| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 63 | RuvA N terminal domain
| 9.6e-15 | - |
| pf:HHH_5 | 73 | 130 | Helix-hairpin-helix domain
| 4e-12 | - |
| pf:HHH_8 | 104 | 126 | Helix-hairpin-helix domain
| 0.42 | - |
| pf:HHH | 108 | 126 | Helix-hairpin-helix motif
| 0.0023 | - |
| pf:5_3_exonuc | 109 | 128 | 5'-3' exonuclease, C-terminal SAM fold
| 0.17 | - |
| pf:RecR_HhH | 109 | 129 | | 0.094 | - |
| pf:IMS_HHH | 110 | 125 | IMS family HHH motif
| 0.022 | - |
| pf:MUC20_C | 120 | 139 | | 0.13 | - |
| pf:RuvA_C | 161 | 198 | RuvA, C-terminal domain
| 0.0052 | - |