Spreadsheet: 5ea8c513-65bb-4117-aef1-690f1753fb66
Sheet: Sheet1

Table S2
Genes significantly upregulated (>1.5X) at 48hr novel to this study (compared to expression of >1.5X in both amplicon and oligo array data reported by [NAME] et. [NAME] (ref 29)
Time |  |  | 2hr | Day 2 | Day 4 | Day 6 | Day 8 | Day 10 | Day 12 | Day 14
Gene | Common | Synonym | Ratio | Ratio | Ratio | Ratio | Ratio | Ratio | Ratio | Ratio | Description (Tuberculist annotation)
MT0124 |  |  | 1.7689117 | 4.026796 | 2.7577345 | 2.3442175 | 2.6540885 | 2.2886982 | 2.2591145 | 1.94514 | hypothetical protein
MT0694 |  |  | 1.1501758 | 1.5901787 | 1.4023086 | 1.3186834 | 1.4005833 | 1.4222254 | 1.6583034 | 1.3128511 | hypothetical protein
MT0717.1 |  |  | 1.4581599 | 1.5377007 | 1.3853663 | 1.3265592 | 1.2690513 | 1.3766468 | 1.9336553 | 0.9140154 | hypothetical protein
MT0740.1 |  |  | 1.2609595 | 1.9776475 | 1.5703299 | 1.4634637 | 1.7002368 | 1.8569165 | 2.1166818 | 2.3796024 | hypothetical protein
MT0761 |  |  | 1.2240155 | 1.8881094 | 1.3669933 | 1.2910825 | 1.6480802 | 1.7317286 | 2.3044395 | 2.760593 | hypothetical protein
MT0762.1 |  |  | 1.1621966 | 1.5028175 | 1.357628 | 1.2399293 | 1.3163179 | 1.2719258 | 1.1917446 | 1.0338496 | Hypothetical protein
MT0772.5 |  |  | 0.93576777 | 1.661515 | 1.4397347 | 1.4685245 | 1.6336201 | 1.3813215 | 1.419673 | 1.4824384 | PE_PGRS family protein
[NAME] |  |  | 0.9717996 | 1.7971921 | 1.3634436 | 1.2267283 | 1.5497382 | 1.4304655 | 1.1863557 | 1.6932197 | hypothetical protein
MT1122.1 |  |  | 2.148673 | 5.6059527 | 3.8778093 | 3.401173 | 3.66193 | 3.4593477 | 3.4318426 | 2.6949577 | hypothetical protein
MT1181 |  |  | 1.3739469 | 1.5259012 | 1.4126176 | 1.0913103 | 1.688729 | 1.2156761 | 2.0579183 | 2.0408287 | hypothetical protein
MT1560 |  |  | 1.019806 | 1.9045134 | 1.780676 | 1.6643282 | 2.0801492 | 1.6320122 | 1.3276829 | 1.3283768 | hypothetical protein
MT1676 |  | Rv1638A | 1.1753049 | 1.6511337 | 1.2919831 | 1.2366234 | 1.3235515 | 1.1350824 | 1.2320856 | 1.2052249 | conserved hypothetical protein
MT1717 |  |  | 1.1810586 | 1.5114889 | 1.0649043 | 1.0683612 | 1.1247761 | 1.1604129 | 1.0448202 | 0.9494662 | hypothetical protein
MT1800 |  |  | 1.1636838 | 1.5010282 | 1.101141 | 1.1038585 | 1.2604926 | 1.3415377 | 1.3246526 | 1.6484084 | glycosyl transferase
MT1968 |  |  | 0.7983342 | 1.5311773 | 1.1575938 | 1.0243471 | 1.1679 | 1.1023422 | 1.1678848 | 1.1326197 | PPE family protein
MT2365 |  | Rv2307A | 1.3068107 | 2.0773003 | 1.5845301 | 1.4954295 | 1.4731607 | 1.5957986 | 1.4072702 | 1.3317354 | hypothetical protein
MT2365.1 |  | Rv2307B | 0.8770917 | 1.5575262 | 1.5579904 | 1.5209386 | 1.4587404 | 1.4006821 | 1.5684366 | 1.3217386 | hypothetical protein
MT2401.2 |  |  | 1.1593908 | 1.727471 | 1.2446427 | 1.2492783 | 1.2063924 | 1.4966044 | 1.8795224 | 1.5898457 | hypothetical protein
MT2466 |  | aprA | 2.7788808 | 6.181613 | 4.0122037 | 3.66206 | 3.4403553 | 4.163733 | 4.506817 | 4.286457 | hypothetical protein
MT2467 |  | aprB | 3.3149943 | 5.69993 | 3.115224 | 2.9149303 | 2.7285745 | 3.3959775 | 3.5960865 | 3.6653252 | hypothetical protein
MT2565 |  |  | 1.1645608 | 1.9035735 | 1.5085922 | 1.3150561 | 1.5027993 | 1.6561646 | 1.919253 | 2.0891442 | hypothetical protein
MT2941 |  |  | 1.5480894 | 2.4583092 | 2.5229394 | 2.61176 | 2.6901546 | 2.4721491 | 2.6374462 | 2.4225714 | hypothetical protein
MT3106.1 |  |  | 1.0862747 | 1.5198506 | 2.271633 | 2.1894655 | 2.8268163 | 1.7127818 | 0.9874985 | 0.88859457 | PE family protein
MT3220.2 |  |  | 1.6979771 | 1.7138972 | 1.6874273 | 1.7288402 | 1.9042068 | 1.5375726 | 1.3846658 | 1.5045704 | PE family protein
MT3222 |  |  | 0.9925938 | 1.53829 | 1.4500372 | 1.3689702 | 1.3902184 | 1.0970979 | 1.1643947 | 1.1644272 | conserved hypothetical
MT3290.1 |  | whiB7;Rv3197A | 1.4549447 | 2.1729727 | 1.2925236 | 1.2032608 | 1.1391157 | 1.0619205 | 1.2679497 | 1.2034955 | conserved hypothetic
MT3290.2 |  |  | 1.5085682 | 2.2408338 | 1.4344695 | 1.1934496 | 1.248231 | 1.3605652 | 1.5281228 | 1.5742217 | hypothetical protein
MT3412 |  |  | 1.1439263 | 1.6056477 | 1.2560813 | 1.15472 | 1.213997 | 1.0339264 | 1.579864 | 1.5427016 | hypothetical protein
MT3413 |  |  | 1.7450156 | 2.5304663 | 2.1536334 | 1.9576601 | 2.169384 | 2.4031346 | 2.5844958 | 2.6157951 | hypothetical protein
MT3762 |  |  | 1.1481909 | 1.9531498 | 1.5137255 | 1.4532577 | 1.6261982 | 1.6141238 | 1.9470413 | 2.0674963 | hypothetical protein
MT3994 |  |  | 1.371726 | 1.5012732 | 1.4067193 | 1.3483483 | 1.411276 | 1.3036993 | 1.2987996 | 1.2546464 | hypothetical protein
plcd | Rv1755c |  | 1.1331252 | 1.9990737 | 1.4102899 | 1.3354696 | 1.4647671 | 1.5858666 | 1.9094137 | 2.6452103 | Protein sequence is in conflict with the conceptual translation; [NAME], (MTCY28.21c), len: 203. Partial CDS for phospholipase C, highly similar to C-terminus of Q50771 phospholipaseC from M. tuberculosis (512 aa) (71.1% identity in 284 aa overlap). CDS has been interrupted by insertion of IS6110 element
roda | Rv0017c |  | 1.3930346 | 1.8906052 | 1.5477118 | 1.6086311 | 1.58728 | 1.7728117 | 2.1081138 | 2.3083315 | Rv0017c, (MTCY10H4.17c), len: 469, highly similar to M. [NAME], (465 aa),opt: 2475 z-score: 3029.6E(): 0; E235744 cell division protein, (81.9% identity in469 aa overlap). Also similar to MTCY270_14, (524, 32.2% identity in 369 aa overlap)
Rv0093c | Rv0093c |  | 0.9659244 | 1.5496012 | 1.2238206 | 1.1975397 | 1.1776062 | 1.1609652 | 1.0989667 | 0.98940736 | Rv0093c, (MTCY251.12c), len: 282, unknown
Rv0140 | Rv0140 |  | 0.95884806 | 1.6377747 | 1.728005 | 1.544966 | 1.6554174 | 1.2239892 | 0.96966964 | 0.9203259 | [NAME], (MTCI5.14), len: 126 , unknown, but similarto D90916_48 Synechocystis sp./P74567 HYPOTHETICAL 20.8 KDPROTEIN (180 aa); opt: 229 z-score: 315.5 E(): 4.7e-10; 36.1% identity in 108 aa overlap. Also similar to MTV017_9 andMTV047_5
Rv0141c | Rv0141c |  | 1.2801889 | 1.5631616 | 1.4429843 | 1.3694186 | 1.5484376 | 1.4116253 | 1.4067553 | 1.2579474 | Rv0141c, (MTCI5.15c), unknown, len: 136 aa
Rv0142 | Rv0142 |  | 0.89412415 | 1.7177293 | 1.778324 | 1.8430463 | 1.9993091 | 1.6514243 | 1.5856898 | 1.6667682 | Rv0142, ([NAME]), len: 208. unknown.
