| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 61 | RuvA N terminal domain
| 7.2e-18 | - |
| pf:FliO | 66 | 114 | Flagellar biosynthesis protein, FliO
| 0.22 | - |
| pf:HHH_5 | 71 | 127 | Helix-hairpin-helix domain
| 8.4e-12 | - |
| pf:HHH_3 | 74 | 123 | Helix-hairpin-helix motif
| 0.018 | - |
| pf:HHH | 74 | 90 | Helix-hairpin-helix motif
| 0.079 | - |
| pf:RecR_HhH | 106 | 127 | | 0.033 | - |
| pf:RuvA_C | 151 | 195 | RuvA, C-terminal domain
| 2.8e-08 | - |