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 3.1e-08 5e-05 26.2 0.1 16 103 4 89 1 107 0.88

2 2 8.9 1.4e+04 -1.2 0.0 37 52 89 104 80 117 0.67

#	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	3.1e-08	5e-05	26.2	0.1	16	103	4	89	1	107	0.88
2	2	8.9	1.4e+04	-1.2	0.0	37	52	89	104	80	117	0.67

Coding Sequence: atgcCTAGACGCCATTTAAGTGAAAATGAGATGTTGAGAGCTGTGGGAATGCTTGAGGCCGGAATTCTTCAAGTTCATgtagcaaatgctatagaaacTACTCAGAGTGTTATCTCGCGCCTCTGGAATCCTTATCGCGAAACTGGAACAGTACGGGAGAGGCATTTGGGTCGGCCAAGAATAACTACGCCTCATATGGATCGGTATGTCCAGCTAGAAGCCCGAAGAAATGACACAGTGACTGCATCTCAAttaattaatcacttgcacacagCTCGTCAAGTAAGGGTTTCCAGACATACCATCTACAGAAGGTTAAGAGAAGCTAATCTAGTCAGCAGAAGGCCTAGGAGATGTCAACCTCTAAACCGAGGAAATCGCGCAACTCGATTAGCCCTGGGCTCAAGAACATGTTATCTGGACTGA
Protein Sequence: MPRRHLSENEMLRAVGMLEAGILQVHVANAIETTQSVISRLWNPYRETGTVRERHLGRPRITTPHMDRYVQLEARRNDTVTASQLINHLHTARQVRVSRHTIYRRLREANLVSRRPRRCQPLNRGNRATRLALGSRTCYLD

Sequence clustering based on sequence similarity using MMseqs2

100% Identity: iTF_00847556; iTF_00847557; iTF_00847558; iTF_00847560; iTF_00847569;
90% Identity: iTF_00847574;
80% Identity: -