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dc.contributor.authorBeattie, Kirsten
dc.contributor.authorDe Ferrari, Luna
dc.contributor.authorMitchell, John B. O.
dc.date.accessioned2016-01-12T12:10:07Z
dc.date.available2016-01-12T12:10:07Z
dc.date.issued2015-12-29
dc.identifier.citationBeattie , K , De Ferrari , L & Mitchell , J B O 2015 , ' Why do sequence signatures predict enzyme mechanism? Homology versus Chemistry ' , Evolutionary Bioinformatics , vol. 2015 , no. 11 , pp. 267-274 . https://doi.org/10.4137/EBO.S31482en
dc.identifier.issn1176-9343
dc.identifier.otherPURE: 229654774
dc.identifier.otherPURE UUID: d6a2a86e-76ab-4237-9cdd-db9bf6bd9077
dc.identifier.otherScopus: 84956959645
dc.identifier.otherORCID: /0000-0002-0379-6097/work/34033380
dc.identifier.otherWOS: 000367286500001
dc.identifier.urihttps://hdl.handle.net/10023/8004
dc.description.abstractWe identify, firstly, InterPro sequence signatures representing evolutionary relatedness and, secondly, signatures identifying specific chemical machinery. Thus, we predict the chemical mechanisms of enzyme catalysed reactions from “catalytic” and “non-catalytic” subsets of InterPro signatures. We first scanned our 249 sequences with InterProScan and then used the MACiE database to identify those amino acid residues which are important for catalysis. The sequences were mutated in silico to replace these catalytic residues with glycine, and then again scanned with InterProScan. Those signature matches from the original scan which disappeared on mutation were called “catalytic”. Mechanism was predicted using all signatures, only the 78 “catalytic” signatures, or only the 519 “non-catalytic” signatures. The noncatalytic signatures gave results indistinguishable from those for the whole feature set, with precision of 0.991 and sensitivity of 0.970. The catalytic signatures alone gave less impressive predictivity, with precision and sensitivity of 0.791 and 0.735, respectively. These results show that our successful prediction of enzyme mechanism is mostly by homology rather than by identifying catalytic machinery.
dc.language.isoeng
dc.relation.ispartofEvolutionary Bioinformaticsen
dc.rightsCopyright © the authors, publisher and licensee Libertas Academica Limited. This is an open access article distributed under the terms of the creative commons CC-By 3.0 license.en
dc.subjectSequence signaturesen
dc.subjectInterProen
dc.subjectEnzyme catalysisen
dc.subjectReaction mechanismen
dc.subjectActive siteen
dc.subjectEvolutionen
dc.subjectHomologyen
dc.subjectQD Chemistryen
dc.subjectQH301 Biologyen
dc.subjectNDASen
dc.subject.lccQDen
dc.subject.lccQH301en
dc.titleWhy do sequence signatures predict enzyme mechanism? Homology versus Chemistryen
dc.typeJournal articleen
dc.contributor.sponsorBBSRCen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Chemistryen
dc.contributor.institutionUniversity of St Andrews. Biomedical Sciences Research Complexen
dc.contributor.institutionUniversity of St Andrews. EaSTCHEMen
dc.identifier.doihttps://doi.org/10.4137/EBO.S31482
dc.description.statusPeer revieweden
dc.identifier.grantnumberBB/I00596X/1en


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