TABLE 3.
Summary of ORFs identified by significant homology (BLAST search) or GENEMARK prediction
| ORF | No. of amino acids | Coding sequence position (start codon-stop codon)a | Gene or function of closest relative (source), identified protein domains | Data bank reference no. | No. of amino acids with identity/total (%) | E valueb |
|---|---|---|---|---|---|---|
| 1 | 278 | 759-1592c | Hypothetical protein (Rhodopseudomonas palustris), related to IS511, transposase OrfB (Caulobacter crescentus CB15), pfam00665 | ZP_00008656 | 111/265 (41%) | 7e−45 |
| AAK24707 | 103/271 (38%) | 1e−37 | ||||
| 2 | 97 | 1622-1912c | Hypothetical protein (Magnetospirillum magnetotacticum), related to IS1477 transposase (Xanthomonas campestris pv. campestris), pfam01527 | ZP_00053525 | 38/90 (42%) | 3e−09 |
| NP_637161 | 29/69 (42%) | 4e−04 | ||||
| 3 | 89 | 1992-2258 | GENEMARK prediction; no homology | |||
| 4 | 398 | 2241-3434c | GENEMARK prediction; no homology | |||
| 5 | 177 | 3431-3961c | Cinorf13 protein (Streptomyces cinnamoneus) | CAD60535 | 45/161 (27%) | 5e−06 |
| 6 | 282 | 4068-4913 | Epoxide hydrolase homolog YfhM (Bacillus subtilis), pfam00561 | BAA24479 | 91/277 (32%) | 1e−32 |
| 7 | 76 | 5017-5244 | GENEMARK prediction; no homology | |||
| 8 | 680 | 5404-7443 | GENEMARK prediction; no homology | |||
| 9 | 238 | 7882-8595 | Putative chromosome-partitioning ATPase-like protein (R. equi), COG1192 | BAB16660 | 144/232 (62%) | 2e−70 |
| 10 | 109 | 8754-9080 | Hypothetical protein (R. equi) | NP_858507 | 25/59 (42%) | 5e−04 |
| 11 | 293 | 9214-10092 | Putative mycobacteriophage excisionase (R. equi) | NP_066806 | 51/121 (42%) | 1e−10 |
| 12 | 109 | 10285-10611 | GENEMARK prediction; no homology | |||
| 13 | 69 | 10608-10814 | GENEMARK prediction; no homology | |||
| 14 | 217 | 10901-11551 | p24 (human immunodeficiency virus 1) | CAB87182 | 25/62 (40%) | 0.037 |
| 15 | 78 | 11867-12100c | GENEMARK prediction; no homology | |||
| 16 | 169 | 12431-12937 | gp8 (mycobacteriophage Bxb1), related to l-alanoyl-d-glutamate peptidase (bacteriophage A500) | NP_075275 | 44/132 (33%) | 2e−10 |
| CAA59365 | 25/71 (35%) | 4e−04 | ||||
| 17 | 90 | 13247-13516 | GENEMARK prediction; no homology | |||
| 18 | 547 | 13601-15241 | IS1554, transposase (M. tuberculosis CDC1551) | AAK45194 | 358/415 (86%) | 0.0 |
| 19 | 176 | 15242-15769 | GENEMARK prediction; no homology | |||
| 20 | 145 | 16137-16571 | GENEMARK prediction; no homology | |||
| 21 | 392 | 16831-18006 | Hypothetical protein (Nitrosomonas europaea ATCC 19718) | CAD84656 | 100/340 (29%) | 1e−27 |
| 22 | 186 | 18097-18654c | GENEMARK prediction; no homology | |||
| 23 | 220 | 18932-19591 | Predicted protein (Methanosarcina acetivorans C2A) | AAM07556 | 36/100 (36%) | 1e−05 |
| 24 | 323 | 19721-20689c | Hypothetical transmembrane protein (Bifidobacterium longum NCC2705), COG3021, related to iron deficiency-induced protein A (Synechococcus sp. PCC7942), pfam03372 | AAN25527 | 74/244 (30%) | 2e−18 |
