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 0.0025 59 3.8 2.0 11 16 13 18 11 20 0.83

2 5 0.029 6.9e+02 0.4 0.5 12 15 32 35 31 36 0.93

3 5 3.6e-10 8.6e-06 25.7 2.2 4 21 51 68 49 69 0.89

4 5 0.63 1.5e+04 -3.8 6.9 10 15 82 87 81 88 0.83

5 5 1 2.4e+04 -5.3 1.3 6 9 92 95 91 95 0.72

#	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	0.0025	59	3.8	2.0	11	16	13	18	11	20	0.83
2	5	0.029	6.9e+02	0.4	0.5	12	15	32	35	31	36	0.93
3	5	3.6e-10	8.6e-06	25.7	2.2	4	21	51	68	49	69	0.89
4	5	0.63	1.5e+04	-3.8	6.9	10	15	82	87	81	88	0.83
5	5	1	2.4e+04	-5.3	1.3	6	9	92	95	91	95	0.72

Coding Sequence: atgtcgGATGATGGTTCAACAGCCGTTGAGAAGAAAGGACGCGGCAGACCTAAATCTAATGGAACACAATcaGAATCTAAAGATATCAAAAAACGAGGAAGACCGGCTGCACCGCCAAAAGCGAAAGAGTCAACAAAATCATCAGATGATGAACAACCTGTAGCCAAACGGGGACGTGGGAGACCCAAGGGTTCAAAAAAGAAGGCATCTGCTCCTAAAGCAAAGagTGGTTCCGGAGAGGGTAGAGGTCGTGGGCGACCACGTAAAGATGCCCCTCCACCCaaaaaggatgcagcttcTACTGAAGAAGAACAAGATGATGAAGAAGAAGATGAAGGCTCTGACCagtaa
Protein Sequence: MSDDGSTAVEKKGRGRPKSNGTQSESKDIKKRGRPAAPPKAKESTKSSDDEQPVAKRGRGRPKGSKKKASAPKAKSGSGEGRGRGRPRKDAPPPKKDAASTEEEQDDEEEDEGSDQ

Sequence clustering based on sequence similarity using MMseqs2