| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 1.7e-26 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 1.3e-15 | - |
| pf:HHH | 74 | 91 | Helix-hairpin-helix motif
| 0.59 | - |
| pf:Transposase_20 | 109 | 144 | Transposase IS116/IS110/IS902 family
| 0.013 | - |
| pf:RecR_HhH | 110 | 128 | | 0.0052 | - |
| pf:HHH | 110 | 125 | Helix-hairpin-helix motif
| 0.016 | - |
| pf:IMS_HHH | 112 | 125 | IMS family HHH motif
| 0.14 | - |
| pf:RuvA_C | 157 | 200 | RuvA, C-terminal domain
| 2.7e-16 | - |
| pf:UBA_7 | 160 | 181 | | 0.37 | - |