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progress for methionine
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jorge authored and jorge committed Aug 2, 2024
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146 changes: 133 additions & 13 deletions phaseolus/pvulModelWithBiomass.xml
Original file line number Diff line number Diff line change
Expand Up @@ -16488,6 +16488,7 @@
<rdf:li rdf:resource="http://identifiers.org/biocyc/COMMONBEAN:CPD-14443"/>
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:67139"/>
<rdf:li rdf:resource="http://identifiers.org/pubchem.compound/70678847"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C20258"/>
</rdf:Bag>
</bqbiol:is>
<bqbiol:hasProperty>
Expand Down Expand Up @@ -75373,7 +75374,19 @@
</fbc:or>
</fbc:geneProductAssociation>
</reaction>
<reaction metaid="PYRROLINECARBREDUCT__45__RXN__45__PRO__47__NAD__47____47__L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__47__NADH__47__PROTON__46__54__46__" id="PYRROLINECARBREDUCT__45__RXN__45__PRO__47__NAD__47____47__L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__47__NADH__47__PROTON__46__54__46__" name="PYRROLINECARBREDUCT-RXN-PRO/NAD//L-DELTA1-PYRROLINE_5-CARBOXYLATE/NADH/PROTON.54." reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
<reaction metaid="PYRROLINECARBREDUCT__45__RXN__45__PRO__47__NAD__47____47__L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__47__NADH__47__PROTON__46__54__46__" id="R01248" name="PYRROLINECARBREDUCT-RXN-PRO/NAD//L-DELTA1-PYRROLINE_5-CARBOXYLATE/NADH/PROTON.54." 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="#R01248">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.2"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01248"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="NADH__91__c__93__" stoichiometry="1" constant="true"/>
Expand Down Expand Up @@ -77180,6 +77193,7 @@
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/biocyc/COMMONBEAN:PYRROLINECARBDEHYDROG-RXN"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00707"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
Expand Down Expand Up @@ -104270,7 +104284,19 @@
<fbc:geneProductRef fbc:geneProduct="G_PHVUL__46__010G045600"/>
</fbc:geneProductAssociation>
</reaction>
<reaction metaid="RXN__45__14014__45__DELTA1__45__PIPERIDEINE__45__2__45__6__45__DICARBOXYLATE__47__NADP__47__WATER__47____47__CPD__45__14443__47__NADPH__47__PROTON__46__72__46__" id="RXN__45__14014__45__DELTA1__45__PIPERIDEINE__45__2__45__6__45__DICARBOXYLATE__47__NADP__47__WATER__47____47__CPD__45__14443__47__NADPH__47__PROTON__46__72__46__" name="RXN-14014-DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE/NADP/WATER//CPD-14443/NADPH/PROTON.72." reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
<reaction metaid="RXN__45__14014__45__DELTA1__45__PIPERIDEINE__45__2__45__6__45__DICARBOXYLATE__47__NADP__47__WATER__47____47__CPD__45__14443__47__NADPH__47__PROTON__46__72__46__" id="R04199" name="RXN-14014-DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE/NADP/WATER//CPD-14443/NADPH/PROTON.72." 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="#R04199">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/1.17.1.8"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04199"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="CPD__45__14443__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="NADPH__91__c__93__" stoichiometry="1" constant="true"/>
Expand Down Expand Up @@ -128157,7 +128183,19 @@
<fbc:geneProductRef fbc:geneProduct="G_PHVUL__46__L001386"/>
</fbc:geneProductAssociation>
</reaction>
