KBase 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:
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.
Narrative Tutorial and FAQ
Build and Gapfill Metabolic Model
Flux Balance Analysis
Evaluate, Compare and Edit Models
Phenotype and Expression
Publications about Metabolic Modeling in KBase