Spreadsheet: 6fbab3d5-c39a-4bff-9e10-897ce188c640
Sheet: Sheet1

Table S1
Genes with peak induction at Day 2 followed by gradual decline toward control levels.
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
MT0855 |  |  | 1.0023141 | 1.4846891 | 1.2346361 | 1.3263266 | 1.3384452 | 1.1833216 | 1.1175786 | 1.1385212 | PE_PGRS family protein
MT1122.1 |  |  | 2.148673 | 5.6059527 | 3.8778093 | 3.401173 | 3.66193 | 3.4593477 | 3.4318426 | 2.6949577 | hypothetical protein
MT2558 |  |  | 1.0314893 | 1.445228 | 1.3442992 | 1.3303162 | 1.3614413 | 1.318265 | 1.1765016 | 1.1601255 | hypothetical protein
MT3222 |  |  | 0.9925938 | 1.53829 | 1.4500372 | 1.3689702 | 1.3902184 | 1.0970979 | 1.1643947 | 1.1644272 | conserved hypothetical
Rv0077c | Rv0077c |  | 1.0541072 | 1.5027956 | 1.370285 | 1.4232521 | 1.3659298 | 1.2979865 | 1.2805219 | 1.1195228 | Rv0077c, (MTV030.21c), possible oxidoreductase, len: 276 aa; weakly similar to many eg. BPA1_STRAU P33912 non-haem bromoperoxidase bpo-a1 (274 aa), [NAME] scores; opt: 230 z-score: 264.8 E(): 1.5e-07, 26.1% identity in 249 aa overlap. Also similar to MTCY05A6_35 and MTCY1A11_10.
Rv0093c | Rv0093c |  | 0.9659244 | 1.5496012 | 1.2238206 | 1.1975397 | 1.1776062 | 1.1609652 | 1.0989667 | 0.98940736 | Rv0093c, (MTCY251.12c), len: 282, unknown
Rv0188 | Rv0188 |  | 0.9446364 | 3.108065 | 2.3431466 | 1.9941442 | 2.0085783 | 1.3764853 | 0.9789934 | 0.87406236 | Rv0188, (MTCI28.27), len: 143, unknown, but some similarity to N-terminus of sp|P80185|MTRC_METTH [NAME] (266 aa), opt: 125 z-score: 174.8 E(): 0.033; 31.6% identity in 98 aa overlap
Rv0246 | Rv0246 |  | 0.9448341 | 1.238223 | 1.2323165 | 1.1550968 | 1.1303203 | 1.0416214 | 1.0751417 | 0.94116807 | Rv0246, (MTV034.12), len: 436. Probable membrane protein similar to Mycobacterium tuberculosis MTCY190.20 (512aa). Start uncertain. FASTA scores Z70283|MTCY190_20 (512aa) opt: 712 z-score: 876.5 E(): 0; 33.2% identity in 422 aa overlap.
