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 7.1e-08 0.00011 22.7 0.1 26 72 11 57 4 94 0.81

2 2 0.81 1.2e+03 -0.2 0.0 49 72 59 82 50 108 0.65

#	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	7.1e-08	0.00011	22.7	0.1	26	72	11	57	4	94	0.81
2	2	0.81	1.2e+03	-0.2	0.0	49	72	59	82	50	108	0.65

Coding Sequence: ATGGACACAACAACCGATTTAGCAGCTCAAGCGATCACCCTATTGCGACAAGGCCAGAGCCAGCGTGAAGTGGCACGTGCACTGAACGTGAGCCAGTCTGCTGTTTCCAGAGTTTACCGTCGTTACcaggagactggtggctttaatCGAAGACGCGGTTCCGGTAGAAAAAGGTGTACATCAGAGAGAGATGACCGATTTATTGTCAGCACATCGTTAAGAAATCGGGCCCTCACTGGCGTTCAAGTCCAACAAGAGCTCAGAGAAACGCGAGGAGTAGATGTGAGTGGCTGGACAGTCAGAAGACGACTTAAGGCAGCTAGGCTTGAGTCAAAAAGGTAG
Protein Sequence: MDTTTDLAAQAITLLRQGQSQREVARALNVSQSAVSRVYRRYQETGGFNRRRGSGRKRCTSERDDRFIVSTSLRNRALTGVQVQQELRETRGVDVSGWTVRRRLKAARLESKR

Sequence clustering based on sequence similarity using MMseqs2