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Propagate Model to New Genome


By: chenry


Translate the metabolic model of one organism to another, using a mapping of similar proteins between their genomes.

Accurate metabolic models are based on well-curated genome annotations which are labor intensive and thus highly valuable. This method permits users to construct a metabolic model of a new organism based on a previously published model in another organism rather than constructing and curating it from scratch. The proteome comparison map between the source and the target organism generated by the Compare Two Proteomes method method is used to identify genes encoding potentially orthologous proteins in the two organisms. The method works best when the two organisms are closely related since that allows a large fraction of annotations to be accurately transferred to the target genome. Additionally, the transferred model may suggest missing annotations in the target genome thus improving the quality of its annotation.

The method applies the following rules in order to decide whether to propagate a reaction or not:

  1. If the reaction has one or more genes in the original model, but none of those genes has an ortholog in the new genome, the reaction is always deleted (or should be at least).
  2. If the reaction has no genes in the original model, then what happens depends on whether the "Keep reactions with no genes" is checked. If checked, the reaction is retained, otherwise it is removed. If checked, the user is making the assumption that both species have the same gaps in the enzymatic annotation of their genomes.
  3. If the reaction has one or more genes in the original model and at least one has a homolog in the new genome, then the reaction is retained, and all genes with homologs are translated and retained.

Team members who developed & deployed algorithm in KBase: Chris Henry, Janaka Edirisinghe, Sam Seaver, and Neal Conrad. For questions, e-mail

App Specification:

Module Commit: 584206644abfeb5f3184783aaa27b3a0993ca583