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
Full text article
Chubukov_2013.pdf
Project name
not specified
Temperature (°C)
37.0
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
Sampling method:
Sampling method: Two samples for intracellular metabolite quantification were taken within 5 min of each other from the shake flask cultures during exponential growth at an OD600 between 0.8 and 1.2.
Quenching procedure:
—
Extraction technique:
hot ethanol
Sample analyzing method:
HPLC-MS
Methods description - Notes
In all, 2 ml of culture was vacuum filtered on a 0.45‐μm pore size nitrocellulose filter (Millipore) and immediately washed with two volumes of fresh M9 medium containing the respective carbon source and adjusted to the pH of the culture at the time of sampling. Sampling was
...
performed in a room kept at 37°C. After washing, the filter was directly transferred for extraction into 4 ml of 60% (v/v) ethanol/water and kept at 78°C for 2 min. The metabolite extract was separated from cell debris and nitrocellulose by centrifugation at 14 000 g at 4°C for 10 min. The supernatants were dried at 0.12 mbar to complete dryness in a speed vac set‐up (Christ, Osterode am Harz, Germany). Dry metabolite extracts were stored at −80°C until analysis.
Metabolite concentrations were determined by using an ion‐pairing ultrahigh performance liquid chromatography‐tandem mass spectrometry method [1]. Dry metabolite extracts were resuspended in 100 μl, 10 μl of which was injected on a Waters Acquity UPLC with a Waters Acquity T3 end‐capped reverse phase column (150 × 2.1 mm × 1.8 μm; Waters Corporation, Milford, MA, USA). Metabolites were detected on a tandem mass spectrometer (Thermo TSQ Quantum Triple Quadropole with Electron‐Spray Ionization; Thermo Scientific, Waltham, MA, USA). --------------------------------------------References---------------------------------------
[1] Büscher JM, Moco S, Sauer U, Zamboni N (2010). Anal Chem 82: 4403–4412. http://doi.org/dsp5gb
Read more
Data file
KIMODATAID88_v3.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
88
Entered by
Administrator KiMoSys
Date Added
2015-05-05
Version
3
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
metabolites at steady-state
Data units
mMol/L cell volume
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
Sampling method: Two samples for intracellular metabolite quantification were taken within 5 min of each other from the shake flask cultures during exponential growth at an OD600 between 0.8 and 1.2.
Quenching procedure: —
Extraction technique: hot ethanol
Sample analyzing method: HPLC-MS
Methods description - Notes
In all, 2 ml of culture was vacuum filtered on a 0.45‐μm pore size nitrocellulose filter (Millipore) and immediately washed with two volumes of fresh M9 medium containing the respective carbon source and adjusted to the pH of the culture at the time of sampling. Sampling was performed in a room kept at 37°C. After washing, the filter was directly transferred for extraction into 4 ml of 60% (v/v) ethanol/water and kept at 78°C for 2 min. The metabolite extract was separated from cell debris and nitrocellulose by centrifugation at 14 000 g at 4°C for 10 min. The supernatants were dried at 0.12 mbar to complete dryness in a speed vac set‐up (Christ, Osterode am Harz, Germany). Dry metabolite extracts were stored at −80°C until analysis.
