| ETS domain |
1awcA, 1bc8C, 1pueE |
| Helix–loop–helix |
1am9A |
| Cro and repressor |
1lmb3, 1lmb4, 1rpeL, 3croL |
| Trp repressor |
1troA |
| Integration host factor |
1ihfA |
| DNA repair protein |
1e3mA |
| Recombinase DNA binding domain |
1hcrA |
| Homeodomain |
1akhB, 1au7A, 1b72A, 1b72B, 1fjlA, 1mnmC, 1mnmD, 2hddA, 9antA |
| RAP1 |
1ignA |
| TC3 transposase |
1tc3C |
| Interferon regulatory factor like |
2irfL |
| Paired domain |
1pdnC |
| DNA polymerase |
1bpyA |
| REL homology |
1a3qA, 1a3qB, 1tsrB, 2ramA |
| STAT family |
1bg1A |
| Single-strand DNA binding domain |
1jmcA |
| Transcription factor T domain |
1xbrA |
| Lambda integrase like N terminal domain |
1crxA |
| Transcription factor DNA binding domain |
1sknP |
| Transcription factor IIB |
1aisA |
| SRF like |
1egwA, 1mnmA |
| TATA box binding domain |
1ytbA |
| Histone like protein |
1azpA |
| DNA repair glycosylase |
1ebmA |
| Endonuclease |
1bgbA, 1bhmA, 3pviA, 1a73A |
| DNAQ Like 3′–5′ Exonuclease |
2kfnA, 4bdpA |
| Methyl transferase |
6mhtA |
| Zinc finger |
1a1gA, 1meyC, 1ubdC |
| Zn6/Cys6 DNA binding domain |
1zmeD |
| Leucine Zipper domain |
1gd2E, 2dgcA |
| Hormone receptor |
1hcqA, 1latA, 2nllB |
