150c (See Datta et al., 2006). Cleavage of PbpB|Rv2163c by Rv2869c under conditions of oxidative stress is prevented by Wag31|Rv2145c (See Mukherjee et al., 2009).	L0T911	No	cell wall and cell processes	ML0908	MMAR_3200	MSMEG_4233	Mb2187c				
NC_000962.3	Mycobrowser_v3	CDS	2432235	2432855	.	+	0	Rv2170	Rv2170	Acetylation, substrate unknown	GCN5-related N-acetyltransferase	Rv2170, (MTV021.03), len: 206 aa. Probable acetyltransferase. Contains GNAT (Gcn5-related N-acetyltransferase) domain in C-terminal part. See Vetting et al. 2005. Equivalent to hypothetical protein ML0903 (210 aa) from Mycobacterium leprae. FASTA scores: ML0903 conserved hypothetical protein (210 aa) opt: 1045, E(): 9.1e-57; 77.143% identity in 210 aa overlap. >emb|CAA18679.1| (AL022602) >gi|13092973|emb|CAC31284.1| (AL583920). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	O53504	No	intermediary metabolism and respiration	ML0903,ML0903c	MMAR_3205	MSMEG_4238	Mb2192				
NC_000962.3	Mycobrowser_v3	CDS	2626654	2626980	.	-	0	Rv2348c	Rv2348c	Unknown	Hypothetical protein	Rv2348c, (MTCY98.17c), len: 108 aa. Hypothetical unknown protein.	P95244	No	unknown		MMAR_3655						
NC_000962.3	Mycobrowser_v3	CDS	2437941	2439140	.	+	0	Rv2176	pknL	Involved in signal transduction (via phosphorylation). May be involved in transcriptional mechanism.	Probable transmembrane serine/threonine-protein kinase L PknL (protein kinase L) (STPK L)	Rv2176, (MTV021.09), len: 399 aa. Probable pknL, transmembrane serine/threonine-protein kinase (see citation below), similar to many e.g. MLCB1770_9 (622 aa). Lacks C-terminal domain and ends with putative transmembrane segment. Contains PS00108 Serine/Threonine protein kinases active-site signature. FASTA scores: Z70722|MLC B1770_9 Mycobacterium leprae cosmid B1770 (622 aa) opt: 732, E(): 5.9e-23; 44.4% identity in 266 aa overlap. Also similar to several Mycobacterium tuberculosis STPK proteins e.g. Rv0014c|PKNB, Rv0015c|PKNA, Rv1743|PKNE, Rv1266c|PKNH etc. Contains Hank's kinase subdomain. Belongs to the Ser/Thr family of protein kinases.	P9WI63	No	regulatory proteins	ML0897,ML0897c	MMAR_3211	MSMEG_4243	Mb2198				
NC_000962.3	Mycobrowser_v3	CDS	2440332	2441720	.	-	0	Rv2178c	aroG	Chorismate biosynthesis	3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG (DAHP synthetase, phenylalanine-repressible)	Rv2178c, (MTV021.11c), len: 462 aa. aroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase similar to many, especially those from plants. FASTA scores: Y15113|M C3DDAH7P_1Morinda citrifolia mRNA for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (535 aa) opt: 1421, E(): 0; 48.3% identity in 443 aa overlap.	O53512	No	intermediary metabolism and respiration	ML0896	MMAR_1854,MMAR_3222	MSMEG_4244	Mb2200c				
NC_000962.3	Mycobrowser_v3	CDS	2444586	2445329	.	-	0	Rv2182c	Rv2182c	Transfer of fatty acyl groups	1-acylglycerol-3-phosphate O-acyltransferase	Rv2182c, (MTV021.15c), len: 247 aa. Probable 1-acylglycerol-3-phosphate O-acyltransferase, similar to many e.g. in Streptomyces. Contains PS00017 ATP/GTP-binding site motif A (P-loop). FASTA scores: pir||T35503 1-acylglycerol-3-phosphate O-acyltransferase homolog SC6E10.16c - Streptomyces coelicolor >gi|5689932|emb|CAB51970.1| (AL109661) hypothetical protein [Streptomyces coelicolor A3(2)] Length = 262, Expect = 6e-61 (54% identity in 215 aa overlap).	O53516	No	conserved hypotheticals	ML0892	MMAR_3226	MSMEG_4248	Mb2204c				
NC_000962.3	Mycobrowser_v3	CDS	2461504	2462148	.	-	0	Rv2197c	Rv2197c	Unknown	Probable conserved transmembrane protein	Rv2197c, (MTCY190.08c), len: 214 aa. Probable conserved transmembrane protein, equivalent to ML0878 conserved hypothetical protein (212 aa) of Mycobacterium leprae. FASTA scores: opt: 858; 62.559% identity in 211 aa overlap CAC31259.1|(AL583920). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WLI9	No	cell wall and cell processes	ML0878	MMAR_3241	MSMEG_4264	Mb2220c				
NC_000962.3	Mycobrowser_v3	CDS	3491808	3492122	.	-	0	Rv3126c	Rv3126c	Unknown	Hypothetical protein	Rv3126c, (MTCY164.36c), unknown, len: 104 aa. Hypothetical unknown protein. Shortened version of MTCY164.36c, avoiding overlap. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WL09	No	conserved hypotheticals				Mb3149c				
NC_000962.3	Mycobrowser_v3	CDS	2448160	2449962	.	+	0	Rv2187	fadD15	Function unknown, but involved in lipid degradation.	Long-chain-fatty-acid-CoA ligase FadD15 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv2187, (MTV021.20), len: 600 aa. fadD15, long-chain-fatty-acid-CoA ligase, similar to several e.g. P44446|LCFH_HAEIN putative long-chain-fatty-acid--CoA ligase from Haemophilus influenzae (607 aa), FASTA scores: (607 aa) opt: 992, E(): 0, (31.5% identity in 578 aa overlap); etc. Contains PS00455 Putative AMP-binding domain signature. Belongs to the ATP-dependent AMP-binding enzyme family.	O53521	No	lipid metabolism	ML0887,ML0887c	MMAR_3231	MSMEG_4254	Mb2209,Mb2210				
NC_000962.3	Mycobrowser_v3	CDS	2453819	2455756	.	+	0	Rv2191	Rv2191	Unknown	Conserved hypothetical protein	Rv2191, (MTCY190.02), len: 645 aa. Conserved hypothetical protein, similar to SW:DP3A_B ACSU P13267 DNA polymerase III, alpha chain (31.3% identity in 249 aa overlap) and SW:UVRC_ECOLI P07028 excinuclease ABC subunit C (25.7% identity in 230 aa overlap). Also similar to M. tuberculosis Rv3711c (dnaQ DNA polymerase III e chain) and Rv1420 (uvrC excinuclease ABC subunit C)	P9WLJ1	No	information pathways	ML0884,ML0884c	MMAR_3235	MSMEG_4259	Mb2214				
NC_000962.3	Mycobrowser_v3	CDS	2459678	2461327	.	+	0	Rv2196	qcrB	Respiration	Probable ubiquinol-cytochrome C reductase QcrB (cytochrome B subunit)	Rv2196, (MTCY190.07), len: 549 aa. Probable qcrB, Ubiquinol-cytochrome C reductase cytochrome B subunit (cytB), integral membrane protein, low similarity in amino-terminal half to cytochrome b subunits, highly similar at C-terminus to SW:12KD_MYCLE P15878 12 KD protein PIR:S08427 (86.9% identity in 153 aa overlap). FASTA scores: sp|Q45658|QCRB_BACST menaquinol-cytochrome C reductase (224 aa) opt: 341, E(): 6.8e-15; 28.0% identity in 207 aa overlap	P9WP37	No	intermediary metabolism and respiration	ML0879,ML0879c	MMAR_3240	MSMEG_4263	Mb2219				
NC_000962.3	Mycobrowser_v3	CDS	2687128	2687973	.	+	0	Rv2393	che1	Possibly involved in inserting FE2+ into sirohydrochlorin to produce siroheme, required for SIRA (Rv2391) function	Ferrochelatase Che1	Rv2393, (MTCY253.28c), len: 281 aa. Che1, ferrochelatase (See Pinto et al., 2007). Conserved protein, with some similarity to Q9L2E8|SC7A8.10c putative secreted protein from Streptomyces coelicolor (274 aa), FASTA scores: opt: 407, E(): 2.8e-18, (37% identity in 246 aa overlap); CAC38793|SCI39.05 Conserved hypothetical protein from Streptomyces coelicolor (305 aa), FASTA scores: opt: 394, E(): 2e-17, (35.0% identity in 251 aa overlap); AAK44492|MT0272 Chalcone/stilbene synthase family protein from Mycobacterium tuberculosis (247 aa), FASTA scores: opt: 350, E(): 9.2e-15, (34.0% identity in 235 aa overlap); P95216|Rv0259c|MTCY06A4.03c|Z86089 hypothetical protein from Mycobacterium tuberculosis (247 aa), FASTA scores: opt: 345, E(): 1.9e-14,(33.6% identity in 235 aa overlap).	P71751	No	intermediary metabolism and respiration		MMAR_3418,MMAR_3712	MSMEG_4529	Mb2414				
NC_000962.3	Mycobrowser_v3	CDS	2468231	2468923	.	+	0	Rv2203	Rv2203	Unknown	Possible conserved membrane protein	Rv2203, (MTCY190.14), len: 230 aa. Possible conserved membrane protein; has single hydrophobic stretch from aa 75 to 97 and is equivalent to Mycobacterium leprae ML0872 putative membrane protein (171 aa). FASTA scores: opt: 821, E(): 3.4e-42; 72.353% identity in 170 aa overlap - CAC31253.1| (AL583920). 2468411. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WLI7	No	cell wall and cell processes	ML0872,ML0872c	MMAR_3247	MSMEG_4271	Mb2226				
NC_000962.3	Mycobrowser_v3	CDS	2477190	2478326	.	+	0	Rv2212	Rv2212	Possibly involved in cAMP synthesis [catalytic activity: ATP = 3',5'-cyclic AMP + diphosphate]	Adenylyl cyclase (ATP pyrophosphate-lyase) (adenylate cyclase)	Rv2212, (MTCY190.23), len: 378 aa. Adenylyl cyclase (See Abdel Motaal et al., 2006). Some similarity to e.g. SW:CYAA_STRCO P40135 adenylate cyclase (29.2% identity in 291 aa overlap); ttg at 24614 in MTCY190 has a better rbs. Contains possible helix-turn-helix motif at aa 64- 85, (+2.72 SD). Also similar to Rv1264 and Rv1647	P9WMU7	No	intermediary metabolism and respiration		MMAR_3257	MSMEG_4279	Mb2235				
NC_000962.3	Mycobrowser_v3	CDS	2478338	2479885	.	+	0	Rv2213	pepB	Protein degradation	Probable aminopeptidase PepB	Rv2213, (MTCY190.24), len: 515 aa. Probable pepB, leucine aminopeptidase, similar to many e.g. SW:AMPA_ECOLI P11648 aminopeptidase a/I, (41.4% identity in 309 aa overlap). Equivalent to Z98741|MLCB22_6 Mycobacterium leprae cosmid B22; Am (524 aa), FASTA scores: opt: 2793, E(): 0; 83.1% identity in 522 aa overlap. Contains PS00631 Cytosol aminopeptidase signature, ntdaegrl. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P9WHT3	No	intermediary metabolism and respiration	ML0864,ML0864c	MMAR_3258	MSMEG_4281	Mb2236				
NC_000962.3	Mycobrowser_v3	CDS	2481965	2483626	.	+	0	Rv2215	dlaT	Involved in tricarboxylic acid cycle; converts pyruvate to acetyl-CoA and CO2. Also involved in antioxidant defense; LPDC|Rv0462, DLAT|Rv2215, AHPD|Rv2429, and AHPC|Rv2428 constitute an NADH-dependent peroxidase and peroxynitrite reductase that provides protection against oxidative stress.	DlaT, dihydrolipoamide acyltransferase, E2 component of pyruvate dehydrogenase	Rv2215, (MTCY190.26), len: 553 aa. DlaT, dihydrolipoamide acyltransferase, E2 component of pyruvate dehydrogenase, proven biochemically (see Tian et al. 2005), similar to e.g. SW:O PD2_ACHLA P35489 dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex (35.3% identity in 552 aa overlap); contains PS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. Rhodanine compounds inhibit DlaT|Rv2215 and can kill non-replicating mycobacteria in mouse bone marrow-derived macrophages (See Bryk et al., 2008). LpdC|Rv0462 co-immunoprecipitates with DlaT|Rv2215 (in lpdC|Rv0462 mutant) and with BkdC|Rv2495c (in dlaT|Rv2215 mutant) (See Venugopal et al., 2011).	P9WIS7	No	intermediary metabolism and respiration	ML0861,ML0861c	MMAR_3260	MSMEG_4283	Mb2238				
NC_000962.3	Mycobrowser_v3	CDS	2487615	2489051	.	+	0	Rv2220	glnA1	Involved in glutamine biosynthesis [catalytic activity: ATP + L-glutamate + NH(3) = ADP + glutamine + orthophosphate].	Glutamine synthetase GlnA1 (glutamine synthase) (GS-I)	Rv2220, (MTCY190.31, MTCY427.01), len: 478 aa. glnA1, glutamine synthetase class I (see Tullius et al., 2001), similar to many e.g. GLNA_STRCO|P15106 from Streptomyces coelicolor, FASTA score: (71.4% identity in 475 aa overlap); etc. Also similar to three other potential glutamine synthetases in Mycobacterium tuberculosis: Rv2222c|glnA2, Rv2860c|glnA4, and Rv1878|glnA3. Contains PS00180 Glutamine synthetase signature 1, PS00181 Glutamine synthetase putative ATP-binding region signature, and PS00182 Glutamine synthetase class-I adenylation site. Belongs to the glutamine synthetase family. Note has shown to be essential for M. tuberculosis virulence.	P9WN39	No	intermediary metabolism and respiration	ML0925	MMAR_3289	MSMEG_4290	Mb2244				
NC_000962.3	Mycobrowser_v3	CDS	2489369	2492353	.	-	0	Rv2221c	glnE	Regulatory protein involved in the regulation of glutamine synthetase activity. Adenylylation and deadenylylation of glutamine synthetase. Possibly regulates GLNB|Rv2919c [catalytic activity: ATP + [L-glutamate:ammonia ligase (ADP-forming)] = pyrophosphate + adenylyl-[L-glutamate:ammonia ligase (ADP-forming)]].	Glutamate-ammonia-ligase adenylyltransferase GlnE (glutamine-synthetase adenylyltransferase)	Rv2221c, (MTCY190.32c, MTCY427.02c), len: 994 aa. glnE, glutamate-ammonia-ligase adenylyltransferase (see citations below), similar to others e.g. GLNE_ECOLI|P30870 glutamate-ammonia-ligase adenylyltransferase from Escherichia coli, FASTA score: (24.4% identity in 721 aa overlap); GLNE_HAEIN|P44419 Glutamate-ammonia-ligase adenylyltransferase from Haemophilus influenzae (981 aa), FASTA score: (28.1% identity in 199 aa overlap); etc. Note that initiation codon uncertain.	P9WN27	No	intermediary metabolism and respiration	ML1630,ML1630c	MMAR_3293	MSMEG_4293	Mb2245c				
NC_000962.3	Mycobrowser_v3	CDS	2495461	2497023	.	-	0	Rv2224c	caeA	Converts unknown esters to corresponding free acid and alcohol	Probable carboxylesterase CaeA	Rv2224c, (MTCY427.05c), len: 520 aa. Probable caeA, carboxylesterase; has signal sequence and lipoprotein motif at N-terminal end. Very similar to three proteases/peptidases from Streptomyces spp.: L42758, L42759, L27466. FASTA score: L4 2758|STMSLPD STMSLPD NID: g940302 - Streptomyces (539 aa) opt: 1032 E(): 0, (37.5% identity in 533 aa overlap). Similar to hypothetical protein SW:YZZE_ECOLI P34211 (27.7% identity in 412 aa overlap) and highly similar to Rv2224c and Rv2672 (49.3% identity in 507 aa overlap); contains PS00013, Prokaryotic membrane lipoprotein lipid attachment site, and PS00120 Lipases, serine active site. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007). Predicted to be an outer membrane protein (See Song et al., 2008).	P9WHR3	No	cell wall and cell processes	ML1633,ML1633c	MMAR_3297	MSMEG_4296	Mb2248c				
NC_000962.3	Mycobrowser_v3	CDS	2497742	2498587	.	+	0	Rv2225	panB	Involved in pantothenate biosynthesis.	3-methyl-2-oxobutanoate hydroxymethyltransferase PanB	Rv2225, (MTCY427.06), len: 281 aa. panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase, similar to PANB_ECOLI|P31057 3-methyl-2-oxobutanoate hydroxymethyltransferase from Escherichia coli (45.9% identity in 257 aa overlap). Identified as a substrate for proteasomal degradation (See Pearce et al., 2006).	P9WIL7	No	intermediary metabolism and respiration	ML1635	MMAR_3299	MSMEG_4298	Mb2249				
NC_000962.3	Mycobrowser_v3	CDS	2501644	2502738	.	-	0	Rv2228c	Rv2228c	Unknown	Multifunctional protein. Has RNASE H, alpha-ribazole phosphatase, and acid phosphatase activities.	Rv2228c, (MTCY427.09c), len: 364 aa. Multifunctional protein with RNase H, alpha-ribazole phosphatase, and acid phosphatase activities. Some similarity to phosphoglycerate mutase and ribonuclease H. Similar to CAB88177.1|AL352972 putative bifunctional protein (ribonuclease H/phosphoglycerate mutase) from Streptomyces coelicolor A3(2) (497 aa); Smith-Waterman scores: 107 bits (424), Expect = 4e-41 Identities = 160/485 (32%). Also similar in C-terminal part to Rv2419c and Rv2135c.	P9WLH5	No	information pathways	ML1637,ML1637c	MMAR_3304	MSMEG_4305	Mb2253c				
NC_000962.3	Mycobrowser_v3	CDS	2504605	2505699	.	-	0	Rv2231c	cobC	Involved in cobalamin biosynthesis	Possible aminotransferase CobC	Rv2231c, (MTCY427.12c), len: 364 aa. Possible cobC, aminotransferase. Note that initiation codon uncertain. Similar to CobC aminotransferases e.g. sp|P21633|COBC_PSEDE COBC protein (333 aa) opt: 277, E(): 1.7e-11; 28.8% identity in 313 aa overlap and also to e.g. SW:HIS8_ECOLI P06986 histidinol-phosphate aminotransferase (27.0% identity in 289 aa overlap), contains PS00105 aminotransferases class-I pyridoxal-phosphate attachment site. Real Mycobacterium tuberculosis histidinol-phosphate aminotransferase, hisC, is Rv1600 (MTCY336.04c).	P9WQ89	No	intermediary metabolism and respiration	ML1640,ML1640c	MMAR_3307		Mb2256c				
NC_000962.3	Mycobrowser_v3	CDS	2506278	2507153	.	+	0	Rv2232	ptkA	Involved in signal transduction (via phosphorylation). Can phosphorylate PTPA|Rv2234 and the peptide substrate myelin basic protein (MBP) [catalytic activity: ATP + a protein = ADP + a phosphoprotein]	Protein tyrosine kinase transcriptional regulatory protein PtkA	Rv2232, (MTCY427.13), len: 291 aa. PtkA, protein tyrosine kinase, similar to members of haloacid dehalogenase-like family from several bacteria and to putative phosphatases e.g. Q9I767 and AAK78398. Contains N-terminal extension. FASTA scores: Q9I767 hypothetical protein PA0065 (221 aa) opt: 439 E(): 3.2e-18; 38.679% identity (40.196% ungapped) in 212 aa overlap; >>tr|AAK78398 Predicted phosphatase, had family (216 aa) opt: 427, E(): 1.5e-17; 34.762% identity (35.437% ungapped) in 210 aa overlap. Replaces previous Rv2232 and Rv2233. Predicted to be an outer membrane protein (See Song et al., 2008).	P9WPI9	No	regulatory proteins	ML1641	MMAR_3308	MSMEG_4308	Mb2257				
NC_000962.3	Mycobrowser_v3	CDS	2512539	2515244	.	+	0	Rv2241	aceE	Involved in energy metabolism; contributes to acetyl-CoA production as part of pyruvate dehydrogenase complex [catalytic activity: pyruvate + lipoamide = S-acetyl-dihydro-lipoamide + CO(2)].	Pyruvate dehydrogenase E1 component AceE (pyruvate decarboxylase) (pyruvate dehydrogenase) (pyruvic dehydrogenase)	Rv2241, (MTCY427.22), len: 901 aa. AceE, pyruvate dehydrogenase E1 component, similar to others e.g. ODP1_ECOLI|P06958 pyruvate dehydrogenase E1 component from Escherichia coli, FASTA score: (51.2% identity in 891 aa overlap); etc.	P9WIS9	No	intermediary metabolism and respiration	ML1651	MMAR_3334	MSMEG_4323	Mb2265				
NC_000962.3	Mycobrowser_v3	CDS	2516787	2517695	.	+	0	Rv2243	fabD	Catalyzes malonyl-CoA-ACP transacylase (MCAT) activity using holo-ACPM as substrate for transacylation [catalytic activity: malonyl-CoA + [acyl-carrier protein] = CoA + malonyl-[acyl-carrier protein]].	Malonyl CoA-acyl carrier protein transacylase FabD (malonyl CoA:ACPM acyltransferase) (MCT)	Rv2243, (MTCY427.24), len: 302 aa. FabD (alternate gene name: mtFabD), malonyl CoA-acyl carrier protein transacylase (see citations below), highly similar to e.g. A57356 acyl-CoA carrier protein malonyltransferase from Streptomyces coelicolor (316 aa), FASTA score: opt: 955, E(): 0, (52.6% identity in 304 aa overlap); FABD_HAEIN|P43712 malonyl CoA-acyl carrier protein transacylase from Haemophilus influenzae, FASTA score: (30.5% identity in 308 aa overlap); and FABD_ECOLI|P25715 from Escherichia coli, FASTA score: (31.4% identity in 309 aa overlap). Identified as a substrate for proteasomal degradation (See Pearce et al., 2006).	P9WNG5	No	lipid metabolism	ML1653	MMAR_3336	MSMEG_4325	Mb2267				
NC_000962.3	Mycobrowser_v3	CDS	2519396	2520712	.	+	0	Rv2246	kasB	Involved in fatty acid biosynthesis (mycolic acids synthesis); involved in meromycolate extension. Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP [catalytic activity: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + [acyl-carrier protein] + CO(2)].	3-oxoacyl-[acyl-carrier protein] synthase 2 KasB (beta-ketoacyl-ACP synthase) (KAS I)	Rv2246, (MTCY427.27), len: 438 aa. KasB, beta-ketoacyl-ACP synthase, involved in meromycolate extension (see citations below). Highly similar or similar to others e.g. L43074|STMFABD3|g870805 beta-ketoacyl-ACP synthase from Streptomyces glaucescens (423 aa), FASTA scores: opt: 1091, E(): 0, (44.7% identity in 416 aa overlap); FABF_ECOLI|P39435 3-oxoacyl-[acyl-carrier-protein] synthase II from Escherichia coli, FASTA score: (37.0% identity in 411 aa overlap); FABB_HORVU|P23902 3-oxoacyl-[acyl-carrier-protein] synthase I, FASTA score: (32.5% identity in 415 aa overlap); etc. Strongest similarity to upstream ORF Rv2245|kasA|MTCY427.26 3-oxoacyl-[acyl-carrier-protein] synthase 1 from Mycobacterium tuberculosis (416 aa), FASTA score: (66.3% identity in 409 aa overlap). Belongs to the beta-ketoacyl-ACP synthases family.	P9WQD7	No	lipid metabolism	ML1656	MMAR_3339	MSMEG_4328	Mb2270				
NC_000962.3	Mycobrowser_v3	CDS	2525565	2526992	.	+	0	Rv2251	Rv2251	Electron acceptor	Possible flavoprotein	Rv2251, (MTV022.01), len: 475 aa. Possible flavoprotein, probably continuation of Rv2250A, similar to MTCY164.18 from Mycobacterium tuberculosis and to several alkyldihydroxyacetonephosphate synthases (e.g. O00116). Also some similarity to D-lactate dehydrogenases. FASTA scores: sptr|O05784|O05784 hypothetical 56.5 kDa protein. (527 aa) opt: 1019 E(): 0; (38.6% identity in 487 aa overlap) and sp|O00116|ADAS_HUMAN alkyldihydroxyaceton ephosphate synthase precursor (658 aa) opt: 558 E(): 6.2e-27; (31.3% identity in 447 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008).	L0TBR2	No	intermediary metabolism and respiration	ML1779	MMAR_3344	MSMEG_4334	Mb2275				
NC_000962.3	Mycobrowser_v3	CDS	2532245	2533330	.	+	0	Rv2259	mscR	Involved in the reduction of S-nitroglutathione	S-nitrosomycothiol reductase MscR	Rv2259, (MTV022.09), len: 361 aa. MscR, S-nitrosomycothiol reductase (see Vogt et al., 2003), similar to several zinc-containing alcohol dehydrogenases especially from Amycolatopsis methanolica P80094 (360 aa), FASTA scores: sp|P80094|FADH_AMYME NAD/mycothiol-dependent formaldehyde dehydrogenase (MD-FALDH) Length = 360, Expect = e-156, Identities = 268/358 (74%). Also similar to Rv0162c, (MTCI28.02c, 35.0% identity in 371 aa overlap). Contains PS00059 Zinc-containing alcohol dehydrogenases signature. Note previously known as adhE2	O53533	No	intermediary metabolism and respiration	ML1784	MMAR_3350	MSMEG_4340	Mb2283				
NC_000962.3	Mycobrowser_v3	CDS	2534470	2535552	.	-	0	Rv2262c	Rv2262c	Function unknown; thought to be involved in lipid metabolism.	Conserved hypothetical protein	Rv2262c, (MTV022.12c), len: 360 aa. Conserved hypothetical protein, with function unknown but some similarity to N-terminal 70% of P23930|P77703|LNT_ECOLI|cute|B0657 apolipoprotein N-acyltransferase from Escherichia coli strain K12 (512 aa), FASTA scores: opt: 239, E(): 1.6e-07, (30.4% identity in 359 aa overlap). Note that neighboring ORF shows similarity to N -terminal part of PCC6803 apolipoprotein N-acyltransferase from Synechocystis sp., suggesting possibility of frameshift. Sequence of clones from two sources has been checked but no error found. Appear to be two extra bases at position 1876970 compared to CDC1551 strain.	O53536	No	lipid metabolism		MMAR_3354		Mb2285c				
NC_000962.3	Mycobrowser_v3	CDS	2540104	2541390	.	+	0	Rv2266	cyp124	Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	Probable cytochrome P450 124 Cyp124	Rv2266, (MT2328, MTCY339.44c), len: 428 aa. Probable cyp124, cytochrome P450, similar to e.g. G405543 cytochrome P450 (406 aa), FASTA scores, opt: 763,E(): 0, (35.4% identity in 393 aa overlap), similar to e.g. MTCY50.26, 33.8% identity in 370 aa overlap	P9WPP3	No	intermediary metabolism and respiration	ML1787	MMAR_3361	MSMEG_3551	Mb2289				
NC_000962.3	Mycobrowser_v3	CDS	2553173	2554831	.	+	0	Rv2281	pitB	Involved in phosphate transport.	Putative phosphate-transport permease PitB	Rv2281, (MTCY339.29c), len: 552 aa. Putative pitB, phosphate-transport permease, integral membrane protein, similar to YG04_HAEIN P45268 putative phosphate permease hi1604 (420 aa). FASTA scores, opt: 484, E(): 5e-23, (33.5% identity in 498 aa overlap) also to G399598 amphotropic murine retrovirus receptor (656 aa) FASTA scores, opt: 453, E(): 5.8e-21, (26.8% identity in 645 aa overlap). Also similar to Rv0545c|pitA from M. tuberculosis. Belongs to the pit subfamily.	P9WIA5	No	cell wall and cell processes		MMAR_3415		Mb2302				
NC_000962.3	Mycobrowser_v3	CDS	2572076	2573008	.	-	0	Rv2300c	Rv2300c	Function unknown	Conserved protein	Rv2300c, (MTCY339.09), len: 310 aa (start uncertain). Conserved protein, similar to others e.g. Q9RXY2|DR0172 conserved hypothetical protein from Deinococcus radiodurans (271 aa), FASTA scores: opt: 306, E(): 1.3e-12, (34.6% identity in 229 aa overlap); Q9HZH1|PA3037 hypothetical protein from Pseudomonas aeruginosa (288 aa), FASTA scores: opt: 248, E(): 7.9e-09, (31.5% identity in 238 aa overlap); Q9PDL8|XF1361 hypothetical protein from Xylella fastidiosa (279 aa), FASTA scores: opt: 236, E(): 4.6e-08, (29.7% identity in 249 aa overlap); U70053|XCU70053_3 GumP protein from Xanthomonas campestris (282 aa), FASTA scores: opt: 222, E(): 3.7e-07, (30.1% identity in 248 aa overlap); etc.	P9WLD7	No	conserved hypotheticals		MMAR_3523		Mb2322c				
NC_000962.3	Mycobrowser_v3	CDS	2561675	2562457	.	+	0	Rv2289	cdh	Involved in phospholipid biosynthesis [catalytic activity: CDP-diacylglycerol + H(2)O = CMP + phosphatidate].	Probable CDP-diacylglycerol pyrophosphatase Cdh (CDP-diacylglycerol diphosphatase) (CDP-diacylglycerol phosphatidylhydrolase)	Rv2289, (MTCY339.21c), len: 260 aa. Probable cdh, CDP-diacylglycerol pyrophosphatase, similar to CDH_SALTY|P26219 cdp-diacylglycerol pyrophosphatase (251 aa), FASTA scores: opt: 395, E(): 5.9e-20, (33.5% identity in 221 aa overlap).	P9WPG9	No	lipid metabolism	ML1417	MMAR_3445		Mb2311				
NC_000962.3	Mycobrowser_v3	CDS	2565327	2566550	.	+	0	Rv2294	Rv2294	Unknown	Probable aminotransferase	Rv2294, (MTCY339.16c), len: 407 aa. Probable aminotransferase, similar to others in M. tuberculosis e.g. MTV030_19, also similar to PATB_BACSU|Q08432 putative aminotransferase b from Bacillus subtilis (387 aa), FASTA scores: opt: 563, E(): 2.8e-29, (31.4% identity in 408 aa overlap); and to MALY_ECOLI|P23256 maly protein from Escherichia coli (390 aa), FASTA scores: opt: 530, E(): 3.6e-27, (31.3% identity in 384 aa overlap). Belongs to class-II of pyridoxal-phosphate-dependent aminotransferases.	P9WQ83	No	intermediary metabolism and respiration	ML1794	MMAR_3453		Mb2316				
NC_000962.3	Mycobrowser_v3	CDS	2570059	2572002	.	-	0	Rv2299c	htpG	Molecular chaperone involved in protein folding. Has ATPase activity.	Probable chaperone protein HtpG (heat shock protein) (HSP90 family protein) (high temperature protein G)	Rv2299c, (MTCY339.11), len: 647 aa. HtpG, probable chaperone, heat shock protein 90 family. Similar to HTPG_BACSU|P46208 heat shock protein htpG homologue from Bacillus subtilis (626 aa), FASTA scores: opt: 1551, E(): 0, (39.6% identity in 631 aa overlap). Contains possible helix-turn-helix motif at aa 519-540 (+3.77 SD).	P9WMJ7	No	virulence, detoxification, adaptation	ML1623	MMAR_3521		Mb2321c				
NC_000962.3	Mycobrowser_v3	CDS	2574096	2575019	.	-	0	Rv2303c	Rv2303c	Could be involved in antibiotic-resistance.	Probable antibiotic-resistance protein	Rv2303c, (MTCY339.06, MT2360), len: 307 aa. Probable antibiotic-resistance protein, with some similarity to Q54229|G153373 macrotetrolide antibiotic-resistance protein (NONR) from Streptomyces griseus (347 aa) (see Plater and Robinson, 1992), FASTA scores: opt: 438, E(): 3.1e-21, (33.2% identity in 226 aa overlap); and other hypothetical proteins e.g. P95886 ORF C02006 from Sulfolobus solfataricus (269 aa), FASTA scores: opt: 252, E(): 3.5e-09, (25.5% identity in 286 aa overlap); etc. Also similar to Mycobacterium tuberculosis Rv3510c|O53555|MTV023.17. Note that the protein Q9XDF3|NONC from Streptomyces griseus subsp. griseus (317 aa) is equivalent to Q54229|G153373|NONR however the N-terminal end is shorter (30 aa) owing to a changed start codon (see Walczak et al., 2000). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	Q50662	No	virulence, detoxification, adaptation		MMAR_4012		Mb2325c				
NC_000962.3	Mycobrowser_v3	CDS	2577108	2577701	.	+	0	Rv2306A	Rv2306A	Unknown	Possible conserved membrane protein	Rv2306A, len: 197 aa. Possible conserved membrane protein, similar to several hypothetical membrane proteins from Mycobacterium tuberculosis and Streptomyces coelicolor, e.g. Rv0625c|P96915|Y625_MYCTU hypothetical 25.2 KDA protein from Mycobacterium tuberculosis (246 aa), FASTA scores: opt: 410, E(): 2.7e-17, (53.25% identity in 139 aa overlap). First 140 aa show high similarity, this then decreases but continues in next ORF Rv2306B, suggesting a frameshift near nt 2577473. However the sequence has been checked and no error found. The sequence is identical in CDC1551 and Mycobacterium bovis. Replaces original Rv2306c on other strand. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	Q79FG5	No	cell wall and cell processes				Mb2328				
NC_000962.3	Mycobrowser_v3	CDS	2583435	2583779	.	+	0	Rv2310	Rv2310	Use for sequence excision.	Possible excisionase	Rv2310, (MT2372, MTCY3G12.24c), len: 114 aa. Possible excisionase, showing some similarity to others e.g. Q9LCU5 putative excisionase from Arthrobacter sp. TM1 (174 aa) FASTA scores: opt: 341, E(): 6.6e-15, (48.2% identity in 110 aa overlap); O85865 putative excisionase from Sphingomonas aromaticivorans (152 aa), FASTA scores: opt: 205, E(): 2.2e-06, (41.25% identity in 80 aa overlap); etc. Also similar to Rv3750c|O69717 hypothetical protein from Mycobacterium tuberculosis (130 aa), FASTA scores: opt: 228, E(): 6.9e-08, (43.9% identity in 82 aa overlap). Contains possible helix-turn-helix motif at aa 20-41 (Score 2181, +6.62 SD). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WLC3	No	insertion seqs and phages				Mb2337				
NC_000962.3	Mycobrowser_v3	CDS	2584486	2584755	.	+	0	Rv2312	Rv2312	Unknown	Hypothetical protein	Rv2312, (MTCY3G12.22c), len: 89 aa. Hypothetical unknown protein. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WLB9	No	conserved hypotheticals				Mb2339				
NC_000962.3	Mycobrowser_v3	CDS	2587287	2588804	.	-	0	Rv2315c	Rv2315c	Function unknown	Conserved protein	Rv2315c, (MTCY3G12.19), len: 505 aa. Conserved protein, highly similar to Q9S273|SCI28.10 hypothetical 47.1 KDA protein from Streptomyces coelicolor (435 aa), FASTA scores: opt: 1768, E():5.6e-101, (63.2% identity in 432 overlap); and similar to others e.g. AAK24787|CC2823 hypothetical protein (TldD/PmbA family) from Caulobacter crescentus (543 aa), FASTA scores: opt: 876, E():3.1e-46, (42.8% identity in 505 overlap); O58578|PH0848 hypothetical 54.4 KDA protein from Pyrococcus horikoshii (481 aa), FASTA scores: opt: 661, E(): 4.3e-33, (29.95% identity in 484 aa overlap); Q9UZ95|PAB1547 hypothetical 53.6 KDA protein from Pyrococcus abyssi (473 aa), FASTA scores: opt: 656, E(): 8.6e-33, (29.1% identity in 481 aa overlap); etc.	P71897	No	conserved hypotheticals	ML1767,ML1767c	MMAR_3616	MSMEG_4464	Mb2342c				
NC_000962.3	Mycobrowser_v3	CDS	2588838	2589710	.	+	0	Rv2316	uspA	Thought to be involved in active transport of sugar across the membrane (import). Responsible for the translocation of the substrate across the membrane.	Probable sugar-transport integral membrane protein ABC transporter UspA	Rv2316, (MTCY3G12.18c), len: 290 aa. Probable uspA, sugar-transport integral membrane protein ABC transporter (see citation below), most similar to Q9CBN8|USPA|ML1768 sugar transport integral membrane protein from Mycobacterium leprae (328 aa), FASTA scores: opt: 1593, E(): 1.9e-93, (82.35% identity in 289 aa overlap); and similar to O32940|ML1426|MLCB2052.28 possible sugar transport protein (probable ABC-transport protein, inner membrane component) from Mycobacterium leprae (319 aa), FASTA scores: opt: 600, E(): 9.2e-31, (34.25% identity in 295 aa overlap). Also similar to other proteins involved in transport e.g. Q9X860|SCE134.05c putative binding protein dependent transport protein from Streptomyces coelicolor (327 aa), FASTA scores: opt: 639, E(): 3.2e-33, (40.45% identity in 272 aa overlap); Q9K6N9|BH3689 sugar transport system (permease) from Bacillus halodurans (300 aa), FASTA scores: opt: 590, E(): 3.7e-30, (35.65% identity in 289 aa overlap); etc.	P71896	No	cell wall and cell processes	ML1768	MMAR_3617	MSMEG_4466	Mb2343				
NC_000962.3	Mycobrowser_v3	CDS	2594154	2594699	.	-	0	Rv2321c	rocD2	Involved in arginine metabolism [catalytic activity: L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid].	Probable ornithine aminotransferase (C-terminus part) RocD2 (ornithine--oxo-acid aminotransferase)	Rv2321c, (MTCY3G12.13), len: 181 aa. Probable rocD2, ornithine aminotransferase, highly similar to C-terminal region of other ornithine aminotransferases, e.g. Q9FC90|ROCD from Streptomyces coelicolor (407 aa), FASTA scores: opt: 628, E(): 1.2e-32, (55.35% identity in 168 aa overlap); P3802|OAT_BACSU|ROCD from Bacillus subtilis (401 aa), FASTA scores: opt: 477, E(): 4.3e-23, (42.1% identity in 178 aa overlap); BAB42057|ROCD|SA0818 from Staphylococcus aureus subsp. aureus N315 (396 aa), FASTA scores: opt: 437, E(): 1.5e-20, (41.3% identity in 170 aa overlap); etc. Contains PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site. Belongs to class-III of pyridoxal-phosphate-dependent aminotransferases. Rv2322c|MTCY3G12.12 (upstream ORF) and Rv2321c|MTCY3G12.13 appear to be an ornithine aminotransferase homologue but are frameshifted - we can find no sequence error in the cosmid to account for this.	P71891	No	intermediary metabolism and respiration	ML1773,ML1773c			Mb2348c				
NC_000962.3	Mycobrowser_v3	CDS	2597009	2597857	.	-	0	Rv2325c	Rv2325c	Function unknown	Conserved hypothetical protein	Rv2325c, (MTCY3G12.09), len: 282 aa. Conserved hypothetical protein, equivalent to O32970|MLCB22.37c|ML0849 hypothetical protein from Mycobacterium leprae (283 aa), FASTA scores: opt: 1405, E(): 1.8e-78, (77.7% identity in 282 aa overlap). Also some similarity to other proteins e.g. Q9Z9J1|YBAF|BH0166 YBAF protein (BH0166 protein) (hypothetical protein) from Bacillus halodurans (265 aa), FASTA scores: opt: 288, E(): 2.8e-10, (25.8% identity in 264 aa overlap); P70972|YBAF YBAF protein (hypothetical protein) from Bacillus subtilis (265 aa), FASTA scores: opt: 259, E(): 1.5e-08, (25.45% identity in 224 aa overlap); AAK34821|SPY2193|Q99X13 Conserved hypothetical protein from Streptococcus pyogenes (266 aa), FASTA scores: opt: 232, E(): 6.5e-07, (25.1% identity in 267 aa overlap); etc.	P9WPI7	No	conserved hypotheticals	ML0849	MMAR_3625	MSMEG_4469	Mb2352c				
NC_000962.3	Mycobrowser_v3	CDS	2597854	2599947	.	-	0	Rv2326c	Rv2326c	Probably involved in active transport accross the membrane. Thought to be responsible for energy coupling to the transport system and the translocation of the substrate across the membrane.	Possible transmembrane ATP-binding protein ABC transporter	Rv2326c, (MTC3G12.08), len: 697 aa. Possible transmembrane ATP-binding protein ABC transporter (see citation below). Equivalent to Q9CCF9|ML0848 ABC transporter from Mycobacterium leprae (724 aa), FASTA scores: opt: 3482, E(): 2.8e-182, (76.9% identity in 697 aa overlap) and also to O32971|MLCB22.38c ABC-type transporter from Mycobacterium leprae (726 aa), FASTA scores: opt: 3482, E(): 2.8e-182, (76.9% identity in 697 aa overlap). Similar in part to other ABC transporters e.g. Q9WY65|TM0222 from Thermotoga maritima (266 aa), FASTA scores: opt: 407, E(): 4.2e-15, (38.0% identity in 213 aa overlap); etc. Contains 2 X PS00017 ATP/GTP-binding site motif A (P-loop); and 2 x PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters).	P9WQI7	No	cell wall and cell processes	ML0848	MMAR_3626	MSMEG_4470	Mb2353c				
NC_000962.3	Mycobrowser_v3	CDS	2605108	2606754	.	+	0	Rv2332	mez	Catalyzes the oxidative decarboxylation of malate into pyruvate, important for a wide range of metabolic pathways [catalytic activity: (S)-malate + NAD(+) = pyruvate + CO(2) + NADH].	Probable [NAD] dependent malate oxidoreductase Mez (malic enzyme) (NAD-malic enzyme) (malate dehydrogenase (oxaloacetate decarboxylating)) (pyruvic-malic carboxylase) (NAD-me)	Rv2332, (MTCY3G12.02c, MTCY98.01, MT2394), len: 548 aa. Probable mez, malate oxidoreductase [NAD] dependent (malic enzyme), highly similar to others e.g. O34389|MALS putative malolactic enzyme [includes: malic enzyme ; L-lactate dehydrogenase] from Bacillus subtilis (566 aa), FASTA scores: opt: 1927, E(): 5.5e-111, (52.9% identity in 539 aa overlap); P45868|MAO2_BACSU|YWKA probable NAD-dependent malic enzyme from Bacillus subtilis (582 aa), FASTA scores: opt: 1849, E(): 3.6e-106, (50.45% identity in 543 aa overlap); Q48796|MLES_OENOE malolactic enzyme from Oenococcus oeni (541 aa), FASTA scores: opt: 1540, E(): 3.6e-87, (44.2% identity in 536 aa overlap); etc. Belongs to the malic enzymes family. N-terminus shortened since first submission (previously 652 aa).	P9WK25	No	intermediary metabolism and respiration	ML0835,ML0835c	MMAR_3643		Mb2360				
NC_000962.3	Mycobrowser_v3	CDS	2608796	2609728	.	+	0	Rv2334	cysK1	Involved in cysteine biosynthesis [catalytic activity: O3-acetyl-L-serine + H(2)S = L-cysteine + acetate].	Cysteine synthase a CysK1 (O-acetylserine sulfhydrylase A) (O-acetylserine (thiol)-lyase A) (CSASE A)	Rv2334, (MT2397, MTCY98.03), len: 310 aa. cysK1, cysteine synthase A, equivalent to O32978|CYSK_MYCLE|ML0839|MLCB22.47 cysteine synthase a from Mycobacterium leprae (310 aa), FASTA scores: opt: 1756, E(): 8.6e-96, (85.8% identity in 310 aa overlap). Also highly similar to other cysteine synthases e.g. Q9JQL6|CYSK|NMA0974|NMB0763 putative cysteine synthase from Neisseria meningitidis (serogroup a and B) (310 aa), FASTA scores: opt: 1368, E(): 4.6e-73, (66.45% identity in 310 aa overlap); P73410|CYSK_SYNY3|SLR1842 from Synechocystis sp (312 aa), FASTA scores: opt: 1310, E(): 1.2e-69, (64.65% identity in 311 aa overlap); Q43725|CYSM_ARATH|OASC|ACS1|AT3G59760|F24G16.30 cysteine synthase (mitochondrial precursor) from Arabidopsis thaliana (Mouse-ear cress) (424 aa), FASTA scores: opt: 1253, E(): 3.2e-66, (59.2% identity in 309 aa overlap) (has its N-terminus longer 104 aa); etc. Contains PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. Belongs to the cysteine synthase/cystathionine beta-synthase family. Note that previously known as cysK.	P9WP55	No	intermediary metabolism and respiration	ML0839,ML0839c	MMAR_3645		Mb2362				
NC_000962.3	Mycobrowser_v3	CDS	2613107	2614063	.	-	0	Rv2338c	moeW	Involved in molybdoptenum cofactor biosynthesis; thought to be involved in the biosynthesis of a demolybdo-cofactor (molybdopterin), necessary for molybdo-enzymes.	Possible molybdopterin biosynthesis protein MoeW	Rv2338c, (MTCY98.07c), len: 318 aa. Possible moeW, molybdoptenum biosynthesis protein, showing some similarity to several molybdopterin biosynthesis proteins e.g. O27613|MTH1571 molybdopterin biosynthesis protein MOEB homolog from Methanobacterium thermoautotrophicum (251 aa), FASTA scores: opt: 309, E(): 4.7e-14; (30.7% identity in 254 aa overlap); Q9KPQ5|VC2311 HESA/MOEB/THIF family protein from Vibrio cholerae (273 aa), FASTA scores: opt: 255, E(): 4e-09, (36.25% identity in 149 aa overlap); Q9PD34|XF1545 molybdopterin biosynthesis protein from Xylella fastidiosa (276 aa), FASTA scores: opt: 233,E(): 1e-07, (33.6% identity in 128 aa overlap); etc. Seems to belong to the HESA/MOEB/THIF family. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P95234	No	intermediary metabolism and respiration				Mb2366c				
NC_000962.3	Mycobrowser_v3	CDS	2620533	2622452	.	-	0	Rv2343c	dnaG	DNA primase is the polymerase that synthesizes small RNA primers for the okazaki fragments on both template strands replication FORKS during chromosomal DNA synthesis.	Probable DNA primase DnaG	Rv2343c, (MTCY98.12c), len: 639 aa. Probable dnaG, DNA primase, equivalent to O52200|PRIM_MYCSM|DNAG DNA primase from Mycobacterium smegmatis (636 aa), FASTA scores: opt: 3504, E(): 5.5e-202, (81.55% identity in 639 aa overlap); and Q9CCG2|DNAG|ML0833 DNA primase from Mycobacterium leprae (642 aa), FASTA scores: opt: 3443, E(): 2.5e-198, (80.4% identity in 642 aa overlap). Also highly similar to many DNA primases e.g. Q9S1N4|PRIM_STRCO|DNAG|SC7A8.07c from Streptomyces coelicolor (641 aa), FASTA scores: opt: 1899, E(): 5.1e-106, (47.9% identity in 643 aa overlap); P74893|PRIM_SYNP7|DNAG from Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) (616 aa), FASTA scores: opt: 860, E(): 6.6e-44, (35.3% identity in 513 aa overlap); P05096|PRIM_BACSU from Bacillus subtilis (603 aa) FASTA scores: opt: 800, E(): 2.5e-40, (33.7% identity in 430 aa overlap); etc.	P9WNW1	No	information pathways	ML0833	MMAR_3650	MSMEG_4482	Mb2372c				
NC_000962.3	Mycobrowser_v3	CDS	2627172	2628698	.	-	0	Rv2349c	plcC	Hydrolyzes sphingomyelin in addition to phosphatidylcholine. Probable virulence factor implicated in the pathogenesis of Mycobacterium tuberculosis at the level of intracellular survival, by the alteration of cell signaling events or by direct cytotoxicity [catalytic activity: a phosphatidylcholine + H(2)O = 1,2- diacylglycerol + choline phosphate].	Probable phospholipase C 3 PlcC	Rv2349c, (MT2414, MTCY98.18c), len: 508 aa. Probable plcC, phospolipase C 3 (see citations below), similar to other precursors of several phospolipases C e.g. P15713|PHLN_PSEAE|PA3319 non-hemolytic phospholipase C precursor from Pseudomonas aeruginosa (692 aa), FASTA scores: opt: 1013, E(): 9.3e-54, (38.85% identity in 525 aa overlap); P06200|PHLC_PSEAE hemolytic phospholipase C precursor from Pseudomonas aeruginosa (730 aa), FASTA scores: opt: 630, E(): 1.5e-30, (35.15% identity in 535 aa overlap); Q9S816|T12J13.18|T21P5.4 putative phospholipase from Arabidopsis thaliana (Mouse-ear cress) (521 aa), FASTA scores: opt: 218, E(): 1e-05, (27.05% identity in 451 aa overlap); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. Q9XB13|PLCD|Rv1755c|MT1799|MTCY28.21C phospholipase C 4 (514 aa), FASTA scores: opt: 2497, E(): 9e-144, (68.35% identity in 509 aa overlap); Q50560|Rv2351c|PLCA|MTP40|MT2416|MTCY98.20c phospholipase C 1 (520 aa), FASTA scores: opt: 2494, E(): 1.4e-143, (68.1% identity in 514 aa overlap); P95246|PLCB|MPCB|Rv2350c|MT2415|MTCY98.19c phospholipase C 2 (512 aa), FASTA scores: opt: 2474, E(): 2.2e-142, (67.65% identity in 513 aa overlap); etc. Belongs to the bacterial phospholipase C family.	P9WIB1	No	intermediary metabolism and respiration		MMAR_3656						
NC_000962.3	Mycobrowser_v3	CDS	2634528	2635592	.	-	0	Rv2353c	PPE39	Function unknown	PPE family protein PPE39	Rv2353c, (MTCY98.22c), len: 354 aa. PPE39, Member of Mycobacterium tuberculosis PPE family, highly similar to many e.g. near ORF P95249|Rv2356c|MTCY98.25 from Mycobacterium tuberculosis (615 aa), FASTA scores: opt: 1566, E(): 3.2e-69, (66.1% identity in 349 aa overlap); Q10778|MTCY48.17, Q10540|MTCY31.06c, E241779|MTCY98, Q10813|MTCY274.23c, P71868|MTCY03C7.23, P71869|MTCY03C7.24c, P42611|MTV037.06C, E64997|MTCY98, Q10707|MTCY49.38C, P71657|MTCY02B10.25c, etc. Note that the ATG and RBS appear to be provided by the IR of neighbouring IS6110. Predicted to be an outer membrane protein (See Song et al., 2008).	Q79FF3	No	PE/PPE								
NC_000962.3	Mycobrowser_v3	CDS	2639673	2641064	.	-	0	Rv2357c	glyS	Involved in translation mechanisms [catalytic activity: ATP + L-glycine + tRNA(GLY) = AMP + pyrophosphate + L-glycyl-tRNA(GLY)].	Probable glycyl-tRNA synthetase GlyS (glycine--tRNA ligase) (GLYRS)	Rv2357c, (MTCY27.23, MTCY98.26), len: 463 aa. Probable glyS, glycyl-tRNA synthetase, equivalent to Q9CCG4|GLYS|ML0826 putative glycyl-tRNA synthase from Mycobacterium leprae (463 aa), FASTA scores: opt: 2898, E(): 1e-179, (90.2% identity in 459 aa overlap). Also highly similar to others e.g. Q9L2H9|SYG_STRCO|SCC121.07c from Streptomyces coelicolor (460 aa), FASTA scores: opt: 2210, E(): 2.9e-135, (68.3% identity in 457 aa overlap); Q9PPZ7|SYG_UREPA|GLYS|UU493 glycyl-tRNA synthetase from Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (473 aa), FASTA scores: opt: 1254, E(): 1.7e-73, (45.25% identity in 462 aa overlap); P75425|SYG_MYCPN|GLYS|MPN354|MP482 glycyl-tRNA synthetase from Mycoplasma pneumoniae (449 aa), FASTA scores: opt: 1074, E(): 6.9e-62, (39.45% identity in 454 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1. Belongs to class-II aminoacyl-tRNA synthetase family.	P9WFV7	No	information pathways	ML0826	MMAR_3667	MSMEG_4485	Mb2378c				
NC_000962.3	Mycobrowser_v3	CDS	2643461	2644258	.	-	0	Rv2362c	recO	Involved in DNA repair and RECF pathway recombination	Possible DNA repair protein RecO	Rv2362c, (MTCY27.18), len: 265 aa. RecO, DNA repair protein, equivalent to Q9CCN0|ML0633 Mycobacterium leprae Hypothetical protein (268 aa), FASTA scores: opt: 1560, E(): 8.5e-93, (86.6% identity in 268 aa overlap). Also highly similar to others e.g. Q9L2H3|SCC121.13c DNA repair protein recO from Streptomyces coelicolor (251 aa), FASTA scores: opt: 843, E(): 6.9e-47, (52.2% identity in 249 aa overlap); and similar to other hypothetical proteins. Weak similarity with P42095|RECO_BACSU DNA repair protein recombinase from Bacillus subtilis (255 aa), FASTA scores: opt: 270, E(): 3.6e-10, (26.4% identity in 182 aa overlap). Maybe involved in modulating assembly and disassembly of RECA filaments (with RECF|Rv0003 and RECR|Rv3715c) (see citation below). Contains match to Pfam entry PF02565 Recombination protein O. Belongs to the RECO family.	P9WHI5	No	information pathways	ML0633	MMAR_3672	MSMEG_4491	Mb2383c				
