title: Genome-Wide Semi-Automated Annotation of Transporter Systems.
abstract: Usually, transport reactions are added to genome-scale metabolic models (GSMMs) based on experimental data and literature. This approach does not allow associating specific genes with transport reactions, which impairs the ability of the model to predict effects of gene deletions. Novel methods for systematic genome-wide transporter functional annotation and their integration into GSMMs are therefore necessary. In this work, an automatic system to detect and classify all potential membrane transport proteins for a given genome and integrate the related reactions into GSMMs is proposed, based on the identification and classification of genes that encode transmembrane proteins. The Transport Reactions Annotation and Generation (TRIAGE) tool identifies the metabolites transported by each transmembrane protein and its transporter family. The localization of the carriers is also predicted and, consequently, their action is confined to a given membrane. The integration of the data provided by TRIAGE with highly curated models allowed the identification of new transport reactions. TRIAGE is included in the new release of merlin, a software tool previously developed by the authors, which expedites the GSMM reconstruction processes.
authors.forename: Oscar
authors.initials: O
authors.lastname: Dias
authors.forename: Daniel
authors.initials: D
authors.lastname: Gomes
authors.forename: Paulo
authors.initials: P
authors.lastname: Vilaca
authors.forename: Joao
authors.initials: J
authors.lastname: Cardoso
authors.forename: Miguel
authors.initials: M
authors.lastname: Rocha
authors.forename: Eugenio C
authors.initials: EC
authors.lastname: Ferreira
authors.forename: Isabel
authors.initials: I
authors.lastname: Rocha
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods*; D026901:Membrane Transport Proteins / Q000235:genetics* / Q000378:metabolism; D055442:Metabolome / Q000235:genetics*; D008954:Models, Biological; D058977:Molecular Sequence Annotation / Q000379:methods*; D049490:Systems Biology
chemical_list: D001426:Bacterial Proteins; D026901:Membrane Transport Proteins