TABLE 1.
Selected ORFs predicted on pRHL3 of Rhodococcus sp. strain RHA1
| RHL3 ORF | Start coordi- nate (bp) | Stop coordi- nate (bp) | Strand type | Product size (no. of amino acids) | % Identitya | Gene product descriptionb | Closest organism(s)a |
|---|---|---|---|---|---|---|---|
| RHL3.14 | 12172 | 11930 | − | 81 | Hypothetical protein/some similarity with two- component histidine kinase | ||
| RHL3.15 | 13116 | 12187 | − | 310 | Conserved hypothetical protein/putative endonuclease | ||
| RHL3.16a | 13528 | 13815 | + | 96 | Hypothetical protein/methyltransferase/possible pseudogene | ||
| RHL3.16b | 13814 | 14131 | + | 106 | 20 | Hypothetical protein/possible pseudogene | C. equii (R. equi) |
| RHL3.24 | 22119 | 21229 | − | 297 | 43 | Putative transposase | S. violaceoruber |
| RHL3.25 | 22466 | 22119 | − | 116 | 82 | Conserved transposase | Rhodococcus sp. strain I24 |
| RHL3.36 | 34389 | 33994 | − | 132 | Putative recombinase/integrase | ||
| RHL3.37 | 34679 | 35092 | + | 138 | 27 | Hypothetical protein/putative transposase | Micrococcus sp. strain 28 |
| RHL3.41 | 40363 | 39539 | − | 275 | 50 | Conserved carveol dehydrogenase | R. erythropolis |
| RHL3.42 | 41024 | 42184 | + | 387 | 44 | Putative limonene monooxygenase | R. erythropolis |
| RHL3.46 | 44886 | 44254 | − | 211 | 20 | Hypothetical protein/putative transposase | R. erythropolis |
| RHL3.55 | 58568 | 59461 | + | 298 | 67 | Conserved GND protein/6-phosphogluconate dehydrogenase | M. smegmatis |
| RHL3.56 | 59461 | 60462 | + | 334 | 85 | Conserved F420-dependent glucose 6-phosphate dehydrogenase | M. phlei |
| RHL3.57 | 60462 | 62114 | + | 551 | 67 | Conserved glucose 6-phosphate isomerase | M. tuberculosis and M. bovis |
| RHL3.59a | 63480 | 63989 | + | 170 | 31 | Putative transposase/possible pseudogene | S. coelicolor |
| RHL3.59b | 63956 | 64327 | + | 134 | 30 | Putative transposase/possible pseudogene | S. avermitilis |
| RHL3.60 | 65785 | 64430 | − | 452 | 43 | Conserved reductase | P. putida |
| RHL3.61 | 66164 | 65754 | − | 137 | 43 | Putative ferredoxin | B. japonicum |
| RHL3.62 | 67411 | 66167 | − | 415 | 27 | Putative cytochrome P450 | S. avermitilis |
| RHL3.65 | 70574 | 70368 | − | 69 | − | Hypothetical protein | |
| RHL3.66 | 71454 | 70582 | − | 291 | Conserved hypothetical protein/possible endonuclease | ||
| RHL3.85 | 91424 | 92161 | + | 246 | Putative transposase | ||
| RHL3.88 | 95128 | 97482 | + | 785 | 44 | Conserved putative ABC transporter ATP-binding protein | S. avermitilis |
| RHL3.91 | 102553 | 100637 | − | 639 | 25 | Probable serine/threonine-protein kinase | M. tuberculosis and M. bovis |
| RHL3.112 | 119957 | 121129 | + | 391 | 53 | Conserved transposase | S. coelicolor |
| RHL3.135 | 144075 | 143851 | − | 75 | Hypothetical protein | ||
| RHL3.136 | 144427 | 146160 | + | 578 | 52 | Putative methylase | C. crescentus |
| RHL3.137 | 146217 | 147332 | + | 372 | 25 | Putative type I restriction modification system enzyme | M. acetivorans |
| RHL3.138 | 147322 | 150444 | + | 1,041 | 41 | Putative DNA helicase | C. efficiens |
| RHL3.139 | 150662 | 152125 | + | 488 | 42 | Putative ABC transporter ATP-binding protein | Synechococcus sp. strain PCC 7942) (A. nidulans R2) |
