Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies
Figure 7
Changes in Function within 276 Superfamilies.
A: A heatmap showing the cumulative changes in all superfamilies where a change is observed based on the differences in E.C. annotations at the class level in a superfamily and uses the phylogenetic tree to infer the order in which changes have occurred. These counts do not take into account changes that occur between SSGs and so need to be viewed in conjunction with the counts in B (right of the diagonal). The colour intensity indicates the number of times a change in E.C. class occurs. The matrix shows the percentage of changes (with total counts in brackets) in E.C. class observed across all 276 superfamilies. Along the matrix diagonal the number of changes occurring within the E.C. class to the 4th level of the E.C. number. B. A similar heatmap to that described for A, but using all the possible combinations of E.C. found in a superfamily. The top right of the matrix shows the observed percentage of changes, with actual count totals in brackets, while the lower right half shows the percentage of changes expected based on a random simulation of E.C. changes. To the right of the matrix the observed (OBS) and expected (EXP) percentage of changes for each E.C. class are shown. C. The same exchanges as described for B but concentrating on the interchanges between classes. D. A box plot showing the proportion of E.C. changes in a superfamily by E.C. level (i.e. derived from data in A top right of matrix). For example if a superfamily has 2 changes at E.C. level 1 and 3 changes at level 4, then the primary E.C. level has contributed 2/5 and the fourth level has contributed 3/5. These fractions are catalogued across all superfamilies in the plot. The insert shows the total number of observed exchanges at each class level. All interchanges shown in A to D exclude those that are being contributed by ‘confusion domains’ detailed in Figure S12.