Spreadsheet: ac578abb-dfa4-4d56-b7da-031b68dc776f
Sheet: Sheet1

Table S11
Figure 6B - Genes with hspX-like temporal profiles
 |  |  | 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)
MT2068 |  |  | 0.9615226 | 1.2188765 | 1.165327 | 1.1655384 | 1.2404845 | 1.0865029 | 1.0365596 | 1.0193313 | hypothetical protein
MT3222 |  |  | 0.9925938 | 1.53829 | 1.4500372 | 1.3689702 | 1.3902184 | 1.0970979 | 1.1643947 | 1.1644272 | conserved hypothetical
MT3919 |  |  | 1.0042764 | 1.1082212 | 1.129253 | 1.1130922 | 1.0972469 | 1.0138702 | 0.98647374 | 0.98911655 | hypothetical protein
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
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
Rv0250c | Rv0250c |  | 0.9359968 | 1.824673 | 1.8478292 | 1.881163 | 1.9915913 | 1.5572616 | 1.2651976 | 1.0681518 | Rv0250c, (MTV034.16c), len: 97. Unknown. TBparse score is 0.902
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
Rv0373c | Rv0373c |  | 1.1091594 | 1.1763214 | 1.1725489 | 1.1643348 | 1.1982992 | 1.0507717 | 1.0593834 | 1.066252 | Rv0373c, (MTV036.08c), len: 799. Probable dehydrogenase similar ORF3 of the O. carboxidovorans coxMSLgene cluster and the P.thermocarboxydovorans (X77931|PTC2CUTAC_3) cut gene cluster. FASTA scores: gp|X82447|OCCOXMSL4_3 O. carboxidovorans MSLgene cluster(809 aa)opt: 2484 z-score: 2967.6 E(): 0.56.0% identity in 804 aa overlap.
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.
Rv0486 | Rv0486 | mshA | 0.8819722 | 1.0839806 | 1.028564 | 1.0963458 | 1.0629843 | 0.9690928 | 0.975853 | 0.94203824 | Rv0486, (MTCY20G9.12), len: 480, highly similar to M. leprae U00018_39 cosmid B2168 YV12_MYCLE (409 aa) FASTAscores, opt: 2375 z-score: 2633.1 E(): 0, (86.4% identity in 413 aa overlap); Also similar to O26550 LPS BIOSYNTHESISRFBU RELATED PROTEIN (411 aa),in U67601_1 Methanococcus jannaschii (25.3% identity in 387 aa overlap); contains PS00039 DEAD-box subfamily ATP-dependent helicases signature
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
Rv0586 | Rv0586 |  | 0.9491926 | 1.2319858 | 1.270801 | 1.2329557 | 1.3399156 | 1.1034293 | 0.9052641 | 0.88081723 | Rv0586, (MTCY19H5.36c), len: 240, probable transcriptional regulator, similar to many eg. LLDR_ECOLI P33233 putative l-lactate dehydrogenase operon regulatory protein (258 aa), [NAME] scores; opt: 225 z-score: 265.0 E(): 9.3e-08,26.7% identity in 232 aa overlap. Contains PS00043 Bacterial regulatory proteins, gntR family signature and probable helix-turn helix motif from aa 36-57. Also similar to other M. tuberculosis proteins eg. [NAME] (32.1% identity in237 aa overlap)
Rv0607 | Rv0607 |  | 1.0152688 | 1.8144853 | 1.6384906 | 1.6116354 | 1.5803007 | 1.2671956 | 1.2429243 | 1.3719641 | Rv0607, (MTCY19H5.15c), len: 128, unknown
ats | Rv0711 |  | 0.8186294 | 1.2022806 | 1.231477 | 1.087224 | 1.109901 | 0.8538429 | 0.93605244 | 0.9851124 | Rv0711, (MTCY210.30), len: 787, atsA, arylsulfatase, similar to eg ARS_PSEAE P51691 arylsulfatase (ec 3.1.6.1) (532 aa), [NAME] scores, opt: 439, E(): 2.9e-21, (30.8% identity in 552 aa overlap); also similar to MTCI418A_1, (38.4% identity in 797 aa overlap); and MTCI376_1; contains PS00523 Sulfatases signature 1, PS00149 Sulfatases signature 2
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
Rv0743c | Rv0743c |  | 1.0800121 | 1.2361667 | 1.2517828 | 1.2341146 | 1.226341 | 1.0048643 | 0.9900064 | 0.9718807 | Rv0743c, (MTV041.17c), len: 185. Unknown. TBparse score is 0.918
Rv0807 | Rv0807 |  | 1.048562 | 1.1610216 | 1.1274318 | 1.106297 | 1.1008241 | 1.0189494 | 1.0294327 | 1.0303957 | Rv0807, (MTCY07H7A.02c), len: 129 aa, unknown, buthighly similar to sp|O05761|O05761 HYPOTHETICAL 14.0 KD PROTEIN in MLCB5_31 Mycobacterium leprae (131 aa); E(): 0; 73.4% identity in 128 aa overlap.
