This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
What is Protein Homology?
A homologous protein is when two species share the same protein as a common ancestor. The species do not necessarily need to have highly conserved DNA sequences to have homologous proteins. Protein homology can be used to understand the functions of highly conserved proteins among model organisms and the evolutionary events leading to the divergence of species. Homologous proteins can also be used to study diseases by comparing conserved and un-conserved sequences and functions.
SEMA5A Protein Sequences
BLAST Alignment
BLAST, or The Basic Local Alignment Search Tool, looks at the similarity between multiple nucleotide or protein sequences. BLAST compares these sequences to other sequence databases to statistically calculate matches. The results can be used to analyze protein functionality and evolutionary events between sequences [1].
The BLAST results are displayed by [2]:
The BLAST results are displayed by [2]:
- E-value- the probability that the match occurs by random chance
- Percent similarity- the percent of the nucleotide or protein sequence that matched
- Percent identity- the percent of amino acids that matched
Figure 1. BLAST alignment. This is an example of the distribution of 100 BLAST hits from the SEMA5A protein sequence. The results are color coded, by score, which is indicated by the color key.
Clustal Omega Alignment
Clustal Omega uses multiple sequence alignment to highlight the similarity between sequences so that the conservation of each region can be determined. The results can be used for phylogenetic analysis, which can determine when evolutionary events between sequences might have occurred.
Clustal Omega was used for multiple sequence alignment of the SEMA5A protein for this project. The alignment results can be found here.
Clustal Omega was used for multiple sequence alignment of the SEMA5A protein for this project. The alignment results can be found here.
Figure 2. Clustal Omega alignment. This is an example of a small region of the Clustal Omega highlighted alignment for the SEMA5A protein.
Discussion
The SEMA5A protein was found to be relatively well conserved among vertebrates and some non-vertebrates. These results explain why a chromosomal deletion of the SEMA5A gene, which results in a loss of SEMA5A protein, has drastic phenotypic results, as seen in individuals with Cri du Chat syndrome.
References
Figure 1. Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
Figure 2. Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins D
Molecular Systems Biology 7 Article number: 539 doi:10.1038/msb.2011.75
[1] Basic Local Alignment Search Tool. (n.d.). Retrieved February 21, 2015, from http://blast.ncbi.nlm.nih.gov/Blast.cgi
[2] Wheeler D, Bhagwat M. BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial. In: Bergman NH, editor. Comparative Genomics: Volumes 1 and 2. Totowa (NJ): Humana Press; 2007. Chapter 9. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1734/
Figure 2. Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins D
Molecular Systems Biology 7 Article number: 539 doi:10.1038/msb.2011.75
[1] Basic Local Alignment Search Tool. (n.d.). Retrieved February 21, 2015, from http://blast.ncbi.nlm.nih.gov/Blast.cgi
[2] Wheeler D, Bhagwat M. BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial. In: Bergman NH, editor. Comparative Genomics: Volumes 1 and 2. Totowa (NJ): Humana Press; 2007. Chapter 9. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1734/