| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 59 | RuvA N terminal domain
| 2.6e-16 | - |
| pf:HHH_2 | 70 | 101 | Helix-hairpin-helix motif
| 0.11 | - |
| pf:HHH_5 | 71 | 129 | Helix-hairpin-helix domain
| 3.3e-16 | - |
| pf:HHH | 101 | 124 | Helix-hairpin-helix motif
| 6.7e-06 | - |
| pf:HHH_2 | 102 | 124 | Helix-hairpin-helix motif
| 0.16 | - |
| pf:HHH_3 | 103 | 124 | Helix-hairpin-helix motif
| 0.0019 | - |
| pf:RecR_HhH | 106 | 127 | | 0.0022 | - |
| pf:RuvA_C | 152 | 196 | RuvA, C-terminal domain
| 7.1e-08 | - |