TABLE 2.
Conserved RpoHII target sequences upstream of protein coding genesa
| Target sequence | ATG distance (bp) | Locus tag | Annotated protein(s) | 5′ end |
|---|---|---|---|---|
| Energy metabolism | ||||
| TGT-N17-CTAGAT | 33 | RSP2785-2784 | CycF, cytochrome 554 | + |
| TTG-N17-CTAGAT | 35 | RSP3212-3210 | QxtA, quinol oxidase subunit I | |
| TCG-N19-CTAGAT | 82 | RSP3831 | Cox15, putative cytochrome oxidase assembly factor | |
| Transport | ||||
| TTG-N19-CTAGAT | 31 | RSP0367 | Preprotein translocase SecG subunit | |
| TGG-N19-CTAGCT | 40 | RSP0759 | Putative capsule polysaccharide exporter | + |
| TTG-N19-CTAGGT | 34 | RSP1053 | Signal recognition particle Ffh | |
| TGC-N18-CTAGCT | −28 | RSP1497 | Putative outer membrane lipoprotein carrier protein | + |
| TTG-N19-CTAGCT | 8 | RSP1803-1805 | CcmC, ABC heme transporter | + |
| TTC-N19-CTAGGT | −2 | RSP1843 | FtsY, signal recognition particle-docking protein | |
| TTG-N18-CTAGCT | 129 | RSP1882-1886 | ABC polyamine transporter, ATPase subunit | |
| Regulatory proteins | ||||
| TGG-N19-CTAGGT | 29 | RSP0269 | TspO, tryptophane-rich sensory protein | |
| TTG-N19-CTAGGT | 42 | RSP0762-0761 | Transcriptional regulator XRE family | |
| TGG-N19-CTAGAT | 83 | RSP2165 | PutR, transcriptional regulator, AsnC family | |
| TTT-N19-CTAGCT | 43 | RSP3217 | Cache sensor signal transduction histidine kinase | |
| TCG-N18-CTAGCT | 20 | RSP3430-3431 | Transcriptional regulator, winged helix family | |
| TTG-N19-CTAGCT | 8 | RSP3865 | Predicted transcriptional regulator | + |
| TTG-N19-CTAGGT | 133 | RSP4257-4258 | Anti-sigma factor antagonist STAS | + |
| Protein turnover and amino acid metabolism | ||||
| GTG-N19-CTAGCT | 49 | RSP0398 | GdhA, glutamate/leucine dehydrogenase | |
| TTT-N19-CTAGAT | 34 | RSP2627 | HisI, Phosphoribosyl-AMP cyclohydrolase | |
| TTT-N18-CTAGGT | 27 | RSP4043-4042 | Peptidylprolyl isomerase | + |
| TTG-N19-CTAGAT | 364 | RSP4294 | 16S rRNA | |
| TTG-N19-CTAGAT | 65 | RSP4330 | tRNA-Ala-GGC | |
| TTG-N19-CTAGAT | 364 | RSP4347 | 16S rRNA | + |
| TTG-N18-CTAGCT | 30 | RSP6044 | Serine/alanine racemase | |
| Stress response | ||||
| TTT-N19-CTAGCT | 29 | RSP0392 | GloA, probable lactothioglutathione synthetase | |
| TCG-N19-CTAGAT | 42 | RSP0663 | Formate-tetrahydrofolate ligase | |
| GTC-N19-CTAGAT | −2 | RSP0817-0816 | Aminodeoxychorismate synthase | |
| TTG-N17-CTAGCT | 18 | RSP1591 | Predicted glutathione S-transferase | + |
| TGG-N19-CTAGCT | 21 | RSP1869 | 2-octaprenyl-6-methoxyphenyl hydroxylase | + |
| TTT-N19-CTAGAT | 8 | RSP2092 | Putative uvrD/DNA helicase II | + |
| GGT-N18-CTAGCT | 202 | RSP2123 | Radical SAM domain protein and/or SplB, DNA repair photolyase domain | |
| TTG-N18-CTAGAT | 62 | RSP2617 | Peptide methionine sulfoxide reductase | + |
| TGT-N18-CTAGGT | 394 | RSP2647-2648 | Predicted SAM-dependent methyltransferase | + |
| TTG-N18-CTAGGT | 27 | RSP3164-3162 | Ferredoxin-like protein | + |
| TTG-N17-CTAGAT | 35 | RSP3212-3210 | QxtA, Quinol oxidase subunit I | |
| Hypothetical | ||||
| TTC-N19-CTAGCT | 29 | RSP0238 | Hypothetical protein | |
| TTC-N17-CTAGCT | 28 | RSP0855 | Hypothetical protein | + |
| TTG-N18-CTAGCT | 110 | RSP1366 | Hypothetical protein | |
| TGG-N19-CTAGAT | 30 | RSP1421 | Hypothetical protein | + |
| GTG-N19-CTAGCT | 27 | RSP3075-3076 | Hypothetical protein | + |
| TTG-N19-CTAGCT | 29 | RSP6001 | Hypothetical protein | + |
| TTC-N19-CTAGCT | 237 | RSP6037 | Hypothetical protein | |
| TTG-N19-CTAGCT | 31 | RSP6232 | Hypothetical protein | |
| Other functions | ||||
| GGT-N18-CTAGAT | 121 | RSP1502 | GAF domain protein | |
| TTT-N19-CTAGGT | 16 | RSP1896 | Guanine deaminase | |
| TTT-N18-CTAGAT | 36 | RSP2268 | Metallo-beta-lactamase family | |
| TCT-N19-CTAGAT | 70 | RSP2468-2470 | Putative portal protein | |
| TCG-N19-CTAGAT | 30 | RSP3261-3262 | BioA, aminotransferase |
a
The target sequences listed were searched using the RSA tools and the consensus sequence KBB-N17-19-CTAGVT. The distance to the translational start site is listed, and it is indicated if downstream genes might be cotranscribed and, hence, may form an operon. Negative distances to the translational start sites indicate that the start codon might have been annotated incorrectly. Positives (+) in the “5′ end” column indicate that primary transcripts were found using 454 pyrosequencing (4) and that the respective sigma factor target sequence is located directly upstream of the 5′ end.