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 2.2e-09 3.1e-06 28.0 0.2 23 94 7 81 3 104 0.88

2 2 6.4 9e+03 -2.6 0.0 83 115 154 187 110 191 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	2.2e-09	3.1e-06	28.0	0.2	23	94	7	81	3	104	0.88
2	2	6.4	9e+03	-2.6	0.0	83	115	154	187	110	191	0.54

Coding Sequence: atgaatttaaaagaaaagagagACGCGGTAATGTCTTTACATAAAAgtggtaaaaataaatcggaGATTGTGAAGTTGTTAAAACCACAAAATATCTGTAAAATGTTCGTGTATCGTACTATTAAACGTTATGAGGAAACTGGCTCTCTTGATAACAGAACAAATAGTGGTGCTAAAGCTAGTGCTACCAGTCCGGATATGGTGAAGAAAGTGCGAGAGCGGTTAAGAAGAAATCCACGTTGTAGCGGCAATCAGATGGCTAAACAACTCGGAATTTCACCGAGAAGTGTCCAACGCATTTTGCATAATAAACTTAAGGTTAAGGgctacaaaatacaaaaaggcCAGGAACTTTCTGCAGCACAAATTACTAAGCGACTCGAAAGATGCAAACAGCTGAAACAGTGGCACGCTGATGGACGAATTCCGAACATTGTCTTCTCGGATGagaaaattttcaccattCAACAAGtgataaacaaacaaaatgatCGTGTTTACTTAGCGCCAGACCAAAAGCATCTACTAAAACAATACACAGCCACTCGCCAACAAAAACCTGCTTCGTTGATGGTTTGGGCTGGTATTACTCGTGAAGGACGAACACCATTGCTTATCGTACCTGCTGGTGTAAAGATAAATCAAGAAACTTACTGCAAATTAGTTTTGGAGGATTGTTTACTACCGTGGTCACGGAAACAATTCGGTTCCAGACGTTGGACATTTCAGCAGGACTCCGCACCAGCCCACAAAGCGAAAAAAACTCAAGAGTGGCTAAAAAACAACGTTCCTGTGCACATTCCTCACAATGCTTGGCCACCGAATTCTCCGGATTTAAATCCATTAGATTTCTGTGTTTGGAGTATGTTAGAGGCCAAGGTCAGTCAAATACGCCATACAAGTTTGGACGCTCTTGAAAAATCACTTCGGCTGGAATGGAAGAAAATACCACAAGAACACTTTCGTGCCGCGTATGACTCCTTCTTTAAGAGACTTAACCTTATAACTCGATTCAAAGGTCAACGAATCGAAAATTGA
Protein Sequence: MNLKEKRDAVMSLHKSGKNKSEIVKLLKPQNICKMFVYRTIKRYEETGSLDNRTNSGAKASATSPDMVKKVRERLRRNPRCSGNQMAKQLGISPRSVQRILHNKLKVKGYKIQKGQELSAAQITKRLERCKQLKQWHADGRIPNIVFSDEKIFTIQQVINKQNDRVYLAPDQKHLLKQYTATRQQKPASLMVWAGITREGRTPLLIVPAGVKINQETYCKLVLEDCLLPWSRKQFGSRRWTFQQDSAPAHKAKKTQEWLKNNVPVHIPHNAWPPNSPDLNPLDFCVWSMLEAKVSQIRHTSLDALEKSLRLEWKKIPQEHFRAAYDSFFKRLNLITRFKGQRIEN

Sequence clustering based on sequence similarity using MMseqs2