| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 5.8e-22 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 3.3e-16 | - |
| pf:HHH | 75 | 91 | Helix-hairpin-helix motif
| 0.79 | - |
| pf:HHH | 106 | 124 | Helix-hairpin-helix motif
| 0.00054 | - |
| pf:HHH_8 | 106 | 123 | Helix-hairpin-helix domain
| 0.37 | - |
| pf:RecR_HhH | 109 | 125 | | 0.00021 | - |
| pf:Transposase_20 | 110 | 132 | Transposase IS116/IS110/IS902 family
| 0.56 | - |
| pf:IMS_HHH | 111 | 124 | IMS family HHH motif
| 0.029 | - |
| pf:RuvA_C | 158 | 201 | RuvA, C-terminal domain
| 1.1e-15 | - |
| pf:DUF3173 | 166 | 182 | Domain of unknown function (DUF3173)
| 1 | - |