hsp | Rv0251c | acr2 | 0.99633616 | 2.3809607 | 1.8828884 | 1.9288802 | 1.6514275 | 1.892626 | 1.4909279 | 1.2519497 | Rv0251c, (MTV034.17c), len: 159. hsp, possibly heat shock protein belonging to HSP20 family, some similarity to many eukaryotic proteins e.g. CHLAMYDOMONAS REINHARDTII P12811|HS2C_CHLRE. Also similar to Synechocystis sp. PCC6803 Spore protein sp21 (146 aa). FASTA scores D90902|D90902_44 Synechocystis sp. [NAME] complete (146 aa) opt: 213 z-score:271.7 E(): 1.2e-07; 30.3% identity in 145 aa overlap; and sp|P12811|HS2C_CHLRE CHLOROPLAST HEAT SHOCK 22KD PROT (157 aa) opt: 184 z-score: 236.3 E(): 1.2e-05;32.4% identity in 142 aa overla. TBparse score is 0.881
fadd27 | Rv0275c |  | 1.1356806 | 2.1483674 | 1.6959293 | 1.643613 | 1.6874965 | 1.7522805 | 1.2520128 | 1.3090913 | Rv0275c, (MTV035.03c), len: 241. fadD27, similar togp|AL022004|MTV043_17 Mycobacterium tuberculosis seque (213aa), FASTA scores: opt: 230 z-score: 266.0 E(): 2.7e-07; 32.6% identity in 190 aa overlap.TBparse score is 0.896
Rv0276 | Rv0276 |  | 1.1893375 | 1.4732774 | 1.409649 | 1.3338935 | 1.3159944 | 1.313627 | 1.2567905 | 1.203873 | Rv0276, (MTV035.04), len: 306. Unknown but similar to Mycobacterium tuberculosis MTCY427.18 (296 aa). FASTA scores: Z70692|MTCY427_18 Mycobacterium tuberculosis cosmid (296 aa) opt: 874 z-score: 1042.8 E(): 0; 49.6% identity in 282 aa overlap. TBparse score is 0.894
dnaK | Rv0350 |  | 1.1666281 | 1.5897613 | 1.4056219 | 1.3394165 | 1.2555459 | 1.2358084 | 1.1798621 | 1.1572704 | Rv0350, (MTCY13E10.10), len: 625. Function: DnaK, 70 kD heat shock protein. FASTA best: DNAK_MYCPA [NAME] (623aa) opt: 3678, E(): 0, (92.3% identity in 625 aa overlap),note that this sequence differs from DNAK_MYCTU P32723 (609 aa), due to a frameshift near the N-terminus
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.
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
Rv0465c | Rv0465c |  | 1.0090375 | 1.473851 | 1.2336339 | 1.1983708 | 1.1052744 | 1.1713997 | 1.0921326 | 1.0709295 | Rv0465c, (MTV038.09c), len: 474. Possible transcriptional regulator very similar to Mycobacterium tuberculosisMTCY22G8.18c (486 aa). Also some similarity in N-terminal region (1-100 aa) with repressors e.g. P06153|RPC_BPPH1 (144 aa). FASTA scores: Z95585|MTCY22G8_18 (486 aa) opt: 1475 z-score: 1794.4 E():0; 47.4% identity in 468 aa overlap; sp|P06153|RPC_BPPH1 IMMUNITY REPRESSOR PROTEIN (144 aa) opt: 130 z-score: 167.1 E(): 0.084; 27.0% identity in 100 aa overlap. TBparse score is 0.896. Contains probablehelix-turn-helix motif at aa 20-41 (1765, +5.20 SD)
fadB2 | Rv0468 |  | 1.1724573 | 1.722551 | 1.540149 | 1.5414381 | 1.577932 | 1.500644 | 1.3075881 | 1.3817303 | Rv0468, (MTV038.12), len: 286. fadB2, Probable 3-hydroxyacyl-CoA dehydrogenase similar to many, e.g. Bradyrhizobium japonicum BJU32229_1 (293 aa) beta-hydroxybutyryl coenzyme Adehydrogenase (HbdA). FASTA scores: U32229|BJU32229_1 (293aa) opt: 771 z-score: 939.6 E(): 0; 45.7% identity in 282 aa overlap. TBparse score is 0.894
Rv0575c | Rv0575c |  | 1.0081505 | 2.1304173 | 1.7575717 | 1.875553 | 1.6958207 | 1.2272571 | 1.1749854 | 0.9543543 | Rv0575c, (MTV039.13c), len: 388. Possible oxidoreductase, weakly similar to many diverse oxidoreductases eg. TR:P96555 (EMBL:AB000564) SALICYLATE HYDROXYLASE from SPHINGOMONAS (395 aa) FASTA scores: opt: 267 z-score: 326.3 E():5e-11, 26.4% identity in 390 aa overlap also similar to Mycobacterium tuberculosis MTCY50.22C (372 aa). FASTA scores:[NAME] (372 aa) opt: 762 z-score: 913.5 E(): 0;40.9% identity in 345 aa overlap. TBparse score is 0.868
