What are protein domains?
Protein domains are unique sections on a protein sequence that have a specific function. Proteins can have one or multiple domains that give it specific properties that relate to its biological and molecular function. By analyzing the domains of a protein, we can identify which regions of the protein are responsible for biological and molecular function. [1]
Results
SMART domain analysis revealed that all the potential model organisms only had one pfam domain. SMART domain analysis did not detect any further functional domains of motifs in the amino acid sequences of HCRT. This tells us that HCRT has a very specific and yet highly conserved function across organisms.
However, according to further research, HCRT has three functional domains coding for a signal sequence, orexin A, and orexin B peptides. Manual alignment of the orexin A and orexin B domains showed a motif that was conserved between the two domains [2].
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References
[1] Pearson WR. An introduction to sequence similarity ("homology") searching. Curr Protoc Bioinformatics. 2013 Jun;Chapter 3:3.1.1-3.1.8. doi: 10.1002/0471250953.bi0301s42. PMID: 23749753; PMCID: PMC3820096.
[2] Wang C, Wang Q, Ji B, Pan Y, Xu C, Cheng B, Bai B, Chen J. The Orexin/Receptor System: Molecular Mechanism and Therapeutic Potential for Neurological Diseases. Front Mol Neurosci. 2018 Jun 28;11:220. doi: 10.3389/fnmol.2018.00220. PMID: 30002617; PMCID: PMC6031739.
[2] Wang C, Wang Q, Ji B, Pan Y, Xu C, Cheng B, Bai B, Chen J. The Orexin/Receptor System: Molecular Mechanism and Therapeutic Potential for Neurological Diseases. Front Mol Neurosci. 2018 Jun 28;11:220. doi: 10.3389/fnmol.2018.00220. PMID: 30002617; PMCID: PMC6031739.
This page was produced as an assignment for Genetics 564, a capstone course at UW-Madison.