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 2e-08 2.1e-05 24.8 0.2 25 99 11 84 3 122 0.92

2 2 4.8 5.2e+03 -2.3 0.0 34 59 151 176 147 209 0.71

#	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	2e-08	2.1e-05	24.8	0.2	25	99	11	84	3	122	0.92
2	2	4.8	5.2e+03	-2.3	0.0	34	59	151	176	147	209	0.71

Coding Sequence: ATGGCGAGATTATCGGAAGTGGACATGGGAAGAGCCCTCGAAATGTCAGCGGCAGGTCAAACCCAACGCGATATCGCAAACTCGATCGGGACGAGCGTGTCGGTAATTAACCGATTACTTGCCCGAAATAATCAAACCGGCAGTCCGCGGTATCGACACGGTGGTGGCAGGCAACGCGTGACGACACCTCGGGAGGATAGACAAATCGTCCAGCAAGTGCGGCAAACACCCGGAGTCAGTGCAAACGAGGTTATCGCGACGATTCCTCATAGAGTGTCGCAACGCACGATCGGACGACGACTGGCGGAGCAAGGTCTGCGATCTCGGCGTCCGGTTATCAAACCGACACTGAGCGTTCGGCATCGGGCTGCTCGAAGAGGTTTTGCTGAGAACCACGAAAATTGGACTCTGGAGCAGTGGCGGCAATGCCTCTTCACCGACGAAGCAAAAATTCAGATCTGCGACAATTCGCGAAACGCGCGAGTGTGGCGCCGAACAGGAGAGCGGATGAACGAACGCTTCCAAAGCCATTCGCGAGCTTTCGGTGGAGGTTCCATTACCGTATGGGGTGGAATCTCACTTGAATCTCGGACGGAATTGGTAGTGTTCCGTAACCAGATTGTTAGAGGGCAAGTGTACATCGATCGAATCTTTGCTCCTGTCGTCGTTCCGGAAGCTCGACGAGTCGGAGACGGCTTCGTCTTCATTGACGACAACGCTCCGGCTCATCGAGCCCGGATTGTCAACAGATTCCTCGATGAGCAAGGAATCGACCGAAGTGACTGGCCTGCTAACAGTCCGGATTTGAATCCGATAGAAAACGTTTGGGCGTTACTAAAGCGAAGAATTCGATCGAGAAGGCCGGCACCGAGAACACTCGATGAGCTTGAGGTCGCAGCCCGAGAGGAATGGCTTGCCATTCCTCAAGAACAAATCACGGCAACGATCGCAAGCATGAATCGCCGCTGTCTAGCTGTCACTCGAGCTCGAGGGGGCGCTCTCAAATATTGA
Protein Sequence: MARLSEVDMGRALEMSAAGQTQRDIANSIGTSVSVINRLLARNNQTGSPRYRHGGGRQRVTTPREDRQIVQQVRQTPGVSANEVIATIPHRVSQRTIGRRLAEQGLRSRRPVIKPTLSVRHRAARRGFAENHENWTLEQWRQCLFTDEAKIQICDNSRNARVWRRTGERMNERFQSHSRAFGGGSITVWGGISLESRTELVVFRNQIVRGQVYIDRIFAPVVVPEARRVGDGFVFIDDNAPAHRARIVNRFLDEQGIDRSDWPANSPDLNPIENVWALLKRRIRSRRPAPRTLDELEVAAREEWLAIPQEQITATIASMNRRCLAVTRARGGALKY

Sequence clustering based on sequence similarity using MMseqs2

100% Identity: iTF_00057898;
90% Identity: iTF_00058657; iTF_00057893; iTF_00057895; iTF_00057896; iTF_00057897; iTF_00057899; iTF_00057901; iTF_00058655; iTF_00058656; iTF_00057898; iTF_00058658; iTF_00057900;
80% Identity: iTF_00057895;