Rv0607 | Rv0607 |  | 1.0152688 | 1.8144853 | 1.6384906 | 1.6116354 | 1.5803007 | 1.2671956 | 1.2429243 | 1.3719641 | Rv0607, (MTCY19H5.15c), len: 128, unknown
Rv0712 | Rv0712 |  | 0.9144661 | 1.1529131 | 1.1480689 | 1.1089915 | 1.1441368 | 1.0320399 | 0.9782902 | 1.0150483 | Rv0712, (MTCY210.31), len: 299 aa, unknown, similarto hypothetical proteins e.g.D90901_33 Synechocystis sp P72841 HYPOTHETICAL 48.1 KD PROTEIN.(410 aa), E(): 1.1e-07; (28.8% identity in 299 aa overlap). slight similarity to carboxykinases
Rv0897c | Rv0897c |  | 0.9150098 | 1.3138696 | 1.2075988 | 1.2500515 | 1.1413198 | 1.1489633 | 1.1599431 | 1.1064289 | Rv0897c, (MTCY31.25c), len: 535. Possible oxidoreductase, some similarity to oxidoreductases from diverse organisms eg. CRTD_RHOSH [NAME] dehydrogenase from Rhodobacter sphaeroides (495 aa), [NAME] scores; opt:139, E(): 2.6e-06, 23.8% identity in 538 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
Rv1128c | Rv1128c |  | 1.0158479 | 1.8396633 | 1.5741498 | 1.3843194 | 1.3496058 | 1.1716067 | 0.9907828 | 0.89183396 | Rv1128c, (MTCY22G8.17c), len: 451. Unknown ORF in REP13E12 degenerate repeat, highly similar to several M.tuberculosis proteins in REP13E12 repeats eg. Q50655 (317 aa),fasta scores; opt: 1329 z-score: 1558.9 E(): 0, 61.1% identity in 316 aa overlap
Rv1129c | Rv1129c |  | 1.0574329 | 1.707216 | 1.526408 | 1.4326794 | 1.500051 | 1.3464204 | 1.2807288 | 1.2051686 | Rv1129c, (MTCY22G8.18c), len: 486. Unknown, possible regulator, 47.4% identity in 468 aa overlap with M. tuberculosis Rv0465c(MTV038.09c)(474 aa) E(): 0. Helix turn helix motif present from aa 32-53
Rv1130 | Rv1130 |  | 1.1160221 | 2.008276 | 1.844206 | 1.814805 | 1.8884158 | 1.7159778 | 1.3441496 | 1.1874472 | Rv1130, (MTCY22G8.19), len: 526. Some similarity toeg.PRPD_ECOLI P77243 prpd protein. escherichia coli (483aa), [NAME] scores; opt: 234 z-score: 273.3 E(): 3.3e-08, 27.0% identity in 429 aa overlap
gltA1 | Rv1131 |  | 0.92045045 | 1.2735193 | 1.2514244 | 1.2146909 | 1.2091206 | 1.1593086 | 1.1143167 | 1.1160665 | Rv1131, (MTCY22G8.20), gltA1, len: 393. Probable citrate synthase, highly similar to eg.[NAME] P26491 citrate synthase (ec4.1.3.7) (375 aa), [NAME] scores; opt: 1942z-score: 2334.7E(): 0, 80.0% identity in 375 aa overlap; contains PS00480Citrate synthase signature. Similar to two other M. tuberculosis citrate synthases MTCY31.24 (33.1% identity in 381 aa overlap) and MTCY31.17c (31.8% identity in 371 aa overlap)
Rv1188 | Rv1188 |  | 0.93025416 | 3.3026469 | 2.0818017 | 1.957907 | 1.9006206 | 1.4112574 | 1.531237 | 1.5707599 | Rv1188, (MTV005.24), [NAME], len: 329. Possible proline dehydrogenase, similar to part of eg. TR:Q52711 (EMBL:X78346) proline dehydrogenase from Rhodobacter capsulatus (1127 aa), [NAME] scores; opt: 194 z-score: 264.3 E(): 1.5e-07,31.2%identity in 349 aa overlap. Also similar to all of twoB. subtilis proteins TR:E1184363 (EMBL:Z99120) (302 aa),fastascores; opt: 509 z-score: 919.0 E(): 0, 37.1% identityin313 aa overlap; and TR:E1182272 (EMBL:Z99105) (303 aa),fastascores; opt: 513 z-score: 783.3 E(): 0, 32.5% identityin311 aa overlapscore is 0.889
Rv1265 | Rv1265 |  | 1.2399546 | 1.941037 | 1.7096931 | 1.6553885 | 1.8462597 | 1.5090932 | 1.4412637 | 1.2679963 | Rv1265, (MTCY50.17c), len: 226. Unknown.
