Merge pull request #237 from SysBioChalmers/fix/misc

fix: multiple small curations
SysBioChalmers · Jul 16, 2020 · 0e3253a · 0e3253a
2 parents 5d0d311 + 23d9218
commit 0e3253a
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diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt
@@ -1,4 +1,4 @@
-MATLAB	9.7.0.1190202 (R2019b)
+MATLAB	9.7.0.1319299 (R2019b) Update 5
 libSBML	5.17.0
 RAVEN_toolbox	2.4.0
 COBRA_toolbox	commit 8204bb7

diff --git a/ModelFiles/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt
@@ -215,7 +215,7 @@ r_0237	s_0794[c] + s_1212[c] + s_1579[c]  -> s_1207[c] + s_1569[c] 	YLR100W	  0.
 r_0238	s_0296[c] + s_0794[c] + s_1212[c] + s_1275[c]  -> s_0803[c] + s_1207[c] + s_1576[c] 	YGR060W	  0.00	1000.00	  0.00
 r_0239	s_0794[c] + s_1212[c] + s_1275[c] + s_1576[c]  -> 2 s_0803[c] + s_1207[c] + s_1577[c] 	YGR060W	  0.00	1000.00	  0.00
 r_0240	s_1212[c] + s_1275[c] + s_1577[c]  -> s_0803[c] + s_1207[c] + s_1578[c] 	YGR060W	  0.00	1000.00	  0.00
-r_0241	s_0122[c] + 2 s_0794[c] + 3 s_1212[c] + 3 s_1275[c]  -> s_0297[c] + 4 s_0803[c] + 3 s_1207[c] 	YGR060W	  0.00	1000.00	  0.00
+r_0241	s_0122[c] + 5 s_0794[c] + 3 s_1275[c] + 6 s_3825[er]  -> s_0297[c] + 4 s_0803[c] + 6 s_3824[er] 	YGR060W	  0.00	1000.00	  0.00
 r_0242	s_0657[c] + s_0794[c] + s_1212[c] + s_1275[c]  -> s_0664[c] + 2 s_0803[c] + s_1207[c] 	YLR056W	  0.00	1000.00	  0.00
 r_0243	s_0700[c]  -> s_0657[c] 	YMR202W	  0.00	1000.00	  0.00
 r_0244	s_0663[er] + s_0795[er] + s_1213[er]  -> s_0667[er] + s_1208[er] 	YGL012W	  0.00	1000.00	  0.00
@@ -622,8 +622,8 @@ r_0770	s_0794[c] + s_1203[c] + s_1537[m]  -> s_1198[c] + s_1535[m] 	( YDL085W or
 r_0771	s_0434[c] + s_1203[c]  -> s_0394[c] + s_0794[c] + s_1212[c] 	( YEL041W or YJR049C )	  0.00	1000.00	  0.00
 r_0772	s_0437[m] + s_1205[m]  -> s_0397[m] + s_0799[m] + s_1214[m] 	( YEL041W or YJR049C or YPL188W )	  0.00	1000.00	  0.00
 r_0773	s_0799[m] + s_1205[m] + s_1537[m]  -> s_1200[m] + s_1535[m] 	YML120C	  0.00	1000.00	  0.00
-r_0774	s_0794[c] + s_1219[c] + s_1386[c]  -> s_0633[c] + s_1222[c] 	YOR209C	  0.00	1000.00	  0.00
-r_0775	s_0799[m] + s_1221[m] + s_1387[m]  -> s_0636[m] + s_1223[m] 	YOR209C	  0.00	1000.00	  0.00
+r_0774	s_0434[c] + s_0794[c] + s_1219[c] + s_1386[c]  -> s_0394[c] + s_0633[c] + s_1222[c] + s_1322[c] 	YOR209C	  0.00	1000.00	  0.00
+r_0775	s_0437[m] + s_0799[m] + s_1221[m] + s_1387[m]  -> s_0397[m] + s_0636[m] + s_1223[m] + s_1326[m] 	YOR209C	  0.00	1000.00	  0.00
 r_0781	s_0803[c] + s_1216[c]  -> s_0419[c] + s_1219[c] 	YGL037C	  0.00	1000.00	  0.00
 r_0782	s_1216[c] + s_1416[c]  -> s_0087[c] + s_1413[c] 	YLR285W	  0.00	1000.00	  0.00
 r_0783	s_0434[c] + s_0794[c] + s_1224[c]  -> s_0633[c] + s_1198[c] 	( YCL047C or YLR328W )	  0.00	1000.00	  0.00
@@ -2005,7 +2005,7 @@ r_3329	s_3657[lp] + s_3688[lp]  -> s_0798[lp] + s_2852[lp] + s_3687[lp] 	YKR089C
 r_3330	s_3657[lp] + s_3690[lp]  -> s_0798[lp] + s_2852[lp] + s_3689[lp] 	YKR089C	  0.00	1000.00	  0.00
 r_3331	s_3657[lp] + s_3692[lp]  -> s_0798[lp] + s_2852[lp] + s_3691[lp] 	YKR089C	  0.00	1000.00	  0.00
 r_4039	s_0365[m] + s_1464[m]  <=> s_0376[m] + s_1460[m] 	YBL015W	-1000.00	1000.00	  0.00
-r_4042	s_0805[e] + s_3715[e]  -> s_0554[e] + s_3716[e] 	YIL020C	  0.00	1000.00	  0.00
+r_4042	s_0805[e] + s_3715[e]  -> s_0554[e] + s_3716[e] 		  0.00	1000.00	  0.00
 r_4045	s_0803[c] + s_1556[c]  -> s_0575[c] + s_1550[c] 	YDR400W	  0.00	1000.00	  0.00
 r_0964	s_0434[c] + s_0750[c] + s_0803[c]  -> s_0394[c] + s_0753[v] + s_0794[c] + s_1322[c] 	YDR135C	  0.00	1000.00	  0.00
 r_1028	s_0434[c] + s_0803[c] + s_1473[c]  -> s_0394[c] + s_0794[c] + s_1322[c] + s_1474[v] 	YLL048C	  0.00	1000.00	  0.00

diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml
@@ -49736,7 +49736,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="s_3884__91__c__93__" sboTerm="SBO:0000247" id="s_3884__91__c__93__" name="Protein [cytoplasm]" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H4NOR">
+      <species metaid="s_3884__91__c__93__" sboTerm="SBO:0000247" id="s_3884__91__c__93__" name="generic protein [cytoplasm]" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H4NOR">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
             <p>NOTES: added after new annotation (PR #142); General type</p>
@@ -66860,14 +66860,14 @@
         </annotation>
         <listOfReactants>
           <speciesReference species="s_0122__91__c__93__" stoichiometry="1" constant="true"/>
-          <speciesReference species="s_0794__91__c__93__" stoichiometry="2" constant="true"/>
-          <speciesReference species="s_1212__91__c__93__" stoichiometry="3" constant="true"/>
+          <speciesReference species="s_0794__91__c__93__" stoichiometry="5" constant="true"/>
           <speciesReference species="s_1275__91__c__93__" stoichiometry="3" constant="true"/>
+          <speciesReference species="s_3825__91__er__93__" stoichiometry="6" constant="true"/>
         </listOfReactants>
         <listOfProducts>
           <speciesReference species="s_0297__91__c__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_0803__91__c__93__" stoichiometry="4" constant="true"/>
-          <speciesReference species="s_1207__91__c__93__" stoichiometry="3" constant="true"/>
+          <speciesReference species="s_3824__91__er__93__" stoichiometry="6" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
           <fbc:geneProductRef fbc:geneProduct="G_YGR060W"/>
@@ -84062,13 +84062,16 @@
           </rdf:RDF>
         </annotation>
         <listOfReactants>
+          <speciesReference species="s_0434__91__c__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_0794__91__c__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_1219__91__c__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_1386__91__c__93__" stoichiometry="1" constant="true"/>
         </listOfReactants>
         <listOfProducts>
+          <speciesReference species="s_0394__91__c__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_0633__91__c__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_1222__91__c__93__" stoichiometry="1" constant="true"/>
+          <speciesReference species="s_1322__91__c__93__" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
           <fbc:geneProductRef fbc:geneProduct="G_YOR209C"/>
@@ -84100,13 +84103,16 @@
           </rdf:RDF>
         </annotation>
         <listOfReactants>
+          <speciesReference species="s_0437__91__m__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_0799__91__m__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_1221__91__m__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_1387__91__m__93__" stoichiometry="1" constant="true"/>
         </listOfReactants>
         <listOfProducts>
+          <speciesReference species="s_0397__91__m__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_0636__91__m__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_1223__91__m__93__" stoichiometry="1" constant="true"/>
+          <speciesReference species="s_1326__91__m__93__" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
           <fbc:geneProductRef fbc:geneProduct="G_YOR209C"/>
@@ -140979,7 +140985,6 @@
               </bqbiol:isDescribedBy>
               <bqbiol:is>
                 <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.16"/>
                   <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02410"/>
                   <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103420"/>
                 </rdf:Bag>
@@ -141000,9 +141005,6 @@
           <speciesReference species="s_0554__91__e__93__" stoichiometry="1" constant="true"/>
           <speciesReference species="s_3716__91__e__93__" stoichiometry="1" constant="true"/>
         </listOfProducts>
-        <fbc:geneProductAssociation>
-          <fbc:geneProductRef fbc:geneProduct="G_YIL020C"/>
-        </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="r_4045" sboTerm="SBO:0000176" id="r_4045" name="uridine hydrolase" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
         <notes>
@@ -204863,7 +204865,6 @@
           <groups:member groups:idRef="r_0909"/>
           <groups:member groups:idRef="r_0910"/>
           <groups:member groups:idRef="r_2116"/>
-          <groups:member groups:idRef="r_4042"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group sboTerm="SBO:0000633" groups:id="group29" groups:name="sce00350  Tyrosine metabolism" groups:kind="partonomy">
@@ -207498,7 +207499,6 @@
           <groups:member groups:idRef="r_3329"/>
           <groups:member groups:idRef="r_3330"/>
           <groups:member groups:idRef="r_3331"/>
-          <groups:member groups:idRef="r_4042"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group sboTerm="SBO:0000633" groups:id="group71" groups:name="sce01130  Biosynthesis of antibiotics" groups:kind="partonomy">
@@ -208198,7 +208198,6 @@
           <groups:member groups:idRef="r_2126"/>
           <groups:member groups:idRef="r_2131"/>
           <groups:member groups:idRef="r_2305"/>
-          <groups:member groups:idRef="r_4042"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group sboTerm="SBO:0000633" groups:id="group76" groups:name="sce02010  ABC transporters" groups:kind="partonomy">

diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml
@@ -25778,7 +25778,7 @@
       - sbo: SBO:0000247
   - !!omap
     - id: s_3884
-    - name: Protein
+    - name: generic protein
     - compartment: c
     - formula: C2H4NOR
     - charge: 1
@@ -34400,11 +34400,11 @@
     - metabolites: !!omap
       - s_0122: -1
       - s_0297: 1
-      - s_0794: -2
+      - s_0794: -5
       - s_0803: 4
-      - s_1207: 3
-      - s_1212: -3
       - s_1275: -3
+      - s_3824: 6
+      - s_3825: -6
     - lower_bound: 0
     - upper_bound: 1000
     - gene_reaction_rule: YGR060W
@@ -43451,10 +43451,13 @@
     - id: r_0774
     - name: NAPRtase
     - metabolites: !!omap
+      - s_0394: 1
+      - s_0434: -1
       - s_0633: 1
       - s_0794: -1
       - s_1219: -1
       - s_1222: 1
+      - s_1322: 1
       - s_1386: -1
     - lower_bound: 0
     - upper_bound: 1000
@@ -43471,10 +43474,13 @@
     - id: r_0775
     - name: NAPRtase
     - metabolites: !!omap
+      - s_0397: 1
+      - s_0437: -1
       - s_0636: 1
       - s_0799: -1
       - s_1221: -1
       - s_1223: 1
+      - s_1326: 1
       - s_1387: -1
     - lower_bound: 0
     - upper_bound: 1000
@@ -89859,13 +89865,7 @@
       - s_3716: 1
     - lower_bound: 0
     - upper_bound: 1000
-    - gene_reaction_rule: YIL020C
-    - subsystem:
-        - sce00340  Histidine metabolism
-        - sce01110  Biosynthesis of secondary metabolites
-        - sce01230  Biosynthesis of amino acids
     - annotation: !!omap
-      - ec-code: 5.3.1.16
       - kegg.reaction: R02410
       - metanetx.reaction: MNXR103420
       - pmid: 4967422

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 **GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media;
 
-* Last update: 2020-06-19
+* Last update: 2020-07-15
 
 * Main Model Descriptors: