Table 1.

Information included in the B. subtilis ME-model iJT964-ME.

Information type	Description/Notes	Containing script	Source
Core metabolic network	Stoichiometric matrix, metabolic reactions, and metabolites included in the network. Exchange reaction constraints are adopted as well.	generate_flatfiles	iYO8447
Gene-reaction rules	Enzyme-reaction associations were taken from the available M-model iYO844. Several new transporters were added and corrected as listed in Supplementary Table 1.	Metacyc_dependent_files	iYO8447
Genome	Genbank file containing gene names, positions, compositions, lengths, and primary structure.	build_me_model	Genbank
Protein complexes	All possible protein complexes in B. subtilis, as well as which monomers that are contained in each complex.	Metacyc_dependent_files	BsubCyc23
Protein stoichiometry	Monomer composition of complexes. All available enzyme stoichiometries in BsubCyc were used, while unavailable ones were defined by homology with E. coli.	Metacyc_dependent_files	BsubCyc23 EcoCyc24
Post-translational modification	Protein modification information was taken from BsubCyc and was also defined by homology with E. coli.	Metacyc_dependent_files	BsubCyc23 EcoCyc24
Transcription Units	List of transcription unit names, lengths, positions, strands, sigma factors, and rho dependence.	Metacyc_dependent_files	BsubCyc23
Cleaved methionine	List of proteins that undergo N-terminal methionine excision.	Metacyc_dependent_files	BsubCyc23
Ribosome composition and synthesis	Subunit composition of the ribosome and synthesis subreactions.	build_me_model	SubtiWiki25 BsubCyc23
Protein compartment and secretory pathway	Final compartment of translated proteins and the secretory pathways by which they reach their final destinations. Tat-pathway signal peptides were predicted by SignalP 5.0.	Metacyc_dependent_files	BsubCyc23 SignalP 5.026
rRNA modifications	List of rRNA modifications and catalyzing enzymes.	ribosome	Desmolaize et al.27
RNA degradosome	Composition of the RNA degradosome	transcription	Lehnik-Habrink et al.28
Excision machinery	Composition of rRNA-containing, monocistronic, and polycistronic rRNA machinery.	transcription	BsubCyc23
Initiation, elongation, and termination subreactions	Translation initiation, elongation, and termination subreactions.	translation	BsubCyc23
Codon usage	Codon usage table for B. subtilis.	build_me_model	Nakamura et al.29
Protein folding	Independent and GroEL-dependent folding.	translation	Endo & Kurusu30
Translocation pathways	Mechanism of translocation: Sec-SRP, SRP, and Tat pathways. Sec-SRP, SRP, and Tat translocation pathways were described by Simonen & Palva31 (Sec-SRP and SRP) and Fu et al.32 (Tat).	translation	Fu et al.32 Simonen & Palva31
Enzyme turnover rates (Keff)	Coefficients that link enzyme usage with reaction fluxes, as described by Lloyd et al.20. Effective coefficients ($K_{eff}$) were assigned depending on the enzyme’s role in primary or secondary metabolism, as reported by Bar-Even et al.33.	build_me_model	Bar-Even et al.33