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
Rv1461 | Rv1461 |  | 1.1665843 | 1.7153934 | 1.7199373 | 1.6489171 | 1.5510399 | 1.3459792 | 1.5325565 | 1.3257666 | Rv1461, (MTV007.08), len: 846. Equivalent of spliced protein from Mycobacterium leprae MLCL536.28c len: 869. Residues1 -253 represent N-extein, and 613 - 846 the C-extein. The intein present from residues 254 - 612 is differentin sequence and site of insertion from the one present in MLCL536.28c. FASTA scores: gp|Z99125|MLCL536_23 Mycobacteriumleprae cosmid L536. (869 aa) opt: 1498 z-score: 1726.9 E():0;54.1% identity in 917 aa overlap. The mature protein issimilar to hypothetical B. subtilis protein FASTA scores:gp|Z99120|BSUB0017_150 Bacillus subtilis complete geno (465aa)opt:1053 z-score: 1216.6 E(): 0; 34.8% identity in 821aa overlap. The intein shows some similarity to inteinsfromMethanococcus jannaschii. FASTA scores: gp|U67548|MJU67548_6Methanococcus jannaschii from bas (895 aa) opt: 181 z-score:210.6 E(): 0.00023; 25.2% identity in 274 aa overlap.TBparsescore is 0.913
Rv1465 | Rv1465 |  | 0.86422825 | 1.3555763 | 1.18852 | 1.0993952 | 1.2100811 | 1.0526752 | 1.0023742 | 0.89832973 | Rv1465, (MTV007.12), len: 162. Equivalent to Mycobacterium leprae hypothetical protein MLCL536.24c, 165. FASTAscores: gp|Z99125|MLCL536_19 Mycobacterium leprae cosmid L536. (165 aa) opt: 870 z-score: 1057.6 E(): 0; 81.8% identity in 165aa overlap. Also similar to hypothetical [NAME] protein YURV, FASTA Score: Z99120|BSUB0017_151 (147 aa) opt: 354 z-score: 439.4 E(): 4.1e-17; 38.3% identity in 141aa overlap. TBparse score is 0.898
Rv1588c | Rv1588c |  | 0.9623549 | 1.4779545 | 1.2952147 | 1.4330595 | 1.3555422 | 1.202357 | 1.1609124 | 1.2000133 | Rv1588c, (MTCY336.16), len: 222. ORF in REP13E12 repeat, nearly identical to ORF's in other Rep13E12 repeats,including [NAME] and MTCY09F9.19c. FASTA results, Y05E_MYCTU Q10891 hypothetical 15.4 kd protein cy251.14 (136 aa) opt: 613; E(): 9.9e-29; 86.5% identity in 111 aaoverlap;MTCY09F9.19c, 5e-21
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)
Rv1725c | Rv1725c |  | 0.99983734 | 1.218221 | 1.1404124 | 1.1467935 | 1.0768814 | 1.1104091 | 1.1023794 | 1.0596945 | Rv1725c, (MTCY04C12.10c), len: 236. Similar to hypothetical proteins from diverse organisms e.g. TR:P70885 (EMBL:U44893) ORF108 from BUTYRIVIBRIO FIBRISOLVENS, (108 aa),fasta scores; opt: 223 z-score: 298.5 E(): 2e-09, 39.1% identity in 92 aa overlap
ndh | Rv1854c |  | 1.0346313 | 1.7389507 | 1.5288166 | 1.4740702 | 1.517592 | 1.2581888 | 1.3977664 | 1.3316532 | Rv1854c, (MTCY359.19), len: 463. Function: ndh, probable NADH dehydrogenase, similar to several - e.g. S74826 NADH dehydrogenase - Synechocystis s (445 aa) FASTA score: opt: 1228 z-score: 1387.4 E(): 0; 46.3% identity in 432 aa overlap. Highly similar to MTCY04D9.04c Z84725| NID: g1817703 - Mycobacterium tuberculosis (470 aa) opt: 1911, E(): 0;64.7% identity in 459 aa overlap. TBPARSE score is 0.897
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
Rv2053c | Rv2053c |  | 1.166256 | 1.375019 | 1.3034446 | 1.335892 | 1.3007958 | 1.30344 | 1.2368038 | 1.1889428 | Rv2053c, (MTV018.40c-MTCY63A.07), len: 175 unknown YJEG_SERMAP37148 hypothetical protein in aspa 5'region (139aa) opt: 148; E(): 0.00033; 28.9% identity in 97 aa overlap. TBparse score is 0.891 FASTA scores: Z97984|MTCY63A_7 (101 aa) opt: 194 z-score: 246.0 E(): 3.3e-06; 100.0% identity in 33 aa overlap.
