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 2.2e-08 2.2e-05 25.2 0.2 22 103 16 96 6 110 0.89

2 2 8.6 8.7e+03 -2.6 0.0 99 122 109 134 106 137 0.48

#	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	2.2e-08	2.2e-05	25.2	0.2	22	103	16	96	6	110	0.89
2	2	8.6	8.7e+03	-2.6	0.0	99	122	109	134	106	137	0.48

Coding Sequence: ATGCAAATGGCAAATATGACTAGGAAGAAGCAACTATCGATTGGATGCAAGAAAGCAATAATTAACGCTGCTAACAACGGAAGATTAATGCAGGATATCGCTTTGGAGTTTTGTGTAGCAACATCAACAATATCGCGTATTATATCCCGATATCGGGAACAAGGGGATATCAATCGCAAAGTGGGAAGTGGCCGTCCACGCAAAACAACTTCCAGATTAGATCGTGAGATCATAAGACAGGTTAAAGTTAATCCCTTTAAAACTGCAGTGGAAGTTACTCAGGACTTGAATGAACATTTTGATGTTAACGTAGGGGTACACACAGTTAGGCGACGATTAGTGGAGTCAAAACTGTATGCAAGACGACCAGCTAGAAAACCATTCATCAGTTCCATCAAGAGGAAGAAACGGCTAGATTTTGCAAAGCGCCATATGCATTGGACAAGTGAGCAATGGACAAAAGTTTTATGGAGTGATGAGAGCAGTTTCAACTTGTTCTCGTCAGATGGCATTAGGTATGTGCGAAGGCCCCCGGGACAAAGGTACAGCCCTAGATATCAAGTTCCAACAATTAAACATGGGGGAGGGTCAGTAATGGTGTGGGGCTCATTTTCTCGTCAAGGCGTGGGCCCGACTGAATGGGAACAAATACCTGCGAGCTATTTGGTGTCGTtgattgactcaatgcctaaaaggttacgcgccgttattgccaataaaggtttcgcaacaaaatattaa
Protein Sequence: MQMANMTRKKQLSIGCKKAIINAANNGRLMQDIALEFCVATSTISRIISRYREQGDINRKVGSGRPRKTTSRLDREIIRQVKVNPFKTAVEVTQDLNEHFDVNVGVHTVRRRLVESKLYARRPARKPFISSIKRKKRLDFAKRHMHWTSEQWTKVLWSDESSFNLFSSDGIRYVRRPPGQRYSPRYQVPTIKHGGGSVMVWGSFSRQGVGPTEWEQIPASYLVSLIDSMPKRLRAVIANKGFATKY

Sequence clustering based on sequence similarity using MMseqs2