Rv1062 | Rv1062 |  | 0.8852393 | 1.094384 | 1.0600663 | 1.1024659 | 1.1327918 | 1.0040672 | 1.0000778 | 0.9603943 | Rv1062, (MTV017.15), len: 285. Unknown but some similarity tohypothetical protein in Bacillus subtilis,BSUB0008_176 (260aa) . FASTA scores: Z99111|BSUB0008_176 (260 aa)opt: 163z-score: 199.1 E(): 0.0013; 27.4% identity in 179aaoverlap. TBparse score is 0.902
Rv1168c | Rv1168c | PPE17 | 1.0304137 | 1.9105203 | 1.6610872 | 1.4293978 | 1.4072455 | 1.0575486 | 0.8639491 | 0.89597994 | Rv1168c, (MTV005.04c), len: 346. Member of the M. tuberculosis PPE-family, similar to many eg. TR:E332789 (EMBL:Z98268) [NAME] (385 aa), [NAME] scores; opt: 504 z-score: 780.2 E(): 0, 36.6% identity in 388 aa overlap
Rv1192 | Rv1192 |  | 0.8724579 | 1.0187943 | 1.0167226 | 1.0170964 | 0.9703269 | 0.9239741 | 0.8484585 | 0.84745914 | Rv1192, (MTCI364.04), len: 275. Unknown, contains PS00120 Lipases, serine active site
Rv1265 | Rv1265 |  | 1.2399546 | 1.941037 | 1.7096931 | 1.6553885 | 1.8462597 | 1.5090932 | 1.4412637 | 1.2679963 | Rv1265, (MTCY50.17c), len: 226. Unknown.
lspA | Rv1539 |  | 0.77829516 | 0.8868809 | 0.8667343 | 0.90623754 | 0.93931484 | 0.8381433 | 0.7641436 | 0.7864647 | Rv1539, (MTCY48.26c), lspA, len: 202. Probable lipoprotein signal peptidase, similar to eg LSPA_PSEFL P17942,(170 aa) FASTA scores, opt: 299, z-score: 338.6, E(): 2.6e-12, (38.3% identity in 167 aa overlap)
Rv1673c | Rv1673c |  | 0.9730325 | 1.1119485 | 1.1627151 | 1.1793398 | 1.1344436 | 1.0525111 | 1.0363758 | 1.0340663 | Rv1673c, (MTV047.08c), len: 310. Unknown, but showsweak similarity YA48_HAEIN P44103 hypothetical protein hi1048 precursor (369 aa), [NAME] scores; z-score: 323.3 E(): 8.3e-11, 26.1% identity in 330 aa overlap
Rv1767 | Rv1767 |  | 1.0870967 | 1.5880903 | 1.6296167 | 1.6183916 | 1.6507446 | 1.3742256 | 1.3404831 | 1.2008497 | Rv1767, (MTCY28.33), len: 119 aa; unknown similar to eg. sp|Q57498|YA53_HAEIN HYPOTHETICAL PROTEIN HI1053. (113 aa) opt: 233 z-score: 313.0 E(): 6.4e-10; 40.0% identity in 90 aa overlap
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
Rv2018 | Rv2018 |  | 1.082362 | 1.2288969 | 1.2944489 | 1.2211072 | 1.2688886 | 1.1212906 | 1.0457371 | 1.0250428 | Rv2018, (MTV018.05), len: 239. Unknown but similar to MTCY339.01c (238 aa). FASTA scores: Z77163|MTCY339_1 Mycobacterium tuberculosis cosmid (238 aa) opt: 142 z-score: 175.1 E(): 0.029; 24.8% identity in 250 aa overlap. TBparse score is 0.929. Contains probable helix-turn-helix motif at aa 215-236 (Score 1175, +3.19 SD)
hspX | 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
Rv2032 | Rv2032 | [NAME] | 0.86200106 | 1.3209773 | 1.2021996 | 1.3046063 | 1.2742609 | 0.92441064 | 0.9143886 | 0.9288279 | Rv2032, (MTV018.19), len: 331. Unknown but similar to hypothetical mycobacterial proteins MTCY164.37 (344 aa) and [NAME] (332 aa). FASTA scores: Z95150|MTCY164_38 Mycobacterium tuberculosis cosmid (344 aa) opt: 1208 z-score: 1416.0 E(): 0; 56.4% identity in 321 aa overlap; Z83867|MTCY3A2_27 Mycobacterium tuberculosis cosmid (332 aa) opt:568 z-score: 669.3 E(): 8.6e-30; 36.8% identity in 321 aaoverlap. TBparse score is 0.931
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
Rv2438c | Rv2438c | nadE | 1.0024769 | 1.2591583 | 1.2343953 | 1.1880056 | 1.3417522 | 1.103419 | 1.0917066 | 1.0675415 | Rv2438c, (MTCY428.08), len: 738. Similar to YHN4_YEAST P38795 hypothetical 80.7 kd protein in erg7- (714 aa), [NAME] scores, opt: 339, E(): 5.1e-14, (24.7% identity in 653 aa overlap), also NADE_RHOCA Q03638 nh(3)-dependent nad(+) synthetase (552 aa), [NAME] scores, opt: 288, E(): 6.3e-11, (26.3% identity in 560 aa overlap), contains PS00591 Glycosyl hydrolases family 10 active site
