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Figure 4-1 Time and distance scales in functional genomics
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Figure 4-2 Pairwise alignment
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Figure 4-3 Plot of percentage of protein pairs having the same biochemical function as sequence changes
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Figure 4-4 Multiple alignment
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Figure 4-5 Phylogenetic tree comparing the three major MAP kinase subgroups
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Figure 4-6 Representative examples of small functional domains found in proteins
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Figure 4-7 Representative examples of short contiguous binding motifs
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Figure 4-8 Construction of a profile
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Figure 4-9 The growth of DNA and protein sequence information collected by GenBank over 20 years
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Figure 4-10 Table of the sizes of the genomes of some representative organisms
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Figure 4-11 Relationship of sequence similarity to similarity of function
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Figure 4-12 The P loop of the Walker motif
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Figure 4-13 Analysis of the functions of the protein-coding sequences in the yeast genome
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Figure 4-14 DNA microarray
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Figure 4-15 2-D protein gel
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Figure 4-16 The phenotype of a gene knockout can give clues to the role of the gene
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Figure 4-17 Protein localization in the cell
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Figure 4-18 Two-hybrid system for finding interacting proteins
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Figure 4-19 Relationship between sequence and structural divergence of proteins
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Figure 4-20 Ribbon diagram of the structure of a monomer of benzoylformate decarboxylase (BFD) and pyruvate decarboxylase (PDC)
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Figure 4-21 Superposition of the three-dimensional structures of steroid-delta-isomerase, nuclear transport factor-2 and scytalone dehydratase
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Figure 4-22 The threshold for structural homology
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Figure 4-23 Evolutionary conservation and interactions between residues in the protein-interaction domain PDZ and in rhodopsin
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Figure 4-24 Structural changes in closely related proteins
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Figure 4-25 The method of profile-based threading
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Figure 4-26 Some decoy structures produced by the Rosetta method
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Figure 4-27 Examples of the best-center cluster found by Rosetta for a number of different test proteins
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Figure 4-28 Growth in the number of structures in the protein data bank
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Figure 4-29 The overall folds of two members of different superfamilies of serine proteases
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Figure 4-30 A comparison of primer–template DNA bound to three DNA polymerases
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Figure 4-31 Example of the use of GRID
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Figure 4-32 Some organic solvents used as probes for binding sites for functional groups
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Figure 4-33 Structure of subtilisin in 100% acetonitrile
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Figure 4-34 Ribbon representation showing the experimentally derived functionality map of thermolysin
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Figure 4-35 An active-site template
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Figure 4-36 Theoretical microscopic titration curves
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Figure 4-37 Residues that show abnormal ionization behavior with changing pH define the active site
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Figure 4-38 The chemical reaction catalyzed by mandelate racemase
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Figure 4-39 The chemical reaction catalyzed by muconate lactonizing enzyme
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Figure 4-40 Mandelate racemase (top) and muconate lactonizing enzyme (bottom) have almost identical folds
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Figure 4-41 A comparison of the active sites of mandelate racemase (left) and muconate lactonizing enzyme (right)
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Figure 4-42 The overall reaction catalyzed by the pyridoxal phosphate-dependent enzyme L-aspartate aminotransferase
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Figure 4-43 The general mechanism for PLP-dependent catalysis of transamination, the interconversion of a-amino acids and a-keto acids
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Figure 4-44 The three-dimensional structures of L-aspartate aminotransferase (left) and D-amino acid aminotransferase (right)
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Figure 4-45 Comparison of the active sites of L-aspartate aminotransferase (left) and D-amino acid aminotransferase (right)
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Figure 4-46 The three-dimensional structures of bacterial D-amino acid aminotransferase (top) and human mitochondrial branched-chain L-amino acid aminotransferase (bottom)
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Figure 4-47 Some examples of multifunctional proteins with their various functions
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Figure 4-48 The three-dimensional structure of the monomer of macrophage inhibitory factor, MIF
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Figure 4-49 Chameleon sequences
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Figure 4-50 Chameleon sequence in the DNA-binding protein Fis
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Figure 4-51 Chameleon sequence in the DNA-binding protein MATa2 from yeast
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Figure 4-52 The prion protein
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Figure 4-53 A possible mechanism for the formation of amyloid fibrils by a globular protein
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Figure 4-54 Structural transformation in a serine protease inhibitor on binding protease
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Figure 4-55 Active sites of MR, MLE, and enolase
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Figure 4-56 The pathway for the utilization of galactonate in E. coli
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Figure 4-57 Structure of galactonate dehydratase
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Figure 4-58 Schematic diagram of a model of the active site of galactonate dehydratase with substrate bound
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Figure 4-59 The three-dimensional structures of bacterial alanine racemase and yeast YBL036c
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Figure 4-60 Comparison of the active sites of bacterial alanine racemase and YBL036c
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