| Motif id | From | To | Definition | E value | Score |
| pf:HTH_40 | 11 | 44 | Helix-turn-helix domain
| 0.046 | - |
| pf:HTH_IclR | 12 | 43 | IclR helix-turn-helix domain
| 0.0087 | - |
| pf:HTH_28 | 13 | 43 | Helix-turn-helix domain
| 0.026 | - |
| pf:HTH_23 | 15 | 43 | Homeodomain-like domain
| 0.0029 | - |
| pf:HTH_38 | 16 | 40 | Helix-turn-helix domain
| 0.00012 | - |
| pf:HTH_35 | 16 | 52 | Winged helix-turn-helix DNA-binding
| 0.016 | - |
| pf:RepB | 16 | 49 | RepB plasmid partitioning protein
| 0.035 | - |
| pf:TnsD | 16 | 49 | Tn7-like transposition protein D
| 0.18 | - |
| pf:HTH_3 | 17 | 52 | Helix-turn-helix
| 6.9e-09 | - |
| pf:HTH_26 | 17 | 65 | Cro/C1-type HTH DNA-binding domain
| 0.0028 | - |
| pf:HTH_5 | 17 | 43 | Bacterial regulatory protein, arsR family
| 0.021 | - |
| pf:HTH_37 | 17 | 45 | Helix-turn-helix domain
| 0.037 | - |
| pf:HNF-1_N | 17 | 43 | Hepatocyte nuclear factor 1 (HNF-1), N terminus
| 0.15 | - |
| pf:HTH_29 | 17 | 43 | Winged helix-turn helix
| 0.36 | - |
| pf:HTH_19 | 18 | 50 | Helix-turn-helix domain
| 8.5e-07 | - |
| pf:HTH_11 | 18 | 42 | HTH domain
| 0.23 | - |
| pf:HTH_31 | 19 | 46 | Helix-turn-helix domain
| 2.3e-05 | - |
| pf:HTH_24 | 19 | 43 | Winged helix-turn-helix DNA-binding
| 0.014 | - |
| pf:Xre-like-HTH | 20 | 53 | | 0.041 | - |
| pf:MarR_2 | 20 | 43 | MarR family
| 0.12 | - |
| pf:Sigma70_r4_2 | 21 | 42 | Sigma-70, region 4
| 0.066 | - |
| pf:HTH_Crp_2 | 21 | 43 | Crp-like helix-turn-helix domain
| 0.3 | - |
| pf:Fer4_21 | 88 | 115 | 4Fe-4S dicluster domain
| 0.00058 | - |
| pf:Fer4_22 | 96 | 113 | 4Fe-4S dicluster domain
| 0.23 | - |
| pf:Fer4_21 | 97 | 145 | 4Fe-4S dicluster domain
| 1.7e-06 | - |
| pf:Fer4_10 | 97 | 140 | 4Fe-4S dicluster domain
| 1.4e-05 | - |
| pf:Fer4 | 98 | 115 | 4Fe-4S binding domain
| 0.0003 | - |
| pf:Fer4_4 | 98 | 112 | 4Fe-4S binding domain
| 0.0053 | - |
| pf:Fer4_2 | 98 | 110 | 4Fe-4S binding domain
| 0.0076 | - |
| pf:Fer4_15 | 98 | 111 | 4Fe-4S single cluster domain
| 0.21 | - |
| pf:Fer4_8 | 99 | 112 | 4Fe-4S dicluster domain
| 0.76 | - |
| pf:Fer4_7 | 100 | 142 | 4Fe-4S dicluster domain
| 1.8e-07 | - |
| pf:Fer4_9 | 100 | 143 | 4Fe-4S dicluster domain
| 2.8e-06 | - |
| pf:Fer4_16 | 100 | 123 | 4Fe-4S double cluster binding domain
| 0.077 | - |
| pf:Fer4_6 | 100 | 112 | 4Fe-4S binding domain
| 0.26 | - |
| pf:Fer4_17 | 100 | 113 | 4Fe-4S dicluster domain
| 0.12 | - |
| pf:Fer4_3 | 100 | 112 | 4Fe-4S binding domain
| 0.051 | - |
| pf:Fer4_6 | 122 | 144 | 4Fe-4S binding domain
| 0.23 | - |
| pf:Fer4 | 123 | 145 | 4Fe-4S binding domain
| 0.00037 | - |