{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1363670321106487296.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1038/msb.2012.13"}},{"identifier":{"@type":"URI","@value":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1038%2Fmsb.2012.13"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/pdf/10.1038/msb.2012.13"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/full-xml/10.1038/msb.2012.13"}},{"identifier":{"@type":"URI","@value":"https://www.embopress.org/doi/pdf/10.1038/msb.2012.13"}},{"identifier":{"@type":"PMID","@value":"22569339"}}],"dc:title":[{"@value":"Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours"}],"description":[{"notation":[{"@value":"Despite the current wealth of sequencing data, one-third of all biochemically characterized metabolic enzymes lack a corresponding gene or protein sequence, and as such can be considered orphan enzymes. They represent a major gap between our molecular and biochemical knowledge, and consequently are not amenable to modern systemic analyses. As 555 of these orphan enzymes have metabolic pathway neighbours, we developed a global framework that utilizes the pathway and (meta)genomic neighbour information to assign candidate sequences to orphan enzymes. For 131 orphan enzymes (37% of those for which (meta)genomic neighbours are available), we associate sequences to them using scoring parameters with an estimated accuracy of 70%, implying functional annotation of 16,345 gene sequences in numerous (meta)genomes. As a case in point, two of these candidate sequences were experimentally validated to encode the predicted activity. In addition, we augmented the currently available genome-scale metabolic models with these new sequence-function associations and were able to expand the models by on average 8%, with a considerable change in the flux connectivity patterns and improved essentiality prediction."}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1383670321106487172","@type":"Researcher","foaf:name":[{"@value":"Takuji Yamada"}],"jpcoar:affiliationName":[{"@value":"Structural and Computational Biology Unit, European Molecular Biology Laboratory  Heidelberg Germany"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487174","@type":"Researcher","foaf:name":[{"@value":"Alison S Waller"}],"jpcoar:affiliationName":[{"@value":"Structural and Computational Biology Unit, European Molecular Biology Laboratory  Heidelberg Germany"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487169","@type":"Researcher","foaf:name":[{"@value":"Jeroen Raes"}],"jpcoar:affiliationName":[{"@value":"Molecular and Cellular Interactions Department, VIB  Brussels Belgium"},{"@value":"Vrije Universiteit Brussel  Brussels Belgium"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487297","@type":"Researcher","foaf:name":[{"@value":"Aleksej Zelezniak"}],"jpcoar:affiliationName":[{"@value":"Structural and Computational Biology Unit, European Molecular Biology Laboratory  Heidelberg Germany"},{"@value":"Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark  Lyngby Denmark"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487173","@type":"Researcher","foaf:name":[{"@value":"Nadia Perchat"}],"jpcoar:affiliationName":[{"@value":"Commissariat à l'Energie Atomique  Evry France"},{"@value":"Centre National de la Recherche Scientifique  Evry France"},{"@value":"Université d'Evry Val d'Essonne, boulevard François Mitterrand  Evry France"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487170","@type":"Researcher","foaf:name":[{"@value":"Alain Perret"}],"jpcoar:affiliationName":[{"@value":"Commissariat à l'Energie Atomique  Evry France"},{"@value":"Centre National de la Recherche Scientifique  Evry France"},{"@value":"Université d'Evry Val d'Essonne, boulevard François Mitterrand  Evry France"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487296","@type":"Researcher","foaf:name":[{"@value":"Marcel Salanoubat"}],"jpcoar:affiliationName":[{"@value":"Commissariat à l'Energie Atomique  Evry France"},{"@value":"Centre National de la Recherche Scientifique  Evry France"},{"@value":"Université d'Evry Val d'Essonne, boulevard François Mitterrand  Evry France"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487171","@type":"Researcher","foaf:name":[{"@value":"Kiran R Patil"}],"jpcoar:affiliationName":[{"@value":"Structural and Computational Biology Unit, European Molecular Biology Laboratory  Heidelberg Germany"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487175","@type":"Researcher","foaf:name":[{"@value":"Jean Weissenbach"}],"jpcoar:affiliationName":[{"@value":"Commissariat à l'Energie Atomique  Evry France"},{"@value":"Centre National de la Recherche Scientifique  Evry France"},{"@value":"Université d'Evry Val d'Essonne, boulevard François Mitterrand  Evry France"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670321106487168","@type":"Researcher","foaf:name":[{"@value":"Peer Bork"}],"jpcoar:affiliationName":[{"@value":"Structural and Computational Biology Unit, European Molecular Biology Laboratory  Heidelberg Germany"},{"@value":"Max‐Delbruck‐Centre for Molecular Medicine  Berlin Germany"}]}],"contributor":[{"@id":"https://cir.nii.ac.jp/crid/1892273590587832068","@type":"Researcher","foaf:name":[{"@value":"EMBL Heidelberg"}]},{"@id":"https://cir.nii.ac.jp/crid/1892273590587832073","@type":"Researcher","foaf:name":[{"@value":"European Molecular Biology Laboratory"}]},{"@id":"https://cir.nii.ac.jp/crid/1892273590587832080","@type":"Researcher","foaf:name":[{"@value":"European Molecular Biology Laboratory [Heidelberg] (EMBL)"}]},{"@id":"https://cir.nii.ac.jp/crid/1892273590587832074","@type":"Researcher","foaf:name":[{"@value":"Génomique métabolique (UMR 8030) ; Genoscope - Centre national de séquençage [Evry] (GENOSCOPE) ; Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)"}]},{"@id":"https://cir.nii.ac.jp/crid/1892273590587832067","@type":"Researcher","foaf:name":[{"@value":"Department of Bio-engineering 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