iWP3, Genome-scale metabolic model of Shewanella piezotolerans WP3

Files in this repository represent the GEM of Shewanella piezotolerans WP3. A manuscript associated with this repository is currently under review at the ASM journal mSystems:

A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation; Keith Dufault-Thompson, Huahua Jian, Ruixue Cheng, Jiefu Li, Fengping Wang, Ying Zhang; mSystems Mar 2017, 2 (2) e00165-16; DOI: 10.1128/mSystems.00165-16

List of files

• model.yaml:

  YAML configuration file for PSAMM. Designates the biomass equation and file paths to the reaction database, compound database, model reactions (defines a list of reactions included in the model), and media definition (defines exchange reactions and constraints). The model contains no special constraints to internal reactions, and the internal reaction constrains will be assigned in PSAMM based on reversibility of reactions.

• reactions.yaml:

  YAML file that defines reactions in the model. This file includes the id, name, equation, gene associations, subsystem assignments, and category of each reaction. The category information indicates the classification of reactions based on how they were added to the WP3 metabolic reconstruction during the annotation process. "Mapping And": functions that are conserved between WP3 and all of the previously modeled Shewanella (Ong, et al., 2014); "Mapping Or": functions that are conserved between WP3 and some but not all of the previously modeled Shewanella; "Annotated 1": functions included through manual curations of the WP3 genome, which were indicated as gap reactions in other Shewanella metabolic reconstructions or were associated with non-homologous genes; "Annotated 2": functions included through a second iteration of manual curations; "Synthesis": synthesis reactions that represent the biosynthesis of macromolecules; "Diffusion": represents the diffusion of small molecules cross the cell membrane; "Gap": Gap filling reactions.

• basal_constraints.yaml

  YAML file that defines the exchange reactions and the basal constraints used for model simulations. Carbon sources and electron acceptors are restricted to [0,1000] in the basal constraints, so the model would require change of these constraints to provide at least one carbon source and one electron acceptor in order to perform growth simulations.

• compounds.tsv:

  TSV file that defines compounds in the model. This file includes the id, name, formula, and charge of each compound.