Parameters

Processes
CentralMetabolismODE
FBA_to_ODE_est_init_biomass_ratio (dimensionless)
InitialConcentration_Biomass (g/L)
InitialConcentration_G6P (u-mol/gDCW)
InitialConcentration_G6Pxt (mM)
InitialConcentration_GLCxt (mM)
InitialConcentration_LACZ (normalized)
InitialConcentration_LCTSxt (mM)
InitialConcentration_PEP (u-mol/gDCW)
InitialConcentration_PTSG (normalized)
InitialConcentration_PYR (u-mol/gDCW)
InitialConcentration_UHPT (normalized)
InitialPhosphorylation_XP (fraction)
K (u-mol/gDW)
K1 (u-mol/gDW)
k1 (u-mol/gDW/h)
K2 (u-mol/gDW)
k2 (u-mol/gDW/h)
K3 (u-mol/gDW)
k3 (u-mol/gDW/h)
kb (dimensionless)
kd (1/h)
Keiiap (u-mol/gDW)
Kg6p (g/L)
kg6p (1/h)
Kglc (g/L)
kgly (1/h)
KI (u-mol/gDW)
Kieiia (dimensionless)
klac (1/h)
Klac (g/L)
km_pts (1/(u-mol/gDW)/g)
kpdh (1/h)
kpts (1/(u-mol/gDW)/g)
Kpts (dimensionless)
kptsup (1/h)
kpyk (1/(u-mol/gDW)^3/h)
ksyn (dimensionless)
m (dimensionless)
MolecularWeight_Biomass (Da)
MolecularWeight_G6P (Da)
MolecularWeight_G6Pxt (Da)
MolecularWeight_GLCxt (Da)
MolecularWeight_LACZ (Da)
MolecularWeight_LCTSxt (Da)
MolecularWeight_PEP (Da)
MolecularWeight_PTSG (Da)
MolecularWeight_PYR (Da)
MolecularWeight_UHPT (Da)
MolecularWeight_XP (Da)
mw1 (g-substrate/u-mol-substrate)
mw2 (g-substrate/u-mol-substrate)
mw3 (g-substrate/u-mol-substrate)
n (dimensionless)
x0 (u-mol/gDW)
Y (g-TM/u-mol-substrate)
Y1_sim (gDW/u-mol)
Y2_sim (gDW/u-mol)
Y3_sim (gDW/u-mol)
ChromosomeCondensation
smcSepNt (nt) 7130
smcSepProbCenter (nt) 2800
ChromosomeSegregation
gtpCost (molecules) 1
Cytokinesis
rateFilamentBindingMembrane (1/s) 0.7
rateFilamentDissociation (1/s) 0.7
rateFtsZGtpHydrolysis (1/s) 0.15
DNARepair
HR_PolA_ResectionLength (nt) 8
HR_RecA_Spacing (nt) 3
HR_RecU_CleavagePosition (nt) 3
HR_RecU_CleavageSequence WTTS
HR_RuvAB_JunctionMigrationHop (nt) 2.2
NER_PcrA_StepSize (nt) 1
NER_UvrABC_IncisionMargin3 (nt) 4
NER_UvrABC_IncisionMargin5 (nt) 7
RM_EcoD_MethylationPosition (nt) 3
RM_EcoD_RecognitionSequence TTANNNNNNNGTCY
RM_EcoD_RestrictionPosition (nt)
RM_MunI_MethylationPosition (nt) 3
RM_MunI_RecognitionSequence CAATTG
RM_MunI_RestrictionPosition (nt) 1
DNASupercoiling
foldChangeIntercepts (dimensionless) [3.57, 1.07, 0.56]
foldChangeLowerSigmaLimit (dimensionless) -0.08
foldChangeSlopes (dimensionless) [42.8, 1.1, -7.4]
foldChangeUpperSigmaLimit (dimensionless) 0.07
gyraseActivityRate (1/s) 1.2
gyraseATPCost (molecules) 2
gyraseDeltaLK (links) -2
gyraseMeanDwellTime (s) 45
gyraseSigmaLimit (dimensionless) -0.1
gyrLogisiticConst (dimensionless) -100
topoIActivityRate (1/s) 1
topoIATPCost (molecules)
topoIDeltaLK (links) 1
topoILogisiticConst (dimensionless) 100
topoISigmaLimit (dimensionless)
topoIVActivityRate (1/s) 2.5
topoIVATPCost (molecules) 2
topoIVDeltaLK (links) -2
topoIVSigmaLimit (dimensionless)
FtsZPolymerization
activationFwd (1/s) 1.1
activationRev (1/s) 0.01
elongationFwd (1/(M*s)) 5100000
elongationRev (1/s) 2.9
exchangeFwd (1/(M*s)) 10000
exchangeRev (1/(M*s)) 5000
nucleationFwd (1/(M*s)) 4200000
nucleationRev (1/s) 40
GlobalMetabolismRFBA
InitialConcentration_13PDG (u-mol/gDCW)
InitialConcentration_2PG (u-mol/gDCW)
InitialConcentration_3PG (u-mol/gDCW)
InitialConcentration_AC (u-mol/gDCW)
InitialConcentration_ACCOA (u-mol/gDCW)
InitialConcentration_ACTP (u-mol/gDCW)
InitialConcentration_ACxt (mM)
InitialConcentration_ADP (u-mol/gDCW)
InitialConcentration_AKG (u-mol/gDCW)
InitialConcentration_AMP (u-mol/gDCW)
InitialConcentration_ATP (u-mol/gDCW)
InitialConcentration_bDGLAC (u-mol/gDCW)
InitialConcentration_bDGLC (u-mol/gDCW)
InitialConcentration_Biomass (g/L)
InitialConcentration_CIT (u-mol/gDCW)
InitialConcentration_CO2 (u-mol/gDCW)
InitialConcentration_CO2xt (mM)
InitialConcentration_COA (u-mol/gDCW)
InitialConcentration_D6PGC (u-mol/gDCW)
InitialConcentration_D6PGL (u-mol/gDCW)
InitialConcentration_E4P (u-mol/gDCW)
InitialConcentration_ETH (u-mol/gDCW)
InitialConcentration_ETHxt (mM)
InitialConcentration_F6P (u-mol/gDCW)
InitialConcentration_FAD (u-mol/gDCW)
InitialConcentration_FADH (u-mol/gDCW)
InitialConcentration_FDP (u-mol/gDCW)
InitialConcentration_FOR (u-mol/gDCW)
InitialConcentration_FORxt (mM)
InitialConcentration_FUM (u-mol/gDCW)
InitialConcentration_G1P (u-mol/gDCW)
InitialConcentration_G6P (u-mol/gDCW)
InitialConcentration_G6Pxt (mM)
InitialConcentration_GAL1P (u-mol/gDCW)
InitialConcentration_GL (u-mol/gDCW)
InitialConcentration_GL3P (u-mol/gDCW)
InitialConcentration_GLAC (u-mol/gDCW)
InitialConcentration_GLC (u-mol/gDCW)
InitialConcentration_GLCxt (mM)
InitialConcentration_GLX (u-mol/gDCW)
InitialConcentration_GLxt (mM)
InitialConcentration_HEXT (u-mol/gDCW)
InitialConcentration_ICIT (u-mol/gDCW)
InitialConcentration_LAC (u-mol/gDCW)
InitialConcentration_LACxt (mM)
InitialConcentration_LCTS (u-mol/gDCW)
InitialConcentration_LCTSxt (mM)
InitialConcentration_MAL (u-mol/gDCW)
InitialConcentration_NAD (u-mol/gDCW)
InitialConcentration_NADH (u-mol/gDCW)
InitialConcentration_NADP (u-mol/gDCW)
InitialConcentration_NADPH (u-mol/gDCW)
InitialConcentration_O2 (u-mol/gDCW)
InitialConcentration_O2xt (mM)
InitialConcentration_OA (u-mol/gDCW)
InitialConcentration_PEP (u-mol/gDCW)
InitialConcentration_PI (u-mol/gDCW)
InitialConcentration_PIxt (mM)
InitialConcentration_PPI (u-mol/gDCW)
InitialConcentration_PYR (u-mol/gDCW)
InitialConcentration_PYRxt (mM)
InitialConcentration_Q (u-mol/gDCW)
InitialConcentration_QH2 (u-mol/gDCW)
InitialConcentration_R5P (u-mol/gDCW)
InitialConcentration_RIB (u-mol/gDCW)
InitialConcentration_RIBxt (mM)
InitialConcentration_RL5P (u-mol/gDCW)
InitialConcentration_S7P (u-mol/gDCW)
InitialConcentration_SUCC (u-mol/gDCW)
InitialConcentration_SUCCOA (u-mol/gDCW)
InitialConcentration_SUCCxt (mM)
InitialConcentration_T3P1 (u-mol/gDCW)
InitialConcentration_T3P2 (u-mol/gDCW)
InitialConcentration_UDPG (u-mol/gDCW)
InitialConcentration_UDPGAL (u-mol/gDCW)
InitialConcentration_UTP (u-mol/gDCW)
InitialConcentration_X5P (u-mol/gDCW)
Metabolism
exchangeRateUpperBound_carbon (mmol/gDCW/h) 12
exchangeRateUpperBound_noncarbon (mmol/gDCW/h) 20
growthAssociatedMaintenance (mmol ATP/gDCW) 59.81
macromoleculeStateInitializationGrowthFactor (dimensionless) 1
nonGrowthAssociatedMaintenance (mmol ATP/gDCW) 8.39
ProteinDecay
ftsHProteaseEnergyCost (ATP/cleavage) 8.3
ftsHProteaseFragmentLength (aa) 15
ftsHProteaseSpecificRate (1/s) 3
lonProteaseEnergyCost (ATP/cleavage) 6
lonProteaseFragmentLength (aa) 20
lonProteaseSpecificRate (1/s) 1.667
oligoendopeptidaseFSpecificRate (1/s) 27.474
proteinMisfoldingRate (1/s) 1e-06
ProteinProcessingI
deformylaseSpecificRate (1/s) 38
methionineAminoPeptidaseSpecificRate (1/s) 6
