Medium composition
M9 minimal medium (per liter): 8.5 g Na2HPO4·2H2O, 3 g KH2PO4, 1 g NH4Cl, 0.5 g NaCl. The following components were sterilized separately and then added (per liter of final medium): 1 ml 0.1 M CaCl2, 1 ml 1 M MgSO4, 1 ml 50 mM FeCl3 and 10 ml trace salts solution. The trace salts solution contained (per liter): 170 mg ZnCl2, 100 mg MnCl2·4H2O, 60.0 mg CoCl2·6H2O, 60.0 mg Na2MoO4·2H2O and 43.0 mg CuCl2·2H2O. Filter‐sterilized carbon sources were added separately to the medium, pH neutralized with 4 M NaOH where necessary.
Methods description - Notes
Extracellular substrate and byproduct concentrations were measured by HPLC analysis using an Agilent 1100 series HPLC stack (Agilent Technologies, Waldbronn, Germany) in combination with an Aminex HPX‐87H polymer column (Bio‐Rad, Hercules, CA, USA). Sugars were detected with
...
a refractive index detector and organic acids with an UV/Vis detector. Substrate or product yields were calculated by linear regression of external concentration against biomass, and specific rates were calculated as yield multiplied by the growth rate. At least five time points during the exponential growth phase were used for the regression analysis. Cell growth was monitored photometrically at 600 nm and cell dry weight was inferred from a predetermined conversion factor of 0.48 g cells/OD600 [1]. All measurement errors for physiological parameters are reported as the standard deviation of 2–3 biological replicates.
Metabolic flux analysis
Biomass sample processing and GC‐MS analysis to determine isotopomer fractions of proteinogenic amino acids was performed as previously described [2]. Stoichiometric network models were based on a core model containing the reactions of central carbon metabolism [3]. When unconstrained by labeling information, futile cycle fluxes were set to zero. The growth rate‐dependent biomass requirements of B. subtilis were previously established [4] and added to the network as unidirectional biomass precursor withdrawing reactions. Metabolic fluxes were derived using the whole isotopomer modeling approach [5]. The procedure uses the cumomer balances and cumomer to isotopomer mapping matrices [6] to calculate the isotopomer distributions of metabolites in a predefined stoichiometric network model for a given flux set. The flux set that gives the best correspondence between the measured and simulated 13C‐label distribution is determined by non‐linear optimization and denoted as the optimal flux fit. All calculations were performed in Matlab 7.6.0 (The Mathworks Inc, Natick, MA, USA). --------------------------------------------References---------------------------------------
[1] Tännler S, Decasper S, Sauer U (2008). Microb Cell Fact 7: 19. http://doi.org/cjbk3x
[2] Zamboni N, Fendt S‐M, Rühl M, Sauer U (2009). Nat Protoc 4: 878–892. http://doi.org/b8ck9w
[3] Oh Y‐K, Palsson BO, Park SM, Schilling CH, Mahadevan R (2007). J Biol Chem 282: 28791–28799. http://doi.org/bvbtsq
[4] Dauner M, Storni T, Sauer U (2001). J Bacteriol 183: 7308–7317. http://doi.org/cs9gqv
[5] Van Winden WA, van Dam JC, Ras C, Kleijn RJ, Vinke JL, van Gulik WM, Heijnen JJ (2005). FEMS Yeast Res 5: 559–568. http://doi.org/cgg3tw
[6] Wiechert W, Möllney M, Isermann N, Wurzel M, de Graaf AA (1999). Biotechnol Bioeng 66: 69–85. http://doi.org/ctxdtx
Read more
Data file
KIMODATAID89_v0.xlsx
Preview file
Information
glucose_carbon source
fructose_carbon source
gluconate_carbon source
succinate_carbon source
glycerol_carbon source
malate_carbon source
mal_gluc_carbon source
pyruvate_carbon source
Metadata
Data EntryID
89
Entered by
Administrator KiMoSys
Date Added
2015-05-12
Version
0
General Information
Manuscript title
Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis.
PubMed ID
24281055
Journal
Molecular Systems Biology
Year
2013
Authors
Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich,
Joerg Stelling and Uwe Sauer
Affiliations
Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland.
