Basic Information

Transcription Factor Domain

TF Family: PAX
Domain: PAX domain
PFAM: PF00292
TF Group: Helix-turn-helix
Description: The paired domain, a ~126 amino acid DNA-binding domain, is found in eukaryotic transcription regulatory proteins involved in embryogenesis. Initially identified in Drosophila’s paired (prd) protein, it typically resides in the N-terminal region and may be followed by an octapeptide, a homeodomain, or a Pro-Ser-Thr-rich C terminus. Paired domain proteins act as transcription repressors or activators, with DNA-binding specificity mediated by three subdomains. Crystal structures reveal a bipartite DNA-binding paired domain: an N-terminal subdomain (PAI) and a C-terminal subdomain (RED), linked by a flexible linker. Both subdomains contain a helix-turn-helix motif that binds DNA's major groove, while the linker may bind the minor groove. Variations in domain usage across Pax proteins and isoforms determine sequence specificity.
Hmmscan Out: # of c-Evalue i-Evalue score bias hmm coord from hmm coord to ali coord from ali coord to env coord from env coord to acc

1 5 2.5e-35 1.5e-31 110.7 0.6 1 64 13 76 13 85 0.94

2 5 2.8e-09 1.7e-05 26.6 0.8 9 61 77 151 70 156 0.71

3 5 1.1e-16 6.6e-13 50.5 0.1 8 52 154 198 149 201 0.94

4 5 8.8e-17 5.2e-13 50.8 0.6 22 63 203 244 200 252 0.91

5 5 0.00047 2.8 9.7 0.0 17 44 261 288 244 291 0.81

#	of	c-Evalue	i-Evalue	score	bias	hmm coord from	hmm coord to	ali coord from	ali coord to	env coord from	env coord to	acc
1	5	2.5e-35	1.5e-31	110.7	0.6	1	64	13	76	13	85	0.94
2	5	2.8e-09	1.7e-05	26.6	0.8	9	61	77	151	70	156	0.71
3	5	1.1e-16	6.6e-13	50.5	0.1	8	52	154	198	149	201	0.94
4	5	8.8e-17	5.2e-13	50.8	0.6	22	63	203	244	200	252	0.91
5	5	0.00047	2.8	9.7	0.0	17	44	261	288	244	291	0.81

Coding Sequence: ATGGAACGCCACCAAAATGGTATGGATGTGTGGGTAGGTCAAGGCCGCGTCAACCAGCTCGGAGGCCTTTTCATCAACGGGCGGCCTCTGCCGAACCACATCAGACTGAAGATCGTGGAAATGGCTGCGGCTGGAGTCAGGCCCTGCGTCATATCACGACAGCTGCGCGTCTCCCATGGCTGCGTCTCCAAGATCCTCAACAGATACCAGGTATGTAATGAAATAGTTAATGGCTTCTTAATCAACGTCTGGCCCCTGCTGCACCACATCAGACTTCAGTCTGATGTGATGCACGATCTTCAGATCGTGGAAATGGCAGAAGCTGGAGACAAGTTCTGCGTCATATCACGACAGCTGCACGGACTGGAGACAAGCACTGCATCATATCACGACCAGCTGCGAGTCTGCCATGGCTGCGTCTCCAAGATCCTCAATATCTACCAGGTTTGTAAAGAAATAGTTAATGGCCTCTTCATCAACGTCTGGCCCCTGCCGAACCACATCAGACTGCAGATCGTAGAGATGGCAGGGACTGGAAAAAAGCATTGCGTCATATCACGACAGCTGCGCGTCTCGCATGGTGCGTCTTCAAGATCCTCAATAGATACCAGATTGAAGATCGTAGAGATGGCAAGGACTGGAGACCAGCACTGCGTCATATCACGACAGCTGCGTGTTTCCCATGGCTGCGTCTCCAAGCTCCTCAATAGATACCAGATATGTAAAGAAATAGTTGATGGTCTCTTCATTATTGTCTGGCCCCTGCCGTCAACGTCTGGCCCCTGCTTAAACCACATCAGATTGCAGTTCGTGGAGATGGCAGGGGCTGGAGACAAGCCTGCTGGAGTTTCTAACATCCTTAATAGATACCAGATTTAA
Protein Sequence: MERHQNGMDVWVGQGRVNQLGGLFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQVCNEIVNGFLINVWPLLHHIRLQSDVMHDLQIVEMAEAGDKFCVISRQLHGLETSTASYHDQLRVCHGCVSKILNIYQVCKEIVNGLFINVWPLPNHIRLQIVEMAGTGKKHCVISRQLRVSHGASSRSSIDTRLKIVEMARTGDQHCVISRQLRVSHGCVSKLLNRYQICKEIVDGLFIIVWPLPSTSGPCLNHIRLQFVEMAGAGDKPAGVSNILNRYQI

Sequence clustering based on sequence similarity using MMseqs2