Rv0146 | Rv0146 |  | 1.0868639 | 1.6173438 | 1.605457 | 1.5160557 | 1.5895293 | 1.4435457 | 1.1137991 | 1.026208 | Rv0146, (MTCI5.20), len: 310 aa, similar to eg YZ21_MYCTU Q10552 hypothetical 36.1 kd protein cy31.21c (325 aa), [NAME] scores, opt: 784, E(): 0, (43.5% identity in 308 aa overlap), Y09U_MYCTU Q50726 hypothetical 38.1 kd protein cy78.29c (348 aa), [NAME] scores, opt: 753, E(): 0, (42.6% identity in 312 aa overlap) also similar to MTCI5.19, (52.9%identity in 293 aa overlap) also similar to [NAME], (49.3 % identity in 306 aa overlap)
Rv0209 | Rv0209 |  | 1.1359147 | 1.5777154 | 1.2575768 | 1.3331943 | 1.2836883 | 1.3186655 | 1.672566 | 1.5061044 | Rv0209, (MTCY08D5.04), unknown, len: 361 aa
naru | Rv0267 |  | 1.6499991 | 2.5149083 | 1.7371174 | 1.5006742 | 1.852225 | 2.3543377 | 2.584959 | 2.9669046 | Rv0267, (MTCY06A4.11), len: 463 aa, similar to nitrite extrusion proteins eg NARU_ECOLI P37758 nitrite extrusion protein 2 (462 aa), [NAME] scores, opt: 630, E(): 4.4e-33, (38.9% identity in 463 aa overlap), and NARK_ECOLI P10903nitrite extrusion protein 1 (463 aa), [NAME] scores, opt: 607, E(): 1.3e-31, (42.0% identity in 457 aa overlap) ALSO similar to MTCY6A4_5, and to MLCB22_25 Mycobacterium leprae cosmid B22; P (517 aa), 35.1% identity in 459 aa overlap
Rv0274 | Rv0274 |  | 1.1273469 | 1.5977678 | 1.3622533 | 1.2707741 | 1.2997184 | 1.1334993 | 0.962922 | 0.8424976 | Rv0274, (MTV035.02), len: 193. Unknown, but some similarity to gp|AJ002571|BSAJ2571_7 Bacillus subtilis 168 56kb DNA (316 aa), opt: 138 z-score: 174.8 E(): 0.033; 27.1% identity in 133 aa overlap. Previous hits with FOSFOMYCIN-RESISTANCE PROTEIN from SERRATIA MARCESCENS. Contains PS00082 Extradiol ring-cleavage dioxygenases signature near C-terminus. FASTA scores: TR:Q56415 (EMBL:M85195) FOSFOMYCIN-RESISTANCE PROTEIN (141 aa), opt: 82 z-score: 285.5 E(): 1.1e-08, 29.1% identity in 151 aa overlap. TBparse score is 0.914
Rv0358 | Rv0358 |  | 1.078655 | 1.955609 | 1.7479777 | 1.6460272 | 1.8181955 | 1.3972259 | 1.2066367 | 1.072163 | Rv0358, (MTCY13E10.20), len: 215. Function: unknown
Rv0380c | Rv0380c |  | 1.0112059 | 2.4940693 | 2.021921 | 1.7432805 | 1.7638968 | 1.2815676 | 0.9478173 | 0.9045283 | Rv0380c, (MTV036.15c), len: 183. Unknown but shows some similarity with methyltransferases. e.g. sp|P19396|SPOU_ECOLI SPOU PROTEIN (229aa) opt: 227 z-score: 306.4 E(): 1.4e-09. 28.9% identity in 166 aa overlap.
Rv0387c | Rv0387c |  | 1.6989814 | 2.2133303 | 1.3901781 | 1.1843228 | 1.3324705 | 1.5961378 | 0.9725072 | 0.8530116 | Rv0387c, (MTV036.22c), len: 244. Unknown; shows some similarity to [NAME], and elastin. FASTA scores: gp|M17282|HUMEL20_1 Human elastin gene, exon 1. Elasti (687 aa)opt: 193 z-score: 156.1 E(): 0.35. 34.4% identity in 189 aa overlap.TBparse score is 0.915
groel2 | Rv0440 |  | 1.2335526 | 2.0220332 | 1.6823547 | 1.5043626 | 1.372462 | 1.3351018 | 1.3222829 | 1.1326671 | Rv0440, (MTV037.04), len: 539. [NAME], identical toM. tuberculosis GroEL-2. Has PS00296 [NAME] cpn60 signature. FASTA scores: sp|P06806|CH62_MYCTU 60 KD CHAPERONIN2(PROTEIN CPN60 (539 aa) opt: 3318 z-score: 3673.1 E(): 0; 100.0% identity in 539 aa overlap. TBparse score is 0.847
Rv0493c | Rv0493c |  | 1.2527701 | 1.8231797 | 1.8956304 | 2.1844077 | 2.3920913 | 2.4289026 | 1.9029526 | 1.8122064 | Rv0493c, (MTCY20G9.19), len: 329, unknown, some similarity to U00018_33 Mycobacterium leprae cosmid B2168 B2168_F2_93 (167 aa) FASTA scores, opt: 166, z-score: 193.6, E(): 0.00077, (35.9% identity in 131 aa overlap)
Rv0532 | Rv0532 | PE_PGRS6 | 1.1219043 | 1.7038234 | 1.4507673 | 1.6116629 | 1.5597947 | 1.760816 | 1.9094288 | 2.2677183 | Rv0532, (MTCY25D10.11), len: 594 aa, member of the M. tuberculosis PGRS family, similar to eg Y0DP_MYCTU Q50615 hypothetical glycine-rich 40.8 kd protein (498 aa) opt: 1703 z-score: 1219.4 E(): 0, (58.2% identity in 536 aa overlap)
Rv0559c | Rv0559c |  | 1.4252266 | 1.5160329 | 1.3184599 | 1.20522 | 1.2868721 | 1.2600155 | 1.1471915 | 1.0556136 | Rv0559c, (MTCY25D10.38c), len: 112, unknown, similar to eg Y08B_MYCTU Q11048 hypothetical 11.6 kd protein [NAME] also to MTV004_9, [NAME] scores, opt: 111 z-score: 156.1E(): 011, (25.4% identity in 114 aa overlap). Contains possible N-terminal signal sequence
Rv0577 | Rv0577 | TB27.3 | 1.0151315 | 2.1460752 | 2.0667098 | 2.1008625 | 2.11902 | 2.1497753 | 2.3423848 | 2.2083285 | Rv0577, (MTV039.15), len: 261. Unknown but similar to sevral hypothetical proteins from Steptomyces sp: SSU50973_2 Streptomyces sp|Q55078|Q55078 DAUNOMYCIN C-14 HYDROXYLASE (DOXA); E(): 1.5e-19, (38.6% identity in 264 aa overlap), and D89734_1 Streptomyces griseus DNA for SgaA P95754 SGAA PROTEIN.;and Streptomyces coelicolor SC9B10_20 (267 aa, 38.9% identity in 252 aa overlap). Also similar to MTCY21C12.05 (257 aa), E(): 1.1e-20, 32.0% identity in 259 aa overlap TBparse score is 0.899
Rv0581 | Rv0581 |  | 1.5769573 | 1.7021295 | 1.4545399 | 1.3776926 | 1.407555 | 1.3179598 | 0.8910284 | 0.9716468 | Rv0581, (MTV039.19), len: 71. Unknown but some similarity to Mycobacterium tuberculosis [NAME] (81 aa) and to Streptomyces [NAME] (77 aa). FASTAscores: Z83863|MTCY159_6 (81 aa) opt: 93 z-score: 138.6E(): 3.2; 25.7% identity in 70 aa overlap; and X05648|SGSPH_1 (77 aa) opt: 92 z-score: 137.6 E(): 3.6; 35.4%identity in 65 aa overlap. TBparse score is 0.864
