From ef44666ba35c09a016d25515857e951d1860fb0e Mon Sep 17 00:00:00 2001
From: Devlin-Moyer <devmoy@gmail.com>
Date: Mon, 23 Oct 2023 18:51:32 -0400
Subject: [PATCH 1/2] feat: added MAM20019c to represent cytosolic FMNH2

---
 model/Human-GEM.yml   | 8 ++++++++
 model/metabolites.tsv | 1 +
 2 files changed, 9 insertions(+)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 6c7c5541..a43481da 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -66657,6 +66657,14 @@
       - charge: 0
       - inchis: ""
       - metFrom: ""
+    - !!omap
+      - id: "MAM20019c"
+      - name: "FMNH2"
+      - compartment: "c"
+      - formula: "C17H21N4O9P"
+      - charge: -2
+      - inchis: ""
+      - metFrom: ""
     - !!omap
       - id: "MAM20019r"
       - name: "FMNH2"
diff --git a/model/metabolites.tsv b/model/metabolites.tsv
index a87f5787..a82aa727 100644
--- a/model/metabolites.tsv
+++ b/model/metabolites.tsv
@@ -8335,6 +8335,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM20021i"	"MAM20021"	""	""	""	"CHEBI:132024"	""	""	""	""	""	"MNXM163133"	""	""
 "MAM02040i"	"MAM02040"	""	""	""	"CHEBI:15377"	""	""	""	""	""	"WATER"	""	""
 "MAM02630i"	"MAM02630"	""	""	""	"CHEBI:15379"	""	""	""	""	""	"MNXM735438"	""	""
+"MAM20019c"	"MAM20019"	"C01847"	""	""	"CHEBI:57618"	""	""	""	""	""	"MNXM1107623"	""	""
 "MAM20019i"	"MAM20019"	"C01847"	""	""	"CHEBI:57618"	""	""	""	""	""	"MNXM1107623"	""	"MAM20022i"
 "MAM01828i"	"MAM01828"	"C00061"	""	""	"CHEBI:58210"	""	""	""	""	""	"MNXM1105928"	""	"MAM20023i"
 "MAM02457i"	"MAM02457"	""	""	""	"CHEBI:78043"	""	""	""	""	""	"MNXM735122"	""	""

From 5491db3423b2963d8b555ccb97f8b842427c25fa Mon Sep 17 00:00:00 2001
From: Devlin-Moyer <devmoy@gmail.com>
Date: Mon, 23 Oct 2023 19:02:06 -0400
Subject: [PATCH 2/2] fix: replaced ubiquinone metabolites with FMN metabolites
 in MAR04575 and added new FMN/ubiquinone redox reaction MAR20167

---
 model/Human-GEM.yml | 22 ++++++++++++++++++++--
 model/reactions.tsv |  1 +
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index a43481da..1a313d79 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -74296,9 +74296,9 @@
       - name: "(S)-dihydroorotate:NAD+ oxidoreductase"
       - metabolites: !!omap
           - MAM00180c: -1
+          - MAM01828c: -1
           - MAM02659c: 1
-          - MAM03102m: 1
-          - MAM03103m: -1
+          - MAM20019c: 1
       - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000102967"
@@ -305329,6 +305329,24 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
+    - !!omap
+      - id: "MAR20167"
+      - name: "MAR20167"
+      - metabolites: !!omap
+          - MAM01828c: 1
+          - MAM03102m: 1
+          - MAM03103m: -1
+          - MAM20019c: -1
+      - lower_bound: -1000
+      - upper_bound: 1000
+      - gene_reaction_rule: "ENSG00000102967"
+      - rxnNotes: ""
+      - rxnFrom: ""
+      - eccodes: ""
+      - references: "PMID:34428349"
+      - subsystem:
+          - "Miscellaneous"
+      - confidence_score: 0
 - genes:
     - !!omap
       - id: "ENSG00000000419"
diff --git a/model/reactions.tsv b/model/reactions.tsv
index 5de1d8ae..01a33724 100644
--- a/model/reactions.tsv
+++ b/model/reactions.tsv
@@ -12997,3 +12997,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20164"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
 "MAR20165"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
 "MAR20166"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
+"MAR20167"	""	""	""	""	""	""	""	""	""	""	0	""	""	""