Enzyme Function Initiative Tools

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).

The tools are available without charge or license to both academic and commercial users.

Please cite your use of the EFI tools:

Rémi Zallot, Nils Oberg, and John A. Gerlt, The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019 58 (41), 4169-4182. https://doi.org/10.1021/acs.biochem.9b00735

Nils Oberg, Rémi Zallot, and John A. Gerlt, EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023. https://doi.org/10.1016/j.jmb.2023.168018

An article in the 2023 Journal of Molecular Biology Computation Resources for Molecular Biology was recently published and is available on the training resources page.

The web tools have been described in five publications:

Nils Oberg, Rémi Zallot, and John A. Gerlt, EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. Journal of Molecular Biology 2023. https://doi.org/10.1016/j.jmb.2023.168018

Rémi Zallot, Nils Oberg, and John A. Gerlt, The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019 58 (41), 4169-4182. https://doi.org/10.1021/acs.biochem.9b00735

Rémi Zallot, Nils Oberg, John A. Gerlt, "Democratized" genomic enzymology web tools for functional assignment, Current Opinion in Chemical Biology, Volume 47, 2018, Pages 77-85, https://doi.org/10.1016/j.cbpa.2018.09.009

John A. Gerlt, Genomic enzymology: Web tools for leveraging protein family sequence–function space and genome context to discover novel functions, Biochemistry. Volume 56, 2017, Pages 4293-4308. https://doi.org/10.1021/acs.biochem.7b00614

John A. Gerlt, Jason T. Bouvier, Daniel B. Davidson, Heidi J. Imker, Boris Sadkhin, David R. Slater, Katie L. Whalen, Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1854, Issue 8, 2015, Pages 1019-1037, ISSN 1570-9639, https://dx.doi.org/10.1016/j.bbapap.2015.04.015

SSN Creation

SSN creation from sequences, Pfam or InterPro famil(ies), and UniProt and/or NCBI protein accession IDs.

GNN Creation

GNN creation from sequence similarity networks.

Genome neighborhood diagrams

Genome neighborhood diagrams from sequences, sequence IDs, or GNNs.

Functional Profiling

Computationally-guided functional profiling using ShortBRED and the CGFP tools from the Balskus and Huttenhower Labs at Harvard University.

These webtools use NCBI BLAST and CD-HIT to create SSNs and GNNs. The computationally-guided functional profiling tool uses the CGFP programs from the Balskus Lab (https://bitbucket.org/biobakery/cgfp/src) and ShortBRED from the Huttenhower Lab (http://huttenhower.sph.harvard.edu/shortbred). The data used originate from the UniProt Consortium databases and the InterPro and ENA databases from EMBL-EBI.