| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 2.1e-26 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 3e-15 | - |
| pf:HHH | 75 | 91 | Helix-hairpin-helix motif
| 0.14 | - |
| pf:HHH | 106 | 124 | Helix-hairpin-helix motif
| 0.0045 | - |
| pf:RecR_HhH | 108 | 125 | | 0.00016 | - |
| pf:HHH_3 | 108 | 130 | Helix-hairpin-helix motif
| 0.79 | - |
| pf:IMS_HHH | 111 | 124 | IMS family HHH motif
| 0.23 | - |
| pf:RuvA_C | 157 | 198 | RuvA, C-terminal domain
| 3.2e-12 | - |