Metabolic Modeling in KBase

Modeling flow chart-NHmodelsKBase has a suite of analysis tools (Apps) and data that support the reconstruction, prediction, and design of metabolic models in microbes and plants. These tools can help advance efforts to optimize microbial production of a certain biofuel, find the minimal media conditions under which that fuel is generated, or predict soil amendments that improve the productivity of plant bioenergy feedstocks.

In KBase, genome-scale metabolic models are primarily reconstructed from protein functional annotations originally derived from literature and subsequently propagated from genome to genome by sequence similarity. When a genome is functionally annotated, its metabolic genes are mapped onto biochemical reactions. This information is integrated with data about reaction stoichiometry, subcellular localization, biomass composition, estimation of energy requirements (directionality of reactions), and other constraints into a detailed stoichiometric model of metabolism. Metabolic models can be used to evaluate an organism’s metabolic capability by simulating growth under different conditions to answer important biological questions such as:

  • What biochemical pathways are present?
  • What are the high flux pathways under a certain growth condition?
  • Could the organism grow anaerobically?
  • Would it grow under certain minimal media conditions?
  • Could the organism be optimized to produce a particular drug molecule or industrially important biofuel?

The flowchart above shows KBase’s metabolic modeling tools (green) as well as some other analysis tools. Check the App Catalog for the latest set of metabolic modeling analysis tools (Apps). The “Microbial Metabolic Model Reconstruction and Analysis” Narrative tutorial lets you see some of this functionality in action.

Common questions and answers about KBase’s metabolic modeling tools can be found in the Metabolic Modeling FAQ.

 

Metabolic Modeling Resources in KBase

 

Narrative Tutorial and FAQ

Build and Gapfill Metabolic Model

Flux Balance Analysis

Evaluate, Compare and Edit Models

Phenotype and Expression

Community Modeling

Publications about Metabolic Modeling in KBase