| Motif id | From | To | Definition | E value | Score |
| pf:RuvB_N | 11 | 73 | Holliday junction DNA helicase ruvB N-terminus
| 0.00031 | - |
| pf:AAA_16 | 19 | 143 | AAA ATPase domain
| 0.005 | - |
| pf:DNA_pol3_delta2 | 20 | 178 | DNA polymerase III, delta subunit
| 5.6e-43 | - |
| pf:TsaE | 36 | 68 | Threonylcarbamoyl adenosine biosynthesis protein TsaE
| 0.4 | - |
| pf:AAA_7 | 37 | 69 | P-loop containing dynein motor region D3
| 0.91 | - |
| pf:PIF1 | 38 | 144 | PIF1-like helicase
| 0.14 | - |
| pf:nSTAND3 | 38 | 64 | | 0.28 | - |
| pf:AAA_14 | 40 | 153 | AAA domain
| 0.023 | - |
| pf:AAA_2 | 41 | 145 | AAA domain (Cdc48 subfamily)
| 0.0089 | - |
| pf:AAA | 42 | 170 | ATPase family associated with various cellular activities (AAA)
| 1.6e-10 | - |
| pf:AAA_22 | 42 | 156 | AAA domain
| 3.3e-05 | - |
| pf:AAA_5 | 42 | 149 | AAA domain (dynein-related subfamily)
| 0.00016 | - |
| pf:AAA_30 | 42 | 151 | AAA domain
| 0.034 | - |
| pf:AAA_18 | 43 | 126 | AAA domain
| 0.0029 | - |
| pf:ResIII | 87 | 145 | Type III restriction enzyme, res subunit
| 0.46 | - |
| pf:DNAX_ATPase_lid | 182 | 230 | | 1.2e-23 | - |
| pf:AAA_assoc_2 | 194 | 235 | AAA C-terminal domain
| 0.3 | - |
| pf:DNA_pol3_gamma3 | 232 | 358 | DNA polymerase III subunits gamma and tau domain III
| 2.1e-26 | - |
| pf:DNA_pol3_tau_4 | 416 | 497 | DNA polymerase III subunits tau domain IV DnaB-binding
| 5e-27 | - |
| pf:DNA_pol3_tau_5 | 499 | 639 | DNA polymerase III tau subunit V interacting with alpha
| 2.5e-57 | - |