TABLE 3.
AphA ChIP-seq data
| Gene IDa | Annotation | AphA box-like sequence | Avg fold enrichment | Microarray (V. harveyi)b | P value |
|---|---|---|---|---|---|
| VEPGS-03659 | Excinuclease ATPase subunit | TCATTCAAGATGATTCATT | 8.8 | N | <0.001 |
| VEPGS-03814 | NADPH:quinone reductase and related Zn-dependent oxidoreductases | TCGGAGAACCTTATGTTTA | 8.45 | N | <0.001 |
| VEPGS-03822 | Alanine-alpha-ketoisovalerate (or valine-pyruvate) aminotransferase | AAAGGGAAGCTTATGCTTC | 8 | N | <0.001 |
| VEPGS-03826 | Type IIA topoisomerase (DNA gyrase/topoisomerase II, topoisomerase IV), B subunit | TCTTCACGCTCAGAGTTAA | 8.1 | N | <0.001 |
| VEPGS-03844 | FoF1-type ATP synthase, subunit b | TGATTAACCTAGTTGACCA | 7.75 | N | <0.001 |
| VEPGS-03847 | FoF1-type ATP synthase, gamma subunit | TATTCAACAAGTTTGTAAA | 8.3 | N | <0.001 |
| VEPGS-03856 | Dihydroxyacid dehydratase/phosphogluconate dehydratase | TGATTCGTCATCTTGCTCG | 8.15 | N | <0.001 |
| VEPGS-03880 | Zn finger domain associated with topoisomerase type I | ATGTGACCATCATTGCTGT | 8.1 | N | <0.001 |
| VEPGS-03964 | Aspartate ammonia-lyase | TGGTCTCCTTCTTTTTTAG | 13.6 | N | <0.001 |
| VEPGS-04037 | Exoribonuclease R | TCGTTTGACGACATGGATT | 8.65 | Y | <0.001 |
| VEPGS-04051 | Iron-sulfur cluster-binding protein | CTTTCAATCTCTTGCATAT | 8.85 | N | <0.001 |
| VEPGS-04106 | Predicted transcriptional regulators (AphA) | TATTCCACTTCATGCTTAT | 14.62 | Y | <0.001 |
| VEPGS-04284 | Small RNA, CsrB family | CATTGAATTTAATACTCAT | 8.75 | N | <0.001 |
| VEPGS-04291 | Putative multidrug resistance protein | TCATTCCGGCTTTAGCTCC | 7.7 | N | <0.001 |
| VEPGS-04316 | Regulator of sigma D (anti-σD) | TTATCGTTAAGTAAATGTG | 7.9 | N | <0.001 |
| VEPGS-04317 | DNA-directed RNA polymerase beta′ subunit | TATAGATCGTTAAGATCAG | 7.55 | Y | <0.001 |
| VEPGS-04318 | DNA-directed RNA polymerase beta subunit | ACAGGCGAGATCATTGTTA | 7.55 | N | <0.001 |
| VEPGS-04329 | Vitamin B12 receptor | TATTCGCACTCTTGTCTTT | 7.95 | N | <0.001 |
| VEPGS-04332 | Transcriptional regulator (FabR) | TATGTCTATAAATTGCATC | 12.6 | N | <0.001 |
| VEPGS-04337 | Glycerol-3-phosphate acyltransferase | TAATTGCCCAAATGCTCAT | 8.1 | N | <0.001 |
| VEPGS-04385 | Adenylate cyclase | TATGGTTTTGTATCCAGAT | 7.7 | N | <0.001 |
| VEPGS-04400 | Predicted transcriptional regulators | TTTTACCCTCTAATCTTCT | 8.35 | N | <0.001 |
| VEPGS-04448 | d-Erythrose 4-phosphate dehydrogenase | TATGCAACTTAGTGTCCAC | 11.45 | N | <0.001 |
| VEPGS-04453 | UDP-N-acetylmuramate dehydrogenase | ACCGATCCCCTGATTCACA | 9.75 | N | <0.001 |
| VEPGS-04457 | Putative translation factor | AACGCGGCATCAAAGTTAT | 7.9 | N | <0.001 |
| VEPGS-04459 | Shikimate 5-dehydrogenase | TGCACCTGTTGATGGTTTT | 8.85 | N | <0.001 |
| VEPGS-01281 | Transcriptional regulators of sugar metabolism | TATAAAGCGTTTTGCCTTT | 8.8 | N | <0.001 |
| VEPGS-01343 | 5′-Nucleotidase/2′,3′-cyclic phosphodiesterase and related esterases | TCTGCGCCTTCTTTCTTCA | 9.65 | N | <0.001 |
| VEPGS-01349 | Hypothetical protein | AAAGTGGCCTGATGGACAT | 8.1 | N | <0.001 |
| VEPGS-01356 | 50S ribosomal protein L15p | TAGTTGCCATGGTGTTCTT | 7.6 | N | <0.001 |
| VEPGS-01395 | UDP-glucose 6-dehydrogenase | TGATAAGCTTTCTGCTTAT | 8.45 | N | <0.001 |
| VEPGS-01401 | Hypothetical protein | CGTATCACCTGTTACTGAT | 7.95 | N | <0.001 |
| VEPGS-01451 | ABC-type oligopeptide transport system, periplasmic component | AAAGCCAAATCGTGCTTTT | 8.4 | N | <0.001 |
| VEPGS-01456 | Biopolymer transport proteins | TAGTTCAGTCAGCTGCTTA | 7.85 | N | <0.001 |
| VEPGS-01492 | Disulfide bond chaperones of the HSP33family | TGCTTTGCCTTCATGCTCA | 7.75 | N | <0.001 |
| VEPGS-01503 | Signal transduction histidine kinase, nitrogen specific | TGAACAATCACTTTCTCAA | 8.75 | N | <0.001 |
| VEPGS-01511 | Cytochrome c553 | TATAAAGCGTTTTGCCTTT | 7.9 | N | <0.001 |
| VEPGS-01513 | 5′-3′ exonuclease (including N-terminal domain of polymerase I) | TAAGCTGATTTTTGCCTTT | 7.65 | Y | <0.001 |
| VEPGS-01530 | Hypothetical protein | ATATGCCACTCCTTATTTA | 7.65 | N | <0.001 |
| VEPGS-01564 | Hypothetical protein | ACTGGCAACCTGATTGTTC | 8.6 | N | <0.001 |
| VEPGS-01566 | Peptide ABC transporter, permease protein | TCTATCGACATCATGGATT | 8 | N | <0.001 |
| VEPGS-01569 | Peptide ABC transporter, ATP-binding protein | CATTAACCATATTATTCAT | 8.95 | N | <0.001 |
| VEPGS-01574 | Transcriptional regulator | TTGGTATCTTGATACTCGT | 8.7 | N | <0.001 |
| VEPGS-01579 | Transcriptional regulator | TCTTTGGCTTTATTTTCAT | 8.75 | N | <0.001 |
| VEPGS-01835 | OpaR (LuxR) | TAGTGTATCACCACGTTCA | 4.11 | N | <0.001 |
| VEPGS-02615 | RNA polymerase sigma factor | TATTCGCACTCTTGTCTTT | 7.75 | N | <0.001 |
| VEPGS-02635 | Glutamine synthetase adenylyltransferase | CCTTCACGATCTTTCACAT | 8.2 | N | <0.001 |
| VEPGS-02651 | Cytochrome b subunit of the bc complex | TACTCTACATCACGCATAA | 7.95 | N | <0.001 |
| VEPGS-02767 | Hypothetical protein | TTATTAAACTATATTCATA | 15.5 | N | <0.001 |