4. Architecture of coralME

coralME is composed of 4 main classes that process and exchange organism-specific information for the reconstruction of a ME-model. The classes are:

class Organism()

class MEBuilder()

class MEReconstruction()

class Homology()

Drawing

4.1. Organism()

class coralme.builder.organism.Organism(config, is_reference, available_reference_models=None)[source]

Organism class for storing information about an organism

This class acts as a database containing all necessary information to reconstruct a ME-model. It is used to retrieve and store information of the main (org) and the reference (ref) organisms. Information in Organism is read and manipulated by methods in the MEBuilder class.

Parameters:

  • config (dict) – Dictionary containing configuration and settings.

  • is_reference (bool) – If True, process as reference organism.

Role: Store information about an organism

This class acts as a database containing all necessary information to reconstruct a ME-model. It is used to retrieve and store information of the main (org) and the reference (ref) organisms. Information in Organism() is read and manipulated by methods in the MEBuilder() class. The reference can be set as any of the provided organisms in coralME, available here, although we advise to choose E. coli and B. subtilis for gram-negative and gram-positive bacteria, respectively.

4.2. MEBuilder()

class coralme.builder.main.MEBuilder(*args, m_model_path=False, genbank_path=False, locus_tag='locus_tag', blast_threads=None, df_gene_cplxs_mods_rxns='automated-org-with-refs.xlsx', df_TranscriptionalUnits='', df_matrix_stoichiometry='', df_matrix_subrxn_stoich='', df_metadata_orphan_rxns='', df_metadata_metabolites='', out_directory='./', log_directory='./', debug=False, **kwargs)[source]

MEBuilder class to coordinate the reconstruction of ME-models.

Parameters:

  • *args – Positional arguments are passed as paths to JSON files that update the configuration of the parent class.

  • **kwargs – Further keyword arguments are passed on as dictionaries to update the configuration of the parent class.

Role: Coordinate the roles of other classes.

This class acts as the main coordinator between other objects, e.g. Organism, Homology, MEProcesser, and METroubleshooter. It contains methods to manipulate class Organism by using attributes in class Homology, and manually curated files in the folder containing the main organism. Moreover, it is called by objects to access stored information in other objects.

4.3. MEReconstruction()

class coralme.builder.main.MEReconstruction(builder)[source]

MEReconstruction class for reconstructing a ME-model from user/automated input

Parameters:

MEBuilder (coralme.builder.main.MEBuilder)

Role: Reconstruct a ME-model from the information contained in class Organism.

This class was based almost entirely from the original ECOLIme code in build_me_model.py. Adaptations to this code were necessary to make it applicable to other organisms.

4.4. Homology()

class coralme.builder.homology.Homology(org, ref, evalue=False, verbose=False)[source]

Homology class for storing information about homology of the main and reference organisms.

This class contains methods to predict and process homology of the main and reference organisms. Homology is inferred from the reciprocal best hits of a BLAST. The results are used to update and complement the attributes of the class Organism.

Parameters:

  • org (str) – Identifier of the main organism. Has to be the same as its containing folder name.

  • ref (str) – Identifier of the reference organism. Has to be the same as its containing folder name.

  • evalue (float) – E-value cutoff to call enzyme homologs from the BLAST. Two reciprocal best hits are considered homologs if their E-value is less than this parameter.

Role: Generate and store information about homology of the main and reference organisms.

This class contains methods to predict and process homology of the main and reference organisms. Homology is inferred from the reciprocal best hits of a BLAST. The results are used to update and complement the attributes of the class Organism.

4.5. Curation()

Role: Handle manual curation.

This class contains methods to handle the manual curation that is in building_data/

  • termination_subreactions.txt

    Input here will define translation termination subreactions and their machinery.

class coralme.builder.curation.TerminationSubreactions(org, id='termination_subreactions', config={}, file='termination_subreactions.txt', name='Translation termination subreactions')[source]

Reads manual input to define translation termination subreactions.

