Kluyveromyces lactis metabolic model
Sara Calhoun
Generated September 9, 2020

Kluyveromyces lactis metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Kluyveromyces lactis, which was built, manually curated, and validated by Dias et al. (2014). The Kluyveromyces lactis genome was retrieved from NCBI RefSeq (GCF_000027005.1) and is 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/Klula1

References:

  • Dias O, Pereira, Gombert AK, Ferreira EC, and Rocha I. iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis. Biotechnol J. 2014 Jun;9(6):776-90. doi: 10.1002/biot.201300242
  • Dujon B, et al. Genome evolution in yeasts. Nature. 2004 Jul 1;430(6995):35-44. doi: 10.1038/nature02579

Kluyveromyces lactis metabolic model

iOD907_KBase
v3 - KBaseFBA.FBAModel-11.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70255

Flux balance analysis run on the Kluyveromyces lactis 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 2m 47s.
Objects
Created Object Name Type Description
iOD907_FBA FBA FBA-13 iOD907_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 70255/6/3 growing in 70255/7/1 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/70255

Kluyveromyces lactis genome imported into KBase

GCF_000002515.2
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/70255

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 59s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/70255
  • Klula1_SpeciesTree.newick
  • Klula1_SpeciesTree-labels.newick
  • Klula1_SpeciesTree.png
  • Klula1_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