| RHL3.141a | 152739 | 153395 | + | 219 | 26 | Putative transposase/possible pseudogene | M. abscessus |
| RHL3.141b | 153148 | 153597 | + | 150 | 30 | Putative transposase/possible pseudogene | M. abscessus |
| RHL3.150 | 161508 | 162518 | + | 337 | 84 | Conserved F420-dependent glucose 6-phosphate dehydrogenase | M. phlei |
| RHL3.151 | 162550 | 164199 | + | 550 | 69 | Conserved glucose 6-phosphate isomerase | M. tuberculosis and M. bovis |
| RHL3.156 | 172382 | 171159 | − | 408 | 31 | Putative permease transporter | S. coelicolor |
| RHL3.157 | 174191 | 173097 | − | 365 | 21 | Putative transporter bacterial inner membrane translocator RbsC | P. multocida |
| RHL3.158 | 175723 | 174203 | − | 507 | 38 | Putative ABC transporter ATP-binding protein | S. coelicolor |
| RHL3.159 | 176971 | 175808 | − | 388 | Putative ABC-type sugar transport system peri- plasmic component | ||
| RHL3.183 | 202742 | 203497 | + | 252 | 53 | Putative sensory transduction protein/two-component regulatory system | C. efficiens |
| RHL3.184 | 203497 | 204651 | + | 385 | 36 | Putative two-component system/sensory transduction histidine kinase | C. glutamicum (B. flavum) |
| RHL3.235 | 256695 | 255916 | − | 260 | 34 | Putative plasmid partioning protein (ParA) | R. erythropolis |
| RHL3.237 | 261733 | 260402 | − | 444 | 25 | Rep-like protein | M. celatum |
| RHL3.246 | 269639 | 268476 | − | 388 | 31 | Putative cytochrome P450 | S. avermitilis |
| RHL3.276 | 307112 | 306021 | − | 364 | 46 | Conserved alcohol dehydrogenase class IV | C. acidovorans (P. acidovorans) |
| RHL3.277 | 308001 | 307105 | − | 299 | 43 | Conserved dioxygenase | A. tumefaciens strain C58 (ATCC 33970) |
| RHL3.279 | 308851 | 308336 | − | 172 | 36 | Putative oxidoreductase | S. coelicolor |
| RHL3.280 | 310077 | 308857 | − | 407 | 30 | Putative indole dioxygenase | S. avermitilis |
| RHL3.281 | 310249 | 311304 | + | 352 | 30 | Probable the operon regulatory protein/AraC family | R. erythropolis |
| RHL3.284 | 313807 | 314808 | + | 334 | 33 | Probable the operon regulatory protein/AraC family | R. erythropolis |
| RHL3.286 | 315759 | 316727 | + | 323 | 20 | Putative ferredoxin/reductase | Rhodococcus sp. strain NCIMB 9784 |
| RHL3.287 | 316809 | 318125 | + | 439 | 26 | Conserved cytochrome P450 | Rhodococcus sp. strain NCIMB 9784 |
| RHL3.294 | 324660 | 322984 | − | 559 | 70 | Conserved G6PI | M. tuberculosis and M. bovis |
| RHL3.295 | 325563 | 324667 | − | 299 | 63 | Conserved GND protein/6-phosphogluconate dehydrogenase | M. smegmatis |
| RHL3.299 | 329871 | 328591 | − | 427 | 90 | Putative G6PDH | R. opacus |
a
Based on BLASTP alignment with members of the nonredundant SPtrEMBL protein database only. B. japonicum, Bradyrhizobium japonicum; M. acetivorans, Methanosarcina acetivorans; A. nidulans, Anacystis nidulans; B. flavum, Brevibacterium flavum; P. multocida, Pasteurella multocida; C. acidovorans, Comamonas acidovorans; C. crescentus, Caulobacter crescentus; C. efficiens, Corynebacterium efficiens.
b
Gene product description was inferred by BLAST sequence similarity of predicted genes with annotated proteins of the nr-SPtrEMBL, NCBI-nr, and Rhodococcus sp. strain I24 protein databases and identification of protein motifs from a collection of protein domain databases as described in Materials and Methods.