Spreadsheet: 58680505-5ae0-4d1b-b9f8-2683be800885
Sheet: Sheet1

Table S7
Figure 5B (black) - Genes with Early Repressed, Sustained 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)
MT1342 |  |  | 1.0142603 | 0.7801663 | 0.8219401 | 0.79251695 | 0.80617493 | 0.83481556 | 0.7893314 | 0.82105803 | hypothetical protein
MT1924.1 |  |  | 1.111669 | 0.501735 | 0.55596834 | 0.53885496 | 0.5514794 | 0.60733205 | 0.5908508 | 0.6008797 | hypothetical protein
rpli | Rv0056 |  | 1.1400968 | 0.8437115 | 0.8509727 | 0.8579025 | 0.84131926 | 0.8337165 | 0.8396317 | 0.8214467 | Rv0056, (MTCY21D4.19), len: 152, highly similar to RL9_MYCLE P46385 50s ribosomal protein l9 (152 aa), [NAME] scores, opt: 847, E(): 0, (88.7% identity in 150 aa overlap); contains PS00651 Ribosomal protein L9 signature
Rv0483 | Rv0483 | lprQ | 1.0197823 | 0.7831892 | 0.78820544 | 0.749037 | 0.76723605 | 0.7673756 | 0.74021894 | 0.75632846 | Rv0483, (MTCY20G9.09), len: 451, unknown, similar to several M. tuberculosis hypothetical proteins, e.g, MTV009_3, [NAME], MTCI28_32, MTV031_10, also similarity toMycobacterium leprae MLCL383_24 O07707 HYPOTHETICAL 43.6 KDPROTEIN and to Q49706 B1496_F2_81 (271 aa). FASTA scores,opt: 324, z-score: 344.1, E(): 3.2e-12, (29.8% identity [NAME] overlap)
Rv0635 | Rv0635 |  | 1.2112653 | 0.91791207 | 0.9279351 | 0.8715129 | 0.91510963 | 0.9354035 | 0.921623 | 0.95510584 | Rv0635, (MTCY20H10.16), len: 158, unknown similar to YV31_MYCTU Q11168 hypothetical 18.4 kd protein cy20g9.31 (166 aa), [NAME] scores, opt: 405, E(): 3.2e-22, (45.0% identity in 140 aa overlap) and YV31_MYCLE P54879 hypothetical 18.7 kd protein b2168_f2 (166 aa), [NAME] scores, opt: 387, E(): 5.9e-21, (43.4% identity in 145 aa overlap) also similar to [NAME] (2 ORFs downstream, 48.7% identity in 150aa overlap, )
rplJ | Rv0651 |  | 1.1723669 | 0.89765924 | 0.88986653 | 0.8734191 | 0.8634551 | 0.9040672 | 0.8692504 | 0.8691606 | Rv0651, (MTCY20H10.32), len: 178 aa, rplJ, similarto eg RL10_STRGR STREPTOMYCES GRISEUS, P36257 50s ribosomalprotein l10. (185 aa), [NAME] scores, opt: 633, E(): 0, (59.0% identity in 173 aa overlap)
[NAME] | [NAME] |  | 1.3233392 | 0.92074245 | 0.9060361 | 0.9356541 | 0.8583097 | 0.9601587 | 0.91030955 | 0.88058954 | Rv0669c, (MTCI376.05), len: 637 unknown, but similarto SLIME MOLD DDU82513_1 Dictyostelium discoideum sp|O15913|O15913 RANDOM SLUG CDNA25 PROTEIN (FRAGMENT) (702 aa), FASTA scores: opt: 756 z-score: 822.1 E(): 0; 35.5% identity in 676 aa overlap Contains PS00017 [NAME]/GTP-binding site motif A
rplV | [NAME] |  | 0.8900457 | 0.64951116 | 0.6727541 | 0.65030056 | 0.6277723 | 0.67528176 | 0.67200655 | 0.6579724 | [NAME], ([NAME]), len: 197 aa, rplV, almost identical to MBS10OPER_7 Mycobacterium bovis BCG and MLCB2492_7 Mycobacterium leprae RIBOSOMAL PROTEIN L22. Also similarto eg RL22_BACSU P42060 50s ribosomal protein l22 (113 aa),fasta scores, opt: 368, E(): 2.4e-13, (52.8% identity in 108 aa overlap); contains PS00464 Ribosomal protein L22 signature, contains repetitive sequence at C-terminus
