| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 1.5e-24 | - |
| pf:HHH_5 | 72 | 130 | Helix-hairpin-helix domain
| 9.2e-17 | - |
| pf:HHH | 74 | 91 | Helix-hairpin-helix motif
| 0.33 | - |
| pf:HHH_2 | 80 | 124 | Helix-hairpin-helix motif
| 0.44 | - |
| pf:HHH_8 | 106 | 123 | Helix-hairpin-helix domain
| 0.24 | - |
| pf:HHH | 109 | 125 | Helix-hairpin-helix motif
| 0.00035 | - |
| pf:RecR_HhH | 109 | 126 | | 0.00061 | - |
| pf:Transposase_20 | 109 | 147 | Transposase IS116/IS110/IS902 family
| 0.0066 | - |
| pf:IMS_HHH | 110 | 125 | IMS family HHH motif
| 0.0044 | - |
| pf:5_3_exonuc | 110 | 129 | 5'-3' exonuclease, C-terminal SAM fold
| 0.45 | - |
| pf:DNA_pol_lambd_f | 110 | 124 | Fingers domain of DNA polymerase lambda
| 0.67 | - |
| pf:RuvA_C | 158 | 201 | RuvA, C-terminal domain
| 1.5e-16 | - |