pqqe | Rv0693 |  | 1.0145541 | 1.593854 | 1.6379765 | 1.5560223 | 1.5023861 | 1.4250165 | 1.9618955 | 1.9115431 | Rv0693, (MTCY210.10), len: 391 aa, similar to eg AE001109_9 Archaeoglobus fulgidus O30258 COENZYME PQQ SYNTHESIS PROTEIN (PQQE) (375 aa), E(): 1.6e-16, 28.1% identity in377 aa overlap; and PQQE_ACICA P07782 coenzyme pqq synthesis protein e (384 aa),fasta scores, opt: 302, E(): 1.8e-12,(23.9% identity in 377 aa overlap), also similar to C-terminus of O28270 HEME BIOSYNTHESIS PROTEIN (NIRJ-2)(468 aa).TBparse score is 0.919
phoy2 | Rv0821c |  | 1.201599 | 1.7602023 | 1.4640312 | 1.4097545 | 1.3936986 | 1.3495411 | 1.4738773 | 1.3448889 | Rv0821c, (MTV043.13c), len: 213. phoY-2, probable phosphate transport system regulatory protein, equivalent toMycobacterium leprae PhoY protein MLU15182_29 (222 aa), andvery similar to Mycobacterium tuberculosis MTCI418A.03c (221 aa), also known as PhoY-1. FASTA scores: U15182|MLU15182_29 Mycobacterium l(222 aa) opt: 1268 z-score: 1515.2 E():0; 93.0% identity in 213 aa overlap; [NAME] aa) opt: 937 z-score: 1123.0 E(): 0; 63.4% identity in 213 aa overlap. TBparse score is 0.910
[NAME] | [NAME] | ercC3 | 1.2504736 | 2.167206 | 1.6815454 | 1.6345716 | 1.676157 | 1.8522702 | 1.8338687 | 2.0156767 | [NAME], (MTV043.54c), len: 542. Probable DNA helicase similar to but shorter than several eukaryotic enzymese.g. . FASTA scores: sp|Q00578|RA25_YEAST DNA REPAIR HELICASE RAD25. (843 aa) opt: 777 z-score: 925.3 E(): 0;30.4% identity in 605 aa overlap; and sp|P49135|XPB_MOUSEDNA-REPAIR PROTEIN COMPLEMENTING X (783 aa) opt: 761 z-score: 906.6 E(): 0; 36.3% identity in 375 aa overlapTBparse score is 0.899
Rv0872c | Rv0872c | PE_PGRS15 | 1.1653444 | 1.9019924 | 1.7365053 | 1.4393759 | 1.5316167 | 1.5905625 | 1.0531423 | 1.1811286 | Rv0872c, (MTV043.65c), len: 606. Member of Gly-richPGRS subfamily of the Mycobacterium tuberculosis PE family,similar to many eg. MTCY24A1.04c. FASTA scores: gp|Z95207|MTCY24A1_4 Mycobacterium tuberculosis cosmid (615 aa)initn:1361 init1: 1361 opt: 2636 z-score: 1525.9 E(): 0; 64.6% identity in 619 aa overlap.
Rv0885 | Rv0885 |  | 1.259492 | 1.7764628 | 1.79496 | 1.8981416 | 2.1027725 | 1.8692504 | 2.0166569 | 1.695616 | Rv0885, (MTCY31.13), len: 340, unknown, TRANSMEMBRANE PROTEIN, equivalentto MLCB57_18 Mycobacterium leprae cosmid B57 O33063 HYPOTHETICAL 40.2 KD PROTEIN; 83.9% identity in 341 aa overlap
Rv0937c | Rv0937c |  | 1.117628 | 1.5344478 | 1.4046512 | 1.4338082 | 1.5040116 | 1.426667 | 1.2965463 | 1.2125162 | Rv0937c, (MTCY08D9.02), len: 273. Some similarity to hypothetical proteins from B. subtilis and [NAME]:O28548 (EMBL:AE000984) AF1726 (286 aa), [NAME] scores; opt: 583, E(): 0, 36.6% identity in 262 aa overlap
uvrd | Rv0949 | uvrD1 | 1.1535796 | 1.611184 | 1.4586096 | 1.3791437 | 1.4363401 | 1.4216006 | 1.1794152 | 1.1168959 | Rv0949, (MTCY10D7.25c), len: 771. Probable DNA helicase similar to many eg. YAY5_SCHPO Q10213 probable atp-dependent dna helicase c (887 aa), FASTA scores, opt: 927, z-score: 1046.0, E(): 0, (33.5% identity in 659 aa overlap); contains PS00017 [NAME]/GTP-binding site motif A
Rv1034c | Rv1034c |  | 1.1134573 | 1.932075 | 1.6466879 | 1.6831609 | 1.7658849 | 1.6178187 | 1.1406214 | 1.1566975 | Rv1034c, (MTCY10G2.15), len: 129. Probable IS1560 transposase fragment, similar to part of TR:E1202305 MTV004.45 (225 aa), 65.1% identity in 129 aa overlap
Rv1036c | Rv1036c |  | 1.1310058 | 1.6492583 | 1.549861 | 1.380223 | 1.4314423 | 1.4023687 | 1.1956099 | 1.213878 | Rv1036c, (MTCY10G2.13), len: 112. Probable IS1560transposase fragment, similar to part of TR:E1202304 MTV004.44 (234 aa) 82.8% identity in 87 aa overlap
Rv1042c | Rv1042c |  | 1.0895423 | 1.5307649 | 1.3488253 | 1.294951 | 1.3000332 | 1.3088311 | 1.0915807 | 1.0297359 | Rv1042c, (MTCY10G2.07), len: 135. Probable transposase, similar to insertion element orf eg M tuberculosis Q50761 TRANSPOSASE (308 aa), opt: 823, E(): 0, (99.1% identityin 117 aa overlap)
Rv1149 | Rv1149 |  | 1.3608764 | 1.8441837 | 1.6117376 | 1.566006 | 1.5106841 | 1.5580474 | 1.294629 | 1.2080003 | [NAME], (MTCI65.16), len: 135. Identical to 117 aaN-terminal region of transposase of putative M. tuberculosisIS element. FASTA scores: S21394 transposase - Mycobacterium tuberculosis (308 aa) opt: 823; E(): 0; 99.1% identityin 117 aa overlap. Second copy is MTCY10G2.07. TBparse scoreis 0.926
pks3 | Rv1180 |  | 1.8065536 | 3.246143 | 2.4866872 | 2.209356 | 2.4427984 | 2.1859128 | 2.1038952 | 2.7812557 | Rv1180, (MTV005.16), len: 488. Probable polyketidesynthase beta-ketoacyl synthase domain, similar to the N-terminus of many polyketide synthases eg. MCAS_MYCBO Q02251 mycocerosicacid synthase from mycobacterium bovis (2110 aa),fasta scores; opt: 2115 z-score: 2182.0 E(): 0, 66.5% identity in 472 aa overlap. Also similar to, and same length asM. tuberculosis TR:P96284 (EMBL:[NAME]) MTCY24G1.02 (496aa),fastascores; opt: 1424 z-score: 1408.6 E(): 0, 50.9% identity in444 aa overlap. Contains possible signal sequence andPS00013 Prokaryotic membrane lipoprotein lipid attachment site,also PS00606 Beta-ketoacyl synthases active site
pks4 | Rv1181 |  | 1.3460608 | 2.0790284 | 1.6662058 | 1.4804721 | 1.6012082 | 1.6477209 | 1.80854 | 1.7096602 | Rv1181, (MTV005.17), len: 1582. Probable polyketidesynthase, similar to many eg. MCAS_MYCBO Q02251 mycocerosicacid synthase from mycobacterium bovis (2110 aa), [NAME] scores; opt: 3518 z-score: 6207.2 E(): 0, 59.7% identity in1614 aaoverlap. Note that this similarity extends upstreamofthefirst initiation codon into the upstream CDS MTV005.16;however the stop codon at the end of MTV005.16 is presentin atleast 4 independent clones (BAC, cosmid and pUC) fromthe genome. The two CDS's may represent separate modulesofthepolyketide synthase.
