├── .gitignore ├── BayesianApproach ├── Code │ ├── Analysis │ │ ├── Figure4acdef_S11acdef_RMSEandVarianceSingleModel.m │ │ ├── Figure4b_S11b_simulateGrowth.m │ │ ├── Figure5ab_kcatcoverage.m │ │ ├── Figure5c_RMSEphen.m │ │ ├── Figure5d_S13_GrowthResult.m │ │ ├── Figure5e_SimulateProteomeSimplied.m │ │ ├── Figure6b_CrabtreeProteinEfficiency.m │ │ ├── Figure6c_SignEnzyme.m │ │ ├── FigureS10_TestSMCABC.m │ │ ├── FigureS12.m │ │ ├── FigureS1c_kcat_org.m │ │ ├── FigureS7_DLnumber.m │ │ ├── FigureS8a_pathway_kcat.m │ │ ├── FigureS8b_general_special_kcat.m │ │ ├── FigureS9_CollecedPhen.m │ │ ├── PCAsampledKcatsOneSpecies.m │ │ ├── SimulatePhenotype.m │ │ ├── SupplementaryTableS6_sigChangedEnzyme.m │ │ ├── calculateproteome.m │ │ ├── convert2panID.m │ │ ├── kcatSignAnalysis.m │ │ └── simulatecarbonsource.m │ ├── ForKcatPrediction │ │ ├── WriteFile_pre_cluster.m │ │ ├── sub1.sh │ │ └── writeFileForKcatPrediction.m │ ├── common │ │ ├── addrxnBack.m │ │ ├── biomassCompData.mat │ │ ├── changeGAM.m │ │ ├── changeMedia.m │ │ ├── getNewIndex.m │ │ ├── getflux.m │ │ ├── getflux_ec.m │ │ ├── minimal_Y6.m │ │ ├── pval_adjust.m │ │ ├── splitModel.m │ │ └── sumBioMass.m │ └── ecGEMconstruction │ │ ├── BayesianModelGeneration_cluster.m │ │ ├── Corefunction │ │ ├── ECprepPanGEM.m │ │ ├── abc_matlab_max.m │ │ ├── addCarbonNum.m │ │ ├── anaerobicModel.m │ │ ├── balancecarbon.m │ │ ├── blockRxns.m │ │ ├── collectPredictedKcat.m │ │ ├── collectkcats.m │ │ ├── convertToGeckoModel.m │ │ ├── fitGAM.m │ │ ├── getProteinMW.m │ │ ├── getcarbonnum.m │ │ ├── getrSample.m │ │ ├── loadkcats.m │ │ ├── searchkcat.m │ │ ├── searchkcat_predict.m │ │ ├── solveModel.m │ │ ├── topUsedEnzymes.m │ │ ├── truncateValues.m │ │ ├── updatekcats.m │ │ ├── updateprior.m │ │ └── writeClusterFile.m │ │ ├── ManualChange.m │ │ ├── Manulchange_for_checklist.m │ │ ├── Strain.txt │ │ ├── TestBayesianModelGeneration.m │ │ ├── classicDLModelGeneration.m │ │ ├── classicDLModelGeneration_cluster.m │ │ ├── conserveMets.mat │ │ ├── ecdata.mat │ │ ├── getEmodel.m │ │ ├── initcluster.m │ │ ├── rxn2block.mat │ │ ├── species_withdata.mat │ │ └── strains.mat ├── Data │ ├── 343_phenotype_clade.tsv │ ├── Proteome_ref.xlsx │ ├── Saccharomyces_cerevisiae.tsv │ ├── SubstrateUsageInfo.tsv │ ├── database │ │ ├── Kcat_combination_41559.tsv │ │ ├── Kcat_combination_wildtype_mutant_withUniprot.json │ │ ├── MNX_met_yeast8.3.4.txt │ │ ├── MNXpropExtract.m │ │ ├── analysis │ │ │ ├── Max_combined.txt │ │ │ ├── brenda_parser │ │ │ │ ├── findMaxKvalues_AllOrgs.m │ │ │ │ ├── max_data │ │ │ │ │ ├── max_KCAT.txt │ │ │ │ │ ├── max_MW.txt │ │ │ │ │ └── max_SA.txt │ │ │ │ ├── retrieveBRENDA.py │ │ │ │ └── stringSplit.m │ │ │ ├── ec_number_kegg.txt │ │ │ └── sabiork │ │ │ │ └── Kcat_sabio.txt │ │ ├── conserverMets.txt │ │ ├── kcatrange.mat │ │ ├── kcatrange_generation.m │ │ └── pdbe │ │ │ ├── PDBe_search.csv │ │ │ ├── Protein_stoichiometry.mat │ │ │ ├── Readme4PDBe.txt │ │ │ ├── Yeast_homologue_genes.xlsx │ │ │ ├── pdbe.m │ │ │ └── pdbe_processing.m │ ├── growthratedata.xlsx │ ├── module_ec.txt │ └── ortholog_changedtoPanID.mat ├── README.rst └── Results │ └── README.rst ├── DeeplearningApproach ├── Code │ ├── analysis │ │ ├── Fig2a_DLRMSE.py │ │ ├── Fig2b_Performance_correlation.py │ │ ├── Fig2c_Enzyme_promiscuity_all.py │ │ ├── Fig2d_Enzyme_promiscuity_case.py │ │ ├── Fig3a_Wildtype_all.py │ │ ├── Fig3b_Mutant_all.py │ │ ├── Fig3c_Mutacorrelation.py │ │ ├── Fig3d_Decreased&Like.py │ │ ├── Fig3e_Attention.py │ │ ├── Fig3f_Compareweight.py │ │ ├── SuppleFig1a_Distribution.py │ │ ├── SuppleFig1b_ECdistribution.py │ │ ├── SuppleFig3a_five_times_validation.py │ │ ├── SuppleFig3b_five_times_test.py │ │ ├── SuppleFig4a_Hyperparameter_radius.py │ │ ├── SuppleFig4b_Hyperparameter_dim.py │ │ ├── SuppleFig4c_Hyperparameter_gnn&cnn.py │ │ ├── SuppleFig5a_Prediction_test.py │ │ ├── SuppleFig5b_Prediction_test_subset.py │ │ ├── SuppleFig5c_Pre_subsystem.py │ │ ├── SuppleFig5d_Enzyme_promiscuity_test.py │ │ ├── SuppleFig6a_Compare_wildtype_mutant.py │ │ ├── SuppleFig6b_Wildtype_test.py │ │ ├── SuppleFig6c_Mutant_test.py │ │ ├── SuppleFig8a_Gen&Spe.py │ │ ├── SuppleFig8b_DNDS.py │ │ ├── model.py │ │ └── subsequence_model.py │ ├── example │ │ ├── input.tsv │ │ ├── model.py │ │ ├── output.tsv │ │ └── prediction_for_input.py │ ├── model │ │ ├── model.py │ │ ├── preprocess_all.py │ │ └── run_model.py │ ├── prediction │ │ └── predict_kcat_343_species.py │ └── preprocess │ │ ├── brenda_download.py │ │ ├── brenda_get_smiles.py │ │ ├── brenda_kcat_clean.py │ │ ├── brenda_kcat_preprocess.py │ │ ├── brenda_retrieve.py │ │ ├── brenda_sequence.py │ │ ├── brenda_sequence_organism.py │ │ ├── combination_brenda_sabio.py │ │ ├── combination_database_data.py │ │ ├── findMaxKvalues_AllOrgs.py │ │ ├── sabio_download.py │ │ ├── sabio_get_smiles.py │ │ ├── sabio_kcat_clean.py │ │ ├── sabio_kcat_clean_unisubstrate.py │ │ ├── sabio_kcat_unisubstrate.py │ │ ├── sabio_kcat_unisubstrate_mutant.py │ │ └── uniprot_sequence.py ├── Data │ ├── EC_enzyme │ │ ├── README │ │ ├── enzclass.txt │ │ └── enzyme.dat │ ├── database │ │ ├── Kcat_combination_0918.json │ │ └── Kcat_combination_0918_wildtype_mutant.json │ ├── enzyme_promiscuity │ │ ├── all_preferred_alternative_random.txt │ │ ├── human_aldo-keto-reductase.tsv │ │ └── test_preferred_alternative_random.txt │ ├── five_fold │ │ ├── MAEs--all--radius2--ngram3--dim20--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50_fold_1.txt │ │ ├── MAEs--all--radius2--ngram3--dim20--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50_fold_2.txt │ │ ├── MAEs--all--radius2--ngram3--dim20--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50_fold_3.txt │ │ ├── MAEs--all--radius2--ngram3--dim20--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50_fold_4.txt │ │ └── MAEs--all--radius2--ngram3--dim20--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50_fold_5.txt │ ├── gene_dn_ds.csv │ ├── input.zip │ ├── output_hyper │ │ ├── MAEs--all--radius0--ngram1--dim10--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50.txt │ │ ├── MAEs--all--radius1--ngram2--dim10--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50.txt │ │ ├── MAEs--all--radius2--ngram3--dim10--layer_gnn2--window11--layer_cnn2--layer_output2--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50.txt │ │ ├── MAEs--all--radius2--ngram3--dim10--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50.txt │ │ ├── MAEs--all--radius2--ngram3--dim10--layer_gnn4--window11--layer_cnn4--layer_output4--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50.txt │ │ ├── MAEs--all--radius2--ngram3--dim20--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50.txt │ │ └── MAEs--all--radius2--ngram3--dim5--layer_gnn3--window11--layer_cnn3--layer_output3--lr1e-3--lr_decay0.5--decay_interval10--weight_decay1e-6--iteration50.txt │ ├── subsystem │ │ └── module_ec.txt │ └── test_dataset │ │ ├── test_out.txt │ │ └── test_out_subset.txt ├── README.rst └── Results │ ├── figures │ ├── Fig2a.pdf │ ├── Fig2b.pdf │ ├── Fig2c.pdf │ ├── Fig2d.pdf │ ├── Fig3a.pdf │ ├── Fig3b.pdf │ ├── Fig3c.pdf │ ├── Fig3d.pdf │ ├── Fig3e.pdf │ ├── Fig3f.pdf │ ├── SuppleFig1a.pdf │ ├── 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