Aspergillus oryzae metabolic model
Sara Calhoun
Generated September 21, 2020

Aspergillus oryzae metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Aspergillus oryzae RIB40, which was built, manually curated, and validated by Vongsangnak et al. (2008). The Aspergillus oryzae RIB40 genome was retrieved from NCBI RefSeq (GCF_000184455.2) and is described in the publication by Machida, et al. (2005).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/Aspor1

References:

  • Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics. 2008 May 23;9:245. doi:10.1186/1471-2164-9-245
  • Machida M, et al. Genome sequencing and analysis of Aspergillus oryzae. Nature. 2005 Dec 22;438(7071):1157-61. doi: 10.1038/nature04300

Metabolic model of Aspergillus oryzae

iWV1314_KBase3
v3 - KBaseFBA.FBAModel-12.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70436

Flux balance analysis run on the Aspergillus oryzae 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 54s.
Objects
Created Object Name Type Description
iWV1314_FBA FBA FBA-13 iWV1314_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 70436/16/3 growing in 70436/4/1 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/70436

Aspergillus oryzae genome imported into KBase

GCF_000184455.2
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/70436

Species tree

Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 4m 58s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/70436
  • Aspor1_SpeciesTree.newick
  • Aspor1_SpeciesTree-labels.newick
  • Aspor1_SpeciesTree.png
  • Aspor1_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