| Motif id | From | To | Definition | E value | Score |
| pf:Sigma54_AID | 6 | 50 | Sigma-54 factor, Activator interacting domain (AID)
| 2.3e-17 | - |
| pf:Sigma54_CBD | 134 | 321 | Sigma-54 factor, core binding domain
| 1e-52 | - |
| pf:Sigma54_DBD | 336 | 496 | Sigma-54, DNA binding domain
| 7.6e-67 | - |
| pf:HTH_IclR | 380 | 404 | IclR helix-turn-helix domain
| 0.12 | - |
| pf:HTH_3 | 385 | 412 | Helix-turn-helix
| 0.55 | - |