ProteinProcessingII
lipoproteinDiacylglycerylTransferaseSpecificRate (1/s) 0.0165
lipoproteinSignalPeptidaseSpecificRate (1/s) 11
ProteinTranslocation
preproteinTranslocase_aaTranslocatedPerATP (aa/ATP) 35
SRP_GTPUsedPerMonomer (GTP/monomer) 2
translocaseSpecificRate (aa/s) 2.71e+12
Replication
dnaPolymeraseElongationRate (nt/s) 100
laggingBackupClampReloadingLength (nt) 750
ligaseRate (1/s) 0.04
okazakiFragmentMeanLength (nt) 1500
primerLength (nt) 11
rnaPolymeraseCollisionMeanDwellTime (s) 1.7
ssbComplexSpacing (nt) 30
ssbDissociationRate (1/s) 0.3
startingOkazakiLoopLength (nt) 50
ReplicationInitiation
kb1ADP (1/(nM*h)) 2.5
kb1ATP (1/(nM*h)) 25
kb2ADP (1/(nM*h)) 0.61
kb2ATP (1/(nM*h)) 0.61
kd1ADP (1/h) 20
kd1ATP (1/h) 20
k_inact (1/g) 4.24e+14
k_Regen (1/h) 125
K_Regen_P4 (g/L) 0.018
siteCooperativity (dimensionless) 170
stateCooperativity (dimensionless)
RNADecay
peptidylTRNAHydrolaseSpecificRate (1/s) 0.7
ribonucleaseRFragmentLength (nt) 5
RNAProcessing
enzymeEnergyCost_DeaD (ATP/cleavage) 2.37
enzymeEnergyCost_RsgA (GTP/cleavage) 1
enzymeSpecificRate_DeaD (1/s) 1.48
enzymeSpecificRate_RNAseIII (1/s) 7.7
enzymeSpecificRate_RNAseJ (1/s) 0.37
enzymeSpecificRate_RNAseP (1/s) 6
enzymeSpecificRate_RsgA (1/s) 0.2917
Transcription
rnaPolymeraseElongationRate (nt/s) 50
Translation
ribosomeElongationRate (aa/s) 16
tmRNABindingProbability (dimensionless) 1e-05
States
Chromosome
equilibriumSuperhelicalDensity (dimensionless) -0.06
relaxedBasesPerTurn (links/nt) 10.4999218193
supercoiledSuperhelicalDensityTolerance (dimensionless) 0.1
FtsZRing
numFtsZSubunitsPerFilament (subunits/filament) 9
numFtsZSubunitsPerNm (subunits/nm) 0.23
Geometry
density (g/L) 1100
Mass
cellInitialDryWeight (g) 3.93e-15
cellInitialMassVariation (dimensionless) 0.05
dryWeightFractionCarbohydrate (fraction) 0.00516418150588
dryWeightFractionDNA (fraction) 0.1688
dryWeightFractionIon (fraction) 0.00980392156863
dryWeightFractionLipid (fraction) 0.0568059965647
dryWeightFractionNucleotide (fraction) 0.01833748
dryWeightFractionPolyamine (fraction) 0.0132352941176
dryWeightFractionProtein (fraction) 0.619701780706
dryWeightFractionRNA (fraction) 0.0929552671059
dryWeightFractionVitamin (fraction) 0.0151960784314
fractionWetWeight (fraction) 0.7
initialBiomassConcentration (g/L) 0.003
initialFractionAAsInMonomers (fraction) 0.99
initialFractionNTPsInRNAs (fraction) 1
timeAveragedCellWeight (dimensionless) 1.4427
MetabolicReaction
initialGrowthFilterWidth (dimensionless) 0.25
meanInitialGrowthRate (cells/s) 2.1393e-05
Metabolite
meanNDPConcentration (mM) 0.5
meanNMPConcentration (mM) 0.2
meanNTPConcentration (mM) 5
ProteinComplex
minimumAverageExpression (molecules) 12
ProteinMonomer
macromoleculeStateInitializationVariation (dimensionless) 2.9
minimumAverageExpression (molecules) 12
Rna
geneExpressionRobustness (dimensionless) 1
minTRnaCnt (molecules) 7
weightFractionMRNA (fraction) 0.2
weightFractionRRNA16S (fraction) 0.166481
weightFractionRRNA23S (fraction) 0.334408
weightFractionRRNA5S (fraction) 0.01311
weightFractionSRNA (fraction) 0.024
weightFractionTRNA (fraction) 0.262
RNAPolymerase
stateExpectations (%) [0.86, 0.01, 0.12, 0.01]
Time
cellCycleLength (s) 32400
cytokinesisDuration (s) 3869
replicationDuration (s) 15571
replicationInitiationDuration (s) 12960