| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 1.1e-22 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 4.4e-14 | - |
| pf:HHH | 74 | 91 | Helix-hairpin-helix motif
| 0.052 | - |
| pf:HHH | 106 | 124 | Helix-hairpin-helix motif
| 0.00028 | - |
| pf:RecR_HhH | 108 | 125 | | 0.00017 | - |
| pf:HHH_8 | 109 | 123 | Helix-hairpin-helix domain
| 0.93 | - |
| pf:Transposase_20 | 110 | 152 | Transposase IS116/IS110/IS902 family
| 0.17 | - |
| pf:IMS_HHH | 110 | 124 | IMS family HHH motif
| 0.047 | - |
| pf:RuvA_C | 163 | 205 | RuvA, C-terminal domain
| 1.8e-15 | - |