Spreadsheet: 6a3c5184-c755-4ddb-974a-796557bb8944
Sheet: Sheet1

Table S9
Figure 5D -Genes with Steady, sustained repression temporal profile
 |  |  | 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)
MT0031 |  |  | 1.3013283 | 1.2609632 | 1.2238029 | 1.1592401 | 1.1528093 | 1.0369257 | 1.0076208 | 0.96714705 | hypothetical protein
MT0085 |  | Rv0078A | 1.0422889 | 0.9119864 | 0.84979206 | 0.82019216 | 0.8535054 | 0.82332605 | 0.72702587 | 0.7228285 | hypothetical protein
MT0603 |  |  | 1.3779404 | 1.3863435 | 1.1454897 | 1.0781622 | 0.9967128 | 1.1257426 | 0.9615105 | 0.9782039 | hypothetical protein
MT1483 |  |  | 1.1731459 | 1.0952611 | 1.0691836 | 1.0311761 | 0.9853275 | 0.98069125 | 0.92852944 | 0.95714253 | transcriptional regulator
MT2510 |  |  | 1.2560965 | 1.2246437 | 0.97363484 | 0.8932613 | 0.9449924 | 0.9641078 | 0.79976743 | 0.8603434 | hypothetical protein
MT2606 |  | Rv2530A | 0.95390576 | 0.9232337 | 0.9008783 | 0.83294 | 0.84392476 | 0.8709394 | 0.80901426 | 0.8327009 | hypothetical protein
MT3483 |  |  | 1.2402059 | 1.1899935 | 1.1577536 | 1.0799974 | 1.0919422 | 1.1112298 | 1.009437 | 1.0077326 | hypothetical protein
Rv2086 | Rv2086 |  | 1.0222464 | 0.85399187 | 0.82428527 | 0.7895904 | 0.829072 | 0.8065783 | 0.73616314 | 0.7049157 | Protein sequence is in conflict with the conceptual translation; Rv2086, (MTCY49.25), len: 217, low similarity to transposases; orfs MTCY49.24, 25, 26, and 27 all show similarity to transposases but we can find no sequence errors to account for the frameshifts
Rv0012 | Rv0012 |  | 1.0059367 | 0.8939485 | 0.87115216 | 0.8709368 | 0.8454302 | 0.8283652 | 0.84237623 | 0.8254595 | Rv0012, (MTCY10H4.12), unknown, len: 262, some similarity to BLU01958_3 5A2 [NAME] (fragment) (188 aa), [NAME] scores, opt: 204, E(): 8.9e-07, (35.6% identity in 90 aa overlap) and B. subtilis ddS G1129091 cell division and sporulation protein (231 aa), [NAME] scores, opt: 180, E(): 3.8e-05, (30.7% identity in 101 aa overlap), also similar to MTCY1A11_20, (30.1% identity in 246 aa overlap) and MTCY1A11_18 (25.5% identity in 235 aa overlap). Contains probable N-terminal signal sequence
Rv0031 | Rv0031 |  | 1.2012212 | 0.92128557 | 0.8549767 | 0.76614946 | 0.80161935 | 0.8561353 | 0.72186387 | 0.66260177 | Rv0031, (MTCY10H4.31), len: 70, Possible transposase remnant, partial similarity to mycobacterial transposases in a short overlap: e.g. MTV002_57, (459 aa) 72.2% identity in 36 aa overlap, MTCY349_9, MTCY19H5_16, MTCY409_3, CY274_16c (58.3% identity in 36aa overlap)
Rv0046c | Rv0046c | ino1 | 0.9704706 | 0.9152053 | 0.8245354 | 0.7968701 | 0.79112446 | 0.8117031 | 0.7733043 | 0.76163375 | Rv0046c, (MTCY21D4.09c), unknown, len: 367, highly similar to M. leprae U00015_14/G466956 B1620_F3_113(369 aa), [NAME] scores, opt: 2221, E(): 0, (91.8% identity in 366 aa overlap) and to a conserved protein in AE000881_1 M. thermoautotrophi (368 aa) low level matches to eg INO1_SPIPO P42803 myo-inositol-1-phosphate synthase (510 aa), [NAME] scores, opt: 144, E(): 0.021, (25.2% identity in 365 aa overlap)
Rv0116c | Rv0116c |  | 0.9857712 | 0.98911023 | 0.95053434 | 0.85643584 | 0.8727994 | 0.88298345 | 0.88194126 | 0.8236385 | Rv0116c, (MTV031.10c), len: 251. Unknown but showssimilarity to several hypothetical mycobacterial proteinse.g. throughout its length to [NAME] (271 aa) and [NAME] (EMBL; [NAME]) (271 aa) to the C-terminal regions of others like MTCI28.31 (366 aa). FASTA scores: opt: 451 z-score: 520.5 E(): 1.7e-21. 46.7% identityin 270 aaoverlap; and Z97050|MTCI28_32 Mycobacterium tuberculosis cosmid (366 aa) opt: 699 z-score: 799.0 E(): 0;45.7% identity in 221 aa overlap. TBparse score is 0.932
