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 1 7.3e-74 8.6e-71 235.4 0.2 2 124 20 142 19 143 0.99

#	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	1	7.3e-74	8.6e-71	235.4	0.2	2	124	20	142	19	143	0.99

Coding Sequence: ATGGATCTCTCCACGGCCTACAGATACAATCAAAACATGATGGAATATTATACGTGTCATGGCGGCGTGAATCAATTAGGAGGCGTTTTCGTCAACGGAAGACCACTTCCGGACGTAGTCAGACAACGAATAGTCGAATTAGCCCACAACGGCGTACGACCCTGTGATATTTCACGGCAACTGAGGGTGTCGCACGGATGCGTGTCCAAAATTTTATCAAGgTATTACGAAACGGGTAGCTTTAAGGCGGGCGTGATCGGCGGCTCGAAGCCGAAGGTGGCCACGCCGCCGGTGGTGGACGCGATCGCGAATTACAAGAGAGAGAATCCGACGATGTTCGCGTGGGAGATTCGCGACAGGCTGCTGGCGGAAGGCATCTGCTCCCAGGACAACGTACCTAGCGTGTCGTCGATTAACAGATTCGTGAAATCGAGACCGAACCGATATCCGGCTCCTATGCTCGGCGATGCTGCAAAACGTTGA
Protein Sequence: MDLSTAYRYNQNMMEYYTCHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRYYETGSFKAGVIGGSKPKVATPPVVDAIANYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRFVKSRPNRYPAPMLGDAAKR

Sequence clustering based on sequence similarity using MMseqs2

100% Identity: iTF_00812705; iTF_00600259; iTF_01522595; iTF_01237604; iTF_00739910; iTF_00415016; iTF_00133193; iTF_00013962; iTF_00030154; iTF_00644042; iTF_00957003; iTF_01276907; iTF_00278092; iTF_00503212; iTF_01318188; iTF_01461100; iTF_00877037; iTF_01288077; iTF_00118639; iTF_01049616; iTF_01350640; iTF_00176337; iTF_00612017; iTF_00665586; iTF_00549491; iTF_00334036; iTF_00628244; iTF_01480820; iTF_01276214; iTF_01329750; iTF_00056536; iTF_01163896; iTF_01567834; iTF_00450939; iTF_00830235; iTF_00917147; iTF_01559707; iTF_01249052; iTF_00630462; iTF_00937246; iTF_01058366; iTF_00641407; iTF_00672800; iTF_01046208; iTF_01183776; iTF_01055171; iTF_00672170; iTF_00716591; iTF_00937968; iTF_00442616; iTF_00919770; iTF_00732572;
90% Identity: iTF_00018133;
80% Identity: iTF_00812705; iTF_00600259; iTF_01522595; iTF_00739910; iTF_00133193; iTF_00013962; iTF_00644042; iTF_00957003; iTF_01276907; iTF_00503212; iTF_01318188; iTF_01461100; iTF_00877037; iTF_01288077; iTF_00118639; iTF_01049616; iTF_01350640; iTF_00176337; iTF_00612017; iTF_00665586; iTF_00549491; iTF_00334036; iTF_00628244; iTF_01276214; iTF_00056536; iTF_01163896; iTF_00450939; iTF_00917147; iTF_01559707; iTF_01249052; iTF_00937246; iTF_00672800; iTF_01183776; iTF_00672170; iTF_00919770;