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 4 7.9e-26 3.8e-22 79.6 0.0 23 108 79 159 68 161 0.90

2 4 6.3e-19 3.1e-15 57.3 0.1 65 108 157 200 155 202 0.93

3 4 4.4e-19 2.1e-15 57.8 0.1 67 108 200 241 198 243 0.94

4 4 4.9e-08 0.00024 22.1 0.1 65 94 239 268 237 271 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	4	7.9e-26	3.8e-22	79.6	0.0	23	108	79	159	68	161	0.90
2	4	6.3e-19	3.1e-15	57.3	0.1	65	108	157	200	155	202	0.93
3	4	4.4e-19	2.1e-15	57.8	0.1	67	108	200	241	198	243	0.94
4	4	4.9e-08	0.00024	22.1	0.1	65	94	239	268	237	271	0.91

Coding Sequence: ATGTTGATATCTGCGGGCAGCGGCCCCACGCCCGAGTTCTCCCCAGCCTCGTGCTGCGCGTCCTGGAAGATGGAGCCGGCACCTCCAGCGTCTGCCATCACACAACCCCTCAATATTTCACCCAACGtGCCAGTATCGCCGTCGTCCTCGGCTTCAGGCGGAgtgggcggcggcggcgcgggcgcggcgcTGTACCCCGGCGCGACGGCGCACCCGCTGTCGTCCCTGCTGTCTCAGCAGCGACTGCTAGAGCTGTCTCGCTTCGGGCTGCGCCACTACGACATCGCGCACCACGTGCTCTCCCAGCAAGGTGCTGTTACCAAGTTGCTTGGAACCCTTCGGCCGCCCGGGCTGATAGGCGGCAGCAAGCCGAAGGTGGCAACCCCGGCCGTGGTGTCCAAGATCGAGCAGTACAAGCGGGAGAACCCCACCATCTTTGCCTGGGAGATCCGCGAGCGGCTCATCTCCGAAGGTACGTTAGTTGGCAGCAAGCCGAAGGTGGTAACCCCGGCCGTGGTGTCCAAGATCGAGCAGTACAAGCGGGAGAACCCCACCATCTTTGCCTGGGAGATCCGCGAGCGGCTCATCTCCGAAGGTACGTTAGTTGGCAGCAAGCCGAAGGTGGCAACCCCGGCCGTGGTGTCCAAGATCGAGCAGTACAAGCGGGAGAACCCCACCATCTTTGCCTGGGAGATCCGCGAGCGGCTCATCTCCGAAGGTACGTTAGTTGGCAGCAAGCCGAAGGTGGCAACCCCGGCCGTGGTGTCCAAGATCGAGCTGTACAAGCGAACCCCACCATCTTTGCCTGGGATTCAAAACTAA
Protein Sequence: MLISAGSGPTPEFSPASCCASWKMEPAPPASAITQPLNISPNVPVSPSSSASGGVGGGGAGAALYPGATAHPLSSLLSQQRLLELSRFGLRHYDIAHHVLSQQGAVTKLLGTLRPPGLIGGSKPKVATPAVVSKIEQYKRENPTIFAWEIRERLISEGTLVGSKPKVVTPAVVSKIEQYKRENPTIFAWEIRERLISEGTLVGSKPKVATPAVVSKIEQYKRENPTIFAWEIRERLISEGTLVGSKPKVATPAVVSKIELYKRTPPSLPGIQN

Sequence clustering based on sequence similarity using MMseqs2