Keywords
central carbon metabolism, metabolic flux, transcriptional regulation
Project name
not specified
Experiment Description
Organism
Bacillus subtilis
Strain
BSB168
Data type
flux measurements
Data units
mmol/gcdw/h
Execution date
not specified
Experimental Details
Temperature (0C)
37
pH
—
Carbon Source
glucose, fructose, gluconate, succinate+glutamate, glycerol, malate, malate, malate+glucose, pyruvate
Culture mode
batch
Process condition
aerobic
Dilution rate (h-1)
—
Working volume (L)
0.03
Biomass concentration (g/L)
3.0 g cells/OD600
Medium composition
M9 minimal medium (per liter): 8.5 g Na2HPO4·2H2O, 3 g KH2PO4, 1 g NH4Cl, 0.5 g NaCl. The following components were sterilized separately and then added (per liter of final medium): 1 ml 0.1 M CaCl2, 1 ml 1 M MgSO4, 1 ml 50 mM FeCl3 and 10 ml trace salts solution. The trace salts solution contained (per liter): 170 mg ZnCl2, 100 mg MnCl2·4H2O, 60.0 mg CoCl2·6H2O, 60.0 mg Na2MoO4·2H2O and 43.0 mg CuCl2·2H2O. Filter‐sterilized carbon sources were added separately to the medium, pH neutralized with 4 M NaOH where necessary.
General protocol information
Flux analysis method: 13C constrained MFA
Platform: GC-MS
Methods description - Notes
Extracellular substrate and byproduct concentrations were measured by HPLC analysis using an Agilent 1100 series HPLC stack (Agilent Technologies, Waldbronn, Germany) in combination with an Aminex HPX‐87H polymer column (Bio‐Rad, Hercules, CA, USA). Sugars were detected with a refractive index detector and organic acids with an UV/Vis detector. Substrate or product yields were calculated by linear regression of external concentration against biomass, and specific rates were calculated as yield multiplied by the growth rate. At least five time points during the exponential growth phase were used for the regression analysis. Cell growth was monitored photometrically at 600 nm and cell dry weight was inferred from a predetermined conversion factor of 0.48 g cells/OD600 [1]. All measurement errors for physiological parameters are reported as the standard deviation of 2–3 biological replicates.
Metabolic flux analysis
Biomass sample processing and GC‐MS analysis to determine isotopomer fractions of proteinogenic amino acids was performed as previously described [2]. Stoichiometric network models were based on a core model containing the reactions of central carbon metabolism [3]. When unconstrained by labeling information, futile cycle fluxes were set to zero. The growth rate‐dependent biomass requirements of B. subtilis were previously established [4] and added to the network as unidirectional biomass precursor withdrawing reactions. Metabolic fluxes were derived using the whole isotopomer modeling approach [5]. The procedure uses the cumomer balances and cumomer to isotopomer mapping matrices [6] to calculate the isotopomer distributions of metabolites in a predefined stoichiometric network model for a given flux set. The flux set that gives the best correspondence between the measured and simulated 13C‐label distribution is determined by non‐linear optimization and denoted as the optimal flux fit. All calculations were performed in Matlab 7.6.0 (The Mathworks Inc, Natick, MA, USA). --------------------------------------------References--------------------------------------- [1] Tännler S, Decasper S, Sauer U (2008). Microb Cell Fact 7: 19. [2] Zamboni N, Fendt S‐M, Rühl M, Sauer U (2009). Nat Protoc 4: 878–892. [3] Oh Y‐K, Palsson BO, Park SM, Schilling CH, Mahadevan R (2007). J Biol Chem 282: 28791–28799 [4] Dauner M, Storni T, Sauer U (2001). J Bacteriol 183: 7308–7317. [5] Van Winden WA, van Dam JC, Ras C, Kleijn RJ, Vinke JL, van Gulik WM, Heijnen JJ (2005). FEMS Yeast Res 5: 559–568. [6] Wiechert W, Möllney M, Isermann N, Wurzel M, de Graaf AA (1999). Biotechnol Bioeng 66: 69–85
Data URL
http://kimosys.org/repository/89
Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
7.63
0.08010599645258878
mmol/gcdw/h
fructose uptake
0.0
0.0
mmol/gcdw/h
gluconate uptake
0.0
0.0
mmol/gcdw/h
glycerol uptake
0.0
0.0
mmol/gcdw/h
malate uptake
0.0
0.0
mmol/gcdw/h
pyruvate uptake
0.0
0.0
mmol/gcdw/h
glutamate uptake
0.0
0.0
mmol/gcdw/h
succinate uptake
0.0
0.0
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 4.158781574736097
0.6963237648426251
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 6.005036410947437
0.23924503371429154
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 0.0
0.0
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 6.005036410947525
0.23924503371436776
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 6.005036410947483
0.23924503371433048
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 11.577311098530272
0.27153352272342046
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 0.0
0.0
mmol/gcdw/h
Pgk;Pgm;Eno
11.577311098529858
0.2715335227231045
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 11.943913249734537
1.049749255375099
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 3.297143161464449
0.6990177045465705
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 3.297143161464449
0.6990177045465705
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 1.8462548362116582
0.6990177045465705
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 1.4508883252527907
0.23315518807957714
