| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 2.8e-23 | - |
| pf:HHH_5 | 72 | 129 | Helix-hairpin-helix domain
| 2e-17 | - |
| pf:HHH | 72 | 91 | Helix-hairpin-helix motif
| 0.55 | - |
| pf:HHH_8 | 103 | 124 | Helix-hairpin-helix domain
| 0.22 | - |
| pf:Cdd1 | 105 | 125 | Pathogenicity locus
| 0.69 | - |
| pf:HHH_3 | 106 | 124 | Helix-hairpin-helix motif
| 0.75 | - |
| pf:Transposase_20 | 108 | 132 | Transposase IS116/IS110/IS902 family
| 0.27 | - |
| pf:RecR_HhH | 109 | 128 | | 0.0024 | - |
| pf:HHH | 110 | 125 | Helix-hairpin-helix motif
| 0.0045 | - |
| pf:IMS_HHH | 110 | 124 | IMS family HHH motif
| 0.03 | - |
| pf:RuvA_C | 148 | 191 | RuvA, C-terminal domain
| 3.4e-13 | - |