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 3 1.4e-35 4e-32 111.4 0.6 1 61 13 73 13 80 0.95

2 3 7.3e-19 2.1e-15 57.4 0.3 24 61 82 119 75 127 0.91

3 3 6.1e-19 1.7e-15 57.7 0.6 24 58 128 162 122 166 0.93

#	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	3	1.4e-35	4e-32	111.4	0.6	1	61	13	73	13	80	0.95
2	3	7.3e-19	2.1e-15	57.4	0.3	24	61	82	119	75	127	0.91
3	3	6.1e-19	1.7e-15	57.7	0.6	24	58	128	162	122	166	0.93

Coding Sequence: ATGGAACGCCACCAGAATGGTATGGATGTGTGGGTAGGACAAGGACGCGTGAACCAGCTAGGAGGTCTGTTCATCAATGGGAGACCGCTTCCGAACCACATCAGGCTGAAGATCGTGGAGATGGCAGCGGCGGGCGTGCGGCCCTGCGTCATCTCGCGCCAGCTGCGAGTCTCTCACGGATGTGTCTCCAAGATCCTTAACAGATACCAGATACCAGGTATTACAGCAACACCTAGATACTACCTGAAGATTGTAGAGATGGTGGCGTCGGGCGTGCGGCCCTGCGTCATCTCGCGCCAGCTGCGATTCTCGCACGGATGTGTCTCCAAGATCCTCAACAGATACCAGATACCAGGTATTACAGCAACACCTAGACACTACCTGAAGATTGTAGAGATGGTGGCAGCGGGCGTGCGGCCCTGCGTCATCTCGCGCCAGCTGCGAGTCTCGCACGGATGTGTCTCCAAGATCCTCAACAGATACCAGGTATTACAGCAACACCTAGACACTACCTGA
Protein Sequence: MERHQNGMDVWVGQGRVNQLGGLFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQIPGITATPRYYLKIVEMVASGVRPCVISRQLRFSHGCVSKILNRYQIPGITATPRHYLKIVEMVAAGVRPCVISRQLRVSHGCVSKILNRYQVLQQHLDTT

Sequence clustering based on sequence similarity using MMseqs2