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 5 0.94 2.1e+04 -1.1 0.0 41 60 69 88 36 93 0.78

2 5 0.0039 87 6.6 0.0 41 78 95 133 90 137 0.82

3 5 0.0027 59 7.1 0.0 41 67 136 162 130 168 0.90

4 5 0.02 4.5e+02 4.3 0.0 48 69 169 190 165 203 0.83

5 5 0.0011 25 8.3 0.0 41 72 203 234 192 249 0.82

#	of	c-Evalue	i-Evalue	score	hmm coord from	hmm coord to	ali coord from	ali coord to	env coord from	env coord to	acc
1	5	0.94	2.1e+04	-1.1	41	60	69	88	36	93	0.78
2	5	0.0039	87	6.6	41	78	95	133	90	137	0.82
3	5	0.0027	59	7.1	41	67	136	162	130	168	0.90
4	5	0.02	4.5e+02	4.3	48	69	169	190	165	203	0.83
5	5	0.0011	25	8.3	41	72	203	234	192	249	0.82

Coding Sequence: ATGGCGACAACTCGACCACGACAGCCCAAACAGTATCGATCAGAGGAAGTCCCTCGTGAGCTGCTAACTTGTCAGAACCACGCTTGCCTCTCGCATGACGTTACAATGTCAGTTAACTCTCGCACGTTGAGAGCGACGCGACGCGAGGATGCGCGCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTAGTCCCAAATCTATGCCGACTACGAGGCTACAGCAAGTGTTAGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCACATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCACATCTACGCCGACTACGAGGTTACAGCCAGTGTTCGTCCCAAATCTACGCCGACTACGAGGCTACAGCAAGTGTTAGTCCCAAATCTACGCCGACTACGAGGTTACAGCCAGTGTTAG
Protein Sequence: MATTRPRQPKQYRSEEVPRELLTCQNHACLSHDVTMSVNSRTLRATRREDARKSTPTTRLQPVFVPNLRRLRGYSQCSSQIYADYEVTVFVPNLRRLRGYSQCSSQIYADYEVTASVSPKSMPTTRLQQVLVPNLRRLRGYSQCSSQIYADYEVTASVRPKSTPTTRLQCSSQIYADYEVTASVRPKSTPTTRLQPVFVPHLRRLRGYSQCSSHIYADYEVTASVRPKSTPTTRLQQVLVPNLRRLRGYSQC

Sequence clustering based on sequence similarity using MMseqs2