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 3.7e-44 2.2e-40 139.3 0.3 1 77 3 79 3 84 0.97

2 2 3.4e-14 2e-10 42.5 0.1 31 65 89 122 85 123 0.91

#	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	3.7e-44	2.2e-40	139.3	0.3	1	77	3	79	3	84	0.97
2	2	3.4e-14	2e-10	42.5	0.1	31	65	89	122	85	123	0.91

Coding Sequence: ATGTCAAGCCAAGCGGGCGTTAACCAACTGGGGGGCGTTTTCGTAAACGGCCGGCCCCTCCCCGACGTGGTGCGCAAGAGGATAGTCGAGCTGGCCATCATGGGCGTCCGGCCCTGCGACATCAGCCGGCAGCTGCTGGTGTCACACGGCTGCGTCTCCAAGATCCTCACCAGGTTCTACGAGACCGGGTCTATTAGACCCGGGTCGATTGGCGGCAGTAAGACTAAGGTCAgttgttattatatttattggtTTAATAGCTGCCACCATGGCCGGTCCTGCTACGTCAGCCGGCAGCTGCTGGTGTCACACGGCTGCGTCTCCAAGATCCTCACCAGGTTCTACGAGATCGGGTCTTTTAGACCCGAGTAA
Protein Sequence: MSSQAGVNQLGGVFVNGRPLPDVVRKRIVELAIMGVRPCDISRQLLVSHGCVSKILTRFYETGSIRPGSIGGSKTKVSCYYIYWFNSCHHGRSCYVSRQLLVSHGCVSKILTRFYEIGSFRPE

Sequence clustering based on sequence similarity using MMseqs2