ephF | Rv0134 |  | 1.2005357 | 1.1143569 | 1.0604149 | 1.0565884 | 1.0120411 | 1.069252 | 0.9649459 | 0.91764325 | Rv0134, (MTCI5.08), len: 300 aa,[NAME], similar to eg Q39856 epoxide hydrolase (341 aa), [NAME] scores, opt: 369, E(): 4.6e-17, (27.2% identity in 335 aa overlap), also similarto MTCY09F9.26c (29.5% identity in 346 aa overlap)
[NAME] | Rv0179c |  | 1.0364941 | 0.9287552 | 0.85915416 | 0.8589615 | 0.8101206 | 0.82332593 | 0.708379 | 0.6721971 | Rv0179c, (MTCI28.19c), len: 369 aa; possible lipoprotein, contains possible M-terminal signal sequencem and contains PS00013 Prokaryotic membrane lipoprotein lipid attachment site
Rv0239 | Rv0239 |  | 1.2027568 | 0.9739994 | 0.8705062 | 0.7848674 | 0.794617 | 0.8489286 | 0.6832159 | 0.6425063 | Rv0239, (MTV034.05), len: 77. Unknown but similar to Mycobacterium tuberculosis protein MTCY359.34 (87 aa). FASTA [NAME] (87 aa) opt: 88 z-score: 135.1 E(): 5; 40.0% identity in 45 aa overlap. TBparse score is 0.922
[NAME] | Rv0254c |  | 1.0401404 | 0.9447526 | 0.9417541 | 0.96530104 | 0.85033756 | 0.86255586 | 0.87427783 | 0.8260824 | Rv0254c, (MTV034.20), [NAME], len: 174. Probable cobinamide kinase similar to many e.g. sp|Q05599|COBU_SALTY (181 aa). Contains PS00017 [NAME]/GTP-binding site motif A (P-loop). FASTA scores sp|Q05599|COBU_SALTY COBINAMIDE KINASE / COBINAMIDE PH (181 aa) opt: 308 z-score: 398.2 E(): 1.1e-14; 38.7% identity in 181 aa overla. TBparse score is 0.919
Rv0258c | Rv0258c |  | 1.2413708 | 1.2051529 | 1.1596863 | 1.0574273 | 1.0442116 | 1.0538388 | 0.94828534 | 0.8745075 | Rv0258c, ([NAME]), len: 151, unknown, alternative start possible, some similarity to MTCI125_6 (207 aa),E(): 9.3e-07; 32.1% identity in 140 aa overlap
Rv0264c | Rv0264c |  | 1.1080863 | 0.9949481 | 0.839988 | 0.73454213 | 0.7563168 | 0.76340765 | 0.73396313 | 0.74155635 | Rv0264c, (MTCY06A4.08c), unknown, len: 320 aa, similar to sp|P75744|YBGJ_ECOLI HYPOTHETICAL 23.9 KD PROTEIN INP (218 aa); E(): 2.1e-14; 35.7% identity in 182 aa overlap.Also similar to YH31_HAEIN P44299 hypothetical protein hi1731. (213 aa), [NAME] scores, opt: 252, E(): 8.3e-10, (31.1%identity in 183 aa overlap)
galE1 | Rv0501 |  | 1.1557336 | 1.1040416 | 1.0296341 | 0.9988201 | 0.9838794 | 1.0345334 | 0.9887446 | 0.96853304 | Rv0501, (MTCY20G9.28), len: 376,galE1, possible udp-glucose 4-epimerase, highly similar to 2 M. leprae orfs, N-terminal region, Q49830 B2168_C1_174 FASTA scores, opt: 934, z-score: 1093.7, E(): 0, (89.6% identity in 164 aa overlap), C-terminal region, Q49813 B2168_C2_214 (168 aa) FASTA scores, opt: 928, z-score: 1087.2, E(): 0, (82.7% identity in 168 aa overlap), overall similarity to GALE_ECOLI P09147 udp-glucose 4-epimerase (338 aa), FASTA scores, opt: 241, z-score: 284.5, E(): 6.7e-09, (28.2% identity in 294 aa overlap)
Rv0502 | Rv0502 |  | 0.915968 | 0.8968255 | 0.8700133 | 0.8609484 | 0.8398175 | 0.8734944 | 0.8425884 | 0.82550454 | Rv0502, (MTCY20G9.29), len: 358, unknown, but highly similar to U00018_22 M. leprae P54878 YV29_MYCLE B2168_C1_175 (367 aa) opt: 2042, z-score: 2363.3, E(): 0, (84.1% identity in 365 aa overlap) ALSO C-terminal similar to AL021529|SC10A5_4 Streptomyces coelicolor cosmid 10 (295 aa, 57.8% identity in 263 aa overlap) and MTCY493_26,(275 aa; 32.6% identity in 273 aa overlap)
Rv0516c | Rv0516c |  | 0.97569174 | 0.8721579 | 0.81644434 | 0.7910399 | 0.8003345 | 0.7638377 | 0.7267571 | 0.7659246 | Rv0516c, (MTCY20G10.06c, unknown), len: 158 aa. some similarity to MTCY02B10_29 (128 aa), E(): 0.0012, 27.4% identity in 124 aa overlap.
