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 2e-33 5.7e-30 104.4 0.4 1 59 18 76 18 77 0.98

2 2 5.2e-13 1.5e-09 38.5 0.1 23 57 74 108 73 118 0.94

#	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	2e-33	5.7e-30	104.4	0.4	1	59	18	76	18	77	0.98
2	2	5.2e-13	1.5e-09	38.5	0.1	23	57	74	108	73	118	0.94

Coding Sequence: ATGCACAGCGCTGCGATGGGCGGAGGGGCACTCTTCGGGTGCTCCTCCGCCGGCCACAGTGGAGTCAATCAGCTCGGTGGAGTCTACGTCAACGGGAGGCCCTTGCCTGACTCCACGCGCCAGAAGATCGTGGAGCTGGCGCACTCGGGAGCCCGGCCCTGCGACATCAGCCGCATCCTGCAGGTCTCCAACGGCTGCGTGAGCAAGATACTCGGCAGGCGCCAGGAGATTTTGGAGCTAGCGCATTCAGGAGCCAAGCCCTGCAACGTCAGCCTCATTCTGCAGGTCTCCAACGACTGTGTCAGCAAGATATTCGGCAGGTCAGTTGCACTCCAACCATTTAATGCAGTAGCAGACCCTTTCTGTAGACCTTTAACGACCACTTCACCAAGGTACTCACCAAGTCTATTCTTACCGCAAAAGAAACACCTGCTACTATCAGCTTTAAGTTGCACTGATATCCACTCTGCAGTAGAAGATTCTTATTTCACACCACCTCGGCTTTTAGAGTAA
Protein Sequence: MHSAAMGGGALFGCSSAGHSGVNQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRRQEILELAHSGAKPCNVSLILQVSNDCVSKIFGRSVALQPFNAVADPFCRPLTTTSPRYSPSLFLPQKKHLLLSALSCTDIHSAVEDSYFTPPRLLE

Sequence clustering based on sequence similarity using MMseqs2