| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 26 | 86 | RuvA N terminal domain
| 1.4e-18 | - |
| pf:HHH_2 | 85 | 123 | Helix-hairpin-helix motif
| 0.11 | - |
| pf:HHH_5 | 96 | 153 | Helix-hairpin-helix domain
| 8.2e-16 | - |
| pf:HHH | 98 | 115 | Helix-hairpin-helix motif
| 0.021 | - |
| pf:RecR_HhH | 133 | 152 | | 0.57 | - |
| pf:RuvA_C | 178 | 228 | RuvA, C-terminal domain
| 2.3e-09 | - |