diff --git a/.circleci/config.yml b/.circleci/config.yml index 76ae6899..b91c614b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,6 +2,7 @@ version: 2.1 orbs: win: circleci/windows@2.2.0 + linux: cloudesire/openjdk-install@1.2.3 commands: install-conda: diff --git a/BFAIR/atom_mapping/__init__.py b/BFAIR/atom_mapping/__init__.py new file mode 100644 index 00000000..87a4e1d1 --- /dev/null +++ b/BFAIR/atom_mapping/__init__.py @@ -0,0 +1,23 @@ +from BFAIR.atom_mapping.atom_mapping import ( + MolfileDownloader, + write_rxn_files, + obtain_atom_mappings, + parse_reaction_mappings, + parse_metabolite_mappings, + generate_INCA_mapping_input, + check_symmetry, + clean_output, +) + +__version__ = '0.0.1' + +__all__ = [ + 'MolfileDownloader', + 'write_rxn_files', + 'obtain_atom_mappings', + 'parse_reaction_mappings', + 'parse_metabolite_mappings', + 'generate_INCA_mapping_input', + 'check_symmetry', + 'clean_output', +] diff --git a/BFAIR/atom_mapping/atom_mapping.py b/BFAIR/atom_mapping/atom_mapping.py new file mode 100644 index 00000000..146155f3 --- /dev/null +++ b/BFAIR/atom_mapping/atom_mapping.py @@ -0,0 +1,739 @@ +"""Atom Mapping. +Module that automatically performs atom-atom mapping of reactions, +when provided a metabolic model with suitable annotations. +Relies heavily on: +Reaction Decoder Tool (RDT) (https://github.com/asad/ReactionDecoder) +to map the reactions; +CADD Group Chemoinformatics Tools and User Services (https://cactus.nci.nih.gov/chemical/structure) +to resolve InChI strings from given InChI keys; +Java, to run RDT""" + +import requests +import os +import glob +import platform +import subprocess +import pandas as pd +from rdkit import Chem, RDLogger +from pymatgen.symmetry import analyzer +from pymatgen.core import structure + +__version__ = "0.0.1" + + +class MolfileDownloader: + def __init__(self, metabolite_data, db_preference=(0, 1, 2, 3)): + """ Class to find and download metabolite structures in + Molfile format. + + Parameters + ---------- + metabolite_data : pandas.DataFrame + Dataframe that contains information about metabolites + the model. Obtain from INCA_input_parser module. + db_preference : tuple of int, optional + Four integers specify the order of preference of + databases to obtain the metabolite structures from: + 0: Using InChI key > InChI string conversion + 1: KEGG Compound database + 2: HMDB database + 3: CHEBI database + """ + self.database_dict = {0: 'get_from_inchi_key', + 1: 'get_from_kegg', + 2: 'get_from_hmdb', + 3: 'get_from_chebi'} + + self.metabolite_data = metabolite_data + self.db_preference = db_preference + + def generate_molfile_database(self): + """ Main method that calls other methods and performs + most sanity checks on obtained files. + + Outputs + ------- + Molfiles : .mol files + """ + print('Fetching metabolite structures...') + + if not os.path.isdir('metabolites'): + os.mkdir('metabolites') + # Disable RDKit warnings + RDLogger.DisableLog('rdApp.*') + + for i, met in self.metabolite_data.iterrows(): + self.filename = met.met_id + '.mol' + + get_from_inchi_keyBool = False + get_from_keggBool = False + get_from_hmdbBool = False + get_from_chebiBool = False + + # Check for annotations and set bool values for those + # present. + if 'inchi_key' in met.annotations: + self.inchi_key = met.annotations['inchi_key'][0] + get_from_inchi_keyBool = True # noqa: F841 + if 'kegg.compound' in met.annotations: + self.keggIDs = [ + keggID for keggID in met.annotations['kegg.compound']] + get_from_keggBool = True # noqa: F841 + if 'hmdb' in met.annotations: + self.hmdbIDnums = ['0' * (7 - len(hmdbID[4:])) + hmdbID[4:] + for hmdbID in met.annotations['hmdb']] + get_from_hmdbBool = True # noqa: F841 + if 'chebi' in met.annotations: + self.chebiIDs = [ + chebiID for chebiID in met.annotations['chebi']] + get_from_chebiBool = True # noqa: F841 + + # Call helper functions according to order of preference + # and available references (specified by previous bool values). + for opt in self.db_preference: + if eval(self.database_dict.get(opt) + 'Bool'): + getattr(self, self.database_dict.get(opt))() + else: + continue + + try: + # Rewrites the .mol file. This removes hydrogens from + # structure, lowkey standardizes molecules, and works + # as a failswitch to see if file is of correct format. + m = Chem.MolFromMolFile(f'metabolites/{self.filename}') + with open(f'metabolites/{self.filename}', "w+") as f: + print(Chem.MolToMolBlock(m), file=f) + + # Add metabolite ID to the first line of Molfile + with open(f'metabolites/{self.filename}', 'r') as f: + lines = f.readlines() + lines.insert(0, self.filename[:-4]) + with open(f'metabolites/{self.filename}', 'w') as wf: + wf.writelines(lines) + break + except BaseException: + os.remove(f'metabolites/{self.filename}') + continue + + print( + f"Successfully fetched {len(os.listdir('metabolites'))}/{self.metabolite_data.shape[0]} metabolites") + + def get_from_inchi_key(self): + """ Helper method to obtain InChI string from InChI key, + and generate the Molfile from the string. + """ + url = f'https://cactus.nci.nih.gov/chemical/structure/{self.inchi_key}/stdinchi' + r = requests.get(url, allow_redirects=False) + inchi_string = r.text + + try: + molfile = Chem.inchi.MolFromInchi(inchi_string) + with open(f'metabolites/{self.filename}', "w+") as f: + print(Chem.MolToMolBlock(molfile), file=f) + except BaseException: + return + + def get_from_kegg(self): + """ Helper method to obtain Molfile from KEGG Compound database + """ + for keggID in self.keggIDs: + url = f'https://www.genome.jp/dbget-bin/www_bget?-f+m+compound+{keggID}' + r = requests.get(url, allow_redirects=False) + open(f'metabolites/{self.filename}', 'wb').write(r.content) + if os.path.getsize(f'metabolites/{self.filename}') != 0: + break + + def get_from_hmdb(self): + """ Helper method to obtain Molfile from HMDB database + """ + for hmdbID in self.hmdbIDnums: + url = f'https://hmdb.ca/structures/metabolites/HMDB{hmdbID}.mol' + r = requests.get(url, allow_redirects=False) + open(f'metabolites/{self.filename}', 'wb').write(r.content) + if os.path.getsize(f'metabolites/{self.filename}') != 0: + break + + def get_from_chebi(self): + """ Helper method to obtain Molfile from CHEBI database + """ + for chebiID in self.chebiIDs: + url = f'https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId={chebiID}&imageId=0' + r = requests.get(url, allow_redirects=False) + open(f'metabolites/{self.filename}', 'wb').write(r.content) + if os.path.getsize(f'metabolites/{self.filename}') != 0: + break + + +def write_rxn_files(rxn_data): + """ Generates RXN files in RDT suitable format. + Requires Molfiles of all metabolites to be present + in the working directory/metabolites folder. + + Parameters + ---------- + rxn_data : pandas.DataFrame + Dataframe that contains information about reactions + in the model. Obtained from INCA_input_parser module. + + Outputs + ------- + RXN files : .rxn files + """ + met_filter = ['h_e', 'h_c', 'h_p', 'h2_e', 'h2_c', 'h2_p'] + biomass_filter = ['Biomass', 'biomass', 'BIOMASS'] + + if not os.path.isdir('unmappedRxns'): + os.mkdir('unmappedRxns') + + path = os.path.join(os.getcwd(), 'unmappedRxns') + + for i, rxn in rxn_data.iterrows(): + # Filter out biomass reaction + if any(biomass_id in rxn.rxn_id for biomass_id in biomass_filter): + print(f'Excluded {rxn.rxn_id} reaction from mapping') + continue + + rxn_filename = rxn.rxn_id + '.rxn' + # Use copies to avoid messing up the original dataframe + reactants = rxn.reactants_ids.copy() + reactants_st = [int(abs(s)) + for s in rxn.reactants_stoichiometry.copy()] + products = rxn.products_ids.copy() + products_st = [int(abs(s)) for s in rxn.products_stoichiometry.copy()] + + # Filter out unwanted molecules + react_indexes = [] + prod_indexes = [] + for i, met in enumerate(reactants): + if met in met_filter: + react_indexes.append(i) + if len(react_indexes) != 0: + for i in sorted(react_indexes, reverse=True): + del reactants[i] + del reactants_st[i] + + for i, met in enumerate(products): + if met in met_filter: + prod_indexes.append(i) + if len(prod_indexes) != 0: + for i in sorted(prod_indexes, reverse=True): + del products[i] + del products_st[i] + + metabolites = reactants + products + metabolites_st = reactants_st + products_st + + # Check if all metabolite structures are present + if not all( + [os.path.isfile(f'metabolites/{met}.mol') for met in metabolites]): + print( + f"Metabolite structures missing for reaction {rxn.rxn_id}") + continue + else: + with open(os.path.join(path, rxn_filename), "w") as f: + # Write first three lines, including reaction equation + f.write(f"$RXN\n{rxn.rxn_id}\n\n{rxn.equation}\n") + + # Write export reactions (1 reactant) + if not products_st and abs(int(sum(reactants_st))) == 1: + f.write( + f'{abs(int(sum(reactants_st)))} {int(sum(reactants_st))}\n') + met = metabolites[0] + with open(f'metabolites/{met}.mol', 'r') as wf: + structure = wf.read() + f.write(f'$MOL\n{structure}') + f.write(f'$MOL\n{structure}') + + # Write all the other reactions with at least 1 metabolite on + # each side + else: + f.write( + f'{abs(int(sum(reactants_st)))} {int(sum(products_st))}\n') + for s, met in zip(metabolites_st, metabolites): + with open(f'metabolites/{met}.mol', 'r') as wf: + structure = wf.read() + # Repeat structure based on stoichiometry + for i in range(s): + f.write(f'$MOL\n{structure}') + print(f"Generated {len(os.listdir('unmappedRxns'))}/{rxn_data.shape[0]}") + + +def obtain_atom_mappings(max_time=120): + """ Performs atom mapping by using RDT. + Only maps reactions that are available in .rxn format, + in the working_directory/unmappedRxns folder. + + Parameters + ---------- + max_time : int, optional + Specifies time limit for single reaction mapping + in seconds. Default: 120s. + + Outputs + ------- + mapped RXN files : .rxn files + mapped TXT files : .txt files + Mappings in SMILES format + pictures of mappings : .png files + """ + # Check if Java is installed + if os.system('java -version') != 0: + raise RuntimeError('Java installation not found') + + print('Mapping reactions...') + # Set the original working dir + owd = os.getcwd() + + # Check if RDT is present in working dir, download if not + if not os.path.isfile('RDT.jar'): + url = 'https://github.com/asad/ReactionDecoder/releases/download/v2.4.1/rdt-2.4.1-jar-with-dependencies.jar' + r = requests.get(url) + open(os.getcwd() + '/RDT.jar', 'wb').write(r.content) + + # Check if required directories are present + if not os.path.isdir('mappedRxns'): + os.makedirs('mappedRxns/rxnFiles') + os.makedirs('mappedRxns/txtFiles') + os.makedirs('mappedRxns/pngFiles') + + rxn_list = os.listdir('unmappedRxns') + + # Change working dir to keep the output organized + os.chdir('mappedRxns') + try: + for rxnFile in rxn_list: + # Check if reaction is mapped, and run RDT with specified time + # limit if not + try: + if not os.path.isfile(f'rxnFiles/{rxnFile}'): + subprocess.run(['java', '-jar', + '../RDT.jar', '-Q', + 'RXN', '-q', + f'../unmappedRxns/{rxnFile}', + '-g', '-j', + 'AAM', '-f', + 'TEXT'], timeout=max_time) + except BaseException: + continue + # Obtain filenames of generated files and simplify them to respective + # reaction IDs + for name in glob.glob('ECBLAST*'): + os.rename(name, name[8:-8] + name[-4:]) + + # Move all generated files to different directories, in respect to + # their filetype + if platform.system() == 'Windows': + os.system('move *.png pngFiles') + os.system('move *.rxn rxnFiles') + os.system('move *.txt txtFiles') + else: + os.system('mv *.png ./pngFiles') + os.system('mv *.rxn ./rxnFiles') + os.system('mv *.txt ./txtFiles') + + except BaseException: + # Make sure that wd is back to normal no matter what + os.chdir(owd) + + print( + f"Reactions mapped in total: {len(os.listdir('rxnFiles'))}/{len(rxn_list)}") + # Change working dir back to original + os.chdir(owd) + + # Remove RDT.jar from working dir + os.remove('RDT.jar') + + +def parse_reaction_mappings(): + """ Parses reaction mappings from mapped RXN files + to a dataframe in suitable format for INCA. Requires + all mapped RXN files to be present in the working_dir/ + mappedRxns/rxnFiles folder. For unmapped reactions, + data is picked from working_dir/unmappedRxns folder + and all mapping data is represented as blanks. + + Returns + ------- + mapping_data : pandas.DataFrame + Reaction mapping data. + """ + if not os.path.isdir('mappedRxns'): + raise RuntimeError( + "'mappedRxns' directory not present in current working directory") + + rxn_list = sorted(os.listdir('unmappedRxns')) + # Compile list of reactions that do not have any mapping + unmapped_list = list(set(os.listdir('unmappedRxns')) - set(os.listdir('mappedRxns/rxnFiles'))) + + keys = ['Unnamed: 0', + 'Unnamed: 0.1', + 'id', + 'mapping_id', + 'rxn_id', + 'rxn_description', + 'reactants_stoichiometry_tracked', + 'products_stoichiometry_tracked', + 'reactants_ids_tracked', + 'products_ids_tracked', + 'reactants_mapping', + 'products_mapping', + 'rxn_equation', + 'used_', + 'comment_', + 'reactants_elements_tracked', + 'products_elements_tracked', + 'reactants_positions_tracked', + 'products_positions_tracked' + ] + mapping_dict_tmp = {} + + for i, rxn in enumerate(rxn_list): + mapping_dict = {k: [] for k in keys} + met_mapping = [] + react_cnt = 0 + prod_cnt = 0 + productBool = False + + if rxn not in unmapped_list: + # Extract info from mapped .rxn files + with open(f'mappedRxns/rxnFiles/{rxn}', 'r') as f: + lines = f.readlines() + for j, line in enumerate(lines): + if line.rstrip() == '$RXN': + # Extract number of reactants + react_lim = int(lines[j + 4].split()[0]) + # Extract number of products + prod_lim = int(lines[j + 4].split()[1]) + if line.rstrip() == '$MOL': + met_id = lines[j + 1].rstrip() + + # Hard-coded, since 16 columns is standard for Molfile atom rows, + # and 15 can occur if we have >100 atoms on one side (cols + # merge) + if len(line.split()) in (15, 16): + atom_row = line.split() + if atom_row[3] == 'C': + # Split columns if they get merged + if atom_row[-3][0] == '0': + atom_row[-3] = atom_row[-3][1:] + met_mapping.append(atom_row[-3]) + + # Check if reached the last atom row + if len(lines[j + 1].split()) not in (15, 16): + # Check if current metabolite is reactant or + # product + if not productBool: + # Check if any carbons are present + if met_mapping: + c_tracked = ['C' for atom in met_mapping] + pos_tracked = list(range(len(met_mapping))) + mapping_dict['reactants_ids_tracked'].append( + met_id) + mapping_dict['reactants_mapping'].append( + met_mapping) + mapping_dict['reactants_elements_tracked'].append( + c_tracked) + mapping_dict['reactants_positions_tracked'].append( + pos_tracked) + react_cnt += 1 + if react_cnt == react_lim: + productBool = True + + # Assign metabolite to products if reached reactant + # limit + else: + if met_mapping: + c_tracked = ['C' for atom in met_mapping] + pos_tracked = list(range(len(met_mapping))) + mapping_dict['products_ids_tracked'].append( + met_id) + mapping_dict['products_mapping'].append( + met_mapping) + mapping_dict['products_elements_tracked'].append( + c_tracked) + mapping_dict['products_positions_tracked'].append( + pos_tracked) + prod_cnt += 1 + + if prod_cnt == prod_lim: + react_stoich = [ + '-1' for met in range(len(mapping_dict['reactants_mapping']))] + prod_stoich = ['1' for met in range( + len(mapping_dict['products_mapping']))] + mapping_dict['reactants_stoichiometry_tracked'] = react_stoich + mapping_dict['products_stoichiometry_tracked'] = prod_stoich + + met_mapping = [] + + mapping_dict['rxn_id'] = rxn[:-4] + mapping_dict['used_'] = True + # Fill all empty fields + mapping_dict['Unnamed: 0'] = 'NULL' + mapping_dict['Unnamed: 0.1'] = 'NULL' + mapping_dict['id'] = 'NULL' + mapping_dict['mapping_id'] = 'NULL' + mapping_dict['rxn_description'] = 'NULL' + mapping_dict['rxn_equation'] = 'NULL' + mapping_dict['comment_'] = 'NULL' + + mapping_dict_tmp[i] = mapping_dict + + mapping_data = pd.DataFrame.from_dict(mapping_dict_tmp, 'index') + + # alphabet for number-letter matching. Max capacity is 63 characters, + # which is a limit set in INCA for this format. + alphabet = list(map(chr, range(97, 123))) + list(map(chr, + range(65, 91))) + list(map(chr, range(48, 58))) + ['_'] + + # Loop through all reactions + for i, rxn in mapping_data.iterrows(): + try: + # Convert number mappings to letters + carbons_list = [atom for met in rxn['reactants_mapping'] + for atom in met] + carbon_map_dict = dict(zip(carbons_list, alphabet)) + + # Compile alphabetical mapping in curly bracket format + carbon_str = '{' + for j, met in enumerate(rxn['reactants_mapping']): + if j != 0: + carbon_str += ',' + for atom in met: + carbon_str += carbon_map_dict[atom] + carbon_str += '}' + mapping_data.at[i, 'reactants_mapping'] = carbon_str + + carbon_str = '{' + for j, met in enumerate(rxn['products_mapping']): + if j != 0: + carbon_str += ',' + for atom in met: + carbon_str += carbon_map_dict[atom] + carbon_str += '}' + mapping_data.at[i, 'products_mapping'] = carbon_str + + except KeyError: + if len(carbons_list) > 63: + print( + f'Reaction {rxn["rxn_id"]} contains more than 63 carbon atoms') + else: + # Mostly happens when one of the metabolites has (R) + # group in the Molfile, and other has a C in that spot + print(f'{rxn["rxn_id"]} has unmapped carbon(-s)') + mapping_data.at[i, 'reactants_mapping'] = '{}' + mapping_data.at[i, 'products_mapping'] = '{}' + + # Convert metabolite lists/stoichiometries to strings in curly brackets + metabolite_str = '{%s}' % (','.join(rxn['reactants_ids_tracked'])) + mapping_data.at[i, 'reactants_ids_tracked'] = metabolite_str + + metabolite_str = '{%s}' % (','.join(rxn['products_ids_tracked'])) + mapping_data.at[i, 'products_ids_tracked'] = metabolite_str + + stoich_str = '{%s}' % (','.join( + rxn['reactants_stoichiometry_tracked'])) + mapping_data.at[i, 'reactants_stoichiometry_tracked'] = stoich_str + + stoich_str = '{%s}' % (','.join(rxn['products_stoichiometry_tracked'])) + mapping_data.at[i, 'products_stoichiometry_tracked'] = stoich_str + + return mapping_data + + +def parse_metabolite_mappings(): + """ Parses metabolite mapping and symmetry data into + INCA suitable format. Requires all Molfiles to be present + in the working_dir/metabolites directory. + + Returns + ------- + metabolite_data : pandas.DataFrame + Dataframe containing mapped metabolite data. + """ + metabolite_list = sorted(os.listdir('metabolites')) + keys = ['mapping_id', + 'met_id', + 'met_elements', + 'met_atompositions', + 'met_symmetry_elements', + 'met_symmetry_atompositions', + 'used_', + 'comment_', + 'met_mapping', + 'base_met_ids', + 'base_met_elements', + 'base_met_atompositions', + 'base_met_symmetry_elements', + 'base_met_symmetry_atompositions', + 'base_met_indices' + ] + metabolite_dict_tmp = {} + + # Works in a similar fashion to parse_reaction_mappings() + for i, met in enumerate(metabolite_list): + met_dict = {k: 'NULL' for k in keys} + with open(f'metabolites/{met}', 'r') as f: + lines = f.readlines() + carbon_count = 0 + for j, line in enumerate(lines): + if j == 0: + met_dict['met_id'] = line.rstrip() + if len(line.split()) == 16: + atom_row = line.split() + if atom_row[3] == 'C': + carbon_count += 1 + # Generate carbon atom lists/mappings + carbon_count_list = ['C' for x in range(carbon_count)] + carbon_count_string = '{%s}' % (','.join(carbon_count_list)) + carbon_count_range = '{%s}' % ( + ','.join([str(x) for x in range(carbon_count)])) + + met_dict['met_elements'] = carbon_count_string + met_dict['met_atompositions'] = carbon_count_range + # Check if the metabolite is symmetrical + if check_symmetry(met): + carbon_count_range_rev = '{%s}' % ( + ','.join([str(x) for x in range(carbon_count - 1, -1, -1)])) + met_dict["met_symmetry_elements"] = carbon_count_string + met_dict['met_symmetry_atompositions'] = carbon_count_range_rev + + metabolite_dict_tmp[i] = met_dict + + metabolite_data = pd.DataFrame.from_dict(metabolite_dict_tmp, 'index') + + return metabolite_data + + +def generate_INCA_mapping_input(reaction_df, metabolite_df): + """ Function to export reaction and metabolite mapping dataframes + to CSV files. + + Parameters + ---------- + reaction_df : pandas.DataFrame + Dataframe that contains reaction mapping data. + metabolite_df : pandas.DataFrame + Dataframe that contains metabolite mapping data. + + Outputs + ------- + MappingReactions : .csv file + MappingMetabolites : .csv file + """ + # Would be a good idea to make the filenames more informative. + reaction_df.to_csv( + path_or_buf=os.path.join( + os.getcwd(), + 'MappingReactions.csv')) + metabolite_df.to_csv( + path_or_buf=os.path.join( + os.getcwd(), + 'MappingMetabolites.csv')) + + +def check_symmetry(met_filename): + """ Function that checks if the given metabolite is symmetric. + Uses pymatgen package for symmetry related operations, and + RDKit for Molfile conversion to XYZ format. Requires Molfiles + of the metabolites to be present in the working_dir/metabolites + folder. + Current criterion for symmetricity is for every carbon except one + (central, if molecule consists of odd number of carbons) to have + at least one equivalent carbon in the structure. + + Parameters + ---------- + met_filename : str + Filename of the specific Molfile + + Returns + ------- + symmetrical : bool + True if metabolite is symmetric, False if not. + + """ + symmetrical = False + # Disable RDKit warnings + RDLogger.DisableLog('rdApp.*') + # Counter for non symmetrical carbon atoms + non_eq_carbons = 0 + carbons = 0 + # Convert Molfile to XYZ string + molecule = Chem.MolFromMolFile(f'metabolites/{met_filename}') + molecule_xyz = Chem.rdmolfiles.MolToXYZBlock(molecule) + + # Create IMolecule object to analyze its' symmetricity + try: + molecule_obj = structure.IMolecule.from_str(molecule_xyz, fmt='xyz') + if len(molecule_obj) == 1: + return symmetrical + # Initialize point group analyzer + pg_analyzer = analyzer.PointGroupAnalyzer(molecule_obj) + + except (IndexError, ValueError): + # '*' is unrecognized in particular + print(f'{met_filename} contains unrecognized symbols') + return symmetrical + # Extract equal atom sets + eq_atoms = pg_analyzer.get_equivalent_atoms() + for i in eq_atoms['eq_sets'].keys(): + if str(molecule_obj[i].specie) == 'C': + carbons += 1 + if len(eq_atoms['eq_sets'].get(i)) == 1: + non_eq_carbons += 1 + if non_eq_carbons > 1: + return symmetrical + + # Molecule has more than 1 carbon, and at most 1 non-symmetrical carbon + if carbons > 1: + symmetrical = True + + return symmetrical + + +def clean_output(metabolites=True, + reactions=True, + mappings=True, + csv=True): + """ Utility function. + Deletes all possible output of other mapping functions. + Deletes everything by default. + + Parameters + ---------- + metabolites : bool, optional + Removes /metabolites folder recursively. + reactions : bool, optional + Removes /unmappedRxns folder recursively. + mappings : bool, optional + Removes /mappedRxns folder recursively. + csv : bool, optional + Removes MappingReactions.csv and MappingMetabolites.csv. + """ + if metabolites: + os.rmdir('metabolites') + if reactions: + os.rmdir('unmappedRxns') + if mappings: + os.rmdir('mappedRxns') + if csv: + os.remove('MappingReactions.csv') + os.remove('MappingMetabolites.csv') + + +# molfile_downloader_descr = MolfileDownloader() +# """A class to find and fetch metabolite structures in Molfile +# format. + +# Examples +# -------- +# >>> downloader = MolfileDownloader(met_df) +# >>> downloader.generate_molfile_database() +# The database will be generated in working_dir/metabolites folder + +# To change the order of databases for fetching, pass a tuple of +# integers when initiating an instance, f.e.: +# >>> downloader = MolfileDownloader(met_df, (2,1,0,3)) +# >>> downloader.generate_molfile_database() + +# For full workflow check, the example notebook. """ diff --git a/BFAIR/mfa/INCA/INCA_input_parser.py b/BFAIR/mfa/INCA/INCA_input_parser.py index 1f4e2e77..7d5b8aaa 100644 --- a/BFAIR/mfa/INCA/INCA_input_parser.py +++ b/BFAIR/mfa/INCA/INCA_input_parser.py @@ -158,6 +158,7 @@ def _parse_json_sbml_cobra_model( "charge": met.charge, "compartment": met.compartment, "bound": met._bound, + "annotations": met.annotation, "used_": True, } metabolite_data_tmp[cnt] = metabolite_data_dict diff --git a/docs/examples/atom_mapping_example_notebook.ipynb b/docs/examples/atom_mapping_example_notebook.ipynb new file mode 100644 index 00000000..3e98a0c0 --- /dev/null +++ b/docs/examples/atom_mapping_example_notebook.ipynb @@ -0,0 +1,296 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "8ed0c5fa", + "metadata": {}, + "source": [ + "# Automatic atom mapping - example" + ] + }, + { + "cell_type": "markdown", + "id": "5aefa4d6", + "metadata": {}, + "source": [ + "This notebook demonstrates how the `atom_mapping` module works in practice. It's purpose is to reduce the workload when preparing input data for MFA analysis on INCA. " + ] + }, + { + "cell_type": "markdown", + "id": "5b362b76", + "metadata": {}, + "source": [ + "The only input required is the COBRA model that contains all reaction data, and, most importantly, references for metabolite structures in KEGG Compound, HMDB, CHEBI databases, or an InChI key." + ] + }, + { + "cell_type": "markdown", + "id": "21edabd6", + "metadata": {}, + "source": [ + "#### First, import required modules:" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "75aa4c2e", + "metadata": {}, + "outputs": [], + "source": [ + "from BFAIR import atom_mapping\n", + "from BFAIR.mfa.INCA import INCA_input_parser" + ] + }, + { + "cell_type": "markdown", + "id": "9b99ccdd", + "metadata": {}, + "source": [ + "#### Prepare input dataframes" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "2e216f79", + "metadata": {}, + "outputs": [], + "source": [ + "model, reaction_data, metabolite_data = INCA_input_parser.parse_cobra_model('data/atom_mapping_Data/e_coli_core.json', 'e_coli_core', '2021-07-15')" + ] + }, + { + "cell_type": "markdown", + "id": "fd095c49", + "metadata": {}, + "source": [ + "Workflow continues by fetching and storing all of the available metabolite structures in Molfile format." + ] + }, + { + "cell_type": "markdown", + "id": "006b1329", + "metadata": {}, + "source": [ + "#### Initialise MolfileDownloader and fetch the structures" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "4bdc27aa", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Fetching metabolite structures...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "RDKit WARNING: [23:06:57] WARNING: not removing hydrogen atom without neighbors\n", + "RDKit WARNING: [23:06:57] WARNING: not removing hydrogen atom without neighbors\n", + "RDKit WARNING: [23:06:57] WARNING: not removing hydrogen atom without neighbors\n", + "RDKit WARNING: [23:06:57] WARNING: not removing hydrogen atom without neighbors\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Successfully fetched 72/72 metabolites\n" + ] + } + ], + "source": [ + "downloader = atom_mapping.MolfileDownloader(metabolite_data)\n", + "downloader.generate_molfile_database()" + ] + }, + { + "cell_type": "markdown", + "id": "e2fd2df9", + "metadata": {}, + "source": [ + "Note: MolfileDownloader takes a second optional argument that allows user to specify preference of databases to search first. By default, 'InChI key -> InChI string -> structure' approach is preferred, and then databases are used for search. Check documentation for more information." + ] + }, + { + "cell_type": "markdown", + "id": "e807e9a6", + "metadata": {}, + "source": [ + "#### Write reactions in RXN format" + ] + }, + { + "cell_type": "markdown", + "id": "23e9e707", + "metadata": {}, + "source": [ + "Here, all of the obtained compound structure files are used to write reactions in RXN format, using `reaction_data` dataframe as a reference." + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "df313fe0", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Excluded BIOMASS_Ecoli_core_w_GAM reaction from mapping\n", + "Generated 94/95\n" + ] + } + ], + "source": [ + "atom_mapping.write_rxn_files(reaction_data)" + ] + }, + { + "cell_type": "markdown", + "id": "39bfd6e0", + "metadata": {}, + "source": [ + "#### Run RDT to obtain atom mappings" + ] + }, + { + "cell_type": "markdown", + "id": "5e24a2e5", + "metadata": {}, + "source": [ + "RDT algorithm is downloaded and stored in the working directory (deleted after function is done). " + ] + }, + { + "cell_type": "markdown", + "id": "459d6b6e", + "metadata": {}, + "source": [ + "**NOTE**: Java is required to run the algorithm, please make sure it's installed on your computer." + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "f7d50194", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Mapping reactions...\n", + "Reactions mapped in total: 85/94\n" + ] + } + ], + "source": [ + "atom_mapping.obtain_atom_mappings(max_time=20) # specify time limit for single reaction" + ] + }, + { + "cell_type": "markdown", + "id": "29fd3bab", + "metadata": {}, + "source": [ + "#### Parse data from generated mappings to suitable format for INCA" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "841634e1", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "RDKit WARNING: [23:23:18] WARNING: not removing hydrogen atom without neighbors\n", + "RDKit WARNING: [23:23:18] WARNING: not removing hydrogen atom without neighbors\n" + ] + } + ], + "source": [ + "reaction_mapping_df = atom_mapping.parse_reaction_mappings()\n", + "met_mapping_df = atom_mapping.parse_metabolite_mappings()" + ] + }, + { + "cell_type": "markdown", + "id": "0afc3974", + "metadata": {}, + "source": [ + "#### Generate CSV output of mapping data" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "92f7ec99", + "metadata": {}, + "outputs": [], + "source": [ + "atom_mapping.generate_INCA_mapping_input(reaction_mapping_df, met_mapping_df)" + ] + }, + { + "cell_type": "markdown", + "id": "ba2dd63b", + "metadata": {}, + "source": [ + "The generated CSV files can be used in general MFA workflow, as atom mapping inputs." + ] + }, + { + "cell_type": "markdown", + "id": "871a16f2", + "metadata": {}, + "source": [ + "#### Clear the working directory of generated output (optional)" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "e8b0ba00", + "metadata": {}, + "outputs": [], + "source": [ + "atom_mapping.clean_output()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python [conda env:test]", + "language": "python", + "name": "conda-env-test-py" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/examples/data/atom_mapping_Data/e_coli_core.json b/docs/examples/data/atom_mapping_Data/e_coli_core.json new file mode 100644 index 00000000..39db7732 --- /dev/null +++ b/docs/examples/data/atom_mapping_Data/e_coli_core.json @@ -0,0 +1,14786 @@ +{ +"metabolites":[ +{ +"id":"glc__D_e", +"name":"D-Glucose", +"compartment":"e", +"charge":0, +"formula":"C6H12O6", +"notes":{ +"original_bigg_ids":[ +"glc_D_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glc__D" +], +"biocyc":[ +"META:Glucopyranose" +], +"chebi":[ +"CHEBI:12965", +"CHEBI:20999", +"CHEBI:4167", +"CHEBI:17634" +], +"hmdb":[ +"HMDB00122", +"HMDB06564" +], +"inchi_key":[ +"WQZGKKKJIJFFOK-GASJEMHNSA-N" +], +"kegg.compound":[ +"C00031" +], +"kegg.drug":[ +"D00009" +], +"metanetx.chemical":[ +"MNXM41" +], +"sabiork":[ +"1406", +"1407" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd26821", +"cpd00027" +] +} +}, +{ +"id":"gln__L_c", +"name":"L-Glutamine", +"compartment":"c", +"charge":0, +"formula":"C5H10N2O3", +"notes":{ +"original_bigg_ids":[ +"gln_L_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"gln__L" +], +"biocyc":[ +"META:GLN" +], +"chebi":[ +"CHEBI:42943", +"CHEBI:42899", +"CHEBI:32679", +"CHEBI:32678", +"CHEBI:58359", +"CHEBI:28300", +"CHEBI:42812", +"CHEBI:13110", +"CHEBI:18050", +"CHEBI:32666", +"CHEBI:6227", +"CHEBI:32665", +"CHEBI:21308", +"CHEBI:42814", +"CHEBI:5432", +"CHEBI:24316" +], +"hmdb":[ +"HMDB00641" +], +"inchi_key":[ +"ZDXPYRJPNDTMRX-VKHMYHEASA-N" +], +"kegg.compound":[ +"C00064", +"C00303" +], +"kegg.drug":[ +"D00015" +], +"metanetx.chemical":[ +"MNXM37" +], +"reactome.compound":[ +"113522", +"212615", +"29472" +], +"sabiork":[ +"2011", +"74" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00253", +"cpd00053" +] +} +}, +{ +"id":"gln__L_e", +"name":"L-Glutamine", +"compartment":"e", +"charge":0, +"formula":"C5H10N2O3", +"notes":{ +"original_bigg_ids":[ +"gln_L_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"gln__L" +], +"biocyc":[ +"META:GLN" +], +"chebi":[ +"CHEBI:42943", +"CHEBI:42899", +"CHEBI:32679", +"CHEBI:32678", +"CHEBI:58359", +"CHEBI:28300", +"CHEBI:42812", +"CHEBI:13110", +"CHEBI:18050", +"CHEBI:32666", +"CHEBI:6227", +"CHEBI:32665", +"CHEBI:21308", +"CHEBI:42814", +"CHEBI:5432", +"CHEBI:24316" +], +"hmdb":[ +"HMDB00641" +], +"inchi_key":[ +"ZDXPYRJPNDTMRX-VKHMYHEASA-N" +], +"kegg.compound":[ +"C00064", +"C00303" +], +"kegg.drug":[ +"D00015" +], +"metanetx.chemical":[ +"MNXM37" +], +"reactome.compound":[ +"113522", +"212615", +"29472" +], +"sabiork":[ +"2011", +"74" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00253", +"cpd00053" +] +} +}, +{ +"id":"glu__L_c", +"name":"L-Glutamate", +"compartment":"c", +"charge":-1, +"formula":"C5H8NO4", +"notes":{ +"original_bigg_ids":[ +"glu_L_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glu__L" +], +"biocyc":[ +"META:Glutamates", +"META:GLT" +], +"chebi":[ +"CHEBI:76051", +"CHEBI:21301", +"CHEBI:29985", +"CHEBI:42825", +"CHEBI:29987", +"CHEBI:18237", +"CHEBI:24314", +"CHEBI:16015", +"CHEBI:13107", +"CHEBI:5431", +"CHEBI:21304", +"CHEBI:6224", +"CHEBI:14321", +"CHEBI:29988" +], +"hmdb":[ +"HMDB00148", +"HMDB60475" +], +"inchi_key":[ +"WHUUTDBJXJRKMK-VKHMYHEASA-M" +], +"kegg.compound":[ +"C00025", +"C00302" +], +"kegg.drug":[ +"D00007", +"D04341" +], +"metanetx.chemical":[ +"MNXM89557" +], +"reactome.compound":[ +"428614", +"29404", +"113552", +"210382" +], +"sabiork":[ +"73", +"2010" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27177", +"cpd00023", +"cpd19002" +] +} +}, +{ +"id":"glu__L_e", +"name":"L-Glutamate", +"compartment":"e", +"charge":-1, +"formula":"C5H8NO4", +"notes":{ +"original_bigg_ids":[ +"glu_L_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glu__L" +], +"biocyc":[ +"META:Glutamates", +"META:GLT" +], +"chebi":[ +"CHEBI:76051", +"CHEBI:21301", +"CHEBI:29985", +"CHEBI:42825", +"CHEBI:29987", +"CHEBI:18237", +"CHEBI:24314", +"CHEBI:16015", +"CHEBI:13107", +"CHEBI:5431", +"CHEBI:21304", +"CHEBI:6224", +"CHEBI:14321", +"CHEBI:29988" +], +"hmdb":[ +"HMDB00148", +"HMDB60475" +], +"inchi_key":[ +"WHUUTDBJXJRKMK-VKHMYHEASA-M" +], +"kegg.compound":[ +"C00025", +"C00302" +], +"kegg.drug":[ +"D00007", +"D04341" +], +"metanetx.chemical":[ +"MNXM89557" +], +"reactome.compound":[ +"428614", +"29404", +"113552", +"210382" +], +"sabiork":[ +"73", +"2010" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27177", +"cpd00023", +"cpd19002" +] +} +}, +{ +"id":"glx_c", +"name":"Glyoxylate", +"compartment":"c", +"charge":-1, +"formula":"C2H1O3", +"notes":{ +"original_bigg_ids":[ +"glx_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glx" +], +"biocyc":[ +"META:GLYOX" +], +"chebi":[ +"CHEBI:24420", +"CHEBI:36655", +"CHEBI:14368", +"CHEBI:24421", +"CHEBI:42767", +"CHEBI:16891", +"CHEBI:35977", +"CHEBI:5509" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/cdffdb1a-3322-4cc1-9171-d857bfaa198a", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/aecbda66-6e98-4c11-aeaf-6a072f4f963c", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/9dc0aa3b-447a-4b5d-8157-501b036f9626", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/43b74f4f-bc8a-4b8b-b587-c97d8e9eed48" +], +"hmdb":[ +"HMDB00119" +], +"inchi_key":[ +"HHLFWLYXYJOTON-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00048" +], +"metanetx.chemical":[ +"MNXM69" +], +"reactome.compound":[ +"904849", +"389678" +], +"sabiork":[ +"1838" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00040" +] +} +}, +{ +"id":"h2o_c", +"name":"H2O H2O", +"compartment":"c", +"charge":0, +"formula":"H2O", +"notes":{ +"original_bigg_ids":[ +"h2o_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h2o" +], +"biocyc":[ +"META:CPD-15815", +"META:OXONIUM", +"META:HYDROXYL-GROUP", +"META:WATER", +"META:OH" +], +"chebi":[ +"CHEBI:13352", +"CHEBI:30490", +"CHEBI:43228", +"CHEBI:33813", +"CHEBI:44292", +"CHEBI:44641", +"CHEBI:27313", +"CHEBI:42043", +"CHEBI:44819", +"CHEBI:29356", +"CHEBI:5594", +"CHEBI:10743", +"CHEBI:15377", +"CHEBI:42857", +"CHEBI:13365", +"CHEBI:29412", +"CHEBI:16234", +"CHEBI:13419", +"CHEBI:5585", +"CHEBI:44701" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/799908db-b8c9-4982-86cb-1f225e2ad08c", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/e7f34a8e-cded-4793-b6d5-792335b38636", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/969d0227-3069-4e44-9525-7ae7bad84170" +], +"hmdb":[ +"HMDB02111", +"HMDB01039" +], +"inchi_key":[ +"XLYOFNOQVPJJNP-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00001", +"C01328" +], +"kegg.drug":[ +"D00001", +"D06322" +], +"metanetx.chemical":[ +"MNXM2" +], +"reactome.compound":[ +"113521", +"141343", +"2022884", +"5278291", +"29356", +"189422", +"5668574", +"5693747", +"109276", +"113519", +"1605715", +"8851517", +"113518", +"351603" +], +"sabiork":[ +"40" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27222", +"cpd00001", +"cpd15275" +] +} +}, +{ +"id":"h2o_e", +"name":"H2O H2O", +"compartment":"e", +"charge":0, +"formula":"H2O", +"notes":{ +"original_bigg_ids":[ +"h2o_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h2o" +], +"biocyc":[ +"META:CPD-15815", +"META:OXONIUM", +"META:HYDROXYL-GROUP", +"META:WATER", +"META:OH" +], +"chebi":[ +"CHEBI:13352", +"CHEBI:30490", +"CHEBI:43228", +"CHEBI:33813", +"CHEBI:44292", +"CHEBI:44641", +"CHEBI:27313", +"CHEBI:42043", +"CHEBI:44819", +"CHEBI:29356", +"CHEBI:5594", +"CHEBI:10743", +"CHEBI:15377", +"CHEBI:42857", +"CHEBI:13365", +"CHEBI:29412", +"CHEBI:16234", +"CHEBI:13419", +"CHEBI:5585", +"CHEBI:44701" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/799908db-b8c9-4982-86cb-1f225e2ad08c", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/e7f34a8e-cded-4793-b6d5-792335b38636", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/969d0227-3069-4e44-9525-7ae7bad84170" +], +"hmdb":[ +"HMDB02111", +"HMDB01039" +], +"inchi_key":[ +"XLYOFNOQVPJJNP-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00001", +"C01328" +], +"kegg.drug":[ +"D00001", +"D06322" +], +"metanetx.chemical":[ +"MNXM2" +], +"reactome.compound":[ +"113521", +"141343", +"2022884", +"5278291", +"29356", +"189422", +"5668574", +"5693747", +"109276", +"113519", +"1605715", +"8851517", +"113518", +"351603" +], +"sabiork":[ +"40" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27222", +"cpd00001", +"cpd15275" +] +} +}, +{ +"id":"h_c", +"name":"H+", +"compartment":"c", +"charge":1, +"formula":"H", +"notes":{ +"original_bigg_ids":[ +"h_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h" +], +"biocyc":[ +"META:PROTON" +], +"chebi":[ +"CHEBI:5584", +"CHEBI:13357", +"CHEBI:15378", +"CHEBI:10744" +], +"hmdb":[ +"HMDB59597" +], +"inchi_key":[ +"GPRLSGONYQIRFK-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00080" +], +"metanetx.chemical":[ +"MNXM1" +], +"reactome.compound":[ +"2000349", +"425978", +"74722", +"428040", +"427899", +"428548", +"156540", +"70106", +"425969", +"1132304", +"5668577", +"1470067", +"163953", +"193465", +"113529", +"351626", +"425999", +"194688", +"374900", +"2872447", +"372511" +], +"sabiork":[ +"39" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00067" +] +} +}, +{ +"id":"h_e", +"name":"H+", +"compartment":"e", +"charge":1, +"formula":"H", +"notes":{ +"original_bigg_ids":[ +"h_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h" +], +"biocyc":[ +"META:PROTON" +], +"chebi":[ +"CHEBI:5584", +"CHEBI:13357", +"CHEBI:15378", +"CHEBI:10744" +], +"hmdb":[ +"HMDB59597" +], +"inchi_key":[ +"GPRLSGONYQIRFK-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00080" +], +"metanetx.chemical":[ +"MNXM1" +], +"reactome.compound":[ +"2000349", +"425978", +"74722", +"428040", +"427899", +"428548", +"156540", +"70106", +"425969", +"1132304", +"5668577", +"1470067", +"163953", +"193465", +"113529", +"351626", +"425999", +"194688", +"374900", +"2872447", +"372511" +], +"sabiork":[ +"39" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00067" +] +} +}, +{ +"id":"icit_c", +"name":"Isocitrate", +"compartment":"c", +"charge":-3, +"formula":"C6H5O7", +"notes":{ +"original_bigg_ids":[ +"icit_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"icit" +], +"chebi":[ +"CHEBI:16087", +"CHEBI:36454", +"CHEBI:5998", +"CHEBI:24886", +"CHEBI:36453", +"CHEBI:14465", +"CHEBI:30887", +"CHEBI:24884" +], +"hmdb":[ +"HMDB00193" +], +"inchi_key":[ +"ODBLHEXUDAPZAU-UHFFFAOYSA-K" +], +"kegg.compound":[ +"C00311" +], +"metanetx.chemical":[ +"MNXM89661" +], +"sabiork":[ +"2013" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00260" +] +} +}, +{ +"id":"lac__D_c", +"name":"D-Lactate", +"compartment":"c", +"charge":-1, +"formula":"C3H5O3", +"notes":{ +"original_bigg_ids":[ +"lac_D_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"lac__D" +], +"biocyc":[ +"META:D-LACTATE" +], +"chebi":[ +"CHEBI:16004", +"CHEBI:341", +"CHEBI:18684", +"CHEBI:43701", +"CHEBI:11001", +"CHEBI:42111", +"CHEBI:42105" +], +"hmdb":[ +"HMDB01311", +"HMDB00171" +], +"inchi_key":[ +"JVTAAEKCZFNVCJ-UWTATZPHSA-M" +], +"kegg.compound":[ +"C00256" +], +"metanetx.chemical":[ +"MNXM285" +], +"sabiork":[ +"1997", +"2284" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00221" +] +} +}, +{ +"id":"lac__D_e", +"name":"D-Lactate", +"compartment":"e", +"charge":-1, +"formula":"C3H5O3", +"notes":{ +"original_bigg_ids":[ +"lac_D_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"lac__D" +], +"biocyc":[ +"META:D-LACTATE" +], +"chebi":[ +"CHEBI:16004", +"CHEBI:341", +"CHEBI:18684", +"CHEBI:43701", +"CHEBI:11001", +"CHEBI:42111", +"CHEBI:42105" +], +"hmdb":[ +"HMDB01311", +"HMDB00171" +], +"inchi_key":[ +"JVTAAEKCZFNVCJ-UWTATZPHSA-M" +], +"kegg.compound":[ +"C00256" +], +"metanetx.chemical":[ +"MNXM285" +], +"sabiork":[ +"1997", +"2284" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00221" +] +} +}, +{ +"id":"mal__L_c", +"name":"L-Malate", +"compartment":"c", +"charge":-2, +"formula":"C4H4O5", +"notes":{ +"original_bigg_ids":[ +"mal_L_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"mal__L" +], +"biocyc":[ +"META:MAL" +], +"chebi":[ +"CHEBI:15589", +"CHEBI:30797", +"CHEBI:423", +"CHEBI:18784", +"CHEBI:18785", +"CHEBI:13140", +"CHEBI:11066" +], +"hmdb":[ +"HMDB00156" +], +"inchi_key":[ +"BJEPYKJPYRNKOW-REOHCLBHSA-L" +], +"kegg.compound":[ +"C00149" +], +"metanetx.chemical":[ +"MNXM98" +], +"reactome.compound":[ +"198498", +"113544" +], +"sabiork":[ +"1918" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00130" +] +} +}, +{ +"id":"mal__L_e", +"name":"L-Malate", +"compartment":"e", +"charge":-2, +"formula":"C4H4O5", +"notes":{ +"original_bigg_ids":[ +"mal_L_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"mal__L" +], +"biocyc":[ +"META:MAL" +], +"chebi":[ +"CHEBI:15589", +"CHEBI:30797", +"CHEBI:423", +"CHEBI:18784", +"CHEBI:18785", +"CHEBI:13140", +"CHEBI:11066" +], +"hmdb":[ +"HMDB00156" +], +"inchi_key":[ +"BJEPYKJPYRNKOW-REOHCLBHSA-L" +], +"kegg.compound":[ +"C00149" +], +"metanetx.chemical":[ +"MNXM98" +], +"reactome.compound":[ +"198498", +"113544" +], +"sabiork":[ +"1918" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00130" +] +} +}, +{ +"id":"nad_c", +"name":"Nicotinamide adenine dinucleotide", +"compartment":"c", +"charge":-1, +"formula":"C21H26N7O14P2", +"notes":{ +"original_bigg_ids":[ +"nad_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nad" +], +"biocyc":[ +"META:NAD" +], +"chebi":[ +"CHEBI:7422", +"CHEBI:44215", +"CHEBI:13394", +"CHEBI:21901", +"CHEBI:57540", +"CHEBI:15846", +"CHEBI:44281", +"CHEBI:44214", +"CHEBI:13393", +"CHEBI:29867" +], +"hmdb":[ +"HMDB00902" +], +"inchi_key":[ +"BAWFJGJZGIEFAR-NNYOXOHSSA-M" +], +"kegg.compound":[ +"C00003" +], +"kegg.drug":[ +"D00002" +], +"metanetx.chemical":[ +"MNXM8" +], +"reactome.compound":[ +"352330", +"192307", +"194653", +"113526", +"29360" +], +"sabiork":[ +"37" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00003" +] +} +}, +{ +"id":"nadh_c", +"name":"Nicotinamide adenine dinucleotide - reduced", +"compartment":"c", +"charge":-2, +"formula":"C21H27N7O14P2", +"notes":{ +"original_bigg_ids":[ +"nadh_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nadh" +], +"biocyc":[ +"META:NADH" +], +"chebi":[ +"CHEBI:13395", +"CHEBI:21902", +"CHEBI:7423", +"CHEBI:44216", +"CHEBI:57945", +"CHEBI:16908", +"CHEBI:13396" +], +"hmdb":[ +"HMDB01487" +], +"inchi_key":[ +"BOPGDPNILDQYTO-NNYOXOHSSA-L" +], +"kegg.compound":[ +"C00004" +], +"metanetx.chemical":[ +"MNXM10" +], +"reactome.compound":[ +"192305", +"73473", +"29362", +"194697" +], +"sabiork":[ +"38" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00004" +] +} +}, +{ +"id":"nadp_c", +"name":"Nicotinamide adenine dinucleotide phosphate", +"compartment":"c", +"charge":-3, +"formula":"C21H25N7O17P3", +"notes":{ +"original_bigg_ids":[ +"nadp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nadp" +], +"biocyc":[ +"META:NADP" +], +"chebi":[ +"CHEBI:29868", +"CHEBI:44405", +"CHEBI:25523", +"CHEBI:13397", +"CHEBI:18009", +"CHEBI:7424", +"CHEBI:13398", +"CHEBI:21903", +"CHEBI:58349", +"CHEBI:44409" +], +"hmdb":[ +"HMDB00217" +], +"inchi_key":[ +"XJLXINKUBYWONI-NNYOXOHSSA-K" +], +"kegg.compound":[ +"C00006" +], +"metanetx.chemical":[ +"MNXM5" +], +"reactome.compound":[ +"194668", +"113563", +"6790191", +"5623650", +"2000348", +"389556", +"29366", +"351628", +"113564" +], +"sabiork":[ +"1263" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00006" +] +} +}, +{ +"id":"nadph_c", +"name":"Nicotinamide adenine dinucleotide phosphate - reduced", +"compartment":"c", +"charge":-4, +"formula":"C21H26N7O17P3", +"notes":{ +"original_bigg_ids":[ +"nadph_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nadph" +], +"biocyc":[ +"META:NADPH" +], +"chebi":[ +"CHEBI:16474", +"CHEBI:7425", +"CHEBI:57783", +"CHEBI:21904", +"CHEBI:13399", +"CHEBI:13400", +"CHEBI:44286" +], +"hmdb":[ +"HMDB06341", +"HMDB00221", +"HMDB00799" +], +"inchi_key":[ +"ACFIXJIJDZMPPO-NNYOXOHSSA-J" +], +"kegg.compound":[ +"C00005" +], +"metanetx.chemical":[ +"MNXM6" +], +"reactome.compound":[ +"113600", +"6790135", +"113602", +"113601", +"2000347", +"351627", +"29364", +"5623644", +"194725" +], +"sabiork":[ +"1262" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00005" +] +} +}, +{ +"id":"nh4_c", +"name":"Ammonium", +"compartment":"c", +"charge":1, +"formula":"H4N", +"notes":{ +"original_bigg_ids":[ +"nh4_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nh4" +], +"biocyc":[ +"META:AMMONIUM", +"META:AMMONIA" +], +"chebi":[ +"CHEBI:44284", +"CHEBI:135980", +"CHEBI:22533", +"CHEBI:13406", +"CHEBI:29337", +"CHEBI:29340", +"CHEBI:13771", +"CHEBI:16134", +"CHEBI:28938", +"CHEBI:22534", +"CHEBI:13405", +"CHEBI:49783", +"CHEBI:7434", +"CHEBI:7435", +"CHEBI:44269", +"CHEBI:44404", +"CHEBI:13407" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/96667bd9-aeae-4e8f-89d3-100d0396af05", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/27a89bdf-42f7-478f-91d8-e39881581096" +], +"hmdb":[ +"HMDB00051", +"HMDB41827" +], +"inchi_key":[ +"QGZKDVFQNNGYKY-UHFFFAOYSA-O" +], +"kegg.compound":[ +"C00014", +"C01342" +], +"kegg.drug":[ +"D02916", +"D02915" +], +"metanetx.chemical":[ +"MNXM15" +], +"reactome.compound":[ +"5693978", +"1132163", +"29382", +"76230", +"140912", +"389843", +"2022135", +"31633", +"113561" +], +"sabiork":[ +"1268", +"43" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19013", +"cpd00013" +] +} +}, +{ +"id":"13dpg_c", +"name":"3-Phospho-D-glyceroyl phosphate", +"compartment":"c", +"charge":-4, +"formula":"C3H4O10P2", +"notes":{ +"original_bigg_ids":[ +"13dpg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"13dpg" +], +"biocyc":[ +"META:DPG" +], +"chebi":[ +"CHEBI:57604", +"CHEBI:20189", +"CHEBI:11881", +"CHEBI:16001", +"CHEBI:1658" +], +"hmdb":[ +"HMDB62758" +], +"inchi_key":[ +"LJQLQCAXBUHEAZ-UWTATZPHSA-J" +], +"kegg.compound":[ +"C00236" +], +"metanetx.chemical":[ +"MNXM261" +], +"reactome.compound":[ +"29800" +], +"sabiork":[ +"21215" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00203" +] +} +}, +{ +"id":"nh4_e", +"name":"Ammonium", +"compartment":"e", +"charge":1, +"formula":"H4N", +"notes":{ +"original_bigg_ids":[ +"nh4_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nh4" +], +"biocyc":[ +"META:AMMONIUM", +"META:AMMONIA" +], +"chebi":[ +"CHEBI:44284", +"CHEBI:135980", +"CHEBI:22533", +"CHEBI:13406", +"CHEBI:29337", +"CHEBI:29340", +"CHEBI:13771", +"CHEBI:16134", +"CHEBI:28938", +"CHEBI:22534", +"CHEBI:13405", +"CHEBI:49783", +"CHEBI:7434", +"CHEBI:7435", +"CHEBI:44269", +"CHEBI:44404", +"CHEBI:13407" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/96667bd9-aeae-4e8f-89d3-100d0396af05", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/27a89bdf-42f7-478f-91d8-e39881581096" +], +"hmdb":[ +"HMDB00051", +"HMDB41827" +], +"inchi_key":[ +"QGZKDVFQNNGYKY-UHFFFAOYSA-O" +], +"kegg.compound":[ +"C00014", +"C01342" +], +"kegg.drug":[ +"D02916", +"D02915" +], +"metanetx.chemical":[ +"MNXM15" +], +"reactome.compound":[ +"5693978", +"1132163", +"29382", +"76230", +"140912", +"389843", +"2022135", +"31633", +"113561" +], +"sabiork":[ +"1268", +"43" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19013", +"cpd00013" +] +} +}, +{ +"id":"o2_c", +"name":"O2 O2", +"compartment":"c", +"charge":0, +"formula":"O2", +"notes":{ +"original_bigg_ids":[ +"o2_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"o2" +], +"biocyc":[ +"META:OXYGEN-MOLECULE" +], +"chebi":[ +"CHEBI:7860", +"CHEBI:26689", +"CHEBI:29097", +"CHEBI:15379", +"CHEBI:13416", +"CHEBI:27140", +"CHEBI:29793", +"CHEBI:30491", +"CHEBI:44742", +"CHEBI:23833", +"CHEBI:25366", +"CHEBI:10745" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4" +], +"hmdb":[ +"HMDB01377" +], +"inchi_key":[ +"MYMOFIZGZYHOMD-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00007" +], +"kegg.drug":[ +"D00003" +], +"metanetx.chemical":[ +"MNXM4" +], +"reactome.compound":[ +"113534", +"113535", +"113685", +"5668566", +"189461", +"113533", +"1131511", +"352327", +"351593", +"29368", +"1236709" +], +"sabiork":[ +"1264" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00007" +] +} +}, +{ +"id":"2pg_c", +"name":"D-Glycerate 2-phosphate", +"compartment":"c", +"charge":-3, +"formula":"C3H4O7P", +"notes":{ +"original_bigg_ids":[ +"2pg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"2pg" +], +"biocyc":[ +"META:2-PG" +], +"chebi":[ +"CHEBI:39868", +"CHEBI:21028", +"CHEBI:58289", +"CHEBI:24344", +"CHEBI:12986", +"CHEBI:17835", +"CHEBI:11651", +"CHEBI:1267", +"CHEBI:88350" +], +"hmdb":[ +"HMDB00362", +"HMDB62707", +"HMDB03391" +], +"inchi_key":[ +"GXIURPTVHJPJLF-UWTATZPHSA-K" +], +"kegg.compound":[ +"C00631" +], +"metanetx.chemical":[ +"MNXM275" +], +"reactome.compound":[ +"30485" +], +"sabiork":[ +"31" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00482" +] +} +}, +{ +"id":"o2_e", +"name":"O2 O2", +"compartment":"e", +"charge":0, +"formula":"O2", +"notes":{ +"original_bigg_ids":[ +"o2_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"o2" +], +"biocyc":[ +"META:OXYGEN-MOLECULE" +], +"chebi":[ +"CHEBI:7860", +"CHEBI:26689", +"CHEBI:29097", +"CHEBI:15379", +"CHEBI:13416", +"CHEBI:27140", +"CHEBI:29793", +"CHEBI:30491", +"CHEBI:44742", +"CHEBI:23833", +"CHEBI:25366", +"CHEBI:10745" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4" +], +"hmdb":[ +"HMDB01377" +], +"inchi_key":[ +"MYMOFIZGZYHOMD-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00007" +], +"kegg.drug":[ +"D00003" +], +"metanetx.chemical":[ +"MNXM4" +], +"reactome.compound":[ +"113534", +"113535", +"113685", +"5668566", +"189461", +"113533", +"1131511", +"352327", +"351593", +"29368", +"1236709" +], +"sabiork":[ +"1264" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00007" +] +} +}, +{ +"id":"3pg_c", +"name":"3-Phospho-D-glycerate", +"compartment":"c", +"charge":-3, +"formula":"C3H4O7P", +"notes":{ +"original_bigg_ids":[ +"3pg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"3pg" +], +"biocyc":[ +"META:G3P" +], +"chebi":[ +"CHEBI:11879", +"CHEBI:11880", +"CHEBI:17794", +"CHEBI:21029", +"CHEBI:1657", +"CHEBI:58272", +"CHEBI:12987" +], +"hmdb":[ +"HMDB60180" +], +"inchi_key":[ +"OSJPPGNTCRNQQC-UWTATZPHSA-K" +], +"kegg.compound":[ +"C00197" +], +"metanetx.chemical":[ +"MNXM126" +], +"reactome.compound":[ +"6799493", +"29728" +], +"sabiork":[ +"21216" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00169" +] +} +}, +{ +"id":"oaa_c", +"name":"Oxaloacetate", +"compartment":"c", +"charge":-2, +"formula":"C4H2O5", +"notes":{ +"original_bigg_ids":[ +"oaa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"oaa" +], +"biocyc":[ +"META:OXALACETIC_ACID" +], +"chebi":[ +"CHEBI:25731", +"CHEBI:24959", +"CHEBI:12820", +"CHEBI:16452", +"CHEBI:30744", +"CHEBI:14703", +"CHEBI:24958", +"CHEBI:7812", +"CHEBI:25734", +"CHEBI:29049" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/133a11f3-81b0-4384-837e-1ccdd0a2a645", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/40afaad4-431a-4e3c-b4c7-020dbe4bdd2a", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/be7c543c-40bd-4698-9821-22f2e65c38f3" +], +"hmdb":[ +"HMDB00223" +], +"inchi_key":[ +"KHPXUQMNIQBQEV-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00036" +], +"lipidmaps":[ +"LMFA01170120" +], +"metanetx.chemical":[ +"MNXM46" +], +"reactome.compound":[ +"6810070", +"113587", +"76213" +], +"sabiork":[ +"1915" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00032" +] +} +}, +{ +"id":"pep_c", +"name":"Phosphoenolpyruvate", +"compartment":"c", +"charge":-3, +"formula":"C3H2O6P", +"notes":{ +"original_bigg_ids":[ +"pep_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pep" +], +"biocyc":[ +"META:PHOSPHO-ENOL-PYRUVATE" +], +"chebi":[ +"CHEBI:18021", +"CHEBI:44894", +"CHEBI:26054", +"CHEBI:14812", +"CHEBI:26055", +"CHEBI:8147", +"CHEBI:58702", +"CHEBI:44897" +], +"hmdb":[ +"HMDB00263" +], +"inchi_key":[ +"DTBNBXWJWCWCIK-UHFFFAOYSA-K" +], +"kegg.compound":[ +"C00074" +], +"metanetx.chemical":[ +"MNXM73" +], +"reactome.compound":[ +"372364", +"29492" +], +"sabiork":[ +"32" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00061" +] +} +}, +{ +"id":"6pgc_c", +"name":"6-Phospho-D-gluconate", +"compartment":"c", +"charge":-3, +"formula":"C6H10O10P", +"notes":{ +"original_bigg_ids":[ +"6pgc_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"6pgc" +], +"biocyc":[ +"META:CPD-2961" +], +"chebi":[ +"CHEBI:33851", +"CHEBI:2231", +"CHEBI:16863", +"CHEBI:40282", +"CHEBI:12232", +"CHEBI:48928", +"CHEBI:58759" +], +"hmdb":[ +"HMDB01316", +"HMDB62800" +], +"inchi_key":[ +"BIRSGZKFKXLSJQ-SQOUGZDYSA-K" +], +"kegg.compound":[ +"C00345" +], +"metanetx.chemical":[ +"MNXM325" +], +"reactome.compound":[ +"29996" +], +"sabiork":[ +"22801", +"2024" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00284" +] +} +}, +{ +"id":"pi_c", +"name":"Phosphate", +"compartment":"c", +"charge":-2, +"formula":"HO4P", +"notes":{ +"original_bigg_ids":[ +"pi_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pi" +], +"biocyc":[ +"META:Pi", +"META:CPD-16459", +"META:PHOSPHATE-GROUP" +], +"chebi":[ +"CHEBI:26078", +"CHEBI:18367", +"CHEBI:29139", +"CHEBI:39739", +"CHEBI:43470", +"CHEBI:35780", +"CHEBI:43474", +"CHEBI:26020", +"CHEBI:45024", +"CHEBI:39745", +"CHEBI:29137", +"CHEBI:14791", +"CHEBI:7793" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/db5219ee-60cb-4370-b066-340c9faf069c", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/84684967-eade-48d4-b25d-c4aede0a0836", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/ad82c39b-2edb-4953-b971-79a2d2ea6e26", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/aac01fea-4223-49c1-8b12-cd50f11ebfc8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04" +], +"hmdb":[ +"HMDB02105", +"HMDB00973", +"HMDB01429", +"HMDB02142", +"HMDB05947" +], +"inchi_key":[ +"NBIIXXVUZAFLBC-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00009" +], +"kegg.drug":[ +"D05467" +], +"metanetx.chemical":[ +"MNXM9" +], +"reactome.compound":[ +"5228339", +"113550", +"8851513", +"113551", +"109277", +"29372", +"8851226", +"113548" +], +"sabiork":[ +"36" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27787", +"cpd00009" +] +} +}, +{ +"id":"6pgl_c", +"name":"6-phospho-D-glucono-1,5-lactone", +"compartment":"c", +"charge":-2, +"formula":"C6H9O9P", +"notes":{ +"original_bigg_ids":[ +"6pgl_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"6pgl" +], +"biocyc":[ +"META:D-6-P-GLUCONO-DELTA-LACTONE" +], +"chebi":[ +"CHEBI:12233", +"CHEBI:4160", +"CHEBI:57955", +"CHEBI:16938", +"CHEBI:20989", +"CHEBI:12958" +], +"hmdb":[ +"HMDB62628", +"HMDB01127" +], +"inchi_key":[ +"IJOJIVNDFQSGAB-SQOUGZDYSA-L" +], +"kegg.compound":[ +"C01236" +], +"metanetx.chemical":[ +"MNXM429" +], +"reactome.compound":[ +"31467" +], +"sabiork":[ +"1366" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00911" +] +} +}, +{ +"id":"pi_e", +"name":"Phosphate", +"compartment":"e", +"charge":-2, +"formula":"HO4P", +"notes":{ +"original_bigg_ids":[ +"pi_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pi" +], +"biocyc":[ +"META:Pi", +"META:CPD-16459", +"META:PHOSPHATE-GROUP" +], +"chebi":[ +"CHEBI:26078", +"CHEBI:18367", +"CHEBI:29139", +"CHEBI:39739", +"CHEBI:43470", +"CHEBI:35780", +"CHEBI:43474", +"CHEBI:26020", +"CHEBI:45024", +"CHEBI:39745", +"CHEBI:29137", +"CHEBI:14791", +"CHEBI:7793" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/db5219ee-60cb-4370-b066-340c9faf069c", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/84684967-eade-48d4-b25d-c4aede0a0836", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/ad82c39b-2edb-4953-b971-79a2d2ea6e26", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/aac01fea-4223-49c1-8b12-cd50f11ebfc8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04" +], +"hmdb":[ +"HMDB02105", +"HMDB00973", +"HMDB01429", +"HMDB02142", +"HMDB05947" +], +"inchi_key":[ +"NBIIXXVUZAFLBC-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00009" +], +"kegg.drug":[ +"D05467" +], +"metanetx.chemical":[ +"MNXM9" +], +"reactome.compound":[ +"5228339", +"113550", +"8851513", +"113551", +"109277", +"29372", +"8851226", +"113548" +], +"sabiork":[ +"36" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27787", +"cpd00009" +] +} +}, +{ +"id":"ac_c", +"name":"Acetate", +"compartment":"c", +"charge":-1, +"formula":"C2H3O2", +"notes":{ +"original_bigg_ids":[ +"ac_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"ac" +], +"biocyc":[ +"META:ACET" +], +"chebi":[ +"CHEBI:13704", +"CHEBI:22165", +"CHEBI:22169", +"CHEBI:40480", +"CHEBI:15366", +"CHEBI:2387", +"CHEBI:30089", +"CHEBI:40486" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/9e26dcbe-4db9-46a0-8614-9f03545032d2", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/5e4989fc-13d3-45d4-ad57-3be380a9d3c0", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/a8f0be58-24e8-441b-8d81-a516a0ead4b3", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/d45256fe-61fa-4f5b-bb16-91a3d615e3d8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/3e2d750f-df31-4445-9255-163c627e9b4a" +], +"hmdb":[ +"HMDB00042" +], +"inchi_key":[ +"QTBSBXVTEAMEQO-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00033" +], +"kegg.drug":[ +"D00010" +], +"lipidmaps":[ +"LMFA01010002" +], +"metanetx.chemical":[ +"MNXM26" +], +"reactome.compound":[ +"1524044", +"390305", +"113539", +"2022890", +"29416" +], +"sabiork":[ +"1278" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00029" +], +"slm":[ +"000000449" +] +} +}, +{ +"id":"pyr_c", +"name":"Pyruvate", +"compartment":"c", +"charge":-1, +"formula":"C3H3O3", +"notes":{ +"original_bigg_ids":[ +"pyr_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pyr" +], +"biocyc":[ +"META:PYRUVATE" +], +"chebi":[ +"CHEBI:26462", +"CHEBI:26466", +"CHEBI:8685", +"CHEBI:32816", +"CHEBI:45253", +"CHEBI:14987", +"CHEBI:15361" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ccc99777-54dc-42d4-a97e-009b780d3905", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc01020e-8c7e-4087-9f56-cf8c962b7437" +], +"hmdb":[ +"HMDB00243" +], +"inchi_key":[ +"LCTONWCANYUPML-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00022" +], +"lipidmaps":[ +"LMFA01060077" +], +"metanetx.chemical":[ +"MNXM23" +], +"reactome.compound":[ +"1130930", +"5357717", +"113557", +"29398", +"389680" +], +"sabiork":[ +"33" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00020" +] +} +}, +{ +"id":"pyr_e", +"name":"Pyruvate", +"compartment":"e", +"charge":-1, +"formula":"C3H3O3", +"notes":{ +"original_bigg_ids":[ +"pyr_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pyr" +], +"biocyc":[ +"META:PYRUVATE" +], +"chebi":[ +"CHEBI:26462", +"CHEBI:26466", +"CHEBI:8685", +"CHEBI:32816", +"CHEBI:45253", +"CHEBI:14987", +"CHEBI:15361" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ccc99777-54dc-42d4-a97e-009b780d3905", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc01020e-8c7e-4087-9f56-cf8c962b7437" +], +"hmdb":[ +"HMDB00243" +], +"inchi_key":[ +"LCTONWCANYUPML-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00022" +], +"lipidmaps":[ +"LMFA01060077" +], +"metanetx.chemical":[ +"MNXM23" +], +"reactome.compound":[ +"1130930", +"5357717", +"113557", +"29398", +"389680" +], +"sabiork":[ +"33" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00020" +] +} +}, +{ +"id":"q8_c", +"name":"Ubiquinone-8", +"compartment":"c", +"charge":0, +"formula":"C49H74O4", +"notes":{ +"original_bigg_ids":[ +"q8_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"q8" +], +"biocyc":[ +"META:UBIQUINONE-8" +], +"chebi":[ +"CHEBI:61683" +], +"inchi_key":[ +"ICFIZJQGJAJRSU-SGHXUWJISA-N" +], +"kegg.compound":[ +"C17569" +], +"lipidmaps":[ +"LMPR02010005" +], +"metanetx.chemical":[ +"MNXM232" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd15560" +] +} +}, +{ +"id":"q8h2_c", +"name":"Ubiquinol-8", +"compartment":"c", +"charge":0, +"formula":"C49H76O4", +"notes":{ +"original_bigg_ids":[ +"q8h2_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"q8h2" +], +"biocyc":[ +"META:CPD-9956" +], +"chebi":[ +"CHEBI:61682" +], +"hmdb":[ +"HMDB01060" +], +"inchi_key":[ +"LOJUQFSPYHMHEO-SGHXUWJISA-N" +], +"metanetx.chemical":[ +"MNXM191" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd29608", +"cpd15561" +] +} +}, +{ +"id":"r5p_c", +"name":"Alpha-D-Ribose 5-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C5H9O8P", +"notes":{ +"original_bigg_ids":[ +"r5p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"r5p" +], +"biocyc":[ +"META:CPD-15318" +], +"chebi":[ +"CHEBI:18189", +"CHEBI:22413", +"CHEBI:12331", +"CHEBI:10270" +], +"inchi_key":[ +"KTVPXOYAKDPRHY-AIHAYLRMSA-L" +], +"kegg.compound":[ +"C03736" +], +"metanetx.chemical":[ +"MNXM15900" +], +"sabiork":[ +"1473" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19028" +] +} +}, +{ +"id":"ru5p__D_c", +"name":"D-Ribulose 5-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C5H9O8P", +"notes":{ +"original_bigg_ids":[ +"ru5p_D_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"ru5p__D" +], +"biocyc":[ +"META:RIBULOSE-5P" +], +"chebi":[ +"CHEBI:40192", +"CHEBI:21088", +"CHEBI:17363", +"CHEBI:26572", +"CHEBI:13040", +"CHEBI:37455", +"CHEBI:58121", +"CHEBI:13018", +"CHEBI:4243" +], +"hmdb":[ +"HMDB02033", +"HMDB02694", +"HMDB00618" +], +"inchi_key":[ +"FNZLKVNUWIIPSJ-UHNVWZDZSA-L" +], +"kegg.compound":[ +"C00199" +], +"metanetx.chemical":[ +"MNXM145" +], +"reactome.compound":[ +"29732" +], +"sabiork":[ +"22814", +"1313" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00171" +] +} +}, +{ +"id":"ac_e", +"name":"Acetate", +"compartment":"e", +"charge":-1, +"formula":"C2H3O2", +"notes":{ +"original_bigg_ids":[ +"ac_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"ac" +], +"biocyc":[ +"META:ACET" +], +"chebi":[ +"CHEBI:13704", +"CHEBI:22165", +"CHEBI:22169", +"CHEBI:40480", +"CHEBI:15366", +"CHEBI:2387", +"CHEBI:30089", +"CHEBI:40486" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/9e26dcbe-4db9-46a0-8614-9f03545032d2", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/5e4989fc-13d3-45d4-ad57-3be380a9d3c0", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/a8f0be58-24e8-441b-8d81-a516a0ead4b3", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/d45256fe-61fa-4f5b-bb16-91a3d615e3d8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/3e2d750f-df31-4445-9255-163c627e9b4a" +], +"hmdb":[ +"HMDB00042" +], +"inchi_key":[ +"QTBSBXVTEAMEQO-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00033" +], +"kegg.drug":[ +"D00010" +], +"lipidmaps":[ +"LMFA01010002" +], +"metanetx.chemical":[ +"MNXM26" +], +"reactome.compound":[ +"1524044", +"390305", +"113539", +"2022890", +"29416" +], +"sabiork":[ +"1278" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00029" +], +"slm":[ +"000000449" +] +} +}, +{ +"id":"acald_c", +"name":"Acetaldehyde", +"compartment":"c", +"charge":0, +"formula":"C2H4O", +"notes":{ +"original_bigg_ids":[ +"acald_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"acald" +], +"biocyc":[ +"META:ACETALD" +], +"chebi":[ +"CHEBI:40533", +"CHEBI:13703", +"CHEBI:2383", +"CHEBI:22158", +"CHEBI:15343" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/9c8865b2-a99d-42e4-a042-c88504f04b51", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/47aa8e53-36ae-4be3-987c-c1cfab66af78", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ee2c714d-ff9d-4df8-b343-48c1ec76ef0e", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/78f3645f-408e-4001-9dda-a52ea62a15d4" +], +"hmdb":[ +"HMDB00990" +], +"inchi_key":[ +"IKHGUXGNUITLKF-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00084" +], +"metanetx.chemical":[ +"MNXM75" +], +"reactome.compound":[ +"113532", +"29510", +"113681", +"113745" +], +"sabiork":[ +"1292" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00071" +] +} +}, +{ +"id":"s7p_c", +"name":"Sedoheptulose 7-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C7H13O10P", +"notes":{ +"original_bigg_ids":[ +"s7p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"s7p" +], +"biocyc":[ +"META:D-SEDOHEPTULOSE-7-P" +], +"chebi":[ +"CHEBI:4244", +"CHEBI:15073", +"CHEBI:15721", +"CHEBI:26621", +"CHEBI:9083", +"CHEBI:15074", +"CHEBI:57483" +], +"hmdb":[ +"HMDB01068", +"HMDB62754" +], +"inchi_key":[ +"JDTUMPKOJBQPKX-GBNDHIKLSA-L" +], +"kegg.compound":[ +"C05382" +], +"metanetx.chemical":[ +"MNXM271" +], +"reactome.compound":[ +"29882" +], +"sabiork":[ +"1618", +"1325" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00238" +] +} +}, +{ +"id":"acald_e", +"name":"Acetaldehyde", +"compartment":"e", +"charge":0, +"formula":"C2H4O", +"notes":{ +"original_bigg_ids":[ +"acald_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"acald" +], +"biocyc":[ +"META:ACETALD" +], +"chebi":[ +"CHEBI:40533", +"CHEBI:13703", +"CHEBI:2383", +"CHEBI:22158", +"CHEBI:15343" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/9c8865b2-a99d-42e4-a042-c88504f04b51", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/47aa8e53-36ae-4be3-987c-c1cfab66af78", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ee2c714d-ff9d-4df8-b343-48c1ec76ef0e", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/78f3645f-408e-4001-9dda-a52ea62a15d4" +], +"hmdb":[ +"HMDB00990" +], +"inchi_key":[ +"IKHGUXGNUITLKF-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00084" +], +"metanetx.chemical":[ +"MNXM75" +], +"reactome.compound":[ +"113532", +"29510", +"113681", +"113745" +], +"sabiork":[ +"1292" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00071" +] +} +}, +{ +"id":"accoa_c", +"name":"Acetyl-CoA", +"compartment":"c", +"charge":-4, +"formula":"C23H34N7O17P3S", +"notes":{ +"original_bigg_ids":[ +"accoa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"accoa" +], +"biocyc":[ +"META:ACETYL-COA" +], +"chebi":[ +"CHEBI:57288", +"CHEBI:22192", +"CHEBI:15351", +"CHEBI:13712", +"CHEBI:2408", +"CHEBI:40470" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11" +], +"hmdb":[ +"HMDB01206" +], +"inchi_key":[ +"ZSLZBFCDCINBPY-ZSJPKINUSA-J" +], +"kegg.compound":[ +"C00024" +], +"lipidmaps":[ +"LMFA07050029", +"LMFA07050281" +], +"metanetx.chemical":[ +"MNXM21" +], +"reactome.compound":[ +"727753", +"76183", +"113560", +"353123", +"113559" +], +"sabiork":[ +"1276" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00022" +], +"slm":[ +"000000297" +] +} +}, +{ +"id":"succ_c", +"name":"Succinate", +"compartment":"c", +"charge":-2, +"formula":"C4H4O4", +"notes":{ +"original_bigg_ids":[ +"succ_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"succ" +], +"biocyc":[ +"META:SUC" +], +"chebi":[ +"CHEBI:22941", +"CHEBI:26803", +"CHEBI:15741", +"CHEBI:132287", +"CHEBI:45639", +"CHEBI:30779", +"CHEBI:15125", +"CHEBI:22943", +"CHEBI:26807", +"CHEBI:9304", +"CHEBI:90372", +"CHEBI:30031" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/cc98aff0-7f64-4db4-9d59-de961c228496", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/6377658b-03f6-4fed-a5bf-ff0f2389b693", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/600b74d3-8fe5-426d-bedf-291175bd23e4", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8fdfd425-4343-4bf2-8427-b2ffa57fdbd7" +], +"hmdb":[ +"HMDB00254" +], +"inchi_key":[ +"KDYFGRWQOYBRFD-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00042" +], +"lipidmaps":[ +"LMFA01170043" +], +"metanetx.chemical":[ +"MNXM25" +], +"reactome.compound":[ +"389583", +"5278787", +"159939", +"433123", +"29434", +"113536" +], +"sabiork":[ +"1924" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00036" +] +} +}, +{ +"id":"succ_e", +"name":"Succinate", +"compartment":"e", +"charge":-2, +"formula":"C4H4O4", +"notes":{ +"original_bigg_ids":[ +"succ_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"succ" +], +"biocyc":[ +"META:SUC" +], +"chebi":[ +"CHEBI:22941", +"CHEBI:26803", +"CHEBI:15741", +"CHEBI:132287", +"CHEBI:45639", +"CHEBI:30779", +"CHEBI:15125", +"CHEBI:22943", +"CHEBI:26807", +"CHEBI:9304", +"CHEBI:90372", +"CHEBI:30031" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/cc98aff0-7f64-4db4-9d59-de961c228496", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/6377658b-03f6-4fed-a5bf-ff0f2389b693", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/600b74d3-8fe5-426d-bedf-291175bd23e4", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8fdfd425-4343-4bf2-8427-b2ffa57fdbd7" +], +"hmdb":[ +"HMDB00254" +], +"inchi_key":[ +"KDYFGRWQOYBRFD-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00042" +], +"lipidmaps":[ +"LMFA01170043" +], +"metanetx.chemical":[ +"MNXM25" +], +"reactome.compound":[ +"389583", +"5278787", +"159939", +"433123", +"29434", +"113536" +], +"sabiork":[ +"1924" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00036" +] +} +}, +{ +"id":"succoa_c", +"name":"Succinyl-CoA", +"compartment":"c", +"charge":-5, +"formula":"C25H35N7O19P3S", +"notes":{ +"original_bigg_ids":[ +"succoa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"succoa" +], +"biocyc":[ +"META:SUC-COA" +], +"chebi":[ +"CHEBI:57292", +"CHEBI:10746", +"CHEBI:15127", +"CHEBI:15380", +"CHEBI:9310", +"CHEBI:45541", +"CHEBI:26811" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/359075fb-98d9-458d-ba82-db4020e753f3" +], +"hmdb":[ +"HMDB01022" +], +"inchi_key":[ +"VNOYUJKHFWYWIR-ITIYDSSPSA-I" +], +"kegg.compound":[ +"C00091" +], +"lipidmaps":[ +"LMFA07050370" +], +"metanetx.chemical":[ +"MNXM92" +], +"reactome.compound":[ +"70958" +], +"sabiork":[ +"1931" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00078" +] +} +}, +{ +"id":"acon_C_c", +"name":"Cis-Aconitate", +"compartment":"c", +"charge":-3, +"formula":"C6H3O6", +"notes":{ +"original_bigg_ids":[ +"acon_C_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"acon_C" +], +"biocyc":[ +"META:CIS-ACONITATE" +], +"chebi":[ +"CHEBI:23306", +"CHEBI:16383", +"CHEBI:12798", +"CHEBI:32805", +"CHEBI:23308", +"CHEBI:10482" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/643481e5-a35b-477e-8665-70f4dca66baa" +], +"hmdb":[ +"HMDB00461", +"HMDB00072" +], +"inchi_key":[ +"GTZCVFVGUGFEME-IWQZZHSRSA-K" +], +"kegg.compound":[ +"C00417" +], +"metanetx.chemical":[ +"MNXM813" +], +"sabiork":[ +"2043" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00331" +] +} +}, +{ +"id":"xu5p__D_c", +"name":"D-Xylulose 5-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C5H9O8P", +"notes":{ +"original_bigg_ids":[ +"xu5p_D_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"xu5p__D" +], +"biocyc":[ +"META:XYLULOSE-5-PHOSPHATE" +], +"chebi":[ +"CHEBI:13036", +"CHEBI:27354", +"CHEBI:4269", +"CHEBI:16332", +"CHEBI:57737", +"CHEBI:21121" +], +"hmdb":[ +"HMDB06212", +"HMDB00868" +], +"inchi_key":[ +"FNZLKVNUWIIPSJ-RFZPGFLSSA-L" +], +"kegg.compound":[ +"C00231" +], +"metanetx.chemical":[ +"MNXM186" +], +"reactome.compound":[ +"29790" +], +"sabiork":[ +"1317" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00198" +] +} +}, +{ +"id":"actp_c", +"name":"Acetyl phosphate", +"compartment":"c", +"charge":-2, +"formula":"C2H3O5P", +"notes":{ +"original_bigg_ids":[ +"actp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"actp" +], +"biocyc":[ +"META:ACETYL-P" +], +"chebi":[ +"CHEBI:13711", +"CHEBI:46262", +"CHEBI:15350", +"CHEBI:22191", +"CHEBI:2407" +], +"hmdb":[ +"HMDB01494" +], +"inchi_key":[ +"LIPOUNRJVLNBCD-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00227" +], +"metanetx.chemical":[ +"MNXM280" +], +"sabiork":[ +"1316" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00196" +] +} +}, +{ +"id":"adp_c", +"name":"ADP C10H12N5O10P2", +"compartment":"c", +"charge":-3, +"formula":"C10H12N5O10P2", +"notes":{ +"original_bigg_ids":[ +"adp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"adp" +], +"biocyc":[ +"META:ADP" +], +"chebi":[ +"CHEBI:2342", +"CHEBI:16761", +"CHEBI:456216", +"CHEBI:40553", +"CHEBI:22244", +"CHEBI:87518", +"CHEBI:13222" +], +"hmdb":[ +"HMDB01341" +], +"inchi_key":[ +"XTWYTFMLZFPYCI-KQYNXXCUSA-K" +], +"kegg.compound":[ +"C00008" +], +"kegg.glycan":[ +"G11113" +], +"metanetx.chemical":[ +"MNXM7" +], +"reactome.compound":[ +"114565", +"211606", +"114564", +"6798177", +"5632457", +"5696026", +"8869360", +"29370", +"113581", +"113582" +], +"sabiork":[ +"35" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00008" +] +} +}, +{ +"id":"akg_c", +"name":"2-Oxoglutarate", +"compartment":"c", +"charge":-2, +"formula":"C5H4O5", +"notes":{ +"original_bigg_ids":[ +"akg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"akg" +], +"biocyc":[ +"META:2-KETOGLUTARATE" +], +"chebi":[ +"CHEBI:40661", +"CHEBI:16810", +"CHEBI:11638", +"CHEBI:30916", +"CHEBI:19749", +"CHEBI:1253", +"CHEBI:30915", +"CHEBI:19748" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/6557f3f2-0ab8-494b-a865-8ce0eae788a9" +], +"hmdb":[ +"HMDB00208", +"HMDB02812", +"HMDB62781" +], +"inchi_key":[ +"KPGXRSRHYNQIFN-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00026" +], +"metanetx.chemical":[ +"MNXM20" +], +"reactome.compound":[ +"113594", +"561075", +"5278317", +"113671", +"29406", +"389537" +], +"sabiork":[ +"1922" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00024" +] +} +}, +{ +"id":"akg_e", +"name":"2-Oxoglutarate", +"compartment":"e", +"charge":-2, +"formula":"C5H4O5", +"notes":{ +"original_bigg_ids":[ +"akg_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"akg" +], +"biocyc":[ +"META:2-KETOGLUTARATE" +], +"chebi":[ +"CHEBI:40661", +"CHEBI:16810", +"CHEBI:11638", +"CHEBI:30916", +"CHEBI:19749", +"CHEBI:1253", +"CHEBI:30915", +"CHEBI:19748" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/6557f3f2-0ab8-494b-a865-8ce0eae788a9" +], +"hmdb":[ +"HMDB00208", +"HMDB02812", +"HMDB62781" +], +"inchi_key":[ +"KPGXRSRHYNQIFN-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00026" +], +"metanetx.chemical":[ +"MNXM20" +], +"reactome.compound":[ +"113594", +"561075", +"5278317", +"113671", +"29406", +"389537" +], +"sabiork":[ +"1922" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00024" +] +} +}, +{ +"id":"amp_c", +"name":"AMP C10H12N5O7P", +"compartment":"c", +"charge":-2, +"formula":"C10H12N5O7P", +"notes":{ +"original_bigg_ids":[ +"amp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"amp" +], +"biocyc":[ +"META:AMP-GROUP", +"META:AMP" +], +"chebi":[ +"CHEBI:13736", +"CHEBI:2356", +"CHEBI:13234", +"CHEBI:22242", +"CHEBI:40786", +"CHEBI:16027", +"CHEBI:40721", +"CHEBI:40510", +"CHEBI:456215", +"CHEBI:13235", +"CHEBI:22245", +"CHEBI:40726", +"CHEBI:47222", +"CHEBI:13740", +"CHEBI:40826", +"CHEBI:12056" +], +"hmdb":[ +"HMDB00045" +], +"inchi_key":[ +"UDMBCSSLTHHNCD-KQYNXXCUSA-L" +], +"kegg.compound":[ +"C00020" +], +"kegg.drug":[ +"D02769" +], +"metanetx.chemical":[ +"MNXM14" +], +"reactome.compound":[ +"389620", +"159448", +"76577", +"109275", +"164121" +], +"sabiork":[ +"1273" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd22272", +"cpd00018" +] +} +}, +{ +"id":"atp_c", +"name":"ATP C10H12N5O13P3", +"compartment":"c", +"charge":-4, +"formula":"C10H12N5O13P3", +"notes":{ +"original_bigg_ids":[ +"atp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"atp" +], +"biocyc":[ +"META:ATP" +], +"chebi":[ +"CHEBI:15422", +"CHEBI:10789", +"CHEBI:10841", +"CHEBI:2359", +"CHEBI:22249", +"CHEBI:13236", +"CHEBI:237958", +"CHEBI:30616", +"CHEBI:57299", +"CHEBI:40938" +], +"hmdb":[ +"HMDB00538" +], +"inchi_key":[ +"ZKHQWZAMYRWXGA-KQYNXXCUSA-J" +], +"kegg.compound":[ +"C00002" +], +"kegg.drug":[ +"D08646" +], +"metanetx.chemical":[ +"MNXM3" +], +"reactome.compound":[ +"8878982", +"389573", +"8938081", +"211579", +"113593", +"113592", +"5632460", +"5696069", +"29358", +"8869363", +"6798184" +], +"sabiork":[ +"34" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00002" +] +} +}, +{ +"id":"cit_c", +"name":"Citrate", +"compartment":"c", +"charge":-3, +"formula":"C6H5O7", +"notes":{ +"original_bigg_ids":[ +"cit_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"cit" +], +"biocyc":[ +"META:CIT" +], +"chebi":[ +"CHEBI:35802", +"CHEBI:133748", +"CHEBI:35809", +"CHEBI:76049", +"CHEBI:41523", +"CHEBI:35810", +"CHEBI:30769", +"CHEBI:13999", +"CHEBI:23322", +"CHEBI:35808", +"CHEBI:42563", +"CHEBI:16947", +"CHEBI:132362", +"CHEBI:35804", +"CHEBI:23321", +"CHEBI:3727", +"CHEBI:35806" +], +"hmdb":[ +"HMDB00094" +], +"inchi_key":[ +"KRKNYBCHXYNGOX-UHFFFAOYSA-K" +], +"kegg.compound":[ +"C00158" +], +"kegg.drug":[ +"D00037" +], +"metanetx.chemical":[ +"MNXM131" +], +"reactome.compound":[ +"29654", +"433138", +"76190" +], +"sabiork":[ +"1952" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00137" +] +} +}, +{ +"id":"co2_c", +"name":"CO2 CO2", +"compartment":"c", +"charge":0, +"formula":"CO2", +"notes":{ +"original_bigg_ids":[ +"co2_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"co2" +], +"biocyc":[ +"META:CARBON-DIOXIDE" +], +"chebi":[ +"CHEBI:23011", +"CHEBI:3283", +"CHEBI:48829", +"CHEBI:16526", +"CHEBI:13283", +"CHEBI:13285", +"CHEBI:13284", +"CHEBI:13282" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379" +], +"hmdb":[ +"HMDB01967" +], +"inchi_key":[ +"CURLTUGMZLYLDI-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00011" +], +"kegg.drug":[ +"D00004" +], +"metanetx.chemical":[ +"MNXM13" +], +"reactome.compound":[ +"29376", +"5668565", +"189480", +"1132345", +"113528", +"1237009", +"159751", +"389536", +"159942" +], +"sabiork":[ +"1266" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00011" +] +} +}, +{ +"id":"co2_e", +"name":"CO2 CO2", +"compartment":"e", +"charge":0, +"formula":"CO2", +"notes":{ +"original_bigg_ids":[ +"co2_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"co2" +], +"biocyc":[ +"META:CARBON-DIOXIDE" +], +"chebi":[ +"CHEBI:23011", +"CHEBI:3283", +"CHEBI:48829", +"CHEBI:16526", +"CHEBI:13283", +"CHEBI:13285", +"CHEBI:13284", +"CHEBI:13282" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379" +], +"hmdb":[ +"HMDB01967" +], +"inchi_key":[ +"CURLTUGMZLYLDI-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00011" +], +"kegg.drug":[ +"D00004" +], +"metanetx.chemical":[ +"MNXM13" +], +"reactome.compound":[ +"29376", +"5668565", +"189480", +"1132345", +"113528", +"1237009", +"159751", +"389536", +"159942" +], +"sabiork":[ +"1266" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00011" +] +} +}, +{ +"id":"coa_c", +"name":"Coenzyme A", +"compartment":"c", +"charge":-4, +"formula":"C21H32N7O16P3S", +"notes":{ +"original_bigg_ids":[ +"coa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"coa" +], +"biocyc":[ +"META:COA-GROUP", +"META:CO-A" +], +"chebi":[ +"CHEBI:41631", +"CHEBI:41597", +"CHEBI:741566", +"CHEBI:23355", +"CHEBI:13295", +"CHEBI:13298", +"CHEBI:57287", +"CHEBI:15346", +"CHEBI:3771", +"CHEBI:13294" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/19310484-6aa5-4dcf-b1da-855a8c21ecfd" +], +"hmdb":[ +"HMDB01423", +"HMDB62184" +], +"inchi_key":[ +"RGJOEKWQDUBAIZ-IBOSZNHHSA-J" +], +"kegg.compound":[ +"C00010" +], +"metanetx.chemical":[ +"MNXM12" +], +"reactome.compound":[ +"193514", +"162743", +"2485002", +"1678675", +"29374", +"76194", +"8939024" +], +"sabiork":[ +"1265" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd22528", +"cpd00010" +] +} +}, +{ +"id":"dhap_c", +"name":"Dihydroxyacetone phosphate", +"compartment":"c", +"charge":-2, +"formula":"C3H5O6P", +"notes":{ +"original_bigg_ids":[ +"dhap_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"dhap" +], +"biocyc":[ +"META:DIHYDROXY-ACETONE-PHOSPHATE" +], +"chebi":[ +"CHEBI:14341", +"CHEBI:5454", +"CHEBI:16108", +"CHEBI:14342", +"CHEBI:24355", +"CHEBI:39571", +"CHEBI:57642" +], +"hmdb":[ +"HMDB11735", +"HMDB01473" +], +"inchi_key":[ +"GNGACRATGGDKBX-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00111" +], +"metanetx.chemical":[ +"MNXM77" +], +"reactome.compound":[ +"390404", +"75970", +"188451" +], +"sabiork":[ +"28" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00095" +] +} +}, +{ +"id":"e4p_c", +"name":"D-Erythrose 4-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C4H7O7P", +"notes":{ +"original_bigg_ids":[ +"e4p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"e4p" +], +"biocyc":[ +"META:ERYTHROSE-4P" +], +"chebi":[ +"CHEBI:4114", +"CHEBI:20927", +"CHEBI:12921", +"CHEBI:48153", +"CHEBI:16897", +"CHEBI:42349" +], +"hmdb":[ +"HMDB01321" +], +"inchi_key":[ +"NGHMDNPXVRFFGS-IUYQGCFVSA-L" +], +"kegg.compound":[ +"C00279" +], +"metanetx.chemical":[ +"MNXM258" +], +"reactome.compound":[ +"29878" +], +"sabiork":[ +"1324" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00236" +] +} +}, +{ +"id":"etoh_c", +"name":"Ethanol", +"compartment":"c", +"charge":0, +"formula":"C2H6O", +"notes":{ +"original_bigg_ids":[ +"etoh_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"etoh" +], +"biocyc":[ +"META:ETOH" +], +"chebi":[ +"CHEBI:42377", +"CHEBI:23978", +"CHEBI:30880", +"CHEBI:16236", +"CHEBI:52092", +"CHEBI:30878", +"CHEBI:4879", +"CHEBI:44594", +"CHEBI:14222" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/a4a354fd-5003-4b7b-b11b-f54204aea384", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/f89efe7c-1a6a-4d21-b99c-e3e1070a8062", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/56e18a05-c059-433a-94f6-0e26c01b010f", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9fb1fbdf-101b-4b82-a596-d2f52c870e4f" +], +"hmdb":[ +"HMDB00108" +], +"inchi_key":[ +"LFQSCWFLJHTTHZ-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00469" +], +"kegg.drug":[ +"D06542", +"D02798", +"D00068", +"D04855" +], +"metanetx.chemical":[ +"MNXM303" +], +"reactome.compound":[ +"113748", +"30203" +], +"sabiork":[ +"56" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00363" +] +} +}, +{ +"id":"etoh_e", +"name":"Ethanol", +"compartment":"e", +"charge":0, +"formula":"C2H6O", +"notes":{ +"original_bigg_ids":[ +"etoh_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"etoh" +], +"biocyc":[ +"META:ETOH" +], +"chebi":[ +"CHEBI:42377", +"CHEBI:23978", +"CHEBI:30880", +"CHEBI:16236", +"CHEBI:52092", +"CHEBI:30878", +"CHEBI:4879", +"CHEBI:44594", +"CHEBI:14222" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/a4a354fd-5003-4b7b-b11b-f54204aea384", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/f89efe7c-1a6a-4d21-b99c-e3e1070a8062", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/56e18a05-c059-433a-94f6-0e26c01b010f", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9fb1fbdf-101b-4b82-a596-d2f52c870e4f" +], +"hmdb":[ +"HMDB00108" +], +"inchi_key":[ +"LFQSCWFLJHTTHZ-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00469" +], +"kegg.drug":[ +"D06542", +"D02798", +"D00068", +"D04855" +], +"metanetx.chemical":[ +"MNXM303" +], +"reactome.compound":[ +"113748", +"30203" +], +"sabiork":[ +"56" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00363" +] +} +}, +{ +"id":"f6p_c", +"name":"D-Fructose 6-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C6H11O9P", +"notes":{ +"original_bigg_ids":[ +"f6p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"f6p" +], +"biocyc":[ +"META:FRUCTOSE-6P" +], +"chebi":[ +"CHEBI:16084", +"CHEBI:12352", +"CHEBI:57634", +"CHEBI:22768", +"CHEBI:10375", +"CHEBI:42378" +], +"hmdb":[ +"HMDB03971" +], +"inchi_key":[ +"BGWGXPAPYGQALX-ARQDHWQXSA-L" +], +"kegg.compound":[ +"C05345" +], +"metanetx.chemical":[ +"MNXM89621" +], +"sabiork":[ +"25" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19035" +] +} +}, +{ +"id":"fdp_c", +"name":"D-Fructose 1,6-bisphosphate", +"compartment":"c", +"charge":-4, +"formula":"C6H10O12P2", +"notes":{ +"original_bigg_ids":[ +"fdp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fdp" +], +"chebi":[ +"CHEBI:37736", +"CHEBI:49299" +], +"inchi_key":[ +"RNBGYGVWRKECFJ-VRPWFDPXSA-J" +], +"kegg.compound":[ +"C00354" +], +"metanetx.chemical":[ +"MNXM417" +], +"sabiork":[ +"1465" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00290" +] +} +}, +{ +"id":"for_c", +"name":"Formate", +"compartment":"c", +"charge":-1, +"formula":"CH1O2", +"notes":{ +"original_bigg_ids":[ +"for_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"for" +], +"biocyc":[ +"META:CPD1G-1532", +"META:CPD1G-1535", +"META:FORMATE", +"META:CPD-9845", +"META:CPD1G-1534", +"META:CARBOXYL-GROUP", +"META:CPD1G-1533" +], +"chebi":[ +"CHEBI:24081", +"CHEBI:30751", +"CHEBI:15740", +"CHEBI:5145", +"CHEBI:42460", +"CHEBI:14276", +"CHEBI:24082" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/9a9d20ae-b6ec-40a9-93ca-1de20597b1ed", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/09c1ad08-016e-4477-8840-b97a031eae23", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/bf16ab32-cb3c-4427-a65a-089ab754823e", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/34fe3cd9-9b0b-46b0-a1c5-8a66509f1919", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/1d077cf2-3f9f-4163-aa49-0fca1b2b3ab3" +], +"hmdb":[ +"HMDB00142" +], +"inchi_key":[ +"BDAGIHXWWSANSR-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00058" +], +"metanetx.chemical":[ +"MNXM39" +], +"reactome.compound":[ +"29460", +"194712", +"389585", +"6801451" +], +"sabiork":[ +"1285" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00047", +"cpd22511" +] +} +}, +{ +"id":"for_e", +"name":"Formate", +"compartment":"e", +"charge":-1, +"formula":"CH1O2", +"notes":{ +"original_bigg_ids":[ +"for_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"for" +], +"biocyc":[ +"META:CPD1G-1532", +"META:CPD1G-1535", +"META:FORMATE", +"META:CPD-9845", +"META:CPD1G-1534", +"META:CARBOXYL-GROUP", +"META:CPD1G-1533" +], +"chebi":[ +"CHEBI:24081", +"CHEBI:30751", +"CHEBI:15740", +"CHEBI:5145", +"CHEBI:42460", +"CHEBI:14276", +"CHEBI:24082" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/9a9d20ae-b6ec-40a9-93ca-1de20597b1ed", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/09c1ad08-016e-4477-8840-b97a031eae23", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/bf16ab32-cb3c-4427-a65a-089ab754823e", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/34fe3cd9-9b0b-46b0-a1c5-8a66509f1919", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/1d077cf2-3f9f-4163-aa49-0fca1b2b3ab3" +], +"hmdb":[ +"HMDB00142" +], +"inchi_key":[ +"BDAGIHXWWSANSR-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00058" +], +"metanetx.chemical":[ +"MNXM39" +], +"reactome.compound":[ +"29460", +"194712", +"389585", +"6801451" +], +"sabiork":[ +"1285" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00047", +"cpd22511" +] +} +}, +{ +"id":"fru_e", +"name":"D-Fructose", +"compartment":"e", +"charge":0, +"formula":"C6H12O6", +"notes":{ +"original_bigg_ids":[ +"fru_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fru" +], +"biocyc":[ +"META:D-Fructopyranose", +"META:Fructofuranose", +"META:CPD-15382", +"META:FRU" +], +"chebi":[ +"CHEBI:47424", +"CHEBI:28757", +"CHEBI:24110", +"CHEBI:20929", +"CHEBI:4119", +"CHEBI:15824", +"CHEBI:5172", +"CHEBI:24104", +"CHEBI:12923", +"CHEBI:4118", +"CHEBI:37714", +"CHEBI:37721", +"CHEBI:48095" +], +"hmdb":[ +"HMDB62538" +], +"inchi_key":[ +"RFSUNEUAIZKAJO-VRPWFDPXSA-N" +], +"kegg.compound":[ +"C01496", +"C05003", +"C00095", +"C10906" +], +"kegg.drug":[ +"D00114" +], +"metanetx.chemical":[ +"MNXM175" +], +"reactome.compound":[ +"189049", +"29532" +], +"sabiork":[ +"25055", +"1463", +"1464" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00082", +"cpd19015", +"cpd27040" +] +} +}, +{ +"id":"fum_c", +"name":"Fumarate", +"compartment":"c", +"charge":-2, +"formula":"C4H2O4", +"notes":{ +"original_bigg_ids":[ +"fum_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fum" +], +"biocyc":[ +"META:FUM" +], +"chebi":[ +"CHEBI:36180", +"CHEBI:37155", +"CHEBI:42511", +"CHEBI:5190", +"CHEBI:18012", +"CHEBI:42743", +"CHEBI:22956", +"CHEBI:22957", +"CHEBI:24124", +"CHEBI:14284", +"CHEBI:37154", +"CHEBI:29806", +"CHEBI:22958", +"CHEBI:24122" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b" +], +"hmdb":[ +"HMDB00134" +], +"inchi_key":[ +"VZCYOOQTPOCHFL-OWOJBTEDSA-L" +], +"kegg.compound":[ +"C00122" +], +"kegg.drug":[ +"D02308" +], +"metanetx.chemical":[ +"MNXM93" +], +"reactome.compound":[ +"113588", +"29586" +], +"sabiork":[ +"1910" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00106" +] +} +}, +{ +"id":"fum_e", +"name":"Fumarate", +"compartment":"e", +"charge":-2, +"formula":"C4H2O4", +"notes":{ +"original_bigg_ids":[ +"fum_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fum" +], +"biocyc":[ +"META:FUM" +], +"chebi":[ +"CHEBI:36180", +"CHEBI:37155", +"CHEBI:42511", +"CHEBI:5190", +"CHEBI:18012", +"CHEBI:42743", +"CHEBI:22956", +"CHEBI:22957", +"CHEBI:24124", +"CHEBI:14284", +"CHEBI:37154", +"CHEBI:29806", +"CHEBI:22958", +"CHEBI:24122" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b" +], +"hmdb":[ +"HMDB00134" +], +"inchi_key":[ +"VZCYOOQTPOCHFL-OWOJBTEDSA-L" +], +"kegg.compound":[ +"C00122" +], +"kegg.drug":[ +"D02308" +], +"metanetx.chemical":[ +"MNXM93" +], +"reactome.compound":[ +"113588", +"29586" +], +"sabiork":[ +"1910" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00106" +] +} +}, +{ +"id":"g3p_c", +"name":"Glyceraldehyde 3-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C3H5O6P", +"notes":{ +"original_bigg_ids":[ +"g3p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"g3p" +], +"biocyc":[ +"META:GAP" +], +"chebi":[ +"CHEBI:5446", +"CHEBI:14333", +"CHEBI:12984", +"CHEBI:181", +"CHEBI:17138", +"CHEBI:21026", +"CHEBI:12983", +"CHEBI:18324", +"CHEBI:58027", +"CHEBI:59776", +"CHEBI:29052" +], +"hmdb":[ +"HMDB01112" +], +"inchi_key":[ +"LXJXRIRHZLFYRP-VKHMYHEASA-L" +], +"kegg.compound":[ +"C00661", +"C00118" +], +"metanetx.chemical":[ +"MNXM74" +], +"reactome.compound":[ +"29578" +], +"sabiork":[ +"27", +"1687" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00102", +"cpd19005" +] +} +}, +{ +"id":"g6p_c", +"name":"D-Glucose 6-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C6H11O9P", +"notes":{ +"original_bigg_ids":[ +"g6p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"g6p" +], +"biocyc":[ +"META:D-glucopyranose-6-phosphate" +], +"chebi":[ +"CHEBI:61548", +"CHEBI:14314", +"CHEBI:4170" +], +"hmdb":[ +"HMDB01549", +"HMDB01401", +"HMDB06793" +], +"inchi_key":[ +"NBSCHQHZLSJFNQ-GASJEMHNSA-L" +], +"kegg.compound":[ +"C00092" +], +"metanetx.chemical":[ +"MNXM160" +], +"reactome.compound":[ +"1629756" +], +"sabiork":[ +"1404", +"1405" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00079", +"cpd26836" +] +} +} +], +"reactions":[ +{ +"id":"PFK", +"name":"Phosphofructokinase", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"f6p_c":-1.0, +"fdp_c":1.0, +"h_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3916 or b1723", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PFK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PFK" +], +"ec-code":[ +"2.7.1.11" +], +"metanetx.reaction":[ +"MNXR102507" +], +"rhea":[ +"16111", +"16109", +"16110", +"16112" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"PFL", +"name":"Pyruvate formate lyase", +"metabolites":{ +"accoa_c":1.0, +"coa_c":-1.0, +"for_c":1.0, +"pyr_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"((b0902 and b0903) and b2579) or (b0902 and b0903) or (b0902 and b3114) or (b3951 and b3952)", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"PFL" +] +}, +"annotation":{ +"bigg.reaction":[ +"PFL" +], +"biocyc":[ +"META:PYRUVFORMLY-RXN" +], +"ec-code":[ +"2.3.1.54" +], +"kegg.reaction":[ +"R00212" +], +"metanetx.reaction":[ +"MNXR102514" +], +"rhea":[ +"11847", +"11845", +"11844", +"11846" +], +"sabiork":[ +"146" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00157" +] +} +}, +{ +"id":"PGI", +"name":"Glucose-6-phosphate isomerase", +"metabolites":{ +"f6p_c":1.0, +"g6p_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4025", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PGI" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGI" +], +"biocyc":[ +"META:PGLUCISOM-RXN" +], +"ec-code":[ +"5.3.1.9" +], +"metanetx.reaction":[ +"MNXR102535" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"PGK", +"name":"Phosphoglycerate kinase", +"metabolites":{ +"13dpg_c":1.0, +"3pg_c":-1.0, +"adp_c":1.0, +"atp_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2926", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PGK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGK" +], +"biocyc":[ +"META:PHOSGLYPHOS-RXN" +], +"ec-code":[ +"2.7.2.3" +], +"kegg.reaction":[ +"R01512" +], +"metanetx.reaction":[ +"MNXR102538" +], +"reactome.reaction":[ +"R-ATH-71850", +"R-DME-71850", +"R-GGA-71850", +"R-SPO-71850", +"R-OSA-71850", +"R-GGA-353039", +"R-GGA-353023", +"R-BTA-71850", +"R-CFA-70486", +"R-MMU-71850", +"R-DME-70486", +"R-PFA-71850", +"R-SPO-70486", +"R-SCE-70486", +"R-PFA-70486", +"R-SSC-70486", +"R-ATH-70486", +"R-DRE-70486", +"R-HSA-70486", +"R-OSA-70486", +"R-XTR-71850", +"R-MMU-70486", +"R-RNO-70486", +"R-TGU-70486", +"R-DRE-71850", +"R-SSC-71850", +"R-SCE-71850", +"R-CFA-71850", +"R-XTR-70486", +"R-DDI-70486", +"R-DDI-71850", +"R-RNO-71850", +"R-BTA-70486", +"R-CEL-70486", +"R-HSA-71850", +"R-CEL-71850", +"R-GGA-70486", +"R-TGU-71850" +], +"rhea":[ +"14801", +"14804", +"14802", +"14803" +], +"sabiork":[ +"7644" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01100" +] +} +}, +{ +"id":"PGL", +"name":"6-phosphogluconolactonase", +"metabolites":{ +"6pgc_c":1.0, +"6pgl_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0767", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"PGL" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGL" +], +"biocyc":[ +"META:6PGLUCONOLACT-RXN" +], +"ec-code":[ +"3.1.1.31" +], +"kegg.reaction":[ +"R02035" +], +"metanetx.reaction":[ +"MNXR102539" +], +"reactome.reaction":[ +"R-OSA-71296", +"R-CFA-71296", +"R-CEL-71296", +"R-GGA-71296", +"R-MMU-71296", +"R-SSC-71296", +"R-BTA-71296", +"R-ATH-71296", +"R-DME-71296", +"R-DRE-71296", +"R-SCE-71296", +"R-HSA-71296", +"R-XTR-71296", +"R-RNO-71296", +"R-DDI-71296", +"R-SPO-71296" +], +"rhea":[ +"12559", +"12556", +"12557", +"12558" +], +"sabiork":[ +"109" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01476" +] +} +}, +{ +"id":"ACALD", +"name":"Acetaldehyde dehydrogenase (acetylating)", +"metabolites":{ +"acald_c":-1.0, +"accoa_c":1.0, +"coa_c":-1.0, +"h_c":1.0, +"nad_c":-1.0, +"nadh_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0351 or b1241", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"ACALD" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACALD" +], +"biocyc":[ +"META:ACETALD-DEHYDROG-RXN" +], +"ec-code":[ +"1.2.1.10" +], +"kegg.reaction":[ +"R00228" +], +"metanetx.reaction":[ +"MNXR95210" +], +"rhea":[ +"23290", +"23291", +"23289", +"23288" +], +"sabiork":[ +"163" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00171" +] +} +}, +{ +"id":"AKGt2r", +"name":"2 oxoglutarate reversible transport via symport", +"metabolites":{ +"akg_c":1.0, +"akg_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2587", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"AKGt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"AKGt2r" +], +"biocyc":[ +"META:TRANS-RXN-23" +], +"metanetx.reaction":[ +"MNXR95661" +], +"rhea":[ +"29011", +"29013", +"29012", +"29014" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05493", +"rxn08095", +"rxn09827" +] +} +}, +{ +"id":"PGM", +"name":"Phosphoglycerate mutase", +"metabolites":{ +"2pg_c":-1.0, +"3pg_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3612 or b4395 or b0755", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PGM" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGM" +], +"biocyc":[ +"META:3PGAREARR-RXN", +"META:RXN-15513" +], +"ec-code":[ +"5.4.2.1", +"5.4.2.11", +"5.4.2.12" +], +"kegg.reaction":[ +"R01518" +], +"metanetx.reaction":[ +"MNXR102547" +], +"reactome.reaction":[ +"R-XTR-71654", +"R-SSC-71654", +"R-DME-71445", +"R-XTR-71445", +"R-RNO-71445", +"R-GGA-71654", +"R-SSC-71445", +"R-GGA-71445", +"R-DDI-71654", +"R-SPO-71654", +"R-MMU-71445", +"R-BTA-71445", +"R-CFA-71445", +"R-PFA-71445", +"R-GGA-352994", +"R-TGU-71654", +"R-SPO-71445", +"R-HSA-71445", +"R-ATH-71654", +"R-MMU-71654", +"R-BTA-71654", +"R-GGA-353014", +"R-DRE-71654", +"R-HSA-71654", +"R-CFA-71654", +"R-OSA-71654", +"R-DDI-71445", +"R-RNO-71654", +"R-DRE-71445", +"R-OSA-71445", +"R-PFA-71654", +"R-DME-71654", +"R-TGU-71445", +"R-SCE-71445", +"R-ATH-71445", +"R-SCE-71654" +], +"rhea":[ +"15902", +"15903", +"15901", +"15904" +], +"sabiork":[ +"7641" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01106" +] +} +}, +{ +"id":"PIt2r", +"name":"Phosphate reversible transport via symport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"pi_c":1.0, +"pi_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2987 or b3493", +"subsystem":"Inorganic Ion Transport and Metabolism", +"notes":{ +"original_bigg_ids":[ +"PIt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"PIt2r" +], +"biocyc":[ +"META:TRANS-RXN-114" +], +"metanetx.reaction":[ +"MNXR102872" +], +"rhea":[ +"29939", +"29941", +"29940", +"29942" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05312", +"rxn09833", +"rxn09811", +"rxn09872", +"rxn09723", +"rxn09120" +] +} +}, +{ +"id":"ALCD2x", +"name":"Alcohol dehydrogenase (ethanol)", +"metabolites":{ +"acald_c":1.0, +"etoh_c":-1.0, +"h_c":1.0, +"nad_c":-1.0, +"nadh_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0356 or b1478 or b1241", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"ALCD2x" +] +}, +"annotation":{ +"bigg.reaction":[ +"ALCD2x" +], +"biocyc":[ +"META:ALCOHOL-DEHYDROG-RXN" +], +"ec-code":[ +"1.1.1.71", +"1.1.1.1" +], +"kegg.reaction":[ +"R00754" +], +"metanetx.reaction":[ +"MNXR95725" +], +"reactome.reaction":[ +"R-MMU-71707", +"R-XTR-71707", +"R-CFA-71707", +"R-OSA-71707", +"R-RNO-71707", +"R-HSA-71707", +"R-SSC-71707", +"R-GGA-71707", +"R-SPO-71707", +"R-DME-71707", +"R-DRE-71707", +"R-BTA-71707", +"R-ATH-71707", +"R-SCE-71707", +"R-TGU-71707", +"R-CEL-71707", +"R-DDI-71707" +], +"rhea":[ +"25292", +"25290", +"25291", +"25293" +], +"sabiork":[ +"597" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00543" +] +} +}, +{ +"id":"ACALDt", +"name":"Acetaldehyde reversible transport", +"metabolites":{ +"acald_c":1.0, +"acald_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"ACALDt" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACALDt" +], +"metanetx.reaction":[ +"MNXR95212" +], +"reactome.reaction":[ +"R-HSA-449872" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09700", +"rxn08033", +"rxn13212", +"rxn08032" +] +} +}, +{ +"id":"ACKr", +"name":"Acetate kinase", +"metabolites":{ +"ac_c":-1.0, +"actp_c":1.0, +"adp_c":1.0, +"atp_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3115 or b2296 or b1849", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"ACKr" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACKr" +], +"biocyc":[ +"META:ACETATEKIN-RXN" +], +"ec-code":[ +"2.7.2.15", +"2.7.2.1" +], +"kegg.reaction":[ +"R00315" +], +"metanetx.reaction":[ +"MNXR95269" +], +"rhea":[ +"11354", +"11355", +"11353", +"11352" +], +"sabiork":[ +"71" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00225" +] +} +}, +{ +"id":"PPC", +"name":"Phosphoenolpyruvate carboxylase", +"metabolites":{ +"co2_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"oaa_c":1.0, +"pep_c":-1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3956", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"PPC" +] +}, +"annotation":{ +"bigg.reaction":[ +"PPC" +], +"ec-code":[ +"4.1.1.31" +], +"kegg.reaction":[ +"R00345" +], +"metanetx.reaction":[ +"MNXR103096" +], +"rhea":[ +"23073", +"23072", +"23075", +"23074" +], +"sabiork":[ +"150" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00251" +] +} +}, +{ +"id":"ACONTa", +"name":"Aconitase (half-reaction A, Citrate hydro-lyase)", +"metabolites":{ +"acon_C_c":1.0, +"cit_c":-1.0, +"h2o_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0118 or b1276", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"ACONTa" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACONTa" +], +"biocyc":[ +"META:ACONITATEDEHYDR-RXN" +], +"ec-code":[ +"4.2.1.3" +], +"kegg.reaction":[ +"R01325" +], +"metanetx.reaction":[ +"MNXR95386" +], +"rhea":[ +"10230", +"10229", +"10231", +"10228" +], +"sabiork":[ +"268" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00974" +] +} +}, +{ +"id":"ACONTb", +"name":"Aconitase (half-reaction B, Isocitrate hydro-lyase)", +"metabolites":{ +"acon_C_c":-1.0, +"h2o_c":-1.0, +"icit_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0118 or b1276", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"ACONTb" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACONTb" +], +"ec-code":[ +"4.2.1.3" +], +"kegg.reaction":[ +"R01900" +], +"metanetx.reaction":[ +"MNXR95387" +], +"rhea":[ +"22145", +"22144", +"22146", +"22147" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01388" +] +} +}, +{ +"id":"ATPM", +"name":"ATP maintenance requirement", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"pi_c":1.0 +}, +"lower_bound":8.39, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Biomass and maintenance functions", +"notes":{ +"original_bigg_ids":[ +"ATPM" +] +}, +"annotation":{ +"bigg.reaction":[ +"ATPM" +], +"biocyc":[ +"META:ATPASE-RXN" +], +"ec-code":[ +"3.6.1.5", +"3.6.3.34", +"3.6.3.20", +"3.6.3.53", +"3.6.3.8", +"3.6.3.32", +"3.6.4.12", +"3.6.3.48", +"3.6.3.40", +"3.6.3.9", +"3.6.3.23", +"3.6.3.22", +"3.6.3.54", +"3.6.3.1", +"3.6.1.8", +"3.6.3.29", +"3.6.3.17", +"3.6.3.50", +"3.6.3.39", +"3.6.3.19", +"3.6.3.4", +"3.6.3.35", +"3.6.3.16", +"3.6.4.4", +"3.6.3.37", +"3.6.4.8", +"3.6.3.31", +"3.6.3.6", +"3.6.4.5", +"3.6.3.52", +"3.6.3.2", +"3.6.3.14", +"3.6.3.51", +"3.6.3.25", +"3.6.3.38", +"3.6.3.33", +"3.6.3.43", +"3.6.4.10", +"3.6.4.13", +"3.6.3.3", +"3.6.3.10", +"3.6.3.24", +"3.6.3.44", +"3.6.3.15", +"3.6.3.5", +"3.6.1.3", +"3.6.1.15", +"3.6.4.2", +"3.6.4.3", +"3.6.3.42", +"3.6.3.11", +"3.6.3.28", +"3.6.3.30", +"3.6.4.1", +"3.6.4.11", +"3.6.3.47", +"3.6.4.6", +"3.6.3.36", +"3.6.3.21", +"3.6.3.12", +"3.6.3.18", +"3.6.3.26", +"3.6.3.27", +"3.6.3.7", +"3.6.4.9", +"3.6.4.7", +"3.6.3.46", +"3.6.3.41", +"3.6.3.49" +], +"kegg.reaction":[ +"R00086" +], +"metanetx.reaction":[ +"MNXR96131" +], +"rhea":[ +"13066", +"13065", +"13068", +"13067" +], +"sabiork":[ +"75" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn11300", +"rxn09694", +"rxn00062" +] +} +}, +{ +"id":"PPCK", +"name":"Phosphoenolpyruvate carboxykinase", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"co2_c":1.0, +"oaa_c":-1.0, +"pep_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3403", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"PPCK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PPCK" +], +"biocyc":[ +"META:PEPCARBOXYKIN-RXN" +], +"ec-code":[ +"4.1.1.49" +], +"kegg.reaction":[ +"R00341" +], +"metanetx.reaction":[ +"MNXR103099" +], +"rhea":[ +"18620", +"18618", +"18617", +"18619" +], +"sabiork":[ +"151" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00247" +] +} +}, +{ +"id":"ACt2r", +"name":"Acetate reversible transport via proton symport", +"metabolites":{ +"ac_c":1.0, +"ac_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"ACt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACt2r" +], +"biocyc":[ +"META:TRANS-RXN0-571" +], +"metanetx.reaction":[ +"MNXR95429" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08061", +"rxn05488" +] +} +}, +{ +"id":"PPS", +"name":"Phosphoenolpyruvate synthase", +"metabolites":{ +"amp_c":1.0, +"atp_c":-1.0, +"h2o_c":-1.0, +"h_c":2.0, +"pep_c":1.0, +"pi_c":1.0, +"pyr_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1702", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PPS" +] +}, +"annotation":{ +"bigg.reaction":[ +"PPS" +], +"biocyc":[ +"META:PEPSYNTH-RXN" +], +"ec-code":[ +"2.7.9.2" +], +"kegg.reaction":[ +"R00199" +], +"metanetx.reaction":[ +"MNXR103140" +], +"rhea":[ +"11364", +"11367", +"11366", +"11365" +], +"sabiork":[ +"148" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00147" +] +} +}, +{ +"id":"ADK1", +"name":"Adenylate kinase", +"metabolites":{ +"adp_c":2.0, +"amp_c":-1.0, +"atp_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0474", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"ADK1" +] +}, +"annotation":{ +"bigg.reaction":[ +"ADK1" +], +"biocyc":[ +"META:ADENYL-KIN-RXN" +], +"ec-code":[ +"2.7.4.3" +], +"kegg.reaction":[ +"R00127" +], +"metanetx.reaction":[ +"MNXR95450" +], +"reactome.reaction":[ +"R-ATH-110145", +"R-SSC-110144", +"R-ATH-110144", +"R-SSC-110145", +"R-GGA-110145", +"R-PFA-110144", +"R-HSA-110145", +"R-RNO-110144", +"R-OSA-110145", +"R-SCE-110145", +"R-RNO-110145", +"R-XTR-110144", +"R-SCE-110144", +"R-PFA-110145", +"R-OSA-110144", +"R-HSA-110144", +"R-BTA-110144", +"R-DRE-110145", +"R-DRE-110144", +"R-SPO-110145", +"R-CEL-110144", +"R-CFA-110144", +"R-XTR-110145", +"R-MMU-110144", +"R-DME-110144", +"R-SPO-110144", +"R-DDI-110145", +"R-GGA-110144", +"R-TGU-110144", +"R-BTA-110145", +"R-CEL-110145", +"R-CFA-110145", +"R-DME-110145", +"R-TGU-110145", +"R-DDI-110144", +"R-MMU-110145" +], +"rhea":[ +"12975", +"12973", +"12976", +"12974" +], +"sabiork":[ +"82" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00097" +] +} +}, +{ +"id":"AKGDH", +"name":"2-Oxogluterate dehydrogenase", +"metabolites":{ +"akg_c":-1.0, +"co2_c":1.0, +"coa_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"succoa_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0116 and b0726 and b0727", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"AKGDH" +] +}, +"annotation":{ +"bigg.reaction":[ +"AKGDH" +], +"biocyc":[ +"META:2OXOGLUTARATEDEH-RXN" +], +"ec-code":[ +"1.2.1.52", +"2.3.1.61", +"1.8.1.4", +"1.2.4.2" +], +"kegg.reaction":[ +"R08549" +], +"metanetx.reaction":[ +"MNXR95655" +], +"reactome.reaction":[ +"R-PFA-71401", +"R-XTR-71401", +"R-SCE-71401", +"R-SSC-71401", +"R-TGU-71401", +"R-ATH-71401", +"R-OSA-71401", +"R-SPO-71401", +"R-CEL-71401", +"R-RNO-71401", +"R-DRE-71401", +"R-GGA-373042", +"R-DDI-71401", +"R-CFA-71401", +"R-HSA-71401", +"R-BTA-71401", +"R-DME-71401", +"R-MMU-71401", +"R-GGA-71401" +], +"rhea":[ +"27789", +"27788", +"27786", +"27787" +], +"sabiork":[ +"8163" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn08094" +] +} +}, +{ +"id":"ATPS4r", +"name":"ATP synthase (four protons for one ATP)", +"metabolites":{ +"adp_c":-1.0, +"atp_c":1.0, +"h2o_c":1.0, +"h_c":3.0, +"h_e":-4.0, +"pi_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"((b3736 and b3737 and b3738) and (b3731 and b3732 and b3733 and b3734 and b3735)) or ((b3736 and b3737 and b3738) and (b3731 and b3732 and b3733 and b3734 and b3735) and b3739)", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"ATPS4r" +] +}, +"annotation":{ +"bigg.reaction":[ +"ATPS4r" +], +"biocyc":[ +"META:ATPSYN-RXN" +], +"ec-code":[ +"3.6.3.14" +], +"metanetx.reaction":[ +"MNXR96136" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08173", +"rxn10042" +] +} +}, +{ +"id":"PTAr", +"name":"Phosphotransacetylase", +"metabolites":{ +"accoa_c":-1.0, +"actp_c":1.0, +"coa_c":1.0, +"pi_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2297 or b2458", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"PTAr" +] +}, +"annotation":{ +"bigg.reaction":[ +"PTAr" +], +"biocyc":[ +"META:PHOSACETYLTRANS-RXN" +], +"ec-code":[ +"2.3.1.8" +], +"kegg.reaction":[ +"R00230" +], +"metanetx.reaction":[ +"MNXR103319" +], +"rhea":[ +"19521", +"19523", +"19522", +"19524" +], +"sabiork":[ +"72" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00173" +] +} +}, +{ +"id":"PYK", +"name":"Pyruvate kinase", +"metabolites":{ +"adp_c":-1.0, +"atp_c":1.0, +"h_c":-1.0, +"pep_c":-1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1854 or b1676", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PYK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PYK" +], +"biocyc":[ +"META:PEPDEPHOS-RXN" +], +"ec-code":[ +"2.7.1.40" +], +"kegg.reaction":[ +"R00200" +], +"metanetx.reaction":[ +"MNXR103371" +], +"reactome.reaction":[ +"R-SSC-71670", +"R-GGA-353056", +"R-DRE-71670", +"R-OSA-71670", +"R-SPO-71670", +"R-DDI-71670", +"R-SCE-71670", +"R-CEL-71670", +"R-PFA-71670", +"R-HSA-71670", +"R-TGU-71670", +"R-DME-71670", +"R-ATH-71670", +"R-BTA-71670", +"R-MMU-71670", +"R-RNO-71670", +"R-GGA-71670", +"R-CFA-71670", +"R-XTR-71670" +], +"rhea":[ +"18160", +"18159", +"18158", +"18157" +], +"sabiork":[ +"9" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00148" +] +} +}, +{ +"id":"BIOMASS_Ecoli_core_w_GAM", +"name":"Biomass Objective Function with GAM", +"metabolites":{ +"3pg_c":-1.496, +"accoa_c":-3.7478, +"adp_c":59.81, +"akg_c":4.1182, +"atp_c":-59.81, +"coa_c":3.7478, +"e4p_c":-0.361, +"f6p_c":-0.0709, +"g3p_c":-0.129, +"g6p_c":-0.205, +"gln__L_c":-0.2557, +"glu__L_c":-4.9414, +"h2o_c":-59.81, +"h_c":59.81, +"nad_c":-3.547, +"nadh_c":3.547, +"nadp_c":13.0279, +"nadph_c":-13.0279, +"oaa_c":-1.7867, +"pep_c":-0.5191, +"pi_c":59.81, +"pyr_c":-2.8328, +"r5p_c":-0.8977 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"objective_coefficient":1.0, +"subsystem":"Biomass and maintenance functions", +"notes":{ +"original_bigg_ids":[ +"Biomass_Ecoli_core_w_GAM" +] +}, +"annotation":{ +"bigg.reaction":[ +"BIOMASS_Ecoli_core_w_GAM" +], +"metanetx.reaction":[ +"MNXR96280" +], +"sbo":"SBO:0000629" +} +}, +{ +"id":"PYRt2", +"name":"Pyruvate transport in via proton symport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"pyr_c":1.0, +"pyr_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"PYRt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"PYRt2" +], +"metanetx.reaction":[ +"MNXR103385" +], +"reactome.reaction":[ +"R-RNO-372347", +"R-HSA-372342", +"R-GGA-372359" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05469", +"rxn09832", +"rxn09717", +"rxn09217" +] +} +}, +{ +"id":"CO2t", +"name":"CO2 transporter via diffusion", +"metabolites":{ +"co2_c":1.0, +"co2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"CO2t" +] +}, +"annotation":{ +"bigg.reaction":[ +"CO2t" +], +"biocyc":[ +"META:TRANS-RXN0-545" +], +"metanetx.reaction":[ +"MNXR96810" +], +"reactome.reaction":[ +"R-DDI-1247645", +"R-CFA-1237069", +"R-TGU-1247649", +"R-CFA-1237042", +"R-CEL-1247645", +"R-XTR-1237069", +"R-HSA-1247645", +"R-OSA-1237042", +"R-GGA-1237042", +"R-BTA-1247645", +"R-GGA-1247649", +"R-RNO-1247645", +"R-XTR-1247645", +"R-TGU-1237042", +"R-SCE-1247649", +"R-MMU-1247649", +"R-CFA-1247649", +"R-GGA-1247645", +"R-SSC-1247645", +"R-BTA-1237069", +"R-RNO-1237069", +"R-SCE-1237042", +"R-DDI-1247649", +"R-SSC-1237042", +"R-DRE-1247649", +"R-DRE-1237042", +"R-DDI-1237042", +"R-DME-1237042", +"R-MMU-1237042", +"R-SSC-1247649", +"R-TGU-1237069", +"R-BTA-1247649", +"R-CFA-1247645", +"R-RNO-1247649", +"R-HSA-1237069", +"R-CEL-1237069", +"R-DDI-1237069", +"R-MMU-1237069", +"R-DME-1247645", +"R-ATH-1237042", +"R-OSA-1247649", +"R-HSA-1237042", +"R-DRE-1247645", +"R-HSA-1247649", +"R-MMU-1247645", +"R-DME-1237069", +"R-RNO-1237042", +"R-TGU-1247645", +"R-BTA-1237042", +"R-GGA-1237069", +"R-DME-1247649", +"R-SSC-1237069", +"R-DRE-1237069", +"R-ATH-1247649" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05467", +"rxn08237", +"rxn09706", +"rxn09821", +"rxn09775", +"rxn09876", +"rxn08238", +"rxn09860" +] +} +}, +{ +"id":"RPE", +"name":"Ribulose 5-phosphate 3-epimerase", +"metabolites":{ +"ru5p__D_c":-1.0, +"xu5p__D_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3386 or b4301", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"RPE" +] +}, +"annotation":{ +"bigg.reaction":[ +"RPE" +], +"biocyc":[ +"META:RIBULP3EPIM-RXN" +], +"ec-code":[ +"5.1.3.1" +], +"kegg.reaction":[ +"R01529" +], +"metanetx.reaction":[ +"MNXR104083" +], +"reactome.reaction":[ +"R-SPO-71303", +"R-CFA-199803", +"R-ATH-71303", +"R-SCE-71303", +"R-CFA-71303", +"R-DME-199803", +"R-XTR-199803", +"R-SSC-199803", +"R-GGA-199803", +"R-TGU-71303", +"R-OSA-199803", +"R-SSC-71303", +"R-MMU-71303", +"R-OSA-71303", +"R-HSA-71303", +"R-MMU-199803", +"R-XTR-71303", +"R-SPO-199803", +"R-SCE-199803", +"R-DDI-71303", +"R-RNO-71303", +"R-DME-71303", +"R-HSA-199803", +"R-DRE-71303", +"R-PFA-199803", +"R-CEL-199803", +"R-RNO-199803", +"R-PFA-71303", +"R-CEL-71303", +"R-TGU-199803", +"R-GGA-71303", +"R-DDI-199803", +"R-BTA-71303", +"R-ATH-199803", +"R-DRE-199803", +"R-BTA-199803" +], +"rhea":[ +"13677", +"13680", +"13678", +"13679" +], +"sabiork":[ +"62" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01116" +] +} +}, +{ +"id":"CS", +"name":"Citrate synthase", +"metabolites":{ +"accoa_c":-1.0, +"cit_c":1.0, +"coa_c":1.0, +"h2o_c":-1.0, +"h_c":1.0, +"oaa_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0720", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"CS" +] +}, +"annotation":{ +"bigg.reaction":[ +"CS" +], +"biocyc":[ +"META:CITSYN-RXN", +"META:RXN-14905" +], +"ec-code":[ +"2.3.3.16", +"2.3.3.1", +"2.3.3.3" +], +"kegg.reaction":[ +"R00351" +], +"metanetx.reaction":[ +"MNXR96920" +], +"reactome.reaction":[ +"R-GGA-373006", +"R-GGA-70975", +"R-CEL-70975", +"R-HSA-70975", +"R-DRE-70975", +"R-MMU-70975", +"R-ATH-70975", +"R-SPO-70975", +"R-OSA-70975", +"R-SCE-70975", +"R-SSC-70975", +"R-DDI-70975", +"R-RNO-70975", +"R-DME-70975", +"R-PFA-70975", +"R-XTR-70975", +"R-CFA-70975", +"R-BTA-70975" +], +"rhea":[ +"16847", +"16846", +"16845", +"16848" +], +"sabiork":[ +"267" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00256" +] +} +}, +{ +"id":"RPI", +"name":"Ribose-5-phosphate isomerase", +"metabolites":{ +"r5p_c":-1.0, +"ru5p__D_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2914 or b4090", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"RPI" +] +}, +"annotation":{ +"bigg.reaction":[ +"RPI" +], +"ec-code":[ +"5.3.1.6" +], +"metanetx.reaction":[ +"MNXR104084" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"SUCCt2_2", +"name":"Succinate transport via proton symport (2 H)", +"metabolites":{ +"h_c":2.0, +"h_e":-2.0, +"succ_c":1.0, +"succ_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3528", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"SUCCt2_2" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCCt2_2" +], +"biocyc":[ +"META:TRANS-RXN-121" +], +"metanetx.reaction":[ +"MNXR104620" +], +"rhea":[ +"29305", +"29306", +"29304", +"29303" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10154", +"rxn09269" +] +} +}, +{ +"id":"CYTBD", +"name":"Cytochrome oxidase bd (ubiquinol-8: 2 protons)", +"metabolites":{ +"h2o_c":1.0, +"h_c":-2.0, +"h_e":2.0, +"o2_c":-0.5, +"q8_c":1.0, +"q8h2_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"(b0978 and b0979) or (b0733 and b0734)", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"CYTBD" +] +}, +"annotation":{ +"bigg.reaction":[ +"CYTBD" +], +"metanetx.reaction":[ +"MNXR97031" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn12494", +"rxn10112", +"rxn08288" +] +} +}, +{ +"id":"D_LACt2", +"name":"D lactate transport via proton symport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"lac__D_c":1.0, +"lac__D_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2975 or b3603", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"D_LACt2" +] +}, +"annotation":{ +"bigg.reaction":[ +"D_LACt2" +], +"biocyc":[ +"META:TRANS-RXN0-515" +], +"metanetx.reaction":[ +"MNXR97838" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10171", +"rxn09772", +"rxn08350" +] +} +}, +{ +"id":"ENO", +"name":"Enolase", +"metabolites":{ +"2pg_c":-1.0, +"h2o_c":1.0, +"pep_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2779", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"ENO" +] +}, +"annotation":{ +"bigg.reaction":[ +"ENO" +], +"biocyc":[ +"META:2PGADEHYDRAT-RXN" +], +"ec-code":[ +"4.2.1.11" +], +"kegg.reaction":[ +"R00658" +], +"metanetx.reaction":[ +"MNXR97932" +], +"reactome.reaction":[ +"R-BTA-71660", +"R-RNO-70494", +"R-TGU-71660", +"R-SSC-71660", +"R-GGA-352981", +"R-DME-70494", +"R-CFA-70494", +"R-OSA-70494", +"R-SCE-71660", +"R-GGA-353044", +"R-CFA-71660", +"R-GGA-70494", +"R-PFA-71660", +"R-SPO-71660", +"R-SPO-70494", +"R-DDI-70494", +"R-RNO-71660", +"R-MMU-70494", +"R-ATH-70494", +"R-SCE-70494", +"R-SSC-70494", +"R-HSA-70494", +"R-DME-71660", +"R-CEL-71660", +"R-HSA-71660", +"R-TGU-70494", +"R-XTR-71660", +"R-DRE-70494", +"R-DRE-71660", +"R-MMU-71660", +"R-ATH-71660", +"R-BTA-70494", +"R-CEL-70494", +"R-XTR-70494", +"R-DDI-71660", +"R-OSA-71660", +"R-PFA-70494", +"R-GGA-71660" +], +"rhea":[ +"10166", +"10165", +"10164", +"10167" +], +"sabiork":[ +"8" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00459" +] +} +}, +{ +"id":"SUCCt3", +"name":"Succinate transport out via proton antiport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"succ_c":-1.0, +"succ_e":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"SUCCt3" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCCt3" +], +"metanetx.reaction":[ +"MNXR104623" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09270" +] +} +}, +{ +"id":"ETOHt2r", +"name":"Ethanol reversible transport via proton symport", +"metabolites":{ +"etoh_c":1.0, +"etoh_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"ETOHt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"ETOHt2r" +], +"metanetx.reaction":[ +"MNXR97981" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10146", +"rxn08427" +] +} +}, +{ +"id":"SUCDi", +"name":"Succinate dehydrogenase (irreversible)", +"metabolites":{ +"fum_c":1.0, +"q8_c":-1.0, +"q8h2_c":1.0, +"succ_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0721 and b0722 and b0723 and b0724", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"SUCDi" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCDi" +], +"metanetx.reaction":[ +"MNXR99641" +], +"rhea":[ +"29190", +"29189", +"29187", +"29188" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn09272" +] +} +}, +{ +"id":"SUCOAS", +"name":"Succinyl-CoA synthetase (ADP-forming)", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"coa_c":-1.0, +"pi_c":1.0, +"succ_c":-1.0, +"succoa_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0728 and b0729", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"SUCOAS" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCOAS" +], +"biocyc":[ +"META:SUCCCOASYN-RXN" +], +"ec-code":[ +"6.2.1.5" +], +"kegg.reaction":[ +"R00405" +], +"metanetx.reaction":[ +"MNXR104635" +], +"reactome.reaction":[ +"R-BTA-70997", +"R-GGA-372977", +"R-PFA-70997", +"R-GGA-373134", +"R-TGU-70997", +"R-XTR-70997", +"R-SSC-70997", +"R-HSA-70997", +"R-DRE-70997", +"R-SCE-70997", +"R-SPO-70997", +"R-DDI-70997", +"R-CFA-70997", +"R-OSA-70997", +"R-GGA-70997", +"R-RNO-70997", +"R-ATH-70997", +"R-MMU-70997" +], +"rhea":[ +"17664", +"17663", +"17662", +"17661" +], +"sabiork":[ +"260" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00285" +] +} +}, +{ +"id":"TALA", +"name":"Transaldolase", +"metabolites":{ +"e4p_c":1.0, +"f6p_c":1.0, +"g3p_c":-1.0, +"s7p_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2464 or b0008", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"TALA" +] +}, +"annotation":{ +"bigg.reaction":[ +"TALA" +], +"biocyc":[ +"META:TRANSALDOL-RXN" +], +"ec-code":[ +"2.2.1.2" +], +"kegg.reaction":[ +"R01827" +], +"metanetx.reaction":[ +"MNXR104715" +], +"rhea":[ +"17056", +"17055", +"17054", +"17053" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"THD2", +"name":"NAD(P) transhydrogenase", +"metabolites":{ +"h_c":2.0, +"h_e":-2.0, +"nad_c":1.0, +"nadh_c":-1.0, +"nadp_c":-1.0, +"nadph_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1602 and b1603", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"THD2" +] +}, +"annotation":{ +"bigg.reaction":[ +"THD2" +], +"ec-code":[ +"1.6.1.1" +], +"metanetx.reaction":[ +"MNXR104805" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10125", +"rxn09295" +] +} +}, +{ +"id":"TKT1", +"name":"Transketolase", +"metabolites":{ +"g3p_c":1.0, +"r5p_c":-1.0, +"s7p_c":1.0, +"xu5p__D_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2935 or b2465", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"TKT1" +] +}, +"annotation":{ +"bigg.reaction":[ +"TKT1" +], +"ec-code":[ +"2.2.1.1" +], +"metanetx.reaction":[ +"MNXR104868" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"TKT2", +"name":"Transketolase", +"metabolites":{ +"e4p_c":-1.0, +"f6p_c":1.0, +"g3p_c":1.0, +"xu5p__D_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2935 or b2465", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"TKT2" +] +}, +"annotation":{ +"bigg.reaction":[ +"TKT2" +], +"biocyc":[ +"META:2TRANSKETO-RXN" +], +"ec-code":[ +"2.2.1.1" +], +"kegg.reaction":[ +"R01830" +], +"metanetx.reaction":[ +"MNXR104869" +], +"rhea":[ +"27627", +"27628", +"27626", +"27629" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"TPI", +"name":"Triose-phosphate isomerase", +"metabolites":{ +"dhap_c":-1.0, +"g3p_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3919", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"TPI" +] +}, +"annotation":{ +"bigg.reaction":[ +"TPI" +], +"biocyc":[ +"META:TRIOSEPISOMERIZATION-RXN" +], +"ec-code":[ +"5.3.1.1" +], +"kegg.reaction":[ +"R01015" +], +"metanetx.reaction":[ +"MNXR104918" +], +"reactome.reaction":[ +"R-RNO-70481", +"R-MMU-70481", +"R-XTR-70481", +"R-SSC-70481", +"R-GGA-352927", +"R-SCE-70454", +"R-CEL-70481", +"R-PFA-70454", +"R-XTR-70454", +"R-BTA-70481", +"R-BTA-70454", +"R-GGA-352914", +"R-ATH-70481", +"R-CFA-70454", +"R-OSA-70454", +"R-HSA-70481", +"R-DRE-70454", +"R-DME-70481", +"R-OSA-70481", +"R-DRE-70481", +"R-ATH-70454", +"R-HSA-70454", +"R-SSC-70454", +"R-DDI-70454", +"R-SCE-70481", +"R-CFA-70481", +"R-PFA-70481", +"R-DDI-70481", +"R-SPO-70454", +"R-SPO-70481", +"R-RNO-70454", +"R-MMU-70454", +"R-CEL-70454", +"R-GGA-70481", +"R-GGA-70454", +"R-DME-70454" +], +"rhea":[ +"18587", +"18588", +"18586", +"18585" +], +"sabiork":[ +"4" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00747" +] +} +}, +{ +"id":"EX_ac_e", +"name":"Acetate exchange", +"metabolites":{ +"ac_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_ac_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_ac_e" +], +"biocyc":[ +"META:RXN0-1981", +"META:TRANS-RXN0-567" +], +"metanetx.reaction":[ +"MNXR95431" +], +"rhea":[ +"27817", +"27814", +"27816", +"27815" +], +"sabiork":[ +"12184" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09787", +"rxn09866", +"rxn10904", +"rxn08063" +] +} +}, +{ +"id":"EX_acald_e", +"name":"Acetaldehyde exchange", +"metabolites":{ +"acald_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_acald_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_acald_e" +], +"metanetx.reaction":[ +"MNXR95212" +], +"reactome.reaction":[ +"R-HSA-449872" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09700", +"rxn08033", +"rxn13212", +"rxn08032" +] +} +}, +{ +"id":"EX_akg_e", +"name":"2-Oxoglutarate exchange", +"metabolites":{ +"akg_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_akg_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_akg_e" +], +"metanetx.reaction":[ +"MNXR95663" +], +"sabiork":[ +"13794" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10923", +"rxn08096", +"rxn13220" +] +} +}, +{ +"id":"EX_co2_e", +"name":"CO2 exchange", +"metabolites":{ +"co2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_co2_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_co2_e" +], +"biocyc":[ +"META:TRANS-RXN0-545" +], +"metanetx.reaction":[ +"MNXR96810" +], +"reactome.reaction":[ +"R-DDI-1247645", +"R-CFA-1237069", +"R-TGU-1247649", +"R-CFA-1237042", +"R-CEL-1247645", +"R-XTR-1237069", +"R-HSA-1247645", +"R-OSA-1237042", +"R-GGA-1237042", +"R-BTA-1247645", +"R-GGA-1247649", +"R-RNO-1247645", +"R-XTR-1247645", +"R-TGU-1237042", +"R-SCE-1247649", +"R-MMU-1247649", +"R-CFA-1247649", +"R-GGA-1247645", +"R-SSC-1247645", +"R-BTA-1237069", +"R-RNO-1237069", +"R-SCE-1237042", +"R-DDI-1247649", +"R-SSC-1237042", +"R-DRE-1247649", +"R-DRE-1237042", +"R-DDI-1237042", +"R-DME-1237042", +"R-MMU-1237042", +"R-SSC-1247649", +"R-TGU-1237069", +"R-BTA-1247649", +"R-CFA-1247645", +"R-RNO-1247649", +"R-HSA-1237069", +"R-CEL-1237069", +"R-DDI-1237069", +"R-MMU-1237069", +"R-DME-1247645", +"R-ATH-1237042", +"R-OSA-1247649", +"R-HSA-1237042", +"R-DRE-1247645", +"R-HSA-1247649", +"R-MMU-1247645", +"R-DME-1237069", +"R-RNO-1237042", +"R-TGU-1247645", +"R-BTA-1237042", +"R-GGA-1237069", +"R-DME-1247649", +"R-SSC-1237069", +"R-DRE-1237069", +"R-ATH-1247649" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn05467", +"rxn08237", +"rxn09706", +"rxn09821", +"rxn09775", +"rxn09876", +"rxn08238", +"rxn09860" +] +} +}, +{ +"id":"EX_etoh_e", +"name":"Ethanol exchange", +"metabolites":{ +"etoh_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_etoh_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_etoh_e" +], +"biocyc":[ +"META:TRANS-RXN0-546" +], +"metanetx.reaction":[ +"MNXR97980" +], +"rhea":[ +"35269", +"35267", +"35270", +"35268" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09683", +"rxn08428", +"rxn09764" +] +} +}, +{ +"id":"EX_for_e", +"name":"Formate exchange", +"metabolites":{ +"for_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_for_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_for_e" +], +"biocyc":[ +"META:TRANS-RXN-1" +], +"metanetx.reaction":[ +"MNXR99620" +], +"reactome.reaction":[ +"R-HSA-6803255" +], +"rhea":[ +"29681", +"29680", +"29682", +"29679" +], +"sabiork":[ +"12483" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09754", +"rxn08525", +"rxn09682", +"rxn08526" +] +} +}, +{ +"id":"EX_fru_e", +"name":"D-Fructose exchange", +"metabolites":{ +"fru_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_fru_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_fru_e" +], +"metanetx.reaction":[ +"MNXR99663" +], +"reactome.reaction":[ +"R-OSA-189222", +"R-XTR-189222", +"R-SCE-189222", +"R-ATH-189222", +"R-RNO-189222", +"R-DME-189222", +"R-TGU-189222", +"R-SSC-189222", +"R-CFA-189222", +"R-DRE-189222", +"R-HSA-189222", +"R-GGA-189222", +"R-BTA-189222", +"R-MMU-189222", +"R-DDI-189222" +], +"sabiork":[ +"13415" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn12996", +"rxn08537" +] +} +}, +{ +"id":"EX_fum_e", +"name":"Fumarate exchange", +"metabolites":{ +"fum_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_fum_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_fum_e" +], +"biocyc":[ +"META:TRANS-RXN0-553" +], +"metanetx.reaction":[ +"MNXR99715" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08544", +"rxn11013" +] +} +}, +{ +"id":"EX_glc__D_e", +"name":"D-Glucose exchange", +"metabolites":{ +"glc__D_e":-1.0 +}, +"lower_bound":-10.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_glc_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_glc__D_e" +], +"biocyc":[ +"META:TRANS-RXN0-574" +], +"metanetx.reaction":[ +"MNXR100188" +], +"sabiork":[ +"7002", +"601" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09875", +"rxn09679", +"rxn08617" +] +} +}, +{ +"id":"EX_gln__L_e", +"name":"L-Glutamine exchange", +"metabolites":{ +"gln__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_gln_L_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_gln__L_e" +], +"biocyc":[ +"META:TRANS-RXN-233" +], +"metanetx.reaction":[ +"MNXR100259" +], +"reactome.reaction":[ +"R-HSA-212651", +"R-BTA-212614", +"R-RNO-212614", +"R-SSC-212614", +"R-MMU-212614", +"R-HSA-212614", +"R-GGA-212614", +"R-CFA-212614", +"R-TGU-212614", +"R-SCE-212614" +], +"sabiork":[ +"13421" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08625", +"rxn10928" +] +} +}, +{ +"id":"EX_glu__L_e", +"name":"L-Glutamate exchange", +"metabolites":{ +"glu__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_glu_L_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_glu__L_e" +], +"biocyc":[ +"META:TRANS-RXN-234", +"META:TRANS-RXN-232" +], +"metanetx.reaction":[ +"MNXR100301" +], +"reactome.reaction":[ +"R-HSA-212658", +"R-TGU-210439", +"R-GGA-210439", +"R-XTR-210439", +"R-RNO-210439", +"R-CFA-210439", +"R-CEL-210439", +"R-DME-210439", +"R-SSC-210439", +"R-HSA-210439", +"R-DRE-210439", +"R-MMU-210439", +"R-BTA-210439" +], +"sabiork":[ +"12283" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08633", +"rxn09750", +"rxn13304", +"rxn13120", +"rxn10917" +] +} +}, +{ +"id":"EX_h_e", +"name":"H+ exchange", +"metabolites":{ +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_h_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_h_e" +], +"biocyc":[ +"META:RXN-14452" +], +"metanetx.reaction":[ +"MNXR100765" +], +"reactome.reaction":[ +"R-HSA-2534378", +"R-DDI-74723", +"R-BTA-170026", +"R-CFA-170026", +"R-SCE-74723", +"R-DRE-74723", +"R-HSA-170026", +"R-TGU-2534378", +"R-HSA-74723", +"R-CFA-2534378", +"R-TGU-74723", +"R-OSA-170026", +"R-RNO-2534378", +"R-GGA-2534378", +"R-MMU-2534378", +"R-BTA-2534378", +"R-SSC-2534378", +"R-DRE-170026", +"R-TGU-170026", +"R-GGA-170026", +"R-SCE-170026", +"R-DRE-2534378", +"R-BTA-74723", +"R-SPO-74723", +"R-XTR-74723", +"R-RNO-74723", +"R-XTR-2534378", +"R-MMU-74723", +"R-CFA-74723", +"R-GGA-74723", +"R-CEL-170026", +"R-MMU-170026", +"R-ATH-74723", +"R-DME-74723", +"R-PFA-74723", +"R-SSC-74723", +"R-XTR-170026", +"R-SSC-170026", +"R-CEL-74723", +"R-ATH-170026", +"R-RNO-170026", +"R-DME-170026" +], +"rhea":[ +"34980", +"34981", +"34982", +"34979" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn11009", +"rxn08730" +] +} +}, +{ +"id":"EX_h2o_e", +"name":"H2O exchange", +"metabolites":{ +"h2o_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_h2o_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_h2o_e" +], +"biocyc":[ +"META:TRANS-RXN-145", +"META:TRANS-RXN0-547" +], +"metanetx.reaction":[ +"MNXR98641" +], +"reactome.reaction":[ +"R-ATH-507868", +"R-CFA-432054", +"R-CFA-432010", +"R-RNO-507868", +"R-OSA-432065", +"R-GGA-432010", +"R-SPO-445714", +"R-PFA-445714", +"R-CFA-432065", +"R-GGA-432067", +"R-TGU-432054", +"R-TGU-445714", +"R-OSA-507868", +"R-DRE-507868", +"R-SPO-507868", +"R-BTA-432054", +"R-GGA-507870", +"R-OSA-432010", +"R-DME-432065", +"R-DRE-432067", +"R-PFA-507868", +"R-SSC-432054", +"R-HSA-432065", +"R-OSA-507870", +"R-HSA-432054", +"R-SSC-432065", +"R-CEL-507868", +"R-XTR-507868", +"R-ATH-507870", +"R-SCE-432065", +"R-BTA-507870", +"R-DME-432010", +"R-CFA-445714", +"R-DRE-445714", +"R-BTA-507868", +"R-GGA-507868", +"R-RNO-432054", +"R-RNO-432010", +"R-SSC-432067", +"R-CEL-445714", +"R-DDI-432065", +"R-ATH-432010", +"R-SCE-432054", +"R-MMU-432065", +"R-MMU-445714", +"R-GGA-432065", +"R-HSA-432067", +"R-SSC-507870", +"R-SCE-432067", +"R-RNO-507870", +"R-DME-432054", +"R-ATH-432067", +"R-BTA-445714", +"R-DRE-507870", +"R-DME-507868", +"R-DME-507870", +"R-DRE-432010", +"R-MMU-432010", +"R-HSA-445714", +"R-OSA-432054", +"R-RNO-432067", +"R-TGU-432010", +"R-TGU-507868", +"R-DDI-432054", +"R-PFA-507870", +"R-HSA-507870", +"R-XTR-432067", +"R-HSA-432010", +"R-SSC-507868", +"R-SCE-507870", +"R-CEL-507870", +"R-DDI-507868", +"R-DRE-432054", +"R-XTR-507870", +"R-DDI-432010", +"R-BTA-432065", +"R-CFA-432067", +"R-OSA-432067", +"R-ATH-432065", +"R-GGA-445714", +"R-SCE-507868", +"R-TGU-432065", +"R-MMU-432067", +"R-TGU-507870", +"R-CFA-507870", +"R-RNO-432065", +"R-MMU-432054", +"R-MMU-507868", +"R-SPO-507870", +"R-SCE-432010", +"R-MMU-507870", +"R-SSC-445714", +"R-HSA-507868", +"R-DME-432067", +"R-SSC-432010", +"R-TGU-432067", +"R-GGA-432054", +"R-BTA-432010", +"R-SCE-445714", +"R-DDI-507870", +"R-ATH-432054", +"R-DDI-432067", +"R-XTR-445714", +"R-BTA-432067", +"R-CFA-507868", +"R-RNO-445714" +], +"rhea":[ +"29668", +"29669", +"29667", +"29670" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08687", +"rxn08686", +"rxn09745", +"rxn09838", +"rxn09874", +"rxn09812", +"rxn09643", +"rxn05319" +] +} +}, +{ +"id":"EX_lac__D_e", +"name":"D-lactate exchange", +"metabolites":{ +"lac__D_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_lac_D_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_lac__D_e" +], +"metanetx.reaction":[ +"MNXR97840" +], +"sabiork":[ +"12471" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08351" +] +} +}, +{ +"id":"EX_mal__L_e", +"name":"L-Malate exchange", +"metabolites":{ +"mal__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_mal_L_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_mal__L_e" +], +"biocyc":[ +"META:TRANS-RXN-225", +"META:TRANS-RXN-224" +], +"metanetx.reaction":[ +"MNXR101367" +], +"sabiork":[ +"13793" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10967", +"rxn08868" +] +} +}, +{ +"id":"EX_nh4_e", +"name":"Ammonia exchange", +"metabolites":{ +"nh4_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_nh4_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_nh4_e" +], +"biocyc":[ +"META:TRANS-RXN0-206", +"META:RXN-9615", +"META:TRANS-RXN0-544" +], +"metanetx.reaction":[ +"MNXR101950" +], +"reactome.reaction":[ +"R-CEL-444416", +"R-SSC-444416", +"R-DDI-444416", +"R-MMU-444416", +"R-DRE-444416", +"R-GGA-444416", +"R-CFA-444416", +"R-HSA-444416", +"R-XTR-444416", +"R-BTA-444416", +"R-RNO-444416", +"R-TGU-444416", +"R-DME-444416" +], +"rhea":[ +"28749", +"28748", +"28750", +"28747" +], +"sabiork":[ +"11683" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn13364", +"rxn09835", +"rxn05466", +"rxn08987", +"rxn08986", +"rxn09736" +] +} +}, +{ +"id":"EX_o2_e", +"name":"O2 exchange", +"metabolites":{ +"o2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_o2_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_o2_e" +], +"biocyc":[ +"META:TRANS-RXN0-474" +], +"metanetx.reaction":[ +"MNXR102090" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09641", +"rxn05468", +"rxn09031", +"rxn09032", +"rxn09734" +] +} +}, +{ +"id":"EX_pi_e", +"name":"Phosphate exchange", +"metabolites":{ +"pi_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_pi_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_pi_e" +], +"biocyc":[ +"META:TRANS-RXN0-470" +], +"metanetx.reaction":[ +"MNXR102871" +], +"rhea":[ +"32824", +"32826", +"32825", +"32823" +], +"sabiork":[ +"10985" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10838", +"rxn09722", +"rxn09121", +"rxn13178" +] +} +}, +{ +"id":"EX_pyr_e", +"name":"Pyruvate exchange", +"metabolites":{ +"pyr_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_pyr_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_pyr_e" +], +"biocyc":[ +"META:TRANS-RXN0-506", +"META:TRANS-RXN0-570" +], +"metanetx.reaction":[ +"MNXR103384" +], +"sabiork":[ +"12168" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10929", +"rxn09218" +] +} +}, +{ +"id":"EX_succ_e", +"name":"Succinate exchange", +"metabolites":{ +"succ_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_succ_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_succ_e" +], +"biocyc":[ +"META:TRANS-RXN0-552" +], +"metanetx.reaction":[ +"MNXR104619" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10952", +"rxn09271" +] +} +}, +{ +"id":"FBA", +"name":"Fructose-bisphosphate aldolase", +"metabolites":{ +"dhap_c":1.0, +"fdp_c":-1.0, +"g3p_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2097 or b1773 or b2925", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"FBA" +] +}, +"annotation":{ +"bigg.reaction":[ +"FBA" +], +"ec-code":[ +"4.1.2.13" +], +"kegg.reaction":[ +"R01068" +], +"metanetx.reaction":[ +"MNXR99459" +], +"rhea":[ +"14729", +"14732", +"14731", +"14730" +], +"sabiork":[ +"1338" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00786" +] +} +}, +{ +"id":"FBP", +"name":"Fructose-bisphosphatase", +"metabolites":{ +"f6p_c":1.0, +"fdp_c":-1.0, +"h2o_c":-1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3925 or b4232", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"FBP" +] +}, +"annotation":{ +"bigg.reaction":[ +"FBP" +], +"ec-code":[ +"3.1.3.11" +], +"metanetx.reaction":[ +"MNXR99465" +], +"rhea":[ +"11067", +"11065", +"11066", +"11064" +], +"sabiork":[ +"2084" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"FORt2", +"name":"Formate transport in via proton symport", +"metabolites":{ +"for_c":1.0, +"for_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0904 or b2492", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FORt2" +] +}, +"annotation":{ +"bigg.reaction":[ +"FORt2" +], +"metanetx.reaction":[ +"MNXR99621" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08524", +"rxn05559" +] +} +}, +{ +"id":"FORt", +"name":"Formate transport via diffusion", +"metabolites":{ +"for_c":1.0, +"for_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":0.0, +"gene_reaction_rule":"b0904 or b2492", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FORti" +] +}, +"annotation":{ +"bigg.reaction":[ +"FORt" +], +"biocyc":[ +"META:TRANS-RXN-1" +], +"metanetx.reaction":[ +"MNXR99620" +], +"reactome.reaction":[ +"R-HSA-6803255" +], +"rhea":[ +"29681", +"29680", +"29682", +"29679" +], +"sabiork":[ +"12483" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09754", +"rxn08525", +"rxn09682", +"rxn08526" +] +} +}, +{ +"id":"FRD7", +"name":"Fumarate reductase", +"metabolites":{ +"fum_c":-1.0, +"q8_c":1.0, +"q8h2_c":-1.0, +"succ_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4151 and b4152 and b4153 and b4154", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"FRD7" +] +}, +"annotation":{ +"bigg.reaction":[ +"FRD7" +], +"metanetx.reaction":[ +"MNXR99641" +], +"rhea":[ +"29190", +"29189", +"29187", +"29188" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn09272" +] +} +}, +{ +"id":"FRUpts2", +"name":"Fructose transport via PEP:Pyr PTS (f6p generating)", +"metabolites":{ +"f6p_c":1.0, +"fru_e":-1.0, +"pep_c":-1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1817 and b1818 and b1819 and b2415 and b2416", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FRUpts2" +] +}, +"annotation":{ +"bigg.reaction":[ +"FRUpts2" +], +"metanetx.reaction":[ +"MNXR99662" +], +"sbo":"SBO:0000185" +} +}, +{ +"id":"FUM", +"name":"Fumarase", +"metabolites":{ +"fum_c":-1.0, +"h2o_c":-1.0, +"mal__L_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1612 or b4122 or b1611", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"FUM" +] +}, +"annotation":{ +"bigg.reaction":[ +"FUM" +], +"biocyc":[ +"META:FUMHYDR-RXN" +], +"ec-code":[ +"4.2.1.2" +], +"kegg.reaction":[ +"R01082" +], +"metanetx.reaction":[ +"MNXR99705" +], +"reactome.reaction":[ +"R-TGU-451033", +"R-TGU-70982", +"R-HSA-70982", +"R-ATH-451033", +"R-SPO-70982", +"R-SPO-451033", +"R-XTR-451033", +"R-MMU-70982", +"R-DRE-70982", +"R-DME-70982", +"R-DME-451033", +"R-HSA-451033", +"R-SCE-451033", +"R-DDI-451033", +"R-OSA-451033", +"R-CFA-70982", +"R-XTR-70982", +"R-MMU-451033", +"R-OSA-70982", +"R-BTA-70982", +"R-DRE-451033", +"R-GGA-373141", +"R-RNO-451033", +"R-CEL-451033", +"R-ATH-70982", +"R-GGA-373145", +"R-CEL-70982", +"R-BTA-451033", +"R-SSC-451033", +"R-SCE-70982", +"R-CFA-451033", +"R-RNO-70982", +"R-GGA-70982", +"R-DDI-70982", +"R-GGA-451033", +"R-SSC-70982" +], +"rhea":[ +"12463", +"12461", +"12462", +"12460" +], +"sabiork":[ +"256" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00799" +] +} +}, +{ +"id":"FUMt2_2", +"name":"Fumarate transport via proton symport (2 H)", +"metabolites":{ +"fum_c":1.0, +"fum_e":-1.0, +"h_c":2.0, +"h_e":-2.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3528", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FUMt2_2" +] +}, +"annotation":{ +"bigg.reaction":[ +"FUMt2_2" +], +"biocyc":[ +"META:TRANS-RXN-121B" +], +"metanetx.reaction":[ +"MNXR99711" +], +"rhea":[ +"29332", +"29334", +"29333", +"29331" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08542", +"rxn10152" +] +} +}, +{ +"id":"G6PDH2r", +"name":"Glucose 6-phosphate dehydrogenase", +"metabolites":{ +"6pgl_c":1.0, +"g6p_c":-1.0, +"h_c":1.0, +"nadp_c":-1.0, +"nadph_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1852", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"G6PDH2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"G6PDH2r" +], +"biocyc":[ +"META:GLU6PDEHYDROG-RXN" +], +"ec-code":[ +"1.1.1.363", +"1.1.1.49" +], +"kegg.reaction":[ +"R00835" +], +"metanetx.reaction":[ +"MNXR99907" +], +"rhea":[ +"15842", +"15843", +"15841", +"15844" +], +"sabiork":[ +"1176", +"6509" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00604" +] +} +}, +{ +"id":"GAPD", +"name":"Glyceraldehyde-3-phosphate dehydrogenase", +"metabolites":{ +"13dpg_c":1.0, +"g3p_c":-1.0, +"h_c":1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pi_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1779", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"GAPD" +] +}, +"annotation":{ +"bigg.reaction":[ +"GAPD" +], +"biocyc":[ +"META:GAPOXNPHOSPHN-RXN" +], +"ec-code":[ +"1.2.1.12", +"1.2.1.59" +], +"kegg.reaction":[ +"R01061" +], +"metanetx.reaction":[ +"MNXR100040" +], +"reactome.reaction":[ +"R-ATH-70482", +"R-DME-70449", +"R-PFA-70482", +"R-SPO-70449", +"R-DRE-70449", +"R-CEL-70449", +"R-CEL-70482", +"R-CFA-70449", +"R-MMU-70482", +"R-HSA-70449", +"R-OSA-70482", +"R-GGA-352956", +"R-RNO-70449", +"R-SCE-70449", +"R-SSC-70482", +"R-ATH-70449", +"R-GGA-70482", +"R-OSA-70449", +"R-GGA-352921", +"R-DDI-70449", +"R-SPO-70482", +"R-TGU-70482", +"R-SCE-70482", +"R-HSA-70482", +"R-DME-70482", +"R-PFA-70449", +"R-XTR-70449", +"R-DRE-70482", +"R-XTR-70482", +"R-GGA-70449", +"R-RNO-70482", +"R-SSC-70449", +"R-DDI-70482", +"R-TGU-70449", +"R-MMU-70449", +"R-CFA-70482", +"R-BTA-70449", +"R-BTA-70482" +], +"rhea":[ +"10303", +"10300", +"10302", +"10301" +], +"sabiork":[ +"7844" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00781" +] +} +}, +{ +"id":"GLCpts", +"name":"D-glucose transport via PEP:Pyr PTS", +"metabolites":{ +"g6p_c":1.0, +"glc__D_e":-1.0, +"pep_c":-1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"(b2417 and b1101 and b2415 and b2416) or (b1817 and b1818 and b1819 and b2415 and b2416) or (b2417 and b1621 and b2415 and b2416)", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"GLCpts" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLCpts" +], +"metanetx.reaction":[ +"MNXR100237" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08612", +"rxn05226" +] +} +}, +{ +"id":"GLNS", +"name":"Glutamine synthetase", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"gln__L_c":1.0, +"glu__L_c":-1.0, +"h_c":1.0, +"nh4_c":-1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3870 or b1297", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLNS" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLNS" +], +"biocyc":[ +"META:GLUTAMINESYN-RXN" +], +"ec-code":[ +"6.3.1.2" +], +"kegg.reaction":[ +"R00253" +], +"metanetx.reaction":[ +"MNXR100024" +], +"reactome.reaction":[ +"R-GGA-70606", +"R-RNO-70606", +"R-TGU-70606", +"R-DME-70606", +"R-CEL-70606", +"R-DRE-70606", +"R-XTR-70606", +"R-SPO-70606", +"R-ATH-70606", +"R-CFA-70606", +"R-BTA-70606", +"R-OSA-70606", +"R-SSC-70606", +"R-MMU-70606", +"R-HSA-70606", +"R-SCE-70606" +], +"rhea":[ +"16172", +"16171", +"16169", +"16170" +], +"sabiork":[ +"760" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00187" +] +} +}, +{ +"id":"GLNabc", +"name":"L-glutamine transport via ABC system", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"gln__L_c":1.0, +"gln__L_e":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0811 and b0810 and b0809", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"GLNabc" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLNabc" +], +"biocyc":[ +"META:ABC-12-RXN" +], +"ec-code":[ +"3.6.3.21" +], +"metanetx.reaction":[ +"MNXR100258" +], +"rhea":[ +"29895#1", +"29897#1", +"29898#1", +"29896#1" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn11233", +"rxn05196", +"rxn05155", +"rxn11101", +"rxn08624" +] +} +}, +{ +"id":"GLUDy", +"name":"Glutamate dehydrogenase (NADP)", +"metabolites":{ +"akg_c":1.0, +"glu__L_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"nadp_c":-1.0, +"nadph_c":1.0, +"nh4_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1761", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLUDy" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUDy" +], +"biocyc":[ +"META:GLUTDEHYD-RXN" +], +"ec-code":[ +"1.4.1.13", +"1.4.1.3", +"1.4.1.4" +], +"kegg.reaction":[ +"R00248" +], +"metanetx.reaction":[ +"MNXR100086" +], +"rhea":[ +"11613", +"11614", +"11612", +"11615" +], +"sabiork":[ +"757" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00184" +] +} +}, +{ +"id":"GLUN", +"name":"Glutaminase", +"metabolites":{ +"gln__L_c":-1.0, +"glu__L_c":1.0, +"h2o_c":-1.0, +"nh4_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1812 or b0485 or b1524", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLUN" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUN" +], +"biocyc":[ +"META:GLUTAMIN-RXN" +], +"ec-code":[ +"6.3.5.2", +"4.3.3.6", +"6.3.5.5", +"1.4.7.1", +"6.3.5.4", +"3.5.1.2", +"6.3.4.2", +"1.4.1.13", +"3.5.1.38" +], +"kegg.reaction":[ +"R00256" +], +"metanetx.reaction":[ +"MNXR100030" +], +"reactome.reaction":[ +"R-TGU-70609", +"R-XTR-70609", +"R-SSC-70609", +"R-GGA-70609", +"R-DDI-70609", +"R-MMU-70609", +"R-DME-70609", +"R-RNO-70609", +"R-CEL-70609", +"R-BTA-70609", +"R-DRE-70609", +"R-HSA-70609", +"R-CFA-70609" +], +"rhea":[ +"15892", +"15889", +"15891", +"15890" +], +"sabiork":[ +"762" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00189" +] +} +}, +{ +"id":"GLUSy", +"name":"Glutamate synthase (NADPH)", +"metabolites":{ +"akg_c":-1.0, +"gln__L_c":-1.0, +"glu__L_c":2.0, +"h_c":-1.0, +"nadp_c":1.0, +"nadph_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3212 and b3213", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLUSy" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUSy" +], +"biocyc":[ +"META:GLUTAMATESYN-RXN" +], +"ec-code":[ +"1.4.1.13" +], +"kegg.reaction":[ +"R00114" +], +"metanetx.reaction":[ +"MNXR100291" +], +"rhea":[ +"15503", +"15501", +"15504", +"15502" +], +"sabiork":[ +"694" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00085" +] +} +}, +{ +"id":"GLUt2r", +"name":"L glutamate transport via proton symport reversible", +"metabolites":{ +"glu__L_c":1.0, +"glu__L_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4077", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"GLUt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUt2r" +], +"metanetx.reaction":[ +"MNXR100300" +], +"reactome.reaction":[ +"R-SCE-8875623", +"R-MMU-8875623", +"R-TGU-8875623", +"R-XTR-8875623", +"R-SSC-8875623", +"R-DME-8875623", +"R-CEL-8875623", +"R-DRE-8875623", +"R-GGA-8875623", +"R-HSA-8875623", +"R-RNO-8875623", +"R-DDI-8875623", +"R-CFA-8875623", +"R-BTA-8875623" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05297", +"rxn09813", +"rxn13303", +"rxn09751", +"rxn08631" +] +} +}, +{ +"id":"GND", +"name":"Phosphogluconate dehydrogenase", +"metabolites":{ +"6pgc_c":-1.0, +"co2_c":1.0, +"nadp_c":-1.0, +"nadph_c":1.0, +"ru5p__D_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2029", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"GND" +] +}, +"annotation":{ +"bigg.reaction":[ +"GND" +], +"biocyc":[ +"META:RXN-9952" +], +"ec-code":[ +"1.1.1.44", +"1.1.1.351" +], +"kegg.reaction":[ +"R01528" +], +"metanetx.reaction":[ +"MNXR100389" +], +"reactome.reaction":[ +"R-PFA-71299", +"R-GGA-71299", +"R-HSA-71299", +"R-SPO-71299", +"R-XTR-71299", +"R-ATH-71299", +"R-TGU-71299", +"R-OSA-71299", +"R-MMU-71299", +"R-DRE-71299", +"R-SCE-71299", +"R-SSC-71299", +"R-DDI-71299", +"R-CFA-71299", +"R-DME-71299", +"R-BTA-71299", +"R-CEL-71299" +], +"rhea":[ +"10116", +"10117", +"10118", +"10119" +], +"sabiork":[ +"108" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01115" +] +} +}, +{ +"id":"H2Ot", +"name":"H2O transport via diffusion", +"metabolites":{ +"h2o_c":1.0, +"h2o_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0875 or s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"H2Ot" +] +}, +"annotation":{ +"bigg.reaction":[ +"H2Ot" +], +"biocyc":[ +"META:TRANS-RXN-145", +"META:TRANS-RXN0-547" +], +"metanetx.reaction":[ +"MNXR98641" +], +"reactome.reaction":[ +"R-ATH-507868", +"R-CFA-432054", +"R-CFA-432010", +"R-RNO-507868", +"R-OSA-432065", +"R-GGA-432010", +"R-SPO-445714", +"R-PFA-445714", +"R-CFA-432065", +"R-GGA-432067", +"R-TGU-432054", +"R-TGU-445714", +"R-OSA-507868", +"R-DRE-507868", +"R-SPO-507868", +"R-BTA-432054", +"R-GGA-507870", +"R-OSA-432010", +"R-DME-432065", +"R-DRE-432067", +"R-PFA-507868", +"R-SSC-432054", +"R-HSA-432065", +"R-OSA-507870", +"R-HSA-432054", +"R-SSC-432065", +"R-CEL-507868", +"R-XTR-507868", +"R-ATH-507870", +"R-SCE-432065", +"R-BTA-507870", +"R-DME-432010", +"R-CFA-445714", +"R-DRE-445714", +"R-BTA-507868", +"R-GGA-507868", +"R-RNO-432054", +"R-RNO-432010", +"R-SSC-432067", +"R-CEL-445714", +"R-DDI-432065", +"R-ATH-432010", +"R-SCE-432054", +"R-MMU-432065", +"R-MMU-445714", +"R-GGA-432065", +"R-HSA-432067", +"R-SSC-507870", +"R-SCE-432067", +"R-RNO-507870", +"R-DME-432054", +"R-ATH-432067", +"R-BTA-445714", +"R-DRE-507870", +"R-DME-507868", +"R-DME-507870", +"R-DRE-432010", +"R-MMU-432010", +"R-HSA-445714", +"R-OSA-432054", +"R-RNO-432067", +"R-TGU-432010", +"R-TGU-507868", +"R-DDI-432054", +"R-PFA-507870", +"R-HSA-507870", +"R-XTR-432067", +"R-HSA-432010", +"R-SSC-507868", +"R-SCE-507870", +"R-CEL-507870", +"R-DDI-507868", +"R-DRE-432054", +"R-XTR-507870", +"R-DDI-432010", +"R-BTA-432065", +"R-CFA-432067", +"R-OSA-432067", +"R-ATH-432065", +"R-GGA-445714", +"R-SCE-507868", +"R-TGU-432065", +"R-MMU-432067", +"R-TGU-507870", +"R-CFA-507870", +"R-RNO-432065", +"R-MMU-432054", +"R-MMU-507868", +"R-SPO-507870", +"R-SCE-432010", +"R-MMU-507870", +"R-SSC-445714", +"R-HSA-507868", +"R-DME-432067", +"R-SSC-432010", +"R-TGU-432067", +"R-GGA-432054", +"R-BTA-432010", +"R-SCE-445714", +"R-DDI-507870", +"R-ATH-432054", +"R-DDI-432067", +"R-XTR-445714", +"R-BTA-432067", +"R-CFA-507868", +"R-RNO-445714" +], +"rhea":[ +"29668", +"29669", +"29667", +"29670" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08687", +"rxn08686", +"rxn09745", +"rxn09838", +"rxn09874", +"rxn09812", +"rxn09643", +"rxn05319" +] +} +}, +{ +"id":"ICDHyr", +"name":"Isocitrate dehydrogenase (NADP)", +"metabolites":{ +"akg_c":1.0, +"co2_c":1.0, +"icit_c":-1.0, +"nadp_c":-1.0, +"nadph_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1136", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"ICDHyr" +] +}, +"annotation":{ +"bigg.reaction":[ +"ICDHyr" +], +"ec-code":[ +"1.1.1.42" +], +"kegg.reaction":[ +"R00267" +], +"metanetx.reaction":[ +"MNXR100781" +], +"rhea":[ +"19629", +"19630", +"19631", +"19632" +], +"sabiork":[ +"269" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00198" +] +} +}, +{ +"id":"ICL", +"name":"Isocitrate lyase", +"metabolites":{ +"glx_c":1.0, +"icit_c":-1.0, +"succ_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4015", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"ICL" +] +}, +"annotation":{ +"bigg.reaction":[ +"ICL" +], +"ec-code":[ +"4.1.3.1" +], +"kegg.reaction":[ +"R00479" +], +"metanetx.reaction":[ +"MNXR100789" +], +"rhea":[ +"13248", +"13245", +"13246", +"13247" +], +"sabiork":[ +"911" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00336" +] +} +}, +{ +"id":"LDH_D", +"name":"D-lactate dehydrogenase", +"metabolites":{ +"h_c":1.0, +"lac__D_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pyr_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2133 or b1380", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"LDH_D" +] +}, +"annotation":{ +"bigg.reaction":[ +"LDH_D" +], +"biocyc":[ +"META:DLACTDEHYDROGNAD-RXN" +], +"ec-code":[ +"1.1.1.28" +], +"kegg.reaction":[ +"R00704" +], +"metanetx.reaction":[ +"MNXR101037" +], +"rhea":[ +"16370", +"16371", +"16372", +"16369" +], +"sabiork":[ +"155" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00500" +] +} +}, +{ +"id":"MALS", +"name":"Malate synthase", +"metabolites":{ +"accoa_c":-1.0, +"coa_c":1.0, +"glx_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"mal__L_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4014 or b2976", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"MALS" +] +}, +"annotation":{ +"bigg.reaction":[ +"MALS" +], +"biocyc":[ +"META:MALSYN-RXN" +], +"ec-code":[ +"2.3.3.9" +], +"kegg.reaction":[ +"R00472" +], +"metanetx.reaction":[ +"MNXR101347" +], +"rhea":[ +"18181", +"18182", +"18184", +"18183" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00330" +] +} +}, +{ +"id":"MALt2_2", +"name":"Malate transport via proton symport (2 H)", +"metabolites":{ +"h_c":2.0, +"h_e":-2.0, +"mal__L_c":1.0, +"mal__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3528", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"MALt2_2" +] +}, +"annotation":{ +"bigg.reaction":[ +"MALt2_2" +], +"biocyc":[ +"META:TRANS-RXN-121A" +], +"metanetx.reaction":[ +"MNXR101370" +], +"rhea":[ +"29341", +"29340", +"29342", +"29339" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08865", +"rxn10153" +] +} +}, +{ +"id":"MDH", +"name":"Malate dehydrogenase", +"metabolites":{ +"h_c":1.0, +"mal__L_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"oaa_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3236", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"MDH" +] +}, +"annotation":{ +"bigg.reaction":[ +"MDH" +], +"biocyc":[ +"META:MALATE-DEH-RXN" +], +"ec-code":[ +"1.1.1.37", +"1.1.1.299" +], +"kegg.reaction":[ +"R00342" +], +"metanetx.reaction":[ +"MNXR101439" +], +"reactome.reaction":[ +"R-BTA-70979", +"R-BTA-198508", +"R-SCE-70979", +"R-GGA-70979", +"R-MMU-71783", +"R-RNO-71783", +"R-DDI-198508", +"R-CFA-71783", +"R-CFA-198508", +"R-ATH-70979", +"R-DME-198508", +"R-TGU-71783", +"R-HSA-71783", +"R-BTA-71783", +"R-DRE-198508", +"R-SPO-70979", +"R-GGA-71783", +"R-TGU-198508", +"R-GGA-372422", +"R-CEL-71783", +"R-XTR-70979", +"R-RNO-198508", +"R-MMU-70979", +"R-SPO-71783", +"R-ATH-71783", +"R-MMU-198508", +"R-DME-70979", +"R-TGU-70979", +"R-CEL-198508", +"R-DME-71783", +"R-DRE-70979", +"R-OSA-71783", +"R-SSC-198508", +"R-GGA-372855", +"R-SSC-70979", +"R-OSA-70979", +"R-GGA-373047", +"R-GGA-198508", +"R-SSC-71783", +"R-HSA-70979", +"R-CFA-70979", +"R-XTR-71783", +"R-HSA-198508", +"R-XTR-198508", +"R-SCE-71783", +"R-RNO-70979", +"R-DRE-71783", +"R-CEL-70979" +], +"rhea":[ +"21432", +"21433", +"21434", +"21435" +], +"sabiork":[ +"113" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00248" +] +} +}, +{ +"id":"ME1", +"name":"Malic enzyme (NAD)", +"metabolites":{ +"co2_c":1.0, +"mal__L_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1479", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"ME1" +] +}, +"annotation":{ +"bigg.reaction":[ +"ME1" +], +"biocyc":[ +"META:1.1.1.39-RXN" +], +"ec-code":[ +"1.1.1.38", +"1.1.1.39" +], +"kegg.reaction":[ +"R00214" +], +"metanetx.reaction":[ +"MNXR101446" +], +"rhea":[ +"12655", +"12654", +"12653", +"12656" +], +"sabiork":[ +"141" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00159" +] +} +}, +{ +"id":"ME2", +"name":"Malic enzyme (NADP)", +"metabolites":{ +"co2_c":1.0, +"mal__L_c":-1.0, +"nadp_c":-1.0, +"nadph_c":1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2463", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"ME2" +] +}, +"annotation":{ +"bigg.reaction":[ +"ME2" +], +"biocyc":[ +"META:MALIC-NADP-RXN" +], +"ec-code":[ +"1.1.1.40" +], +"kegg.reaction":[ +"R00216" +], +"metanetx.reaction":[ +"MNXR101443" +], +"rhea":[ +"18255", +"18256", +"18254", +"18253" +], +"sabiork":[ +"142" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00161" +] +} +}, +{ +"id":"NADH16", +"name":"NADH dehydrogenase (ubiquinone-8 & 3 protons)", +"metabolites":{ +"h_c":-4.0, +"h_e":3.0, +"nad_c":1.0, +"nadh_c":-1.0, +"q8_c":-1.0, +"q8h2_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2276 and b2277 and b2278 and b2279 and b2280 and b2281 and b2282 and b2283 and b2284 and b2285 and b2286 and b2287 and b2288", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"NADH16" +] +}, +"annotation":{ +"bigg.reaction":[ +"NADH16" +], +"ec-code":[ +"1.6.5.3" +], +"metanetx.reaction":[ +"MNXR101864" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08972" +] +} +}, +{ +"id":"NADTRHD", +"name":"NAD transhydrogenase", +"metabolites":{ +"nad_c":-1.0, +"nadh_c":1.0, +"nadp_c":1.0, +"nadph_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3962 or (b1602 and b1603)", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"NADTRHD" +] +}, +"annotation":{ +"bigg.reaction":[ +"NADTRHD" +], +"biocyc":[ +"META:PYRNUTRANSHYDROGEN-RXN" +], +"ec-code":[ +"1.6.1.3", +"1.6.1.2", +"1.6.1.1" +], +"kegg.reaction":[ +"R00112" +], +"metanetx.reaction":[ +"MNXR101898" +], +"rhea":[ +"11692", +"11695", +"11694", +"11693" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00083" +] +} +}, +{ +"id":"NH4t", +"name":"Ammonia reversible transport", +"metabolites":{ +"nh4_c":1.0, +"nh4_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001 or b0451", +"subsystem":"Inorganic Ion Transport and Metabolism", +"notes":{ +"original_bigg_ids":[ +"NH4t" +] +}, +"annotation":{ +"bigg.reaction":[ +"NH4t" +], +"biocyc":[ +"META:TRANS-RXN0-206", +"META:RXN-9615", +"META:TRANS-RXN0-544" +], +"metanetx.reaction":[ +"MNXR101950" +], +"reactome.reaction":[ +"R-CEL-444416", +"R-SSC-444416", +"R-DDI-444416", +"R-MMU-444416", +"R-DRE-444416", +"R-GGA-444416", +"R-CFA-444416", +"R-HSA-444416", +"R-XTR-444416", +"R-BTA-444416", +"R-RNO-444416", +"R-TGU-444416", +"R-DME-444416" +], +"rhea":[ +"28749", +"28748", +"28750", +"28747" +], +"sabiork":[ +"11683" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn13364", +"rxn09835", +"rxn05466", +"rxn08987", +"rxn08986", +"rxn09736" +] +} +}, +{ +"id":"O2t", +"name":"O2 transport diffusion ", +"metabolites":{ +"o2_c":1.0, +"o2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"O2t" +] +}, +"annotation":{ +"bigg.reaction":[ +"O2t" +], +"biocyc":[ +"META:TRANS-RXN0-474" +], +"metanetx.reaction":[ +"MNXR102090" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09641", +"rxn05468", +"rxn09031", +"rxn09032", +"rxn09734" +] +} +}, +{ +"id":"PDH", +"name":"Pyruvate dehydrogenase", +"metabolites":{ +"accoa_c":1.0, +"co2_c":1.0, +"coa_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pyr_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0114 and b0115 and b0116", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PDH" +] +}, +"annotation":{ +"bigg.reaction":[ +"PDH" +], +"biocyc":[ +"META:PYRUVDEH-RXN" +], +"ec-code":[ +"1.2.1", +"1.8.1.4", +"1.2.1.51", +"1.2.4.1", +"2.3.1.12" +], +"kegg.reaction":[ +"R00209" +], +"metanetx.reaction":[ +"MNXR102425" +], +"reactome.reaction":[ +"R-RNO-71397", +"R-OSA-71397", +"R-GGA-373177", +"R-DME-71397", +"R-TGU-71397", +"R-XTR-71397", +"R-CFA-71397", +"R-BTA-71397", +"R-HSA-71397", +"R-GGA-71397", +"R-SPO-71397", +"R-CEL-71397", +"R-DDI-71397", +"R-DRE-71397", +"R-SSC-71397", +"R-SCE-71397", +"R-ATH-71397", +"R-MMU-71397" +], +"rhea":[ +"28043", +"28045", +"28044", +"28042" +], +"sabiork":[ +"523" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00154" +] +} +} +], +"genes":[ +{ +"id":"b1241", +"name":"adhE", +"notes":{ +"original_bigg_ids":[ +"b1241" +] +}, +"annotation":{ +"asap":[ +"ABE-0004164" +], +"ecogene":[ +"EG10031" +], +"ncbigene":[ +"945837" +], +"ncbigi":[ +"16129202" +], +"refseq_locus_tag":[ +"b1241" +], +"refseq_name":[ +"adhE" +], +"refseq_synonym":[ +"JW1228", +"ECK1235", +"adhC", +"ana" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9Q7" +] +} +}, +{ +"id":"b0351", +"name":"mhpF", +"notes":{ +"original_bigg_ids":[ +"b0351" +] +}, +"annotation":{ +"asap":[ +"ABE-0001207" +], +"ecogene":[ +"EG13625" +], +"ncbigene":[ +"945008" +], +"ncbigi":[ +"16128336" +], +"refseq_locus_tag":[ +"b0351" +], +"refseq_name":[ +"mhpF" +], +"refseq_synonym":[ +"JW0342", +"ECK0348" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77580" +] +} +}, +{ +"id":"s0001", +"name":"", +"notes":{ +"original_bigg_ids":[ +"s0001" +] +}, +"annotation":{ +"sbo":"SBO:0000243" +} +}, +{ +"id":"b1849", +"name":"purT", +"notes":{ +"original_bigg_ids":[ +"b1849" +] +}, +"annotation":{ +"asap":[ +"ABE-0006162" +], +"ecogene":[ +"EG11809" +], +"ncbigene":[ +"946368" +], +"ncbigi":[ +"16129802" +], +"refseq_locus_tag":[ +"b1849" +], +"refseq_name":[ +"purT" +], +"refseq_synonym":[ +"JW1838", +"ECK1850" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33221" +] +} +}, +{ +"id":"b3115", +"name":"tdcD", +"notes":{ +"original_bigg_ids":[ +"b3115" +] +}, +"annotation":{ +"asap":[ +"ABE-0010245" +], +"ecogene":[ +"EG11172" +], +"ncbigene":[ +"947635" +], +"ncbigi":[ +"145698313" +], +"refseq_locus_tag":[ +"b3115" +], +"refseq_name":[ +"tdcD" +], +"refseq_synonym":[ +"JW5806", +"ECK3104", +"yhaA" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P11868" +] +} +}, +{ +"id":"b2296", +"name":"ackA", +"notes":{ +"original_bigg_ids":[ +"b2296" +] +}, +"annotation":{ +"asap":[ +"ABE-0007579" +], +"ecogene":[ +"EG10027" +], +"ncbigene":[ +"946775" +], +"ncbigi":[ +"16130231" +], +"refseq_locus_tag":[ +"b2296" +], +"refseq_name":[ +"ackA" +], +"refseq_synonym":[ +"JW2293", +"ECK2290" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6A3" +] +} +}, +{ +"id":"b1276", +"name":"acnA", +"notes":{ +"original_bigg_ids":[ +"b1276" +] +}, +"annotation":{ +"asap":[ +"ABE-0004283" +], +"ecogene":[ +"EG11325" +], +"ncbigene":[ +"946724" +], +"ncbigi":[ +"16129237" +], +"refseq_locus_tag":[ +"b1276" +], +"refseq_name":[ +"acnA" +], +"refseq_synonym":[ +"JW1268", +"ECK1271", +"acn" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P25516" +] +} +}, +{ +"id":"b0118", +"name":"acnB", +"notes":{ +"original_bigg_ids":[ +"b0118" +] +}, +"annotation":{ +"asap":[ +"ABE-0000411" +], +"ecogene":[ +"EG12316" +], +"ncbigene":[ +"944864" +], +"ncbigi":[ +"16128111" +], +"refseq_locus_tag":[ +"b0118" +], +"refseq_name":[ +"acnB" +], +"refseq_synonym":[ +"ECK0117", +"JW0114", +"yacJ", +"yacI" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P36683" +] +} +}, +{ +"id":"b0474", +"name":"adk", +"notes":{ +"original_bigg_ids":[ +"b0474" +] +}, +"annotation":{ +"asap":[ +"ABE-0001645" +], +"ecogene":[ +"EG10032" +], +"ncbigene":[ +"945097" +], +"ncbigi":[ +"16128458" +], +"refseq_locus_tag":[ +"b0474" +], +"refseq_name":[ +"adk" +], +"refseq_synonym":[ +"plsA", +"JW0463", +"ECK0468", +"dnaW" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69441" +] +} +}, +{ +"id":"b0116", +"name":"lpd", +"notes":{ +"original_bigg_ids":[ +"b0116" +] +}, +"annotation":{ +"asap":[ +"ABE-0000404" +], +"ecogene":[ +"EG10543" +], +"ncbigene":[ +"944854" +], +"ncbigi":[ +"16128109" +], +"refseq_locus_tag":[ +"b0116" +], +"refseq_name":[ +"lpd" +], +"refseq_synonym":[ +"dhl", +"lpdA", +"ECK0115", +"JW0112" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9P0" +] +} +}, +{ +"id":"b0727", +"name":"sucB", +"notes":{ +"original_bigg_ids":[ +"b0727" +] +}, +"annotation":{ +"asap":[ +"ABE-0002480" +], +"ecogene":[ +"EG10980" +], +"ncbigene":[ +"945307" +], +"ncbigi":[ +"16128702" +], +"refseq_locus_tag":[ +"b0727" +], +"refseq_name":[ +"sucB" +], +"refseq_synonym":[ +"JW0716", +"ECK0715" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFG6" +] +} +}, +{ +"id":"b0726", +"name":"sucA", +"notes":{ +"original_bigg_ids":[ +"b0726" +] +}, +"annotation":{ +"asap":[ +"ABE-0002478" +], +"ecogene":[ +"EG10979" +], +"ncbigene":[ +"945303" +], +"ncbigi":[ +"16128701" +], +"refseq_locus_tag":[ +"b0726" +], +"refseq_name":[ +"sucA" +], +"refseq_synonym":[ +"lys", +"JW0715", +"ECK0714" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFG3" +] +} +}, +{ +"id":"b2587", +"name":"kgtP", +"notes":{ +"original_bigg_ids":[ +"b2587" +] +}, +"annotation":{ +"asap":[ +"ABE-0008515" +], +"ecogene":[ +"EG10522" +], +"ncbigene":[ +"947069" +], +"ncbigi":[ +"16130512" +], +"refseq_locus_tag":[ +"b2587" +], +"refseq_name":[ +"kgtP" +], +"refseq_synonym":[ +"ECK2585", +"JW2571", +"witA" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AEX3" +] +} +}, +{ +"id":"b0356", +"name":"frmA", +"notes":{ +"original_bigg_ids":[ +"b0356" +] +}, +"annotation":{ +"asap":[ +"ABE-0001221" +], +"ecogene":[ +"EG50010" +], +"ncbigene":[ +"944988" +], +"ncbigi":[ +"16128341" +], +"refseq_locus_tag":[ +"b0356" +], +"refseq_name":[ +"frmA" +], +"refseq_synonym":[ +"ECK0353", +"adhC", +"JW0347" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P25437" +] +} +}, +{ +"id":"b1478", +"name":"adhP", +"notes":{ +"original_bigg_ids":[ +"b1478" +] +}, +"annotation":{ +"asap":[ +"ABE-0004928" +], +"ecogene":[ +"EG12622" +], +"ncbigene":[ +"946036" +], +"ncbigi":[ +"90111280" +], +"refseq_locus_tag":[ +"b1478" +], +"refseq_name":[ +"adhP" +], +"refseq_synonym":[ +"yddN", +"ECK1472", +"JW1474" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P39451" +] +} +}, +{ +"id":"b3734", +"name":"atpA", +"notes":{ +"original_bigg_ids":[ +"b3734" +] +}, +"annotation":{ +"asap":[ +"ABE-0012213" +], +"ecogene":[ +"EG10098" +], +"ncbigene":[ +"948242" +], +"ncbigi":[ +"16131602" +], +"refseq_locus_tag":[ +"b3734" +], +"refseq_name":[ +"atpA" +], +"refseq_synonym":[ +"uncA", +"papA", +"ECK3727", +"JW3712" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABB0" +] +} +}, +{ +"id":"b3733", +"name":"atpG", +"notes":{ +"original_bigg_ids":[ +"b3733" +] +}, +"annotation":{ +"asap":[ +"ABE-0012211" +], +"ecogene":[ +"EG10104" +], +"ncbigene":[ +"948243" +], +"ncbigi":[ +"16131601" +], +"refseq_locus_tag":[ +"b3733" +], +"refseq_name":[ +"atpG" +], +"refseq_synonym":[ +"uncG", +"ECK3726", +"papC", +"JW3711" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABA6" +] +} +}, +{ +"id":"b3736", +"name":"atpF", +"notes":{ +"original_bigg_ids":[ +"b3736" +] +}, +"annotation":{ +"asap":[ +"ABE-0012217" +], +"ecogene":[ +"EG10103" +], +"ncbigene":[ +"948247" +], +"ncbigi":[ +"16131604" +], +"refseq_locus_tag":[ +"b3736" +], +"refseq_name":[ +"atpF" +], +"refseq_synonym":[ +"uncF", +"JW3714", +"papF", +"ECK3729" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABA0" +] +} +}, +{ +"id":"b3737", +"name":"atpE", +"notes":{ +"original_bigg_ids":[ +"b3737" +] +}, +"annotation":{ +"asap":[ +"ABE-0012220" +], +"ecogene":[ +"EG10102" +], +"ncbigene":[ +"948253" +], +"ncbigi":[ +"16131605" +], +"refseq_locus_tag":[ +"b3737" +], +"refseq_name":[ +"atpE" +], +"refseq_synonym":[ +"uncE", +"JW3715", +"ECK3730", +"papH" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P68699" +] +} +}, +{ +"id":"b3739", +"name":"atpI", +"notes":{ +"original_bigg_ids":[ +"b3739" +] +}, +"annotation":{ +"asap":[ +"ABE-0012224" +], +"ecogene":[ +"EG10106" +], +"ncbigene":[ +"948251" +], +"ncbigi":[ +"90111645" +], +"refseq_locus_tag":[ +"b3739" +], +"refseq_name":[ +"atpI" +], +"refseq_synonym":[ +"uncI", +"JW5611", +"ECK3732" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABC0" +] +} +}, +{ +"id":"b3738", +"name":"atpB", +"notes":{ +"original_bigg_ids":[ +"b3738" +] +}, +"annotation":{ +"asap":[ +"ABE-0012222" +], +"ecogene":[ +"EG10099" +], +"ncbigene":[ +"948252" +], +"ncbigi":[ +"16131606" +], +"refseq_locus_tag":[ +"b3738" +], +"refseq_name":[ +"atpB" +], +"refseq_synonym":[ +"JW3716", +"ECK3731", +"uncB", +"papD" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AB98" +] +} +}, +{ +"id":"b3735", +"name":"atpH", +"notes":{ +"original_bigg_ids":[ +"b3735" +] +}, +"annotation":{ +"asap":[ +"ABE-0012215" +], +"ecogene":[ +"EG10105" +], +"ncbigene":[ +"948254" +], +"ncbigi":[ +"16131603" +], +"refseq_locus_tag":[ +"b3735" +], +"refseq_name":[ +"atpH" +], +"refseq_synonym":[ +"JW3713", +"papE", +"ECK3728", +"uncH" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABA4" +] +} +}, +{ +"id":"b3731", +"name":"atpC", +"notes":{ +"original_bigg_ids":[ +"b3731" +] +}, +"annotation":{ +"asap":[ +"ABE-0012206" +], +"ecogene":[ +"EG10100" +], +"ncbigene":[ +"948245" +], +"ncbigi":[ +"16131599" +], +"refseq_locus_tag":[ +"b3731" +], +"refseq_name":[ +"atpC" +], +"refseq_synonym":[ +"uncC", +"ECK3724", +"papG", +"JW3709" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6E6" +] +} +}, +{ +"id":"b3732", +"name":"atpD", +"notes":{ +"original_bigg_ids":[ +"b3732" +] +}, +"annotation":{ +"asap":[ +"ABE-0012208" +], +"ecogene":[ +"EG10101" +], +"ncbigene":[ +"948244" +], +"ncbigi":[ +"16131600" +], +"refseq_locus_tag":[ +"b3732" +], +"refseq_name":[ +"atpD" +], +"refseq_synonym":[ +"papB", +"ECK3725", +"JW3710", +"uncD" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABB4" +] +} +}, +{ +"id":"b0720", +"name":"gltA", +"notes":{ +"original_bigg_ids":[ +"b0720" +] +}, +"annotation":{ +"asap":[ +"ABE-0002451" +], +"ecogene":[ +"EG10402" +], +"ncbigene":[ +"945323" +], +"ncbigi":[ +"16128695" +], +"refseq_locus_tag":[ +"b0720" +], +"refseq_name":[ +"gltA" +], +"refseq_synonym":[ +"JW0710", +"gluT", +"ECK0709", +"icdB" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABH7" +] +} +}, +{ +"id":"b0733", +"name":"cydA", +"notes":{ +"original_bigg_ids":[ +"b0733" +] +}, +"annotation":{ +"asap":[ +"ABE-0002499" +], +"ecogene":[ +"EG10173" +], +"ncbigene":[ +"945341" +], +"ncbigi":[ +"90111166" +], +"refseq_locus_tag":[ +"b0733" +], +"refseq_name":[ +"cydA" +], +"refseq_synonym":[ +"ECK0721", +"JW0722" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABJ9" +] +} +}, +{ +"id":"b0734", +"name":"cydB", +"notes":{ +"original_bigg_ids":[ +"b0734" +] +}, +"annotation":{ +"asap":[ +"ABE-0002501" +], +"ecogene":[ +"EG10174" +], +"ncbigene":[ +"945347" +], +"ncbigi":[ +"16128709" +], +"refseq_locus_tag":[ +"b0734" +], +"refseq_name":[ +"cydB" +], +"refseq_synonym":[ +"ECK0722", +"JW0723" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABK2" +] +} +}, +{ +"id":"b0979", +"name":"cbdB", +"notes":{ +"original_bigg_ids":[ +"b0979" +] +}, +"annotation":{ +"asap":[ +"ABE-0003302" +], +"ecogene":[ +"EG11379" +], +"ncbigene":[ +"947547" +], +"ncbigi":[ +"16128945" +], +"refseq_locus_tag":[ +"b0979" +], +"refseq_name":[ +"cbdB" +], +"refseq_synonym":[ +"JW0961", +"appB", +"cyxB", +"ECK0970" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P26458" +] +} +}, +{ +"id":"b0978", +"name":"cbdA", +"notes":{ +"original_bigg_ids":[ +"b0978" +] +}, +"annotation":{ +"asap":[ +"ABE-0003300" +], +"ecogene":[ +"EG11380" +], +"ncbigene":[ +"945585" +], +"ncbigi":[ +"16128944" +], +"refseq_locus_tag":[ +"b0978" +], +"refseq_name":[ +"cbdA" +], +"refseq_synonym":[ +"JW0960", +"ECK0969", +"cyxA", +"appC" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P26459" +] +} +}, +{ +"id":"b3603", +"name":"lldP", +"notes":{ +"original_bigg_ids":[ +"b3603" +] +}, +"annotation":{ +"asap":[ +"ABE-0011777" +], +"ecogene":[ +"EG11961" +], +"ncbigene":[ +"948114" +], +"ncbigi":[ +"16131474" +], +"refseq_locus_tag":[ +"b3603" +], +"refseq_name":[ +"lldP" +], +"refseq_synonym":[ +"JW3578", +"ECK3593", +"lct", +"lctP" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33231" +] +} +}, +{ +"id":"b2975", +"name":"glcA", +"notes":{ +"original_bigg_ids":[ +"b2975" +] +}, +"annotation":{ +"asap":[ +"ABE-0009763" +], +"ecogene":[ +"EG12995" +], +"ncbigene":[ +"947259" +], +"ncbigi":[ +"16130875" +], +"refseq_locus_tag":[ +"b2975" +], +"refseq_name":[ +"glcA" +], +"refseq_synonym":[ +"ECK2969", +"JW2942", +"yghK" +], +"sbo":"SBO:0000243", +"uniprot":[ +"Q46839" +] +} +}, +{ +"id":"b2779", +"name":"eno", +"notes":{ +"original_bigg_ids":[ +"b2779" +] +}, +"annotation":{ +"asap":[ +"ABE-0009110" +], +"ecogene":[ +"EG10258" +], +"ncbigene":[ +"945032" +], +"ncbigi":[ +"16130686" +], +"refseq_locus_tag":[ +"b2779" +], +"refseq_name":[ +"eno" +], +"refseq_synonym":[ +"JW2750", +"ECK2773" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6P9" +] +} +}, +{ +"id":"b2925", +"name":"fbaA", +"notes":{ +"original_bigg_ids":[ +"b2925" +] +}, +"annotation":{ +"asap":[ +"ABE-0009600" +], +"ecogene":[ +"EG10282" +], +"ncbigene":[ +"947415" +], +"ncbigi":[ +"16130826" +], +"refseq_locus_tag":[ +"b2925" +], +"refseq_name":[ +"fbaA" +], +"refseq_synonym":[ +"fba", +"ald", +"fda", +"ECK2921", +"JW2892" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AB71" +] +} +}, +{ +"id":"b1773", +"name":"ydjI", +"notes":{ +"original_bigg_ids":[ +"b1773" +] +}, +"annotation":{ +"asap":[ +"ABE-0005906" +], +"ecogene":[ +"EG13485" +], +"ncbigene":[ +"946291" +], +"ncbigi":[ +"16129727" +], +"refseq_locus_tag":[ +"b1773" +], +"refseq_name":[ +"ydjI" +], +"refseq_synonym":[ +"ECK1771", +"JW1762" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77704" +] +} +}, +{ +"id":"b2097", +"name":"fbaB", +"notes":{ +"original_bigg_ids":[ +"b2097" +] +}, +"annotation":{ +"asap":[ +"ABE-0006941" +], +"ecogene":[ +"EG14062" +], +"ncbigene":[ +"946632" +], +"ncbigi":[ +"90111385" +], +"refseq_locus_tag":[ +"b2097" +], +"refseq_name":[ +"fbaB" +], +"refseq_synonym":[ +"dhnA", +"JW5344", +"ECK2090" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A991" +] +} +}, +{ +"id":"b3925", +"name":"glpX", +"notes":{ +"original_bigg_ids":[ +"b3925" +] +}, +"annotation":{ +"asap":[ +"ABE-0012821" +], +"ecogene":[ +"EG11517" +], +"ncbigene":[ +"948424" +], +"ncbigi":[ +"16131763" +], +"refseq_locus_tag":[ +"b3925" +], +"refseq_name":[ +"glpX" +], +"refseq_synonym":[ +"JW3896", +"ECK3917" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9C9" +] +} +}, +{ +"id":"b4232", +"name":"fbp", +"notes":{ +"original_bigg_ids":[ +"b4232" +] +}, +"annotation":{ +"asap":[ +"ABE-0013842" +], +"ecogene":[ +"EG10283" +], +"ncbigene":[ +"948753" +], +"ncbigi":[ +"16132054" +], +"refseq_locus_tag":[ +"b4232" +], +"refseq_name":[ +"fbp" +], +"refseq_synonym":[ +"JW4191", +"ECK4227", +"fdp" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A993" +] +} +}, +{ +"id":"b2492", +"name":"focB", +"notes":{ +"original_bigg_ids":[ +"b2492" +] +}, +"annotation":{ +"asap":[ +"ABE-0008206" +], +"ecogene":[ +"EG14220" +], +"ncbigene":[ +"949032" +], +"ncbigi":[ +"16130417" +], +"refseq_locus_tag":[ +"b2492" +], +"refseq_name":[ +"focB" +], +"refseq_synonym":[ +"JW2477", +"ECK2488" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77733" +] +} +}, +{ +"id":"b0904", +"name":"focA", +"notes":{ +"original_bigg_ids":[ +"b0904" +] +}, +"annotation":{ +"asap":[ +"ABE-0003073" +], +"ecogene":[ +"EG11258" +], +"ncbigene":[ +"945513" +], +"ncbigi":[ +"16128871" +], +"refseq_locus_tag":[ +"b0904" +], +"refseq_name":[ +"focA" +], +"refseq_synonym":[ +"ycaE", +"ECK0895", +"JW0887" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC23" +] +} +}, +{ +"id":"b4152", +"name":"frdC", +"notes":{ +"original_bigg_ids":[ +"b4152" +] +}, +"annotation":{ +"asap":[ +"ABE-0013598" +], +"ecogene":[ +"EG10332" +], +"ncbigene":[ +"948680" +], +"ncbigi":[ +"16131977" +], +"refseq_locus_tag":[ +"b4152" +], +"refseq_name":[ +"frdC" +], +"refseq_synonym":[ +"ECK4148", +"JW4113" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A8Q0" +] +} +}, +{ +"id":"b4154", +"name":"frdA", +"notes":{ +"original_bigg_ids":[ +"b4154" +] +}, +"annotation":{ +"asap":[ +"ABE-0013604" +], +"ecogene":[ +"EG10330" +], +"ncbigene":[ +"948667" +], +"ncbigi":[ +"16131979" +], +"refseq_locus_tag":[ +"b4154" +], +"refseq_name":[ +"frdA" +], +"refseq_synonym":[ +"ECK4150", +"JW4115" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00363" +] +} +}, +{ +"id":"b4153", +"name":"frdB", +"notes":{ +"original_bigg_ids":[ +"b4153" +] +}, +"annotation":{ +"asap":[ +"ABE-0013602" +], +"ecogene":[ +"EG10331" +], +"ncbigene":[ +"948666" +], +"ncbigi":[ +"16131978" +], +"refseq_locus_tag":[ +"b4153" +], +"refseq_name":[ +"frdB" +], +"refseq_synonym":[ +"JW4114", +"ECK4149" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC47" +] +} +}, +{ +"id":"b4151", +"name":"frdD", +"notes":{ +"original_bigg_ids":[ +"b4151" +] +}, +"annotation":{ +"asap":[ +"ABE-0013595" +], +"ecogene":[ +"EG10333" +], +"ncbigene":[ +"948668" +], +"ncbigi":[ +"16131976" +], +"refseq_locus_tag":[ +"b4151" +], +"refseq_name":[ +"frdD" +], +"refseq_synonym":[ +"JW4112", +"ECK4147" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A8Q3" +] +} +}, +{ +"id":"b1819", +"name":"manZ", +"notes":{ +"original_bigg_ids":[ +"b1819" +] +}, +"annotation":{ +"asap":[ +"ABE-0006058" +], +"ecogene":[ +"EG10569" +], +"ncbigene":[ +"946342" +], +"ncbigi":[ +"345452720" +], +"refseq_locus_tag":[ +"b1819" +], +"refseq_name":[ +"manZ" +], +"refseq_synonym":[ +"ptsM", +"ECK1817", +"ptsX", +"gptB", +"mpt", +"JW1808" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69805" +] +} +}, +{ +"id":"b1817", +"name":"manX", +"notes":{ +"original_bigg_ids":[ +"b1817" +] +}, +"annotation":{ +"asap":[ +"ABE-0006054" +], +"ecogene":[ +"EG10567" +], +"ncbigene":[ +"946334" +], +"ncbigi":[ +"16129771" +], +"refseq_locus_tag":[ +"b1817" +], +"refseq_name":[ +"manX" +], +"refseq_synonym":[ +"ECK1815", +"ptsX", +"gptB", +"mpt", +"JW1806", +"ptsL" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69797" +] +} +}, +{ +"id":"b2416", +"name":"ptsI", +"notes":{ +"original_bigg_ids":[ +"b2416" +] +}, +"annotation":{ +"asap":[ +"ABE-0007967" +], +"ecogene":[ +"EG10789" +], +"ncbigene":[ +"946879" +], +"ncbigi":[ +"16130342" +], +"refseq_locus_tag":[ +"b2416" +], +"refseq_name":[ +"ptsI" +], +"refseq_synonym":[ +"ECK2411", +"ctr", +"JW2409" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P08839" +] +} +}, +{ +"id":"b2415", +"name":"ptsH", +"notes":{ +"original_bigg_ids":[ +"b2415" +] +}, +"annotation":{ +"asap":[ +"ABE-0007962" +], +"ecogene":[ +"EG10788" +], +"ncbigene":[ +"946886" +], +"ncbigi":[ +"16130341" +], +"refseq_locus_tag":[ +"b2415" +], +"refseq_name":[ +"ptsH" +], +"refseq_synonym":[ +"ctr", +"hpr", +"JW2408", +"ECK2410", +"iex?" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AA04" +] +} +}, +{ +"id":"b1818", +"name":"manY", +"notes":{ +"original_bigg_ids":[ +"b1818" +] +}, +"annotation":{ +"asap":[ +"ABE-0006056" +], +"ecogene":[ +"EG10568" +], +"ncbigene":[ +"946332" +], +"ncbigi":[ +"16129772" +], +"refseq_locus_tag":[ +"b1818" +], +"refseq_name":[ +"manY" +], +"refseq_synonym":[ +"ptsX", +"pel", +"ECK1816", +"JW1807", +"ptsP" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69801" +] +} +}, +{ +"id":"b1611", +"name":"fumC", +"notes":{ +"original_bigg_ids":[ +"b1611" +] +}, +"annotation":{ +"asap":[ +"ABE-0005380" +], +"ecogene":[ +"EG10358" +], +"ncbigene":[ +"946147" +], +"ncbigi":[ +"16129569" +], +"refseq_locus_tag":[ +"b1611" +], +"refseq_name":[ +"fumC" +], +"refseq_synonym":[ +"JW1603", +"ECK1606" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P05042" +] +} +}, +{ +"id":"b4122", +"name":"fumB", +"notes":{ +"original_bigg_ids":[ +"b4122" +] +}, +"annotation":{ +"asap":[ +"ABE-0013501" +], +"ecogene":[ +"EG10357" +], +"ncbigene":[ +"948642" +], +"ncbigi":[ +"16131948" +], +"refseq_locus_tag":[ +"b4122" +], +"refseq_name":[ +"fumB" +], +"refseq_synonym":[ +"JW4083", +"ECK4115" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P14407" +] +} +}, +{ +"id":"b1612", +"name":"fumA", +"notes":{ +"original_bigg_ids":[ +"b1612" +] +}, +"annotation":{ +"asap":[ +"ABE-0005392" +], +"ecogene":[ +"EG10356" +], +"ncbigene":[ +"946826" +], +"ncbigi":[ +"16129570" +], +"refseq_locus_tag":[ +"b1612" +], +"refseq_name":[ +"fumA" +], +"refseq_synonym":[ +"JW1604", +"ECK1607" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC33" +] +} +}, +{ +"id":"b3528", +"name":"dctA", +"notes":{ +"original_bigg_ids":[ +"b3528" +] +}, +"annotation":{ +"asap":[ +"ABE-0011527" +], +"ecogene":[ +"EG20044" +], +"ncbigene":[ +"948039" +], +"ncbigi":[ +"16131400" +], +"refseq_locus_tag":[ +"b3528" +], +"refseq_name":[ +"dctA" +], +"refseq_synonym":[ +"JW3496", +"ECK3513", +"out" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A830" +] +} +}, +{ +"id":"b1852", +"name":"zwf", +"notes":{ +"original_bigg_ids":[ +"b1852" +] +}, +"annotation":{ +"asap":[ +"ABE-0006171" +], +"ecogene":[ +"EG11221" +], +"ncbigene":[ +"946370" +], +"ncbigi":[ +"16129805" +], +"refseq_locus_tag":[ +"b1852" +], +"refseq_name":[ +"zwf" +], +"refseq_synonym":[ +"JW1841", +"ECK1853" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC53" +] +} +}, +{ +"id":"b1779", +"name":"gapA", +"notes":{ +"original_bigg_ids":[ +"b1779" +] +}, +"annotation":{ +"asap":[ +"ABE-0005920" +], +"ecogene":[ +"EG10367" +], +"ncbigene":[ +"947679" +], +"ncbigi":[ +"16129733" +], +"refseq_locus_tag":[ +"b1779" +], +"refseq_name":[ +"gapA" +], +"refseq_synonym":[ +"ECK1777", +"JW1768" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9B2" +] +} +}, +{ +"id":"b1101", +"name":"ptsG", +"notes":{ +"original_bigg_ids":[ +"b1101" +] +}, +"annotation":{ +"asap":[ +"ABE-0003722" +], +"ecogene":[ +"EG10787" +], +"ncbigene":[ +"945651" +], +"ncbigi":[ +"16129064" +], +"refseq_locus_tag":[ +"b1101" +], +"refseq_name":[ +"ptsG" +], +"refseq_synonym":[ +"car", +"JW1087", +"umg", +"glcA", +"umgC", +"cat", +"CR", +"tgl", +"ECK1087" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69786" +] +} +}, +{ +"id":"b2417", +"name":"crr", +"notes":{ +"original_bigg_ids":[ +"b2417" +] +}, +"annotation":{ +"asap":[ +"ABE-0007971" +], +"ecogene":[ +"EG10165" +], +"ncbigene":[ +"946880" +], +"ncbigi":[ +"16130343" +], +"refseq_locus_tag":[ +"b2417" +], +"refseq_name":[ +"crr" +], +"refseq_synonym":[ +"gsr", +"JW2410", +"ECK2412", +"treD", +"tgs", +"iex" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69783" +] +} +}, +{ +"id":"b1621", +"name":"malX", +"notes":{ +"original_bigg_ids":[ +"b1621" +] +}, +"annotation":{ +"asap":[ +"ABE-0005429" +], +"ecogene":[ +"EG10563" +], +"ncbigene":[ +"946009" +], +"ncbigi":[ +"16129579" +], +"refseq_locus_tag":[ +"b1621" +], +"refseq_name":[ +"malX" +], +"refseq_synonym":[ +"ECK1616", +"JW1613" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P19642" +] +} +}, +{ +"id":"b1297", +"name":"puuA", +"notes":{ +"original_bigg_ids":[ +"b1297" +] +}, +"annotation":{ +"asap":[ +"ABE-0004365" +], +"ecogene":[ +"EG13908" +], +"ncbigene":[ +"946202" +], +"ncbigi":[ +"90111244" +], +"refseq_locus_tag":[ +"b1297" +], +"refseq_name":[ +"puuA" +], +"refseq_synonym":[ +"ECK1292", +"JW5201", +"ycjK" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P78061" +] +} +}, +{ +"id":"b3870", +"name":"glnA", +"notes":{ +"original_bigg_ids":[ +"b3870" +] +}, +"annotation":{ +"asap":[ +"ABE-0012640" +], +"ecogene":[ +"EG10383" +], +"ncbigene":[ +"948370" +], +"ncbigi":[ +"16131710" +], +"refseq_locus_tag":[ +"b3870" +], +"refseq_name":[ +"glnA" +], +"refseq_synonym":[ +"ECK3863", +"JW3841" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9C5" +] +} +}, +{ +"id":"b0809", +"name":"glnQ", +"notes":{ +"original_bigg_ids":[ +"b0809" +] +}, +"annotation":{ +"asap":[ +"ABE-0002764" +], +"ecogene":[ +"EG10389" +], +"ncbigene":[ +"945435" +], +"ncbigi":[ +"16128777" +], +"refseq_locus_tag":[ +"b0809" +], +"refseq_name":[ +"glnQ" +], +"refseq_synonym":[ +"JW0794", +"ECK0798" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P10346" +] +} +}, +{ +"id":"b0811", +"name":"glnH", +"notes":{ +"original_bigg_ids":[ +"b0811" +] +}, +"annotation":{ +"asap":[ +"ABE-0002771" +], +"ecogene":[ +"EG10386" +], +"ncbigene":[ +"944872" +], +"ncbigi":[ +"16128779" +], +"refseq_locus_tag":[ +"b0811" +], +"refseq_name":[ +"glnH" +], +"refseq_synonym":[ +"JW0796", +"ECK0800" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AEQ3" +] +} +}, +{ +"id":"b0810", +"name":"glnP", +"notes":{ +"original_bigg_ids":[ +"b0810" +] +}, +"annotation":{ +"asap":[ +"ABE-0002766" +], +"ecogene":[ +"EG10388" +], +"ncbigene":[ +"945621" +], +"ncbigi":[ +"16128778" +], +"refseq_locus_tag":[ +"b0810" +], +"refseq_name":[ +"glnP" +], +"refseq_synonym":[ +"JW0795", +"ECK0799" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AEQ6" +] +} +}, +{ +"id":"b1761", +"name":"gdhA", +"notes":{ +"original_bigg_ids":[ +"b1761" +] +}, +"annotation":{ +"asap":[ +"ABE-0005865" +], +"ecogene":[ +"EG10372" +], +"ncbigene":[ +"946802" +], +"ncbigi":[ +"16129715" +], +"refseq_locus_tag":[ +"b1761" +], +"refseq_name":[ +"gdhA" +], +"refseq_synonym":[ +"ECK1759", +"JW1750" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00370" +] +} +}, +{ +"id":"b1524", +"name":"glsB", +"notes":{ +"original_bigg_ids":[ +"b1524" +] +}, +"annotation":{ +"asap":[ +"ABE-0005086" +], +"ecogene":[ +"EG13816" +], +"ncbigene":[ +"944973" +], +"ncbigi":[ +"16129483" +], +"refseq_locus_tag":[ +"b1524" +], +"refseq_name":[ +"glsB" +], +"refseq_synonym":[ +"glsA2", +"yneH", +"JW1517", +"ECK1517" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6W0" +] +} +}, +{ +"id":"b0485", +"name":"glsA", +"notes":{ +"original_bigg_ids":[ +"b0485" +] +}, +"annotation":{ +"asap":[ +"ABE-0001688" +], +"ecogene":[ +"EG13247" +], +"ncbigene":[ +"946187" +], +"ncbigi":[ +"16128469" +], +"refseq_locus_tag":[ +"b0485" +], +"refseq_name":[ +"glsA" +], +"refseq_synonym":[ +"glsA1", +"ECK0479", +"ybaS", +"JW0474" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77454" +] +} +}, +{ +"id":"b1812", +"name":"pabB", +"notes":{ +"original_bigg_ids":[ +"b1812" +] +}, +"annotation":{ +"asap":[ +"ABE-0006031" +], +"ecogene":[ +"EG10683" +], +"ncbigene":[ +"946337" +], +"ncbigi":[ +"16129766" +], +"refseq_locus_tag":[ +"b1812" +], +"refseq_name":[ +"pabB" +], +"refseq_synonym":[ +"ECK1810", +"JW1801" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P05041" +] +} +}, +{ +"id":"b3213", +"name":"gltD", +"notes":{ +"original_bigg_ids":[ +"b3213" +] +}, +"annotation":{ +"asap":[ +"ABE-0010547" +], +"ecogene":[ +"EG10404" +], +"ncbigene":[ +"947723" +], +"ncbigi":[ +"16131103" +], +"refseq_locus_tag":[ +"b3213" +], +"refseq_name":[ +"gltD" +], +"refseq_synonym":[ +"psiQ", +"aspB", +"ossB", +"JW3180", +"ECK3203" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P09832" +] +} +}, +{ +"id":"b3212", +"name":"gltB", +"notes":{ +"original_bigg_ids":[ +"b3212" +] +}, +"annotation":{ +"asap":[ +"ABE-0010545" +], +"ecogene":[ +"EG10403" +], +"ncbigene":[ +"947724" +], +"ncbigi":[ +"308209621" +], +"refseq_locus_tag":[ +"b3212" +], +"refseq_name":[ +"gltB" +], +"refseq_synonym":[ +"psiQ", +"aspB", +"ECK3202", +"ossB", +"JW3179" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P09831" +] +} +}, +{ +"id":"b4077", +"name":"gltP", +"notes":{ +"original_bigg_ids":[ +"b4077" +] +}, +"annotation":{ +"asap":[ +"ABE-0013357" +], +"ecogene":[ +"EG10405" +], +"ncbigene":[ +"948591" +], +"ncbigi":[ +"16131903" +], +"refseq_locus_tag":[ +"b4077" +], +"refseq_name":[ +"gltP" +], +"refseq_synonym":[ +"ECK4070", +"JW4038" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P21345" +] +} +}, +{ +"id":"b2029", +"name":"gnd", +"notes":{ +"original_bigg_ids":[ +"b2029" +] +}, +"annotation":{ +"asap":[ +"ABE-0006737" +], +"ecogene":[ +"EG10411" +], +"ncbigene":[ +"946554" +], +"ncbigi":[ +"16129970" +], +"refseq_locus_tag":[ +"b2029" +], +"refseq_name":[ +"gnd" +], +"refseq_synonym":[ +"JW2011", +"ECK2024" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00350" +] +} +}, +{ +"id":"b0875", +"name":"aqpZ", +"notes":{ +"original_bigg_ids":[ +"b0875" +] +}, +"annotation":{ +"asap":[ +"ABE-0002976" +], +"ecogene":[ +"EG13270" +], +"ncbigene":[ +"945497" +], +"ncbigi":[ +"16128843" +], +"refseq_locus_tag":[ +"b0875" +], +"refseq_name":[ +"aqpZ" +], +"refseq_synonym":[ +"bniP", +"JW0859", +"ECK0866" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P60844" +] +} +}, +{ +"id":"b1136", +"name":"icd", +"notes":{ +"original_bigg_ids":[ +"b1136" +] +}, +"annotation":{ +"asap":[ +"ABE-0003823" +], +"ecogene":[ +"EG10489" +], +"ncbigene":[ +"945702" +], +"ncbigi":[ +"16129099" +], +"refseq_locus_tag":[ +"b1136" +], +"refseq_name":[ +"icd" +], +"refseq_synonym":[ +"icdA", +"icdE", +"JW1122", +"ECK1122" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P08200" +] +} +}, +{ +"id":"b4015", +"name":"aceA", +"notes":{ +"original_bigg_ids":[ +"b4015" +] +}, +"annotation":{ +"asap":[ +"ABE-0013128" +], +"ecogene":[ +"EG10022" +], +"ncbigene":[ +"948517" +], +"ncbigi":[ +"16131841" +], +"refseq_locus_tag":[ +"b4015" +], +"refseq_name":[ +"aceA" +], +"refseq_synonym":[ +"JW3975", +"icl", +"ECK4007" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9G6" +] +} +}, +{ +"id":"b1380", +"name":"ldhA", +"notes":{ +"original_bigg_ids":[ +"b1380" +] +}, +"annotation":{ +"asap":[ +"ABE-0004619" +], +"ecogene":[ +"EG13186" +], +"ncbigene":[ +"946315" +], +"ncbigi":[ +"16129341" +], +"refseq_locus_tag":[ +"b1380" +], +"refseq_name":[ +"ldhA" +], +"refseq_synonym":[ +"ECK1377", +"JW1375", +"hslI", +"htpH", +"hslF" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P52643" +] +} +}, +{ +"id":"b2133", +"name":"dld", +"notes":{ +"original_bigg_ids":[ +"b2133" +] +}, +"annotation":{ +"asap":[ +"ABE-0007048" +], +"ecogene":[ +"EG10231" +], +"ncbigene":[ +"946653" +], +"ncbigi":[ +"16130071" +], +"refseq_locus_tag":[ +"b2133" +], +"refseq_name":[ +"dld" +], +"refseq_synonym":[ +"JW2121", +"ECK2126" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P06149" +] +} +}, +{ +"id":"b4014", +"name":"aceB", +"notes":{ +"original_bigg_ids":[ +"b4014" +] +}, +"annotation":{ +"asap":[ +"ABE-0013125" +], +"ecogene":[ +"EG10023" +], +"ncbigene":[ +"948512" +], +"ncbigi":[ +"16131840" +], +"refseq_locus_tag":[ +"b4014" +], +"refseq_name":[ +"aceB" +], +"refseq_synonym":[ +"ECK4006", +"mas", +"JW3974" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P08997" +] +} +}, +{ +"id":"b2976", +"name":"glcB", +"notes":{ +"original_bigg_ids":[ +"b2976" +] +}, +"annotation":{ +"asap":[ +"ABE-0009767" +], +"ecogene":[ +"EG20080" +], +"ncbigene":[ +"948857" +], +"ncbigi":[ +"16130876" +], +"refseq_locus_tag":[ +"b2976" +], +"refseq_name":[ +"glcB" +], +"refseq_synonym":[ +"JW2943", +"glc", +"ECK2970" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P37330" +] +} +}, +{ +"id":"b3236", +"name":"mdh", +"notes":{ +"original_bigg_ids":[ +"b3236" +] +}, +"annotation":{ +"asap":[ +"ABE-0010613" +], +"ecogene":[ +"EG10576" +], +"ncbigene":[ +"947854" +], +"ncbigi":[ +"16131126" +], +"refseq_locus_tag":[ +"b3236" +], +"refseq_name":[ +"mdh" +], +"refseq_synonym":[ +"ECK3225", +"JW3205" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P61889" +] +} +}, +{ +"id":"b1479", +"name":"maeA", +"notes":{ +"original_bigg_ids":[ +"b1479" +] +}, +"annotation":{ +"asap":[ +"ABE-0004931" +], +"ecogene":[ +"EG10948" +], +"ncbigene":[ +"946031" +], +"ncbigi":[ +"90111281" +], +"refseq_locus_tag":[ +"b1479" +], +"refseq_name":[ +"maeA" +], +"refseq_synonym":[ +"JW5238", +"sfcA", +"ECK1473" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P26616" +] +} +}, +{ +"id":"b2463", +"name":"maeB", +"notes":{ +"original_bigg_ids":[ +"b2463" +] +}, +"annotation":{ +"asap":[ +"ABE-0008111" +], +"ecogene":[ +"EG14193" +], +"ncbigene":[ +"946947" +], +"ncbigi":[ +"16130388" +], +"refseq_locus_tag":[ +"b2463" +], +"refseq_name":[ +"maeB" +], +"refseq_synonym":[ +"ECK2458", +"JW2447", +"ypfF" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P76558" +] +} +}, +{ +"id":"b2281", +"name":"nuoI", +"notes":{ +"original_bigg_ids":[ +"b2281" +] +}, +"annotation":{ +"asap":[ +"ABE-0007539" +], +"ecogene":[ +"EG12089" +], +"ncbigene":[ +"946757" +], +"ncbigi":[ +"16130216" +], +"refseq_locus_tag":[ +"b2281" +], +"refseq_name":[ +"nuoI" +], +"refseq_synonym":[ +"ECK2275", +"JW2276" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFD6" +] +} +}, +{ +"id":"b2277", +"name":"nuoM", +"notes":{ +"original_bigg_ids":[ +"b2277" +] +}, +"annotation":{ +"asap":[ +"ABE-0007529" +], +"ecogene":[ +"EG11773" +], +"ncbigene":[ +"947731" +], +"ncbigi":[ +"16130212" +], +"refseq_locus_tag":[ +"b2277" +], +"refseq_name":[ +"nuoM" +], +"refseq_synonym":[ +"JW2272", +"nuoA", +"ECK2271" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFE8" +] +} +}, +{ +"id":"b2280", +"name":"nuoJ", +"notes":{ +"original_bigg_ids":[ +"b2280" +] +}, +"annotation":{ +"asap":[ +"ABE-0007536" +], +"ecogene":[ +"EG12090" +], +"ncbigene":[ +"946756" +], +"ncbigi":[ +"16130215" +], +"refseq_locus_tag":[ +"b2280" +], +"refseq_name":[ +"nuoJ" +], +"refseq_synonym":[ +"ECK2274", +"JW2275" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFE0" +] +} +}, +{ +"id":"b2286", +"name":"nuoC", +"notes":{ +"original_bigg_ids":[ +"b2286" +] +}, +"annotation":{ +"asap":[ +"ABE-0007549" +], +"ecogene":[ +"EG12084" +], +"ncbigene":[ +"946759" +], +"ncbigi":[ +"145698291" +], +"refseq_locus_tag":[ +"b2286" +], +"refseq_name":[ +"nuoC" +], +"refseq_synonym":[ +"ECK2280", +"nuoD", +"nuoCD", +"JW5375" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33599" +] +} +}, +{ +"id":"b2287", +"name":"nuoB", +"notes":{ +"original_bigg_ids":[ +"b2287" +] +}, +"annotation":{ +"asap":[ +"ABE-0007551" +], +"ecogene":[ +"EG12083" +], +"ncbigene":[ +"946738" +], +"ncbigi":[ +"16130222" +], +"refseq_locus_tag":[ +"b2287" +], +"refseq_name":[ +"nuoB" +], +"refseq_synonym":[ +"JW5875", +"ECK2281" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFC7" +] +} +}, +{ +"id":"b2284", +"name":"nuoF", +"notes":{ +"original_bigg_ids":[ +"b2284" +] +}, +"annotation":{ +"asap":[ +"ABE-0007545" +], +"ecogene":[ +"EG11774" +], +"ncbigene":[ +"946753" +], +"ncbigi":[ +"16130219" +], +"refseq_locus_tag":[ +"b2284" +], +"refseq_name":[ +"nuoF" +], +"refseq_synonym":[ +"ECK2278", +"nuoB", +"JW2279" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P31979" +] +} +}, +{ +"id":"b2276", +"name":"nuoN", +"notes":{ +"original_bigg_ids":[ +"b2276" +] +}, +"annotation":{ +"asap":[ +"ABE-0007526" +], +"ecogene":[ +"EG12093" +], +"ncbigene":[ +"945136" +], +"ncbigi":[ +"145698289" +], +"refseq_locus_tag":[ +"b2276" +], +"refseq_name":[ +"nuoN" +], +"refseq_synonym":[ +"JW2271", +"ECK2270" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFF0" +] +} +}, +{ +"id":"b2282", +"name":"nuoH", +"notes":{ +"original_bigg_ids":[ +"b2282" +] +}, +"annotation":{ +"asap":[ +"ABE-0007541" +], +"ecogene":[ +"EG12088" +], +"ncbigene":[ +"946761" +], +"ncbigi":[ +"16130217" +], +"refseq_locus_tag":[ +"b2282" +], +"refseq_name":[ +"nuoH" +], +"refseq_synonym":[ +"JW2277", +"ECK2276" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFD4" +] +} +}, +{ +"id":"b2279", +"name":"nuoK", +"notes":{ +"original_bigg_ids":[ +"b2279" +] +}, +"annotation":{ +"asap":[ +"ABE-0007534" +], +"ecogene":[ +"EG12091" +], +"ncbigene":[ +"947580" +], +"ncbigi":[ +"16130214" +], +"refseq_locus_tag":[ +"b2279" +], +"refseq_name":[ +"nuoK" +], +"refseq_synonym":[ +"JW2274", +"ECK2273" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFE4" +] +} +}, +{ +"id":"b2283", +"name":"nuoG", +"notes":{ +"original_bigg_ids":[ +"b2283" +] +}, +"annotation":{ +"asap":[ +"ABE-0007543" +], +"ecogene":[ +"EG12087" +], +"ncbigene":[ +"946762" +], +"ncbigi":[ +"145698290" +], +"refseq_locus_tag":[ +"b2283" +], +"refseq_name":[ +"nuoG" +], +"refseq_synonym":[ +"JW2278", +"ECK2277" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33602" +] +} +}, +{ +"id":"b2285", +"name":"nuoE", +"notes":{ +"original_bigg_ids":[ +"b2285" +] +}, +"annotation":{ +"asap":[ +"ABE-0007547" +], +"ecogene":[ +"EG12086" +], +"ncbigene":[ +"946746" +], +"ncbigi":[ +"16130220" +], +"refseq_locus_tag":[ +"b2285" +], +"refseq_name":[ +"nuoE" +], +"refseq_synonym":[ +"JW2280", +"ECK2279" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFD1" +] +} +}, +{ +"id":"b2288", +"name":"nuoA", +"notes":{ +"original_bigg_ids":[ +"b2288" +] +}, +"annotation":{ +"asap":[ +"ABE-0007553" +], +"ecogene":[ +"EG12082" +], +"ncbigene":[ +"946764" +], +"ncbigi":[ +"49176207" +], +"refseq_locus_tag":[ +"b2288" +], +"refseq_name":[ +"nuoA" +], +"refseq_synonym":[ +"JW2283", +"ECK2282" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFC3" +] +} +}, +{ +"id":"b2278", +"name":"nuoL", +"notes":{ +"original_bigg_ids":[ +"b2278" +] +}, +"annotation":{ +"asap":[ +"ABE-0007532" +], +"ecogene":[ +"EG12092" +], +"ncbigene":[ +"945540" +], +"ncbigi":[ +"16130213" +], +"refseq_locus_tag":[ +"b2278" +], +"refseq_name":[ +"nuoL" +], +"refseq_synonym":[ +"ECK2272", +"JW2273" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33607" +] +} +}, +{ +"id":"b1603", +"name":"pntA", +"notes":{ +"original_bigg_ids":[ +"b1603" +] +}, +"annotation":{ +"asap":[ +"ABE-0005354" +], +"ecogene":[ +"EG10744" +], +"ncbigene":[ +"946628" +], +"ncbigi":[ +"16129561" +], +"refseq_locus_tag":[ +"b1603" +], +"refseq_name":[ +"pntA" +], +"refseq_synonym":[ +"JW1595", +"ECK1598" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P07001" +] +} +}, +{ +"id":"b3962", +"name":"sthA", +"notes":{ +"original_bigg_ids":[ +"b3962" +] +}, +"annotation":{ +"asap":[ +"ABE-0012975" +], +"ecogene":[ +"EG11428" +], +"ncbigene":[ +"948461" +], +"ncbigi":[ +"90111670" +], +"refseq_locus_tag":[ +"b3962" +], +"refseq_name":[ +"sthA" +], +"refseq_synonym":[ +"ECK3954", +"udhA", +"JW5551", +"sth" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P27306" +] +} +}, +{ +"id":"b1602", +"name":"pntB", +"notes":{ +"original_bigg_ids":[ +"b1602" +] +}, +"annotation":{ +"asap":[ +"ABE-0005352" +], +"ecogene":[ +"EG10745" +], +"ncbigene":[ +"946144" +], +"ncbigi":[ +"16129560" +], +"refseq_locus_tag":[ +"b1602" +], +"refseq_name":[ +"pntB" +], +"refseq_synonym":[ +"ECK1597", +"JW1594" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AB67" +] +} +}, +{ +"id":"b0451", +"name":"amtB", +"notes":{ +"original_bigg_ids":[ +"b0451" +] +}, +"annotation":{ +"asap":[ +"ABE-0001564" +], +"ecogene":[ +"EG11821" +], +"ncbigene":[ +"945084" +], +"ncbigi":[ +"16128436" +], +"refseq_locus_tag":[ +"b0451" +], +"refseq_name":[ +"amtB" +], +"refseq_synonym":[ +"JW0441", +"ECK0445", +"ybaG" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69681" +] +} +}, +{ +"id":"b0114", +"name":"aceE", +"notes":{ +"original_bigg_ids":[ +"b0114" +] +}, +"annotation":{ +"asap":[ +"ABE-0000397" +], +"ecogene":[ +"EG10024" +], +"ncbigene":[ +"944834" +], +"ncbigi":[ +"16128107" +], +"refseq_locus_tag":[ +"b0114" +], +"refseq_name":[ +"aceE" +], +"refseq_synonym":[ +"ECK0113", +"JW0110" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFG8" +] +} +}, +{ +"id":"b0115", +"name":"aceF", +"notes":{ +"original_bigg_ids":[ +"b0115" +] +}, +"annotation":{ +"asap":[ +"ABE-0000400" +], +"ecogene":[ +"EG10025" +], +"ncbigene":[ +"944794" +], +"ncbigi":[ +"16128108" +], +"refseq_locus_tag":[ +"b0115" +], +"refseq_name":[ +"aceF" +], +"refseq_synonym":[ +"ECK0114", +"JW0111" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P06959" +] +} +}, +{ +"id":"b3916", +"name":"pfkA", +"notes":{ +"original_bigg_ids":[ +"b3916" +] +}, +"annotation":{ +"asap":[ +"ABE-0012789" +], +"ecogene":[ +"EG10699" +], +"ncbigene":[ +"948412" +], +"ncbigi":[ +"16131754" +], +"refseq_locus_tag":[ +"b3916" +], +"refseq_name":[ +"pfkA" +], +"refseq_synonym":[ +"JW3887", +"ECK3908" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A796" +] +} +}, +{ +"id":"b1723", +"name":"pfkB", +"notes":{ +"original_bigg_ids":[ +"b1723" +] +}, +"annotation":{ +"asap":[ +"ABE-0005748" +], +"ecogene":[ +"EG10700" +], +"ncbigene":[ +"946230" +], +"ncbigi":[ +"49176138" +], +"refseq_locus_tag":[ +"b1723" +], +"refseq_name":[ +"pfkB" +], +"refseq_synonym":[ +"JW5280", +"ECK1721" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P06999" +] +} +}, +{ +"id":"b3114", +"name":"tdcE", +"notes":{ +"original_bigg_ids":[ +"b3114" +] +}, +"annotation":{ +"asap":[ +"ABE-0010242" +], +"ecogene":[ +"EG12758" +], +"ncbigene":[ +"947623" +], +"ncbigi":[ +"49176316" +], +"refseq_locus_tag":[ +"b3114" +], +"refseq_name":[ +"tdcE" +], +"refseq_synonym":[ +"JW5522", +"ECK3103", +"yhaS" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P42632" +] +} +}, +{ +"id":"b2579", +"name":"grcA", +"notes":{ +"original_bigg_ids":[ +"b2579" +] +}, +"annotation":{ +"asap":[ +"ABE-0008489" +], +"ecogene":[ +"EG11784" +], +"ncbigene":[ +"947068" +], +"ncbigi":[ +"16130504" +], +"refseq_locus_tag":[ +"b2579" +], +"refseq_name":[ +"grcA" +], +"refseq_synonym":[ +"ECK2577", +"yfiD", +"JW2563" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P68066" +] +} +}, +{ +"id":"b3951", +"name":"pflD", +"notes":{ +"original_bigg_ids":[ +"b3951" +] +}, +"annotation":{ +"asap":[ +"ABE-0012934" +], +"ecogene":[ +"EG11910" +], +"ncbigene":[ +"948454" +], +"ncbigi":[ +"16131789" +], +"refseq_locus_tag":[ +"b3951" +], +"refseq_name":[ +"pflD" +], +"refseq_synonym":[ +"ECK3942", +"yijL", +"JW3923" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P32674" +] +} +}, +{ +"id":"b0902", +"name":"pflA", +"notes":{ +"original_bigg_ids":[ +"b0902" +] +}, +"annotation":{ +"asap":[ +"ABE-0003068" +], +"ecogene":[ +"EG10028" +], +"ncbigene":[ +"945517" +], +"ncbigi":[ +"16128869" +], +"refseq_locus_tag":[ +"b0902" +], +"refseq_name":[ +"pflA" +], +"refseq_synonym":[ +"ECK0893", +"JW0885", +"act" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9N4" +] +} +}, +{ +"id":"b3952", +"name":"pflC", +"notes":{ +"original_bigg_ids":[ +"b3952" +] +}, +"annotation":{ +"asap":[ +"ABE-0012937" +], +"ecogene":[ +"EG11911" +], +"ncbigene":[ +"948453" +], +"ncbigi":[ +"49176447" +], +"refseq_locus_tag":[ +"b3952" +], +"refseq_name":[ +"pflC" +], +"refseq_synonym":[ +"ECK3943", +"JW3924", +"yijM" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P32675" +] +} +}, +{ +"id":"b0903", +"name":"pflB", +"notes":{ +"original_bigg_ids":[ +"b0903" +] +}, +"annotation":{ +"asap":[ +"ABE-0003071" +], +"ecogene":[ +"EG10701" +], +"ncbigene":[ +"945514" +], +"ncbigi":[ +"16128870" +], +"refseq_locus_tag":[ +"b0903" +], +"refseq_name":[ +"pflB" +], +"refseq_synonym":[ +"pfl", +"ECK0894", +"JW0886" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P09373" +] +} +}, +{ +"id":"b4025", +"name":"pgi", +"notes":{ +"original_bigg_ids":[ +"b4025" +] +}, +"annotation":{ +"asap":[ +"ABE-0013163" +], +"ecogene":[ +"EG10702" +], +"ncbigene":[ +"948535" +], +"ncbigi":[ +"16131851" +], +"refseq_locus_tag":[ +"b4025" +], +"refseq_name":[ +"pgi" +], +"refseq_synonym":[ +"JW3985", +"ECK4017" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6T1" +] +} +}, +{ +"id":"b2926", +"name":"pgk", +"notes":{ +"original_bigg_ids":[ +"b2926" +] +}, +"annotation":{ +"asap":[ +"ABE-0009605" +], +"ecogene":[ +"EG10703" +], +"ncbigene":[ +"947414" +], +"ncbigi":[ +"16130827" +], +"refseq_locus_tag":[ +"b2926" +], +"refseq_name":[ +"pgk" +], +"refseq_synonym":[ +"ECK2922", +"JW2893" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A799" +] +} +}, +{ +"id":"b0767", +"name":"pgl", +"notes":{ +"original_bigg_ids":[ +"b0767" +] +}, +"annotation":{ +"asap":[ +"ABE-0002611" +], +"ecogene":[ +"EG13231" +], +"ncbigene":[ +"946398" +], +"ncbigi":[ +"16128735" +], +"refseq_locus_tag":[ +"b0767" +], +"refseq_name":[ +"pgl" +], +"refseq_synonym":[ +"JW0750", +"ybhE", +"ECK0756", +"blu" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P52697" +] +} +}, +{ +"id":"b3612", +"name":"gpmM", +"notes":{ +"original_bigg_ids":[ +"b3612" +] +}, +"annotation":{ +"asap":[ +"ABE-0011818" +], +"ecogene":[ +"EG12296" +], +"ncbigene":[ +"948130" +], +"ncbigi":[ +"16131483" +], +"refseq_locus_tag":[ +"b3612" +], +"refseq_name":[ +"gpmM" +], +"refseq_synonym":[ +"JW3587", +"yibO", +"ECK3602", +"pgmI", +"gpmC", +"gpmI" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P37689" +] +} +}, +{ +"id":"b4395", +"name":"ytjC", +"notes":{ +"original_bigg_ids":[ +"b4395" +] +}, +"annotation":{ +"asap":[ +"ABE-0014416" +], +"ecogene":[ +"EG12164" +], +"ncbigene":[ +"948918" +], +"ncbigi":[ +"16132212" +], +"refseq_locus_tag":[ +"b4395" +], +"refseq_name":[ +"ytjC" +], +"refseq_synonym":[ +"gpmB", +"JW4358", +"ECK4387" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A7A2" +] +} +}, +{ +"id":"b0755", +"name":"gpmA", +"notes":{ +"original_bigg_ids":[ +"b0755" +] +}, +"annotation":{ +"asap":[ +"ABE-0002563" +], +"ecogene":[ +"EG11699" +], +"ncbigene":[ +"945068" +], +"ncbigi":[ +"16128723" +], +"refseq_locus_tag":[ +"b0755" +], +"refseq_name":[ +"gpmA" +], +"refseq_synonym":[ +"JW0738", +"gpm", +"ECK0744" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P62707" +] +} +}, +{ +"id":"b3493", +"name":"pitA", +"notes":{ +"original_bigg_ids":[ +"b3493" +] +}, +"annotation":{ +"asap":[ +"ABE-0011407" +], +"ecogene":[ +"EG12230" +], +"ncbigene":[ +"948009" +], +"ncbigi":[ +"16131365" +], +"refseq_locus_tag":[ +"b3493" +], +"refseq_name":[ +"pitA" +], +"refseq_synonym":[ +"pit", +"ECK3478", +"JW3460" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFJ7" +] +} +}, +{ +"id":"b2987", +"name":"pitB", +"notes":{ +"original_bigg_ids":[ +"b2987" +] +}, +"annotation":{ +"asap":[ +"ABE-0009800" +], +"ecogene":[ +"EG12883" +], +"ncbigene":[ +"947475" +], +"ncbigi":[ +"16130887" +], +"refseq_locus_tag":[ +"b2987" +], +"refseq_name":[ +"pitB" +], +"refseq_synonym":[ +"ECK2981", +"JW2955" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P43676" +] +} +}, +{ +"id":"b3956", +"name":"ppc", +"notes":{ +"original_bigg_ids":[ +"b3956" +] +}, +"annotation":{ +"asap":[ +"ABE-0012950" +], +"ecogene":[ +"EG10756" +], +"ncbigene":[ +"948457" +], +"ncbigi":[ +"16131794" +], +"refseq_locus_tag":[ +"b3956" +], +"refseq_name":[ +"ppc" +], +"refseq_synonym":[ +"glu", +"ECK3947", +"asp", +"JW3928" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00864" +] +} +}, +{ +"id":"b3403", +"name":"pck", +"notes":{ +"original_bigg_ids":[ +"b3403" +] +}, +"annotation":{ +"asap":[ +"ABE-0011106" +], +"ecogene":[ +"EG10688" +], +"ncbigene":[ +"945667" +], +"ncbigi":[ +"16131280" +], +"refseq_locus_tag":[ +"b3403" +], +"refseq_name":[ +"pck" +], +"refseq_synonym":[ +"JW3366", +"pckA", +"ECK3390" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P22259" +] +} +}, +{ +"id":"b1702", +"name":"ppsA", +"notes":{ +"original_bigg_ids":[ +"b1702" +] +}, +"annotation":{ +"asap":[ +"ABE-0005678" +], +"ecogene":[ +"EG10759" +], +"ncbigene":[ +"946209" +], +"ncbigi":[ +"16129658" +], +"refseq_locus_tag":[ +"b1702" +], +"refseq_name":[ +"ppsA" +], +"refseq_synonym":[ +"pps", +"ECK1700", +"JW1692" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P23538" +] +} +}, +{ +"id":"b2297", +"name":"pta", +"notes":{ +"original_bigg_ids":[ +"b2297" +] +}, +"annotation":{ +"asap":[ +"ABE-0007582" +], +"ecogene":[ +"EG20173" +], +"ncbigene":[ +"946778" +], +"ncbigi":[ +"16130232" +], +"refseq_locus_tag":[ +"b2297" +], +"refseq_name":[ +"pta" +], +"refseq_synonym":[ +"JW2294", +"ECK2291" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9M8" +] +} +}, +{ +"id":"b2458", +"name":"eutD", +"notes":{ +"original_bigg_ids":[ +"b2458" +] +}, +"annotation":{ +"asap":[ +"ABE-0008097" +], +"ecogene":[ +"EG14188" +], +"ncbigene":[ +"946940" +], +"ncbigi":[ +"16130383" +], +"refseq_locus_tag":[ +"b2458" +], +"refseq_name":[ +"eutD" +], +"refseq_synonym":[ +"eutI", +"ypfA", +"ECK2453", +"JW2442" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77218" +] +} +}, +{ +"id":"b1676", +"name":"pykF", +"notes":{ +"original_bigg_ids":[ +"b1676" +] +}, +"annotation":{ +"asap":[ +"ABE-0005600" +], +"ecogene":[ +"EG10804" +], +"ncbigene":[ +"946179" +], +"ncbigi":[ +"16129632" +], +"refseq_locus_tag":[ +"b1676" +], +"refseq_name":[ +"pykF" +], +"refseq_synonym":[ +"ECK1672", +"JW1666" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AD61" +] +} +}, +{ +"id":"b1854", +"name":"pykA", +"notes":{ +"original_bigg_ids":[ +"b1854" +] +}, +"annotation":{ +"asap":[ +"ABE-0006182" +], +"ecogene":[ +"EG10803" +], +"ncbigene":[ +"946527" +], +"ncbigi":[ +"16129807" +], +"refseq_locus_tag":[ +"b1854" +], +"refseq_name":[ +"pykA" +], +"refseq_synonym":[ +"JW1843", +"ECK1855" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P21599" +] +} +}, +{ +"id":"b3386", +"name":"rpe", +"notes":{ +"original_bigg_ids":[ +"b3386" +] +}, +"annotation":{ +"asap":[ +"ABE-0011061" +], +"ecogene":[ +"EG11960" +], +"ncbigene":[ +"947896" +], +"ncbigi":[ +"16131264" +], +"refseq_locus_tag":[ +"b3386" +], +"refseq_name":[ +"rpe" +], +"refseq_synonym":[ +"yhfD", +"ECK3373", +"JW3349", +"dod" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AG07" +] +} +}, +{ +"id":"b4301", +"name":"sgcE", +"notes":{ +"original_bigg_ids":[ +"b4301" +] +}, +"annotation":{ +"asap":[ +"ABE-0014097" +], +"ecogene":[ +"EG12553" +], +"ncbigene":[ +"948829" +], +"ncbigi":[ +"16132122" +], +"refseq_locus_tag":[ +"b4301" +], +"refseq_name":[ +"sgcE" +], +"refseq_synonym":[ +"JW4263", +"ECK4290", +"yjhK" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P39362" +] +} +}, +{ +"id":"b2914", +"name":"rpiA", +"notes":{ +"original_bigg_ids":[ +"b2914" +] +}, +"annotation":{ +"asap":[ +"ABE-0009567" +], +"ecogene":[ +"EG11443" +], +"ncbigene":[ +"947407" +], +"ncbigi":[ +"16130815" +], +"refseq_locus_tag":[ +"b2914" +], +"refseq_name":[ +"rpiA" +], +"refseq_synonym":[ +"ECK2910", +"JW5475", +"ygfC" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A7Z0" +] +} +}, +{ +"id":"b4090", +"name":"rpiB", +"notes":{ +"original_bigg_ids":[ +"b4090" +] +}, +"annotation":{ +"asap":[ +"ABE-0013405" +], +"ecogene":[ +"EG11827" +], +"ncbigene":[ +"948602" +], +"ncbigi":[ +"16131916" +], +"refseq_locus_tag":[ +"b4090" +], +"refseq_name":[ +"rpiB" +], +"refseq_synonym":[ +"JW4051", +"alsB", +"alsI", +"yjcA", +"ECK4083" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P37351" +] +} +}, +{ +"id":"b0721", +"name":"sdhC", +"notes":{ +"original_bigg_ids":[ +"b0721" +] +}, +"annotation":{ +"asap":[ +"ABE-0002460" +], +"ecogene":[ +"EG10933" +], +"ncbigene":[ +"945316" +], +"ncbigi":[ +"16128696" +], +"refseq_locus_tag":[ +"b0721" +], +"refseq_name":[ +"sdhC" +], +"refseq_synonym":[ +"JW0711", +"ECK0710", +"cybA" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69054" +] +} +}, +{ +"id":"b0722", +"name":"sdhD", +"notes":{ +"original_bigg_ids":[ +"b0722" +] +}, +"annotation":{ +"asap":[ +"ABE-0002464" +], +"ecogene":[ +"EG10934" +], +"ncbigene":[ +"945322" +], +"ncbigi":[ +"16128697" +], +"refseq_locus_tag":[ +"b0722" +], +"refseq_name":[ +"sdhD" +], +"refseq_synonym":[ +"JW0712", +"ECK0711" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC44" +] +} +}, +{ +"id":"b0724", +"name":"sdhB", +"notes":{ +"original_bigg_ids":[ +"b0724" +] +}, +"annotation":{ +"asap":[ +"ABE-0002468" +], +"ecogene":[ +"EG10932" +], +"ncbigene":[ +"945300" +], +"ncbigi":[ +"16128699" +], +"refseq_locus_tag":[ +"b0724" +], +"refseq_name":[ +"sdhB" +], +"refseq_synonym":[ +"ECK0713", +"JW0714" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P07014" +] +} +}, +{ +"id":"b0723", +"name":"sdhA", +"notes":{ +"original_bigg_ids":[ +"b0723" +] +}, +"annotation":{ +"asap":[ +"ABE-0002466" +], +"ecogene":[ +"EG10931" +], +"ncbigene":[ +"945402" +], +"ncbigi":[ +"16128698" +], +"refseq_locus_tag":[ +"b0723" +], +"refseq_name":[ +"sdhA" +], +"refseq_synonym":[ +"JW0713", +"ECK0712" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC41" +] +} +}, +{ +"id":"b0729", +"name":"sucD", +"notes":{ +"original_bigg_ids":[ +"b0729" +] +}, +"annotation":{ +"asap":[ +"ABE-0002485" +], +"ecogene":[ +"EG10982" +], +"ncbigene":[ +"945314" +], +"ncbigi":[ +"16128704" +], +"refseq_locus_tag":[ +"b0729" +], +"refseq_name":[ +"sucD" +], +"refseq_synonym":[ +"JW0718", +"ECK0717" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AGE9" +] +} +}, +{ +"id":"b0728", +"name":"sucC", +"notes":{ +"original_bigg_ids":[ +"b0728" +] +}, +"annotation":{ +"asap":[ +"ABE-0002483" +], +"ecogene":[ +"EG10981" +], +"ncbigene":[ +"945312" +], +"ncbigi":[ +"16128703" +], +"refseq_locus_tag":[ +"b0728" +], +"refseq_name":[ +"sucC" +], +"refseq_synonym":[ +"JW0717", +"ECK0716" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A836" +] +} +}, +{ +"id":"b0008", +"name":"talB", +"notes":{ +"original_bigg_ids":[ +"b0008" +] +}, +"annotation":{ +"asap":[ +"ABE-0000027" +], +"ecogene":[ +"EG11556" +], +"ncbigene":[ +"944748" +], +"ncbigi":[ +"16128002" +], +"refseq_locus_tag":[ +"b0008" +], +"refseq_name":[ +"talB" +], +"refseq_synonym":[ +"yaaK", +"JW0007", +"ECK0008" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A870" +] +} +}, +{ +"id":"b2464", +"name":"talA", +"notes":{ +"original_bigg_ids":[ +"b2464" +] +}, +"annotation":{ +"asap":[ +"ABE-0008115" +], +"ecogene":[ +"EG11797" +], +"ncbigene":[ +"947006" +], +"ncbigi":[ +"16130389" +], +"refseq_locus_tag":[ +"b2464" +], +"refseq_name":[ +"talA" +], +"refseq_synonym":[ +"ECK2459", +"JW2448" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A867" +] +} +}, +{ +"id":"b2465", +"name":"tktB", +"notes":{ +"original_bigg_ids":[ +"b2465" +] +}, +"annotation":{ +"asap":[ +"ABE-0008117" +], +"ecogene":[ +"EG12100" +], +"ncbigene":[ +"945865" +], +"ncbigi":[ +"16130390" +], +"refseq_locus_tag":[ +"b2465" +], +"refseq_name":[ +"tktB" +], +"refseq_synonym":[ +"JW2449", +"ECK2460" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33570" +] +} +}, +{ +"id":"b2935", +"name":"tktA", +"notes":{ +"original_bigg_ids":[ +"b2935" +] +}, +"annotation":{ +"asap":[ +"ABE-0009625" +], +"ecogene":[ +"EG11427" +], +"ncbigene":[ +"947420" +], +"ncbigi":[ +"49176286" +], +"refseq_locus_tag":[ +"b2935" +], +"refseq_name":[ +"tktA" +], +"refseq_synonym":[ +"JW5478", +"tkt", +"ECK2930" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P27302" +] +} +}, +{ +"id":"b3919", +"name":"tpiA", +"notes":{ +"original_bigg_ids":[ +"b3919" +] +}, +"annotation":{ +"asap":[ +"ABE-0012799" +], +"ecogene":[ +"EG11015" +], +"ncbigene":[ +"948409" +], +"ncbigi":[ +"16131757" +], +"refseq_locus_tag":[ +"b3919" +], +"refseq_name":[ +"tpiA" +], +"refseq_synonym":[ +"JW3890", +"ECK3911", +"tpi" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A858" +] +} +} +], +"id":"e_coli_core", +"compartments":{ +"c":"cytosol", +"e":"extracellular space" +}, +"version":"1" +} \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 2aea1a4d..214c574b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,3 +17,4 @@ nbsphinx == 0.8.3 scipy == 1.6.0 seaborn == 0.11.1 scikit-learn == 0.24.2 +pymatgen == 2022.0.10 diff --git a/setup.py b/setup.py index 676b3000..4a8dce57 100644 --- a/setup.py +++ b/setup.py @@ -56,7 +56,8 @@ "nbsphinx == 0.8.3", "scipy == 1.6.0", "seaborn == 0.11.1", - "scikit-learn == 0.24.2" + "scikit-learn == 0.24.2", + "pymatgen == 2022.0.10" ], # dependency_links= include_package_data=True, diff --git a/tests/test_MFA_visualization.py b/tests/test_MFA_visualization.py index a72a32af..c1a25b5f 100644 --- a/tests/test_MFA_visualization.py +++ b/tests/test_MFA_visualization.py @@ -4,6 +4,7 @@ import cobra import matplotlib import pandas as pd +from numpy import ndarray from BFAIR.mfa.visualization import ( reshape_fluxes_escher, sampled_fluxes_minrange, @@ -25,6 +26,43 @@ class test_methods(unittest.TestCase): maxDiff = None + # Add method for dictionary AlmostEqual assertion + def assertDeepAlmostEqual(self, expected, actual, *args, **kwargs): + """ + Assert that two complex structures have almost equal contents. + + Compares lists, dicts and tuples recursively. Checks numeric values + using test_case's :py:meth:`unittest.TestCase.assertAlmostEqual` and + checks all other values with :py:meth:`unittest.TestCase.assertEqual`. + Accepts additional positional and keyword arguments and pass those + intact to assertAlmostEqual() (that's how you specify comparison + precision). + """ + is_root = '__trace' not in kwargs + trace = kwargs.pop('__trace', 'ROOT') + try: + if isinstance(expected, (int, float, complex)): + self.assertAlmostEqual(expected, actual, *args, **kwargs) + elif isinstance(expected, (list, tuple, ndarray)): + self.assertEqual(len(expected), len(actual)) + for index in range(len(expected)): + v1, v2 = expected[index], actual[index] + self.assertDeepAlmostEqual(v1, v2, + __trace=repr(index), *args, **kwargs) + elif isinstance(expected, dict): + self.assertEqual(set(expected), set(actual)) + for key in expected: + self.assertDeepAlmostEqual(expected[key], actual[key], + __trace=repr(key), *args, **kwargs) + else: + self.assertEqual(expected, actual) + except AssertionError as exc: + exc.__dict__.setdefault('traces', []).append(trace) + if is_root: + trace = ' -> '.join(reversed(exc.traces)) + exc = AssertionError("%s\nTRACE: %s" % (exc.message, trace)) + raise exc + # Create method to compare dataframes def assertDataframeEqual(self, a, b, msg): try: @@ -71,7 +109,7 @@ def test_reshape_fluxes_escher(self): self.assertEqual(self.fluxes_relaxed, fluxes_relaxed_) relaxed_fluxes_sampling_ = reshape_fluxes_escher( self.relaxed_sampled_fluxes) - self.assertEqual( + self.assertDeepAlmostEqual( self.relaxed_fluxes_sampling, relaxed_fluxes_sampling_) def test_sampled_fluxes_minrange(self): diff --git a/tests/test_atom_mapping.py b/tests/test_atom_mapping.py new file mode 100644 index 00000000..d98eade5 --- /dev/null +++ b/tests/test_atom_mapping.py @@ -0,0 +1,224 @@ +import unittest +import pandas as pd +import pickle +import pathlib +import os +import shutil +from numpy import ndarray +from BFAIR.atom_mapping import (MolfileDownloader, + write_rxn_files, + obtain_atom_mappings, + parse_reaction_mappings, + parse_metabolite_mappings, + generate_INCA_mapping_input, + check_symmetry, + ) + +original_wd = os.getcwd() +current_dir = str(pathlib.Path(__file__).parent.absolute()) + + +class test_methods(unittest.TestCase): + + # Add method for list AlmostEqual assertion + def assertDeepAlmostEqual(self, expected, actual, *args, **kwargs): + """ + Assert that two complex structures have almost equal contents. + + Compares lists, dicts and tuples recursively. Checks numeric values + using test_case's :py:meth:`unittest.TestCase.assertAlmostEqual` and + checks all other values with :py:meth:`unittest.TestCase.assertEqual`. + Accepts additional positional and keyword arguments and pass those + intact to assertAlmostEqual() (that's how you specify comparison + precision). + """ + is_root = '__trace' not in kwargs + trace = kwargs.pop('__trace', 'ROOT') + try: + if isinstance(expected, (int, float, complex)): + self.assertAlmostEqual(expected, actual, *args, **kwargs) + elif isinstance(expected, (list, tuple, ndarray)): + self.assertEqual(len(expected), len(actual)) + for index in range(len(expected)): + v1, v2 = expected[index], actual[index] + self.assertDeepAlmostEqual( + v1, v2, __trace=repr(index), *args, **kwargs) + elif isinstance(expected, dict): + self.assertEqual(set(expected), set(actual)) + for key in expected: + self.assertDeepAlmostEqual( + expected[key], actual[key], __trace=repr(key), *args, **kwargs) + else: + self.assertEqual(expected, actual) + except AssertionError as exc: + exc.__dict__.setdefault('traces', []).append(trace) + if is_root: + trace = ' -> '.join(reversed(exc.traces)) + exc = AssertionError("%s\nTRACE: %s" % (exc.message, trace)) + raise exc + + # Create method to compare dataframes + + def assertDataframeEqual(self, a, b, msg): + try: + pd.testing.assert_frame_equal(a, b) + except AssertionError as e: + raise self.failureException(msg) from e + + @classmethod + def setUpClass(cls): + # Working directory changed to make sure that all generated + # test data is contained properly. + os.chdir(current_dir) + file_obj = open( + current_dir + '/test_data/atom_mapping_Data/test_data.obj', + 'rb') + ( + metabolites, + unmapped_rxns, + mapped_rxns, + reaction_df, + metabolite_df, + reaction_df_csv, + metabolite_df_csv, + model_reaction_df, + model_metabolite_df, + ) = pickle.load(file_obj) + + file_obj.close() + + cls.metabolites = metabolites + cls.unmapped_rxns = unmapped_rxns + cls.mapped_rxns = mapped_rxns + cls.reaction_df = reaction_df + cls.metabolite_df = metabolite_df + cls.reaction_df_csv = reaction_df_csv + cls.metabolite_df_csv = metabolite_df_csv + cls.model_reaction_df = model_reaction_df + cls.model_metabolite_df = model_metabolite_df + + @classmethod + def tearDownClass(cls): + shutil.rmtree(current_dir + '/metabolites') + shutil.rmtree(current_dir + '/unmappedRxns') + shutil.rmtree(current_dir + '/mappedRxns') + os.remove(current_dir + '/MappingReactions.csv') + os.remove(current_dir + '/MappingMetabolites.csv') + os.chdir(original_wd) + + def setUp(self): + # Add the method to compare dataframes in the class + self.addTypeEqualityFunc(pd.DataFrame, self.assertDataframeEqual) + + # Currently, tests are supposed to be run in alphabetical order + # i.e. "test_a_" first, then "test_b_", because their output + # depends on the output of other tests. + + def test_g_check_symmetry(self): + """ Tests check_symmetry() function + Makes sure that symmetric and non-symmetric compounds + are reported correctly """ + self.assertTrue(check_symmetry('succ_c.mol')) + self.assertFalse(check_symmetry('f6p_c.mol')) + + def test_f_generate_INCA_mapping_input(self): + """ Tests generate_INCA_mapping_input() function + Compares the resulting output to the previously generated results """ + reaction_df_csv = self.reaction_df_csv + metabolite_df_csv = self.metabolite_df_csv + reaction_df_ = parse_reaction_mappings() + metabolite_df_ = parse_metabolite_mappings() + + generate_INCA_mapping_input(reaction_df_, metabolite_df_) + + reaction_df_csv_ = pd.read_csv(current_dir + '/MappingReactions.csv') + metabolite_df_csv_ = pd.read_csv( + current_dir + '/MappingMetabolites.csv') + + self.assertEqual(reaction_df_csv, reaction_df_csv_) + self.assertEqual(metabolite_df_csv, metabolite_df_csv_) + + def test_e_parse_metabolite_mappings(self): + """ Tests parse_metabolite_mappings() function. + Compares the resulting output to the previously generated results """ + metabolite_df = self.metabolite_df + metabolite_df_ = parse_metabolite_mappings() + self.assertEqual(metabolite_df, metabolite_df_) + + def test_d_parse_reaction_mappings(self): + """ Tests parse_reaction_mappings function. + Compares the resulting output to the previously generated results """ + reaction_df = self.reaction_df + reaction_df_ = parse_reaction_mappings() + self.assertEqual(reaction_df, reaction_df_) + + def test_c_obtain_atom_mappings(self): + """ Tests obtain_atom_mapppings() function. + Compares the resulting output to the previously generated results """ + mapped_rxns = self.mapped_rxns + + obtain_atom_mappings() + + mapped_rxns_ = sorted(os.listdir(current_dir + '/mappedRxns/rxnFiles')) + for i, rxn_file in enumerate(mapped_rxns_): + with open(current_dir + f'/mappedRxns/rxnFiles/{rxn_file}', 'r') as f: + lines = f.readlines() + atom_rows = [] + for j, line in enumerate(lines): + if len(line.split()) in (15, 16): + # Only append rows containing atom mappings + atom_rows.append(line.split()) + mapped_rxns_[i] = atom_rows + + self.assertEqual(mapped_rxns, mapped_rxns_) + + def test_b_write_rxn_files(self): + """ Tests write_rxn_files function. + Compares the resulting output to the previously generated results """ + unmapped_rxns = self.unmapped_rxns + model_reaction_df = self.model_reaction_df + write_rxn_files(model_reaction_df) + + # Store all file contents in one list, and convert all numerics to + # floats + unmapped_rxns_ = sorted(os.listdir(current_dir + '/unmappedRxns')) + for i, rxn_file in enumerate(unmapped_rxns_): + with open(current_dir + f'/unmappedRxns/{rxn_file}', 'r') as f: + unmapped_rxns_[i] = f.readlines() + for j, line in enumerate(unmapped_rxns_[i]): + unmapped_rxns_[i][j] = unmapped_rxns_[i][j].split() + for k, val in enumerate(unmapped_rxns_[i][j]): + try: + unmapped_rxns_[i][j][k] = float(val) + except BaseException: + pass + + self.assertDeepAlmostEqual(unmapped_rxns, unmapped_rxns_) + + def test_a_MolfileDownloader(self): + """ Tests the MolfileDownloader class with all of its' methods. + Compares downloaded files to the ones downloaded previously """ + metabolites = self.metabolites + model_metabolite_df = self.model_metabolite_df + downloader = MolfileDownloader(model_metabolite_df) + downloader.generate_molfile_database() + + # Store all file contents in one list, and convert all numerics to + # floats + metabolites_ = sorted(os.listdir(current_dir + '/metabolites')) + for i, molfile in enumerate(metabolites_): + with open(current_dir + f'/metabolites/{molfile}', 'r') as f: + metabolites_[i] = f.readlines() + for j, met in enumerate(metabolites_[i]): + metabolites_[i][j] = metabolites_[i][j].split() + for k, val in enumerate(metabolites_[i][j]): + try: + metabolites_[i][j][k] = float(val) + except BaseException: + pass + + self.assertDeepAlmostEqual(metabolites, metabolites_) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_data/atom_mapping_Data/e_coli_core.json b/tests/test_data/atom_mapping_Data/e_coli_core.json new file mode 100644 index 00000000..39db7732 --- /dev/null +++ b/tests/test_data/atom_mapping_Data/e_coli_core.json @@ -0,0 +1,14786 @@ +{ +"metabolites":[ +{ +"id":"glc__D_e", +"name":"D-Glucose", +"compartment":"e", +"charge":0, +"formula":"C6H12O6", +"notes":{ +"original_bigg_ids":[ +"glc_D_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glc__D" +], +"biocyc":[ +"META:Glucopyranose" +], +"chebi":[ +"CHEBI:12965", +"CHEBI:20999", +"CHEBI:4167", +"CHEBI:17634" +], +"hmdb":[ +"HMDB00122", +"HMDB06564" +], +"inchi_key":[ +"WQZGKKKJIJFFOK-GASJEMHNSA-N" +], +"kegg.compound":[ +"C00031" +], +"kegg.drug":[ +"D00009" +], +"metanetx.chemical":[ +"MNXM41" +], +"sabiork":[ +"1406", +"1407" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd26821", +"cpd00027" +] +} +}, +{ +"id":"gln__L_c", +"name":"L-Glutamine", +"compartment":"c", +"charge":0, +"formula":"C5H10N2O3", +"notes":{ +"original_bigg_ids":[ +"gln_L_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"gln__L" +], +"biocyc":[ +"META:GLN" +], +"chebi":[ +"CHEBI:42943", +"CHEBI:42899", +"CHEBI:32679", +"CHEBI:32678", +"CHEBI:58359", +"CHEBI:28300", +"CHEBI:42812", +"CHEBI:13110", +"CHEBI:18050", +"CHEBI:32666", +"CHEBI:6227", +"CHEBI:32665", +"CHEBI:21308", +"CHEBI:42814", +"CHEBI:5432", +"CHEBI:24316" +], +"hmdb":[ +"HMDB00641" +], +"inchi_key":[ +"ZDXPYRJPNDTMRX-VKHMYHEASA-N" +], +"kegg.compound":[ +"C00064", +"C00303" +], +"kegg.drug":[ +"D00015" +], +"metanetx.chemical":[ +"MNXM37" +], +"reactome.compound":[ +"113522", +"212615", +"29472" +], +"sabiork":[ +"2011", +"74" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00253", +"cpd00053" +] +} +}, +{ +"id":"gln__L_e", +"name":"L-Glutamine", +"compartment":"e", +"charge":0, +"formula":"C5H10N2O3", +"notes":{ +"original_bigg_ids":[ +"gln_L_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"gln__L" +], +"biocyc":[ +"META:GLN" +], +"chebi":[ +"CHEBI:42943", +"CHEBI:42899", +"CHEBI:32679", +"CHEBI:32678", +"CHEBI:58359", +"CHEBI:28300", +"CHEBI:42812", +"CHEBI:13110", +"CHEBI:18050", +"CHEBI:32666", +"CHEBI:6227", +"CHEBI:32665", +"CHEBI:21308", +"CHEBI:42814", +"CHEBI:5432", +"CHEBI:24316" +], +"hmdb":[ +"HMDB00641" +], +"inchi_key":[ +"ZDXPYRJPNDTMRX-VKHMYHEASA-N" +], +"kegg.compound":[ +"C00064", +"C00303" +], +"kegg.drug":[ +"D00015" +], +"metanetx.chemical":[ +"MNXM37" +], +"reactome.compound":[ +"113522", +"212615", +"29472" +], +"sabiork":[ +"2011", +"74" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00253", +"cpd00053" +] +} +}, +{ +"id":"glu__L_c", +"name":"L-Glutamate", +"compartment":"c", +"charge":-1, +"formula":"C5H8NO4", +"notes":{ +"original_bigg_ids":[ +"glu_L_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glu__L" +], +"biocyc":[ +"META:Glutamates", +"META:GLT" +], +"chebi":[ +"CHEBI:76051", +"CHEBI:21301", +"CHEBI:29985", +"CHEBI:42825", +"CHEBI:29987", +"CHEBI:18237", +"CHEBI:24314", +"CHEBI:16015", +"CHEBI:13107", +"CHEBI:5431", +"CHEBI:21304", +"CHEBI:6224", +"CHEBI:14321", +"CHEBI:29988" +], +"hmdb":[ +"HMDB00148", +"HMDB60475" +], +"inchi_key":[ +"WHUUTDBJXJRKMK-VKHMYHEASA-M" +], +"kegg.compound":[ +"C00025", +"C00302" +], +"kegg.drug":[ +"D00007", +"D04341" +], +"metanetx.chemical":[ +"MNXM89557" +], +"reactome.compound":[ +"428614", +"29404", +"113552", +"210382" +], +"sabiork":[ +"73", +"2010" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27177", +"cpd00023", +"cpd19002" +] +} +}, +{ +"id":"glu__L_e", +"name":"L-Glutamate", +"compartment":"e", +"charge":-1, +"formula":"C5H8NO4", +"notes":{ +"original_bigg_ids":[ +"glu_L_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glu__L" +], +"biocyc":[ +"META:Glutamates", +"META:GLT" +], +"chebi":[ +"CHEBI:76051", +"CHEBI:21301", +"CHEBI:29985", +"CHEBI:42825", +"CHEBI:29987", +"CHEBI:18237", +"CHEBI:24314", +"CHEBI:16015", +"CHEBI:13107", +"CHEBI:5431", +"CHEBI:21304", +"CHEBI:6224", +"CHEBI:14321", +"CHEBI:29988" +], +"hmdb":[ +"HMDB00148", +"HMDB60475" +], +"inchi_key":[ +"WHUUTDBJXJRKMK-VKHMYHEASA-M" +], +"kegg.compound":[ +"C00025", +"C00302" +], +"kegg.drug":[ +"D00007", +"D04341" +], +"metanetx.chemical":[ +"MNXM89557" +], +"reactome.compound":[ +"428614", +"29404", +"113552", +"210382" +], +"sabiork":[ +"73", +"2010" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27177", +"cpd00023", +"cpd19002" +] +} +}, +{ +"id":"glx_c", +"name":"Glyoxylate", +"compartment":"c", +"charge":-1, +"formula":"C2H1O3", +"notes":{ +"original_bigg_ids":[ +"glx_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glx" +], +"biocyc":[ +"META:GLYOX" +], +"chebi":[ +"CHEBI:24420", +"CHEBI:36655", +"CHEBI:14368", +"CHEBI:24421", +"CHEBI:42767", +"CHEBI:16891", +"CHEBI:35977", +"CHEBI:5509" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/cdffdb1a-3322-4cc1-9171-d857bfaa198a", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/aecbda66-6e98-4c11-aeaf-6a072f4f963c", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/9dc0aa3b-447a-4b5d-8157-501b036f9626", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/43b74f4f-bc8a-4b8b-b587-c97d8e9eed48" +], +"hmdb":[ +"HMDB00119" +], +"inchi_key":[ +"HHLFWLYXYJOTON-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00048" +], +"metanetx.chemical":[ +"MNXM69" +], +"reactome.compound":[ +"904849", +"389678" +], +"sabiork":[ +"1838" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00040" +] +} +}, +{ +"id":"h2o_c", +"name":"H2O H2O", +"compartment":"c", +"charge":0, +"formula":"H2O", +"notes":{ +"original_bigg_ids":[ +"h2o_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h2o" +], +"biocyc":[ +"META:CPD-15815", +"META:OXONIUM", +"META:HYDROXYL-GROUP", +"META:WATER", +"META:OH" +], +"chebi":[ +"CHEBI:13352", +"CHEBI:30490", +"CHEBI:43228", +"CHEBI:33813", +"CHEBI:44292", +"CHEBI:44641", +"CHEBI:27313", +"CHEBI:42043", +"CHEBI:44819", +"CHEBI:29356", +"CHEBI:5594", +"CHEBI:10743", +"CHEBI:15377", +"CHEBI:42857", +"CHEBI:13365", +"CHEBI:29412", +"CHEBI:16234", +"CHEBI:13419", +"CHEBI:5585", +"CHEBI:44701" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/799908db-b8c9-4982-86cb-1f225e2ad08c", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/e7f34a8e-cded-4793-b6d5-792335b38636", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/969d0227-3069-4e44-9525-7ae7bad84170" +], +"hmdb":[ +"HMDB02111", +"HMDB01039" +], +"inchi_key":[ +"XLYOFNOQVPJJNP-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00001", +"C01328" +], +"kegg.drug":[ +"D00001", +"D06322" +], +"metanetx.chemical":[ +"MNXM2" +], +"reactome.compound":[ +"113521", +"141343", +"2022884", +"5278291", +"29356", +"189422", +"5668574", +"5693747", +"109276", +"113519", +"1605715", +"8851517", +"113518", +"351603" +], +"sabiork":[ +"40" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27222", +"cpd00001", +"cpd15275" +] +} +}, +{ +"id":"h2o_e", +"name":"H2O H2O", +"compartment":"e", +"charge":0, +"formula":"H2O", +"notes":{ +"original_bigg_ids":[ +"h2o_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h2o" +], +"biocyc":[ +"META:CPD-15815", +"META:OXONIUM", +"META:HYDROXYL-GROUP", +"META:WATER", +"META:OH" +], +"chebi":[ +"CHEBI:13352", +"CHEBI:30490", +"CHEBI:43228", +"CHEBI:33813", +"CHEBI:44292", +"CHEBI:44641", +"CHEBI:27313", +"CHEBI:42043", +"CHEBI:44819", +"CHEBI:29356", +"CHEBI:5594", +"CHEBI:10743", +"CHEBI:15377", +"CHEBI:42857", +"CHEBI:13365", +"CHEBI:29412", +"CHEBI:16234", +"CHEBI:13419", +"CHEBI:5585", +"CHEBI:44701" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/799908db-b8c9-4982-86cb-1f225e2ad08c", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/e7f34a8e-cded-4793-b6d5-792335b38636", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/969d0227-3069-4e44-9525-7ae7bad84170" +], +"hmdb":[ +"HMDB02111", +"HMDB01039" +], +"inchi_key":[ +"XLYOFNOQVPJJNP-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00001", +"C01328" +], +"kegg.drug":[ +"D00001", +"D06322" +], +"metanetx.chemical":[ +"MNXM2" +], +"reactome.compound":[ +"113521", +"141343", +"2022884", +"5278291", +"29356", +"189422", +"5668574", +"5693747", +"109276", +"113519", +"1605715", +"8851517", +"113518", +"351603" +], +"sabiork":[ +"40" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27222", +"cpd00001", +"cpd15275" +] +} +}, +{ +"id":"h_c", +"name":"H+", +"compartment":"c", +"charge":1, +"formula":"H", +"notes":{ +"original_bigg_ids":[ +"h_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h" +], +"biocyc":[ +"META:PROTON" +], +"chebi":[ +"CHEBI:5584", +"CHEBI:13357", +"CHEBI:15378", +"CHEBI:10744" +], +"hmdb":[ +"HMDB59597" +], +"inchi_key":[ +"GPRLSGONYQIRFK-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00080" +], +"metanetx.chemical":[ +"MNXM1" +], +"reactome.compound":[ +"2000349", +"425978", +"74722", +"428040", +"427899", +"428548", +"156540", +"70106", +"425969", +"1132304", +"5668577", +"1470067", +"163953", +"193465", +"113529", +"351626", +"425999", +"194688", +"374900", +"2872447", +"372511" +], +"sabiork":[ +"39" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00067" +] +} +}, +{ +"id":"h_e", +"name":"H+", +"compartment":"e", +"charge":1, +"formula":"H", +"notes":{ +"original_bigg_ids":[ +"h_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"h" +], +"biocyc":[ +"META:PROTON" +], +"chebi":[ +"CHEBI:5584", +"CHEBI:13357", +"CHEBI:15378", +"CHEBI:10744" +], +"hmdb":[ +"HMDB59597" +], +"inchi_key":[ +"GPRLSGONYQIRFK-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00080" +], +"metanetx.chemical":[ +"MNXM1" +], +"reactome.compound":[ +"2000349", +"425978", +"74722", +"428040", +"427899", +"428548", +"156540", +"70106", +"425969", +"1132304", +"5668577", +"1470067", +"163953", +"193465", +"113529", +"351626", +"425999", +"194688", +"374900", +"2872447", +"372511" +], +"sabiork":[ +"39" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00067" +] +} +}, +{ +"id":"icit_c", +"name":"Isocitrate", +"compartment":"c", +"charge":-3, +"formula":"C6H5O7", +"notes":{ +"original_bigg_ids":[ +"icit_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"icit" +], +"chebi":[ +"CHEBI:16087", +"CHEBI:36454", +"CHEBI:5998", +"CHEBI:24886", +"CHEBI:36453", +"CHEBI:14465", +"CHEBI:30887", +"CHEBI:24884" +], +"hmdb":[ +"HMDB00193" +], +"inchi_key":[ +"ODBLHEXUDAPZAU-UHFFFAOYSA-K" +], +"kegg.compound":[ +"C00311" +], +"metanetx.chemical":[ +"MNXM89661" +], +"sabiork":[ +"2013" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00260" +] +} +}, +{ +"id":"lac__D_c", +"name":"D-Lactate", +"compartment":"c", +"charge":-1, +"formula":"C3H5O3", +"notes":{ +"original_bigg_ids":[ +"lac_D_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"lac__D" +], +"biocyc":[ +"META:D-LACTATE" +], +"chebi":[ +"CHEBI:16004", +"CHEBI:341", +"CHEBI:18684", +"CHEBI:43701", +"CHEBI:11001", +"CHEBI:42111", +"CHEBI:42105" +], +"hmdb":[ +"HMDB01311", +"HMDB00171" +], +"inchi_key":[ +"JVTAAEKCZFNVCJ-UWTATZPHSA-M" +], +"kegg.compound":[ +"C00256" +], +"metanetx.chemical":[ +"MNXM285" +], +"sabiork":[ +"1997", +"2284" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00221" +] +} +}, +{ +"id":"lac__D_e", +"name":"D-Lactate", +"compartment":"e", +"charge":-1, +"formula":"C3H5O3", +"notes":{ +"original_bigg_ids":[ +"lac_D_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"lac__D" +], +"biocyc":[ +"META:D-LACTATE" +], +"chebi":[ +"CHEBI:16004", +"CHEBI:341", +"CHEBI:18684", +"CHEBI:43701", +"CHEBI:11001", +"CHEBI:42111", +"CHEBI:42105" +], +"hmdb":[ +"HMDB01311", +"HMDB00171" +], +"inchi_key":[ +"JVTAAEKCZFNVCJ-UWTATZPHSA-M" +], +"kegg.compound":[ +"C00256" +], +"metanetx.chemical":[ +"MNXM285" +], +"sabiork":[ +"1997", +"2284" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00221" +] +} +}, +{ +"id":"mal__L_c", +"name":"L-Malate", +"compartment":"c", +"charge":-2, +"formula":"C4H4O5", +"notes":{ +"original_bigg_ids":[ +"mal_L_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"mal__L" +], +"biocyc":[ +"META:MAL" +], +"chebi":[ +"CHEBI:15589", +"CHEBI:30797", +"CHEBI:423", +"CHEBI:18784", +"CHEBI:18785", +"CHEBI:13140", +"CHEBI:11066" +], +"hmdb":[ +"HMDB00156" +], +"inchi_key":[ +"BJEPYKJPYRNKOW-REOHCLBHSA-L" +], +"kegg.compound":[ +"C00149" +], +"metanetx.chemical":[ +"MNXM98" +], +"reactome.compound":[ +"198498", +"113544" +], +"sabiork":[ +"1918" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00130" +] +} +}, +{ +"id":"mal__L_e", +"name":"L-Malate", +"compartment":"e", +"charge":-2, +"formula":"C4H4O5", +"notes":{ +"original_bigg_ids":[ +"mal_L_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"mal__L" +], +"biocyc":[ +"META:MAL" +], +"chebi":[ +"CHEBI:15589", +"CHEBI:30797", +"CHEBI:423", +"CHEBI:18784", +"CHEBI:18785", +"CHEBI:13140", +"CHEBI:11066" +], +"hmdb":[ +"HMDB00156" +], +"inchi_key":[ +"BJEPYKJPYRNKOW-REOHCLBHSA-L" +], +"kegg.compound":[ +"C00149" +], +"metanetx.chemical":[ +"MNXM98" +], +"reactome.compound":[ +"198498", +"113544" +], +"sabiork":[ +"1918" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00130" +] +} +}, +{ +"id":"nad_c", +"name":"Nicotinamide adenine dinucleotide", +"compartment":"c", +"charge":-1, +"formula":"C21H26N7O14P2", +"notes":{ +"original_bigg_ids":[ +"nad_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nad" +], +"biocyc":[ +"META:NAD" +], +"chebi":[ +"CHEBI:7422", +"CHEBI:44215", +"CHEBI:13394", +"CHEBI:21901", +"CHEBI:57540", +"CHEBI:15846", +"CHEBI:44281", +"CHEBI:44214", +"CHEBI:13393", +"CHEBI:29867" +], +"hmdb":[ +"HMDB00902" +], +"inchi_key":[ +"BAWFJGJZGIEFAR-NNYOXOHSSA-M" +], +"kegg.compound":[ +"C00003" +], +"kegg.drug":[ +"D00002" +], +"metanetx.chemical":[ +"MNXM8" +], +"reactome.compound":[ +"352330", +"192307", +"194653", +"113526", +"29360" +], +"sabiork":[ +"37" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00003" +] +} +}, +{ +"id":"nadh_c", +"name":"Nicotinamide adenine dinucleotide - reduced", +"compartment":"c", +"charge":-2, +"formula":"C21H27N7O14P2", +"notes":{ +"original_bigg_ids":[ +"nadh_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nadh" +], +"biocyc":[ +"META:NADH" +], +"chebi":[ +"CHEBI:13395", +"CHEBI:21902", +"CHEBI:7423", +"CHEBI:44216", +"CHEBI:57945", +"CHEBI:16908", +"CHEBI:13396" +], +"hmdb":[ +"HMDB01487" +], +"inchi_key":[ +"BOPGDPNILDQYTO-NNYOXOHSSA-L" +], +"kegg.compound":[ +"C00004" +], +"metanetx.chemical":[ +"MNXM10" +], +"reactome.compound":[ +"192305", +"73473", +"29362", +"194697" +], +"sabiork":[ +"38" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00004" +] +} +}, +{ +"id":"nadp_c", +"name":"Nicotinamide adenine dinucleotide phosphate", +"compartment":"c", +"charge":-3, +"formula":"C21H25N7O17P3", +"notes":{ +"original_bigg_ids":[ +"nadp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nadp" +], +"biocyc":[ +"META:NADP" +], +"chebi":[ +"CHEBI:29868", +"CHEBI:44405", +"CHEBI:25523", +"CHEBI:13397", +"CHEBI:18009", +"CHEBI:7424", +"CHEBI:13398", +"CHEBI:21903", +"CHEBI:58349", +"CHEBI:44409" +], +"hmdb":[ +"HMDB00217" +], +"inchi_key":[ +"XJLXINKUBYWONI-NNYOXOHSSA-K" +], +"kegg.compound":[ +"C00006" +], +"metanetx.chemical":[ +"MNXM5" +], +"reactome.compound":[ +"194668", +"113563", +"6790191", +"5623650", +"2000348", +"389556", +"29366", +"351628", +"113564" +], +"sabiork":[ +"1263" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00006" +] +} +}, +{ +"id":"nadph_c", +"name":"Nicotinamide adenine dinucleotide phosphate - reduced", +"compartment":"c", +"charge":-4, +"formula":"C21H26N7O17P3", +"notes":{ +"original_bigg_ids":[ +"nadph_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nadph" +], +"biocyc":[ +"META:NADPH" +], +"chebi":[ +"CHEBI:16474", +"CHEBI:7425", +"CHEBI:57783", +"CHEBI:21904", +"CHEBI:13399", +"CHEBI:13400", +"CHEBI:44286" +], +"hmdb":[ +"HMDB06341", +"HMDB00221", +"HMDB00799" +], +"inchi_key":[ +"ACFIXJIJDZMPPO-NNYOXOHSSA-J" +], +"kegg.compound":[ +"C00005" +], +"metanetx.chemical":[ +"MNXM6" +], +"reactome.compound":[ +"113600", +"6790135", +"113602", +"113601", +"2000347", +"351627", +"29364", +"5623644", +"194725" +], +"sabiork":[ +"1262" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00005" +] +} +}, +{ +"id":"nh4_c", +"name":"Ammonium", +"compartment":"c", +"charge":1, +"formula":"H4N", +"notes":{ +"original_bigg_ids":[ +"nh4_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nh4" +], +"biocyc":[ +"META:AMMONIUM", +"META:AMMONIA" +], +"chebi":[ +"CHEBI:44284", +"CHEBI:135980", +"CHEBI:22533", +"CHEBI:13406", +"CHEBI:29337", +"CHEBI:29340", +"CHEBI:13771", +"CHEBI:16134", +"CHEBI:28938", +"CHEBI:22534", +"CHEBI:13405", +"CHEBI:49783", +"CHEBI:7434", +"CHEBI:7435", +"CHEBI:44269", +"CHEBI:44404", +"CHEBI:13407" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/96667bd9-aeae-4e8f-89d3-100d0396af05", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/27a89bdf-42f7-478f-91d8-e39881581096" +], +"hmdb":[ +"HMDB00051", +"HMDB41827" +], +"inchi_key":[ +"QGZKDVFQNNGYKY-UHFFFAOYSA-O" +], +"kegg.compound":[ +"C00014", +"C01342" +], +"kegg.drug":[ +"D02916", +"D02915" +], +"metanetx.chemical":[ +"MNXM15" +], +"reactome.compound":[ +"5693978", +"1132163", +"29382", +"76230", +"140912", +"389843", +"2022135", +"31633", +"113561" +], +"sabiork":[ +"1268", +"43" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19013", +"cpd00013" +] +} +}, +{ +"id":"13dpg_c", +"name":"3-Phospho-D-glyceroyl phosphate", +"compartment":"c", +"charge":-4, +"formula":"C3H4O10P2", +"notes":{ +"original_bigg_ids":[ +"13dpg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"13dpg" +], +"biocyc":[ +"META:DPG" +], +"chebi":[ +"CHEBI:57604", +"CHEBI:20189", +"CHEBI:11881", +"CHEBI:16001", +"CHEBI:1658" +], +"hmdb":[ +"HMDB62758" +], +"inchi_key":[ +"LJQLQCAXBUHEAZ-UWTATZPHSA-J" +], +"kegg.compound":[ +"C00236" +], +"metanetx.chemical":[ +"MNXM261" +], +"reactome.compound":[ +"29800" +], +"sabiork":[ +"21215" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00203" +] +} +}, +{ +"id":"nh4_e", +"name":"Ammonium", +"compartment":"e", +"charge":1, +"formula":"H4N", +"notes":{ +"original_bigg_ids":[ +"nh4_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"nh4" +], +"biocyc":[ +"META:AMMONIUM", +"META:AMMONIA" +], +"chebi":[ +"CHEBI:44284", +"CHEBI:135980", +"CHEBI:22533", +"CHEBI:13406", +"CHEBI:29337", +"CHEBI:29340", +"CHEBI:13771", +"CHEBI:16134", +"CHEBI:28938", +"CHEBI:22534", +"CHEBI:13405", +"CHEBI:49783", +"CHEBI:7434", +"CHEBI:7435", +"CHEBI:44269", +"CHEBI:44404", +"CHEBI:13407" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/96667bd9-aeae-4e8f-89d3-100d0396af05", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/27a89bdf-42f7-478f-91d8-e39881581096" +], +"hmdb":[ +"HMDB00051", +"HMDB41827" +], +"inchi_key":[ +"QGZKDVFQNNGYKY-UHFFFAOYSA-O" +], +"kegg.compound":[ +"C00014", +"C01342" +], +"kegg.drug":[ +"D02916", +"D02915" +], +"metanetx.chemical":[ +"MNXM15" +], +"reactome.compound":[ +"5693978", +"1132163", +"29382", +"76230", +"140912", +"389843", +"2022135", +"31633", +"113561" +], +"sabiork":[ +"1268", +"43" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19013", +"cpd00013" +] +} +}, +{ +"id":"o2_c", +"name":"O2 O2", +"compartment":"c", +"charge":0, +"formula":"O2", +"notes":{ +"original_bigg_ids":[ +"o2_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"o2" +], +"biocyc":[ +"META:OXYGEN-MOLECULE" +], +"chebi":[ +"CHEBI:7860", +"CHEBI:26689", +"CHEBI:29097", +"CHEBI:15379", +"CHEBI:13416", +"CHEBI:27140", +"CHEBI:29793", +"CHEBI:30491", +"CHEBI:44742", +"CHEBI:23833", +"CHEBI:25366", +"CHEBI:10745" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4" +], +"hmdb":[ +"HMDB01377" +], +"inchi_key":[ +"MYMOFIZGZYHOMD-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00007" +], +"kegg.drug":[ +"D00003" +], +"metanetx.chemical":[ +"MNXM4" +], +"reactome.compound":[ +"113534", +"113535", +"113685", +"5668566", +"189461", +"113533", +"1131511", +"352327", +"351593", +"29368", +"1236709" +], +"sabiork":[ +"1264" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00007" +] +} +}, +{ +"id":"2pg_c", +"name":"D-Glycerate 2-phosphate", +"compartment":"c", +"charge":-3, +"formula":"C3H4O7P", +"notes":{ +"original_bigg_ids":[ +"2pg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"2pg" +], +"biocyc":[ +"META:2-PG" +], +"chebi":[ +"CHEBI:39868", +"CHEBI:21028", +"CHEBI:58289", +"CHEBI:24344", +"CHEBI:12986", +"CHEBI:17835", +"CHEBI:11651", +"CHEBI:1267", +"CHEBI:88350" +], +"hmdb":[ +"HMDB00362", +"HMDB62707", +"HMDB03391" +], +"inchi_key":[ +"GXIURPTVHJPJLF-UWTATZPHSA-K" +], +"kegg.compound":[ +"C00631" +], +"metanetx.chemical":[ +"MNXM275" +], +"reactome.compound":[ +"30485" +], +"sabiork":[ +"31" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00482" +] +} +}, +{ +"id":"o2_e", +"name":"O2 O2", +"compartment":"e", +"charge":0, +"formula":"O2", +"notes":{ +"original_bigg_ids":[ +"o2_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"o2" +], +"biocyc":[ +"META:OXYGEN-MOLECULE" +], +"chebi":[ +"CHEBI:7860", +"CHEBI:26689", +"CHEBI:29097", +"CHEBI:15379", +"CHEBI:13416", +"CHEBI:27140", +"CHEBI:29793", +"CHEBI:30491", +"CHEBI:44742", +"CHEBI:23833", +"CHEBI:25366", +"CHEBI:10745" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4" +], +"hmdb":[ +"HMDB01377" +], +"inchi_key":[ +"MYMOFIZGZYHOMD-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00007" +], +"kegg.drug":[ +"D00003" +], +"metanetx.chemical":[ +"MNXM4" +], +"reactome.compound":[ +"113534", +"113535", +"113685", +"5668566", +"189461", +"113533", +"1131511", +"352327", +"351593", +"29368", +"1236709" +], +"sabiork":[ +"1264" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00007" +] +} +}, +{ +"id":"3pg_c", +"name":"3-Phospho-D-glycerate", +"compartment":"c", +"charge":-3, +"formula":"C3H4O7P", +"notes":{ +"original_bigg_ids":[ +"3pg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"3pg" +], +"biocyc":[ +"META:G3P" +], +"chebi":[ +"CHEBI:11879", +"CHEBI:11880", +"CHEBI:17794", +"CHEBI:21029", +"CHEBI:1657", +"CHEBI:58272", +"CHEBI:12987" +], +"hmdb":[ +"HMDB60180" +], +"inchi_key":[ +"OSJPPGNTCRNQQC-UWTATZPHSA-K" +], +"kegg.compound":[ +"C00197" +], +"metanetx.chemical":[ +"MNXM126" +], +"reactome.compound":[ +"6799493", +"29728" +], +"sabiork":[ +"21216" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00169" +] +} +}, +{ +"id":"oaa_c", +"name":"Oxaloacetate", +"compartment":"c", +"charge":-2, +"formula":"C4H2O5", +"notes":{ +"original_bigg_ids":[ +"oaa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"oaa" +], +"biocyc":[ +"META:OXALACETIC_ACID" +], +"chebi":[ +"CHEBI:25731", +"CHEBI:24959", +"CHEBI:12820", +"CHEBI:16452", +"CHEBI:30744", +"CHEBI:14703", +"CHEBI:24958", +"CHEBI:7812", +"CHEBI:25734", +"CHEBI:29049" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/133a11f3-81b0-4384-837e-1ccdd0a2a645", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/40afaad4-431a-4e3c-b4c7-020dbe4bdd2a", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/be7c543c-40bd-4698-9821-22f2e65c38f3" +], +"hmdb":[ +"HMDB00223" +], +"inchi_key":[ +"KHPXUQMNIQBQEV-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00036" +], +"lipidmaps":[ +"LMFA01170120" +], +"metanetx.chemical":[ +"MNXM46" +], +"reactome.compound":[ +"6810070", +"113587", +"76213" +], +"sabiork":[ +"1915" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00032" +] +} +}, +{ +"id":"pep_c", +"name":"Phosphoenolpyruvate", +"compartment":"c", +"charge":-3, +"formula":"C3H2O6P", +"notes":{ +"original_bigg_ids":[ +"pep_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pep" +], +"biocyc":[ +"META:PHOSPHO-ENOL-PYRUVATE" +], +"chebi":[ +"CHEBI:18021", +"CHEBI:44894", +"CHEBI:26054", +"CHEBI:14812", +"CHEBI:26055", +"CHEBI:8147", +"CHEBI:58702", +"CHEBI:44897" +], +"hmdb":[ +"HMDB00263" +], +"inchi_key":[ +"DTBNBXWJWCWCIK-UHFFFAOYSA-K" +], +"kegg.compound":[ +"C00074" +], +"metanetx.chemical":[ +"MNXM73" +], +"reactome.compound":[ +"372364", +"29492" +], +"sabiork":[ +"32" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00061" +] +} +}, +{ +"id":"6pgc_c", +"name":"6-Phospho-D-gluconate", +"compartment":"c", +"charge":-3, +"formula":"C6H10O10P", +"notes":{ +"original_bigg_ids":[ +"6pgc_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"6pgc" +], +"biocyc":[ +"META:CPD-2961" +], +"chebi":[ +"CHEBI:33851", +"CHEBI:2231", +"CHEBI:16863", +"CHEBI:40282", +"CHEBI:12232", +"CHEBI:48928", +"CHEBI:58759" +], +"hmdb":[ +"HMDB01316", +"HMDB62800" +], +"inchi_key":[ +"BIRSGZKFKXLSJQ-SQOUGZDYSA-K" +], +"kegg.compound":[ +"C00345" +], +"metanetx.chemical":[ +"MNXM325" +], +"reactome.compound":[ +"29996" +], +"sabiork":[ +"22801", +"2024" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00284" +] +} +}, +{ +"id":"pi_c", +"name":"Phosphate", +"compartment":"c", +"charge":-2, +"formula":"HO4P", +"notes":{ +"original_bigg_ids":[ +"pi_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pi" +], +"biocyc":[ +"META:Pi", +"META:CPD-16459", +"META:PHOSPHATE-GROUP" +], +"chebi":[ +"CHEBI:26078", +"CHEBI:18367", +"CHEBI:29139", +"CHEBI:39739", +"CHEBI:43470", +"CHEBI:35780", +"CHEBI:43474", +"CHEBI:26020", +"CHEBI:45024", +"CHEBI:39745", +"CHEBI:29137", +"CHEBI:14791", +"CHEBI:7793" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/db5219ee-60cb-4370-b066-340c9faf069c", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/84684967-eade-48d4-b25d-c4aede0a0836", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/ad82c39b-2edb-4953-b971-79a2d2ea6e26", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/aac01fea-4223-49c1-8b12-cd50f11ebfc8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04" +], +"hmdb":[ +"HMDB02105", +"HMDB00973", +"HMDB01429", +"HMDB02142", +"HMDB05947" +], +"inchi_key":[ +"NBIIXXVUZAFLBC-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00009" +], +"kegg.drug":[ +"D05467" +], +"metanetx.chemical":[ +"MNXM9" +], +"reactome.compound":[ +"5228339", +"113550", +"8851513", +"113551", +"109277", +"29372", +"8851226", +"113548" +], +"sabiork":[ +"36" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27787", +"cpd00009" +] +} +}, +{ +"id":"6pgl_c", +"name":"6-phospho-D-glucono-1,5-lactone", +"compartment":"c", +"charge":-2, +"formula":"C6H9O9P", +"notes":{ +"original_bigg_ids":[ +"6pgl_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"6pgl" +], +"biocyc":[ +"META:D-6-P-GLUCONO-DELTA-LACTONE" +], +"chebi":[ +"CHEBI:12233", +"CHEBI:4160", +"CHEBI:57955", +"CHEBI:16938", +"CHEBI:20989", +"CHEBI:12958" +], +"hmdb":[ +"HMDB62628", +"HMDB01127" +], +"inchi_key":[ +"IJOJIVNDFQSGAB-SQOUGZDYSA-L" +], +"kegg.compound":[ +"C01236" +], +"metanetx.chemical":[ +"MNXM429" +], +"reactome.compound":[ +"31467" +], +"sabiork":[ +"1366" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00911" +] +} +}, +{ +"id":"pi_e", +"name":"Phosphate", +"compartment":"e", +"charge":-2, +"formula":"HO4P", +"notes":{ +"original_bigg_ids":[ +"pi_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pi" +], +"biocyc":[ +"META:Pi", +"META:CPD-16459", +"META:PHOSPHATE-GROUP" +], +"chebi":[ +"CHEBI:26078", +"CHEBI:18367", +"CHEBI:29139", +"CHEBI:39739", +"CHEBI:43470", +"CHEBI:35780", +"CHEBI:43474", +"CHEBI:26020", +"CHEBI:45024", +"CHEBI:39745", +"CHEBI:29137", +"CHEBI:14791", +"CHEBI:7793" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/db5219ee-60cb-4370-b066-340c9faf069c", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/84684967-eade-48d4-b25d-c4aede0a0836", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/ad82c39b-2edb-4953-b971-79a2d2ea6e26", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/aac01fea-4223-49c1-8b12-cd50f11ebfc8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04" +], +"hmdb":[ +"HMDB02105", +"HMDB00973", +"HMDB01429", +"HMDB02142", +"HMDB05947" +], +"inchi_key":[ +"NBIIXXVUZAFLBC-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00009" +], +"kegg.drug":[ +"D05467" +], +"metanetx.chemical":[ +"MNXM9" +], +"reactome.compound":[ +"5228339", +"113550", +"8851513", +"113551", +"109277", +"29372", +"8851226", +"113548" +], +"sabiork":[ +"36" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd27787", +"cpd00009" +] +} +}, +{ +"id":"ac_c", +"name":"Acetate", +"compartment":"c", +"charge":-1, +"formula":"C2H3O2", +"notes":{ +"original_bigg_ids":[ +"ac_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"ac" +], +"biocyc":[ +"META:ACET" +], +"chebi":[ +"CHEBI:13704", +"CHEBI:22165", +"CHEBI:22169", +"CHEBI:40480", +"CHEBI:15366", +"CHEBI:2387", +"CHEBI:30089", +"CHEBI:40486" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/9e26dcbe-4db9-46a0-8614-9f03545032d2", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/5e4989fc-13d3-45d4-ad57-3be380a9d3c0", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/a8f0be58-24e8-441b-8d81-a516a0ead4b3", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/d45256fe-61fa-4f5b-bb16-91a3d615e3d8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/3e2d750f-df31-4445-9255-163c627e9b4a" +], +"hmdb":[ +"HMDB00042" +], +"inchi_key":[ +"QTBSBXVTEAMEQO-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00033" +], +"kegg.drug":[ +"D00010" +], +"lipidmaps":[ +"LMFA01010002" +], +"metanetx.chemical":[ +"MNXM26" +], +"reactome.compound":[ +"1524044", +"390305", +"113539", +"2022890", +"29416" +], +"sabiork":[ +"1278" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00029" +], +"slm":[ +"000000449" +] +} +}, +{ +"id":"pyr_c", +"name":"Pyruvate", +"compartment":"c", +"charge":-1, +"formula":"C3H3O3", +"notes":{ +"original_bigg_ids":[ +"pyr_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pyr" +], +"biocyc":[ +"META:PYRUVATE" +], +"chebi":[ +"CHEBI:26462", +"CHEBI:26466", +"CHEBI:8685", +"CHEBI:32816", +"CHEBI:45253", +"CHEBI:14987", +"CHEBI:15361" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ccc99777-54dc-42d4-a97e-009b780d3905", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc01020e-8c7e-4087-9f56-cf8c962b7437" +], +"hmdb":[ +"HMDB00243" +], +"inchi_key":[ +"LCTONWCANYUPML-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00022" +], +"lipidmaps":[ +"LMFA01060077" +], +"metanetx.chemical":[ +"MNXM23" +], +"reactome.compound":[ +"1130930", +"5357717", +"113557", +"29398", +"389680" +], +"sabiork":[ +"33" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00020" +] +} +}, +{ +"id":"pyr_e", +"name":"Pyruvate", +"compartment":"e", +"charge":-1, +"formula":"C3H3O3", +"notes":{ +"original_bigg_ids":[ +"pyr_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"pyr" +], +"biocyc":[ +"META:PYRUVATE" +], +"chebi":[ +"CHEBI:26462", +"CHEBI:26466", +"CHEBI:8685", +"CHEBI:32816", +"CHEBI:45253", +"CHEBI:14987", +"CHEBI:15361" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ccc99777-54dc-42d4-a97e-009b780d3905", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc01020e-8c7e-4087-9f56-cf8c962b7437" +], +"hmdb":[ +"HMDB00243" +], +"inchi_key":[ +"LCTONWCANYUPML-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00022" +], +"lipidmaps":[ +"LMFA01060077" +], +"metanetx.chemical":[ +"MNXM23" +], +"reactome.compound":[ +"1130930", +"5357717", +"113557", +"29398", +"389680" +], +"sabiork":[ +"33" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00020" +] +} +}, +{ +"id":"q8_c", +"name":"Ubiquinone-8", +"compartment":"c", +"charge":0, +"formula":"C49H74O4", +"notes":{ +"original_bigg_ids":[ +"q8_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"q8" +], +"biocyc":[ +"META:UBIQUINONE-8" +], +"chebi":[ +"CHEBI:61683" +], +"inchi_key":[ +"ICFIZJQGJAJRSU-SGHXUWJISA-N" +], +"kegg.compound":[ +"C17569" +], +"lipidmaps":[ +"LMPR02010005" +], +"metanetx.chemical":[ +"MNXM232" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd15560" +] +} +}, +{ +"id":"q8h2_c", +"name":"Ubiquinol-8", +"compartment":"c", +"charge":0, +"formula":"C49H76O4", +"notes":{ +"original_bigg_ids":[ +"q8h2_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"q8h2" +], +"biocyc":[ +"META:CPD-9956" +], +"chebi":[ +"CHEBI:61682" +], +"hmdb":[ +"HMDB01060" +], +"inchi_key":[ +"LOJUQFSPYHMHEO-SGHXUWJISA-N" +], +"metanetx.chemical":[ +"MNXM191" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd29608", +"cpd15561" +] +} +}, +{ +"id":"r5p_c", +"name":"Alpha-D-Ribose 5-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C5H9O8P", +"notes":{ +"original_bigg_ids":[ +"r5p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"r5p" +], +"biocyc":[ +"META:CPD-15318" +], +"chebi":[ +"CHEBI:18189", +"CHEBI:22413", +"CHEBI:12331", +"CHEBI:10270" +], +"inchi_key":[ +"KTVPXOYAKDPRHY-AIHAYLRMSA-L" +], +"kegg.compound":[ +"C03736" +], +"metanetx.chemical":[ +"MNXM15900" +], +"sabiork":[ +"1473" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19028" +] +} +}, +{ +"id":"ru5p__D_c", +"name":"D-Ribulose 5-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C5H9O8P", +"notes":{ +"original_bigg_ids":[ +"ru5p_D_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"ru5p__D" +], +"biocyc":[ +"META:RIBULOSE-5P" +], +"chebi":[ +"CHEBI:40192", +"CHEBI:21088", +"CHEBI:17363", +"CHEBI:26572", +"CHEBI:13040", +"CHEBI:37455", +"CHEBI:58121", +"CHEBI:13018", +"CHEBI:4243" +], +"hmdb":[ +"HMDB02033", +"HMDB02694", +"HMDB00618" +], +"inchi_key":[ +"FNZLKVNUWIIPSJ-UHNVWZDZSA-L" +], +"kegg.compound":[ +"C00199" +], +"metanetx.chemical":[ +"MNXM145" +], +"reactome.compound":[ +"29732" +], +"sabiork":[ +"22814", +"1313" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00171" +] +} +}, +{ +"id":"ac_e", +"name":"Acetate", +"compartment":"e", +"charge":-1, +"formula":"C2H3O2", +"notes":{ +"original_bigg_ids":[ +"ac_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"ac" +], +"biocyc":[ +"META:ACET" +], +"chebi":[ +"CHEBI:13704", +"CHEBI:22165", +"CHEBI:22169", +"CHEBI:40480", +"CHEBI:15366", +"CHEBI:2387", +"CHEBI:30089", +"CHEBI:40486" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/9e26dcbe-4db9-46a0-8614-9f03545032d2", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/5e4989fc-13d3-45d4-ad57-3be380a9d3c0", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/a8f0be58-24e8-441b-8d81-a516a0ead4b3", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/d45256fe-61fa-4f5b-bb16-91a3d615e3d8", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/3e2d750f-df31-4445-9255-163c627e9b4a" +], +"hmdb":[ +"HMDB00042" +], +"inchi_key":[ +"QTBSBXVTEAMEQO-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00033" +], +"kegg.drug":[ +"D00010" +], +"lipidmaps":[ +"LMFA01010002" +], +"metanetx.chemical":[ +"MNXM26" +], +"reactome.compound":[ +"1524044", +"390305", +"113539", +"2022890", +"29416" +], +"sabiork":[ +"1278" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00029" +], +"slm":[ +"000000449" +] +} +}, +{ +"id":"acald_c", +"name":"Acetaldehyde", +"compartment":"c", +"charge":0, +"formula":"C2H4O", +"notes":{ +"original_bigg_ids":[ +"acald_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"acald" +], +"biocyc":[ +"META:ACETALD" +], +"chebi":[ +"CHEBI:40533", +"CHEBI:13703", +"CHEBI:2383", +"CHEBI:22158", +"CHEBI:15343" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/9c8865b2-a99d-42e4-a042-c88504f04b51", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/47aa8e53-36ae-4be3-987c-c1cfab66af78", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ee2c714d-ff9d-4df8-b343-48c1ec76ef0e", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/78f3645f-408e-4001-9dda-a52ea62a15d4" +], +"hmdb":[ +"HMDB00990" +], +"inchi_key":[ +"IKHGUXGNUITLKF-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00084" +], +"metanetx.chemical":[ +"MNXM75" +], +"reactome.compound":[ +"113532", +"29510", +"113681", +"113745" +], +"sabiork":[ +"1292" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00071" +] +} +}, +{ +"id":"s7p_c", +"name":"Sedoheptulose 7-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C7H13O10P", +"notes":{ +"original_bigg_ids":[ +"s7p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"s7p" +], +"biocyc":[ +"META:D-SEDOHEPTULOSE-7-P" +], +"chebi":[ +"CHEBI:4244", +"CHEBI:15073", +"CHEBI:15721", +"CHEBI:26621", +"CHEBI:9083", +"CHEBI:15074", +"CHEBI:57483" +], +"hmdb":[ +"HMDB01068", +"HMDB62754" +], +"inchi_key":[ +"JDTUMPKOJBQPKX-GBNDHIKLSA-L" +], +"kegg.compound":[ +"C05382" +], +"metanetx.chemical":[ +"MNXM271" +], +"reactome.compound":[ +"29882" +], +"sabiork":[ +"1618", +"1325" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00238" +] +} +}, +{ +"id":"acald_e", +"name":"Acetaldehyde", +"compartment":"e", +"charge":0, +"formula":"C2H4O", +"notes":{ +"original_bigg_ids":[ +"acald_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"acald" +], +"biocyc":[ +"META:ACETALD" +], +"chebi":[ +"CHEBI:40533", +"CHEBI:13703", +"CHEBI:2383", +"CHEBI:22158", +"CHEBI:15343" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/9c8865b2-a99d-42e4-a042-c88504f04b51", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/47aa8e53-36ae-4be3-987c-c1cfab66af78", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ee2c714d-ff9d-4df8-b343-48c1ec76ef0e", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/78f3645f-408e-4001-9dda-a52ea62a15d4" +], +"hmdb":[ +"HMDB00990" +], +"inchi_key":[ +"IKHGUXGNUITLKF-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00084" +], +"metanetx.chemical":[ +"MNXM75" +], +"reactome.compound":[ +"113532", +"29510", +"113681", +"113745" +], +"sabiork":[ +"1292" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00071" +] +} +}, +{ +"id":"accoa_c", +"name":"Acetyl-CoA", +"compartment":"c", +"charge":-4, +"formula":"C23H34N7O17P3S", +"notes":{ +"original_bigg_ids":[ +"accoa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"accoa" +], +"biocyc":[ +"META:ACETYL-COA" +], +"chebi":[ +"CHEBI:57288", +"CHEBI:22192", +"CHEBI:15351", +"CHEBI:13712", +"CHEBI:2408", +"CHEBI:40470" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11" +], +"hmdb":[ +"HMDB01206" +], +"inchi_key":[ +"ZSLZBFCDCINBPY-ZSJPKINUSA-J" +], +"kegg.compound":[ +"C00024" +], +"lipidmaps":[ +"LMFA07050029", +"LMFA07050281" +], +"metanetx.chemical":[ +"MNXM21" +], +"reactome.compound":[ +"727753", +"76183", +"113560", +"353123", +"113559" +], +"sabiork":[ +"1276" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00022" +], +"slm":[ +"000000297" +] +} +}, +{ +"id":"succ_c", +"name":"Succinate", +"compartment":"c", +"charge":-2, +"formula":"C4H4O4", +"notes":{ +"original_bigg_ids":[ +"succ_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"succ" +], +"biocyc":[ +"META:SUC" +], +"chebi":[ +"CHEBI:22941", +"CHEBI:26803", +"CHEBI:15741", +"CHEBI:132287", +"CHEBI:45639", +"CHEBI:30779", +"CHEBI:15125", +"CHEBI:22943", +"CHEBI:26807", +"CHEBI:9304", +"CHEBI:90372", +"CHEBI:30031" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/cc98aff0-7f64-4db4-9d59-de961c228496", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/6377658b-03f6-4fed-a5bf-ff0f2389b693", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/600b74d3-8fe5-426d-bedf-291175bd23e4", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8fdfd425-4343-4bf2-8427-b2ffa57fdbd7" +], +"hmdb":[ +"HMDB00254" +], +"inchi_key":[ +"KDYFGRWQOYBRFD-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00042" +], +"lipidmaps":[ +"LMFA01170043" +], +"metanetx.chemical":[ +"MNXM25" +], +"reactome.compound":[ +"389583", +"5278787", +"159939", +"433123", +"29434", +"113536" +], +"sabiork":[ +"1924" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00036" +] +} +}, +{ +"id":"succ_e", +"name":"Succinate", +"compartment":"e", +"charge":-2, +"formula":"C4H4O4", +"notes":{ +"original_bigg_ids":[ +"succ_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"succ" +], +"biocyc":[ +"META:SUC" +], +"chebi":[ +"CHEBI:22941", +"CHEBI:26803", +"CHEBI:15741", +"CHEBI:132287", +"CHEBI:45639", +"CHEBI:30779", +"CHEBI:15125", +"CHEBI:22943", +"CHEBI:26807", +"CHEBI:9304", +"CHEBI:90372", +"CHEBI:30031" +], +"envipath":[ +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/cc98aff0-7f64-4db4-9d59-de961c228496", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/6377658b-03f6-4fed-a5bf-ff0f2389b693", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/600b74d3-8fe5-426d-bedf-291175bd23e4", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8fdfd425-4343-4bf2-8427-b2ffa57fdbd7" +], +"hmdb":[ +"HMDB00254" +], +"inchi_key":[ +"KDYFGRWQOYBRFD-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00042" +], +"lipidmaps":[ +"LMFA01170043" +], +"metanetx.chemical":[ +"MNXM25" +], +"reactome.compound":[ +"389583", +"5278787", +"159939", +"433123", +"29434", +"113536" +], +"sabiork":[ +"1924" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00036" +] +} +}, +{ +"id":"succoa_c", +"name":"Succinyl-CoA", +"compartment":"c", +"charge":-5, +"formula":"C25H35N7O19P3S", +"notes":{ +"original_bigg_ids":[ +"succoa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"succoa" +], +"biocyc":[ +"META:SUC-COA" +], +"chebi":[ +"CHEBI:57292", +"CHEBI:10746", +"CHEBI:15127", +"CHEBI:15380", +"CHEBI:9310", +"CHEBI:45541", +"CHEBI:26811" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/359075fb-98d9-458d-ba82-db4020e753f3" +], +"hmdb":[ +"HMDB01022" +], +"inchi_key":[ +"VNOYUJKHFWYWIR-ITIYDSSPSA-I" +], +"kegg.compound":[ +"C00091" +], +"lipidmaps":[ +"LMFA07050370" +], +"metanetx.chemical":[ +"MNXM92" +], +"reactome.compound":[ +"70958" +], +"sabiork":[ +"1931" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00078" +] +} +}, +{ +"id":"acon_C_c", +"name":"Cis-Aconitate", +"compartment":"c", +"charge":-3, +"formula":"C6H3O6", +"notes":{ +"original_bigg_ids":[ +"acon_C_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"acon_C" +], +"biocyc":[ +"META:CIS-ACONITATE" +], +"chebi":[ +"CHEBI:23306", +"CHEBI:16383", +"CHEBI:12798", +"CHEBI:32805", +"CHEBI:23308", +"CHEBI:10482" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/643481e5-a35b-477e-8665-70f4dca66baa" +], +"hmdb":[ +"HMDB00461", +"HMDB00072" +], +"inchi_key":[ +"GTZCVFVGUGFEME-IWQZZHSRSA-K" +], +"kegg.compound":[ +"C00417" +], +"metanetx.chemical":[ +"MNXM813" +], +"sabiork":[ +"2043" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00331" +] +} +}, +{ +"id":"xu5p__D_c", +"name":"D-Xylulose 5-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C5H9O8P", +"notes":{ +"original_bigg_ids":[ +"xu5p_D_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"xu5p__D" +], +"biocyc":[ +"META:XYLULOSE-5-PHOSPHATE" +], +"chebi":[ +"CHEBI:13036", +"CHEBI:27354", +"CHEBI:4269", +"CHEBI:16332", +"CHEBI:57737", +"CHEBI:21121" +], +"hmdb":[ +"HMDB06212", +"HMDB00868" +], +"inchi_key":[ +"FNZLKVNUWIIPSJ-RFZPGFLSSA-L" +], +"kegg.compound":[ +"C00231" +], +"metanetx.chemical":[ +"MNXM186" +], +"reactome.compound":[ +"29790" +], +"sabiork":[ +"1317" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00198" +] +} +}, +{ +"id":"actp_c", +"name":"Acetyl phosphate", +"compartment":"c", +"charge":-2, +"formula":"C2H3O5P", +"notes":{ +"original_bigg_ids":[ +"actp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"actp" +], +"biocyc":[ +"META:ACETYL-P" +], +"chebi":[ +"CHEBI:13711", +"CHEBI:46262", +"CHEBI:15350", +"CHEBI:22191", +"CHEBI:2407" +], +"hmdb":[ +"HMDB01494" +], +"inchi_key":[ +"LIPOUNRJVLNBCD-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00227" +], +"metanetx.chemical":[ +"MNXM280" +], +"sabiork":[ +"1316" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00196" +] +} +}, +{ +"id":"adp_c", +"name":"ADP C10H12N5O10P2", +"compartment":"c", +"charge":-3, +"formula":"C10H12N5O10P2", +"notes":{ +"original_bigg_ids":[ +"adp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"adp" +], +"biocyc":[ +"META:ADP" +], +"chebi":[ +"CHEBI:2342", +"CHEBI:16761", +"CHEBI:456216", +"CHEBI:40553", +"CHEBI:22244", +"CHEBI:87518", +"CHEBI:13222" +], +"hmdb":[ +"HMDB01341" +], +"inchi_key":[ +"XTWYTFMLZFPYCI-KQYNXXCUSA-K" +], +"kegg.compound":[ +"C00008" +], +"kegg.glycan":[ +"G11113" +], +"metanetx.chemical":[ +"MNXM7" +], +"reactome.compound":[ +"114565", +"211606", +"114564", +"6798177", +"5632457", +"5696026", +"8869360", +"29370", +"113581", +"113582" +], +"sabiork":[ +"35" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00008" +] +} +}, +{ +"id":"akg_c", +"name":"2-Oxoglutarate", +"compartment":"c", +"charge":-2, +"formula":"C5H4O5", +"notes":{ +"original_bigg_ids":[ +"akg_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"akg" +], +"biocyc":[ +"META:2-KETOGLUTARATE" +], +"chebi":[ +"CHEBI:40661", +"CHEBI:16810", +"CHEBI:11638", +"CHEBI:30916", +"CHEBI:19749", +"CHEBI:1253", +"CHEBI:30915", +"CHEBI:19748" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/6557f3f2-0ab8-494b-a865-8ce0eae788a9" +], +"hmdb":[ +"HMDB00208", +"HMDB02812", +"HMDB62781" +], +"inchi_key":[ +"KPGXRSRHYNQIFN-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00026" +], +"metanetx.chemical":[ +"MNXM20" +], +"reactome.compound":[ +"113594", +"561075", +"5278317", +"113671", +"29406", +"389537" +], +"sabiork":[ +"1922" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00024" +] +} +}, +{ +"id":"akg_e", +"name":"2-Oxoglutarate", +"compartment":"e", +"charge":-2, +"formula":"C5H4O5", +"notes":{ +"original_bigg_ids":[ +"akg_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"akg" +], +"biocyc":[ +"META:2-KETOGLUTARATE" +], +"chebi":[ +"CHEBI:40661", +"CHEBI:16810", +"CHEBI:11638", +"CHEBI:30916", +"CHEBI:19749", +"CHEBI:1253", +"CHEBI:30915", +"CHEBI:19748" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/6557f3f2-0ab8-494b-a865-8ce0eae788a9" +], +"hmdb":[ +"HMDB00208", +"HMDB02812", +"HMDB62781" +], +"inchi_key":[ +"KPGXRSRHYNQIFN-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00026" +], +"metanetx.chemical":[ +"MNXM20" +], +"reactome.compound":[ +"113594", +"561075", +"5278317", +"113671", +"29406", +"389537" +], +"sabiork":[ +"1922" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00024" +] +} +}, +{ +"id":"amp_c", +"name":"AMP C10H12N5O7P", +"compartment":"c", +"charge":-2, +"formula":"C10H12N5O7P", +"notes":{ +"original_bigg_ids":[ +"amp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"amp" +], +"biocyc":[ +"META:AMP-GROUP", +"META:AMP" +], +"chebi":[ +"CHEBI:13736", +"CHEBI:2356", +"CHEBI:13234", +"CHEBI:22242", +"CHEBI:40786", +"CHEBI:16027", +"CHEBI:40721", +"CHEBI:40510", +"CHEBI:456215", +"CHEBI:13235", +"CHEBI:22245", +"CHEBI:40726", +"CHEBI:47222", +"CHEBI:13740", +"CHEBI:40826", +"CHEBI:12056" +], +"hmdb":[ +"HMDB00045" +], +"inchi_key":[ +"UDMBCSSLTHHNCD-KQYNXXCUSA-L" +], +"kegg.compound":[ +"C00020" +], +"kegg.drug":[ +"D02769" +], +"metanetx.chemical":[ +"MNXM14" +], +"reactome.compound":[ +"389620", +"159448", +"76577", +"109275", +"164121" +], +"sabiork":[ +"1273" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd22272", +"cpd00018" +] +} +}, +{ +"id":"atp_c", +"name":"ATP C10H12N5O13P3", +"compartment":"c", +"charge":-4, +"formula":"C10H12N5O13P3", +"notes":{ +"original_bigg_ids":[ +"atp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"atp" +], +"biocyc":[ +"META:ATP" +], +"chebi":[ +"CHEBI:15422", +"CHEBI:10789", +"CHEBI:10841", +"CHEBI:2359", +"CHEBI:22249", +"CHEBI:13236", +"CHEBI:237958", +"CHEBI:30616", +"CHEBI:57299", +"CHEBI:40938" +], +"hmdb":[ +"HMDB00538" +], +"inchi_key":[ +"ZKHQWZAMYRWXGA-KQYNXXCUSA-J" +], +"kegg.compound":[ +"C00002" +], +"kegg.drug":[ +"D08646" +], +"metanetx.chemical":[ +"MNXM3" +], +"reactome.compound":[ +"8878982", +"389573", +"8938081", +"211579", +"113593", +"113592", +"5632460", +"5696069", +"29358", +"8869363", +"6798184" +], +"sabiork":[ +"34" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00002" +] +} +}, +{ +"id":"cit_c", +"name":"Citrate", +"compartment":"c", +"charge":-3, +"formula":"C6H5O7", +"notes":{ +"original_bigg_ids":[ +"cit_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"cit" +], +"biocyc":[ +"META:CIT" +], +"chebi":[ +"CHEBI:35802", +"CHEBI:133748", +"CHEBI:35809", +"CHEBI:76049", +"CHEBI:41523", +"CHEBI:35810", +"CHEBI:30769", +"CHEBI:13999", +"CHEBI:23322", +"CHEBI:35808", +"CHEBI:42563", +"CHEBI:16947", +"CHEBI:132362", +"CHEBI:35804", +"CHEBI:23321", +"CHEBI:3727", +"CHEBI:35806" +], +"hmdb":[ +"HMDB00094" +], +"inchi_key":[ +"KRKNYBCHXYNGOX-UHFFFAOYSA-K" +], +"kegg.compound":[ +"C00158" +], +"kegg.drug":[ +"D00037" +], +"metanetx.chemical":[ +"MNXM131" +], +"reactome.compound":[ +"29654", +"433138", +"76190" +], +"sabiork":[ +"1952" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00137" +] +} +}, +{ +"id":"co2_c", +"name":"CO2 CO2", +"compartment":"c", +"charge":0, +"formula":"CO2", +"notes":{ +"original_bigg_ids":[ +"co2_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"co2" +], +"biocyc":[ +"META:CARBON-DIOXIDE" +], +"chebi":[ +"CHEBI:23011", +"CHEBI:3283", +"CHEBI:48829", +"CHEBI:16526", +"CHEBI:13283", +"CHEBI:13285", +"CHEBI:13284", +"CHEBI:13282" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379" +], +"hmdb":[ +"HMDB01967" +], +"inchi_key":[ +"CURLTUGMZLYLDI-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00011" +], +"kegg.drug":[ +"D00004" +], +"metanetx.chemical":[ +"MNXM13" +], +"reactome.compound":[ +"29376", +"5668565", +"189480", +"1132345", +"113528", +"1237009", +"159751", +"389536", +"159942" +], +"sabiork":[ +"1266" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00011" +] +} +}, +{ +"id":"co2_e", +"name":"CO2 CO2", +"compartment":"e", +"charge":0, +"formula":"CO2", +"notes":{ +"original_bigg_ids":[ +"co2_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"co2" +], +"biocyc":[ +"META:CARBON-DIOXIDE" +], +"chebi":[ +"CHEBI:23011", +"CHEBI:3283", +"CHEBI:48829", +"CHEBI:16526", +"CHEBI:13283", +"CHEBI:13285", +"CHEBI:13284", +"CHEBI:13282" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379" +], +"hmdb":[ +"HMDB01967" +], +"inchi_key":[ +"CURLTUGMZLYLDI-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00011" +], +"kegg.drug":[ +"D00004" +], +"metanetx.chemical":[ +"MNXM13" +], +"reactome.compound":[ +"29376", +"5668565", +"189480", +"1132345", +"113528", +"1237009", +"159751", +"389536", +"159942" +], +"sabiork":[ +"1266" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00011" +] +} +}, +{ +"id":"coa_c", +"name":"Coenzyme A", +"compartment":"c", +"charge":-4, +"formula":"C21H32N7O16P3S", +"notes":{ +"original_bigg_ids":[ +"coa_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"coa" +], +"biocyc":[ +"META:COA-GROUP", +"META:CO-A" +], +"chebi":[ +"CHEBI:41631", +"CHEBI:41597", +"CHEBI:741566", +"CHEBI:23355", +"CHEBI:13295", +"CHEBI:13298", +"CHEBI:57287", +"CHEBI:15346", +"CHEBI:3771", +"CHEBI:13294" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/19310484-6aa5-4dcf-b1da-855a8c21ecfd" +], +"hmdb":[ +"HMDB01423", +"HMDB62184" +], +"inchi_key":[ +"RGJOEKWQDUBAIZ-IBOSZNHHSA-J" +], +"kegg.compound":[ +"C00010" +], +"metanetx.chemical":[ +"MNXM12" +], +"reactome.compound":[ +"193514", +"162743", +"2485002", +"1678675", +"29374", +"76194", +"8939024" +], +"sabiork":[ +"1265" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd22528", +"cpd00010" +] +} +}, +{ +"id":"dhap_c", +"name":"Dihydroxyacetone phosphate", +"compartment":"c", +"charge":-2, +"formula":"C3H5O6P", +"notes":{ +"original_bigg_ids":[ +"dhap_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"dhap" +], +"biocyc":[ +"META:DIHYDROXY-ACETONE-PHOSPHATE" +], +"chebi":[ +"CHEBI:14341", +"CHEBI:5454", +"CHEBI:16108", +"CHEBI:14342", +"CHEBI:24355", +"CHEBI:39571", +"CHEBI:57642" +], +"hmdb":[ +"HMDB11735", +"HMDB01473" +], +"inchi_key":[ +"GNGACRATGGDKBX-UHFFFAOYSA-L" +], +"kegg.compound":[ +"C00111" +], +"metanetx.chemical":[ +"MNXM77" +], +"reactome.compound":[ +"390404", +"75970", +"188451" +], +"sabiork":[ +"28" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00095" +] +} +}, +{ +"id":"e4p_c", +"name":"D-Erythrose 4-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C4H7O7P", +"notes":{ +"original_bigg_ids":[ +"e4p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"e4p" +], +"biocyc":[ +"META:ERYTHROSE-4P" +], +"chebi":[ +"CHEBI:4114", +"CHEBI:20927", +"CHEBI:12921", +"CHEBI:48153", +"CHEBI:16897", +"CHEBI:42349" +], +"hmdb":[ +"HMDB01321" +], +"inchi_key":[ +"NGHMDNPXVRFFGS-IUYQGCFVSA-L" +], +"kegg.compound":[ +"C00279" +], +"metanetx.chemical":[ +"MNXM258" +], +"reactome.compound":[ +"29878" +], +"sabiork":[ +"1324" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00236" +] +} +}, +{ +"id":"etoh_c", +"name":"Ethanol", +"compartment":"c", +"charge":0, +"formula":"C2H6O", +"notes":{ +"original_bigg_ids":[ +"etoh_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"etoh" +], +"biocyc":[ +"META:ETOH" +], +"chebi":[ +"CHEBI:42377", +"CHEBI:23978", +"CHEBI:30880", +"CHEBI:16236", +"CHEBI:52092", +"CHEBI:30878", +"CHEBI:4879", +"CHEBI:44594", +"CHEBI:14222" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/a4a354fd-5003-4b7b-b11b-f54204aea384", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/f89efe7c-1a6a-4d21-b99c-e3e1070a8062", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/56e18a05-c059-433a-94f6-0e26c01b010f", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9fb1fbdf-101b-4b82-a596-d2f52c870e4f" +], +"hmdb":[ +"HMDB00108" +], +"inchi_key":[ +"LFQSCWFLJHTTHZ-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00469" +], +"kegg.drug":[ +"D06542", +"D02798", +"D00068", +"D04855" +], +"metanetx.chemical":[ +"MNXM303" +], +"reactome.compound":[ +"113748", +"30203" +], +"sabiork":[ +"56" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00363" +] +} +}, +{ +"id":"etoh_e", +"name":"Ethanol", +"compartment":"e", +"charge":0, +"formula":"C2H6O", +"notes":{ +"original_bigg_ids":[ +"etoh_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"etoh" +], +"biocyc":[ +"META:ETOH" +], +"chebi":[ +"CHEBI:42377", +"CHEBI:23978", +"CHEBI:30880", +"CHEBI:16236", +"CHEBI:52092", +"CHEBI:30878", +"CHEBI:4879", +"CHEBI:44594", +"CHEBI:14222" +], +"envipath":[ +"5882df9c-dae1-4d80-a40e-db4724271456/compound/a4a354fd-5003-4b7b-b11b-f54204aea384", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/f89efe7c-1a6a-4d21-b99c-e3e1070a8062", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/56e18a05-c059-433a-94f6-0e26c01b010f", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9fb1fbdf-101b-4b82-a596-d2f52c870e4f" +], +"hmdb":[ +"HMDB00108" +], +"inchi_key":[ +"LFQSCWFLJHTTHZ-UHFFFAOYSA-N" +], +"kegg.compound":[ +"C00469" +], +"kegg.drug":[ +"D06542", +"D02798", +"D00068", +"D04855" +], +"metanetx.chemical":[ +"MNXM303" +], +"reactome.compound":[ +"113748", +"30203" +], +"sabiork":[ +"56" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00363" +] +} +}, +{ +"id":"f6p_c", +"name":"D-Fructose 6-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C6H11O9P", +"notes":{ +"original_bigg_ids":[ +"f6p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"f6p" +], +"biocyc":[ +"META:FRUCTOSE-6P" +], +"chebi":[ +"CHEBI:16084", +"CHEBI:12352", +"CHEBI:57634", +"CHEBI:22768", +"CHEBI:10375", +"CHEBI:42378" +], +"hmdb":[ +"HMDB03971" +], +"inchi_key":[ +"BGWGXPAPYGQALX-ARQDHWQXSA-L" +], +"kegg.compound":[ +"C05345" +], +"metanetx.chemical":[ +"MNXM89621" +], +"sabiork":[ +"25" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd19035" +] +} +}, +{ +"id":"fdp_c", +"name":"D-Fructose 1,6-bisphosphate", +"compartment":"c", +"charge":-4, +"formula":"C6H10O12P2", +"notes":{ +"original_bigg_ids":[ +"fdp_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fdp" +], +"chebi":[ +"CHEBI:37736", +"CHEBI:49299" +], +"inchi_key":[ +"RNBGYGVWRKECFJ-VRPWFDPXSA-J" +], +"kegg.compound":[ +"C00354" +], +"metanetx.chemical":[ +"MNXM417" +], +"sabiork":[ +"1465" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00290" +] +} +}, +{ +"id":"for_c", +"name":"Formate", +"compartment":"c", +"charge":-1, +"formula":"CH1O2", +"notes":{ +"original_bigg_ids":[ +"for_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"for" +], +"biocyc":[ +"META:CPD1G-1532", +"META:CPD1G-1535", +"META:FORMATE", +"META:CPD-9845", +"META:CPD1G-1534", +"META:CARBOXYL-GROUP", +"META:CPD1G-1533" +], +"chebi":[ +"CHEBI:24081", +"CHEBI:30751", +"CHEBI:15740", +"CHEBI:5145", +"CHEBI:42460", +"CHEBI:14276", +"CHEBI:24082" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/9a9d20ae-b6ec-40a9-93ca-1de20597b1ed", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/09c1ad08-016e-4477-8840-b97a031eae23", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/bf16ab32-cb3c-4427-a65a-089ab754823e", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/34fe3cd9-9b0b-46b0-a1c5-8a66509f1919", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/1d077cf2-3f9f-4163-aa49-0fca1b2b3ab3" +], +"hmdb":[ +"HMDB00142" +], +"inchi_key":[ +"BDAGIHXWWSANSR-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00058" +], +"metanetx.chemical":[ +"MNXM39" +], +"reactome.compound":[ +"29460", +"194712", +"389585", +"6801451" +], +"sabiork":[ +"1285" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00047", +"cpd22511" +] +} +}, +{ +"id":"for_e", +"name":"Formate", +"compartment":"e", +"charge":-1, +"formula":"CH1O2", +"notes":{ +"original_bigg_ids":[ +"for_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"for" +], +"biocyc":[ +"META:CPD1G-1532", +"META:CPD1G-1535", +"META:FORMATE", +"META:CPD-9845", +"META:CPD1G-1534", +"META:CARBOXYL-GROUP", +"META:CPD1G-1533" +], +"chebi":[ +"CHEBI:24081", +"CHEBI:30751", +"CHEBI:15740", +"CHEBI:5145", +"CHEBI:42460", +"CHEBI:14276", +"CHEBI:24082" +], +"envipath":[ +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/9a9d20ae-b6ec-40a9-93ca-1de20597b1ed", +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/09c1ad08-016e-4477-8840-b97a031eae23", +"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/bf16ab32-cb3c-4427-a65a-089ab754823e", +"5882df9c-dae1-4d80-a40e-db4724271456/compound/34fe3cd9-9b0b-46b0-a1c5-8a66509f1919", +"650babc9-9d68-4b73-9332-11972ca26f7b/compound/1d077cf2-3f9f-4163-aa49-0fca1b2b3ab3" +], +"hmdb":[ +"HMDB00142" +], +"inchi_key":[ +"BDAGIHXWWSANSR-UHFFFAOYSA-M" +], +"kegg.compound":[ +"C00058" +], +"metanetx.chemical":[ +"MNXM39" +], +"reactome.compound":[ +"29460", +"194712", +"389585", +"6801451" +], +"sabiork":[ +"1285" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00047", +"cpd22511" +] +} +}, +{ +"id":"fru_e", +"name":"D-Fructose", +"compartment":"e", +"charge":0, +"formula":"C6H12O6", +"notes":{ +"original_bigg_ids":[ +"fru_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fru" +], +"biocyc":[ +"META:D-Fructopyranose", +"META:Fructofuranose", +"META:CPD-15382", +"META:FRU" +], +"chebi":[ +"CHEBI:47424", +"CHEBI:28757", +"CHEBI:24110", +"CHEBI:20929", +"CHEBI:4119", +"CHEBI:15824", +"CHEBI:5172", +"CHEBI:24104", +"CHEBI:12923", +"CHEBI:4118", +"CHEBI:37714", +"CHEBI:37721", +"CHEBI:48095" +], +"hmdb":[ +"HMDB62538" +], +"inchi_key":[ +"RFSUNEUAIZKAJO-VRPWFDPXSA-N" +], +"kegg.compound":[ +"C01496", +"C05003", +"C00095", +"C10906" +], +"kegg.drug":[ +"D00114" +], +"metanetx.chemical":[ +"MNXM175" +], +"reactome.compound":[ +"189049", +"29532" +], +"sabiork":[ +"25055", +"1463", +"1464" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00082", +"cpd19015", +"cpd27040" +] +} +}, +{ +"id":"fum_c", +"name":"Fumarate", +"compartment":"c", +"charge":-2, +"formula":"C4H2O4", +"notes":{ +"original_bigg_ids":[ +"fum_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fum" +], +"biocyc":[ +"META:FUM" +], +"chebi":[ +"CHEBI:36180", +"CHEBI:37155", +"CHEBI:42511", +"CHEBI:5190", +"CHEBI:18012", +"CHEBI:42743", +"CHEBI:22956", +"CHEBI:22957", +"CHEBI:24124", +"CHEBI:14284", +"CHEBI:37154", +"CHEBI:29806", +"CHEBI:22958", +"CHEBI:24122" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b" +], +"hmdb":[ +"HMDB00134" +], +"inchi_key":[ +"VZCYOOQTPOCHFL-OWOJBTEDSA-L" +], +"kegg.compound":[ +"C00122" +], +"kegg.drug":[ +"D02308" +], +"metanetx.chemical":[ +"MNXM93" +], +"reactome.compound":[ +"113588", +"29586" +], +"sabiork":[ +"1910" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00106" +] +} +}, +{ +"id":"fum_e", +"name":"Fumarate", +"compartment":"e", +"charge":-2, +"formula":"C4H2O4", +"notes":{ +"original_bigg_ids":[ +"fum_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"fum" +], +"biocyc":[ +"META:FUM" +], +"chebi":[ +"CHEBI:36180", +"CHEBI:37155", +"CHEBI:42511", +"CHEBI:5190", +"CHEBI:18012", +"CHEBI:42743", +"CHEBI:22956", +"CHEBI:22957", +"CHEBI:24124", +"CHEBI:14284", +"CHEBI:37154", +"CHEBI:29806", +"CHEBI:22958", +"CHEBI:24122" +], +"envipath":[ +"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b" +], +"hmdb":[ +"HMDB00134" +], +"inchi_key":[ +"VZCYOOQTPOCHFL-OWOJBTEDSA-L" +], +"kegg.compound":[ +"C00122" +], +"kegg.drug":[ +"D02308" +], +"metanetx.chemical":[ +"MNXM93" +], +"reactome.compound":[ +"113588", +"29586" +], +"sabiork":[ +"1910" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00106" +] +} +}, +{ +"id":"g3p_c", +"name":"Glyceraldehyde 3-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C3H5O6P", +"notes":{ +"original_bigg_ids":[ +"g3p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"g3p" +], +"biocyc":[ +"META:GAP" +], +"chebi":[ +"CHEBI:5446", +"CHEBI:14333", +"CHEBI:12984", +"CHEBI:181", +"CHEBI:17138", +"CHEBI:21026", +"CHEBI:12983", +"CHEBI:18324", +"CHEBI:58027", +"CHEBI:59776", +"CHEBI:29052" +], +"hmdb":[ +"HMDB01112" +], +"inchi_key":[ +"LXJXRIRHZLFYRP-VKHMYHEASA-L" +], +"kegg.compound":[ +"C00661", +"C00118" +], +"metanetx.chemical":[ +"MNXM74" +], +"reactome.compound":[ +"29578" +], +"sabiork":[ +"27", +"1687" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00102", +"cpd19005" +] +} +}, +{ +"id":"g6p_c", +"name":"D-Glucose 6-phosphate", +"compartment":"c", +"charge":-2, +"formula":"C6H11O9P", +"notes":{ +"original_bigg_ids":[ +"g6p_c" +] +}, +"annotation":{ +"bigg.metabolite":[ +"g6p" +], +"biocyc":[ +"META:D-glucopyranose-6-phosphate" +], +"chebi":[ +"CHEBI:61548", +"CHEBI:14314", +"CHEBI:4170" +], +"hmdb":[ +"HMDB01549", +"HMDB01401", +"HMDB06793" +], +"inchi_key":[ +"NBSCHQHZLSJFNQ-GASJEMHNSA-L" +], +"kegg.compound":[ +"C00092" +], +"metanetx.chemical":[ +"MNXM160" +], +"reactome.compound":[ +"1629756" +], +"sabiork":[ +"1404", +"1405" +], +"sbo":"SBO:0000247", +"seed.compound":[ +"cpd00079", +"cpd26836" +] +} +} +], +"reactions":[ +{ +"id":"PFK", +"name":"Phosphofructokinase", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"f6p_c":-1.0, +"fdp_c":1.0, +"h_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3916 or b1723", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PFK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PFK" +], +"ec-code":[ +"2.7.1.11" +], +"metanetx.reaction":[ +"MNXR102507" +], +"rhea":[ +"16111", +"16109", +"16110", +"16112" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"PFL", +"name":"Pyruvate formate lyase", +"metabolites":{ +"accoa_c":1.0, +"coa_c":-1.0, +"for_c":1.0, +"pyr_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"((b0902 and b0903) and b2579) or (b0902 and b0903) or (b0902 and b3114) or (b3951 and b3952)", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"PFL" +] +}, +"annotation":{ +"bigg.reaction":[ +"PFL" +], +"biocyc":[ +"META:PYRUVFORMLY-RXN" +], +"ec-code":[ +"2.3.1.54" +], +"kegg.reaction":[ +"R00212" +], +"metanetx.reaction":[ +"MNXR102514" +], +"rhea":[ +"11847", +"11845", +"11844", +"11846" +], +"sabiork":[ +"146" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00157" +] +} +}, +{ +"id":"PGI", +"name":"Glucose-6-phosphate isomerase", +"metabolites":{ +"f6p_c":1.0, +"g6p_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4025", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PGI" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGI" +], +"biocyc":[ +"META:PGLUCISOM-RXN" +], +"ec-code":[ +"5.3.1.9" +], +"metanetx.reaction":[ +"MNXR102535" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"PGK", +"name":"Phosphoglycerate kinase", +"metabolites":{ +"13dpg_c":1.0, +"3pg_c":-1.0, +"adp_c":1.0, +"atp_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2926", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PGK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGK" +], +"biocyc":[ +"META:PHOSGLYPHOS-RXN" +], +"ec-code":[ +"2.7.2.3" +], +"kegg.reaction":[ +"R01512" +], +"metanetx.reaction":[ +"MNXR102538" +], +"reactome.reaction":[ +"R-ATH-71850", +"R-DME-71850", +"R-GGA-71850", +"R-SPO-71850", +"R-OSA-71850", +"R-GGA-353039", +"R-GGA-353023", +"R-BTA-71850", +"R-CFA-70486", +"R-MMU-71850", +"R-DME-70486", +"R-PFA-71850", +"R-SPO-70486", +"R-SCE-70486", +"R-PFA-70486", +"R-SSC-70486", +"R-ATH-70486", +"R-DRE-70486", +"R-HSA-70486", +"R-OSA-70486", +"R-XTR-71850", +"R-MMU-70486", +"R-RNO-70486", +"R-TGU-70486", +"R-DRE-71850", +"R-SSC-71850", +"R-SCE-71850", +"R-CFA-71850", +"R-XTR-70486", +"R-DDI-70486", +"R-DDI-71850", +"R-RNO-71850", +"R-BTA-70486", +"R-CEL-70486", +"R-HSA-71850", +"R-CEL-71850", +"R-GGA-70486", +"R-TGU-71850" +], +"rhea":[ +"14801", +"14804", +"14802", +"14803" +], +"sabiork":[ +"7644" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01100" +] +} +}, +{ +"id":"PGL", +"name":"6-phosphogluconolactonase", +"metabolites":{ +"6pgc_c":1.0, +"6pgl_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0767", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"PGL" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGL" +], +"biocyc":[ +"META:6PGLUCONOLACT-RXN" +], +"ec-code":[ +"3.1.1.31" +], +"kegg.reaction":[ +"R02035" +], +"metanetx.reaction":[ +"MNXR102539" +], +"reactome.reaction":[ +"R-OSA-71296", +"R-CFA-71296", +"R-CEL-71296", +"R-GGA-71296", +"R-MMU-71296", +"R-SSC-71296", +"R-BTA-71296", +"R-ATH-71296", +"R-DME-71296", +"R-DRE-71296", +"R-SCE-71296", +"R-HSA-71296", +"R-XTR-71296", +"R-RNO-71296", +"R-DDI-71296", +"R-SPO-71296" +], +"rhea":[ +"12559", +"12556", +"12557", +"12558" +], +"sabiork":[ +"109" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01476" +] +} +}, +{ +"id":"ACALD", +"name":"Acetaldehyde dehydrogenase (acetylating)", +"metabolites":{ +"acald_c":-1.0, +"accoa_c":1.0, +"coa_c":-1.0, +"h_c":1.0, +"nad_c":-1.0, +"nadh_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0351 or b1241", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"ACALD" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACALD" +], +"biocyc":[ +"META:ACETALD-DEHYDROG-RXN" +], +"ec-code":[ +"1.2.1.10" +], +"kegg.reaction":[ +"R00228" +], +"metanetx.reaction":[ +"MNXR95210" +], +"rhea":[ +"23290", +"23291", +"23289", +"23288" +], +"sabiork":[ +"163" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00171" +] +} +}, +{ +"id":"AKGt2r", +"name":"2 oxoglutarate reversible transport via symport", +"metabolites":{ +"akg_c":1.0, +"akg_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2587", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"AKGt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"AKGt2r" +], +"biocyc":[ +"META:TRANS-RXN-23" +], +"metanetx.reaction":[ +"MNXR95661" +], +"rhea":[ +"29011", +"29013", +"29012", +"29014" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05493", +"rxn08095", +"rxn09827" +] +} +}, +{ +"id":"PGM", +"name":"Phosphoglycerate mutase", +"metabolites":{ +"2pg_c":-1.0, +"3pg_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3612 or b4395 or b0755", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PGM" +] +}, +"annotation":{ +"bigg.reaction":[ +"PGM" +], +"biocyc":[ +"META:3PGAREARR-RXN", +"META:RXN-15513" +], +"ec-code":[ +"5.4.2.1", +"5.4.2.11", +"5.4.2.12" +], +"kegg.reaction":[ +"R01518" +], +"metanetx.reaction":[ +"MNXR102547" +], +"reactome.reaction":[ +"R-XTR-71654", +"R-SSC-71654", +"R-DME-71445", +"R-XTR-71445", +"R-RNO-71445", +"R-GGA-71654", +"R-SSC-71445", +"R-GGA-71445", +"R-DDI-71654", +"R-SPO-71654", +"R-MMU-71445", +"R-BTA-71445", +"R-CFA-71445", +"R-PFA-71445", +"R-GGA-352994", +"R-TGU-71654", +"R-SPO-71445", +"R-HSA-71445", +"R-ATH-71654", +"R-MMU-71654", +"R-BTA-71654", +"R-GGA-353014", +"R-DRE-71654", +"R-HSA-71654", +"R-CFA-71654", +"R-OSA-71654", +"R-DDI-71445", +"R-RNO-71654", +"R-DRE-71445", +"R-OSA-71445", +"R-PFA-71654", +"R-DME-71654", +"R-TGU-71445", +"R-SCE-71445", +"R-ATH-71445", +"R-SCE-71654" +], +"rhea":[ +"15902", +"15903", +"15901", +"15904" +], +"sabiork":[ +"7641" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01106" +] +} +}, +{ +"id":"PIt2r", +"name":"Phosphate reversible transport via symport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"pi_c":1.0, +"pi_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2987 or b3493", +"subsystem":"Inorganic Ion Transport and Metabolism", +"notes":{ +"original_bigg_ids":[ +"PIt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"PIt2r" +], +"biocyc":[ +"META:TRANS-RXN-114" +], +"metanetx.reaction":[ +"MNXR102872" +], +"rhea":[ +"29939", +"29941", +"29940", +"29942" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05312", +"rxn09833", +"rxn09811", +"rxn09872", +"rxn09723", +"rxn09120" +] +} +}, +{ +"id":"ALCD2x", +"name":"Alcohol dehydrogenase (ethanol)", +"metabolites":{ +"acald_c":1.0, +"etoh_c":-1.0, +"h_c":1.0, +"nad_c":-1.0, +"nadh_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0356 or b1478 or b1241", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"ALCD2x" +] +}, +"annotation":{ +"bigg.reaction":[ +"ALCD2x" +], +"biocyc":[ +"META:ALCOHOL-DEHYDROG-RXN" +], +"ec-code":[ +"1.1.1.71", +"1.1.1.1" +], +"kegg.reaction":[ +"R00754" +], +"metanetx.reaction":[ +"MNXR95725" +], +"reactome.reaction":[ +"R-MMU-71707", +"R-XTR-71707", +"R-CFA-71707", +"R-OSA-71707", +"R-RNO-71707", +"R-HSA-71707", +"R-SSC-71707", +"R-GGA-71707", +"R-SPO-71707", +"R-DME-71707", +"R-DRE-71707", +"R-BTA-71707", +"R-ATH-71707", +"R-SCE-71707", +"R-TGU-71707", +"R-CEL-71707", +"R-DDI-71707" +], +"rhea":[ +"25292", +"25290", +"25291", +"25293" +], +"sabiork":[ +"597" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00543" +] +} +}, +{ +"id":"ACALDt", +"name":"Acetaldehyde reversible transport", +"metabolites":{ +"acald_c":1.0, +"acald_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"ACALDt" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACALDt" +], +"metanetx.reaction":[ +"MNXR95212" +], +"reactome.reaction":[ +"R-HSA-449872" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09700", +"rxn08033", +"rxn13212", +"rxn08032" +] +} +}, +{ +"id":"ACKr", +"name":"Acetate kinase", +"metabolites":{ +"ac_c":-1.0, +"actp_c":1.0, +"adp_c":1.0, +"atp_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3115 or b2296 or b1849", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"ACKr" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACKr" +], +"biocyc":[ +"META:ACETATEKIN-RXN" +], +"ec-code":[ +"2.7.2.15", +"2.7.2.1" +], +"kegg.reaction":[ +"R00315" +], +"metanetx.reaction":[ +"MNXR95269" +], +"rhea":[ +"11354", +"11355", +"11353", +"11352" +], +"sabiork":[ +"71" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00225" +] +} +}, +{ +"id":"PPC", +"name":"Phosphoenolpyruvate carboxylase", +"metabolites":{ +"co2_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"oaa_c":1.0, +"pep_c":-1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3956", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"PPC" +] +}, +"annotation":{ +"bigg.reaction":[ +"PPC" +], +"ec-code":[ +"4.1.1.31" +], +"kegg.reaction":[ +"R00345" +], +"metanetx.reaction":[ +"MNXR103096" +], +"rhea":[ +"23073", +"23072", +"23075", +"23074" +], +"sabiork":[ +"150" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00251" +] +} +}, +{ +"id":"ACONTa", +"name":"Aconitase (half-reaction A, Citrate hydro-lyase)", +"metabolites":{ +"acon_C_c":1.0, +"cit_c":-1.0, +"h2o_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0118 or b1276", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"ACONTa" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACONTa" +], +"biocyc":[ +"META:ACONITATEDEHYDR-RXN" +], +"ec-code":[ +"4.2.1.3" +], +"kegg.reaction":[ +"R01325" +], +"metanetx.reaction":[ +"MNXR95386" +], +"rhea":[ +"10230", +"10229", +"10231", +"10228" +], +"sabiork":[ +"268" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00974" +] +} +}, +{ +"id":"ACONTb", +"name":"Aconitase (half-reaction B, Isocitrate hydro-lyase)", +"metabolites":{ +"acon_C_c":-1.0, +"h2o_c":-1.0, +"icit_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0118 or b1276", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"ACONTb" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACONTb" +], +"ec-code":[ +"4.2.1.3" +], +"kegg.reaction":[ +"R01900" +], +"metanetx.reaction":[ +"MNXR95387" +], +"rhea":[ +"22145", +"22144", +"22146", +"22147" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01388" +] +} +}, +{ +"id":"ATPM", +"name":"ATP maintenance requirement", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"pi_c":1.0 +}, +"lower_bound":8.39, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Biomass and maintenance functions", +"notes":{ +"original_bigg_ids":[ +"ATPM" +] +}, +"annotation":{ +"bigg.reaction":[ +"ATPM" +], +"biocyc":[ +"META:ATPASE-RXN" +], +"ec-code":[ +"3.6.1.5", +"3.6.3.34", +"3.6.3.20", +"3.6.3.53", +"3.6.3.8", +"3.6.3.32", +"3.6.4.12", +"3.6.3.48", +"3.6.3.40", +"3.6.3.9", +"3.6.3.23", +"3.6.3.22", +"3.6.3.54", +"3.6.3.1", +"3.6.1.8", +"3.6.3.29", +"3.6.3.17", +"3.6.3.50", +"3.6.3.39", +"3.6.3.19", +"3.6.3.4", +"3.6.3.35", +"3.6.3.16", +"3.6.4.4", +"3.6.3.37", +"3.6.4.8", +"3.6.3.31", +"3.6.3.6", +"3.6.4.5", +"3.6.3.52", +"3.6.3.2", +"3.6.3.14", +"3.6.3.51", +"3.6.3.25", +"3.6.3.38", +"3.6.3.33", +"3.6.3.43", +"3.6.4.10", +"3.6.4.13", +"3.6.3.3", +"3.6.3.10", +"3.6.3.24", +"3.6.3.44", +"3.6.3.15", +"3.6.3.5", +"3.6.1.3", +"3.6.1.15", +"3.6.4.2", +"3.6.4.3", +"3.6.3.42", +"3.6.3.11", +"3.6.3.28", +"3.6.3.30", +"3.6.4.1", +"3.6.4.11", +"3.6.3.47", +"3.6.4.6", +"3.6.3.36", +"3.6.3.21", +"3.6.3.12", +"3.6.3.18", +"3.6.3.26", +"3.6.3.27", +"3.6.3.7", +"3.6.4.9", +"3.6.4.7", +"3.6.3.46", +"3.6.3.41", +"3.6.3.49" +], +"kegg.reaction":[ +"R00086" +], +"metanetx.reaction":[ +"MNXR96131" +], +"rhea":[ +"13066", +"13065", +"13068", +"13067" +], +"sabiork":[ +"75" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn11300", +"rxn09694", +"rxn00062" +] +} +}, +{ +"id":"PPCK", +"name":"Phosphoenolpyruvate carboxykinase", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"co2_c":1.0, +"oaa_c":-1.0, +"pep_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3403", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"PPCK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PPCK" +], +"biocyc":[ +"META:PEPCARBOXYKIN-RXN" +], +"ec-code":[ +"4.1.1.49" +], +"kegg.reaction":[ +"R00341" +], +"metanetx.reaction":[ +"MNXR103099" +], +"rhea":[ +"18620", +"18618", +"18617", +"18619" +], +"sabiork":[ +"151" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00247" +] +} +}, +{ +"id":"ACt2r", +"name":"Acetate reversible transport via proton symport", +"metabolites":{ +"ac_c":1.0, +"ac_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"ACt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"ACt2r" +], +"biocyc":[ +"META:TRANS-RXN0-571" +], +"metanetx.reaction":[ +"MNXR95429" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08061", +"rxn05488" +] +} +}, +{ +"id":"PPS", +"name":"Phosphoenolpyruvate synthase", +"metabolites":{ +"amp_c":1.0, +"atp_c":-1.0, +"h2o_c":-1.0, +"h_c":2.0, +"pep_c":1.0, +"pi_c":1.0, +"pyr_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1702", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PPS" +] +}, +"annotation":{ +"bigg.reaction":[ +"PPS" +], +"biocyc":[ +"META:PEPSYNTH-RXN" +], +"ec-code":[ +"2.7.9.2" +], +"kegg.reaction":[ +"R00199" +], +"metanetx.reaction":[ +"MNXR103140" +], +"rhea":[ +"11364", +"11367", +"11366", +"11365" +], +"sabiork":[ +"148" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00147" +] +} +}, +{ +"id":"ADK1", +"name":"Adenylate kinase", +"metabolites":{ +"adp_c":2.0, +"amp_c":-1.0, +"atp_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0474", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"ADK1" +] +}, +"annotation":{ +"bigg.reaction":[ +"ADK1" +], +"biocyc":[ +"META:ADENYL-KIN-RXN" +], +"ec-code":[ +"2.7.4.3" +], +"kegg.reaction":[ +"R00127" +], +"metanetx.reaction":[ +"MNXR95450" +], +"reactome.reaction":[ +"R-ATH-110145", +"R-SSC-110144", +"R-ATH-110144", +"R-SSC-110145", +"R-GGA-110145", +"R-PFA-110144", +"R-HSA-110145", +"R-RNO-110144", +"R-OSA-110145", +"R-SCE-110145", +"R-RNO-110145", +"R-XTR-110144", +"R-SCE-110144", +"R-PFA-110145", +"R-OSA-110144", +"R-HSA-110144", +"R-BTA-110144", +"R-DRE-110145", +"R-DRE-110144", +"R-SPO-110145", +"R-CEL-110144", +"R-CFA-110144", +"R-XTR-110145", +"R-MMU-110144", +"R-DME-110144", +"R-SPO-110144", +"R-DDI-110145", +"R-GGA-110144", +"R-TGU-110144", +"R-BTA-110145", +"R-CEL-110145", +"R-CFA-110145", +"R-DME-110145", +"R-TGU-110145", +"R-DDI-110144", +"R-MMU-110145" +], +"rhea":[ +"12975", +"12973", +"12976", +"12974" +], +"sabiork":[ +"82" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00097" +] +} +}, +{ +"id":"AKGDH", +"name":"2-Oxogluterate dehydrogenase", +"metabolites":{ +"akg_c":-1.0, +"co2_c":1.0, +"coa_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"succoa_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0116 and b0726 and b0727", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"AKGDH" +] +}, +"annotation":{ +"bigg.reaction":[ +"AKGDH" +], +"biocyc":[ +"META:2OXOGLUTARATEDEH-RXN" +], +"ec-code":[ +"1.2.1.52", +"2.3.1.61", +"1.8.1.4", +"1.2.4.2" +], +"kegg.reaction":[ +"R08549" +], +"metanetx.reaction":[ +"MNXR95655" +], +"reactome.reaction":[ +"R-PFA-71401", +"R-XTR-71401", +"R-SCE-71401", +"R-SSC-71401", +"R-TGU-71401", +"R-ATH-71401", +"R-OSA-71401", +"R-SPO-71401", +"R-CEL-71401", +"R-RNO-71401", +"R-DRE-71401", +"R-GGA-373042", +"R-DDI-71401", +"R-CFA-71401", +"R-HSA-71401", +"R-BTA-71401", +"R-DME-71401", +"R-MMU-71401", +"R-GGA-71401" +], +"rhea":[ +"27789", +"27788", +"27786", +"27787" +], +"sabiork":[ +"8163" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn08094" +] +} +}, +{ +"id":"ATPS4r", +"name":"ATP synthase (four protons for one ATP)", +"metabolites":{ +"adp_c":-1.0, +"atp_c":1.0, +"h2o_c":1.0, +"h_c":3.0, +"h_e":-4.0, +"pi_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"((b3736 and b3737 and b3738) and (b3731 and b3732 and b3733 and b3734 and b3735)) or ((b3736 and b3737 and b3738) and (b3731 and b3732 and b3733 and b3734 and b3735) and b3739)", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"ATPS4r" +] +}, +"annotation":{ +"bigg.reaction":[ +"ATPS4r" +], +"biocyc":[ +"META:ATPSYN-RXN" +], +"ec-code":[ +"3.6.3.14" +], +"metanetx.reaction":[ +"MNXR96136" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08173", +"rxn10042" +] +} +}, +{ +"id":"PTAr", +"name":"Phosphotransacetylase", +"metabolites":{ +"accoa_c":-1.0, +"actp_c":1.0, +"coa_c":1.0, +"pi_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2297 or b2458", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"PTAr" +] +}, +"annotation":{ +"bigg.reaction":[ +"PTAr" +], +"biocyc":[ +"META:PHOSACETYLTRANS-RXN" +], +"ec-code":[ +"2.3.1.8" +], +"kegg.reaction":[ +"R00230" +], +"metanetx.reaction":[ +"MNXR103319" +], +"rhea":[ +"19521", +"19523", +"19522", +"19524" +], +"sabiork":[ +"72" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00173" +] +} +}, +{ +"id":"PYK", +"name":"Pyruvate kinase", +"metabolites":{ +"adp_c":-1.0, +"atp_c":1.0, +"h_c":-1.0, +"pep_c":-1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1854 or b1676", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PYK" +] +}, +"annotation":{ +"bigg.reaction":[ +"PYK" +], +"biocyc":[ +"META:PEPDEPHOS-RXN" +], +"ec-code":[ +"2.7.1.40" +], +"kegg.reaction":[ +"R00200" +], +"metanetx.reaction":[ +"MNXR103371" +], +"reactome.reaction":[ +"R-SSC-71670", +"R-GGA-353056", +"R-DRE-71670", +"R-OSA-71670", +"R-SPO-71670", +"R-DDI-71670", +"R-SCE-71670", +"R-CEL-71670", +"R-PFA-71670", +"R-HSA-71670", +"R-TGU-71670", +"R-DME-71670", +"R-ATH-71670", +"R-BTA-71670", +"R-MMU-71670", +"R-RNO-71670", +"R-GGA-71670", +"R-CFA-71670", +"R-XTR-71670" +], +"rhea":[ +"18160", +"18159", +"18158", +"18157" +], +"sabiork":[ +"9" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00148" +] +} +}, +{ +"id":"BIOMASS_Ecoli_core_w_GAM", +"name":"Biomass Objective Function with GAM", +"metabolites":{ +"3pg_c":-1.496, +"accoa_c":-3.7478, +"adp_c":59.81, +"akg_c":4.1182, +"atp_c":-59.81, +"coa_c":3.7478, +"e4p_c":-0.361, +"f6p_c":-0.0709, +"g3p_c":-0.129, +"g6p_c":-0.205, +"gln__L_c":-0.2557, +"glu__L_c":-4.9414, +"h2o_c":-59.81, +"h_c":59.81, +"nad_c":-3.547, +"nadh_c":3.547, +"nadp_c":13.0279, +"nadph_c":-13.0279, +"oaa_c":-1.7867, +"pep_c":-0.5191, +"pi_c":59.81, +"pyr_c":-2.8328, +"r5p_c":-0.8977 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"objective_coefficient":1.0, +"subsystem":"Biomass and maintenance functions", +"notes":{ +"original_bigg_ids":[ +"Biomass_Ecoli_core_w_GAM" +] +}, +"annotation":{ +"bigg.reaction":[ +"BIOMASS_Ecoli_core_w_GAM" +], +"metanetx.reaction":[ +"MNXR96280" +], +"sbo":"SBO:0000629" +} +}, +{ +"id":"PYRt2", +"name":"Pyruvate transport in via proton symport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"pyr_c":1.0, +"pyr_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"PYRt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"PYRt2" +], +"metanetx.reaction":[ +"MNXR103385" +], +"reactome.reaction":[ +"R-RNO-372347", +"R-HSA-372342", +"R-GGA-372359" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05469", +"rxn09832", +"rxn09717", +"rxn09217" +] +} +}, +{ +"id":"CO2t", +"name":"CO2 transporter via diffusion", +"metabolites":{ +"co2_c":1.0, +"co2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"CO2t" +] +}, +"annotation":{ +"bigg.reaction":[ +"CO2t" +], +"biocyc":[ +"META:TRANS-RXN0-545" +], +"metanetx.reaction":[ +"MNXR96810" +], +"reactome.reaction":[ +"R-DDI-1247645", +"R-CFA-1237069", +"R-TGU-1247649", +"R-CFA-1237042", +"R-CEL-1247645", +"R-XTR-1237069", +"R-HSA-1247645", +"R-OSA-1237042", +"R-GGA-1237042", +"R-BTA-1247645", +"R-GGA-1247649", +"R-RNO-1247645", +"R-XTR-1247645", +"R-TGU-1237042", +"R-SCE-1247649", +"R-MMU-1247649", +"R-CFA-1247649", +"R-GGA-1247645", +"R-SSC-1247645", +"R-BTA-1237069", +"R-RNO-1237069", +"R-SCE-1237042", +"R-DDI-1247649", +"R-SSC-1237042", +"R-DRE-1247649", +"R-DRE-1237042", +"R-DDI-1237042", +"R-DME-1237042", +"R-MMU-1237042", +"R-SSC-1247649", +"R-TGU-1237069", +"R-BTA-1247649", +"R-CFA-1247645", +"R-RNO-1247649", +"R-HSA-1237069", +"R-CEL-1237069", +"R-DDI-1237069", +"R-MMU-1237069", +"R-DME-1247645", +"R-ATH-1237042", +"R-OSA-1247649", +"R-HSA-1237042", +"R-DRE-1247645", +"R-HSA-1247649", +"R-MMU-1247645", +"R-DME-1237069", +"R-RNO-1237042", +"R-TGU-1247645", +"R-BTA-1237042", +"R-GGA-1237069", +"R-DME-1247649", +"R-SSC-1237069", +"R-DRE-1237069", +"R-ATH-1247649" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05467", +"rxn08237", +"rxn09706", +"rxn09821", +"rxn09775", +"rxn09876", +"rxn08238", +"rxn09860" +] +} +}, +{ +"id":"RPE", +"name":"Ribulose 5-phosphate 3-epimerase", +"metabolites":{ +"ru5p__D_c":-1.0, +"xu5p__D_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3386 or b4301", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"RPE" +] +}, +"annotation":{ +"bigg.reaction":[ +"RPE" +], +"biocyc":[ +"META:RIBULP3EPIM-RXN" +], +"ec-code":[ +"5.1.3.1" +], +"kegg.reaction":[ +"R01529" +], +"metanetx.reaction":[ +"MNXR104083" +], +"reactome.reaction":[ +"R-SPO-71303", +"R-CFA-199803", +"R-ATH-71303", +"R-SCE-71303", +"R-CFA-71303", +"R-DME-199803", +"R-XTR-199803", +"R-SSC-199803", +"R-GGA-199803", +"R-TGU-71303", +"R-OSA-199803", +"R-SSC-71303", +"R-MMU-71303", +"R-OSA-71303", +"R-HSA-71303", +"R-MMU-199803", +"R-XTR-71303", +"R-SPO-199803", +"R-SCE-199803", +"R-DDI-71303", +"R-RNO-71303", +"R-DME-71303", +"R-HSA-199803", +"R-DRE-71303", +"R-PFA-199803", +"R-CEL-199803", +"R-RNO-199803", +"R-PFA-71303", +"R-CEL-71303", +"R-TGU-199803", +"R-GGA-71303", +"R-DDI-199803", +"R-BTA-71303", +"R-ATH-199803", +"R-DRE-199803", +"R-BTA-199803" +], +"rhea":[ +"13677", +"13680", +"13678", +"13679" +], +"sabiork":[ +"62" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01116" +] +} +}, +{ +"id":"CS", +"name":"Citrate synthase", +"metabolites":{ +"accoa_c":-1.0, +"cit_c":1.0, +"coa_c":1.0, +"h2o_c":-1.0, +"h_c":1.0, +"oaa_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0720", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"CS" +] +}, +"annotation":{ +"bigg.reaction":[ +"CS" +], +"biocyc":[ +"META:CITSYN-RXN", +"META:RXN-14905" +], +"ec-code":[ +"2.3.3.16", +"2.3.3.1", +"2.3.3.3" +], +"kegg.reaction":[ +"R00351" +], +"metanetx.reaction":[ +"MNXR96920" +], +"reactome.reaction":[ +"R-GGA-373006", +"R-GGA-70975", +"R-CEL-70975", +"R-HSA-70975", +"R-DRE-70975", +"R-MMU-70975", +"R-ATH-70975", +"R-SPO-70975", +"R-OSA-70975", +"R-SCE-70975", +"R-SSC-70975", +"R-DDI-70975", +"R-RNO-70975", +"R-DME-70975", +"R-PFA-70975", +"R-XTR-70975", +"R-CFA-70975", +"R-BTA-70975" +], +"rhea":[ +"16847", +"16846", +"16845", +"16848" +], +"sabiork":[ +"267" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00256" +] +} +}, +{ +"id":"RPI", +"name":"Ribose-5-phosphate isomerase", +"metabolites":{ +"r5p_c":-1.0, +"ru5p__D_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2914 or b4090", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"RPI" +] +}, +"annotation":{ +"bigg.reaction":[ +"RPI" +], +"ec-code":[ +"5.3.1.6" +], +"metanetx.reaction":[ +"MNXR104084" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"SUCCt2_2", +"name":"Succinate transport via proton symport (2 H)", +"metabolites":{ +"h_c":2.0, +"h_e":-2.0, +"succ_c":1.0, +"succ_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3528", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"SUCCt2_2" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCCt2_2" +], +"biocyc":[ +"META:TRANS-RXN-121" +], +"metanetx.reaction":[ +"MNXR104620" +], +"rhea":[ +"29305", +"29306", +"29304", +"29303" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10154", +"rxn09269" +] +} +}, +{ +"id":"CYTBD", +"name":"Cytochrome oxidase bd (ubiquinol-8: 2 protons)", +"metabolites":{ +"h2o_c":1.0, +"h_c":-2.0, +"h_e":2.0, +"o2_c":-0.5, +"q8_c":1.0, +"q8h2_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"(b0978 and b0979) or (b0733 and b0734)", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"CYTBD" +] +}, +"annotation":{ +"bigg.reaction":[ +"CYTBD" +], +"metanetx.reaction":[ +"MNXR97031" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn12494", +"rxn10112", +"rxn08288" +] +} +}, +{ +"id":"D_LACt2", +"name":"D lactate transport via proton symport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"lac__D_c":1.0, +"lac__D_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2975 or b3603", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"D_LACt2" +] +}, +"annotation":{ +"bigg.reaction":[ +"D_LACt2" +], +"biocyc":[ +"META:TRANS-RXN0-515" +], +"metanetx.reaction":[ +"MNXR97838" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10171", +"rxn09772", +"rxn08350" +] +} +}, +{ +"id":"ENO", +"name":"Enolase", +"metabolites":{ +"2pg_c":-1.0, +"h2o_c":1.0, +"pep_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2779", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"ENO" +] +}, +"annotation":{ +"bigg.reaction":[ +"ENO" +], +"biocyc":[ +"META:2PGADEHYDRAT-RXN" +], +"ec-code":[ +"4.2.1.11" +], +"kegg.reaction":[ +"R00658" +], +"metanetx.reaction":[ +"MNXR97932" +], +"reactome.reaction":[ +"R-BTA-71660", +"R-RNO-70494", +"R-TGU-71660", +"R-SSC-71660", +"R-GGA-352981", +"R-DME-70494", +"R-CFA-70494", +"R-OSA-70494", +"R-SCE-71660", +"R-GGA-353044", +"R-CFA-71660", +"R-GGA-70494", +"R-PFA-71660", +"R-SPO-71660", +"R-SPO-70494", +"R-DDI-70494", +"R-RNO-71660", +"R-MMU-70494", +"R-ATH-70494", +"R-SCE-70494", +"R-SSC-70494", +"R-HSA-70494", +"R-DME-71660", +"R-CEL-71660", +"R-HSA-71660", +"R-TGU-70494", +"R-XTR-71660", +"R-DRE-70494", +"R-DRE-71660", +"R-MMU-71660", +"R-ATH-71660", +"R-BTA-70494", +"R-CEL-70494", +"R-XTR-70494", +"R-DDI-71660", +"R-OSA-71660", +"R-PFA-70494", +"R-GGA-71660" +], +"rhea":[ +"10166", +"10165", +"10164", +"10167" +], +"sabiork":[ +"8" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00459" +] +} +}, +{ +"id":"SUCCt3", +"name":"Succinate transport out via proton antiport", +"metabolites":{ +"h_c":1.0, +"h_e":-1.0, +"succ_c":-1.0, +"succ_e":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"SUCCt3" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCCt3" +], +"metanetx.reaction":[ +"MNXR104623" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09270" +] +} +}, +{ +"id":"ETOHt2r", +"name":"Ethanol reversible transport via proton symport", +"metabolites":{ +"etoh_c":1.0, +"etoh_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"ETOHt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"ETOHt2r" +], +"metanetx.reaction":[ +"MNXR97981" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10146", +"rxn08427" +] +} +}, +{ +"id":"SUCDi", +"name":"Succinate dehydrogenase (irreversible)", +"metabolites":{ +"fum_c":1.0, +"q8_c":-1.0, +"q8h2_c":1.0, +"succ_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0721 and b0722 and b0723 and b0724", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"SUCDi" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCDi" +], +"metanetx.reaction":[ +"MNXR99641" +], +"rhea":[ +"29190", +"29189", +"29187", +"29188" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn09272" +] +} +}, +{ +"id":"SUCOAS", +"name":"Succinyl-CoA synthetase (ADP-forming)", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"coa_c":-1.0, +"pi_c":1.0, +"succ_c":-1.0, +"succoa_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0728 and b0729", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"SUCOAS" +] +}, +"annotation":{ +"bigg.reaction":[ +"SUCOAS" +], +"biocyc":[ +"META:SUCCCOASYN-RXN" +], +"ec-code":[ +"6.2.1.5" +], +"kegg.reaction":[ +"R00405" +], +"metanetx.reaction":[ +"MNXR104635" +], +"reactome.reaction":[ +"R-BTA-70997", +"R-GGA-372977", +"R-PFA-70997", +"R-GGA-373134", +"R-TGU-70997", +"R-XTR-70997", +"R-SSC-70997", +"R-HSA-70997", +"R-DRE-70997", +"R-SCE-70997", +"R-SPO-70997", +"R-DDI-70997", +"R-CFA-70997", +"R-OSA-70997", +"R-GGA-70997", +"R-RNO-70997", +"R-ATH-70997", +"R-MMU-70997" +], +"rhea":[ +"17664", +"17663", +"17662", +"17661" +], +"sabiork":[ +"260" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00285" +] +} +}, +{ +"id":"TALA", +"name":"Transaldolase", +"metabolites":{ +"e4p_c":1.0, +"f6p_c":1.0, +"g3p_c":-1.0, +"s7p_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2464 or b0008", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"TALA" +] +}, +"annotation":{ +"bigg.reaction":[ +"TALA" +], +"biocyc":[ +"META:TRANSALDOL-RXN" +], +"ec-code":[ +"2.2.1.2" +], +"kegg.reaction":[ +"R01827" +], +"metanetx.reaction":[ +"MNXR104715" +], +"rhea":[ +"17056", +"17055", +"17054", +"17053" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"THD2", +"name":"NAD(P) transhydrogenase", +"metabolites":{ +"h_c":2.0, +"h_e":-2.0, +"nad_c":1.0, +"nadh_c":-1.0, +"nadp_c":-1.0, +"nadph_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1602 and b1603", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"THD2" +] +}, +"annotation":{ +"bigg.reaction":[ +"THD2" +], +"ec-code":[ +"1.6.1.1" +], +"metanetx.reaction":[ +"MNXR104805" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn10125", +"rxn09295" +] +} +}, +{ +"id":"TKT1", +"name":"Transketolase", +"metabolites":{ +"g3p_c":1.0, +"r5p_c":-1.0, +"s7p_c":1.0, +"xu5p__D_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2935 or b2465", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"TKT1" +] +}, +"annotation":{ +"bigg.reaction":[ +"TKT1" +], +"ec-code":[ +"2.2.1.1" +], +"metanetx.reaction":[ +"MNXR104868" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"TKT2", +"name":"Transketolase", +"metabolites":{ +"e4p_c":-1.0, +"f6p_c":1.0, +"g3p_c":1.0, +"xu5p__D_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2935 or b2465", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"TKT2" +] +}, +"annotation":{ +"bigg.reaction":[ +"TKT2" +], +"biocyc":[ +"META:2TRANSKETO-RXN" +], +"ec-code":[ +"2.2.1.1" +], +"kegg.reaction":[ +"R01830" +], +"metanetx.reaction":[ +"MNXR104869" +], +"rhea":[ +"27627", +"27628", +"27626", +"27629" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"TPI", +"name":"Triose-phosphate isomerase", +"metabolites":{ +"dhap_c":-1.0, +"g3p_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3919", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"TPI" +] +}, +"annotation":{ +"bigg.reaction":[ +"TPI" +], +"biocyc":[ +"META:TRIOSEPISOMERIZATION-RXN" +], +"ec-code":[ +"5.3.1.1" +], +"kegg.reaction":[ +"R01015" +], +"metanetx.reaction":[ +"MNXR104918" +], +"reactome.reaction":[ +"R-RNO-70481", +"R-MMU-70481", +"R-XTR-70481", +"R-SSC-70481", +"R-GGA-352927", +"R-SCE-70454", +"R-CEL-70481", +"R-PFA-70454", +"R-XTR-70454", +"R-BTA-70481", +"R-BTA-70454", +"R-GGA-352914", +"R-ATH-70481", +"R-CFA-70454", +"R-OSA-70454", +"R-HSA-70481", +"R-DRE-70454", +"R-DME-70481", +"R-OSA-70481", +"R-DRE-70481", +"R-ATH-70454", +"R-HSA-70454", +"R-SSC-70454", +"R-DDI-70454", +"R-SCE-70481", +"R-CFA-70481", +"R-PFA-70481", +"R-DDI-70481", +"R-SPO-70454", +"R-SPO-70481", +"R-RNO-70454", +"R-MMU-70454", +"R-CEL-70454", +"R-GGA-70481", +"R-GGA-70454", +"R-DME-70454" +], +"rhea":[ +"18587", +"18588", +"18586", +"18585" +], +"sabiork":[ +"4" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00747" +] +} +}, +{ +"id":"EX_ac_e", +"name":"Acetate exchange", +"metabolites":{ +"ac_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_ac_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_ac_e" +], +"biocyc":[ +"META:RXN0-1981", +"META:TRANS-RXN0-567" +], +"metanetx.reaction":[ +"MNXR95431" +], +"rhea":[ +"27817", +"27814", +"27816", +"27815" +], +"sabiork":[ +"12184" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09787", +"rxn09866", +"rxn10904", +"rxn08063" +] +} +}, +{ +"id":"EX_acald_e", +"name":"Acetaldehyde exchange", +"metabolites":{ +"acald_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_acald_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_acald_e" +], +"metanetx.reaction":[ +"MNXR95212" +], +"reactome.reaction":[ +"R-HSA-449872" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09700", +"rxn08033", +"rxn13212", +"rxn08032" +] +} +}, +{ +"id":"EX_akg_e", +"name":"2-Oxoglutarate exchange", +"metabolites":{ +"akg_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_akg_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_akg_e" +], +"metanetx.reaction":[ +"MNXR95663" +], +"sabiork":[ +"13794" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10923", +"rxn08096", +"rxn13220" +] +} +}, +{ +"id":"EX_co2_e", +"name":"CO2 exchange", +"metabolites":{ +"co2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_co2_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_co2_e" +], +"biocyc":[ +"META:TRANS-RXN0-545" +], +"metanetx.reaction":[ +"MNXR96810" +], +"reactome.reaction":[ +"R-DDI-1247645", +"R-CFA-1237069", +"R-TGU-1247649", +"R-CFA-1237042", +"R-CEL-1247645", +"R-XTR-1237069", +"R-HSA-1247645", +"R-OSA-1237042", +"R-GGA-1237042", +"R-BTA-1247645", +"R-GGA-1247649", +"R-RNO-1247645", +"R-XTR-1247645", +"R-TGU-1237042", +"R-SCE-1247649", +"R-MMU-1247649", +"R-CFA-1247649", +"R-GGA-1247645", +"R-SSC-1247645", +"R-BTA-1237069", +"R-RNO-1237069", +"R-SCE-1237042", +"R-DDI-1247649", +"R-SSC-1237042", +"R-DRE-1247649", +"R-DRE-1237042", +"R-DDI-1237042", +"R-DME-1237042", +"R-MMU-1237042", +"R-SSC-1247649", +"R-TGU-1237069", +"R-BTA-1247649", +"R-CFA-1247645", +"R-RNO-1247649", +"R-HSA-1237069", +"R-CEL-1237069", +"R-DDI-1237069", +"R-MMU-1237069", +"R-DME-1247645", +"R-ATH-1237042", +"R-OSA-1247649", +"R-HSA-1237042", +"R-DRE-1247645", +"R-HSA-1247649", +"R-MMU-1247645", +"R-DME-1237069", +"R-RNO-1237042", +"R-TGU-1247645", +"R-BTA-1237042", +"R-GGA-1237069", +"R-DME-1247649", +"R-SSC-1237069", +"R-DRE-1237069", +"R-ATH-1247649" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn05467", +"rxn08237", +"rxn09706", +"rxn09821", +"rxn09775", +"rxn09876", +"rxn08238", +"rxn09860" +] +} +}, +{ +"id":"EX_etoh_e", +"name":"Ethanol exchange", +"metabolites":{ +"etoh_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_etoh_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_etoh_e" +], +"biocyc":[ +"META:TRANS-RXN0-546" +], +"metanetx.reaction":[ +"MNXR97980" +], +"rhea":[ +"35269", +"35267", +"35270", +"35268" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09683", +"rxn08428", +"rxn09764" +] +} +}, +{ +"id":"EX_for_e", +"name":"Formate exchange", +"metabolites":{ +"for_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_for_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_for_e" +], +"biocyc":[ +"META:TRANS-RXN-1" +], +"metanetx.reaction":[ +"MNXR99620" +], +"reactome.reaction":[ +"R-HSA-6803255" +], +"rhea":[ +"29681", +"29680", +"29682", +"29679" +], +"sabiork":[ +"12483" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09754", +"rxn08525", +"rxn09682", +"rxn08526" +] +} +}, +{ +"id":"EX_fru_e", +"name":"D-Fructose exchange", +"metabolites":{ +"fru_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_fru_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_fru_e" +], +"metanetx.reaction":[ +"MNXR99663" +], +"reactome.reaction":[ +"R-OSA-189222", +"R-XTR-189222", +"R-SCE-189222", +"R-ATH-189222", +"R-RNO-189222", +"R-DME-189222", +"R-TGU-189222", +"R-SSC-189222", +"R-CFA-189222", +"R-DRE-189222", +"R-HSA-189222", +"R-GGA-189222", +"R-BTA-189222", +"R-MMU-189222", +"R-DDI-189222" +], +"sabiork":[ +"13415" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn12996", +"rxn08537" +] +} +}, +{ +"id":"EX_fum_e", +"name":"Fumarate exchange", +"metabolites":{ +"fum_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_fum_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_fum_e" +], +"biocyc":[ +"META:TRANS-RXN0-553" +], +"metanetx.reaction":[ +"MNXR99715" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08544", +"rxn11013" +] +} +}, +{ +"id":"EX_glc__D_e", +"name":"D-Glucose exchange", +"metabolites":{ +"glc__D_e":-1.0 +}, +"lower_bound":-10.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_glc_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_glc__D_e" +], +"biocyc":[ +"META:TRANS-RXN0-574" +], +"metanetx.reaction":[ +"MNXR100188" +], +"sabiork":[ +"7002", +"601" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09875", +"rxn09679", +"rxn08617" +] +} +}, +{ +"id":"EX_gln__L_e", +"name":"L-Glutamine exchange", +"metabolites":{ +"gln__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_gln_L_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_gln__L_e" +], +"biocyc":[ +"META:TRANS-RXN-233" +], +"metanetx.reaction":[ +"MNXR100259" +], +"reactome.reaction":[ +"R-HSA-212651", +"R-BTA-212614", +"R-RNO-212614", +"R-SSC-212614", +"R-MMU-212614", +"R-HSA-212614", +"R-GGA-212614", +"R-CFA-212614", +"R-TGU-212614", +"R-SCE-212614" +], +"sabiork":[ +"13421" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08625", +"rxn10928" +] +} +}, +{ +"id":"EX_glu__L_e", +"name":"L-Glutamate exchange", +"metabolites":{ +"glu__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_glu_L_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_glu__L_e" +], +"biocyc":[ +"META:TRANS-RXN-234", +"META:TRANS-RXN-232" +], +"metanetx.reaction":[ +"MNXR100301" +], +"reactome.reaction":[ +"R-HSA-212658", +"R-TGU-210439", +"R-GGA-210439", +"R-XTR-210439", +"R-RNO-210439", +"R-CFA-210439", +"R-CEL-210439", +"R-DME-210439", +"R-SSC-210439", +"R-HSA-210439", +"R-DRE-210439", +"R-MMU-210439", +"R-BTA-210439" +], +"sabiork":[ +"12283" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08633", +"rxn09750", +"rxn13304", +"rxn13120", +"rxn10917" +] +} +}, +{ +"id":"EX_h_e", +"name":"H+ exchange", +"metabolites":{ +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_h_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_h_e" +], +"biocyc":[ +"META:RXN-14452" +], +"metanetx.reaction":[ +"MNXR100765" +], +"reactome.reaction":[ +"R-HSA-2534378", +"R-DDI-74723", +"R-BTA-170026", +"R-CFA-170026", +"R-SCE-74723", +"R-DRE-74723", +"R-HSA-170026", +"R-TGU-2534378", +"R-HSA-74723", +"R-CFA-2534378", +"R-TGU-74723", +"R-OSA-170026", +"R-RNO-2534378", +"R-GGA-2534378", +"R-MMU-2534378", +"R-BTA-2534378", +"R-SSC-2534378", +"R-DRE-170026", +"R-TGU-170026", +"R-GGA-170026", +"R-SCE-170026", +"R-DRE-2534378", +"R-BTA-74723", +"R-SPO-74723", +"R-XTR-74723", +"R-RNO-74723", +"R-XTR-2534378", +"R-MMU-74723", +"R-CFA-74723", +"R-GGA-74723", +"R-CEL-170026", +"R-MMU-170026", +"R-ATH-74723", +"R-DME-74723", +"R-PFA-74723", +"R-SSC-74723", +"R-XTR-170026", +"R-SSC-170026", +"R-CEL-74723", +"R-ATH-170026", +"R-RNO-170026", +"R-DME-170026" +], +"rhea":[ +"34980", +"34981", +"34982", +"34979" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn11009", +"rxn08730" +] +} +}, +{ +"id":"EX_h2o_e", +"name":"H2O exchange", +"metabolites":{ +"h2o_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_h2o_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_h2o_e" +], +"biocyc":[ +"META:TRANS-RXN-145", +"META:TRANS-RXN0-547" +], +"metanetx.reaction":[ +"MNXR98641" +], +"reactome.reaction":[ +"R-ATH-507868", +"R-CFA-432054", +"R-CFA-432010", +"R-RNO-507868", +"R-OSA-432065", +"R-GGA-432010", +"R-SPO-445714", +"R-PFA-445714", +"R-CFA-432065", +"R-GGA-432067", +"R-TGU-432054", +"R-TGU-445714", +"R-OSA-507868", +"R-DRE-507868", +"R-SPO-507868", +"R-BTA-432054", +"R-GGA-507870", +"R-OSA-432010", +"R-DME-432065", +"R-DRE-432067", +"R-PFA-507868", +"R-SSC-432054", +"R-HSA-432065", +"R-OSA-507870", +"R-HSA-432054", +"R-SSC-432065", +"R-CEL-507868", +"R-XTR-507868", +"R-ATH-507870", +"R-SCE-432065", +"R-BTA-507870", +"R-DME-432010", +"R-CFA-445714", +"R-DRE-445714", +"R-BTA-507868", +"R-GGA-507868", +"R-RNO-432054", +"R-RNO-432010", +"R-SSC-432067", +"R-CEL-445714", +"R-DDI-432065", +"R-ATH-432010", +"R-SCE-432054", +"R-MMU-432065", +"R-MMU-445714", +"R-GGA-432065", +"R-HSA-432067", +"R-SSC-507870", +"R-SCE-432067", +"R-RNO-507870", +"R-DME-432054", +"R-ATH-432067", +"R-BTA-445714", +"R-DRE-507870", +"R-DME-507868", +"R-DME-507870", +"R-DRE-432010", +"R-MMU-432010", +"R-HSA-445714", +"R-OSA-432054", +"R-RNO-432067", +"R-TGU-432010", +"R-TGU-507868", +"R-DDI-432054", +"R-PFA-507870", +"R-HSA-507870", +"R-XTR-432067", +"R-HSA-432010", +"R-SSC-507868", +"R-SCE-507870", +"R-CEL-507870", +"R-DDI-507868", +"R-DRE-432054", +"R-XTR-507870", +"R-DDI-432010", +"R-BTA-432065", +"R-CFA-432067", +"R-OSA-432067", +"R-ATH-432065", +"R-GGA-445714", +"R-SCE-507868", +"R-TGU-432065", +"R-MMU-432067", +"R-TGU-507870", +"R-CFA-507870", +"R-RNO-432065", +"R-MMU-432054", +"R-MMU-507868", +"R-SPO-507870", +"R-SCE-432010", +"R-MMU-507870", +"R-SSC-445714", +"R-HSA-507868", +"R-DME-432067", +"R-SSC-432010", +"R-TGU-432067", +"R-GGA-432054", +"R-BTA-432010", +"R-SCE-445714", +"R-DDI-507870", +"R-ATH-432054", +"R-DDI-432067", +"R-XTR-445714", +"R-BTA-432067", +"R-CFA-507868", +"R-RNO-445714" +], +"rhea":[ +"29668", +"29669", +"29667", +"29670" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08687", +"rxn08686", +"rxn09745", +"rxn09838", +"rxn09874", +"rxn09812", +"rxn09643", +"rxn05319" +] +} +}, +{ +"id":"EX_lac__D_e", +"name":"D-lactate exchange", +"metabolites":{ +"lac__D_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_lac_D_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_lac__D_e" +], +"metanetx.reaction":[ +"MNXR97840" +], +"sabiork":[ +"12471" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn08351" +] +} +}, +{ +"id":"EX_mal__L_e", +"name":"L-Malate exchange", +"metabolites":{ +"mal__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_mal_L_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_mal__L_e" +], +"biocyc":[ +"META:TRANS-RXN-225", +"META:TRANS-RXN-224" +], +"metanetx.reaction":[ +"MNXR101367" +], +"sabiork":[ +"13793" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10967", +"rxn08868" +] +} +}, +{ +"id":"EX_nh4_e", +"name":"Ammonia exchange", +"metabolites":{ +"nh4_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_nh4_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_nh4_e" +], +"biocyc":[ +"META:TRANS-RXN0-206", +"META:RXN-9615", +"META:TRANS-RXN0-544" +], +"metanetx.reaction":[ +"MNXR101950" +], +"reactome.reaction":[ +"R-CEL-444416", +"R-SSC-444416", +"R-DDI-444416", +"R-MMU-444416", +"R-DRE-444416", +"R-GGA-444416", +"R-CFA-444416", +"R-HSA-444416", +"R-XTR-444416", +"R-BTA-444416", +"R-RNO-444416", +"R-TGU-444416", +"R-DME-444416" +], +"rhea":[ +"28749", +"28748", +"28750", +"28747" +], +"sabiork":[ +"11683" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn13364", +"rxn09835", +"rxn05466", +"rxn08987", +"rxn08986", +"rxn09736" +] +} +}, +{ +"id":"EX_o2_e", +"name":"O2 exchange", +"metabolites":{ +"o2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_o2_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_o2_e" +], +"biocyc":[ +"META:TRANS-RXN0-474" +], +"metanetx.reaction":[ +"MNXR102090" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn09641", +"rxn05468", +"rxn09031", +"rxn09032", +"rxn09734" +] +} +}, +{ +"id":"EX_pi_e", +"name":"Phosphate exchange", +"metabolites":{ +"pi_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_pi_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_pi_e" +], +"biocyc":[ +"META:TRANS-RXN0-470" +], +"metanetx.reaction":[ +"MNXR102871" +], +"rhea":[ +"32824", +"32826", +"32825", +"32823" +], +"sabiork":[ +"10985" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10838", +"rxn09722", +"rxn09121", +"rxn13178" +] +} +}, +{ +"id":"EX_pyr_e", +"name":"Pyruvate exchange", +"metabolites":{ +"pyr_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_pyr_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_pyr_e" +], +"biocyc":[ +"META:TRANS-RXN0-506", +"META:TRANS-RXN0-570" +], +"metanetx.reaction":[ +"MNXR103384" +], +"sabiork":[ +"12168" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10929", +"rxn09218" +] +} +}, +{ +"id":"EX_succ_e", +"name":"Succinate exchange", +"metabolites":{ +"succ_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"", +"subsystem":"Extracellular exchange", +"notes":{ +"original_bigg_ids":[ +"EX_succ_e" +] +}, +"annotation":{ +"bigg.reaction":[ +"EX_succ_e" +], +"biocyc":[ +"META:TRANS-RXN0-552" +], +"metanetx.reaction":[ +"MNXR104619" +], +"sbo":"SBO:0000627", +"seed.reaction":[ +"rxn10952", +"rxn09271" +] +} +}, +{ +"id":"FBA", +"name":"Fructose-bisphosphate aldolase", +"metabolites":{ +"dhap_c":1.0, +"fdp_c":-1.0, +"g3p_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2097 or b1773 or b2925", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"FBA" +] +}, +"annotation":{ +"bigg.reaction":[ +"FBA" +], +"ec-code":[ +"4.1.2.13" +], +"kegg.reaction":[ +"R01068" +], +"metanetx.reaction":[ +"MNXR99459" +], +"rhea":[ +"14729", +"14732", +"14731", +"14730" +], +"sabiork":[ +"1338" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00786" +] +} +}, +{ +"id":"FBP", +"name":"Fructose-bisphosphatase", +"metabolites":{ +"f6p_c":1.0, +"fdp_c":-1.0, +"h2o_c":-1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3925 or b4232", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"FBP" +] +}, +"annotation":{ +"bigg.reaction":[ +"FBP" +], +"ec-code":[ +"3.1.3.11" +], +"metanetx.reaction":[ +"MNXR99465" +], +"rhea":[ +"11067", +"11065", +"11066", +"11064" +], +"sabiork":[ +"2084" +], +"sbo":"SBO:0000176" +} +}, +{ +"id":"FORt2", +"name":"Formate transport in via proton symport", +"metabolites":{ +"for_c":1.0, +"for_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0904 or b2492", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FORt2" +] +}, +"annotation":{ +"bigg.reaction":[ +"FORt2" +], +"metanetx.reaction":[ +"MNXR99621" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08524", +"rxn05559" +] +} +}, +{ +"id":"FORt", +"name":"Formate transport via diffusion", +"metabolites":{ +"for_c":1.0, +"for_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":0.0, +"gene_reaction_rule":"b0904 or b2492", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FORti" +] +}, +"annotation":{ +"bigg.reaction":[ +"FORt" +], +"biocyc":[ +"META:TRANS-RXN-1" +], +"metanetx.reaction":[ +"MNXR99620" +], +"reactome.reaction":[ +"R-HSA-6803255" +], +"rhea":[ +"29681", +"29680", +"29682", +"29679" +], +"sabiork":[ +"12483" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09754", +"rxn08525", +"rxn09682", +"rxn08526" +] +} +}, +{ +"id":"FRD7", +"name":"Fumarate reductase", +"metabolites":{ +"fum_c":-1.0, +"q8_c":1.0, +"q8h2_c":-1.0, +"succ_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4151 and b4152 and b4153 and b4154", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"FRD7" +] +}, +"annotation":{ +"bigg.reaction":[ +"FRD7" +], +"metanetx.reaction":[ +"MNXR99641" +], +"rhea":[ +"29190", +"29189", +"29187", +"29188" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn09272" +] +} +}, +{ +"id":"FRUpts2", +"name":"Fructose transport via PEP:Pyr PTS (f6p generating)", +"metabolites":{ +"f6p_c":1.0, +"fru_e":-1.0, +"pep_c":-1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1817 and b1818 and b1819 and b2415 and b2416", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FRUpts2" +] +}, +"annotation":{ +"bigg.reaction":[ +"FRUpts2" +], +"metanetx.reaction":[ +"MNXR99662" +], +"sbo":"SBO:0000185" +} +}, +{ +"id":"FUM", +"name":"Fumarase", +"metabolites":{ +"fum_c":-1.0, +"h2o_c":-1.0, +"mal__L_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1612 or b4122 or b1611", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"FUM" +] +}, +"annotation":{ +"bigg.reaction":[ +"FUM" +], +"biocyc":[ +"META:FUMHYDR-RXN" +], +"ec-code":[ +"4.2.1.2" +], +"kegg.reaction":[ +"R01082" +], +"metanetx.reaction":[ +"MNXR99705" +], +"reactome.reaction":[ +"R-TGU-451033", +"R-TGU-70982", +"R-HSA-70982", +"R-ATH-451033", +"R-SPO-70982", +"R-SPO-451033", +"R-XTR-451033", +"R-MMU-70982", +"R-DRE-70982", +"R-DME-70982", +"R-DME-451033", +"R-HSA-451033", +"R-SCE-451033", +"R-DDI-451033", +"R-OSA-451033", +"R-CFA-70982", +"R-XTR-70982", +"R-MMU-451033", +"R-OSA-70982", +"R-BTA-70982", +"R-DRE-451033", +"R-GGA-373141", +"R-RNO-451033", +"R-CEL-451033", +"R-ATH-70982", +"R-GGA-373145", +"R-CEL-70982", +"R-BTA-451033", +"R-SSC-451033", +"R-SCE-70982", +"R-CFA-451033", +"R-RNO-70982", +"R-GGA-70982", +"R-DDI-70982", +"R-GGA-451033", +"R-SSC-70982" +], +"rhea":[ +"12463", +"12461", +"12462", +"12460" +], +"sabiork":[ +"256" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00799" +] +} +}, +{ +"id":"FUMt2_2", +"name":"Fumarate transport via proton symport (2 H)", +"metabolites":{ +"fum_c":1.0, +"fum_e":-1.0, +"h_c":2.0, +"h_e":-2.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3528", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"FUMt2_2" +] +}, +"annotation":{ +"bigg.reaction":[ +"FUMt2_2" +], +"biocyc":[ +"META:TRANS-RXN-121B" +], +"metanetx.reaction":[ +"MNXR99711" +], +"rhea":[ +"29332", +"29334", +"29333", +"29331" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08542", +"rxn10152" +] +} +}, +{ +"id":"G6PDH2r", +"name":"Glucose 6-phosphate dehydrogenase", +"metabolites":{ +"6pgl_c":1.0, +"g6p_c":-1.0, +"h_c":1.0, +"nadp_c":-1.0, +"nadph_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1852", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"G6PDH2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"G6PDH2r" +], +"biocyc":[ +"META:GLU6PDEHYDROG-RXN" +], +"ec-code":[ +"1.1.1.363", +"1.1.1.49" +], +"kegg.reaction":[ +"R00835" +], +"metanetx.reaction":[ +"MNXR99907" +], +"rhea":[ +"15842", +"15843", +"15841", +"15844" +], +"sabiork":[ +"1176", +"6509" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00604" +] +} +}, +{ +"id":"GAPD", +"name":"Glyceraldehyde-3-phosphate dehydrogenase", +"metabolites":{ +"13dpg_c":1.0, +"g3p_c":-1.0, +"h_c":1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pi_c":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1779", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"GAPD" +] +}, +"annotation":{ +"bigg.reaction":[ +"GAPD" +], +"biocyc":[ +"META:GAPOXNPHOSPHN-RXN" +], +"ec-code":[ +"1.2.1.12", +"1.2.1.59" +], +"kegg.reaction":[ +"R01061" +], +"metanetx.reaction":[ +"MNXR100040" +], +"reactome.reaction":[ +"R-ATH-70482", +"R-DME-70449", +"R-PFA-70482", +"R-SPO-70449", +"R-DRE-70449", +"R-CEL-70449", +"R-CEL-70482", +"R-CFA-70449", +"R-MMU-70482", +"R-HSA-70449", +"R-OSA-70482", +"R-GGA-352956", +"R-RNO-70449", +"R-SCE-70449", +"R-SSC-70482", +"R-ATH-70449", +"R-GGA-70482", +"R-OSA-70449", +"R-GGA-352921", +"R-DDI-70449", +"R-SPO-70482", +"R-TGU-70482", +"R-SCE-70482", +"R-HSA-70482", +"R-DME-70482", +"R-PFA-70449", +"R-XTR-70449", +"R-DRE-70482", +"R-XTR-70482", +"R-GGA-70449", +"R-RNO-70482", +"R-SSC-70449", +"R-DDI-70482", +"R-TGU-70449", +"R-MMU-70449", +"R-CFA-70482", +"R-BTA-70449", +"R-BTA-70482" +], +"rhea":[ +"10303", +"10300", +"10302", +"10301" +], +"sabiork":[ +"7844" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00781" +] +} +}, +{ +"id":"GLCpts", +"name":"D-glucose transport via PEP:Pyr PTS", +"metabolites":{ +"g6p_c":1.0, +"glc__D_e":-1.0, +"pep_c":-1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"(b2417 and b1101 and b2415 and b2416) or (b1817 and b1818 and b1819 and b2415 and b2416) or (b2417 and b1621 and b2415 and b2416)", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"GLCpts" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLCpts" +], +"metanetx.reaction":[ +"MNXR100237" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08612", +"rxn05226" +] +} +}, +{ +"id":"GLNS", +"name":"Glutamine synthetase", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"gln__L_c":1.0, +"glu__L_c":-1.0, +"h_c":1.0, +"nh4_c":-1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3870 or b1297", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLNS" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLNS" +], +"biocyc":[ +"META:GLUTAMINESYN-RXN" +], +"ec-code":[ +"6.3.1.2" +], +"kegg.reaction":[ +"R00253" +], +"metanetx.reaction":[ +"MNXR100024" +], +"reactome.reaction":[ +"R-GGA-70606", +"R-RNO-70606", +"R-TGU-70606", +"R-DME-70606", +"R-CEL-70606", +"R-DRE-70606", +"R-XTR-70606", +"R-SPO-70606", +"R-ATH-70606", +"R-CFA-70606", +"R-BTA-70606", +"R-OSA-70606", +"R-SSC-70606", +"R-MMU-70606", +"R-HSA-70606", +"R-SCE-70606" +], +"rhea":[ +"16172", +"16171", +"16169", +"16170" +], +"sabiork":[ +"760" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00187" +] +} +}, +{ +"id":"GLNabc", +"name":"L-glutamine transport via ABC system", +"metabolites":{ +"adp_c":1.0, +"atp_c":-1.0, +"gln__L_c":1.0, +"gln__L_e":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"pi_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0811 and b0810 and b0809", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"GLNabc" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLNabc" +], +"biocyc":[ +"META:ABC-12-RXN" +], +"ec-code":[ +"3.6.3.21" +], +"metanetx.reaction":[ +"MNXR100258" +], +"rhea":[ +"29895#1", +"29897#1", +"29898#1", +"29896#1" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn11233", +"rxn05196", +"rxn05155", +"rxn11101", +"rxn08624" +] +} +}, +{ +"id":"GLUDy", +"name":"Glutamate dehydrogenase (NADP)", +"metabolites":{ +"akg_c":1.0, +"glu__L_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"nadp_c":-1.0, +"nadph_c":1.0, +"nh4_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1761", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLUDy" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUDy" +], +"biocyc":[ +"META:GLUTDEHYD-RXN" +], +"ec-code":[ +"1.4.1.13", +"1.4.1.3", +"1.4.1.4" +], +"kegg.reaction":[ +"R00248" +], +"metanetx.reaction":[ +"MNXR100086" +], +"rhea":[ +"11613", +"11614", +"11612", +"11615" +], +"sabiork":[ +"757" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00184" +] +} +}, +{ +"id":"GLUN", +"name":"Glutaminase", +"metabolites":{ +"gln__L_c":-1.0, +"glu__L_c":1.0, +"h2o_c":-1.0, +"nh4_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1812 or b0485 or b1524", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLUN" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUN" +], +"biocyc":[ +"META:GLUTAMIN-RXN" +], +"ec-code":[ +"6.3.5.2", +"4.3.3.6", +"6.3.5.5", +"1.4.7.1", +"6.3.5.4", +"3.5.1.2", +"6.3.4.2", +"1.4.1.13", +"3.5.1.38" +], +"kegg.reaction":[ +"R00256" +], +"metanetx.reaction":[ +"MNXR100030" +], +"reactome.reaction":[ +"R-TGU-70609", +"R-XTR-70609", +"R-SSC-70609", +"R-GGA-70609", +"R-DDI-70609", +"R-MMU-70609", +"R-DME-70609", +"R-RNO-70609", +"R-CEL-70609", +"R-BTA-70609", +"R-DRE-70609", +"R-HSA-70609", +"R-CFA-70609" +], +"rhea":[ +"15892", +"15889", +"15891", +"15890" +], +"sabiork":[ +"762" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00189" +] +} +}, +{ +"id":"GLUSy", +"name":"Glutamate synthase (NADPH)", +"metabolites":{ +"akg_c":-1.0, +"gln__L_c":-1.0, +"glu__L_c":2.0, +"h_c":-1.0, +"nadp_c":1.0, +"nadph_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3212 and b3213", +"subsystem":"Glutamate Metabolism", +"notes":{ +"original_bigg_ids":[ +"GLUSy" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUSy" +], +"biocyc":[ +"META:GLUTAMATESYN-RXN" +], +"ec-code":[ +"1.4.1.13" +], +"kegg.reaction":[ +"R00114" +], +"metanetx.reaction":[ +"MNXR100291" +], +"rhea":[ +"15503", +"15501", +"15504", +"15502" +], +"sabiork":[ +"694" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00085" +] +} +}, +{ +"id":"GLUt2r", +"name":"L glutamate transport via proton symport reversible", +"metabolites":{ +"glu__L_c":1.0, +"glu__L_e":-1.0, +"h_c":1.0, +"h_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4077", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"GLUt2r" +] +}, +"annotation":{ +"bigg.reaction":[ +"GLUt2r" +], +"metanetx.reaction":[ +"MNXR100300" +], +"reactome.reaction":[ +"R-SCE-8875623", +"R-MMU-8875623", +"R-TGU-8875623", +"R-XTR-8875623", +"R-SSC-8875623", +"R-DME-8875623", +"R-CEL-8875623", +"R-DRE-8875623", +"R-GGA-8875623", +"R-HSA-8875623", +"R-RNO-8875623", +"R-DDI-8875623", +"R-CFA-8875623", +"R-BTA-8875623" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn05297", +"rxn09813", +"rxn13303", +"rxn09751", +"rxn08631" +] +} +}, +{ +"id":"GND", +"name":"Phosphogluconate dehydrogenase", +"metabolites":{ +"6pgc_c":-1.0, +"co2_c":1.0, +"nadp_c":-1.0, +"nadph_c":1.0, +"ru5p__D_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2029", +"subsystem":"Pentose Phosphate Pathway", +"notes":{ +"original_bigg_ids":[ +"GND" +] +}, +"annotation":{ +"bigg.reaction":[ +"GND" +], +"biocyc":[ +"META:RXN-9952" +], +"ec-code":[ +"1.1.1.44", +"1.1.1.351" +], +"kegg.reaction":[ +"R01528" +], +"metanetx.reaction":[ +"MNXR100389" +], +"reactome.reaction":[ +"R-PFA-71299", +"R-GGA-71299", +"R-HSA-71299", +"R-SPO-71299", +"R-XTR-71299", +"R-ATH-71299", +"R-TGU-71299", +"R-OSA-71299", +"R-MMU-71299", +"R-DRE-71299", +"R-SCE-71299", +"R-SSC-71299", +"R-DDI-71299", +"R-CFA-71299", +"R-DME-71299", +"R-BTA-71299", +"R-CEL-71299" +], +"rhea":[ +"10116", +"10117", +"10118", +"10119" +], +"sabiork":[ +"108" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn01115" +] +} +}, +{ +"id":"H2Ot", +"name":"H2O transport via diffusion", +"metabolites":{ +"h2o_c":1.0, +"h2o_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0875 or s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"H2Ot" +] +}, +"annotation":{ +"bigg.reaction":[ +"H2Ot" +], +"biocyc":[ +"META:TRANS-RXN-145", +"META:TRANS-RXN0-547" +], +"metanetx.reaction":[ +"MNXR98641" +], +"reactome.reaction":[ +"R-ATH-507868", +"R-CFA-432054", +"R-CFA-432010", +"R-RNO-507868", +"R-OSA-432065", +"R-GGA-432010", +"R-SPO-445714", +"R-PFA-445714", +"R-CFA-432065", +"R-GGA-432067", +"R-TGU-432054", +"R-TGU-445714", +"R-OSA-507868", +"R-DRE-507868", +"R-SPO-507868", +"R-BTA-432054", +"R-GGA-507870", +"R-OSA-432010", +"R-DME-432065", +"R-DRE-432067", +"R-PFA-507868", +"R-SSC-432054", +"R-HSA-432065", +"R-OSA-507870", +"R-HSA-432054", +"R-SSC-432065", +"R-CEL-507868", +"R-XTR-507868", +"R-ATH-507870", +"R-SCE-432065", +"R-BTA-507870", +"R-DME-432010", +"R-CFA-445714", +"R-DRE-445714", +"R-BTA-507868", +"R-GGA-507868", +"R-RNO-432054", +"R-RNO-432010", +"R-SSC-432067", +"R-CEL-445714", +"R-DDI-432065", +"R-ATH-432010", +"R-SCE-432054", +"R-MMU-432065", +"R-MMU-445714", +"R-GGA-432065", +"R-HSA-432067", +"R-SSC-507870", +"R-SCE-432067", +"R-RNO-507870", +"R-DME-432054", +"R-ATH-432067", +"R-BTA-445714", +"R-DRE-507870", +"R-DME-507868", +"R-DME-507870", +"R-DRE-432010", +"R-MMU-432010", +"R-HSA-445714", +"R-OSA-432054", +"R-RNO-432067", +"R-TGU-432010", +"R-TGU-507868", +"R-DDI-432054", +"R-PFA-507870", +"R-HSA-507870", +"R-XTR-432067", +"R-HSA-432010", +"R-SSC-507868", +"R-SCE-507870", +"R-CEL-507870", +"R-DDI-507868", +"R-DRE-432054", +"R-XTR-507870", +"R-DDI-432010", +"R-BTA-432065", +"R-CFA-432067", +"R-OSA-432067", +"R-ATH-432065", +"R-GGA-445714", +"R-SCE-507868", +"R-TGU-432065", +"R-MMU-432067", +"R-TGU-507870", +"R-CFA-507870", +"R-RNO-432065", +"R-MMU-432054", +"R-MMU-507868", +"R-SPO-507870", +"R-SCE-432010", +"R-MMU-507870", +"R-SSC-445714", +"R-HSA-507868", +"R-DME-432067", +"R-SSC-432010", +"R-TGU-432067", +"R-GGA-432054", +"R-BTA-432010", +"R-SCE-445714", +"R-DDI-507870", +"R-ATH-432054", +"R-DDI-432067", +"R-XTR-445714", +"R-BTA-432067", +"R-CFA-507868", +"R-RNO-445714" +], +"rhea":[ +"29668", +"29669", +"29667", +"29670" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08687", +"rxn08686", +"rxn09745", +"rxn09838", +"rxn09874", +"rxn09812", +"rxn09643", +"rxn05319" +] +} +}, +{ +"id":"ICDHyr", +"name":"Isocitrate dehydrogenase (NADP)", +"metabolites":{ +"akg_c":1.0, +"co2_c":1.0, +"icit_c":-1.0, +"nadp_c":-1.0, +"nadph_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1136", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"ICDHyr" +] +}, +"annotation":{ +"bigg.reaction":[ +"ICDHyr" +], +"ec-code":[ +"1.1.1.42" +], +"kegg.reaction":[ +"R00267" +], +"metanetx.reaction":[ +"MNXR100781" +], +"rhea":[ +"19629", +"19630", +"19631", +"19632" +], +"sabiork":[ +"269" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00198" +] +} +}, +{ +"id":"ICL", +"name":"Isocitrate lyase", +"metabolites":{ +"glx_c":1.0, +"icit_c":-1.0, +"succ_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4015", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"ICL" +] +}, +"annotation":{ +"bigg.reaction":[ +"ICL" +], +"ec-code":[ +"4.1.3.1" +], +"kegg.reaction":[ +"R00479" +], +"metanetx.reaction":[ +"MNXR100789" +], +"rhea":[ +"13248", +"13245", +"13246", +"13247" +], +"sabiork":[ +"911" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00336" +] +} +}, +{ +"id":"LDH_D", +"name":"D-lactate dehydrogenase", +"metabolites":{ +"h_c":1.0, +"lac__D_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pyr_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2133 or b1380", +"subsystem":"Pyruvate Metabolism", +"notes":{ +"original_bigg_ids":[ +"LDH_D" +] +}, +"annotation":{ +"bigg.reaction":[ +"LDH_D" +], +"biocyc":[ +"META:DLACTDEHYDROGNAD-RXN" +], +"ec-code":[ +"1.1.1.28" +], +"kegg.reaction":[ +"R00704" +], +"metanetx.reaction":[ +"MNXR101037" +], +"rhea":[ +"16370", +"16371", +"16372", +"16369" +], +"sabiork":[ +"155" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00500" +] +} +}, +{ +"id":"MALS", +"name":"Malate synthase", +"metabolites":{ +"accoa_c":-1.0, +"coa_c":1.0, +"glx_c":-1.0, +"h2o_c":-1.0, +"h_c":1.0, +"mal__L_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b4014 or b2976", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"MALS" +] +}, +"annotation":{ +"bigg.reaction":[ +"MALS" +], +"biocyc":[ +"META:MALSYN-RXN" +], +"ec-code":[ +"2.3.3.9" +], +"kegg.reaction":[ +"R00472" +], +"metanetx.reaction":[ +"MNXR101347" +], +"rhea":[ +"18181", +"18182", +"18184", +"18183" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00330" +] +} +}, +{ +"id":"MALt2_2", +"name":"Malate transport via proton symport (2 H)", +"metabolites":{ +"h_c":2.0, +"h_e":-2.0, +"mal__L_c":1.0, +"mal__L_e":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3528", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"MALt2_2" +] +}, +"annotation":{ +"bigg.reaction":[ +"MALt2_2" +], +"biocyc":[ +"META:TRANS-RXN-121A" +], +"metanetx.reaction":[ +"MNXR101370" +], +"rhea":[ +"29341", +"29340", +"29342", +"29339" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08865", +"rxn10153" +] +} +}, +{ +"id":"MDH", +"name":"Malate dehydrogenase", +"metabolites":{ +"h_c":1.0, +"mal__L_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"oaa_c":1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3236", +"subsystem":"Citric Acid Cycle", +"notes":{ +"original_bigg_ids":[ +"MDH" +] +}, +"annotation":{ +"bigg.reaction":[ +"MDH" +], +"biocyc":[ +"META:MALATE-DEH-RXN" +], +"ec-code":[ +"1.1.1.37", +"1.1.1.299" +], +"kegg.reaction":[ +"R00342" +], +"metanetx.reaction":[ +"MNXR101439" +], +"reactome.reaction":[ +"R-BTA-70979", +"R-BTA-198508", +"R-SCE-70979", +"R-GGA-70979", +"R-MMU-71783", +"R-RNO-71783", +"R-DDI-198508", +"R-CFA-71783", +"R-CFA-198508", +"R-ATH-70979", +"R-DME-198508", +"R-TGU-71783", +"R-HSA-71783", +"R-BTA-71783", +"R-DRE-198508", +"R-SPO-70979", +"R-GGA-71783", +"R-TGU-198508", +"R-GGA-372422", +"R-CEL-71783", +"R-XTR-70979", +"R-RNO-198508", +"R-MMU-70979", +"R-SPO-71783", +"R-ATH-71783", +"R-MMU-198508", +"R-DME-70979", +"R-TGU-70979", +"R-CEL-198508", +"R-DME-71783", +"R-DRE-70979", +"R-OSA-71783", +"R-SSC-198508", +"R-GGA-372855", +"R-SSC-70979", +"R-OSA-70979", +"R-GGA-373047", +"R-GGA-198508", +"R-SSC-71783", +"R-HSA-70979", +"R-CFA-70979", +"R-XTR-71783", +"R-HSA-198508", +"R-XTR-198508", +"R-SCE-71783", +"R-RNO-70979", +"R-DRE-71783", +"R-CEL-70979" +], +"rhea":[ +"21432", +"21433", +"21434", +"21435" +], +"sabiork":[ +"113" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00248" +] +} +}, +{ +"id":"ME1", +"name":"Malic enzyme (NAD)", +"metabolites":{ +"co2_c":1.0, +"mal__L_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b1479", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"ME1" +] +}, +"annotation":{ +"bigg.reaction":[ +"ME1" +], +"biocyc":[ +"META:1.1.1.39-RXN" +], +"ec-code":[ +"1.1.1.38", +"1.1.1.39" +], +"kegg.reaction":[ +"R00214" +], +"metanetx.reaction":[ +"MNXR101446" +], +"rhea":[ +"12655", +"12654", +"12653", +"12656" +], +"sabiork":[ +"141" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00159" +] +} +}, +{ +"id":"ME2", +"name":"Malic enzyme (NADP)", +"metabolites":{ +"co2_c":1.0, +"mal__L_c":-1.0, +"nadp_c":-1.0, +"nadph_c":1.0, +"pyr_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2463", +"subsystem":"Anaplerotic reactions", +"notes":{ +"original_bigg_ids":[ +"ME2" +] +}, +"annotation":{ +"bigg.reaction":[ +"ME2" +], +"biocyc":[ +"META:MALIC-NADP-RXN" +], +"ec-code":[ +"1.1.1.40" +], +"kegg.reaction":[ +"R00216" +], +"metanetx.reaction":[ +"MNXR101443" +], +"rhea":[ +"18255", +"18256", +"18254", +"18253" +], +"sabiork":[ +"142" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00161" +] +} +}, +{ +"id":"NADH16", +"name":"NADH dehydrogenase (ubiquinone-8 & 3 protons)", +"metabolites":{ +"h_c":-4.0, +"h_e":3.0, +"nad_c":1.0, +"nadh_c":-1.0, +"q8_c":-1.0, +"q8h2_c":1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b2276 and b2277 and b2278 and b2279 and b2280 and b2281 and b2282 and b2283 and b2284 and b2285 and b2286 and b2287 and b2288", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"NADH16" +] +}, +"annotation":{ +"bigg.reaction":[ +"NADH16" +], +"ec-code":[ +"1.6.5.3" +], +"metanetx.reaction":[ +"MNXR101864" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn08972" +] +} +}, +{ +"id":"NADTRHD", +"name":"NAD transhydrogenase", +"metabolites":{ +"nad_c":-1.0, +"nadh_c":1.0, +"nadp_c":1.0, +"nadph_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b3962 or (b1602 and b1603)", +"subsystem":"Oxidative Phosphorylation", +"notes":{ +"original_bigg_ids":[ +"NADTRHD" +] +}, +"annotation":{ +"bigg.reaction":[ +"NADTRHD" +], +"biocyc":[ +"META:PYRNUTRANSHYDROGEN-RXN" +], +"ec-code":[ +"1.6.1.3", +"1.6.1.2", +"1.6.1.1" +], +"kegg.reaction":[ +"R00112" +], +"metanetx.reaction":[ +"MNXR101898" +], +"rhea":[ +"11692", +"11695", +"11694", +"11693" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00083" +] +} +}, +{ +"id":"NH4t", +"name":"Ammonia reversible transport", +"metabolites":{ +"nh4_c":1.0, +"nh4_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001 or b0451", +"subsystem":"Inorganic Ion Transport and Metabolism", +"notes":{ +"original_bigg_ids":[ +"NH4t" +] +}, +"annotation":{ +"bigg.reaction":[ +"NH4t" +], +"biocyc":[ +"META:TRANS-RXN0-206", +"META:RXN-9615", +"META:TRANS-RXN0-544" +], +"metanetx.reaction":[ +"MNXR101950" +], +"reactome.reaction":[ +"R-CEL-444416", +"R-SSC-444416", +"R-DDI-444416", +"R-MMU-444416", +"R-DRE-444416", +"R-GGA-444416", +"R-CFA-444416", +"R-HSA-444416", +"R-XTR-444416", +"R-BTA-444416", +"R-RNO-444416", +"R-TGU-444416", +"R-DME-444416" +], +"rhea":[ +"28749", +"28748", +"28750", +"28747" +], +"sabiork":[ +"11683" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn13364", +"rxn09835", +"rxn05466", +"rxn08987", +"rxn08986", +"rxn09736" +] +} +}, +{ +"id":"O2t", +"name":"O2 transport diffusion ", +"metabolites":{ +"o2_c":1.0, +"o2_e":-1.0 +}, +"lower_bound":-1000.0, +"upper_bound":1000.0, +"gene_reaction_rule":"s0001", +"subsystem":"Transport, Extracellular", +"notes":{ +"original_bigg_ids":[ +"O2t" +] +}, +"annotation":{ +"bigg.reaction":[ +"O2t" +], +"biocyc":[ +"META:TRANS-RXN0-474" +], +"metanetx.reaction":[ +"MNXR102090" +], +"sbo":"SBO:0000185", +"seed.reaction":[ +"rxn09641", +"rxn05468", +"rxn09031", +"rxn09032", +"rxn09734" +] +} +}, +{ +"id":"PDH", +"name":"Pyruvate dehydrogenase", +"metabolites":{ +"accoa_c":1.0, +"co2_c":1.0, +"coa_c":-1.0, +"nad_c":-1.0, +"nadh_c":1.0, +"pyr_c":-1.0 +}, +"lower_bound":0.0, +"upper_bound":1000.0, +"gene_reaction_rule":"b0114 and b0115 and b0116", +"subsystem":"Glycolysis/Gluconeogenesis", +"notes":{ +"original_bigg_ids":[ +"PDH" +] +}, +"annotation":{ +"bigg.reaction":[ +"PDH" +], +"biocyc":[ +"META:PYRUVDEH-RXN" +], +"ec-code":[ +"1.2.1", +"1.8.1.4", +"1.2.1.51", +"1.2.4.1", +"2.3.1.12" +], +"kegg.reaction":[ +"R00209" +], +"metanetx.reaction":[ +"MNXR102425" +], +"reactome.reaction":[ +"R-RNO-71397", +"R-OSA-71397", +"R-GGA-373177", +"R-DME-71397", +"R-TGU-71397", +"R-XTR-71397", +"R-CFA-71397", +"R-BTA-71397", +"R-HSA-71397", +"R-GGA-71397", +"R-SPO-71397", +"R-CEL-71397", +"R-DDI-71397", +"R-DRE-71397", +"R-SSC-71397", +"R-SCE-71397", +"R-ATH-71397", +"R-MMU-71397" +], +"rhea":[ +"28043", +"28045", +"28044", +"28042" +], +"sabiork":[ +"523" +], +"sbo":"SBO:0000176", +"seed.reaction":[ +"rxn00154" +] +} +} +], +"genes":[ +{ +"id":"b1241", +"name":"adhE", +"notes":{ +"original_bigg_ids":[ +"b1241" +] +}, +"annotation":{ +"asap":[ +"ABE-0004164" +], +"ecogene":[ +"EG10031" +], +"ncbigene":[ +"945837" +], +"ncbigi":[ +"16129202" +], +"refseq_locus_tag":[ +"b1241" +], +"refseq_name":[ +"adhE" +], +"refseq_synonym":[ +"JW1228", +"ECK1235", +"adhC", +"ana" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9Q7" +] +} +}, +{ +"id":"b0351", +"name":"mhpF", +"notes":{ +"original_bigg_ids":[ +"b0351" +] +}, +"annotation":{ +"asap":[ +"ABE-0001207" +], +"ecogene":[ +"EG13625" +], +"ncbigene":[ +"945008" +], +"ncbigi":[ +"16128336" +], +"refseq_locus_tag":[ +"b0351" +], +"refseq_name":[ +"mhpF" +], +"refseq_synonym":[ +"JW0342", +"ECK0348" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77580" +] +} +}, +{ +"id":"s0001", +"name":"", +"notes":{ +"original_bigg_ids":[ +"s0001" +] +}, +"annotation":{ +"sbo":"SBO:0000243" +} +}, +{ +"id":"b1849", +"name":"purT", +"notes":{ +"original_bigg_ids":[ +"b1849" +] +}, +"annotation":{ +"asap":[ +"ABE-0006162" +], +"ecogene":[ +"EG11809" +], +"ncbigene":[ +"946368" +], +"ncbigi":[ +"16129802" +], +"refseq_locus_tag":[ +"b1849" +], +"refseq_name":[ +"purT" +], +"refseq_synonym":[ +"JW1838", +"ECK1850" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33221" +] +} +}, +{ +"id":"b3115", +"name":"tdcD", +"notes":{ +"original_bigg_ids":[ +"b3115" +] +}, +"annotation":{ +"asap":[ +"ABE-0010245" +], +"ecogene":[ +"EG11172" +], +"ncbigene":[ +"947635" +], +"ncbigi":[ +"145698313" +], +"refseq_locus_tag":[ +"b3115" +], +"refseq_name":[ +"tdcD" +], +"refseq_synonym":[ +"JW5806", +"ECK3104", +"yhaA" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P11868" +] +} +}, +{ +"id":"b2296", +"name":"ackA", +"notes":{ +"original_bigg_ids":[ +"b2296" +] +}, +"annotation":{ +"asap":[ +"ABE-0007579" +], +"ecogene":[ +"EG10027" +], +"ncbigene":[ +"946775" +], +"ncbigi":[ +"16130231" +], +"refseq_locus_tag":[ +"b2296" +], +"refseq_name":[ +"ackA" +], +"refseq_synonym":[ +"JW2293", +"ECK2290" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6A3" +] +} +}, +{ +"id":"b1276", +"name":"acnA", +"notes":{ +"original_bigg_ids":[ +"b1276" +] +}, +"annotation":{ +"asap":[ +"ABE-0004283" +], +"ecogene":[ +"EG11325" +], +"ncbigene":[ +"946724" +], +"ncbigi":[ +"16129237" +], +"refseq_locus_tag":[ +"b1276" +], +"refseq_name":[ +"acnA" +], +"refseq_synonym":[ +"JW1268", +"ECK1271", +"acn" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P25516" +] +} +}, +{ +"id":"b0118", +"name":"acnB", +"notes":{ +"original_bigg_ids":[ +"b0118" +] +}, +"annotation":{ +"asap":[ +"ABE-0000411" +], +"ecogene":[ +"EG12316" +], +"ncbigene":[ +"944864" +], +"ncbigi":[ +"16128111" +], +"refseq_locus_tag":[ +"b0118" +], +"refseq_name":[ +"acnB" +], +"refseq_synonym":[ +"ECK0117", +"JW0114", +"yacJ", +"yacI" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P36683" +] +} +}, +{ +"id":"b0474", +"name":"adk", +"notes":{ +"original_bigg_ids":[ +"b0474" +] +}, +"annotation":{ +"asap":[ +"ABE-0001645" +], +"ecogene":[ +"EG10032" +], +"ncbigene":[ +"945097" +], +"ncbigi":[ +"16128458" +], +"refseq_locus_tag":[ +"b0474" +], +"refseq_name":[ +"adk" +], +"refseq_synonym":[ +"plsA", +"JW0463", +"ECK0468", +"dnaW" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69441" +] +} +}, +{ +"id":"b0116", +"name":"lpd", +"notes":{ +"original_bigg_ids":[ +"b0116" +] +}, +"annotation":{ +"asap":[ +"ABE-0000404" +], +"ecogene":[ +"EG10543" +], +"ncbigene":[ +"944854" +], +"ncbigi":[ +"16128109" +], +"refseq_locus_tag":[ +"b0116" +], +"refseq_name":[ +"lpd" +], +"refseq_synonym":[ +"dhl", +"lpdA", +"ECK0115", +"JW0112" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9P0" +] +} +}, +{ +"id":"b0727", +"name":"sucB", +"notes":{ +"original_bigg_ids":[ +"b0727" +] +}, +"annotation":{ +"asap":[ +"ABE-0002480" +], +"ecogene":[ +"EG10980" +], +"ncbigene":[ +"945307" +], +"ncbigi":[ +"16128702" +], +"refseq_locus_tag":[ +"b0727" +], +"refseq_name":[ +"sucB" +], +"refseq_synonym":[ +"JW0716", +"ECK0715" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFG6" +] +} +}, +{ +"id":"b0726", +"name":"sucA", +"notes":{ +"original_bigg_ids":[ +"b0726" +] +}, +"annotation":{ +"asap":[ +"ABE-0002478" +], +"ecogene":[ +"EG10979" +], +"ncbigene":[ +"945303" +], +"ncbigi":[ +"16128701" +], +"refseq_locus_tag":[ +"b0726" +], +"refseq_name":[ +"sucA" +], +"refseq_synonym":[ +"lys", +"JW0715", +"ECK0714" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFG3" +] +} +}, +{ +"id":"b2587", +"name":"kgtP", +"notes":{ +"original_bigg_ids":[ +"b2587" +] +}, +"annotation":{ +"asap":[ +"ABE-0008515" +], +"ecogene":[ +"EG10522" +], +"ncbigene":[ +"947069" +], +"ncbigi":[ +"16130512" +], +"refseq_locus_tag":[ +"b2587" +], +"refseq_name":[ +"kgtP" +], +"refseq_synonym":[ +"ECK2585", +"JW2571", +"witA" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AEX3" +] +} +}, +{ +"id":"b0356", +"name":"frmA", +"notes":{ +"original_bigg_ids":[ +"b0356" +] +}, +"annotation":{ +"asap":[ +"ABE-0001221" +], +"ecogene":[ +"EG50010" +], +"ncbigene":[ +"944988" +], +"ncbigi":[ +"16128341" +], +"refseq_locus_tag":[ +"b0356" +], +"refseq_name":[ +"frmA" +], +"refseq_synonym":[ +"ECK0353", +"adhC", +"JW0347" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P25437" +] +} +}, +{ +"id":"b1478", +"name":"adhP", +"notes":{ +"original_bigg_ids":[ +"b1478" +] +}, +"annotation":{ +"asap":[ +"ABE-0004928" +], +"ecogene":[ +"EG12622" +], +"ncbigene":[ +"946036" +], +"ncbigi":[ +"90111280" +], +"refseq_locus_tag":[ +"b1478" +], +"refseq_name":[ +"adhP" +], +"refseq_synonym":[ +"yddN", +"ECK1472", +"JW1474" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P39451" +] +} +}, +{ +"id":"b3734", +"name":"atpA", +"notes":{ +"original_bigg_ids":[ +"b3734" +] +}, +"annotation":{ +"asap":[ +"ABE-0012213" +], +"ecogene":[ +"EG10098" +], +"ncbigene":[ +"948242" +], +"ncbigi":[ +"16131602" +], +"refseq_locus_tag":[ +"b3734" +], +"refseq_name":[ +"atpA" +], +"refseq_synonym":[ +"uncA", +"papA", +"ECK3727", +"JW3712" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABB0" +] +} +}, +{ +"id":"b3733", +"name":"atpG", +"notes":{ +"original_bigg_ids":[ +"b3733" +] +}, +"annotation":{ +"asap":[ +"ABE-0012211" +], +"ecogene":[ +"EG10104" +], +"ncbigene":[ +"948243" +], +"ncbigi":[ +"16131601" +], +"refseq_locus_tag":[ +"b3733" +], +"refseq_name":[ +"atpG" +], +"refseq_synonym":[ +"uncG", +"ECK3726", +"papC", +"JW3711" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABA6" +] +} +}, +{ +"id":"b3736", +"name":"atpF", +"notes":{ +"original_bigg_ids":[ +"b3736" +] +}, +"annotation":{ +"asap":[ +"ABE-0012217" +], +"ecogene":[ +"EG10103" +], +"ncbigene":[ +"948247" +], +"ncbigi":[ +"16131604" +], +"refseq_locus_tag":[ +"b3736" +], +"refseq_name":[ +"atpF" +], +"refseq_synonym":[ +"uncF", +"JW3714", +"papF", +"ECK3729" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABA0" +] +} +}, +{ +"id":"b3737", +"name":"atpE", +"notes":{ +"original_bigg_ids":[ +"b3737" +] +}, +"annotation":{ +"asap":[ +"ABE-0012220" +], +"ecogene":[ +"EG10102" +], +"ncbigene":[ +"948253" +], +"ncbigi":[ +"16131605" +], +"refseq_locus_tag":[ +"b3737" +], +"refseq_name":[ +"atpE" +], +"refseq_synonym":[ +"uncE", +"JW3715", +"ECK3730", +"papH" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P68699" +] +} +}, +{ +"id":"b3739", +"name":"atpI", +"notes":{ +"original_bigg_ids":[ +"b3739" +] +}, +"annotation":{ +"asap":[ +"ABE-0012224" +], +"ecogene":[ +"EG10106" +], +"ncbigene":[ +"948251" +], +"ncbigi":[ +"90111645" +], +"refseq_locus_tag":[ +"b3739" +], +"refseq_name":[ +"atpI" +], +"refseq_synonym":[ +"uncI", +"JW5611", +"ECK3732" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABC0" +] +} +}, +{ +"id":"b3738", +"name":"atpB", +"notes":{ +"original_bigg_ids":[ +"b3738" +] +}, +"annotation":{ +"asap":[ +"ABE-0012222" +], +"ecogene":[ +"EG10099" +], +"ncbigene":[ +"948252" +], +"ncbigi":[ +"16131606" +], +"refseq_locus_tag":[ +"b3738" +], +"refseq_name":[ +"atpB" +], +"refseq_synonym":[ +"JW3716", +"ECK3731", +"uncB", +"papD" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AB98" +] +} +}, +{ +"id":"b3735", +"name":"atpH", +"notes":{ +"original_bigg_ids":[ +"b3735" +] +}, +"annotation":{ +"asap":[ +"ABE-0012215" +], +"ecogene":[ +"EG10105" +], +"ncbigene":[ +"948254" +], +"ncbigi":[ +"16131603" +], +"refseq_locus_tag":[ +"b3735" +], +"refseq_name":[ +"atpH" +], +"refseq_synonym":[ +"JW3713", +"papE", +"ECK3728", +"uncH" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABA4" +] +} +}, +{ +"id":"b3731", +"name":"atpC", +"notes":{ +"original_bigg_ids":[ +"b3731" +] +}, +"annotation":{ +"asap":[ +"ABE-0012206" +], +"ecogene":[ +"EG10100" +], +"ncbigene":[ +"948245" +], +"ncbigi":[ +"16131599" +], +"refseq_locus_tag":[ +"b3731" +], +"refseq_name":[ +"atpC" +], +"refseq_synonym":[ +"uncC", +"ECK3724", +"papG", +"JW3709" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6E6" +] +} +}, +{ +"id":"b3732", +"name":"atpD", +"notes":{ +"original_bigg_ids":[ +"b3732" +] +}, +"annotation":{ +"asap":[ +"ABE-0012208" +], +"ecogene":[ +"EG10101" +], +"ncbigene":[ +"948244" +], +"ncbigi":[ +"16131600" +], +"refseq_locus_tag":[ +"b3732" +], +"refseq_name":[ +"atpD" +], +"refseq_synonym":[ +"papB", +"ECK3725", +"JW3710", +"uncD" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABB4" +] +} +}, +{ +"id":"b0720", +"name":"gltA", +"notes":{ +"original_bigg_ids":[ +"b0720" +] +}, +"annotation":{ +"asap":[ +"ABE-0002451" +], +"ecogene":[ +"EG10402" +], +"ncbigene":[ +"945323" +], +"ncbigi":[ +"16128695" +], +"refseq_locus_tag":[ +"b0720" +], +"refseq_name":[ +"gltA" +], +"refseq_synonym":[ +"JW0710", +"gluT", +"ECK0709", +"icdB" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABH7" +] +} +}, +{ +"id":"b0733", +"name":"cydA", +"notes":{ +"original_bigg_ids":[ +"b0733" +] +}, +"annotation":{ +"asap":[ +"ABE-0002499" +], +"ecogene":[ +"EG10173" +], +"ncbigene":[ +"945341" +], +"ncbigi":[ +"90111166" +], +"refseq_locus_tag":[ +"b0733" +], +"refseq_name":[ +"cydA" +], +"refseq_synonym":[ +"ECK0721", +"JW0722" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABJ9" +] +} +}, +{ +"id":"b0734", +"name":"cydB", +"notes":{ +"original_bigg_ids":[ +"b0734" +] +}, +"annotation":{ +"asap":[ +"ABE-0002501" +], +"ecogene":[ +"EG10174" +], +"ncbigene":[ +"945347" +], +"ncbigi":[ +"16128709" +], +"refseq_locus_tag":[ +"b0734" +], +"refseq_name":[ +"cydB" +], +"refseq_synonym":[ +"ECK0722", +"JW0723" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0ABK2" +] +} +}, +{ +"id":"b0979", +"name":"cbdB", +"notes":{ +"original_bigg_ids":[ +"b0979" +] +}, +"annotation":{ +"asap":[ +"ABE-0003302" +], +"ecogene":[ +"EG11379" +], +"ncbigene":[ +"947547" +], +"ncbigi":[ +"16128945" +], +"refseq_locus_tag":[ +"b0979" +], +"refseq_name":[ +"cbdB" +], +"refseq_synonym":[ +"JW0961", +"appB", +"cyxB", +"ECK0970" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P26458" +] +} +}, +{ +"id":"b0978", +"name":"cbdA", +"notes":{ +"original_bigg_ids":[ +"b0978" +] +}, +"annotation":{ +"asap":[ +"ABE-0003300" +], +"ecogene":[ +"EG11380" +], +"ncbigene":[ +"945585" +], +"ncbigi":[ +"16128944" +], +"refseq_locus_tag":[ +"b0978" +], +"refseq_name":[ +"cbdA" +], +"refseq_synonym":[ +"JW0960", +"ECK0969", +"cyxA", +"appC" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P26459" +] +} +}, +{ +"id":"b3603", +"name":"lldP", +"notes":{ +"original_bigg_ids":[ +"b3603" +] +}, +"annotation":{ +"asap":[ +"ABE-0011777" +], +"ecogene":[ +"EG11961" +], +"ncbigene":[ +"948114" +], +"ncbigi":[ +"16131474" +], +"refseq_locus_tag":[ +"b3603" +], +"refseq_name":[ +"lldP" +], +"refseq_synonym":[ +"JW3578", +"ECK3593", +"lct", +"lctP" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33231" +] +} +}, +{ +"id":"b2975", +"name":"glcA", +"notes":{ +"original_bigg_ids":[ +"b2975" +] +}, +"annotation":{ +"asap":[ +"ABE-0009763" +], +"ecogene":[ +"EG12995" +], +"ncbigene":[ +"947259" +], +"ncbigi":[ +"16130875" +], +"refseq_locus_tag":[ +"b2975" +], +"refseq_name":[ +"glcA" +], +"refseq_synonym":[ +"ECK2969", +"JW2942", +"yghK" +], +"sbo":"SBO:0000243", +"uniprot":[ +"Q46839" +] +} +}, +{ +"id":"b2779", +"name":"eno", +"notes":{ +"original_bigg_ids":[ +"b2779" +] +}, +"annotation":{ +"asap":[ +"ABE-0009110" +], +"ecogene":[ +"EG10258" +], +"ncbigene":[ +"945032" +], +"ncbigi":[ +"16130686" +], +"refseq_locus_tag":[ +"b2779" +], +"refseq_name":[ +"eno" +], +"refseq_synonym":[ +"JW2750", +"ECK2773" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6P9" +] +} +}, +{ +"id":"b2925", +"name":"fbaA", +"notes":{ +"original_bigg_ids":[ +"b2925" +] +}, +"annotation":{ +"asap":[ +"ABE-0009600" +], +"ecogene":[ +"EG10282" +], +"ncbigene":[ +"947415" +], +"ncbigi":[ +"16130826" +], +"refseq_locus_tag":[ +"b2925" +], +"refseq_name":[ +"fbaA" +], +"refseq_synonym":[ +"fba", +"ald", +"fda", +"ECK2921", +"JW2892" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AB71" +] +} +}, +{ +"id":"b1773", +"name":"ydjI", +"notes":{ +"original_bigg_ids":[ +"b1773" +] +}, +"annotation":{ +"asap":[ +"ABE-0005906" +], +"ecogene":[ +"EG13485" +], +"ncbigene":[ +"946291" +], +"ncbigi":[ +"16129727" +], +"refseq_locus_tag":[ +"b1773" +], +"refseq_name":[ +"ydjI" +], +"refseq_synonym":[ +"ECK1771", +"JW1762" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77704" +] +} +}, +{ +"id":"b2097", +"name":"fbaB", +"notes":{ +"original_bigg_ids":[ +"b2097" +] +}, +"annotation":{ +"asap":[ +"ABE-0006941" +], +"ecogene":[ +"EG14062" +], +"ncbigene":[ +"946632" +], +"ncbigi":[ +"90111385" +], +"refseq_locus_tag":[ +"b2097" +], +"refseq_name":[ +"fbaB" +], +"refseq_synonym":[ +"dhnA", +"JW5344", +"ECK2090" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A991" +] +} +}, +{ +"id":"b3925", +"name":"glpX", +"notes":{ +"original_bigg_ids":[ +"b3925" +] +}, +"annotation":{ +"asap":[ +"ABE-0012821" +], +"ecogene":[ +"EG11517" +], +"ncbigene":[ +"948424" +], +"ncbigi":[ +"16131763" +], +"refseq_locus_tag":[ +"b3925" +], +"refseq_name":[ +"glpX" +], +"refseq_synonym":[ +"JW3896", +"ECK3917" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9C9" +] +} +}, +{ +"id":"b4232", +"name":"fbp", +"notes":{ +"original_bigg_ids":[ +"b4232" +] +}, +"annotation":{ +"asap":[ +"ABE-0013842" +], +"ecogene":[ +"EG10283" +], +"ncbigene":[ +"948753" +], +"ncbigi":[ +"16132054" +], +"refseq_locus_tag":[ +"b4232" +], +"refseq_name":[ +"fbp" +], +"refseq_synonym":[ +"JW4191", +"ECK4227", +"fdp" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A993" +] +} +}, +{ +"id":"b2492", +"name":"focB", +"notes":{ +"original_bigg_ids":[ +"b2492" +] +}, +"annotation":{ +"asap":[ +"ABE-0008206" +], +"ecogene":[ +"EG14220" +], +"ncbigene":[ +"949032" +], +"ncbigi":[ +"16130417" +], +"refseq_locus_tag":[ +"b2492" +], +"refseq_name":[ +"focB" +], +"refseq_synonym":[ +"JW2477", +"ECK2488" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77733" +] +} +}, +{ +"id":"b0904", +"name":"focA", +"notes":{ +"original_bigg_ids":[ +"b0904" +] +}, +"annotation":{ +"asap":[ +"ABE-0003073" +], +"ecogene":[ +"EG11258" +], +"ncbigene":[ +"945513" +], +"ncbigi":[ +"16128871" +], +"refseq_locus_tag":[ +"b0904" +], +"refseq_name":[ +"focA" +], +"refseq_synonym":[ +"ycaE", +"ECK0895", +"JW0887" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC23" +] +} +}, +{ +"id":"b4152", +"name":"frdC", +"notes":{ +"original_bigg_ids":[ +"b4152" +] +}, +"annotation":{ +"asap":[ +"ABE-0013598" +], +"ecogene":[ +"EG10332" +], +"ncbigene":[ +"948680" +], +"ncbigi":[ +"16131977" +], +"refseq_locus_tag":[ +"b4152" +], +"refseq_name":[ +"frdC" +], +"refseq_synonym":[ +"ECK4148", +"JW4113" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A8Q0" +] +} +}, +{ +"id":"b4154", +"name":"frdA", +"notes":{ +"original_bigg_ids":[ +"b4154" +] +}, +"annotation":{ +"asap":[ +"ABE-0013604" +], +"ecogene":[ +"EG10330" +], +"ncbigene":[ +"948667" +], +"ncbigi":[ +"16131979" +], +"refseq_locus_tag":[ +"b4154" +], +"refseq_name":[ +"frdA" +], +"refseq_synonym":[ +"ECK4150", +"JW4115" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00363" +] +} +}, +{ +"id":"b4153", +"name":"frdB", +"notes":{ +"original_bigg_ids":[ +"b4153" +] +}, +"annotation":{ +"asap":[ +"ABE-0013602" +], +"ecogene":[ +"EG10331" +], +"ncbigene":[ +"948666" +], +"ncbigi":[ +"16131978" +], +"refseq_locus_tag":[ +"b4153" +], +"refseq_name":[ +"frdB" +], +"refseq_synonym":[ +"JW4114", +"ECK4149" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC47" +] +} +}, +{ +"id":"b4151", +"name":"frdD", +"notes":{ +"original_bigg_ids":[ +"b4151" +] +}, +"annotation":{ +"asap":[ +"ABE-0013595" +], +"ecogene":[ +"EG10333" +], +"ncbigene":[ +"948668" +], +"ncbigi":[ +"16131976" +], +"refseq_locus_tag":[ +"b4151" +], +"refseq_name":[ +"frdD" +], +"refseq_synonym":[ +"JW4112", +"ECK4147" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A8Q3" +] +} +}, +{ +"id":"b1819", +"name":"manZ", +"notes":{ +"original_bigg_ids":[ +"b1819" +] +}, +"annotation":{ +"asap":[ +"ABE-0006058" +], +"ecogene":[ +"EG10569" +], +"ncbigene":[ +"946342" +], +"ncbigi":[ +"345452720" +], +"refseq_locus_tag":[ +"b1819" +], +"refseq_name":[ +"manZ" +], +"refseq_synonym":[ +"ptsM", +"ECK1817", +"ptsX", +"gptB", +"mpt", +"JW1808" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69805" +] +} +}, +{ +"id":"b1817", +"name":"manX", +"notes":{ +"original_bigg_ids":[ +"b1817" +] +}, +"annotation":{ +"asap":[ +"ABE-0006054" +], +"ecogene":[ +"EG10567" +], +"ncbigene":[ +"946334" +], +"ncbigi":[ +"16129771" +], +"refseq_locus_tag":[ +"b1817" +], +"refseq_name":[ +"manX" +], +"refseq_synonym":[ +"ECK1815", +"ptsX", +"gptB", +"mpt", +"JW1806", +"ptsL" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69797" +] +} +}, +{ +"id":"b2416", +"name":"ptsI", +"notes":{ +"original_bigg_ids":[ +"b2416" +] +}, +"annotation":{ +"asap":[ +"ABE-0007967" +], +"ecogene":[ +"EG10789" +], +"ncbigene":[ +"946879" +], +"ncbigi":[ +"16130342" +], +"refseq_locus_tag":[ +"b2416" +], +"refseq_name":[ +"ptsI" +], +"refseq_synonym":[ +"ECK2411", +"ctr", +"JW2409" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P08839" +] +} +}, +{ +"id":"b2415", +"name":"ptsH", +"notes":{ +"original_bigg_ids":[ +"b2415" +] +}, +"annotation":{ +"asap":[ +"ABE-0007962" +], +"ecogene":[ +"EG10788" +], +"ncbigene":[ +"946886" +], +"ncbigi":[ +"16130341" +], +"refseq_locus_tag":[ +"b2415" +], +"refseq_name":[ +"ptsH" +], +"refseq_synonym":[ +"ctr", +"hpr", +"JW2408", +"ECK2410", +"iex?" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AA04" +] +} +}, +{ +"id":"b1818", +"name":"manY", +"notes":{ +"original_bigg_ids":[ +"b1818" +] +}, +"annotation":{ +"asap":[ +"ABE-0006056" +], +"ecogene":[ +"EG10568" +], +"ncbigene":[ +"946332" +], +"ncbigi":[ +"16129772" +], +"refseq_locus_tag":[ +"b1818" +], +"refseq_name":[ +"manY" +], +"refseq_synonym":[ +"ptsX", +"pel", +"ECK1816", +"JW1807", +"ptsP" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69801" +] +} +}, +{ +"id":"b1611", +"name":"fumC", +"notes":{ +"original_bigg_ids":[ +"b1611" +] +}, +"annotation":{ +"asap":[ +"ABE-0005380" +], +"ecogene":[ +"EG10358" +], +"ncbigene":[ +"946147" +], +"ncbigi":[ +"16129569" +], +"refseq_locus_tag":[ +"b1611" +], +"refseq_name":[ +"fumC" +], +"refseq_synonym":[ +"JW1603", +"ECK1606" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P05042" +] +} +}, +{ +"id":"b4122", +"name":"fumB", +"notes":{ +"original_bigg_ids":[ +"b4122" +] +}, +"annotation":{ +"asap":[ +"ABE-0013501" +], +"ecogene":[ +"EG10357" +], +"ncbigene":[ +"948642" +], +"ncbigi":[ +"16131948" +], +"refseq_locus_tag":[ +"b4122" +], +"refseq_name":[ +"fumB" +], +"refseq_synonym":[ +"JW4083", +"ECK4115" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P14407" +] +} +}, +{ +"id":"b1612", +"name":"fumA", +"notes":{ +"original_bigg_ids":[ +"b1612" +] +}, +"annotation":{ +"asap":[ +"ABE-0005392" +], +"ecogene":[ +"EG10356" +], +"ncbigene":[ +"946826" +], +"ncbigi":[ +"16129570" +], +"refseq_locus_tag":[ +"b1612" +], +"refseq_name":[ +"fumA" +], +"refseq_synonym":[ +"JW1604", +"ECK1607" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC33" +] +} +}, +{ +"id":"b3528", +"name":"dctA", +"notes":{ +"original_bigg_ids":[ +"b3528" +] +}, +"annotation":{ +"asap":[ +"ABE-0011527" +], +"ecogene":[ +"EG20044" +], +"ncbigene":[ +"948039" +], +"ncbigi":[ +"16131400" +], +"refseq_locus_tag":[ +"b3528" +], +"refseq_name":[ +"dctA" +], +"refseq_synonym":[ +"JW3496", +"ECK3513", +"out" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A830" +] +} +}, +{ +"id":"b1852", +"name":"zwf", +"notes":{ +"original_bigg_ids":[ +"b1852" +] +}, +"annotation":{ +"asap":[ +"ABE-0006171" +], +"ecogene":[ +"EG11221" +], +"ncbigene":[ +"946370" +], +"ncbigi":[ +"16129805" +], +"refseq_locus_tag":[ +"b1852" +], +"refseq_name":[ +"zwf" +], +"refseq_synonym":[ +"JW1841", +"ECK1853" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC53" +] +} +}, +{ +"id":"b1779", +"name":"gapA", +"notes":{ +"original_bigg_ids":[ +"b1779" +] +}, +"annotation":{ +"asap":[ +"ABE-0005920" +], +"ecogene":[ +"EG10367" +], +"ncbigene":[ +"947679" +], +"ncbigi":[ +"16129733" +], +"refseq_locus_tag":[ +"b1779" +], +"refseq_name":[ +"gapA" +], +"refseq_synonym":[ +"ECK1777", +"JW1768" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9B2" +] +} +}, +{ +"id":"b1101", +"name":"ptsG", +"notes":{ +"original_bigg_ids":[ +"b1101" +] +}, +"annotation":{ +"asap":[ +"ABE-0003722" +], +"ecogene":[ +"EG10787" +], +"ncbigene":[ +"945651" +], +"ncbigi":[ +"16129064" +], +"refseq_locus_tag":[ +"b1101" +], +"refseq_name":[ +"ptsG" +], +"refseq_synonym":[ +"car", +"JW1087", +"umg", +"glcA", +"umgC", +"cat", +"CR", +"tgl", +"ECK1087" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69786" +] +} +}, +{ +"id":"b2417", +"name":"crr", +"notes":{ +"original_bigg_ids":[ +"b2417" +] +}, +"annotation":{ +"asap":[ +"ABE-0007971" +], +"ecogene":[ +"EG10165" +], +"ncbigene":[ +"946880" +], +"ncbigi":[ +"16130343" +], +"refseq_locus_tag":[ +"b2417" +], +"refseq_name":[ +"crr" +], +"refseq_synonym":[ +"gsr", +"JW2410", +"ECK2412", +"treD", +"tgs", +"iex" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69783" +] +} +}, +{ +"id":"b1621", +"name":"malX", +"notes":{ +"original_bigg_ids":[ +"b1621" +] +}, +"annotation":{ +"asap":[ +"ABE-0005429" +], +"ecogene":[ +"EG10563" +], +"ncbigene":[ +"946009" +], +"ncbigi":[ +"16129579" +], +"refseq_locus_tag":[ +"b1621" +], +"refseq_name":[ +"malX" +], +"refseq_synonym":[ +"ECK1616", +"JW1613" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P19642" +] +} +}, +{ +"id":"b1297", +"name":"puuA", +"notes":{ +"original_bigg_ids":[ +"b1297" +] +}, +"annotation":{ +"asap":[ +"ABE-0004365" +], +"ecogene":[ +"EG13908" +], +"ncbigene":[ +"946202" +], +"ncbigi":[ +"90111244" +], +"refseq_locus_tag":[ +"b1297" +], +"refseq_name":[ +"puuA" +], +"refseq_synonym":[ +"ECK1292", +"JW5201", +"ycjK" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P78061" +] +} +}, +{ +"id":"b3870", +"name":"glnA", +"notes":{ +"original_bigg_ids":[ +"b3870" +] +}, +"annotation":{ +"asap":[ +"ABE-0012640" +], +"ecogene":[ +"EG10383" +], +"ncbigene":[ +"948370" +], +"ncbigi":[ +"16131710" +], +"refseq_locus_tag":[ +"b3870" +], +"refseq_name":[ +"glnA" +], +"refseq_synonym":[ +"ECK3863", +"JW3841" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9C5" +] +} +}, +{ +"id":"b0809", +"name":"glnQ", +"notes":{ +"original_bigg_ids":[ +"b0809" +] +}, +"annotation":{ +"asap":[ +"ABE-0002764" +], +"ecogene":[ +"EG10389" +], +"ncbigene":[ +"945435" +], +"ncbigi":[ +"16128777" +], +"refseq_locus_tag":[ +"b0809" +], +"refseq_name":[ +"glnQ" +], +"refseq_synonym":[ +"JW0794", +"ECK0798" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P10346" +] +} +}, +{ +"id":"b0811", +"name":"glnH", +"notes":{ +"original_bigg_ids":[ +"b0811" +] +}, +"annotation":{ +"asap":[ +"ABE-0002771" +], +"ecogene":[ +"EG10386" +], +"ncbigene":[ +"944872" +], +"ncbigi":[ +"16128779" +], +"refseq_locus_tag":[ +"b0811" +], +"refseq_name":[ +"glnH" +], +"refseq_synonym":[ +"JW0796", +"ECK0800" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AEQ3" +] +} +}, +{ +"id":"b0810", +"name":"glnP", +"notes":{ +"original_bigg_ids":[ +"b0810" +] +}, +"annotation":{ +"asap":[ +"ABE-0002766" +], +"ecogene":[ +"EG10388" +], +"ncbigene":[ +"945621" +], +"ncbigi":[ +"16128778" +], +"refseq_locus_tag":[ +"b0810" +], +"refseq_name":[ +"glnP" +], +"refseq_synonym":[ +"JW0795", +"ECK0799" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AEQ6" +] +} +}, +{ +"id":"b1761", +"name":"gdhA", +"notes":{ +"original_bigg_ids":[ +"b1761" +] +}, +"annotation":{ +"asap":[ +"ABE-0005865" +], +"ecogene":[ +"EG10372" +], +"ncbigene":[ +"946802" +], +"ncbigi":[ +"16129715" +], +"refseq_locus_tag":[ +"b1761" +], +"refseq_name":[ +"gdhA" +], +"refseq_synonym":[ +"ECK1759", +"JW1750" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00370" +] +} +}, +{ +"id":"b1524", +"name":"glsB", +"notes":{ +"original_bigg_ids":[ +"b1524" +] +}, +"annotation":{ +"asap":[ +"ABE-0005086" +], +"ecogene":[ +"EG13816" +], +"ncbigene":[ +"944973" +], +"ncbigi":[ +"16129483" +], +"refseq_locus_tag":[ +"b1524" +], +"refseq_name":[ +"glsB" +], +"refseq_synonym":[ +"glsA2", +"yneH", +"JW1517", +"ECK1517" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6W0" +] +} +}, +{ +"id":"b0485", +"name":"glsA", +"notes":{ +"original_bigg_ids":[ +"b0485" +] +}, +"annotation":{ +"asap":[ +"ABE-0001688" +], +"ecogene":[ +"EG13247" +], +"ncbigene":[ +"946187" +], +"ncbigi":[ +"16128469" +], +"refseq_locus_tag":[ +"b0485" +], +"refseq_name":[ +"glsA" +], +"refseq_synonym":[ +"glsA1", +"ECK0479", +"ybaS", +"JW0474" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77454" +] +} +}, +{ +"id":"b1812", +"name":"pabB", +"notes":{ +"original_bigg_ids":[ +"b1812" +] +}, +"annotation":{ +"asap":[ +"ABE-0006031" +], +"ecogene":[ +"EG10683" +], +"ncbigene":[ +"946337" +], +"ncbigi":[ +"16129766" +], +"refseq_locus_tag":[ +"b1812" +], +"refseq_name":[ +"pabB" +], +"refseq_synonym":[ +"ECK1810", +"JW1801" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P05041" +] +} +}, +{ +"id":"b3213", +"name":"gltD", +"notes":{ +"original_bigg_ids":[ +"b3213" +] +}, +"annotation":{ +"asap":[ +"ABE-0010547" +], +"ecogene":[ +"EG10404" +], +"ncbigene":[ +"947723" +], +"ncbigi":[ +"16131103" +], +"refseq_locus_tag":[ +"b3213" +], +"refseq_name":[ +"gltD" +], +"refseq_synonym":[ +"psiQ", +"aspB", +"ossB", +"JW3180", +"ECK3203" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P09832" +] +} +}, +{ +"id":"b3212", +"name":"gltB", +"notes":{ +"original_bigg_ids":[ +"b3212" +] +}, +"annotation":{ +"asap":[ +"ABE-0010545" +], +"ecogene":[ +"EG10403" +], +"ncbigene":[ +"947724" +], +"ncbigi":[ +"308209621" +], +"refseq_locus_tag":[ +"b3212" +], +"refseq_name":[ +"gltB" +], +"refseq_synonym":[ +"psiQ", +"aspB", +"ECK3202", +"ossB", +"JW3179" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P09831" +] +} +}, +{ +"id":"b4077", +"name":"gltP", +"notes":{ +"original_bigg_ids":[ +"b4077" +] +}, +"annotation":{ +"asap":[ +"ABE-0013357" +], +"ecogene":[ +"EG10405" +], +"ncbigene":[ +"948591" +], +"ncbigi":[ +"16131903" +], +"refseq_locus_tag":[ +"b4077" +], +"refseq_name":[ +"gltP" +], +"refseq_synonym":[ +"ECK4070", +"JW4038" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P21345" +] +} +}, +{ +"id":"b2029", +"name":"gnd", +"notes":{ +"original_bigg_ids":[ +"b2029" +] +}, +"annotation":{ +"asap":[ +"ABE-0006737" +], +"ecogene":[ +"EG10411" +], +"ncbigene":[ +"946554" +], +"ncbigi":[ +"16129970" +], +"refseq_locus_tag":[ +"b2029" +], +"refseq_name":[ +"gnd" +], +"refseq_synonym":[ +"JW2011", +"ECK2024" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00350" +] +} +}, +{ +"id":"b0875", +"name":"aqpZ", +"notes":{ +"original_bigg_ids":[ +"b0875" +] +}, +"annotation":{ +"asap":[ +"ABE-0002976" +], +"ecogene":[ +"EG13270" +], +"ncbigene":[ +"945497" +], +"ncbigi":[ +"16128843" +], +"refseq_locus_tag":[ +"b0875" +], +"refseq_name":[ +"aqpZ" +], +"refseq_synonym":[ +"bniP", +"JW0859", +"ECK0866" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P60844" +] +} +}, +{ +"id":"b1136", +"name":"icd", +"notes":{ +"original_bigg_ids":[ +"b1136" +] +}, +"annotation":{ +"asap":[ +"ABE-0003823" +], +"ecogene":[ +"EG10489" +], +"ncbigene":[ +"945702" +], +"ncbigi":[ +"16129099" +], +"refseq_locus_tag":[ +"b1136" +], +"refseq_name":[ +"icd" +], +"refseq_synonym":[ +"icdA", +"icdE", +"JW1122", +"ECK1122" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P08200" +] +} +}, +{ +"id":"b4015", +"name":"aceA", +"notes":{ +"original_bigg_ids":[ +"b4015" +] +}, +"annotation":{ +"asap":[ +"ABE-0013128" +], +"ecogene":[ +"EG10022" +], +"ncbigene":[ +"948517" +], +"ncbigi":[ +"16131841" +], +"refseq_locus_tag":[ +"b4015" +], +"refseq_name":[ +"aceA" +], +"refseq_synonym":[ +"JW3975", +"icl", +"ECK4007" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9G6" +] +} +}, +{ +"id":"b1380", +"name":"ldhA", +"notes":{ +"original_bigg_ids":[ +"b1380" +] +}, +"annotation":{ +"asap":[ +"ABE-0004619" +], +"ecogene":[ +"EG13186" +], +"ncbigene":[ +"946315" +], +"ncbigi":[ +"16129341" +], +"refseq_locus_tag":[ +"b1380" +], +"refseq_name":[ +"ldhA" +], +"refseq_synonym":[ +"ECK1377", +"JW1375", +"hslI", +"htpH", +"hslF" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P52643" +] +} +}, +{ +"id":"b2133", +"name":"dld", +"notes":{ +"original_bigg_ids":[ +"b2133" +] +}, +"annotation":{ +"asap":[ +"ABE-0007048" +], +"ecogene":[ +"EG10231" +], +"ncbigene":[ +"946653" +], +"ncbigi":[ +"16130071" +], +"refseq_locus_tag":[ +"b2133" +], +"refseq_name":[ +"dld" +], +"refseq_synonym":[ +"JW2121", +"ECK2126" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P06149" +] +} +}, +{ +"id":"b4014", +"name":"aceB", +"notes":{ +"original_bigg_ids":[ +"b4014" +] +}, +"annotation":{ +"asap":[ +"ABE-0013125" +], +"ecogene":[ +"EG10023" +], +"ncbigene":[ +"948512" +], +"ncbigi":[ +"16131840" +], +"refseq_locus_tag":[ +"b4014" +], +"refseq_name":[ +"aceB" +], +"refseq_synonym":[ +"ECK4006", +"mas", +"JW3974" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P08997" +] +} +}, +{ +"id":"b2976", +"name":"glcB", +"notes":{ +"original_bigg_ids":[ +"b2976" +] +}, +"annotation":{ +"asap":[ +"ABE-0009767" +], +"ecogene":[ +"EG20080" +], +"ncbigene":[ +"948857" +], +"ncbigi":[ +"16130876" +], +"refseq_locus_tag":[ +"b2976" +], +"refseq_name":[ +"glcB" +], +"refseq_synonym":[ +"JW2943", +"glc", +"ECK2970" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P37330" +] +} +}, +{ +"id":"b3236", +"name":"mdh", +"notes":{ +"original_bigg_ids":[ +"b3236" +] +}, +"annotation":{ +"asap":[ +"ABE-0010613" +], +"ecogene":[ +"EG10576" +], +"ncbigene":[ +"947854" +], +"ncbigi":[ +"16131126" +], +"refseq_locus_tag":[ +"b3236" +], +"refseq_name":[ +"mdh" +], +"refseq_synonym":[ +"ECK3225", +"JW3205" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P61889" +] +} +}, +{ +"id":"b1479", +"name":"maeA", +"notes":{ +"original_bigg_ids":[ +"b1479" +] +}, +"annotation":{ +"asap":[ +"ABE-0004931" +], +"ecogene":[ +"EG10948" +], +"ncbigene":[ +"946031" +], +"ncbigi":[ +"90111281" +], +"refseq_locus_tag":[ +"b1479" +], +"refseq_name":[ +"maeA" +], +"refseq_synonym":[ +"JW5238", +"sfcA", +"ECK1473" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P26616" +] +} +}, +{ +"id":"b2463", +"name":"maeB", +"notes":{ +"original_bigg_ids":[ +"b2463" +] +}, +"annotation":{ +"asap":[ +"ABE-0008111" +], +"ecogene":[ +"EG14193" +], +"ncbigene":[ +"946947" +], +"ncbigi":[ +"16130388" +], +"refseq_locus_tag":[ +"b2463" +], +"refseq_name":[ +"maeB" +], +"refseq_synonym":[ +"ECK2458", +"JW2447", +"ypfF" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P76558" +] +} +}, +{ +"id":"b2281", +"name":"nuoI", +"notes":{ +"original_bigg_ids":[ +"b2281" +] +}, +"annotation":{ +"asap":[ +"ABE-0007539" +], +"ecogene":[ +"EG12089" +], +"ncbigene":[ +"946757" +], +"ncbigi":[ +"16130216" +], +"refseq_locus_tag":[ +"b2281" +], +"refseq_name":[ +"nuoI" +], +"refseq_synonym":[ +"ECK2275", +"JW2276" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFD6" +] +} +}, +{ +"id":"b2277", +"name":"nuoM", +"notes":{ +"original_bigg_ids":[ +"b2277" +] +}, +"annotation":{ +"asap":[ +"ABE-0007529" +], +"ecogene":[ +"EG11773" +], +"ncbigene":[ +"947731" +], +"ncbigi":[ +"16130212" +], +"refseq_locus_tag":[ +"b2277" +], +"refseq_name":[ +"nuoM" +], +"refseq_synonym":[ +"JW2272", +"nuoA", +"ECK2271" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFE8" +] +} +}, +{ +"id":"b2280", +"name":"nuoJ", +"notes":{ +"original_bigg_ids":[ +"b2280" +] +}, +"annotation":{ +"asap":[ +"ABE-0007536" +], +"ecogene":[ +"EG12090" +], +"ncbigene":[ +"946756" +], +"ncbigi":[ +"16130215" +], +"refseq_locus_tag":[ +"b2280" +], +"refseq_name":[ +"nuoJ" +], +"refseq_synonym":[ +"ECK2274", +"JW2275" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFE0" +] +} +}, +{ +"id":"b2286", +"name":"nuoC", +"notes":{ +"original_bigg_ids":[ +"b2286" +] +}, +"annotation":{ +"asap":[ +"ABE-0007549" +], +"ecogene":[ +"EG12084" +], +"ncbigene":[ +"946759" +], +"ncbigi":[ +"145698291" +], +"refseq_locus_tag":[ +"b2286" +], +"refseq_name":[ +"nuoC" +], +"refseq_synonym":[ +"ECK2280", +"nuoD", +"nuoCD", +"JW5375" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33599" +] +} +}, +{ +"id":"b2287", +"name":"nuoB", +"notes":{ +"original_bigg_ids":[ +"b2287" +] +}, +"annotation":{ +"asap":[ +"ABE-0007551" +], +"ecogene":[ +"EG12083" +], +"ncbigene":[ +"946738" +], +"ncbigi":[ +"16130222" +], +"refseq_locus_tag":[ +"b2287" +], +"refseq_name":[ +"nuoB" +], +"refseq_synonym":[ +"JW5875", +"ECK2281" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFC7" +] +} +}, +{ +"id":"b2284", +"name":"nuoF", +"notes":{ +"original_bigg_ids":[ +"b2284" +] +}, +"annotation":{ +"asap":[ +"ABE-0007545" +], +"ecogene":[ +"EG11774" +], +"ncbigene":[ +"946753" +], +"ncbigi":[ +"16130219" +], +"refseq_locus_tag":[ +"b2284" +], +"refseq_name":[ +"nuoF" +], +"refseq_synonym":[ +"ECK2278", +"nuoB", +"JW2279" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P31979" +] +} +}, +{ +"id":"b2276", +"name":"nuoN", +"notes":{ +"original_bigg_ids":[ +"b2276" +] +}, +"annotation":{ +"asap":[ +"ABE-0007526" +], +"ecogene":[ +"EG12093" +], +"ncbigene":[ +"945136" +], +"ncbigi":[ +"145698289" +], +"refseq_locus_tag":[ +"b2276" +], +"refseq_name":[ +"nuoN" +], +"refseq_synonym":[ +"JW2271", +"ECK2270" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFF0" +] +} +}, +{ +"id":"b2282", +"name":"nuoH", +"notes":{ +"original_bigg_ids":[ +"b2282" +] +}, +"annotation":{ +"asap":[ +"ABE-0007541" +], +"ecogene":[ +"EG12088" +], +"ncbigene":[ +"946761" +], +"ncbigi":[ +"16130217" +], +"refseq_locus_tag":[ +"b2282" +], +"refseq_name":[ +"nuoH" +], +"refseq_synonym":[ +"JW2277", +"ECK2276" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFD4" +] +} +}, +{ +"id":"b2279", +"name":"nuoK", +"notes":{ +"original_bigg_ids":[ +"b2279" +] +}, +"annotation":{ +"asap":[ +"ABE-0007534" +], +"ecogene":[ +"EG12091" +], +"ncbigene":[ +"947580" +], +"ncbigi":[ +"16130214" +], +"refseq_locus_tag":[ +"b2279" +], +"refseq_name":[ +"nuoK" +], +"refseq_synonym":[ +"JW2274", +"ECK2273" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFE4" +] +} +}, +{ +"id":"b2283", +"name":"nuoG", +"notes":{ +"original_bigg_ids":[ +"b2283" +] +}, +"annotation":{ +"asap":[ +"ABE-0007543" +], +"ecogene":[ +"EG12087" +], +"ncbigene":[ +"946762" +], +"ncbigi":[ +"145698290" +], +"refseq_locus_tag":[ +"b2283" +], +"refseq_name":[ +"nuoG" +], +"refseq_synonym":[ +"JW2278", +"ECK2277" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33602" +] +} +}, +{ +"id":"b2285", +"name":"nuoE", +"notes":{ +"original_bigg_ids":[ +"b2285" +] +}, +"annotation":{ +"asap":[ +"ABE-0007547" +], +"ecogene":[ +"EG12086" +], +"ncbigene":[ +"946746" +], +"ncbigi":[ +"16130220" +], +"refseq_locus_tag":[ +"b2285" +], +"refseq_name":[ +"nuoE" +], +"refseq_synonym":[ +"JW2280", +"ECK2279" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFD1" +] +} +}, +{ +"id":"b2288", +"name":"nuoA", +"notes":{ +"original_bigg_ids":[ +"b2288" +] +}, +"annotation":{ +"asap":[ +"ABE-0007553" +], +"ecogene":[ +"EG12082" +], +"ncbigene":[ +"946764" +], +"ncbigi":[ +"49176207" +], +"refseq_locus_tag":[ +"b2288" +], +"refseq_name":[ +"nuoA" +], +"refseq_synonym":[ +"JW2283", +"ECK2282" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFC3" +] +} +}, +{ +"id":"b2278", +"name":"nuoL", +"notes":{ +"original_bigg_ids":[ +"b2278" +] +}, +"annotation":{ +"asap":[ +"ABE-0007532" +], +"ecogene":[ +"EG12092" +], +"ncbigene":[ +"945540" +], +"ncbigi":[ +"16130213" +], +"refseq_locus_tag":[ +"b2278" +], +"refseq_name":[ +"nuoL" +], +"refseq_synonym":[ +"ECK2272", +"JW2273" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33607" +] +} +}, +{ +"id":"b1603", +"name":"pntA", +"notes":{ +"original_bigg_ids":[ +"b1603" +] +}, +"annotation":{ +"asap":[ +"ABE-0005354" +], +"ecogene":[ +"EG10744" +], +"ncbigene":[ +"946628" +], +"ncbigi":[ +"16129561" +], +"refseq_locus_tag":[ +"b1603" +], +"refseq_name":[ +"pntA" +], +"refseq_synonym":[ +"JW1595", +"ECK1598" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P07001" +] +} +}, +{ +"id":"b3962", +"name":"sthA", +"notes":{ +"original_bigg_ids":[ +"b3962" +] +}, +"annotation":{ +"asap":[ +"ABE-0012975" +], +"ecogene":[ +"EG11428" +], +"ncbigene":[ +"948461" +], +"ncbigi":[ +"90111670" +], +"refseq_locus_tag":[ +"b3962" +], +"refseq_name":[ +"sthA" +], +"refseq_synonym":[ +"ECK3954", +"udhA", +"JW5551", +"sth" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P27306" +] +} +}, +{ +"id":"b1602", +"name":"pntB", +"notes":{ +"original_bigg_ids":[ +"b1602" +] +}, +"annotation":{ +"asap":[ +"ABE-0005352" +], +"ecogene":[ +"EG10745" +], +"ncbigene":[ +"946144" +], +"ncbigi":[ +"16129560" +], +"refseq_locus_tag":[ +"b1602" +], +"refseq_name":[ +"pntB" +], +"refseq_synonym":[ +"ECK1597", +"JW1594" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AB67" +] +} +}, +{ +"id":"b0451", +"name":"amtB", +"notes":{ +"original_bigg_ids":[ +"b0451" +] +}, +"annotation":{ +"asap":[ +"ABE-0001564" +], +"ecogene":[ +"EG11821" +], +"ncbigene":[ +"945084" +], +"ncbigi":[ +"16128436" +], +"refseq_locus_tag":[ +"b0451" +], +"refseq_name":[ +"amtB" +], +"refseq_synonym":[ +"JW0441", +"ECK0445", +"ybaG" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69681" +] +} +}, +{ +"id":"b0114", +"name":"aceE", +"notes":{ +"original_bigg_ids":[ +"b0114" +] +}, +"annotation":{ +"asap":[ +"ABE-0000397" +], +"ecogene":[ +"EG10024" +], +"ncbigene":[ +"944834" +], +"ncbigi":[ +"16128107" +], +"refseq_locus_tag":[ +"b0114" +], +"refseq_name":[ +"aceE" +], +"refseq_synonym":[ +"ECK0113", +"JW0110" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFG8" +] +} +}, +{ +"id":"b0115", +"name":"aceF", +"notes":{ +"original_bigg_ids":[ +"b0115" +] +}, +"annotation":{ +"asap":[ +"ABE-0000400" +], +"ecogene":[ +"EG10025" +], +"ncbigene":[ +"944794" +], +"ncbigi":[ +"16128108" +], +"refseq_locus_tag":[ +"b0115" +], +"refseq_name":[ +"aceF" +], +"refseq_synonym":[ +"ECK0114", +"JW0111" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P06959" +] +} +}, +{ +"id":"b3916", +"name":"pfkA", +"notes":{ +"original_bigg_ids":[ +"b3916" +] +}, +"annotation":{ +"asap":[ +"ABE-0012789" +], +"ecogene":[ +"EG10699" +], +"ncbigene":[ +"948412" +], +"ncbigi":[ +"16131754" +], +"refseq_locus_tag":[ +"b3916" +], +"refseq_name":[ +"pfkA" +], +"refseq_synonym":[ +"JW3887", +"ECK3908" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A796" +] +} +}, +{ +"id":"b1723", +"name":"pfkB", +"notes":{ +"original_bigg_ids":[ +"b1723" +] +}, +"annotation":{ +"asap":[ +"ABE-0005748" +], +"ecogene":[ +"EG10700" +], +"ncbigene":[ +"946230" +], +"ncbigi":[ +"49176138" +], +"refseq_locus_tag":[ +"b1723" +], +"refseq_name":[ +"pfkB" +], +"refseq_synonym":[ +"JW5280", +"ECK1721" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P06999" +] +} +}, +{ +"id":"b3114", +"name":"tdcE", +"notes":{ +"original_bigg_ids":[ +"b3114" +] +}, +"annotation":{ +"asap":[ +"ABE-0010242" +], +"ecogene":[ +"EG12758" +], +"ncbigene":[ +"947623" +], +"ncbigi":[ +"49176316" +], +"refseq_locus_tag":[ +"b3114" +], +"refseq_name":[ +"tdcE" +], +"refseq_synonym":[ +"JW5522", +"ECK3103", +"yhaS" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P42632" +] +} +}, +{ +"id":"b2579", +"name":"grcA", +"notes":{ +"original_bigg_ids":[ +"b2579" +] +}, +"annotation":{ +"asap":[ +"ABE-0008489" +], +"ecogene":[ +"EG11784" +], +"ncbigene":[ +"947068" +], +"ncbigi":[ +"16130504" +], +"refseq_locus_tag":[ +"b2579" +], +"refseq_name":[ +"grcA" +], +"refseq_synonym":[ +"ECK2577", +"yfiD", +"JW2563" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P68066" +] +} +}, +{ +"id":"b3951", +"name":"pflD", +"notes":{ +"original_bigg_ids":[ +"b3951" +] +}, +"annotation":{ +"asap":[ +"ABE-0012934" +], +"ecogene":[ +"EG11910" +], +"ncbigene":[ +"948454" +], +"ncbigi":[ +"16131789" +], +"refseq_locus_tag":[ +"b3951" +], +"refseq_name":[ +"pflD" +], +"refseq_synonym":[ +"ECK3942", +"yijL", +"JW3923" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P32674" +] +} +}, +{ +"id":"b0902", +"name":"pflA", +"notes":{ +"original_bigg_ids":[ +"b0902" +] +}, +"annotation":{ +"asap":[ +"ABE-0003068" +], +"ecogene":[ +"EG10028" +], +"ncbigene":[ +"945517" +], +"ncbigi":[ +"16128869" +], +"refseq_locus_tag":[ +"b0902" +], +"refseq_name":[ +"pflA" +], +"refseq_synonym":[ +"ECK0893", +"JW0885", +"act" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9N4" +] +} +}, +{ +"id":"b3952", +"name":"pflC", +"notes":{ +"original_bigg_ids":[ +"b3952" +] +}, +"annotation":{ +"asap":[ +"ABE-0012937" +], +"ecogene":[ +"EG11911" +], +"ncbigene":[ +"948453" +], +"ncbigi":[ +"49176447" +], +"refseq_locus_tag":[ +"b3952" +], +"refseq_name":[ +"pflC" +], +"refseq_synonym":[ +"ECK3943", +"JW3924", +"yijM" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P32675" +] +} +}, +{ +"id":"b0903", +"name":"pflB", +"notes":{ +"original_bigg_ids":[ +"b0903" +] +}, +"annotation":{ +"asap":[ +"ABE-0003071" +], +"ecogene":[ +"EG10701" +], +"ncbigene":[ +"945514" +], +"ncbigi":[ +"16128870" +], +"refseq_locus_tag":[ +"b0903" +], +"refseq_name":[ +"pflB" +], +"refseq_synonym":[ +"pfl", +"ECK0894", +"JW0886" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P09373" +] +} +}, +{ +"id":"b4025", +"name":"pgi", +"notes":{ +"original_bigg_ids":[ +"b4025" +] +}, +"annotation":{ +"asap":[ +"ABE-0013163" +], +"ecogene":[ +"EG10702" +], +"ncbigene":[ +"948535" +], +"ncbigi":[ +"16131851" +], +"refseq_locus_tag":[ +"b4025" +], +"refseq_name":[ +"pgi" +], +"refseq_synonym":[ +"JW3985", +"ECK4017" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A6T1" +] +} +}, +{ +"id":"b2926", +"name":"pgk", +"notes":{ +"original_bigg_ids":[ +"b2926" +] +}, +"annotation":{ +"asap":[ +"ABE-0009605" +], +"ecogene":[ +"EG10703" +], +"ncbigene":[ +"947414" +], +"ncbigi":[ +"16130827" +], +"refseq_locus_tag":[ +"b2926" +], +"refseq_name":[ +"pgk" +], +"refseq_synonym":[ +"ECK2922", +"JW2893" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A799" +] +} +}, +{ +"id":"b0767", +"name":"pgl", +"notes":{ +"original_bigg_ids":[ +"b0767" +] +}, +"annotation":{ +"asap":[ +"ABE-0002611" +], +"ecogene":[ +"EG13231" +], +"ncbigene":[ +"946398" +], +"ncbigi":[ +"16128735" +], +"refseq_locus_tag":[ +"b0767" +], +"refseq_name":[ +"pgl" +], +"refseq_synonym":[ +"JW0750", +"ybhE", +"ECK0756", +"blu" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P52697" +] +} +}, +{ +"id":"b3612", +"name":"gpmM", +"notes":{ +"original_bigg_ids":[ +"b3612" +] +}, +"annotation":{ +"asap":[ +"ABE-0011818" +], +"ecogene":[ +"EG12296" +], +"ncbigene":[ +"948130" +], +"ncbigi":[ +"16131483" +], +"refseq_locus_tag":[ +"b3612" +], +"refseq_name":[ +"gpmM" +], +"refseq_synonym":[ +"JW3587", +"yibO", +"ECK3602", +"pgmI", +"gpmC", +"gpmI" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P37689" +] +} +}, +{ +"id":"b4395", +"name":"ytjC", +"notes":{ +"original_bigg_ids":[ +"b4395" +] +}, +"annotation":{ +"asap":[ +"ABE-0014416" +], +"ecogene":[ +"EG12164" +], +"ncbigene":[ +"948918" +], +"ncbigi":[ +"16132212" +], +"refseq_locus_tag":[ +"b4395" +], +"refseq_name":[ +"ytjC" +], +"refseq_synonym":[ +"gpmB", +"JW4358", +"ECK4387" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A7A2" +] +} +}, +{ +"id":"b0755", +"name":"gpmA", +"notes":{ +"original_bigg_ids":[ +"b0755" +] +}, +"annotation":{ +"asap":[ +"ABE-0002563" +], +"ecogene":[ +"EG11699" +], +"ncbigene":[ +"945068" +], +"ncbigi":[ +"16128723" +], +"refseq_locus_tag":[ +"b0755" +], +"refseq_name":[ +"gpmA" +], +"refseq_synonym":[ +"JW0738", +"gpm", +"ECK0744" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P62707" +] +} +}, +{ +"id":"b3493", +"name":"pitA", +"notes":{ +"original_bigg_ids":[ +"b3493" +] +}, +"annotation":{ +"asap":[ +"ABE-0011407" +], +"ecogene":[ +"EG12230" +], +"ncbigene":[ +"948009" +], +"ncbigi":[ +"16131365" +], +"refseq_locus_tag":[ +"b3493" +], +"refseq_name":[ +"pitA" +], +"refseq_synonym":[ +"pit", +"ECK3478", +"JW3460" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AFJ7" +] +} +}, +{ +"id":"b2987", +"name":"pitB", +"notes":{ +"original_bigg_ids":[ +"b2987" +] +}, +"annotation":{ +"asap":[ +"ABE-0009800" +], +"ecogene":[ +"EG12883" +], +"ncbigene":[ +"947475" +], +"ncbigi":[ +"16130887" +], +"refseq_locus_tag":[ +"b2987" +], +"refseq_name":[ +"pitB" +], +"refseq_synonym":[ +"ECK2981", +"JW2955" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P43676" +] +} +}, +{ +"id":"b3956", +"name":"ppc", +"notes":{ +"original_bigg_ids":[ +"b3956" +] +}, +"annotation":{ +"asap":[ +"ABE-0012950" +], +"ecogene":[ +"EG10756" +], +"ncbigene":[ +"948457" +], +"ncbigi":[ +"16131794" +], +"refseq_locus_tag":[ +"b3956" +], +"refseq_name":[ +"ppc" +], +"refseq_synonym":[ +"glu", +"ECK3947", +"asp", +"JW3928" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00864" +] +} +}, +{ +"id":"b3403", +"name":"pck", +"notes":{ +"original_bigg_ids":[ +"b3403" +] +}, +"annotation":{ +"asap":[ +"ABE-0011106" +], +"ecogene":[ +"EG10688" +], +"ncbigene":[ +"945667" +], +"ncbigi":[ +"16131280" +], +"refseq_locus_tag":[ +"b3403" +], +"refseq_name":[ +"pck" +], +"refseq_synonym":[ +"JW3366", +"pckA", +"ECK3390" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P22259" +] +} +}, +{ +"id":"b1702", +"name":"ppsA", +"notes":{ +"original_bigg_ids":[ +"b1702" +] +}, +"annotation":{ +"asap":[ +"ABE-0005678" +], +"ecogene":[ +"EG10759" +], +"ncbigene":[ +"946209" +], +"ncbigi":[ +"16129658" +], +"refseq_locus_tag":[ +"b1702" +], +"refseq_name":[ +"ppsA" +], +"refseq_synonym":[ +"pps", +"ECK1700", +"JW1692" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P23538" +] +} +}, +{ +"id":"b2297", +"name":"pta", +"notes":{ +"original_bigg_ids":[ +"b2297" +] +}, +"annotation":{ +"asap":[ +"ABE-0007582" +], +"ecogene":[ +"EG20173" +], +"ncbigene":[ +"946778" +], +"ncbigi":[ +"16130232" +], +"refseq_locus_tag":[ +"b2297" +], +"refseq_name":[ +"pta" +], +"refseq_synonym":[ +"JW2294", +"ECK2291" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9M8" +] +} +}, +{ +"id":"b2458", +"name":"eutD", +"notes":{ +"original_bigg_ids":[ +"b2458" +] +}, +"annotation":{ +"asap":[ +"ABE-0008097" +], +"ecogene":[ +"EG14188" +], +"ncbigene":[ +"946940" +], +"ncbigi":[ +"16130383" +], +"refseq_locus_tag":[ +"b2458" +], +"refseq_name":[ +"eutD" +], +"refseq_synonym":[ +"eutI", +"ypfA", +"ECK2453", +"JW2442" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77218" +] +} +}, +{ +"id":"b1676", +"name":"pykF", +"notes":{ +"original_bigg_ids":[ +"b1676" +] +}, +"annotation":{ +"asap":[ +"ABE-0005600" +], +"ecogene":[ +"EG10804" +], +"ncbigene":[ +"946179" +], +"ncbigi":[ +"16129632" +], +"refseq_locus_tag":[ +"b1676" +], +"refseq_name":[ +"pykF" +], +"refseq_synonym":[ +"ECK1672", +"JW1666" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AD61" +] +} +}, +{ +"id":"b1854", +"name":"pykA", +"notes":{ +"original_bigg_ids":[ +"b1854" +] +}, +"annotation":{ +"asap":[ +"ABE-0006182" +], +"ecogene":[ +"EG10803" +], +"ncbigene":[ +"946527" +], +"ncbigi":[ +"16129807" +], +"refseq_locus_tag":[ +"b1854" +], +"refseq_name":[ +"pykA" +], +"refseq_synonym":[ +"JW1843", +"ECK1855" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P21599" +] +} +}, +{ +"id":"b3386", +"name":"rpe", +"notes":{ +"original_bigg_ids":[ +"b3386" +] +}, +"annotation":{ +"asap":[ +"ABE-0011061" +], +"ecogene":[ +"EG11960" +], +"ncbigene":[ +"947896" +], +"ncbigi":[ +"16131264" +], +"refseq_locus_tag":[ +"b3386" +], +"refseq_name":[ +"rpe" +], +"refseq_synonym":[ +"yhfD", +"ECK3373", +"JW3349", +"dod" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AG07" +] +} +}, +{ +"id":"b4301", +"name":"sgcE", +"notes":{ +"original_bigg_ids":[ +"b4301" +] +}, +"annotation":{ +"asap":[ +"ABE-0014097" +], +"ecogene":[ +"EG12553" +], +"ncbigene":[ +"948829" +], +"ncbigi":[ +"16132122" +], +"refseq_locus_tag":[ +"b4301" +], +"refseq_name":[ +"sgcE" +], +"refseq_synonym":[ +"JW4263", +"ECK4290", +"yjhK" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P39362" +] +} +}, +{ +"id":"b2914", +"name":"rpiA", +"notes":{ +"original_bigg_ids":[ +"b2914" +] +}, +"annotation":{ +"asap":[ +"ABE-0009567" +], +"ecogene":[ +"EG11443" +], +"ncbigene":[ +"947407" +], +"ncbigi":[ +"16130815" +], +"refseq_locus_tag":[ +"b2914" +], +"refseq_name":[ +"rpiA" +], +"refseq_synonym":[ +"ECK2910", +"JW5475", +"ygfC" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A7Z0" +] +} +}, +{ +"id":"b4090", +"name":"rpiB", +"notes":{ +"original_bigg_ids":[ +"b4090" +] +}, +"annotation":{ +"asap":[ +"ABE-0013405" +], +"ecogene":[ +"EG11827" +], +"ncbigene":[ +"948602" +], +"ncbigi":[ +"16131916" +], +"refseq_locus_tag":[ +"b4090" +], +"refseq_name":[ +"rpiB" +], +"refseq_synonym":[ +"JW4051", +"alsB", +"alsI", +"yjcA", +"ECK4083" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P37351" +] +} +}, +{ +"id":"b0721", +"name":"sdhC", +"notes":{ +"original_bigg_ids":[ +"b0721" +] +}, +"annotation":{ +"asap":[ +"ABE-0002460" +], +"ecogene":[ +"EG10933" +], +"ncbigene":[ +"945316" +], +"ncbigi":[ +"16128696" +], +"refseq_locus_tag":[ +"b0721" +], +"refseq_name":[ +"sdhC" +], +"refseq_synonym":[ +"JW0711", +"ECK0710", +"cybA" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69054" +] +} +}, +{ +"id":"b0722", +"name":"sdhD", +"notes":{ +"original_bigg_ids":[ +"b0722" +] +}, +"annotation":{ +"asap":[ +"ABE-0002464" +], +"ecogene":[ +"EG10934" +], +"ncbigene":[ +"945322" +], +"ncbigi":[ +"16128697" +], +"refseq_locus_tag":[ +"b0722" +], +"refseq_name":[ +"sdhD" +], +"refseq_synonym":[ +"JW0712", +"ECK0711" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC44" +] +} +}, +{ +"id":"b0724", +"name":"sdhB", +"notes":{ +"original_bigg_ids":[ +"b0724" +] +}, +"annotation":{ +"asap":[ +"ABE-0002468" +], +"ecogene":[ +"EG10932" +], +"ncbigene":[ +"945300" +], +"ncbigi":[ +"16128699" +], +"refseq_locus_tag":[ +"b0724" +], +"refseq_name":[ +"sdhB" +], +"refseq_synonym":[ +"ECK0713", +"JW0714" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P07014" +] +} +}, +{ +"id":"b0723", +"name":"sdhA", +"notes":{ +"original_bigg_ids":[ +"b0723" +] +}, +"annotation":{ +"asap":[ +"ABE-0002466" +], +"ecogene":[ +"EG10931" +], +"ncbigene":[ +"945402" +], +"ncbigi":[ +"16128698" +], +"refseq_locus_tag":[ +"b0723" +], +"refseq_name":[ +"sdhA" +], +"refseq_synonym":[ +"JW0713", +"ECK0712" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC41" +] +} +}, +{ +"id":"b0729", +"name":"sucD", +"notes":{ +"original_bigg_ids":[ +"b0729" +] +}, +"annotation":{ +"asap":[ +"ABE-0002485" +], +"ecogene":[ +"EG10982" +], +"ncbigene":[ +"945314" +], +"ncbigi":[ +"16128704" +], +"refseq_locus_tag":[ +"b0729" +], +"refseq_name":[ +"sucD" +], +"refseq_synonym":[ +"JW0718", +"ECK0717" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AGE9" +] +} +}, +{ +"id":"b0728", +"name":"sucC", +"notes":{ +"original_bigg_ids":[ +"b0728" +] +}, +"annotation":{ +"asap":[ +"ABE-0002483" +], +"ecogene":[ +"EG10981" +], +"ncbigene":[ +"945312" +], +"ncbigi":[ +"16128703" +], +"refseq_locus_tag":[ +"b0728" +], +"refseq_name":[ +"sucC" +], +"refseq_synonym":[ +"JW0717", +"ECK0716" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A836" +] +} +}, +{ +"id":"b0008", +"name":"talB", +"notes":{ +"original_bigg_ids":[ +"b0008" +] +}, +"annotation":{ +"asap":[ +"ABE-0000027" +], +"ecogene":[ +"EG11556" +], +"ncbigene":[ +"944748" +], +"ncbigi":[ +"16128002" +], +"refseq_locus_tag":[ +"b0008" +], +"refseq_name":[ +"talB" +], +"refseq_synonym":[ +"yaaK", +"JW0007", +"ECK0008" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A870" +] +} +}, +{ +"id":"b2464", +"name":"talA", +"notes":{ +"original_bigg_ids":[ +"b2464" +] +}, +"annotation":{ +"asap":[ +"ABE-0008115" +], +"ecogene":[ +"EG11797" +], +"ncbigene":[ +"947006" +], +"ncbigi":[ +"16130389" +], +"refseq_locus_tag":[ +"b2464" +], +"refseq_name":[ +"talA" +], +"refseq_synonym":[ +"ECK2459", +"JW2448" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A867" +] +} +}, +{ +"id":"b2465", +"name":"tktB", +"notes":{ +"original_bigg_ids":[ +"b2465" +] +}, +"annotation":{ +"asap":[ +"ABE-0008117" +], +"ecogene":[ +"EG12100" +], +"ncbigene":[ +"945865" +], +"ncbigi":[ +"16130390" +], +"refseq_locus_tag":[ +"b2465" +], +"refseq_name":[ +"tktB" +], +"refseq_synonym":[ +"JW2449", +"ECK2460" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33570" +] +} +}, +{ +"id":"b2935", +"name":"tktA", +"notes":{ +"original_bigg_ids":[ +"b2935" +] +}, +"annotation":{ +"asap":[ +"ABE-0009625" +], +"ecogene":[ +"EG11427" +], +"ncbigene":[ +"947420" +], +"ncbigi":[ +"49176286" +], +"refseq_locus_tag":[ +"b2935" +], +"refseq_name":[ +"tktA" +], +"refseq_synonym":[ +"JW5478", +"tkt", +"ECK2930" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P27302" +] +} +}, +{ +"id":"b3919", +"name":"tpiA", +"notes":{ +"original_bigg_ids":[ +"b3919" +] +}, +"annotation":{ +"asap":[ +"ABE-0012799" +], +"ecogene":[ +"EG11015" +], +"ncbigene":[ +"948409" +], +"ncbigi":[ +"16131757" +], +"refseq_locus_tag":[ +"b3919" +], +"refseq_name":[ +"tpiA" +], +"refseq_synonym":[ +"JW3890", +"ECK3911", +"tpi" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A858" +] +} +} +], +"id":"e_coli_core", +"compartments":{ +"c":"cytosol", +"e":"extracellular space" +}, +"version":"1" +} \ No newline at end of file diff --git a/tests/test_data/atom_mapping_Data/generate_atom_mapping_test_data.py b/tests/test_data/atom_mapping_Data/generate_atom_mapping_test_data.py new file mode 100644 index 00000000..59cbd30e --- /dev/null +++ b/tests/test_data/atom_mapping_Data/generate_atom_mapping_test_data.py @@ -0,0 +1,141 @@ +import pickle +import os +import pandas as pd +import pathlib +from BFAIR.mfa.INCA import INCA_input_parser +from BFAIR.atom_mapping import (MolfileDownloader, + write_rxn_files, + obtain_atom_mappings, + parse_reaction_mappings, + parse_metabolite_mappings, + generate_INCA_mapping_input, + clean_output, + ) + +original_wd = os.getcwd() +current_dir = str(pathlib.Path(__file__).parent.absolute()) +os.chdir(current_dir) + +# Load e_coli_core model +model, reaction_data, metabolite_data = INCA_input_parser.parse_cobra_model( + 'e_coli_core.json', 'e_coli_core', '2021-07-15') + +# Subset handpicked reactions +model_reaction_df = pd.DataFrame() +model_reaction_df = model_reaction_df.append( + reaction_data[reaction_data['rxn_id'] == 'PFK']) +model_reaction_df = model_reaction_df.append( + reaction_data[reaction_data['rxn_id'] == 'BIOMASS_Ecoli_core_w_GAM']) +model_reaction_df = model_reaction_df.append( + reaction_data[reaction_data['rxn_id'] == 'EX_pyr_e']) +model_reaction_df = model_reaction_df.append( + reaction_data[reaction_data['rxn_id'] == 'ICL']) + +# And metabolites from these reactions +model_metabolite_df = pd.DataFrame() +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'atp_c']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'f6p_c']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'adp_c']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'fdp_c']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'h_c']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'pyr_e']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'icit_c']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'succ_c']) +model_metabolite_df = model_metabolite_df.append( + metabolite_data[metabolite_data['met_id'] == 'glx_c']) + +# Obtain all required files +# Metabolite Molfiles +downloader = MolfileDownloader(model_metabolite_df) +downloader.generate_molfile_database() + +# Rxn files +write_rxn_files(model_reaction_df) + +# Mapped Rxn files +obtain_atom_mappings() + +# Parsed dataframes of mappings +reaction_df = parse_reaction_mappings() +metabolite_df = parse_metabolite_mappings() + +# CSV outputs of these dataframes +generate_INCA_mapping_input(reaction_df, metabolite_df) + + +# Load all the generated files in Python +# Molfiles in a single list. +# All numerics converted to floats. +metabolites = os.listdir('metabolites') +for i, molfile in enumerate(metabolites): + with open(f'metabolites/{molfile}', 'r') as f: + metabolites[i] = f.readlines() + for j, met in enumerate(metabolites[i]): + metabolites[i][j] = metabolites[i][j].split() + for k, val in enumerate(metabolites[i][j]): + try: + metabolites[i][j][k] = float(val) + except BaseException: + pass + +# Rxn files in a single list. +# All numerics converted to floats. +unmapped_rxns = os.listdir('unmappedRxns') +for i, rxn_file in enumerate(unmapped_rxns): + with open(f'unmappedRxns/{rxn_file}', 'r') as f: + unmapped_rxns[i] = f.readlines() + for j, line in enumerate(unmapped_rxns[i]): + unmapped_rxns[i][j] = unmapped_rxns[i][j].split() + for k, val in enumerate(unmapped_rxns[i][j]): + try: + unmapped_rxns[i][j][k] = float(val) + except BaseException: + pass + +# Mapped Rxn files in a single list +mapped_rxns = os.listdir('mappedRxns/rxnFiles') +for i, rxn_file in enumerate(mapped_rxns): + with open(f'mappedRxns/rxnFiles/{rxn_file}', 'r') as f: + lines = f.readlines() + atom_rows = [] + for j, line in enumerate(lines): + if len(line.split()) in (15, 16): + # Only append rows containing atom mappings + atom_rows.append(line.split()) + mapped_rxns[i] = atom_rows + +# CSV outputs of parsed mapping data +reaction_df_csv = pd.read_csv('MappingReactions.csv') +metabolite_df_csv = pd.read_csv('MappingMetabolites.csv') + +# Pickle all the variables using pickle +filehandler = open("test_data.obj", "wb") + +pickle.dump( + [ + metabolites, + unmapped_rxns, + mapped_rxns, + reaction_df, + metabolite_df, + reaction_df_csv, + metabolite_df_csv, + model_reaction_df, + model_metabolite_df, + ], + filehandler +) + +filehandler.close() + +clean_output() + +os.chdir(original_wd) diff --git a/tests/test_data/atom_mapping_Data/test_data.obj b/tests/test_data/atom_mapping_Data/test_data.obj new file mode 100644 index 00000000..528873a2 Binary files /dev/null and b/tests/test_data/atom_mapping_Data/test_data.obj differ