Metabolite concentrations were determined by using an ion‐pairing ultrahigh performance liquid chromatography‐tandem mass spectrometry method [1]. Dry metabolite extracts were resuspended in 100 μl, 10 μl of which was injected on a Waters Acquity UPLC with a Waters Acquity T3 end‐capped reverse phase column (150 × 2.1 mm × 1.8 μm; Waters Corporation, Milford, MA, USA). Metabolites were detected on a tandem mass spectrometer (Thermo TSQ Quantum Triple Quadropole with Electron‐Spray Ionization; Thermo Scientific, Waltham, MA, USA). --------------------------------------------References--------------------------------------- [1] Büscher JM, Moco S, Sauer U, Zamboni N (2010). Anal Chem 82: 4403–4412
Data URL
http://kimosys.org/repository/88
Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 24.91518850544861
1.3581877679937104
mM
asparagine
ChEBI:22653 0.2504073938435929
0.02099381478957779
mM
glutamine
ChEBI:28300 15.05742118928206
0.3367698891560398
mM
disaccharides
ChEBI:36233 0.20534978597509584
0.049033580967262555
mM
tyrosine
ChEBI:18186 0.13297267294883108
0.0012286971847166456
mM
adenine
ChEBI:16708 0.009127165443714695
0.0020116981317648834
mM
phenylalanine
ChEBI:28044 0.07398987922951049
0.005864880237886019
mM
aspartate
ChEBI:29990 4.827604190189284
0.24928662762535359
mM
glutamate
ChEBI:29986 228.50502591097228
8.728312570341686
mM
glucose-6-phosphate (G6P)
ChEBI:17665 1.272903816052215
0.034951183683848086
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.14298942265782988
0.012178794865617362
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 0.8499747783795233
0.0019284828446252122
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 2.6310472714915996
0.10530751253272919
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.28993877255581785
0.04176896758048419
mM
dihydroxyacetone-phosphate (DHAP)
1.7632578988482044
0.01608057916269323
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.475197535964314
0.05347737489286811
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.13281786937859102
0.004433315970108945
mM
pantothenate
ChEBI:16454 0.01719004664658521
0.007558117807861199
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.10736321735707773
0.0050629842753159154
mM
succinate
ChEBI:30779 2.0723770105501806
0.393466070543097
mM
malate
ChEBI:6650 31.047181582189783
20.67430458105456
mM
alpha-ketoglutarate
1.301971772650298
0.014324010125531195
mM
fumarate
ChEBI:37154 0.42195304118156474
0.08668561442402203
mM
phospho-glycerate (2PG+3PG)
3.2788015594700024
0.12536283000153903
mM
6-phospho-gluconate
ChEBI:16863 2.320320661739981
0.0002943984587049364
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.22900217002131867
0.010916208822261783
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.634432188785067
0.10741665972071057
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 0.47592822943377905
0.004604957138314325
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 1.3773363509573455
0.03836724378072798
mM
citrate
ChEBI:35804 5.203695513297346
0.06487345690637758
mM
isocitrate
ChEBI:30887 0.09677491001478378
0.007757958389602471
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.7723388075704656
0.06358330591089245
mM
adenosine triphosphate (ATP)
CHEBI:15422 2.572888375070979
0.5561235824025896
mM
bis-phosho-glycerate (BPG)
0.007723738798237255
0.00526478881721109
mM
Graph
Loading...
Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 29.823059949592114
11.584216872746689
mM
asparagine
ChEBI:22653 0.4347033171245732
0.005110825151688647
mM
glutamine
ChEBI:28300 15.62133242207966
0.11492256685956548
mM
disaccharides
ChEBI:36233 0.36327956012653595
0.07331748539502536
mM
tyrosine
ChEBI:18186 0.09404036360502083
0.007628581698555452
mM
adenine
ChEBI:16708 0.006606075623418004
0.001202645605471305
mM
phenylalanine
ChEBI:28044 0.07433492641746636
0.0027553870367016883
mM
aspartate
ChEBI:29990 5.335024604703328
0.023027140335032836
mM
glutamate
ChEBI:29986 236.82808079605337
7.903765410504647
mM
glucose-6-phosphate (G6P)
ChEBI:17665 0.8234174871718796
0.009424973583497698
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.14885366369858233
0.00939244240155182
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 0.9361821957315277
0.09217642117296188
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 2.7605493207137233
0.13592491905441562
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.38616892384448376
0.06214732299873732
mM
dihydroxyacetone-phosphate (DHAP)
2.247378463618791
0.0794379783760839
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.3573998069822673
0.12457628271309086
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.11277963833966714
0.020797997190007654
mM
pantothenate
ChEBI:16454 0.036710896675679804
0.0023029433876985417
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.14275873490290614
0.013138868822389335
mM
succinate
ChEBI:30779 1.9173083478275346
0.09865593987459176
mM
malate
ChEBI:6650 13.321421258288275
6.106559898748657
mM
alpha-ketoglutarate
0.8559275686758658
0.023357304946402424
mM
fumarate
ChEBI:37154 0.3723775222145719
0.041961775111755945
mM
phospho-glycerate (2PG+3PG)
5.94864389029794
0.021710154915178137
mM
6-phospho-gluconate
ChEBI:16863 1.1197561690164362
0.1405428310333381
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.21446206672469426
0.02006614146282701
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.5670468047287311
0.06417330476540833
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 1.0517888258971464
0.0877666209439042
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 1.4435493818102643
0.11381527878504583
mM
citrate
ChEBI:35804 5.468300564802842
0.01818295880115306
mM
isocitrate
ChEBI:30887 0.0854757943341845
0.001782314344128108
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.7307154620440399
0.005518013870973337
mM
adenosine triphosphate (ATP)
CHEBI:15422 2.216887809943693
0.2041277477506589
mM
bis-phosho-glycerate (BPG)
0.004168878183983961
0.0017710116151457814
mM
Graph
Loading...
Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 8.051595589088876
2.7179479084528975
mM
asparagine
ChEBI:22653 0.09597212784866146
0.0056936937925346
mM
glutamine
ChEBI:28300 21.74619209383076
2.1264371768964843
mM
disaccharides
ChEBI:36233 0.3965365069632501
0.07555813656570348
mM
tyrosine
ChEBI:18186 0.16071466670054724
0.0021590942672528313
mM
adenine
ChEBI:16708 0.00866100884771374
0.0006024010501502032
mM
phenylalanine
ChEBI:28044 0.08712462771073211
0.0005438994196494129
mM
aspartate
ChEBI:29990 4.862269085468398
0.17434361402680976
mM
glutamate
ChEBI:29986 251.52533014530178
13.494406214485934
mM
glucose-6-phosphate (G6P)
ChEBI:17665 0.7710842094854156
0.08660191147204882
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.1446447417669544
0.002882664915892161
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 0.9226872273187938
0.023685383029122986
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 2.652204050404295
0.00857900696277647
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.23201882540557203
0.02234964086528554
mM
dihydroxyacetone-phosphate (DHAP)
2.038664006779687
0.13024053063366003
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.636217814975752
0.06094787081193631
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.08877714116910557
0.028748000621446345
mM
pantothenate
ChEBI:16454 0.019440334602124718
0.0055309631039480245
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.13854883680718477
0.03200822987298527
mM
succinate
ChEBI:30779 1.548789612586523
0.05059302138402055
mM
malate
ChEBI:6650 2.5650190375858863
1.271944303102345
mM
alpha-ketoglutarate
0.7850595875220594
0.06150586228113053
mM
fumarate
ChEBI:37154 0.2953150063496357
0.005101909766162621
mM
phospho-glycerate (2PG+3PG)
3.6277534603497257
0.04880799290628812
mM
6-phospho-gluconate
ChEBI:16863 9.184286751581553
0.23951409290446168
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.1686974456635576
0.00598335474124069
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.506267062240216
0.05518602888414992
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 0.3398257942935527
0.023327807538070566
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 1.1348498366692743
0.10649063259239255
mM
citrate
ChEBI:35804 4.155049940446716
0.12459814990064588
mM
isocitrate
ChEBI:30887 0.12183407461121365
0.002451252805392677
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.6882963701956211
0.03251749689465705
mM
adenosine triphosphate (ATP)
CHEBI:15422 3.1795147634103493
0.5410699521810585
mM
bis-phosho-glycerate (BPG)
0.003394972551328993
0.0017788452952311345
mM
Graph
Loading...
Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 6.121961338263404
0.9630766058152425
mM
asparagine
ChEBI:22653 0.1622295564726894
0.02847678173967841
mM
glutamine
ChEBI:28300 43.24288089189058
2.49787136467182
mM
disaccharides
ChEBI:36233 0.12081005578323031
0.02675549298532797
mM
tyrosine
ChEBI:18186 0.12642355257342147
0.010927493548484123
mM
adenine
ChEBI:16708 0.010479751015850846
0.0015536035737137213
mM
phenylalanine
ChEBI:28044 0.06526575774837926
0.00035682898596792884
mM
aspartate
ChEBI:29990 24.505762403928756
0.34188737022794946
mM
glutamate
ChEBI:29986 n/a
0.0
mM
glucose-6-phosphate (G6P)
ChEBI:17665 0.9414173680526843
0.07453451141852935
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.11842114034321145
0.010348716548668493
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 0.7409774921501787
0.010002405196489761
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 2.3467828548480165
0.07452335033528645
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.28763017830158444
0.11247727091357843
mM
dihydroxyacetone-phosphate (DHAP)
0.5376961104037102
0.011742345960310319
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.45031007405309287
0.1135974090139247
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.12115224820626583
0.008086524343029013
mM
pantothenate
ChEBI:16454 0.030643532163301117
0.006296963597522109
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.17205076948166143
0.012388857158494207
mM
succinate
ChEBI:30779 0.0
0.0
mM
malate
ChEBI:6650 5.678383828655971
1.2979895598932853
mM
alpha-ketoglutarate
1.475774117660614
0.17022772370951977
mM
fumarate
ChEBI:37154 0.6602496256577651
0.12376728939171966
mM
phospho-glycerate (2PG+3PG)
2.2082627237101176
0.04143846562093456
mM
6-phospho-gluconate
ChEBI:16863 0.7434075165962362
0.02792173911135687
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.1619419723297128
0.0015992253091198505
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.4205138221120369
0.02601979738329685
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 2.201673192455539
0.06267192242356301
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 0.17945103393005823
0.0020599200569193094
mM
citrate
ChEBI:35804 5.407264272683581
0.2517143859329334
mM
isocitrate
ChEBI:30887 0.10925710747707931
0.00640594413527245
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.7659638433489182
0.0774729160397532
mM
adenosine triphosphate (ATP)
CHEBI:15422 3.2058273062415763
0.31632548256259274
mM
bis-phosho-glycerate (BPG)
0.0037135164457449284
0.0023851759246914027
mM
Graph
Loading...
Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 22.67337913721712
10.618048855244702
mM
asparagine
ChEBI:22653 0.08549450265476047
0.014917515190559956
mM
glutamine
ChEBI:28300 13.93854998673934
0.5969375675140398
mM
disaccharides
ChEBI:36233 0.17258960693433043
0.06941428211540726
mM
tyrosine
ChEBI:18186 0.08844867427802583
0.009107481717686959
mM
adenine
ChEBI:16708 0.007586954348827328
5.9654489964236414e-05
mM
phenylalanine
ChEBI:28044 0.06288010650554508
0.008440460796655919
mM
aspartate
ChEBI:29990 5.953863628505462
0.36050099373362343
mM
glutamate
ChEBI:29986 230.2585850395946
13.504029637629642
mM
glucose-6-phosphate (G6P)
ChEBI:17665 0.3618973353403583
0.035499977929463106
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.15708878157673117
0.015499598677073567
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 18.364691342801066
0.7293058049795338
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 2.949426418613524
0.1920154718267253
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.7696307199830774
0.38110229150282593
mM
dihydroxyacetone-phosphate (DHAP)
2.6908995048308038
0.22643240845093215
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.423167290548464
0.051998843685286705
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.11052784149397595
0.023361363820857448
mM
pantothenate
ChEBI:16454 0.06499626290445082
0.04486079116748169
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.1585030902120778
0.030346627901696302
mM
succinate
ChEBI:30779 1.7080929876288078
0.27157444179338375
mM
malate
ChEBI:6650 4.941558249279139
2.9875515095073033
mM
alpha-ketoglutarate
0.9480738296684343
0.1362228121310159
mM
fumarate
ChEBI:37154 1.1170804317307232
0.74628902558907
mM
phospho-glycerate (2PG+3PG)
3.0613868842371144
0.27541498413981613
mM
6-phospho-gluconate
ChEBI:16863 0.7989452118433704
0.03146920859334934
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.19995472507278145
0.015799818671711055
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.7278108873530793
0.029816918895172018
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 0.4033635802768732
0.0055055027783200705
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 0.4632091808868316
0.013665978668437218
mM
citrate
ChEBI:35804 4.5445269352617705
0.06667149786694537
mM
isocitrate
ChEBI:30887 0.08671280482769037
0.00320532667844093
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.73047968039749
0.004553645332370293
mM
adenosine triphosphate (ATP)
CHEBI:15422 2.599364668716743
0.07250833140612145
mM
bis-phosho-glycerate (BPG)
0.0029821995411085604
0.0002882807030726313
mM
Graph
