Komagataella phaffii metabolic model
Sara Calhoun
Generated September 21, 2020

Komagataella phaffii metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Komagataella phaffii (also, known as Pichia pastoris), which was built, manually curated, and validated by Andersen et al. (2008). The Komagataella phaffii genome was retrieved from NCBI RefSeq (GCF_000027005.1) and is described in the publication by Pel et al. (2007).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/Picpa1

References:

  • Caspeta L, Shoaie S, Agren R, Nookaew I, and Nielsen J. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol. 2012 Apr 4;6:24. doi: 10.1186/1752-0509-6-24.
  • De Schutter K, et al. Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol. 2009 Jun;27(6):561-6. doi: 10.1038/nbt.1544

Metabolic model of Komagataella phaffii

iLC915_KBase3
v7 - KBaseFBA.FBAModel-12.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70432

Flux balance analysis run on the Komagataella phaffii 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 17s.
Objects
Created Object Name Type Description
iLC915_FBA FBA FBA-13 iLC915_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 70432/11/7 growing in 70432/8/1 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/70432

Komagataella phaffii genome imported into KBase

GCF_000027005.1
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/70432

Species tree

Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 3m 40s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/70432
  • Picpa1_SpeciesTree.newick
  • Picpa1_SpeciesTree-labels.newick
  • Picpa1_SpeciesTree.png
  • Picpa1_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