
*** Escherichia Coli Core Metabolism Model ***
***              EMP Pathway
*** source:    http://gcrg.ucsd.edu/Downloads/Flux_Balance_Analysis


require(LIM)
#source('C:/Shared/LIM/LIM/inst/examples/Reactions/newxranges.r')

#liminput <-Read("E_coli.lim")

lim <-Setup("E_coli.lim")
pars<-Ldei(lim)
xr<-Xranges(lim,central=TRUE, full=TRUE)
LP<-Linp(lim)
data.frame(pars=pars$X, t(LP$X),xr[,1:3])
# show position of the range solutions
plot(xr[1,],xr[2,])
# and the central value...
points(xr[1,3],xr[2,3],col="red",pch=16)

# Show that central value is a valid solution
X <- xr[,3]
max(abs(lim$A%*%X-lim$B))
min(lim$G%*%X-lim$H)
# Use this value as initial condition for rda sampling
xs<-Xsample(lim,iter=50000,out=10000,type="cda",test=TRUE,x0=X)  #))
pairs(xs[,1:10],pch=".",cex=2)

# Sample solution space  - takes a while
#print(system.time(
#xs<-Xsample(lim,iter=10000,out=5000,jmp=50,type="mirror",test=TRUE)  #))
xs<-Xsample(lim,iter=5000,type="mirror",test=TRUE)  #))
#xs<-Xsample(lim,iter=5,jmp=100,type="mirror",test=TRUE)  #
pairs(xs[,1:10],pch=".",cex=2)

data.frame(Mean=colMeans(xs), sd=sd(xs))
rr <- NULL
for (i in 1:5000)
{X <- xs[i,]
rr <-max(rr,sum(abs( lim$A%*%X-lim$B)))
}
rr
##############################################


## REACTIONS
!gene:  Reaction                                        enzyme                                              Gene              EC Number
GLK1:  GLC + ATP -> G6P + ADP                    !      Glucokinase                                         glk     2.7.1.2
PGI1:  G6P <-> F6P                               !      Phosphoglucose isomerase                            pgi     5.3.1.9
PFKA:  F6P + ATP -> FDP + ADP                    !      Phosphofructokinase                                 pfkA        2.7.1.11
FBP:   FDP -> F6P + PI                           !      Fructose-1,6-bisphosphatase                         fbp     3.1.3.11
FBA:   FDP <-> T3P1 + T3P2                       !      Fructose-1,6-bisphosphatate aldolase                fba     4.1.2.13
TPIA:  T3P2 <-> T3P1                             !      Triosphosphate Isomerase                            tpiA        5.3.1.1
GAPA:  T3P1 + PI + NAD <->  NADH + 13PDG         !      Glyceraldehyde-3-phosphate dehydrogenase-A complex  gapA        1.2.1.12
PGK:   13PDG + ADP <-> 3PG + ATP                 !      Phosphoglycerate kinase                             pgk     2.7.2.3
GPMA:  3PG <-> 2PG                               !      Phosphoglycerate mutase 1                           gpmA        5.4.2.1
ENO:   2PG <-> PEP                               !      Enolase                                             eno     4.2.1.11
PPSA:  PYR + ATP -> PEP + AMP + PI               !      Phosphoenolpyruvate synthase                        ppsA        2.7.9.2
PYKA:  PEP + ADP -> PYR + ATP                    !      Pyruvate Kinase II                                  pykA        2.7.1.40
!      PYKF: PEP + ADP -> PYR + ATP              !      Pyruvate Kinase I                                   pykF        2.7.1.40
ACEE:  PYR + COA + NAD -> NADH + CO2 + ACCOA     !      Pyruvate dehydrogenase                              lpdA, aceEF     1.2.4.1, 2.3.1.12, 1.8.6.4

!Pentose Phosphate Pathway
ZWF:   G6P + NADP <-> D6PGL + NADPH              !      Glucose 6-phosphate-1-dehydrogenase                 zwf     1.1.1.49
PGL:   D6PGL -> D6PGC                            !      6-Phosphogluconolactonase                           pgl     3.1.1.31
GND:   D6PGC + NADP -> NADPH + CO2 + RL5P        !      6-Phosphogluconate dehydrogenase (decarboxylating)  gnd     1.1.1.44
RPIA:  RL5P <-> R5P                              !      Ribose-5-phosphate isomerase A                      rpiA        5.3.1.6
RPE:   RL5P <-> X5P                              !      Ribulose phosphate 3-epimerase                      rpe     5.1.3.1
TKTA1: R5P + X5P <-> T3P1 + S7P                  !      Transketolase I                                     tktA        2.2.1.1
!  TKTB1: R5P + X5P <-> T3P1 + S7P               !      Transketolase II                                    tktB        2.2.1.1
TKTA2: X5P + E4P <-> F6P + T3P1                  !      Transketolase I                                     tktA        2.2.1.1
!  TKTB2: X5P + E4P <-> F6P + T3P1               !      Transketolase II                                    tktB        2.2.1.1
TALA:  T3P1 + S7P <-> E4P + F6P                  !      Transaldolase A                                     talB        2.2.1.2

!The Tricarboxylic Acid Cycle
GLTA:  ACCOA + OA -> COA + CIT                   !      Citrate synthase                                    gltA        4.1.3.7
ACNA:  CIT <-> ICIT                              !      Aconitase A                                         acnA        4.2.1.3
ICDA:  ICIT + NADP <-> CO2 + NADPH + AKG         !      Isocitrate dehydrogenase                            icdA        1.1.1.42
SUCA:  AKG + NAD + COA -> CO2 + NADH + SUCCOA    !      2-Ketoglutarate dehyrogenase                        sucAB, lpdA     1.2.4.2,2.3.1.61,1.8.1.4
SUCC1: SUCCOA + ADP + PI <-> ATP + COA + SUCC    !      Succinyl-CoA synthetase                             sucCD       6.2.1.5
SDHA1: SUCC + FAD -> FADH + FUM                  !      Succinate dehydrogenase                             sdhABCD     1.3.99.1
FRDA:  FUM + FADH -> SUCC + FAD                  !      Fumurate reductase                                  frdABCD     1.3.99.1
FUMA:  FUM <-> MAL                               !      Fumarase A                                          fumA        4.2.1.2
MDH:   MAL + NAD <-> NADH + OA                   !      Malate dehydrogenase                                mdh     1.1.1.37

!Pyruvate Metabolism
DLD1:  PYR + NADH <-> NAD + LAC                  !      D-Lactate dehydrogenase 1                           dld     1.1.1.28
ADHE2: ACCOA +2*NADH <-> ETH +2*NAD + COA        !      Acetaldehyde dehydrogenase                          adhE        1.2.1.10
PFLA:  PYR + COA -> ACCOA + FOR                  !      Pyruvate formate lyase 1                            pflAB       2.3.1.54
PTA:   ACCOA + PI <-> ACTP + COA                 !      Phosphotransacetylase                               pta     2.3.1.8
ACKA:  ACTP + ADP <-> ATP + AC                   !      Acetate kinase A                                    ackA        2.7.2.1
ACS:   ATP + AC + COA -> AMP + PPI + ACCOA       !      Acetyl-CoA synthetase                               acs     6.2.1.1