NC_000962.3	Mycobrowser_v3	CDS	2644320	2645774	.	+	0	Rv2363	amiA2	Generates monocarboxylate from monocarboxylic acid amide [catalytic activity: a monocarboxylic acid amide + H(2)O = a monocarboxylate + NH(3)].	Probable amidase AmiA2 (aminohydrolase)	Rv2363, (MTCY27.17c), len: 484 aa. Probable amiA2, amidase, highly similar or similar to others e.g. O28325|YJ54_ARCFU|AF1954 putative amidase from Archaeoglobus fulgidus (453 aa), FASTA scores: opt: 777, E(): 1.1e-38, (35.0% identity in 474 aa overlap); Q55424|AMID_SYNY3|SLL0828 putative amidase from Synechocystis sp. strain PCC 6803 (506 aa), FASTA scores: opt: 770, E(): 3e-38, (36.4% identity in 456 aa overlap); Q53116|AMDA enantiomerase-selective amidase from Rhodococcus sp. (462 aa), FASTA scores: opt: 701, E(): 3.5e-34, (32.7% identity in 468 aa overlap); etc. Also highly similar to others from Mycobacterium tuberculosis e.g. AMI2_MYCTU|AMIB2|Q11056|Rv1263|MT1301|MTCY50.19c|cy50.19c amidase (462 aa), FASTA scores: opt: 1141, E(): 2.9e-60, (45.4% identity in 454 aa overlap); etc. Contains PS00571 Amidases signature, and PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the amidase family.	P9WQ99	No	intermediary metabolism and respiration	ML0632,ML0632c	MMAR_3673	MSMEG_4492	Mb2384				
NC_000962.3	Mycobrowser_v3	CDS	2648916	2649974	.	-	0	Rv2368c	phoH1	Unknown	Probable PHOH-like protein PhoH1 (phosphate starvation-inducible protein PSIH)	Rv2368c, (MTCY27.12), len: 352 aa. Probable phoH1, phoH-like protein (phosphate starvation-induced protein), probably ATP-binding protein, equivalent to Q49751|PHOL_MYCLE| ML0627|B1937_F1_20 PHOH-like protein from Mycobacterium leprae (349 aa), FASTA scores: opt: 1952, E(): 4.7e-107, (88.9% identity in 352 aa overlap). Also highly similar to Q9L2L5|SCC117.05 PHOH-like protein from Streptomyces coelicolor (359 aa), FASTA scores: opt: 1407, E(): 3.6e-75, (63.6% identity in 349 aa overlap); Q9RSY1|DR1988 PHOH-related protein from Deinococcus radiodurans (380 aa), FASTA scores: opt: 1053, E(): 1.9e-54, (53.3% identity in 349 aa overlap); Q9KD58|PHOH|BH1361 phosphate starvation-induced protein from Bacillus halodurans (320 aa), FASTA scores: opt: 1019, E(): 1.6e-52, (54.35% identity in 300 aa overlap); P46343|PHOL_BACSU PHOH-like protein from Bacillus subtilis (319 aa), FASTA scores: opt: 1014, E(): 3.2e-52, (50.8% identity in 303 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the PHOH family. Note that previously known as phoH.	P9WIA3	No	intermediary metabolism and respiration	ML0627	MMAR_3678	MSMEG_4497	Mb2389c				
NC_000962.3	Mycobrowser_v3	CDS	2652037	2652825	.	-	0	Rv2372c	Rv2372c	Function unknown	Conserved hypothetical protein	Rv2372c, (MTCY27.08), len: 262 aa. Conserved hypothetical protein, equivalent to Q9CCN1|ML0626 hypothetical protein from Mycobacterium leprae (257 aa), FASTA scores: opt: 1277, E(): 3e-71, (77.25% identity in 255 aa overlap). Also highly similar to others e.g. Q9RDD9|SDRD hypothetical 26.1 KDA protein from Streptomyces coelicolor (249 aa), FASTA scores: opt: 624, E(): 3.2e-31, (45.05% identity in 253 aa overlap); P54461|YQEU_BACSU hypothetical 28.8 kDa protein from Bacillus subtilis (256 aa), FASTA scores: opt: 375, E(): 6e-16, (32.5% identity in 234 aa overlap); etc. C-terminal half highly similar to Q49763|B1937_F2_57 from Mycobacterium leprae (128 aa), FASTA scores: opt: 577, E(): 1.4e-28, (75.8% identity in 124 aa overlap). Belongs to the UPF0088 family.	P9WGX1	No	conserved hypotheticals	ML0626	MMAR_3682	MSMEG_4502	Mb2393c				
NC_000962.3	Mycobrowser_v3	CDS	2654062	2655093	.	-	0	Rv2374c	hrcA	Involved in transcriptional regulation (repression) of class I heat shock proteins e.g. DNAK-GRPE-DNAJ1 and groels operons). Prevents heat-shock induction of these operons.	Probable heat shock protein transcriptional repressor HrcA	Rv2374c, (MTCY27.06), len: 343 aa. Probable hrcA, heat-inducible transcriptional repressor (see citation below), equivalent to Q9CCN2|HRCA|ML0624 putative heat-inducible transcriptional regulator from Mycobacterium leprae (343 aa), FASTA scores: opt: 1926, E(): 3.9e-107, (89.8% identity in 343 aa overlap). Also highly similar to other heat-inducible transcription repressor proteins e.g. Q9RDD6|HRCA|SCC77.22c from Streptomyces coelicolor (338 aa), FASTA scores: opt: 1227, E(): 1.1e-65, (58.8% identity in 335 aa overlap); O52163|HRCA_STRAL from Streptomyces albus (338 aa), FASTA scores: opt: 1196, E(): 7.7e-64, (56.1% identity in 335 aa overlap); P25499|HRCA_BACSU heat-inducible transcription repressor from Bacillus subtilis (343 aa), FASTA scores: opt: 538, E(): 8.4e-25, (28.9% identity in 325 aa overlap); etc. Almost identical, but conflict at C-terminus, to Q49749|YGRP|B1937_F1_18 putative heat-inducible transcription repressor from Mycobacterium leprae (197 aa) FASTA scores: opt: 1126, E(): 6.9e-60, (91.8% identity in 195 aa overlap). Belongs to the HRCA family.	P9WMK3	No	virulence, detoxification, adaptation	ML0624	MMAR_3684	MSMEG_4505	Mb2395c				
NC_000962.3	Mycobrowser_v3	CDS	2656215	2656430	.	-	0	Rv2377c	mbtH	Thought to be involved in the biogenesis of the hydroxyphenyloxazoline-containing siderophore mycobactins.	Putative conserved protein MbtH	Rv2377c, (MT2445.1, MTCY27.03), len: 71 aa. Putative mbtH, conserved protein with no function assigned (see Quadri et al., 1998; De Voss et al., 1999), similar to hypothetical proteins or proteins found in several gene clusters for biosynthesis or transport of siderophores and other nonribosomally synthesized peptides e.g. Q9Z388|SCE8.11c putative small conserved hypothetical protein from Streptomyces coelicolor (71 aa), FASTA scores: opt: 345, E(): 1.4e-19, (68.2% identity in 66 aa overlap); Q9F8V3|CUMB COUY protein (probably involved in the biosynthesis of aminocoumarin antibiotic coumermycin a(1)) (see Wang et al., 2000) from Streptomyces rishiriensis (71 aa), FASTA scores: opt: 329, E(): 2.2e-18, (63.2% identity in 68 aa overlap); Q9F5J2|SIM-CB MBTH-like protein (probably protein involved in the biosynthesis of aminocoumarin antibiotic coumermycin a(1)) from Streptomyces antibioticus (70 aa), FASTA scores: opt: 308, E(): 8.4e-17, (65.6% identity in 64 aa overlap); Q9FB14 MBTH-like protein (involved in the biosynthesis of the antitumor drug bleomycin) (see Du et al., 2000) from Streptomyces verticillus FASTA scores: opt: 220, E(): 8.8e-10, (41.2% identity in 68 aa overlap); etc.	P9WIP5	No	lipid metabolism		MMAR_0097,MMAR_2519,MMAR_3173,MMAR_3265,MMAR_3696	MSMEG_0399,MSMEG_4508	Mb2398c				
NC_000962.3	Mycobrowser_v3	CDS	2656408	2657703	.	-	0	Rv2378c	mbtG	Involved in the biogenesis of the hydroxyphenyloxazoline-containing siderophore mycobactins. This hydroxylase is possibly required for N-hydroxylation of the two lysine residues at some stage during mycobactin assembly [catalytic activity: L-lysine + O(2) = N6-hydroxy-L-lysine + H(2)O. No information can be found if this enzyme is NADPH dependent or independent].	Lysine-N-oxygenase MbtG (L-lysine 6-monooxygenase) (lysine N6-hydroxylase)	Rv2378c, (MTCY27.02), len: 431 aa. MbtG, lysine-N-oxygenase (hydroxylase) (EC 1.13.12.10 or 1.14.13.59; depending if enzyme is NADPH dependent or independent) (see citations below), showing some similarity with various proteins including ornithine and lysine-N-oxygenases, e.g. Q9K6Q1|TRKA|BH3677 potassium uptake protein from Bacillus halodurans (350 aa), FASTA scores: opt: 153, E(): 0.016, (25.2% identity in 246 aa overlap); P56584|SID1_USTMA L-ornithine 5-monooxygenase from Ustilago maydis (Smut fungus) (570 aa), FASTA scores: opt: 136, E(): 0.31, (22.85% identity in 127 aa overlap); Q9HHV0|HXYA|VNG6214G monooxygenase from Halobacterium sp. strain NRC-1 (477 aa), FASTA scores: opt: 119, E(): 3.4, (40.0% identity in 70 aa overlap); O69828|SC1A6.23 putative lysine N-hydroxlase (fragment) from Streptomyces coelicolor (134 aa), blast score: 76 (similarity in part for this one); etc. Cofactors: FAD (by similarity).	P9WKF7	No	lipid metabolism		MMAR_3697	MSMEG_4509	Mb2399c				
NC_000962.3	Mycobrowser_v3	CDS	2720776	2721777	.	-	0	Rv2424c	Rv2424c	Required for the transposition of the insertion element IS1558.	Probable transposase	Rv2424c, (MTCY428.23), len: 333 aa. Probable transposase for IS1558, similar to is element proteins e.g. AL021957|Rv2177c|MTV021_10 from Mycobacterium tuberculosis (221 aa), FASTA scores: opt: 1491, E(): 6.2e-87, (98.6% identity in 221 aa overlap); P19780|YIS1_STRCO hypothetical insertion element IS110 from Streptomyces coelicolor (45 aa), FASTA scores: opt: 203, E(): 1.7e-05; (27.3% identity in 238 aa overlap); etc. Contains PS01159 WW/rsp5/WWP domain signature.	P71924	No	insertion seqs and phages				Mb2447c,Mb2448c				
NC_000962.3	Mycobrowser_v3	CDS	2667255	2670269	.	-	0	Rv2381c	mbtD	Involved in the biogenesis of the hydroxyphenyloxazoline-containing siderophore mycobactins.	Polyketide synthetase MbtD (polyketide synthase)	Rv2381c, (MTCY22H8.04), len: 1004 aa. MbtD, polyketide synthase (see citations below), similar in part to several synthases e.g. Q03132|ERY2_SACER|ERYA erythronolide synthase, modules 3 and 4 from Saccharopolyspora erythraea (Streptomyces erythraeus) (3567 aa), FASTA scores: opt: 971, E(): 1e-46, (29.35% identity in 1043 aa overlap); Q9F829|megaii megalomicin 6-deoxyerythronolide B synthase 2 from Micromonospora megalomicea subsp. nigra (3562 aa), FASTA scores: opt: 787, E(): 2.4e-36, (29.35% identity in 1032 aa overlap); Q9L4W4|NYSB polyketide synthase from Streptomyces noursei (3192 aa), FASTA scores: opt: 761, E(): 6.6e-35, (29.55% identity in 1086 aa overlap); O30764|NIDA1 polyketide synthase modules 1 and 2 from Streptomyces caelestis (4340 aa), FASTA scores: opt: 726, E(): 7.8e-33, (27.3% identity in 1052 aa overlap); etc. Contains PS00012 Phosphopantetheine attachment site.	P71719	No	lipid metabolism			MSMEG_4512	Mb2402c				
NC_000962.3	Mycobrowser_v3	CDS	2677729	2678649	.	+	0	Rv2385	mbtJ	Involved in the biogenesis of the hydroxyphenyloxazoline-containing siderophore mycobactins. Possibly required for N-hydroxylation of the two lysine residues at some stage during mycobactin assembly.	Putative acetyl hydrolase MbtJ	Rv2385, (MTCY253.36c), len: 306 aa. Putative mbtJ, acetyl hydrolase (see citations below), showing some similarity with various hydrolases including acetyl hydrolases e.g. Q9ZBM4|MLCB1450.08|ML0314 putative hydrolase/esterase from Mycobacterium leprae (335 aa), FASTA scores: opt: 449, E(): 6.7e-21, (33.85% identity in 313 aa overlap); AAK47950|MT3591 Esterase from M. tuberculosis strain CDC1551 (327 aa), FASTA scores: opt: 469, E(): 3.6e-22, (35% identity in 283 aa overlap); Q9X8J4|SCE9.22 putative esterase from Streptomyces coelicolor (266 aa), FASTA scores: opt: 430,E(): 8.5e-20, (38% identity in 245 aa overlap); Q01109|BAH_STRHY acetyl-hydrolase from Streptomyces hygroscopicus (299 aa), FASTA scores: opt: 420, E(): 4e-19, (35.1% identity in 265 aa overlap). Equivalent to AAK46748 from Mycobacterium tuberculosis strain CDC1551 (327 aa) but shorter 21 aa. Note that previously known as lipK.	Q79FE8	No	lipid metabolism				Mb2406				
NC_000962.3	Mycobrowser_v3	CDS	2678653	2680005	.	-	0	Rv2386c	mbtI	Involved in the biogenesis of the hydroxyphenyloxazoline-containing siderophore mycobactins. Possibly plays a role in the conversion of chorismate to salicilate (the starter unit for mycobactin siderophore construction).	Isochorismate synthase MbtI	Rv2386c, (MTCY253.35), len: 450 aa. mbtI, isochorismate synthase (see citations below), similar to Q9X9I8|IRP9 salicylate synthetase from Yersinia enterocolitica (434 aa), FASTA scores: opt: 887, E(): 7.5e-48, (37.45% identity in 422 aa overlap); and similar in C-terminal region to many anthranilate synthases component I e.g. Q9Z4W7|TRPE_STRCO|SCE8.07c from Streptomyces coelicolor (511 aa), FASTA scores: opt: 509, E(): 3e-24, (40.4% identity in 255 aa overlap); P33975|TRPE_HALVO from Halobacterium volcanii (Haloferax volcanii) (523 aa) FASTA scores: opt: 488, E(): 6.2e-23, (34.2% identity in 298 aa overlap); and similar to Q08653|TRPE_THEMA|TM0142 anthranilate synthase component I from Thermotoga maritima (461 aa), FASTA scores: opt: 478, E(): 2.3e-22, (28.4% identity in 440 aa overlap); etc. Could be belong to the anthranilate synthase component I family. Note that previously known as trpE2, an anthranilate synthase component I.	P9WFX1	No	lipid metabolism		MMAR_3706	MSMEG_4524	Mb2407c				
NC_000962.3	Mycobrowser_v3	CDS	2690072	2692075	.	+	0	Rv2395	Rv2395	Function unknown (possibly involved in transport across the membrane).	Probable conserved integral membrane protein	Rv2395, (MTCY253.26c), len: 667 aa. Probable conserved integral membrane protein, similar to AAK24613|CC2646 oligopeptide transporter/opt family protein from Caulobacter crescentus (666 aa), FASTA scores: opt: 1638, E(): 4.8e-86, (51.0% identity in 658 aa overlap); Q9PIS5|CJ0204 putative integral membrane protein from Campylobacter jejuni (665 aa), FASTA scores: opt: 1484, E(): 2.9e-77, (40.6% identity in 658 aa overlap); and P44016|Y561_HAEIN hypothetical integral membrane protein from Haemophilus influenzae (635 aa), FASTA scores: opt: 1449, E(): 2.8e-75, (42.15% identity in 624 aa overlap).	P71749	No	cell wall and cell processes		MMAR_3714	MSMEG_1311	Mb2416,Mb2417				
NC_000962.3	Mycobrowser_v3	CDS	2696644	2697714	.	-	0	Rv2400c	subI	Involved in the active transport across the membrane of multiple sulfur-containing compounds, including sulfate and thiosulfate (import).	Probable sulfate-binding lipoprotein SubI	Rv2400c, (MTCY253.21), len: 356 aa. Probable subI, sulfate-binding lipoprotein component of sulfate transport system (see citations below), equivalent to Q9CCN3|SUBI|ML0615 (alias Q49748|B1937_F1_11, 358 aa) putative sulphate-binding protein from Mycobacterium leprae (348 aa), FASTA scores: opt: 1775, E(): 2.3e-102, (76.45% identity in 340 aa overlap). Also similar to others and other substrate-binding proteins e.g. P27366|SUBI_SYNP7|SBPA sulfate-binding protein precursor from Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) (350 aa), FASTA scores: opt: 703, E(): 4.6e-36, (35.6% identity in 351 aa overlap); Q9I6K7|SBP|PA0283 sulfate-binding protein precursor from Pseudomonas aeruginosa (332 aa), FASTA scores: opt: 591, E(): 3.7e-29, (36.9% identity in 317 aa overlap); CAC49112|SMB21133 putative sulfate uptake ABC transporter periplasmic solute-binding protein precursor from Rhizobium meliloti (Sinorhizobium meliloti) (341 aa), FASTA scores: opt: 569, E(): 8.8e-28, (36.15% identity in 321 aa overlap); etc. Belongs to the prokaryotic sulfate binding protein family.	P71744	No	cell wall and cell processes	ML0615	MMAR_3718	MSMEG_4533	Mb2422c				
NC_000962.3	Mycobrowser_v3	CDS	2701287	2703248	.	-	0	Rv2404c	lepA	Involved in translation.	Probable GTP-binding protein LepA (GTP-binding elongation factor)	Rv2404c, (MT2476, MTCY253.16), len: 653 aa. Probable lepA, GTP-binding protein (a protein of unknown function, but apparently with membrane-related functions and very similar to protein synthesis elongation factors; see citations below). Equivalent to P53530|LEPA_MYCLE|ML0611|B1937_F3_81 GTP-binding protein from Mycobacterium leprae (646 aa), FASTA scores: opt: 3610, E(): 1.2e-205, (88.0% identity in 649 aa overlap). Also highly similar to many GTP-binding proteins LEPA e.g. Q9RDC9|LEPA_STRCO|SCC77.29c from Streptomyces coelicolor (622 aa), FASTA scores: opt: 3046, E(): 2.3e-172, (74.3% identity in 626 aa overlap); P37949|LEPA_BACSU from B. subtilis (612 aa), FASTA scores: opt: 2430, E(): 5.3e-136, (58.7% identity in 610 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00301 GTP-binding elongation factors signature. Belongs to the GTP-binding elongation factor family, LEPA subfamily.	P9WK97	No	intermediary metabolism and respiration	ML0611	MMAR_3724	MSMEG_4556	Mb2427c				
NC_000962.3	Mycobrowser_v3	CDS	2721866	2723308	.	-	0	Rv2425c	Rv2425c	Function unknown	Conserved hypothetical protein	Rv2425c, (MTCY428.22), len: 480 aa. Hypothetical protein; C-terminal half shares similarity to other unknown conserved proteins e.g. Q53065 hypothetical 24.3 KDA protein from Rhodococcus erythropolis (219 aa), FASTA scores: opt: 398, E(): 9.9e-17, (34.15% identity in 202 aa overlap); C-terminus of O27843|MTH1815 conserved protein from Methanothermobacter thermautotrophicus (346 aa), FASTA scores: opt: 341, E(): 3.7e-13, (31.35% identity in 233 aa overlap); etc.	P71923	No	conserved hypotheticals	ML1456,ML1456c	MMAR_3751	MSMEG_4582	Mb2449c				
NC_000962.3	Mycobrowser_v3	CDS	2706494	2707333	.	-	0	Rv2409c	Rv2409c	Function unknown	Conserved protein	Rv2409c, (MTCY253.11), len: 279 aa. Conserved protein, equivalent to Q49757|YP69_MYCLE|G466976|B1937_F2_39 hypothetical protein from Mycobacterium leprae (279 aa), FASTA scores: opt: 1564, E(): 4.6e-95, (82.1% identity in 279 aa overlap). Also similar to others e.g. Q9RSX6|DR1993 from Deinococcus radiodurans (274 aa), FASTA scores: opt: 494, E(): 4e-25, (35.1% identity in 282 aa overlap); BAB49898|Mll2875 from Rhizobium loti (Mesorhizobium loti) (294 aa), FASTA scores: opt: 382, E(): 8.9e-18, (29.75% identity in 269 aa overlap); Q9I305|PA1732 from Pseudomonas aeruginosa (266 aa), FASTA scores: opt: 326, E(): 3.7e-14, (31.25% identity in 275 aa overlap); etc. Also similar to Rv2569c|MTCY227.32 from Mycobacterium tuberculosis.	P71734	No	conserved hypotheticals	ML0607	MMAR_3730	MSMEG_4567	Mb2432c				
NC_000962.3	Mycobrowser_v3	CDS	2708310	2709965	.	-	0	Rv2411c	Rv2411c	Function unknown	Conserved hypothetical protein	Rv2411c, (MTCY253.09c), len: 551 aa. Hypothetical protein, highly similar to Q49755|YO11_MYCLE|ML0605|MLCL536.05c|U1937B|B1937_F1_4 hypothetical 61.8 KDA protein from Mycobacterium leprae (561 aa), FASTA scores, opt: 3163, E(): 4.1e-178, (87.35% identity in 554 aa overlap). Also highly similar, except in N-terminus, to others e.g. Q55587|Y335_SYNY3|SLL0335 hypothetical protein from Synechocystis sp. strain PCC 6803 (481 aa), FASTA scores: opt: 1620, E(): 1.2e-87, (52.8% identity in 468 aa overlap); Q9I307|PA1730 hypothetical protein from Pseudomonas aeruginosa (470 aa), FASTA scores: opt: 1574, E(): 5.8e-85, (52.7% identity in 467 aa overlap); Q9RST1|DR2042 conserved hypothetical protein from Deinococcus radiodurans (655 aa), FASTA scores: opt: 1561, E(): 4.4e-84, (53.3% identity in 467 aa overlap); etc.	P9WLA9	No	conserved hypotheticals	ML0605	MMAR_3732	MSMEG_4570	Mb2434c				
NC_000962.3	Mycobrowser_v3	CDS	2712891	2713784	.	-	0	Rv2415c	Rv2415c	Function unknown	Conserved hypothetical protein	Rv2415c, (MTCY253.05), len: 297 aa. Hypothetical protein, with some similarity in C-terminal part to comE operon proteins 1 e.g. Q9EU10|come|COME4|COME1|COME2|COME3 come protein (a competence protein with DNA-binding activity) from Neisseria gonorrhoeae (99 aa), FASTA scores: opt: 190, E(): 0.0032, (49.2% identity in 61 aa overlap); Q9JYB8|NMB1657 from Neisseria meningitidis (205 aa) FASTA scores: opt: 191, E(): 0.0052, (49.2% identity in 61 aa overlap); CME1_BACSU|P39694 come operon protein 1 from Bacillus subtilis (205 aa), FASTA scores, opt: 181, E(): 0.017 (29.8% identity in 218 aa overlap); etc.	P71728	No	conserved hypotheticals	ML0601	MMAR_3736	MSMEG_4574	Mb2438c				
NC_000962.3	Mycobrowser_v3	CDS	2724230	2725477	.	-	0	Rv2427c	proA	Involved in proline biosynthesis pathway (at the second step). Catalyzes the NADPH dependent reduction of L-gamma- glutamyl 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate. [catalytic activity: L-glutamate 5-semialdehyde + phosphate + NADP(+) = L-gamma-glutamyl 5-phosphate + NADPH].	Probable gamma-glutamyl phosphate reductase protein ProA (GPR) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)	Rv2427c, (MTCY428.20), len: 415 aa. Probable proA, gamma-glutamyl phosphate reductase protein, equivalent to Q9CBZ7|ML1458|PROA [gamma]-glutamyl phosphate reductase from Mycobacterium leprae (409 aa), FASTA scores: opt: 2120, E(): 7.4e-118, (81.9% identity in 409 aa overlap). Also highly similar or similar to other gamma-glutamyl phosphate reductases proteins (GPR) e.g. Q9RDK1|PROA from Streptomyces coelicolor (428 aa), FASTA scores: opt: 1073, E(): 4.6e-56, (60.4% identity in 429 aa overlap); P45638|PROA_CORGL from Corynebacterium glutamicum (432 aa), FASTA scores: opt: 993, E(): 2.4e-51, (58.5% identity in 417 aa overlap); P96489|PROA_STRTR gamma-glutamyl phosphate reductase from Streptococcus thermophilus (416 aa), FASTA scores: opt: 863, E(): 1.1e-43, (49.15% identity in 413 aa overlap); etc. Belongs to the gamma-glutamyl phosphate reductase family.	P9WHV1	No	intermediary metabolism and respiration	ML1458,ML1458c	MMAR_3753	MSMEG_4584	Mb2451c				
NC_000962.3	Mycobrowser_v3	CDS	2726806	2727339	.	+	0	Rv2429	ahpD	Involved in oxidative stress response. LPDC|Rv0462, DLAT|Rv2215, AHPD|Rv2429, and AHPC|Rv2428 constitute an NADH-dependent peroxidase and peroxynitrite reductase that provides protection against oxidative stress.	Alkyl hydroperoxide reductase D protein AhpD (alkyl hydroperoxidase D)	Rv2429, (MTCY428.17c), len: 177 aa. AhpD, alkyl hydroperoxide reductase, similar to other alkyl hydroperoxide reductases D proteins e.g. Q9RN73|AHPD from Streptomyces coelicolor (178 aa), FASTA scores: opt: 611, E(): 1.4e-33, (57.4% identity in 169 aa overlap); Q50441|AHPD_MYCSM AHPD protein (fragment) from Mycobacterium smegmatis (52 aa), FASTA score: opt:196.	P9WQB5	No	virulence, detoxification, adaptation	ML2043	MMAR_2754	MSMEG_4890	Mb2455				
NC_000962.3	Mycobrowser_v3	CDS	2728844	2729134	.	-	0	Rv2433c	Rv2433c	Unknown	Hypothetical protein	Rv2433c, (MTCY428.13), len: 96 aa. Hypothetical unknown protein.	P71916	No	conserved hypotheticals				Mb2459c				
NC_000962.3	Mycobrowser_v3	CDS	2729115	2730560	.	-	0	Rv2434c	Rv2434c	Unknown	Probable conserved transmembrane protein	Rv2434c, (MTCY428.12), len: 481 aa. Probable conserved transmembrane protein, with some similarity to BAB48444|MLR0973 probable integral membrane protein from Rhizobium loti (410 aa), FASTA scores: opt: 298, E(): 4.1e-11, (27.25% identity in 389 aa overlap); and also similarity with other hypothetical proteins and/or putative integral membrane proteins.	P71915	No	cell wall and cell processes		MMAR_3756	MSMEG_3579	Mb2460c				
NC_000962.3	Mycobrowser_v3	CDS	2733230	2734144	.	+	0	Rv2436	rbsK	Involved in ribose metabolism (in the first step) [catalytic activity: ATP + D-ribose = ADP + D-ribose 5-phosphate].	Ribokinase RbsK	Rv2436, (MTCY428.10c), len: 304 aa. Probable rbsK, ribokinase, similar to others e.g. Q9RZ99|DRA0055 from Deinococcus radiodurans (300 aa) FASTA scores: opt: 485, E(): 9.1e-21, (44.55% identity in 301 aa overlap); P36945|P96733|RBSK_BACSU from Bacillus subtilis (293 aa), FASTA scores: opt: 398, E(): 8.5e-16, (36.35% identity in 297 aa overlap); P05054|RBSK_ECOLI|B3752|Z5253|ECS4694 from Escherichia coli strain K12 (309 aa), FASTA scores: opt: 387, E(): 3.8e-15, (34.7% identity in 314 aa overlap); etc. Contains PS00583 pfkB family of carbohydrate kinases signature 1. Belongs to the PFKB family of carbohydrate kinases.	P71913	No	intermediary metabolism and respiration	ML1461		MSMEG_4585	Mb2462				
NC_000962.3	Mycobrowser_v3	CDS	2734792	2736831	.	-	0	Rv2438c	nadE	Involved in biosynthesis of NAD. Can use both glutamine or ammonia as a nitrogen source [catalytic activity: ATP + deamido-NAD(+) + L-glutamine + H(2)O = AMP + diphosphate + NAD(+) + L-glutamate].	Glutamine-dependent NAD(+) synthetase NadE (NAD(+) synthase [glutamine-hydrolysing])	Rv2438c, (MT2513, MTCY428.08), len: 679 aa. NadE, glutamine-dependent NAD(+) synthetase (see citation below), equivalent to Q9CBZ6|NADE_MYCLE|ML1463 Glutamine-dependent NAD(+) synthetase from Mycobacterium leprae (680 aa), FASTA scores: opt: 3877, E(): 0. Also similar to others e.g. O83759|NADE_TREPA|TP0780 from Treponema pallidum (679 aa), FASTA scores: opt: 543, E(): 1.1e-25; O74940|NADE_SCHPO|SPCC553.02 from Schizosaccharomyces pombe (Fission yeast) (700 aa), FASTA scores: opt: 354, E(): 4.7e-14 ; P38795|NADE_YEAST|YHR074W from Saccharomyces cerevisiae (Baker's yeast) (714 aa), FASTA scores: opt: 339, E(): 4e-13; etc. Contains PS00591 Glycosyl hydrolases family 10 active site. Belongs to the NAD synthetase family in the C-terminal section. N-terminus shorter since first submission.	P9WJJ3	No	intermediary metabolism and respiration	ML1463,ML1463c	MMAR_3759	MSMEG_4617	Mb2464c				
NC_000962.3	Mycobrowser_v3	CDS	2737117	2738247	.	-	0	Rv2439c	proB	Involved in proline biosynthesis pathway (at the first step). Catalyzes the transfer of a phosphate group to glutamate to form glutamate 5-phosphate which rapidly cyclizes to 5-oxoproline [catalytic activity: ATP + L-glutamate = ADP + L-glutamate 5- phosphate].	Probable glutamate 5-kinase protein ProB (gamma-glutamyl kinase) (GK)	Rv2439c, (MTCY428.07), len: 376 aa. Probable proB, glutamate 5-kinase protein (GK), equivalent to Q9CBZ5|prob|ML1464 from Mycobacterium leprae (367 aa) FASTA scores: opt: 1937, E(): 1.1e-102, (84.4% identity in 366 aa overlap). Also highly similar to other glutamate 5-kinase proteins e.g. P46546|PROB_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (369 aa), FASTA scores: opt: 1241, E(): 3e-63, (54.35% identity in 368 aa overlap); Q9ZG98|PROB_MEIRU glutamate 5-kinase from Meiothermus ruber (390 aa), FASTA scores: opt: 825, E(): 1.2e-39, (45.05% identity in 353 aa overlap); Q9RDJ9|prob|SCC123.25c from Streptomyces coelicolor (374 aa), FASTA scores: opt: 1193, E(): 1.6e-60, (55.85% identity in 367 aa overlap); etc. Contains PS00902 Glutamate 5-kinase signature. Belongs to the glutamate 5-kinase family.	P9WHU9	No	intermediary metabolism and respiration	ML1464,ML1464c	MMAR_3764	MSMEG_4621	Mb2466c				
NC_000962.3	Mycobrowser_v3	CDS	2752262	2752660	.	+	0	Rv2451	Rv2451	Unknown	Hypothetical proline and serine rich protein	Rv2451, (MTV008.07), len: 132 aa. Hypothetical unknown pro-, ser-rich protein.	O53178	No	conserved hypotheticals				Mb2478				
NC_000962.3	Mycobrowser_v3	CDS	2738247	2739686	.	-	0	Rv2440c	obg	Essential GTP-binding protein.	Probable GTP1/Obg-family GTP-binding protein Obg	Rv2440c, (MTCY428.06), len: 479 aa. Probable obg, nucleotide-binding protein, equivalent to Q9CBZ4|ML1465 GTP1/OBG-family GTP-binding protein from Mycobacterium leprae (478 aa), FASTA scores: opt: 1328, E(): 8.4e-70, (58.9% identity in 479 aa overlap). Also highly similar to others e.g. P95722|OBG GTP-binding protein from Streptomyces coelicolor (478 aa), FASTA scores: opt: 1311, E(): 8.2e-69, (60.7% identity in 476 aa overlap); P20964|OBG_BACSU SPO0B-associated GTP-binding protein from Bacillus subtilis (428 aa), FASTA scores: opt: 1006, E(): 3.9e-51, (42.9% identity in 436 aa overlap); Q9KDK0|OBG|BH1213 GTP-binding protein involved in initiation of sporulation from Bacillus halodurans (427 aa), FASTA scores: opt: 978, E(): 1.7e-49, (41.95% identity in 436 aa overlap); etc. Highly similar (identical but shorter 5 aa) to AAK46813|MT2516 GTP-binding protein from Mycobacterium tuberculosis strain CDC1551 (484 aa), FASTA scores: opt: 3205, E(): 7.9e-179, (100% identity in 479 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the GTP1/OBG family.	P9WMT1	No	intermediary metabolism and respiration	ML1465,ML1465c	MMAR_3765	MSMEG_4623	Mb2467c				
NC_000962.3	Mycobrowser_v3	CDS	2740709	2742184	.	+	0	Rv2443	dctA	Involved in the transport of dicarboxylates such as succinate, fumarate, and malate from the periplasm across the inner membrane. Responsible for the translocation of the substrate across the membrane.	Probable C4-dicarboxylate-transport transmembrane protein DctA	Rv2443, (MTCY428.03c), len: 491 aa. Probable dctA, C4-dicarboxylate-transport transmembrane protein, similar to other C4-dicarboxylate transport proteins e.g. AAK46817|MT2519 from Mycobacterium tuberculosis strain CDC1551 (491 aa); Q9L1K8|SC6A11.12 putative sodium:dicarboxylate symporter from Streptomyces coelicolor (466 aa), FASTA scores: opt: 1797, E(): 2.9e-98, (61.3% identity in 452 aa overlap); Q9RRG7|DR2525 from Deinococcus radiodurans (463 aa); P50334|DCTA_SALTY from Salmonella typhimurium (428 aa) FASTA scores: opt: 1241, E(): 1.3e-65, (47.2% identity in 415 aa overlap); etc. Belongs to the sodium dicarboxylate symporter family (SDF) (DAACS family).	P71906	No	cell wall and cell processes		MMAR_3814	MSMEG_5302	Mb2470				
NC_000962.3	Mycobrowser_v3	CDS	2746135	2747598	.	-	0	Rv2447c	folC	Conversion of folates to polyglutamate derivatives. Bacteria require folate for the biosynthesis of glycine, methionine, formyl-met-tRNA, thymidylates, purines, and pantothenate [catalytic activity: ATP + {tetrahydrofolyl-[GLU]}(N) + L-glutamate = ADP + phosphate + {tetrahydrofolyl-[GLU]}(N+1)].	Probable folylpolyglutamate synthase protein FolC (folylpoly-gamma-glutamate synthetase) (FPGS)	Rv2447c, (MTV008.03c), len: 487 aa. Probable folC, folylpolyglutamate synthase, equivalent to Q9CBY8|FOLC|ML1471 from Mycobacterium leprae (485 aa), FASTA scores: opt: 2425, E(): 2.2e-134, (78.7% identity in 483 aa overlap). Also highly similar to others e.g. Q9L1G4|FPGS|O08416|Y13070 from Streptomyces coelicolor (444 aa), FASTA scores: opt: 774, E(): 6.3e-38, (53.9% identity in 462 aa overlap); P15925|FOLC_LACCA|FGS from Lactobacillus casei (428 aa), FASTA scores: opt: 631, E(): 1.4e-29, (34.55% identity in 437 aa overlap); Q05865|FOLC_BACSU from Bacillus subtilis (430 aa), FASTA scores: opt: 421, E(): 2.6e-17, (32.9% identity in 383 aa overlap); etc. Contains PS01012 Folylpolyglutamate synthase signature 2. Belongs to the folylpolyglutamate synthase family.	I6Y0R5	No	intermediary metabolism and respiration	ML1471,ML1471c	MMAR_3771		Mb2474c				
NC_000962.3	Mycobrowser_v3	CDS	2747595	2750225	.	-	0	Rv2448c	valS	Involved in translation mechanisms [catalyic activity: ATP + L-valine + tRNA(val) = AMP + diphosphate + L-valyl-tRNA(val)].	Probable valyl-tRNA synthase protein ValS (valyl-tRNA synthetase) (valine--tRNA ligase) (valine translase)	Rv2448c, (MTV008.04c), len: 876 aa. Probable valS, valyl-tRNA synthetases, equivalent to Q9CBY7|VALS|ML1472 valyl-tRNA synthase from Mycobacterium leprae (886 aa), FASTA scores: opt: 5181,E(): 0, (85.4% identity in 876 aa overlap). Also highly similar to others e.g. O06851|SYV_STRCO from Streptomyces coelicolor (874 aa), FASTA scores: opt: 2470, E(): 1.6e-143, (60.45% identity in 880 aa overlap); Q9X2D7|SYV_THEMA|VALS|TM1817 from Thermotoga maritima (865 aa), FASTA scores: opt: 2418, E(): 2.4e-140, (44.2% identity in 891 aa overlap); Q05873|SYV_BACSU|VALS from Bacillus subtilis (880 aa), FASTA scores: opt: 2063, E(): 1.4e-118, (46.08% identity in 894 aa overlap); etc. Contains PS00178 Aminoacyl-transfer RNA synthetases class-I signature. Contains probable coiled-coil from aa 810 to 846. Belongs to class-I aminoacyl-tRNA synthetase family.	P9WFS9	No	information pathways	ML1472,ML1472c	MMAR_3772	MSMEG_4630	Mb2475c				
NC_000962.3	Mycobrowser_v3	CDS	2751662	2752180	.	-	0	Rv2450c	rpfE	Thought to promote the resuscitation and growth of dormant, nongrowing cells. Could also stimulate the growth of several other high G+C gram+ organisms, e.g. Mycobacterium avium, Mycobacterium bovis (BCG), Mycobacterium kansasii, Mycobacterium smegmatis.	Probable resuscitation-promoting factor RpfE	Rv2450c, (MTV008.06c), len: 172 aa. Probable rpfE, resuscitation-promoting factor (see Mukamolova et al., 1998), similar to O86308|Z96935|MLRPF_1 RPF protein precursor from Micrococcus luteus (220 aa), FASTA scores: opt: 291, E(): 3e-7, (48.75% identity in 80 aa overlap). C-terminus is similar to other Mycobacterial rpf proteins e.g. O05594|Rv1009|MTCI237.26|RPFB probable resuscitation-promoting factor from Mycobacterium tuberculosis (362 aa), FASTA scores: opt: 344, E(): 1.4e-09, (42.85% identity in 147 aa overlap); etc. C-terminal region similar to N-terminal region of Q9F2Q2|SCE41.06c putative secreted protein from Streptomyces coelicolor (244 aa), FASTA scores: opt: 355, E(): 3.1e-10, (56.65% identity in 90 aa overlap). Also similar to Q9F2Q1|SCE41.07c putative secreted protein from Streptomyces coelicolor (near Q9F2Q2|SCE41.06c) (341 aa) FASTA scores: opt: 317, E(): 2.5e-08, (51.7% identity in 87 aa overlap). With Mycobacterium leprae, high similarity between the two corresponding C-terminal regions of two hypothetical proteins, Q9CD53|ML0240 (375 aa), FASTA scores: opt: 339, E(): 2.5e-09, (59.15% identity in 93 aa overlap) and O33049|MLCB57.05c|ML2151 (174 aa), FASTA scores: opt: 329, E(): 4e-09, (58.14% identity in 86 aa overlap). Contains a possible secretory signal sequence in N-terminus. Possible autocrine and/or paracrine bacterial growth factor or cytokine (see citations below). Interacts with RipA (see Hett et al., 2007). Predicted possible vaccine candidate (See Zvi et al., 2008).	O53177	No	cell wall and cell processes		MMAR_3776		Mb2477c				
NC_000962.3	Mycobrowser_v3	CDS	2758208	2759488	.	-	0	Rv2457c	clpX	ATP-dependent specificity component of the CLP protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of CLPP).	Probable ATP-dependent CLP protease ATP-binding subunit ClpX	Rv2457c, (MTV008.13c), len: 426 aa. Probable clpX, ATP-dependent clp protease ATP-binding subunit clpX, equivalent to Q9CBY6|CLPX|ML1477 ATP-dependent CLP protease ATP-binding protein from Mycobacterium leprae (426 aa), FASTA scores: opt: 2652, E(): 1.4e-142, (96.0% identity in 426 aa overlap). Also highly similar to others e.g. Q9F316|CLPX from Streptomyces coelicolor (428 aa) FASTA scores: opt: 2178, E(): 8.2e-116, (77.8% identity in 428 aa overlap); P50866|CLPX_BACSU from Bacillus subtilis (420 aa), FASTA scores: opt: 1788, E(): 8.5e-94, (63.6% identity in 426 aa overlap); P33138|CLPX_ECOLI from Escherichia coli (423 aa), FASTA scores: opt: 1694, E(): 1.7e-88, (62.4% identity in 415 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the CLPX chaperone family. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P9WPB9	No	intermediary metabolism and respiration	ML1477,ML1477c	MMAR_3805	MSMEG_4671	Mb2484c				
NC_000962.3	Mycobrowser_v3	CDS	2763172	2763774	.	-	0	Rv2461c	clpP1	CLP cleaves peptides in various proteins in a process that requires ATP hydrolysis. CLP may be responsible for a fairly general and central housekeeping function rather than for the degradation of specific substrates.	Probable ATP-dependent CLP protease proteolytic subunit 1 ClpP1 (endopeptidase CLP)	Rv2461c, (MT2536, MTV008.17c), len: 200 aa. Probable clpP1, ATP-dependent clp protease proteolytic subunit 1, equivalent to Q9CBY3|CLP1_MYCLE ATP-dependent CLP protease proteolytic subunit from Mycobacterium leprae (224 aa), FASTA scores: opt: 1226, E(): 1.3e-71, (95.0% identity in 200 aa overlap). Also highly similar to others e.g. Q9F315|CLPP1 from Streptomyces coelicolor (219 aa), FASTA scores: opt: 713, E(): 9.3e-39, (61.75% identity in 183 aa overlap); P80244|CLPP_BACSU from Bacillus subtilis (197 aa), FASTA scores: opt: 658, E(): 2.8e-35, (54% identity in 187 aa overlap); Q9WZF9|CLPP_THEMA|TM0695 from Thermotoga maritima (203 aa), FASTA scores: opt: 653, E(): 6.1e-35, (55.25% identity in 172 aa overlap); etc. Also similar to downstream ORF Rv2460c|MTV008.16c|clpP2 (214 aa), FASTA score: (48.3% identity in 172 aa overlap). Belongs to peptidase family S14, also known as CLPP family. Note that previously known as clp. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P9WPC5	No	intermediary metabolism and respiration	ML1480,ML1480c	MMAR_3808	MSMEG_4673	Mb2488c				
NC_000962.3	Mycobrowser_v3	CDS	2924817	2925383	.	-	0	Rv2594c	ruvC	Nuclease that resolves holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous ARMS and leaves a 5'terminal phosphate and a 3'terminal hydroxyl group [catalytic activity: endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (holliday junction)].	Probable crossover junction endodeoxyribonuclease RuvC (holliday junction nuclease) (holliday junction resolvase)	Rv2594c, (MTCY227.07), len: 188 aa. Probable ruvC, Holliday junction resolvase (see citations below), equivalent to P40834|RUVC_MYCLE|ML0481|B1177_C3_226 crossover junction endodeoxyribonuclease from Mycobacterium leprae (188 aa), FASTA scores: opt: 984, E(): 2.3e-55, (81.0% identity in 184 aa overlap). Also highly similar to others e.g. Q9AE11|RUVC from Corynebacterium glutamicum (Brevibacterium flavum) (221 aa), FASTA scores: opt: 713, E(): 3.6e-38, (56.9% identity in 188 aa overlap); Q9L289|RUVC_STRCO|SCL2.10c from Streptomyces coelicolor (188 aa), FASTA scores: opt: 704, E(): 1.2e-37, (60.65% identity in 178 aa overlap); P24239|RUVC_ECOLI|B1863 from Escherichia coli strain K12 (172 aa), FASTA scores: opt: 322, E(): 1.6e-13, (38.65% identity in 163 aa overlap); etc. Belongs to the RUVC family. Cofactor: magnesium.	P9WGV9	No	information pathways	ML0481	MMAR_2109	MSMEG_2943	Mb2625c				
NC_000962.3	Mycobrowser_v3	CDS	2765655	2766839	.	+	0	Rv2463	lipP	Function unknown; lipolytic enzyme involved in cellular metabolism.	Probable esterase/lipase LipP	Rv2463, (MTV008.19), len: 394 aa. Probable lipP, esterase, lipase similar to others eg O87861|ESTA esterase a from Streptomyces chrysomallus (389 aa), FASTA scores: opt: 964, E(): 1.9e-53, (44.35% identity in 399 aa overlap); Q9I4S7|PA1047 probable esterase from Pseudomonas aeruginosa (392 aa), FASTA scores: opt: 863, E(): 4.6e-47, (40.05% identity in 377 aa overlap); Q53403|ESTC esterase III from Pseudomonas fluorescens (382 aa), FASTA scores: opt: 753, E(): 3.9e-40, (36.3% identity in 380 aa overlap); etc.	O53190	No	intermediary metabolism and respiration	ML1482	MMAR_3810	MSMEG_4680	Mb2490				
NC_000962.3	Mycobrowser_v3	CDS	2767671	2768159	.	-	0	Rv2465c	rpiB	Interconverts ribose-5-phosphate and ribulose-5-phosphate	Ribose-5-phosphate isomerase	Rv2465c, (MTV008.21c), len: 162 aa. RpiB, Ribose-5-phosphate isomerase, proven biochemically (see Roos et al., 2004) equivalent to AAK46840|MT2540 putative carbohydrate-phosphate isomerase from Mycobacterium tuberculosis strain CDC1551 (159 aa). Equivalent to Q9CBY1|ML1484 possible phosphopentose isomerase from Mycobacterium leprae (162 aa), FASTA scores: opt: 992, E(): 7.1e-59, (89.5% identity in 162 aa overlap). Also highly similar or similar to several diverse isomerases e.g. Q9L206|SC8E4.02c putative isomerase from Streptomyces coelicolor (159 aa), FASTA scores: opt: 661, E(): 6.1e-37, (61.45% identity in 153 aa overlap); P47636|Y396_MYCGE|MG396 hypothetical LACA/RPIB family protein from Mycoplasma genitalium (152 aa), FASTA scores: opt: 357, E(): 8.2e-17, (42% identity in 150 aa overlap); P53527|Y396_MYCPN|MPN595|MP247 hypothetical LACA/RPIB family protein from Mycoplasma pneumoniae (152 aa), FASTA scores: opt: 340, E(): 1.1e-15, (38.6% identity in 145 aa overlap); P26592|LACB_STAAU galactose-6-phosphate isomerase from Staphylococcus aureus (171 aa), FASTA scores: opt: 296, E(): 1e-12, (35.4% identity in 158 aa overlap) and P37351|RPIB_ECOLI ribose 5-phosphate isomerase b from Escherichia coli (149 aa), FASTA scores: opt: 262, E(): 1.6e-10, (32.2% identity in 146 aa overlap); etc. Could belong to the LACA/RPIB family.	P9WKD7	No	intermediary metabolism and respiration	ML1484,ML1484c	MMAR_3813	MSMEG_4684	Mb2492c				
NC_000962.3	Mycobrowser_v3	CDS	2772367	2773035	.	-	0	Rv2469c	Rv2469c	Function unknown	Conserved hypothetical protein	Rv2469c, (MTV008.25c), len: 222 aa. Conserved hypothetical protein, highly similar to other hypothetical proteins e.g. Q9X7B4|MLCB1610.15|ML1254 from Mycobacterium leprae (215 aa), FASTA scores: opt: 1183, E(): 3.3e-70, (77.9% identity in 222 aa overlap); Q9L1Y0|SC8E4A.25c from Streptomyces coelicolor (178 aa), FASTA scores: opt: 589, E(): 1.7e-31, (53.4% identity in 161 aa overlap) (N-terminal region is shorter 50 aa approximately); Q9RRS6|DR2409 conserved hypothetical protein from Deinococcus radiodurans (186 aa), FASTA scores: opt: 440, E(): 9.6e-22, (42.25% identity in 168 aa overlap) (N-terminal region is shorter 30 aa approximately); etc.	O53196	No	conserved hypotheticals	ML1254	MMAR_3820	MSMEG_4694	Mb2496c				
NC_000962.3	Mycobrowser_v3	CDS	2773564	2775204	.	+	0	Rv2471	aglA	Involved in sugar metabolism (hydrolysis of terminal, non-reducing 1,4-linked D-glucose residues with release of D-glucose).	Probable alpha-glucosidase AglA (maltase) (glucoinvertase) (glucosidosucrase) (maltase-glucoamylase) (lysosomal alpha-glucosidase) (acid maltase)	Rv2471, (MTV008.27), len: 546 aa. Probable aglA, maltase (alpha-glucosidase), highly similar or similar to several e.g. Q60027|AGLA from Thermomonospora curvata (544 aa), FASTA scores: opt: 2071, E(): 4e-116, (57.7% identity in 525 aa overlap); Q9KZE3|AGLAE from Streptomyces coelicolor (534 aa), FASTA scores: opt: 1475, E(): 1.5e-80, (50.1% identity in 537 aa overlap); O86874|AGLA from Streptomyces lividans (534 aa), FASTA scores: opt: 1473, E(): 2e-80, (50.1% identity in 537 aa overlap); etc. Seems to belong to family 13 of glycosyl hydrolases, also known as the alpha-amylase family.	O53198	No	intermediary metabolism and respiration	ML1252,ML1252c	MMAR_3822	MSMEG_4696	Mb2498				
NC_000962.3	Mycobrowser_v3	CDS	2823256	2824593	.	-	0	Rv2508c	Rv2508c	Unknown	Probable conserved integral membrane leucine and alanine rich protein	Rv2508c, (MTCY07A7.14c), len: 445 aa. Probable conserved integral membrane leu-, ala-rich protein, equivalent to Q9CCU4|ML0430 putative membrane protein from Mycobacterium leprae (454 aa) (alias O07710|MLCL383.37 longer 10 aa), FASTA scores: opt: 2205, E(): 2.5e-124, (75.75% identity in 441 aa overlap). Also similar to hypothetical or membrane proteins e.g. BAB50841|MLL4103 hypothetical protein from Rhizobium loti (Mesorhizobium loti) (458 aa), FASTA scores: opt: 396, E(): 2.4e-16, (27.75% identity in 447 aa overlap); Q9RKX9|SC6D7.19c putative integral membrane protein from Streptomyces coelicolor (486 aa), FASTA scores: opt: 323, E(): 5.7e-12, (28.95% identity in 428 aa overlap); P42306|YXIO_BACSU probable integral membrane protein from Bacillus subtilis (428 aa), FASTA scores: opt: 220, E(): 7.2e-06, (20.35% identity in 413 aa overlap); etc. Also similar to proteins from Mycobacterium tuberculosis e.g. Q10564|Y876_MYCTU|Rv0876c|MT0899|MTCY31.04c (548 aa), FASTA scores: opt: 184, E(): 0.0012, (24.7% identity in 466 aa overlap).	O06171	No	cell wall and cell processes	ML0430		MSMEG_4721	Mb2536c				
NC_000962.3	Mycobrowser_v3	CDS	2777388	2782262	.	-	0	Rv2476c	gdh	Catabolic glutdh involved in the utilization of glutamate and other amino acids of the glutamate family. Generates 2-oxoglutarate from L-glutamate [catalytic activity: L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH].	Probable NAD-dependent glutamate dehydrogenase Gdh (NAD-Gdh) (NAD-dependent glutamic dehydrogenase)	Rv2476c, (MTV008.32c), len: 1624 aa. Probable gdh, glutamate dehydrogenase. Highly similar to Q9X7B2|MLCB1610.10|ML1249 hypothetical 177.9 KDA protein from Mycobacterium leprae (1622 aa), FASTA scores: opt: 8630,E(): 0, (81.45% identity in 1634 aa overlap). But highly similar to Q9F0J1|GDH NAD-glutamate dehydrogenase from Streptomyces clavuligerus (1651 aa), FASTA scores: opt: 3833, E(): 0, (45.8% identity in 1600 aa overlap); (see Minambres et al., 2000). Also similar with others e.g. AAG53963|PA3068|GDHB hypothetical (NAD(+)-dependent glutamate dehydrogenase from Pseudomonas aeruginosa (1620 aa), FASTA scores: opt: 2214, E(): 1e-124, (40.1% identity in 1561 aa overlap) (see Lu & Abdelal 2001); and Q9Y8G5|GDHB NAD-specific glutamate dehydrogenase from Agaricus bisporus (1029 aa), FASTA scores: opt: 194, E(): 0.00099, (22.7% identity in 647 aa overlap) (see Kersten et al., 1999); etc. Contains possible Helix-turn-helix motif at aa 1568 to 1589 (score 1098, +2.93 SD).	O53203	No	intermediary metabolism and respiration	ML1249	MMAR_3829	MSMEG_4699	Mb2503c				
