bacillus_megaterium_metabolism — Bacillus megaterium metabolic network (2019)

Description

Metabolic network of the bacterium Bacillus megaterium strain DSM319, from the manually curated genome-scale metabolic model iJA1121 of Aminian-Dehkordi et al. The model was reconstructed from a draft network obtained by aligning the genome of DSM319 with those of other B. megaterium strains and comparing with the existing models of the strain WSH002 and of B. subtilis, followed by manual curation and gap filling, and was validated against growth phenotypes on different carbon and nitrogen sources. The model contains 1,709 reactions, 1,349 metabolites in two compartments (cytosol and extracellular space), and 1,121 genes, and it is distributed in the SBML format for flux balance analysis.

The network is bipartite and directed, with reactions on one side, and metabolites and genes on the other. Each reactant (substrate) of a reaction points to the reaction, and each reaction points to its products, as written in the model (reversible reactions can also proceed in the reverse direction). Each gene associated with a reaction (as a catalysing enzyme, or a subunit of an enzyme complex) points to the reaction. The same compound in different compartments corresponds to different metabolite nodes. Exchange reactions, which model the uptake and secretion of extracellular metabolites, have a single metabolite. The 46 genes of the model that are not associated with any reaction (some of which have malformed identifiers in the model, such as "orBMD_0557") are isolated nodes.

The network has the following properties:

All nodes: name, the name of the metabolite or reaction, or the locus tag of the gene; id, the identifier in the SBML model; kind, either "metabolite", "reaction", or "gene"; is_reaction, whether the node is a reaction.
Metabolites: compartment ("c" for cytosol, "e" for extracellular); formula, the chemical formula; charge; kegg, the KEGG compound identifier, if available.
Reactions: subsystem, the metabolic subsystem (e.g. "Amino acid metabolism", "Transporting system"); ec, the EC number(s) of the enzyme, if available; reversible, whether the reaction is reversible; lower_bound and upper_bound, the flux bounds in the model (in mmol per gram dry weight per hour); gene_rule, the gene-reaction rule, as a boolean expression of the genes required by the reaction ("and" for enzyme complexes and "or" for isozymes).
Edges: role, either "reactant", "product", or "gene"; stoichiometry, the stoichiometric coefficient of the metabolite in the reaction (1 for genes).

Tags

Biological Metabolic Unweighted Metadata

Citation

J. Aminian-Dehkordi, S. M. Mousavi, A. Jafari, I. Mijakovic, S.-A. Marashi, "Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319." Scientific Reports 9, 18762 (2019) 10.1038/s41598-019-55041-w Sci-Hub

Upstream URL OK

https://doi.org/10.1038/s41598-019-55041-w

Upstream license

CC BY 4.0, https://creativecommons.org/licenses/by/4.0/

Networks

Tip: hover over a column header for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
bacillus_megaterium_metabolism	4,179	9,662	2.31	15.87	24.76	28.73	-0.10	0.00	12	0.98	Directed	Bipartite	name id kind is_reaction compartment formula charge kegg subsystem ec reversible lower_bound upper_bound gene_rule	role stoichiometry	66 KiB	100 KiB	97 KiB	107 KiB