| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 7.4e-24 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 8e-15 | - |
| pf:HHH | 72 | 91 | Helix-hairpin-helix motif
| 0.33 | - |
| pf:HTH_78 | 92 | 131 | | 0.47 | - |
| pf:HHH_8 | 107 | 124 | Helix-hairpin-helix domain
| 0.45 | - |
| pf:RecR_HhH | 109 | 125 | | 0.00026 | - |
| pf:HHH | 110 | 124 | Helix-hairpin-helix motif
| 0.0041 | - |
| pf:Transposase_20 | 110 | 132 | Transposase IS116/IS110/IS902 family
| 0.51 | - |
| pf:IMS_HHH | 111 | 124 | IMS family HHH motif
| 0.048 | - |
| pf:RuvA_C | 158 | 201 | RuvA, C-terminal domain
| 2.7e-16 | - |