| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 60 | RuvA N terminal domain
| 6.1e-12 | - |
| pf:DUF4391 | 13 | 178 | Domain of unknown function (DUF4391)
| 0.21 | - |
| pf:Nse4_C | 27 | 59 | Nse4 C-terminal
| 0.45 | - |
| pf:HHH_5 | 70 | 127 | Helix-hairpin-helix domain
| 1.1e-14 | - |
| pf:HHH | 73 | 89 | Helix-hairpin-helix motif
| 0.07 | - |
| pf:Transposase_20 | 106 | 150 | Transposase IS116/IS110/IS902 family
| 0.75 | - |
| pf:IMS_HHH | 107 | 121 | IMS family HHH motif
| 0.35 | - |
| pf:RecR_HhH | 108 | 126 | | 0.0055 | - |
| pf:5_3_exonuc | 109 | 183 | 5'-3' exonuclease, C-terminal SAM fold
| 0.038 | - |
| pf:HHH | 112 | 123 | Helix-hairpin-helix motif
| 0.11 | - |
| pf:RuvA_C | 151 | 194 | RuvA, C-terminal domain
| 2.6e-10 | - |