This class creates the property “termination_subreactions” from the manual inputs in termination_subreactions.txt in an instance of Organism.

Input here will define translation termination subreactions and their machinery.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

termination_subreactions.txt :

subreaction enzymes PrfA_mono_mediated_termination PrfA_mono …

  • peptide_release_factors.txt

    Input here will define peptide release factors.

class coralme.builder.curation.PeptideReleaseFactors(org, id='peptide_release_factors', config={}, file='peptide_release_factors.txt', name='Peptide release factors')[source]

Reads manual input to define peptide release factors.

This class creates the property “peptide_release_factors” from the manual inputs in peptide_release_factors.txt in an instance of Organism.

Input here will define peptide release factors.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

peptide_release_factors.txt :

release_factor enzyme UAA generic_RF …

  • rna_degradosome.txt

    Input here will define the composition of the RNA degradosome.

class coralme.builder.curation.RNADegradosome(org, id='rna_degradosome', config={}, file='rna_degradosome.txt', name='RNA degradosome composition')[source]

Reads manual input to add RNA degradosome composition.

This class creates the property “rna_degradosome” from the manual inputs in rna_degradosome.txt in an instance of Organism.

Input here will define the composition of the RNA degradosome.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

rna_degradosome.txt :

enzymes Eno_dim_mod_mg2(4) …

  • special_trna_subreactions.txt

    Input here will define special tRNA subreactions, such as tRNA-Sec (selenocysteine) synthesis from tRNA-Ser.

class coralme.builder.curation.SpecialtRNASubreactions(org, id='special_trna_subreactions', config={}, file='special_trna_subreactions.txt', name='Special tRNA subreactions')[source]

Reads manual input to define special tRNA subreactions.

This class creates the property “special_trna_subreactions” from the manual inputs in special_trna_subreactions.txt in an instance of Organism.

Input here will define special tRNA subreactions, such as tRNA-Sec (selenocysteine) synthesis from tRNA-Ser.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

special_trna_subreactions.txt :

subreaction enzymes PrfA_mono_mediated_termination PrfA_mono …

  • lipoprotein_precursors.txt

    Input here will add lipoprotein precursors.

class coralme.builder.curation.LipoproteinPrecursors(org, id='lipoprotein_precursors', config={}, file='lipoprotein_precursors.txt', name='Lipoprotein precursors')[source]

Reads manual input to add lipoprotein precursors.

This class creates the property “lipoprotein_precursors” from the manual inputs in lipoprotein_precursors.txt in an instance of Organism.

Input here will add lipoprotein precursors.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

lipoprotein_precursors.txt :

name,gene AcrA,b0463 …

  • special_modifications.txt

    Input here will define machinery for special modifications. These modifications are a set of pre-defined modifications that are used in ME-models.

class coralme.builder.curation.SpecialModifications(org, id='special_modifications', config={}, file='special_modifications.txt', name='Special protein modifications')[source]

Reads manual input to define machinery for special modifications.

This class creates the property “special_modifications” from the manual inputs in special_modifications.txt in an instance of Organism.

Input here will define machinery for special modifications. These modifications are a set of pre-defined modifications that are used in ME-models.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

special_modifications.txt :

modification enzymes stoich fes_transfer CPLX0-7617,IscA_tetra,CPLX0-7824 …

  • excision_machinery.txt

    Input here will define machinery for excision.

class coralme.builder.curation.ExcisionMachinery(org, id='excision_machinery', config={}, file='excision_machinery.txt', name='Excision machinery')[source]

Reads manual input to define machinery for excision.

This class creates the property “excision_machinery” from the manual inputs in excision_machinery.txt in an instance of Organism.

Input here will define machinery for excision.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

excision_machinery.txt :

mechanism enzymes rRNA_containing RNase_E_tetra_mod_zn2(2), … …

  • orphan_and_spont_reactions.txt

    Input here will mark reactions as orphan or spontaneous. Orphan reactions will be associated with CPLX_dummy, and spontaneous ones will not require enzymes for flux.

class coralme.builder.curation.OrphanSpontReactions(org, id='orphan_and_spont_reactions', config={}, file='orphan_and_spont_reactions.txt', name='Orphan and spontaneous reactions')[source]

Reads manual input to add reactions to the ME-model.