Rv0523c | Rv0523c |  | 1.0333323 | 0.9168569 | 0.87926817 | 0.7953807 | 0.8278629 | 0.84212244 | 0.7591348 | 0.7780256 | Rv0523c, (MTCY25D10.02, unknown), len: 131 aa, somesimilarity to M. tuberculosis MTCY336_06 O06592 (136 aa);fasta scores, opt: 197 z-score: 236.8 E(): 5e-08, (38.4% identity in 99 aa overlap)
Rv0531 | Rv0531 |  | 1.0395297 | 0.9740361 | 0.9459072 | 0.8833709 | 0.8986429 | 0.89244705 | 0.7741463 | 0.8041745 | Rv0531, (MTCY25D10.10), len: 105, unknown membrane protein, similar to Y13803|MLB1306_1 Mycobacterium leprae cosmid B1306 O07133 (86 aa) PROTEIN (FRAGMENT);E(): 2.1e-24; 74.4% identity in 86 aa overlap
mce2 | Rv0589 | mce2A | 1.3031793 | 1.2148411 | 1.1915364 | 1.0583206 | 1.1013906 | 1.0852497 | 0.9813092 | 1.0474159 | Rv0589, ([NAME]), len: 404; mce2, highly similar to TR:P72013 M. tuberculosis Mcep protein (EM_BA:MTMCE X70901) (MTCI28.08), [NAME] scores; opt: 1324 z-score: 1780.7 E(): 0, 62.6% identity in 436 aa overlap. See [NAME] et al, Science v261 p1454. Similar to MTCI28_9, MTV023_6, Contains a possible N-terminal signal sequence
Rv0606 | Rv0606 |  | 1.1055115 | 1.0911802 | 1.0483415 | 0.9459736 | 0.9818536 | 0.98187286 | 0.9019955 | 0.9426828 | Rv0606, (MTCY19H5.16c, possible truncated transposase for IS_1536 element), len: 247 aa; highly similar to N-termius of YX16_MYCTU Q10809 hypothetical 51.3 kd protein cy274.16 (460 aa), [NAME] scores opt: 1368, E(): 0, (83.5% identity in 237 aa overlap) Similar to MTV002_57 (87.4% identity in 238 aa overlap)
Rv0634c | Rv0634c |  | 1.2350767 | 1.0330782 | 0.91630006 | 0.8378423 | 0.81010497 | 0.89440614 | 0.7639333 | 0.68324816 | Rv0634c, (MTCY20H10.15c), len: 237, putative glyoxylase, similar to U00011_3 Mycobacterium leprae Y0BK_MYCLE Q49649 hypothetical 23.9 kd protein b1177_c3 (218 aa), [NAME] scores, opt: 281, E(): 3.9e-12, (31.8% identity in 201 aaoverlap), also to several other hypothetical proteins e.g.YG63_HAEIN [NAME] hypothetical protein hi1663. [NAME] (212 aa), [NAME] scores, opt: 272, E(): 1.5e-11, (31.8% identity in 192 aaoverlap)
Rv0742 | Rv0742 | PE_PGRS8 | 1.0738608 | 1.0099106 | 1.0325372 | 0.9852638 | 0.95416534 | 0.974524 | 0.9555804 | 0.9479445 | Rv0742, (MTV041.16), len: 175. Unknown, member of PE-family, PGRS subfamily of glycine-rich protein, similar to many M. tuberculosis PGRS-type proteins. e.g. gp|Z78020|MTCY1A11_25 M. tuberculosis cosmi (498 aa). Similarity suggests ORF starts with [NAME] start codon. FASTA scores:opt: 766 z-score: 582.4 E(): 6.1e-25. 73.6% identity in 178 aa overlap. TBparse score is 0.846
[NAME] | Rv0847 |  | 1.1548704 | 0.75040466 | 0.68005013 | 0.6456066 | 0.6758737 | 0.64338297 | 0.46863833 | 0.5068435 | Rv0847, (MTV043.40), len: 130. Unknown, possibly lipoprotein contains possible signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. TBparse score is 0.920
Rv0854 | Rv0854 |  | 1.1117392 | 0.8457083 | 0.894657 | 0.82155514 | 0.8055363 | 0.8349959 | 0.747893 | 0.7013712 | Rv0854, (MTV043.47), len: 147. Unknown but some similarity to mycobacterial proteins Mycobacterium leprae MLCL622.27c (156 aa) and Mycobacterium tuberculosis [NAME] (184 aa). FASTA scores: [NAME] (156 aa) opt: 193z-score: 251.9 E(): 1.6e-06; 24.6% identity in 134 aa overlap; and Z97050|MTCI28_4 (184 aa) opt: 171 z-score: 223.8 E(): 5.8e-05; 21.5% identity in 135 aa overlap. Alsohighly similar to downstream ORFS MTV043_50 and MTV043_49.TBparse score is 0.903
Rv0857 | Rv0857 |  | 1.1187382 | 1.0537176 | 0.9937243 | 0.92299926 | 0.91565496 | 0.94867533 | 0.82763433 | 0.81993127 | Rv0857, (MTV043.50), len: 124. Unknown but some similarity to mycobacterial proteins, like the upstream ORFs MTV043_49 (134 aa; E(): 9.6e-28; 61.6% identity in 99 aa overlap), and MTV043_47 (147 aa; E(): 2.8e-18; 42.7% identity in 117 aa overlap), and MTCI28.04 (184 aa) and MLCL622.27c (156 aa). FASTA scores: Z97050|MTCI28_4 (184 aa) opt: 122 z-score: 174.9 E(): 0.031; 29.4% identity in 85 aa overlap; and [NAME] (156 aa) opt: 114 z-score:165.4 E(): 0.1; 30.9% identity in 55 aa overlap. TBparse score is 0.910