<reaction metaid="PYRROLINECARBREDUCT__45__RXN__45__PRO__47__NADP__47____47__L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__47__NADPH__47__PROTON__46__56__46__" id="PYRROLINECARBREDUCT__45__RXN__45__PRO__47__NADP__47____47__L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__47__NADPH__47__PROTON__46__56__46__" name="PYRROLINECARBREDUCT-RXN-PRO/NADP//L-DELTA1-PYRROLINE_5-CARBOXYLATE/NADPH/PROTON.56." reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
<reaction metaid="PYRROLINECARBREDUCT__45__RXN__45__PRO__47__NADP__47____47__L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__47__NADPH__47__PROTON__46__56__46__" id="R01251" name="PYRROLINECARBREDUCT-RXN-PRO/NADP//L-DELTA1-PYRROLINE_5-CARBOXYLATE/NADPH/PROTON.56." 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="#R01251">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.2"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01251"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="L__45__DELTA1__45__PYRROLINE_5__45__CARBOXYLATE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="NADPH__91__c__93__" stoichiometry="1" constant="true"/>
Expand Down Expand Up @@ -135383,7 +135421,19 @@
</fbc:or>
</fbc:geneProductAssociation>
</reaction>
<reaction metaid="RXN__45__14014__45__DELTA1__45__PIPERIDEINE__45__2__45__6__45__DICARBOXYLATE__47__NAD__47__WATER__47____47__CPD__45__14443__47__NADH__47__PROTON__46__70__46__" id="RXN__45__14014__45__DELTA1__45__PIPERIDEINE__45__2__45__6__45__DICARBOXYLATE__47__NAD__47__WATER__47____47__CPD__45__14443__47__NADH__47__PROTON__46__70__46__" name="RXN-14014-DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE/NAD/WATER//CPD-14443/NADH/PROTON.70." reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
<reaction metaid="RXN__45__14014__45__DELTA1__45__PIPERIDEINE__45__2__45__6__45__DICARBOXYLATE__47__NAD__47__WATER__47____47__CPD__45__14443__47__NADH__47__PROTON__46__70__46__" id="R04198" name="RXN-14014-DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE/NAD/WATER//CPD-14443/NADH/PROTON.70." 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="#R04198">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/1.17.1.8"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04198"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="CPD__45__14443__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="NADH__91__c__93__" stoichiometry="1" constant="true"/>
Expand Down Expand Up @@ -148686,6 +148736,7 @@
<speciesReference species="AMMONIA__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="PYRUVATE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="HOMO__45__CYS__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="PROTON__91__c__93__" stoichiometry="1" constant="true"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_PHVUL__46__001G125400"/>
Expand Down Expand Up @@ -148877,6 +148928,65 @@
</fbc:or>
</fbc:geneProductAssociation>
</reaction>
<reaction metaid="R01777" id="R01777" name="succinyl-CoA:L-homoserine O-succinyltransferase" 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="#R01777">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.46"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01777"/>
</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="SUC__45__COA__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="HOMO__45__SER__91__c__93__" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="CO__45__A__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="O__45__SUCCINYL__45__L__45__HOMOSERINE__91__c__93__" stoichiometry="1" constant="true"/>
</listOfProducts>
</reaction>
<reaction metaid="R07392" id="R07392" name="S-methyl-5-thio-D-ribulose-1-phosphate hydro-lyase" 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="#R07392">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.109"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07392"/>
</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="CPD__45__1063__91__c__93__" stoichiometry="1" constant="true"/>

