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Pyrimidine ribonucleotides can be synthesize in two ways, de novo biosynthesis and salvaging pathways. In salvaging pathways nucleosides from RNA and DNA breakdown can reenter pyrimidine ribonucleotide de novo biosynthesis.
Website=www.biocyc.org/Ecoli/Pathways/
free text=Voet and Voet  (textbook)  Biochemistry
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<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
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<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00043" kind="mole"/>
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<compartment metaid="default" id="default" size="1" units="volume"/>
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<listOfSpecies>
<species metaid="s1" id="s1" name="cytosine" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  cytosine
Synonym:  Synonym not specified
Accession:  S04144
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>cytosine</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s2" id="s2" name="H_sub_2_endsub_O" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  H2O
Synonym:  Synonym not specified
Accession:  S04147
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>H_sub_2_endsub_O</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3" id="s3" name="NH_sub_3" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  NH3
Synonym:  Synonym not specified
Accession:  S04141
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>NH_sub_3</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s4" id="s4" name="uracil" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  uracil
Synonym:  Synonym not specified
Accession:  S04149
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>uracil</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s5" id="s5" name="PRPP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  PRPP
Synonym:  Synonym not specified
Accession:  S04143
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>PRPP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s6" id="s6" name="PP_sub_i" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  PPi
Synonym:  Synonym not specified
Accession:  S04155
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>PP_sub_i</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s7" id="s7" name="UMP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  UMP
Synonym:  Synonym not specified
Accession:  S04157
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>UMP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s8" id="s8" name="uridine" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  uridine
Synonym:  Synonym not specified
Accession:  S04153
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>uridine</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s9" id="s9" name="ribose-1-phosphate" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  ribose-1-phosphate
Synonym:  Synonym not specified
Accession:  S04152
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>ribose-1-phosphate</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s10" id="s10" name="PO_sub_4" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  PO4
Synonym:  Synonym not specified
Accession:  S04151
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>PO_sub_4</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s11" id="s11" name="GTP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  GTP
Synonym:  Synonym not specified
Accession:  S04150
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>GTP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s12" id="s12" name="GDP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  GDP
Synonym:  Synonym not specified
Accession:  S04142
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>GDP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s13" id="s13" name="cytidine" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  cytidine
Synonym:  Synonym not specified
Accession:  S04146
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>cytidine</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s14" id="s14" name="CMP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  CMP
Synonym:  Synonym not specified
Accession:  S04140
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>CMP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s15" id="s15" name="CDP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  CDP
Synonym:  Synonym not specified
Accession:  S04156
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>CDP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s16" id="s16" name="CTP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  CTP
Synonym:  Synonym not specified
Accession:  S04148
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>CTP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s17" id="s17" name="ATP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  ATP
Synonym:  Synonym not specified
Accession:  S04145
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>ATP</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s18" id="s18" name="ADP" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  ADP
Synonym:  Synonym not specified
Accession:  S04154
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
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</celldesigner:speciesIdentity>
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</annotation>
</species>
<species metaid="s19" id="s19" name="Cytosine_br_deaminase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  Cytosine deaminase
Synonym:  Synonym not specified
Accession:  P03155
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
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<celldesigner:proteinReference>p1</celldesigner:proteinReference>
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<species metaid="s20" id="s20" name="Uridine_br_phosphorylase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  Uridine phosphorylase
Synonym:  Synonym not specified
Accession:  P03152
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p2</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="r2"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s21" id="s21" name="Uridine kinase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  Uridine kinase
Synonym:  Synonym not specified
Accession:  P03150
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p3</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="r4"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s22" id="s22" name="Uracil phosphoribosyl_br_ transferase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  Uracil phosphoribosyltransferase
Synonym:  Synonym not specified
Accession:  P03151
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p4</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="r3"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s23" id="s23" name="Cytodine deaminase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  Cytidine deaminase
Synonym:  Synonym not specified
Accession:  P03154
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p5</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="r5"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s24" id="s24" name="Cytidine kinase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  Cytidine kinase
Synonym:  Synonym not specified
Accession:  P03149
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p6</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="r6"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s25" id="s25" name="Cytidylate kinase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  Cytidylate kinase
Synonym:  Synonym not specified
Accession:  P03153
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p7</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="r7"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s26" id="s26" name="CDP kinase" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
