Yarrowia lipolytica metabolic model
Sara Calhoun
Generated September 9, 2020

Yarrowia lipolytica metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Yarrowia lipolytica, which was built, manually curated, and validated by Loira et al. (2012). The Yarrowia lipolytica genome was retrieved from NCBI RefSeq (GCF_000002525.2) and was described in the publication by Dujon et al. (2004).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/Yarli1

References:

  • Loira N, Dulermo T, Nicaud JM, Sherman DJ. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Syst Biol. 2012 May 4;6:35. doi: 10.1186/1752-0509-6-35
  • Dujon B, Sherman D, Fischer G, et al. Genome evolution in yeasts. Nature. 2004;430(6995):35-44. doi:10.1038/nature02579

Metabolic model of Yarrowia lipolytica

iNL895_KBase2
v4 - KBaseFBA.FBAModel-11.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70456

Flux balance analysis run on the Yarrowia lipolytica metabolic model

Run Flux Balance Analysis
Use flux balance analysis to predict metabolic fluxes in a metabolic model of an organism grown on a given media.
This app completed without errors in 1m 45s.
Objects
Created Object Name Type Description
iNL895_FBA FBA FBA-13 iNL895_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 70456/28/4 growing in 70456/4/1 media.
Output from Run Flux Balance Analysis
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/70456

Yarrowia lipolytica genome imported into KBase

GCF_000002525.2
v1 - KBaseGenomes.Genome-8.2
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70456

Species tree

Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 5m 17s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/70456
  • Yarli1_SpeciesTree.newick
  • Yarli1_SpeciesTree-labels.newick
  • Yarli1_SpeciesTree.png
  • Yarli1_SpeciesTree.pdf

Apps

  1. Insert Genome Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  2. Run Flux Balance Analysis
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • Orth JD, Thiele I, Palsson B . What is flux balance analysis? Nature Biotechnology. 2010;28: 245 248. doi:10.1038/nbt.1614