| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 6.7e-24 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 1.3e-12 | - |
| pf:HHH | 106 | 124 | Helix-hairpin-helix motif
| 0.0012 | - |
| pf:RecR_HhH | 107 | 126 | | 0.0003 | - |
| pf:HHH_8 | 108 | 125 | Helix-hairpin-helix domain
| 0.59 | - |
| pf:IMS_HHH | 111 | 124 | IMS family HHH motif
| 0.13 | - |
| pf:RuvA_C | 159 | 203 | RuvA, C-terminal domain
| 1.5e-17 | - |
| pf:RHH_1 | 186 | 201 | Ribbon-helix-helix protein, copG family
| 0.49 | - |