Reason for two kcat values in each PredcitedKcat343species file

[HettieC]

Hi,

I am currently trying to use the PredcitedKcat343species results from https://zenodo.org/record/6438262#.Y3NLqi8w0dU , and I would like to know what the two different kcat values for each reaction refer to.

For example, the first reaction of the Saccharomyces_cerevisiae has

rxnID	MNXID	met_model	met_standard_name	Smiles	genes	refID	Kcat_value (substrate_first)

r_0001_1	MNXM731834;MNXM731974	(R)-lactate;ferricytochrome c	(R)-lactate;ferricytochrome c	C[C@@H](O)C([O-])=O;	YDL174C;YEL039C	chebi:16004;chebi:15991	13.8553,3.7425;

I see that it is "substrate first", but am I correct in thinking that this means that the first value gives the turnover number for the forward reaction and the second value is for the backwards reaction? If so, what do the two values mean when there are forward and backward reactions given, eg here:

r_0018_1_fwd	MNXM263;MNXM741173	2-oxoadipic acid;L-glutamate	2-oxoadipate;L-glutamate	[O-]C(=O)CCCC(=O)C([O-])=O;[NH3+][C@@H](CCC([O-])=O)C([O-])=O	YER152C	chebi:57499;chebi:29985	6.3271;3.6237
r_0018_1_rvs	MNXM20;MNXM268	2-oxoglutarate;L-2-aminoadipate	2-oxoglutarate;L-2-aminoadipate	[O-]C(=O)CCC(=O)C([O-])=O;[NH3+][C@@H](CCCC([O-])=O)C([O-])=O	YER152C	chebi:16810;chebi:58672	9.5759;3.3994

An explanation of which of the two values I should use in enzyme constrained modelling would be much appreciated.

Thanks,
Hettie

[feiranl]

Thanks for the interest, kcat values are predicted for pairs of all subunits and all substrates for each enzymatic reaction, that is the reason for multiple values for each rxn. If you are interested in the kcat values used in the ecModels, we use the maximum values, and you can find the kcat values in the zenode model_build_files/model_dl/. Load the mat file, and the kcat values are documented in the enzymedata, enzymedata.kcat are kcat values used for each rxn: enzymedata.rxn_list.