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Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 47.67451554520204
0.4708817629868953
mM
asparagine
ChEBI:22653 0.05186870774283531
0.013812595518038127
mM
glutamine
ChEBI:28300 33.17882781517628
3.1882597726656545
mM
disaccharides
ChEBI:36233 0.08180229817431994
0.010895527484450003
mM
tyrosine
ChEBI:18186 0.1035718058228493
0.0002678359657001944
mM
adenine
ChEBI:16708 0.008390102146145035
0.0013423660994658338
mM
phenylalanine
ChEBI:28044 0.07024002984834599
0.0014458958331425575
mM
aspartate
ChEBI:29990 16.53819154065137
0.6697678797363231
mM
glutamate
ChEBI:29986 268.6601588061497
19.08899375895851
mM
glucose-6-phosphate (G6P)
ChEBI:17665 0.7971096922785729
0.10784942508067785
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.14955388273618225
0.054377441320487094
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 0.6469002086998634
0.03151398873076977
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 2.7506269316917873
0.3374203817298176
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.07464762584495394
0.007281845592613488
mM
dihydroxyacetone-phosphate (DHAP)
0.9072612610144314
0.011650649319738693
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.2639204062831334
0.07687255565750804
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.058468790762110416
0.004244602398935961
mM
pantothenate
ChEBI:16454 0.05174370329021749
0.014583671687345697
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.12089132272306684
0.0096834823868608
mM
succinate
ChEBI:30779 40.82479505869556
2.085877001702162
mM
malate
ChEBI:6650 n/a
0.0
mM
alpha-ketoglutarate
2.938832396700759
0.3886565449951358
mM
fumarate
ChEBI:37154 9.888668188990025
1.2483886812421359
mM
phospho-glycerate (2PG+3PG)
2.0510797717399134
0.04287834765749321
mM
6-phospho-gluconate
ChEBI:16863 0.3993151444104067
0.0005363360919177218
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.21713809851391042
0.005418603480631015
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.4616903716938869
0.007234587609272258
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 2.7140904862220463
0.13187663770655678
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 0.18896430823693894
0.003475604427171805
mM
citrate
ChEBI:35804 4.8006627650725555
0.045483985774327884
mM
isocitrate
ChEBI:30887 0.12966437240173745
0.008191095396829162
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.6524899228188257
0.07221239665411777
mM
adenosine triphosphate (ATP)
CHEBI:15422 2.166924763790286
0.2551991406466908
mM
bis-phosho-glycerate (BPG)
0.0019645168276370036
0.0002321162468296716
mM
Graph
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Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 58.22231934835713
13.679839621962305
mM
asparagine
ChEBI:22653 0.2446824697302957
0.028411283410047533
mM
glutamine
ChEBI:28300 16.424229237539237
1.2159086989068726
mM
disaccharides
ChEBI:36233 0.07019778640496185
1.869666879450449e-05
mM
tyrosine
ChEBI:18186 0.09863439260341755
0.0018238239425087538
mM
adenine
ChEBI:16708 0.006724672003590983
0.00048687912159909013
mM
phenylalanine
ChEBI:28044 0.06304781336287581
0.010050232365537703
mM
aspartate
ChEBI:29990 27.09538232702637
3.47389410638719
mM
glutamate
ChEBI:29986 235.65948264347657
18.860742691333144
mM
glucose-6-phosphate (G6P)
ChEBI:17665 0.8900988749442253
0.01427165531470237
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.10624759908666476
0.014120962869868976
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 0.6988215073504676
0.0008394825434558384
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 1.8154237851859796
0.07038023195655585
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.16097361363381502
0.010703357529533317
mM
dihydroxyacetone-phosphate (DHAP)
2.110679743881333
0.18676600325817028
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.9963410232028111
0.016423538565177198
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.11071559471277914
0.041229665442300785
mM
pantothenate
ChEBI:16454 0.031017816560846866
0.010093196763305801
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.14329801767360145
0.03552788109949888
mM
succinate
ChEBI:30779 32.838932031335844
4.459908649746776
mM
malate
ChEBI:6650 n/a
0.0
mM
alpha-ketoglutarate
2.608871832366205
0.14279747810999477
mM
fumarate
ChEBI:37154 10.19773306098729
1.675825429699385
mM
phospho-glycerate (2PG+3PG)
2.7711751892580883
0.15350412608105968
mM
6-phospho-gluconate
ChEBI:16863 1.6690839111361828
0.1345098624585659
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.22532483068441936
0.014345015041683201
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.4611044055661738
0.02437605872284021
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 0.5615177802300942
0.04484043293293605
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 1.122506896211707
0.132756388871358
mM
citrate
ChEBI:35804 4.041119907495907
0.04927463131337251
mM
isocitrate
ChEBI:30887 0.10141167284707485
0.002232596299715811
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.7216906374033267
0.00956692142832044
mM
adenosine triphosphate (ATP)
CHEBI:15422 2.5004086512226866
0.07892549953087014
mM
bis-phosho-glycerate (BPG)
0.002527878622697387
0.0005937590962705498
mM
Graph
Loading...
