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 4.9e-23 1.1e-18 70.7 0.0 65 111 25 71 15 82 0.92

2 2 0.99 2.2e+04 -1.3 0.1 41 55 92 106 73 130 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	4.9e-23	1.1e-18	70.7	0.0	65	111	25	71	15	82	0.92
2	2	0.99	2.2e+04	-1.3	0.1	41	55	92	106	73	130	0.65

Coding Sequence: ATGACTGAAGTAAAATCAGCATTAAGATCTTTATCAGTGAGTGATACAGACCTACAGAGAACATTGAGACCTCCAGGGTTAATTGGTGGTAGTAAACCAAAGGTagcaacacctgcagttgtttcaAAGATTGAACAGTACAAAAGAGAAAATCCAACAATTTTCGCTTGGGAAATTAGGGAACGGTTAATATCTGAAGGGTGCTGCGGCGAAATGGTGCTGCGACGAAATGGTGCCGCCACGAAAGGATGCTGCGGCGAAAAAATGCTGCGGCGAAAGGATGCTATGACAAAAGGGTGCTGTAGCGAAAGGGTGCTACGGCGAAAGGGTGCTACGACAAAAGGGTGCTACGGCGAAAGGGTGCTACGGCGAAAGGGCGCTACGACAAACGGTTGCTGCGGCGAAAGGGTGTCTCGGCGAAAGGGTGCTGTGGTGTTGTTGGAGCGAAAGAGTGCTGTGGTGAAAGGGTGCTGTGGTGAAAGGTGCTGCGGCCAAAGGTTTCTACGGCAAAAGGTTTCTGCGGCGAAAGGTTTCTGCGGCGAAATATTTCTACGGGAAAAGGGTACTGGGGCGAAAGGGTACTGGGGCGAAAGGGTGCTATGGCGAAAGAGTACTGAAGTGAAAGTGTAA
Protein Sequence: MTEVKSALRSLSVSDTDLQRTLRPPGLIGGSKPKVATPAVVSKIEQYKRENPTIFAWEIRERLISEGCCGEMVLRRNGAATKGCCGEKMLRRKDAMTKGCCSERVLRRKGATTKGCYGERVLRRKGATTNGCCGERVSRRKGAVVLLERKSAVVKGCCGERCCGQRFLRQKVSAAKGFCGEIFLREKGTGAKGYWGERVLWRKSTEVKV

Sequence clustering based on sequence similarity using MMseqs2