| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 1.1e-24 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 2e-13 | - |
| pf:HHH | 74 | 91 | Helix-hairpin-helix motif
| 0.9 | - |
| pf:HTH_78 | 102 | 131 | | 0.86 | - |
| pf:HHH_8 | 105 | 125 | Helix-hairpin-helix domain
| 0.41 | - |
| pf:RecR_HhH | 107 | 126 | | 0.00011 | - |
| pf:HHH | 108 | 124 | Helix-hairpin-helix motif
| 0.0011 | - |
| pf:IMS_HHH | 110 | 124 | IMS family HHH motif
| 0.12 | - |
| pf:DUF2497 | 157 | 203 | Protein of unknown function (DUF2497)
| 0.78 | - |
| pf:RuvA_C | 161 | 203 | RuvA, C-terminal domain
| 1.7e-16 | - |
| pf:RHH_1 | 184 | 203 | Ribbon-helix-helix protein, copG family
| 0.24 | - |