Docstoc

File S3 - PLANT PHYSIOLOGY®

Document Sample
File S3 - PLANT PHYSIOLOGY® Powered By Docstoc
					File S3. Complete metabolic model (13C-FLUX network definition) used for fitting

PROJECT
           NAME        VERSION       FORMAT   DATE      COMMENT
           AtMFA                 1                      //Model used for parameter fitting

NETWORK
                   E                        PRODUCT_2
           FLUX_NAME DUCT_1 EDUCT_2 PRODUCT_1

//glucose uptake

           upt         Glc1                   Glc6P                 //glucose uptake
                       #ABCDEF                #ABCDEF

//CO2 output

           CO2         intCO2                 extCO2                //CO2 output
                       #A                     #A

//methyl THF output

           metTHFsinkMetTHF                   sinkMetTHF            //methyl THF output
                     #A                       #A

// cytosolic hexose catabolism

           chex1       Glc6P                  Fru6P                 //cytosolic phosphoglucose isomerase
                       #ABCDEF                #ABCDEF

           chex2       Fru6P                  GA3P      GA3P        //cytosolic phosphofructokinase, cytosolic aldolase and
                       #ABCDEF                #CBA      #DEF

           chex3       PEP                    cPYR                  //cytosolic pyruvate kinase
                       #ABC                   #ABC

//cytosolic plastid exchange

           cpex        Glc6P                  pHexP                 //plastidic hexose phosphate uptake
                       #ABCDEF                #ABCDEF

//plastidic hexose catabolism

           phex1       pHexP                  GA3P      GA3P        //plastidic aldolase
                       #ABCDEF                #CBA      #DEF

           phex2       PEP                    pPYR                  //plastidic pyruvate production
                       #ABC                   #ABC
//cytosolic & plastidic hexose catabolism

            cphex          GA3P              PEP                  //glyceraldehyde 3-phosphate dehydrogenase, phospho
                           #ABC              #ABC

//cell wall biosynthesis

            hcellwall      Glc6P             hcellwall            //hexose cell wall component synthesis
                           #ABCDEF           #ABCDEF

                       hcellwall
            hcellwallOUT                     hcellwallOUT         //hexose cell wall component output
                       #ABCDEF               #ABCDEF

            pcellwall      Glc6P             pcellwall   intCO2   //pentose cell wall component synthesis
                           #ABCDEF           #ABCDE      #F

                       pcellwall
            pcellwallOUT                     pcellwallOUT         //pentose cell wall component output
                       #ABCDE                #ABCDE

//starch biosynthesis

            starch         pHexP             Starch               //starch synthesis
                           #ABCDEF           #ABCDEF

            starchOUT Starch                 StarchOUT            //starch output
                      #ABCDEF                #ABCDEF

//pentose phosphate pathway

            ppp1           pHexP             intCO2      PenP     //glucose-6-phosphate dehydrogenase, 6-phosphogluco
                           #ABCDEF           #A          #BCDEF

            ppp2           PenP              GA3P        EnC2     //transketolase & transaldolase half reactions
                           #ABCDE            #CDE        #AB

            ppp3           PenP       EnC2   Sed7P                //transketolase & transaldolase half reactions
                           #ABCDE     #ab    #abABCDE

            ppp4           Ery4P      EnC2   pHexP                //transketolase & transaldolase half reactions
                           #ABCD      #ab    #abABCD

            ppp5           GA3P       EnC3   pHexP                //transketolase & transaldolase half reactions
                           #ABC       #abc   #abcABC

            ppp6           Sed7P             Ery4P       EnC3     //transketolase & transaldolase half reactions
                           #ABCDEFG          #DEFG       #ABC
//mitochondria cytosol exchange

           cmex       cPYR                 mPYR               //mitochondrial pyruvate uptake
                      #ABC                 #ABC

