- A GEM is primarily a set of reactions: here are all the reaction equations occurring in bigg_e_coli_core. NB: here the reac label is the one produced while compiling MetaNetX
- Building on example 10. ...in addition reactions are endowed with a direction, flux bounds and possibly the description of the enzymes that catalyze it.
- For the KEGG compound C01732, retrieve the MNXref identifier, name and reference
- Given the protein with UniProt accession number P0ABU7 (Biopolymer transport protein ExbB) retrieve all reactions and models in which this polypeptide appears.
- Given the protein with UniProt accession number P42588 (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) retrieve all reactions and models in which this polypeptide appears.
- List all GEMs currently in the MetaNetX repository, with their numbers of reactions, chemical, compartments and genes/proteins.
- List the external identifiers that correspond to the KEGG reaction R00703 (lactate dehydrogenase). This crosslinking of external identifiers is the core of MNXref
- Retrieve the MNXref metabolite with name N,N-dimethyl-beta-alanine, together with molecular information.
- Retrieve the MNXref reaction identifier, that corresponds to the KEGG reaction R00703 (lactate dehydrogenase).
- Retrieve the identifiers for N,N-dimethyl-beta-alanine in external databases. This crosslinking of external identifiers is the core of MNXref.
- Show the reaction equation catalyzed by lactate dehydrogenase (KEGG reaction R00703). NB: Stoichiometric coefficients for substrates are given a negative value.
- Show the reaction equation for ATP synthase (reaction ATPS4m from BiGG). NB: there are two types of protons here, as MetaNetX distinguishes protons used for balancing (MNXM1) from those that are translocated (MNXM01).
- Show the reaction equation for the tartrate/succinate antiporter (rhea:34763). NB: there are two generic compartments here.)