A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annotations being limited to a set of already known reactions. Here, we introduce Network Integrated Computational Explorer for Gap Annotation of Metabolism (NICEgame), a workflow to identify and curate nonannotated metabolic functions in genomes using the ATLAS of Biochemistry and genome-scale metabolic models (GEMs). To resolve gaps in GEMs, NICEgame provides alternative sets of known and hypothetical reactions, assesses their thermodynamic feasibility, and suggests candidate genes to catalyze these reactions. We identified metabolic gaps and applied NICEgame in the latest GEM of Escherichia coli, iML1515, and enhanced the E. coli genome annotation by resolving 47% of these gaps. NICEgame, applicable to any GEM and functioning from open-source software, should thus enhance all GEM-based predictions and subsequent biotechnological and biomedical applications.