Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1134362 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29772300_1.fastq.gz | Fastqsanger.gz | |||
| SRR29772301_1.fastq.gz | Fastqsanger.gz | |||
| SRR29772302_1.fastq.gz | Fastqsanger.gz | |||
| SRR29772303_1.fastq.gz | Fastqsanger.gz | |||
| SRR29772304_1.fastq.gz | Fastqsanger.gz |
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Project description:Henry2009 - Genome-scale metabolic network of
Bacillus subtilis (iBsu1103)
This model is described in the article:
iBsu1103: a new genome-scale
metabolic model of Bacillus subtilis based on SEED
annotations.
Henry CS, Zinner JF, Cohoon MP,
Stevens RL.
Genome Biol. 2009; 10(6): R69
Abstract:
BACKGROUND: Bacillus subtilis is an organism of interest
because of its extensive industrial applications, its
similarity to pathogenic organisms, and its role as the model
organism for Gram-positive, sporulating bacteria. In this work,
we introduce a new genome-scale metabolic model of B. subtilis
168 called iBsu1103. This new model is based on the annotated
B. subtilis 168 genome generated by the SEED, one of the most
up-to-date and accurate annotations of B. subtilis 168
available. RESULTS: The iBsu1103 model includes 1,437 reactions
associated with 1,103 genes, making it the most complete model
of B. subtilis available. The model also includes Gibbs free
energy change (DeltarG' degrees ) values for 1,403 (97%) of the
model reactions estimated by using the group contribution
method. These data were used with an improved reaction
reversibility prediction method to identify 653 (45%)
irreversible reactions in the model. The model was validated
against an experimental dataset consisting of 1,500 distinct
conditions and was optimized by using an improved model
optimization method to increase model accuracy from 89.7% to
93.1%. CONCLUSIONS: Basing the iBsu1103 model on the
annotations generated by the SEED significantly improved the
model completeness and accuracy compared with the most recent
previously published model. The enhanced accuracy of the
iBsu1103 model also demonstrates the efficacy of the improved
reaction directionality prediction method in accurately
identifying irreversible reactions in the B. subtilis
metabolism. The proposed improved model optimization
methodology was also demonstrated to be effective in minimally
adjusting model content to improve model accuracy.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180015.
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2015-07-30 | MODEL1507180015 | BioModels
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