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 0.0048 12 7.1 0.0 29 103 67 140 59 148 0.83

2 3 0.0052 13 6.9 0.0 29 103 153 226 151 236 0.82

3 3 0.0046 12 7.1 0.0 29 103 239 312 235 325 0.83

#	of	c-Evalue	i-Evalue	score	hmm coord from	hmm coord to	ali coord from	ali coord to	env coord from	env coord to	acc
1	3	0.0048	12	7.1	29	103	67	140	59	148	0.83
2	3	0.0052	13	6.9	29	103	153	226	151	236	0.82
3	3	0.0046	12	7.1	29	103	239	312	235	325	0.83

Coding Sequence: ATGGTTTACAATACGCTTCGGCATGTTGAAGAATTTGGAACCATTCAAAACATGGAGCAATGTCCTCGTAAAAGGAAGACCACACCAAAAGAAGACAAAGTAATTTATCGTTTGTCAGCCAAGGGTCCGTTTCAGAGCTCCAGTGCCATGCGCAACGAACTGAAAGAAAATTATGATGTCAACATATCACCAAGGACGATGAAAGACAAGGGAAGGACAGTTTCTGATATATCCAAGCTGTTGGAGTTCTCCAGAAAAATGGTTTACAATACGCTTCGGCATGTTGAAGAATTTGGAACCATTCAAAACATGGAGCAATGTCCTCGTAAAAGGAAGACCACACCAAAAGAAGACAAAGTAATTTATCGTTTGTCAGCCAAGGGTCCGTTTCAGAGCTCCAGTGCCATGCGCAACGAACTGAAAGAAAATTATGATGTCAACATATCACCAAGGACGATGAAAGACAAGGGAAGGACAGTTTCTGATATATCCAAGCTGTTGGAGTTCTCCAGAAAAATGGTTTACAATACGCTTCGGCATGTTGAAGAATTTGGAACCATTCAAAACATGGAGCAATGTCCTCGTAAAAGGAAGACCACACCAAAAGAAGACAAAGTAATTTATCGTTTGTCAGCCAAGGGTCCGTTTCAGAGCTCCAGTGCCATGCGCAACGAACTGAAAGAAAATTATGATGTCAACATATCACCAAGGACGATGAAAGACAAGGGAAGGACAGTTTCTGATATATCCAAGCTGTTGGAGTTCTCCAGAAAAATGGTTTACAATACGCTTCGGCATGTTGAAGAATTTGGAACCATTCAAAACATGGAGCAATGTCCTCGTAAAAGGAAGACCACACCAAAAGAAGACAAAGTAATTTATCGTTTGTCAGCCAAGGGTCCGTTTCAGAGCTCCAGTGCCATGCGCAACGAACTGAAAGAAAATTATGATGTCAACATATCACCAAGGACGGTAATTTATGTACAATACATGAACATTGGTGAATTATATTAA
Protein Sequence: MVYNTLRHVEEFGTIQNMEQCPRKRKTTPKEDKVIYRLSAKGPFQSSSAMRNELKENYDVNISPRTMKDKGRTVSDISKLLEFSRKMVYNTLRHVEEFGTIQNMEQCPRKRKTTPKEDKVIYRLSAKGPFQSSSAMRNELKENYDVNISPRTMKDKGRTVSDISKLLEFSRKMVYNTLRHVEEFGTIQNMEQCPRKRKTTPKEDKVIYRLSAKGPFQSSSAMRNELKENYDVNISPRTMKDKGRTVSDISKLLEFSRKMVYNTLRHVEEFGTIQNMEQCPRKRKTTPKEDKVIYRLSAKGPFQSSSAMRNELKENYDVNISPRTVIYVQYMNIGELY

Sequence clustering based on sequence similarity using MMseqs2