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Enzyme Function Initiative (EFI) Tools Workshop

Event Type
Conference/Workshop
Sponsor
Professor John Gerlt
Location
Carl R. Woese Institute of Genomic Biology, Room 607
Date
May 9, 2019   9:00 am - 2:30 pm  
Registration
Registration
Contact
Professor John Gerlt
E-Mail
j-gerlt@illinois.edu
Views
210
Originating Calendar
IHSI Events

The protein databases contain an exponentially growing number of sequences as a result of the recent increase in ease and decrease in cost of genome sequencing. The rate of data accumulation far exceeds the rate of functional studies, producing an increase in genomic ‘dark matter’, sequences for which no precise and validated function is defined.

We have now entered the metagenomics era, and the challenges of dealing with the ‘dark matter’ remains even with this new type of information generated. The “chemically guided functional profiling” (CGFP) approach uses a molecular understanding of a large enzyme superfamily to guide and prioritize the identification and quantitation of different family members in metagenomes and metatranscriptomes.

We developed the Enzyme Function Initiative (EFI) tools, accessible at efi.igb.illinois.edu, to identify, explore, and leverage the protein and genome databases for discovery of the in vitro activities and in vivo functions of novel enzymes and proteins belonging to the dark matter.

The EFI workshop focuses on 3 genomic enzymology web tools that assist the discovery novel metabolic pathways:

  • Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence-function space in protein families
  • Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes
  • Enzyme Function Initiative-Chemically Guided Functional Profiling (EFI-CGFP) for mapping metagenome protein abundance to clusters in SSNs
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