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 6.1e-69 1.6e-65 219.6 0.2 1 117 30 146 30 147 0.99

2 3 1.6e-23 4.2e-20 72.8 0.0 68 117 146 195 145 197 0.97

3 3 6.5e-20 1.7e-16 61.2 0.0 74 118 196 240 194 240 0.98

#	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	6.1e-69	1.6e-65	219.6	0.2	1	117	30	146	30	147	0.99
2	3	1.6e-23	4.2e-20	72.8	0.0	68	117	146	195	145	197	0.97
3	3	6.5e-20	1.7e-16	61.2	0.0	74	118	196	240	194	240	0.98

Coding Sequence: ATGctgccagcgcagcagctgGCCCCGATCAGCCCCTGGCCCCCTGACTCCAACCTGCTGGACCGCATGGACGACCTGGCGCACAAAGGTCACAGCGGTGTTAACCAGCTCGGCGGCGTGTTTGTAGGAGGCAGACCTCTCCCAGACTCGACGCGGCAGAAGATTGTGGAGCTGGCGCACTCGGGGGCCAGGCCGTGTGATATCAGCAGGATCCTGCAAGTCTCCAACGGCTGCGTGTCCAAGATCCTCGGCAGGTACTACGAGACCGGCTCCATCAGGCCGCGTGCGATCGGCGGCTCCAAGCCCAGGGTAGCCACAGCCGAGGTGGTGAGCAAGATAGCGCAGTACAAGCGGGAGTGCCCCTCGATCTTCGCCTGGGAGATCAGGGACCGTCTGCTGAGTGAAGGCGTCTGCACCTCGGATAACATACCCTCTATTGACGGCTCCAAGCCCAGGGTAGCCACAGCCGAGGTGGTCAGCAAGATAGCGCAGTACAAGCGGGAGTGTCCCTCGATCTTCGCCTGGGAGATCAGGGACCGTCTGCTGAGTGAAGGCGTCTGCACCTCGGATAATATTCCCTCTCTCAGGGTAGCCACAGCCGAGGTGGTCAGCAAGATAGCGCAGTACAAGCGGGAGTGCCCCTCGATCTTCGCCTGGGAGATGAGGGACCGTCTCCTCAGTGAAGGCGTCTGCACGTCGGATAATATTCCCTCTGTGAGTTGA
Protein Sequence: MLPAQQLAPISPWPPDSNLLDRMDDLAHKGHSGVNQLGGVFVGGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATAEVVSKIAQYKRECPSIFAWEIRDRLLSEGVCTSDNIPSIDGSKPRVATAEVVSKIAQYKRECPSIFAWEIRDRLLSEGVCTSDNIPSLRVATAEVVSKIAQYKRECPSIFAWEMRDRLLSEGVCTSDNIPSVS

Sequence clustering based on sequence similarity using MMseqs2