Penicillium chrysogenum metabolic model
Sara Calhoun
Generated September 9, 2020

Penicillium chrysogenum metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Penicillium chrysogenum Wisconsin 54-1255, which was built, manually curated, and validated by Agren et al. (2013). The Penicillium chrysogenum Wisconsin 54-1255 genome was retrieved from NCBI RefSeq (GCF_000226395.1) and is described in the publication by ven den Berg et al. (2008).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/PenchWisc1_1

References:

  • Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol. 2013;9(3):e1002980. doi:10.1371/journal.pcbi.1002980
  • van den Berg MA, et al. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol. 2008 Oct;26(10):1161-8. doi: 10.1038/nbt.1498

Metabolic model of Penicillium chrysogenum

iAL1006_KBase3
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/70449

Flux balance analysis run on the Penicillium chrysogenum 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 44s.
Objects
Created Object Name Type Description
iAL1006_FBA FBA FBA-13 iAL1006_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 70449/16/3 growing in 70449/4/1 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/70449

Species tree

GCF_000226395.1
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/70449

Penicillium chrysogenum genome imported into KBase

Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app is still in progress.
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