moeA | Rv0994 | moeA1 | 1.114771 | 1.057391 | 0.97861004 | 0.9384805 | 0.92577857 | 0.98295194 | 0.9264789 | 0.9122501 | Rv0994, (MTCI237.08), moeA, len: 426. Probable MoeAprotein, similar to e.g. MOEA_ECOLI P12281 molybdopterin biosynthesis moea protein (411 aa), [NAME] scores, opt: 519 z-score: 567.7 E(): 1.3e-24, (32.3% identity in 402 aa overlap)
Rv0997 | Rv0997 |  | 1.2079246 | 1.1913085 | 0.95945936 | 0.94825613 | 0.93742824 | 0.9347924 | 0.87025195 | 0.8305721 | Rv0997, (MTCI237.11), len: 143 aa. Unknown
arcA | Rv1001 |  | 1.354207 | 1.3278279 | 1.2135006 | 1.1500812 | 1.1589057 | 1.1483016 | 1.0832282 | 1.0106905 | Rv1001, (MTCI237.16), [NAME], len: 402. Probable arginine deiminase, similar to e.g. [NAME] P13981 argininedeiminase (ec 3.5.3.6) (417 aa), [NAME] scores, opt:581 z-score: 692.9 E(): 1.4e-31, (39.4% identity in 411 aaoverlap),also similar to SAGP_STRPY P16962 streptococcal acid glycoprotein (410 aa), [NAME] scores, opt: 823 z-score:980.7 E():0,(38.3% identity in 402 aa overlap)
Rv1066 | Rv1066 |  | 1.0267634 | 1.0084491 | 0.98858654 | 0.91672534 | 0.93558663 | 0.8583704 | 0.8168199 | 0.8489266 | Rv1066, (MTV017.19), len: 131. Unknown but strong similarity to hypothetical Streptomyces coelicolor protein [NAME] (132 aa). FASTA scores: gp|AL0209|SC4H8_10 (132 aa) opt: 429 z-score: 547.6 E(): 5.2e-23; 57.1% identity in 119 aa overlap. TBparse score is 0.859
Rv1081c | Rv1081c |  | 1.2993076 | 1.0509578 | 0.9545866 | 0.8613678 | 0.8737289 | 0.9144481 | 0.8965248 | 0.8188437 | Rv1081c, (MTV017.34c), len: 144. Unknown but hydrophobic stretch from aa 26 - 48. TBparse score is 0.906
Rv1086 | Rv1086 |  | 1.0402828 | 1.0308397 | 0.9505854 | 0.94884664 | 0.89369243 | 0.90432566 | 0.87431794 | 0.86890554 | Rv1086, (MTV017.39), len: 262. Unknown but member of the UPF0015 FAMILY similar to family members from Streptomyces fradiae P20182|YT14_STRFR (259 aa) and Corynebacterium glutamicicum P38118|YARF_CORGL (234 aa). Contains PS01066 Uncharacterized protein family UPF0015 signature. FASTA scores: sp|P20182|YT14_STRFR HYPOTHETICAL 29.1 KD PROTEIN (259 aa) opt: 840 z-score: 1078.8 E(): 0; 51.0% identityin 259 aaoverlap; and sp|P38118|YARF_CORGL HYPOTHETICAL 26.1 KD PROTEIN (234 aa) opt: 729 z-score: 937.8 E(): 0; 56.0% identity in 209 aa overlap. Also similar to Rv2361c(MTCY27.19)(296 aa,35.6% identity in 233 aa overlap)
echA11 | Rv1141c |  | 1.3243228 | 1.2129397 | 1.076842 | 1.054968 | 1.0647781 | 1.0351753 | 0.9882338 | 0.97827864 | Rv1141c, (MTCI65.08c), len: 268. echA11, Similar toenoyl-CoA hydratases and naphthoate synthases. FASTA scores: D907776NID: g1742263 - Escherichia coli (262 aa) opt: 513; E():1e-25; 36.1% identity in 249 aa overlap. Also very similartoupstream ORF MTCI65.09c, (268 aa). FASTA score: opt: 1225;E(): 0; 72.3% identity in 267 aa overlap. TBparse scoreis 0.910
echA10 | Rv1142c |  | 1.083213 | 0.96112067 | 0.9121288 | 0.8990955 | 0.89397615 | 0.8967455 | 0.85693663 | 0.84670514 | Rv1142c, (MTCI65.09c), len: 268. echA10, Similar toenoyl-CoAhydratases and naphthoate synthases. FASTA scores: D907776D90777 NID: g1742263 - Escherichia coli (262 aa)opt: 525; E(): 1.3e-26; 35.1% identity in 251 aa overlap.Highlysimilar to downstream ORF MTCI65.08c, (268 aa). FASTA score: opt: 1225; E(): 0; 72.3% identity in 267 aa overlap. TBparse score is 0.891
