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 3 3.7e-07 0.0011 21.4 0.0 15 92 3 79 1 103 0.84

2 3 9.5 2.8e+04 -2.6 0.0 74 88 97 111 81 114 0.75

3 3 0.41 1.2e+03 1.9 0.0 3 37 193 226 191 251 0.81

#	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	3	3.7e-07	0.0011	21.4	15	92	3	79	1	103	0.84
2	3	9.5	2.8e+04	-2.6	74	88	97	111	81	114	0.75
3	3	0.41	1.2e+03	1.9	3	37	193	226	191	251	0.81

Coding Sequence: ATGCCTGGAAAATGTTTAAGTGAAGATATTCTCAATCGAGCTGCACAGTTAGTACGGCAAGGTGCTCGGCAAAGACAGGTCGGTCGAGTGTTAAACATGTCACATAGAGTCATAGGAAGAGCTTTAAACCGTTTTCATTTAACTGGTGCTGTGGCATTTTGGCATGGGGGAAGTCGAAGACGATCTACAACTCAAGCTCAGGATCAATTTCTAAGACTGTTGGCAAGAATAAATCCCAGAAATAAtgcttcaatattaaataatgccTTACATGCCGCTGCTGGAGTAACAATATCGACTCCAACTGTAAGGAGAAGGTTGCACGAGTATAACCTTAGAGCTAGACTTGCTAGACGACCACCAACTTGTCTGCATTTAAATGCACAACACCGTGAAGCACGGAGAAATTGGGCTCGAGATCATTTACACTGGAACCTTCATGAATGGGGATCGTGCATGTTCTCAGATGAATCAAGATTCACTTTAAACCGTTCAGACGGACGAATTTTAGTGTGGCGAAGGCCTGGTGAAAGATATCGCGAAGATTTGATGTCTCCAAGAATAGCTTTTGGAGGTGGCGGTGTTACGGTATGGGGAggcattattttaaatggccGCACAGAACTCGTTGTTTTTAGATATGAAACTGTTAATGCACAACGGTATGTGGACCAGTGTGTATTACTAGTAGTGGTACCACTTGCCCAAAAGTTTGGAAACGAATTCATATTTATGTACGACAACGCCCGTCCTCATCGTGCGCAGATTGTGAATAACGTATTTGAACAGCACGGAATAGCTAGAATGATATGGCCTCCACATTCACCCGACTGTAATCCCATAGAATATATATGggataaattaaaaagacaAATGACACAACGACAACAGCCTCCAGAAACGCTACAGCAGTTGGAAAATGCGATTTTGGAGGAATGGGAATTGATTCCTCAAGAACTCGTTAATAACCTTATCAGAAGTATGCCTGGAAGGTGTCAAGAGGTACATCGTGTTAGAGGAGGTcccataaaatattaa
Protein Sequence: MPGKCLSEDILNRAAQLVRQGARQRQVGRVLNMSHRVIGRALNRFHLTGAVAFWHGGSRRRSTTQAQDQFLRLLARINPRNNASILNNALHAAAGVTISTPTVRRRLHEYNLRARLARRPPTCLHLNAQHREARRNWARDHLHWNLHEWGSCMFSDESRFTLNRSDGRILVWRRPGERYREDLMSPRIAFGGGGVTVWGGIILNGRTELVVFRYETVNAQRYVDQCVLLVVVPLAQKFGNEFIFMYDNARPHRAQIVNNVFEQHGIARMIWPPHSPDCNPIEYIWDKLKRQMTQRQQPPETLQQLENAILEEWELIPQELVNNLIRSMPGRCQEVHRVRGGPIKY

Sequence clustering based on sequence similarity using MMseqs2