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 1.6e-08 6.7e-05 24.0 0.0 19 71 5 57 2 106 0.88

2 2 2.5 1.1e+04 -2.5 0.0 77 95 114 132 83 139 0.60

#	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	1.6e-08	6.7e-05	24.0	0.0	19	71	5	57	2	106	0.88
2	2	2.5	1.1e+04	-2.5	0.0	77	95	114	132	83	139	0.60

Coding Sequence: ATGGCCACCACGCCCCATCAAGCGGCTCAAGTTATAACCCTATTGTCGCATGAAGGGCTCGGTCAGCGAGCCGTCTCTCGCCAGCTTCAAATGAGTCAGTCTGCTGTTTCAAGATTGTACAGGAGATTTCAAGCGACTGGTGCCTTTAATCCGAGACCAAGAACGGGCCGCCATCGATCCACTTCAGAGAGAGACAACCGTTTTATCGTTTCAACCGCGTTGCGAAATCAGCACTTCACGGCTGTTGATGTGCAGCAGGAACTGAGGCGTATTCGCGGAGTAGGTGTCAGCGAGTCAACAGTGAAAAGACTATTGAGGGAAGCCAAACTGACTTCAAGACGGCCTGCCACGGGCCCCAAATTGACTGCACGGCGCCGACAAGCGCCCCTCTTATTTACTCCAGAACATCTCAATTGGAGCATCACGCAATGGCGGTCTGTTATGTTTACTGACGAGTCCAGAATGTGTCtgcatggcagtgacagaagacgCCGAGTCTACAGGCATTCGGGTGAGCAATTTGCGGAGTGCTGTTTCGTTGAAACGGTTGCATACGGCGGCGGTTCCTGCATGATGAGGGCTGGTATTTCCTTGGAGGGAGAATCGGAGCTCGTTTTCGTGCCCAGAGGAGGCCGAGGAGGAAGGCTGACAGCTGATCGGTACATTGCCGATATTCTCCGGGTCCACGTTGTGCCCCACGCAGCATTTATTGGCAAGTACTTCGCATTGATGTATCACAAAGCTCGGTGTCACATGTTGCGTCTTACTCGGCAGTGCCTAGACGAAGCGAATATaccgacaattgactggcctgcactcAGTCCAGACACGAATCCCATTTATCACTTGTGGGGCGAGCTCAAGAGAAGATTCCGAGCCAGAAATCGAGTTCCTTCGTCCACTAAAGAATTGAAGGCAACCTAA
Protein Sequence: MATTPHQAAQVITLLSHEGLGQRAVSRQLQMSQSAVSRLYRRFQATGAFNPRPRTGRHRSTSERDNRFIVSTALRNQHFTAVDVQQELRRIRGVGVSESTVKRLLREAKLTSRRPATGPKLTARRRQAPLLFTPEHLNWSITQWRSVMFTDESRMCLHGSDRRRRVYRHSGEQFAECCFVETVAYGGGSCMMRAGISLEGESELVFVPRGGRGGRLTADRYIADILRVHVVPHAAFIGKYFALMYHKARCHMLRLTRQCLDEANIPTIDWPALSPDTNPIYHLWGELKRRFRARNRVPSSTKELKAT

Sequence clustering based on sequence similarity using MMseqs2