NC_000962.3	Mycobrowser_v3	CDS	2786914	2789283	.	-	0	Rv2482c	plsB2	Involved in phospholipid biosynthesis (at the first step). May also function in the regulation of membrane biogenesis [catalytic activity: acyl-CoA + SN-glycerol 3-phosphate = CoA + 1-acyl-SN-glycerol 3-phosphate].	Probable glycerol-3-phosphate acyltransferase PlsB2 (GPAT)	Rv2482c, (MT2555, MTV008.38c), len: 789 aa. Probable plsB2, glycerol-3-phosphate acyltransferase, highly similar to Q9X7B0|PLSB_MYCLE probable glycerol-3-phosphate acyltransferase from Mycobacterium leprae (775 aa), FASTA scores: opt: 4210, E(): 0, (80.7% identity in 783 aa overlap). Also similar to others e.g. P00482|PLSB_ECOLI from Escherichia coli (806 aa), FASTA scores: opt: 521, E(): 3e-24, (24.35 identity in 612 aa overlap); Q9CLN7|PLSB_PASMU from Pasteurella multocida (809 aa), FASTA scores: opt: 529, E(): 9.7e-25, (27.05% identity in 540 aa overlap); Q9KVP8|PLSB_VIBCH from Vibrio cholerae (811 aa), FASTA scores: opt: 510, E(): 1.4e-23, (26.0% identity in 639 aa overlap); etc. Also highly similar to Q10775|PLSB1|Rv1551|MTCY48.14c from M. tuberculosis (621 aa), FASTA scores: opt: 1013, E(): 1.5e-54, (34.65% identity in 586 aa overlap). Belongs to the GPAT/DAPAT family.	P9WI61	No	lipid metabolism	ML1246	MMAR_3833	MSMEG_4703	Mb2507c				
NC_000962.3	Mycobrowser_v3	CDS	2792723	2793988	.	-	0	Rv2485c	lipQ	Function unknown; lipolytic enzyme involved in cellular metabolism.	Probable carboxylesterase LipQ	Rv2485c, (MTV008.41c), len: 421 aa. Probable lipQ, carboxylesterase protein (lipase). Similar (greater at the C-terminal end) to AAK46626|MT2342 putative carboxylesterase from Mycobacterium tuberculosis strain CDC1551 (431 aa), FASTA scores: opt: 1134, E(): 4.3e-60, (46.25% identity in 428 aa overlap); and Q50681|Rv2284|MTCY339.26c hypothetical protein from M. tuberculosis strain H37Rv (431 aa), FASTA scores: opt: 1134, E(): 4.3e-60, (46.25% identity in 428 aa overlap). Also similar in part to other putative lipases/esterases e.g. AAK44451|MT0230 from Mycobacterium tuberculosis strain CDC1551 (403 aa), FASTA scores: opt: 763, E(): 4.6e-38, (37.95% identity in 390 aa overlap); Q9RY19|DR0133 from Deinococcus radiodurans (296 aa), FASTA scores: opt: 392, E(): 4e-16, (33.7% identity in 276 aa overlap); Q9Z545|SC9B2.14 from Streptomyces coelicolor (502 aa) FASTA scores: opt: 279, E(): 3.2e-09, (31.15% identity in 292 aa overlap); etc.	I6Y9F7	No	intermediary metabolism and respiration	ML1243	MMAR_3836		Mb2510c				
NC_000962.3	Mycobrowser_v3	CDS	2801254	2806236	.	-	0	Rv2490c	PE_PGRS43	Function unknown	PE-PGRS family protein PE_PGRS43	Rv2490c, (MTV008.46c), len: 1660 aa. PE_PGRS43, Member of the Mycobacterium tuberculosis PE family, PGRS-subfamily of Gly-rich proteins (see Brennan and Delogu, 2002), similar to many e.g. AAK47971|MT3612.1 PE_PGRS family protein from Mycobacterium tuberculosis strain CDC1551 (1715 aa), FASTA scores: opt: 5161, E(): 1.5e-187, (51.7% identity in 1752 aa overlap); etc.	Q79FD4	No	PE/PPE				Mb2517c,Mb2518c				
NC_000962.3	Mycobrowser_v3	CDS	2808758	2809939	.	-	0	Rv2495c	bkdC	Involved in energy metabolism. The branched-chain alpha-keto acid dehydrogenase complex catalyzes the overall conversion of branched chain alpha-keto acids to acyl-CoA and CO2. It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3).	Probable branched-chain keto acid dehydrogenase E2 component BkdC	Rv2495c, (MTCY07A7.01c-MTV008.51c), len: 393 aa. Probable bkdC, branched-chain keto acid dehydrogenase, E2 component, similar to others e.g. Q9XA49|SCGD3.30c from Streptomyces coelicolor (491 aa) FASTA scores: opt: 615, E(): 1.2e-28, (36.45% identity in 491 aa overlap; several gaps); P19262|ODO2_YEAST|KGD2|YDR148C|YD8358.05c from Saccharomyces cerevisiae (Baker's yeast) (463 aa) FASTA scores: opt: 533, E(): 7.1e-24, (28.55% identity in 396 aa overlap); Q9HN75|DSA|VNG2219G from Halobacterium sp. strain NRC-1 (478 aa), FASTA scores: opt: 521, E(): E(): 3.7e-23, (30.25% identity in 486 aa overlap; in part); etc. Belongs to the 2-oxoacid dehydrogenase family. Alternative nucleotide at position 2809621 (T->C; T107A) has been observed. LpdC|Rv0462 co-immunoprecipitates with DlaT|Rv2215 (in lpdC|Rv0462 mutant) and with BkdC|Rv2495c (in dlaT|Rv2215 mutant) (See Venugopal et al., 2011). Previously known as pdhC.	O06159	No	intermediary metabolism and respiration	ML0443	MMAR_3842	MSMEG_4710	Mb2523c				
NC_000962.3	Mycobrowser_v3	CDS	2814916	2816880	.	-	0	Rv2501c	accA1	This protein carries two functions: biotin carboxyl carrier protein and biotin carboxyltransferase. Involved in the first step of long-chain fatty acid synthesis [catalytic activity: ATP + biotin-carboxyl-carrier protein + CO(2) = ADP + phosphate + carboxybiotin-carboxyl-carrier protein].	Probable acetyl-/propionyl-coenzyme A carboxylase alpha chain (alpha subunit) AccA1: biotin carboxylase + biotin carboxyl carrier protein (BCCP)	Rv2501c, (MTCY07A7.07c, P46401), len: 654 aa. Probable accA1 (alternate gene name: bccA), acetyl-/propionyl-coenzyme A carboxylase (alpha subunit) [includes: biotin carboxylase ; biotin carboxyl carrier protein (BCCP)], similar to others eg Q9L076|FABG from Streptomyces coelicolor (646 aa), FASTA scores: opt: 2071, E(): 1e-113, (57.8% identity in 659 aa overlap); AAK24139|Q9A6C6|CC2168 from Caulobacter crescentus (654 aa), FASTA scores: opt: 1754, E(): 3.7e-95, (47.2% identity in 661 aa overlap); etc. Contains PS00188 Biotin-requiring enzymes attachment site, PS00866 Carbamoyl-phosphate synthase subdomain signature 1, and PS00867 Carbamoyl-phosphate synthase subdomain signature 2.	P9WPQ3	No	lipid metabolism	ML0437	MMAR_3848	MSMEG_4716	Mb2529c				
NC_000962.3	Mycobrowser_v3	CDS	2821712	2822359	.	+	0	Rv2506	Rv2506	Involved in transcriptional mechanism.	Probable transcriptional regulatory protein (probably TetR-family)	Rv2506, (MTCY07A7.12), len: 215 aa. Probable transcriptional regulator, TetR family, similar to many others e.g. Q9L078|SCC105.06c putative TetR-family regulatory protein from Streptomyces coelicolor (208 aa), FASTA scores: opt: 333, E(): 1.5e-14, (48.75% identity in 197 aa overlap); Q9X7X6|SC6A5.30c putative regulatory protein from Streptomyces coelicolor (404 aa), FASTA scores: opt: 267, E(): 4.8e-10, (30.45% identity in 207 aa overlap) (similarity only with C-terminus for this one); Q9FBI8|SCP8.33c putative TetR-family transcriptional regulator from Streptomyces coelicolor (213 aa), FASTA scores: opt: 239, E(): 1.8e-08, (29.9% identity in 184 aa overlap); etc. Also similar to transcriptional regulatory proteins from Mycobacterium tuberculosis e.g. O05858|Rv3208|MTCY07D11.18c (228 aa), FASTA scores: opt: 218, E(): 4.4e-07, (30.35% identity in 191 aa overlap); C-terminus of P95251|Rv1963c|MTV051.01c|MTCY09F9.01 (406 aa), FASTA scores: opt: 238, E(): 3.6e-08, (28.25% identity in 177 aa overlap); P96839|Rv3557c|MTCY06G11.04c (200 aa), FASTA scores: opt: 215, E(): 6.2e-07, (38.25% identity in 148 aa overlap); etc. Equivalent to AAK46885 from Mycobacterium tuberculosis strain CDC1551 (231 aa) but shorter 16 aa. Contains probable helix-turn-helix motif at aa 46-67, (Score 1660, +4.84 SD). Belongs to the TetR/AcrR family of transcriptional regulators.	O06169	No	regulatory proteins	ML0432,ML0432c	MMAR_3853	MSMEG_4718	Mb2534				
NC_000962.3	Mycobrowser_v3	CDS	2925734	2926138	.	+	0	Rv2596	vapC40	Unknown	Possible toxin VapC40. Contains PIN domain.	Rv2596, (MTCY227.05c), len: 134 aa. Possible vapC40, toxin, part of toxin-antitoxin (TA) operon with Rv2595, contains PIN domain, see Arcus et al. 2005. Similar to others in Mycobacterium tuberculosis e.g. O07780|Rv0598c|MTCY19H5.24 hypothetical 14.8 KDA protein from (137 aa), FASTA scores: opt: 254, E(): 8.8e-11, (41.55% identity in 130 aa overlap).	P9WF61	No	virulence, detoxification, adaptation				Mb2627				
NC_000962.3	Mycobrowser_v3	CDS	2824678	2825484	.	+	0	Rv2509	Rv2509	Function unknown; possibly involved in cellular metabolism.	Probable short-chain type dehydrogenase/reductase	Rv2509, (MTCY07A7.15), len: 268 aa. Probable ala-rich oxidoreductase, short-chain dehydrogenase/reductase, equivalent to O07709|MLCL383.36c|ML0429 dehydrogenase (putative oxidoreductase) from Mycobacterium leprae (268 aa), FASTA scores: opt: 1509, E(): 2.6e-84, (88.75% identity in 267 aa overlap). Also highly similar to others e.g. O86553|SC1F2.16c putative dehydrogenase from Streptomyces coelicolor (276 aa), FASTA scores: opt: 492, E(): 9.5e-23, (38.15% identity in 262 aa overlap); Q9I5R3|PA0658 probable short-chain dehydrogenase from Pseudomonas aeruginosa (266 aa), FASTA scores: opt: 472, E(): 1.5e-21, (37.8% identity in 246 aa overlap); AAK22120|CC0133 oxidoreductase (short-chain dehydrogenase/reductase family) from Caulobacter crescentus (266 aa), FASTA scores: opt: 428, E(): 6.9e-19, (35.8% identity in 243 aa overlap); etc. Also highly similar or similar to oxidoreductases from Mycobacterium tuberculosis e.g. Q10782|Rv1544|MTCY48.21 putative ketoacyl reductase (267 aa), FASTA scores: opt: 656, E(): 1.1e-32, (43.05% identity in 267 aa overlap). Contains PS00061 Short-chain alcohol dehydrogenase family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	I6Y9I3	No	intermediary metabolism and respiration	ML0429,ML0429c	MMAR_3856	MSMEG_4722	Mb2537				
NC_000962.3	Mycobrowser_v3	CDS	2834109	2835335	.	-	0	Rv2518c	ldtB	Involved in peptidoglycan synthesis. Catalyzes the formation of 3->3 crosslinks between peptidoglycan subunits.	Probable L,D-transpeptidase LdtB	Rv2518c, (MTV009.03c), len: 408 aa. Probable ldtB, L,D-transpeptidase, highly similar to O07707|MLCL383.3 hypothetical 43.6 KDA protein from Mycobacterium leprae (407 aa), FASTA scores: opt: 2300, E(): 1.2e-130, (82.5% identity in 406 aa overlap); Q9CCU5|LPPS|ML0426 putative secreted protein from Mycobacterium leprae (404 aa), FASTA scores: opt: 2279, E(): 2.3e-129, (82.4% identity in 403 aa overlap); and Q9CB49|ML2446 possible lipoprotein from Mycobacterium leprae (441 aa), FASTA scores: opt: 736, E(): 8.4e-37, (35.6% identity in 399 aa overlap). Also similar to other proteins from several organisms e.g. Q9X811|SC6G10.26c putative secreted protein from Streptomyces coelicolor (424 aa), FASTA scores: opt: 867, E(): 1.1e-44, (32.25% identity in 403 aa overlap); Q9L1E8|SC3D11.14 putative lipoprotein from Streptomyces coelicolor (416 aa), FASTA scores: opt: 737, E(): 7e-37, (32.95% identity in 413 aa overlap); Q9KYV1|SCE22.11 putative lipoprotein from Streptomyces coelicolor (407 aa), FASTA scores: opt: 721, E(): 6.2e-36, (33.5% identity in 400 aa overlap). And similar to several hypothetical mycobacterial proteins e.g. Q11149|Y483_MYCTU|Rv0483|MT0501|MTCY20G9.09 (451 aa), FASTA scores: opt: 763, E(): 2.1e-38, (34.85% identity in 402 aa overlap). Has very long signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Note that previously known as lppS	I6Y9J2	No	cell wall and cell processes	ML0426	MMAR_3872	MSMEG_4745	Mb2547c				
NC_000962.3	Mycobrowser_v3	CDS	2838129	2839541	.	-	0	Rv2522c	Rv2522c	Function unknown	Conserved hypothetical protein	Rv2522c, (MTV009.07c), len: 470 aa. Conserved hypothetical protein, equivalent, but longer 20 aa, to Q9X7E4|ML1193|MLCB458.08 from hypothetical 46.6 KDA protein Mycobacterium leprae (442 aa), FASTA scores: opt: 2521, E(): 4.1e-142, (86.35% identity in 440 aa overlap). Also similar to various proteins e.g. Q9K425|SCG22.20 putative peptidase from Streptomyces coelicolor (451 aa), FASTA scores: opt: 1097, E(): 1.1e-57, (42.5% identity in 451 aa overlap); Q9FCK3|2SC3B6.09 putative peptidase from Streptomyces coelicolor (470 aa), FASTA scores: opt: 669, E(): 2.8e-32, (34.2% identity in 462 aa overlap); Q98AF9|MLL6018 hypothetical protein from Rhizobium loti (Mesorhizobium loti) (486 aa), FASTA scores: opt: 622, E(): 1.7e-29, (33.95% identity in 442 aa overlap); Q9RSU7|DR2025 ARGE/DAPE/ACY1 family protein from Deinococcus radiodurans (459 aa), FASTA scores: opt: 616, E(): 3.7e-29, (34.15% identity in 442 aa overlap); etc (include some similarity to hypothetical proteins from C. elegans and yeast). Alternative start possible at 6687 but then no RBS obvious.	I6X4J0	No	conserved hypotheticals	ML1193	MMAR_3957	MSMEG_4755	Mb2551c				
NC_000962.3	Mycobrowser_v3	CDS	2839538	2839930	.	-	0	Rv2523c	acpS	Biosynthesis of fatty acids and lipids. Transfers the 4'-phosphopantetheine moiety from coenzyme A to a SER of acyl-carrier protein. Catalyzes the formation of holo-ACP, which mediates the transfer of acyl fatty-acid intermediates during the biosynthesis of fatty acids and lipids [catalytic activity: CoA + APO-[acyl-carrier protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier protein] ].	holo-[acyl-carrier protein] synthase AcpS (holo-ACP synthase) (CoA:APO-[ACP]pantetheinephosphotransferase) (CoA:APO-[acyl-carrier protein]pantetheinephosphotransferase)	Rv2523c, (MT2599, MTV009.08c), len: 130 aa. AcpS, holo-[Acyl Carrier Protein] synthase (see citation below), equivalent to Q9X7E3|ACPS_MYCLE|ML1192|MLCB458.07 holo-[acyl-carrier protein] synthase from Mycobacterium leprae (130 aa), FASTA scores: opt: 732, E(): 5.5e-42, (87.5% identity in 128 aa overlap). Also similar to others e.g. O86785|ACPS_STRCO|SC6G4.22c from Streptomyces coelicolor (123 aa), FASTA scores: opt: 204, E(): 6.6e-07, (36.7% identity in 139 aa overlap); Q9KPB6|VC2457 from Vibrio cholerae (126 aa), FASTA scores: opt: 163, E(): 0.00036, (32.55% identity in 129 aa overlap); P24224|ACPS_ECOLI|DPJ|B2563 from Escherichia coli strain K12 (125 aa), FASTA scores: opt: 151, E(): 0.0022, (30.55% identity in 131 aa overlap); etc. Belongs to the ACPS family. Acts on fas-I enzymes in C. glutamicum (See Chalut et al., 2006).	P9WQD3	No	lipid metabolism	ML1192	MMAR_3961	MSMEG_4756	Mb2552c				
NC_000962.3	Mycobrowser_v3	CDS	2851751	2852671	.	-	0	Rv2528c	mrr	Involved in the acceptance of foreign DNA which is modified. Restricts both adenine- and cytosine-methylated DNA.	Probable restriction system protein Mrr	Rv2528c, (MTCY159.28), len: 306 aa. Probable mrr, restriction system protein, similar to other mrr proteins e.g. Q9RWS8|DR0587|MRR from Deinococcus radiodurans (306 aa), FASTA scores: opt: 776, E(): 4.2e-40, (40.45% identity in 309 aa overlap); P24202|MRR_ECOLI|B4351 from Escherichia coli strain K12 (304 aa), FASTA scores: opt: 647, E(): 2.9e-32, (35.25% identity in 309 aa overlap); Q9RX07|DR0508 from Deinococcus radiodurans (336 aa), FASTA scores: opt: 456, E(): 1.3e-20, (37.3% identity in 319 aa overlap); etc.	I6Y9K2	No	information pathways				Mb2557c				
NC_000962.3	Mycobrowser_v3	CDS	2858727	2859290	.	-	0	Rv2534c	efp	Involved in peptide bond synthesis. Stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.	Probable elongation factor P Efp	Rv2534c, (MTCY159.22), len: 187 aa. Probable efp, elongation factor P, equivalent to Q9CCS0|EFP|ML0522 elongation factor P from Mycobacterium leprae (187 aa), FASTA scores: opt: 1158, E(): 2.1e-67, (94.1% identity in 186 aa overlap). Also highly similar to many e.g. Q45288|EFP_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (187 aa), FASTA scores: opt: 843, E(): 3.4e-47, (69.5% identity in 187 aa overlap); Q9KXQ9|EFP from Streptomyces coelicolor (188 aa), FASTA scores: opt: 833, E(): 1.5e-46, (67.0% identity in 188 aa overlap); P49778|EFP_BACSU from Bacillus subtilis (185 aa), FASTA scores: opt: 607, E(): 4.6e-32, (47.8% identity in 182 aa overlap); P33398|EFP_ECOLI|B4147 from Escherichia coli strain K12 (187 aa), FASTA scores: opt: 503, E(): 1.8e-27, (42.3% identity in 182 aa overlap); etc. Belongs to the elongation factor P family.	P9WNM3	No	information pathways	ML0522	MMAR_2181	MSMEG_3035	Mb2563c				
NC_000962.3	Mycobrowser_v3	CDS	2859300	2860418	.	-	0	Rv2535c	pepQ	Function unknown; hydrolyses peptides.	Probable cytoplasmic peptidase PepQ	Rv2535c, (MTCY159.21), len: 372 aa. Probable pepQ, cytoplasmic peptidase, equivalent to Q9CCS1|PEPQ|ML0521 putative cytoplasmic peptidase from Mycobacterium leprae (376 aa), FASTA scores: opt: 1954, E(): 1.1e-105, (82.7% identity in 376 aa overlap). Also similar to other peptidases e.g. P54518|YQHT_BACSU putative peptidase (belongs to peptidase family M24B) from Bacillus subtilis (353 aa), FASTA scores: opt: 808, E(): 1.6e-39, (39.65% identity in 368 aa overlap); Q9KXQ8|SC9C5.16c putative peptidase from Streptomyces coelicolor (368 aa), FASTA scores: opt: 803, E(): 3.2e-39, (43.15% identity in 380 aa overlap); Q9K950|BH2800 XAA-pro dipeptidase from Bacillus halodurans (355 aa), FASTA scores: opt: 801, E(): 4.1e-39, (39.45% identity in 365 aa overlap); etc. Note that second part of protein is similar to second part of MTCY49.29c|Rv2089c|MT2150|MTCY49.29c probable dipeptidase; belongs to peptidase family M24B from Mycobacterium tuberculosis (375 aa) (33.9% identity in 354 aa overlap) blast results: Score: 142 bits (359), E: 4e-33, Identities: 86/224 (38%), Positives: 119/224 (52%), Gaps: 4/224 (1%). Could be belong to peptidase family M24B. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	I6YDN6	No	intermediary metabolism and respiration	ML0521	MMAR_2180	MSMEG_3034	Mb2564c				
NC_000962.3	Mycobrowser_v3	CDS	2860452	2861144	.	+	0	Rv2536	Rv2536	Unknown	Probable conserved transmembrane protein	Rv2536, (MTCY159.20c), len: 230 aa. Probable conserved transmembrane protein, equivalent to Q9CCS2|ML0520 putative membrane protein from Mycobacterium leprae (202 aa), FASTA scores: opt: 812, E(): 2e-41, (63.2% identity in 201 aa overlap). Also similar in part to Q9HMD5|VNG2594c from Halobacterium sp. strain NRC-1 (117 aa), FASTA scores: opt: 33.6, E(): 1.8, (33.6% identity in 116 aa overlap); and perhaps AAK65752|SMA1996 putative ABC transporter permease protein from Rhizobium meliloti (Sinorhizobium meliloti) plasmid pSymA (323 aa), FASTA scores: opt: 117, E(): 6.1, (30.6% identity in 121 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P95017	No	cell wall and cell processes	ML0520,ML0520c		MSMEG_3032	Mb2565				
NC_000962.3	Mycobrowser_v3	CDS	2861148	2861591	.	-	0	Rv2537c	aroD	Involved at the third step in the biosynthesis of chorismate within the biosynthesis of aromatic amino acids (the shikimate pathway). Catalyze a trans-dehydration via an enolate intermediate [catalytic activity: 3-dehydroquinate = 3-dehydroshikimate + H(2)O].	3-dehydroquinate dehydratase AroD (AROQ) (3-dehydroquinase) (type II dhqase)	Rv2537c, (MTCY159.19), len: 147 aa. AroD (alternate gene name: aroQ), 3-dehydroquinate dehydratase (see citation below), equivalent to Q9CCS3|AROD|ML0519 3-dehydroquinate dehydratase from Mycobacterium leprae (145 aa), FASTA scores: opt: 803, E(): 3.4e-46, (85.9% identity in 142 aa overlap). Also highly similar to many e.g. P96750|AROQ_CORPS from Corynebacterium pseudotuberculosis (146 aa), FASTA scores: opt: 559, E(): 4.1e-30, (61.05% identity in 136 aa overlap); Q9K949|BH2801 from Bacillus halodurans (145 aa), FASTA scores: opt: 453, E(): 4e-23, (52.15% identity in 138 aa overlap); P54517|AROQ_BACSU|YQHS from Bacillus subtilis (148 aa), FASTA scores: opt: 419, E(): 7.1e-21, (45.3% identity in 139 aa overlap); etc. Contains PS01029 Dehydroquinase class II signature. Belongs to the type-II 3-dehydroquinase family.	P9WPX7	No	intermediary metabolism and respiration	ML0519	MMAR_2178		Mb2566c				
NC_000962.3	Mycobrowser_v3	CDS	2861588	2862676	.	-	0	Rv2538c	aroB	Involved at the second step in the biosynthesis of chorismate within the biosynthesis of aromatic amino acids (the shikimate pathway) [catalytic activity: 7-phospho-3-deoxy-arabino-heptulosonate = 3-dehydroquinate + orthophosphate].	3-dehydroquinate synthase AroB	Rv2538c, (MTCY159.18), len: 362 aa. AroB, 3-dehydroquinate synthase (see citations below), equivalent to Q9CCS4|AROB_MYCLE|ML0518 3-dehydroquinate synthase from Mycobacterium leprae (361 aa), FASTA scores: opt: 2059, E(): 3.3e-117, (87.25% identity in 361 aa overlap). Also highly similar to many e.g. Q9KXQ6|AROB from Streptomyces coelicolor (363 aa), FASTA scores: opt: 1363, E(): 4e-75, (60.05% identity in 358 aa overlap); Q9X5D2|AROB_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (366 aa), FASTA scores: opt: 1154, E(): 1.7e-62, (50.95% identity in 359 aa overlap); P07639|AROB_ECOLI|B3389 from Escherichia coli strain K12 (362 aa), FASTA scores: opt: 771, E(): 2.4e-39, (40.6% identity in 345 aa overlap); etc. Belongs to the dehydroquinate synthase family.	P9WPX9	No	intermediary metabolism and respiration	ML0518	MMAR_2177	MSMEG_3033	Mb2567c				
NC_000962.3	Mycobrowser_v3	CDS	2868860	2869237	.	+	0	Rv2548	vapC19	Unknown	Possible toxin VapC19	Rv2548, (MTCY159.08c), len: 125 aa. Possible vapC19, toxin, part of toxin-antitoxin (TA) operon with Rv2547, contains PIN domain (See Arcus et al., 2005; Pandey and Gerdes, 2005). Similarity to others in Mycobacterium tuberculosis e.g. P71665|Rv1397c|MTCY21B4.14c hypothetical 15.0 KDA protein (133 aa), FASTA scores: opt: 265, E(): 7.1e-12, (42.3% identity in 123 aa overlap); and to Q97WY5|SSO1975 hypothetical protein from Sulfolobus solfataricus (125 aa), FASTA scores: opt: 131, E(): 0.018, (30.0% identity in 110 aa overlap); O52285|YLE hypothetical 14.9 KDA protein from Agrobacterium radiobacter (133 aa), FASTA scores: opt: 128, E(): 0.03, (32.8% identity in 125 aa overlap); etc.	P9WF93	No	virulence, detoxification, adaptation				Mb2578				
NC_000962.3	Mycobrowser_v3	CDS	2871206	2872015	.	-	0	Rv2552c	aroE	Possibly involved at the fourth step in the biosynthesis of chorismate within the biosynthesis of aromatic amino acids (the shikimate pathway) [catalytic activity: shikimate + NADP(+) = 5-dehydroshikimate + NADPH].	Probable shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)	Rv2552c, (MTCY159.04), len: 269 aa. Probable aroE, shikimate 5-dehydrogenase, equivalent to Q9CCS7|AROE|ML0515 putative shikimate 5-dehydrogenase from Mycobacterium leprae (278 aa), FASTA scores: opt: 1452, E(): 1.8e-77, (81.5% identity in 270 aa overlap). Also highly similar, but longer 101 aa, to Q9KH59|AROE putative shikimate dehydrogenase (fragment) from Mycobacterium marinum (148 aa), FASTA scores: opt: 729, E(): 1.3e-35, (76.35% identity in 148 overlap); Q9F7W3|AROE from Mycobacterium ulcerans (148 aa), FASTA scores: opt: 718, E(): 5.9e-35, (75.7% identity in 148 aa overlap). And also similar to to others e.g. Q9KXQ2|AROE from Streptomyces coelicolor (255 aa), FASTA scores: opt: 572, E(): 2.8e-26, (43.4% identity in 251 aa overlap); Q98DY3|MLR4492 from Rhizobium loti (Mesorhizobium loti) (280 aa), FASTA scores: opt: 385, E(): 2.2e-15, (34.85% identity in 284 aa overlap); P74591|AROE_SYNY3|SLR1559 from Synechocystis sp. strain PCC 6803 (290 aa), FASTA scores: opt: 347, E(): 3.7e-13, (30.9% identity in 275 aa overlap); P15770|AROE_ECOLI|B3281 from Escherichia coli strain K12 (272 aa), FASTA scores: opt: 230, E(): 7.7e-08, (29.5% identity in 251 aa overlap); etc. Belongs to the shikimate dehydrogenase family.	I6Y120	No	intermediary metabolism and respiration	ML0515	MMAR_2173	MSMEG_3028	Mb2582c				
NC_000962.3	Mycobrowser_v3	CDS	2873771	2876485	.	-	0	Rv2555c	alaS	Involved in translation mechanism [catalytic activity: ATP + L-alanine + tRNA(ala) = AMP + pyrophosphate + L-alanyl-tRNA (ala)].	Probable alanyl-tRNA synthetase AlaS (alanine--tRNA ligase) (alanine translase) (ALARS)	Rv2555c, (MTCY318.01c-MTCY159.01), len: 904 aa. Probable alaS, alanyl-tRNA synthetase, equivalent to Q9CCT0|alas|ML0512 alanyl-tRNA synthetase from Mycobacterium leprae (908 aa), FASTA scores: opt: 5013, E(): 0, (84.65% identity in 907 aa overlap). Also highly similar to many e.g. Q9KXP9|alas from Streptomyces coelicolor (890 aa), FASTA scores: opt: 2159, E(): 3.8e-118, (53.45% identity in 907 aa overlap); Q9FFC7 Arabidopsis thaliana (Mouse-ear cress) (954 aa), FASTA scores: opt: 1963, E(): 1.1e-106, (41.1% identity in 925 aa overlap); Q9RS27|DR2300 from Deinococcus radiodurans (890 aa), FASTA scores: opt: 1352, E(): 4.1e-71, (38.05% identity in 915 aa overlap); etc. Belongs to class-II aminoacyl-tRNA synthetase family.	P9WFW7	No	information pathways	ML0512	MMAR_2170	MSMEG_3025	Mb2585c				
NC_000962.3	Mycobrowser_v3	CDS	2878571	2879929	.	-	0	Rv2559c	Rv2559c	Function unknown	Conserved hypothetical alanine leucine valine rich protein	Rv2559c, (MTCY9C4.09), len: 452 aa. Conserved hypothetical ala-, leu-, val-rich protein, equivalent to Q9CCT1|ML0510 hypothetical protein from Mycobacterium leprae (473 aa), FASTA scores: opt: 2411, E(): 3.9e-121, (83.4% identity in 452 aa overlap); O69490|O69490 hypothetical 47.1 KDA protein from Mycobacterium leprae (447 aa), FASTA scores: opt: 2406, E(): 6.9e-121, (83.95% identity in 448 aa overlap). Also highly similar to Q9KXP4|SC9C5.30c conserved ATP/GTP binding protein from Streptomyces coelicolor (451 aa), FASTA scores: opt: 1742, E(): 1.5e-85, (64.4% identity in 430 aa overlap); Q9RT67|DR1898 conserved hypothetical protein from Deinococcus radiodurans (434 aa), FASTA scores: opt: 1147, E(): 6.6e-54, (46.0% identity in 415 aa overlap); P45262|YCAJ_HAEIN|HI1590 hypothetical protein from Haemophilus influenzae (446 aa), FASTA scores: opt: 1140, E(): 1.6e-53, (42.5% identity in 428 aa overlap); etc. Also similar to Q50629|MTCY227.09|RUVB|Rv2592c|MT2669|MTCY227.09 holliday junction DNA helicase from Mycobacterium tuberculosis (344 aa), (30.1% identity in 296 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop).	P9WQN1	No	conserved hypotheticals	ML0510	MMAR_2167	MSMEG_3021	Mb2589c				
NC_000962.3	Mycobrowser_v3	CDS	2883342	2884334	.	+	0	Rv2564	glnQ	Thought to be involved in active transport of glutamine across the membrane (import). Responsible for the translocation of the substrate across the membrane.	Probable glutamine-transport ATP-binding protein ABC transporter GlnQ	Rv2564, (MTCY9C4.04c), len: 330 aa. Probable glnQ, glutamine-transport ATP-binding protein ABC transporter (see citation below), highly similar to many e.g. Q9L0J9|SCD40A.12c putative ABC-transporter ATP-binding protein from Streptomyces coelicolor (246 aa), FASTA scores: opt: 598, E(): 2.5e-26, (46.35% identity in 218 aa overlap); O54136|SC2E9.11 from Streptomyces coelicolor (230 aa), FASTA scores: opt: 592, E(): 5.1e-26, (46.55% identity in 219 aa overlap); O29244|AF1018 from Archaeoglobus fulgidus (228 aa), FASTA scores: opt: 580, E(): 2.4e-25, (42.4% identity in 210 aa overlap); P75831|YBJZ_ECOLI|B0879 from Escherichia coli strain K12 (648 aa), FASTA scores: opt: 555, E(): 1.3e-23, (39.65% identity in 232 aa overlap); etc. Also highly similar to O53618|Rv0073|MTV030.17 ABC-transporter ATP-binding subunit from Mycobacterium tuberculosis (330 aa), FASTA scores: opt: 1782, E(): 4.7e-92, (83.65% identity in 330 aa overlap); etc. Shows some similarity to Q11040|YC81_MYCTU|MTCY50.01|Rv1281c|MT1318 hypothetical ABC transporter ATP-binding protein from Mycobacterium tuberculosis (612 aa) (32.9 % identity in 234 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and PS00889 Cyclic nucleotide-binding domain signature 2. Belongs to the ATP-binding transport protein family (ABC transporters).	P9WQI5	No	cell wall and cell processes	ML2675		MSMEG_1614	Mb2593				
NC_000962.3	Mycobrowser_v3	CDS	2884611	2886362	.	+	0	Rv2565	Rv2565	Function unknown	Conserved protein	Rv2565, (MTCY9C4.03c), len: 583 aa. Conserved protein, similar in part to Q9A6C3|CC2171 hypothetical protein from Caulobacter crescentus (610 aa), FASTA scores: opt: 765, E(): 2.8e-37, (32.15% identity in 575 aa overlap). C-terminus also highly similar to various bacterial proteins e.g. O34731|YLBK_BACSU hypothetical 28.3 KDA protein from Bacillus subtilis (260 aa), FASTA scores: opt: 386, E(): 2.2e-15, (33.05% identity in 245 aa overlap); CAC45997|SMC01003 conserved hypothetical protein from Rhizobium meliloti (Sinorhizobium meliloti) (321 aa), FASTA scores: opt: 352, E(): 2.5e-13, (29.65% identity in 280 aa overlap); Q9K9Q8|BH2587 hypothetical protein from Bacillus halodurans (275 aa), FASTA scores: opt: 334, E(): 2.5e-12, (33.7% identity in 175 aa overlap); etc. And shows similarity to C-terminal half of some eukaryotic proteins e.g. Q9R114|NTE neuropathy target esterase homolog from Mus musculus (Mouse) (1327 aa), FASTA scores: opt: 411, E(): 2.7e-16, (24.45% identity in 626 aa overlap); O60859 neuropathy target esterase from Homo sapiens (Human) (1327 aa), FASTA scores: opt: 410, E(): 3.1e-16, (24.1% identity in 627 aa overlap); Q9U969|SWS|CG2212 swiss cheese protein from Drosophila melanogaster (Fruit fly) (1425 aa), FASTA scores: opt: 401, E(): 1.1e-15, (27.75% identity in 544 aa overlap); etc. Also shows strong similarity to C-terminal half of O05884|Z95121|Rv3239c|MTY20B11.14c hypothetical 110.2 KDA protein from Mycobacterium tuberculosis (1048 aa), FASTA scores: opt: 648, E(): 3e-30, (36.55% identity in 572 aa overlap); and O69695|Rv3728|MTV025.076 putative two-domain membrane protein from Mycobacterium tuberculosis (1065 aa), FASTA scores: opt: 643, E(): 6e-30, (34.3% identity in 595 aa overlap). Predicted to be an outer membrane protein (See Song et al., 2008).	P9WIY7	No	conserved hypotheticals				Mb2594				
NC_000962.3	Mycobrowser_v3	CDS	2886373	2889795	.	+	0	Rv2566	Rv2566	Function unknown	Long conserved protein	Rv2566, (MTCY9C4.02c), len: 1140 aa. Long conserved protein, equivalent to O53120|ML2678 or MLCB1913.12 hypothetical protein from Mycobacterium leprae (1000 aa), FASTA scores: opt: 760, E(): 7.1e-38, (50.2% identity in 1128 aa overlap); and middle part equivalent to Q9ZB40 72.2 KDA protein (fragment) from Mycobacterium leprae (644 aa), FASTA scores: opt: 1017, E(): 1.5e-65, (45.65% identity in 655 aa overlap). Also highly similar to Q98HG6|MLL2877 hypothetical protein from Rhizobium loti (Mesorhizobium loti) (1119 aa), FASTA scores: opt: 1413, E(): 3.7e-77, (52.4% identity in 1148 aa overlap); and N-terminus shows similarity with other proteins e.g. Q9HUN8|PA4926 hypothetical protein from Pseudomonas aeruginosa (311 aa), FASTA scores: opt: 278, E(): 3e-09, (29.95% identity in 284 aa overlap); and upstream ORF Q50652|YP69_MYCTU|Rv2569c|MT2645|MTCY227.32 conserved hypothetical protein from Mycobacterium tuberculosis (314 aa), FASTA scores: opt: 252, E(): 1.1e-07, (28.9% identity in 315 aa overlap). Equivalent to AAK46955 from Mycobacterium tuberculosis strain CDC1551 (1156 aa) but shorter 16 aa.	Q50732	No	conserved hypotheticals	ML2678	MMAR_2165	MSMEG_3016	Mb2595,Mb2596				
NC_000962.3	Mycobrowser_v3	CDS	2889795	2892449	.	+	0	Rv2567	Rv2567	Function unknown	Conserved hypothetical alanine and leucine rich protein	Rv2567, (MTCY227.34c, MTCY9C4.01c), len: 884 aa. Conserved hypothetical ala-, leu-rich protein, equivalent to O53121|ML2679|MLCB1913.13 hypothetical protein from Mycobacterium leprae (893 aa), FASTA scores: opt: 4326, E(): 0, (75.2% identity in 883 aa overlap); and similar to Q49755|YO11_MYCLE|ML0605|MLCL536.05c|U1937B|B1937_F1_4 hypothetical 61.8 KDA protein from Mycobacterium leprae (561 aa), FASTA scores: opt: 758, E(): 1.2e-38, (32.2% identity in 537 aa overlap). Also similar to others e.g. Q9HUN7|PA4927 hypothetical protein from Pseudomonas aeruginosa (830 aa), FASTA scores: opt: 1247, E(): 2.2e-68, (38.25% identity in 831 aa overlap); Q98HG7|MLL2876 hypothetical protein from Rhizobium loti (Mesorhizobium loti) (803 aa), FASTA scores: opt: 937, E(): 1.9e-49, (32.15% identity in 828 aa overlap); CAC47419|SMC04057 conserved hypothetical protein from Rhizobium meliloti (Sinorhizobium meliloti) (802 aa), FASTA scores: opt: 900, E(): 3.4e-47, (30.85% identity in 852 aa overlap); etc. And similar to P71732|YO11_MYCTU|Rv2411c|MT2484|MTCY253.09 conserved hypothetical protein from Mycobacterium tuberculosis (551 aa), FASTA scores: opt: 781, E(): 4.6e-40, (33.75% identity in 495 aa overlap).	P9WL97	No	conserved hypotheticals	ML2679	MMAR_2164	MSMEG_3017	Mb2597				
NC_000962.3	Mycobrowser_v3	CDS	2896013	2897803	.	-	0	Rv2572c	aspS	Involved in translation mechanism [catalytic activity: ATP + L-aspartate + tRNA(asp) = AMP + pyrophosphate + L-aspartyl-tRNA(asp)].	Probable aspartyl-tRNA synthetase AspS (aspartate--tRNA ligase) (ASPRS) (aspartic acid translase)	Rv2572c, (MTCY227.29), len: 596 aa. Probable aspS, aspartyl-tRNA synthetase, equivalent to P36429|SYD_MYCLE|ML0501|MLCB1259.19 aspartyl-tRNA synthetase from Mycobacterium leprae (589 aa), FASTA scores: opt: 3534, E(): 1.8e-215, (87.85% identity in 592 aa overlap). Also highly similar to many e.g. O67589|SYD_AQUAE|AQ_1677 from Aquifex aeolicus (603 aa), FASTA scores: opt: 1829, E(): 8.2e-108, (47.5% identity in 598 aa overlap); O32038|SYD_BACSU from Bacillus subtilis (592 aa), FASTA scores: opt: 1732, E(): 1.1e-101, (46.25% identity in 597 aa overlap); P21889|SYD_ECOLI|TLS|B1866 from Escherichia coli strain K12 (590 aa), FASTA scores: opt: 1588, E(): 1.3e-92, (47.35% identity in 581 aa overlap); etc. Contains PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1. Belongs to class-II aminoacyl-tRNA synthetase family.	P9WFW3	No	information pathways	ML0501	MMAR_2158	MSMEG_3003	Mb2602c				
NC_000962.3	Mycobrowser_v3	CDS	2899339	2900220	.	+	0	Rv2575	Rv2575	Unknown	Possible conserved membrane glycine rich protein	Rv2575, (MTCY227.26c), len: 293 aa. Possible conserved membrane gly-rich protein, highly similar to hypothetical proteins e.g. Q9RR98|DR2596 conserved hypothetical protein from Deinococcus radiodurans (313 aa), FASTA scores: opt: 734, E(): 2.8e-38, (42.95% identity in 291 aa overlap); Q9HV81|PA4717 from Pseudomonas aeruginosa (297 aa), FASTA scores: opt: 641, E(): 1.5e-32, (43.35% identity in 300 aa overlap); Q98IA4|MLL2493 from Rhizobium loti (Mesorhizobium loti) (306 aa), FASTA scores: opt: 628, E(): 1e-31, (38.45% identity in 307 aa overlap); etc. Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature.	P9WL85	No	cell wall and cell processes	ML0499,ML0499c	MMAR_2155	MSMEG_3000	Mb2605				
NC_000962.3	Mycobrowser_v3	CDS	2900226	2900690	.	-	0	Rv2576c	Rv2576c	Unknown	Possible conserved membrane protein	Rv2576c, (MTCY227.25), len: 154 aa. Possible conserved membrane protein, showing similarity with Q9ZFC2 hypothetical 15.7 KDA protein from Mycobacterium sp. FM10 (146 aa), FASTA scores: opt: 235, E(): 4.1e-08, (31.35% identity in 150 aa overlap).	P9WL83	No	cell wall and cell processes	ML0498	MMAR_2151	MSMEG_2983	Mb2606c				
NC_000962.3	Mycobrowser_v3	CDS	2900918	2902507	.	+	0	Rv2577	Rv2577	Unknown	Conserved protein	Rv2577, (MTCY227.24c), len: 529 aa. Conserved protein, showing similarity with various proteins from eukaryotes, in particular phosphatases, e.g. Q9SE01|pap purple acid phosphatase precursor from Glycine max (Soybean) (464 aa), FASTA scores: opt: 190, E(): 0.00026, (27.3% identity in 388 aa overlap); Q9SVP2|F18A5.90|AT4G13700 hypothetical 53.4 KDA protein from Arabidopsis thaliana (Mouse-ear cress) (474 aa), FASTA scores: opt: 280, E(): 6.6e-10, (27.2% identity in 331 aa overlap); Q9FK32 similarity to unknown protein from Arabidopsis thaliana (Mouse-ear cress) (529 aa), FASTA scores: opt: 249, E(): 6.2e-08, (25.3% identity in 435 aa overlap); Q12546|APHA acid phosphatase precursor from Aspergillus ficuum (614 aa), FASTA scores: opt: 207, E(): 2.9e-05, (22.95% identity in 458 aa overlap); etc.	P9WL81	No	conserved hypotheticals	ML0497,ML0497c	MMAR_2149		Mb2607,Mb2608				
NC_000962.3	Mycobrowser_v3	CDS	2902509	2903531	.	-	0	Rv2578c	Rv2578c	Function unknown	Conserved hypothetical protein	Rv2578c, (MTCY227.23), len: 340 aa. Conserved hypothetical protein, highly similar to hypothetical proteins (conserved or not) e.g. Q9ZBJ3|SC9C7.17c from Streptomyces coelicolor (348 aa), FASTA scores: opt: 998, E(): 1.6e-55, (47.6% identity in 355 aa overlap); Q9I763|PA0069 from Pseudomonas aeruginosa (352 aa), FASTA scores: opt: 560, E(): 6e-28, (36.6% identity in 284 aa overlap); Q986C9|MLL7417 from Rhizobium loti (Mesorhizobium loti) (356 aa), FASTA scores: opt: 550, E(): 2.6e-27, (39.15% identity in 240 aa overlap); etc.	P9WL79	No	conserved hypotheticals	ML0496	MMAR_2148	MSMEG_2990	Mb2609c				
NC_000962.3	Mycobrowser_v3	CDS	2903639	2904541	.	+	0	Rv2579	dhaA	Generates a primary alcohol and halide from 1-haloalkane and H2O [catalytic activity: 1-haloalkane + H2O = a primary alcohol + halide].	Possible haloalkane dehalogenase DhaA (1-chlorohexane halidohydrolase)	Rv2579, (MTCY227.22c), len: 300 aa. Possible dhaA, haloalkane dehalogenase, strictly equivalent to Q9XB14|ISO-RV2579 haloalkane dehalogenase (1-chlorohexane halidohydrolase) from Mycobacterium bovis (300 aa), FASTA scores: opt: 2075, E(): 7.1e-125, (99.35% identity in 300 aa overlap); note that only two residues, 120 and 293 are different. Also highly similar to others e.g. Q9ZER0|DHAAF haloalkane dehalogenase from Mycobacterium sp strain GP1 (307 aa), FASTA scores: opt: 842, E(): 2.3e-46, (44.95% identity in 298 aa overlap); Q53042|DHAA haloalkane dehalogenase from Rhodococcus rhodochrous, and Pseudomonas pavonaceae (293 aa), FASTA scores: opt: 837, E(): 4.5e-46, (44.6% identity in 298 aa overlap); etc. Note that this protein may also be a 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase, because also highly similar to P51698|LINB_PSEPA 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase from Pseudomonas paucimobilis (Sphingomonas paucimobilis) (see Nagata et al., 1993) (296 aa), FASTA scores: opt: 1494, E(): 6.8e-88, (69.5% identity in 295 aa overlap). Also shows some similarity with proteins from Mycobacterium tuberculosis e.g. Q50670|YM96_MYCTU|Rv2296|MT2353|MTCY339.14c putative haloalkane dehalogenase (300 aa), FASTA scores: opt: 302, E(): 5.3e-12, (30.85% identity in 295 aa overlap); and Q50600|YJ33_MYCTU|Rv1833c|MT1881|MTCY1A11.10 hypothetical 32.2 KDA protein (286 aa), FASTA scores: opt: 286, E(): 5.3e-11, (29.85% identity in 288 aa overlap). May belong to alpha/beta hydrolase fold family. Note that previously known as linB.	P9WMR9	No	intermediary metabolism and respiration		MMAR_0112	MSMEG_6837	Mb2610				
NC_000962.3	Mycobrowser_v3	CDS	2904821	2906092	.	-	0	Rv2580c	hisS	Involved in translation mechamism [catalytic activity: ATP + L-histidine + tRNA(his) = AMP + pyrophosphate + L-histidyl-tRNA(his)].	Probable histidyl-tRNA synthetase HisS (histidine--tRNA ligase) (HISRS) (histidine--translase)	Rv2580c, (MT2657, MTCY227.21), len: 423 aa. Probable hisS, histidyl-tRNA synthetase, equivalent to P46696|SYH_MYCLE|hiss|ML0494|MLCB1259.12|B1177_C3_248 histidyl-tRNA synthetase from Mycobacterium leprae (427 aa), FASTA scores: opt: 2380, E(): 2.1e-131, (85.85% identity in 417 aa overlap). Also highly similar to many e.g. Q9KXP2|hiss from Streptomyces coelicolor (425 aa), FASTA scores: opt: 1542, E(): 1.4e-82, (56.0% identity in 418 aa overlap); O32422|SYH_STAAU|hiss from Staphylococcus aureus (420 aa), FASTA scores: opt: 1135, E(): 7.4e-59, (44.9% identity in 412 aa overlap); P04804|SYH_ECOLI|hiss|B2514 from Escherichia coli strain K12 (423 aa), FASTA scores: opt: 1099, E(): 9.4e-57, (43.9% identity in 417 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to class-II aminoacyl-tRNA synthetase family.	P9WFV5	No	information pathways	ML0494	MMAR_2127	MSMEG_2976	Mb2611c				
NC_000962.3	Mycobrowser_v3	CDS	2906089	2906763	.	-	0	Rv2581c	Rv2581c	Involved in glyoxal pathway. Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid [catalytic activity: (S)-(2-hydroxyacyl)glutathione + H(2)O = glutathione + a 2-hydroxy acid anion].	Possible glyoxalase II (hydroxyacylglutathione hydrolase) (GLX II)	Rv2581c, (MTCY227.20), len: 224 aa. Possible glyoxalase II, equivalent to Q49649|YP81_MYCLE|ML0493|MLCB1259.11|B1177_C3_247 hypothetical 23.9 KDA protein from Mycobacterium leprae (218 aa), FASTA scores: opt: 1264, E(): 7.8e-73, (82.0% identity in 222 aa overlap). Also highly similar to Q9KXP1|SC9C5.33c possible hydrolase from Streptomyces coelicolor (235 aa), FASTA scores: opt: 654, E(): 2.9e-34, (46.8% identity in 220 aa overlap); and similar to Q9CI24|YFCI hypothetical protein from Lactococcus lactis (subsp. lactis) (Streptococcus lactis) (210 aa), FASTA scores: opt: 360, E(): 9.9e-16, (35.0% identity in 217 aa overlap); AAK75726|SP1646 metallo-beta-lactamase superfamily protein from Streptococcus pneumoniae (209 aa), FASTA scores: opt: 320, E(): 3.3e-13, (35.85% identity in 198 aa overlap); AAK80229|CAC2272 predicted Zn-dependent hydrolase of metallo-beta-lactamase superfamily from Clostridium acetobutylicum (199 aa), FASTA scores: opt: 282, E(): 8e-11, (32.7% identity in 217 aa overlap); etc. Equivalent to AAK46971 from Mycobacterium tuberculosis strain CDC1551 (246 aa) but shorter 22 aa. Belongs to the glyoxalase II family. Cofactor: binds two zinc ions.	P9WMW3	No	virulence, detoxification, adaptation	ML0493	MMAR_2126	MSMEG_2975	Mb2612c				
NC_000962.3	Mycobrowser_v3	CDS	2906814	2907740	.	+	0	Rv2582	ppiB	PPIases accelerate the folding of proteins [catalytic activity: cis-trans isomerization of proline imidic peptide bonds inoligopeptides].	Probable peptidyl-prolyl cis-trans isomerase B PpiB (cyclophilin) (PPIase) (rotamase) (peptidylprolyl isomerase)	Rv2582, (MTCY227.19c), len: 308 aa. Probable ppiB (alternate gene name: ppi), cyclophilin (peptidyl-prolyl cis-trans isomerase), equivalent to P46697|PPIB_MYCLE|PPI|ML0492|MLCB1259.10c|B1177_F3_97 probable peptidyl-prolyl cis-trans isomerase B from Mycobacterium leprae (295 aa), FASTA scores: opt: 1423, E(): 1.3e-66, (72.2% identity in 295 aa overlap). Also similar to others e.g. Q9KJG8|PPIB peptidyl-prolyl cis-trans isomerase from Streptomyces lividans (277 aa), FASTA scores: opt: 485, E(): 3.2e-18, (38.35% identity in 292 aa overlap); Q9KXP0|SC9C5.34 peptidyl-prolyl cis-trans isomerase from Streptomyces coelicolor (277 aa), FASTA scores: opt: 483, E(): 4.1e-18, (38.35% identity in 292 aa overlap); Q9RT72|DR1893 peptidyl-prolyl cis-trans isomerase from Deinococcus radiodurans (350 aa), FASTA scores: opt: 296, E(): 2.2e-08, (29.0% identity in 276 aa overlap); etc. Belongs to the cyclophilin-type PPIase family.	P9WHW1	No	information pathways	ML0492,ML0492c	MMAR_2125	MSMEG_2973,MSMEG_2974	Mb2613				
NC_000962.3	Mycobrowser_v3	CDS	2939012	2939962	.	-	0	Rv2611c	Rv2611c	Catalyzes the acylation of the 6-position of the mannose residue linked to position 2 of the myo-inositol in phosphatylinositol mono- and DI-mannosides.	Probable acyltransferase	Rv2611c, (MTCY01A10.22), len: 316 aa. Probable acyltransferase , equivalent to O07148|MLCL581.15c|ML0453 hypothetical 35.4 KDA protein from Mycobacterium leprae (320 aa), FASTA scores: opt: 1529, E(): 5e-90, (71.45% identity in 312 aa overlap); and equivalent to Q9F7Y8 putative acyltransferase from Mycobacterium smegmatis (303 aa), FASTA scores: opt: 1464, E(): 6.5e-86, (72.15% identity in 291 aa overlap) (see citation below). Also highly similar to Q9L283|SCL2.16c putative acyltransferase from Streptomyces coelicolor (311 aa), FASTA scores: opt: 810, E(): 2.8e-44, (47.7% identity in 302 aa overlap); and similar to other acyltransferases e.g. Q9F0N3 acyltransferase from Campylobacter jejuni (295 aa), FASTA scores: opt: 207, E(): 6.4e-06, (20.45% identity in 220 aa overlap); Q9K379 acyltransferase (lipid a biosynthesis acyltransferase) from Campylobacter jejuni (295 aa), FASTA scores: opt: 203, E(): 1.1e-05, (20.0% identity in 220 aa overlap); etc.	P9WMB5	No	lipid metabolism	ML0453,ML0453c	MMAR_2091	MSMEG_2934	Mb2643c				
NC_000962.3	Mycobrowser_v3	CDS	2907826	2910198	.	-	0	Rv2583c	relA	Involved in the metabolism of PPGPP (at the first step). In eubacteria PPGPP (guanosine 3'-diphosphate 5-'diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes the formation of PPPGPP which is then hydrolysed to form PPGPP [catalytic activity: ATP + GTP = AMP + guanosine 3'-diphosphate 5-'triphosphate].	Probable GTP pyrophosphokinase RelA (ATP:GTP 3'- pyrophosphotransferase) (PPGPP synthetase I) ((P)PPGPP synthetase) (GTP diphosphokinase)	Rv2583c, (MTCY227.18), len: 790 aa. Probable relA, GTP pyrophosphokinase, equivalent to Q49640|RELA_MYCLE|ML0491|MLCB1259.09|B1177_C1_168 probable GTP pyrophosphokinase from Mycobacterium leprae (787 aa), FASTA scores: opt: 4834, E(): 0, (93.4% identity in 790 aa overlap). Also highly similar to others e.g. O87331|RELA_CORGL|RELA|rel from Corynebacterium glutamicum (Brevibacterium flavum) (760 aa), FASTA scores: opt: 3375, E(): 1.6e-196, (67.0% identity in 758 aa overlap); O85709|RELA_STRAT from Streptomyces antibioticus (841 aa), FASTA scores: opt: 3209, E(): 1.9e-186, (63.85% identity in 786 aa overlap); Q9KDH1|RELA|BH1242 from Bacillus halodurans (728 aa), FASTA scores: opt: 2195,E(): 3.8e-125, (45.65% identity in 714 aa overlap); etc. Belongs to the RELA / spot family.	P9WHG9	No	intermediary metabolism and respiration	ML0491	MMAR_2124	MSMEG_2965	Mb2614c				
