| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 62 | RuvA N terminal domain
| 1.7e-22 | - |
| pf:HHH_2 | 68 | 90 | Helix-hairpin-helix motif
| 0.36 | - |
| pf:HHH | 69 | 91 | Helix-hairpin-helix motif
| 0.048 | - |
| pf:HHH_5 | 72 | 129 | Helix-hairpin-helix domain
| 6.7e-18 | - |
| pf:HHH_8 | 95 | 123 | Helix-hairpin-helix domain
| 0.078 | - |
| pf:Cdd1 | 105 | 125 | Pathogenicity locus
| 0.42 | - |
| pf:HHH_3 | 106 | 124 | Helix-hairpin-helix motif
| 0.36 | - |
| pf:Transposase_20 | 108 | 132 | Transposase IS116/IS110/IS902 family
| 0.25 | - |
| pf:RecR_HhH | 109 | 128 | | 0.0016 | - |
| pf:HHH | 110 | 125 | Helix-hairpin-helix motif
| 0.0031 | - |
| pf:IMS_HHH | 110 | 124 | IMS family HHH motif
| 0.019 | - |
| pf:5_3_exonuc | 111 | 128 | 5'-3' exonuclease, C-terminal SAM fold
| 0.93 | - |
| pf:RuvA_C | 147 | 191 | RuvA, C-terminal domain
| 5.6e-14 | - |