reaction-network

A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-reaction-network

Required or used by

anvi-get-metabolic-model-file

Description

This artifact represents the metabolic reaction network stored in a contigs-db or a pan-db by anvi-reaction-network.

The program, anvi-reaction-network, generates a reaction network from genes encoding enzymes in the contigs-db or from gene clusters with consensus enzyme annotations in the pan-db. The reaction network represents biochemical reactions and the constituent metabolites predicted from the genome or pangenome. The program relies upon KEGG Orthology (KO) annotations of protein-coding genes and reference data in the ModelSEED Biochemistry database, and is therefore subject to all the limitations thereof, including incomplete annotation of genes with protein orthologs and imprecise knowledge of the reactions catalyzed by enzymes.

The representation of the reaction network in two tables of the contigs-db, gene_function_reactions and gene_function_metabolites, is generalizable to other sources of metabolic data, linking genes to predicted functional orthologs and the associated reactions and metabolites. Reaction and metabolite data are likewise stored in the identically formatted tables, gene_cluster_function_reactions and gene_cluster_function_metabolites, in the pan-db. This data can be exported to a JSON-formatted file by anvi-get-metabolic-model-file for inspection and metabolic model analyses.

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