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 8.8e-63 1.5e-59 199.3 0.2 3 125 27 144 25 144 0.97

2 2 4e-15 6.8e-12 45.3 0.2 3 35 239 271 237 271 0.96

#	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	8.8e-63	1.5e-59	199.3	0.2	3	125	27	144	25	144	0.97
2	2	4e-15	6.8e-12	45.3	0.2	3	35	239	271	237	271	0.96

Coding Sequence: ATGTCCTTCTGTTTGTCCACAGATCCCAGTGCAGCGGGCATGGGCCAGCCGGGCGTGGGGGGTGCAGCACAACAGTACGGGGAGGTGAACCAGCTCGGGGGGGTGTTCGTGAACGGGCGGCCGCTGCCCAATGCGGTGCGGCTGCGGATAGTCGAACTAGCACAATTAGGCATCAGGCCATGCGACATCAGCCGGCAACTACGCGTGTCCCACGGCTGCGTGTCCAAGATACTGGCGCGCTACCACGAGACCGGATCCATCCTGCCCGGCGCCATCGGGGGGTCCAAGCCCAGGGTGGTGTCGTACATAAAGCAGCTGAAAGCCAAGGACCCCGGCATCTTCGCGTGGGAGATCCGCGACCGACTCCTCGCCGACGGCGTCTGCGACAAGTACAACGTGCCCTCGGTGTCGTCCATCAGTCGGATACTGAGGAACAAGCTCGGAGGGGGCGCGCTCTACCCCGTGCCCCCGCTCTACCCCGTGCCCCCGCAGCGGTGCTGGCCGCTGCACCAGCCCTACGATTACTACGTGTATCTACAGGTACCTACGAATAGTCTATCTACAGAATTTACAACGTGCCCTCGATGTCGTCCATCATCGGACCATCCACCATCGTCGGATACTGAGGAACAAGCTCGGAGGGAGCGCGCTTTACCCCATCCCAGTGCAGCGGGCATGGGCCAGCCGGGCGTGGGGGGTGCAGCACAACAGTACGGGGAGGTGAACCAGCTCGGGGGGGTGTTCGTGAACGGGCGGCCGCTGCCCAATGCGGTGCGGCTGCGGATAGTCGAACTAGCGCAATTAGGCATCAGGTAA
Protein Sequence: MSFCLSTDPSAAGMGQPGVGGAAQQYGEVNQLGGVFVNGRPLPNAVRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVVSYIKQLKAKDPGIFAWEIRDRLLADGVCDKYNVPSVSSISRILRNKLGGGALYPVPPLYPVPPQRCWPLHQPYDYYVYLQVPTNSLSTEFTTCPRCRPSSDHPPSSDTEEQARRERALPHPSAAGMGQPGVGGAAQQYGEVNQLGGVFVNGRPLPNAVRLRIVELAQLGIR

Sequence clustering based on sequence similarity using MMseqs2