papa3 | [NAME] |  | 1.1402601 | 1.9393406 | 1.6443888 | 1.5045505 | 1.7627631 | 1.6142035 | 1.9672724 | 2.1086571 | [NAME], (MTV005.18), len: 472. Similar to other Mycobacterial hypothetical proteins eg. TR:Q49618 (EMBL:U00010)B1170_C1_180 from M. leprae (471 aa), [NAME] scores; opt: 2526 z-score: 3476.5 E(): 0, 75.6% identity in 471 aa overlap
fadd21 | Rv1185c |  | 1.2375727 | 1.519568 | 1.2374948 | 1.0954922 | 1.2396473 | 1.1395187 | 1.4578328 | 1.4041061 | Rv1185c, (MTV005.21c), len: 578. fadD21, Probable acyl-coAsynthase, similar to eg. TR:P71495 (EMBL:U75685) ACYL-COA SYNTHASE from Mycobacterium bovis (582 aa), [NAME] scores; opt: 2388 z-score: 2929.0 E(): 0, 61.8% identity in 579 aa overlap
sigi | Rv1189 |  | 0.9349557 | 1.9401171 | 1.1841468 | 1.137687 | 1.0950822 | 1.112359 | 1.2101058 | 1.2895586 | Rv1189, (MTV005.25-MTCI364.01), len: 290. Probablesigma factor, similar to eg. TR:[NAME] (EMBL:U87307) extracytoplasmic function alternative sigma factor (sigE) fromM. smegmatis (204 aa), [NAME] scores; opt: 239 z-score: 301.4 E(): 1.3e-09, 32.9% identity in 167 aa overlap.
Rv1269c | Rv1269c |  | 1.1687788 | 1.7119439 | 1.499374 | 1.5433052 | 1.4573152 | 1.452269 | 1.7447263 | 1.6174203 | Rv1269c, (MTCY50.13), len: 124. Similar to M. tuberculosis protein Y0DU_MYCTU Q50620 hypothetical protein cy1a11.30 (137 aa), [NAME] scores; E(): 9e-21, 41.6% identity in 137 aa overlap
Rv1284 | Rv1284 |  | 1.5044042 | 1.7609495 | 1.4730192 | 1.3612243 | 1.4642136 | 1.4323717 | 0.9573175 | 0.9680559 | Rv1284, (MTCY373.03), len: 163. Unknown, some similarity to hypothetical protein from Methanobacterium thermoautotrophicum. Weak similarity to carbonic anhydrases. FASTAscore: U51624|MTU516242 NID: g1272328 - Methanob (171 aa)opt: 305 z-score: 390.7 E(): 1.2e-14; 35.2% identity in 165aa overlap
qor | Rv1454c |  | 1.1281838 | 1.9034504 | 1.2350719 | 1.1865438 | 1.0150468 | 1.3772874 | 1.3720751 | 0.80688256 | Rv1454c, (MTV007.01c), qor, len: 328. Probable quinone oxidoreductase (EC 1.6.5.5) (NADPH:QUINONE REDUCTASE).FASTA scores: U87282|RCU87282_2 Rhodobacter capsulatus cbbIIoper (323aa) opt: 849 E(): 0; (44.7% identity in 329 aaoverlap). Contains PS01162 [NAME] oxidoreductase / zeta-crystallin signature. Also similar to MTCY180.06, FASTA scores:cY180.seq 6203:7204 MW:35814 (334 aa) opt: 430 z-score:353.9E(): 2e-14; (32.3% identity in 350 aa overlap). TBparsescore is 0.887
Rv1460 | Rv1460 |  | 1.0448674 | 2.2742755 | 1.9762721 | 1.8725966 | 2.048823 | 1.7473862 | 1.6170869 | 1.4753458 | Rv1460, (MTV007.07), len: 278. Equivalent to Mycobacterium leprae hypothetical protein [NAME]. Possible helix-turn-helix motif between aa 68 - 89. FASTA scores: gp|Z99125|MLCL536_25 Mycobacterium leprae cosmid L536. (254 aa) opt: 1273 z-score: 1384.7 E(): 0; 79.6% identity in 250aa overlap. Alternative start possible at 6754. TBparse score is 0.904
fadd24 | Rv1529 |  | 1.3347648 | 1.5167607 | 1.5386417 | 1.3868868 | 1.3727419 | 1.3437483 | 1.2776973 | 1.2111942 | Rv1529, (MTV045.03), len: 584. fadD24, but highlysimilar to possible polyketide synthase MTCY409.04c (584 aa),63.2% identity in 584 aa overlap, or MBU75685_1 M. bovisacyl-CoA synt (582 aa), 65.6% identity in 582 aa overlap and many other mycobacterial hypothetical proteins: MTCY19G5_7(583 aa) 68.7% identity in 584 aa overlap or MTCY24G1_8(580 aa),66.0% identity in 582 aa overlap, or U00010_6 M.leprae [NAME], (372 aa), 57.6% identity in 342 aa overlap.TBparse score is 0.951
cydd | Rv1621c |  | 1.3257716 | 1.8593527 | 1.5926445 | 1.4772996 | 1.6004096 | 1.353858 | 1.4536536 | 1.2806897 | Rv1621c, (MTCY01B2.13c), len: 527. cydD, Function: probable ABC transporter, similar to many, possibly CydD, contains an ATP/GTP-binding site motif A (P-loop, PS00017) and ABC transporters family signature (PS00211). FASTA best:Q11019 Y07D_MYCTU (579 aa) opt: 530; E(): 6.9e-25; (29.1% identity in 530 aa overlap). Relatives in M. tuberculosis: MTCY02B10.13, 2.4e-21; MTCY50.10, 3.6e-20; MTCY50.09, 1.9e-16; MTCY01B2.12c,4.7e-15; MTCY02B10.12, 3.7e-14.
Rv1639c | Rv1639c |  | 1.3230984 | 1.9433283 | 1.6677707 | 1.4116359 | 1.5358889 | 1.3715366 | 1.3048624 | 1.2436036 | Rv1639c, (MTCY06H11.03c), len: 489. Some similarityto YLI2_CORGL P35866 hypothetical 45.7 kd protein in lysi(426aa), [NAME] scores opt: 511, E(): 2.4e-23, (28.9% identityin 370 aa overlap); contains PS00904 Protein phenyltransferases alpha subunit repeat signature
Rv1646 | Rv1646 | PE17 | 1.0518955 | 1.5909978 | 1.4050303 | 1.3157467 | 1.2668978 | 1.160619 | 1.2156456 | 1.0694087 | Rv1646, (MTCY06H11.11), len: 310. Member of the M.tuberculosis [NAME] family of proteins, similar to eg YW36_MYCTUQ10873 hypothetical 53.7 kd protein cy39.36c (558aa), fastascores, opt: 411, E(): 1.3e-15, (34.4% identityin 320 aa overlap)
Rv1686c | Rv1686c |  | 0.83469003 | 1.598468 | 1.4635829 | 1.6574174 | 1.7668126 | 1.4365612 | 1.649464 | 1.6320707 | Rv1686c, (MTCI125.08c), len: 226. Possible transmembrane protein, some similarity to TR:Q53627 (EMBL:U43537) STREPTOMYCES ARGILLACEUS MEMBRANE PROTEIN INVOLVED IN MITHRAMYCIN RESISTANCE (233 aa), [NAME] scores; opt: 222 z-score:304.1 E(): 5.4e-10, 28.7% identity in 216 aa overla
Rv1687c | Rv1687c |  | 0.9470041 | 1.658409 | 1.5764408 | 1.6735134 | 1.7622682 | 1.3239137 | 1.5056071 | 1.4098151 | Rv1687c, (MTCI125.09c), len: 255. Probable ABC-typetransport protein, similar to many ABC-type transporters eg. NODI_RHISN P55476 nodulation atp-binding protein I (343 aa), [NAME] scores; opt: 479 z-score: 540.4 E(): 3.7e-23, 34.6% identity in 243 aa overlap. Contains PS00211 ABC transporters family signature and PS00017 ATP/GTP-binding site motif A (P-loop). Also contains PS00039 DEAD-box subfamily ATP-dependenthelicases signature, though this may be spurious.Also similar to many other M. tuberculosis ABC-type transporters e.g. [NAME] (34.5% identity in 238 aa overlap)
Rv1734c | Rv1734c |  | 1.1146287 | 1.5051074 | 1.1055317 | 1.0679464 | 1.2530322 | 1.4116076 | 1.4261777 | 1.4810265 | Rv1734c, (MTCY04C12.19c), len: 80. Unknown.
