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 1e-07 0.00013 22.8 0.2 15 106 4 94 2 102 0.93

2 2 4.6 5.9e+03 -1.9 0.0 96 108 258 270 212 277 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	1e-07	0.00013	22.8	0.2	15	106	4	94	2	102	0.93
2	2	4.6	5.9e+03	-1.9	0.0	96	108	258	270	212	277	0.76

Coding Sequence: ATGCCTAGAGGAAAACATTTGTCGGTTGATATCAAAACGCGTATTGTAGATTTATACCAAAGTGGTGAAAAGCAAATCAATATTGCAAAAAGGTTTAACTTGAATAAATCTATAGTTTCTCGTATTATAAATGGTTTTGTAACATTCGGGCATGTTTTGCCTAAAAAGAAATCTGGAAGACCGAGAAAGACGAATAAATATCaagataaacaaattttaaaaataacaaaaagtgaGCCTTTTTTGAGTtctatcaaaataaagcaacaTGTATCCAAAGAACTAGGCGTACAATTGTCTTCAAGAACAATATGGAATGGACAATGTGAGGCTGGACTCTTTGCCAGAAGACCTGCCAAAAAACCGTTGTTGTCTGCAAAAAACAGACGGTCCCGTCTTAATTTTGCAAGAGCGCATTTACACTGGACACTTCAAGACtggaaaaaagtaatatttagcGATGAATCAAagtttaatttgtttcaaagtGACGGGATGGTGTATGTACGACGCCCTATCAACCAAAGATTGAATCCTAAATATACGCGCCCAACAGTCAAGCATGGCGGAGGGTCACTTATGGTTTGGGGTTGTTTTTCTGGTTTTGGAATGGGTCCTCTCCACAAAATTGATAGAATTATGGATAGGTTTATTTACAAAGATATCCTAGAATGCAGAATGATTCCATATGCAGAAGAAAAAATGCCACTGAGACATATTTTTCAACAGGATAACGATCCGAAACACTcctctaaatatttaaaagAGAACCTATGGGAAATTTTGGACAGAAAAATAAGAGATAAAACATACACCAATAGGGAAGAATTGTTTAATGCATTGAACCAAGCATGGAATAACATGGACCCTgtaataatttctaaattatTACAATCTATGCAACGCCGTTGTGAAGaggttattaaaaataaaggatattttacaaaatactga
Protein Sequence: MPRGKHLSVDIKTRIVDLYQSGEKQINIAKRFNLNKSIVSRIINGFVTFGHVLPKKKSGRPRKTNKYQDKQILKITKSEPFLSSIKIKQHVSKELGVQLSSRTIWNGQCEAGLFARRPAKKPLLSAKNRRSRLNFARAHLHWTLQDWKKVIFSDESKFNLFQSDGMVYVRRPINQRLNPKYTRPTVKHGGGSLMVWGCFSGFGMGPLHKIDRIMDRFIYKDILECRMIPYAEEKMPLRHIFQQDNDPKHSSKYLKENLWEILDRKIRDKTYTNREELFNALNQAWNNMDPVIISKLLQSMQRRCEEVIKNKGYFTKY

Sequence clustering based on sequence similarity using MMseqs2