TABLE 1.
Designations, coordinates, and annotations of ORFs in Nine Mile strain deletions
| ORF no. | Designation | Coordinatesa | No. of codons | 9MIIb | 514 | Best homology | E valuec | Conserved domain | E valuec | pfam no. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | JB167-1 | 138-1151 | 337 | + | +/− | dTDP-glucose 4,6-dehydratase | 5.00E-30 | NAD-dependent epimerase/dehydratase, nucleotide-sugar substrates | 7.00E-40 | pfam01370 |
| 2 | JB167-2 | 1151-2185 | 344 | + | − | GDP-d-mannose dehydratase | 2.00E-46 | NAD-dependent epimerase/dehydratase, nucleotide-sugar substrates | 1.00E-67 | pfam01370 |
| 3 | JB167-3 | 2160-3740 | 526 | +/− | − | ADP-heptose synthase | 2.00E-15 | pfkB family carbohydrate kinase | 9.00E-18 | pfam00294 |
| Cytidylyltransferase | 1.00E-11 | pfam01467 | ||||||||
| 4 | JB167-4 | 3743-4887 | 314 | − | − | No significant homology | Oxidoreductase, NADP or NAD | 7.00E-07 | pfam01408 | |
| 5 | JB167-5 | 4672-5982 | 436 | − | − | UDP-glucose 6-dehydrogenase | 3.00E-32 | UDP-glucose/GDP-mannose dehydrogenase | 2.00E-48 | pfam00984 |
| 6 | JB167-6 | 5975-6880 | 301 | − | − | UDP-glucose 4-epimerase | 1.00E-14 | NAD-dependent epimerase/dehydratase, nucleotide-sugar substrates | 6.00E-25 | pfam01370 |
| 7 | JB153-1 | 6994-7536 | 180 | − | − | No significant homology | RNA adenine dimethylases | 1.00E-05 | smart00650 | |
| UbIE/COQ5 methyltransferase family | 6.00E-04 | pfam01209 | ||||||||
| 8 | JB153-2 | (7533-8720) | 395 | − | − | No significant homology | ||||
| 9 | JB153-3 | 9134-10552 | 472 | − | − | 3-Alpha-hydroxysteroid sulfotransferase | 1.3 | |||
| 10 | JB153-4 | 10997-14335 | 1112 | − | − | No significant homology | ||||
| 11 | JB153-5 | 14566-15273 | 235 | − | − | Acetoin:2,6-dichlorophenolindophenol oxidoreductase, beta subunit | 2.00E-16 | Transketolase, C-terminal domainDehydrogenase E1 component | 9.00E-23 2.00E-05 | pfam02780 pfam00676 |
| 12 | JB153-6 | 15290-16933 | 547 | − | − | No significant homology | ||||
| 13 | JB153-7 | 17313-18311 | 332 | − | − | GDP-l-fucose synthetase | 6.00E-82 | NAD-dependent epimerase/dehydratase, nucleotide-sugar substrates | 4.00E-19 | pfam01370 |
| 14 | JB153-8 | 18304-19350 | 348 | − | − | GDP-d-mannose dehydratase | 1.00E-134 | NAD-dependent epimerase/dehydratase, nucleotide-sugar substrates | 8.00E-34 | pfam01370 |
| 15 | JB153-9 | 19377-20216 | 279 | − | − | Glycosyl transferase | 2.00E-19 | Glycosyl transferase | 1.00E-13 | pfam00535 |
| 16 | JB153-10 | 20209-21447 | 412 | − | − | NDP-hexose 3-c-methyltransferase | 1.00E-103 | |||
| 17 | JB153-11 | (21468-22478) | 336 | − | − | Pyruvate dehydrogenase, beta subunit | 1.00E-56 | Transketolase, C-terminal domain | 1.00E-22 | pfam02780 |
| Transketolase, pyridine binding domain | 1.00E-22 | pfam02779 | ||||||||
| 18 | JB153-12 | (22526-23551) | 341 | − | − | Pyruvate dehydrogenase, alpha subunit | 1.00E-52 | Dehydrogenase E1 component | 2.00E-54 | pfam00676 |
| 19 | JB153-13 | (23702-24814) | 370 | − | − | Glycosyl transferase | 5.00E-09 | Glycosyl transferase | 1.00E-13 | pfam00535 |
| 20 | JB153-14 | (24876-26252) | 458 | − | − | No significant homology | ||||
| 21 | JB153-15 | (26245-27393) | 382 | − | − | Pleiotropic transcriptional control | 2.00E-72 | DegT-DnrJ-EryC1-StrS family, DNA binding proteins | 2.00E-85 | pfam01041 |
| 22 | JB153-16 | (27430-28590) | 386 | − | − | Pleiotropic transcriptional control | 3.00E-74 | DegT-DnrJ-EryC1-StrS family, DNA binding proteins | 3.00E-102 | pfam01041 |
| 23 | JB153-17 | (28613-29782) | 389 | +/− | − | No significant homology | ||||
| 24 | JB153-18 | 29985-31544 | 519 | + | − | Sterold sulfotransferase-like protein | 3.4 | Sulfotransferase | 4.00E-05 | pfam00685 |
| 25 | JB153-19 | (31580-33241) | 553 | + | +/− | ATP sulfurylase | 1.00E-140 | Sulfate adenylyltransferase | 1.00E-90 | pfam01747 |
| Adenylylsulfate kinase | 4.00E-55 | pfam01583 | ||||||||
| 26 | JB153-20 | (33319-34152) | 277 | + | + | Sulfur assimilation | 2.00E-45 | Inositol monophosphatase | 4.00E-41 | pfam00459 |
| 27 | JB153-21 | 34289-35038 | 249 | + | + | 3-Oxoacyl-(acyl-carrier protein) reductase | 1.00E-10 | Short-chain dehydrogenase | 8.00E-12 | pfam00106 |
| 28 | JB153-22 | 35048-35911 | 287 | + | + | ABC transporter permease, O-antigen export | 2.00E-35 | ABC-2-type transporter | 1.00E-21 | pfam01061 |
| 29 | JB153-23 | 35921-36697 | 258 | + | + | ABC transporter permease, O-antigen export | 2.00E-63 | ABC transporter | 2.00E-26 | pfam00005 |
| 30 | JB153-24 | (37409-37738) | 109 | + | + | No significant homology | ||||
| 31 | JB153-25 | (37755-38485) | 236 | + | + | No significant homology |
a
Parentheses indicate the complementary strand.
b
+, presence of ORFs; +/−, partial ORFs; −, absence of ORFs.
c
BLASTP similarity score (see explanation at www.ncbi.nlm.nih.gov).