I did alignment for 9 protein sequence.However, from the alignment I got only 1 dot resembles semi-conservation protein residue. The residue conserved were P (proline) ans S (serine). How do I explain this?
2 answers
do you have 9 protein sequences true? what did you do? multiple alignment of all of these? or you used psi-blast?
i dont know about the protein that you have used. but in generally during the evolution, the residues that are important for the function of the protein often are well conserved. this is the generalised concept.
i suggest first of all (if your protein is a studied protein), try to search on PDB database if it exist as experimentally determined structure and than with the help of a reference(scientific literature) to have the answer that you search. generally scientific literature reports information about what you are looking for.
As a general phenomenon 'similar sequences will have similar structure & similar structures have similar function'. It may not hold true in every case. In your case the conserved residues are proline and serine. Most of the times these residues are conserved due to structural constraints throughout the evolution. Some times the length of the proteins is also important during alignment. Just try to check in all the 9 proteins in which secondary structure proline and serine is present. If these 2 residues are present in the same secondary structure in each case then the structural constraints are dominating during the evolution.
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What is it that you would like explained? Why there is not more conservation in your alignment? Or why P + S are considered as semi-conserved?