| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 59 | RuvA N terminal domain
| 1.5e-17 | - |
| pf:HHH_5 | 69 | 126 | Helix-hairpin-helix domain
| 1.6e-14 | - |
| pf:HHH | 72 | 88 | Helix-hairpin-helix motif
| 0.097 | - |
| pf:HHH_3 | 72 | 121 | Helix-hairpin-helix motif
| 0.22 | - |
| pf:HH_CyaD | 83 | 142 | | 0.00097 | - |
| pf:RecR_HhH | 105 | 125 | | 0.019 | - |
| pf:IMS_HHH | 107 | 120 | IMS family HHH motif
| 0.83 | - |
| pf:HHH | 111 | 122 | Helix-hairpin-helix motif
| 0.51 | - |
| pf:RuvA_C | 148 | 192 | RuvA, C-terminal domain
| 1.5e-11 | - |