| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 67 | RuvA N terminal domain
| 5.8e-18 | - |
| pf:HHH_5 | 77 | 135 | Helix-hairpin-helix domain
| 8.2e-16 | - |
| pf:HHH_2 | 77 | 130 | Helix-hairpin-helix motif
| 0.069 | - |
| pf:HHH_3 | 112 | 138 | Helix-hairpin-helix motif
| 0.089 | - |
| pf:HHH_8 | 112 | 129 | Helix-hairpin-helix domain
| 0.35 | - |
| pf:RecR_HhH | 115 | 133 | | 0.02 | - |
| pf:HHH | 116 | 130 | Helix-hairpin-helix motif
| 0.096 | - |
| pf:RuvA_C | 159 | 194 | RuvA, C-terminal domain
| 7.5e-06 | - |