Web-Based Resource for Genomic Enzymology Tools

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PROJECT SUMMARY/ABSTRACT This application requests support for a web-based resource that provides community access to “genomic enzymology” tools to 1) enable identification of uncharacterized proteins for functional discovery, including those that are present in human microbiome and other metagenomic communities; 2) facilitate assignment of function to uncharacterized proteins by providing easy access to genome context/functional linkage; and 3) survey sequence-function space in protein families for identification of candidates for functional screening and improvement of desired biochemical/biophysical properties (useful for systems biology as well as the pharmaceutical and chemical applications). The resource provides three integrated tools: 1) EFI-EST for visualization/analysis of sequence-function space in proteins families using sequence similarity networks (SSNs); 2) EFI-GNT for visualization/analysis of genome context for microbial and fungal proteins in SSNs using genome neighborhood networks and genome neighborhood diagrams to identify functionally linked proteins (e.g., enzymes, transporters, and transcriptional regulators in novel metabolic pathways); and 3) EFI-CGFP for chemically guided functional profiling that maps metagenome and/or meta-transcriptome abundance to clusters in SSNs for identification of important microbiome targets for functional characterization. The resource enables access to the tools without the need for users to have computer programming expertise and/or local access to the necessary computational infrastructure. The resource has been available since 2014; its development and dissemination have been supported by U54GM093342 and P01GM118303. The resource has been accessed by >5,000 domestic and international users and cited in >300 publications and patents, confirming its ease-of- use, popularity, and impact.