Rv2115c | Rv2115c |  | 0.97014123 | 1.2152411 | 1.1979817 | 1.1828779 | 1.1841596 | 1.1119245 | 1.1198344 | 1.0621912 | Rv2115c, (MTCY261.11c), len: 609 aa. Probable ATPase, similar to eg. [NAME] Q58556 cell division cycle protein 48 homolog (903 aa), [NAME] scores; opt: 423 z-score: 695.8 E(): 8.1e-32, 45.8% identity in 249 aa overlap. Contains PS00674 AAA-protein family signature and PS00017 ATP/GTP-binding site motif A (P-loop). Also some similarity to other M. tuberculosis atpases eg. MTCY22G10.32c (36.2% identity in 290 aa overlap). Equivalent to Mycobacterium leprae U00017|U00017_18 (609 aa) [NAME] scores; opt: 3670 z-score: 4031.4 E(): 0; 92.9% identity in 609 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
uspE | Rv2317 | uspB | 0.9832743 | 1.3376563 | 1.2099429 | 1.2082322 | 1.2348669 | 1.2151475 | 1.1547408 | 1.1437067 | Rv2317, (MTC3G12.17c), len: 274. uspB, membrane protein probably involved in sugar transport, most similar to G296356 putative transport system permease protein (275 aa)fasta scores, opt: 562, E(): 3.8e-32, (33.8% identity in 275 aa overlap)
uspC | Rv2318 |  | 0.9386471 | 1.1410251 | 1.0694442 | 1.0198143 | 0.97828174 | 1.0356055 | 0.97465664 | 0.9620622 | Rv2318, (MTCY3G12.16c), len: 440. uspC, probably component of sugar transport system, has hydrophobic stretch possibly signal peptide at N-terminus. Similar to AF012836|AF012836_1 Thermococcus [NAME] (450 aa) opt: 202 z-score: 238.9 E(): 8.8e-06; 24.8% identity in 431 aaoverlap; also slight similarity to MALX_STRPN P29850 maltose/maltodextrin-binding protein (423 aa), [NAME] scores, opt:144, E(): 0.023, (21.1% identity in 440 aa overlap)
rocD1 | Rv2322c |  | 0.9700177 | 1.2971112 | 1.1982942 | 1.1545721 | 1.1307513 | 1.0413043 | 0.9640131 | 0.91664135 | Rv2322c, (MTCY3G12.12), len: 221. Probable rocD, similar to N-terminal region of ornithine aminotransferase len: 221, eg OAT_BACSU P38021 (401 aa) [NAME] scores, opt: 626, E(): 3.5e-32, (43.1% identity in 218 aa overlap); MTCY3G12.12 and .13 appear to be an ornithine aminotransferase homologue but are frameshifted - we can find no sequence errorin the cosmid to account for this
Rv2342 | Rv2342 |  | 0.98383754 | 1.1968788 | 1.151952 | 1.1253904 | 1.1097846 | 1.0837812 | 1.0272117 | 0.96976495 | Rv2342, (MTCY98.11), len: 85, function: unknown, TBPARSE score is 0.887
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
scoa | Rv2504c |  | 1.0127431 | 1.4869858 | 1.3390216 | 1.4147403 | 1.3920927 | 1.2128294 | 1.2277995 | 1.2282356 | Rv2504c, (MTCY07A7.10c), len: 248 aa. scoA, 3-Oxo Acid:CoA Transferase, A Subunit, similar to eg PCAI_BACSU P42315 probable 3-oxoadipate coa-transferase SUBUNIT A (EC 2.8.3.6) (238 aa) opt: 562 z-score: 664.0 E(): 5.7e-30, (55.6% identity in 248 aa overlap)
Rv2557 | Rv2557 |  | 1.3153374 | 2.9417238 | 2.3522995 | 2.203846 | 2.2016926 | 1.9133629 | 2.0446684 | 1.8128449 | Rv2557, (MTCY9C4.11c), unknown, len: 224, highly similar to MTCY9C4.10c (69.2% identity in 224 aa overlap)
Rv2570 | Rv2570 |  | 1.0530304 | 1.3089626 | 1.3149846 | 1.2371501 | 1.2498707 | 1.1395102 | 1.154102 | 1.0358161 | Rv2570, ([NAME]), len: 129. Unknown
Rv2619c | Rv2619c |  | 0.8362862 | 1.4989748 | 1.3889343 | 1.4408263 | 1.4088818 | 1.1877064 | 1.0902011 | 1.1124022 | Rv2619c, (MTCY01A10.14), len: 117 aa. Unknown
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
[NAME] | [NAME] |  | 0.9979684 | 1.5425711 | 1.3933893 | 1.2423148 | 1.2514092 | 1.0904526 | 0.99024963 | 1.030977 | Rv2659c, (MTCY441.28c), len: 375. Integrase, similar to many eg to VINT_BPML5 P22884 integrase. mycobacteriophage l5 (371 aa), [NAME] scores, opt: 836, E(): 0, (39.0% identity in 372 aa overlap)
Rv2693c | Rv2693c |  | 0.9998595 | 1.2941867 | 1.2100707 | 1.1977566 | 1.2220011 | 1.1771269 | 1.0977697 | 1.0350292 | Rv2693c, (MTCY05A6.14c), len: 223. Function: unknown but some similarity to AL021530|SC2E9_15 Streptomyces coelicolor cosmid 2E (272 aa) opt: 212 z-score: 272.1 E(): 1.3e-07; 23.5% identity in 247 aa overlap. TBparse score is 0.902
sigB | Rv2710 |  | 1.091392 | 1.793394 | 1.4804809 | 1.4306308 | 1.4189283 | 1.3495831 | 1.2834346 | 1.2472188 | Rv2710, (MTCY05A6.31), len: 323. Function: sigB, RNA polymerase sigma factor (formerly MysB). Contains sigma-70 factors family signatures 1 and 2 (PS00715; PS00716)FASTA best: G1171103 (323 aa) opt: 2062; E(): 0; 100.0% identity in 323 aa overlap. Highly similar to sigA, MTCY05A6.24, (528 aa) E(): 0; 62.9% identity in 315 aa overlap. TBparse score is 0.894 Contains possible helix-turn-helix motif at aa 283-304(+5.31 SD)
Rv2777c | Rv2777c |  | 1.2857325 | 1.9949317 | 1.6116695 | 1.4760903 | 1.4815235 | 1.4668669 | 1.4160664 | 1.3299356 | Rv2777c, (MTV002.42c), len: 356 aa. Unknown
Rv2821c | Rv2821c |  | 1.1194758 | 1.5603753 | 1.6148798 | 1.435436 | 1.3216174 | 1.4342365 | 1.3338686 | 1.2432721 | Rv2821c, (MTCY16B7.21), len: 236. Some similarity to CONSERVED PROTEIN AE000879|AE000879_5 Methanobacterium thermoautotrop (245 aa) [NAME] score, opt: 294 z-score: 366.8 E(): 6.6e-13; 34.8% identity in 224 aa overlap
Rv2829c | Rv2829c |  | 0.98907846 | 2.0354912 | 1.5825948 | 1.5174003 | 1.5156227 | 1.3013759 | 1.1886853 | 1.2980042 | Rv2829c, (MTCY16B7.13), unknown, len: 130, slight similarity to G1001388 hypothetical 15.1 kDa protein,(131 aa), [NAME] scores, opt: 128, E(): 0.0093, (26.4% identity in 125 aa overlap)
hupB | Rv2986c |  | 0.9779357 | 1.2271452 | 1.1224458 | 1.1406908 | 1.0806793 | 1.0911615 | 0.993681 | 0.9622424 | Rv2986c, (MTCY349.01), len: 214 aa. Probable hupB, resembles fusion between [NAME] and histone. Equivalent to M. leprae sp|O33125|O33125 HISTONE-LIKE DNA BINDING PROTEIN. (200 aa) opt: 914 z-score: 751.6 E(): 0; 80.1% identity in 216 aa overlap; also similar at N-terminus to DBH_BACST P02346 dna-binding protein ii (hb) (hu). [NAME] (90 aa),fasta scores, opt: 286, E(): 1e-13, (48.3% identity in 89 aa overlap) and to G777718 histone H1 (182 aa), [NAME] scores, opt: 293, E(): 7.6e-08, (48.8% identity in 162 aa overlap); contains PS00045 Bacterial histone-like DNA-binding proteins signature. C-terminal domain is very rich in lysine and alanine
ilvC | Rv3001c |  | 1.0754238 | 1.3786211 | 1.2795559 | 1.3854649 | 1.299646 | 1.256495 | 1.2166387 | 1.1725086 | Rv3001c, ([NAME]), len: 333. Ketol-acid reductoisomerase, ilvC, similar to many eg. ILVC_MYCAV Q59500 (333aa). FASTA score: sp|Q59500|ILVC_MYCAV KETOL-ACID REDUCTOISOMERASE (333 aa) opt: 1977 z-score: 2361.0 E(): 0; (87.7% identity in 333 aa overlap). TBparse score is 0.871
Rv3142c | Rv3142c |  | 1.069729 | 1.2749331 | 1.271646 | 1.2655568 | 1.2519251 | 1.1254343 | 1.1144865 | 1.0736947 | Rv3142c, (MTCY03A2.16), len: 142. Function: unknownTBparse score is 0.921
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)
[NAME] | Rv3250c |  | 0.8998009 | 1.8524032 | 1.6294333 | 1.5417775 | 1.6910472 | 1.3193876 | 1.2194417 | 1.1391535 | Rv3250c, (MTCY20B11.25c), len: 60, rubredoxin,, similar to P42453|RUBR_ACICA RUBREDOXIN; contains rubredoxin signature (PS00202), also similar to neighbouring ORF M. tuberculosis RubA (MTCY20B11.26c, 7.3e-11). FASTA best: RUBR_ACICA P42453 rubredoxin (rd). [NAME] (54 aa) opt: 315 z-score: 437.2 E(): 2.3e-17; (69.8% identity in 53 aa overlap)
rubA | [NAME] |  | 0.8893118 | 2.783888 | 2.363966 | 2.0450034 | 2.328545 | 1.8072299 | 1.3542173 | 1.2127013 | [NAME], (MTCY20B11.26c), len: 55. Function: rubredoxin, most similar to X65936|POOCT_3 P;oleovorans; contains rubredoxin signature (PS00202). Similar to neighbouring ORF M. tuberculosis rubB, MTCY20B11.25c, 7.3e-11. FASTA best: RUB2_PSEOL P00272 rubredoxin 2. pseudomonas oleovorans. (172 aa) opt: 278 z-score: 379.4 E(): 3.8e-14; (65.3% identity in 49 aa overlap)
Rv3252c | Rv3252c | alkB | 0.9187559 | 1.9020381 | 1.6722882 | 1.6712751 | 1.7400151 | 1.4897649 | 1.0003669 | 1.0390537 | Rv3252c, (MTCY20B11.27c), len: 416, unknown but similar to monoxygenases, has possible transmembrane stretches. FASTA best: ALKB_PSEOL P12691 alkane-1 monooxygenase (ec 1.14.15.3) (401 aa) opt: 975 z-score: 1144.2 E(): 0; Smith-Waterman score: 1197; (44.4% identity in 399 aa overlap)
