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 2 2.4e-09 6.3e-06 27.0 0.1 24 112 9 96 2 103 0.89

2 2 2.6 6.8e+03 -2.2 0.0 71 90 109 128 97 138 0.73

#	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	2	2.4e-09	6.3e-06	27.0	0.1	24	112	9	96	2	103	0.89
2	2	2.6	6.8e+03	-2.2	0.0	71	90	109	128	97	138	0.73

Coding Sequence: ATGGCGGTTAACGAAAATGATTCTGCCCGTATTGTTGCTTTGTTGGAGGAAGGCTTTAGTCAGCGATACGTCGCTGAAAGATTGGGCATCAATCAGTCGACCGTCTCACGGATTTCGAACCGATTTCGGGAAACTGGAAGATATGGCCGCAGAATAGGATCAGGTAGAGGACGCGTCACAACTGCAAAGGAGGACAGGAATTTGGCTCAAGCGGCGATACGGAATCCAGTGCTTGTAGCGCAACAAATCGCGCATGCTGTTATGCCGAATAAACAGATAAGTGATGAAACTGTGAGGAGACGCTTACACGAACAGGGTTTACGATCGCGTGCTCGTGTCCAAGCGCCGTTACTTCTGGGCCGTCATAAAGAAAGCCGAAGACAATATGCACGAAATCATGCGAATTGGATTTGGAGGGAATGA
Protein Sequence: MAVNENDSARIVALLEEGFSQRYVAERLGINQSTVSRISNRFRETGRYGRRIGSGRGRVTTAKEDRNLAQAAIRNPVLVAQQIAHAVMPNKQISDETVRRRLHEQGLRSRARVQAPLLLGRHKESRRQYARNHANWIWRE

Sequence clustering based on sequence similarity using MMseqs2