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 0.15 5.1e+02 1.5 0.0 40 90 13 66 4 72 0.69

2 2 7.9e-22 2.8e-18 67.0 0.1 61 106 71 117 68 117 0.92

#	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	0.15	5.1e+02	1.5	0.0	40	90	13	66	4	72	0.69
2	2	7.9e-22	2.8e-18	67.0	0.1	61	106	71	117	68	117	0.92

Coding Sequence: ATGGGCCACCGAAAAGGTTGCGGTGcaggctgcggctcggctcgccttgaCTCGGCTACCGGTTGTGTGTACGCTCAGGGCGAGAGCCTGACCAGGAATCAGGGCCCCGGTTTCCTTTCAGCTCGCCCCGGGGTCGAAACTTCACCTGCAAGCGCAGCGCACAGCGTCGAGACATGGCacgagaAATACCGGAGTGGGTGTGATGTTGCAGGGACTCTTCGACCGCCGGGCCTCATCGGCGGAAGCAAACCCAAGGTGGCCACCCCAACCGTGGTCTCCAAGATCGAGCAGTACAAGCGGGAGAACCCGACCATCTTCGCCTGGGAGATACGGGAGAGGCTGATATCAGAAG
Protein Sequence: MGHRKGCGAGCGSARLDSATGCVYAQGESLTRNQGPGFLSARPGVETSPASAAHSVETWHEKYRSGCDVAGTLRPPGLIGGSKPKVATPTVVSKIEQYKRENPTIFAWEIRERLISE

Sequence clustering based on sequence similarity using MMseqs2