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 3.3e-09 1.7e-06 28.6 0.1 24 63 9 48 4 61 0.88

2 2 4.8 2.5e+03 -1.0 0.0 56 80 66 90 55 109 0.54

#	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	3.3e-09	1.7e-06	28.6	0.1	24	63	9	48	4	61	0.88
2	2	4.8	2.5e+03	-1.0	0.0	56	80	66	90	55	109	0.54

Coding Sequence: ATGGAAACCACAACTGCAGAAGCCGCTCAAATCGTCATCTTAATCCAGCAAGGGTTGTCTCAGTGTAATATTGCTCGACAGCTTCATCTAAGCCAGCCTTGTGTCTCGAAGGTGTACAGAAGGTTCAGGGCGACTGGAAACTTTGTCTGGAGACCAGGATCTGGAAGACAGCGTTGCACTTCAGTGAGAGATGACCGATTCATTGTCACCACTTCCCTCCGAAATCGACAACTAACCGGCGTGGACATCCAACGGCAGCTCAGAGAAGTTCGAGAGAGGGCTGTTAGCGAGTGGTCAAGGAGGCGAAGACTTAAAGAAGTGAATTTGACCCCAAGAAGGCCAGCTACGGGGCCCAAATTGTCTCCAGCCCACCGAGAAGCCCGGCTTCAGTTTGCAAGCGATTACTTAGATTGGGATATAGAGCCATGGAGTCGAGTCCTGTTCTCGGACGAAACAAGGATGTGCCTGCATGGTAGCGACAGTCGACTGAGAGTCTATAGAAGACCGGGGGAGCGATTTGCACAATGCTGTTTTGCGGAAATAGTGGCATACGGGGGCGGGTCCTGTATGATATGGGCGGGGATTTCTATAGAAGCAAAAATGGAGCTGGTATTCGTACCTGGTGGTGGTCGGGGAGGGGGCCTAACTGCGGAAAGATACATCAACGACATTCTGCTAGGCCATGTGCTCCCGTACGGTTTATTGGCGAATATTTCCTgctaa
Protein Sequence: METTTAEAAQIVILIQQGLSQCNIARQLHLSQPCVSKVYRRFRATGNFVWRPGSGRQRCTSVRDDRFIVTTSLRNRQLTGVDIQRQLREVRERAVSEWSRRRRLKEVNLTPRRPATGPKLSPAHREARLQFASDYLDWDIEPWSRVLFSDETRMCLHGSDSRLRVYRRPGERFAQCCFAEIVAYGGGSCMIWAGISIEAKMELVFVPGGGRGGGLTAERYINDILLGHVLPYGLLANISC

Sequence clustering based on sequence similarity using MMseqs2