</listOfReactants>
<listOfProducts>
<speciesReference species="CPD__45__8999__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="WATER__91__c__93__" stoichiometry="1" constant="true"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:or>
<fbc:geneProductRef fbc:geneProduct="G_PHVUL__46__005G072900"/>
</fbc:or>
</fbc:geneProductAssociation>
</reaction>



Expand Down Expand Up @@ -149958,20 +150068,28 @@
<speciesReference species="OXYGEN__45__MOLECULE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="L__45__ALPHA__45__ALANINE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="L__45__ASPARTATE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="GLN__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="VAL__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="LEU__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="ARG__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="SER__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="HIS__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="ASN__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="CYS__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="GLN__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="GLT__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="GLY__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="THR__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="HIS__91__c__93__" stoichiometry="1" constant="true"/>
<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="PHE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="TYR__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"/>
<speciesReference species="THR__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="TRP__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="CYS__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="ASN__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="TYR__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="VAL__91__c__93__" stoichiometry="1" constant="true"/>



<speciesReference species="ADENINE__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="GUANINE__91__c__93__" stoichiometry="1" constant="true"/>
Expand Down Expand Up @@ -150006,6 +150124,7 @@
<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"/>



Expand Down Expand Up @@ -155570,6 +155689,7 @@
<fbc:geneProduct metaid="G_PHVUL__46__007G250300" sboTerm="SBO:0000243" fbc:id="G_PHVUL__46__007G250300" fbc:name="Phvul.007G250300" fbc:label="G_PHVUL__46__007G250300"/>
<fbc:geneProduct metaid="G_PHVUL__46__008G210100" sboTerm="SBO:0000243" fbc:id="G_PHVUL__46__008G210100" fbc:name="Phvul.008G210100" fbc:label="G_PHVUL__46__008G210100"/>
<fbc:geneProduct metaid="G_PHVUL__46__011G0558000" sboTerm="SBO:0000243" fbc:id="G_PHVUL__46__011G0558000" fbc:name="Phvul.011G0558000" fbc:label="G_PHVUL__46__011G0558000"/>
<fbc:geneProduct metaid="G_PHVUL__46__005G072900" sboTerm="SBO:0000243" fbc:id="G_PHVUL__46__005G072900" fbc:name="Phvul.005G072900" fbc:label="G_PHVUL__46__005G072900"/>
</fbc:listOfGeneProducts>
</model>
</sbml>
65 changes: 60 additions & 5 deletions phaseolus/pvulModelWithBiomass_selectedReactions.txt
Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,9 @@ PEPCARBOX__45__RXN
ALANINE__45__AMINOTRANSFERASE__45__RXN
ASPAMINOTRANS__45__RXN

##Ala Asp Glt
ALANINE__45____45__GLYOXYLATE__45__AMINOTRANSFERASE__45__RXN

#Krebs basic
#PYRUVATE-SYNTHASE-MANUAL No enzymes in P vulgaris
PEPCARBOXYKIN__45__RXN
Expand Down Expand Up @@ -243,9 +246,6 @@ FORMATETHFLIG__45__RXN
#_3__46__7__46__1__46__9__45__RXN HYDROXYMUCONATE__45__SALD__91__c__93__





#Histidine metabolism
ATPPHOSPHORIBOSYLTRANS__45__RXN
HISTPRATPHYD__45__RXN
Expand Down Expand Up @@ -287,7 +287,38 @@ ARGINASE__45__RXN
UREASE__45__RXN
#NITRIC__45__OXIDE__45__SYNTHASE__45__RXN Ok but blocked by now. Requires oxygen and produces nitric oxide

#Ser, Gly, Thre
#Arg, Pro metabolism
GLUTKIN__45__RXN
GLUTSEMIALDEHYDROG__45__RXN
RXN__45__14116
ORNITHINE__45__GLU__45__AMINOTRANSFERASE__45__RXN
SPONTPRO__45__RXN
R01248
R01251


ORNDECARBOX__45__RXN
PYRROLINECARBDEHYDROG__45__RXN
#RXN__45__13565

#
#RXN__45__13564


ARGDECARBOX__45__RXN
AGMATINE__45__DEIMINASE__45__RXN
N__45__CARBAMOYLPUTRESCINE__45__AMIDASE__45__RXN

#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
PSERTRANSAM__45__RXN
RXN0__45__5114
Expand All @@ -306,6 +337,13 @@ GCVT__45__RXN
GCVP__45__RXN
RXN__45__8629

DIHYDRODIPICSYN__45__RXN
R04198
R04199
RXN__45__7737
DIAMINOPIMEPIM__45__RXN
DIAMINOPIMDECARB__45__RXN

#Val, ISO, Leu,
ACETOLACTSYN__45__RXN
ACETOLACTREDUCTOISOM__45__RXN
Expand Down Expand Up @@ -366,7 +404,24 @@ R07274


R00782

R01777
O__45__SUCCHOMOSERLYASE__45__RXN
R01286
#HOMOCYSMET__45__RXN Requires 5-Methyltetrahydropteroyltri-L-glutamate


##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
_5__46__3__46__1__46__23__45__RXN
R07392
R82__45__RXN
R83__45__RXN
R147__45__RXN
RXN__45__15650

#R01286
#DCYSDESULF__45__RXN Disconnected
Expand Down

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