NC_000962.3	Mycobrowser_v3	tRNA	2969497	2969568	.	-	0	MTB000035	valT	-	tRNA-Val (CAC)	valT, tRNA-Val, anticodon cac, length = 72		No	stable RNAs								
NC_000962.3	Mycobrowser_v3	CDS	2910229	2910900	.	-	0	Rv2584c	apt	Involved in purine salvage. Catalyses a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis [catalytic activity: AMP + pyrophosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate].	Adenine phosphoribosyltransferase Apt (APRT) (AMP diphosphorylase) (AMP pyrophosphorylase) (transphosphoribosidase)	Rv2584c, (MTCY227.17), len: 223 aa. Probable apt, adenine phosphoribosyltransferase, similar, but longer in N-terminus, to others e.g. O87330|APT_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (185 aa), FASTA scores: opt: 524, E(): 1.3e-24, (50.95% identity in 159 aa overlap); P52561|APT_STRCO from Streptomyces coelicolor (182 aa), FASTA scores: opt: 503, E(): 2.3e-23, (51.85% identity in 164 aa overlap); P47956|APT_MUSPA|APRT from Mus pahari (Shrew mouse) (180 aa), FASTA scores: opt: 419, E(): 2.5e-18, (44.7% identity in 170 aa overlap); P07672|P09993|P77121|APT_ECOLI|B0469 from Escherichia coli strain K12 (183 aa), FASTA scores: opt: 393, E(): 1.9e-18, (42.6% identity in 162 aa overlap); etc. Contains PS00103 Purine/ pyrimidine phosphoribosyl transferases signature, and PS00144 Asparaginase / glutaminase active site signature 1. Belongs to the purine/pyrimidine phosphoribosyltransferase family. Nearest initiation codon indicated by homology is TTG at 17426 or GTG at 17465.	P9WQ07	No	intermediary metabolism and respiration	ML0490	MMAR_2123	MSMEG_2964	Mb2615c				
NC_000962.3	Mycobrowser_v3	CDS	2911004	2912677	.	-	0	Rv2585c	Rv2585c	Unknown	Possible conserved lipoprotein	Rv2585c, (MT2662, MTCY227.16), len: 557 aa. Possible conserved lipoprotein precursor, possibly attached to the membrane by a lipid anchor and substrate-binding protein involved in transport, equivalent to Q49646|YP85_MYCLE|ML0489|MLCB1259.07|B1177_C2_197 hypothetical lipoprotein precursor from Mycobacterium leprae (555 aa), FASTA scores: opt: 2812, E(): 9.8e-158, (78.95% identity in 546 aa overlap); and C-terminus highly similar to C-terminus of Q49638|DCIAE|B1177_C1_166 DCIAE protein from Mycobacterium leprae (344 aa), FASTA scores: opt: 1177, E(): 7.4e-62, (78.6% identity in 229 aa overlap). Also similar in part to various proteins, principally substrate-binding proteins, e.g. O87329|DCIAE dipeptide-binding protein from Corynebacterium glutamicum (Brevibacterium flavum) (502 aa), FASTA scores: opt: 614, E(): 1.2e-28, (30.7% identity in 427 aa overlap); Q9AKR0|OPPA|CAC49261 putative oligopeptide uptake ABC transporter periplasmic solute-binding protein precursor from Rhizobium meliloti (Sinorhizobium meliloti) (532 aa), FASTA scores: opt: 209, E(): 7.7e-05, (22.85% identity in 460 aa overlap); P76128|YDDS_ECOLI|B1487|P77769|P76874 putative ABC transporter periplasmic binding protein from Escherichia coli strain K12 (516 aa), FASTA scores: opt: 182, E(): 0.0029, (20.0% identity in 315 aa overlap); etc.	P9WL77	No	cell wall and cell processes	ML0489	MMAR_2122	MSMEG_2963	Mb2616c				
NC_000962.3	Mycobrowser_v3	CDS	2912683	2914011	.	-	0	Rv2586c	secF	Involved in protein export. Part of the prokaryotic protein translocation apparatus which comprise SECA, SECB, SECD, SECE, SECF, SECG and SECY.	Probable protein-export membrane protein SecF	Rv2586c, (MT2663, MTCY227.15), len: 442 aa. Probable secF, protein-export membrane protein (integral membrane protein) (see citation below), equivalent to P38386|SECF_MYCLE|SECF|ML0488|MLCB1259.06|B1177_C3_239 protein-export membrane protein from Mycobacterium leprae (471 aa), FASTA scores: opt: 1910, E(): 2.9e-104, (72.15% identity in 456 aa overlap). Also similar to others e.g. Q9AE06|SECF from Corynebacterium glutamicum (Brevibacterium flavum) (403 aa), FASTA scores: opt: 1198, E(): 9.8e-63, (47.1% identity in 399 aa overlap); Q53956|SECF_STRCO|SCL2.05c from Streptomyces coelicolor (373 aa), FASTA scores: opt: 670, E(): 6.4e-32, (39.25% identity in 400 aa overlap); Q55611|SECF_SYNY3|SLR0775 from Synechocystis sp. strain PCC 6803 (315 aa), FASTA scores: opt: 416, E(): 3.8e-17, (33.8% identity in 296 aa overlap); etc. Belongs to the SECD/SECF family, SECF family. Part of the prokaryotic protein translocation apparatus which comprise SECA|Rv3240c, SECD|Rv2587c, SECE|Rv0638, SECF, SECG|Rv1440 and SECY|Rv0732.	P9WGN9	No	cell wall and cell processes	ML0488	MMAR_2121	MSMEG_2962	Mb2617c				
NC_000962.3	Mycobrowser_v3	CDS	2915846	2916193	.	-	0	Rv2588c	yajC	Thought to be involved in secretion apparatus.	Probable conserved membrane protein secretion factor YajC	Rv2588c, (MTCY227.13), len: 115 aa. Probable yajC, secretion factor, a conserved membrane protein (see Braunstein & Belisle 2000), equivalent to Q49647|YP88_MYCLE|ML0486|MLCB1259.04|B1177_C3_235 hypothetical 12.8 KDA protein from Mycobacterium leprae (114 aa), FASTA scores: opt: 499, E(): 2.7e-26, (77.0% identity in 100 aa overlap). Also similar to other proteins e.g. Q9AE08 hypothetical 13.5 KDA protein from Corynebacterium glutamicum (Brevibacterium flavum) (121 aa), FASTA scores: opt: 222, E(): 5e-08, (39.8% identity in 103 aa overlap); Q9L292|SCL2.07c putative secreted protein from Streptomyces coelicolor (169 aa), FASTA scores: opt: 203, E(): 1.2e-06, (32.05% identity in 106 aa overlap); Q9CDT0|YWAB unknown protein from Lactococcus lactis (subsp. lactis) (Streptococcus lactis) (110 aa), FASTA scores: opt: 150, E(): 0.0026, (30.85% identity in 94 aa overlap); etc.	P9WL75	No	cell wall and cell processes	ML0486	MMAR_2119	MSMEG_2960	Mb2619c				
NC_000962.3	Mycobrowser_v3	CDS	2916360	2917709	.	+	0	Rv2589	gabT	Involved in 4-aminobutyrate (GABA) degradation pathway [catalytic activity: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate].	4-aminobutyrate aminotransferase GabT (gamma-amino-N-butyrate transaminase) (GABA transaminase) (glutamate:succinic semialdehyde transaminase) (GABA aminotransferase) (GABA-at)	Rv2589, (MTCY227.12c), len: 449 aa. Probable gabT, 4-aminobutyrate aminotransferase, equivalent to P40829|GABT_MYCLE|ML0485|MLCB1259.03c|B1177_F2_67 4-aminobutyrate aminotransferase (446 aa), FASTA scores: opt: 2468, E(): 4.5e-141, (83.75% identity in 449 aa overlap). Also highly similar to others e.g. O86823|GABT from Streptomyces coelicolor (444 aa), FASTA scores: opt: 1832, E(): 8e-103, (63.9% identity in 443 aa overlap); AAK79395|CAC1427 from Clostridium acetobutylicum (445 aa), FASTA scores: opt: 1283, E(): 8.4e-70, (45.75% identity in 433 aa overlap); Q9KE66|BH0991 from Bacillus halodurans (443 aa), FASTA scores: opt: 1224, E(): 2.9e-66, (44.55% identity in 431 aa overlap); etc. Contains PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site. Belongs to class-III of pyridoxal-phosphate-dependent aminotransferases. Cofactor: pyridoxal phosphate.	P9WQ79	No	intermediary metabolism and respiration	ML0485,ML0485c	MMAR_2118	MSMEG_2959	Mb2620				
NC_000962.3	Mycobrowser_v3	CDS	2917871	2921377	.	+	0	Rv2590	fadD9	Function unknown, but involved in lipid degradation.	Probable fatty-acid-CoA ligase FadD9 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)	Rv2590, (MTCY227.11c), len: 1168 aa. Probable fadD9, fatty-acid-CoA synthetase, highly similar to O69484|FADD9 (alias Q9CCT4|FADD9|ML0484 but longer 14 aa) putative acyl-CoA synthetase from Mycobacterium leprae (1174 aa), FASTA scores: opt: 5247, E(): 0, (68.0% identity in 1178 aa overlap). N-terminal (approximately 700 residues) similar to other long chain fatty acid ligases. And C-terminus highly similar to C-terminus of Q9XCF2|PSTB PSTB protein from Mycobacterium avium (2552 aa), FASTA scores: opt: 2083, E(): 8.4e-116, (40.8% identity in 1150 aa overlap) (and weak similarity on N-terminus). C-terminal part highly similar to polyketide synthases and peptides synthases (weak similarity on N-terminus) e.g. Q10896|Rv0101|MTCY251.20|NRP probable peptide synthetase from Mycobacterium tuberculosis (2512 aa), FASTA scores: opt: 1988, E(): 3.7e-110, (40.2% identity in 1181 aa overlap); etc. Contains PS00455 putative AMP-binding domain signature, and PS00061 Short-chain alcohol dehydrogenase family signature. Seems to belong to the ATP-dependent AMP-binding enzyme family, and to the short-chain dehydrogenases/reductases (SDR) family.	Q50631	No	lipid metabolism	ML0484,ML0484c	MMAR_2117	MSMEG_2956	Mb2621				
NC_000962.3	Mycobrowser_v3	CDS	2924230	2924820	.	-	0	Rv2593c	ruvA	forms a complex with RUVB. RUVA stimulates, in the presence of DNA, the weak ATPase activity of RUVB. The RUVA-RUVB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RUVAB is an helicase that mediates the holliday junction migration by localized denaturation and reanneling.	Probable holliday junction DNA helicase RuvA	Rv2593c, (MTCY227.08), len: 196 aa. Probable ruvA, Holliday junction binding protein (see citations below), equivalent to P40832|RUVA_MYCLE|ML0482|B1177_C2_188 holliday junction DNA helicase from Mycobacterium leprae (203 aa), FASTA scores: opt: 923, E(): 9.9e-50, (76.85% identity in 203 aa overlap). Also highly similar to others e.g. Q9L290|RUVA from Streptomyces coelicolor (201 aa) (201 aa), FASTA scores: opt: 549, E(): 8.2e-27, (47.55% identity in 204 aa overlap); Q9AE10|RUVA from Corynebacterium glutamicum (Brevibacterium flavum) (206 aa), FASTA scores: opt: 440, E(): 4e-20, (47.1% identity in 206 aa overlap); P08576|RUVA_ECOLI|B1861|Z2913|ECS2571 from Escherichia coli strains K12 and O157:H7 (203 aa), FASTA scores: opt: 312, E(): 2.8e-12, (34.85% identity in 201 aa overlap); etc. Belongs to the RuvA family.	P9WGW3	No	information pathways	ML0482	MMAR_2110	MSMEG_2944	Mb2624c				
NC_000962.3	Mycobrowser_v3	CDS	2927990	2928391	.	+	0	Rv2600	Rv2600	Unknown	Probable conserved integral membrane protein	Rv2600, (MTCY277.01c, MTV001.01), len: 133 aa. Probable conserved integral membrane protein, equivalent (but shorter 18 aa) to Q9K537|YQ00_MYCPA hypothetical protein RV2600 homolog from Mycobacterium paratuberculosis (151 aa), FASTA scores: opt: 543, E(): 4.2e-28, (62.9% identity in 132 aa overlap). Also some similarity with other hypothetical or membrane proteins e.g. Q9L090|SCC24.27c putative integral membrane protein from Streptomyces coelicolor (146 aa), FASTA scores: opt: 241, E(): 8.7e-09, (34.8% identity in 135 aa overlap); O58487|PH0773 hypothetical 15.0 KDA protein from Pyrococcus horikoshii (138 aa), FASTA scores: opt: 116, E(): 0.84, (34.35% identity in 96 aa overlap); etc. Equivalent to AAK46990 from Mycobacterium tuberculosis strain CDC1551 (152 aa) but shorter 19 aa.	P9WFG5	No	cell wall and cell processes	ML0477,ML0477c			Mb2631				
NC_000962.3	Mycobrowser_v3	CDS	2928388	2929959	.	+	0	Rv2601	speE	Involved in the biosynthesis of spermidine from arginine (at the fifth, last step). The activity is thought to be regulated mainly by the availability of decarboxylated S-adenosylmethionine [catalytic activity: S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine].	Probable spermidine synthase SpeE (putrescine aminopropyltransferase) (aminopropyltransferase) (SPDSY)	Rv2601, (MTCI270.04c-MTV001.02), len: 523 aa. Probable speE, spermidine synthase, highly similar to many e.g. Q9L091|SCC24.26c from Streptomyces coelicolor (531 aa), FASTA scores: opt: 1493, E(): 1.3e-79, (48.45% identity in 514 aa overlap); Q9X8S2|SCH10.33c from Streptomyces coelicolor (554 aa), FASTA scores: opt: 1045, E(): 1.7e-53, (40.55% identity in 525 aa overlap); P09158|SPEE_ECOLI|B0121 from Escherichia coli strain K12 (287 aa), FASTA scores: opt: 368, E(): 2.9e-14, (30.5% identity in 272 aa overlap); etc.	P9WGE5	No	intermediary metabolism and respiration	ML0476,ML0476c	MMAR_2104		Mb2632				
NC_000962.3	Mycobrowser_v3	CDS	2930344	2930784	.	+	0	Rv2602	vapC41	Unknown	Possible toxin VapC41. Contains PIN domain.	Rv2602, (MTCI270A.03c), len: 146 aa. Possible vapC41, toxin, part of toxin-antitoxin (TA) operon with Rv2601A, contains PIN domain, see Arcus et al. 2005. Similar to others in Mycobacterium tuberculosis (strains H37Rv and CDC1551) e.g. O50457|Rv1242|MTV006.14 (143 aa), FASTA scores: opt: 147, E(): 0.0021, (26.25% identity in 141 aa overlap); P95023|Rv2530c|MTCY159.26 (139 aa), FASTA scores: opt: 131, E(): 0.027, (33.35% identity in 135 aa overlap); O53812|Rv0749|MTV041.23 (142 aa), FASTA scores: opt: 125, E(): 0.072, (26.45% identity in 140 aa overlap).	P9WF59	No	virulence, detoxification, adaptation				Mb2634				
NC_000962.3	Mycobrowser_v3	CDS	2930805	2931560	.	-	0	Rv2603c	Rv2603c	Function unknown	Highly conserved protein	Rv2603c, (MTCI270A.02), len: 251 aa. Highly conserved protein, equivalent to Q49645|YQ03_MYCLE|ML0475|U1177B|B1177_C2_181 hypothetical 26.6 KDA protein from Mycobacterium leprae (251 aa), FASTA scores: opt: 1514, E(): 2.2e-84, (92.45% identity in 251 aa overlap). Also highly similar to Q9L288|SCL2.11c hypothetical 26.8 KDA protein from Streptomyces coelicolor (250 aa), FASTA scores: opt: 1268, E(): 1.5e-69, (76.7% identity in 249 aa overlap); Q9AE12|YFCA hypothetical structural protein from Corynebacterium glutamicum (Brevibacterium flavum) (251 aa), FASTA scores: opt: 1231, E(): 2.6e-67, (72.9% identity in 251 aa overlap); O83487|Y474_TREPA|TP0474 hypothetical protein from Treponema pallidum (245 aa), FASTA scores: opt: 780, E(): 4.4e-40, (47.75% identity in 245 aa overlap); P24237|YEBC_ECOLI|B1864 protein YEBC from Escherichia coli strain K12 (246 aa), FASTA scores: opt: 776, E(): 7.6e-40, (47.8% identity in 249 aa overlap); etc.	P9WGA5	No	conserved hypotheticals	ML0475	MMAR_2098	MSMEG_2940	Mb2635c				
NC_000962.3	Mycobrowser_v3	CDS	2931693	2932289	.	-	0	Rv2604c	snoP	Possibly involved in the biosynthesis of pyridoxine/pyridoxal 5-phosphate biosynthesis	Probable glutamine amidotransferase SnoP	Rv2604c, (MTCY01A10.29, MTCI270A.01), len: 198 aa. Probable snoP, glutamine amidotransferase, equivalent (but shorter 21 aa) to Q49637|HISH|B1177_C1_149 HISH protein (belongs to the YFL060C/YAAE/HI1648 family) (alias Q9CCT5|ML0474 hypothetical protein 223 aa) from Mycobacterium leprae (219 aa), FASTA scores: opt: 1069, E(): 1.7e-60, (83.35% identity in 198 aa overlap). Also highly similar to hypothetical proteins or amidotransferases e.g. Q9L287|SCL2.12c hypothetical 21.5 KDA protein from Streptomyces coelicolor (202 aa), FASTA scores: opt: 702, E(): 2.3e-37, (56.75% identity in 192 aa overlap); P37528|YAAE_BACSU hypothetical 21.4 KDA protein from Bacillus subtilis (196 aa), FASTA scores: opt: 608, E(): 1.9e-31, (48.7% identity in 189 aa overlap); Q9KGN5|BH0023 amidotransferase from Bacillus halodurans (196 aa), FASTA scores: opt: 583, E(): 7.4e-30, (48.7% identity in 195 aa overlap); etc. Also some similarity with several proteins from Mycobacterium tuberculosis e.g. O06589|HIS5_MYCTU|Rv1602|MT1638|MTCY336.02c amidotransferase (206 aa), FASTA scores: opt: 154, E(): 0.00036, (30.6% identity in 193 aa overlap). Contains a Pfam match to entry PF01174 SNO glutamine amidotransferase family. Note possibly co-regulated with snzP (Rv2606c).	P9WII7	No	intermediary metabolism and respiration	ML0474	MMAR_2096	MSMEG_2939	Mb2636c				
NC_000962.3	Mycobrowser_v3	CDS	2933171	2934070	.	-	0	Rv2606c	snzP	Possibly involved in the biosynthesis of pyridoxine/pyridoxal 5-phosphate biosynthesis	Possible pyridoxine biosynthesis protein SnzP	Rv2606c, (MTCY01A10.27), len: 299 aa. Probable snzP, pyridoxine biosynthesis protein. Highly similar to O07145|YQ06_MYCLE|ML0450|MLCL581.12c possible pyridoxine biosynthesis protein from Mycobacterium leprae (307 aa), FASTA scores: opt: 1686, E(): 1.5e-95, (89.7% identity in 291 aa overlap). Also highly similar to several pyridoxine biosynthesis proteins and hypothetical proteins e.g. Q9L286|SCL2.13c hypothetical 32.2 KDA protein from Streptomyces coelicolor (303 aa), FASTA scores: opt: 1461, E(): 7.6e-82, (76.8% identity in 293 aa overlap); O14027|YEM4_SCHPO|SPAC29B12.04 putative stress-induced protein from Schizosaccharomyces pombe (Fission yeast) (296 aa), FASTA scores: opt: 1318, E(): 3.8e-73, (70.35% identity in 290 aa overlap); Q9UW83|PYROA protein involved in pyridoxine biosynthesis from Emericella nidulans (Aspergillus nidulans) (see citation below) (304 aa), FASTA scores: opt: 1288, E(): 2.6e-71, (67.9% identity in 302 aa overlap); etc. Contains Pfam match to entry PF01680, SOR_SNZ family. Contains PS01235 Uncharacterized protein family UPF0019 signature. Belongs to the SOR_SNZ family. Note possibly co-regulated with snoP (Rv2604c).	P9WII9	No	intermediary metabolism and respiration	ML0450,ML0450c	MMAR_2094	MSMEG_2937	Mb2638c				
NC_000962.3	Mycobrowser_v3	CDS	2934198	2934872	.	+	0	Rv2607	pdxH	Involved in biosynthesis of pyridoxine (vitamin B6) and pyridoxal phosphate. Oxidize PNP and PMP into pyridoxal 5'-phosphate (PLP)[catalytic activity: pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)].	Probable pyridoxamine 5'-phosphate oxidase PdxH (PNP/PMP oxidase) (pyridoxinephosphate oxidase) (PNPOX) (pyridoxine 5'-phosphate oxidase)	Rv2607, (MTCY01A10.26c), len: 224 aa. Probable pdxH, pyridoxinephosphate oxidase, equivalent to O33065|PDXH_MYCLE|ML2131|MLCB57.46 pyridoxamine 5'-phosphate oxidase from Mycobacterium leprae (219 aa), FASTA scores: opt: 1038, E(): 8.3e-61, (67.1% identity in 219 aa overlap). Also similar to others e.g. Q9I4S5|PDXH|PA1049 from Pseudomonas aeruginosa (215 aa), FASTA scores: opt: 608, E(): 1.1e-32, (49.55% identity in 218 aa overlap); Q9K3V7|SCD10.19c from Streptomyces coelicolor (234 aa), FASTA scores: opt: 600, E(): 3.9e-32, (42.3% identity in 234 aa overlap); P28225|PDXH_ECOLI|B1638 from Escherichia coli strain K12 (217 aa), FASTA scores: opt: 533, E(): 8.9e-28, (40.3% identity in 216 aa overlap); etc. Contains a match to Pfam entry PF01243 Pyridoxamine 5'-phosphate oxidase. Belongs to the pyridoxamine 5'-phosphate oxidase family. Cofactor: FMN.	P9WIJ1	No	intermediary metabolism and respiration	ML2131,ML2131c	MMAR_4642	MSMEG_5675	Mb2639				
NC_000962.3	Mycobrowser_v3	CDS	2935046	2936788	.	+	0	Rv2608	PPE42	Function unknown	PPE family protein PPE42	Rv2608, (MTCY01A10.25c), len: 580 aa. PPE42, Member of the Mycobacterium tuberculosis PPE family, highly similar to many e.g. O06828|Rv1430|MTCY493.24c from Mycobacterium tuberculosis (528 aa), FASTA scores: opt: 1004, E(): 5.9e-48, (56.05% identity in 307 aa overlap).	P9WHZ5	No	PE/PPE				Mb2640				
NC_000962.3	Mycobrowser_v3	CDS	2937865	2939001	.	-	0	Rv2610c	pimA	Involved in the first mannosylation step in phosphatidylinositol mannoside biosynthesis (transfer of mannose residues onto PI, leading to the synthesis of phosphatidylinositol monomannoside).	Alpha-mannosyltransferase PimA	Rv2610c, (MTCY01A10.23), len: 378 aa. PimA, alpha-mannosyltransferase (see citations below), equivalent to O07147|MLCL581.14c|ML0452 putative glycosyltransferase from Mycobacterium leprae (374 aa), FASTA scores: opt: 2044, E(): 8.8e-118, (82.25% identity in 378 aa overlap). N-terminus (from aa 1 to 27) equivalent to Q9FY7 putative alpha-mannosyl transferase (fragment) from Mycobacterium smegmatis (27 aa), blastp scores: 57.4 bits (137), E(): 3e-8, Identities = 25/27 (92%), Positives = 27/27 (99%) (see citation below). Also highly similar to Q9L284|SCL2.15c putative sugar transferase from Streptomyces coelicolor (387 aa), FASTA scores: opt: 1222, E(): 1.8e-67, (52.95% identity in 376 aa overlap); and similar in part to various proteins e.g. Q9YA73|APE2066 long hypothetical N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein from Aeropyrum pernix (392 aa), FASTA scores: opt: 434, E(): 3e-19, (31.5% identity in 378 aa overlap); Q9UZA1|PAB0827 galactosyltransferase or LPS biosynthesis RFBU related protein from Pyrococcus abyssi (371 aa), FASTA scores: opt: 382, E(): 4.3e-16, (28.2% identity in 383 aa overlap); O26275|MTH173 LPS biosynthesis RFBU related protein from Methanothermobacter thermautotrophicus (382 aa), FASTA scores: opt: 372, E(): 1.8e-15, (28.4% identity in 391 aa overlap); etc. Shows also some similarity with O05313|Rv1212c|MTCI364.24c hypothetical 41.5 KDA protein from Mycobacterium tuberculosis (387 aa), FASTA scores: opt: 232, E(): 1.1e -07, (28.4% identity in 402 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop).	P9WMZ5	No	lipid metabolism	ML0452,ML0452c	MMAR_2092	MSMEG_2935	Mb2642c				
NC_000962.3	Mycobrowser_v3	CDS	2939959	2940612	.	-	0	Rv2612c	pgsA1	Catalyzes the transfer of a free alcohol (inositol) onto CDP-diacylglycerol. The product of this putative ORF seems be essential to mycobacteria [catalytic activity: CDP-diacylglycerol + myo-inositol = CMP + phosphatidyl 1D-myo-inositol].	PI synthase PgsA1 (phosphatidylinositol synthase) (CDP-diacylglycerol--inositol-3-phosphatidyltransferase)	Rv2612c, (MTCY01A10.21), len: 217 aa. pgsA1 (previously known as pgsA), PI synthase/CDP-diacylglyceride--inositol phosphatidyltransferase, transmembrane protein, equivalent to O07149|MLCL581.16c|PGSA|ML0454 putative phosphatidyltransferase from Mycobacterium leprae (239 aa), FASTA scores: opt: 1141, E(): 4.1e-70, (79.35% identity in 213 aa overlap); and Q9F7Y9|PGSA phosphatidylinositol synthase from Mycobacterium smegmatis (222 aa), FASTA scores: opt: 981, E(): 2.7e-59, (67.3% identity in 217 aa overlap) (see citation below). Also similar to other proteins e.g. Q9L282|SCL2.17c putative membrane transferase from Streptomyces coelicolor (241 aa), FASTA scores: opt: 564, E(): 4.9e-31, (43.4% identity in 212 aa overlap); Q9UYD0|PGSA-like|PAB1041 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase from Pyrococcus abyssi (186 aa), FASTA scores: opt: 264, E(): 8.4e-11, (33.15% identity in 190 aa overlap); Q9HQS2|PGSA|VNG1030G CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase from Halobacterium sp. strain NRC-1 (199 aa), FASTA scores: opt: 249, E(): 9.1e-10, (32.1% identity in 193 aa overlap); etc. Contains PS00379 CDP-alcohol phosphatidyltransferases signature. Belongs to the CDP-alcohol phosphatidyltransferase class-I family. Note that in Mycobacterium smegmatis, the psgA homologue is essential to the survival of the bacteria and seems cannot be compensated by any other enzyme of Mycobacterium smegmatis.	P9WPG7	No	lipid metabolism	ML0454,ML0454c	MMAR_2090	MSMEG_2933	Mb2644c				
NC_000962.3	Mycobrowser_v3	CDS	2940609	2941196	.	-	0	Rv2613c	Rv2613c	Function unknown; but could be involved in lipid metabolism.	Conserved protein	Rv2613c, (MTCY01A10.20A), len: 195 aa. Conserved protein, equivalent to Q9CCU0|ML0455 hypothetical protein from Mycobacterium leprae (206 aa), FASTA scores: opt: 1074, E(): 7.4e-62, (84.7% identity in 196 aa overlap); and highly similar, but longer 18 aa, to O07150|MLCL581.17c hypothetical 20.7 KDA protein from Mycobacterium leprae (186 aa), FASTA scores: opt: 1038, E(): 1.4e-59, (89.7% identity in 175 aa overlap). Also highly similar to other hypothetical proteins (often Hit family member) e.g. Q9F7Z0 from Mycobacterium smegmatis (see citation below) (205 aa), FASTA scores: opt: 975, E(): 1.6e-55, (79.35% identity in 184 aa overlap); Q9L279|SCL2.20 from Streptomyces coelicolor (186 aa), FASTA scores: opt: 638, E(): 5.8e-34, (52.85% identity in 176 aa overlap); Q9YFX8|APE0122 from Aeropyrum pernix (184 aa), FASTA scores: opt: 515, E(): 4.4e-26, (45.9% identity in 159 aa overlap); etc. It seems the Rv2613c and downstream ORF Rv2612c|psgA1 are expressed from the same promoter (see citation below) and that Rv2613c should be involved in lipid metabolism.	P9WMK9	No	lipid metabolism	ML0455,ML0455c	MMAR_2089	MSMEG_2932	Mb2645c				
NC_000962.3	Mycobrowser_v3	CDS	2941189	2943267	.	-	0	Rv2614c	thrS	Involved in translation mechanism [catalytic activity: ATP + L-threonine + tRNA(THR) = AMP + pyrophosphate + L-threonyl-tRNA(THR)].	Probable threonyl-tRNA synthetase ThrS (threonine-tRNA synthetase)(ThrRS) (threonine-tRNA ligase)	Rv2614c, (MT2689, MTCY01A10.20), len: 692 aa. Probable thrS, threonyl-tRNA synthetase (Threonine--tRNA ligase), equivalent to O07151|SYT_MYCLE|THRS|ML0456|MLCL581.18c threonyl-tRNA synthetase from Mycobacterium leprae (702 aa), FASTA scores: opt: 3988, E(): 0, (84.05% identity in 702 aa overlap). Also highly similar to others e.g. Q9L278|THRS from Streptomyces coelicolor (658 aa), FASTA scores: opt: 1982, E(): 5.1e-114, (65.1% identity in 659 aa overlap); P56881|SYT_THETH|THRS from Thermus aquaticus (subsp. thermophilus) (659 aa), FASTA scores: opt: 1551, E(): 1.5e-87, (46.5% identity in 650 aa overlap); P00955|SYT_ECOLI from Escherichia coli (642 aa), FASTA scores: opt: 946, E(): 0, (40.7% identity in 612 aa overl ap); etc. Contains PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2. Belongs to class-II aminoacyl-tRNA synthetase family. Cofactor: binds 1 zinc ion (by similarity).	P9WFT5	No	information pathways	ML0456,ML0456c	MMAR_2088	MSMEG_2931	Mb2646c				
NC_000962.3	Mycobrowser_v3	CDS	2948636	2949457	.	+	0	Rv2622	Rv2622	Causes methylation	Possible methyltransferase (methylase)	Rv2622, (MTCY01A10.10c), len: 273 aa. Possible methyltransferase, similar in part to others e.g. AAK75664|SP1578 putative methyltransferase from Streptococcus pneumoniae (252 aa), FASTA scores: opt: 406, E(): 6.6e-18, (32.65% identity in 251 aa overlap); Q9F8B8 methyltransferase from Streptococcus agalactiae (254 aa), FASTA scores: opt: 381, E(): 2.3e-16, (31.75% identity in 252 aa overlap); Q9RJB6|SCF91.08 putative methyltransferase from Streptomyces coelicolor (231 aa), FASTA scores: opt: 159, E(): 0.0091, (33.1% identity in 151 aa overlap); etc. Also similar in part to several hypothetical proteins e.g. Q99YR0|SPY1582 hypothetical protein from Streptococcus pyogenes (251 aa), FASTA scores: opt: 397, E(): 2.3e-17, (36.3% identity in 248 aa overlap).	I6XES4	No	intermediary metabolism and respiration		MMAR_2078	MSMEG_5310	Mb2655				
NC_000962.3	Mycobrowser_v3	CDS	2949593	2950486	.	+	0	Rv2623	TB31.7	Function unknown	Universal stress protein family protein TB31.7	Rv2623, (MTCY01A10.09c), len: 297 aa. TB31.7, universal stress protein family protein, highly similar to hypothetical proteins from Mycobacterium tuberculosis e.g. Q10851|YK05_MYCTU|Rv2005c|MT2061|MTCY39.12 (295 aa), FASTA scores: opt: 1076, E(): 1.4e-60, (55.25% identity in 295 aa overlap); O53472|Rv2026c|MTV018.13c (294 aa), FASTA scores: opt: 988, E(): 4.8e-55, (51.5% identity in 295 aa overlap); Q10862|YJ96_MYCTU|Rv1996|MT2052|MTCY39.23c (317 aa), FASTA scores: opt: 688, E(): 4.1e-36, (45.1% identity in 315 aa overlap); etc. Also similar to several Streptomyces proteins e.g. Q9RIZ8|SCJ1.16c conserved hypothetical protein from Streptomyces coelicolor (294 aa), FASTA scores: opt: 407, E(): 2e-18, (32.65% identity in 303 aa overlap); and other bacterial hypothetical proteins e.g. Q9HPP5|VNG1536 from Halobacterium sp (147 aa), FASTA scores: opt: 180, E(): 0.00022, (31.65% identity in 139 aa overlap). Predicted possible vaccine candidate (See Zvi et al., 2008). Binds ATP.	P9WFD7	No	virulence, detoxification, adaptation		MMAR_2077	MSMEG_3945	Mb2656				
NC_000962.3	Mycobrowser_v3	CDS	2977231	2978658	.	-	0	Rv2655c	Rv2655c	Unknown	Possible PhiRv2 prophage protein	Rv2655c, (MTCY441.24c), len: 475 aa. Hypothetical protein, possibly phiRv2 phage protein (putative primase-like protein) (see citation below). C-terminus similar to P22875|YXIS_SACER hypothetical 28.9 KDA protein (probably does not play a direct role in plasmid integration or excision) from Saccharopolyspora erythraea (Streptomyces erythraeus) plasmid pSE211 (263 aa), FASTA scores: opt: 389, E(): 2.7e-15, (33.45% identity in 269 aa overlap). Weak similarity in N-terminus to O06608|MTCY336.22|Rv1582c Probable phiRV1 phage protein from Mycobacterium tuberculosis (471 aa), FASTA scores: opt: 133, E(): 2.5, (36.0% identity in 75 aa overlap).	I6Y1F0	No	insertion seqs and phages								
NC_000962.3	Mycobrowser_v3	CDS	2957572	2958870	.	+	0	Rv2631	Rv2631	Function unknown	Conserved hypothetical protein	Rv2631, (MTCY441.01, MTCY01A10.01c), len: 432 aa. Conserved hypothetical protein, highly similar to several conserved hypothetical proteins from various species e.g. O29399|AF0862 conserved hypothetical protein from Archaeoglobus fulgidus (482 aa), FASTA scores: opt: 1496, E(): 2.1e-80, (52.3% identity in 432 aa overlap) (has its N-terminus longer 30 aa); O27634|MTH1597 conserved protein from Methanothermobacter thermautotrophicus (488 aa), FASTA scores: opt: 1428, E(): 2.1e-76, (50.9% identity in 432 aa overlap); Q9YB37|APE1758 hypothetical 53.7 KDA protein APE1758 from Aeropyrum pernix (483 aa), FASTA scores: opt: 1422, E(): 4.6e-76, (49.3% identity in 432 aa overlap) (has its N-terminus longer 30 aa); etc. Equivalent to AAK47022 from Mycobacterium tuberculosis strain CDC1551 (432 aa). 3' part extended since first submission (+175 aa).	P9WGW5	No	conserved hypotheticals	ML2103,ML2103c			Mb2664				
NC_000962.3	Mycobrowser_v3	CDS	2963586	2964242	.	+	0	Rv2637	dedA	Unknown	Possible transmembrane protein DedA	Rv2637, (MTCY441.07), len: 218 aa. Possible dedA, transmembrane protein, equivalent to Q49642|YQ37_MYCLE|ML0467|MLCL581.27|B1177_C2_172/B1177_C1_140 hypothetical 23.1 KDA protein (potential integral membrane protein, belongs to the DedA family) from Mycobacterium leprae (214 aa), FASTA scores: opt: 1160, E(): 4.4e-64, (82.75% identity in 209 aa overlap); and O69601|Y364_MYCLE|ML0287|MLCB4.30 hypothetical protein (potential integral membrane protein) (222 aa), FASTA scores: opt: 292, E(): 6.6e-11, (32.25% identity in 189 aa overlap). Also highly similar to other membrane proteins e.g. CAC42863|SCBAC36F5.27c putative integral membrane from Streptomyces coelicolor (211 aa), FASTA scores: opt: 837, E(): 2.6e-44, (59.2% identity in 201 aa overlap); Q55705|Y232_SYNY3|SLR0232 potential integral membrane protein from Synechocystis sp. strain PCC 6803 (218 aa), FASTA scores: opt: 415, E(): 1.9e-18, (37.85% identity in 206 aa overlap); Q9RV63|DR1167 DEDA protein from Deinococcus radiodurans (200 aa); P09548|DEDA_ECOLI|B2317|Z3579|ECS3201 DEDA protein (DSG-1 protein) from Escherichia coli strains K12 and O157:H7 (219 aa), blast scores: 178, E(): 1.8e-13, Identities = 53/175 (30%); etc. Also similar to O06314|Y364_MYCTU|Rv0364|MT0380|MTCY13E10.26 hypothetical 24.5 KDA protein (potential integral membrane protein) from Mycobacterium tuberculosis (227 aa), FASTA scores: opt: 293, E(): 5.8e-11, (35.85% identity in 184 aa overlap). Belongs to the DedA family.	P9WP07	No	cell wall and cell processes	ML0467	MMAR_2063		Mb2670				
NC_000962.3	Mycobrowser_v3	CDS	2965026	2965358	.	-	0	Rv2639c	Rv2639c	Unknown	Probable conserved integral membrane protein	Rv2639c, (MTCY441.09c), len: 110 aa. Probable conserved integral membrane protein, highly similar to many bacterial hypothetical or membrane proteins e.g. Q9X889|YE14_STRCO|SCE15.14 potential integral membrane protein from Streptomyces coelicolor (112 aa), FASTA scores: opt: 597, E(): 3.1e-31, (73.15% identity in 108 aa overlap); Q55939|Y793_SYNY3|SLL0793 potential integral membrane protein from Synechocystis sp. strain PCC 6803 (108 aa), FASTA scores: opt: 341, E(): 4.9e-15, (51.4% identity in 109 aa overlap); O31553|YFJF_BACSU potential integral membrane protein from Bacillus subtilis (109 aa), FASTA scores: opt: 334, E(): 1.4e-14, (47.5% identity in 109 aa overlap); etc.	P9WFN9	No	cell wall and cell processes		MMAR_2961	MSMEG_3252	Mb2672c				
NC_000962.3	Mycobrowser_v3	CDS	2965478	2965837	.	-	0	Rv2640c	Rv2640c	Involved in transcriptional mechanism.	Possible transcriptional regulatory protein (probably ArsR-family)	Rv2640c, (MTCY441.10c), len: 119 aa. Possible transcriptional regulator, arsR family, highly similar to many e.g. Q9L1V5|SC4A9.07 putative ArsR-family transcriptional regulator from Streptomyces coelicolor (117 aa), FASTA scores: opt: 261, E(): 5.6e-10, (47.75% identity in 103 aa overlap); Q9X8X8|SCH35.28c putative transcriptional regulator from Streptomyces coelicolor (122 aa), FASTA scores: opt: 252, E(): 2.2e-09, (37.05% identity in 116 aa overlap); Q9L220|SC1A2.21 putative ArsR-family transcriptional from Streptomyces coelicolor (119 aa), FASTA scores: opt: 252, E(): 2.2e-09, (37.05% identity in 116 aa overlap); P77295|YGAV_ECOLI|B2667 hypothetical transcriptional regulator from Escherichia coli strain K12 (99 aa), FASTA scores: opt: 156, E(): 0.0023, (34.1% identity in 88 aa overlap); etc. Also similar to upstream ORF P71941|Rv2642|MTCY441.12 putative transcriptional regulatory protein from Mycobacterium tuberculosis (126 aa), FASTA scores: opt: 237, E(): 2e-08, (38.55% identity in 109 aa overlap). Contains helix-turn-helix motif at aa 59-80 (Score 1166, +3.16 SD). Belongs to the ArsR family of transcriptional regulators.	I6Y1A7	No	regulatory proteins		MMAR_2058	MSMEG_1175	Mb2673c				
NC_000962.3	Mycobrowser_v3	CDS	2966910	2968406	.	+	0	Rv2643	arsC	Involved in transport of arsenic compounds across the membrane (export): arsenic resistance by an export mechanism. Responsible for the translocation of the substrate across the membrane.	Probable arsenic-transport integral membrane protein ArsC	Rv2643, (MTCY441.13), len: 498 aa. Probable arsC, arsenical resistance transport integral membrane protein, highly similar or similar to others e.g. Q9L1X4|SC3D9.05 possible arsenic resistance membrane transport protein from Streptomyces coelicolor (368 aa), FASTA scores: opt: 1729, E(): 2.2e-96, (74.3% identity in 358 aa overlap); Q9X8Y0|SCH35.26 putative heavy metal resistance membrane protein from Streptomyces coelicolor (369 aa), FASTA scores: opt: 1729, E(): 2.2e-96, (73.8% identity in 359 aa overlap); Q06598|ACR3_YEAST|ACR3|YPR201W|P9677.2 arsenical-resistance protein from Saccharomyces cerevisiae (Baker's yeast) (404 aa), FASTA scores: opt: 591, E(): 4e-28, (36.6% identity in 380 aa overlap); etc. Belongs to the ACR3 family.	I6X4W4	No	cell wall and cell processes		MMAR_2055	MSMEG_1172	Mb2676				
NC_000962.3	Mycobrowser_v3	CDS	2979691	2980818	.	-	0	Rv2659c	Rv2659c	Sequence integration. Integrase is necessary for integration of a phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome.	Probable PhiRv2 prophage integrase	Rv2659c, (MTCY441.28c), len: 375 aa. Probable integrase, phiRv2 phage protein: putative member of the phage integrase family of tyrosine recombinases (see Hatfull 2000), highly similar to others e.g. P22884|VINT_BPML5|33|int from Mycobacteriophage L5 (371 aa), FASTA scores: opt: 836, E(): 1.2e-44, (39.0% identity in 372 aa overlap); Q38361|VINT_BPMD2|33|int from Mycobacteriophage D29 (333 aa), FASTA scores: opt: 786, E(): 1.4e-41, (40.55% identity in 338 aa overlap); etc. Seems belongs to the 'phage' integrase family.	P9WMB3	No	insertion seqs and phages		MMAR_4848						
NC_000962.3	Mycobrowser_v3	CDS	2983071	2983874	.	+	0	Rv2666	Rv2666	Required for the transposition of the insertion element IS1081.	Probable transposase for insertion sequence element IS1081 (fragment)	Rv2666, (MTCY441.35), len: 267 aa. Probable transposase (fragment), identical in region of overlap to P35882|TRA1_MYCBO|TRA1_MYCTU transposase for insertion sequence element IS1081 from Mycobacterium tuberculosis or bovis (415 aa). Last 4 codons not part of gene. Contains PS01007 Transposases, Mutator family, signature.	P71963	No	insertion seqs and phages				Mb2685				
NC_000962.3	Mycobrowser_v3	CDS	2985283	2985753	.	+	0	Rv2669	Rv2669	Acetylation, substrate unknown	GCN5-related N-acetyltransferase	Rv2669, (MTCY441.38), len: 156 aa. Probable acetyltransferase. Contains GNAT (Gcn5-related N-acetyltransferase) domain. See Vetting et al. 2005. Similarity to several proteins e.g. Q9A6M0|CC2073 acetyltransferase (GNAT family) from Caulobacter crescentus (178 aa), FASTA scores: opt: 242, E(): 1.2e-09, (30.9% identity in 165 aa overlap); Q99RQ8|SA2159 hypothetical protein similar to transcription repressor of sporulation, septation and degradation paiA from Staphylococcus aureus subsp. aureus N315 (171 aa), FASTA scores: opt: 214, E(): 9.8e-08, (27.5% identity in 160 aa overlap); BAB58531|SAV2369 hypothetical 20.1 KDA protein from Staphylococcus aureus subsp. aureus Mu50 (171 aa), FASTA scores: opt: 214, E(): 9.8e-08, (27.5% identity in 160 aa overlap); P21340|PAIA_BACSU|O32112 protease synthase and sporulation from Bacillus subtilis (171 aa), FASTA scores: opt: 209, E(): 2.1e-07, (22.85% identity in 162 aa overlap); etc.	P9WQG5	No	intermediary metabolism and respiration	ML1342,ML1342c	MMAR_5575	MSMEG_2789	Mb2688				
NC_000962.3	Mycobrowser_v3	CDS	2985731	2986840	.	-	0	Rv2670c	Rv2670c	Function unknown	Conserved hypothetical protein	Rv2670c, (MTCY441.39c), len: 369 aa. Conserved hypothetical protein, equivalent, but longer 164 aa, to O05683|MLC1351.22c hypothetical 17.3 KDA protein from Mycobacterium leprae (160 aa), FASTA scores: opt: 847, E(): 1.2e-45, (82.4% identity in 159 aa overlap). And highly similar to Q9X824|SC9B1.04c putative ATP/GTP-binding integral membrane protein from Streptomyces coelicolor (350 aa), FASTA scores: opt: 1169, E(): 2e-65, (56.85% identity in 343 aa overlap); and Q9RWB0|DR0759 conserved hypothetical protein from Deinococcus radiodurans (351 aa), FASTA scores: opt: 859, E(): 4e-46, (45.9% identity in 331 aa overlap). Also some similarity with other proteins e.g. P46442|YHCM_ECOLI|AAG58360|BAB37528 hypothetical protein from Escherichia coli strains K12 and O157:H7 (375 aa), FASTA scores: opt: 237, E(): 2.1e-07, (28.0% identity in 325 aa overlap); Q9JRK2|NMA1520|NMB1306 putative nucleotide-binding protein from Neisseria meningitidis (serogroup a and B) (383 aa), FASTA scores: opt: 221, E(): 2.1e-06, (27.8% identity in 356 aa overlap); Q9HVX7|PA4438 hypothetical protein from Pseudomonas aeruginosa (364 aa), FASTA scores: opt: 211, E(): 8.5e-06, (28.9% identity in 353 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop).	I6Y1G3	No	conserved hypotheticals	ML1341	MMAR_2046	MSMEG_2788	Mb2689c				
NC_000962.3	Mycobrowser_v3	CDS	3001983	3003269	.	+	0	Rv2685	arsB1	Thought to be involved in transport of arsenical compounds across the membrane (export): arsenic resistance by an export mechanism. Responsible for the translocation of the substrate across the membrane.	Probable arsenic-transport integral membrane protein ArsB1	Rv2685, (MTCY05A6.06), len: 428 aa. Probable arsB1, arsenic-transport integral membrane protein, equivalent to P46838|AG45_MYCLE|ML1036 46 KDA probable integral membrane protein (antigen 45, a transmembrane protein related to arsenical pumps) from Mycobacterium leprae (429 aa), FASTA scores: opt: 2048, E(): 7.3e-120, (74.25% identity in 427 aa overlap); and downstream ORF O07186|YQ84_MYCTU|ARSA|Rv2684|MT2758|MTCY05A6.05 probable integral membrane protein ARSA from Mycobacterium tuberculosis (429 aa), FASTA scores: opt: 2154, E(): 1.9e-126, (76.8% identity in 427 aa overlap). Also highly similar to other proteins e.g. O59575|PH1912 hypothetical 46.0 KDA protein from Pyrococcus horikoshii (424 aa), FASTA scores: opt: 1075, E(): 1.9e-59, (43.55% identity in 427 aa overlap); Q9UY19|PAB1107 transport protein from Pyrococcus abyssi (425 aa), FASTA scores: opt: 1062, E(): 1.3e-58, (41.8% identity in 428 aa overlap); Q9KDI2|BH1231 hypothetical 46.0 KDA protein from Bacillus halodurans (428 aa), FASTA scores: opt: 993, E(): 2.4e-54, (39.55% identity in 430 aa overlap); etc. Belongs to the NADC/P/PHO87 family of transporters, P subfamily. Note that previously known as arsB.	P9WPD7	No	cell wall and cell processes		MMAR_2029	MSMEG_0851	Mb2704				
NC_000962.3	Mycobrowser_v3	CDS	2989291	2990592	.	+	0	Rv2673	aftC	Involved in the biosynthesis of the mycobacterial cell wall arabinan	Possible arabinofuranosyltransferase AftC	Rv2673, (MTCY441.42), len: 433 aa. Possible aftC, arabinofuranosyltransferase (See Birch et al., 2008). Predicted to be in the GT-C superfamily of glycosyltransferases (See Liu and Mushegian, 2003). Possible conserved integral membrane protein, equivalent to MLC1351.25|ML1338 possible conserved integral membrane protein from Mycobacterium leprae (440 aa), FASTA scores: opt: 2410, E(): 5.3e-143, (82.05% identity in 434 aa overlap); and showing some similarity with Q9CBX0|ML1504 probable conserved membrane protein from Mycobacterium leprae (430 aa), FASTA scores: opt: 159, E(): 0.014, (24.4% identity in 340 aa overlap). Also similar to Q53873|SC6G4.11 putative integral membrane protein from Streptomyces coelicolor (411 aa), FASTA scores: opt: 383, E(): 1.4e-16, (29.6% identity in 422 aa overlap); and with weak similarity with P71061|YVFB hypothetical protein from Bacillus subtilis (396 aa), FASTA scores: opt: 136, E(): 0.36, (24.35% identity in 279 aa overlap); and BAB60134|TVG1014811 hypothetical protein from Thermoplasma volcanium (695 aa), FASTA scores: opt: 133, E(): 0.85, (26.45% identity in 280 aa overlap). Shows also some similarity with O06557|Rv1159|MTCI65.26 hypothetical 47.1 KDA protein from Mycobacterium tuberculosis (431 aa), FASTA scores: opt: 149, E(): 0.059, (22.45% identity in 410 aa overlap); and O53515|Rv2181|MTV021.14 putative membrane protein from Mycobacterium tuberculosis (427 aa), FASTA scores: opt: 129, E(): 1, (24.8% identity in 367 aa overlap).	P9WMZ7	No	cell wall and cell processes	ML1338,ML1338c	MMAR_2043	MSMEG_2785	Mb2692				
NC_000962.3	Mycobrowser_v3	CDS	2992634	2993992	.	-	0	Rv2677c	hemY	Involved in heme and porphyrin biosynthesis (at the penultimate step). Catalyzes the 6-electron oxidation of protoporphyrinogen IX to form protoporphyrin IX [catalytic activity: protoporphyrinogen-IX + O(2) = protoporphyrin-IX + H(2)O(2)].	Probable protoporphyrinogen oxidase HemY (protoporphyrinogen-IX oxidase) (protoporphyrinogenase) (PPO)	Rv2677c, (MT2751, MTV010.01c), len: 452 aa. Probable hemY, protoporphyrinogen oxidase, equivalent to Q50008|PPOX_MYCLE|HEMY|ML1044 protoporphyrinogen oxidase from Mycobacterium leprae (451 aa), FASTA scores: opt: 2211, E(): 8.8e-118, (75.4% identity in 455 aa overlap). Also similar to others e.g. Q9RV99|DR1130 from Deinococcus radiodurans (462 aa), FASTA scores: opt: 523, E(): 2.7e-22, (29.8% identity in 453 aa overlap); O32434|PPOX_PROFR|HEMY from Propionibacterium freudenreichii shermanii (527 aa), FASTA scores: opt: 344, E(): 4e-12, (32.1% identity in 495 aa overlap); P32397|PPOX_BACSU|HEMY|HEMG from Bacillus subtilis (470 aa), FASTA scores: opt: 305, E(): 5.9e-10, (26.8% identity in 463 aa overlap); etc. Belongs to the protoporphyrinogen oxidase family. Cofactor: contains one FAD per homodimer.	P9WMP1	No	intermediary metabolism and respiration	ML1044	MMAR_2039	MSMEG_2781	Mb2696c				
NC_000962.3	Mycobrowser_v3	CDS	2993989	2995062	.	-	0	Rv2678c	hemE	Involved in porphyrin biosynthesis [catalytic activity: uroporphyrinogen III = coproporphyrinogen + 4 CO(2)].	Probable uroporphyrinogen decarboxylase HemE (uroporphyrinogen III decarboxylase) (URO-D) (UPD)	Rv2678c, (MTV010.02c), len: 357 aa. Probable hemE, uroporphyrinogen decarboxylase, equivalent to P46809|DCUP_MYCLE|heme|ML1043 uroporphyrinogen decarboxylase from Mycobacterium leprae (357 aa), FASTA scores: opt: 2017, E(): 8.2e-111, (83.75% identity in 357 aa overlap). Also highly similar to many e.g. O69861|DCUP_STRCO|heme|SC1C3.19 from Streptomyces coelicolor (355 aa), FASTA scores: opt: 1165, E(): 5.6e-61, (58.15% identity in 349 aa overlap); P32395|DCUP_BACSU|heme from Bacillus subtilis (353 aa), FASTA scores: opt: 859, E(): 4.5e-43, (44.1% identity in 356 aa overlap); Q9RV96|DCUP_DEIRA|heme|DR1133 from Deinococcus radiodurans (344 aa), FASTA scores: opt: 850, E(): 1.5e-42, (43.0% identity in 349 aa overlap); etc. Equivalent to AAK47067 from Mycobacterium tuberculosis strain CDC1551 (372 aa) but shorter 15 aa. Contains PS00907 Uroporphyrinogen decarboxylase signature 2. Belongs to the uroporphyrinogen decarboxylase family.	P9WFE1	No	intermediary metabolism and respiration	ML1043	MMAR_2038	MSMEG_2780	Mb2697c				
