| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 5.4e-23 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 1.2e-13 | - |
| pf:Cdd1 | 104 | 125 | Pathogenicity locus
| 0.8 | - |
| pf:HHH_3 | 107 | 134 | Helix-hairpin-helix motif
| 0.024 | - |
| pf:HHH_8 | 107 | 124 | Helix-hairpin-helix domain
| 0.39 | - |
| pf:Transposase_20 | 108 | 130 | Transposase IS116/IS110/IS902 family
| 0.21 | - |
| pf:RecR_HhH | 109 | 125 | | 4.6e-05 | - |
| pf:IMS_HHH | 109 | 124 | IMS family HHH motif
| 0.022 | - |
| pf:HHH | 110 | 124 | Helix-hairpin-helix motif
| 0.013 | - |
| pf:RuvA_C | 165 | 206 | RuvA, C-terminal domain
| 7.1e-14 | - |