rplF | Rv0719 |  | 1.0605956 | 0.8512767 | 0.89527965 | 0.84407955 | 0.8236695 | 0.8440967 | 0.84714 | 0.8582251 | Rv0719, (MTCY210.38), len: 179 aa, rplF, almost identical to MLCB2492_19 Mycobacterium leprae O32998 RIBOSOMALPROTEIN L6; also highly similar to RL6_STRCO P46786 50s ribosomal protein l6. streptomyces (179 aa), [NAME] scores, opt: 872, E(): 0, (70.4% identity in 179 aa overlap); containsPS00525 Ribosomal protein L6 signature 1
Rv0846c | Rv0846c |  | 1.1041169 | 0.6787096 | 0.6802551 | 0.7084039 | 0.7365617 | 0.6777447 | 0.65907186 | 0.67499775 | Rv0846c, (MTV043.39c), len: 504. Unknown but similar to several L-ascorbate oxidases e.g. (579 aa). Contains [NAME] oxidases signature 2 at C-terminus. FASTA scores: sp|P24792|ASO_CUCMA L-ASCORBATE OXIDASE PRECURSOR(579 aa) opt: 423 z-score: 457.2 E(): 5.8e-18; 28.4% identity in 493 aa overlap. TBparse score is 0.904
Rv0849 | Rv0849 |  | 1.1080099 | 0.76430196 | 0.7303331 | 0.7470594 | 0.6741064 | 0.7390263 | 0.74090713 | 0.7369862 | Rv0849, (MTV043.42), len: 419. Probable integral membrane transport protein, some similarity to quinolone efflux pumps e.g. [NAME] S74031_1 (388 aa). FASTA scores: [NAME] (402 aa) opt: 447 z-score: 559.5 E():1.2e-23; 26.2% identity in 385 aa overlap; and S74031|S74031_1 (388 aa) opt: 250 z-score: 315.1 E(): 4.8e-10; 21.3% identity in 394 aa overlap. TBparse score is 0.908
Rv0942 | Rv0942 |  | 1.0125216 | 0.80860287 | 0.8556778 | 0.8081836 | 0.79447085 | 0.81132996 | 0.81914717 | 0.8485949 | Rv0942, (MTCY10D7.32c), len: 92.
accA2 | Rv0973c |  | 1.2410811 | 0.79528415 | 0.78313303 | 0.7782291 | 0.75603175 | 0.78026205 | 0.73364085 | 0.77097523 | Rv0973c, (MTV044.01c-MTCY10D7.01), len: 667,accA2, Probable carbamoyl-phosphate synthase, biotin dependent,similar to pyruvate- or urea- carboxylases, similar to many e.g. MTCY349_20. FASTA scores: gp|Z83018|MTCY349_20 M. tuberculosis cosmid (1127 aa) opt: 838 z-score: 961.3 E(): 0. 40.2% identity in 500 aa overlap; contains PS00867 Carbamoyl-phosphate synthase subdomain signature 2MTCY10D7.01, partial orf, similar to BCCA_MYCTU P46401 acetyl-/propionyl-coenzyme a carboxylase alpha chain, (654 aa) FASTA scores, opt:250,z-score: 288.8, E(): 4e-09, (28.6% identity in 182 aa overlap); contains [NAME] enzymes attachment site
Rv1199c | Rv1199c |  | 1.0165571 | 0.7305258 | 0.74339515 | 0.7360882 | 0.7210581 | 0.7511476 | 0.72992676 | 0.7817907 | Rv1199c, (MTCI364.11c), len: 415. Transposase for IS1081, identical to TRA1_MYCBO P35882 transposase for insertion sequence element (415 aa), region identical to MTCY441.35, (100.0% identity in 261 aa overlap), almost identicalto MTCY10G2.02c (415 aa) (99.8% identity in 415 aa overlap);contains PS01007 Transposases, Mutator family, signature,PS00435 Peroxidases proximal heme-ligand signature
Rv1519 | Rv1519 |  | 1.2296137 | 0.5978402 | 0.691476 | 0.6443365 | 0.6352013 | 0.7037567 | 0.6423675 | 0.6802348 | Rv1519, (MTCY19G5.09c), len: 89. Unknown, high similarity to C-terminus of MTCY78.26, 58.1% identity in 74aa overlap.