NC_000962.3	Mycobrowser_v3	CDS	2996105	2996737	.	+	0	Rv2680	Rv2680	Function unknown	Conserved protein	Rv2680, (MTV010.04), len: 210 aa. Conserved protein, equivalent to Q50005|ML1041|U1764V hypothetical protein from Mycobacterium leprae (196 aa), FASTA scores: opt: 1136, E(): 9.7e-66, (83.95% identity in 193 aa overlap). Also similar to O69860|SC1C3.18c hypothetical 24.7 KDA protein from Streptomyces coelicolor (238 aa), FASTA scores: opt: 516, E(): 5.7e-26, (45.5% identity in 189 aa overlap); and similar in part to Q9I6V4|PA0178 probable two-component sensor from Pseudomonas aeruginosa (639 aa), FASTA scores: opt: 120, E(): 3.1, (33.05% identity in 115 aa overlap); and a few other proteins. Equivalent to AAK47069 from Mycobacterium tuberculosis strain CDC1551 (178 aa) but longer 32 aa; and N-terminus highly similar to N-terminus of AAK48352|MT3984 hypothetical 4.2 KDA protein from Mycobacterium tuberculosis strain CDC1551 (38 aa), FASTA scores: opt: 102, E(): 3.6, (62.05% identity in 29 aa overlap). Nucleotide position 2996194 in the genome sequence has been corrected, T:A resulting in V30V.	O86317	No	conserved hypotheticals	ML1041,ML1041c	MMAR_2036	MSMEG_2779	Mb2699				
NC_000962.3	Mycobrowser_v3	CDS	3010024	3010686	.	+	0	Rv2692	ceoC	Part of a potassium transport system.	TRK system potassium uptake protein CeoC	Rv2692, (MTCY05A6.13), len: 220 aa. CeoC (alternate gene names: trkA and trkB), TRK system potassium uptake protein (see citation below), highly similar to others e.g. O54141|SC2E9.16c from Streptomyces coelicolor (226 aa), FASTA scores: opt: 870, E(): 9.4e-48, (58.8% identity in 216 aa overlap); Q58505|TRKA_METJA|MJ1105 from Methanococcus jannaschii (218 aa), FASTA scores: opt: 361, E(): 9.7e-16, (29.8% identity in 218 aa overlap); O27333|TRKA_METTH|MTH1265 from Methanobacterium thermoautotrophicum (216 aa), FASTA scores: opt: 326, E(): 1.5e-13, (30.1% identity in 216 aa overlap); etc. Also similar to downstream orf O07193|CEOB|TRKA|Rv2691|MTCY05A6.12 TRK system potassium uptake protein from Mycobacterium tuberculosis (227 aa), FASTA scores: opt: 259, E(): 2.6e-09, (26.55% identity in 226 aa overlap). Contains a motif common to NAD+ binding pockets (see citation below). Belongs to the TrkA family.	P9WFZ3	No	cell wall and cell processes	ML1033,ML1033c	MMAR_2022	MSMEG_2769	Mb2711				
NC_000962.3	Mycobrowser_v3	CDS	3013683	3014147	.	-	0	Rv2697c	dut	Involved in biosynthesis of thymidylate. This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA [catalytic activity: dUTP + H(2)O = dUMP + pyrophosphate].	Probable deoxyuridine 5'-triphosphate nucleotidohydrolase Dut (dUTPase) (dUTP pyrophosphatase) (deoxyuridine 5'-triphosphatase) (dUTP diphosphatase) (deoxyuridine-triphosphatase)	Rv2697c, (MT2771, MTCY05A6.18c), len: 154 aa. Probable dut, deoxyuridine 5'-triphosphate nucleotidohydrolase (see citation below), equivalent to Q49992|DUT_MYCLE|ML1028 deoxyuridine 5'-triphosphate nucleotidohydrolase from Mycobacterium leprae (154 aa), FASTA scores: opt: 928, E(): 2.1e-51, (90.25% identity in 154 aa overlap). Also highly similar to others e.g. O54134|DUT_STRCO|SC2E9.09 from Streptomyces coelicolor (183 aa), FASTA scores: opt: 534, E(): 1.2e-26, (56.1% identity in 148 aa overlap); O66592|DUT_AQUAE|AQ_220 from Aquifex aeolicus (150 aa), FASTA scores: opt: 398, E(): 3.3e-18, (48.05% identity in 152 aa overlap); Q9X3X5|DUT_ZYMMO from Zymomonas mobilis (146 aa), FASTA scores: opt: 396, E(): 4.4e-18, (49.0% identity in 147 aa overlap); etc. Belongs to the dUTPase family.	P9WNS5	No	intermediary metabolism and respiration	ML1028	MMAR_2017	MSMEG_2765	Mb2716c				
NC_000962.3	Mycobrowser_v3	CDS	3015203	3015853	.	+	0	Rv2700	Rv2700	Unknown	Possible conserved secreted alanine rich protein	Rv2700, (MTCY05A6.21), len: 216 aa. Possible secreted ala-rich protein, equivalent to Q4998|ML1025|U1764H possible secreted protein from Mycobacterium leprae (216 aa), FASTA scores: opt: 1198, E(): 1.2e-65, (82.4% identity in 216 aa overlap). Also showing some similarity with Q9AK75|2SCD60.08c conserved hypothetical protein from Streptomyces coelicolor (204 aa), FASTA scores: opt: 193, E(): 8.9e-05, (31.25% identity in 192 aa overlap). A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	I6Y1I5	No	cell wall and cell processes	ML1025,ML1025c	MMAR_2014	MSMEG_2761	Mb2719				
NC_000962.3	Mycobrowser_v3	CDS	3016858	3017655	.	+	0	Rv2702	ppgK	Catalyzes the phosphorylation of glucose using polyphosphate or ATP as the phosphoryl donor. GTP, UTP and CTP can replace ATP as phosphoryl donor [catalytic activity: (phosphate)(N) + D-glucose = (phosphate)(N-1) + D-glucose 6-phosphate].	Polyphosphate glucokinase PpgK (polyphosphate-glucose phosphotransferase)	Rv2702, (MTCY05A6.23), len: 265 aa. PpgK, polyphosphate glucokinase (see citations below), equivalent, but shorter 60 aa, to Q49988|PPGK_MYCLE|ML1023|U1764FG polyphosphate glucokinase from Mycobacterium leprae (324 aa), FASTA scores: opt: 1411, E(): 5.6e-80, (82.8% identity in 262 aa overlap). Also highly similar (or just similar) to others e.g. Q9ADE8|PPGK from Streptomyces coelicolor (246 aa), FASTA scores: opt: 912, E(): 3e-49, (57.3% identity in 239 aa overlap); Q9AGV8|PPGK from Corynebacterium ammoniagenes (Brevibacterium ammoniagenes) (277 aa), FASTA scores: opt: 890, E(): 7.5e-48, (57.75% identity in 239 aa overlap); P40184|GLK_STRCO|SC6E10.20c from Streptomyces coelicolor (317 aa), FASTA scores: opt: 233, E(): 3.2e-07, (31.3% identity in 163 aa overlap); etc.	P9WIN1	No	intermediary metabolism and respiration	ML1023,ML1023c	MMAR_2012	MSMEG_2760	Mb2721				
NC_000962.3	Mycobrowser_v3	CDS	3022461	3023432	.	+	0	Rv2710	sigB	The sigma factor is an initiation factor that promotes attachment of the RNA polymerase to specific initiation sites and then is released. May control the regulons of stationary phase and general stress resistance. Seems to be regulated by sigh (Rv3223c product) and SIGE (Rv1221 product). Seems to regulate KATG|Rv1908c and the heat-shock response.	RNA polymerase sigma factor SigB	Rv2710, (MTCY05A6.31), len: 323 aa. SigB (formerly known as mysB), RNA polymerase sigma factor (see citations below), equivalent to Q59531|ML1014 RNA polymerase sigma factor from Mycobacterium leprae (319 aa), FASTA scores: opt: 1935, E(): 1.9e-109, (96.2% identity in 316 aa overlap). Also highly similar to others e.g. Q59553|MYSB from Mycobacterium smegmatis (319 aa), FASTA scores: opt: 1874, E(): 9.1e-106, (92.4% identity in 316 aa overlap); Q9ANT6|SIGB from Brevibacterium flavum (331 aa), FASTA scores: opt: 1525, E(): 9.9e-85, (78.9% identity in 303 aa overlap); Q60158|RPOV from Mycobacterium bovis (528 aa), FASTA scores: opt: 1246, E(): 9.3e-68, (62.85% identity in 315 aa overlap); etc. Contains sigma-70 factors family signatures 1 and 2 (PS00715 and PS00716). And contains possible helix-turn-helix motif at aa 282-303 (Score 1887, +5.61 SD). Belongs to the sigma-70 factor family.	P9WGI5	No	information pathways	ML1014,ML1014c	MMAR_2003	MSMEG_2752	Mb2729				
NC_000962.3	Mycobrowser_v3	CDS	3034909	3036102	.	+	0	Rv2723	Rv2723	Unknown	Probable conserved integral membrane protein	Rv2723, (MTCY154.03), len: 397 aa. Probable conserved integral membrane protein, highly similar to others e.g. Q9Z503|SCC54.23c putative integral membrane export protein from Streptomyces coelicolor (333 aa), FASTA scores: opt: 883, E(): 2.4e-48, (46.4% identity in 332 aa overlap); Q9RD18|SCM1.25c putative integral membrane protein from Streptomyces coelicolor (316 aa), FASTA scores: opt: 865, E(): 3.1e-47, (47.55% identity in 324 aa overlap); P96554|Y319_MYXXA integral membrane protein (probable) from Myxococcus xanthus (319 aa), FASTA scores: opt: 626, E(): 3.4e-32, (34.65% identity in 323 aa overlap); P42601|YGJT_ECOLI|B3088 from Escherichia coli strain K12 integral membrane protein (probable) (321 aa), FASTA scores: opt: 541, E(): 7.7e-27, (35.1% identity in 279 aa overlap); etc.	P9WG93	No	cell wall and cell processes		MMAR_1990		Mb2742				
NC_000962.3	Mycobrowser_v3	CDS	3025441	3026847	.	+	0	Rv2713	sthA	Conversion of NADPH, generated by peripheral catabolic pathways, to NADH, which can enter the respiratory chain for energy generation [catalytic activity: NADPH + NAD(+) = NADP(+) + NADH].	Probable soluble pyridine nucleotide transhydrogenase SthA (STH) (NAD(P)(+) transhydrogenase [B-specific]) (nicotinamide nucleotide transhydrogenase)	Rv2713, (MT2786, MTCY05A6.34), len: 468 aa. Probable sthA, soluble pyridine nucleotide transhydrogenase, highly similar to others e.g. Q983E2|MLR8366 from Rhizobium loti (Mesorhizobium loti) (481 aa), FASTA scores: opt: 1447, E(): 4.1e-78, (49.55% identity in 460 aa overlap); P27306|STHA_ECOLI|STH|UDHA|B3962 from Escherichia coli strain K12 (465 aa), FASTA scores: opt: 1267, E(): 1.7e-67, (43.05% identity in 462 aa overlap); O05139|STHA_PSEFL|STH from Pseudomonas fluorescens (463 aa), FASTA scores: opt: 1257, E(): 6.6e-67, (43.8% identity in 461 aa overlap); etc. Also highly similar to CAC46308|SMC00300 putative oxidoreductase protein from Rhizobium meliloti (Sinorhizobium meliloti) (467 aa), FASTA scores: opt: 1466, E(): 3e-79, (49.55% identity in 462 aa overlap). Shows some similarity to MTCY359.04, E(): 3.1e-08; MTCY210.05, E(): 3.4e-08. Contains ATP/GTP-binding site motif A (P-loop; PS00017). Belongs to the pyridine nucleotide-disulfide oxidoreductases class-I. Cofactor: FAD (by similarity).	P9WHH5	No	intermediary metabolism and respiration	ML1012,ML1012c	MMAR_2000	MSMEG_2748	Mb2732				
NC_000962.3	Mycobrowser_v3	CDS	3027065	3028039	.	+	0	Rv2714	Rv2714	Function unknown	Conserved alanine and leucine rich protein	Rv2714, (MTCY05A6.35), len: 324 aa. Conserved ala-, leu-rich protein, equivalent to Q49847|ML1009|B2235_F1_6 hypothetical protein from Mycobacterium leprae (326 aa), FASTA scores: opt: 1881, E(): 5.8e-107, (89.7% identity in 320 aa overlap); and similar to Q49797|MLCB2533.03c|B2126_F1_36 hypothetical protein from Mycobacterium leprae (317 aa), FASTA scores: opt: 376, E(): 1.2e-15, (30.1% identity in 279 aa overlap); and Q9CC38|ML1306 hypothetical protein from Mycobacterium leprae (274 aa), FASTA scores: opt: 367, E(): 3.6e-15, (29.8% identity in 275 aa overlap). Also highly similar to Q9S2K6|SC7H2.11c hypothetical 34.2 KDA protein from Streptomyces coelicolor (312 aa), FASTA scores: opt: 770, E(): 1.4e-39, (40.9% identity in 286 aa overlap); and similar to Q9ADA5|SCI52.04 conserved hypothetical protein from Streptomyces coelicolor (333 aa), FASTA scores: opt: 386, E(): 3e-16, (29.05% identity in 296 aa overlap). Also similar to O33260|Rv2125|MTCY261.21 hypothetical protein from Mycobacterium tuberculosis (292 aa), FASTA scores: opt: 387, E(): 2.3e-16, (29.45% identity in 292 aa overlap).	I6YA29	No	conserved hypotheticals	ML1009,ML1009c	MMAR_1998	MSMEG_2746	Mb2733				
NC_000962.3	Mycobrowser_v3	CDS	3031788	3032498	.	+	0	Rv2720	lexA	Involved in regulation of nucleotide excision repair and sos response. Represses a number of genes involved in the response to DNA damage (sos response), including RECA and LEXA. Has been shown to bind to the 14 bp palindromic sequence 5'-cgaacnnnngttcg-3'. In the presence of single-stranded DNA, RECA interacts with LEXA causing an autocatalytic cleavage which disrupts the DNA-binding part of LEXA, leading to derepression of the sos regulon and eventually DNA repair [catalytic activity: hydrolysis of ala-|-GLY bond in repressor LEXA].	Repressor LexA	Rv2720, (MTCY05A6.41), len: 236 aa. LexA repressor (see citations below), equivalent to Q49848|LEXA_MYCLE|ML1003|B2235_F2_55 LEXA repressor from Mycobacterium leprae (217 aa), FASTA scores: opt: 1255, E(): 7.1e-70, (89.8% identity in 216 aa overlap). Also highly similar to others e.g. O69979|LEXA_STRCO|SC4H2.24c from Streptomyces coelicolor (234 aa), FASTA scores: opt: 1034, E(): 2.6e-56, (70.5% identity in 217 aa overlap); O86847|LEXA_STRCL from Streptomyces clavuligerus (239 aa), FASTA scores: opt: 1021, E(): 1.6e-55, (69.1% identity in 217 aa overlap); Q9KAD3|LEXA_BACHD from Bacillus halodurans (207 aa), FASTA scores: opt: 645, E(): 1.5e-32, (47.9% identity in 213 aa overlap); etc. Belongs to peptidase family S24; also known as the UMUD/LEXA family. Start changed since first submission (+19 aa).	P9WHR7	No	regulatory proteins	ML1003,ML1003c	MMAR_1992	MSMEG_2740	Mb2739				
NC_000962.3	Mycobrowser_v3	CDS	3037427	3038914	.	-	0	Rv2725c	hflX	Possibly a putative GTPase, modulating activity of HFLK and HFLC proteins.	Probable GTP-binding protein HflX	Rv2725c, (MTCY154.05c), len: 495 aa. Probable hflX (hfl for high frequency of lysogenization), GTP-binding protein ,equivalent to Q9CCC0|ML0997 (alias Q49843|HFLX but longer) possible ATP/GTP-binding protein from Mycobacterium leprae (488 aa), FASTA scores: opt: 2562, E(): 1.1e-133, (84.55% identity in 485 aa overlap). Also highly similar to many e.g. Q9XCC1 from Streptomyces fradiae (425 aa), FASTA scores: opt: 1280, E(): 3.2e-63, (57.7% identity in 423 aa overlap); P73965|HFLX|SLR1521 from Synechocystis sp. strain PCC 6803 (534 aa), FASTA scores: opt: 1028, E(): 2.8e-49, (44.7% identity in 414 aa overlap); P25519|HFLX_ECOLI|B4173 from Escherichia coli strain K12 (426 aa), FASTA scores: opt: 916, E(): 3.4e-43, (40.1% identity in 414 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	O33230	No	intermediary metabolism and respiration	ML0997	MMAR_1988	MSMEG_2736	Mb2744c				
NC_000962.3	Mycobrowser_v3	CDS	3039825	3040769	.	-	0	Rv2727c	miaA	Catalyzes the first step in the biosynthesis of 2-methylthio-N6-(delta(2)-isopentenyl)-adenosine (ms[2]I[6]a]) adjacent to the anticodon of several tRNA species [catalytic activity: isopentenyl diphosphate + tRNA = pyrophosphate + tRNA containing 6-isopentenyladenosine].	Probable tRNA delta(2)-isopentenylpyrophosphate transferase MiaA (IPP transferase) (isopentenyl-diphosphate:tRNA isopentenyltransferase) (iptase) (IPPT)	Rv2727c, (MTCY154.07c), len: 314 aa. Probable miaA, tRNA delta(2)-isopentenylpyrophosphate transferase, equivalent to P46811|MIAA_MYCLE|ML0995|B2235_C3_232 tRNA delta(2)-isopentenylpyrophosphate transferase from Mycobacterium leprae (311 aa), FASTA scores: opt: 1679, E(): 3.2e-89, (81.85% identity in 314 aa overlap). Also highly similar to many e.g. O69967|MIAA_STRCO|SC4H2.12 from Streptomyces coelicolor (312 aa), FASTA scores: opt: 1006, E(): 1.2e-50, (55.5% identity in 301 aa overlap); O31795|MIAA_BACSU from Bacillus subtilis (314 aa), FASTA scores: opt: 671, E(): 1.9e-31, (38.55% identity in 293 aa overlap);P16384|MIAA_ECOLI|TRPX|B4171 from Escherichia coli strain K12 and Shigella flexneri (316 aa), FASTA scores: opt: 565, E(): 2.3e-25, (35.2% identity in 307 aa overlap);etc. Contains PS00017 ATP/GTP-binding site motif A (P -loop). Belongs to the IPP transferase family.	P9WJW1	No	intermediary metabolism and respiration	ML0995	MMAR_1986	MSMEG_2734	Mb2746c				
NC_000962.3	Mycobrowser_v3	CDS	3043026	3044378	.	+	0	Rv2731	Rv2731	Function unknown	Conserved alanine and arginine rich protein	Rv2731, (MTCY174.11), len: 450 aa. Conserved ala-, arg-rich protein, highly similar in part to Q49849|B2235_F2_77 hypothetical protein from Mycobacterium leprae (266 aa), FASTA scores: opt: 368, E(): 1e-10, (73.5% identity in 83 aa overlap); and Q9KXN9|SC9C5.35 hypothetical 6.5 KDA protein (fragment) from Streptomyces coelicolor (58 aa), FASTA scores: opt: 214, E(): 0.00065, (51.7% identity in 58 aa overlap). Also similar to Q9L296|SCL2.01 hypothetical 37.4 KDA protein (fragment) from Streptomyces coelicolor (328 aa), FASTA scores: opt: 843, E(): 3.7e-33, (45.95% identity in 296 aa overlap) (but N-terminus shorter); and shows some similarity with other proteins e.g. Q26938 kinetoplast-associated protein (KAP) from Trypanosoma cruzi (1052 aa), FASTA scores: opt: 223, E(): 0.0022, (30.3% identity in 297 aa overlap). Start site chosen by RBS and to avoid overlap, although there are several other possible start sites further upstream.	I6XF60	No	conserved hypotheticals	ML0991,ML0991c	MMAR_1981	MSMEG_2731	Mb2750				
NC_000962.3	Mycobrowser_v3	CDS	3044986	3046524	.	-	0	Rv2733c	Rv2733c	Unknown	Conserved hypothetical alanine, arginine-rich protein	Rv2733c, (MTCY154.13c), len: 512 aa. Conserved hypothetical ala-, arg-rich protein. Similar to other hypothetical proteins from a range of organisms e.g. Y195_MYCLE|Q49842 hypothetical 56.0 kDa protein b2235_c2_195 from Mycobacterium leprae (516 aa), FASTA scores: opt: 2689, E(): 0, (80.4% identity in 509 aa overlap).	P9WK05	No	conserved hypotheticals	ML0989	MMAR_1979	MSMEG_2729	Mb2752c				
NC_000962.3	Mycobrowser_v3	CDS	3052023	3053189	.	-	0	Rv2739c	Rv2739c	Function unknown; probably involved in cellular metabolism.	Possible alanine rich transferase	Rv2739c, (MTV002.04c), len: 388 aa. Possible ala-rich transferase, equivalent to Q49841|ML0985|MLCB33.02c|U2235C possible glycosyltransferase from Mycobacterium leprae (392 aa), FASTA scores: opt: 2112, E(): 5.1e-114, (80.95% identity in 388 aa overlap). Shows some similarity with other transferases e.g. Q9S1V2|SCJ4.21 putative glycosyl transferase from Streptomyces coelicolor (407 aa), FASTA scores: opt: 290, E(): 2e-09, (27.75% identity in 382 aa overlap); Q9RYI3|DRA0329 putative glycosyltransferase from Deinococcus radiodurans (418 aa), FASTA scores: opt: 267, E(): 4.3e-08, (29.05% identity in 396 aa overlap); P96560|GTFC glycosyltransferase from Amycolatopsis orientalis (409 aa), FASTA scores: opt: 253, E(): 2.7e-07, (27.75% identity in 418 aa overlap); etc. Equivalent to AAK47130 from Mycobacterium tuberculosis strain CDC1551 (420 aa) but shorter 32 aa.	O33282	No	intermediary metabolism and respiration	ML0985			Mb2759c				
NC_000962.3	Mycobrowser_v3	CDS	3068189	3068464	.	-	0	Rv2755c	hsdS.1	Implicated in restriction/modification of DNA. Component of type I restriction/modification system. It's possible that the M and S subunits together form a methyltransferase (MTASE) that methylates two adenine residues in complementary strands of bipartite DNA recognition sequence.	Possible type I restriction/modification system specificity determinant (fragment) HsdS.1 (S protein)	Rv2755c, (MTV002.20c), len: 91 aa. Possible hsdS.1, fragment of type I restriction/modification system specificity determinant (S protein), similar to the N-terminus of other hsdS proteins e.g. O34140|HSDS from Klebsiella pneumoniae (439 aa), FASTA scores: opt: 303, E(): 2.1e-13, (46.65% identity in 90 aa overlap); P72419|sty|SBLI from Salmonella typhimurium (434 aa), FASTA scores: opt: 278, E(): 1.1e-11, (47.65% identity in 86 aa overlap); and Q9P9X9|XF2741 from Xylella fastidiosa (412 aa), FASTA scores: opt: 144, E(): 0.015, (31.7% identity in 82 aa overlap). Also some similarity with O33303|Rv2761c|MTV002.26c|HSDS possible type I restriction/modification system specificity determinant from Mycobacterium tuberculosis (364 aa), FASTA scores: opt: 145, E(): 0.012, (29.9% identity in 87 aa overlap). Note that previously known as hsdS'.	I6XF84	No	information pathways				Mb2776c				
NC_000962.3	Mycobrowser_v3	CDS	3057251	3058063	.	-	0	Rv2744c	35kd_ag	Unknown	Conserved 35 kDa alanine rich protein	Rv2744c, (MTV002.09c), len: 270 aa. 35kd_ag, conserved ala-rich protein 35-kd antigen (see O'Connor et al., 1990). N-terminal part is equivalent to Q49840|MLCB33.06c|B2235_C2_187 hypothetical protein from Mycobacterium leprae (167 aa), FASTA scores: opt: 789, E(): 3.4e-35, (85.05% identity in 147 aa overlap); and C-terminal part equivalent to Q49845|MLCB33.05c|B2235_C3_214 hypothetical protein from Mycobacterium leprae (114 aa), FASTA scores: opt: 465, E(): 3.6e-18, (65.8% identity in 114 aa overlap); note that these two proteins from Mycobacterium leprae are adjacent. Shows some similarity with Q55707||Y617_SYNY3|SLL0617 hypothetical 28.9 KDA protein from Synechocystis sp. strain PCC 6803 (267 aa), FASTA scores: opt: 155, E(): 0.19, (23.4% identity in 252 aa overlap); and C-terminus of Q9L4N1|EMM M protein from Streptococcus equisimilis (592 aa), FASTA scores: opt: 165, E(): 0.11, (23.45% identity in 260 aa overlap). C-terminus also similar to AAK45945|MT1676 conserved hypothetical protein from Mycobacterium tuberculosis strain CDC1551 (85 aa), FASTA scores: opt: 159, E(): 0.047, (50.9% identity in 55 aa overlap). Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WHP5	No	conserved hypotheticals	ML0981	MMAR_1971	MSMEG_2695	Mb2765c				
NC_000962.3	Mycobrowser_v3	CDS	3058602	3059231	.	-	0	Rv2746c	pgsA3	Involved in acidic phospholipid biosynthesis. This protein probably catalyzes the committed step to the synthesis of the acidic phospholipids [catalytic activity: CDP-diacylglycerol + glycerol-3-phosphate = CMP + 3-(3-phosphatidyl)-glycerol 1-phosphate].	Probable PGP synthase PgsA3 (CDP-diacylglycerol--glycerol-3-phosphate 3- phosphatidyltransferase) (phosphatidylglycerophosphate synthase)	Rv2746c, (MTV002.11c), len: 209 aa. Probable pgsA3, PGP synthase (see citation below), transmembrane protein, equivalent, but longer 19 aa, to Q49839|O08087|PGSA|ML0979 PGSA from Mycobacterium leprae (193 aa), FASTA scores: opt: 925, E(): 3.7e-53, (77.15% identity in 188 aa overlap). Also highly similar to O86813|PGSA phosphatidylglycerophosphate synthase from Streptomyces coelicolor (263 aa), FASTA scores: opt: 692, E(): 6.6e-38, (57.85% identity in 185 aa overlap) (has its N-terminus longer); and similar to others (generally with N-terminus shorter) e.g. Q99XI0|PGSA|SPY2196 phosphatidylglycerophosphate synthase from Streptococcus pyogenes (180 aa), FASTA scores: opt: 368, E(): 5.4e-17, (39.9% identity in 168 aa overlap); Q9ZE96|PGSA_RICPR|PGSA|RP049 CDP-diacylglycerol--glycerol-3-phosphate 3- phosphatidyltransferase from Rickettsia prowazekii (181 aa), FASTA scores: opt: 343, E(): 2.3e-15, (40.1% identity in 172 aa overlap); P06978|PGSA_ECOLI|PGSA|B1912|Z3000|ECS2650 CDP-diacylglycerol--glycerol-3-phosphate 3- phosphatidyltransferase from Escherichia coli strains K12 and O157:H7 (181 aa), FASTA scores: opt: 322, E(): 5.3e-14, (34.45% identity in 180 aa overlap); etc. Also some similarity to PGSA2|Rv1822|MTCY1A11.21c probable CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase from Mycobacterium tuberculosis (209 aa), FASTA score: (27.1% identity in 166 aa overlap). Contains PS00379 CDP-alcohol phosphatidyltransferases signature. Belongs to the CDP-alcohol phosphatidyltransferase class-I family.	P9WPG3	No	lipid metabolism	ML0979	MMAR_1969	MSMEG_2692	Mb2767c				
NC_000962.3	Mycobrowser_v3	CDS	3062816	3063634	.	+	0	Rv2750	Rv2750	Function unknown; possibly involved in cellular metabolism.	Probable dehydrogenase	Rv2750, (MTV002.15), len: 272 aa. Probable dehydrogenase, highly similar to other dehydrogenases/reductases e.g. Q9L5X5|cox cholesterol oxidase from Nocardioides simplex (Arthrobacter simplex) (270 aa), FASTA scores: opt: 836, E(): 1.8e-43, (55.7% identity in 264 aa overlap); Q9RA05|LIMC carveol dehydrogenase from Rhodococcus erythropolis (277 aa), FASTA scores: opt: 792, E(): 8.6e-41, (48.55% identity in 274 aa overlap); Q9F5J1|SIM-NJ1|SIMD2 putative 3-keto-acyl-reductase from Streptomyces antibioticus (273 aa), FASTA scores: opt: 435, E(): 3.7e-19, (35.75% identity in 263 aa overlap); etc. Also highly similar to AAK44941MT0715 oxidoreductase (short-chain dehydrogenase/reductase family) from Mycobacterium tuberculosis strain CDC1551 (275 aa), FASTA scores: opt: 702, E(): 2.4e-35, (44.45% identity in 270 aa overlap); and similar to many other Mycobacterium tuberculosis dehydrogenases.	P9WGS5	No	intermediary metabolism and respiration	ML0975,ML0975c			Mb2771				
NC_000962.3	Mycobrowser_v3	CDS	3068461	3070083	.	-	0	Rv2756c	hsdM	Implicated in methylation of DNA. Component of type I restriction/modification system. It is possible that the M and S subunits together form a methyltransferase (MTASE) that methylates two adenine residues in complementary strands of bipartite DNA recognition sequence.	Possible type I restriction/modification system DNA methylase HsdM (M protein) (DNA methyltransferase)	Rv2756c, (MTV002.21c), len: 540 aa. Possible hsdM, type I restriction/modification system DNA methylase (M protein), highly similar to others e.g. Q9P9X8|XF2742 from Xylella fastidiosa (519 aa), FASTA scores: opt: 1613, E(): 1.9e-96, (52.3% identity in 543 aa overlap); O34139|HSDM from Klebsiella pneumoniae (539 aa), FASTA scores: opt: 1267, E(): 4.4e-74, (45.9% identity in 549 aa overlap); P72418|sty|SBLI|HSDM from Salmonella typhimurium (539 aa), FASTA scores: opt: 1263, E(): 8e-74, (45.7% identity in 549 aa overlap); etc. Possible alternative start site (GTG) overlapping with termination codon of previous ORF 90 bp upstream. Note that the corresponding endonuclease (M protein) does not appear to be present in Mycobacterium tuberculosis.	O33298	No	information pathways	ML1516,ML1516c	MMAR_1959		Mb2777c				
NC_000962.3	Mycobrowser_v3	CDS	3071546	3072640	.	-	0	Rv2761c	hsdS	Implicated in restriction/modification of DNA. Component of type I restriction/modification system. It is thought that the M and S subunits together form a methyltransferase (MTASE) that methylates two adenine residues in complementary strands of bipartite DNA recognition sequence.	Possible type I restriction/modification system specificity determinant HsdS (S protein)	Rv2761c, (MTV002.26c), len: 364 aa. Possible hsdS, type I restriction/modification system specificity determinant (S protein), similar in part to other hsdS protein (S proteins) e.g. Q9P9X9|XF2741 from Xylella fastidiosa (412 aa), FASTA scores: opt: 252, E(): 7.4e-09, (24.95% identity in 401 aa overlap); N-terminus of Q9RC12 type I S-subunit from Lactobacillus delbrueckii (subsp. lactis) (389 aa), FASTA scores: opt: 232, E(): 1.4e-07, (28.1% identity in 185 aa overlap); N-terminus of P72419|sty|SBLI from Salmonella typhimurium (434 aa), FASTA scores: opt: 221, E(): 8e-07, (28.45% identity in 130 aa overlap); C-terminus of P17222|PRRB_ECOLI from Escherichia coli strain CTR5X (401 aa), FASTA scores: opt: 197, E(): 2.8e-05, (27.05% identity in 148 aa overlap); etc. Seems to belong to type-I restriction system S methylase family.	I6YEB1	No	information pathways	ML1515,ML1515c	MMAR_1960		Mb2782c				
NC_000962.3	Mycobrowser_v3	CDS	3074636	3075373	.	+	0	Rv2765	Rv2765	Function unknown; probably involved in cellular metabolism.	Probable alanine rich hydrolase	Rv2765, (MTV002.30), len: 245 aa. Probable ala-rich hydrolase, similar to various hydrolases or hypothetical proteins e.g. Q9KYM6|SC9H11.13c putative hydrolase from Streptomyces coelicolor (251 aa), FASTA scores: opt: 630, E(): 1.4e-33, (43.1% identity in 246 aa overlap); Q9A5T9|CC2358 dienelactone hydrolase family protein from Caulobacter crescentus (286 aa), FASTA scores: opt: 592, E(): 4.5e-31, (38.45% identity in 242 aa overlap); Q9FCF1|2SCD46.33 putative hydrolase (dienelactone hydrolase family) from Streptomyces coelicolor (254 aa), FASTA scores: opt: 500, E(): 3.9e-25, (37.7% identity in 252 aa overlap); P73163|DLHH_SYNY3|SLL1298 putative carboxymethylenebutenolidase (dienelactone hydrolase) from Synechocystis sp. (strain PCC 6803) (246 aa), FASTA scores: opt: 276, E(): 1.3e-10, (26.95% identity in 230 aa overlap); etc.	I6XF92	No	intermediary metabolism and respiration	ML1520	MMAR_1955	MSMEG_2669	Mb2787				
NC_000962.3	Mycobrowser_v3	CDS	3079309	3080457	.	-	0	Rv2770c	PPE44	Function unknown. May be involved in virulence.	PPE family protein PPE44	Rv2770c, (MTV002.35c), len: 382 aa. PPE44, Member of the Mycobacterium tuberculosis PPE family, highly similar to many e.g. downstream ORF O33310|Rv2768c|MTV002.33c from M. tuberculosis (394 aa), FASTA scores: opt: 1135, E(): 2.2e-53, (62.15% identity in 391 aa overlap); and P96362|Rv1039c|MTCY10G2.10 from Mycobacterium tuberculosis (391 aa), FASTA scores: opt: 1010, E(): 1e-46, (55.95% identity in 395 aa overlap). Equivalent to AAK47159 from Mycobacterium tuberculosis strain CDC1551 (402 aa) but shorter 20 aa. Start changed since first submission (-20 aa).	P9WHZ3	No	PE/PPE		MMAR_1947		Mb2792c				
NC_000962.3	Mycobrowser_v3	CDS	3108416	3110065	.	+	0	Rv2800	Rv2800	Function unknown; probably involved in cellular metabolism.	Possible hydrolase	Rv2800, (MTCY16B7.43c), len: 549 aa. Possible hydrolase, an esterase or an acylase. Similar, but longer in N-terminus, to esterases or acylases e.g. Q9L9D7|COCE cocaine esterase from Rhodococcus sp. MB1 'Bresler 1999' (574 aa), FASTA scores: opt: 510, E(): 3.1e-23, (33.6% identity in 571 aa overlap); Q9L3U2|STTE putative acylase from Streptomyces rochei (Streptomyces parvullus) (554 aa), FASTA scores: opt: 492, E(): 3.7e-22, (34.45% identity in 569 aa overlap); CAC49652|SMB21424 putative esterase or acylase protein from Rhizobium meliloti (Sinorhizobium meliloti) plasmid pSymB (578 aa), FASTA scores: opt: 405, E(): 7.1e-17, (34.45% identity in 569 aa overlap); etc.	I6YEE6	No	intermediary metabolism and respiration	ML1550	MMAR_1910	MSMEG_2644	Mb2823				
NC_000962.3	Mycobrowser_v3	CDS	3081604	3082341	.	-	0	Rv2773c	dapB	Involved in biosynthesis of diaminopimelate and lysine from aspartate semialdehyde (at the second step) [catalytic activity: 2,3,4,5-tetrahydrodipicolinate + NAD(P)(+) = 2,3-dihydrodipicolinate + NAD(P)H].	Dihydrodipicolinate reductase DapB (DHPR)	Rv2773c, (MTV002.38c), len: 245 aa. DapB, dihydrodipicolinate reductase (see Pavelka et al., 1997), highly similar to many e.g. P40110|DAPB_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (248 aa), FASTA scores: opt: 1030, E(): 1.8e-58, (65.45% identity in 246 aa overlap); O86836|DAPB_STRCO|SC9A10.03 from Streptomyces coelicolor (250 aa), FASTA scores: opt: 997, E(): 2.3e-56, (61.15% identity in 247 aa overlap); P42976|DAPB_BACSU from Bacillus subtilis (267 aa), FASTA scores: opt: 608, E(): 1.7e-31, (45.95% identity in 209 aa overlap); P46829|DAPB_MYCBO from Mycobacterium bovis (see Cirillo et al., 1994) (271 aa), FASTA scores: opt: 505, E(): 6.3e-25, (36.2% identity in 246 aa overlap); etc. Belongs to the dihydrodipicolinate reductase family.	P9WP23	No	intermediary metabolism and respiration	ML1527,ML1527c	MMAR_1938	MSMEG_2664	Mb2795c				
NC_000962.3	Mycobrowser_v3	CDS	3083374	3084303	.	-	0	Rv2776c	Rv2776c	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase	Rv2776c, (MTV002.41c), len: 309 aa. Probable oxidoreductase, similar to other oxidoreductases e.g. Q9KZ15|SC10B7.17 putative iron-sulfur oxidoreductase from Streptomyces coelicolor (364 aa), FASTA scores: opt: 846, E(): 1.2e-45, (46.75% identity in 308 aa overlap); O88034|SC5A7.28c iron-sulfur oxidoreductase beta subunit from Streptomyces coelicolor (313 aa), FASTA scores: opt: 745, E(): 2.3e-39, (41.45% identity in 316 aa overlap); P33164|PDR_BURCE|OPHA1 phthalate dioxygenase reductase from Burkholderia cepacia (Pseudomonas cepacia) (321 aa), FASTA scores: opt: 616, E(): 2.9e-31, (33.65% identity in 309 aa overlap); etc. Equivalent to AAK47165 from Mycobacterium tuberculosis strain CDC1551 (363 aa) but shorter 54 aa. Contains PS00197 2Fe-2S ferredoxins, iron-sulfur binding region signature and PS00063 Aldo/keto reductase family putative active site signature. Seems to belong to the 2FE2S plant-type ferredoxin family in the C-terminal section.	O86347	No	intermediary metabolism and respiration	ML1529,ML1529c	MMAR_1933	MSMEG_3676	Mb2798c				
NC_000962.3	Mycobrowser_v3	CDS	3086820	3087935	.	+	0	Rv2780	ald	May play a role in cell wall synthesis as L-alanine is an important constituent of the peptidoglycan layer [catalytic activity: L-alanine + H(2)O + NAD(+) = pyruvate + NH(3) + NADH].	Secreted L-alanine dehydrogenase Ald (40 kDa antigen) (TB43)	Rv2780, (MT2850, MTV002.45), len: 371 aa. Ald, secreted L-alanine dehydrogenase (40 kd antigen); equivalent to Q9CBV6|ALD|ML1532 L-alanine dehydrogenase from Mycobacterium leprae (371 aa), FASTA scores: opt: 2081, E(): 4e-115, (85.45% identity in 371 aa overlap). Also highly similar to others e.g. Q9S227|SCI51.13c from Streptomyces coelicolor (371 aa), FASTA scores: opt: 1575, E(): 2.3e-85, (66.05% identity in 371 aa overlap); Q9K827|BH3180 from Bacillus halodurans (371 aa), FASTA scores: opt: 1341, E(): 1.4e-71, (56.45% identity in 372 aa overlap); Q9RT70|DR1895 from Deinococcus radiodurans (390 aa), FASTA scores: opt: 1319, E(): 2.8e-70, (54.2% identity in 371 aa overlap); etc. Contains PS00836 and PS00837 Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1 and 2. Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WQB1	No	intermediary metabolism and respiration	ML1532	MMAR_1928	MSMEG_2659	Mb2802,Mb2803				
NC_000962.3	Mycobrowser_v3	CDS	3089045	3090361	.	-	0	Rv2782c	pepR	Function unknown; possibly hydrolyzes peptides and/or proteins	Probable zinc protease PepR	Rv2782c, (MTV002.47c), len: 438 aa. Probable pepR, protease/peptidase, equivalent to O32965|YR82_MYCLE|ML0855|MLCB22.26c hypothetical zinc protease from Mycobacterium leprae (445 aa), FASTA scores: opt: 2346, E(): 4.3e-146, (84.3% identity in 421 aa overlap). Also highly similar to others e.g. O86835|YA12_STRCO|SC9A10.02 from Streptomyces coelicolor (459 aa), FASTA scores: opt: 1394, E(): 1.1e-83, (51.9% identity in 416 aa overlap); Q04805|YMXG_BACSU|YMXG from Bacillus subtilis (409 aa), FASTA scores: opt: 1014, E(): 7.9e-59, (37.55% identity in 410 aa overlap); Q9KA85|BH2405 from Bacillus halodurans (413 aa), FASTA scores: opt: 967, E(): 9.6e-56, (38.6% identity in 417 aa overlap); etc. Contains PS00143 Insulinase family, zinc-binding region signature. Belongs to peptidase family M16, also known as the insulinase family. Cofactor: requires divalent cations for activity. Binds zinc. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P9WHT5	No	intermediary metabolism and respiration	ML0855	MMAR_1926	MSMEG_2657	Mb2805c				
NC_000962.3	Mycobrowser_v3	CDS	3212162	3212956	.	-	0	Rv2902c	rnhB	Degrades the ribonucleotide moiety on RNA-DNA hybrid molecules [catalytic activity: endonucleolytic cleavage to 5'- phosphomonoester].	Probable ribonuclease HII protein RnhB (RNase HII)	Rv2902c, (MT2970, MTCY274.33c), len: 264 aa. Probable rnhB, ribonuclease HII, equivalent to O33022|RNH2_MYCLE|RNHB|ML1611|MLCB250.40 ribonuclease HII from Mycobacterium leprae (240 aa), FASTA scores: opt: 1242, E(): 6.9e-72, (76.75% identity in 245 aa overlap). Also similar (but longer ~20 aa) to others e.g. Q9HXY9|RNHB|PA3642 ribonuclease HII from Pseudomonas aeruginosa (201 aa), FASTA scores: opt: 572, E(): 3.1e-29, (52.7% identity in 184 aa overlap); Q9PEI7|RNH2_XYLFA|RNHB|XF1041 ribonuclease HII from Xylella fastidiosa (234 aa), FASTA scores: opt: 556, E(): 3.6e-28, (50.25% identity in 185 aa overlap); P10442|RNH2_ECOLI|RNHB|B0183 ribonuclease HII from Escherichia coli strain K-12 (213 aa), FASTA scores: opt: 519, E(): 7.4e-26, (48.65% identity in 183 aa overlap); etc. Belongs to the RNASE HII family. Cofactor: manganese (by similarity).	P9WH01	No	information pathways	ML1611,ML1611c	MMAR_1806	MSMEG_2442	Mb2926c				
NC_000962.3	Mycobrowser_v3	CDS	3093905	3094900	.	-	0	Rv2786c	ribF	Involved in FAD biosynthesis [catalytic activity 1: ATP + riboflavin = ADP + FMN] [catalytic activity 2: ATP + FMN = diphosphate + FAD].	Probable bifunctional FAD synthetase/riboflavin biosynthesis protein RibF: riboflavin kinase (flavokinase) + FMN adenylyltransferase (FAD pyrophosphorylase) (FAD synthetase)(FAD diphosphorylase) (flavin adenine dinucleotide synthetase)	Rv2786c, (MTV002.51c), len: 331 aa. Probable ribF, FAD synthetase/riboflavin biosynthesis protein, bifunctional enzyme, equivalent to O32968|RIBF|ML0852 riboflavin kinase from Mycobacterium leprae (331 aa), FASTA scores: opt: 1923, E(): 2.3e-115, (87.45% identity in 327 aa overlap). Also highly similar to many e.g. Q59263|RIBF_CORAM from Corynebacterium ammoniagenes (Brevibacterium ammoniagenes) (338 aa), FASTA scores: opt: 899, E(): 5.7e-50, (45.8% identity in 321 aa overlap); Q9Z530|SC9F2.05c from Streptomyces coelicolor (318 aa), FASTA scores: opt: 862, E(): 1.3e-47, (52.45% identity in 324 aa overlap); P08391|RIBF_ECOLI|B0025|Z0029ECS0028 from Escherichia coli strains K12 and O157:H7 (313 aa), FASTA scores: opt: 517, E(): 1.3e-25, (36.05% identity in 305 aa overlap); etc.	I6X5C9	No	intermediary metabolism and respiration	ML0852	MMAR_1921	MSMEG_2653	Mb2809c				
NC_000962.3	Mycobrowser_v3	CDS	3098964	3100169	.	-	0	Rv2790c	ltp1	Possibly catalyzes the transfer of a great variety of lipids between membranes.	Probable lipid-transfer protein Ltp1	Rv2790c, (MTV002.55c), len: 401 aa. Probable ltp1, lipid-transfer protein, highly similar to many eukaryotic sterol-carrier proteins/lipid-transfer protein precursors (see Ossendorp & Wirtz 1993) e.g. O62742|SCP2 sterol carrier protein X from Oryctolagus cuniculus (Rabbit) (547 aa), FASTA scores: opt: 1710, E(): 6e-102, (63.7% identity in 394 aa overlap); Q9QW19 3-oxoacyl-CoA thiolase homolog (fragment) from Rattus sp. (405 aa), FASTA scores: opt: 1696, E(): 3.8e-101, (63.2% identity in 394 aa overlap); P11915|NLTP_RAT|SCP2|SCP-2 nonspecific lipid-transfer protein precursor from Rattus norvegicus (Rat) (547 aa), FASTA scores: opt: 1696, E(): 4.8e-101, (63.2% identity in 394 aa overlap); P32020|NLTP_MOUSE|SCP2|SCP-2 nonspecific lipid-transfer protein precursor from Mus musculus (Mouse) (547 aa), FASTA scores: opt: 1681, E(): 4.3e-100, (62.7% identity in 394 aa overlap); etc. Contains PS00098 Thiolases acyl-enzyme intermediate signature and PS00737 Thiolases signature 2. Also similar to other M. tuberculosis proteins e.g. O06144|Rv1627c|MTCY01B2.19c (402 aa) (35.8% identity in 413 aa overlap).	O33332	No	cell wall and cell processes	ML0850			Mb2813c				
NC_000962.3	Mycobrowser_v3	CDS	3113658	3114812	.	+	0	Rv2807	Rv2807	Function unknown	Conserved hypothetical protein	Rv2807, (MTCY16B7.36c), len: 384 aa. Conserved hypothetical protein, highly similar, but shorter 35 aa, to Q9KK74 hypothetical 47.4 KDA protein from Brevibacterium linens (418 aa), FASTA scores: opt: 1865, E(): 9.4e-116, (69.75% identity in 380 aa overlap); and with similarity with other hypothetical proteins or transposases e.g. Q981U5|MLR9230 protein from Rhizobium loti (Mesorhizobium loti) (504 aa), FASTA scores: opt: 636,, (36.05% identity in 377 aa overlap); CAC47689 putative transposase for insertion sequence ISRM18 from Rhizobium meliloti (Sinorhizobium meliloti) (507 aa), FASTA scores: opt: 553, E(): 6.6e-29, (33.5% identity in 370 aa overlap); etc. Also similar to Rv3128c|MTCY164.38c (336 aa) (47.2% identity in 339 aa overlap); and high similarity at N-terminal region with Rv2805|MTCY16B7.38c (79.2% identity in 101 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P71644	No	conserved hypotheticals				Mb2830				
NC_000962.3	Mycobrowser_v3	CDS	3118224	3119036	.	+	0	Rv2813	Rv2813	Function unknown	Conserved hypothetical protein	Rv2813, (MTCY16B7.30c), len: 270 aa. Conserved hypothetical protein, similar to various proteins (notably secreted proteins) e.g. Q9ZFL2 hypothetical 30.4 KDA protein from Bacillus stearothermophilus (266 aa), FASTA scores: opt: 518, E(): 1.4e-26, (33.85% identity in 266 aa overlap); P45754|GSPA_AERHY|EXEA general secretion pathway protein from Aeromonas hydrophila (547 aa), FASTA scores: opt: 386, E(): 1.1e-17, (32.05% identity in 265 aa overlap); Q9KPC7|VC2445 general secretion pathway protein A from Vibrio cholerae (529 aa), FASTA scores: opt: 366, E(): 2.2e-16, (31.1% identity in 270 aa overlap); Q56674|VC0403 mannose-sensitive hemagglutinin D from Vibrio cholerae (281 aa), FASTA scores: opt: 317, E(): 2.1e-13, (27.85% identity in 262 aa overlap); etc. Also highly similar to AAK40072 Rv2813-like protein from Mycobacterium celatum (270 aa), FASTA scores: opt: 1628, E(): 2.8e-99, (90.75% identity in 270 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6XFD1	No	conserved hypotheticals				Mb2837				
NC_000962.3	Mycobrowser_v3	CDS	3120566	3121552	.	-	0	Rv2814c	Rv2814c	Required for the transposition of the insertion element IS6110.	Probable transposase	Rv2814c, (MTCY16B7.29), len: 328 aa. Probable transposase subunit for IS6110. Identical to many other M. tuberculosis IS6110 transposase subunits. The transposase described here may be made by a frame shifting mechanism during translation that fuses Rv2814c and Rv2815c, the sequence UUUUAAAG (directly upstream of Rv2814c) maybe responsible for such a frameshifting event (see McAdam et al., 1990). Start changed since first submission (+ 16 aa). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WKH9	No	insertion seqs and phages				Mb2838c				
NC_000962.3	Mycobrowser_v3	CDS	3397214	3398290	.	-	0	Rv3037c	Rv3037c	Function unknown	Conserved hypothetical protein	Rv3037c, (MTV012.52c), len: 358 aa. Conserved hypothetical protein, similar in part to others e.g. O86799|SC6G4.36c from Streptomyces coelicolor (426 aa), FASTA scores: opt: 545, E(): 5.5e-27, (36.15% identity in 354 aa overlap); Q9UZW6|PAB0687 from Pyrococcus abyssi (386 aa), FASTA scores: opt: 262, E(): 3.5e-09, (31.0% identity in 200 aa overlap).	P9WJZ3	No	conserved hypotheticals	ML1722,ML1722c	MMAR_1664	MSMEG_2330	Mb3063c				
NC_000962.3	Mycobrowser_v3	CDS	3128253	3128963	.	-	0	Rv2821c	Rv2821c	Function unknown	Conserved hypothetical protein	Rv2821c, (MTCY16B7.21), len: 236 aa. Conserved hypothetical protein, similar to several hypothetical proteins e.g. Q9X2C9|TM1809 conserved hypothetical protein from Thermotoga maritima (247 aa), FASTA scores: opt: 318, E(): 8.2e-15, (39.45% identity in 213 aa overlap); O27152|MTH1080 conserved hypothetical protein from Methanothermobacter thermautotrophicus (245 aa), FASTA scores: opt: 294, E(): 3.9e-13, (34.8% identity in 224 aa overlap); BAB59251|TVG0114661 hypothetical protein from Thermoplasma volcanium (229 aa), FASTA scores: opt: 252, E(): 3.3e-10, (33.8% identity in 225 aa overlap); etc. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WJF9	No	conserved hypotheticals				Mb2845c				
NC_000962.3	Mycobrowser_v3	CDS	3137271	3138020	.	+	0	Rv2831	echA16	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Probable enoyl-CoA hydratase EchA16 (enoyl hydrase) (unsaturated acyl-CoA hydratase) (crotonase)	Rv2831, (MTCY16B7.11c), len: 249 aa. Probable echA16, enoyl-CoA hydratase, similar to others e.g. O23468|AT4G16210 from Arabidopsis thaliana (Mouse-ear cress) (244 aa), FASTA scores: opt: 491, E(): 7.3e-25, (42.1% identity in 190 aa overlap); Q98LI4|MLL1009 from Rhizobium loti (Mesorhizobium loti) (258 aa), FASTA scores: opt: 491, E(): 7.6e-25, (40.75% identity in 248 aa overlap); O07137|ECH8_MYCLE|ML2402|MLCB1306.05c from Mycobacterium leprae (257 aa), FASTA scores: opt: 478, E(): 5.3e-24, (38.05% identity in 226 aa overlap); P76082|PAAF_ECOLI|B1393 from scherichia coli strain K12 (255 aa), FASTA scores: opt: 439, E(): 1.9e-21, (37.55% identity in 221 aa overlap); etc. Also similar to O53418|ECH8_MYCTU|ECHA8|Rv1070c|MT1100|MTV017.23c from Mycobacterium tuberculosis (257 aa), FASTA scores: opt: 471, E(): 1.5e-23, (38.05% identity in 226 aa overlap).	I6YEH6	No	lipid metabolism	ML1552	MMAR_1903	MSMEG_2641	Mb2855				
NC_000962.3	Mycobrowser_v3	CDS	3138099	3139181	.	-	0	Rv2832c	ugpC	Thought to be involved in active transport of Sn-glycerol-3-phosphate across the membrane (import). Responsible for energy coupling to the transport system.	Probable Sn-glycerol-3-phosphate transport ATP-binding protein ABC transporter UgpC	Rv2832c, (MTCY16B7.10), len: 360 aa. Probable ugpC, Sn-glycerol-3-phosphate transport ATP-binding protein ABC transporter (see Braibant et al., 2000), similar to others: CAC48805 probable glycerol-3-phosphate ABC transporter ATP-binding protein from Rhizobium meliloti (Sinorhizobium meliloti) plasmid pSymB (349 aa), FASTA scores: opt: 1018, E(): 4.1e-53, (48.6% identity in 356 aa overlap); Q98G42|MLL3499|UGPC SN-glycerol-3-phosphate transport ATP-binding protein from Rhizobium loti (Mesorhizobium loti) (366 aa), FASTA scores: opt: 1016, E(): 5.6e-53, (48.5% identity in 367 aa overlap). But also highly similar to many msiK proteins, ABC transporter ATP-binding proteins possibly involved in transport of cellolbiose and maltose (see Schlosser et al., 1997) e.g. P96483|MSIK MSIK protein from Streptomyces reticuli (377 aa), FASTA scores: opt: 1277, E(): 1.9e-68, (58.05% identity in 379 aa overlap); Q9L0Q1|MSIK ABC transporter ATP-binding protein from Streptomyces coelicolor (378 aa), FASTA scores: opt: 1276, E(): 2.1e-68, (57.65% identity in 380 aa overlap); Q54333|MSIK from Streptomyces lividans (314 aa), FASTA scores: opt: 1217, E(): 5.9e-65, (63.7% identity in 292 aa overlap); and other ABC-type sugar transport proteins. Also highly similar to O53482|Rv2038c|MTV018.25c ABC-type sugar transport protein from Mycobacterium tuberculosis (357 aa), FASTA scores: opt: 1248, E(): 9.4e-67, (56.8% identity in 354 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters).	I6X5H3	No	cell wall and cell processes		MMAR_1901	MSMEG_0508	Mb2856c				
