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 1.5e-34 3.2e-31 108.2 0.9 1 59 3 61 3 69 0.96

2 2 5.8e-23 1.2e-19 70.8 0.6 13 56 223 266 216 268 0.95

#	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	1.5e-34	3.2e-31	108.2	0.9	1	59	3	61	3	69	0.96
2	2	5.8e-23	1.2e-19	70.8	0.6	13	56	223	266	216	268	0.95

Coding Sequence: ATGTTTGGTCACGGCGGCGTCAACCAACTTGGTGGGGTGTTCGTAAACGGGCGGCCGTTGCCCGACGTCGTGCGACAACGGATAGTGGAGCTGGCCCACAGCGGCGTCCGGCCGTGCGACATCAGCCGACAGCTGCGGGTCTCCCACGGCTGCGTCTCTAAGATCCTGTCCAGGTCAGTGGAAGGTTTACTCCACCAAGTTGGTTCTGACTTCCATGCCTCGAGCTCCACTGCGTCTGATCAACAGCCTGCGGATCCGGAAAAACCGGATGGTTCTGACTACTATGCAGGGGCTGACTCCACTGCGTCTGACCTCCAGCCTGCGGACCCTGAAAGACTCTCAGCTGGGTTTGATGAACTTCGATCTACCTCGGCAAGGTCTGAGCCTGCGTCTCATGACTCTACGATTGAGTTTACGAATCCTGAAAGAACTGCTCGGAGATTTTATGAACTCCAAACCACTGCGAGGTTTGAAGAGCCTCCTGAGAGGTTAGACGATCTTCATAATGCCTCTAGGAGGTTAGAGAACCTCCAATCGCACGCGGAGAGGCTCCAAACTGCTTTAACAAGGGCTGAAGAGCTTGAGCGGTTAGACAATCACGCTGTCTCTGGGATAGAGCAATCGCATTCTGAGAGGATAGAAGATTTCTACCTCCACCAAGGGTCTATAAACGGCAGACCATTGCCAGAAGCAGTCAGACGCAGGATAGTGGAGCTGGCTCGCAGTGGCGTGAGGGCTTGCGACATCAGCCGGCGGCTACGGGTCTCTCATGGCTGCGTGTCCAAGATCCTGTCGAGGTCAGTCTAA
Protein Sequence: MFGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHSGVRPCDISRQLRVSHGCVSKILSRSVEGLLHQVGSDFHASSSTASDQQPADPEKPDGSDYYAGADSTASDLQPADPERLSAGFDELRSTSARSEPASHDSTIEFTNPERTARRFYELQTTARFEEPPERLDDLHNASRRLENLQSHAERLQTALTRAEELERLDNHAVSGIEQSHSERIEDFYLHQGSINGRPLPEAVRRRIVELARSGVRACDISRRLRVSHGCVSKILSRSV

Sequence clustering based on sequence similarity using MMseqs2