| Motif id | From | To | Definition | E value | Score |
| pf:FleQ | 6 | 114 | Flagellar regulatory protein FleQ
| 4.1e-31 | - |
| pf:Sigma54_activat | 137 | 304 | Sigma-54 interaction domain
| 1e-74 | - |
| pf:AAA_16 | 137 | 200 | AAA ATPase domain
| 9.4e-06 | - |
| pf:Sigma54_activ_2 | 138 | 308 | Sigma-54 interaction domain
| 1.7e-17 | - |
| pf:AAA_7 | 146 | 185 | P-loop containing dynein motor region D3
| 0.026 | - |
| pf:bpMoxR | 149 | 277 | | 0.02 | - |
| pf:nSTAND3 | 154 | 182 | | 0.51 | - |
| pf:MCM | 157 | 276 | MCM2/3/5 family
| 0.039 | - |
| pf:AAA_5 | 160 | 279 | AAA domain (dynein-related subfamily)
| 1.5e-06 | - |
| pf:AAA | 161 | 286 | ATPase family associated with various cellular activities (AAA)
| 0.054 | - |
| pf:AAA_lid_14 | 309 | 385 | | 5.9e-23 | - |
| pf:HTH_50 | 439 | 487 | | 0.00031 | - |
| pf:HTH_8 | 444 | 484 | Bacterial regulatory protein, Fis family
| 3.1e-13 | - |