NC_000962.3	Mycobrowser_v3	CDS	3140487	3141314	.	-	0	Rv2834c	ugpE	Involved in active transport of Sn-glycerol-3-phosphate across the membrane (import). Responsible for the translocation of the substrate across the membrane.	Probable Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter UgpE	Rv2834c, (MTCY16B7.08), len: 275 aa. Probable ugpE, Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter (see citation below), similar to various permeases e.g. Q9KDY3|BH1078 glycerol-3-phosphate ABC transporter from Bacillus halodurans (270 aa), FASTA scores: opt: 620, E(): 4.3e-32, (34.7% identity in 268 aa overlap); Q9X0K6|TM1122 glycerol-3-phosphate ABC transporter permease protein from Thermotoga maritima (276 aa), FASTA scores: opt: 605, E(): 3.9e-31, (32.5% identity in 274 aa overlap); AAG58557|UGPE SN-glycerol 3-phosphate transport system (integral membrane protein) from Escherichia coli strain O157:H7 and EDL933 (281 aa), FASTA scores: opt: 574, E(): 3.7e-29, (32.95% identity in 264 aa overlap); P10906|UGPE_ECOLI|B3451 SN-glycerol-3-phosphate transport system permease protein from Escherichia coli strain K12 (281 aa), FASTA scores: opt: 569, E(): 7.6e-29, (32.6% identity in 264 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.	I6Y1U3	No	cell wall and cell processes		MMAR_1899		Mb2858c				
NC_000962.3	Mycobrowser_v3	CDS	3141311	3142222	.	-	0	Rv2835c	ugpA	Involved in active transport of Sn-glycerol-3-phosphate across the membrane (import). Responsible for the translocation of the substrate across the membrane.	Probable Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter UgpA	Rv2835c, (MTCY1B7.07), len: 303 aa. Probable ugpA, Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter (see citation below), similar to various permeases e.g. Q9RK71|SCF11.19 probable sugar transporter inner membrane protein from Streptomyces coelicolor (316 aa), FASTA scores: opt: 643, E(): 3.1e-35, (38.85% identity in 291 aa overlap); Q9KDY4|BH1077 glycerol-3-phosphate ABC transporter (permease) from Bacillus halodurans (315 aa), FASTA scores: opt: 548, E(): 6.2e-29, (31.5% identity in 295 aa overlap); AAK78407|CAC0427 glycerol-3-phosphate ABC-transporter, permease component from Clostridium acetobutylicum (304 aa), FASTA scores: opt: 538, E(): 2.8e-28, (29.1% identity in 292 aa overlap); etc. Contains PS00062 Aldo/keto reductase family signature 2, and PS00402 Binding-protein-dependent transport systems inner membrane comp signature.	I6XFF3	No	cell wall and cell processes		MMAR_1898		Mb2859c,Mb2860c				
NC_000962.3	Mycobrowser_v3	CDS	3728624	3729355	.	+	0	Rv3342	Rv3342	Causes methylation	Possible methyltransferase (methylase)	Rv3342, (MTV016.42), len: 243 aa. Possible methyltransferase, similar to various proteins e.g. Q9I5X8|PA0558 hypothetical protein from Pseudomonas aeruginosa (255 aa), FASTA scores: opt: 496, E(): 4.4e-24, (39.85% identity in 236 aa overlap); Q9XBC9|CZA382.22c putative rRNA methylase from Amycolatopsis orientalis (259 aa), FASTA scores: opt: 473, E(): 1.2e-22, (42.45% identity in 245 aa overlap); Q9UTA8|SPAC25B8.10 putative methyltransferase from Schizosaccharomyces pombe (Fission yeast) (256 aa), FASTA scores: opt: 470, E(): 1.9e-22, (35.7% identity in 238 aa overlap); and Q9UTA9|SPAC25B8.09 putative methyltransferase from Schizosaccharomyces pombe (Fission yeast) (251 aa), FASTA scores: opt: 418, E(): 3.4e-19, (31.2% identity in 237 aa overlap); etc. Start uncertain. Belongs to the methyltransferase superfamily.	P9WK01	No	intermediary metabolism and respiration	ML0681,ML0681c	MMAR_1183	MSMEG_1650	Mb3374				
NC_000962.3	Mycobrowser_v3	CDS	3148385	3149428	.	-	0	Rv2841c	nusA	Could participates in both the termination and antitermination of transcription.	Probable N utilization substance protein A NusA	Rv2841c, (MTCY24A1.16, MTCY16B7.01), len: 347 aa. Probable nusA, N-utilization substance protein A, equivalent to Q9Z5J1|NUSA|ML1558 probable transcription termination/antitermination factor from Mycobacterium leprae (347 aa), FASTA scores: opt: 2054, E(): 5.4e-120, (91.95% identity in 347 aa overlap). Also highly similar to others e.g. Q9KYR1|SC5H4.28 putative transcriptional termination/antitermination factor from Streptomyces coelicolor (340 aa), FASTA scores: opt: 1346, E(): 4.3e-76, (63.35% identity in 341 aa overlap); P32727|NUSA_BACSU N utilization substance protein A (371 aa), FASTA scores: opt: 847, E(): 4.1e-45, (43.95% identity in 346 aa overlap); Q9KA74|NUSA|BH2416 transcriptional terminator from Bacillus halodurans (382 aa), FASTA scores: opt: 846, E(): 4.8e-45, (43.15% identity in 373 aa overlap); etc. Belongs to the NUSA family.	P9WIV3	No	information pathways		MMAR_1892	MSMEG_2625	Mb2866c				
NC_000962.3	Mycobrowser_v3	CDS	3151202	3152950	.	-	0	Rv2845c	proS	Involved in translation mechanism [catalytic activity: ATP + L-proline + tRNA(pro) = AMP + pyrophosphate + L-prolyl-tRNA(pro)].	Probable prolyl-tRNA synthetase ProS (proline--tRNA ligase) (PRORS) (global RNA synthesis factor) (proline translase)	Rv2845c, (MTCY24A1.12), len: 582 aa. Probable proS, prolyl-tRNA synthetase, highly similar to others e.g. Q9KYR6|SYP_STRCO|pros|SC5H4.23 from Streptomyces coelicolor (567 aa), FASTA scores: opt: 1161, E(): 9e-64, (57.15% identity in 574 aa overlap); P56124|SYP_HELPY|pros|HP0238 from Helicobacter pylori (Campylobacter pylori) (577 aa), FASTA scores: opt: 1082, E(): 6.6e-59, (37.8% identity in 553 aa overlap); P16659|SYP_ECOLI|pros|DRPA|B0194 from Escherichia coli strain K12 (572 aa), FASTA scores: opt: 926, E(): 2.6e-49, (39.85% identity in 587 aa overlap); etc. Contains PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1. Belongs to class-II aminoacyl-tRNA synthetase family.	P9WFT9	No	information pathways		MMAR_1888	MSMEG_2621	Mb2870c				
NC_000962.3	Mycobrowser_v3	CDS	3156148	3157521	.	-	0	Rv2848c	cobB	Involved in the cobalamin biosynthesis. Responsible for the amidation of carboxylic groups at position a and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation.	Probable cobyrinic acid A,C-diamide synthase CobB	Rv2848c, (MTCY24A1.09), len: 457 aa. Probable cobB, cobyrinic acid A,C-diamide synthase, highly similar to others e.g. O27509|COBB_METTH|MTH1460 from Methanobacterium thermoautotrophicum (447 aa), FASTA scores: opt: 980, E(): 1.3e-49, (39.65% identity in 454 aa overlap); Q9KBM8|BH1898 from Bacillus halodurans (465 aa), FASTA scores: opt: 928, E(): 1.4e-46, (37.0% identity in 457 aa overlap); O68108|COBB_RHOCA from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (435 aa), FASTA scores: opt: 921, E(): 3.3e-46, (39.35% identity in 437 aa overlap); etc. Belongs to the COBB/COBQ family, COBB subfamily.	P9WP97	No	intermediary metabolism and respiration	ML1564,ML1564c	MMAR_1885	MSMEG_2617	Mb2873c				
NC_000962.3	Mycobrowser_v3	CDS	3398425	3399408	.	-	0	Rv3038c	Rv3038c	Function unknown	Conserved protein	Rv3038c, (MTV012.53c), len: 327 aa. Conserved protein, equivalent to Q9CBQ9|ML1723 hypothetical protein from Mycobacterium leprae (327 aa), FASTA scores: opt: 1843, E(): 6.1e-108, (80.75% identity in 327 aa overlap). Weak similarity with e.g. Q9KZI3|SCG8A.16 putative methyltransferase from Streptomyces coelicolor (199 aa), FASTA scores: opt: 227, E(): 3.9e-07, (31.95% identity in 191 aa overlap) and O52570 methyltransferase from Amycolatopsis mediterranei (272 aa), FASTA scores: opt: 228, E(): 4.3e-07, (31.7% identity in 164 aa overlap). Contains PS00044 Bacterial regulatory proteins, lysR family signature but shows no similarity to known LysR family members.	I6YAZ1	No	conserved hypotheticals	ML1723,ML1723c	MMAR_1663	MSMEG_2329	Mb3064c				
NC_000962.3	Mycobrowser_v3	CDS	3160580	3162061	.	-	0	Rv2852c	mqo	Involved in tricarboxylic acid cycle [catalytic activity: (S)-malate + acceptor = oxaloacetate + reduced acceptor].	Probable malate:quinone oxidoreductase Mqo (malate dehydrogenase [acceptor])	Rv2852c, (MT2918, MTCY24A1.05), len: 493 aa. Probable mqo, malate:quinone oxidoreductase, highly similar to others e.g. O69282|MQO_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (499 aa), FASTA scores: opt: 1701, E(): 1.2e-101, (50.7% identity in 495 aa overlap); Q9Z9Q7|BH3960 from Bacillus halodurans (500 aa), FASTA scores: opt: 1632, E(): 3.3e-97, (48.55% identity in 486 aa overlap); Q9HYF4|MQOA|PA3452 from Pseudomonas aeruginosa (523 aa), FASTA scores: opt: 1604, E(): 2.1e-95, (49.1% identity in 487 aa overlap) (N-terminus longer); P33940|MQO_ECOLI|B2210 from Escherichia coli strain K12 (548 aa), FASTA scores: opt: 1525, E(): 2.7e-90, (48.15% identity in 492 aa overlap); etc. Belongs to the MQO family. Cofactors: FAD.	P9WJP5	No	intermediary metabolism and respiration	ML1568,ML1568c	MMAR_1881	MSMEG_2613	Mb2877c				
NC_000962.3	Mycobrowser_v3	CDS	3165205	3166584	.	+	0	Rv2855	mtr	Involved in reduction of mycothiol.	NADPH-dependent mycothiol reductase Mtr	Rv2855, (MTCY24A1.02c), len: 459 aa. Mtr, NADPH-dependent mycothiol reductase, proven enzymatically but previously described as glutathione reductase homolog (gene name: gorA) (see citation below). Similar to others e.g. Q9L7K8|MERA mercuric reductase from Streptomyces sp. CHR28 (474 aa), FASTA scores: opt: 719, E(): 9e-38, (35.2% identity in 460 aa overlap); P30341|MERA_STRLI mercuric reductase from Streptomyces lividans (474 aa), FASTA scores: opt: 712, E(): 2.5e-37, (34.95% identity in 455 aa overlap); Q98ED5|MLL4296 ferric leghemoglobin reductase-2 precursor, dihydrolipoamide dehydrogenase from Rhizobium loti (Mesorhizobium loti) (468 aa), FASTA scores: opt: 670, E(): 1.1e-34, (30.8% identity in 471 aa overlap); etc. Belongs to the pyridine nucleotide-disulphide oxidoreductases class-I. Cofactor: FAD.	P9WHH3	No	intermediary metabolism and respiration	ML1570	MMAR_1875	MSMEG_2611	Mb2880				
NC_000962.3	Mycobrowser_v3	CDS	3166684	3167802	.	+	0	Rv2856	nicT	Seems involved in nickel incorporation. Thought to be involved in transport of nickel across the membrane. Responsible for the translocation of the substrate across the membrane.	Possible nickel-transport integral membrane protein NicT	Rv2856, (MTCY24A1.01c), len: 372 aa. Possible nicT, nickel-transport integral membrane protein, similar to transport proteins and hydrogenase cluster proteins e.g. BAB58860|SAV2698 hypothetical 37.9 KDA protein from Staphylococcus aureus subsp. aureus Mu50 (338 aa), FASTA scores: opt: 1082, E(): 7.1e-60, (48.05% identity in 335 aa overlap); Q97ZB2|HOXN high-affinity nickel-transport protein from Sulfolobus solfataricus (373 aa), FASTA scores: opt: 922, E(): 6.6e-50, (42.2% identity in 372 aa overlap); P23516|HOXN_ALCEU high-affinity nickel transport protein (integral membrane protein) from Alcaligenes eutrophus (Ralstonia eutropha) (351 aa), FASTA scores: opt: 904, E(): 8.3e-49, (41.9% identity in 339 aa overlap); Q45247|HUPN_BRAJA hydrogenase nickel incorporation protein from Bradyrhizobium japonicum (381 aa), FASTA scores: opt: 853, E(): 1.3e-45, (41.65% identity in 329 aa overlap); etc. Seems to belong to the HOXN/HUPN/NIXA family of nickel transporters (NiCoT family).	I6YEJ7	No	cell wall and cell processes	ML1571	MMAR_1873		Mb2881				
NC_000962.3	Mycobrowser_v3	CDS	3169356	3170723	.	-	0	Rv2858c	aldC	Oxidizes a wide variety of aldehydes [catalytic activity: aldehyde + NAD(+) + H(2)O = acid + NADH].	Probable aldehyde dehydrogenase AldC	Rv2858c, (MTV003.04c), len: 455 aa. Probable aldC, aldehyde dehydrogenase, similar to many e.g. O88069|SCI35.34c putative aldehyde dehydrogenase from Streptomyces coelicolor (483 aa), FASTA scores: opt: 1872, E(): 6.4e-109, (64.5% identity in 448 aa overlap); Q9FAB1|ALDH|BT-ALDH aldehyde dehydrogenase from Bacillus thermoleovorans (497 aa), FASTA scores: opt: 1157, E(): 2.1e-64, (44.3% identity in 458 aa overlap); O33455|CYMC P-CUMIC aldehyde dehydrogenase from Pseudomonas putida (494 aa), FASTA scores: opt: 1149, E(): 6.5e-64, (43.15% identity in 452 aa overlap); P40047|DHA5_YEAST|ALD5|ALDH5|ALD3|YER073W aldehyde dehydrogenase from Saccharomyces cerevisiae (Baker's yeast) (519 aa), FASTA scores: opt: 1091, E(): 2.7e-60, (38.55% identity in 459 aa overlap); P80668|FEAB_ECOLI|PADA|MAOB|B1385 phenylacetaldehyde dehydrogenase from Escherichia coli strain K12 (499 aa), FASTA scores: opt: 1074, E(): 3e-59, (42.2% identity in 462 aa overlap); etc. Also similar to many M. tuberculosis dehydrogenases e.g. P71823|Rv0768|MTCY369.13 (489 aa), FASTA score: (38.1% identity in 467 aa overlap). Contains PS00687 Aldehyde dehydrogenases glutamic acid active site and PS00070 Aldehyde dehydrogenases cysteine active site. Belongs to the aldehyde dehydrogenases family.	O33340	No	intermediary metabolism and respiration			MSMEG_2597	Mb2883c				
NC_000962.3	Mycobrowser_v3	CDS	3170720	3171646	.	-	0	Rv2859c	Rv2859c	Function unknown; probably involved in cellular metabolism.	Possible amidotransferase	Rv2859c, (MTV003.05c), len: 308 aa. Possible amidotransferase, equivalent (but longer 58 aa) to Q9CBU9|ML1573 possible amidotransferase from Mycobacterium leprae (249 aa), FASTA scores: opt: 1226, E(): 3e-64, (71.55% identity in 239 aa overlap). Also similar to other amidotransferases and hypothetical proteins, but shorter in N-terminus e.g. O88072|SCI35.37 hypothetical 25.3 KDA protein from Streptomyces coelicolor (242 aa), FASTA scores: opt: 683, E(): 1.2e-32, (47.65% identity in 235 aa overlap); AAK79730|Q97I88|CAC1764 predicted glutamine amidotransferase from Clostridium acetobutylicum (241 aa), FASTA scores: opt: 458, E(): 1.6e-19, (32.95% identity in 246 aa overlap); AAK75201|Q97QV9|SP1089 glutamine amidotransferase class I from Streptococcus pneumoniae (229 aa), FASTA scores: opt: 431, E(): 5.6e-18, (34.75% identity in 236 aa overlap); etc. Contains three 17 aa repeats at the N-terminus very similar to those in other Mycobacterium tuberculosis proteins e.g. Q10699|YY30_MYCTU|Rv2090|MT2151|MTCY49.30 putative 5'-3' exonuclease RV2090.	O33341	No	intermediary metabolism and respiration	ML1573,ML1573c	MMAR_1844	MSMEG_2596	Mb2884c				
NC_000962.3	Mycobrowser_v3	CDS	3175454	3177265	.	-	0	Rv2864c	Rv2864c	Function unknown, possibly involved in cell wall biosynthesis.	Possible penicillin-binding lipoprotein	Rv2864c, (MTV003.10c), len: 603 aa. Possible penicillin-binding lipoprotein, probably located in periplasm, equivalent to Q9CBU6|ML1577 probable penicillin binding protein from Mycobacterium leprae (608 aa), FASTA scores: opt: 3352, E(): 2.1e-193, (81.5% identity in 606 aa overlap). Also shows some similarity to others e.g. P72405|PCBR from Streptomyces clavuligerus (551 aa), FASTA scores: opt: 543, E(): 6.1e-25, (28.4% identity in 567 aa overlap); Q9F2L0|SCH63.18c from Streptomyces coelicolor (546 aa), FASTA scores: opt: 519, E(): 1.7e-23, (29.3% identity in 577 aa overlap); Q9RKD1|SCE87.07 from Streptomyces coelicolor (541 aa), FASTA scores: opt: 472, E(): 1.1e-20, (34.3% identity in 318 aa overlap); etc. Equivalent to AAK47258 from Mycobacterium tuberculosis strain CDC1551 (618 aa) but shorter 15 aa. Contains signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site, and PS00017 ATP/GTP-binding site motif A (P-loop).	O33346	No	cell wall and cell processes	ML1577,ML1577c			Mb2889c				
NC_000962.3	Mycobrowser_v3	CDS	3180548	3181762	.	-	0	Rv2869c	rip	Controls membrane composition	Membrane bound metalloprotease	Rv2869c, (MTV003.15c), len: 404 aa. Rip, metalloprotease, regulates intramembrane proteolysis and controls membrane composition (rip, see Makinoshima and Glickman, 2005). Similar to site two protease (S2P) in higher eukaryotes. Conserved transmembrane protein, equivalent to Q9CBU4|ML1582 probable integral membrane protein from Mycobacterium leprae (404 aa), FASTA scores: opt: 2250, E(): 1.1e-128, (82.2% identity in 404 aa overlap). Also weakly similar to other membrane proteins or hypothetical proteins e.g. Q9A710|CC1916 putative membrane-associated zinc metalloprotease from Caulobacter crescentus (398 aa), FASTA scores: opt: 368, E(): 7.8e-15, (28.1% identity in 427 aa overlap). Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007). Cleaves PbpB|Rv2163c in a Zn2+ -dependent manner (See Mukherjee et al., 2009). Cleaves proteins RskA|Rv0444c, RslA|Rv0736, and Rv3912, in M. tuberculosis Erdman (See Sklar et al., 2010).	P9WHS3	No	cell wall and cell processes	ML1582,ML1582c	MMAR_1837	MSMEG_2579	Mb2894c				
NC_000962.3	Mycobrowser_v3	CDS	3184847	3186934	.	+	0	Rv2874	dipZ	Could be involved in cytochrome-C biogenesis.	Possible integral membrane C-type cytochrome biogenesis protein DipZ	Rv2874, (MT2942, MTCY274.05), len: 695 aa. Possible dipZ, cytochrome c-type biogenesis protein (see citation below), probable integral membrane protein, similar in part to others or hypothetical proteins e.g. CAC48606|SMB20213 conserved hypothetical protein from Rhizobium meliloti (Sinorhizobium meliloti) (627 aa), FASTA scores: opt: 844, E(): 7.3e-43, (32.65% identity in 643 aa overlap); Q9ZMH0|CCDA or JHP0250 putative cytochrome C-type biogenesis protein from Helicobacter pylori J99 (Campylobacter pylori J99) (239 aa), FASTA scores: opt: 250, E(): 1.4e-07, (27.3% identity in 227 aa overlap); Q9LA04|CCDA C-type cytochrome biogenesis protein from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (252 aa), FASTA scores: opt: 245, E(): 2.9e-07, (27.85% identity in 244 aa overlap); etc. Also similar to O06393|CCSA|Rv0527|MTCY25D10.06 cytochrome C-type biogenesis protein from Mycobacterium tuberculosis (259 aa), FASTA scores: opt: 280, E(): 2.4e-09, (29.3% identity in 239 aa overlap).	P9WG63	No	intermediary metabolism and respiration		MMAR_1835		Mb2899				
NC_000962.3	Mycobrowser_v3	CDS	3188008	3188871	.	-	0	Rv2877c	Rv2877c	Unknown; possibly involved in transport of mercury across the membrane.	Probable conserved integral membrane protein	Rv2877c, (MTCY274.08c), len: 287 aa. Probable conserved integral membrane protein, Mer family possibly involved in transport of mercury, similar to others, and to the fourth protein of the mercury resistance operon of Streptomyces sp (or other organisms), and to putative cytochrome-c biogenesis proteins e.g. Q9XBD1|CZA382.20C putative integral membrane transporter from Amycolatopsis orientalis (298 aa), FASTA scores: opt: 913, E(): 7.6e-46, (51.55% identity in 293 aa overlap); P30344|MER4_STRLI mercury resistance probable HG transport protein from Streptomyces lividans (319 aa), FASTA scores: opt: 427, E(): 1.2e-17, (32.85% identity in 289 aa overlap); Q9M5P3 putative cytochrome C biogenesis protein precursor from Arabidopsis thaliana (Mouse-ear cress) (354 aa), FASTA scores: opt: 229, E(): 4e-06, (29.85% identity in 221 aa overlap); etc. Contains PS00044 Bacterial regulatory proteins, lysR family signature. Note that previously known as merT.	I6YEL8	No	cell wall and cell processes	ML1585,ML1585c	MMAR_1832	MSMEG_3541	Mb2902c				
NC_000962.3	Mycobrowser_v3	CDS	3383885	3385066	.	-	0	Rv3025c	iscS	Catalyzes the removal of elemental sulfur from cysteine to produce alanine.	Cysteine desulfurase IscS (NIFS protein homolog) (nitrogenase metalloclusters biosynthesis protein NIFS)	Rv3025c, (MTV012.40c), len: 393 aa. IscS (alternate gene name: nifS), cysteine desulfurase (NifS-like protein) , equivalent to MLCB637.06|O33098 NIFS-like protein from Mycobacterium leprae (396 aa), FASTA scores: opt: 2186, E(): 2.7e-122, (84.9% identity in 391 aa overlap). Also highly similar to many e.g. O86581|SC2A11.20 putative pyridoxal-phosphate-dependent aminotransferase from Streptomyces coelicolor (389 aa), FASTA scores: opt: 1568, E(): 1.1e-85, (61.7% identity in 389 aa overlap); P57795|ISCS|NIFS cysteine desulfurase (NIFS protein homolog) from Methanosarcina thermophila (404 aa), FASTA scores: opt: 1059, E(): 1.6e-55, (46.2% identity in 381 aa overlap); O54055|ISCS_RUMFL|ISCS|NIFS cysteine desulfurase from Ruminococcus flavefaciens (396 aa), FASTA scores: opt: 973, E(): 2e-50, (43.3% identity in 381 aa overlap); P57794|NIFS_ACEDI cysteine desulfurase from Acetobacter diazotrophicus (400 aa), FASTA scores: opt: 958, E(): 1.6e-49, (41.1% identity in 392 aa overlap); etc. Also similar to Rv1464|MTV007.11 from Mycobacterium tuberculosis. Contains PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site. Belongs to class-V of pyridoxal-phosphate-dependent aminotransferases, NIFS/ISCS subfamily. Cofactor: pyridoxal phosphate (by similarity).	P9WQ71	No	intermediary metabolism and respiration	ML1708,ML1708c	MMAR_1689	MSMEG_2357	Mb3051c				
NC_000962.3	Mycobrowser_v3	CDS	3189583	3190152	.	-	0	Rv2879c	Rv2879c	Function unknown	Conserved hypothetical protein	Rv2879c, (MTCY274.10c), len: 189 aa. Conserved hypothetical protein, similar to others e.g. C-terminus of Q9RVT6|DR0936 conserved hypothetical protein from Deinococcus radiodurans (346 aa), FASTA scores: opt: 505, E(): 1e-26, (46.5% identity in 185 aa overlap); O34617|YLON_BACSU hypothetical 41.6 KDA protein from Bacillus subtilis (363 aa), FASTA scores: opt: 459, E(): 1.2e-24, (40.5% identity in 185 aa overlap); YFGB_ECOLI|P36979 hypothetical 43.1 kDa protein from Escherichia coli (384 aa), FASTA scores, opt: 410, E(): 2.8e-21, (41.7% identity in 187 aa overlap); etc. Appears to be a frame shift with respect to following ORF but we can detect no error in the cosmid sequence to account for this.	P0A644	No	conserved hypotheticals	ML1587,ML1587c		MSMEG_2545	Mb2904c				
NC_000962.3	Mycobrowser_v3	CDS	3190701	3191621	.	-	0	Rv2881c	cdsA	Involved in the phospholipid biosynthesis [catalytic activity: CTP + phosphatidate = pyrophosphate + CDP-diacylglycerol].	Probable integral membrane phosphatidate cytidylyltransferase CdsA (CDP-diglyceride synthetase) (CDP-diglyceride pyrophosphorylase) (CDP-diacylglycerol synthase) (CDS) (CTP:phosphatidate cytidylyltransferase) (CDP-DAG synthase) (CDP-DG synthetase)	Rv2881c, (MTCY274.12c), len: 306 aa. Probable cdsA, phosphatidate cytidylyltransferase, integral membrane protein, equivalent to Q9CBU1|CDSA_MYCLE|ML1589 phosphatidate cytidylyltransferase from Mycobacterium leprae (312 aa), FASTA scores: opt: 1470, E(): 1.1e-84, (70.3% identity in 313 aa overlap). Also similar to others e.g. Q9KPV7|VC2255 from Vibrio cholerae (280 aa), FASTA scores: opt: 383, E(): 1.1e-16, (29.3% identity in 280 aa overlap); Q9CDT2|CDSA from Lactococcus lactis (subsp. lactis) (Streptococcus lactis) (267 aa), FASTA scores: opt: 361, E(): 2.6e-15, (29.05% identity in 265 aa overlap); P06466|CDSA_ECOLI|CDS|B0175|Z0186|ECS0177 from Escherichia coli strains K12 and O157:H7 (249 aa), FASTA scores: opt: 352, E(): 9.2e-15, (40.4% identity in 156 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Belongs to the CDS family.	P9WPF7	No	lipid metabolism	ML1589,ML1589c	MMAR_1828	MSMEG_2543	Mb2905c				
NC_000962.3	Mycobrowser_v3	CDS	3193393	3194151	.	+	0	Rv2884	Rv2884	Involved in transcriptional mechanism	Probable transcriptional regulatory protein	Rv2884, (MTCY274.15), len: 252 aa. Probable transcriptional regulatory protein, highly similar to others e.g. Q05943|GLNR_STRCO|SCD84.26c transcriptional regulatory protein from Streptomyces coelicolor (267 aa), FASTA scores: opt: 609, E(): 2.7e-34, (46.4% identity in 224 aa overlap); Q55733|SLL0396 regulatory components of sensory transduction system from Synechocystis sp. strain PCC 6803 (224 aa), FASTA scores: opt: 330, E(): 3e-15, (31.8% identity in 217 aa overlap); Q9A4S3|CC2757 DNA-binding response regulator from Caulobacter crescentus (223 aa), FASTA scores: opt: 311, E(): 6e-14, (30.3% identity in 221 aa overlap); etc. Also highly similar to O53830|Rv0818|MTV043.10 putative regulatory protein from Mycobacterium tuberculosis (255 aa), FASTA scores: opt: 665, E(): 3.8e-38, (47.6% identity in 227 aa overlap). The N-terminal region is similar to that of other regulatory components of sensory transduction systems.	I6X5M3	No	regulatory proteins	ML1592	MMAR_1825		Mb2908				
NC_000962.3	Mycobrowser_v3	CDS	3198292	3199107	.	-	0	Rv2889c	tsf	Associates with the EF-TU.GDP complex and induces the exchange of GDP to GTP, it remains bound to the aminoacyl-tRNA. EF-TU.GTP complex up to the GTP hydrolysis stage on the ribosome.	Probable elongation factor Tsf (EF-ts)	Rv2889c, (MTCY274.20c), len: 271 aa. Probable tsf, elongation factor, equivalent to O33039|EFTS_MYCLE|TSF|ML1597|MLCB250.64 elongation factor from Mycobacterium leprae (276 aa), FASTA scores: opt: 1430, E(): 1.9e-80, (83.7% identity in 276 aa overlap). Also highly similar to others e.g. Q9X5Z9|EFTS_STRRA|TSF from Streptomyces ramocissimus (278 aa), FASTA scores: opt: 928, E(): 1.1e-49, (57.05% identity in 277 aa overlap); O31213|EFTS_STRCO|TSF|SC2E1.42 from Streptomyces coelicolor (278 aa), FASTA scores: opt: 927, E(): 1.3e-49, (56.3% identity in 277 aa overlap); P80700|EFTS_BACSU|TSF from Bacillus subtilis (292 aa), FASTA scores: opt: 650, E(): 1.3e-32, (43.85% identity in 276 aa overlap); etc. Contains PS01127 Elongation factor Ts signature 2. Belongs to the EF-ts family.	P9WNM1	No	information pathways	ML1597,ML1597c	MMAR_1820	MSMEG_2520	Mb2913c				
NC_000962.3	Mycobrowser_v3	CDS	3202420	3203397	.	+	0	Rv2893	Rv2893	Function unknown; probably involved in cellular metabolism.	Possible oxidoreductase	Rv2893, (MTCY274.24), len: 325 aa. Possible oxidoreductase, showing similarity with various proteins and/or oxidoreductases e.g. Q9AE05|RIF11 eleventh protein in the rif biosynthetic gene cluster from Amycolatopsis mediterranei (Nocardia mediterranei) (294 aa), FASTA scores: opt: 270, E(): 4.8e-10, (34.5% identity in 313 aa overlap); O52567 reductase from Amycolatopsis mediterranei (Nocardia mediterranei) (153 aa), FASTA scores: opt: 251, E(): 5e-09, (42.4% identity in 125 aa overlap); Q58929|mer|MJ1534 F420-dependent methylenetetrahydromethanopterin reductase from Methanococcus jannaschii (331 aa), FASTA scores: opt: 249, E(): 1.2e-08, (29.7% identity in 283 aa overlap); etc. Also some similarity with others proteins from Mycobacterium tuberculosis strains H37Rv and CDC1551 e.g. P71844|Rv0791c|MTCY369.35c putative oxidoreductase (347 aa), FASTA scores: opt: 264, E(): 1.3e-09, (29.05% identity in 272 aa overlap); and P96809|Rv0132|MTCI5.06c putative oxidoreductase (360 aa), FASTA scores: opt: 260, E(): 2.4e-09, (33.05% identity in 239 aa overlap).	I6YEN3	No	intermediary metabolism and respiration		MMAR_2775	MSMEG_2516	Mb2917				
NC_000962.3	Mycobrowser_v3	CDS	3206431	3207942	.	-	0	Rv2897c	Rv2897c	Function unknown	Conserved hypothetical protein	Rv2897c, (MTCY274.28c), len: 503 aa. Conserved hypothetical protein, possibly Mg-chelatase, highly similar to hypothetical proteins and chelatases e.g. Q9RTV0|DR1656 mg(2+) chelatase family protein from Deinococcus radiodurans (519 aa), FASTA scores: opt: 1333, E(): 3.6e-68, (46.55% identity in 505 aa overlap);Q55372|SLR0904 hypothetical 55.1 KDA protein from Synechocystis sp. strain PCC 6803 (509 aa), FASTA scores: opt: 1271, E(): 1.2e-64, (42.65% identity in 504 aa overlap); Q9HTR4|PA5290 hypothetical protein from Pseudomonas aeruginosa (497 aa), FASTA scores: opt: 1248, E(): 2.3e-63, (45.9% identity in 503 aa overlap); Q9K0Z6|comm|NMB0405 competence protein (mg-chelatase) from Neisseria meningitidis (serogroup B), FASTA scores: opt: 1229, E(): 2.8e-62, (43.2% identity in 509 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop).	P9WPR1	No	conserved hypotheticals	ML1606,ML1606c	MMAR_1813	MSMEG_2509	Mb2921c				
NC_000962.3	Mycobrowser_v3	CDS	3207942	3208328	.	-	0	Rv2898c	Rv2898c	Function unknown	Conserved hypothetical protein	Rv2898c, (MTCY274.29c), len: 128 aa. Conserved hypothetical protein, highly similar to O33024|YS98_MYCLE|ML1607|MLCB250.49 hypothetical 11.0 KDA protein from Mycobacterium leprae (96 aa), FASTA scores: opt: 318, E(): 2.3e-16, (58.35% identity in 96 aa overlap). Also similar to other hypothetical proteins e.g. O69890|YE19_STRCO|SC2E1.19 from Streptomyces coelicolor (130 aa), FASTA scores: opt: 253, E(): 1.7e-11, (39.65% identity in 121 aa overlap); Q9HVZ1|PA4424 from Pseudomonas aeruginosa (125 aa), FASTA scores: opt: 234, E(): 4.2e-10, (40.85% identity in 115 aa overlap); O86871 from Streptomyces lividans (85 aa), FASTA scores: opt: 224, E(): 1.8e-09, (46.45% identity in 84 aa overlap); etc. Equivalent to AAK47292 from Mycobacterium tuberculosis strain CDC1551 (141 aa) but shorter 13 aa. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WFM9	No	conserved hypotheticals	ML1607,ML1607c	MMAR_1812	MSMEG_2508	Mb2922c				
NC_000962.3	Mycobrowser_v3	CDS	3209406	3211745	.	-	0	Rv2900c	fdhF	Decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors [catalytic activity: formate + NAD(+) = CO(2) + NADH].	Possible formate dehydrogenase H FdhF (formate-hydrogen-lyase-linked, selenocysteine-containing polypeptide) (formate dehydrogenase-H alpha subunit) (FDH-H)	Rv2900c, (MTCY274.31c), len: 779 aa. Possible fdhF, formate dehydrogenase, highly similar to others formate dehydrogenases and prokaryotic molybdopterin-containing oxidoreductases e.g. Q9S2J9|SC7H2.18 putative formate dehydrogenase from Streptomyces coelicolor (759 aa), FASTA scores: opt: 3038, E(): 2.7e-180, (59.7% identity in 767 aa overlap); Q9HU08|PA5181 probable oxidoreductase from Pseudomonas aeruginosa (773 aa), FASTA scores: opt: 2560, E(): 1.1e-150, (53.2% identity in 761 aa overlap); P78160 formate dehydrogenase a chain (fragment) from Escherichia coli strain K12 (740 aa), FASTA scores: opt: 2002, E(): 3.7e-116, (43.1% identity in 733 aa overlap); P07658|FDHF_ECOLI|P78137|B4079 formate dehydrogenase from Escherichia coli strain K12 (715 aa), FASTA scores: opt: 305, E(): 5.6e-13, (25.5% identity in 748 aa overlap); etc. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family.	P9WJP9	No	intermediary metabolism and respiration	ML1609,ML1609c	MMAR_0121	MSMEG_4668	Mb2924c				
NC_000962.3	Mycobrowser_v3	CDS	3213912	3214253	.	-	0	Rv2904c	rplS	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 RplS	Rv2904c, (MTCY274.35c), len: 113 aa. rplS, 50S ribosomal protein L19, equivalent to O33020|RL19_MYCLE 50S ribosomal protein L19 from Mycobacterium leprae (113 aa), FASTA scores: opt: 702, E(): 1.4e-45, (93.8% identity in 113 aa overlap). Also highly similar to others e.g. O69883|RL19_STRCO from Streptomyces coelicolor (116 aa), FASTA scores: opt: 571, E(): 9.5e-36, (77.25% identity in 110 aa overlap); O31742|RL19_BACSU from Bacillus subtilis (115 aa), FASTA scores: opt: 523, E(): 3.8e-32, (72.9% identity in 107 aa overlap); RL19_BACST|P30529 from Bacillus stearothermophilus (116 aa), FASTA scores: opt: 518, E(): 9.1e-32, (71.7% identity in 106 aa overlap); etc. Belongs to the L19P family of ribosomal proteins.	P9WHC9	No	information pathways	ML1613,ML1613c	MMAR_1804	MSMEG_2440	Mb2928c				
NC_000962.3	Mycobrowser_v3	CDS	3215665	3216357	.	-	0	Rv2906c	trmD	Specifically methylates guanosime-37 in various TRNAS [catalytic activity S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine].	Probable tRNA (guanine-N1)-methyltransferase TrmD (M1G-methyltransferase) (tRNA [GM37] methyltransferase)	Rv2906c, (MTCY274.37c), len: 230 aa. Probable trmD, tRNA m1G methyltransferase, equivalent to O33017|TRMD_MYCLE from Mycobacterium leprae (238 aa), FASTA scores: opt: 1363, E(): 8.1e-86, (87.2% identity in 227 aa overlap). Also highly similar to others e.g. O69882|TRMD_STRCO from Streptomyces coelicolor and S. lividans (277 aa), FASTA scores: opt: 841, E(): 4.5e-50, (55.55% identity in 234 aa overlap); Q9A0B6 from Streptococcus pyogenes (243 aa), FASTA scores: opt: 698, E(): 2.5e-40, (47.6% identity in 227 aa overlap); P07020|TRMD_ECOLI|TRMD|B2607|Z3901|ECS3470 from Escherichia coli strain O157:H7 (255 aa), FASTA scores: opt: 573, E(): 3.8e-33, (42.1% identity in 228 aa overlap); etc. Belongs to the RNA methyltransferase TRMD family.	P9WFY7	No	information pathways	ML1615,ML1615c	MMAR_1802	MSMEG_2438	Mb2930c				
NC_000962.3	Mycobrowser_v3	CDS	3216361	3216891	.	-	0	Rv2907c	rimM	Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. It could be some accessory protein needed for efficient assembly of the 30S subunit. RIMM is needed in a step prior to RBFA during the maturation of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes.	Probable 16S rRNA processing protein RimM	Rv2907c, (MTCY274.38c), len: 176 aa. Probable rimM, 16S rRNA processing protein, equivalent to O33016|RIMM_MYCLE probable 16S rRNA processing protein from Mycobacterium leprae (179 aa), FASTA scores: opt: 797, E(): 2.4e-46, (73.15% identity in 175 aa overlap). Also highly similar to others e.g. O69881|RIMM_STRCO from Streptomyces coelicolor (188 aa), FASTA scores: opt: 485, E(): 2.3e-25, (48.85% identity in 176 aa overlap); Q9KA14|RIMM_BACHD from Bacillus halodurans (173 aa), FASTA scores: opt: 289, E(): 3.2e-12, (30.65% identity in 173 aa overlap); P21504|RIMM_ECOLI|RIMM|B2608 from Escherichia coli strain K12 (182 aa), FASTA scores: opt: 237, E(): 1e-08, (29.4% identity in 177 aa overlap). Belongs to the RimM family.	P9WH19	No	information pathways	ML1616,ML1616c	MMAR_1801	MSMEG_2437	Mb2931c				
NC_000962.3	Mycobrowser_v3	CDS	3218339	3219214	.	+	0	Rv2911	dacB2	Involved in peptidoglycan synthesis (at final stages). Hydrolyzes the bound D-alanyl-D-alanine [catalytic activity: D-alanyl-D-alanine + H(2)O = 2 D-alanine].	Probable penicillin-binding protein DacB2 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD-carboxypeptidase) (PBP) (DD-transpeptidase) (serine-type D-ala-D-ala carboxypeptidase) (D-amino acid hydrolase)	Rv2911, (MTCY274.43), len: 291 aa. Probable dacB2, D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein), an ala-rich protein. Highly similar (except in N-terminus) to Q9CCM2|ML0691 putative D-alanyl-D-alanine carboxypeptidase from Mycobacterium leprae (411 aa), FASTA scores: opt: 749, E(): 9.3e-39, (46.75% identity in 276 aa overlap). Also similar to penicillin binding proteins / D-alanyl-D-alanine carboxypeptidases e.g. Q9KCJ8|SC4G1.16c D-alanyl-D-alanine carboxypeptidase from Streptomyces coelicolor (382 aa), FASTA scores: opt: 386, E(): 2.1e-16, (31.25% identity in 285 aa overlap); P35150|DACB_BACSU penicillin-binding protein 5* precursor from Bacillus subtilis (382 aa), FASTA scores: opt: 384, E(): 3.6e-17, (30.7% identity in 244 aa overlap); Q9K8X5|DACB|BH2877 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) from Bacillus halodurans (395 aa), FASTA scores: opt: 359, E(): 9.7e-15, (30.3% identity in 241 aa overlap); P33364|PBP7_ECOLI|PBPG|B2134 penicillin-binding protein 7 precursor from Escherichia coli strain K12 (313 aa), FASTA scores: opt: 273, E(): 7.5e-10, (27.8% identity in 263 aa overlap); etc. Also similar to O53380|Rv3330|MTV016.30 penicillin-binding protein from Mycobacterium tuberculosis (405 aa), FASTA scores: opt: 746, E(): 1.4e-38, (47.0% identity in 266 aa overlap). Seems to contain PF00768 Peptidase_S11 domain PFAM. Belongs to peptidase family S11; also known as the D-alanyl-D-alanine carboxypeptidase 1 family. Thought to be a membrane-bound protein. Note that previously known as dacB.	I6Y204	No	cell wall and cell processes		MMAR_1797	MSMEG_2433	Mb2935				
NC_000962.3	Mycobrowser_v3	CDS	3219863	3221698	.	-	0	Rv2913c	Rv2913c	Hydrolyzes specific D-amino acid.	Possible D-amino acid aminohydrolase (D-amino acid hydrolase)	Rv2913c, (MTCY338.01c, MTCY274.45c), len: 611 aa. Possible D-amino acid aminohydrolase, similar (principally in N-terminus) to D-amino acid aminohydrolases e.g. Q9V2D3|NDAD|PAB0090 D-aminoacylase (aspartate, glutamate etc) from Pyrococcus abyssi (526 aa), FASTA scores: opt: 336, E(): 2.2e-13, (27.55% identity in 581 aa overlap); P94212|NDDD_ALCXX N-acyl-D-aspartate deacylase (N-acyl-D-aspartate amidohydrolase) from Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans) (498 aa), FASTA scores: opt: 221, E(): 3.4e-06, (25.95% identity in 532 aa overlap); Q9AGH8 D-aminoacylase from Alcaligenes faecalis (484 aa), FASTA scores: opt: 218, E(): 5.1e-06, (28.35% identity in 434 aa overlap); etc.	P9WJH9	No	intermediary metabolism and respiration		MMAR_1795	MSMEG_6141	Mb2937c				
NC_000962.3	Mycobrowser_v3	CDS	3385163	3386077	.	-	0	Rv3026c	Rv3026c	Function unknown	Conserved hypothetical protein	Rv3026c, (MTV012.41c), len: 304 aa. Conserved hypothetical protein, similar to Q9RCZ0|SCM10.08C putative acyltransferase from Streptomyces coelicolor (275 aa), FASTA scores: opt: 393, E(): 2.2e-17, (41.4% identity in 299 aa overlap). Similar in part to other hypothetical proteins and acyltransferases e.g. BAB51968|MLR5533 from Rhizobium loti (266 aa), FASTA scores: opt: 280, E(): 2.4e-10, (29.45% identity in 258 aa overlap); Q9KIH9 putative acyltransferase (putative acyltransferase transmembrane protein) from Rhizobium meliloti (Sinorhizobium meliloti) (292 aa), FASTA scores: opt: 252, E(): 1.4e-08, (30.5% identity in 210 aa overlap); O69114|PLSC putative 1-acyl-SN-glycerol-3-phosphate acyltransferase from Burkholderia pseudomallei (Pseudomonas pseudomallei) (289 aa), FASTA scores: opt: 216, E(): 2.4e-06, (30.85% identity in 269 aa overlap); etc. So may be a member of acyltransferase family protein.	I6XFY8	No	conserved hypotheticals	ML1709,ML1709c	MMAR_1687	MSMEG_2356	Mb3052c				
NC_000962.3	Mycobrowser_v3	CDS	3226363	3228243	.	+	0	Rv2917	Rv2917	Function unknown	Conserved hypothetical alanine and arginine rich protein	Rv2917, (MTCY338.05), len: 626 aa. Conserved hypothetical ala-, arg-rich protein, highly similar (but longer 34 aa) to O33011|ML1624|MLCB250.18C hypothetical 65.2 KDA protein from Mycobacterium leprae (596 aa), FASTA scores: opt: 3117, E(): 9e-183, (79.8% identity in 584 aa overlap). Also highly similar to Q9S2E8|SCE19A.36C hypothetical 66.2 KDA protein from Streptomyces coelicolor (598 aa), FASTA scores: opt: 1921, E(): 1.1e-109, (56.08% identity in 567 aa overlap); and Q9S3Y6|SDRA SDRA protein from Streptomyces coelicolor (597 aa), FASTA scores: opt: 1896, E(): 3.6e-108, (55.75% identity in 567 aa overlap). And shows some similarity with others proteins from other organisms. Equivalent to AAK47311 putative RNA helicase from Mycobacterium tuberculosis strain CDC1551 (602 aa) but longer 24 aa. Contains PS00017 ATP/GTP-binding site motif A (P-loop).	P9WL21	No	conserved hypotheticals	ML1624	MMAR_1790	MSMEG_0866	Mb2941				
NC_000962.3	Mycobrowser_v3	CDS	3228254	3230680	.	-	0	Rv2918c	glnD	Modifies, by uridylylation or deuridylylation the PII (GLNB|Rv2919c) regulatory protein [catalytic activity: UTP + [protein-PII] = diphosphate + uridylyl-[protein-PII]].	Probable [protein-PII] uridylyltransferase GlnD (PII uridylyl- transferase) (uridylyl removing enzyme) (UTASE)	Rv2918c, (MTCY338.07c), len: 808 aa. Probable glnD, uridylyltransferase (ala-rich protein), similar to other uridylyltransferases e.g. O69873||SC2E1.02 from Streptomyces coelicolor (835 aa), FASTA scores: opt: 1473, E(): 2.8e-81, (41.03% identity in 858 aa overlap); P43919|GLND_HAEIN from Haemophilus influenzae (863 aa), FASTA scores: opt: 333, E(): 2.5e-12, (25.4% identity in 819 aa overlap); P27249|GLND_ECOLI|GLND|B0167 from Escherichia coli strain K12 (890 aa), FASTA scores: opt: 306, E(): 1.1e-10, (27.75% identity in 858 aa overlap); etc. Belongs to the GlnD family.	P9WN29	No	intermediary metabolism and respiration	ML1625,ML1625c	MMAR_1789	MSMEG_2427	Mb2942c				
NC_000962.3	Mycobrowser_v3	CDS	3231073	3232506	.	-	0	Rv2920c	amt	Thought to be involved in transport of ammonium across the membrane (export). Responsible for the translocation of the substrate across the membrane.	Probable ammonium-transport integral membrane protein Amt	Rv2920c, (MTCY338.09c), len: 477 aa. Probable amt, ammonium-transport integral membrane protein (ala-, gly-, leu-, val-rich protein), highly similar to others e.g. Q9ZBP6|SC7A1.27 ammonium transporter from Streptomyces coelicolor (448 aa), FASTA scores: opt: 1246, E(): 7.3e-67, (54.1% identity in 462 aa overlap); P54146|AMT_CORGL ammonium transport system from Corynebacterium glutamicum (452 aa), FASTA scores: opt: 953, E(): 2.1e-49, (41.45% identity in 475 aa overlap); Q07429|NRGA_BACSU probable ammonium transporter (membrane protein NRGA) from Bacillus subtilis (404 aa), FASTA scores: opt: 721, E(): 0, (44.4% identity in 430 aa overlap); etc. Belongs to the AMT1/MEP/NRGA family of ammonium transporters (TC 2.49).	P9WQ65	No	cell wall and cell processes	ML1627,ML1627c	MMAR_1787	MSMEG_2425	Mb2944c				
NC_000962.3	Mycobrowser_v3	CDS	3232871	3234139	.	-	0	Rv2921c	ftsY	Probably involved in the reception and insertion of a subset of proteins at the membrane: possibly membrane receptor for FFH|Rv2916c.	Probable cell division protein FtsY (SRP receptor) (signal recognition particle receptor)	Rv2921c, (MTCY338.10c, MT2989), len: 422 aa. Probable ftsY, signal recognition particle (SRP) receptor, a membrane-associated cell division protein (see citation below), equivalent to O33010|FTSY_MYCLE cell division protein FTSY homolog from Mycobacterium leprae (430 aa), FASTA scores: opt: 1760, E(): 1.1e-108, (81.35% identity in 429 aa overlap). Also similar to others e.g. Q9I6C1|FTSY|PA0373 signal recognition particle receptor FTSY from Pseudomonas aeruginosa (455 aa), FASTA scores: opt: 882, E(): 5.1e-40, (42.08% identity in 385 aa overlap); Q9KVJ6|FTSY cell division protein from Vibrio cholerae (391 aa), FASTA scores: opt: 837, E(): 1.2e-37, (36.3% identity in 394 aa overlap); P10121|FTSY_ECOLI|FTSY|B3464 cell division protein from Escherichia coli strain K12 (497 aa), FASTA scores: opt: 800, E(): 1.3e-35, (39.75% identity in 327 aa overlap); etc. Also similar to Q9ZBP9|SC7A1.24 putative prokaryotic docking protein from Streptomyces coelicolor (412 aa), FASTA scores: opt: 1461, E(): 4.3e-71, (60.3% identity in 423 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00300 SRP54-type proteins GTP-binding domain signature. Belongs to the SRP family of GTP-binding proteins.	P9WGD9	No	cell wall and cell processes	ML1628,ML1628c	MMAR_1786	MSMEG_2424	Mb2945c				
NC_000962.3	Mycobrowser_v3	CDS	3241222	3241959	.	-	0	Rv2927c	Rv2927c	Function unknown	Conserved hypothetical protein	Rv2927c, (MTCY338.16c), len: 245 aa. Conserved hypothetical protein, equivalent to Q9CBS6|ML1661|MLCB1243.13 (alias O69467) hypothetical protein from Mycobacterium leprae (247 aa), FASTA scores: opt: 1440, E(): 4.9e-76, (90.6% identity in 245 aa overlap). Also similar to many hypothetical proteins from other organisms e.g. Q9ZBR0|SC7A1.13 hypothetical 41.0 KDA protein from Streptomyces coelicolor (379 aa), FASTA scores: opt: 266, E(): 3.4e-08, (29.9% identity in 234 aa overlap); etc. Also some similarity with P46815|AG84_MYCLE|ML0922 antigen 84 from Mycobacterium leprae (266 aa), FASTA scores: opt: 193, E(): 0.00043, (28.7% identity in 136 aa overlap) (see citation below); and P46816|AG84_MYCTU|WAG31|Rv2145c|MT2204|MTCY270.23 antigen 84 from Mycobacterium tuberculosis (260 aa), FASTA scores: opt: 178, E(): 0.0031, (34.35% identity in 131 aa overlap) (see citation below). Contains potential coiled-coil region.	P9WL15	No	conserved hypotheticals	ML1661,ML1661c	MMAR_1780	MSMEG_2416	Mb2952c				