| CAC40996 | 57/204 (27%) | 0.13 | ||||
| 25 | 121 | 21894-22256 | Conserved hypothetical protein (M. bovis subsp. bovis AF2122/97), related to membrane proteins related to metalloendopeptidases (Corynebacterium glutamicum ATCC 13032), pfam01551 | CAD93836 | 66/117 (56%) | 5e−35 |
| BAB98251 | 66/115 (57%) | 5e−32 | ||||
| 26 | 105 | 22532-22846c | GENEMARK prediction; no homology | |||
| 27 | 520 | 22970-24529c | Conserved hypothetical protein (M. tuberculosis CDC1551), related to ResB protein required for cytochrome c biosynthesis (C. glutamicum ATCC 13032), COG1333, pfam05140 | AAK44773 | 254/488 (52%) | e−134 |
| NP_599688 | 237/491 (48%) | e−117 | ||||
| 28 | 415 | 25001-26245 | Divalent cation-transport integral membrane protein MNTH (M. bovis subsp. bovis AF2122/97), pfam01566, COG1914 | CAD93809 | 233/391 (59%) | e−111 |
| 29 | 166 | 26272-26769c | Lipoprotein signal peptidase (Brucella melitensis 16M), pfam01252 | AAL52980 | 56/127 (44%) | 1e−10 |
| 30 | 118 | 26766-27119c | Hypothetical protein (Thermobifida fusca), related to transcriptional regulator (Nostoc sp. PCC 7120), smart00418, pfam01022 | ZP_00056748 | 67/97 (69%) | 3e−27 |
| BAB74465 | 27/67 (40%) | 1e−07 | ||||
| 31 | 207 | 27221-27841 | Hypothetical methyltransferase (Shewanella oneidensis MR-1), COG2226, pfam01209, related to menaquinone biosynthesis methyltransferase (2-heptaprenyl-1,4-naphthoquinone methyltransferase) (Methanosarcina acetivorans C2A) | NP_717595 | 70/189 (37%) | 1e−27 |
| NP_619210 | 35/116 (30%) | 3e−05 | ||||
| 32 | 391 | 28126-29298 | Probable conserved lipoprotein LppS (M. bovis subsp. bovis AF2122/97), pfam03734, COG1376 | CAD97408 | 174/386 (45%) | 6e−88 |
| 33 | 140 | 29414-29833 | cadC (Listeria monocytogenes), pfam01022 | AAA25276 | 36/98 (36%) | 4e−11 |
| 34 | 731 | 29826-32018 | Probable cation transport ATPase (M. tuberculosis), COG2217, pfam00122 | F70757 | 378/647 (58%) | e−151 |
| 35 | 501 | 32034-33536c | Putative polyprenol-phosphate-mannose synthase 2 (Ppm2) (M. smegmatis), COG0815, pfam00745 | CAC15462 | 205/483 (42%) | 5e−86 |
| 36 | 215 | 33754-34398 | Putative membrane protein (Corynebacterium efficiens), COG1651, related to thiol-disulfide oxidoreductase BdbD (B. cereus ATCC 14579), pfam01323 | BAC19796 | 95/209 (45%) | 8e−40 |
| NP_830362 | 49/217 (22%) | 6e−06 | ||||
| 37 | 191 | 34464-35036 | Hypothetical integral membrane protein (M. smegmatis), COG4243 | AAG30410 | 93/190 (48%) | 1e−41 |
| 38 | 314 | 35135-36076c | Hypothetical protein (Bifidobacterium longum DJO10A), related to cobalt-zinc-cadmium resistance protein (Xanthomonas axonopodis pv. citri 306), COG1230, pfam01545 | ZP_00120702 | 125/297 (42%) | 1e−49 |
| NP_641652 | 106/298 (35%) | 5e−38/PICK> | ||||
