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 1.4e-08 6.9e-06 27.4 0.1 16 93 3 79 1 91 0.80

2 2 7.9 4e+03 -0.9 0.0 33 49 98 115 78 120 0.66

#	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	1.4e-08	6.9e-06	27.4	0.1	16	93	3	79	1	91	0.80
2	2	7.9	4e+03	-0.9	0.0	33	49	98	115	78	120	0.66

Coding Sequence: ATGCCAAGAGGATTATCAGAAGTTTTGCGAGCAAGAATAGTAACTTTGAGGGAAGAAGGATACACCACGACAGAAATAGCACGCAGAGTTGCTATATCCCAATCCTGTGTCGTGACCACGTTGCAAAGGTACCACGCAATGGGTAATTTTGCTGACCGACCCCGCAGTGGTCGCCCAACTGTTTTGACTGCTGCCCAAAAGCGCTATATTATATTCCTGGTAGCCCGTGATCCGACAATCAAcggtactaaaataaaagcagaaGTTCGGCCGCCTCTGGGCTTGCAGTTAGCACTCAGACCATGCGGAATTGCTTGCACCAGACTGGATTACGAGCACGGAGGTCTTGACGAGCTCCTCTGA
Protein Sequence: MPRGLSEVLRARIVTLREEGYTTTEIARRVAISQSCVVTTLQRYHAMGNFADRPRSGRPTVLTAAQKRYIIFLVARDPTINGTKIKAEVRPPLGLQLALRPCGIACTRLDYEHGGLDELL

Sequence clustering based on sequence similarity using MMseqs2