Eremothecium gossypii metabolic model
Sara Calhoun
Generated September 9, 2020

Eremothecium gossypii metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Eremothecium gossypii ATCC 10895 (also, known as Ashbya gossypii), which was built, manually curated, and validated by Ledesma-Amaro et al. (2014). The Eremothecium gossypii ATCC 10895 genome was retrieved from NCBI RefSeq (GCF_000091025.4) and is described in the publication by Dietrich et al. (2004).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/Ashgo1_1

References:

  • Ledesma-Amaro R, Kerkhoven EJ, Revuelta JL, Nielsen J. Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii. Biotechnol Bioeng. 2014;111(6):1191-1199. doi:10.1002/bit.25167
  • Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pöhlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004 Apr 9;304(5668):304-7. doi: 10.1126/science.1095781

Metabolic model of Eremothecium gossypii

iRL766_KBase2
v5 - KBaseFBA.FBAModel-11.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70448

Flux balance analysis run on the Eremothecium gossypii 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 is still in progress.
No output found.

Eremothecium gossypii genome imported into KBase

GCF_000091025.4
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/70448

Species tree

Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app produced errors.
No output found.

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