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 4.1 9.6e+03 -2.8 0.0 106 123 5 22 2 24 0.70

2 2 1.9e-34 4.4e-31 108.1 1.3 1 56 48 103 48 103 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	2	4.1	9.6e+03	-2.8	0.0	106	123	5	22	2	24	0.70
2	2	1.9e-34	4.4e-31	108.1	1.3	1	56	48	103	48	103	0.98

Coding Sequence: ATGCTCATCTTGAAGCCAATATCTAAAAATCAAAACATACCCGGGTATCGATCCCAGGACAGGGCGTGCCGGATCGATGTGGCCGTCACGCCCGGCGCCCTCCCTCGCCCGGGCATAACCGGGGATAATACCCGGCTCCACGGCCACGGAGGAGTCAATCAACTAGGTGGCGTGTTCGTCAACGGTCGGCCTCTGCCCGATGTCGTCCGACAAAGAATAGTCGAGCTGGCCCACAGCGGCGTGCGGCCTTGCGACATCAGCAGACAGTTGCGGGTGTCTCATGGATGCGTGTCGAAGATATTGTCTAGGTGA
Protein Sequence: MLILKPISKNQNIPGYRSQDRACRIDVAVTPGALPRPGITGDNTRLHGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHSGVRPCDISRQLRVSHGCVSKILSR

Sequence clustering based on sequence similarity using MMseqs2