NC_000962.3	Mycobrowser_v3	CDS	3272214	3273209	.	+	0	Rv2936	drrA	Probably involved in active transport of antibiotic and phthiocerol dimycocerosate (dim) across the membrane (export). DRRA, DRRB|Rv2936|MTCY19H9.05 and DRRC|Rv2938|MTCY19H9.06 may act jointly to confer daunorubicin and doxorubicin resistance by an export mechanism. Responsible for energy coupling to the transport system.	Daunorubicin-dim-transport ATP-binding protein ABC transporter DrrA	Rv2936, (MTCY19H9.04), len: 331 aa. drrA, daunorubicin-dim-transport resistance ATP-binding protein ABC transporter, probably involved in daunorubicin resistance and phthiocerol dimycocerosate transport (see citations below), equivalent to Q49938|DRRA|ML2352|L518_F2_43|DRRA probable daunorubicin resistance ATP-binding protein from Mycobacterium leprae (331 aa), FASTA scores: opt: 1842, E(): 4.2e-103, (85.2% identity in 331 aa overlap). Also highly similar to others e.g. Q9XCF7 DRRA from Mycobacterium avium (315 aa), FASTA scores: opt: 1040, E(): 4.7e-55, (54.35% identity in 309 aa overlap); Q9X5J8 daunorubicin resistance protein A from Mycobacterium avium (315 aa), FASTA scores: opt: 1030, E(): 1.9e-54, (53.7% identity in 309 aa overlap); P32010|DRRA_STRPE daunorubicin resistance ATP-binding protein from Streptomyces peucetius (330 aa), FASTA scores: opt: 852, E(): 9e-44, (47.15% identity in 318 aa overlap); etc. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and PS00211 ABC transporters family signature. Belongs to the ATP-binding transport protein family (ABC transporters). Note that Rv2936|drrA belongs to the transcriptional unit Rv2930|fadD26-Rv2939|papA5 (proven experimentally).	P9WQL9	No	cell wall and cell processes	ML2352,ML2352c	MMAR_1771		Mb2961				
NC_000962.3	Mycobrowser_v3	CDS	3274072	3274902	.	+	0	Rv2938	drrC	Probably involved in active transport of antibiotic and phthiocerol dimycocerosate (dim) across the membrane (export). DRRA|Rv2934|MTCY19H9.04, DRRB|Rv2937|MTCY19H9.05 and DRRC may act jointly to confer daunorubicin and doxorubicin resistance by an export mechanism. Probably responsible for the translocation of the substrate across the membrane and localization of dim into the cell wall.	Probable daunorubicin-dim-transport integral membrane protein ABC transporter DrrC	Rv2938, (MTCY19H9.06), len: 276 aa. Probable drrC, daunorubicin-dim-transport integral membrane protein ABC transporter, probably involved in daunorubicin resistance and phthiocerol dimycocerosate transport (see citations below), equivalent to Q9CB71|ML2350 probable antibiotic resistance membrane protein from Mycobacterium leprae (276 aa), FASTA scores: opt: 1434, E(): 1.2e-81, (79.0% identity in 276 aa overlap); and Q49941|DRRC|L518_F3_76 putative daunorubicin resistance transmembrane protein from Mycobacterium leprae (244 aa), FASTA scores: opt: 1194, E(): 8.3e-67, (76.85% identity in 242 aa overlap). Also similar to others e.g. Q9XCF9 DRRC protein from Mycobacterium avium (263 aa), FASTA scores: opt: 538, E(): 3.7e-26, (32.65% identity in 251 aa overlap); Q9S6H3 daunorubicin resistance protein C from Mycobacterium avium (263 aa), FASTA scores: opt: 533, E(): 7.6e-26, (32.25% identity in 251 aa overlap); P32011|DRRB_STRPE daunorubicin resistance transmembrane protein from Streptomyces peucetius (283 aa), FASTA scores: opt: 276, E(): 6.6e-10, (21.07% identity in 261 aa overlap); etc. Note that Rv2938|drrC belongs to the transcriptional unit Rv2930|fadD26-Rv2939|papA5 (proven experimentally).	P9WG21	No	cell wall and cell processes	ML2350,ML2350c	MMAR_1769		Mb2963				
NC_000962.3	Mycobrowser_v3	CDS	3283335	3285077	.	+	0	Rv2941	fadD28	Involved in phthiocerol dimycocerosate (dim) biosynthesis. Thought to be involved in the release and transfer of mycoserosic acid from mas onto the DIOLS.	Fatty-acid-AMP ligase FadD28 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)	Rv2941, (MTCY24G1.08c), len: 580 aa. FadD28 (alternate gene name: acoas), fatty-acid-AMP synthetase (see citations below), almost identical to P71495 acyl-CoA synthase from Mycobacterium bovis (582 aa), FASTA scores: opt: 3828, E(): 0, (99.15% identity in 580 aa overlap); and equivalent to Q9CD79|FADD28|ML0138 acyl-CoA synthetase from Mycobacterium leprae (579 aa), FASTA scores: opt: 3183, E(): 8.8e-186, (81.9% identity in 580 aa overlap). And also highly similar to others Mycobacteria proteins e.g. O07797|FADD23|Rv3826|MTCY409.04c putative fatty-acid-CoA synthetase from Mycobacterium tuberculosis (584 aa); etc. Contains PS00018 EF-hand calcium-binding domain. Note that Rv2941|fadD28 and Rv2942|mmpL7 are transcriptionally coupled (proven experimentally).	P9WQ59	No	lipid metabolism	ML0138,ML0138c	MMAR_1765	MSMEG_4731	Mb2966				
NC_000962.3	Mycobrowser_v3	CDS	3350274	3350993	.	-	0	Rv2993c	Rv2993c	Isomerizes HHDD (2-hydroxy-hept-2,4-diene-1,7-dioate) to OHED (2-oxo-hept-3-ene-1,7-dioate).	Possible 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (HHDD isomerase)	Rv2993c, (MTV012.07c), len: 239 aa. Possible 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase, equivalent to O33119|ML1689|MLCB637.28 possible 2-hydroxyhepta-2,4-diene- 1,7-dioate isomerase from Mycobacterium leprae (242 aa), FASTA scores: opt: 1427, E(): 4.4e-86, (85.9% identity in 241 aa overlap). Also similar to others e.g. Q9LBE3|DR1609 from Deinococcus radiodurans (250 aa), FASTA scores: opt: 723, E(): 5.5e-40, (49.05% identity in 216 aa overlap); O27551|MTH1507 from Methanothermobacter thermautotrophicus (260 aa), FASTA scores: opt: 708, E(): 5.4e-39, (52.1% identity in 213 aa overlap); Q9HQR6|VNG1037G|HPCE from Halobacterium sp. (strain NRC-1) (244 aa), FASTA scores: opt: 590, E(): 2.7e-31, (43.65% identity in 220 aa overlap); etc. Start chosen by homology, but ORF could continue upstream.	I6Y276	No	intermediary metabolism and respiration	ML1689,ML1689c	MMAR_1718	MSMEG_2382	Mb3017c				
NC_000962.3	Mycobrowser_v3	CDS	3290624	3291325	.	-	0	Rv2945c	lppX	Unknown	Probable conserved lipoprotein LppX	Rv2945c, (MTCY24G1.04), len: 233 aa. Probable lppX, conserved lipoprotein, equivalent to Q9CD80 putative lipoprotein from Mycobacterium leprae (233 aa), FASTA scores: opt: 1165, E(): 2.1e-65, (76.4% identity in 233 aa overlap); and similar to Q9CCP6|ML0557 from Mycobacterium leprae (238 aa), FASTA scores: opt: 338, E(): 7.4e-14, (30.75% identity in 231 aa overlap). Also similar to others from Mycobacterium tuberculosis e.g. P71679|LPRG_MYCTU lipoprotein (236 aa), FASTA scores: opt: 342, E(): 4.1e-14, (32.05% identity in 231 aa overlap); etc. Contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site, and has in its N-terminal a signal peptide. Belongs to the LPPX/lprafg family of lipoproteins. A core mycobacterial gene; conserved in mycobacterial strains (See Marmiesse et al., 2004).	P9WK65	No	cell wall and cell processes	ML0136	MMAR_1763		Mb2970c				
NC_000962.3	Mycobrowser_v3	CDS	3297837	3299954	.	-	0	Rv2948c	fadD22	Involved in biosynthesis of phenolic glycolipids (PGLs)	P-hydroxybenzoyl-AMP ligase FadD22	Rv2948c, (MTCY24G1.01), len: 705 aa. FadD22, p-hydroxybenzoyl-AMP ligase. Highly similar to many e.g. Q9CD82|ML0134 putative acyl-CoA synthetase from Mycobacterium leprae (707 aa), fasta scores: opt: 3554, E(): 6.4e-209, (75.9% identity in 705 aa overlap). Almost identical to G560509|Q50468 PKS002A protein from Mycobacterium tuberculosis (705 aa), fasta scores: opt: 4647, E(): 0, (99.7% identity in 705 aa overlap).	P9WQ61	No	lipid metabolism	ML0134	MMAR_1761		Mb2972c				
NC_000962.3	Mycobrowser_v3	CDS	3300596	3302455	.	-	0	Rv2950c	fadD29	Involved in biosynthesis of phenolic glycolipids (PGLs)	Fatty-acid-AMP ligase FadD29 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)	Rv2950c, (MTCY349.40), len: 619 aa. fadD29, fatty-acid-AMP synthetase, similar to various mycobacterial enzymes believed to be involved in polyketide or fatty acid synthesis. Equivalent (but shorter 61 aa) to Q9CD84 from Mycobacterium leprae (680 aa), FASTA scores: opt: 3280, E(): 2.2e-192, (80.15% identity in 620 aa overlap); and highly similar to others from Mycobacterium leprae e.g. Q9Z5K5 probable acyl-CoA synthase (583 aa), FASTA scores: opt: 2358, E(): 3.4e-136, (62.35% identity in 579 aa overlap). Also similar to others from Mycobacterium tuberculosis e.g. Q10976|FD26_MYCTU putative fatty-acid--CoA ligase (583 aa), FASTA scores: opt: 2416, E(): 1e-139, (63.15% identity in 581 aa overlap) (N-terminus shorter); etc. Equivalent to AAK47349 from Mycobacterium tuberculosis strain CDC1551 (582 aa) but longer 37 aa.	P95141	No	lipid metabolism	ML0132	MMAR_1759		Mb2974c				
NC_000962.3	Mycobrowser_v3	CDS	3304441	3305253	.	+	0	Rv2952	Rv2952	Thought to cause methylation.	Possible methyltransferase (methylase)	Rv2952, (MTCY349.38), len: 270 aa. Probable methyltransferase, equivalent to Q9CD86|ML0130 hypothetical protein from Mycobacterium leprae (270 aa), FASTA scores: opt: 1584, E(): 6.1e-99, (83.7% identity in 270 aa overlap). Also highly similar to Q9RMN9|MTF2 putative methyltransferase from Mycobacterium smegmatis (274 aa), FASTA scores: opt: 902, E(): 3.8e-53, (56.35% identity in 252 aa overlap). Also similar to other methyltransferases e.g. Q9ADL4|SORM O-methyltransferase from Polyangium cellulosum (346 aa), FASTA scores: opt: 390, E(): 1.1e-18, (36.25% identity in 251 aa overlap); Q54303|RAPM methyltransferase from Streptomyces hygroscopicus (317 aa), FASTA scores: opt: 315, E(): 1.1e-13, (40.75% identity in 135 aa overlap); etc. Very similar to C-terminal part of Q50584|Rv1523|MTCY19G5.05c hypothetical 37.9 KDA protein from Mycobacterium tuberculosis (358 aa), FASTA score: opt: 965, E(): 2.7e-57, (60.3% identity in 247 aa overlap).	P9WIN3	No	intermediary metabolism and respiration	ML0130,ML0130c	MMAR_3170	MSMEG_0393	Mb2976				
NC_000962.3	Mycobrowser_v3	CDS	3310714	3312000	.	-	0	Rv2958c	Rv2958c	Function unknown; probably involved in cellular metabolism. Possibly involved in resistance to killing by human macrophages.	Possible glycosyl transferase	Rv2958c, (MTCY349.30), len: 428 aa. Possible glycosyl transferase (see citation below), highly similar to Q9CD88|ML0128 putative glycosyl transferase from Mycobacterium leprae (435 aa), FASTA scores: opt: 2116, E(): 5.8e-126, (75.05% identity in 417 aa overlap); and Q9CD91|ML0125 putative glycosyl transferase from Mycobacterium leprae (438 aa), FASTA scores: opt: 2104, E(): 3.3e-125, (74.65% identity in 418 aa overlap). Also shows some similarity to variety of glycosyl transferases e.g. Q9RYI3 putative glycosyltransferase from Deinococcus radiodurans (418 aa), FASTA scores: opt: 317, E(): 1.9e-12, (31.0% identity in 297 aa overlap); Q9S1V2 putative glycosyl transferase from Streptomyces coelicolor (407 aa), FASTA scores: opt: 264, E(): 4.1e-09, (27.2% identity in 342 aa overlap); P72650|CRTX|SLR1125 zeaxanthin glucosyl transferase from Synechocystis sp. strain PCC 6803 (419 aa), FASTA scores: opt: 251, E(): 2.8e-08, (26.8% identity in 295 aa overlap); etc. Very similar to P95130|MTCY349.25 from Mycobacterium tuberculosis (449 aa), FASTA score: opt: 2215, E(): 3.3e-132, (77.25% identity in 422 aa overlap). This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WFR1	No	intermediary metabolism and respiration	ML0128			Mb2982c				
NC_000962.3	Mycobrowser_v3	CDS	3313773	3315122	.	-	0	Rv2962c	Rv2962c	Function unknown; probably involved in cellular metabolism. Possibly involved in resistance to killing by human macrophages.	Possible glycosyl transferase	Rv2962c, (MTCY349.25), len: 449 aa. Possible glycosyl transferase (see citation below), highly similar or identical to Mycobacterium tuberculosis proteins G560522 U0002JA, G560521 U0002H, G560522 U0002JA, G560519 U0002KA. Equivalent (but longer 21 aa) to Q9CD91 putative glycosyl transferase from Mycobacterium leprae (438 aa), FASTA scores: opt: 2229, E(): 1.3e-133, (77.45% identity in 426 aa overlap); and highly similar to Q9CD88 putative glycosyl transferase from Mycobacterium leprae (435 aa), FASTA scores: opt: 2129, E(): 2.7e-127, (74.35% identity in 425 aa overlap); and others from Mycobacterium leprae. Also shows some similarity to variety of glycosyl transferases e.g. Q9RYI3|DRA0329 putative glycosyl transferase from Deinococcus radiodurans (418 aa), FASTA scores: opt: 340, E(): 5.5e-14, (31.2% identity in 330 aa overlap); P72650 zeaxanthin glucosyl transferase from Synechocystis sp. (strain PCC 6803) (419 aa), FASTA scores: opt: 244, E(): 6.6e-08, (26.2% identity in 294 aa overlap); etc. Also highly similar to P95134 hypothetical 46.8 KDA protein from Mycobacterium tuberculosis (428 aa), FASTA scores: opt: 2215, E(): 9.6e-133, (77.25% identity in 422 aa overlap).	P9WN09	No	intermediary metabolism and respiration	ML0125	MMAR_1755		Mb2986c				
NC_000962.3	Mycobrowser_v3	CDS	3316529	3317461	.	+	0	Rv2964	purU	Involved in de novo purine biosynthesis [catalytic activity: 10-formyltetrahydrofolate + H(2)O = formate + tetrahydrofolate].	Probable formyltetrahydrofolate deformylase PurU (formyl-FH(4) hydrolase)	Rv2964, (MTCY349.23c), len: 310 aa. Probable purU, formyltetrahydrofolate deformylase, highly similar to others e.g. Q9RWT1|DR0584 formyltetrahydrofolate deformylase from Deinococcus radiodurans (298 aa), FASTA scores: opt: 1005, E(): 4.9e-52, (52.25% identity in 297 aa overlap); Q9K7U4 formyltetrahydrofolate deformylase from Bacillus halodurans (289 aa), FASTA scores: opt: 982, E(): 1.1e-50, (51.8% identity in 280 aa overlap); Q55135|PURU_SYNY3|SLL0070 formyltetrahydrofolate deformylase from Synechocystis sp. strain PCC 6803 (284 aa), FASTA scores: opt: 839, E(): 2.9e-42, (48.2% identity in 280 aa overlap); etc.	P9WHM3	No	intermediary metabolism and respiration		MMAR_1753	MSMEG_2200	Mb2988				
NC_000962.3	Mycobrowser_v3	CDS	3319663	3323046	.	-	0	Rv2967c	pca	Involved in gluconeogenesis and lipogenesis. Pyruvate carboxylase catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second [catalytic activity: ATP + pyruvate + HCO(3)(-) = ADP + phosphate + oxaloacetate].	Probable pyruvate carboxylase Pca (pyruvic carboxylase)	Rv2967c, (MTCY349.20), len: 1127 aa. Probable pca, pyruvate carboxylase (ala-rich protein), equivalent to Q9F843|PYC pyruvate carboxylase from Mycobacterium smegmatis (1127 aa), FASTA scores: opt: 6232, E(): 0, (83.3% identity in 1127 aa overlap). Also highly similar to others e.g. Q9RK64|SCF11.26c pyruvate carboxylase from Streptomyces coelicolor (1124 aa), FASTA scores: opt: 5526, E(): 0, (74.65% identity in 1125 aa overlap); O54587|PYC pyruvate carboxylase from Corynebacterium glutamicum (Brevibacterium flavum) (1140 aa), FASTA scores: opt: 4811, E(): 0, (64.5% identity in 1132 aa overlap); Q9DDT1 pyruvate carboxylase from Brachydanio rerio (Zebrafish) (1180 aa), FASTA scores: opt: 3133, E(): 1.1e-171, (47.8% identity in 1142 aa overlap); etc. Contains PS00867 Carbamoyl-phosphate synthase subdomain signature 2, PS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site, and PS00188 Biotin-requiring enzymes attachment site.	I6YEU0	No	intermediary metabolism and respiration	ML1665,ML1665c	MMAR_1749	MSMEG_2412	Mb2991c				
NC_000962.3	Mycobrowser_v3	CDS	3323709	3324476	.	-	0	Rv2969c	Rv2969c	Unknown	Possible conserved membrane or secreted protein	Rv2969c, (MTCY349.18), len: 255 aa. Possible conserved membrane or exported protein, equivalent to Q9CBS4|ML1667 possible conserved membrane protein from Mycobacterium leprae (264 aa), FASTA scores: opt: 1101, E(): 9.9e-68, (65.9% identity in 258 aa overlap); and highly similar to O69463 putative transmembrane protein from Mycobacterium leprae (258 aa), FASTA scores: opt: 1097, E(): 1.8e-67, (65.5% identity in 258 aa overlap). C-terminus also highly similar to Q9KK65|996A160 exported protein (fragment) from Mycobacterium avium (85 aa), FASTA scores: opt: 418, E(): 2e-21, (72.95% identity in 85 aa overlap). Also weakly similar to membrane or exported proteins e.g. Q9S2U7|SC4G6.04c putative integral membrane protein from Streptomyces coelicolor (275 aa), FASTA scores: opt: 312, E(): 7.6e-14, (28.25% identity in 230 aa overlap); Q9XAB6|SCC22.22C putative secreted protein from Streptomyces coelicolor (255 aa), FASTA scores: opt: 181, E(): 6.4e-05, (27.0% identity in 226 aa overlap); etc. Also some similarity with P72001|PKNE_MYCTU from Mycobacterium tuberculosis (566 aa), FASTA scores: opt: 264, E(): 2.3e-10, (30.5% identity in 177 aa overlap).	O33272	No	cell wall and cell processes	ML1667,ML1667c	MMAR_1747	MSMEG_2410	Mb2993c				
NC_000962.3	Mycobrowser_v3	CDS	3326101	3326949	.	+	0	Rv2971	Rv2971	Function unknown; probably involved in cellular metabolism.	Probable oxidoreductase	Rv2971, (MTCY349.16c), len: 282 aa. Probable oxidoreductase, possibly aldo/keto reductase, equivalent to O69462 putative oxidoreductase from Mycobacterium leprae (282 aa), FASTA scores: opt: 1495, E(): 4.9e-93, (82.35% identity in 272 aa overlap). Also similar to others e.g. Q9KYM9|SC9H11.10C oxidoreductase from Streptomyces coelicolor (276 aa), FASTA scores: opt: 849, E(): 1.2e-49, (51.7% identity in 267 aa overlap); Q9ZBW7|SC4B5.01C putative oxidoreductase from Streptomyces coelicolor (277 aa), FASTA scores: opt: 847, E(): 1.7e-49, (49.1% identity in 271 aa overlap); Q46857|YQHE_ECOLI|YQHE|B3012 hypothetical oxidoreductase from Escherichia coli strain K12 (275 aa), FASTA scores: opt: 827, E(): 3.7e-48, (47.45% identity in 276 aa overlap); etc. Contains PS00063 Aldo/keto reductase family putative active site signature; and PS00062 Aldo/keto reductase family signature 2.	P9WQA5	No	intermediary metabolism and respiration	ML1669	MMAR_1744	MSMEG_2407	Mb2996				
NC_000962.3	Mycobrowser_v3	CDS	3327023	3327736	.	-	0	Rv2972c	Rv2972c	Unknown	Possible conserved membrane or exported protein	Rv2972c, (MTCY349.15), len: 237 aa. Possible conserved membrane or exported protein, equivalent (but longer 52 aa) to O69461|MLCB1243.02 hypothetical 20.5 KDA protein from Mycobacterium leprae (180 aa), FASTA scores: opt: 581, E(): 8.2e-32, (55.75% identity in 174 aa overlap). Also similar to membrane or exported proteins e.g. Q9F2P3|SCE41.16C putative lipoprotein from Streptomyces coelicolor (258 aa), FASTA scores: opt: 498, E(): 4.1e-26, (44.08% identity in 186 aa overlap); Q99QB5|SCP1.323C putative secreted protein from Streptomyces coelicolor (219 aa), FASTA scores: opt: 329, E(): 8.5e-15, (36.35% identity in 176 aa overlap); Q9ACQ1|SCP1.267 putative secreted protein from Streptomyces coelicolor (219 aa), FASTA scores: opt: 286, E(): 6.6e-12, (32.03% identity in 231 aa overlap); etc.	I6X5W6	No	cell wall and cell processes	ML1670,ML1670c	MMAR_1743	MSMEG_2404	Mb2997c				
NC_000962.3	Mycobrowser_v3	CDS	3332071	3332754	.	-	0	Rv2976c	ung	Involved in base excision repair.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.	Probable uracil-DNA glycosylase Ung (UDG)	Rv2976c, (MTCY349.11), len: 227 aa. Probable ung, uracil-DNA glycosylase (see citation below), equivalent to Q9CBS3 uracil-DNA glycosylase from Mycobacterium leprae (227 aa), FASTA scores: opt: 1394, E(): 8.8e-85, (88.1% identity in 227 aa overlap). Also highly similar to others e.g. Q9EX12 from Streptomyces coelicolor (225 aa), FASTA scores: opt: 1134, E(): 1.3e-67, (72.75% identity in 224 aa overlap); Q9K682|UNG_BACHD from Bacillus halodurans (224 aa), FASTA scores: opt: 652, E(): 8.9e-36, (45.5% identity in 222 aa overlap); P39615|UNG_BACSU from Bacillus subtilis (225 aa), FASTA scores: opt: 625, E(): 5.4e-34, (45.5% identity in 222 aa overlap); etc. Belongs to the uracil-DNA glycosylase family.	P9WFQ9	No	information pathways	ML1675,ML1675c	MMAR_1737	MSMEG_2399	Mb3000c				
NC_000962.3	Mycobrowser_v3	CDS	3332787	3333788	.	-	0	Rv2977c	thiL	Involved in thiamine biosynthesis [catalytic activity: ATP + thiamine phosphate = ADP + thiamine diphosphate].	Probable thiamine-monophosphate kinase ThiL (thiamine-phosphate kinase)	Rv2977c, (MTCY349.10), len: 333 aa. Possible thiL, thiamin-monophosphate kinase, equivalent to Q9CBS2 probable thiamine-monophosphate kinase from Mycobacterium leprae (325 aa), FASTA scores: opt: 1738, E(): 4.5e-98, (80.9% identity in 314 aa overlap). Also highly similar to others e.g. Q9ZBR7|SC7A1.06 putative thiamine monphosphate kinase from Streptomyces coelicolor (322 aa), FASTA scores: opt: 959, E(): 7.8e-51, (51.1% identity in 319 aa overlap); O05514|THIL_BACSU thiamine-monophosphate kinase from Bacillus subtilis (325 aa), FASTA scores: opt: 476, E(): 1.5e-21, (35.15% identity in 273 aa overlap); P77785|THIL_ECOLI|THIL|B0417 thiamine-monophosphate kinase from Escherichia coli strain K12 (325 aa), FASTA scores: opt: 418, E(): 5e-18, (36.9% identity in 282 aa overlap); etc. Belongs to the thiamine-monophosphate kinase family. Note that the start, as given, is in IS1538.	P9WG71	No	intermediary metabolism and respiration	ML1676,ML1676c	MMAR_1735	MSMEG_2398	Mb3001c				
NC_000962.3	Mycobrowser_v3	CDS	3336796	3337917	.	-	0	Rv2981c	ddlA	Involved in cell wall formation. Along with alanine racemase, it MAKES up the D-alanine branch of the peptidoglycan biosynthetic route. [catalytic activity: ATP + D-alanine + D-alanine = ADP + phosphate + D-alanyl-D-alanine].	Probable D-alanine--D-alanine ligase DdlA (D-alanylalanine synthetase) (D-ala-D-ala ligase)	Rv2981c, (MTCY349.06), len: 373 aa. Probable ddlA (alternate gene name: ddl), D-alanine--D-alanine ligase a (see citation below), equivalent to Q9CBS0|Q9CBS0 D-alanine-D-alanine ligase a from Mycobacterium leprae (384 aa), FASTA scores: opt: 2001, E(): 2.4e-115, (81.75% identity in 367 aa overlap); and Q9ZGN0|DDL_MYCSM D-alanine--D-alanine ligase from Mycobacterium smegmatis (373 aa), FASTA scores: opt: 1934, E(): 3.1e-111, (77.95% identity in 372 aa overlap). Also highly similar to others e.g. Q9ZBR9|DDL_STRCO from Streptomyces coelicolor (389 aa), FASTA scores: opt: 1187, E(): 2.2e-65, (52.0% identity in 379 aa overlap); P15051|DDLA_SALTY from Salmonella typhimurium and Salmonella typhi (363 aa), FASTA scores: opt: 946, E(): 1.3e-50, (44.5% identity in 364 aa overlap); P23844|DDLA_ECOLI|DDLA|B0381|Z0477|ECS0431 from Escherichia coli strain O157:H7 and K12 (364 aa), FASTA scores: opt: 938, E(): 3.9e-50, (43.55% identity in 363 aa overlap); etc. Contains PS00843 D-alanine--D-alanine ligase signature 1. Belongs to the D-alanine--D-alanine ligase family.	P9WP31	No	cell wall and cell processes	ML1678,ML1678c	MMAR_1733	MSMEG_2395	Mb3005c				
NC_000962.3	Mycobrowser_v3	CDS	3339854	3342082	.	+	0	Rv2984	ppk1	Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyp) [catalytic activity: ATP + {phosphate}(N) = ADP + {phosphate}(N+1)]. Likely involved in MPRAB-SIGE-rel signalling and the stringent response.	Polyphosphate kinase PPK (polyphosphoric acid kinase) (ATP-polyphosphate phosphotransferase)	Rv2984, (MTCY349.03c), len: 742 aa. Ppk1, polyphosphate kinase (See Sureka et al., 2007), equivalent to O33127|PPK_MYCLE polyphosphate kinase from Mycobacterium leprae (739 aa), FASTA scores: opt: 4264, E(): 0, (87.85% identity in 742 aa overlap). Also highly similar to others e.g. Q9KZV6|PPK_STRCO from Streptomyces coelicolor (746 aa), FASTA scores: opt: 1979, E(): 2.6e-117, (59.9% identity in 701 aa overlap); Q9KD27|PPK_BACHD from Bacillus halodurans (705 aa), FASTA scores: opt: 1319, E(): 1.4e-75, (45.55% identity in 674 aa overlap); Q9PAC7|PPK_XYLFA from Xylella fastidiosa (698 aa), FASTA scores: opt: 1300, E(): 2.2e-74, (43.3% identity in 693 aa overlap); etc. Belongs to the polyphosphate kinase family.	P9WHV9	No	intermediary metabolism and respiration	ML1681	MMAR_1730	MSMEG_2391	Mb3008				
NC_000962.3	Mycobrowser_v3	CDS	3342165	3343118	.	+	0	Rv2985	mutT1	Function unknown; hydrolytic enzyme. Possibly involved in removal of damaged nucleotide.	Possible hydrolase MutT1	Rv2985, (MTCY349.02c), len: 317 aa. Possible mutT1, long MutT protein (hydrolase) (see citation below), highly similar to O33126|MLCB637.35 hypothetical 34.5 KDA protein from Mycobacterium leprae (312 aa), FASTA scores: opt: 1514, E(): 5.1e-91, (71.85% identity in 316 aa overlap); and Q9CBR8|ML1682 hypothetical protein from Mycobacterium leprae (311 aa), FASTA scores: opt: 1510, E(): 9.2e-91, (71.5% identity in 316 aa overlap). Also similar to Q50195|L222-ORF6|ML2698 hypothetical protein from Mycobacterium leprae (251 aa), FASTA scores: opt: 231, E(): 1.1e-07, (36.7% identity in 128 aa overlap). Also similar to shorter mutt proteins and related hypothetical protein e.g. Q9EUS6 hypothetical 16.6 KDA protein from Streptomyces griseus subsp. griseus (152 aa), FASTA scores: opt: 380, E(): 1.7e-17, (50.75% identity in 130 aa overlap); Q9KZV8|SCD84.10C putative mutt-like protein from Streptomyces coelicolor (142 aa), FASTA scores: opt: 376, E(): 2.9e-17, (46.1% identity in 128 aa overlap); P96590|mutt mutt protein from Bacillus subtilis (149 aa), FASTA scores: opt: 180, E(): 0.00017, (35.25% identity in 122 aa overlap); etc. Also similar to O05437 hypothetical 27.1 KDA protein from Mycobacterium tuberculosis (248 aa), FASTA scores: opt: 224, E(): 3.2e-07, (34.03% identity in 144 aa overlap). Contains PS00893 mutT domain signature. Seems to belong to the mutt/NUDIX family protein.	P9WIY3	No	information pathways	ML1682	MMAR_1729	MSMEG_2390	Mb3009				
NC_000962.3	Mycobrowser_v3	CDS	3346147	3346848	.	+	0	Rv2989	Rv2989	Involved in transcriptional mechanism.	Probable transcriptional regulatory protein	Rv2989, (MTV012.03), len: 233 aa. Probable transcriptional regulator (ala-rich protein), highly similar to O86533|SC1C2.33c putative transcriptional regulator from Streptomyces coelicolor (238 aa), FASTA scores: opt: 711, E(): 2.3e-38, (53.05% identity in 230 aa overlap); and similar to others e.g. Q9KND6 putative transcriptional regulator from Vibrio cholerae (244 aa), FASTA scores: opt: 232, E(): 1.2e-07, (29.75% identity in 232 aa overlap); Q9R9U0|SRPS efflux pump regulator from Pseudomonas putida (259 aa), FASTA scores: opt: 224, E(): 4.1e-07, (28.35% identity in 247 aa overlap); etc. Also similar to proteins from Mycobacterium tuberculosis e.g. O06806|Rv1773c|MTCY28.39 hypothetical 26.6 KDA protein (248 aa), FASTA scores: opt: 239, E(): 4.4e-08, (29.85% identity in 231 aa overlap); P71977|RV1719|MTCY04C12.04 hypothetical 27.9 KDA protein (259 aa), FASTA scores: opt: 215, E(): 1.6e-06, (31.85% identity in 223 aa overlap); etc. Equivalent to AAK47396 from Mycobacterium tuberculosis strain CDC1551 (267 aa) but shorter 34 aa. Contains possible helix-turn-helix motif at aa 25-46 (Score 1005, +2.61 SD).	O53238	No	regulatory proteins	ML1686	MMAR_1725	MSMEG_2386	Mb3013				
NC_000962.3	Mycobrowser_v3	CDS	3351269	3352606	.	+	0	Rv2994	Rv2994	Unknown; COULB be involved in efflux system (possibly drug).	Probable conserved integral membrane protein	Rv2994, (MTV012.08), len: 445 aa. Probable conserved integral membrane protein, member of major facilitator superfamily (MFS) possibly involved in transport of drug. C-terminal part highly similar to O33118|MLCB637.27c hypothetical 14.7 KDA protein (probable pseudogene product) from Mycobacterium leprae (134 aa), FASTA scores: opt: 483, E(): 2.7e-21, (60.9% identity in 138 aa overlap). Also similar to various transporters e.g. Q9I5C8|PA0811 probable MFS transporter from Pseudomonas aeruginosa (415 aa), FASTA scores: opt: 289, E(): 1.3e-09, (26.05% identity in 399 aa overlap); O30210|AF0025 cyanate transport protein from Archaeoglobus fulgidus (393 aa), FASTA scores: opt: 281, E(): 3.7e-09, (24.05% identity in 399 aa overlap); Q9RI35|SCJ12.25C putative nitrate/nitrite transporter from Streptomyces coelicolor (412 aa), FASTA scores: opt: 264, E(): 3.8e-08, (24.95% identity in 409 aa overlap); Q9A5N5|CC2412 major facilitator family transporter from Caulobacter crescentus (405 aa), FASTA scores: opt: 263, E(): 4.3e-08, (27.55% identity in 399 aa overlap); etc. First start taken; similarity to P21191|NORA_STAAU quinolone resistance protein from Staphylococcus aureus (388 aa) suggests alternative start at 7319 but then no positively charged aa before first transmembrane segment.	P9WJW7	No	cell wall and cell processes	ML1690	MMAR_1717	MSMEG_2380	Mb3018				
NC_000962.3	Mycobrowser_v3	CDS	3352458	3353468	.	-	0	Rv2995c	leuB	Involved in leucine biosynthesis (at the third step) [catalytic activity: 3-carboxy-2-hydroxy-4-methylpentanoate + NAD(+) = 3-carboxy-4-methyl-2-oxopentanoate + NADH (the product decarboxylates to 4-methyl-2-oxopentanoate)].	Probable 3-isopropylmalate dehydrogenase LeuB (beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	Rv2995c, (MTV012.09), len: 336 aa. Probable leuB, 3-isopropylmalate dehydrogenase, identical except a single bp to P94929|LEU3_MYCBO 3-isopropylmalate dehydrogenase from Mycobacterium bovis (336 aa) (see citation below), FASTA scores: opt: 2168, E(): 5.1e-132, (99.7% identity in 336 aa overlap); and equivalent to O33117|LEU3_MYCLE 3-isopropylmalate dehydrogenase from Mycobacterium leprae (336 aa), FASTA scores: opt: 1864, E(): 1.8e-112, (83.95% identity in 336 aa overlap). Also highly similar to others e.g. P94631|LEU3_CORGL from Corynebacterium glutamicum (340 aa), FASTA scores: opt: 1526, E(): 1e-90, (69.9% identity in 339 aa overlap); O86504 from Streptomyces coelicolor (347 aa), FASTA scores: opt: 1470, E(): 4.2e-87, (67.85% identity in 339 aa overlap); Q9UZ05|PAB2424 from Pyrococcus abyssi (354 aa), FASTA scores: opt: 998, E(): 1e-56, (50.0% identity in 322 aa overlap); etc. Note that also shows high similarity with many tartrate dehydrogenases. Belongs to the isocitrate and isopropylmalate dehydrogenases family.	P9WKK9	No	intermediary metabolism and respiration	ML1691,ML1691c	MMAR_1716	MSMEG_2379	Mb3019c				
NC_000962.3	Mycobrowser_v3	CDS	3357602	3358567	.	+	0	Rv2999	lppY	Unknown	Probable conserved lipoprotein LppY	Rv2999, (MTV012.13), len: 321 aa. Probable lppY, conserved lipoprotein, highly similar to O07774|LPQO|Rv0604|MTCY19H5.18c putative lipoprotein from Mycobacterium tuberculosis (316 aa), FASTA scores: opt: 1153, E(): 5e-62, (53.2% identity in 312 aa overlap); and showing similarity with AAK80743|CAC2799 uncharacterized conserved protein similar to LPPY/LPQO of Mycobacterium tuberculosis from Clostridium acetobutylicum (152 aa), FASTA scores: opt: 165, E(): 0.0077, (26.08% identity in 138 aa overlap); and Q9F2T1|SCD65.01c putative lipoprotein (fragment) from Streptomyces coelicolor (146 aa), FASTA scores: opt: 126, E(): 1.6, (% identity in aa overlap). Equivalent to AAK47407 from Mycobacterium tuberculosis strain CDC1551 (329 aa) but shorter 8 aa. Contains probable N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	O53246	No	cell wall and cell processes				Mb3024				
NC_000962.3	Mycobrowser_v3	CDS	3360624	3361130	.	-	0	Rv3002c	ilvN	Involved in valine and isoleucine biosynthesis (at the first step) [catalytic activity: 2-acetolactate + CO(2) = 2-pyruvate].	Probable acetolactate synthase (small subunit) IlvN (acetohydroxy-acid synthase) (AHAS) (ALS)	Rv3002c, (MT3082, MTV012.16c), len: 168 aa. Probable ilvN (alternate gene name: ilvH), acetolactate synthase, small subunit, equivalent or highly similar to others e.g. O33113|ILVH_MYCLE|MLCB637.21 from Mycobacterium leprae (169 aa), FASTA scores: opt: 843, E(): 5.1e-47, (83.5% identity in 164 aa overlap); Q59499|ILVH_MYCAV|ILVN from Mycobacterium avium (167 aa), FASTA scores: opt: 798, E(): 3.7e-44, (81.05% identity in 169 aa overlap); Q9Z566|ILVN from Streptomyces coelicolor (174 aa), FASTA scores: opt: 678, E(): 1.7e-36, (64.8% identity in 159 aa overlap); etc. Belongs to the acetolactate synthase small subunit family.	P9WKJ3	No	intermediary metabolism and respiration	ML1695,ML1695c	MMAR_1711	MSMEG_2373	Mb3027c				
NC_000962.3	Mycobrowser_v3	CDS	3361130	3362986	.	-	0	Rv3003c	ilvB1	Involved in valine and isoleucine biosynthesis (at the first step) [catalytic activity: 2-acetolactate + CO(2) = 2 pyruvate].	Acetolactate synthase (large subunit) IlvB1 (acetohydroxy-acid synthase)	Rv3003c, (MT3083, MTV012.17c), len: 618 aa. ilvB1, acetolactate synthase, large subunit, equivalent or highly similar to others e.g. O33112|ILVB_MYCLE|MLCB637.20|ML1696 from Mycobacterium leprae (625 aa), FASTA scores: opt: 3653, E(): 5.4e-208, (87.1% identity in 627 aa overlap); Q59498|ILVB_MYCAV from Mycobacterium avium (621 aa), FASTA scores: opt: 3473, E(): 2.3e-197, (84.7% identity in 614 aa overlap); P42463|ILVB_CORGL from Corynebacterium glutamicum (Brevibacterium flavum) (626 aa), FASTA scores: opt: 2754, E(): 5.9e-155, (65.8% identity in 589 aa overlap); etc. Contains PS00187 Thiamine pyrophosphate enzymes signature. Cofactor: thiamine pyrophosphate, and magnesium (by similarity). Note that previously known as ilvB.	P9WG41	No	intermediary metabolism and respiration	ML1696,ML1696c	MMAR_1710	MSMEG_2372	Mb3028c				
NC_000962.3	Mycobrowser_v3	CDS	3372545	3374620	.	-	0	Rv3014c	ligA	This protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA [catalytic activity: NAD(+) + (deoxyribonucleotide)(N) + (deoxyribonucleotide)(M) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(N+M)].	DNA ligase [NAD dependent] LigA (polydeoxyribonucleotide synthase [NAD+])	Rv3014c, (MT3094, MTV012.28c), len: 691 aa. ligA (alternate gene name: lig), DNA ligase NAD-dependent (see citation below), equivalent to O33102|DNLJ_MYCLE|LIGA|LIG|ML1705|MLCB637.10 DNA ligase from Mycobacterium leprae (694 aa), FASTA scores: opt: 3844, E(): 0, (84.7% identity in 687 aa overlap). Also highly similar to many prokaryotic and eukaryotic ligases e.g. Q9Z585|LIGA|SC8D9.06 from Streptomyces coelicolor (735 aa), FASTA scores: opt: 2002, E(): 4e-113, (59.4% identity in 714 aa overlap); P49421|DNLJ_RHOMR|LIGA|LIG from Rhodothermus marinus (712 aa), FASTA scores: opt: 1835, E(): 4.6e-103, (45.55% identity in 685 aa overlap); P15042|DNLJ_ECOLI|LIGA|LIG|DNAL|PDEC|lop|B2411 from Escherichia coli strain K12 (671 aa), FASTA scores: opt: 1696, E(): 1.1e-94, (43.8% identity in 680 aa overlap); etc. Belongs to the NAD-dependent DNA ligase family.	P9WNV1	No	information pathways	ML1705,ML1705c	MMAR_1694	MSMEG_2362	Mb3039c				
NC_000962.3	Mycobrowser_v3	CDS	3376490	3376852	.	-	0	Rv3017c	esxQ	Unknown	ESAT-6 like protein EsxQ (TB12.9) (ESAT-6 like protein 8)	Rv3017c, (MT3097, MTV012.31c), len: 120 aa. EsxQ, ESAT-6 like protein (see citation below), possibly secreted protein, very similar to AAK47433|MT3104 putative secreted ESAT-6 like protein 9 from Mycobacterium tuberculosis strain CDC1551 (96 aa), FASTA scores: opt: 315, E(): 1.2e-14, (65.7% identity in 70 aa overlap); Rv3019c|O53266|MTV012.33c putative secreted ESAT-6 like protein 9 from Mycobacterium tuberculosis (96 aa), FASTA scores: opt: 315, E(): 1.2e-14, (65.7% identity in 70 aa overlap) and Rv0288|O53693|CFP7|MT0301|MTV035.16 10 KDA antigen CFP7 (low molecular weight protein antigen 7) (CFP-7) from Mycobacterium tuberculosis (95 aa), FASTA scores: opt: 303, E(): 7.4e-14, (66.2% identity in 68 aa overlap). An alternative start site exists at 3376801. Belongs to the ESAT6 family. Note previously known as TB12.9.	P9WNJ1	No	cell wall and cell processes				Mb3042c				
NC_000962.3	Mycobrowser_v3	CDS	3387075	3388031	.	-	0	Rv3028c	fixB	The electron transfer flavoprotein serves as a specific electron acceptor for other dehydrogenases. It transfers the electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase (ETF dehydrogenase).	Probable electron transfer flavoprotein (alpha-subunit) FixB (alpha-ETF) (electron transfer flavoprotein large subunit) (ETFLS)	Rv3028c, (MTV012.43c), len: 318 aa. Probable fixB (alternate gene name: etfA), electron transfer flavoprotein (alpha subunit) for various dehydrogenases. Equivalent to O33096|ETFA_MYCLE|FIXB|ML1711|MLCB637.04 electron transfer flavoprotein from Mycobacterium leprae (318 aa), FASTA scores: opt: 1788, E(): 1.1e-87, (89.3% identity in 318 aa overlap). Also highly similar to many e.g. Q9K418|SCG22.27c from Streptomyces coelicolor (320 aa), FASTA scores: opt: 1161, E(): 1.6e-54, (59.45% identity in 323 aa overlap); AAK08137|etfa from Rhodobacter sphaeroides (308 aa), FASTA scores: opt: 792, E(): 5.1e-35, (45.95% identity in 309 aa overlap); P38974|ETFA_PARDE electron transfer flavoprotein from Paracoccus denitrificans (307 aa), FASTA scores: opt: 789, E(): 7.4e-35, (45.95% identity in 309 aa overlap); etc. Belongs to the Etf alpha-subunit / FixB family.	P9WNG9	No	intermediary metabolism and respiration	ML1711,ML1711c	MMAR_1685	MSMEG_2352	Mb3054c				
NC_000962.3	Mycobrowser_v3	CDS	3389922	3391502	.	+	0	Rv3031	Rv3031	Function unknown	Conserved protein	Rv3031, (MTV012.46), len: 526 aa. Conserved protein, equivalent to Q9CBR4|ML1714 hypothetical protein from Mycobacterium leprae (522 aa), FASTA scores: opt: 3167, E(): 4.4e-190, (86.15% identity in 526 aa overlap); and highly similar to truncated O33093|MLCB637.01c hypothetical 37.2 KDA protein (fragment) from Mycobacterium leprae (338 aa), FASTA scores: opt: 2041, E(): 5.7e-120, (84.8% identity in 342 aa overlap). Also some similarity to hypothetical proteins Q9V0M7|PAB1857 from Pyrococcus abyssi (602 aa), FASTA scores: opt: 477, E(): 3.5e-22, (31.2% identity in 556 aa overlap); and Synechocystis P74630|D90916|SLL0735 from Synechocystis sp. strain PCC 6803 (529 aa), FASTA scores: opt: 282, E(): 4.7e-10, (28.6% identity in 560 aa overlap).	P9WQ27	No	conserved hypotheticals	ML1714	MMAR_1682	MSMEG_2349	Mb3057				
NC_000962.3	Mycobrowser_v3	CDS	3399419	3400183	.	-	0	Rv3039c	echA17	Could possibly oxidize fatty acids using specific components [catalytic activity: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O].	Probable enoyl-CoA hydratase EchA17 (crotonase) (unsatured acyl-CoA hydratase) (enoyl hydrase)	Rv3039c, (MTV012.54c), len: 254 aa. Probable echA17, Enoyl-CoA Hydratase/Isomerase Superfamily member (crotonase). Similar to many e.g. Q9L1E6|SC3D11.16 putative enoyl-CoA hydratase from Streptomyces coelicolor (255 aa), FASTA scores: opt: 625, E(): 1.5e-30, (45.55% identity in 224 aa overlap); O07137||ECH8_MYCLE|ML2402|MLCB1306.05c probable enoyl-CoA hydratase ECHA8 from Mycobacterium leprae (257 aa), FASTA scores: opt: 448, E(): 6.4e-20, (35.3% identity in 235 aa overlap), P97087|CRT crotonase / enoyl-CoA hydratase from Clostridium thermosaccharolyticum (Thermoanaerobacterium thermosaccharolyticum) (259 aa), FASTA scores: opt: 420, E(): 3.1e-18, (31.2% identity in 234 aa overlap). Also similar to Mycobacterium tuberculosis AAK45356|O53418|Rv1070c|ECHA8|MT1100|MTV017.23c probable enoyl-CoA hydratase ECHA8 (257 aa), FASTA scores: opt: 450, E(): 4.9e-20, (36.4% identity in 226 aa overlap). Belongs to the enoyl-CoA hydratase/isomerase family.	P9WNN3	No	lipid metabolism	ML1724,ML1724c	MMAR_1662	MSMEG_2328	Mb3065c				
NC_000962.3	Mycobrowser_v3	CDS	3400192	3401058	.	-	0	Rv3040c	Rv3040c	Function unknown	Conserved protein	Rv3040c, (MTV012.55c), len: 288 aa. Conserved protein, highly similar to Q9XA40|SCH17.07c hypothetical protein from Streptomyces coelicolor (312 aa), FASTA scores: opt: 648, E(): 5.2e-34, (50.0% identity in 260 aa overlap). Also similar to Q9F7R7 predicted mutt superfamily hydrolase from uncultured proteobacterium EBAC31A08 (264 aa), FASTA scores: opt: 295, E(): 1.3e-11, (27.2% identity in 257 aa overlap); AAK24293|CC2322 hypothetical protein from Caulobacter crescentus (254 aa), blast scores: 185 (32% identity) and 131 (37% identity), etc.	O53287	No	conserved hypotheticals	ML1725,ML1725c	MMAR_1661	MSMEG_2327	Mb3066c				
NC_000962.3	Mycobrowser_v3	CDS	3405136	3406215	.	+	0	Rv3044	fecB	May be involved in active transport of FeIII-decitrate across the membrane (import).	Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB	Rv3044, (MTV012.59), len: 359 aa. Probable fecB, FeIII dicitrate-binding periplasmic lipoprotein (see citation below), equivalent to Q9CBQ4|FECB|ML1729 putative FEIII-dicitrate transporter lipoprotein from Mycobacterium leprae (364 aa), FASTA scores: opt: 1816, E(): 1.1e-96, (75.65% identity in 357 aa overlap); and Q9LA57|FECB from Mycobacterium avium (364 aa), FASTA scores: opt: 1769, E(): 5.1e-94. Similar to many periplasmic FeIII-dicitrate transporters e.g. P72593|FECB|SLR1319 from Synechocystis sp. strain PCC 6803 (315 aa), FASTA scores: opt: 459, E(): 3.6e-19, (31.35% identity in 303 aa overlap); and P72611|FECB|SLR1492 from Synechocystis sp. strain PCC 6803. N-terminus longer (approximately 30 aa) to AAK47459 from Mycobacterium tuberculosis strain CDC1551 (327 aa). Has signal peptide and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site.	O53291	No	cell wall and cell processes	ML1729	MMAR_1650	MSMEG_2319	Mb3070				
NC_000962.3	Mycobrowser_v3	CDS	3414719	3414958	.	-	0	Rv3053c	nrdH	Involved in electron transfer system for ribonucleotide reductase system NRDEF.	Probable glutaredoxin electron transport component of NRDEF (glutaredoxin-like protein) NrdH	Rv3053c, (MTCY22D7.29), len: 79 aa. Probable nrdH, glutaredoxin-like protein, equivalent to Q9CBP8|NRDH|ML1736 from Mycobacterium leprae (80 aa), FASTA scores: opt: 478, E(): 2.7e-27, (91.15% identity in 79 aa overlap), and similar to many glutaredoxin-like proteins e.g. Q9XD65|NRDH from Corynebacterium glutamicum (Brevibacterium flavum) (77 aa), FASTA scores: opt: 382, E(): 1.5e-20, (72.35% identity in 76 aa overlap); and Q56108|NRDH_SALTY from Salmonella typhimurium (81 aa), FASTA scores: opt: 243, E(): 9.9e-11, (45.85% identity in 72 aa overlap). Belongs to the glutaredoxin family.	I6YB06	No	information pathways	ML1736,ML1736c	MMAR_1640	MSMEG_2297	Mb3079c				
NC_000962.3	Mycobrowser_v3	CDS	3416081	3416695	.	+	0	Rv3055	Rv3055	Involved in transcriptional mechanism.	Possible transcriptional regulatory protein (probably TetR-family)	Rv3055, (MTCY22D7.26c), len: 204 aa. Possible transcriptional regulatory protein, similar to Q9RD23|SCM1.20c putative TetR-family transcriptional regulator from Streptomyces coelicolor (234 aa), FASTA scores: opt: 471, E(): 4.6e-23, (44.9% identity in 187 aa overlap); and with low similarity to other e.g. Q9ADK8|2SCK31.12 putative TetR-family transcriptional regulator from Streptomyces coelicolor (198 aa), FASTA scores: opt: 208, 2.5e-06, (32.9% identity in 155 aa overlap); Q9ADD9|SCBAC20F6.11c putative TetR-family transcriptional from Streptomyces coelicolor (199 aa), FASTA scores: opt: 182, E(): 0.00012, (31.0% identity in 184 aa overlap). Contains potential helix-turn-helix motif from aa 48 to 69 (+3.42 SD). so may belong to the TetR/AcrR family of transcriptional regulators.	P95103	No	regulatory proteins	ML1738	MMAR_1637	MSMEG_2295	Mb3081				
NC_000962.3	Mycobrowser_v3	CDS	3417799	3418662	.	-	0	Rv3057c	Rv3057c	Unknown, but similar to various oxidoreductases and enzymes involved in polyketides synthesis	Probable short chain alcohol dehydrogenase/reductase	Rv3057c, (MTCY22D7.24), len: 287 aa. Probable oxidoreductase, probably short-chain alcohol dehydrogenase/reductase. Equivalent to Q9CBP7|ML1740 possible short chain dehydrogenases/reductase from Mycobacterium leprae (312 aa), FASTA scores: opt: 1563, E(): 6e-89, (81.8% identity in 280 aa overlap). Also similar to many oxidoreductases e.g. Q9ZBX8|SCD78.21c putative oxidoreductase from Streptomyces coelicolor (585 aa), FASTA scores: opt: 541, E(): 6.7e-26, (37.25% identity in 263 aa overlap); AAK47506|MT3170 oxidoreductase, short-chain dehydrogenase/reductase family from Mycobacterium tuberculosis strain CDC1551 (276 aa), FASTA scores: opt: 521, E(): 6.1e-25, (36.25% identity in 276 aa overlap); AAK45541|MT1283 oxidoreductase, short-chain dehydrogenase/reductase family from Mycobacterium tuberculosis strain CDC1551 (276 aa), FASTA scores: opt: 471, E(): 7.2e-22, (32.4% identity in 281 aa overlap). Also similar to O50460|Rv1245c|MTV006.17C dehydrogenase (276 aa). Contains short-chain alcohol dehydrogenase family signature (PS00061). May belong to the short-chain dehydrogenases/reductases (SDR) family.	I6YB11	No	intermediary metabolism and respiration	ML1740,ML1740c	MMAR_1636	MSMEG_2291	Mb3083c				
