TABLE 4.
PhoP-dependent genes of Pve – regulators and unclassified.
| Gene name(s) | Locus_tag(s) | Fold changea | Product(s) | Best operator | Scoreb |
| Regulators | |||||
| glnK | OA04_12080 | 0.49 | Nitrogen regulatory protein P-II | – | – |
| - | OA04_01500 | 0.34 | LysR family transcriptional regulator | – | – |
| sftR | OA04_43750 | 2.34 | LysR family transcriptional regulator SftR | CGGTTTTATTATTTTTTCT | 9.4 |
| cbl | OA04_28870 | 2.71 | Transcriptional regulator CysB-like protein | CCATTTTGCTATGATTTAT | 10.8 |
| Miscellaneous | |||||
| scrK | OA04_04060 | 0.45 | Fructokinase | – | – |
| yjbJ | OA04_05950 | 2.0 | Osmotic stress-induced protein| RpoS regulon | – | – |
| ygdBppdD | OA04_10430-OA04_10440 | 3.58 | Putative pilins | – | – |
| ftp | OA04_17930 | 2.29 | Periplasmic FAD:protein FMN transferase | TTTTTTTCCTTTCATTTGT | 10.3 |
| slyB | OA04_18750 | 2.46 | Outer membrane lipoprotein | CTGTTTATACGCAATTTAA | 9.9 |
| ychH | OA04_21530 | 2.31 | Putative inner membrane stress-induced protein | AATATTTTTTTACGTTTAA | 6 |
| ynfK | OA04_22140 | 5.06 | Putative dithiobiotin synthetase | CATTTTAGCTGTGCTTGTT | 5.7 |
| – | OA04_23860 | 3.76 | hypothetical protein | GGGTATTAATCTTGTTTAA | 7.3 |
| – | OA04_24930 | 2.36 | Protein kinase-like domain protein | ATATTTGATCTGCGTTGAA | 5.4 |
| – | OA04_28020 | 2.03 | 2-dehydropantoate 2-reductase | – | – |
| – | OA04_29260 | 67.65 | Alpha/beta hydrolase superfamily protein | CTATTGAGCCGTGGTTTAA | 8.4 |
| – | OA04_29530 | 2.22 | Putative 2-methylcitrate dehydratase | CGTTTTATTATTTATTTAT | 13.1 |
| – | OA04_29750 | 2.91 | Putative acireductone dioxygenase | TTTTGTTATTTCGATTTAA | 8 |
| – | OA04_32550 | 3.02 | Exported choloylglycine hydrolase | TTGTTTATTTTAGGTTTAT | 13.8 |
| raiA | OA04_34460 | 2.18 | Stationary phase translation inhibitor and ribosome stability factor | CCGTTTTTTTTATGGTTAG | 7.3 |
| gudX | OA04_36650 | 4.2 | Glucarate dehydratase | ACTTTTTACTGAGGTTGGT | 7.5 |
| metF | OA04_43310 | 3.58 | 5,10-methylenetetrahydrofolate reductase | – | – |
aWild type vs. phoP mutant ratio. For operons, the value for the first gene is shown. Supplementary Table 3 contains values for all genes.
bChIPmunk score for the best operator.