| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 61 | RuvA N terminal domain
| 5.5e-20 | - |
| pf:HHH_5 | 71 | 129 | Helix-hairpin-helix domain
| 3.5e-17 | - |
| pf:HHH_8 | 100 | 124 | Helix-hairpin-helix domain
| 0.74 | - |
| pf:HHH_3 | 106 | 145 | Helix-hairpin-helix motif
| 0.48 | - |
| pf:Transposase_20 | 107 | 140 | Transposase IS116/IS110/IS902 family
| 0.8 | - |
| pf:RecR_HhH | 109 | 127 | | 5.7e-05 | - |
| pf:HHH | 109 | 123 | Helix-hairpin-helix motif
| 0.032 | - |
| pf:IMS_HHH | 109 | 123 | IMS family HHH motif
| 0.077 | - |
| pf:DUF655 | 109 | 144 | Protein of unknown function (DUF655)
| 0.22 | - |
| pf:PG_binding_2 | 150 | 181 | Putative peptidoglycan binding domain
| 0.4 | - |
| pf:RuvA_C | 155 | 197 | RuvA, C-terminal domain
| 1e-11 | - |