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 6e-10 1.2e-06 29.1 0.2 18 101 5 87 2 98 0.83

2 2 0.65 1.3e+03 -0.1 0.0 36 49 94 107 71 115 0.69

#	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	6e-10	1.2e-06	29.1	0.2	18	101	5	87	2	98	0.83
2	2	0.65	1.3e+03	-0.1	0.0	36	49	94	107	71	115	0.69

Coding Sequence: ATGCCAAAAAGATTATCAGAAGTTTTACGAGCAAGAATAGTAACTTTGAGGGAAGAAGGATACACCACGAGAGAAATAGCACGCAGAGTTGCTATATCCCAATCCTGTGTCGTGACCACGTTGCAGAGGTACCGCGAGATGGGTAATTTAGCTGACCGACCCCGCAGTGGTCGCCCAACTAATTTGACTGCTGGCCAAAAGCGCTATATTAGATTGCTGGCAGCTCGAGAACCAACAATCAAcgctactaaaataaaaacagaagtTCGGGCCGCTTCTGGGCTTGAAGTTAGCAGACCATTCCGAGTAAACCATGGGCACCGATTTGTACTGGTCGATAGAAAGCTTGATAATTGA
Protein Sequence: MPKRLSEVLRARIVTLREEGYTTREIARRVAISQSCVVTTLQRYREMGNLADRPRSGRPTNLTAGQKRYIRLLAAREPTINATKIKTEVRAASGLEVSRPFRVNHGHRFVLVDRKLDN

Sequence clustering based on sequence similarity using MMseqs2