Rv1861 | Rv1861 |  | 1.2094895 | 1.6367784 | 1.4122019 | 1.31429 | 1.1812377 | 1.27905 | 1.2488536 | 1.1990404 | Rv1861, (MTCY359.12c), len: 101. Function: unknown but contains PS00017 [NAME]/GTP-binding site motif A (P-loop) TBPARSE score is 0.863
Rv1926c | Rv1926c | mpt63;mpb63 | 1.3448339 | 1.6681955 | 1.335315 | 1.1414299 | 1.3617024 | 1.1284755 | 1.3640621 | 1.2669164 | Rv1926c, MTCY09F9.38, len: 159 aa. Unknown, probably exported protein contains N-terminal signal sequence.
Rv1955 | Rv1955 |  | 1.2245443 | 2.2752774 | 2.1418622 | 1.999619 | 2.2917695 | 1.7179446 | 1.4950496 | 1.4146959 | Rv1955, (MTCY09F9.09c), len: 170 aa. Unknown, startoverlaps another ORF
Rv1956 | Rv1956 |  | 1.0150208 | 1.7373061 | 1.7070909 | 1.7024044 | 1.7205809 | 1.5085582 | 1.3698287 | 1.2960787 | Rv1956, (MTCY09F9.08c), len: 149 aa, unknown, possibly involved in regulation, contains probable helix-turn-helix motif at aa 52-73, (+4.78 SD)
Rv1957 | Rv1957 |  | 1.1700335 | 1.7114946 | 1.674389 | 1.6370823 | 1.7006215 | 1.5035497 | 1.4331454 | 1.4441202 | Rv1957, (MTCY09F9.07c), len: 181 aa, unknown
Rv1988 | Rv1988 |  | 1.2095417 | 1.6350414 | 1.272924 | 1.1750327 | 1.1608412 | 1.0723592 | 1.0330302 | 1.1087614 | Rv1988, (MTCY39.31c), len: 179, methyltransferase, similar to eg ERME_SACER P07287 rrna adenine n-6-methyltransferase (370 aa) FASTA scores, opt: 259, z-score: 322.8, E(): 2e-11, (35.1% identity in 171 aa overlap); contains PS00092 [NAME] DNA methylases signature
Rv1998c | Rv1998c |  | 1.023004 | 2.8361235 | 2.1517887 | 2.5104198 | 2.777263 | 1.9246202 | 1.9265553 | 2.4987855 | Rv1998c, (MTCY39.20), len: 258, some similarity with unknown Saccharopolyspora erythraea protein SEU82823_3 (266 aa). FASTA scores, U82823|SEU82823_3 Saccharopolyspora erythraea putat (266 aa) opt: 654 z-score: 771.3 E():0;43.8% identity in 249 aa overlaopt: 114, z-score: 141.6, E(): 0.24, (26.8% identity in 246 aa overlap)
[NAME] | Rv2031c | acr | 0.9498107 | 2.4847236 | 1.9348757 | 1.8930686 | 1.9194276 | 0.99915504 | 0.6271407 | 0.6077577 | Rv2031c, (MTV018.18c), len: 144. hspX. Identical to14 KD ANTIGEN (16 KD ANTIGEN) (HSP 16.3) of M. tuberculosis. BELONGS TO THE SMALL HEAT SHOCK PROTEIN (HSP20) FAMILY. (See [NAME]. 174:1352-1359(1992); INFECT. [NAME]. 60:2066-2074(1992)). FASTA scores: P30223|14KD_MYCTU 14 KD ANTIGEN (16 KD ANTIGEN) (HS (143 aa) opt: 933 z-score: 1119.3E(): 0; 100.0% identity in 143 aa overlap. TBparse score is 0.897
[NAME] | [NAME] | PPE36 | 0.91933155 | 1.6272297 | 1.2806404 | 1.0683906 | 1.2401394 | 1.0814672 | 1.1581757 | 1.1500405 | Rv2108, (MTCY261.04), len: 243 aa; N-terminus is similar to N-terminal region of M. tuberculosis PPE family proteins eg. YX23_MYCTU Q10813 hypothetical 41.1 kd [NAME] (404 aa), [NAME] scores; opt: 431 z-score: 701.6 E(): 3.9e-32, 44.0% identity in 166 aa overlap
Rv2129c | Rv2129c |  | 1.3906277 | 1.6764643 | 1.4367461 | 1.5427649 | 1.4333688 | 1.4195845 | 1.1980004 | 1.1028812 | Rv2129c, (MTCY261.28), len: 293 aa. Probable oxidoreductase, similar to many eg. [NAME] P73826 3-oxoacyl-[acyl-carrier protein] reductase (240 aa), [NAME] scores; opt: 241 z-score: 430.2 E(): 5.1e-17, 32.7% identity in 196 aaoverlap. Also similar to a number of other M. tuberculosisoxidoreductases eg. [NAME] (34.1% identity in 217 aa overlap)
Rv2137c | Rv2137c |  | 1.3526313 | 2.0844257 | 1.6085685 | 1.6411839 | 1.7228097 | 1.754005 | 1.7225924 | 1.5955572 | Rv2137c, (MTCY270.31), len: 137. Function: unknown C-terminus is very similar to hypothetical M. leprae protein [NAME] (150 aa). FASTA best: [NAME]. (150 aa) opt: 469 z-score: 623.7 E(): 9.6e-28; (77.2% identity in 101 aa overlap)
mure | Rv2158c |  | 0.8851536 | 1.6279069 | 1.5330718 | 1.6575351 | 1.6709929 | 1.516077 | 1.9087324 | 1.9544379 | Rv2158c, (MTCY270.10), len: 535. Function murE: probable UDP-N-acetylmuramoylalanyl-D- glutamate-2,6-diaminopimelate ligase (EC 6.3.2.13; UDP-N-ACETYLMURAMYL-TRIPEPTIDE SYNTHETASE) also related to other M. tuberculosis mur gene products. FASTA best: MURE_BACSU Q03523 (494 aa) opt: 1020 z-score: 1110.1 E(): 0; (40.1% identity in 476 aa overlap)
Rv2233 | Rv2233 |  | 1.147152 | 2.0320585 | 1.7998854 | 1.5489817 | 1.7077582 | 1.5068195 | 1.3449088 | 1.2897171 | Rv2233, (MTCY427.14), unknown, len: 135. Similar toC-terminal part of several PHOSPHOGLYCOLATE PHOSPHATASES egsp|P32662|GPH_ECOLI PHOSPHOGLYCOLATE PHOSPHATASE (252 aa).FASTA score: opt: 184 z-score: 250.0 E(): 2.1e-06; 26.5% identity in 132 aa overlap
Rv2288 | Rv2288 |  | 1.0561917 | 2.4737973 | 2.246403 | 1.2354975 | 2.0795493 | 1.6643211 | 1.306671 | 1.6717883 | Rv2288, (MTCY339.22c), len: 125. Unknown
Rv2302 | Rv2302 |  | 1.2442673 | 1.8919384 | 1.6600852 | 1.471648 | 1.4705317 | 1.2895732 | 1.2053206 | 1.0043992 | Rv2302, (MTCY339.07c), len: 80, Similar to Mycobacterium tuberculosis AL021942|MTV039_7 (88 aa) FASTA scores,opt: 300 z-score: 431.5 E(): 1.6e-16; 61.8% identity in76 aa overlap, and similar to M. leprae U650M G699303 (53aa) FASTA scores, opt: 89 z-score: 140.9, E(): 0.66, (45.5% identity in 33 aa overlap)
Rv2305 | Rv2305 |  | 1.1706088 | 1.8377528 | 1.6275525 | 1.4220074 | 1.6669785 | 1.8020937 | 2.0780194 | 2.068527 | Rv2305, (MTCY339.04c), len: 429. Unknown
nark1 | Rv2329c |  | 1.5831475 | 1.5024105 | 1.2204443 | 1.1557127 | 1.3544787 | 1.1872046 | 1.4691504 | 1.4406104 | Rv2329c, (MTCY3G12.05), len: 515. narK1, probale nitrite extrusion protein. Equivalent to Z98741|MLCB22_25 Mycobacterium leprae cosmid B22; P (517 aa). FASTA score: opt: 2224 z-score: 2696.7 E(): 0; 69.3% identity in 488 aa overlap; similar to Z86089|MTCY6A4_5 Mycobacterium tuberculosis cosmid (469 aa) opt: 2000 z-score: 2425.8 E():0; 62.6% identity in 470 aa overlap; and similar toNARK_ECOLI P10903 nitrite extrusion protein (nitrite fa (463 aa) [NAME] scores, opt: 784, E(): 0, (35.3% identity in 468aaoverlap)
Rv2331 | Rv2331 |  | 1.956867 | 2.2020757 | 1.8965311 | 1.726932 | 2.0454526 | 1.7935766 | 1.5288283 | 1.5587568 | Rv2331, (MTCY3G12.03c), len: 128. Unknown, shortened version of MTCY3G12.03c to eliminate overlap with [NAME]