!Anaplerotic Reactions
PCKA:  OA + ATP -> PEP + CO2 + ADP               !      Phosphoenolpyruvate carboxykinase                   pckA        4.1.1.49
PPC:   PEP + CO2 -> OA + PI                      !      Phosphoenolpyruvate carboxylase                     ppc     4.1.1.31
MAEB:  MAL + NADP -> CO2 + NADPH + PYR           !      Malic enzyme (NADP)                                 maeB        1.1.1.40
SFCA:  MAL + NAD -> CO2 + NADH + PYR             !      Malic enzyme (NAD)                                  sfcA        1.1.1.38
ACEA:  ICIT -> GLX + SUCC                        !      Isocitrate lyase                                    aceA        4.1.3.1
ACEB:  ACCOA + GLX -> COA + MAL                  !      Malate synthase A                                   aceB        4.1.3.2
PPA:   PPI -> 2*PI                               !      Inorganic pyrophosphatase                           ppa     3.6.1.1
GLPK:  GL + ATP -> GL3P + ADP                    !      Glycerol kinase                                     glpK        2.7.1.30
GPSA1: GL3P + NADP <-> T3P2 + NADPH              !      Glycerol-3-phosphate-dehydrogenase-[NAD(P)+]        gpsA        1.1.1.94
RBSK:  RIB + ATP -> R5P + ADP                    !      Ribokinase                                          rbsK        2.7.1.15

!Respiration                Note: the P/O ratio is set to 1.5 currently
NUOA:  NADH + Q -> NAD + QH2 +3.5*HEXT           !      NADH dehydrogenase I                                nuoABEFGHIJKLMN     1.6.5.3
FDOH:  FOR + Q -> QH2 + CO2 +2*HEXT              !      Formate dehydrogenase-O                             fdoIHG      1.2.2.1
GLPD:  GL3P + Q -> T3P2 + QH2                    !      Glycerol-3-phosphate dehydrogenase (aerobic)        glpD        1.1.99.5
CYOA:  QH2 +0.5*O2 -> Q + 2.5*HEXT               !      Cytochrome oxidase bo3                              cyoABCD, cycBC, cydAB       1.10.2.2,1.9.3.1
SDHA2: FADH + Q <-> FAD + QH2                    !      Succinate dehydrogenase complex                     sdhABCD     1.3.5.1
PNT1A: NADPH + NAD -> NADP + NADH                !      Pyridine nucleotide transhydrogenase                pntAB       1.6.1.1
PNT2A: NADP + NADH +2*HEXT -> NADPH + NAD        !      Pyridine nucleotide transhydrogenase                pntAB       1.6.1.1
ATPA:  ATP <-> ADP + PI +4*HEXT                  !      F0F1-ATPase                                         atpABCDEFGHI        3.6.1.34

!Membrane Transport
GLCUP: GLCxt + HEXT -> GLC                       !      Glucose/galactose transporter                       gluP            Proton symport
GLCPTS:GLCxt + PEP -> G6P + PYR                  !      Glucose                                             ptsG, crr       PTS
GLUP:  GLxt <-> GL                               !      Glycerol                                            glpF            Facilitated Diffusion
RIBUP: RIBxt + ATP <-> RIB + ADP + PI             !      Ribose                                              rbsABCD, xylH   BPD transport
ACUP:  ACxt + HEXT <-> AC                        !      Acetate transport
LACUP: LACxt + HEXT <-> LAC                      !      L-Lactate                                           lldP
FORUP: FORxt <-> FOR                             !      Formate transport                                   focA        Uniport
ETHUP: ETHxt + HEXT <-> ETH                      !      Ethanol transport                                               diffusion
SUCCUP:SUCCxt + HEXT <-> SUCC                    !      Succinate transport                                 dcuAB       Proton Symport
PYRUP: PYRxt + HEXT <-> PYR                      !      Pyruvate transport                                              Proton Symport
PIUP:  PIxt <-> PI                               !      Phosphate transport                                 pitAB       Proton symport
O2TX:  O2xt <-> O2                               !      Oxygen transport                                                Diffusion
CO2TX: CO2xt <-> CO2                             !      Carbon dioxide transport                                        Diffusion

ATPM: ATP -> ADP + PI                            !      ATP drain flux for constant maintanence requirements
ADK:  ATP + AMP-> 2*ADP                          !      ADK


Growth:                                                           &
41.25*ATP +3.54*NAD +18.22*NADPH +0.2*G6P                         &
 +0.07*F6P +0.89*R5P +0.36*E4P +0.12*T3P1                         &
 +1.49*3PG +0.51*PEP +2.83*PYR +3.74*ACCOA  +1.78*OA +1.07*AKG    &
 -> 3.74*COA +41.25* ADP +41.25* PI                               &
 +3.54* NADH +18.22* NADP +1.00* Biomass
 

### END REACTION

## MAXIMISE

maxgrowth: Growth
maxRBSK  : RBSK         ! not very realistic?

