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 3 0.0017 1.9 9.9 0.2 49 94 18 62 13 100 0.78

2 3 0.0016 1.8 10.0 0.2 49 94 99 143 92 181 0.78

3 3 0.0021 2.5 9.6 0.1 49 84 180 214 175 233 0.73

#	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	3	0.0017	1.9	9.9	0.2	49	94	18	62	13	100	0.78
2	3	0.0016	1.8	10.0	0.2	49	94	99	143	92	181	0.78
3	3	0.0021	2.5	9.6	0.1	49	84	180	214	175	233	0.73

Coding Sequence: ATGGGATTTATTTTCCGTAAATTCGACGACAAACCAGTACCTTCTGTGTCGACAATACACGCCATAATAAAGCGGTTTGAAGAAACAGGTAGTGTCATTCCGAAGAAAAGGGGTGGCAATCGAAGAAGAAATAACGCGCAACTGGAAGAAATGGTGCTGGGAATGATTAATGTTAATCCAACTTTCAGTAGCAGGTATATTGCTCAAGAATGCAATGTATCTCACTCTACTGTAAAGAatatcttaaatttattttccgtaaaATTCGACGACAAACCAGTACCTTCTGTGTCGACAATACACGCCATAATAAAGCGGTTTGAAGAAACAGGTAGTGTCATTCCGAAGAAAAGGGGTGGCAATCGAAGAAGAAATAACGCGCAACTGGAAGAAATGGTGCTGGGAATGATTAATGTTAATCCAACTTTCAGTAGCAGGTATATTGCTCAAGAATGCAATGTATCTCACTCTACTGTAAAGAatatcttaaatttattttccgtaaaATTCGACGACAAACCAGTACCTTCTGTGTCGACAATACACGCCATAATAAAGCGGTTTGAAGAAACAGGTAGTGTCATTCCGAAGAAAAGGGGTGGCAATCGAAGAAGAAATAACGCGCAACTGGAAGAAATGGTGCTGGGAATGATTAATGTTAATCCAACTTTCAGTAGCAGGTATATTGCTCAAGAATGCAATGTATCTCACTCTACTAAGAGATTGCACGCCCTAATGAAGAGGTCTGGTTTCAGCATGATGGGTGTCAGCCCATTTCAGCAGTGGGAAGTAAGAAACTACCTAGATGCTGTTTTTCCTGATCATTGGATTGGACGCGGTGGAGTTATAAATTGGCCAGCCAGATCTCCCTGA
Protein Sequence: MGFIFRKFDDKPVPSVSTIHAIIKRFEETGSVIPKKRGGNRRRNNAQLEEMVLGMINVNPTFSSRYIAQECNVSHSTVKNILNLFSVKFDDKPVPSVSTIHAIIKRFEETGSVIPKKRGGNRRRNNAQLEEMVLGMINVNPTFSSRYIAQECNVSHSTVKNILNLFSVKFDDKPVPSVSTIHAIIKRFEETGSVIPKKRGGNRRRNNAQLEEMVLGMINVNPTFSSRYIAQECNVSHSTKRLHALMKRSGFSMMGVSPFQQWEVRNYLDAVFPDHWIGRGGVINWPARSP

Sequence clustering based on sequence similarity using MMseqs2