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 4 1.7e-32 6.2e-29 101.6 0.4 1 62 18 79 18 90 0.91

2 4 6.2e-10 2.3e-06 28.7 0.3 34 59 91 116 81 128 0.83

3 4 9.9e-10 3.6e-06 28.0 0.2 34 56 132 154 117 165 0.85

4 4 0.00013 0.49 11.5 0.0 18 35 169 186 157 187 0.86

#	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	4	1.7e-32	6.2e-29	101.6	0.4	1	62	18	79	18	90	0.91
2	4	6.2e-10	2.3e-06	28.7	0.3	34	59	91	116	81	128	0.83
3	4	9.9e-10	3.6e-06	28.0	0.2	34	56	132	154	117	165	0.85
4	4	0.00013	0.49	11.5	0.0	18	35	169	186	157	187	0.86

Coding Sequence: ATGCATAGCGCGGCGATGGGCGGAGGGGCGCTTTTCGGGTGCTCCTCCGCCGGCCACAGCGGAATCAATCAGCTCGGAGGAGTTTACGTCAATGGGAGGCCGCTGCCGGACTCCACGAGGCAGAAGATCGTGGAGCTGGCGCACTCGGGCGCGCGGCCCTGCGACATCAGCCGGATCCTGCAGGTCTCCAACGGCTGCGTCTCCAAAATACTCGGCAGGTCAGTTGCATCCGTGGTCTATAGGAGGCAGGCCGCTGCCGGACTCGACGAGGCAGAAGATTGCGACATCAGCCGGATCCTGCAGGTCTCCAACGGCTGCGTCTCCAAAATACTCGGCAGGTCAGTTGCATCCGTGGTCTATAGGAGGCAGGCCGCTGCCGCCGGACTCGACGAGGCAGAAGACTGCGACATCAGCCGGATCCTGCAGGTCTCCAACGGCTGCGTCTCCAAGATACTCGGCAGGCCAGTTGGACGCGTGGTTTGTAGGAATTGTAGGAGGCAGGCCGCCGCGGACTCCACGAGGCAGAAGATCGTGGAGCTGGCGCACTCGGGAGCGCGGCTCTGA
Protein Sequence: MHSAAMGGGALFGCSSAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRSVASVVYRRQAAAGLDEAEDCDISRILQVSNGCVSKILGRSVASVVYRRQAAAAGLDEAEDCDISRILQVSNGCVSKILGRPVGRVVCRNCRRQAAADSTRQKIVELAHSGARL

Sequence clustering based on sequence similarity using MMseqs2