Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

被引：592
作者：
Gerlt, John A. [1 ,2 ,3 ]
Bouvier, Jason T. [1 ,2 ]
Davidson, Daniel B. [1 ]
Imker, Heidi J. [1 ]
Sadkhin, Boris [1 ]
Slater, David R. [1 ]
Whalen, Katie L. [1 ]
机构：
[1] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA
[2] Univ Illinois, Dept Biochem, Urbana, IL 61801 USA
[3] Univ Illinois, Dept Chem, Urbana, IL 61801 USA
来源：
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS | 2015年 / 1854卷 / 08期
关键词：
Enzyme; Protein sequence analysis; Protein family; Function discovery; Web tool; OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE; RIBULOSE MONOPHOSPHATE PATHWAY; D-MANNONATE DEHYDRATASE; PROTON RELAY SYSTEM; ACTIVE-SITE; DISCOVERY; EVOLUTION; SUPRAFAMILY; PREDICTION; DEAMINASE;
D O I：
10.1016/j.bbapap.2015.04.015
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymeffinction.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 (HJ. 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. (C) 2015 Elsevier B.V. All rights reserved.
引用
收藏
页码：1019 / 1037
页数：19
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