Frequently Asked Questions

What is basic helix-loop-helix (bHLH)

Basic Helix Loop Helix (bHLH) proteins are transcription factors with many essential functions such as gender determination, nervous system, and muscle development in many organisms, from yeast to humans [1], [2]. It is also a transcription factor family that has an essential role in plant growth, development, and stress responses [3]. They play an essential role in the development of vertebrates. They play an active role in cell proliferation and differentiation. It has been observed that expression levels are highly increased in the formation of the cardiovascular system [1], [4].

Structure

It contains two alpha-helix structures separated by a loop, followed by a 60 aa DNA binding site (basic). The helix structures allow interaction with other bHLH proteins. Nineteen amino acids of the domain are highly conserved from yeast to human [1], [4]. Members of the bHLH superfamily have two highly conserved and functionally different domains that combined make up a 60-amino-acid-residue region. The basic domain, which binds the transcription factor to DNA at a consensus hexanucleotide sequence known as the E box, is located at the amino-terminal end of this region. Different bHLH family members recognize distinct E-box consensus sequences. The HLH domain, located at the carboxy-terminal end, enables interactions with other protein subunits to create homo- and heterodimeric complexes. Many different combinations of dimeric structures are possible, each with different binding affinities between monomers. The heterogeneity in the E-box sequence that is recognized and the dimers formed by different bHLH proteins determines how they control diverse developmental functions through transcriptional regulation [5].



References

[1] S. Jones, "An overview of the basic helix-loop-helix proteins," Genome Biology, vol. 5, no. 6, pp. 226-226, 2004.

[2] D. Zhang, G. Li and Y. Wang, "A genome-wide identification and analysis of basic helix-loop-helix transcription factors in cattle," Gene, vol. 626, pp. 241-250, 2017.

[3] Y. Wang, S. Wang, Y. Tian, Q. Wang, S. Chen, H. Li, C. Ma and H. Li, "Functional Characterization of a Sugar Beet BvbHLH93 Transcription Factor in Salt Stress Tolerance," International Journal of Molecular Sciences, vol. 22, no. 7, 2021.

[4] V. Ledent and M. Vervoort, "The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis," Genome Res., vol. 11, no. 5, pp. 754-770, 2001.

[5] L. Serna, "bHLH proteins know when to make a stoma," Trends in Plant Science, vol. 12, no. 11, pp. 483-485, 2007.

How can I view sequences?
A list of 166 families can be viewed by clicking the "bHLH Species" tab at the top of the homepage. Also view CDS and PEP sequences by clicking on the desired family.
How can I use the Hidden Markov Model tool?
You can open the tool's page by clicking on the "Hidden Markov Model (HMM)" content just below the slider section on the homepage. When you type the PEP sequence you want to search on the form screen on the page that opens and press the "RUN" button, if your sequence is a bHLH sequence, the search and score results will appear on your screen.
How can I use the Basic Local Alignment Search Tool (BLAST)?
You can open the tool's page by clicking on the "Basic Local Alignment Search Tool (BLAST)" content just below the slider section on the homepage. When you type the PEP sequence you want to search on the form screen on the page that opens and press the "RUN" button, the search and score results will appear on your screen after the query and calculation. Results may take a while to arrive.
How can I use the Deep Learning Model (LSTM) tool?
You can open the tool's page by clicking on the "Deep Learning Model (LSTM)" content just below the slider section on the homepage. When you type the PEP sequence you want to search on the form screen on the page that opens and press the "RUN" button, the transcription factor protein family of the entered PEP sequence will appear on your screen as a result of the prediction made by the deep learning model.
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