Table 2. Known or predicted direct targets of AphA.
| Gene name | Gene ID | AphA box-like sequence | Position& | Score | Reference | Regulation by AphA |
| V. parahaemolyticus RIMD 2210633 | ||||||
| aphA | VP2762 | GTATTCCACTTCATGCTTAT | D-238…-219 | 16.37 | This study | Negative |
| opaR | VP2516 | ATATGCACCATTACACTCAT | D-98…-79 | 18.32 | This study | Negative |
| qrr4 | VPA0199-0200 intergenic | ATATGCCACTTGTTACATTG | R-146…-127 | 10.96 | This study | Negative |
| Vibrio sp. Ex25 | ||||||
| aphA | VEA_002309 | CTATTCCACTTCATGCTTAT | D-240…-221 | 15.71 | Predicted | Negative |
| luxR | VEA_002553 | ATATGCACCATTACACTCAT | D-161…-142 | 18.32 | Predicted | Negative |
| qrr4 | VEA000800-000799 intergenic | ATATGCCACTTCATGCACTG | R-146…-127 | 14.05 | Predicted | Negative |
| Vibrio sp. EJY3 | ||||||
| aphA | VEJY3_14120 | GTATTCCACTTCATGCTTAT | D-242…-223 | 16.37 | Predicted | Negative |
| luxR | VEJY3_12990 | ATATGCACCATTACACTCAT | D-98…-79 | 18.32 | Predicted | Negative |
| qrr4 | VEJY316416-16421 intergenic | ATATGCTACCAACCGCATTG | R-145…-126 | 7.64 | Predicted | Negative |
| V. harveyi ATCC BAA-1116 | ||||||
| aphA | VIBHAR_00046 | CTATTCCACTTCATGCTTAT | D-240…-221 | 15.71 | [7] | Negative |
| luxR | VIBHAR_03459 | ATATGCACCATTACACTCAT | D-101…-82 | 18.32 | [7] | Negative |
| qrr4 | VIBHAR_06697 | ATATGCCACCATGCGCATTG | R-146…-127 | 11.01 | [7] | Negative |
| V. vulnificus YJ016 | ||||||
| aphA | VV3005 | CTATTCCACTTTATGCTTAT | D-238…-219 | 16.45 | Predicted | Negative |
| smcR | VV2770 | ATATGCACCATTACACTCAT | D-110…-91 | 18.32 | Predicted | Negative |
| qrr4 | VVA0457-0458 intergenic | ATACACACAAATTTGCATAT | R-97…-78 | 8.65 | Predicted | Negative |
| V. splendidus LGP32 | ||||||
| aphA | VS_2891 | GTATTCTACTTTATGCTTAT | D-237…-218 | 15.94 | Predicted | Negative |
| luxR | VS_2539 | ATATGCACCATTACACTCAT | D-79…-60 | 18.32 | Predicted | Negative |
| V. anguillarum 775 | ||||||
| aphA | VAA_02615 | GTATTCTACTTTATGCTTAT | D-253…-234 | 15.94 | Predicted | Negative |
| vanT | VAA_00743 | ATATGCAGCAGTACACTCAT | D-99…-80 | 13.81 | Predicted | Negative |
| V. cholerae N16961 | ||||||
| aphA | VC2647 | GTATTCCACTTTATGCTTAT | D-245…-226 | 17.11 | [30] | Negative |
| hapR | VC0583 | ATATGCACCATTACACTCAT | D-101…-82 | 18.32 | Predicted | Negative |
| pva | VCA0877 | ATATGCAACAAATTACACAT | D-178…-159 | 12.75 | [44] | Negative |
| alsR | VC1588 | ATATACACACAGATTCATAT | R-93…-74 | 8.6 | [29] | Negative |
| alsD | VC1589 | ATATACACACAGATTCATAT | D-32…-13 | 8.6 | [29] | Negative |
| vpsT | VCA0952 | ATACGCAAAAAGACTCTTAT | R-242…-223 | 10.7 | [28] | Positive |
| tcpP | VC0826 | TTATGCAATTAAGTTCTCAT | D-110…-91 | 6.71 | [27] | |
| V. furnissii NCTC 11218 | ||||||
| aphA | vfu_A00617 | GTATTCTACTTTATGCTTAT | D-246…-227 | 15.94 | Predicted | Negative |
| luxR | vfu_A00883 | ATGTACGCAATTACACTCAT | D-104…-85 | 9.66 | Predicted | Negative |
&, ‘D’ indicates the direct sequence, and the minus numbers denote nucleotide positions upstream of genes.