NC_000962.3	Mycobrowser_v3	CDS	3418726	3419376	.	-	0	Rv3058c	Rv3058c	Involved in transcriptional mechanism.	Possible transcriptional regulatory protein (probably TetR-family)	Rv3058c, (MTCY22D7.23), len: 216 aa. Possible transcriptional regulatory protein, TetR-family, showing reasonable similarity to others e.g. AAK48337|MT3970 from Mycobacterium tuberculosis strain CDC1551 (216 aa), FASTA scores: opt: 261, E(): 2.8e-10, (31.7% identity in 221 aa overlap); Q49962|ML1070|U1756B from Mycobacterium leprae (217 aa), FASTA scores: opt: 234, E(): 1.8e-08, (27.2% identity in 195 aa overlap); Q9CDD3|ML0064 from Mycobacterium leprae (214 aa), FASTA scores: opt: 199, E(): 3.6e-06, (25.65% identity in 195 aa overlap); O66121|CPRS from Streptomyces coelicolor (215 aa), FASTA scores: opt: 183, E(): 4.2e-05, (26.0% identity in 196 aa overlap). Equivalent to AAK47476|MT3144 from Mycobacterium tuberculosis strain CDC1551 (237 aa) but N-terminus shorter 21 residues. Start was predicted by TBParse but alternatives (ATG) are possible. Could belong to the TetR/AcrR family of transcriptional regulators.	P95100	No	regulatory proteins	ML1741,ML1741c	MMAR_1635	MSMEG_2290	Mb3084c				
NC_000962.3	Mycobrowser_v3	CDS	3419492	3420970	.	+	0	Rv3059	cyp136	Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	Probable cytochrome P450 136 Cyp136	Rv3059, (MTCY22D7.22c), len: 492 aa. Probable cyp136, cytochrome P450 136, similar to other cytochrome P450-dependent oxidases e.g. Q59990|CYP120|CYP|SLR0574 putative cytochrome P450 120 from Synechocystis sp. strain PCC 6803 (444 aa), FASTA scores: opt: 579, E(): 1.5e-29, (27.3% identity in 443 aa overlap); Q64654|CYP51|CP51_RAT cytochrome P450 51 (lanosterol 14-alpha demethylase) from Rattus norvegicus (Rat) (503 aa), FASTA scores: opt: 549, E(): 1.4e-27, (26.2% identity in 458 aa overlap); Q9JIY3|CYP51 lanosterol 14-alpha-demethylase from Mus musculus (Mouse) (486 aa), FASTA scores: opt: 546, E(): 2.1e-27, (25.75% identity in 458 aa overlap). Contains cytochrome P450 cysteine heme-iron ligand signature (PS00086). Belongs to the cytochrome P450 family.	P9WPM7	No	intermediary metabolism and respiration	ML1742	MMAR_1634	MSMEG_2289	Mb3085				
NC_000962.3	Mycobrowser_v3	CDS	3423262	3425427	.	-	0	Rv3061c	fadE22	Function unknown, but involved in lipid degradation.	Probable acyl-CoA dehydrogenase FadE22	Rv3061c, (MTCY22D7.20), len: 721 aa. Probable fadE22, Acyl-CoA Dehydrogenase, similar to many e.g. AAK44503|MT0284 from Mycobacterium tuberculosis strain CDC1551 (731 aa), FASTA scores: opt: 1804, E(): 1.1e-101, (43.45% identity in 743 aa overlap); AAK48037|MT3678 from Mycobacterium tuberculosis strain CDC1551 (711 aa), FASTA scores: opt: 1630, E(): 3.9e-91, (42.55% identity in 733 aa overlap); and extensive similarity in C-terminal part to many acyl-CoA dehydrogenases e.g. Q9A5G9|CC2478 from Caulobacter crescentus (407 aa), FASTA scores: opt: 767, E(): 4.8e-39, (36.7% identity in 376 aa overlap). Also similar to many hypothetical proteins. Could belong to the acyl-CoA dehydrogenases family.	I6X654	No	lipid metabolism	ML1745,ML1745c	MMAR_1625		Mb3087c,Mb3088c				
NC_000962.3	Mycobrowser_v3	CDS	3431979	3433622	.	-	0	Rv3068c	pgmA	This enzyme participates in both the breakdown and synthesis of glucose [catalytic activity: alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate].	Probable phosphoglucomutase PgmA (glucose phosphomutase) (PGM)	Rv3068c, (MTCY22D7.13), len: 547 aa. Probable pgmA, phosphoglucomutase, highly similar to other phosphoglucomutases e.g. Q9L117|PGM from Streptomyces coelicolor (546 aa), FASTA scores: opt: 2569, E(): 2.8e-149, (71.4% identity in 545 aa overlap); Q9ABY5|CC0085 from Caulobacter crescentus (545 aa), FASTA scores: opt: 2465, E(): 6.2e-143, (70.4% identity in 541 aa overlap); P38569|PGMU_ACEXY|CELB from Acetobacter xylinum (555 aa), FASTA scores: opt: 2206, E(): 4e-127, (62.25% identity in 543 aa overlap); P74643|PGM|SLL0726 from Synechocystis sp. strain PCC 6803 (567 aa), FASTA scores: opt: 2168, E(): 8.5e-125, (60.0% identity in 550 aa overlap); P36938|PGMU_ECOLI|PGM|B0688 from Escherichia coli (546 aa), FASTA scores: opt: 2111, E(): 2.5e-121, (58.2% identity in 550 aa overlap). Also similar to other phosphomannomutases. Has phosphoglucomutase and phosphomannomutase signature (PS00710) and ATP/GTP-binding site motif A (P-loop) (PS00017). Belongs to the phosphohexose mutases family.	I6Y2G3	No	intermediary metabolism and respiration	ML1759,ML1759c	MMAR_1591	MSMEG_2136	Mb3095c				
NC_000962.3	Mycobrowser_v3	CDS	3435798	3436322	.	-	0	Rv3072c	Rv3072c	Function unknown	Conserved hypothetical protein	Rv3072c, (MTCY22D7.09), len: 174 aa. Hypothetical protein, similar in part to O87779 hypothetical 18.1 KDA protein (fragment) from Mycobacterium paratuberculosis (166 aa), FASTA scores: opt: 238, E(): 2.5e-08, (42.6% identity in 108 aa overlap); Q9AH10 putative F420-dependent dehydrogenase from Rhodococcus erythropolis (295 aa), FASTA scores: opt: 228, E(): 1.7e-07, (34.25% identity in 111 aa overlap); P71557|Y953_MYCTU|Rv0953c|MTCY10D7.21 possible oxidoreductase from Mycobacterium tuberculosis strain H37Rv (304 aa), FASTA scores: opt: 208, E(): 3.2e-06, (38.9% identity in 108 aa overlap); etc. N-terminal region similar to several proteins from Mycobacterium tuberculosis.	P95086	No	conserved hypotheticals				Mb3099c				
NC_000962.3	Mycobrowser_v3	CDS	3438050	3438973	.	-	0	Rv3075c	Rv3075c	Function unknown	Conserved protein	Rv3075c, (MTCY22D7.06), len: 307 aa. Conserved protein, with some similarity to Q9I562|PA0883 probable acyl-CoA lyase beta chain from Pseudomonas aeruginosa (275 aa), FASTA scores: opt: 408, E(): 9.2e-19, (35.15% identity in 273 aa overlap); Q9S2U9|SC4G6.02 putative citrate lyase beta chain from Streptomyces coelicolor (274 aa), FASTA scores: opt: 384, E(): 3.1e-17, (34.7% identity in 265 aa overlap); O06162|cite|Rv2498c|MTCY07A7.04c from Mycobacterium tuberculosis (273 aa), FASTA scores: opt: 349, E(): 5.1e-15, (35.2% identity in 264 aa overlap); etc. Several initiation codons possible, first one chosen.	I6YF40	No	conserved hypotheticals		MMAR_1583	MSMEG_2667	Mb3102c				
NC_000962.3	Mycobrowser_v3	CDS	3439541	3441352	.	+	0	Rv3077	Rv3077	Function unknown; probably involved in cellular metabolism.	Possible hydrolase	Rv3077, (MTCY22D7.04c), len: 603 aa. Possible hydrolase, with some similarity to variety of hydrolases (aryl- and steryl sulfatases principaly) e.g. Q45087|PEHA phosphonate monoester hydrolase from Burkholderia caryophylli (514 aa), FASTA scores: opt: 239, E(): 7.2e-07, (23.95% identity in 413 aa overlap); Q9I1E5|PA2333 probable sulfatase from Pseudomonas aeruginosa (538 aa), FASTA scores: opt: 231, E(): 2.3e-06, (28.1% identity in 516 aa overlap); P31447|YIDJ_ECOLI|B3678 putative sulfatase from Escherichia coli (497 aa), FASTA scores: opt: 222, E(): 7.4e-06, (27.7% identity in 390 aa overlap); etc. Note that previously known as atsF.	Q6MX15	No	intermediary metabolism and respiration		MMAR_1577	MSMEG_1286	Mb3104				
NC_000962.3	Mycobrowser_v3	CDS	3441770	3442597	.	-	0	Rv3079c	Rv3079c	Function unknown	Conserved protein	Rv3079c, (MTCY22D7.02), len: 275 aa. Conserved protein, similar to other hypothetical mycobacterium proteins e.g. P71557|Y953_MYCTU|Rv0953c|MTCY10D7.21 possible oxidoreductase from Mycobacterium tuberculosis strain H37Rv (282 aa), FASTA scores: opt: 668, E(): 2.4e-34, (40.55% identity in 281 aa overlap); O06216|Rv2161c|MTCY270.07 from Mycobacterium tuberculosis strain H37Rv (288 aa), FASTA scores: opt: 595, E(): 8.5e-30, (40.9% identity in 274 aa overlap); O87779 from Mycobacterium paratuberculosis (166 aa), FASTA scores: opt: 464, E(): 7.2e-22, (41.55% identity in 166 aa overlap); etc. Also some similarity to other proteins e.g. Q9AH10 putative F420-dependent dehydrogenase from Rhodococcus erythropolis (295 aa), FASTA scores: opt: 401, E(): 9.6e-18, (30.2% identity in 288 aa overlap); Q9AE04|RIF17 RIF17 protein from Amycolatopsis mediterranei (356 aa), FASTA scores: opt: 298, E(): 2.8e-11, (35.0% identity in 203 aa overlap); AAK48081|MT3720 luciferase-related protein from Mycobacterium tuberculosis strain CDC1551 (395 aa), FASTA scores: opt: 223, E(): 1.4e-06, (29.4% identity in 211 aa overlap).	I6XG43	No	conserved hypotheticals		MMAR_1575		Mb3106c				
NC_000962.3	Mycobrowser_v3	CDS	3442656	3445988	.	-	0	Rv3080c	pknK	Involved in signal transduction (via phosphorylation). Involved in transcriptional regulatory mechanism and in the regulation of secondary metabolites [catalytic activity: ATP + a protein = ADP + a phosphoprotein].	Serine/threonine-protein kinase transcriptional regulatory protein PknK (protein kinase K) (STPK K)	Rv3080c, (MTV013.01c-MTCY22D7.01), len: 1110 aa. pknK, serine/threonine protein kinase involved in transcriptional regulatory function (see citation below). Similar but shorter in N-terminus (approximately 300 residues) to others e.g. Q48411|ACOK transcriptional regulatory protein of aco ABCD operon from Klebsiella pneumoniae (921 aa), FASTA scores: opt: 886, E(): 7.6e-37, (27.75% identity in 829 aa overlap); Q9HX92|PA3921 probable transcriptional regulator from Pseudomonas aeruginosa (belongs to the LuxR/UhpA family of transcriptional regulators) (906 aa), FASTA scores: opt: 760, E(): 1.5e-30, (29.55% identity in 822 aa overlap); Q9I2X9|PA1760 probable transcriptional regulator from Pseudomonas aeruginosa (belongs to the LuxR/UhpA family of transcriptional regulators) (907 aa), FASTA scores: opt: 696, E(): 2.3e-27, (25.85% identity in 685 aa overlap); P06993|malt (alias BAB37683|ECS4260 and AAG58520|malt) positive regulator of MAL regulon from Escherichia coli strain O157:H7 (901 aa), FASTA scores: opt: 660, E(): 1.4e-25, (29.25% identity in 530 aa overlap); Q9KNF3|VCA0011 malt regulatory protein from Vibrio cholerae (belongs to the LuxR/UhpA family of transcriptional regulators) (921 aa), FASTA scores: opt: 626, E(): 7.2e-24, (25.8% identity in 659 aa overlap); etc. N-terminal region similar to N-terminus of serine/threonine kinases e.g. Q9KK90|PKMA serine/threonine kinase (similar to the Ser/Thr family of protein kinases) from Amycolatopsis mediterranei (589 aa), FASTA scores: opt: 545, E(): 5.7e-20, (34.45% identity in 334 aa overlap); Q9RPT5|AMK serine/threonine protein kinase homolog (similar to the Ser/Thr family of protein kinases) from Amycolatopsis mediterranei (606 aa), FASTA scores: opt: 537, E(): 1.5e-19, (35.55% identity in 346 aa overlap); Q9L0I0|PKAD protein serine/threonine kinase from Streptomyces coelicolor (599 aa), FASTA scores: opt: 520, E(): 1e-18, (36.1% identity in 324 aa overlap); etc. N-terminal part also similar to O53510|PKNL_MYCTU|Rv2176|MT2232|MTV021.09 probable serine/threonine-protein kinase from Mycobacterium tuberculosis strain H37Rv (399 aa), FASTA scores: opt: 511, E(): 2.1e-18, (35.15% identity in 313 aa overlap). Contains PS00107 Protein kinases ATP-binding region signature and PS00017 ATP/GTP-binding site motif A (P-loop). Contains Hank's kinase subdomain. First part of the protein seems belong to the Ser/Thr family of protein kinases, and second parts seems belongs to the LuxR/UhpA family of transcriptional regulators.	P9WI65	No	regulatory proteins		MMAR_2576	MSMEG_0529	Mb3107c				
NC_000962.3	Mycobrowser_v3	CDS	3450920	3451750	.	+	0	Rv3085	Rv3085	Function unknown; supposedly involved in cellular metabolism.	Probable short-chain type dehydrogenase/reductase	Rv3085, (MTV013.06), len: 276 aa. Probable short-chain dehydrogenase/reductase, similar to various oxidoreductases in the short chain dehydrogenases/reductases family e.g. Q9CC98|ML1094 short chain alcohol dehydrogenase from Mycobacterium leprae (277 aa), FASTA scores: opt: 1059, E(): 4.8e-56, (61.65% identity in 266 aa overlap); Q9I3H6|PA1537 probable short-chain dehydrogenase from Pseudomonas aeruginos (295 aa), FASTA scores: opt: 858, E(): 4.7e-44, (48.4% identity in 285 aa overlap); Q9CBP7|ML1740 possible short chain reductase from Mycobacterium leprae (312 aa), FASTA scores: opt: 500, E(): 1e-22, (36.6% identity in 257 aa overlap); etc. Also similar to mycobacterium proteins O50460|Rv1245c|MTV006.17c dehydrogenase similar to the short-chain dehydrogenases/reductases family (276 aa), FASTA scores: opt: 1200, E(): 1.9e-64, (65.2% identity in 273 aa overlap); and P95101|Rv3057c|MTCY22D7.24 hypothetical dehydrogenase (287 aa). Contains PS00061 Short-chain alcohol dehydrogenase family signature. Belongs to the short-chain dehydrogenases/reductases (SDR) family.	P9WGP9	No	intermediary metabolism and respiration				Mb3112				
NC_000962.3	Mycobrowser_v3	CDS	3455761	3457272	.	+	0	Rv3089	fadD13	Function unknown, but involved in lipid degradation.	Probable chain -fatty-acid-CoA ligase FadD13 (fatty-acyl-CoA synthetase)	Rv3089, (MTV013.10), len: 503 aa. Probable fadD13, Acyl-CoA Synthetase, similar to many e.g. MTCI28.06, MTCY08D5.09, MTCY06G11.08 from Mycobacterium tuberculosis strain H37Rv; and to Q9F7P5 predicted acid--CoA ligase FADD13 from uncultured proteobacterium EBAC31A08 (504 aa), FASTA scores: opt: 1126, E(): 2.4e-62, (38.85% identity in 502 aa overlap); Q9EY88|FCS feruloyl-CoA synthetase from Amycolatopsis sp. strain HR167 (491 aa), FASTA scores: opt: 1073, E(): 4.5e-59, (38.5% identity in 504 aa overlap); BAB49118|MLR1843 probable acid-CoA ligase from Rhizobium loti (Mesorhizobium loti) (495 aa), FASTA scores: opt: 937, E(): 1.2e-50, (36.2% identity in 503 aa overlap); Q9KZC1|SC6F7.21 probable long-chain-fatty-acid-CoA ligase from Streptomyces coelicolor (511 aa), FASTA scores: opt: 899, E(): 2.8e-48, (36.1% identity in 510 aa overlap); Q9A5P7|CC2400 putative acid-CoA ligase from Caulobacter crescentus (496 aa), FASTA scores: opt: 874, E(): 9.8e-47, (35.1% identity in 507 aa overlap); etc. Contains PS00455 Putative AMP-binding domain signature and PS00061 Short-chain alcohol dehydrogenase family signature.	P9WQ37	No	lipid metabolism	ML0469	MMAR_2597		Mb3116				
NC_000962.3	Mycobrowser_v3	CDS	3459116	3460807	.	+	0	Rv3091	Rv3091	Function unknown	Conserved protein	Rv3091, (MTCY164.02), len: 563 aa. Conserved protein, similar in part to O60859 neuropathy target esterase from Homo sapiens (Human) (1327 aa), FASTA scores: opt: 177, E(): 0.0062, (30.65% identity in 173 aa overlap); and Q9I385|PA1640 hypothetical protein from Pseudomonas aeruginosa (345 aa), FASTA scores: opt: 152, E(): 0.069, (27.8% identity in 180 aa overlap).	I6YB49	No	conserved hypotheticals		MMAR_1571						
NC_000962.3	Mycobrowser_v3	CDS	3460814	3461734	.	-	0	Rv3092c	Rv3092c	Unknown	Probable conserved integral membrane protein	Rv3092c, (MTCY164.03c), len: 306 aa. Probable conserved integral membrane protein, highly similar to Q9RUT5|DR1297 conserved hypothetical protein from Deinococcus radiodurans (311 aa), FASTA scores: opt: 941, E(): 9.8e-51, (55.65% identity in 309 aa overlap); Q9A8B8|CC1436 hypothetical protein from Caulobacter crescentus (314 aa), FASTA scores: opt: 791, E(): 1.6e-41, (46.9% identity in 305 aa overlap); and also highly similar to Q9I2N8|PA1857 hypothetical protein from Pseudomonas aeruginosa (307 aa), FASTA scores: opt: 373, E(): 8.1e-16, (40.8% identity in 321 aa overlap); BAB36119|ECS2696 putative methyl-independent mismatch repair protein from Escherichia coli strain O157:H7 (305 aa), FASTA scores: opt: 335, E(): 1.7e-13, (39.75% identity in 307 aa overlap).	I6Y2I9	No	cell wall and cell processes		MMAR_1567	MSMEG_0562	Mb3119c				
NC_000962.3	Mycobrowser_v3	CDS	3465778	3467091	.	-	0	Rv3097c	lipY	Generates diacylglycerol and a fatty acid anion from triacylglycerol [catalytic activity: triacylglycerol + H(2)O = diacylglycerol + a fatty acid anion].	PE-PGRS family protein, triacylglycerol lipase LipY (esterase/lipase) (triglyceride lipase) (tributyrase)	Rv3097c, (MTCY164.08c), len: 437 aa. LipY, triacylglycerol lipase. Belongs to the hormone-sensitive lipase family (See Deb et al., 2006) and member of the M. tuberculosis PE-family PGRS subfamily of gly-rich proteins (see citation below); N-terminal part similar to N-terminus of M. tuberculosis PE-PGRS family members e.g. Q10637|Y03A_MYCTU hypothetical glycine-rich 49.6 kDa protein (603 aa). Other relatives include MTCY1A11.25c; MTCY21B4.13c; MTCY270.06; MTCY359.33; MTC1A11.04. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	I6Y2J4	No	PE/PPE		MMAR_1547		Mb3124c				
NC_000962.3	Mycobrowser_v3	CDS	3469301	3469783	.	-	0	Rv3100c	smpB	Binds specifically to the SSRA RNA (TMRNA) and is required for stable association of SSRA with ribosomes. Thought to be implicated in the survival of bacterium within macrophages.	Probable SSRA-binding protein SmpB	Rv3100c, (MTCY164.11c), len: 160 aa. Probable smpB, small protein b related to several bacterial small protein b homologs e.g. O32881|SSRP_MYCLE|ML0671|MLCB1779.19c from Mycobacterium leprae (160 aa), FASTA scores: opt: 914, E(): 1.1e-52, (84.9% identity in 159 aa overlap); Q9L1S9|SMPB from Streptomyces coelicolor (159 aa), FASTA scores: opt: 568, E(): 3.3e-30, (55.15% identity in 145 aa overlap); O32230|SSRP_BACSU from Bacillus subtilis (156 aa), FASTA scores: opt: 511, E(): 1.7e-26, (47.05% identity in 153 aa overlap); etc. Belongs to the SSRP family. Conserved in M. tuberculosis, M. leprae, M. bovis and M. avium paratuberculosis; predicted to be essential for in vivo survival and pathogenicity (See Ribeiro-Guimaraes and Pessolani, 2007).	P9WGD3	No	virulence, detoxification, adaptation	ML0671	MMAR_1532	MSMEG_2091	Mb3127c				
NC_000962.3	Mycobrowser_v3	CDS	3469786	3470679	.	-	0	Rv3101c	ftsX	Involved in growth (principally during log phase cells). Thought to be involved in active transport of septation component across the membrane. Responsible for the translocation of the substrate across the membrane. Is coded in an operon essential for cell division.	Putative cell division protein FtsX (septation component-transport integral membrane protein ABC transporter)	Rv3101c, (MTCY164.12c), len: 297 aa. Putative ftsX, cell division protein, septation component transport integral membrane protein ABC transporter (see citations below), equivalent to O32882|FTSX_MYCLE|ML0670|MLCB1779.20c cell division protein from Mycobacterium leprae (297 aa), FASTA scores: opt: 1597, E(): 9.2e-93, (80.8% identity in 297 aa overlap); and similar to others e.g. Q9L1S7|SCE59.27c from Streptomyces coelicolor (305 aa), FASTA scores: opt: 585, E(): 1.9e-29, (34.55% identity in 304 aa overlap); O34876|FTSX_BACSU from Bacillus subtilis (296 aa), FASTA scores: opt: 318, E(): 9.1e-13, (24.65% identity in 300 aa overlap); Q9K6X3|FTSX|BH3601 from Bacillus halodurans (298 aa), FASTA scores: opt: 290, E(): 5.2e-11, (22.75% identity in 299 aa overlap); etc. Belongs to the FTSX family.	P9WG19	No	cell wall and cell processes	ML0670	MMAR_1531	MSMEG_2090	Mb3128c				
NC_000962.3	Mycobrowser_v3	CDS	3472768	3473904	.	-	0	Rv3105c	prfB	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.	Probable peptide chain release factor 2 PrfB (RF-2)	Rv3105c, (MTCY164.15c), len: 378 aa. Probable prfB, peptide chain release factor 2, equivalent to O32885|RF2_MYCLE|ML0667|MLCB1779.24c from Mycobacterium leprae, FASTA scores: opt: 2197, E(): 1.8e-126, (90.05% identity in 372 aa overlap); and also similar to other peptide chain release factors e.g. Q9L1S3|PRFB from Streptomyces coelicolor (368 aa), FASTA scores: opt: 1674, E(): 1.2e-94, (69.3% identity in 365 aa overlap); O67695|RF2_AQUAE|PRFB|AQ_1840 from Aquifex aeolicus (373 aa), FASTA scores: opt: 1082, E(): 1.3e-58, (44.45% identity in 369 aa overlap); P28367|RF2_BACSU from B. subtilis (366 aa), FASTA scores: opt: 1030, E(): 1.9e-55, (44.0% identity in 359 aa overlap); etc. Also related to Q10605|MTCY373.19|RF1_MYCTU|Rv1299|MT1338 peptide chain release factor 1 (rf-1) (357 aa), FASTA scores: opt: 646, E(): 1.1e-34, (38.6% identity in 350 aa overlap). Contains prokaryotic-type class I peptide chain release factors signature (PS00745). Belongs to the prokaryotic and mitochondrial release factors family.	P9WHG1	No	information pathways	ML0667	MMAR_1527	MSMEG_2086					
NC_000962.3	Mycobrowser_v3	CDS	3475378	3476961	.	-	0	Rv3107c	agpS	Involved in ether lipid biosynthesis [catalytic activity: 1-acyl-glycerone 3-phosphate + a long-chain alcohol = 1-alkyl-glycerone 3-phosphate + a long-chain acid anion].	Possible alkyldihydroxyacetonephosphate synthase AgpS (alkyl-DHAP synthase) (alkylglycerone-phosphate synthase)	Rv3107c, (MTCY164.17c), len: 527 aa. Possible agpS, alkyl-dihydroxyacetonephosphate synthase, similar to others and some various enzymes e.g. AAK46595|MT2311 putative alkyl-dihydroxyacetonephosphate synthase from Mycobacterium tuberculosis strain CDC1551 (529 aa), FASTA scores: opt: 1052, E(): 2.1e-58, (37.1% identity in 542 aa overlap); Q9RJ97|SCF91.28c putative flavoprotein from Streptomyces coelicolor (530 aa), FASTA scores: opt: 972, E(): 2.2e-53, (36.2% identity in 544 aa overlap); O96759|ADAS_DICDI alkyldihydroxyacetonephosphate synthase from Dictyostelium discoideum (Slime mold) (611 aa), FASTA scores: opt: 617, E(): 4.5e-31, (33.95% identity in 480 aa overlap); O97157|ADAS_TRYBB alkyldihydroxyacetonephosphate synthase from Trypanosoma brucei (613 aa), FASTA scores: opt: 567, E(): 6.2e-28, (29.15% identity in 521 aa overlap); etc. Also similar to O53525|Rv2251|MTV022.01 hypothetical 49.8 KDA protein from Mycobacterium tuberculosis strain H37Rv (475 aa), FASTA scores: opt: 1019, E(): 2.3e-56, (38.6% identity in 487 aa overlap). Belongs to the FAD-binding oxidoreductase/transferase family 4. Cofactor: FAD (by similarity).	O05784	No	lipid metabolism	ML0665	MMAR_1525		Mb3134c				
NC_000962.3	Mycobrowser_v3	CDS	3477649	3478728	.	+	0	Rv3109	moaA1	Involved in molybdenum cofactor biosynthesis; involved in the biosynthesis of molybdopterin precursor Z from guanosine.	Probable molybdenum cofactor biosynthesis protein A MoaA1	Rv3109, (MTCY164.19), len: 359 aa. Probable moaA1, molybdenum cofactor biosynthesis protein, highly similar to others e.g. P39757|MOAA_BACSU|NARA|NARAB from Bacillus subtilis (341 aa), FASTA scores: opt: 810, E(): 6.2e-44, (39.75% identity in 327 aa overlap); O67929|MOAA_AQUAE|AQ_2183 from Aquifex aeolicus (320 aa), FASTA scores: opt: 794, E(): 6e-43, (40.55% identity in 323 aa overlap); Q9ZIM6|MOAA_STACA from Staphylococcus carnosus (340 aa), FASTA scores: opt: 783, E(): 3.2e-42, (38.65% identity in 326 aa overlap); etc. Also highly similar to O53143|MOAA3|MOA3_MYCTU|MT3427 molybdenum cofactor biosynthesis protein A 3 from Mycobacterium tuberculosis strain F4 (378 aa), FASTA scores: opt: 1762, E(): 4.7e-104, (74.3% identity in 350 aa overlap); and similar to O53881|MOA2_MYCTU|MOAA2|Rv0869c|MT0892|MTV043.62 molybdenum cofactor biosynthesis protein A 2 from Mycobacterium tuberculosis strain H37Rv (360 aa), FASTA scores: opt: 657, E(): 3e-34, (36.55% identity in 309 aa overlap). Belongs to the MoaA / NifB / PqqE family. Note that previously known as moaA. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WJS3	No	intermediary metabolism and respiration				Mb3136				
NC_000962.3	Mycobrowser_v3	CDS	3480759	3481289	.	+	0	Rv3114	Rv3114	Function unknown	Conserved hypothetical protein	Rv3114, (MTCY164.24), len: 176 aa. Conserved hypothetical protein, with some similarity to Q9F9W7 cytosine deaminase from Bifidobacterium longum (143 aa), FASTA scores: opt: 207, E(): 2.2e-07, (37.05% identity in 108 aa overlap); and Q9RV23|DR1207 cell cycle protein MESJ, putative/cytosine deaminase-related protein from Deinococcus radiodurans (600 aa), FASTA scores: opt: 212, E(): 3.5e-07, (33.35% identity in 177 aa overlap). Equivalent to AAK47536|MT3196 cytidine and deoxycytidylate deaminase family protein from Mycobacterium tuberculosis strain CDC1551 (187 aa) but shorter 11 aa. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	O05791	No	conserved hypotheticals				Mb3141				
NC_000962.3	Mycobrowser_v3	CDS	3482776	3483945	.	+	0	Rv3116	moeB2	Possibly involved in molybdopterin metabolism (synthesis).	Probable molybdenum cofactor biosynthesis protein MoeB2 (MPT-synthase sulfurylase) (molybdopterin synthase sulphurylase)	Rv3116, (MTCY164.26), len: 389 aa. Probable moeB2, molybdopterin cofactor biosynthesis protein, equivalent to Q9CCG8|MOEZ|ML0817 protein probably involved in molybdopterin biosynthesis from Mycobacterium leprae (395 aa), FASTA scores: opt: 1433, E(): 8e-80, (57.8% identity in 384 aa overlap). Very similar to members of the HESA/MOEB/THIF family e.g. Q9FCL0|2SC3B6.02 putative sulfurylase from Streptomyces coelicolor (392 aa), FASTA scores: opt: 1562, E(): 1.1e-87, (58.15% identity in 380 aa overlap); Q9XC37|PDTORFF MOEB-like protein (putative sulfurylase) from Pseudomonas stutzeri (Pseudomonas perfectomarina) (391 aa), FASTA scores: opt: 1311, E(): 2.1e-72, (52.4% identity in 395 aa overlap); O54307|MPT|MOEB MPT-synthase sulfurylase from Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) (391 aa), FASTA scores: opt: 1238, E(): 5.7e-68, (51.4% identity in 393 aa overlap); P74344|MOEB|SLL1536 molybdopterin biosynthesis MOEB protein from Synechocystis sp. strain PCC 6803 (392 aa), FASTA scores: opt: 1212, E(): 2.2e-66, (46.5% identity in 398 aa overlap); etc. Also highly similar to O05860|MTCY07D11.20|MOEB1|Rv3206c putative molybdenum cofactor biosynthesis protein from Mycobacterium tuberculosis strain H37Rv (392 aa), FASTA scores: opt: 1445, E(): 1.5e-80, (56.25% identity in 400 aa overlap). Belongs to the HesA /MoeB/ThiF family. Note that previously known as moeB. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	L7N674	No	intermediary metabolism and respiration				Mb3143				
NC_000962.3	Mycobrowser_v3	CDS	3484809	3485111	.	+	0	Rv3118	sseC1	Thought to be involved in sulphur metabolism.	Conserved hypothetical protein SseC1	Rv3118, (MTCY164.28, O05794), len: 100 aa. SseC1, conserved hypothetical protein, equivalent to Q9CBC7|ML2199 hypothetical protein from Mycobacterium leprae (100 aa), FASTA scores: opt: 545, E(): 3.1e-30, (84.0% identity in 10 aa overlap). Also similar to hypothetical proteins e.g. Q50035 from Saccharopolyspora erythraea (Streptomyces erythraeus) (101 aa), FASTA scores: opt: 345, E(): 9.7e-17, (57.15% identity in 98 aa overlap); and Q9K4H3|SCD66.02 from Streptomyces coelicolor (95 aa), FASTA scores: opt: 249, E(): 2.8e-10, (48.5% identity in 99 aa overlap). Some weak similarity with Q9ZB84|PCAG protocatechuate 3,4-dioxygenase alpha-subunit from Pseudomonas marginata (196 aa), FASTA scores: opt: 109, E(): 1.4, (31.3% identity in 83 aa overlap); and other bacterial proteins. Identical second copy present as Rv0814c|AL022004|MTV043.06c|SSEC2 from Mycobacterium tuberculosis (100 aa) (100.0% identity in 100 aa overlap). Note that previously known as sseC. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P0CG96	No	intermediary metabolism and respiration		MMAR_4869	MSMEG_5790					
NC_000962.3	Mycobrowser_v3	CDS	3485132	3485575	.	+	0	Rv3119	moaE1	Possibly a molybdenum biosynthesis cofactor. Conversion of molybdopterin precursor Z into molybdopterin requires transfer of two sulfur atoms to precursor Z (to generate the dithiolene group). This is catalyzed by the converting factor composed of a small and large subunit.	Probable molybdenum cofactor biosynthesis protein E MoaE1 (molybdopterin converting factor large subunit) (molybdopterin [MPT] converting factor, subunit 2)	Rv3119, (MTCY164.29), len: 147 aa. Probable moaE1, molybdopterin converting factor E (molybdopterin converting factor (subunit 2)), highly similar to others e.g. O31705|MOAE from Bacillus subtilis (157 aa), FASTA scores: opt: 390, E(): 8.6e-19, (43.95% identity in 132 aa overlap); Q9K8I7|MOAE|BH3019 from Bacillus halodurans (156 aa), FASTA scores: opt: 369, E(): 2e-17, (42.4% identity in 132 aa overlap); P30749|MOAE_ECOLI|CHLA5|B0785 from Escherichia coli strain K12 (149 aa), FASTA scores: opt: 312, E(): 1.1e-13, (38.45% identity in 130 aa overlap); etc. Also highly similar (but shorter 74 aa) to O53375|GPHA|Rv3323c|MTV016.23c MOAD-MOAE fusion protein from Mycobacterium tuberculosis (221 aa), FASTA scores: opt: 733, E(): 3.9e-41, (76.2% identity in 143 aa overlap); and highly similar to O53878|MOAE2|Rv0866|MTV043.59 putative molybdopterin synthase large subunit from Mycobacterium tuberculosis (141 aa), FASTA scores: opt: 321, E(): 2.6e-14, (40.9% identity in 132 aa overlap). Note that previously known as moaE. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WJR3	No	intermediary metabolism and respiration								
NC_000962.3	Mycobrowser_v3	CDS	3490476	3491651	.	-	0	Rv3125c	PPE49	Function unknown	PPE family protein PPE49	Rv3125c, (MTCY164.35c), len: 391 aa. PPE49, Member of the Mycobacterium tuberculosis PPE family, similar to other e.g. P95247|Rv2352c|MTCY98.21c (391 aa), FASTA scores: opt: 1576, E(): 3.8e-72, (62.55% identity in 398 aa overlap), MTCY98.0029c, MTCY03A2.22c, MTCY10G2.10, MTCY02B10.25c, MTCI364.08, M TCY21C12.09c, MTCY48.17. This region is a possible MT-complex-specific genomic island (See Becq et al., 2007).	P9WHY5	No	PE/PPE		MMAR_4324		Mb3148c				
NC_000962.3	Mycobrowser_v3	CDS	3496551	3497549	.	+	0	Rv3131	Rv3131	Function unknown	Conserved protein	Rv3131, (MTCY03A2.27c), len: 332 aa. Conserved protein, similar to other hypothetical bacterial proteins e.g. O53476|Rv2032|MTV018.19 (331 aa), FASTA scores: opt: 568, E(): 2.5e-27, (36.7% identity in 321 aa overlap); O05800|Rv3127|MTCY164.37 (344 aa), FASTA scores: opt: 521, E(): 1.9e-24, (34.95% identity in 326 aa overlap); Q9RI33|SCJ12.27c from Streptomyces coelicolor (335 aa), FASTA scores: opt: 441, E(): 1.3e-19, (35.75% identity in 319 aa overlap); Q9RI44|SCJ12.14 from Streptomyces coelicolor (309 aa), FASTA scores: opt: 328, E(): 9.3e-13, (27.9% identity in 308 aa overlap); Q9CBP5|ML1751 from Mycobacterium leprae (721 aa), FASTA scores: opt: 137, E(): 0.78, (26.15% identity in 298 aa overlap); etc. Equivalent to AAK47555 from Mycobacterium tuberculosis strain CDC1551 but shorter 12 aa. Predicted possible vaccine candidate (See Zvi et al., 2008).	P9WIZ7	No	conserved hypotheticals			MSMEG_3955	Mb3155				
NC_000962.3	Mycobrowser_v3	CDS	3499943	3500749	.	-	0	Rv3134c	Rv3134c	Function unknown. Could play a role in the adaptation to hypoxia, participating in the phosphorelay in the two component regulatory system DEVR|Rv3133c/DEVS|Rv3132c.	Universal stress protein family protein	Rv3134c, (MTCY03A2.240, len: 268 aa. Universal stress protein family protein. Ala-, Val- rich (see citations below), related to other hypothetical Mycobacterium tuberculosis proteins e.g. O53474|Rv2028c|MTV018.15c (279 aa), FASTA scores: opt: 562, E(): 3.2e-28, (40.65% identity in 273 aa overlap); O06188|Rv2624c|MTCY01A10.08 (272 aa), FASTA scores: opt: 458, E(): 1.1e-21, (36.55% identity in 271 aa overlap); O53472|R2026c|MTV018.13c (294 aa), FASTA scores: opt: 232, E(): 1.9e-07, (30.45% identity in 276 aa overlap); etc. Shares some similarity with other hypothetical proteins from Streptomyces coelicolor e.g. Q9RIZ8|SCJ1.16c (294 aa), FASTA scores: opt: 207, E(): 6.9e-06, (28.9% identity in 263 aa overlap); Q9K4L5|SC5F8.09 putative stress-inducible protein (312 aa), FASTA scores: opt: 204, E(): 1.1e-05, (28.4% identity in 271 aa overlap); etc. Equivalent to AAK47558|MT3220 Universal stress protein family from Mycobacterium tuberculosis strain CDC1551 (268 aa). Rv3134c seems cotranscribed with devR-devS (see Sherman et al., 2001).	P9WFD3	No	virulence, detoxification, adaptation		MMAR_1515	MSMEG_5245	Mb3158c				
NC_000962.3	Mycobrowser_v3	CDS	3505363	3506769	.	+	0	Rv3139	fadE24	Function unknown, but involved in lipid degradation.	Probable acyl-CoA dehydrogenase FadE24	Rv3139, (MTCY03A2.19c), len: 468 aa. Probable fadE24, acyl-CoA dehydrogenase (1.3.99.-), equivalent to O32890|MLCB1779.30|FADE24|ML0661 putative acyl-CoA dehydrogenase from Mycobacterium leprae (465 aa), FASTA scores: opt: 2587, E(): 4e-153, (83.6% identity in 464 aa overlap). Similar to other e.g. Q9HUH0|PA4995 from Pseudomonas aeruginosa (429 aa), FASTA scores: opt: 1139, E(): 2.8e-63, (45.3% identity in 426 aa overlap); Q9K6D0|MMGC|BH3799 from Bacillus halodurans (379 aa), FASTA scores: opt: 603, E(): 4.7e-30, (30.3% identity in 366 aa overlap); Q9K6D1|ACDA|BH3798 from Bacillus halodurans (380 aa), FASTA scores: opt: 601, E(): 6.3e-30, (32.25% identity in 363 aa overlap); etc. Contains acyl-CoA dehydrogenases signature 2 (PS00073) near C-terminus. Belongs to the acyl-CoA dehydrogenases family.	P95187	No	lipid metabolism	ML0661,ML0661c	MMAR_1510	MSMEG_2081	Mb3163				
NC_000962.3	Mycobrowser_v3	CDS	3508095	3509066	.	+	0	Rv3141	fadB4	Involved in lipid degradation [catalytic activity: NADPH + quinone = NADP(+) + semiquinone].	Probable NADPH quinone oxidoreductase FadB4 (NADPH:quinone reductase) (zeta-crystallin)	Rv3141, (MTCY03A2.17c), len: 323 aa. Probable fadB4, quinone oxidoreductase, showing strong similarity to variety of quinone oxidoreductases and domains in polyketide and fatty acid synthases e.g. Q9HTV6|PA5234 probable oxidoreductase from Pseudomonas aeruginosa (325 aa), FASTA scores: opt: 737, E(): 1.4e-35, (39.65% identity in 328 aa overlap); Q9RYQ7|DRA0251 putative NADPH quinone oxidoreductase from Deinococcus radiodurans (336 aa), FASTA scores: opt: 688, E(): 1e-32, (40.6% identity in 325 aa overlap); Q9RVG8|DR1061 putative NADPH quinone oxidoreductase from Deinococcus radiodurans (388 aa), FASTA scores: opt: 559, E(): 3.3e-25, (36.3% identity in 325 aa overlap); BAB49685|MLL2594 probable quinone oxidoreductase from Rhizobium loti (Mesorhizobium loti) (326 aa), FASTA scores: opt: 519, E(): 5.9e-23, (34.25% identity in 330 aa overlap); Q9LXZ4|T5P19_110 quinone reductase-like protein from Arabidopsis thaliana (348 aa), FASTA scores: opt: 517, E(): 8.1e-23, (33.55% identity in 322 aa overlap); etc. Also similar to Q9AA38|CC0770 zinc-containing alcohol dehydrogenase from Caulobacter crescentus (325 aa), FASTA scores: opt: 673, E(): 7.2e-32, (40.2% identity in 326 aa overlap); and Q9ABX4|CC0096 zinc-containing alcohol dehydrogenase from Caulobacter crescentus (332 aa), FASTA scores: opt: 623, E(): 5.7e-29, (40.7% identity in 334 aa overlap). Also resembles Mycobacterium tuberculosis proteins P96826|Rv0149|MTCI5_23, MTCY13D12.11, MTCY24G1.03, MTCY19H9.01. Belongs to the zinc-containing alcohol dehydrogenase family, quinone oxidoreductase subfamily. Thought to be differentially expressed within host cells (see Triccas et al., 1999).	P95185	No	lipid metabolism	ML0658,ML0658c	MMAR_1498	MSMEG_2033	Mb3165				
NC_000962.3	Mycobrowser_v3	CDS	3512628	3513338	.	+	0	Rv3147	nuoC	Involved in aerobic|anaerobic respiration [catalytic activity: NADH + ubiquinone = NAD(+) + ubiquinol].	Probable NADH dehydrogenase I (chain C) NuoC (NADH-ubiquinone oxidoreductase chain C)	Rv3147, (MTCY03A2.11c), len: 236 aa. Probable nuoC, NADH dehydrogenase, chain C, similar to others e.g. Q9XAQ6|NUOC from Streptomyces coelicolor (251 aa), FASTA scores: opt: 1113, E(): 2.6e-64, (67.35% identity in 236 aa overlap); Q9A6X2|CC1954 from Caulobacter crescentus (197 aa), FASTA scores: opt: 351, E(): 1.6e-15, (41.65% identity in 132 aa overlap); BAB48757|MLL1369 from Rhizobium loti (Mesorhizobium loti) (201 aa), FASTA scores: opt: 347, E(): 3e-15, (42.4% identity in 132 aa overlap); etc. Also similar to Q9UUU0|NUGM NUGM protein precursor from Yarrowia lipolytica (Candida lipolytica) (281 aa), FASTA scores: opt: 356, E(): 1.1e-15, (34.55% identity in 162 aa overlap). Also similar to MTCY251.05, FASTA score: E():4.9e-05. Equivalent to AAK47574 from Mycobacterium tuberculosis strain CDC1551 but longer 26 aa. Belongs to the complex I 30 KDA subunit family.	P9WJH3	No	intermediary metabolism and respiration		MMAR_1481	MSMEG_2061	Mb3171				
NC_000962.3	Mycobrowser_v3	CDS	3515412	3516749	.	+	0	Rv3150	nuoF	Involved in aerobic|anaerobic respiration [catalytic activity: NADH + ubiquinone = NAD(+) + ubiquinol].	Probable NADH dehydrogenase I (chain F) NuoF (NADH-ubiquinone oxidoreductase chain F)	Rv3150, (MTCY03A2.08c), len: 445 aa. Probable nuoF, NADH dehydrogenase, chain F, similar to others e.g. Q9XAQ9|NUOF_STRCO from Streptomyces coelicolor (449 aa), FASTA scores: opt: 2314, E(): 3.5e-139, (76.25% identity in 434 aa overlap); NUF2_RHIME from Rhizobium meliloti (421 aa), FASTA scores: opt: 1545, E(): 1.8e-90, (53.1% identity in 424 aa overlap); Q9RU92|DR1500 from Deinococcus radiodurans (444 aa), FASTA scores: opt: 1445, E(): 4.1e-84, (52.9% identity in 427 aa overlap); etc. Contains respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2 (PS00645). Belongs to the complex I 51 KDA subunit family. Cofactor: FMN and one 4FE-4S cluster (probable).	P9WIV7	No	intermediary metabolism and respiration		MMAR_1478	MSMEG_2058	Mb3174				
NC_000962.3	Mycobrowser_v3	CDS	3519282	3520514	.	+	0	Rv3152	nuoH	Involved in aerobic|anaerobic respiration [catalytic activity: NADH + ubiquinone = NAD(+) + ubiquinol].	Probable NADH dehydrogenase I (chain H) NuoH (NADH-ubiquinone oxidoreductase chain H)	Rv3152, (MTCY03A2.06c), len: 410 aa. Probable nuoH, integral membrane NADH dehydrogenase I, chain H, similar to others e.g. Q9XAR1 Q9XAR1|NUOH from Streptomyces coelicolor (467 aa), FASTA scores: opt: 1630, E(): 3.4e-90, (58.35% identity in 413 aa overlap); Q9RU94|DR1498 from Deinococcus radiodurans (397 aa), FASTA scores: opt: 1081, E(): 2e-57, (45.5% identity in 391 aa overlap); Q9ZCF7|NUOH_RICPR|RP796 from Rickettsia prowazekii (339 aa), FASTA scores: opt: 976, E(): 3.4e-51, (46.2% identity in 329 aa overlap); etc. Contains respiratory-chain NADH dehydrogenase subunit 1 signature 2 (PS00668). Some similarity to MTCY251.02 (FASTA score: E(): 1.2e-07). Belongs to the complex I subunit 1 family.	P9WIX1	No	intermediary metabolism and respiration		MMAR_1476	MSMEG_2056	Mb3176				
NC_000962.3	Mycobrowser_v3	CDS	3521139	3521927	.	+	0	Rv3154	nuoJ	Involved in aerobic|anaerobic respiration [catalytic activity: NADH + ubiquinone = NAD(+) + ubiquinol].	Probable NADH dehydrogenase I (chain J) NuoJ (NADH-ubiquinone oxidoreductase chain J)	Rv3154, (MTCY03A2.04c), len: 262 aa. Probable nuoJ, transmembrane NADH dehydrogenase I, chain J, similar to others e.g. Q9XAR3|NUOJ from Streptomyces coelicolor (285 aa), FASTA scores: opt: 991, E(): 3.2e-52, (63.7% identity in 243 aa overlap); Q9JX90|NUOJ|NMA0006 from Neisseria meningitidis (serogroup A) (223 aa), FASTA scores: opt: 329, E(): 9.6e-13, (34.85% identity in 175 aa overlap); Q9K1B2|NMB0253 from Neisseria meningitidis (serogroup B) (223 aa), FASTA scores: opt: 326, E(): 1.5e-12, (34.85% identity in 175 aa overlap); etc. But also similarity with Q00243|NU6C_PLEBO|NDH6 NADH-plastoquinone oxidoreductase chain 6 homolog (catalytic activity: NADH + plastoquinone = NAD(+) + plastoquinol) from Plectonema boryanum (199 aa), FASTA scores: opt: 287, E(): 2.8e-10, (34.35% identity in 195 aa overlap). Similar to polypeptide 6 of the NADH-ubiquinol oxidoreductase of chloroplasts or mitochondria.	P95172	No	intermediary metabolism and respiration		MMAR_1474	MSMEG_2054	Mb3178				
NC_000962.3	Mycobrowser_v3	CDS	3521924	3522223	.	+	0	Rv3155	nuoK	Involved in aerobic|anaerobic respiration [catalytic activity: NADH + ubiquinone = NAD(+) + ubiquinol].	Probable NADH dehydrogenase I (chain K) NuoK (NADH-ubiquinone oxidoreductase chain K)	Rv3155, (MTCY03A2.03c), len: 99 aa. Probable nuoK, integral membrane NADH dehydrogenase I, chain K, similar to others e.g. Q9XAR4|NUOK from Streptomyces coelicolor (99 aa), FASTA scores: opt: 509, E(): 2.7e-31, (78.55% identity in 98 aa overlap); Q56226|NQOB_THETH|NQO11 from Thermus aquaticus (subsp. thermophilus) (95 aa), blast scores: initn: 298, init1: 180, bits: 85.7, FASTA scores: opt: 313, E(): 9.4e-17, (53.7% identity in 95 aa overlap); Q9RU97|DR1495 from Deinococcus radiodurans (103 aa), FASTA scores: opt: 309, E(): 2e-16, (52.0% identity in 100 aa overlap); etc. But also similarity with NADH-plastoquinone oxidoreductases chain 4L e.g. Q9MUL4|NULC_MESVI|NDHE from Mesostigma viride (catalytic activity: NADH + plastoquinone = NAD(+) + plastoquinol) (101 aa), FASTA scores: opt: 280, E(): 2.8e-14, (40.6% identity in 101 aa overlap); and P06261|NULC_TOBAC|NDHE|NDH4L from Nicotiana tabacum (Common tobacco) (101 aa), FASTA scores: opt: 259, E(): 1e-12, (43.0% identity in 93 aa overlap). Similar to polypeptide 4L of the NADH-ubiquinol oxidoreductase of chloroplasts or mitochondria.	P9WIX3	No	intermediary metabolism and respiration		MMAR_1473	MSMEG_2053	Mb3179				
NC_000962.3	Mycobrowser_v3	CDS	3522234	3524135	.	+	0	Rv3156	nuoL	Involved in aerobic|anaerobic respiration [catalytic activity: NADH + ubiquinone = NAD(+) + ubiquinol].	Probable NADH dehydrogenase I (chain L) NuoL (NADH-ubiquinone oxidoreductase chain L)	Rv3156, (MTCY03A2.02c), len: 633 aa. Probable nuoL, integral membrane NADH dehydrogenase I, chain L, similar to others e.g. Q9XAR5|NUOL_STRCO from Streptomyces coelicolor (654 aa), FASTA scores: opt: 2074, E(): 1.1e-111, (61.1% identity in 648 aa overlap); Q56227|NQOC_THETH|NQO12 from Thermus aquaticus (subsp. thermophilus) (606 aa), FASTA scores: opt: 1420, E(): 3.8e-74, (43.35% identity in 630 aa overlap); Q9ZJV6|NUOL|JHP1192 from Helicobacter pylori J99 (Campylobacter pylori J99) (612 aa), FASTA scores: opt: 1279, E(): 4.7e-66, (41.65% identity in 516 aa overlap); etc. Also similar to MTCY251.04 (FASTA score: E(): 1.3e-11) and MTCY03A2.01c (FASTA score: E(): 2.3e-10). Similar to polypeptide 5 of the NADH-ubiquinol oxidoreductase of chloroplasts or mitochondrial.	P9WIW1	No	intermediary metabolism and respiration		MMAR_1472	MSMEG_2052					
NC_000962.3	Mycobrowser_v3	CDS	3525790	3527385	.	+	0	Rv3158	nuoN	Involved in aerobic|anaerobic respiration [catalytic activity: NADH + ubiquinone = NAD(+) + ubiquinol].	Probable NADH dehydrogenase I (chain N) NuoN (NADH-ubiquinone oxidoreductase chain N)	Rv3158, (MTV014.02c), len: 531 aa. Probable nuoN, integral membrane NADH dehydrogenase I, chain N, similar to others e.g. Q9XAR7|SC10A7.08c from Streptomyces coelicolor (552 aa), FASTA scores: opt: 1493, E(): 1.1e-81, (56.7% identity in 543 aa overlap); Q9PGI2|XF0318 from Xylella fastidiosa (485 aa), FASTA scores: opt: 942, E(): 7.4e-49, (39.6% identity in 379 aa overlap); CAB51628|NUON2 from Rhizobium meliloti (Sinorhizobium meliloti) (479 aa), FASTA scores: opt: 934, E(): 2.2e-48, (35.5% identity in 479 aa overlap); etc. But also similarity with NADH-plastoquinone oxidoreductases chain 4L (catalytic activity: NADH + plastoquinone = NAD(+) + plastoquinol) e.g. P29801|NU2C_SYNP7|NDHB from Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) (521 aa), FASTA scores: opt: 921, E(): 1.4e-47, (40.25% identity in 395 aa overlap). Belongs to the complex I subunit 2 family.	P9WIW9	No	intermediary metabolism and respiration	ML0657,ML0657c	MMAR_1470	MSMEG_2050	Mb3182				
NC_000962.3	Mycobrowser_v3	CDS	3535431	3536057	.	-	0	Rv3167c	Rv3167c	Involved in transcriptional mechanism.	Probable transcriptional regulatory protein (probably TetR-family)	Rv3167c, (MTV014.11c), len: 208 aa. Probable transcriptional regulator, TetR family, similar to several transcriptional regulators e.g. Q9L2A4|SC8F4.22c (TetR/AcrR family) from Streptomyces coelicolor (234 aa), FASTA scores: opt: 317, E(): 7.5e-13, (33.35% identity in 210 aa overlap); Q9RK47|SCF12.11 (TetR/AcrR family) from Streptomyces coelicolor (206 aa), FASTA scores: opt: 293, E(): 2.1e-11, (32.65% identity in 199 aa overlap); Q54288 regulator of antibiotic transport complexes (TetR/AcrR family) (204 aa), FASTA scores: opt: 260, E(): 2.4e-09, (30.75% identity in 205 aa overlap); etc. Equivalent to AAK47595 from Mycobacterium tuberculosis strain CDC1551 but shorter 21 aa. Contains probable helix-turn-helix motif from aa 42 to 63 (Score 1727, +5.07 SD). May belong to the TetR/AcrR family of transcriptional regulators.	O53317	No	regulatory proteins	ML0650			Mb3192c				
NC_000962.3	Mycobrowser_v3	CDS	3538505	3539851	.	+	0	Rv3170	aofH	Possibly catalyzes the oxidative deamination: oxidize on primary amines, and perhaps on secondary and tertiary amines [catalytic activity: RCH(2)NH(2) + H(2)O + O(2) = RCHO + NH(3) + H(2)O(2)]. Must have important function in metabolism. Supposedly involved in stationary-phase survival.	Probable flavin-containing monoamine oxidase AofH (amine oxidase) (MAO)	Rv3170, (MT3259, MTV014.14), len: 448 aa. Probable aofH, flavin-containing (mono)amine oxidase, equivalent to a predicted homologous protein from Mycobacterium smegmatis (see citation below), and similar to many eukaryotic monoamine oxidases e.g. P49253|AOF_ONCMY from Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) (