Fixed methionine cycle

FLAGlab · Aug 6, 2024 · 8e49f4c · 8e49f4c
1 parent 8cba418
commit 8e49f4c
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Showing 2 changed files with 118 additions and 13 deletions.
diff --git a/phaseolus/pvulModelWithBiomass.xml b/phaseolus/pvulModelWithBiomass.xml
@@ -4304,6 +4304,25 @@
  </rdf:RDF>
  </annotation>
  </species>
+ <species metaid="_5__45__METHYL__45__THF__91__c__93__" sboTerm="SBO:0000247" id="_5__45__METHYL__45__THF__91__c__93__" name="5-methyltetrahydrofolate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2" fbc:chemicalFormula="C20H23N7O6">
+ <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#_5__45__METHYL__45__THF__91__c__93__">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/biocyc/COMMONBEAN:5-METHYL-THF-GLU-N"/>
+ <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00440"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:hasProperty>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000247"/>
+ </rdf:Bag>
+ </bqbiol:hasProperty>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
  <species metaid="_5__45__METHYL__45__THF__45__GLU__45__N__91__c__93__" sboTerm="SBO:0000247" id="_5__45__METHYL__45__THF__45__GLU__45__N__91__c__93__" name="a 5-methyltetrahydrofolate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C20H23N7O5X">
  <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
  <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
@@ -114602,7 +114621,21 @@
  </fbc:or>
  </fbc:geneProductAssociation>
  </reaction>
- <reaction metaid="RXN__45__6382__45__CPD__45__6082__47__NAD__47__WATER__47____47__B__45__ALANINE__47__NADH__47__PROTON__46__42__46__" id="RXN__45__6382__45__CPD__45__6082__47__NAD__47__WATER__47____47__B__45__ALANINE__47__NADH__47__PROTON__46__42__46__" name="RXN-6382-CPD-6082/NAD/WATER//B-ALANINE/NADH/PROTON.42." reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
+ <reaction metaid="RXN__45__6382__45__CPD__45__6082__47__NAD__47__WATER__47____47__B__45__ALANINE__47__NADH__47__PROTON__46__42__46__" id="R00904" name="3-aminopropanal:NAD+ oxidoreductase" reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
+ <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#DCYSDESULF__45__RXN">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.3"/>
+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.5"/>
+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.19"/>
+ <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00904"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
  <listOfReactants>
  <speciesReference species="CPD__45__6082__91__c__93__" stoichiometry="1" constant="true"/>
  <speciesReference species="NAD__91__c__93__" stoichiometry="1" constant="true"/>
@@ -121184,7 +121217,6 @@
  <rdf:Bag>
  <rdf:li rdf:resource="http://identifiers.org/biocyc/COMMONBEAN:1.5.1.20-RXN"/>
  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.20"/>
- <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07168"/>
  </rdf:Bag>
  </bqbiol:is>
  </rdf:Description>
@@ -148987,6 +149019,33 @@
  </fbc:or>
  </fbc:geneProductAssociation>
  </reaction>
+ <reaction metaid="R00946" id="R00946" name="5-methyltetrahydrofolate:L-homocysteine S-methyltransferase" reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
+ <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#R00946">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.13"/>
+ <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00946"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:hasProperty>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000176"/>
+ </rdf:Bag>
+ </bqbiol:hasProperty>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="_5__45__METHYL__45__THF__91__c__93__" stoichiometry="1" constant="true"/>
+ <speciesReference species="HOMO__45__CYS__91__c__93__" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="THF__91__c__93__" stoichiometry="1" constant="true"/>
+ <speciesReference species="MET__91__c__93__" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
 
 
 