Rv1154c | Rv1154c |  | 1.2434403 | 1.1858295 | 1.1163008 | 1.1558478 | 1.0691872 | 1.0715472 | 1.0042454 | 1.0012451 | Rv1154c, (MTCI65.21c), len: 213. Unknown, TBparse score is 0.911
Rv1176c | Rv1176c |  | 0.94801354 | 0.80708224 | 0.81207 | 0.72658587 | 0.71220386 | 0.7256689 | 0.655534 | 0.62926435 | Rv1176c, (MTV005.12c), len: 189. some similarity toB. subtilis hypothetical protein TR:P94443 (EMBL:D78508) YFIO (182 aa), [NAME] scores; opt: 219 z-score: 407.3 E(): 1.7e-15, 25.1% identity in 183 aa overlap
glgC | Rv1213 |  | 1.1583608 | 1.0935926 | 0.9676023 | 0.92498964 | 0.9357008 | 0.9728603 | 0.9350486 | 0.91460526 | Rv1213, (MTCI364.25), [NAME], len: 404. Probable glucose-1-phosphate adenylyltransferase, similar to eg GLGC_ECOLI P00584 glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) (430 aa), [NAME] scores, opt: 1075, E(): 0, (40.3% identity in 407 aa overlap), highly similar to Q49961 [NAME] (419aa), [NAME] scores, opt: 2532, E(): 0, (92.6% identity in404aa overlap)
lpqY | Rv1235 |  | 1.0605131 | 0.9750567 | 0.9436937 | 0.91967463 | 0.9610929 | 0.8680689 | 0.8339432 | 0.8615342 | Rv1235, (MTV006.07), len: 468. Unknown lipoprotein highly similar to M. leprae protein u1756v (469 aa), possibly involved in sugar (e.g. maltose) uptake. FASTA scores:MLU1518034opt: 2442 E(): 0; (77.4% identity in 470 aa overlap). Similar to P18815|MALE_ENTAE MALTOSE-BINDING PERIPLASMICPROT (396 aa)FASTA scores: opt: 193 E(): 2.3e-05; (24.2% identityin 297 aa overlap). Contains PS00013 [NAME] lipid attachment site. TBparse score is0.914
Rv1246c | Rv1246c |  | 1.095388 | 1.050758 | 0.9970976 | 0.9349812 | 0.898842 | 0.90778244 | 0.93218714 | 0.87790513 | Rv1246c, (MTV006.18c), len: 97. Unknown, highly similar to hypothetical M. tuberculosis protein MTV003.12, (87aa). FASTAscores: opt: 290, E(): 3.9e-24; (54.1% identityin 85 aaoverlap)
lprC | Rv1275 |  | 1.1443852 | 1.0481216 | 1.0373782 | 1.0068629 | 0.9969492 | 1.035133 | 0.9580585 | 0.9330491 | Rv1275,(MTCY50.07c), len: 180. Unknown, contains possible N-terminal signal sequence and appropriately positioned prokaryotic lipoprotein lipid attachment site (PS00013).
bisc | Rv1442 |  | 1.1687466 | 1.0038918 | 0.886769 | 0.8322265 | 0.86416095 | 0.832562 | 0.86217016 | 0.72535354 | Rv1442, (MTCY493.12c), bisC, len: 766. Biotin sulfoxide reductase, similar to eg. BISC_ECOLI P20099 biotin sulfoxide reductase (739 aa), [NAME] scores; opt: 1271 z-score:1436.6E():0, 40.2% identity in 744 aa overlap
Rv1443c | Rv1443c |  | 1.1144066 | 0.79969543 | 0.8094721 | 0.790693 | 0.7319934 | 0.74139726 | 0.59869194 | 0.63938206 | Rv1443c, (MTCY493.11), len: 161. Unknown.
[NAME] | [NAME] |  | 0.9965357 | 0.92988807 | 0.9071636 | 0.8541331 | 0.8715718 | 0.878902 | 0.85023445 | 0.8707856 | [NAME], (MTV007.21c), len: 187. Probable transcription regulator equivalent to Mycobacterium avium strain GIR10 transcriptional regulator. Also similar to E. coli glucuronide repressor 9GusR/UidR), member of TETR/ACRR FAMILY. Helix-turn-helix motif predicted between aa 33 - 54. FASTAscores: gp|AF0021|AF002133_1 Mycobacterium avium strain GIR10 (82 aa)opt: 490 z-score: 597.2 E(): 6.7e-26; (92.5% identity in80 aa overlap) and Q59431|UIDR_ECOLI UID OPERON REPRESSOR (GUS OPERON (196 aa) opt: 192 z-score: 239.3 E():5.8e-06;28.5% identity in 172 aa overlap. Helix turn helixmotif at aa 33-54(+3.40 SD)
hemZ | Rv1485 |  | 1.2199013 | 1.0058091 | 0.9466717 | 0.87009037 | 0.85337657 | 0.8623028 | 0.8493897 | 0.8610325 | Rv1485, (MTCY277.06), hemZ, len: 344. Ferrochelatase similar to e.g. HEMZ_BACSU P32396 ferrochelatase (310 aa), FASTA scores, opt:490, E(): 2e-24, (30.2% identity in 295 aa overlap)
Rv1762c | Rv1762c |  | 1.1112062 | 0.9736275 | 0.86775166 | 0.8635536 | 0.8296265 | 0.8839633 | 0.79326284 | 0.7623596 | Rv1762c, (MTCY28.28c), len: 262. Unknown.