// TCA cycle

           tca1       mPYR                 mAcCoA    intCO2   //pyruvate dehydrogenase
                      #ABC                 #BC       #A

           tca2       OAA         mAcCoA   mCit               //citrate synthase
                      #ABCD       #ab      #DCBbaA

           tca3       mCit                 AKG       intCO2   //aconitase & isocitrate dehydrogenase
                      #ABCDEF              #ABCDE    #F

           tca4       AKG                  Fum       intCO2   //a-ketoglutarate dehydrogenase and succinate dehydro
                      #ABCDE               #BCDE     #A

           tca5a      Fum                  OAA                //fumarase & malate dehydrogenase
                      #ABCD                #ABCD

           tca5b      Fum                  OAA                //fumarase & malate dehydrogenase
                      #ABCD                #DCBA

// anaplerotic metabolism

           ana1       PEP         intCO2   OAA                // phosphoenolpyruvate carboxylase and phosphoenolp
                      #ABC        #a       #ABCa

           ana2       OAA                  mPYR      intCO2   //mitochondrial NAD dependent malic enyme
                      #ABCD                #ABC      #D

           ana3       OAA                  pPYR      intCO2   //plastidic NADP dependent malic enzyme
                      #ABCD                #ABC      #D

//amino acid biosynthesis

           ala        cPYR                 Ala                //alanine synthesis
                      #ABC                 #ABC

           asp        OAA                  Asp                //aspartate synthesis
                      #ABCD                #ABCD

           thr        Asp                  Thr                //threonine synthesis
                      #ABCD                #ABCD
asn     Asp               Asn                   //asparagine synthesis
        #ABCD             #ABCD

met     Asp               Met                   //methionine synthesis
        #ABCD             #ABCD

glu     AKG               Glu                   //glutamate synthesis
        #ABCDE            #ABCDE

gln     Glu               Gln                   //glutamine synthesis
        #ABCDE            #ABCDE

citru   Glu      intCO2   Citrulline            //citrulline synthesis
        #ABCDE   #a       #ABCDEa

arg     Citrulline Asp    Arg     Fum           //arginine synthesis
        #ABCDEF #abcd     #ABCDEF #abcd

gaba    Glu               GABA         intCO2   //g-aminobutyric acid synthesis
        #ABCDE            #BCDE        #A

ser     GA3P              Ser                   //serine synthesis
        #ABC              #ABC

gly     Ser               Gly          MetTHF   //glycine synthesis
        #ABC              #AB          #C

shik    PEP      Ery4P    Shikim                //shikimate synthesis
        #ABC     #abcd    #ABCabcd

chor    Shikim   PEP      Choris                //chorismate synthesis
        #ABCDEFG #abc     #ABCDEFGabc

phe     Choris            Phe       intCO2      //phenylalanine synthesis
        #ABCDEFGHIJ       #HIJBCDEFG#A

tyr     Choris            Tyr       intCO2      //tyrosine synthesis
        #ABCDEFGHIJ       #HIJBCDEFG#A

val     pPYR     pPYR     Val          intCO2   //valine synthesis
        #ABC     #abc     #ABbcC       #a

lys1a   Asp      pPYR     Lys     intCO2        //lysine synthesis
        #ABCD    #abc     #ABCDcb #a

lys1b   Asp      pPYR     Lys          intCO2   //lysine synthesis
                      #ABCD       #abc     #abcDCB   #A

           leu1       pPYR        pPYR     Isoval    intCO2   //leucine synthesis
                      #ABC        #abc     #ABbcC    #a

           leu2       Isoval      pAcCoA   Leu     intCO2     //leucine synthesis
                      #ABCDE      #ab      #abBCDE #A

           ile        Asp         pPYR     Ile     intCO2     //isoleucine synthesis
                      #ABCD       #abc     #ABbCDc #a

           his        PenP                 His                //histidine synthesis
                      #ABCDE               #EDCBA

//amino acid incorporation into protein

           alaOUT     Ala                  extpAla
                      #ABC                 #ABC

           aspOUT     Asp                  extpAsp
                      #ABCD                #ABCD

           asnOUT     Asn                  extpAsn
                      #ABCD                #ABCD

           thrOUT     Thr                  extpThr
                      #ABCD                #ABCD

           metOUT     Met                  extpMet
                      #ABCD                #ABCD

           gluOUT     Glu                  extpGlu
                      #ABCDE               #ABCDE

           glnOUT     Gln                  extpGln
                      #ABCDE               #ABCDE

           argOUT     Arg                  extpArg
                      #ABCDEF              #ABCDEF