Compound
ChEBI ID
Initial Concentration
Std
Unit
arginine
ChEBI:29016 32.18386664904875
0.27766261775260226
mM
asparagine
ChEBI:22653 0.20891305462002507
0.05115081609350562
mM
glutamine
ChEBI:28300 54.706518566393974
0.7180160621870684
mM
disaccharides
ChEBI:36233 0.13673441528187097
0.027728302713119032
mM
tyrosine
ChEBI:18186 0.2837545002143578
0.007370619287242336
mM
adenine
ChEBI:16708 0.013728789582496062
0.00042228479445183785
mM
phenylalanine
ChEBI:28044 0.10263863170086898
0.014211441156789358
mM
aspartate
ChEBI:29990 4.298333585882476
0.008822960545349812
mM
glutamate
ChEBI:29986 305.1188573069559
0.040542225266875676
mM
glucose-6-phosphate (G6P)
ChEBI:17665 0.794686495318283
0.06786183389560174
mM
ribose-5-phosphate (R5P)
ChEBI:78679 0.08737286047372327
0.0011613365506615014
mM
glycerol-3-phosphate (G3P)
ChEBI:15978 0.508290347096837
0.021796297958706357
mM
ribulose-5-phosphate (Ru5P)
ChEBI:29027 1.9749707048650729
0.009212870857723487
mM
xylulose-5-phosphate (Xu5P)
ChEBI:27354 0.054316746374157926
0.020178029440741926
mM
dihydroxyacetone-phosphate (DHAP)
0.9607491244450139
0.13907281108275993
mM
ribose-1-phosphate (R1P)
ChEBI:35425 0.11135790131781656
0.02390695814831409
mM
guanosine monophosphate (GMP)
ChEBI:74948 0.0838511017685529
0.02408767873620435
mM
pantothenate
ChEBI:16454 0.016790261214375983
0.0015987644300768638
mM
adenosine monophosphate (AMP)
ChEBI:16027 0.09493790295085416
0.023186490137754534
mM
succinate
ChEBI:30779 2.7842230382411772
0.07769104554326667
mM
malate
ChEBI:6650 0.9223817450493517
0.009997532706878254
mM
alpha-ketoglutarate
2.1552138445559015
0.1772812628451037
mM
fumarate
ChEBI:37154 1.9019516027736088
0.6377155939252854
mM
phospho-glycerate (2PG+3PG)
1.037900076879673
0.010554014759781016
mM
6-phospho-gluconate
ChEBI:16863 0.05322710876930267
0.01909583970676887
mM
guanosine diphosphate (GDP)
ChEBI:17552 0.16493736622691677
0.034416570938798074
mM
adenosine diphosphate (ADP)
CHEBI:16761 0.44227130666347253
0.017573851386696537
mM
phosphoenolpyruvate (PEP)
ChEBI:44897 0.7725099803636727
0.024519428786890063
mM
fructose-bis-phosphate (FBP)
ChEBI:40595 0.25344694384884575
0.004380977651108717
mM
citrate
ChEBI:35804 4.918558037649488
0.06449272927503147
mM
isocitrate
ChEBI:30887 0.1293042167338264
0.001377974227113804
mM
guanosine triphosphate (GTP)
ChEBI:15996 0.7205174583320642
0.021476818161530797
mM
adenosine triphosphate (ATP)
CHEBI:15422 3.637998816170775
0.28344494701435496
mM
bis-phosho-glycerate (BPG)
0.0026021745701233024
0.0011600739723496567
mM
Graph
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