Rv1814 | Rv1814 | erg3 | 1.2380097 | 1.1842484 | 1.1786745 | 1.0317042 | 0.9691921 | 1.004062 | 0.9705699 | 0.94718057 | [NAME], (MTCY1A11.29c), unknown, len: 300, weak similarity to eg ERG3_YEAST P32353 c-5 sterol desaturase (365 aa), FASTA scores, opt: 154, z-score: 191.4, E(): 0.0011, (22.9% identity in 288 aa overlap)
[NAME] | [NAME] |  | 1.1740232 | 0.84805113 | 0.8350252 | 0.78178865 | 0.80000794 | 0.7159974 | 0.58221126 | 0.52448475 | [NAME], (MTCY09F9.13), len: 98 aa. Unknown, similar to Rv2541, (135 aa, 40.9% identity in 88 aa overlap)
[NAME] | [NAME] |  | 1.2313926 | 1.0533442 | 1.0587447 | 0.938601 | 0.96520793 | 0.95007175 | 0.8795644 | 0.8812825 | Rv1959c, (MTCY09F9.05), len: 98 aa, unknown, some similarity to E145339 hypothetical protein (103 aa), [NAME] scores, opt: 142,E(): 0.0003,(33.0% identity in 91 aa overlap)
Rv2063c | Rv2063c | Rv2063 | 1.1724614 | 1.110823 | 1.0624958 | 1.0147214 | 1.031032 | 0.91318417 | 0.95176774 | 0.9425006 | Rv2063c, (MTCY49.02c), len: 122. Unknown
Rv2078 | Rv2078 |  | 1.0509526 | 0.7889781 | 0.8097157 | 0.7932976 | 0.72718686 | 0.7181589 | 0.6985246 | 0.6273454 | Rv2078, (MTCY49.17), len: 104. Unknown
Rv2103c | Rv2103c |  | 1.1719799 | 0.98201036 | 0.9852448 | 0.9931381 | 0.9292403 | 0.93837434 | 0.8728882 | 0.8576554 | Rv2103c, (MTV020.03), len: 144. Unknown but similarto hypothetical mycobacterial proteins, B2126_C3_261 (97 aa) and MTCY274_3 (147 aa). FASTA scores: sptr|Q49793|Q49793B2126_C3_261 (97 aa) opt: 331 z-score: 458.4 E(): 4.8e-18; 59.4% identity in 96 aa overlap and gp|Z74024|MTCY274_3 Mycobacterium tuberculosis cosmid (147 aa) opt: 234 z-score: 325.9 E(): 1.2e-10; 34.8% identity in 141 aa overlap. TBparsescore is 0.889
Rv2142c | Rv2142c |  | 1.107839 | 1.0083842 | 1.0292741 | 0.99036413 | 0.9695328 | 0.9257636 | 0.9071052 | 0.91503835 | Rv2142c, (MTCY270.26), len: 105. Function: unknown
Rv2182c | Rv2182c |  | 1.138589 | 1.124581 | 1.0626727 | 1.0450073 | 1.022813 | 1.0522742 | 0.9947905 | 0.9380379 | Rv2182c, (MTV021.15c), len: 247. Unknown but similar to Streptomyces cinnamoneus OrfB SCU80063_3 (199 aa). Contains PS00017 [NAME]/GTP-binding site motif A (P-loop). FASTA scores: gp|U80063|SCU80063_3 Streptomyces cinnamoneus (199 aa) opt: 738 z-score: 905.6 E(): 0; 52.0% identity in 196 aa overlap.TBparse score is 0.926
ahpC | Rv2428 |  | 1.2473252 | 1.1528825 | 1.0688238 | 1.0434085 | 1.0499756 | 1.0156596 | 1.0354452 | 1.0563009 | Rv2428, (MTCY428.18c), len: 195. ahpC gene, alkyl hydroperoxide reductase, identical to G1172078 AHPC
miaA | Rv2727c |  | 1.2492311 | 1.2465148 | 1.1951332 | 1.0530617 | 1.0763768 | 1.0230917 | 1.0758477 | 0.9919183 | Rv2727c, ([NAME]), len: 314. miaA, probable trna delta(2)-isopentenylpyrophosphate transferase, len: 314 aa; similar to many eg. MIAA_ECOLI P16384 trna delta(2)-isopentenylpyrophosphate transferase (316 aa), [NAME] scores; opt: 565 z-score: 528.6 E(): 1.7e-22, 35.2% identity in 307 aa overlap. Contains PS00017 [NAME]/GTP-binding site motif A (P-loop)
[NAME] | [NAME] |  | 1.1951889 | 1.1043204 | 0.99234396 | 0.94317687 | 0.9346293 | 0.9771905 | 0.82593197 | 0.8700978 | [NAME], (MTV003.12), len: 87 aa. Unknown, but similar to AL021006|MTV006_18 Mycobacterium tuberculosis seque (97 aa) [NAME] scores; opt: 290 z-score: 419.6 E(): 7.6e-16; 54.1% identity in 85 aa overlap
lppW | Rv2905 |  | 1.0331672 | 1.0302489 | 0.91256124 | 0.87766695 | 0.8184368 | 0.8283946 | 0.72195715 | 0.67763966 | Rv2905, (MTCY274.36), len: 314. Unknown lipoproteinhas signal peptide and appropriately positioned prokaryoticlipoprotein lipid attachment site. Slight similarity to beta-lactamase. FASTA score: P14559|BLAC_STRAL BETA-LACTAMASEPRECURSOR (EC 3.5 (314 aa) opt: 113 E(): 3.3; 25.2% identityin 278 aa overlap
