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

2. Figure 4.1: Fruit fly
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3. Figure 4.2a: General structure of amino acids

4. Figure 4.2b: Alanine

5. Figure 4.2c: Phenylalanine

6. Figure 4.3a: Aspartate and Glutamate

7. Figure 4.3b: Leucine and Valine

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

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

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

11. Figure 4.7: The PAM250 substitution matrix

12. 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

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