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FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies

By Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed A. Rahman, Roman A. Laskowski, Christine A. Orengo and Janet M. Thornton

Abstract

FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme's sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering ∼1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. The resource is freely available through a web interface: www.ebi.ac.uk/thorton-srv/databases/FunTree

Topics: Articles
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:3245072
Provided by: PubMed Central

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