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 2 1.4e-34 4.2e-31 108.3 1.1 1 59 36 94 36 119 0.88

2 2 2.8e-22 8.3e-19 68.6 0.1 13 57 193 237 183 245 0.93

#	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	2	1.4e-34	4.2e-31	108.3	1.1	1	59	36	94	36	119	0.88
2	2	2.8e-22	8.3e-19	68.6	0.1	13	57	193	237	183	245	0.93

Coding Sequence: ATGTCAGGGTGTTCGTGGTTATGGAGATCGAATTTGAATGGTGGCTCTTACAACATGTTTCCATCGAGATCTATCAGTAGCTTGATGGGGATATTCGGTCATAGTGGTCACGGAGGGGTCAACCAACTTGGTGGAGTGTTCGTAAACGGGCGACCGTTGCCCGACGTCGTCCGACAACGGATAGTGGAACTCGCGCACAGCGGGGTGCGACCCTGCGACATTAGCCGGCAACTCCGGGTGTCCCACGGCTGCGTGTCCAAAATACTATCCAGGTCAGTGGATCATCTCCACCAAGTTGGTTCTACTAGGTCCGGAAACGTGCTGGACTGTCAGCTACTCCAGGGAAACCGAACTGTCGACTCCGTGGAAAGCCCCCAGGAGCCTGGCCGATCTGTGAGGGTAGAAGACAGATTCGAAGATCCTAGGGTTTTTCGACCAGAAATGGACGAAGAACCTTTCCGGGTTGCAAACAGACCAATGCGGAACGAAGACTCCACAAGATTGGAGTCTTTTCAGGAGTCTCGATCGAGGGTAGAAGACTCCAGATTGCAAGAGCTATACCTCCACCAGGGGAGTATAAACGGGCGACCTCTGCCAGAGCCAGTGAGATGGAGAATAATTGAGCTGGCACGCAGCGGCGTCAGGGCATGTGACATCAGCCGGCAACTGAGGATCTCGCACGGCTGTGTGTCCAAAATACTGTCGAGGTCAGTTCCTAACACCTACTACACCAGCCTGTTTAGTccactggacatatgccttccctataagaagggagatatgcccataaccctcacGCTGGGAATGCTGAggatcgtagagcacagcttcttgcaccgctga
Protein Sequence: MSGCSWLWRSNLNGGSYNMFPSRSISSLMGIFGHSGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHSGVRPCDISRQLRVSHGCVSKILSRSVDHLHQVGSTRSGNVLDCQLLQGNRTVDSVESPQEPGRSVRVEDRFEDPRVFRPEMDEEPFRVANRPMRNEDSTRLESFQESRSRVEDSRLQELYLHQGSINGRPLPEPVRWRIIELARSGVRACDISRQLRISHGCVSKILSRSVPNTYYTSLFSPLDICLPYKKGDMPITLTLGMLRIVEHSFLHR

Sequence clustering based on sequence similarity using MMseqs2