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 6 0.062 1.9e+02 3.4 0.0 79 118 23 62 16 68 0.84

2 6 0.062 1.9e+02 3.4 0.0 79 118 71 110 63 115 0.84

3 6 0.062 1.9e+02 3.4 0.0 79 118 119 158 111 163 0.84

4 6 0.062 1.9e+02 3.4 0.0 79 118 167 206 159 211 0.84

5 6 0.064 1.9e+02 3.3 0.0 79 118 215 254 208 259 0.84

6 6 0.049 1.5e+02 3.7 0.0 79 118 263 302 256 308 0.82

#	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	6	0.062	1.9e+02	3.4	79	118	23	62	16	68	0.84
2	6	0.062	1.9e+02	3.4	79	118	71	110	63	115	0.84
3	6	0.062	1.9e+02	3.4	79	118	119	158	111	163	0.84
4	6	0.062	1.9e+02	3.4	79	118	167	206	159	211	0.84
5	6	0.064	1.9e+02	3.3	79	118	215	254	208	259	0.84
6	6	0.049	1.5e+02	3.7	79	118	263	302	256	308	0.82

Coding Sequence: ATGGATGATCGGCAAGCATTTTTAATATTGTTTTCTCTCAGTTTCAGAATCCAATCAGCGGGAGAAAACCTAACAAATTCAATTCAACCTGCCAACATCCAAAACCGGGAATGCCTTGGAGTAGAAACCAGAAAGAAACAACTAACAGAGGCTATTACATTGGAGAATAACTTTCCTTGCACAAGTTTCAGAATCCAATCAGCGGGAGAAAACCTAACAAATTCAATTCAACCTGCCAACATCCAAAACCGGGAATGCCTTGGAGTAGAAACCAGAAAGAAACAACTAACAGAGGCTATTACATTGGAGAATAACTTTCCTTGCACAAGTTTCAGAATCCAATCAGCGGGAGAAAACCTAACAAATTCAATTCAACCTGCCAACATCCAAAACCGGGAATGCCTTGGAGTAGAAACCAGAAAGAAACAACTAACAGAGGCTATTACATTGGAGAATAACTTTCCTTGCACAAGTTTCAGAATCCAATCAGCGGGAGAAAACCTAACAAATTCAATTCAACCTGCCAACATCCAAAACCGGGAATGCCTTGGAGTAGAAACCAGAAAGAAACAACTAACAGAGGCTATTACATTGGAGAATAACTTTCCTTGCACAAGTTTCAGAATCCAATCAGCGGGAGAAAACCTAACAAATTCAATTCAACCTGCCAACATCCAAAACCGGGAATGCCTTGGAGTAGAAACCAGAAAGAAACAACTAACAGAGGCTATTACATTGGAGAATAACTTTCCTTGCACAAGTTTCAGAATCCAATCAGCGGGAGAAAACCTAACAAATTCAATTCAACCTGCCAACATCCAAAACCGGGAATGCCTTGGAGTAGAAACCAGAAAGAAACAACTAACAGAGGCTATTACATTGGAGAATAACTTTCCTTGCACAAGCTTGAGTTGCTGCAATAGACCAAGCCAACTGACGGAAGCTATTGGAGGAGATTATTGGCCCAGACTCGGTGACAATTCATTGTTAGGTGCTCCAGACTGTCTTCGTCTAGGCCTAATTCCACTAGGACAGTGTGATGTTTGA
Protein Sequence: MDDRQAFLILFSLSFRIQSAGENLTNSIQPANIQNRECLGVETRKKQLTEAITLENNFPCTSFRIQSAGENLTNSIQPANIQNRECLGVETRKKQLTEAITLENNFPCTSFRIQSAGENLTNSIQPANIQNRECLGVETRKKQLTEAITLENNFPCTSFRIQSAGENLTNSIQPANIQNRECLGVETRKKQLTEAITLENNFPCTSFRIQSAGENLTNSIQPANIQNRECLGVETRKKQLTEAITLENNFPCTSFRIQSAGENLTNSIQPANIQNRECLGVETRKKQLTEAITLENNFPCTSLSCCNRPSQLTEAIGGDYWPRLGDNSLLGAPDCLRLGLIPLGQCDV

Sequence clustering based on sequence similarity using MMseqs2