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 1.3e-51 6.2e-48 163.9 0.3 14 125 6 114 2 114 0.98

2 3 0.0067 31 6.5 0.0 103 125 134 153 127 153 0.90

3 3 0.003 14 7.6 0.0 102 125 255 275 178 275 0.91

#	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	1.3e-51	6.2e-48	163.9	0.3	14	125	6	114	2	114	0.98
2	3	0.0067	31	6.5	0.0	103	125	134	153	127	153	0.90
3	3	0.003	14	7.6	0.0	102	125	255	275	178	275	0.91

Coding Sequence: ATGGGTGAAGGATTCGACGGGAGACCGCTGCCTCGCCACATTCGTCTGAATATTGTGGAGAtggcggcggcgggcgtgcgGCCCTGTGCGTCATCTCGCGCCAGCTGCGCGTCTCGCACGGCTGTCTCCAAGATCCTCAACGGATATCAGGAGACAGGGTCCATCAGGCCTGGCGTGATTGGGGGCTCCAAACCGCGCGTAGCCACGCCCGAGGTGGAGGCGCGGATCGAGGACCTGAAGCGACAGAACCCGGGGATATTCTCGTGGGAGATCCGGGAGAAATTGATAAAGGAAGGCGTGTCGGACCCGCCTAGCATCTCATCCATCTCTCGGCTgctgcgcggcggcgcgcgggacCCCGAAGGCAAGAAGGACTACAGCATCGACGGGATCCTTGGAGTATTGCAGGAAGGCGTGTCCGACCCGCCCAGCATCTCATCCATCTCGCGGCTactgcgcggcggcgcgcgggacCCCGAAGGCAAGAAGGACTACAGCATCGACGGGATCCTTGGAGGTCAGTATTGCAGGAAGGCGTGTCGGATCCGCTCAGCATCTCATCCATCTCGCGGCTGCTGCGAGGCGGCGCGCGGGACCCCGAAGGCAAGAAGGACTACAGCATCGACGGGATCCTTGGAGGTCAGTATTGCAGGAAGGCGTGTCGGACCCGCCCAGCATCTCATCCATCTCACGGCTgctgcgcggcggcgcgcgggacCCCGAAGGCAAGAAGGACTACAGCATCGACGGGATCCTTGGAGGTCAGTATTGCAGGAAGGCGTGTCGGACCCGCCCAGCATCTCATCCATCTCGCGGCTgctgcgcggcggcgcgcgggacCCCGAAGGCAAGAAGGACTACAGCATCGACGGGATCCTTGGATGTCAGTACTGTAACGGAGAGAAGAGTTAA
Protein Sequence: MGEGFDGRPLPRHIRLNIVEMAAAGVRPCASSRASCASRTAVSKILNGYQETGSIRPGVIGGSKPRVATPEVEARIEDLKRQNPGIFSWEIREKLIKEGVSDPPSISSISRLLRGGARDPEGKKDYSIDGILGVLQEGVSDPPSISSISRLLRGGARDPEGKKDYSIDGILGGQYCRKACRIRSASHPSRGCCEAARGTPKARRTTASTGSLEVSIAGRRVGPAQHLIHLTAAARRRAGPRRQEGLQHRRDPWRSVLQEGVSDPPSISSISRLLRGGARDPEGKKDYSIDGILGCQYCNGEKS

Sequence clustering based on sequence similarity using MMseqs2