           serOUT     Ser                  extpSer
                      #ABC                 #ABC

           glyOUT     Gly                  extpGly
                      #AB                  #AB

           pheOUT     Phe                  extpPhe
                     #ABCDEFGHI     #ABCDEFGHI

          tyrOUT     Tyr            extpTyr
                     #ABCDEFGHI     #ABCDEFGHI

          valOUT     Val            extpVal
                     #ABbcC         #ABbcC

          leuOUT     Leu            extpLeu
                     #ABCDEF        #ABCDEF

          ileOUT     Ile            extpIle
                     #ABCDEF        #ABCDEF

          lysOUT     Lys            extpLys
                     #ABCDEF        #ABCDEF

          hisOUT     His            extpHis
                     #ABCDE         #ABCDE

//soluble metabolite accumulation

          sgluOUT    Glu            extsGlu      //soluble glutamate accumulation
                     #ABCDE         #ABCDE

          salaOUT    Ala            extsAla      //soluble alanine accumulation
                     #ABC           #ABC

          sgabaOUT GABA             extsGABA     //soluble GABA accumulation
                   #ABCD            #ABCD

          sglcOUT    Glc6P          extsGlc      //soluble glucose accumulation
                     #ABCDEF        #ABCDEF

          ssucFOUT Fru6P            extsSucF     //soluble sucrose accumulation
                   #ABCDEF          #ABCDEF

          ssucGOUT Glc6P            extsSucG     //soluble sucrose accumulation
                   #ABCDEF          #ABCDEF

          scit       mCit           sCit         //soluble citrate accumulation
                     #ABCDEF        #ABCDEF

          scitOUT    sCit           extsCit
                     #ABCDEF        #ABCDEF

          smal       OAA            sMal         //soluble malate accumulation
                        #ABCD                #ABCD

            smalOUT sMal                     extsMal
                    #ABCD                    #ABCD

            ssucc       Fum                  sSucc                 //soluble succinate accumulation
                        #ABCD                #ABCD

            ssuccOUT sSucc                   extsSucc
                     #ABCD                   #ABCD

            sfumOUT Fum                      extsFum               //soluble fumarate accumulation
                    #ABCD                    #ABCD

// lipid biosynthesis

            lip1        pPYR                 pAcCoA       intCO2   //plastidic pyruvate dehydrogenase
                        #ABC                 #BC          #A

            lip2        pAcCoA               fattyA                //plastidic fatty acid synthesis
                        #AB                  #AB

            lipidOUT    fattyA               extlfattyA            //fatty acid accumulation in phospholipid
                        #AB                  #AB

                      GA3P
            glycerolOUT                      extlglycerol          //glycerol accumulation in phospholipid
                      #ABC                   #ABC

EQUALITIES
          NET
                        VALUE      FORMULA
                                 0 tca5b-tca5a
                                 0 lys1a-lys1b

            XCH
                        VALUE      FORMULA
                                 0 tca5b-tca5a

INEQUALITIES
          NET
                        VALUE     COMP       FORMULA

                                 0 <=        ppp1
                                 0 <=        ana2
                                 0 <=        ana3

LABEL_INPUT
        ISOTOPOMER
META_NAME       VALUE

Glc1    #000000        0
        #100000    0.945
        #110000    0.011
        #100001    0.011
        #100010    0.011
        #100100    0.011
        #101000    0.011
ucose isomerase


uctokinase, cytosolic aldolase and triose phosphate isomerase"




sphate uptake
osphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase and enolase"




ponent synthesis


ponent output


mponent synthesis


mponent output




e dehydrogenase, 6-phosphogluconolactonase & phosphogluconate dehydrogenase"


saldolase half reactions


saldolase half reactions


saldolase half reactions


saldolase half reactions


saldolase half reactions
e dehydrogenase


ydrogenase and succinate dehydrogenase


dehydrogenase


dehydrogenase




te carboxylase and phosphoenolpyruvate carboxykinase


dependent malic enyme


ndent malic enzyme
cumulation
hydrogenase




ion in phospholipid


n in phospholipid

				
DOCUMENT INFO
Shared By:
Categories:
Tags:
Stats:
views:7
posted:4/24/2010
language:English
pages:15