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 5e-41 3.6e-37 129.0 0.2 1 97 5 101 5 124 0.86

2 2 0.95 6.9e+03 -1.1 0.0 84 105 138 159 124 178 0.63

#	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	5e-41	3.6e-37	129.0	0.2	1	97	5	101	5	124	0.86
2	2	0.95	6.9e+03	-1.1	0.0	84	105	138	159	124	178	0.63

Coding Sequence: ATGCCTCACACTGGCCAAGCGGGAGTGAACCAGCTGGGAGGAGTGTTCGTGAATGGTAGGCCTCTGCCCGACTGTGTTCGCCGGCGAATCGTCGAGTTGGCTCTGATGGGAGTACGACCTTGCGATATCTCTCGCCAGCTCCTAGTCTCTCATGGCTGCGTCTCCAAGATCCTCACAAGGTTTTATGAAACTGGCTCCATTCGTCCAGGCTCTATAGGACCTCCCAAAAACAGAAATGCTTATGGAACCAAGAGACGATGCAAACAAGACACATGGGAAGAGAAGTCGAGAGTGCTCACATGGCAGAACACAAGTTTAGCAACAAAAGGAGAATTGGATAGAACAAAAGAACAGTGGTCATCTAGTGAAGAAGAAGATGAAACCAGATCCATAAAACCACGAGGATATTCTATTGAAGAGATACTGAAAAAGAGTCCACCCCGAAACGCCTGGTCGTCTGTGCAGACACTCCTCAACCAACCCTGTGGTCTCCTTGTCGACAAGCCATGTGACTGTGACCTCAGTAGGCACCTTAGCCCCTACGTCCACTATAACCTCTGA
Protein Sequence: MPHTGQAGVNQLGGVFVNGRPLPDCVRRRIVELALMGVRPCDISRQLLVSHGCVSKILTRFYETGSIRPGSIGPPKNRNAYGTKRRCKQDTWEEKSRVLTWQNTSLATKGELDRTKEQWSSSEEEDETRSIKPRGYSIEEILKKSPPRNAWSSVQTLLNQPCGLLVDKPCDCDLSRHLSPYVHYNL

Sequence clustering based on sequence similarity using MMseqs2