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 2.5e-25 6.8e-22 77.6 0.5 1 45 19 63 19 64 0.97

2 3 1.3e-49 3.7e-46 156.0 0.4 24 106 61 143 60 154 0.96

3 3 3.4e-06 0.0093 15.8 0.1 105 125 176 196 171 196 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	3	2.5e-25	6.8e-22	77.6	0.5	1	45	19	63	19	64	0.97
2	3	1.3e-49	3.7e-46	156.0	0.4	24	106	61	143	60	154	0.96
3	3	3.4e-06	0.0093	15.8	0.1	105	125	176	196	171	196	0.95

Coding Sequence: ATGGCAGTGTCCACCCTCAACATGGCGCCGTACTTCACAGGATACCCGTTCCAAGGTCAGGGCCGCGTCAACCAGCTGGGCGGCGTGTTCATCaacggccggccgctgccgaacCACATCCGCCTCAAGATCgtggagatggcggcggcgggcgtgcggccctGCGTCATCTCGCGCCAGCTGCGCATCgtggagatggcggcggcgggcgtgcggccctGCGTCATCTCGCGCCAGCTGCGCGTGTCGCACGGCTGCGTGTCCAAGATCCTCAACCGCTACCAGGAGACGGGCTCCATCAGGCCGGGCGTCATCGGCGGCTCCAAGCCGCGCGTCGCCACGCCCGAGGTGGAGAAGCGCATCGAGGACTACAAGAAGACCAACCCGGGCATCTTCAGCTGGGAGATCCGCGACAGACTTATCAAGGTGCGTCTCGACTCCTTTCAAGGTCGTGTTTCAGAGGAAACCGACCACCGATCGTTTGCCAATTGCAACCTGACGAATGATGACTCTGTGGGATCCCAGCAGGATGGGATATGCGACAAGACCACGGCGCCGTCCGTGAGCTCCATCAgcaggctgctgcggggcggcaggcgagaCGACTGCGGGGACCCGCGCCGCAACCACTCCATCGACGGCATCCTCGGCGAGTGTGAGTACAAACCTTTACCAGAAACTTGGGGACGGGGACAGAAGGCAGGACctcagtggcgcggcggcaaaCACCGGGGCACGGATGCCGacacagggcggggccggccggccgggccgcga
Protein Sequence: MAVSTLNMAPYFTGYPFQGQGRVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEKRIEDYKKTNPGIFSWEIRDRLIKVRLDSFQGRVSEETDHRSFANCNLTNDDSVGSQQDGICDKTTAPSVSSISRLLRGGRRDDCGDPRRNHSIDGILGECEYKPLPETWGRGQKAGPQWRGGKHRGTDADTGRGRPAGPR

Sequence clustering based on sequence similarity using MMseqs2