The above suggests that we must consider both identities and similarities between the amino acids in calculating the alignment score. On the other hand, substituting V with R may have a dramatic negative effect and destabilize or denature a protein. The same applies, e.g., to K and R substitution, since both these residues are usually located on the surface and primarily interact with solvent or with the acidic side chains of E or D. For example, L and V will be equally tolerated within a protein's hydrophobic core, assuming enough space is available for the slightly larger side chain of leucine to be accommodated. For this reason, this type of conservation is called similarity, and it depends on the demand for the conservation of structure and function. Many replaced residues will be chemically equivalent to the "original" ones. The higher this percentage, the closer the compared sequences will be in terms of their evolutionary origin.Įven though many amino acids in a protein sequence can be invariant, depending on the evolutionary distance between the proteins, there will always be a substantial number of residue substitutions caused by mutations. Using this number, we can count the percentage of identical residues – called the percentage of sequence identity. The most straightforward score to assess how closely related two sequences are can be based on the number of identical amino acids that align against each other. This suggests that the alignment score is essential, and its calculation needs careful consideration. The alignment software sorts the generated alignments according to a calculated score, with the output being the one with the highest score. First, however, we must remember that an alignment generated by software will represent only one of many different possible alignments. There are many ways to align two protein sequences against each other.
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