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 1.6e-10 1.7e-07 32.6 0.7 20 101 2 86 1 100 0.87

2 2 0.47 5.1e+02 2.0 0.0 38 96 83 143 78 165 0.72

#	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	1.6e-10	1.7e-07	32.6	0.7	20	101	2	86	1	100	0.87
2	2	0.47	5.1e+02	2.0	0.0	38	96	83	143	78	165	0.72

Coding Sequence: ATGAACGCAACACGATCACTGATTTTAAATCTACATTTGGAAGGAAAATCGACTTGCAAAATTATCAACTGCTTAAAAGACTTGCAAATAAGCCGGCGATTTGTGCAGCGAACGGTAGCTCGTTTTAGGAGGACTGGCAGCGTTCTTCCAGATTTAAATGGTGGTCCAAAACGGACAGTGAGGACGCCGACCCTGGTTAAAAAGGTGAGGGAAAGAATTCGTAGAAATTGCTCAGTTTCCGGAAGAAAAATCGCACGGGAGCTAAACGTCAGCCAAGACACCATCCATAAGGTCATTTCTGAAGACCTTAAGCTCAAGGCGTATAAAAAGAAGAGGATTCACGGCCTTACGGAACGCCAGCGACTTATGGGAAAGGAAAGAAGTGAGGTTATCCTTCGGAGACACGCTGATTGCAGTATCATATTTTCAGATGAAAAACTGTTCCTTCTACAGGCAAGTCATAACCCCCAAAATGACAGAGTCTACGCGGCAAGCATGGAAgatattcctaaagaaaaaaaatccgttCAAAGGTTTCAAAACGTAACGTCCGTCATGGTTTGGGGTGCTGTTTCTGAAAAAGGAAAATTACCCCTGCTTTTCATAGAAAAAGGGGTCAAAATCAATGCTCAATACTACCTGAACgaggttttaaaaactcatttgcTGCCGTTTGCCAAGCAGATTTACGGAAACGAAGAGTTTTGCTTTCAACAAGATTCCGCTCCAGCCCACAAGGCAAAAATCGTGCAAAGCTGGTGTCGTGCTCATTTGCCAGATTTTATATCTACTGAGGAATGGCCTCCGTCTTCCCCTGACCTTAATCCTCTAGATTTTTCTATTTGGGTTATTATGCTTAGCAAATTaagcaatgttaaaaatatgactGTTGATGgattcaagaaaaaattaaggaaGATATGGGACGATATTTCGGATGAGGAGGTACGTGCCGCGTGCTCATCTTTTAGAAAACGTCTTAAgttggtaaaaaaaatgaaaggcgAACGGTTTGAATTAAATGATGAGAAATTGTGA
Protein Sequence: MNATRSLILNLHLEGKSTCKIINCLKDLQISRRFVQRTVARFRRTGSVLPDLNGGPKRTVRTPTLVKKVRERIRRNCSVSGRKIARELNVSQDTIHKVISEDLKLKAYKKKRIHGLTERQRLMGKERSEVILRRHADCSIIFSDEKLFLLQASHNPQNDRVYAASMEDIPKEKKSVQRFQNVTSVMVWGAVSEKGKLPLLFIEKGVKINAQYYLNEVLKTHLLPFAKQIYGNEEFCFQQDSAPAHKAKIVQSWCRAHLPDFISTEEWPPSSPDLNPLDFSIWVIMLSKLSNVKNMTVDGFKKKLRKIWDDISDEEVRAACSSFRKRLKLVKKMKGERFELNDEKL

Sequence clustering based on sequence similarity using MMseqs2