| 39 | 271 | 36335-37147c | Possible cytochrome c-type biogenesis protein CCDA (M. bovis subsp. bovis), related to a cytochrome c biogenesis protein (C. glutamicum ATCC 13032), pfam02683, COG0785 | CAD93402 | 120/233 (51%) | 4e−49 |
| NP_599687 | 116/254 (45%) | 1e−45 | ||||
| 40 | 209 | 37144-37770c | Hypothetical protein (M. leprae), COG0526, COG1225, related to thiol-disulfide isomerase and thioredoxins (C. glutamicum ATCC 13032) | S72901 | 94/179 (52%) | 4e−41 |
| BAB97832 | 73/174 (41%) | 1e−27 | ||||
| 41 | 309 | 38162-39088 | Hypothetical protein (M. leprae), COG0739, related to membrane proteins related to metalloendopeptidases (C. glutamicum ATCC 13032), pfam01551 | CAB36664 | 64/120 (53%) | 1e−29 |
| BAB98251 | 65/120 (54%) | 5e−27 | ||||
| 42 | 597 | 39321-41111 | Cytochrome c oxidase, subunit 1 (M. tuberculosis CDC1551), COG0843, pfam00115 | NP_337644 | 442/568 (77%) | 0.0 |
| 43 | 91 | 41108-41380 | GENEMARK prediction; no homology | |||
| 44 | 311 | 41762-42694c | Hypothetical protein (T. fusca), COG0501, related to peptidase M48 (C. glutamicum) | ZP_00058818 | 47/117 (40%) | 3e−08 |
| AAL31539 | 37/111 (33%) | 3e−04 | ||||
| 45 | 113 | 42699-43037c | Hypothetical protein (T. fusca), COG3680, pfam03965, related to methicillin resistance regulatory protein (S. aureus subsp. aureus N315) | ZP_00056896 | 45/109 (41%) | 8e−13 |
| NP_373280 | 20/87 (22%) | 0.007 | ||||
| 46 | 730 | 43290-45479 | Cation-transporting ATPase (M. leprae), COG2216, COG2217, pfam00122 | NP_302350 | 337/724 (46%) | 3−148 |
| 47 | 663 | 45417-47405c | Possible membrane protein (M. leprae), related to CtaG (B. subtilis), COG3336 | NP_302349 | 212/598 (35%) | 8e−86 |
| NP_389376 | 50/234 (21%) | 0.004 | ||||
| 48 | 226 | 47520-48197 | Probable conserved integral membrane protein (M. bovis subsp. bovis AF2122/97) | CAD93856 | 50/183 (27%) | 3e−04 |
| 49 | 155 | 48266-48730c | Hypothetical protein (Cytophaga hutchinsonii) | ZP_00117563 | 29/79 (36%) | 2e−08 |
| 50 | 104 | 49143-49454 | Putative modification methylase (Streptomyces lividans) | AAO61179 | 22/64 (34%) | 0.19 |
| 51 | 223 | 49580-50248 | Hypothetical protein Rv1044 (M. tuberculosis H37Rv) | NP_215560 | 62/201 (30%) | 3e−05 |
| 52 | 344 | 50248-51279 | GENEMARK prediction; no homology | |||
| 53 | 164 | 51284-51775c | GENEMARK prediction; no homology | |||
| 54 | 85 | 51807-52061c | GENEMARK prediction; no homology | |||
| 55 | 231 | 52162-52854 | GENEMARK prediction; no homology | |||
| 56 | 125 | 52851-53225 | Helix-turn-helix protein (Pyrobaculum aerophilum IM2), related to SgraIC control protein (Streptomyces griseus), pfam01381 | AAL64755 | 29/61 (47%) | 1e−04 |
| AAG31560 | 24/60 (40%) | 0.002 | ||||
| 57 | 79 | 53531-53767 | Glutaredoxin electron transport component of NrdEF (M. leprae), COG0695, pfam00462 | NP_302197 | 60/77 (77%) | 4e−25 |
| 58 | 138 | 53846-54259 | GENEMARK prediction; no homology | |||