Rv1703c | Rv1703c |  | 0.72091025 | 0.5436524 | 0.5807258 | 0.57004744 | 0.5599814 | 0.56851196 | 0.5845563 | 0.5937724 | Rv1703c, (MTCI125.25c), len: 196. Probable o-methyltransferase, most similar to the soluble form of mammalian catecholo-methyltransferase eg. COMT_HUMAN P21964 catechol o-methyltransferase (271 aa), [NAME] scores; opt: 405 z-score: 642.3 E(): 7.8e-29, 38.9% identity in 190 aa overlap
Rv1749c | Rv1749c |  | 1.1811255 | 0.7887431 | 0.81999415 | 0.8236713 | 0.82965285 | 0.87796116 | 0.84948015 | 0.83194023 | Rv1749c, (MTCY28.12c-MTCY04C12.33c), len: 185. Possible integral membrane protein, similar to hypothetical protein TR:O27914 (EMBL:AE000940) MTH1892 from Methanobacterium thermoautotrophicum (168 aa), [NAME] scores; E(): 9.3e-16,37.4% identity in 123 aa overlap
Rv1778c | Rv1778c |  | 1.0706692 | 0.8705458 | 0.85104126 | 0.8176524 | 0.8146327 | 0.8377278 | 0.8720301 | 0.8465292 | Rv1778c, (MTCY25C11.05c), unknown, len: 149 aa
[NAME] | [NAME] |  | 1.1347756 | 0.92308474 | 0.94041336 | 0.9339009 | 0.9758843 | 0.9361462 | 0.9150476 | 0.9362088 | [NAME], (MTCY09F9.23c), len: 256 aa. Dehydrogenase similar to eg LINC_PSEPA P50197 2,5-dichloro-2,5-cyclohexadiene-1,4-d (250 aa), [NAME] scores, opt: 529, E(): 5.7e-25, (40.6% identity in 251 aa overlap); contains PS00061 Short-chain alcohol dehydrogenase family signature
Rv2791c | Rv2791c |  | 0.83896744 | 0.4478244 | 0.48748112 | 0.47797543 | 0.46035773 | 0.5209471 | 0.4958391 | 0.46318918 | Rv2791c, (MTV002.56c), probable IS1602 transposase len: 459 aa; similar to many eg. TR:[NAME] (EMBL:D38778) TRANSPOSASE-LIKE PROTEIN OF PS3IS (369 aa), [NAME] scores; opt: 327 z-score: 426.0 E(): 1.4e-16, 26.8% identity in 399 aaoverlap
Rv2908c | Rv2908c |  | 0.9628167 | 0.7810619 | 0.78034353 | 0.78110635 | 0.75243884 | 0.7504783 | 0.7644744 | 0.7677148 | Rv2908c, ([NAME]), len: 80. Unknown but equivalent to M. leprae sp|O33015|O33015 HYPOTHETICAL 8.6 KD PROTEIN. (80 aa) opt: 492 z-score: 660.6 E(): 2.8e-29; 93.8% identity in 80 aa overlap
Rv2959c | Rv2959c |  | 1.1091956 | 0.81292725 | 0.7794996 | 0.77918786 | 0.79122806 | 0.7763106 | 0.77322674 | 0.7921843 | Rv2959c, (MTCY349.29), len: 245 aa. Unknown, identical to G560520 U0002JB, some similarity to methyltransferases
Rv2963 | Rv2963 |  | 0.8903979 | 0.5002317 | 0.5610996 | 0.54299116 | 0.55007416 | 0.52533215 | 0.4802025 | 0.5239585 | Rv2963, (MTCY349.24c), len: 406 aa. Unknown, integral membrane protein, identical to G560523 U0002F
[NAME] | Rv3011c |  | 0.8993498 | 0.72866523 | 0.72405285 | 0.71986735 | 0.73056835 | 0.7080315 | 0.7045451 | 0.74370164 | Rv3011c, (MTV012.25c), len: 494. Probable gatA, [NAME]-tRNA-Gln amidotransferase subunit A similar to several e.g. G2589195 (486 aa). See Proc Natl Acad Sci U S A 1997 Oct28;94(22):11819-11826. Similar to many prokaryotic and eukaryotic amidases, best with Mycobacterium leprae MLCB637_13and Synechocystis P73558. FASTA score: Z99263|MLCB637_13 Mycobacterium leprae