| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 1.2e-19 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 3.3e-16 | - |
| pf:HHH_8 | 97 | 123 | Helix-hairpin-helix domain
| 0.13 | - |
| pf:HHH_3 | 106 | 130 | Helix-hairpin-helix motif
| 0.19 | - |
| pf:RecR_HhH | 107 | 128 | | 0.017 | - |
| pf:Transposase_20 | 108 | 130 | Transposase IS116/IS110/IS902 family
| 0.36 | - |
| pf:IMS_HHH | 110 | 124 | IMS family HHH motif
| 0.45 | - |
| pf:RuvA_C | 153 | 196 | RuvA, C-terminal domain
| 1.9e-08 | - |