This class creates the property “orphan_and_spont_reactions” from the manual inputs in orphan_and_spont_reactions.txt in an instance of Organism.

Input here will mark reactions as orphan or spontaneous. Orphan reactions will be associated with CPLX_dummy, and spontaneous ones will not require enzymes for flux.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

orphan_and_spont_reactions.txt :

name description is_reversible is_spontaneous subsystems CODH_Fe_loading Loading of Fe false true …

  • enzyme_reaction_association.txt

    Input here will create the association between enzymes and reactions in the ME-model.

class coralme.builder.curation.EnzymeReactionAssociation(org, id='enz_rxn_assoc_df', config={}, file='enzyme_reaction_association.txt', name='Enzyme-reaction associations')[source]

Reads manual input to specify enzyme-reaction associations.

This class creates the property “enz_rxn_assoc_df” from the manual inputs in enzyme_reaction_association.txt in an instance of Organism.

Input here will create the association between enzymes and reactions in the ME-model.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

enzyme_reaction_association.txt :

Reaction Complexes ADNt2pp NUPG-MONOMER OR NUPC-MONOMER …

  • peptide_compartment_and_pathways.txt

    Input here will modify protein locations, and translocation pathways in the ME-model.

class coralme.builder.curation.ProteinLocation(org, id='protein_location', config={}, file='peptide_compartment_and_pathways.txt', name='Protein location')[source]

Reads manual input to add protein locations.

This class creates the property “protein_location” from the manual inputs in peptide_compartment_and_pathways.txt in an instance of Organism.

Input here will modify protein locations, and translocation pathways in the ME-model.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

peptide_compartment_and_pathways.txt :

Complex Complex_compartment Protein Protein_compartment translocase_pathway BSU02690-MONOMER Plasma_Membrane BSU02690() Plasma_Membrane s …

  • translocation_pathways.txt

    Input here will define translocation pathways and their machinery.

class coralme.builder.curation.TranslocationPathways(org, id='translocation_pathways', config={}, file='translocation_pathways.txt', name='Translocation pathways')[source]

Reads manual input to define translocation pathways.

This class creates the property “translocation_pathways” from the manual inputs in translocation_pathways.txt in an instance of Organism.

Input here will define translocation pathways and their machinery.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

translocation_pathways.txt :

pathway enzyme sec BSU27650-MONOMER sec BSU35300-MONOMER sec secYEG …

  • rna_modification.txt

    Input here will define enzymes that perform RNA modifications for either rRNA or tRNA in the ME-model.

class coralme.builder.curation.RNAModificationMachinery(org, id='rna_modification_df', config={}, file='rna_modification.txt', name='RNA Modification machinery')[source]

Reads manual input to add RNA modification machinery.

This class creates the property “rna_modification_df” from the manual inputs in rna_modification.txt in an instance of Organism.

Input here will define enzymes that perform RNA modifications for either rRNA or tRNA in the ME-model.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

rna_modification.txt :

modification positions type enzymes source D 16,17,20,20A,21 tRNA DusB_mono …

  • ribosomal_proteins.txt

    Input here will define the composition of the ribosome.

class coralme.builder.curation.RibosomeStoich(org, id='ribosome_stoich', config={}, file='ribosomal_proteins.txt', name='Ribosomal proteins')[source]

Reads manual input to define ribosome composition.

This class creates the property “ribosome_stoich” from the manual inputs in ribosomal_proteins.txt in an instance of Organism.

