Basic Information

Transcription Factor Domain

TF Family: HMGA
Domain: HMGA domain
PFAM: AnimalTFDB
TF Group: Unclassified Structure
Description: This entry represents the HMGA family, whose members contain DNA-binding domains, also known as AT hooks due to their ability to interact with the narrow minor groove of AT-rich DNA sequences. They play an important role in chromatin organisation [1]. The high mobility group (HMG) proteins are the most abundant and ubiquitous nonhistone chromosomal proteins. They bind to DNA and to nucleosomes and are involved in the regulation of DNA-dependent processes such as transcription, replication, recombination, and DNA repair. They can be grouped into three families: HMGB (HMG 1/2), HMGN (HMG 14/17) and HMGA (HMG I/Y). The characteristic domains are: AT-hook for the HMGA family, the HMG Box for the HMGB family, and the nucleosome-binding domain (NBD) for the members of the HMGN family [2].
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 0.0026 50 3.8 2.0 11 16 13 18 11 20 0.83

2 5 0.22 4.3e+03 -2.4 4.1 12 15 33 36 32 50 0.69

3 5 5.1e-10 9.8e-06 25.2 1.9 6 21 56 71 52 72 0.86

4 5 0.13 2.5e+03 -1.7 4.6 10 15 85 90 84 91 0.83

5 5 1 1.9e+04 -5.2 1.7 6 9 95 98 94 99 0.74

#	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	0.0026	50	3.8	2.0	11	16	13	18	11	20	0.83
2	5	0.22	4.3e+03	-2.4	4.1	12	15	33	36	32	50	0.69
3	5	5.1e-10	9.8e-06	25.2	1.9	6	21	56	71	52	72	0.86
4	5	0.13	2.5e+03	-1.7	4.6	10	15	85	90	84	91	0.83
5	5	1	1.9e+04	-5.2	1.7	6	9	95	98	94	99	0.74

Coding Sequence: ATGTCGGACGATGGGTCAACAGCAGTTGAAAAGAAAGGACGTGGTAGACCTAAATCTAATGGGACACAATCAGAAGCCAAAGGTGATGGTAAGAAAAGAGGAAGACCAGCAGTACCAGCTGCTAAATCTAAAGAATCAAAAAATTCTTCTGACGATGAACAAGCACCAATAGCAAAACGAGGAAGAGGCAGACCCAAAGGCTCTAAGAAAAAGGCAGCTGCACCTAAATCTAAGagtTCGTCTGGAGAGGGGCGATCTCGTGGCCGGCCACGCAAAGATGCACCTCCACCTAAAAAAGATGCAGGATCTACTGATGAAGAACAAGAAGATGAAGAAGAAGAGGAAGGTTCTGATCAGTAA
Protein Sequence: MSDDGSTAVEKKGRGRPKSNGTQSEAKGDGKKRGRPAVPAAKSKESKNSSDDEQAPIAKRGRGRPKGSKKKAAAPKSKSSSGEGRSRGRPRKDAPPPKKDAGSTDEEQEDEEEEEGSDQ

Sequence clustering based on sequence similarity using MMseqs2