The Natural History of Biocatalytic Mechanisms
Figure 1
The history of biocatalytic mechanisms.
The heat map describes the distribution of presence (red) and absence (yellow) of mechanism step types (y-axis) over fold age (x-axis). Rows of the heat map (mechanisms) are ordered vertically according to the first appearance of the step type in time, with the oldest at the top. The row sidebars at the top of the heat map are used to describe the number of MACiE entries and CATH H-level domain structures (annotated as number of folds) appearing at each fold age, and presence of top-level EC classes that are associated with these H-level structures (see color key). The x-axis scale reflects the different nd values found in our dataset, arranged from the oldest on the left to the youngest on the right. Every unique nd value forms a separate column. The non-linear scale is defined by the number of unique nd values falling in each interval of nd. There are many distinct nd values between 0.0 and 0.3 found in our dataset, so the scale is expanded in this region. There are few distinct nd values between 0.7 and 1.0, so the scale is very condensed in that region. Geological time is taken to be approximately linear with nd, where nd = 0 represents the origin of the protein world approximately 3.8 billion years ago and nd = 1 corresponds to the present [4].