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Bioedit alignment tutorial3/24/2024 The same applies to Lys and Arg, which are usually located on the surface and primarily interact with solvent or with the acidic side chains of Glu or Asp. For example, Leu and Val will be equally tolerated within a hydrophobic core, assuming that there is place for the slightly larger side chain of leucine. Substitution of amino acids by chemically equivalent ones often does not have a dramatic effect on the structure or function of the protein. Similar residues are those that have similar chemical characteristics, like positively charged Lys and Arg, or hydrophobic Leu and Val, etc. This gives the percentage of identical and similar residues – percentage of sequence identity and sequence similarity. The number of identical and similar amino acid residues may then be compared to the total number of amino acids in the protein. Since evolutionary relationships assume that a certain number of the amino acid residues in a protein sequence are conserved, the simplest way to assess the relationships between two sequences would be to count the numbers of identical and similar amino acids. Sequence alignment is crucial in any analyses of evolutionary relationships, in extracting functional and even tertiary structure information from a protein amino acid sequence.
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