| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 61 | RuvA N terminal domain
| 1.2e-19 | - |
| pf:HHH_5 | 71 | 129 | Helix-hairpin-helix domain
| 6.1e-14 | - |
| pf:HHH_2 | 78 | 124 | Helix-hairpin-helix motif
| 0.35 | - |
| pf:SepF | 93 | 140 | | 0.58 | - |
| pf:SLS | 98 | 146 | Mitochondrial inner-membrane-bound regulator
| 0.05 | - |
| pf:HHH_3 | 107 | 124 | Helix-hairpin-helix motif
| 0.22 | - |
| pf:DUF6497 | 107 | 145 | | 0.25 | - |
| pf:HHH | 109 | 124 | Helix-hairpin-helix motif
| 0.013 | - |
| pf:RecR_HhH | 109 | 125 | | 0.04 | - |
| pf:RuvA_C | 150 | 193 | RuvA, C-terminal domain
| 1.2e-05 | - |