Input here will define the composition of the ribosome.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

ribosomal_proteins.txt :

subunits proteins 30S RpsD_mono,… 50S generic_23s_rRNAs,generic_5s_rRNAs,RplA_mono,…

  • rho_independent.txt

    Input here will mark genes with rho independent transcription termination.

class coralme.builder.curation.RhoIndependent(org, id='rho_independent', config={}, file='rho_independent.txt', name='Genes with rho-independent termination')[source]

Reads manual input to define genes with rho independent termination.

This class creates the property “rho_independent” from the manual inputs in rho_independent.txt in an instance of Organism.

Input here will mark genes with rho independent transcription termination.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

rho_independent.txt :

id b0344 …

  • sigma_factors.txt

    Input here will mark proteins for N-terminal methionine cleavage in the ME-model.

class coralme.builder.curation.Sigmas(org, id='sigmas', config={}, file='sigma_factors.txt', name='Sigma factors')[source]

Reads manual input to modify or add sigma factors.

This class creates the property “sigmas” from the manual inputs in sigma_factors.txt in an instance of Organism.

Input here will mark proteins for N-terminal methionine cleavage in the ME-model.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

sigma_factors.txt :

sigma,complex,genes,name RpoH_mono,RNAP_32H,b3461,”RNA polymerase, sigma 32 (sigma H) factor” …

  • cleaved_methionine.txt

    Input here will mark proteins for N-terminal methionine cleavage in the ME-model.

class coralme.builder.curation.CleavedMethionine(org, id='cleaved_methionine', config={}, file='cleaved_methionine.txt', name='Proteins with N-terminal methionine cleavage')[source]

Reads manual input to mark proteins that undergo N-terminal methionine cleavage.

This class creates the property “cleaved_methionine” from the manual inputs in cleaved_methionine.txt in an instance of Organism.

Input here will mark proteins for N-terminal methionine cleavage in the ME-model.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

cleaved_methionine.txt :

cleaved_methionine_genes b4154 …

  • folding_dict.txt

    Input here will define folding pathways for proteins.

class coralme.builder.curation.FoldingDict(org, id='folding_dict', config={}, file='folding_dict.txt', name='Protein to folding machinery associations')[source]

Reads manual input to define folding pathways for proteins.

This class creates the property “folding_dict” from the manual inputs in folding_dict.txt in an instance of Organism.

Input here will define folding pathways for proteins.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

folding_dict.txt :

mechanism enzymes GroEL_dependent_folding b0014, … …

  • translocation_multipliers.txt

    Input here will modify how many pores are required for the translocation of a protein.

class coralme.builder.curation.TranslocationMultipliers(org, id='translocation_multipliers', config={}, file='translocation_multipliers.txt', name='Translocation multipliers')[source]

Reads manual input to define translocation multipliers.

This class creates the property “translocation_multipliers” from the manual inputs in translocation_multipliers.txt in an instance of Organism.

Input here will modify how many pores are required for the translocation of a protein.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

translocation_multipliers.txt :

Gene,YidC_MONOMER,TatE_MONOMER,TatA_MONOMER b1855,2.0,0.0,0.0 …

  • subreaction_matrix.txt

    Input here will define subreactions in the ME-model.

class coralme.builder.curation.SubreactionMatrix(org, id='subreaction_matrix', config={}, file='subreaction_matrix.txt', name='Matrix of subreaction stoichiometries')[source]

Reads manual input to add subreactions.

This class creates the property “subreaction_matrix” from the manual inputs in subreaction_matrix.txt in an instance of Organism.

Input here will define subreactions in the ME-model.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

subreaction_matrix.txt :

Reaction Metabolites Stoichiometry mod_acetyl_c accoa_c -1.0 mod_acetyl_c coa_c +1.0 …

  • me_metabolites.txt

    Input here will mark metabolites in the M-model for replacement with their corrected E-matrix component.

  • elongation_subreactions.txt

    Input here will define translation elongation subreactions and their machinery.

class coralme.builder.curation.MEMetabolites(org, id='me_mets', config={}, file='me_metabolites.txt', name='Metabolites to substitute from M-model')[source]

Reads manual input to replace metabolites in the M-model.

