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PROVIDER: PRJEB14430 | ENA |
REPOSITORIES: ENA
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Project description:Borodina2005 - Genome-scale metabolic network
of Streptomyces coelicolor (iIB711)
This model is described in the article:
Genome-scale analysis of
Streptomyces coelicolor A3(2) metabolism.
Borodina I, Krabben P, Nielsen
J.
Genome Res. 2005 Jun; 15(6):
820-829
Abstract:
Streptomyces are filamentous soil bacteria that produce more
than half of the known microbial antibiotics. We present the
first genome-scale metabolic model of a representative of this
group--Streptomyces coelicolor A3(2). The metabolism
reconstruction was based on annotated genes, physiological and
biochemical information. The stoichiometric model includes 819
biochemical conversions and 152 transport reactions, accounting
for a total of 971 reactions. Of the reactions in the network,
700 are unique, while the rest are iso-reactions. The network
comprises 500 metabolites. A total of 711 open reading frames
(ORFs) were included in the model, which corresponds to 13% of
the ORFs with assigned function in the S. coelicolor A3(2)
genome. In a comparative analysis with the Streptomyces
avermitilis genome, we showed that the metabolic genes are
highly conserved between these species and therefore the model
is suitable for use with other Streptomycetes. Flux balance
analysis was applied for studies of the reconstructed metabolic
network and to assess its metabolic capabilities for growth and
polyketides production. The model predictions of wild-type and
mutants' growth on different carbon and nitrogen sources agreed
with the experimental data in most cases. We estimated the
impact of each reaction knockout on the growth of the in silico
strain on 62 carbon sources and two nitrogen sources, thereby
identifying the "core" of the essential reactions. We also
illustrated how reconstruction of a metabolic network at the
genome level can be used to fill gaps in genome annotation.
This model is hosted on
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MODEL1507180049.
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2015-07-30 | MODEL1507180049 | BioModels
Project description:Ribosome profiling analysis of wild type prototrophic Streptomyces coelicolor A3(2) MT1110 strain to examine global translational vs transcriptional profile change when exposed to cold shock from 30°C to 10°C in minimal liquid medium.
2024-02-22 | GSE230542 | GEO