| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 63 | RuvA N terminal domain
| 2.8e-13 | - |
| pf:HHH_5 | 73 | 130 | Helix-hairpin-helix domain
| 2.1e-14 | - |
| pf:HHH | 107 | 126 | Helix-hairpin-helix motif
| 0.0015 | - |
| pf:RecR_HhH | 108 | 129 | | 0.057 | - |
| pf:HHH_8 | 108 | 126 | Helix-hairpin-helix domain
| 0.96 | - |
| pf:5_3_exonuc | 110 | 129 | 5'-3' exonuclease, C-terminal SAM fold
| 0.19 | - |
| pf:IMS_HHH | 111 | 125 | IMS family HHH motif
| 0.034 | - |
| pf:RuvA_C | 157 | 198 | RuvA, C-terminal domain
| 0.0023 | - |