This class creates the property “me_mets” from the manual inputs in me_metabolites.txt in an instance of Organism.

Input here will mark metabolites in the M-model for replacement with their corrected E-matrix component.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

me_metabolites.txt :

id me_id name formula compartment type sufbcd_c CPLX0-1341 SufBCD complex REPLACE …

  • subsystem_classification.txt

    Input here will classify subsystems in umbrella classifications which are then used to set a median Keff and correct it with the complex SASA.

class coralme.builder.curation.SubsystemClassification(org, id='subsystem_classification', config={}, file='subsystem_classification.txt', name='Classification of subsystems')[source]

Reads manual input to classify subsystems for Keff estimation.

This class creates the property “subsystem_classification” from the manual inputs in subsystem_classification.txt in an instance of Organism.

Input here will classify subsystems in umbrella classifications which are then used to set a median Keff and correct it with the complex SASA.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

subsystem_classification.txt : subsystem central_CE central_AFN intermediate secondary other S_Amino_acids_and_related_molecules 0 1 0 0 0 …

  • reaction_matrix.txt

    Input here will define reactions directly in the ME-model. Definitions here will be added to the ME-model after processing the M-model into the ME-model.

class coralme.builder.curation.ReactionMatrix(org, id='reaction_matrix', config={}, file='reaction_matrix.txt', name='Matrix of reaction stoichiometries')[source]

Reads manual input to add reactions to the ME-model.

This class creates the property “reaction_matrix” from the manual inputs in reaction_matrix.txt in an instance of Organism.

Input here will define reactions directly in the ME-model. Definitions here will be added to the ME-model after processing the M-model into the ME-model.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

reaction_matrix.txt :

Reaction Metabolites Stoichiometry Cs_cyto_import cs_p -1.0 Cs_cyto_import h_c 1.0 Cs_cyto_import cs_c 1.0 Cs_cyto_import h_p -1.0 …

  • lipid_modifications.txt

    Input here will define enzymes that perform lipid modifications.

class coralme.builder.curation.LipidModifications(org, id='lipid_modifications', config={}, file='lipid_modifications.txt', name='Lipid modifications')[source]

Reads manual input to define lipid modification machinery.

This class creates the property “lipid_modifications” from the manual inputs in lipid_modifications.txt in an instance of Organism.

Input here will define enzymes that perform lipid modifications.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

lipid_modifications.txt :

lipid_mod enzymes pg_pe_160 Lgt_MONOMER,LspA_MONOMER …

  • amino_acid_trna_synthetase.txt

    Input here will define amino acid tRNA ligases.

  • initiation_subreactions.txt

    Input here will define translation initiation subreactions and their machinery.

class coralme.builder.curation.AminoacidtRNASynthetase(org, id='amino_acid_trna_synthetase', config={}, file='amino_acid_trna_synthetase.txt', name='Amino acid to tRNA synthetase associations')[source]

Reads manual input to define amino acid tRNA ligases.

This class creates the property “amino_acid_trna_synthetase” from the manual inputs in amino_acid_trna_synthetase.txt in an instance of Organism.

Input here will define amino acid tRNA ligases.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

amino_acid_trna_synthetase.txt :

amino_acid enzyme ala__L_c Ala_RS_tetra_mod_zn2(4) …

  • post_transcriptional_modification_of_RNA.txt

    Input here will define RNA genes that undergo modifications.

class coralme.builder.curation.RNAModificationTargets(org, id='rna_modification_targets', config={}, file='post_transcriptional_modification_of_RNA.txt', name='RNA modification targets')[source]

Reads manual input to add RNA modification targets.

This class creates the property “rna_modification_targets” from the manual inputs in post_transcriptional_modification_of_RNA.txt in an instance of Organism.