Rv2358 | Rv2358 |  | 1.1755011 | 1.51967 | 1.4770669 | 1.4294529 | 1.565087 | 1.448263 | 1.2309604 | 1.1038781 | Rv2358, (MTCY27.22c), len: 135 aa. Probable transcriptional regulator, similar to eg AL022004|MTV043_19 Mycobacterium tuberculosis seque (130 aa) opt: 201 z-score: 248.3 E(): 2.6e-06; 34.3% identity in 108 aa overlap; SMTB_SYNP7 P30340 transcriptional repressor smtb. [NAME] (122 aa), [NAME] scores, opt: 175 z-score: 225.1 E(): 1.6e-05, (32.2% identity in 90 aa overlap), similar to ARR1_ECOLI P15905arsenical resistance operon repressor (117 aa), [NAME] scores, opt: 164 z-score: 212.2 E(): 8.1e-05, (39.1% identity in69 aa overlap) Contains possible helix-turn-helix motif ataa 73-94(+2.78 SD)
Rv2390c | Rv2390c |  | 2.0880604 | 2.5628335 | 1.6372676 | 1.4440625 | 1.5152575 | 1.31893 | 1.0742173 | 1.051312 | Rv2390c, (MTCY253.31), len: 185. Similar to Y07Q_MYCTU Q11032 hypothetical 23.5 kd protein cy02b10 (220 aa), [NAME] scores, opt: 223 z-score: 274.3 E(): 2.8e-08, (26.8% identity in 190 aa overlap) and Y07R_MYCTU Q11033 hypothetical 28.3 kd protein cy02b10. (261 aa), [NAME] scores,opt: 238, E(): 3.4e-09,(27.6% identity in 163 aa overlap)
Rv2396 | Rv2396 | PE_PGRS41 | 1.2861456 | 2.268022 | 1.8226259 | 1.6074978 | 1.6388696 | 1.4353119 | 1.4071285 | 1.3476928 | Rv2396, (MTCY253.25c), len: 361. Member of PE family, PGRS subfamily gly rich protein, len: 361, similar to egY03A_MYCTU Q10637 hypothetical glycine-rich 49.6 kd pro (603 aa), [NAME] scores, opt: 1144, E(): 2.2e-40, (54.8% identity in 372 aa overlap); contains PS00583 pfkB family of carbohydrate kinases signature 1
tig | Rv2462c |  | 1.0743979 | 1.8055555 | 1.512604 | 1.4079877 | 1.459919 | 1.3404157 | 1.3856992 | 1.2550143 | Rv2462c, (MTV008.18c), len: 466 aa. tig, possible chaperone protein; similar to trigger factor from several organisms eg. TIG_BACSU P80698 trigger factor (tf) (423 aa), [NAME] scores; opt: 648 z-score: 578.2 E(): 5.2e-25, 29.9% identity in 411 aa overlap
scob | Rv2503c |  | 1.0242488 | 1.6510581 | 1.4188445 | 1.4739449 | 1.4670273 | 1.2780101 | 1.2433901 | 1.3987175 | Rv2503c, (MTCY07A7.09c), len: 218 aa. scoB, 3-Oxo Acid:CoA Transferase, B Subunit similar to eg PCAJ_BACSU P42316 probable 3-oxoadipate coa-transferase SUBUNIT B (EC 2.8.3.6) (216 aa) opt: 820 z-score: 990.7 E(): 0, (58.2% identity in 201 aa overlap)
lpps | Rv2518c |  | 1.2199014 | 1.6795732 | 1.4648838 | 1.3341571 | 1.3816874 | 1.2454998 | 1.4275441 | 1.3726612 | Rv2518c, (MTV009.03c), len: 408. Unknown but similar to several hypothetical mycobacterial proteins and equivalent to Mycobacterium leprae protein [NAME]; len: 414 aa; also similar to YV09_MYCTU Q11149 hypothetical 47.9 kd protein cY20G9.09 (451 aa). FASTA scores: sptr|O07707|O07707HYPOTHETICAL 43.6 KD PROTEIN (407 aa) opt: 2300 z-score: 2660.7 E(): 0; (82.5% identity in 406 aa overlap); and sp|Q11149|YV09_MYCTU HYPOTHETICAL 47.9 KD PROTEIN CY20 (451 aa)opt: 763 z-score: 885.2 E(): 0; (34.8% identity in 402 aaoverlap). Could be a lipoprotein, has very long signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. TBparse score is 0.881
Rv2615c | Rv2615c | PE_PGRS45 | 0.96709365 | 1.6285038 | 2.071649 | 2.5716305 | 2.6046474 | 3.0427487 | 2.746218 | 2.854787 | Rv2615c, (MTCY01A10.19), len: 461 aa. Member of M. tuberculosis gly-, ala-, asn-rich PE protein family, pgrs subfamily
Rv2617c | Rv2617c |  | 1.0165731 | 2.1267025 | 2.1624336 | 2.0898435 | 2.3624358 | 2.0105593 | 1.5212727 | 1.3833097 | Rv2617c, (MTCY01A10.17), len: 146 aa. Unknown, somesimilarity to [NAME] P54720 hypothetical protein in glvbc 3'region (134 aa), [NAME] scores, opt: 98, E(): 1.2, (30.6% identity in 111 aa overlap)
Rv2632c | Rv2632c |  | 1.4492784 | 2.4203417 | 2.2691593 | 1.9776034 | 2.0104232 | 1.7218938 | 1.4861635 | 1.3755851 | Rv2632c, (MTCY441.02c), len: 93. Highly similar to hypothetical M. tuberculosis protein, MTCY04C12.23. FASTA score: NID: g1654017 - [NAME] (153 aa) opt: 319 E(): 1.3e-16; 53.9% identity in 89 aa overlap
Rv2633c | Rv2633c |  | 1.9707838 | 3.8268821 | 3.2301471 | 2.7632241 | 3.0296586 | 2.4216173 | 2.2221901 | 2.0662396 | Rv2633c, (MTCY441.03c), len: 161. Unknown
Rv2654c | Rv2654c |  | 1.2367063 | 2.8628345 | 2.0806105 | 1.9800223 | 2.0204482 | 1.8290561 | 1.9251347 | 1.8182143 | Rv2654c, (MTCY441.23c), len: 81. Unknown, ala-rich some similarity to antifreeze proteins, possibly phage protein
Rv2657c | Rv2657c |  | 1.4375925 | 1.5380924 | 1.2604907 | 1.1785322 | 1.2481663 | 1.3180431 | 1.3806213 | 1.220221 | Rv2657c, (MTCY441.26c), len: 86. Probable phage protein. Similar to gp36 protein of mycobacteriophage L5 Q05246|VG36_BPML5 GENE 36 PROTEIN (GP36). - MYCOBA (56 aa)opt:169 E(): 8.9e-07 (50.0% identity in 50 aa overlap). Also similar to Mycobacteriophage D29 dCMP deaminase (g1) gene Similarity suggests alternative start at 21737. Contains possible heli-turn-helix motif at aa 34 - 55, (+4.47 SD)
Rv2658c | Rv2658c |  | 1.0572039 | 2.383661 | 1.78474 | 1.7599453 | 1.6031083 | 1.4781361 | 1.8963988 | 1.8470892 | Rv2658c, (MTCY441.27c), len: 120. Unknown, probablyphage protein
Rv2705c | Rv2705c |  | 1.4589903 | 1.6066947 | 1.4199651 | 1.3164057 | 1.3948398 | 1.3318219 | 1.380908 | 1.2645879 | Rv2705c, (MTCY05A6.26c), en: 129. Function: unknownunlikely orf
Rv2758c | Rv2758c |  | 1.8032129 | 1.6365216 | 1.4298146 | 1.0907575 | 1.1904604 | 1.4792331 | 0.92852706 | 1.0134333 | Rv2758c, (MTV002.23c), len: 88 aa. Unknown; similarto several M. tuberculosis hypothetical proteins eg. TR:P95008 MTCY159.11C (92 aa), [NAME] scores; opt: 151 z-score: 268.9 E(): 8e-08, 66.7% identity in 45 aa overlap. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature
fabg5 | [NAME] |  | 1.3928086 | 1.5402353 | 1.3078557 | 1.3952396 | 1.3658549 | 1.5431817 | 1.0532985 | 1.0637746 | [NAME], (MTV002.31c), len: 260 aa. fabG5, probable 3-oxoacyl-[acyl-carrier protein]; Similar to many. [NAME] scores; sp|P51831|FABG_BACSU 3-OXOACYL-[ACYL-CARRIER PROTEIN] (246 aa) opt: 504 z-score: 639.3 E(): 4e-28; 37.2% identity in 247 aa overlap. Also similar to many other M. tuberculosis acyl-carrier proteins eg. [NAME] (38.5% identity in 244 aa overlap). Contains PS00061 Short-chain alcohol dehydrogenase family signature
Rv2797c | Rv2797c |  | 1.1326216 | 1.5459157 | 1.1704844 | 1.2506238 | 1.2826378 | 1.4107306 | 1.4729711 | 1.5875765 | Rv2797c, (MTCY16B7.46), len: 562. Unknown, containsPS00120 Lipases, serine active site, similarity to Z83863|MTCY159_14 Mycobacterium tuberculosis cosmid (403 aa) opt:537 z-score: 530.8 E(): 4.8e-22; 40.8% identity in 292aa overlap
Rv2893 | Rv2893 |  | 1.540343 | 1.6694583 | 1.6704361 | 1.7893027 | 1.7339765 | 1.8912086 | 1.5316243 | 1.3013668 | Rv2893, (MTCY274.24), len: 325, similar in part to gp|AL021959|MTV042_1 Mycobacterium tuberculosis sequen (244aa) opt: 264 z-score: 339.4 E(): 2.2e-11; 34.0% identity in 162 aa overlap; also similar to alkanal monooxygenasealpha chain, eg LUXA_KRYAL P18299 (357 aa), FASTA scores, opt: 130, z-score: 156.1, E(): 0.038, (23.7% identity in 131aa overlap)
rnc | Rv2925c |  | 1.2399595 | 1.6360298 | 1.462796 | 1.377304 | 1.4814101 | 1.2897513 | 1.332753 | 1.2280923 | Rv2925c, (MTCY338.14c), len: 240. RNase III, Q10962; RNC_ECOLI P05797 ribonuclease III, (226 aa) opt: 459, z-score: 563.7, E(): 7.5e-25, (41.8% identity in 213 aa overlap); contains PS00517 [NAME] family signature
Rv3067 | Rv3067 |  | 1.1517347 | 1.6128877 | 1.4459599 | 1.3814449 | 1.6172225 | 1.3821462 | 1.7320824 | 1.537147 | Rv3067, (MTCY22D7.14c), len: 136. Function: unknownhas hydrophobic stretch at N-terminus, some similarity to hypothetical M. tuberculosis proteins such as MTCY50.11 andMTV049_2. TTG start chosen on basis of codon usage but upstream ATG also possible. FASTA scores: AL022021|MTV049_25 Mycobacterium tuberculosis seque (108 aa) opt: 183 z-score:197.9 E(): 0.0017; 36.6% identity in 82 aa overlap; [NAME] hypothetical 11.6 kd protein [NAME] (113 aa), opt: 148, E(): 0.0098; (29.2% identity in 106 aa overlap).
Rv3123 | Rv3123 |  | 1.2554659 | 1.5403272 | 1.4270446 | 1.1953189 | 1.3771307 | 1.2360439 | 1.080879 | 1.1387917 | Rv3123, (MTCY164.33), len: 162 aa. Unknown
whib1 | Rv3219 |  | 1.4399639 | 1.6437924 | 1.4608281 | 1.0947915 | 1.2914675 | 1.2187865 | 1.1028081 | 1.1489242 | Rv3219, (MTCY07D11.07c), len: 84, whiB-homolog, putative regulatory protein, similar to MTCY78_13. FASTA best: SCWHIB_1 S;coelicolor whiB gene; Regulatory (87 aa, E(): 7e-10;43.8% identity in 73 aa overlap. Also similar to U00020_2 Mycobacterium leprae cosmid B229, 42.7% identity in 82 aa overlap
desa3 | Rv3229c |  | 1.1220597 | 1.7903808 | 1.7041906 | 1.5917028 | 1.5903782 | 1.7741995 | 1.5217018 | 1.4526212 | Rv3229c, (MTCY20B11.04c), len: 427. Function: desA3, but shows some similarity to desaturases. FASTA best:D90914_112 Synechocystis Q08871 LINOLEOYL-COA DESATURASE (EC 1.14.99.25) (359 aa), opt: 319 z-score: 380.8 E(): 3.2e-14; (25.1% identity in 295 aa overlap)
Rv3237c | Rv3237c |  | 1.2281644 | 1.513831 | 1.4431354 | 1.5163839 | 1.4643462 | 1.3687972 | 1.2475775 | 1.23948 | Rv3237c, (MTCY20B11.12c), len: 160, unknown some similarity to putative potassium channel protein. FASTA best:YD57_METJA [NAME] putative potassium channel protein (343 aa) opt: 143 z-score: 180.3 E(): 0.0047; (33.8% identity in68 aa overlap). Also similar to AE001018_4 Archaeoglobus fulgidus O29024 HYPOTHETICAL 17.5 KD PROTEIN, 29.0% identityin155 aa overlap
Rv3238c | Rv3238c |  | 1.5244019 | 2.0938537 | 1.8377815 | 1.737404 | 1.5448993 | 1.6525613 | 1.382853 | 1.2334815 | Rv3238c, (MTCY20B11.13c), len: 244, unknown, possible membrane protein
Rv3249c | Rv3249c |  | 1.1339731 | 2.4636168 | 1.8666278 | 1.6455572 | 1.7915144 | 1.4014546 | 1.304103 | 1.0789233 | Rv3249c, (MTCY20B11.24c), len: 211. Function: unknown but some similarity to hypothetical transcriptional regulator in M. tuberculosis. FASTA best: Y08R_MYCTU Q11063 hypothetical transcriptional regulator (202 aa), opt: 191 z-score: 240.3 E(): 2.2e-06; (28.3% identity in 180 aa overlap). Also some similarity to D90899_48 Synechocystis P72624 HYPOTHETICAL 22.6 KD PROTEIN and MTCY63_7. Possible helix-turn helix motif at aa 45-66 (+6.53 SD)
rsbw | Rv3287c |  | 1.0175185 | 1.8687633 | 1.9645153 | 1.9538131 | 1.9840132 | 1.7257565 | 1.8002579 | 1.9823588 | Rv3287c, (MTCY71.27c), len: 242, usfX, hypotheticalprotein, identical to AF001306_2 Mycobacterium tuberculosisP96892 USFX (100.0% identity in 242 aa overlap). Start chosen by similarity, overlapping end of next ORF. Also similar to M. leprae Q49667 B1308_F3_89 (75 aa), [NAME] scores, opt: 308, E(): 2.7e-15, (72.2% identity in 72 aa overlap), also similar to [NAME] P17904 anti-sigma b factor (160 aa), [NAME] scores, opt: 108, E(): 0.35, (21.3% identity in127 aa overlap)
deoa | Rv3314c |  | 0.9753264 | 1.6397827 | 1.4445202 | 1.3916953 | 1.4295303 | 1.2921665 | 1.3412955 | 1.4202156 | Rv3314c, (MTV016.14), len: 427. deoA, probable thymidine phosporylase, similar to many e.g. P77836|PDP_BACST (433 aa) best with human TYPH_HUMAN (482 aa). Contains PS00647 Thymidine and pyrimidine-nucleoside phosphorylases signature. FASTA scores: sp|P19971|TYPH_HUMAN THYMIDINE PHOSPHORYLASE PRECURSOR (482 aa) opt: 957 z-score: 1115.0 E(): 0;44.4% identity in 441 aa overlap and sp|P77836|PDP_BACST PYRIMIDINE-NUCLEOSIDE PHOSPHORYLASE (433 aa) opt: 919 z-score: 1071.6 E(): 0; 44.4% identity in 428 aa overlap. TBparsescore is 0.890
Rv3354 | Rv3354 |  | 1.9370784 | 3.4864547 | 2.0749326 | 1.9941047 | 1.9587772 | 2.1680007 | 1.9077587 | 1.5530618 | Rv3354, (MTV004.11), len: 129, unknown similar to several [NAME] hypothetical proteins eg. TR:[NAME] (EMBL:Z98271) MLCB1779.15 from M. leprae (168 aa), [NAME] scores; opt: 467 z-score: 665.0 E(): 7e-30, 55.9% identity in 127 aa overlap. Also to M. tuberculosis MTCI125.12 (47.0% identity in 115 aa overlap). Also similar to MTCI125_11, [NAME], MTV049_25.