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 1.0550121390860574
0.23315518807957714
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 0.7912426971256008
0.2331488768288133
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 1.0550121390858807
0.2331551880796992
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 7.4050909076325
0.2768651686110098
mmol/gcdw/h
Cit
3.353026004223841
0.2860504573125806
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 3.353026004223599
0.28605045731241446
mmol/gcdw/h
Odh
2.6384248842412568
0.2871917866472469
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
2.6384248842415996
0.2871917866474715
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 1.8783581686034625
0.5753951355504129
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 0.9156838914161167
0.8051705751613757
mmol/gcdw/h
ME
0.7600667854348442
0.3440401177586434
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 3.5038673997711975
0.5191585222157664
mmol/gcdw/h
acetate
3.3718315067836726
0.015141372251415602
mmol/gcdw/h
transport, CO2 excretion
29.07739645873977
2.851896639765874
mmol/gcdw/h
transport, acetate excretion
3.3718315067837414
0.015141372251397604
mmol/gcdw/h
transport, pyruvate excretion
0.0763
0.0
mmol/gcdw/h
G6P efflux to biomass
0.17407526379944213
5.750667215026784e-05
mmol/gcdw/h
G3P efflux to biomass
1.2240044204900344
0.0021632760159146116
mmol/gcdw/h
P5P efflux to biomass
0.39587618616649717
0.0006849375017252292
mmol/gcdw/h
E4P efflux to biomass
0.26376944196009944
0.00027942036596729234
mmol/gcdw/h
PEP efflux to biomass
0.5490817402112911
0.00044716721760387204
mmol/gcdw/h
PYR efflux to biomass
1.71872158817296
0.004326401243782927
mmol/gcdw/h
OAA efflux to biomass
1.1135156727347577
0.0029376038999041876
mmol/gcdw/h
AcCoA efflux to biomass
0.6802333966251187
0.0005739396602354142
mmol/gcdw/h
aKG efflux to biomass
0.7146011199822404
0.0017241439138146791
mmol/gcdw/h
Graph
Loading...
Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
0.0
0.0
mmol/gcdw/h
fructose uptake
5.72
0.0956659688445579
mmol/gcdw/h
gluconate uptake
0.0
0.0
mmol/gcdw/h
glycerol uptake
0.0
0.0
mmol/gcdw/h
malate uptake
0.0
0.0
mmol/gcdw/h
pyruvate uptake
0.0
0.0
mmol/gcdw/h
glutamate uptake
0.0
0.0
mmol/gcdw/h
succinate uptake
0.0
0.0
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 -1.515530245160474
0.6609640853247655
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 0.0
0.0
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 0.92092
0.22012767904454397
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 4.799077676914364
0.17398573214815474
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 4.799077676914342
0.17398573214814606
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 8.705817941836743
0.17503695479030018
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 0.0
0.0
mmol/gcdw/h
Pgk;Pgm;Eno
8.70581794183674
0.17503695479030057
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 8.222367482542687
0.17512883085616435
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 1.3386141325909042
0.6610929655341355
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 1.3386141325909042
0.6610929655341355
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 0.5946079220747937
0.6610929655341355
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 0.7440062105161107
0.2204682299563261
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 0.41157533455062434
0.22036880457324512
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 0.18303258752416937
0.2204682299563261
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 0.4115753345506585
0.22036880457324237
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 5.07183778865539
0.17948790427087186
mmol/gcdw/h
Cit
3.791103596663147
0.18009480758553223
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 3.7911035966631323
0.18009480758553134
mmol/gcdw/h
Odh
3.1651978083068
0.18122381436770238
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
3.1651978083067873
0.18122381436770066
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 2.156565244493213
0.14684436248351426
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 -5.1696955985212865e-08
1.573443087945319e-15
mmol/gcdw/h
ME
1.0086326160327
0.1067716207247965
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 2.599357282580284
0.1050101144960903
mmol/gcdw/h
acetate
0.6275094983738496
0.0010033849879975839
mmol/gcdw/h
transport, CO2 excretion
25.302318365864455
3.886034649438518
mmol/gcdw/h
transport, acetate excretion
0.6275094983738514
0.0010033849879981663
mmol/gcdw/h
transport, pyruvate excretion
0.0572
0.0
mmol/gcdw/h
G6P efflux to biomass
0.1769161125695891
0.00017539326609619538
mmol/gcdw/h
G3P efflux to biomass
1.0753699995161463
0.002457197136066473
mmol/gcdw/h
P5P efflux to biomass
0.33243087596547716
0.00043025674756131283
mmol/gcdw/h
E4P efflux to biomass
0.2285427470264905
0.00033926795768155323
mmol/gcdw/h
PEP efflux to biomass
0.4834504075970655
0.0004554361910769309
mmol/gcdw/h
PYR efflux to biomass
1.502604922901425
0.006002362789866155
mmol/gcdw/h
OAA efflux to biomass
0.9648189821073346
0.005125969175275908
mmol/gcdw/h
AcCoA efflux to biomass
0.6532246936184118
0.001108139906284699
mmol/gcdw/h
aKG efflux to biomass
0.6259057883563267
0.003117795772360965
mmol/gcdw/h
Graph
Loading...
Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
0.0
0.0
mmol/gcdw/h
fructose uptake
0.0
0.0
mmol/gcdw/h
gluconate uptake
5.13
0.1086408645714818
mmol/gcdw/h
glycerol uptake
0.0
0.0
mmol/gcdw/h
malate uptake
0.0
0.0
mmol/gcdw/h
pyruvate uptake
0.0
0.0
mmol/gcdw/h
glutamate uptake
0.0
0.0
mmol/gcdw/h
succinate uptake
0.0
0.0
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 -0.7228025210329124
0.4369812100993314
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 2.824790543957899
0.10589587205644964
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 0.0
0.0
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 2.82479054395776
0.10589587205637982
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 2.8247905439578513
0.10589587205644035
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 6.463069426191855
0.13003062552425396
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 0.0
0.0
mmol/gcdw/h
Pgk;Pgm;Eno
6.463069426191612
0.1300306255239654
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 6.090068761362493
0.17457222555981625
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 0.5338423944754216
0.4386568428389323
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 5.66352
0.4386568428389323
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 3.5475930649903287
0.5472977074104142
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 2.115926935009672
0.1740978281262177
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 1.8629488378206085
0.1740978281262177
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 1.6846442271697195
0.1739729574197407
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 1.8629488378209067
0.1740978281262768
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 3.554329150159393
0.1379188285146579
mmol/gcdw/h
Cit
2.936763449374231
0.13863987847618955
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 2.9367634493741623
0.13863987847609843
mmol/gcdw/h
Odh
2.426939041886173
0.1404676366201142
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
2.426939041886331
0.1404676366203152
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 2.2251080787955555
0.15426781223731342
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 0.01891815841986817
0.07210218858224399
mmol/gcdw/h
ME
0.2018310116825398
0.09256109577249463
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 1.5064024163713747
0.08182559461445
mmol/gcdw/h
acetate
4.8591898154203853e-08
8.45541690369879e-14
mmol/gcdw/h
transport, CO2 excretion
390.286805786424
1713.3156631173163
mmol/gcdw/h
transport, acetate excretion
4.8591788864077826e-08
4.1867539586448433e-13
mmol/gcdw/h
transport, pyruvate excretion
0.0
0.0
mmol/gcdw/h
G6P efflux to biomass
0.18896012655744213
0.001959456998904843
mmol/gcdw/h
G3P efflux to biomass
0.8711558888931551
0.0017319556864727082
mmol/gcdw/h
P5P efflux to biomass
0.25330049166495533
0.0005113628648938859
mmol/gcdw/h
E4P efflux to biomass
0.17830461065121786
0.00025513986237173846
mmol/gcdw/h
PEP efflux to biomass
0.3919188232492072
0.0003613152315592965
mmol/gcdw/h
PYR efflux to biomass
1.231168109330015
0.0037517272621124015
mmol/gcdw/h
OAA efflux to biomass
0.775828887372978
0.004061161002457126
mmol/gcdw/h
AcCoA efflux to biomass
0.617565652193162
0.0009186134689262932
mmol/gcdw/h
aKG efflux to biomass
0.509824407488175
0.0023616049527739706
mmol/gcdw/h
Graph
Loading...
Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
0.0
0.0
mmol/gcdw/h
fructose uptake
0.0
0.0
mmol/gcdw/h
gluconate uptake
0.0
0.0
mmol/gcdw/h
glycerol uptake
0.0
0.0
mmol/gcdw/h
malate uptake
0.0
0.0
mmol/gcdw/h
pyruvate uptake
0.0
0.0
mmol/gcdw/h
glutamate uptake
2.21
0.10355309492022531
mmol/gcdw/h
succinate uptake
3.35
0.07468630747021941
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 -0.39344047285678957
0.04397679378212383
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 0.0
0.0
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 0.35845
0.014646667938964643
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 -0.36009523608529764
0.01464666793896575
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 -0.36009523608531324
0.014646667938966216
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 0.0
0.0
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 1.29645
0.014656299670160012
mmol/gcdw/h
Pgk;Pgm;Eno
-1.2951810605861662
0.01465629967015942
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 2.5461098573016256
1.5635570780478256
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 0.23401207562940868
0.04398602640330908
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 0.23401207562940868
0.04398602640330908
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 0.03334523677151719
0.04398602640330908
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 0.2006668388578915
0.014670688944367776
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 0.06886708651916329
0.0146635475385344
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 -0.0355218497476461
0.014670688944367776
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 0.06886708651919247
0.014663547538534518
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 2.4478448290760153
0.0646299368874709
mmol/gcdw/h
Cit
1.959991549155937
0.06442333718888699
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 1.9599915491559445
0.06442333718888722
mmol/gcdw/h
Odh
3.8521194551280087
0.15256554891784257
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
7.202119455128032
0.1272867265560115
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 6.195089475129529
1.5317622529679285
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 4.0777137081883135
1.5647886762626098
mmol/gcdw/h
ME
1.0070299799984463
1.5510954454589934
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 0.318605044590317
0.11256252675777015
mmol/gcdw/h
acetate
3.850210214147123e-08
1.6333211292869978e-15
mmol/gcdw/h
transport, CO2 excretion
13.646349540689071
0.3261011814863725
mmol/gcdw/h
transport, acetate excretion
3.8502084719126085e-08
1.5386084269989182e-15
mmol/gcdw/h
transport, pyruvate excretion
3.8502084719126085e-08
1.5386084269989182e-15
mmol/gcdw/h
G6P efflux to biomass
0.15942839722738983
0.0002484137237723736
mmol/gcdw/h
G3P efflux to biomass
0.539468738667944
0.0013190813924628705
mmol/gcdw/h
P5P efflux to biomass
0.1317997523387488
0.00014393880575687998
mmol/gcdw/h
E4P efflux to biomass
0.10438893626683161
7.53296395630603e-05
mmol/gcdw/h
PEP efflux to biomass
0.23642279030044028
0.0002837057413941283
mmol/gcdw/h
PYR efflux to biomass
0.7866898866295802
0.0026948641273393994
mmol/gcdw/h
OAA efflux to biomass
0.475989262375611
0.000979095373495237
mmol/gcdw/h
AcCoA efflux to biomass
0.4878532414179519
0.0011552159676210033
mmol/gcdw/h
aKG efflux to biomass
0.3223239198282255
0.00047060123859389715
mmol/gcdw/h
Graph
Loading...
Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
0.0
0.0
mmol/gcdw/h
fructose uptake
0.0
0.0
mmol/gcdw/h
gluconate uptake
0.0
0.0
mmol/gcdw/h
glycerol uptake
6.22
0.08533434181242015
mmol/gcdw/h
malate uptake
0.0
0.0
mmol/gcdw/h
pyruvate uptake
0.0
0.0
mmol/gcdw/h
glutamate uptake
0.0
0.0
mmol/gcdw/h
succinate uptake
0.0
0.0
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 -0.15019729934881415
0.05603537832557634
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 0.0
0.0
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 0.31722
0.018621626226955804
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 -0.3148132414839155
0.018621626226954416
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 5.905186758516101
0.08542739073951705
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 4.780596316350546
0.08702606674263683
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 0.0
0.0
mmol/gcdw/h
Pgk;Pgm;Eno
4.780596316350544
0.08702606674263963
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 4.488671925496549
0.09951821505279364
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 0.00787858667761848
0.056052890044769245
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 0.00787858667761848
0.056052890044769245
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 -0.1646159421351189
0.056052890044769245
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 0.17249452881273736
0.01870850403315652
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 -0.013844537474190103
0.018707764743437907
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 -0.1507714046609288
0.01870850403315652
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 -0.013844537474155705
0.018707764743444245
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 2.592134141893071
0.09530411485805168
mmol/gcdw/h
Cit
2.0043453190251572
0.0962727452397624
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 2.0043453190251546
0.09627274523976105
mmol/gcdw/h
Odh
1.620194249460958
0.09807139237527794
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
1.6201942494609218
0.09807139237528315
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 0.6221830145308971
0.16229427300569643
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 0.0035844098632002736
0.03479697363514469
mmol/gcdw/h
ME
0.9980112900373094
0.12747314957652084
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 1.9681710910982226
0.1270131533132507
mmol/gcdw/h
acetate
0.10985531195359348
4.8478375863739864e-05
mmol/gcdw/h
transport, CO2 excretion
12.071557596549349
2.18913368444804
mmol/gcdw/h
transport, acetate excretion
0.10985531195359148
4.847837586345701e-05
mmol/gcdw/h
transport, pyruvate excretion
5.51072882006028e-08
2.0146587111500978e-15
mmol/gcdw/h
G6P efflux to biomass
0.14231871267117518
0.00012065792794325122
mmol/gcdw/h
G3P efflux to biomass
0.6590057960206858
0.0013255528427749276
mmol/gcdw/h
P5P efflux to biomass
0.18633906628694366
0.0002521293225665285
mmol/gcdw/h
E4P efflux to biomass
0.1369268671867648
0.00011681222348370704
mmol/gcdw/h
PEP efflux to biomass
0.2955088007171569
0.00026868650146897303
mmol/gcdw/h
PYR efflux to biomass
0.9263778723280162
0.003554784798835271
mmol/gcdw/h
OAA efflux to biomass
0.5824243767407259
0.0028363742468209873
mmol/gcdw/h
AcCoA efflux to biomass
0.47793351091434005
0.0009737891236281227
mmol/gcdw/h
aKG efflux to biomass
0.3841510695641892
0.0018471064704760165
mmol/gcdw/h
Graph
Loading...
Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
0.0
0.0
mmol/gcdw/h
fructose uptake
0.0
0.0
mmol/gcdw/h
gluconate uptake
0.0
0.0
mmol/gcdw/h
glycerol uptake
0.0
0.0
mmol/gcdw/h
malate uptake
26.51
0.2252082566800063
mmol/gcdw/h
pyruvate uptake
0.0
0.0
mmol/gcdw/h
glutamate uptake
0.0
0.0
mmol/gcdw/h
succinate uptake
0.0
0.0
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 -2.1952326504349498
0.7508143438222071
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 0.0
0.0
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 1.27248
0.2501457718936623
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 -1.2604015190730342
0.25014577189364195
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 -1.2604015190728464
0.25014577189365433
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 0.0
0.0
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 3.5788500000000005
0.24962686910951476
mmol/gcdw/h
Pgk;Pgm;Eno
-3.587230992776176
0.24962686910950055
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 11.592647440060716
10.312150875323857
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 1.9971627879573408
0.7508140609845839
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 1.9971627879573408
0.7508140609845839
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 0.9348311313616813
0.7508140609845839
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 1.0623316565956595
0.25038926437509884
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 0.6088214021104348
0.25038926437509884
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 0.32600972925124644
0.2502793658881214
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 0.6088214021106885
0.25038926437513853
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 13.980778793162
0.11655594713758197
mmol/gcdw/h
Cit
2.8298806983061024
0.1230309507110634
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 2.8298806983053915
0.12303095071097078
mmol/gcdw/h
Odh
2.0071049904800953
0.12315478932934432
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
2.0071049904804825
0.12315478932938674
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 18.1711784365412
10.260023950970297
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 15.802561867911919
10.390652934733039
mmol/gcdw/h
ME
10.345926553939401
10.22855016973264
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 1.7368856488898576
0.30835201888121805
mmol/gcdw/h
acetate
10.358065726958692
0.02984750738969563
mmol/gcdw/h
transport, CO2 excretion
723.9087223981601
848.202066560462
mmol/gcdw/h
transport, acetate excretion
10.358065726958648
0.02984750738971811
mmol/gcdw/h
transport, pyruvate excretion
3.9765000000000006
0.13255
mmol/gcdw/h
G6P efflux to biomass
0.19806986247741842
3.513011593409204e-05
mmol/gcdw/h
G3P efflux to biomass
1.3924376838819021
0.0007212829888131461
mmol/gcdw/h
P5P efflux to biomass
0.45351025448519655
0.00031472442415313954
mmol/gcdw/h
E4P efflux to biomass
0.28281167285950004
0.00016855769796737184
mmol/gcdw/h
PEP efflux to biomass
0.622683435074873
0.000144410963521222
mmol/gcdw/h
PYR efflux to biomass
2.244408986684697
0.011177787771404659
mmol/gcdw/h
OAA efflux to biomass
1.2756215192129339
0.0005084277812708653
mmol/gcdw/h
AcCoA efflux to biomass
0.7928323678968916
0.0002038273364966729
mmol/gcdw/h
aKG efflux to biomass
0.8227757078245873
0.0003902108690959967
mmol/gcdw/h
Graph
Loading...
Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
5.93
0.10257829801310862
mmol/gcdw/h
fructose uptake
0.0
0.0
mmol/gcdw/h
gluconate uptake
0.0
0.0
mmol/gcdw/h
glycerol uptake
0.0
0.0
mmol/gcdw/h
malate uptake
14.6
0.36776673033347396
mmol/gcdw/h
pyruvate uptake
0.0
0.0
mmol/gcdw/h
glutamate uptake
0.0
0.0
mmol/gcdw/h
succinate uptake
0.0
0.0
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 2.878598218265933
0.46371227453186137
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 4.230082411941233
0.193427203853897
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 0.0
0.0
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 4.230082411941104
0.19342720385387474
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 4.230082411941134
0.19342720385387907
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 7.054363267895905
0.27919700389397134
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 0.0
0.0
mmol/gcdw/h
Pgk;Pgm;Eno
7.0543632678957096
0.2791970038938924
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 16.75856463933747
3.074012577106291
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 2.8942328677867604
0.4318921452609284
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 2.8942328677867604
0.4318921452609284
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 1.351484193675267
0.4318921452609284
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 1.542748674111493
0.14400154354409186
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 0.8822395426864428
0.14389146332262379
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 0.46924465098882445
0.14400154354409186
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 0.8822395426864467
0.14389146332262975
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 10.113746804289585
0.11771503714907507
mmol/gcdw/h
Cit
1.7385509712911875
0.10366141289993634
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 1.7385509712910576
0.10366141289988283
mmol/gcdw/h
Odh
0.6514495042052052
0.10352913394773278
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
0.6514495042054145
0.10352913394781343
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 13.194178931173163
3.0759270783184127
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 10.546407180920102
3.150116678575924
mmol/gcdw/h
ME
2.057270573032371
3.07047242732438
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 0.8188433422943183
0.20534137383208173
mmol/gcdw/h
acetate
7.594591483598996
0.040700899380977755
mmol/gcdw/h
transport, CO2 excretion
28.716437317001397
0.8686506064027721
mmol/gcdw/h
transport, acetate excretion
7.59459148359894
0.04070089938096918
mmol/gcdw/h
transport, pyruvate excretion
4.9639999999999995
0.146
mmol/gcdw/h
G6P efflux to biomass
0.15304464659940922
6.864421136170604e-05
mmol/gcdw/h
G3P efflux to biomass
1.8750462069750902
0.006877628959107896
mmol/gcdw/h
P5P efflux to biomass
0.6605091314250023
0.0013191860672486964
mmol/gcdw/h
E4P efflux to biomass
0.41299489169750864
0.0008896735902884935
mmol/gcdw/h
PEP efflux to biomass
0.8422058094783159
0.0013811887426959221
mmol/gcdw/h
PYR efflux to biomass
2.919244760046885
0.04072953767519536
mmol/gcdw/h
OAA efflux to biomass
1.7280641212562635
0.003707001047266287
mmol/gcdw/h
AcCoA efflux to biomass
0.7806043493994282
0.0008291443410226486
mmol/gcdw/h
aKG efflux to biomass
1.087101467085821
0.0021482438419982743
mmol/gcdw/h
Graph
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Reaction
KEGG ID
Flux
Std
Unit
glucose uptake
