From 7930323aa0fe783615845cef98dea577f9bb0ffe Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Thu, 25 Apr 2024 21:29:53 +0800
Subject: [PATCH] fix: modified unbalance reactions

---
 model/Human-GEM.yml | 67 ++++++++++++++++++++-------------------------
 1 file changed, 29 insertions(+), 38 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 8b5c4bf5..ad067091 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -66422,7 +66422,7 @@
       - name: "(5Z,8Z,11Z,14Z)-eicosatetraenedioate"
       - compartment: "n"
       - formula: "C20H28O4"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66438,7 +66438,7 @@
       - name: "(5Z,8Z,11Z,14Z)-eicosatetraenedioate"
       - compartment: "c"
       - formula: "C20H28O4"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66558,7 +66558,7 @@
       - name: "19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate"
       - compartment: "r"
       - formula: "C20H33O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66590,7 +66590,7 @@
       - name: "19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate"
       - compartment: "i"
       - formula: "C20H33O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66638,7 +66638,7 @@
       - name: "19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate"
       - compartment: "r"
       - formula: "C20H29O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66654,7 +66654,7 @@
       - name: "19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate"
       - compartment: "i"
       - formula: "C20H29O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66662,7 +66662,7 @@
       - name: "21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate"
       - compartment: "r"
       - formula: "C22H31O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66670,7 +66670,7 @@
       - name: "21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate"
       - compartment: "i"
       - formula: "C22H31O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66686,7 +66686,7 @@
       - name: "11-hydroxydodecanoate"
       - compartment: "r"
       - formula: "C12H23O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66702,7 +66702,7 @@
       - name: "11-hydroxydodecanoate"
       - compartment: "i"
       - formula: "C12H23O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66710,7 +66710,7 @@
       - name: "13-hydroxytetradecanoate"
       - compartment: "r"
       - formula: "C14H27O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66718,7 +66718,7 @@
       - name: "13-hydroxytetradecanoate"
       - compartment: "i"
       - formula: "C14H27O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66878,7 +66878,7 @@
       - name: "(E)-hexadec-2-enoate"
       - compartment: "r"
       - formula: "C16H29O2"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66886,7 +66886,7 @@
       - name: "(E)-hexadec-2-enoate"
       - compartment: "c"
       - formula: "C16H29O2"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66894,7 +66894,7 @@
       - name: "22-oxodocosanoate"
       - compartment: "r"
       - formula: "C22H41O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -66902,7 +66902,7 @@
       - name: "22-oxodocosanoate"
       - compartment: "c"
       - formula: "C22H41O3"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -67030,7 +67030,7 @@
       - name: "(2E,6E)-farnesoate"
       - compartment: "r"
       - formula: "C15H23O2"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -67046,7 +67046,7 @@
       - name: "(2E,6E)-farnesoate"
       - compartment: "c"
       - formula: "C15H23O2"
-      - charge: 0
+      - charge: -1
       - inchis: ""
       - metFrom: ""
     - !!omap
@@ -67341,7 +67341,7 @@
       - id: "MAM01657r"
       - name: "dehydrodolichol-diphosphate"
       - compartment: "r"
-      - formula: "C100H161O7P2"
+      - formula: "C40H65O7P2"
       - charge: -3
       - inchis: ""
       - metFrom: ""
@@ -67637,7 +67637,7 @@
       - id: "MAM20082m"
       - name: "S-propanoyldihydrolipoamide"
       - compartment: "m"
-      - formula: ""
+      - formula: "C11H23N1O2S2"
       - charge: 0
       - inchis: ""
       - metFrom: ""
@@ -94679,8 +94679,8 @@
       - name: "superoxide:superoxide oxidoreductase"
       - metabolites: !!omap
           - MAM02039x: -2
-          - MAM01803x: 1
-          - MAM01802x: 1
+          - MAM02630x: 1
+          - MAM02041x: 1
           - MAM02631x: -2
       - lower_bound: 0
       - upper_bound: 1000
@@ -117551,7 +117551,7 @@
           - MAM01285c: 1
           - MAM01371c: -1
           - MAM01597c: 1
-          - MAM02039c: 1
+          - MAM02039c: 2
           - MAM02040c: -2
           - MAM02746x: 1
           - MAM02747c: -1
@@ -161337,8 +161337,8 @@
       - name: "hydrogen-peroxide:hydrogen-peroxide oxidoreductase"
       - metabolites: !!omap
           - MAM02040x: 2
-          - MAM01803x: -2
-          - MAM01802x: 1
+          - MAM02041x: -2
+          - MAM02630x: 1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000121691 or ENSG00000166016"
@@ -223112,7 +223112,6 @@
           - MAM01285c: 1
           - MAM01371c: -1
           - MAM02039c: 1
-          - MAM02039e: -1
           - MAM02040c: -1
           - MAM02200c: 1
           - MAM02200e: -1
@@ -286846,10 +286845,10 @@
           - MAM01597x: -2
           - MAM02039x: 2
           - MAM02040x: -2
-          - MAM01803x: 2
+          - MAM02041x: 2
           - MAM02552x: -2
           - MAM02553x: 2
-          - MAM01802x: -1
+          - MAM02630x: -1
           - MAM03236x: -1
           - MAM03238x: 1
       - lower_bound: 0
@@ -301841,7 +301840,6 @@
       - id: "MAR20021"
       - name: "MAR20021"
       - metabolites: !!omap
-          - MAM02039r: 1
           - MAM02040r: 1
           - MAM02457r: -1
           - MAM02630r: -1
@@ -301862,7 +301860,6 @@
       - id: "MAR20022"
       - name: "MAR20022"
       - metabolites: !!omap
-          - MAM02039i: 1
           - MAM02040i: 1
           - MAM02457i: -1
           - MAM02630i: -1
@@ -301884,7 +301881,6 @@
       - name: "MAR20023"
       - metabolites: !!omap
           - MAM01784r: -1
-          - MAM02039r: 1
           - MAM02040r: 1
           - MAM02630r: -1
           - MAM20019r: -1
@@ -301905,7 +301901,6 @@
       - name: "MAR20024"
       - metabolites: !!omap
           - MAM01784i: -1
-          - MAM02039i: 1
           - MAM02040i: 1
           - MAM02630i: -1
           - MAM20019i: -1
@@ -301926,7 +301921,6 @@
       - name: "MAR20025"
       - metabolites: !!omap
           - MAM01689r: -1
-          - MAM02039r: 1
           - MAM02040r: 1
           - MAM02630r: -1
           - MAM20019r: -1
@@ -301947,7 +301941,6 @@
       - name: "MAR20026"
       - metabolites: !!omap
           - MAM01689i: -1
-          - MAM02039i: 1
           - MAM02040i: 1
           - MAM02630i: -1
           - MAM20019i: -1
@@ -301967,7 +301960,6 @@
       - id: "MAR20027"
       - name: "MAR20027"
       - metabolites: !!omap
-          - MAM02039r: 1
           - MAM02040r: 1
           - MAM02344r: -1
           - MAM02630r: -1
@@ -301988,7 +301980,6 @@
       - id: "MAR20028"
       - name: "MAR20028"
       - metabolites: !!omap
-          - MAM02039i: 1
           - MAM02040i: 1
           - MAM02344i: -1
           - MAM02630i: -1
@@ -302009,7 +302000,6 @@
       - id: "MAR20029"
       - name: "MAR20029"
       - metabolites: !!omap
-          - MAM02039r: 1
           - MAM02040r: 1
           - MAM02494r: -1
           - MAM02630r: -1
@@ -302030,7 +302020,6 @@
       - id: "MAR20030"
       - name: "MAR20030"
       - metabolites: !!omap
-          - MAM02039i: 1
           - MAM02040i: 1
           - MAM02494i: -1
           - MAM02630i: -1
@@ -303481,6 +303470,7 @@
           - MAM02007m: -1
           - MAM02040m: -1
           - MAM02439m: 1
+          - MAM02039m: 1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000125246"
@@ -303501,6 +303491,7 @@
           - MAM02039m: 1
           - MAM02046m: -1
           - MAM02751m: 1
+          - MAM01422m: 1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000076555"