| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 61 | RuvA N terminal domain
| 4e-20 | - |
| pf:HHH_5 | 71 | 129 | Helix-hairpin-helix domain
| 1.3e-17 | - |
| pf:5_3_exonuc | 75 | 107 | 5'-3' exonuclease, C-terminal SAM fold
| 0.68 | - |
| pf:HHH_8 | 93 | 122 | Helix-hairpin-helix domain
| 0.093 | - |
| pf:Cdd1 | 103 | 124 | Pathogenicity locus
| 0.71 | - |
| pf:HHH_3 | 106 | 143 | Helix-hairpin-helix motif
| 0.49 | - |
| pf:Transposase_20 | 107 | 138 | Transposase IS116/IS110/IS902 family
| 0.81 | - |
| pf:RecR_HhH | 109 | 127 | | 3.6e-05 | - |
| pf:HHH | 109 | 123 | Helix-hairpin-helix motif
| 0.022 | - |
| pf:IMS_HHH | 109 | 123 | IMS family HHH motif
| 0.047 | - |
| pf:DUF655 | 109 | 144 | Protein of unknown function (DUF655)
| 0.15 | - |
| pf:PG_binding_2 | 150 | 181 | Putative peptidoglycan binding domain
| 0.28 | - |
| pf:RuvA_C | 155 | 197 | RuvA, C-terminal domain
| 6.7e-12 | - |