| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 5.5e-25 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 1.9e-16 | - |
| pf:HHH | 74 | 91 | Helix-hairpin-helix motif
| 0.48 | - |
| pf:HHH_8 | 107 | 124 | Helix-hairpin-helix domain
| 0.63 | - |
| pf:RecR_HhH | 108 | 127 | | 0.00092 | - |
| pf:HHH | 109 | 125 | Helix-hairpin-helix motif
| 0.00051 | - |
| pf:Transposase_20 | 109 | 147 | Transposase IS116/IS110/IS902 family
| 0.0033 | - |
| pf:IMS_HHH | 110 | 125 | IMS family HHH motif
| 0.0084 | - |
| pf:5_3_exonuc | 110 | 129 | 5'-3' exonuclease, C-terminal SAM fold
| 0.58 | - |
| pf:RuvA_C | 158 | 201 | RuvA, C-terminal domain
| 1.3e-16 | - |