cosmid B637. (497 aa) opt: 2839 z-score:3067.1 E(): 0; (88.8% identity in 492 aa overlap) and sptr|P73558|P73558 AMIDASE (483 aa) opt: 1593 z-score: 1723.4 E(): 0; (55.9% identity in 487 aa overlap) and G2589195 GLU-TRNAGLN AMIDOTRANSFERASE SUBUNITS C (486 aa)opt: 1348 z-score: 1488.1 E(): 0; (50.5% identity in 459 aa overlap). Also similar to other M. tuberculosis proteins e.g. MTV004.33,(475 aa) FASTA score; opt: 563 z-score: 461.5 E(): 2.1e-20; (32.5% identity in 489 aa overlap). Contains PS00017 [NAME]/GTP-binding site motif A (P-loop). TBparse score is 0.868
Rv3234c | Rv3234c |  | 0.91262317 | 0.69799316 | 0.7310543 | 0.7349588 | 0.73179597 | 0.7189333 | 0.76990646 | 0.72189814 | Rv3234c, (MTCY20B11.09c), len: 271, unknown but some similarity to hypothetical M. tuberculosis proteins e.g. MTCY21B4.43, 1.5e-23; MTCY03A2.28, 1.3e-17; [NAME], 8.8e-14., MTCY493_29 , MTCY28_26 , MTV013_8, MTY13E12_33 etc. FASTA best: YZ23_MYCTU Q10554 hypothetical 53.9 kd protein cy31.23. (505 aa) opt: 327 z-score: 384.6 E(): 2e-14; (30.0%identity in 270 aa overlap)
phoY1 | Rv3301c |  | 1.2706301 | 1.0449834 | 0.9909538 | 0.9600031 | 0.9639095 | 0.9948065 | 1.0080501 | 0.97740406 | Rv3301c, (MTCI418A.03c), len: 221 aa phoY, probablephosphate transport system regulatory protein, highly similar to M. leprae Q50047 phoY (222 aa), [NAME] scores; opt:929 z-score: 1110.0 E(): 0, 61.5% identity in 218 aa overlap.Also similar to MTV043_13 (213 aa, 63.4% identity in 213 aaoverlap)
metC | Rv3340 |  | 1.0600365 | 0.7815876 | 0.7696211 | 0.7801528 | 0.7564406 | 0.81845146 | 0.8037889 | 0.8328896 | Rv3340, (MTV016.40), len: 449. Probable homocysteine synthase (EC 4.2.99.10) similar to many fungal enzymes e.g. P50125|CYSD_EMENI (437 aa). Contains PS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. FASTA scores: sp|P50125|CYSD_EMENI O-ACETYLHOMOSERINE (THIOL)-LYASE (437 aa) opt: 1442 z-score: 1703.1 E(): 0; 53.7% identity in 430 aa overlap. TBparse score is 0.869
Rv3353c | Rv3353c |  | 1.2548208 | 0.8780697 | 0.85631305 | 0.85923064 | 0.8793879 | 0.88786 | 0.87556434 | 0.86418796 | Rv3353c, (MTV004.10c), len: 114 aa; unknown, weak similarity to M. leprae hypothetical protein TR:Q49720 (EMBL:U00014) B1549_C3_218 (222 aa), [NAME] scores; opt: 121 z-score: 210.3 E(): 0.00015, 33.0% identity in 100 aa overlap Also similar to part of MTV030_7, E(): 3.4e-14, 51.6% identity in 91 aa overlap
glmS | Rv3436c |  | 1.0185654 | 0.75633496 | 0.7186322 | 0.7124492 | 0.6818114 | 0.74199563 | 0.72929484 | 0.7345246 | Rv3436c, (MTCY77.08c), len: 624 aa. glmS, probableglucosamine-fructose-6-phosphate aminotransferasehighly similar to M. leprae GLMS_MYCLE P40831 probable glucosamine--fructose-6-phosphate aminotransferase (624 aa), [NAME] scores, opt: 3570, E(): 0, (89.0% identity in 627 aa overlap)
Rv3651 | Rv3651 |  | 1.0176004 | 0.7044344 | 0.7192585 | 0.7216701 | 0.7094118 | 0.7101458 | 0.72698605 | 0.7925345 | Rv3651, (MTCY15C10.01c), len: 345. Function: unknown