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scoGEM 1.0
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@sulheim sulheim released this 26 Feb 14:06
· 206 commits to master since this release
v1.0
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Learn about vigilant mode.

First release of scoGEM, the community-developed genome-scale reconstruction of Streptomyces coelicolor.
The reconstruction is created by using iKS1317 as a template, additional genes, reactions and metabolites have been added from Sco4 and iAA1259

Basic stats

  • 1613 genes
  • 2544 reactions
  • 2017 metabolites
  • Memote score of 73

New features

  • Increased coverage compared to previous models
  • Divided the biomass-reaction into pseudo-metabolites:
    • lipid
    • rna
    • dna
    • cell wall
    • protein
    • carbohydrate
    • misc
  • Added SBO annotations to all genes, reactions and metabolites
  • Curated biomass reaction with respect to prosthetic groups
  • Improved coverage and curated annotation of
    • genes: GO, UniProt, AA-sequence, mass, EC-number, PANTHER (all in separate csv-file)
    • reactions: KEGG, BioCyc, MetaNetX
    • metabolites: KEGG, BioCyc, CHEBI, MetaNetX
  • Reviewed and curated reaction bounds by using calculations of the change in Gibbs free energy from eQuilibrator
  • Created an enzyme-constrained model from scoGEM 1.0 by using GECKO
    • Generated generic ec-models with protein pools for both strain M145 and M1152
    • Generated condition-specific proteome-constrained ec-models for both M145 and M1152
Assets 2
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