| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 61 | RuvA N terminal domain
| 1.6e-17 | - |
| pf:FliO | 66 | 117 | Flagellar biosynthesis protein, FliO
| 0.26 | - |
| pf:HHH_5 | 71 | 127 | Helix-hairpin-helix domain
| 2e-11 | - |
| pf:HHH_3 | 74 | 123 | Helix-hairpin-helix motif
| 0.0063 | - |
| pf:HHH | 74 | 90 | Helix-hairpin-helix motif
| 0.11 | - |
| pf:RecR_HhH | 106 | 127 | | 0.057 | - |
| pf:RuvA_C | 150 | 195 | RuvA, C-terminal domain
| 4.7e-08 | - |