| 59 | 141 | 54256-54678 | GENEMARK prediction; no homology | |||
| 60 | 189 | 54682-55248 | gp82 (mycobacteriophage CJW1), GerE (Corynebacterium striatum, plasmid pTP10), COG0305, pfam00772 | AAN01696 | 41/147 (27%) | 0.008 |
| AAG03386 | 5/73 (34%) | 0.014 | ||||
| 61 | 69 | 55270-55476 | GENEMARK prediction; no homology | |||
| 62 | 180 | 55631-56170c | GENEMARK prediction; no homology | |||
| 63 | 171 | 56299-56811c | Hypothetical protein (Nostoc punctiforme) | ZP_00106356 | 34/95 (35%) | 5e−05 |
| 64 | 192 | 57097-57672c | Putative bacteriophage-related protein (Ralstonia solanacearum), related to gene 2.8 (enterobacteria phage T7) | NP_521357 | 33/95 (34%) | 5e−04 |
| NP_041971 | 30/97 (30%) | 0.010 | ||||
| 65 | 113 | 57690-58028c | GENEMARK prediction; no homology | |||
| 66 | 65 | 58573-58767 | GENEMARK prediction; no homology | |||
| 67 | 2,073 | 58773-64991 | TraA-like protein (R. equi), related to TraA (C. glutamicum), COG0507 | NP_066783 | 329/987 (33%) | e−105 |
| NP_776232 | 253/878 (28%) | 3e−56 | ||||
| 68 | 113 | 65072-65410 | GENEMARK prediction; no homology | |||
| 69 | 133 | 65473-65871 | Putative glycosyl transferase (Streptomyces nogalater) | AAF01809 | 28/82 (34%) | 0.032 |
| 70 | 345 | 65928-66962c | Hypothetical protein (Microbulbifer degradans 2-40) | ZP_00068299 | 71/150 (47%) | 2e−27 |
| 71 | 275 | 67047-67871c | Conserved hypothetical protein (C. efficiens YS-314) | NP_736653 | 48/181 (26%) | 1e−09 |
| 72 | 128 | 68071-68454c | Putative membrane protein (Streptomyces avermitilis MA-4680) | NP_825985 | 29/82 (35%) | 0.002 |
| 73 | 144 | 68480-68911c | WD40-repeat-containing protein (Methanosarcina acetivorans C2A) | NP_617428 | 22/70 (31%) | 0.30 |
| 74 | 139 | 69109-69525c | GENEMARK prediction; no homology | |||
| 75 | 1,631 | 69852-74744c | Putative methylase (or helicase) (R. equi), related to helicase SNF2 family (Agrobacterium tumefaciens C58), COG4646 | BAB16635 | 489/1302 (37%) | 0.0 |
| AAL46337 | 399/1325 (30%) | e−125 | ||||
| 76 | 331 | 74754-75746c | Putative transposase (C. efficiens YS-314), related to IS1601-D (Mycobacterium avium), pfam00665, COG2801 | NP_739229 | 186/284 (65%) | 7e−96 |
| AAD44200 | 7e−55 | |||||
| 77 | 104 | 75743-76054c | Putative transposase (C. efficiens YS-314), related to transposase IS911 helix-turn-helix and LZ region (N. europaea ATCC 19718), pfam01527 | NP_739228 | 64/103 (62%) | 1e−23 |
| 78 | 266 | 76073-76870c | Putative methylase (or helicase) (R. equi), related to DNA meth- ylase (Listeria innocua), COG2263 | BAB16635 | 110/264 (41%) | 6e−41 |
| NP_569161 | 65/182 (35%) | 5e−27 | ||||
| 79 | 193 | 76999-77577c | GENEMARK prediction; no homology | |||
| 80 | 90 | 77862-78131c | GENEMARK prediction; no homology | |||
| 81 | 312 | 78251-79186c | GENEMARK prediction; no homology | |||
| 82 | 154 | 79275-79736c | GENEMARK prediction; no homology | |||
