Related Experiment Video
Updated: May 6, 2026
High-Throughput Metabolic Profiling for Model Refinements of Microalgae
Published on: December 4, 2021
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of
Miguel Ponce-de-León, Francisco Montero1, Juli Peretó
1Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain. framonte@quim.ucm.es.
Background:
Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed.
Results:
We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connected through gap metabolites, is proposed. The method has been successfully applied to the curation of iCG238, the genome-scale metabolic model for the bacterium Blattabacterium cuenoti, obligate endosymbiont of cockroaches.
Conclusion:
We found the proposed approach to be a valuable tool for the curation of genome-scale metabolic models. The outcome of its application to the genome-scale model B. cuenoti iCG238 is a more accurate model version named as B. cuenoti iMP240.
