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-11 9e-09 36.1 1.0 18 89 26 97 19 120 0.87

2 2 1.7 6.9e+02 1.0 0.3 13 56 83 124 78 161 0.77

#	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-11	9e-09	36.1	1.0	18	89	26	97	19	120	0.87
2	2	1.7	6.9e+02	1.0	0.3	13	56	83	124	78	161	0.77

Coding Sequence: ATGTTATTTCAGTCGTATTCATGCTGTTTATCTCTTATTCCAGTCGATCCGCTTCCATTTTTGAAGTTTGCCATGGTCTCCGAAGAAGCTCGCCACGCCGTCGTTTCGTTACACAAGCAGGGATGGAAGAATTGCCGGATTTCCAGAACGCTGAAGTTGAAGAAATATGATGTGTCGCGGGTCCTGAAGCGTTACAAGGAAACTGGAAGTGTTGCAGATCGTCCTCGAAGCGGAAGACCCGTCGAAGTGCGTTCAAAAGCTATGAAGAACCGAATTCGATGCCGAGTGAAGCGAAATTCGGAACGATCTCTTAGGAAGATGGCAAAAGAGCTGAAAATTGGCGATGGGAGCGTGCAGCGGATTGTGAAGGAAGATCTGAAGCTCGTCTCTCACAGGAAGATCGCTGCTCACGTTTTGACCGACAAAATGAAGGAGAAACGGCTTGAAAACTGCAAGAGGATGTTGGCCGTGGTCGCAAGTCGAGGTTGTCAGAAAATTCTCTTTTCAGATGAGAAGCTTTTCAACCTGGAACCCGTCCATAATCGCCAGAACGATCGCATACTGCTACCAAAAGGAACTCCTCGAGCTGTGAACATCGAAAGAAGCCACTTCAGCAAGGATTCCGTGATGGTTTGGGCCGGAATCACCGCGAAAGCCAAAACGAAACTGATCTTCCTGGAAAAAGGCGTCAAGATCAACTCCGAAGTGTACCAGAACGCTGTTTTGAAGGCTGAAGTGGTTCCTTTCGCCCAGAAGCACTTCCCGGACGGCAACTGGATCTTCCAACAAGATTGGGCCCCTATCTTGGAGAGCAAGGCGTGCGCTACAAAACACGCCAATGTGGAGTCCCTGAAGTGCGCTCTACAGAAAGCATGGGACGATTTGGACCAGAAGACCCTTgcgaaaatcgcgaaaaatttcaaaacccGTTTGGAGGCCTGCATCGAAGTTGAAGGCGGCCATTTCGAACACTTGTTGTAA
Protein Sequence: MLFQSYSCCLSLIPVDPLPFLKFAMVSEEARHAVVSLHKQGWKNCRISRTLKLKKYDVSRVLKRYKETGSVADRPRSGRPVEVRSKAMKNRIRCRVKRNSERSLRKMAKELKIGDGSVQRIVKEDLKLVSHRKIAAHVLTDKMKEKRLENCKRMLAVVASRGCQKILFSDEKLFNLEPVHNRQNDRILLPKGTPRAVNIERSHFSKDSVMVWAGITAKAKTKLIFLEKGVKINSEVYQNAVLKAEVVPFAQKHFPDGNWIFQQDWAPILESKACATKHANVESLKCALQKAWDDLDQKTLAKIAKNFKTRLEACIEVEGGHFEHLL

Sequence clustering based on sequence similarity using MMseqs2