During the initial phases of the EFI, projects focused on specific enzyme superfamilies that were selected for their ability to contribute to development of a general strategy for functional assignment. Each of theses superfamilies, amidohydrolase (AH), enolase (EN), glutathione transferase (GST), haloacid dehalogenase (HAD), and isoprenoid sythethase type I (IS), had specific challenges that needed to be addressed in order to make accurate functional predictions. For example, we have carried out large-scale characterization of chain elongation enzymes in the IS superfamily, defined domain complexity in the HAD superfamily, and discovered novel biology by starting with a structure of an unknown enzyme from the EN superfamily. Building on these and the EFI's other successes, we now are using the strategies developed for superfamily analyses as tools to inform upon function not only within those specific groups of enzymes but, more critically and interestingly, within the metabolic context in which they function.
By virtue of the large‑scale collaborative nature of the EFI, we are in a fortunate position to be able to combine a wide array of disciplines, including bioinformatics, structural biology, computation, enzymology, metabolomics and microbiology. This organization and synergy is ideal for revealing a high-level understanding of function for both an enzyme and its associated metabolic pathway. Current pathway‑focused projects include identifying and characterizing novel pathways in organisms associated with the human microbome, targeting organisms with suspected highly diverse catabolic metabolism (e.g. Agrobacterium tumefaciens and Sinorhizobium meliloti), and targeting pathways computationally predicted to be incomplete or novel. As needed, specific targets from the enzyme superfamilies represented in EFI Bridging Projects are still selected to address remaining issues in diversity of sequence space, specificity boundaries, and to continue to deorphanize structures solved by the Protein Structure Initiative. Please see our page on target categories for more details on selection of specific protein targets for inclusion into the EFI pipeline.