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 1.2 2.8e+03 -1.1 0.0 80 111 4 35 2 49 0.70

2 3 5.7e-10 1.3e-06 29.0 0.1 16 91 99 174 93 191 0.86

3 3 0.0011 2.4 8.8 0.0 46 91 200 245 184 253 0.78

#	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	1.2	2.8e+03	-1.1	0.0	80	111	4	35	2	49	0.70
2	3	5.7e-10	1.3e-06	29.0	0.1	16	91	99	174	93	191	0.86
3	3	0.0011	2.4	8.8	0.0	46	91	200	245	184	253	0.78

Coding Sequence: ATGGAAGACATTTCGGCAACAGTTGCCAAGATAAAGGAGGAAACGCCCACTACTCACGGGGAGGTCGTAACAGAGATTGAAATCAAAGAAGAAATAACAGAAGCACCTAAAATGAATGCTGGTTCATACCATGAAGATCTAGATGATGAACAGGCTCCTTCAAGCTCATTAGATAGTTTAGCAACCGATGATGAGTGCTTAAAAGAGAAGATAAAAAAAGGTAGTAACAAACAGATTAAATCAAGAACAGAGACGACAGAGCGTATGGGATGTCAGAAAGcCATGGGCTCGCGAAGGAACCTCAATAACATGGAACGCACCAAGATAATTCATCTACGAGACGAAGGAGCAAACATAAGCCAAATAGCCCAAGAGCTTCATATGTCGAGAAATACAGTCCGGCTGTGGCTTAAGCGCTACGACAGCGAGGGGCACGTCGCGCCTAAAGTGCGTTGTTCGCGACCGCGCGTCATCACGCAGGAGCGCCTGGAGCGGATGGTCGCCGCGTACGAGCGGGAGCCGTGCACTCCGACGCGGGTGTTCGCGGACGAGTACGAGTGTAGCTTGCAAGCGATCCGCACGGCTTTGCGTCGGGCGGGCAGAAATACAGTCCGGCTGTGGCTTAAGCGCTACGACAGCGAGGGGCACGTCGCGCCTAAAGTGCGTTGTTCGCGACCGCGCGTCATCACGCAGGAGCGCCTGGAGCGGATGGTCGCCGCGTACGAGCGGGAGCCGTGCACTCCGACGCGGGTGTTCGCGGACGAN
Protein Sequence: MEDISATVAKIKEETPTTHGEVVTEIEIKEEITEAPKMNAGSYHEDLDDEQAPSSSLDSLATDDECLKEKIKKGSNKQIKSRTETTERMGCQKAMGSRRNLNNMERTKIIHLRDEGANISQIAQELHMSRNTVRLWLKRYDSEGHVAPKVRCSRPRVITQERLERMVAAYEREPCTPTRVFADEYECSLQAIRTALRRAGRNTVRLWLKRYDSEGHVAPKVRCSRPRVITQERLERMVAAYEREPCTPTRVFADX

Sequence clustering based on sequence similarity using MMseqs2