The relationship between protein structure and function: a comprehensive survey focusing on enzymes

Figure 4, Structure-function Classes in the Yeast Genome Analyzed
Through a Variety of Classification Schemes

This figure shows the distribution of fold function combinations in the yeast genome as analyzed by a variety of different structure and functional classifications. Each of the figures is a cross tabulation of one structural classification scheme (on the column heads) versus a functional classification (row heads). Part A shows SCOP versus ENZYME; Part B, CATH vs. ENZYME; Part C, SCOP vs. COGs; Part D, SCOP vs. Most Conversed COGs; Part E, SCOP vs. MIPS Functional Catalogue. Each of the grid boxes gives the number of fold-function combinations within a structure-function class. This number is expressed as a percentage of the total number of combinations in the diagram to make the graphs readily comparable. The total number of combinations in each of the sub figures is 141 (A), 77 (B), 1207 (C), 120 (D), and 66 (E). Some notes on the subfigures: Part A is directly comparable with the cross tabulation in table 2B for all of Swissprot. In Parts D and E, we employ the COGs scheme in exactly the same fashion as we did the ENZYME classification. We form combinations between individual yeast COGs and SCOP folds (e.g. COG 0186 with fold 2.26) and then we place these combinations into larger structure-function classes. The COGs overall functional classes are denoted by a single letter and then are in turn grouped into three broader areas (so, for instance, the 0186-2.26 pair would go into the structure-function class all-beta, J). We, likewise, proceed similarly for the MIPS yeast functional catalogue. This gives each function a 2 or 3 component number similar to an EC number (e.g. 07.20.3 or 06.2). We use the first two numbers to create combinations with SCOP folds and then use the top number to create the functional classes shown in the diagram. For Part E we just use the 110 COGs that are present in all 8 genomes in the current COGs analysis (E. coli, H. influenzae, H. pylori, M. genitalium, M. pneumoniae, Synechocystis, M. jannaschii, yeast).