Rv3479 | Rv3479 |  | 1.0250428 | 1.7395339 | 1.5422426 | 1.4637346 | 1.4980214 | 1.2117882 | 1.3628497 | 1.1544499 | Rv3479, (MTCY13E12.32), len: 1075. Function: unknown, first start taken. Hydrophobic stretches at C-terminus
lipf | Rv3487c |  | 1.6046652 | 2.3118389 | 1.8415409 | 1.6405109 | 1.8027685 | 1.5587447 | 1.6511011 | 1.800124 | Rv3487c, (MTCY13E12.41c), len: 277. Function: unknown but similar to esterases and lipases of around 300 aa. Best with M. leprae protein Q50058. FASTA results: Q50058 [NAME] B1740 (143 aa) opt: 565; E(): 3.9e-31; 61.8% identity in 136 aa overlap. Also similar to MTCY253.36c (FASTA score: 1.3e-22; 36.2% identity in 254 aa overlap). TBparse score is 0.940
Rv3612c | Rv3612c |  | 1.3743083 | 1.9302541 | 1.5825727 | 1.3936567 | 1.5018011 | 1.3236463 | 1.2195312 | 1.3001255 | Rv3612c, (MTCY07H7B.10), len: 109. Unknown
[NAME] | [NAME] |  | 1.7707771 | 1.5666978 | 1.3849132 | 1.3465229 | 1.360068 | 1.1369146 | 1.1913252 | 1.1287824 | [NAME], (MTV025.034c), len: 110. Unknown, but similar to Rv3288c (MTCY71.28c),(137 aa, 29.1% identity in 79 aa overlap)
Rv3741c | Rv3741c |  | 1.1530572 | 2.0093758 | 1.3724612 | 1.0642667 | 1.0879686 | 1.2117859 | 0.82503915 | 0.73024166 | Rv3741c, (MTV025.089c), len: 224. Unknown, partially similar to M. tuberculosis probable monoxygenase MTCY01A6.14 (489 aa) and various monoxygenases. FASTA scores: gp|Z83864|MTCY1A6_14 Mycobacterium tuberculosis cosmid (489 aa);opt: 542 z-score: 672.7 E(): 5.8e-30. 50.0% identity in162 aa overlap. Also similar to [NAME]; and MTCY31_22; TBparse score is 0.911, Similarity to MTCY01A6.14 and MTV013_4continuein ORF (MTV025.090c) upstream after a gap of 100.
Rv3749c | Rv3749c |  | 1.1234434 | 1.6655964 | 1.4264932 | 1.2825025 | 1.2824522 | 1.1552274 | 1.339559 | 1.2457021 | Rv3749c, (MTV025.097c), len: 169. Unknown. ContainsPS00092 [NAME]specific DNA methylases signature
Rv3822 | Rv3822 |  | 1.3997802 | 1.768082 | 1.3309832 | 1.2241877 | 1.2879028 | 1.1153946 | 1.1519527 | 1.1140466 | Rv3822, (MTCY409.08c), len: 404. Unknown, similar to M. leprae hypothetical protein Q49633 [NAME] (391 aa),fasta scores; opt: 601 z-score: 485.5 E(): 5e-20, 36.3% identity in 342 aa overlap. Also similar to M. tuberculosis hypothetical proteins e.g. MTCY03C7.17c (38.1% identity in 281 aa overlap). Alsosimilar to Rv1184c, Rv1430, Rv0159c etc.
pks2 | Rv3825c |  | 1.605706 | 2.4516504 | 1.8410461 | 1.6230792 | 1.7687769 | 1.5792075 | 1.8726552 | 1.7393943 | Rv3825c, (MTCY409.05), len: 2126. Probable polyketide synthase, highly similar to MCAS_MYCBO Q02251 mycocerosic acid synthase from Mycobacterium bovis (2110 aa), [NAME] scores; opt: 3495 z-score: 8755.7 E(): 0, 61.6% identity in 2130 aa overlap. Contains PS00606 Beta-ketoacyl synthases active siteand PS00012 [NAME] attachment site. Also similar to many other M. tuberculosis polyketide synthases eg. MTCY24G1.09 (64.3% identity in 2057 aa overlap)
Rv3855 | Rv3855 | ethR;aka;etaR | 0.95242214 | 1.5126826 | 1.5369238 | 1.6487068 | 1.580924 | 1.4467453 | 1.5077399 | 1.3765267 | Rv3855, (MTCY01A6.13c), len: 216. Possible regulatory protein, similar to M. leprae G699124 U1756B (217 aa), [NAME] scores, opt: 786, E(): 0, (60.4% identity in 202 aa overlap). Also similar to M. tuberculosis Rv3058c(MTCY22D7.23)(216 aa, 32.1% identity in 221 aa overlap). Contains helix-turn-helix motif, aa 46-67 , (+3.55 SD)
Rv3865 | Rv3865 |  | 1.0599837 | 1.9201341 | 1.5604652 | 1.5863224 | 1.6159073 | 1.5206752 | 1.7158003 | 1.5882533 | Rv3865, (MTCY01A6.03c), len: 103. Unknown, some similarity to M. leprae G466936 B1620_C2_214, (106 aa), [NAME] scores, opt: 154,E():5.7e-05, (31.1% identity in 103 aa overlap). Also similar to M. tuberculosis [NAME] (MTCY07H7B.07)(103 aa, 36.3% identity in 102 aa overlap)
Rv3866 | Rv3866 |  | 0.97172457 | 1.5103942 | 1.3238944 | 1.3384823 | 1.4390292 | 1.2607703 | 1.2803098 | 1.3202469 | [NAME], (MTCY01A6.01c,MTV027.01), len: 283. Unknownsimilar to M. tuberculosis hypothetical proteins e.g. MTV035.17 (295 aa) E(): 1.2e-08, 28.2% identity in 277 aa overlap
Rv3891c | Rv3891c | esxD | 1.0332378 | 1.6216652 | 1.3079768 | 1.2534275 | 1.2516198 | 1.1380227 | 1.0317316 | 1.0984175 | Rv3891c, (MTCY15F10.21), len: 107. Function: unknown. First GTG taken
Rv3896c | Rv3896c |  | 1.10592 | 1.5852388 | 1.1528703 | 1.1479735 | 1.1089693 | 1.2254605 | 0.9987038 | 0.7283948 | Rv3896c, (MTCY15F10.16), len: 302. Function: unknown Ala-rich protein. First GTG taken, although TBparse suggests TTG at 16079. Related to putative p60 homologue MTCY10H4.24,(281 aa, 29.0% identity in 290 aa overlap) E() 8.1e-09. FASTA best: TR:Q38352 (EMBL:EMBL; L29568) ORF360 from LACTOCOCCUS DELBRUECKII BACTERIOPHAGE LL-H. z-score: 250.8 E(): 5.5e-07, (40.0% identity in 115 aa overlap)