Long Name:  CDP kinase
Synonym:  Synonym not specified
Accession:  P03156
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p8</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="r8"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="r1" id="r1" reversible="false">
<annotation>
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<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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<celldesigner:baseReactant species="s1" alias="a1"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s4" alias="a4"/>
</celldesigner:baseProducts>
<celldesigner:listOfReactantLinks>
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</celldesigner:listOfReactantLinks>
<celldesigner:listOfProductLinks>
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</celldesigner:listOfProductLinks>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="1">
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<celldesigner:line width="1.0" color="ff000000"/>
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</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>a1</celldesigner:alias>
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</annotation>
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<speciesReference metaid="CDMT00003" species="s2">
<annotation>
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</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00004" species="s4">
<annotation>
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<celldesigner:alias>a4</celldesigner:alias>
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</annotation>
</speciesReference>
<speciesReference metaid="CDMT00005" species="s3">
<annotation>
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</annotation>
</speciesReference>
</listOfProducts>
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<annotation>
<celldesigner:extension>
<celldesigner:alias>a25</celldesigner:alias>
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</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
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<annotation>
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</celldesigner:listOfModification>
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</annotation>
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<annotation>
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</annotation>
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<annotation>
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</annotation>
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</annotation>
</speciesReference>
</listOfProducts>
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<annotation>
<celldesigner:extension>
<celldesigner:alias>a26</celldesigner:alias>
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</annotation>
</modifierSpeciesReference>
</listOfModifiers>
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<reaction metaid="r3" id="r3" reversible="false">
<annotation>
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</annotation>
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<speciesReference metaid="CDMT00012" species="s8">
<annotation>
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<celldesigner:alias>a8</celldesigner:alias>
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</annotation>
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</annotation>
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<annotation>
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<celldesigner:alias>a28</celldesigner:alias>
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</annotation>
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<celldesigner:line width="1.0" color="ff000000"/>
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</celldesigner:extension>
</annotation>
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<speciesReference metaid="CDMT00027" species="s13">
<annotation>
<celldesigner:extension>
<celldesigner:alias>a15</celldesigner:alias>
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</annotation>
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<speciesReference metaid="CDMT00028" species="s11">
<annotation>
<celldesigner:extension>
<celldesigner:alias>a16</celldesigner:alias>
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</annotation>
</speciesReference>
</listOfReactants>
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<speciesReference metaid="CDMT00029" species="s14">
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<celldesigner:extension>
<celldesigner:alias>a18</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference metaid="CDMT00030" species="s12">
<annotation>
<celldesigner:extension>
<celldesigner:alias>a17</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
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<modifierSpeciesReference metaid="CDMT00031" species="s24">
<annotation>
<celldesigner:extension>
<celldesigner:alias>a30</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction metaid="r7" id="r7" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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</celldesigner:listOfReactantLinks>
<celldesigner:listOfProductLinks>
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<celldesigner:editPoints>0.33333333333333304,-8.881784197001252E-16 0.666666666666667,0.0</celldesigner:editPoints>
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<speciesReference metaid="CDMT00032" species="s14">
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<celldesigner:extension>
<celldesigner:alias>a18</celldesigner:alias>
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<celldesigner:alias>a23</celldesigner:alias>
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</annotation>
</speciesReference>
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<speciesReference metaid="CDMT00034" species="s15">
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<celldesigner:extension>
<celldesigner:alias>a19</celldesigner:alias>
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</annotation>
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<speciesReference metaid="CDMT00035" species="s18">
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<celldesigner:alias>a24</celldesigner:alias>
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</speciesReference>
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<modifierSpeciesReference metaid="CDMT00037" species="s25">
<annotation>
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<celldesigner:alias>a31</celldesigner:alias>
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</reaction>
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<celldesigner:editPoints>0.3333333333333339,0.0 0.6666666666666665,-8.881784197001252E-16</celldesigner:editPoints>
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<listOfReactants>
<speciesReference metaid="CDMT00038" species="s15">
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<celldesigner:alias>a19</celldesigner:alias>
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</speciesReference>
<speciesReference metaid="CDMT00039" species="s17">
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<celldesigner:alias>a21</celldesigner:alias>
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<speciesReference metaid="CDMT00040" species="s16">
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</speciesReference>
<speciesReference metaid="CDMT00041" species="s18">
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<celldesigner:alias>a22</celldesigner:alias>
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<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00042" species="s26">
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<celldesigner:extension>
<celldesigner:alias>a32</celldesigner:alias>
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</reaction>
</listOfReactions>
</model>
</sbml>

