| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 9.5e-25 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 2e-16 | - |
| pf:HHH | 74 | 91 | Helix-hairpin-helix motif
| 0.41 | - |
| pf:HHH_8 | 106 | 123 | Helix-hairpin-helix domain
| 0.57 | - |
| pf:HHH | 107 | 125 | Helix-hairpin-helix motif
| 0.00069 | - |
| pf:RecR_HhH | 109 | 126 | | 0.00096 | - |
| pf:Transposase_20 | 109 | 142 | Transposase IS116/IS110/IS902 family
| 0.04 | - |
| pf:IMS_HHH | 111 | 125 | IMS family HHH motif
| 0.018 | - |
| pf:RuvA_C | 157 | 200 | RuvA, C-terminal domain
| 3.9e-17 | - |