@@ -149172,6 +149231,40 @@
  </fbc:or>
  </fbc:geneProductAssociation>
  </reaction>
+ <reaction metaid="R07168" id="R07168" name="R07168" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB3N1000">
+ <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#R02236">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.20"/>
+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.54"/>
+ <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07168"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:hasProperty>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000176"/>
+ </rdf:Bag>
+ </bqbiol:hasProperty>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="C00143" stoichiometry="1" constant="true"/>
+ <speciesReference species="NADH__91__c__93__" stoichiometry="1" constant="true"/>
+ <speciesReference species="PROTON__91__c__93__" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="_5__45__METHYL__45__THF__91__c__93__" stoichiometry="1" constant="true"/>
+ <speciesReference species="NAD__91__c__93__" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_PHVUL__46__007G281200"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
  <!--Reactions nucleotides-->
  <reaction metaid="R01868" id="R01868" name="dihydroorotate:quinone oxidoreductase" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB3N1000">
  <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
@@ -150078,9 +150171,7 @@
  <speciesReference species="ILE__91__c__93__" stoichiometry="1" constant="true"/>
  <speciesReference species="LEU__91__c__93__" stoichiometry="1" constant="true"/>
  <speciesReference species="LYS__91__c__93__" stoichiometry="1" constant="true"/>
-
- <speciesReference species="HOMO__45__CYS__91__c__93__" stoichiometry="1" constant="true"/>
-
+ <speciesReference species="MET__91__c__93__" stoichiometry="1" constant="true"/>
  <speciesReference species="PHE__91__c__93__" stoichiometry="1" constant="true"/>
  <speciesReference species="PRO__91__c__93__" stoichiometry="1" constant="true"/>
  <speciesReference species="SER__91__c__93__" stoichiometry="1" constant="true"/>
@@ -150124,7 +150215,8 @@
  <speciesReference species="AICAR__91__c__93__" stoichiometry="1" constant="true"/>
  <speciesReference species="C00672" stoichiometry="1" constant="true"/>
  <speciesReference species="B__45__ALANINE__91__c__93__" stoichiometry="1" constant="true"/>
- <speciesReference species="PUTRESCINE__91__c__93__" stoichiometry="1" constant="true"/>
+ <speciesReference species="SPERMIDINE__91__c__93__" stoichiometry="1" constant="true"/>
+ <speciesReference species="_2__45__KETO__45__GLUTARAMATE__91__c__93__" stoichiometry="1" constant="true"/>
 
 
 

diff --git a/phaseolus/pvulModelWithBiomass_selectedReactions.txt b/phaseolus/pvulModelWithBiomass_selectedReactions.txt
@@ -218,6 +218,8 @@ R02236
 R00937
 R00940
 
+R07168
+
 
 
 #Glyoxylate metabolism (630)
@@ -309,14 +311,22 @@ ARGDECARBOX__45__RXN
 AGMATINE__45__DEIMINASE__45__RXN
 N__45__CARBAMOYLPUTRESCINE__45__AMIDASE__45__RXN
 
+SPERMIDINESYN__45__RXN
+
+#RXN__45__12089
+#R01914 Two reactions alternative. Missing this reaction
+#AMINOBUTDEHYDROG__45__RXN
+#R00904
+
 #PUTRESCINE__45__OXIDASE__45__RXN
 #PROLINE__45__RACEMASE__45__RXN
-#SPERMIDINESYN__45__RXN
-#AMINOBUTDEHYDROG__45__RXN
+
+
 #SPERMINE__45__SYNTHASE__45__RXN
 #RXN0__45__3942
 #RXN__45__9015
-#RXN__45__12089
+
+
 
 #Ser, Gly, Thre, lys
 PGLYCDEHYDROG__45__RXN
@@ -408,20 +418,23 @@ R01777
 O__45__SUCCHOMOSERLYASE__45__RXN
 R01286
 #HOMOCYSMET__45__RXN Requires 5-Methyltetrahydropteroyltri-L-glutamate
-
+R00946
 
 ##Blocked reactions until Met and Spermidine are solved
 S__45__ADENMETSYN__45__RXN
 SAMDECARB__45__RXN
-SPERMIDINESYN__45__RXN
-METHYLTHIOADENOSINE__45__NUCLEOSIDASE__45__RXN
-_5__45__METHYLTHIORIBOSE__45__KINASE__45__RXN
+#SPERMIDINESYN__45__RXN Already in proline metabolsim
+_5__45__METHYLTHIOADENOSINE__45__PHOSPHORYLASE__45__RXN
+#METHYLTHIOADENOSINE__45__NUCLEOSIDASE__45__RXN Two step alternative
+#_5__45__METHYLTHIORIBOSE__45__KINASE__45__RXN
 _5__46__3__46__1__46__23__45__RXN
 R07392
 R82__45__RXN
 R83__45__RXN
 R147__45__RXN
 RXN__45__15650
+##Metabolize _2__45__KETO__45__GLUTARAMATE__91__c__93__
+#RXN__45__13072
 
 #R01286
 #DCYSDESULF__45__RXN Disconnected