Supplementary material for Overbeek et al. (1999) Proc. Natl. Acad. Sci. USA 96(6), 2896-2901.
Examples of metabolic pathways reconstructed from the PCBBHs
The spreadsheets represent reconstructions of some metabolic pathways and the functional subsystems directly from PCBBHs using the algorithm described in the article. The spreadsheets were generated in real time by using the data from 31 genomes currently available in the WIT system. No explicit biochemical expertise was involved in constructing the spreadsheets beyond the selection of the score-threshold by the operator, as discussed in our PNAS paper.
The results are available "with ids" and without. The "ids" refer to the identification numbers used by the WIT system. Clicking on them takes you into the WIT system at Argonne National Laboratory. For most pathways, there is also a link to the "pathway," which, again, takes you into the WIT system and displays information about the pathway.
The results are in the form of two tables, the "Functional Couplings" table and the "Connection Matrix":
- The Functional Couplings table shows the clustering of genes from a particular pathway from a number of genomes. The organism name is given in the form of a two-character code for the organism names (DR, CY, etc.). Click on any one of them to see the full name of the organism. Each row depicts a set of bidirectional best hits associated with the function defined in the leftmost column, and each column represents one or more gene clusters from a single genome (distinct colors indicate distinct clusters). Dashes represent the enzymes that are not forming PCBBHs or were not found in a particular organism.
- The Connection Matrix table gives the coupling scores between the distinct functional roles in the pathway. The values represent the strongest coupling between the designated functions. This data provides evidence indicating whether the clustering of the genes in a pathway is preserved in phylogenetically distant species.
Results for the pathways: