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 6.2e-09 7.2e-06 25.9 0.3 18 103 6 90 1 103 0.85

2 2 1 1.2e+03 -0.7 0.0 13 30 93 111 83 123 0.68

#	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	6.2e-09	7.2e-06	25.9	0.3	18	103	6	90	1	103	0.85
2	2	1	1.2e+03	-0.7	0.0	13	30	93	111	83	123	0.68

Coding Sequence: ATGGAACGGCACGCTTTTCCATCTAATCTTTGCGAAATTATTATGCGAATGCACAAGCAGGGTCACCGACAAGTTGATATTGCTCAAACTATCGGAGTATCCCAAAGTGTGGTCTTTCGCACCTTTTCACGTTTTCGGGAAACAGGAACTACTGCTAGGCGACCTGGTAGTGGATCCCAACGTATTACAACCCCTAGAGAAGAGCGTAACATGGTCATACAAGCGAGACGCAACTCCTTTTTGACTGTGCGTCAGATCCAAAATCAATTACAAAATGTCCGGGGTCGGCCCATTTGCCTTCAAACAGTTCGGAACCGTTTATGGGAAGTTGGACTGTCATCCTATGCTATGTTGAAGACCAGCTTCAACAGCACGTCACTGGCGGTTACGAAGAGCATGGTGTAA
Protein Sequence: MERHAFPSNLCEIIMRMHKQGHRQVDIAQTIGVSQSVVFRTFSRFRETGTTARRPGSGSQRITTPREERNMVIQARRNSFLTVRQIQNQLQNVRGRPICLQTVRNRLWEVGLSSYAMLKTSFNSTSLAVTKSMV

Sequence clustering based on sequence similarity using MMseqs2