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 1.6e-06 0.0021 19.4 0.1 24 66 9 51 3 70 0.86

2 2 0.053 69 4.8 0.0 41 108 50 111 47 121 0.72

#	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	1.6e-06	0.0021	19.4	0.1	24	66	9	51	3	70	0.86
2	2	0.053	69	4.8	0.0	41	108	50	111	47	121	0.72

Coding Sequence: ATGGATACCACACCTGAAGAAGCCGCGCAAGTTGTTGCCTTGTTGGAACAAGGACTTAGCCAGCGAGTAGTCGCTGCCCAGCTTCGCTTAAGCCAGTCTGCTGTGTCCCGGGTCTACAGACGATTTCGAGAGACCGGTGCCTTCAATCGAAGACTAAGAACCAGCCGCCACCGGTGTACTTCTGACAGAGACGACCGTTTCATTGTCTCAACATCGCTGCGCAATCGGCATCTGACGGGTGTTGATGTTCAACAAGAACTCAGGCACGTTCGTGGTGTAGCTGTAAGTGTAAGCGAGTGGACAATAAGAAGACGTCTGAAAGCAGCCAATCTCACTCCAAAAAGGGCTGCGACGGGGCCCAAATTAAACCCAAATACCCACCCACCGACAAGCGCGTCTTCAGTTTGCTCAAGAGCATGTCAATTGGACCATTGCCCAATGGCAGTCGGTTCTCTTTACTGA
Protein Sequence: MDTTPEEAAQVVALLEQGLSQRVVAAQLRLSQSAVSRVYRRFRETGAFNRRLRTSRHRCTSDRDDRFIVSTSLRNRHLTGVDVQQELRHVRGVAVSVSEWTIRRRLKAANLTPKRAATGPKLNPNTHPPTSASSVCSRACQLDHCPMAVGSLY

Sequence clustering based on sequence similarity using MMseqs2