Enzyme function initiative-enzyme similarity tool (EFI-EST)

A web tool for generating protein sequence similarity networks

John Alan Gerlt, Jason T. Bouvier, Daniel B. Davidson, Heidi J Imker, Boris Sadkhin, David R. Slater, Katie L. Whalen

Research output: Contribution to journalReview article

Abstract

The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.

Original languageEnglish (US)
Pages (from-to)1019-1037
Number of pages19
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1854
Issue number8
DOIs
StatePublished - Aug 1 2015

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Enzymes
Proteins
National Institute of General Medical Sciences (U.S.)
Orotidine-5'-Phosphate Decarboxylase
Biota
Protein Databases
Bioinformatics
Computational Biology
Demonstrations
Genes
Genome
Costs and Cost Analysis
Costs

Keywords

  • Enzyme
  • Function discovery
  • Protein family
  • Protein sequence analysis
  • Web tool

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

Enzyme function initiative-enzyme similarity tool (EFI-EST) : A web tool for generating protein sequence similarity networks. / Gerlt, John Alan; Bouvier, Jason T.; Davidson, Daniel B.; Imker, Heidi J; Sadkhin, Boris; Slater, David R.; Whalen, Katie L.

In: Biochimica et Biophysica Acta - Proteins and Proteomics, Vol. 1854, No. 8, 01.08.2015, p. 1019-1037.

Research output: Contribution to journalReview article

Gerlt, John Alan ; Bouvier, Jason T. ; Davidson, Daniel B. ; Imker, Heidi J ; Sadkhin, Boris ; Slater, David R. ; Whalen, Katie L. / Enzyme function initiative-enzyme similarity tool (EFI-EST) : A web tool for generating protein sequence similarity networks. In: Biochimica et Biophysica Acta - Proteins and Proteomics. 2015 ; Vol. 1854, No. 8. pp. 1019-1037.
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