| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 6.7e-08 | - |
| pf:HHH_5 | 72 | 128 | Helix-hairpin-helix domain
| 1.2e-14 | - |
| pf:HHH | 106 | 126 | Helix-hairpin-helix motif
| 0.043 | - |
| pf:RecR_HhH | 108 | 128 | | 0.00037 | - |
| pf:HHH_3 | 108 | 125 | Helix-hairpin-helix motif
| 0.48 | - |
| pf:IMS_HHH | 110 | 124 | IMS family HHH motif
| 0.11 | - |
| pf:RuvA_C | 145 | 191 | RuvA, C-terminal domain
| 2e-07 | - |