| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 1.7e-24 | - |
| pf:HHH_5 | 72 | 128 | Helix-hairpin-helix domain
| 1e-12 | - |
| pf:HHH | 73 | 91 | Helix-hairpin-helix motif
| 0.058 | - |
| pf:Transposase_20 | 109 | 130 | Transposase IS116/IS110/IS902 family
| 0.11 | - |
| pf:HHH_3 | 109 | 125 | Helix-hairpin-helix motif
| 1 | - |
| pf:HHH | 110 | 124 | Helix-hairpin-helix motif
| 0.0044 | - |
| pf:RecR_HhH | 110 | 126 | | 0.013 | - |
| pf:5_3_exonuc | 112 | 165 | 5'-3' exonuclease, C-terminal SAM fold
| 0.083 | - |
| pf:IMS_HHH | 113 | 124 | IMS family HHH motif
| 0.21 | - |
| pf:RuvA_C | 170 | 209 | RuvA, C-terminal domain
| 9e-11 | - |