ftsY | Rv2921c |  | 1.1506196 | 1.1173475 | 1.0598714 | 1.0472968 | 1.0317184 | 1.0237252 | 1.0273832 | 1.0248703 | Rv2921c, (MTCY338.10c), len: 422. ftsY, Probable cell division protein FtsY, Q10969, similar to eg FTSY_ECOLIP10121, cell division protein ftsy (497 aa), FASTA scores,opt: 800, z-score: 819.9, E(): 4e-39, (40.9% identity in 328 aa overlap): contains PS00017 [NAME]/GTP-binding site motif A, PS00300 SRP54-type proteins GTP-binding domain signature
Rv2979c | Rv2979c |  | 1.020427 | 0.9875587 | 0.8518187 | 0.84246886 | 0.8692426 | 0.83514154 | 0.78036916 | 0.8205009 | Rv2979c, ([NAME]), len: 194 aa. probable resolvase for IS1538, low level matches to transposon resolvases,highly similar from aa 101 to YX1C_MYCTU Q10831 hypothetical 31.9 kd protein cy274.17 (295 aa), [NAME] scores, opt: 809, E(): 0, (69.1% identity in 194 aa overlap); contains PS00397 Site-specific recombinases active site and possible helix-turn-helix motiv at aa 2-23
[NAME] | [NAME] |  | 1.1331824 | 0.9850433 | 0.9196472 | 0.8617508 | 0.8217537 | 0.91266644 | 0.7835511 | 0.7655426 | [NAME], (MTCY22D7.23), len: 216. Function: unknownresembles [NAME] and a hypothetical M. leprae protein(U1756B) but also shows some similarity to several repressors in N-terminal segment. Start was predicted by TBparse but alternatives (ATG) are possible. FASTA best: G699124 U1756B (217 aa) opt: 234, E(): 2.1e-09, (27.2% identity in 195aa overlap) TBparse score is 0.913
Rv3070 | Rv3070 |  | 1.1264338 | 1.0381322 | 1.0231315 | 1.0311339 | 0.9531104 | 1.0059232 | 0.9620258 | 0.96345454 | Rv3070, (MTCY22D7.11c), len: 126. Function: unknownmembrane protein with three putative transmembrane segments. Similar to several hypothetical bacterial proteins and related to MTCY22D7.12c. FASTA scores: sp|O25823|O25823 CONSERVED HYPOTHETICAL INTEGRAL MEMBR (130 aa) opt: 225 z-score: 318.7 E(): 3.1e-10; 33.3% identity in 123 aa overlap; and TR:Q58918 Q58918 hypothetical 13.5 kDa protein 1523, [NAME] scores, opt: 157, (38.5% identity in 109 aa overlap)
Rv3073c | Rv3073c |  | 1.2366905 | 1.0050623 | 0.9088519 | 0.8345794 | 0.86799306 | 0.9291745 | 0.73155046 | 0.7075314 | Rv3073c, (MTCY22D7.08), len: 118. Function: unknownbut similar to sp|P76243|YEAO_ECOLI HYPOTHETICAL 14.2 KD PROTEIN (122 aa) FASTA scores, opt: 230 z-score: 302.4 E():2.5e-09; 33.3% identity in 111 aa overlap. TBparse score is 0.885
sseC | Rv3118 | sseC1 | 1.0960248 | 1.0056762 | 0.880723 | 0.85504174 | 0.795985 | 0.85114884 | 0.7971819 | 0.7258532 | Rv3118, (MTCY164.28), len: 100. Unknown but very similar to hypothetical M. leprae protein G699208 U2266J (143aa) and to Saccharopolyspora erythraea sp|Q54084 (HYPOTHETICAL 10.2 KD PROTEIN). FASTA results, opt: 545 E(): 2.1e-31;(84.0% identity in 100 aa overlap). Identical second copypresent as AL022004|MTV043_6 (100 aa); (100.0% identity in100 aa overlap)
[NAME] | Rv3203 |  | 0.9336544 | 0.87178266 | 0.8678034 | 0.84212285 | 0.8291485 | 0.77454305 | 0.8109581 | 0.8206074 | Rv3203, (MTCY07D11.23c), len: 224, unknown but shows some similarity to lipases and contains serine active site signature of lipases (PS00120). FASTA best: P19076 DMPD_PSEPU 2-HYDROXYMUCONIC SEMIALDEHYDE hydrolase (283 aa) opt:171 z-score: 201.7 E(): 0.00012; (26.6% identity in 256 aaoverlap)
