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 1.2e-10 5.2e-07 31.4 0.1 31 86 16 71 2 88 0.82

2 2 1.2 5.5e+03 -1.0 0.0 39 57 84 102 75 111 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	1.2e-10	5.2e-07	31.4	0.1	31	86	16	71	2	88	0.82
2	2	1.2	5.5e+03	-1.0	0.0	39	57	84	102	75	111	0.76

Coding Sequence: ATGGATTTAAAACGAAATACAGTGATTGCTCTTCATTTGGAGGGAAAATCGAATATCGAAATATGTCGAGCGCTGCGAAATCTTCAATTGAACGAGAAATTTGTGCATCGCACTATTCAACGTTATAATGAGACTGGTAGCGTTAAGAAACGCTACGGTGGCGGACGACGCTGTACTACAACGGCGCCAGAAGTTGTCGAAAAGGTGCGTCATCGATTAGACAGAAATCTAGCGCGCTCAGCAAACCAGCTCGCGCAGAATCTCAAGTTGAGCGATCGCAGCGTTCGTcgcatattgaagaaaaagctTAAAGTCAAACCATTAAAAAAGAACCTTTCTCAGGAACTCACTTCTTTACAGCGTAGCTAA
Protein Sequence: MDLKRNTVIALHLEGKSNIEICRALRNLQLNEKFVHRTIQRYNETGSVKKRYGGGRRCTTTAPEVVEKVRHRLDRNLARSANQLAQNLKLSDRSVRRILKKKLKVKPLKKNLSQELTSLQRS

Sequence clustering based on sequence similarity using MMseqs2

100% Identity: iTF_01331493; iTF_00445153; iTF_01246877; iTF_00701962; iTF_01334871; iTF_01246889; iTF_01534800; iTF_01334825; iTF_01246891; iTF_01246939; iTF_00375181; iTF_01246934; iTF_00375185; iTF_01192690;
90% Identity: -
80% Identity: -