## END MAXIMISE

### INEQUALITIES
! Carbon sources...
O2TX  = [0,20]    ! Oxygen input
GLCUP = [0,10]    ! glucose input
GLUP  = [-1000,0] ! glycerol
RIBUP = [-1000,0] ! Ribose uptake   - strange!
SUCCUP= [-1000,0] ! succinate
ACUP  = [-1000,0] ! acetate
LACUP = [-1000,0] ! lactate
PYRUP = [-1000,0] ! pyruvate
! Carbon byproducts
FORup = [-1000,0] ! formate
ETHup = [-1000,0] ! ethanol
CO2TX = [-1000,0] ! CO2
! phosphate
PIUP = [-1000,1000]

SDHA1  <100
FRDA   <100
FORup+ LACUP=[-10,-10]

### END INEQUALITIES
### EQUATIONS

 ATPM = 5.87  ! Non-growth associated ATP drain flux for constant maintenance requirements
### END EQUATIONS

### COMPONENTS
GLC     ! a-D-Glucose
G6P     ! Glucose 6-phosphate
F6P     ! Fructose 6-phosphate
FDP     ! Fructose 1,6-diphosphate
T3P2    ! /DHAP Dihydroxyacetone phosphate
T3P1    ! Glyceraldehyde 3-phosphate
13PDG   ! 1,3-bis-Phosphoglycerate
3PG     ! 3-Phosphoglycerate
2PG     ! 2-Phosphoglycerate
PEP     ! Phosphoenolpyruvate
PYR     ! Pyruvate
ACCOA   ! Acetyl-CoA
CIT     ! Citrate
!  ACO    ! cis-Aconitate
ICIT    ! Isocitrate
AKG     ! a-Ketoglutarate
SUCCOA  ! Succinate CoA
SUCC    ! Succinate
FUM     ! Fumarate
MAL     ! Malate
OA      ! Oxaloacetate
!  ACAL ! Acetaldehyde
ACTP    ! Acetyl-phosphate
ETH     ! Ethanol
AC      ! Acetate
LAC     ! D-Lactate
FOR     ! Formate
D6PGL   ! D-6-Phosphate-glucono-delta-lactone
D6PGC   ! D-6-Phosphate-gluconate
RL5P    ! Ribulose 5-phosphate
X5P     ! Xylulose-5-phosphate
R5P     ! Ribose 5-phosphate
S7P     ! sedo-Heptulose
E4P     ! Erythrose 4-phosphate
RIB     ! Ribose
GLX     ! Glyoxylate
NAD     ! Nicotinamide adenine dinucleotide
NADH    ! Nicotinamide adenine dinucleotide (reduced)
NADP    ! Dihydronicotinamide adenine dinucleotide phosphate
NADPH   ! Dihydronicotinamide adenine dinucleotide phosphate (reduced)
HEXT    ! External Hydrogen Ion (Proton)
Q       ! Ubiquinone

FAD     ! Flavin adenine dinucleotide
FADH    ! Flavin adenine dinucleotide (reduced)
AMP     ! Adenosine monophosphate
ADP     ! Adenosine diphosphate
ATP     ! Adenosine triphosphate
GL3P    ! Glycerol 3-phosphate
CO2     ! Carbon dioxide
PI      ! Inorganic Phosphate
PPI     ! Pyrophosphate


O2      ! Oxygen
COA
GL
QH2     !
### END COMPONENTS

### EXTERNALS

Biomass
GLCxt
GLxt
RIBxt
ACxt
LACxt
FORxt
ETHxt
SUCCxt
PYRxt
PIxt
O2xt
CO2xt

### END EXTERNALS


