title: Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
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.
authors.affiliation: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA. Electronic address: j-gerlt@illinois.edu.
authors.forename: John A
authors.initials: JA
authors.lastname: Gerlt
authors.affiliation: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
authors.forename: Jason T
authors.initials: JT
authors.lastname: Bouvier
authors.affiliation: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Davidson
authors.affiliation: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
authors.forename: Heidi J
authors.initials: HJ
authors.lastname: Imker
authors.affiliation: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
authors.forename: Boris
authors.initials: B
authors.lastname: Sadkhin
authors.affiliation: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Slater
authors.affiliation: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
authors.forename: Katie L
authors.initials: KL
authors.lastname: Whalen
mesh_terms: D030562:Databases, Protein; D020407:Internet; D009964:Orotidine-5'-Phosphate Decarboxylase / Q000737:chemistry* / Q000235:genetics*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D009964:Orotidine-5'-Phosphate Decarboxylase
keywords: Enzyme; Function discovery; Protein family; Protein sequence analysis; Web tool