Input here will define RNA genes that undergo modifications.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

post_transcriptional_modification_of_RNA.txt :

bnum position modification b0202 20A D …

  • protein_corrections.txt

    Input here will add, modify complexes in the ME-model, as well as add, modify their modifications. You can add a complex modification ID in the replace column, which will remove that modified complex and replace it with your manually added one.

class coralme.builder.curation.ManualComplexes(org, id='manual_complexes', config={}, file='protein_corrections.txt', name='Protein corrections')[source]

Reads manual input to modify or add complexes.

This class creates the property “manual_complexes” from the manual inputs in protein_corrections.txt in an instance of Organism.

Input here will add, modify complexes in the ME-model, as well as add, modify their modifications. You can add a complex modification ID in the replace column, which will remove that modified complex and replace it with your manually added one.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

This example adds SufBCD with their subunits and modifications, while removing SufBCD_mod_2fe3s(1).

protein_corrections.txt :

complex_id,name,genes,mod,replace SufBCD,SufBC2D Fe-S cluster scaffold complex,BSU32670(1) AND BSU32710(2) AND BSU32700(1),2fe2s(1),SufBCD_mod_2fe3s(1) …

property org_data

Final dataset stored in Organism instance

  • reaction_median_keffs.txt

    Input here will define median Keffs for estimation of Keffs using the SASA method.

  • transcription_subreactions.txt

    Input here will define machinery for transcription subreactions. These subreactions are a set of pre-defined subreactions that are used in ME-models.

class coralme.builder.curation.TranscriptionSubreactions(org, id='transcription_subreactions', config={}, file='transcription_subreactions.txt', name='Transcription subreactions')[source]

Reads manual input to define transcription subreactions.

This class creates the property “transcription_subreactions” from the manual inputs in transcription_subreactions.txt in an instance of Organism.

Input here will define machinery for transcription subreactions. These subreactions are a set of pre-defined subreactions that are used in ME-models.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

transcription_subreactions.txt :

mechanism enzymes Transcription_normal_rho_independent Mfd_mono_mod_mg2(1),NusA_mono,NusG_mono,GreA_mono,GreB_mono,RpoZ_mono_mod_mg2(1) …

  • generic_dict.txt

    Input here will define generics.

class coralme.builder.curation.GenericDict(org, id='generic_dict', config={}, file='generic_dict.txt', name='Dictionary of generic complexes')[source]

Reads manual input to define generics.

This class creates the property “generic_dict” from the manual inputs in generic_dict.txt in an instance of Organism.

Input here will define generics.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

generic_dict.txt :

generic_component enzymes generic_16Sm4Cm1402 RsmH_mono,RsmI_mono …

  • ribosome_subreactions.txt

    Input here will define enzymes that perform a ribosome subreaction.

class coralme.builder.curation.RibosomeSubreactions(org, id='ribosome_subreactions', config={}, file='ribosome_subreactions.txt', name='Ribosomal subreactions')[source]

Reads manual input to define ribosome subreactions.

This class creates the property “ribosome_subreactions” from the manual inputs in ribosome_subreactions.txt in an instance of Organism.

Input here will define enzymes that perform a ribosome subreaction.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

ribosome_subreactions.txt :

subreaction enzyme gtp_bound_30S_assembly_factor_phase1 BSU16650-MONOMER …

  • reaction_corrections.txt

    Input here will modify reactions at the M-model stage before ME-model building.

class coralme.builder.curation.ReactionCorrections(org, id='reaction_corrections', config={}, file='reaction_corrections.txt', name='Reaction corrections')[source]

Reads manual input to modify reactions in the M-model.

This class creates the property “reaction_corrections” from the manual inputs in reaction_corrections.txt in an instance of Organism.

Input here will modify reactions at the M-model stage before ME-model building.

Parameters:

org (coralme.builder.organism.Organism) – Organism object.

Examples

reaction_corrections.txt :

reaction_id,name,gene_reaction_rule,reaction,notes COBALT2tpp,cobalt transport in via permease (no H+),BSU24740,cobalt2_e –> cobalt2_c,No notes …

  • TUs_from_biocyc.txt

    Input here will modify transcriptional unit information.

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