Scheffersomyces stipitis metabolic model
Sara Calhoun
Generated September 21, 2020

Scheffersomyces stipitis metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Scheffersomyces stipitis (also known as Pichia stipitis), which was built, manually curated, and validated by Caspeta et al. (2012). The Scheffersomyces stipitis genome was retrieved from NCBI RefSeq (GCF_000209165.1) and was sequenced by the Joint Genome Institute (Jeffries et al., 2007).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/Picst3

References:

  • Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol. Apr 4 2012;6:24. doi:10.1186/1752-0509-6-24
  • Jeffries TW, Grigoriev IV, Grimwood J, et al. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol. 2007;25(3):319-326. doi:10.1038/nbt1290

Metabolic model of Scheffersomyces stipitis

iSS884_KBase3
v1 - KBaseFBA.FBAModel-12.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70454
iSS884_KBase2
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/70454

Flux balance analysis run on the Scheffersomyces stipitis 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 produced errors.
No output found.
Gapfill Metabolic Model
Identify the minimal set of biochemical reactions to add to a draft metabolic model to enable it to produce biomass in a specified media.
This app produced errors in 1m 11s.
No output found.

Scheffersomyces stipitis genome imported into KBase

GCF_000209165.1
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/70454

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 48s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/70454
  • Picst3_SpeciesTree.newick
  • Picst3_SpeciesTree-labels.newick
  • Picst3_SpeciesTree.png
  • Picst3_SpeciesTree.pdf

Apps

  1. Gapfill Metabolic Model
    • [1] Henry, C.S., et al., High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol, 2010. 28(9): p. 977-82.
    • [2] Henry, C.S., et al., Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J, 2006. 90(4): p. 1453-61.
    • [3] Jankowski, M.D., et al., Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J, 2008. 95(3): p. 1487-99.
    • [4] Henry, C.S., et al., iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol, 2009. 10(6): p. R69.
    • [5] Orth, J.D., I. Thiele, and B.O. Palsson, What is flux balance analysis? Nat Biotechnol, 2010. 28(3): p. 245-8.
    • [6] Latendresse, M., Efficiently gap-filling reaction networks. BMC Bioinformatics, 2014. 15: p. 225.
    • [7] Dreyfuss, J.M., et al., Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol, 2013. 9(7): p. e1003126.
  2. 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
  3. 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