lat | Rv3290c |  | 1.0509075 | 2.2737095 | 1.8672428 | 1.7590612 | 1.88367 | 1.8199914 | 1.3739222 | 1.4561515 | Rv3290c, (MTCY71.30), len: 449, lat, similar to LAT_NOCLA [NAME] lysine-epsilon aminotransferase (ec 2. (450 aa), [NAME] scores, opt: 1702, E(): 0, (60.4% identity in 439aa overlap)
Rv3466 | Rv3466 |  | 0.93185145 | 1.5092527 | 1.2967943 | 1.3106202 | 1.3318752 | 1.216981 | 1.1775885 | 1.1084061 | Rv3466, (MTCY13E12.19), len: 222. ORF from REP13E12but extending 5' of repeat. Has segment of identity to other REP13E12 ORF's eg. MTCY336.16, MTCI65.15c, [NAME], cMTCY251.14c
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
fdxD | Rv3503c |  | 0.8807251 | 1.4809214 | 1.3843112 | 1.3177825 | 1.3730356 | 1.2026116 | 1.1243657 | 1.0763651 | Rv3503c, (MTV023.10c), len: 63. fdxD. Probable ferredoxin similar to several e.g. FER_CLOTH (63 aa). FASTA scores: sptr|Q49867|Q49867 HYPOTHETICAL 9.3 KD PROTEIN B229_C3(83 aa) opt: 276 z-score: 401.6 E(): 7.3e-15; 75.9% identity in 54 aa overlap; and sp|P00203|FER_CLOTH FERREDOXIN(63 aa) opt: 157 z-score: 239.1 E(): 8.3e-06; 36.7% identity in 60 aa overlap. TBparse score is 0.871
Rv3529c | Rv3529c |  | 1.1615756 | 1.865622 | 1.7994683 | 1.6355399 | 1.7052588 | 1.6496735 | 1.6020392 | 1.3915986 | Rv3529c, (MTCY03C7.27), len: 384 aa. Unknown. Some similarity to Z77163|MTCY339_43 Mycobacterium tuberculosis cosmid (388 aa) [NAME] scores, opt: 261 z-score: 312.2 E():7.2e-10; 27.3% identity in 253 aa overlap
Rv3705c | Rv3705c |  | 1.1289256 | 1.4593545 | 1.3200326 | 1.3509916 | 1.3035773 | 1.2278554 | 1.1475147 | 1.0947851 | Rv3705c, (MTV025.053c), len: 214 Unknown. TBparsescore is0.909
Rv3767c | Rv3767c |  | 1.2641542 | 2.5680263 | 2.3057406 | 2.1205342 | 2.1777859 | 1.9170227 | 1.72528 | 1.4969413 | Rv3767c, ([NAME],[NAME]), len: 314. Unknown, but similar to other hypothetical mycobacterial proteins e.g. Y09U_MYCTU Q50726 hypothetical 38.1 kd protein cy78.29c (348 aa), [NAME] scores; opt: 796 z-score: 1212.1 E():0, 45.4% identity in 302 aa overlap. Also similar to [NAME]; MTCY31_23;MTCY210_45; MTCY4C12_14;MTY13D12_21, MTCI5_19, MTCY180_22. Contains probable N-terminal signal sequence
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
Rv3892c | Rv3892c | PPE69 | 0.9756193 | 1.4027448 | 1.2574208 | 1.3009664 | 1.2373493 | 1.1812682 | 1.2176945 | 1.1195146 | Rv3892c, (MTCY15F10.20), len: 399. Member of the M.tuberculosis PPE family of conserved proteins, similar to many e.g. MTV049.23 (423 aa) E(): 6.1e-06, 28.7% identity in401 aa overlap