| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 3.6e-22 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 5.5e-12 | - |
| pf:HHH | 109 | 125 | Helix-hairpin-helix motif
| 0.00065 | - |
| pf:RecR_HhH | 109 | 124 | | 0.00037 | - |
| pf:IMS_HHH | 110 | 124 | IMS family HHH motif
| 0.044 | - |
| pf:5_3_exonuc | 113 | 138 | 5'-3' exonuclease, C-terminal SAM fold
| 0.97 | - |
| pf:RuvA_C | 161 | 204 | RuvA, C-terminal domain
| 6.7e-15 | - |