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
Rv2626c | Rv2626c |  | 1.0010575 | 1.5443156 | 1.3139611 | 1.3380876 | 1.5295889 | 1.0772221 | 0.89730847 | 0.92653304 | Rv2626c, (MTCY01A10.06), len: 143 aa. Unknown, somesimilarity to B. subtilis O34682|O34682 YLBB PROTEIN. (150 aa) [NAME] score' opt: 258 z-score: 350.2 E(): 5.5e-12; 33.9% identity in 121 aa overlap, alsowith [NAME], (142 aa) opt: 145 z-score: 175.9 E(): 0.00012, (22.3% identity in 112 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
Rv2653c | Rv2653c |  | 1.2186269 | 1.7282012 | 1.7273521 | 1.631048 | 1.709631 | 1.4455984 | 1.1941184 | 1.2697619 | Rv2653c, (MTCY441.22c), len: 107. Unknown, possiblyphage 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)
Rv2743c | Rv2743c |  | 1.0422891 | 1.32159 | 1.3642353 | 1.4319569 | 1.435834 | 1.2381014 | 1.1855665 | 1.0472313 | [NAME], (MTV002.08c), len: 270 aa. Unknown; similar to, but longer than, M. leprae hypothetical protein TR:Q49833 (EMBL:Z94723) MLCB33.04C (B2235_C1_148) (123 aa), [NAME] scores; opt: 639 z-score: 854.8 E(): 0, 74.8% identity in123 aa overlap
Rv2830c | Rv2830c |  | 0.91208 | 1.1445255 | 1.1963413 | 1.2320071 | 1.1947823 | 1.0477818 | 0.9999471 | 0.99124604 | Rv2830c, (MTCY16B7.12), len: 71 aa. Unknown, some similarity to Z97182|MTCY19H5_26 (85 aa) opt: 88 z-score: 145.8 E(): 1.3; 41.7% identity in 36 aa overlap; and to bacteriophage P1 phd gene, PHD_BPP1 Q06253 prevent host death protein (73 aa), [NAME] scores, opt: 79, E(): 3.8, (35.9% identity in 39 aa overlap)
Rv2913c | Rv2913c |  | 1.0829912 | 2.0835037 | 1.863615 | 1.7169905 | 1.8218195 | 1.4213004 | 0.93848497 | 0.8975968 | Rv2913c, (MTCY338.01c-MTCY274.45c), len: 611. Some similarity at N-terminus to D-amino acid aminohydrolases e.g. TR:P94212 P94212 N-ACYL-D-AMINO ACID AMIDOHYDROLASE (498aa) opt: 221; E(): 2.2e-13; 36.9% identity in 198 aa overlap
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
moeZ | Rv3206c | moeB1 | 0.95969206 | 1.1698747 | 1.1802931 | 1.1798371 | 1.2102833 | 1.0862008 | 1.0380359 | 0.9849009 | Rv3206c, (MTCY07D11.20), len: 392. probable MOEB- homolog, possibly involved in cofactor synthesis, shows goodsimilarity to enzymes involved in molbdopterin synthesis. Has hydrophobic segment from 45-71, and belongs to the HesA/MoeB/ThiF family. FASTA best: P51335 YCXH_PORPU HYPOTHETICAL 43.4 KD PROTEIN (382 aa) opt: 739 z-score: 821.8 E(): 0;(36.2% identity in 378 aa overlap) Also highly similar toMTCY164_27 Mycobacterium tuberculosis O05792 MOEB, 57.3% identity in 386 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
[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)
Rv3531c | Rv3531c |  | 0.948023 | 1.4218171 | 1.6354656 | 1.6193252 | 1.5852807 | 1.337764 | 1.0089942 | 0.9876432 | Rv3531c, (MTCY03C7.25), len: 375 aa. Unknown
Rv3675 | Rv3675 |  | 0.9073041 | 1.1565263 | 1.1966933 | 1.1536595 | 1.2217408 | 1.0493839 | 0.8454108 | 0.94959587 | Rv3675, (MTV025.023), len: 125. Unknown, possible membrane protein
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
Rv3862c | Rv3862c | whiB6;whmF | 1.1968904 | 1.4393815 | 1.4746362 | 1.4665508 | 1.4945792 | 1.2871919 | 1.1446446 | 1.2216376 | Rv3862c, whiB6, (MTCY01A6.06), len: 116, unknown