Protein Alignments: Clues to Protein Function Chapter 4 Protein Alignments: Clues to Protein Function

Figure 4.1: Fruit fly © Studiotouch/ShutterStock, Inc.

Figure 4.2a: General structure of amino acids

Figure 4.2b: Alanine

Figure 4.2c: Phenylalanine

Figure 4.3a: Aspartate and Glutamate

Figure 4.3b: Leucine and Valine

Figure 4. 4: Alignment showing identical ( Figure 4.4: Alignment showing identical (*) and similar (:) amino acids

Figure 4.5: “Good” DNA alignment ignoring coding sequence; very little similarity occurs at the protein level

Figure 4.6: Paralogs and orthologs are two kinds of evolutionarily related sequences

Figure 4.7: The PAM250 substitution matrix

Figure 4. T1: Hydrophobicity values for the 20 amino acids Figure 4.T1: Hydrophobicity values for the 20 amino acids. A more positive value represents a more hydrophobic amino acid

Figure 4.8: Example showing how data from a training set can be used to develop a substitution matrix