| 83 | 136 | 79916-80323c | Hypothetical protein (Arthrobacter nicotinovorans) | CAD47981 | 30/68 (44%) | 2e−08 |
| 84 | 630 | 80323-82212c | Conjugative transfer gene complex protein-like protein (R. equi), related to transfer complex protein TrsK (S. aureus), pfam02534, COG3505 | NP_066787 | 187/531 (35%) | 9e−77 |
| C56976 | 28/78 (35%) | 8e−07 | ||||
| 85 | 238 | 82251-82964c | GENEMARK prediction; no homology | |||
| 86 | 183 | 83008-83556c | Hypothetical protein (R. equi) | NP_066788 | 40/161 (24%) | 0.037 |
| 87 | 675 | 83553-85577c | Putative peptidase (R. equi), related to peptidase M23/M37 family (Bacillus anthracis Ames), pfam01551, COG0739 | NP_066789 | 150/318 (47%) | 4e−59 |
| NP_844314 | 38/104 (36%) | 1e−11 | ||||
| 88 | 133 | 85570-85968c | GENEMARK prediction; no homology | |||
| 89 | 653 | 85965-87923c | Hypothetical protein (R. equi), related to ATP binding protein-like protein (R. equi) | NP_858493 | 192/560 (34%) | 1e−70 |
| NP_066791 | 192/560 (34%) | 1e−70 | ||||
| 90 | 353 | 87943-89001c | Integral membrane protein-like protein (R. equi) | NP_066792 | 71/266 (26%) | 3e−06 |
| 91 | 499 | 89029-90525c | Integral membrane protein-like protein (R. equi) | NP_066792 | 174/473 (36%) | 2e−68 |
| 92 | 505 | 90570-92084c | Putative transfer gene complex protein-like protein (A. nicotinovorans) | CAD47985 | 27/72 (37%) | 2e−05 |
| 93 | 301 | 92078-92980c | Hypothetical protein (R. equi) | NP_066795 | 76/258 (29%) | 2e−10 |
| 94 | 198 | 92985-93578c | Hypothetical protein (R. equi) | NP_066796 | 65/191 (34%) | 3e−18 |
| 95 | 90 | 93617-93886c | GENEMARK prediction; no homology | |||
| 96 | 97 | 93912-94202c | Hypothetical protein (Haemophilus somnus 129PT), related to preprotein translocase SecY subunit (Haemophilus influenzae Rd) | ZP_00123677 | 29/80 (36%) | 0.16 |
| NP_438957 | 27/75 (36%) | 0.31 | ||||
| 97 | 211 | 94249-94881c | GENEMARK prediction; no homology | |||
| 98 | 413 | 94887-96125c | GENEMARK prediction; no homology | |||
| 99 | 279 | 96272-97108c | GENEMARK prediction; no homology | |||
| 100 | 109 | 97105-97431c | GENEMARK prediction; no homology | |||
| 101 | 551 | 97778-99430c | Hypothetical protein (R. equi) | NP_066802 | 151/332 (45%) | 3e−58 |
| 102 | 144 | 100135-100566 | Putative repressor protein (R. equi), related to transcriptional repressor (B. cereus ATCC 14579), pfam1381, COG1476 | NP_066803 | 49/141 (34%) | 6e−16 |
| NP_830818 | 20/61 (32%) | 5e−05 | ||||
| 103 | 37 | 100591-100701 | GENEMARK prediction; no homology | |||
| 104 | 59 | 100804-100980c | GENEMARK prediction; no homology | |||
| 105 | 227 | 100858-522 | gp48 (mycobacteriophage Che8), related to methyltransferase-helicase polyprotein (grapevine rootstock stem lesion-associated virus) | NP_817386 | 36/91 (39%) | 4e−08 |
| AAN63466 | 27/92 (29%) | 0.052 |
a
c, complementary strand.
b
An E value of >0.4 indicates no homology.