TABLE 3.
Potential CtrA binding sites in the R. capsulatus genome
| Gene | Description | Location of predicted sitea |
Transcript fold changeb (log phase, stationary phase) | Quantitative proteome datac (log phase, stationary phase) | |
|---|---|---|---|---|---|
| TTAA-N7-TTAAC | TTAACCAT | ||||
| rcc00042 | PAS/PAC sensor domain protein | −47 | 12.6, 14.9 | ND | |
| rcc00222 | DNA repair protein RadC | −30 | 7.6, 21.8 | ND | |
| rcc00280 | Hemolysin-type calcium-binding repeat family protein | −100 | 1.2, −1.1 | ND | |
| rcc00393 | UvrABC system protein C | −372 | −1.3, −1.7 | ND | |
| rcc00434 | Hypothetical protein | −57 | −54 | 1.4, 3.9 | ND |
| rcc00459 | Glutathione S-transferase domain proteind | −49 | −1.4, −1.3 | 0.97, −0.43 | |
| rcc00463 | Protein of unknown function UPF0102 | −315 | 4.4, 13.7 | ND | |
| rcc00498 | Transglycosylase, Slt family | −249 | −1.25, −1.1 | ND | |
| rcc00516 | Tyrosine phenol-lyase | −570 | −1.7, −1.4 | −1.43, −1.47 | |
| rcc00645 | Diguanylate cyclase/phosphodiesterase with PAS/PAC sensor | −68 | 7.7, 25.9 | −1.14, 0.74 | |
| rcc00844 | Conserved hypothetical protein | −82 | −90 | 21.3, 28.7 | ND |
| rcc00845 | Hypothetical protein | −273 | −118 | 5.2, 17.8 | |
| rcc00872 | Alcohol dehydrogenase, zinc-binding domain protein | −193 | −1.3, −1.1 | −0.05, −0.50 | |
| rcc01237 | Glycosyl transferase, family 2 | −166 | 2.4, 5.1 | ND | |
| rcc01324 | Type I restriction-modification system, R subunit | −475 | −1.4. −1.1 | ND | |
| rcc01384 | UvrABC system protein B | −65 | −1.4, 0 | −2.42, 1.25 | |
| rcc01462 | Ribonucleoside-diphosphate reductase NrdJ | −491 | −1.3, 1.6 | −2.06, 1.23 | |
| rcc01749 | Histidine kinase CckA | −96 | 1.4, −1.1 | 1.33, 1.12 | |
| rcc01849 | Protein of unknown function DUF1457 | −40 | 3.3, 1.7 | ND | |
| rcc01932 | Glycosyl transferase, family 4 | −183 | −1.7, −1.4 | ND | |
| rcc01940 | Hemolysin-type calcium-binding repeat family protein | −129 | −5.0, −2.5 | ND | |
| rcc03000 | Conserved hypothetical protein | −241 | 2.0. 1.7 | ND | |
| rcc03209 | Protein containing DUF484 | −46 | 2.6, 2.1 | 1.98, 3.09 | |
| rcc03214 | Protein of unknown function DUF1127 | −131 | −1.3, −2.5 | ND | |
a
Position of the last (3′) base of the predicted binding site relative to the first base of the predicted start codon for the gene.
b
Positive values indicate higher transcript levels in the wild type, and negative values indicate higher levels in the ctrA mutant.
c
Absolute difference in Z-score data for each protein, with positive values representing larger amounts in the wild type and negative values representing larger amounts in the ctrA mutant. ND, not detected.
d
Gene rcc00460 is predicted to be cotranscribed with rcc00459 and is affected by loss of CtrA.