This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
What is homology?
Homology can be conceptualized as similarity resulting from common ancestry. The remarkable similarity of organisms (even between organisms that are distantly related) provides evidence for evolution while also yielding the opportunity to make testable predictions about function or explain observations that might otherwise be puzzling [2]. To examine the similarity between PDK1 proteins in different organisms , the amino acid sequences were aligned using NCBI's basic alignment search tool (BLAST). BLAST compares a query sequence (in this case, human PDK1) to a set of reference genomes within other organisms in order to find similar sequences. The program is also able to provide a measure of the statistical significance of observed relationships between sequences.
In regards to relationships between protein sequences in different organisms, identity refers to the extent that sequences have the same amino acids at each position in the sequence. In contrast, similarity refers to the identity and positive substitutions.
In regards to relationships between protein sequences in different organisms, identity refers to the extent that sequences have the same amino acids at each position in the sequence. In contrast, similarity refers to the identity and positive substitutions.
Analysis of PKD1 protein homology
Identity and similarity between analyzed organisms and human PKD1. More closely related versions of PKD1 share more similarity. Identity is described in blue, similarity in grey.
Analysis
PKD1 is well conserved across species, although the presence of PKD1 was not detected in single-celled organisms such as yeast or bacteria. The presence of PKD1 was also not found in plants, suggesting that the gene is more highly conserved in animals. This makes sense because PKD1 localizes to primary (non-motile) cilia, which are very common in humans and other animals and rare in plants. The identity and similarity in each of the homologues also follows an intuitive pattern; animals that are more closely related to humans evolutionarily have more similar versions of polycystin-1.
References[1] Banner image: http://www.pnas.org/content/102/51/18379/F3.expansion.html
[2] Reece, Jane B., and Neil A. Campbell. "Mechanisms of Evolution." Campbell Biology. Boston. 2011. |
Site created by: Elizabeth Roeske
Last updated: 5.12.2014 University of Wisconsin-Madison: Genetics 564 |