0.0
0.0
mmol/gcdw/h
fructose uptake
0.0
0.0
mmol/gcdw/h
gluconate uptake
0.0
0.0
mmol/gcdw/h
glycerol uptake
0.0
0.0
mmol/gcdw/h
malate uptake
0.0
0.0
mmol/gcdw/h
pyruvate uptake
8.26
0.12866216482592374
mmol/gcdw/h
glutamate uptake
0.0
0.0
mmol/gcdw/h
succinate uptake
0.0
0.0
mmol/gcdw/h
[c] : g6p f6p (pgi)
R00771 -0.15405595638941327
0.020408448273198133
mmol/gcdw/h
[c] : atp + f6p --> adp + fdp + h (Pfk)
R04779 0.0
0.0
mmol/gcdw/h
[c] : fdp + h2o --> f6p + pi (Fbp)
R00762 0.22302
0.006844492939447122
mmol/gcdw/h
[c] : fdp dhap + g3p (Fba)
R01068 -0.21987574132013588
0.00684449293944731
mmol/gcdw/h
[c] : dhap g3p (Tpi)
R01015 -0.21987574132014853
0.006844492939447293
mmol/gcdw/h
[c] : 13dpg + h + nadph --> g3p + nadp + pi (GapA)
R01061 0.0
0.0
mmol/gcdw/h
[c] : g3p + nad + pi --> 13dpg + h + nadh (GapB)
R01061 0.90034
0.0069562191501662644
mmol/gcdw/h
Pgk;Pgm;Eno
-0.898687460687355
0.00695621915016593
mmol/gcdw/h
[c] : adp + h + pep --> atp + pyr (PykA)
R00200 0.8142304333942195
0.6268196513853994
mmol/gcdw/h
[c] : g6p + nadp --> 6pgl + h + nadph (Zwf)
R02736 0.02746146757416978
0.020405210536213702
mmol/gcdw/h
[c] : 6pgc + nadp co2 + nadph + ru5p-D (Gnd)
R01528 0.02746146757416978
0.020405210536213702
mmol/gcdw/h
[c] : ru5p-D xu5p-D (Rpe)
R01529 -0.06581978493073323
0.020405210536213702
mmol/gcdw/h
[c] : r5p ru5p-D (Rpi)
R01056 0.093281252504903
0.006808545421398495
mmol/gcdw/h
[c] : r5p + xu5p-D g3p + s7p (Tkt1)
R01641 0.0031400653121926372
0.0067577071935572795
mmol/gcdw/h
[c] : e4p + xu5p-D f6p + g3p (Tkt2)
R01067 -0.06895985024292586
0.006808545421398495
mmol/gcdw/h
[c] : g3p + s7p e4p + f6p (Tal)
R01827 0.0031400653121986906
0.006757707193557318
mmol/gcdw/h
[c] : coa + nad + pyr --> accoa + co2 + nadh (Pdh)
R00210 6.049276100556576
0.13161152641970048
mmol/gcdw/h
Cit
3.9104670963526647
0.13761279509899668
mmol/gcdw/h
[c] : icit + nadp akg + co2 + nadph (Icd)
R00267 3.9104670963526367
0.13761279509899643
mmol/gcdw/h
Odh
3.6748880590206148
0.13792363561706342
mmol/gcdw/h
Sdh; [c] : fum + h2o mal-L (Fum)
3.6748880590206165
0.13792363561706308
mmol/gcdw/h
[c] : mal-L + nad h + nadh + oaa (Mdh)
R00342 3.174279025223885
0.41536801697207887
mmol/gcdw/h
[c] : atp + oaa --> adp + co2 + pep (Pck)
R00341 1.8843633347243887
0.6273062377230784
mmol/gcdw/h
ME
0.5006091236683995
0.3929417039732451
mmol/gcdw/h
[c] : atp + hco3 + pyr --> adp + h + oaa + pi (Pyc)
R00344 2.9648208756133374
0.2601410021548416
mmol/gcdw/h
acetate
1.7687891000535294
0.005763314645347794
mmol/gcdw/h
transport, CO2 excretion
13.610098946113386
0.7345454129017465
mmol/gcdw/h
transport, acetate excretion
1.7687891000535028
0.005763314645347937
mmol/gcdw/h
transport, pyruvate excretion
8.98716954183994e-08
2.9988343745347276e-16
mmol/gcdw/h
G6P efflux to biomass
0.12659448881514318
0.00012580584978798986
mmol/gcdw/h
G3P efflux to biomass
0.3899761278041335
0.0005705344116674166
mmol/gcdw/h
P5P efflux to biomass
0.09014118719274702
0.00016342954660143567
mmol/gcdw/h
E4P efflux to biomass
0.07209991555512742
0.00010708146642113484
mmol/gcdw/h
PEP efflux to biomass
0.17144544064281494
0.00011141208975205794
mmol/gcdw/h
PYR efflux to biomass
0.5607424011492793
0.0005969222978612891
mmol/gcdw/h
OAA efflux to biomass
0.3442694697601701
0.0004466146579611241
mmol/gcdw/h
AcCoA efflux to biomass
0.37001990415039215
0.0002596007589774414
mmol/gcdw/h
aKG efflux to biomass
0.2355790373320302
0.0003124754264921515
mmol/gcdw/h
Graph
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