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 2.5e-08 7.2e-05 24.3 0.9 24 78 9 62 3 118 0.87

2 2 0.26 7.5e+02 1.7 0.0 13 57 100 143 89 147 0.76

#	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	2.5e-08	7.2e-05	24.3	0.9	24	78	9	62	3	118	0.87
2	2	0.26	7.5e+02	1.7	0.0	13	57	100	143	89	147	0.76

Coding Sequence: ATGGCAGAAAAAGCAATAAGAGCTAGTAAGATTATAGCGCTGCTGGAAGAGGGCTGTAGCCAATGTTACGTCTCACAGCGGTTAAACGTGAGTCGTTCAATCGTCCAAGGAACCTGGAATCGGTACCAAGAGAAAGGTTCCGTTCAGAGAAGGCAAGGTTCAGGGAGAAAACGGTGTACACAACCACGAGACGACCGCTTTTTAGTCACTCAAGCGCTGAGAAACCGCAAATGTAGTTACATAGACCTCAAAAGAAACCTTGAAGAGATACGCGGAGCACAAGTTAGCCTATGGACTGTGAGGAGGAGGCTTTTAGATGCTGATATACGCAATCGACGACCAGCGCGGGCCCCTAAGTTACTTCGTGAGCACCGGATTGCCCGATTGAGGTTCGCTAGAAATTGCCTATCTTGGATACTAGGTAACTGGAGTAGCGTACTCTTCTCCGATGAGGCTCGCATTTGTCTACATGGTGAGGATCGACGTCGGCGAGTGTTACGAAGACCAGGCGAACGCTATGCCGACGTGTGCTTTGAAGAAATCACCCCTTATGGTGGAGGgtccgttatgttttgggcgGGCGTAACTTCTAACTATCGTACCGAGATAGTATTAATTGAAAATGGCTCACTAAATGCGCAAAGGTACATATCAGAAATCCTCTCTCAAAATCCACAACCTGCACTGACTGTAATTAGTGAAGATGCCATTTAcatggacgacaatgctcggGCCCACCGTTCTAGCGACGTAGATGTTTATATGCAAGAGGCCGGGTTCGTCGTTTGGATTGGCCAGCGCGGACCCGACCTCAACCCTACTGAGTCTGGGACCTTCTAA
Protein Sequence: MAEKAIRASKIIALLEEGCSQCYVSQRLNVSRSIVQGTWNRYQEKGSVQRRQGSGRKRCTQPRDDRFLVTQALRNRKCSYIDLKRNLEEIRGAQVSLWTVRRRLLDADIRNRRPARAPKLLREHRIARLRFARNCLSWILGNWSSVLFSDEARICLHGEDRRRRVLRRPGERYADVCFEEITPYGGGSVMFWAGVTSNYRTEIVLIENGSLNAQRYISEILSQNPQPALTVISEDAIYMDDNARAHRSSDVDVYMQEAGFVVWIGQRGPDLNPTESGTF

Sequence clustering based on sequence similarity using MMseqs2

100% Identity: iTF_00124235; iTF_00124227; iTF_00124226; iTF_01415811; iTF_01415810; iTF_01415813; iTF_00124230; iTF_01415807; iTF_01415806; iTF_00447116; iTF_00038745;
90% Identity: iTF_01332605;
80% Identity: -