| Motif id | From | To | Definition | E value | Score |
| pf:RuvA_N | 1 | 61 | RuvA N terminal domain
| 2.1e-14 | - |
| pf:Ist1 | 35 | 77 | Regulator of Vps4 activity in the MVB pathway
| 0.13 | - |
| pf:HHH_2 | 63 | 101 | Helix-hairpin-helix motif
| 0.067 | - |
| pf:HHH_5 | 71 | 126 | Helix-hairpin-helix domain
| 1.4e-12 | - |
| pf:HHH_2 | 101 | 124 | Helix-hairpin-helix motif
| 0.37 | - |
| pf:HHH_8 | 104 | 123 | Helix-hairpin-helix domain
| 0.009 | - |
| pf:Cdd1 | 104 | 124 | Pathogenicity locus
| 0.066 | - |
| pf:HHH_3 | 105 | 124 | Helix-hairpin-helix motif
| 0.053 | - |
| pf:HHH | 106 | 124 | Helix-hairpin-helix motif
| 0.0019 | - |
| pf:IMS_HHH | 109 | 122 | IMS family HHH motif
| 0.52 | - |
| pf:RuvA_C | 139 | 181 | RuvA, C-terminal domain
| 7.9e-13 | - |