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 7.3e-09 1.2e-05 25.8 0.3 19 103 7 90 2 106 0.90

2 2 6.9 1.1e+04 -3.2 0.0 95 111 275 291 269 294 0.76

#	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	7.3e-09	1.2e-05	25.8	0.3	19	103	7	90	2	106	0.90
2	2	6.9	1.1e+04	-3.2	0.0	95	111	275	291	269	294	0.76

Coding Sequence: ATGGCTCGCAATAAATATTCTAATGacgtgaaagaaaaaatagtgTCTGATTTTACTAACGGTGAATCAGTAACATTTATTGCCAATAAATTTGGTATAAGCCATACCGTGATTTCGCGAATATTAGCTCGATTTCGTGCTCGGGGAAATGTTCAAACGGTTCATAGTGGTGGTAGACCCCGAAAAACCAGCAGTCGCGATGATAAAAGAATAATCAGGCTAATTAAAAAGGACCCCTTCATTTCgtcaagaaacataaaaaatgaactAGGCATAGAGATCTCAAGCAGGACGATCCGGCGAAGAGCTGTTGATAGTGGCTTGCTGTCATATCGAGCAATAAAAAAGccatttatttctcaaaaaaatcgaCGTGCACGACTGGAATTTGCAAAGGCGCACTTAAACTGGACTTTGGCAAAATGGAAAACGGTTCTCTTTTCAGacgaatccaaatttaatttaaagggaTCCGACGGATTGCGCATGGTACGGAGGCCGAAGGGCGAACGCCTTAATCCCCGATTCACCAAGGGCACAGTCAAGCACGGTGGAGGCAATATTATTGTCTGGGGATGTTTTTCCAGTCAAGGAGTCGGGCCAATTCACAAGATTAGTGGTATAATGGATCGTTTCATGTACCGGGAGATTCTTCAAAATGTCATGCTTCCTCATGCTGAGGAAAATATGCCGTTGCGATGGATcttccaacatgacaatgatccaaaacataccGCTAAACTTGTGAAGGATTGGCTTACGGAAGGTGGTATTGCTGTTATGAAGTGGCCAGCACAATCCCCTGATCTCAACCCCATAGAAAATCTATGGGAAATTGTAGATCAGAGGATTGATCGCACGAAATGCAGTAATTTAGATTCTCTACTTCACCAAACTCAAATTGCCTGGAGAAACATCCCCATGCATATAATTGACAACCTCATTGCCTCCATGCCTCGTCGATGTACTgcagtaattaaaaataatggttaCGCCACGAAATATtag
Protein Sequence: MARNKYSNDVKEKIVSDFTNGESVTFIANKFGISHTVISRILARFRARGNVQTVHSGGRPRKTSSRDDKRIIRLIKKDPFISSRNIKNELGIEISSRTIRRRAVDSGLLSYRAIKKPFISQKNRRARLEFAKAHLNWTLAKWKTVLFSDESKFNLKGSDGLRMVRRPKGERLNPRFTKGTVKHGGGNIIVWGCFSSQGVGPIHKISGIMDRFMYREILQNVMLPHAEENMPLRWIFQHDNDPKHTAKLVKDWLTEGGIAVMKWPAQSPDLNPIENLWEIVDQRIDRTKCSNLDSLLHQTQIAWRNIPMHIIDNLIASMPRRCTAVIKNNGYATKY

Sequence clustering based on sequence similarity using MMseqs2