Rv3277 | Rv3277 |  | 1.3968138 | 1.1419154 | 1.1951897 | 1.1400894 | 1.0564516 | 1.1255957 | 1.0272772 | 0.9756669 | Rv3277, (MTCY71.17), len: 272 aa, unknown, highly similar to M. [NAME] B1308_C1_121 (228 aa), [NAME] scores, opt: 1266, E(): 0, (84.2% identity in 228 aa overlap); contains PS00044 Bacterial regulatory proteins, [NAME] family signature
lpqC | Rv3298c |  | 1.1554248 | 0.9997507 | 0.91156566 | 0.9465857 | 0.8699437 | 0.89302355 | 0.809869 | 0.7612 | Rv3298c, (MTCY71.38c), len: 304 aa, similar to M. leprae Q49658 B1308_F2_43, (302 aa), [NAME] scores, opt: 1541, E(): 0, (72.0% identity in 300 aa overlap). Possibly esterase or poly(3-hydroxyalkanoate) depolymerases.MTI376.03c Z95972 (280 aa) opt: 519; E(): 1.7e-26; (38.7% identity in 274 aa overlap). Probably lipoprotein with 18 aa signal sequence as it contains appropriately positioned (PS00013) Prokaryotic membrane lipoprotein lipid attachment site. Also similar to Rv0671,lpqP, (MTI376.03c) (280 aa, 38.7% identityin 274 aa overlap)
Rv3478 | Rv3478 | PPE60 | 1.1683536 | 0.84073627 | 0.76850075 | 0.77173066 | 0.72025496 | 0.7853767 | 0.61371374 | 0.58153397 | Rv3478, (MTCY13E12.31), len: 393. Member of M. tuberculosis PPE family. Includes MTCY02B10.25c, [NAME], MTCY10G2.10, MTCY03A2.22c, [NAME], MTCY164.34c, MTCY98.0029c, etc. FASTA scores: Z75555|MTCY02B10_25 Mycobacterium tuberculosis cosm (396 aa) opt: 2165 z-score: 2221.1 E():0; 85.4% identity in 396 aa overlap
Rv3603c | Rv3603c |  | 1.148508 | 0.9844762 | 0.88659996 | 0.79807407 | 0.8109056 | 0.8649017 | 0.66723424 | 0.7017364 | Rv3603c, (MTCY07H7B.19), len: 303. Unknown.
Rv3621c | Rv3621c | PPE65 | 0.8617899 | 0.8289204 | 0.8085246 | 0.7972214 | 0.7906774 | 0.7648322 | 0.76325 | 0.75223994 | Rv3621c, (MTCY15C10.31,MTCY07H7B.01), len: 413. Member of Ala-, Gly-rich protein family in M. tuberculosis (PPE family). FASTA best: [NAME] YX23_MYCTU HYPOTHETICAL 41.1KD PROTEIN CY27 (404 aa) opt: 939 z-score: 914.2 E(): 0; (44.5% identity in 418 aa overlap)
nth | Rv3674c |  | 1.027612 | 0.89577186 | 0.83323365 | 0.8790087 | 0.8290631 | 0.83066803 | 0.7543339 | 0.7100689 | Rv3674c, (MTV025.022c), nth, len: 223. [NAME], (DNA N-GLYCOSYLASE ACTIVITY), similar to many, e.g. sp|P73715|END3_SYNY3 ENDONUCLEASE III (219 aa) FASTA scores: opt: 678 z-score: 839.3 E(): 0. 53.6% identity in 194 aa overlap, or sp|P46303|UVEN_MICLU ULTRAVIOLET N-GLYCOSYLASE/APLYAS (279 aa), 57.1% identity in 231 aa overlap,Contains PS00764 Endonuclease III iron-sulfur binding region signature, and PS01155 Endonuclease III family signature
[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)
Rv3698 | Rv3698 |  | 1.0494118 | 0.98966396 | 0.89349926 | 0.80909324 | 0.8142222 | 0.81441385 | 0.7657916 | 0.7355632 | Rv3698, (MTV025.046), len: 509. Unknown. TBparse score is 0.934
Rv3765c | Rv3765c | tcrX | 1.2364109 | 1.1222862 | 1.1059259 | 1.0795375 | 1.0362353 | 1.0445827 | 0.9862445 | 0.9944716 | Rv3765c, (MTV025.113c), len: 234. Probable response regulator of a two-component regulatory system similar togp|U88959|MTU88959_1 Mycobacterium tuberculosis respon (257aa); opt: 938 z-score: 1160.2 E(): 0. 58.6% identity in 232aa overlap. Also similar to following M. tuberculosis regulatory proteins: MTCY10G2_16; MTCY369_2; MTCY31_34; MTCY19H5_20; MTY13628_5; MTCY20G9_17 and to MLCB57_27 M. leprae;MBY13627_3 M. bovis BCG. TBparse score is 0.899
Rv3882c | Rv3882c |  | 1.0885468 | 1.1044513 | 1.0010982 | 0.97637725 | 0.934356 | 0.9848371 | 0.9061516 | 0.86735713 | Rv3882c, (MTV027.17c,[NAME]), len: 462. Unknown, M.leprae eqivalent is TR:O33077 (EMBL:Y14967) [NAME] (467aa), [NAME] scores; E(): 0, 72.1% identity in 462 aa overlap