Merge pull request #707 from SysBioChalmers/fix/dupe_lipoate_biosynth

Merge Duplicate Lipoic Acid Biosynthesis Pathways
SysBioChalmers · Oct 17, 2023 · 1138c5c · 1138c5c
2 parents 04837d1 + 01a5d1e
commit 1138c5c
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diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2237,6 +2237,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01445m"	"MAM01445"	"cholate"	"C00695"	"HMDB0000619"	"CHEBI:16359"	"221493"	"LMST04010001"	""	"HC00502"	"cholate"	"MNXM450"	"m01445m"	"m01445m"
 "MAM01514m"	"MAM01514"	"cholcoa"	"C01794"	"HMDB0001374"	"CHEBI:15519"	"439573"	""	""	"HC00844"	"cholcoa"	"MNXM162468;MNXM431"	"m01514m"	"m01514m"
 "MAM00759c"	"MAM00759"	""	"C13712"	""	""	""	"LMST02030130"	""	""	"M00759"	"MNXM3494"	"m00759c"	"m00759c"
+"MAM02397c"	"MAM02397"	""	"C16239"	""	""	""	""	""	""	"M02397"	"MNXM19093"	"m02397c"	"m02397c"
 "MAM01268c"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268c"	"m01268c"
 "MAM01268m"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268m"	"m01268m"
 "MAM01268n"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268n"	"m01268n"

diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -230,6 +230,8 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00096"	""	"BUP2"	""	""	""	"BUP2"	"MNXR96346"	""	""	""	0	""	""	"BUP2"
 "MAR02027"	""	"r0193"	""	""	""	"r0193"	"MNXR105313"	""	""	""	0	""	""	"r0193"
 "MAR02006"	""	"CPS_m"	""	""	""	"r0034"	""	""	""	""	0	""	""	"r0034"
+"MAR06400"	"R07768"	""	"R07768C"	""	""	"HMR_6400"	"MNXR111356"	"HMR_6400"	"RCR11944"	""	0	""	""	"HMR_6400"
+"MAR06401"	"R07769"	""	"R07769C"	""	""	"HMR_6401"	"MNXR111357"	"HMR_6401"	"RCR11945"	""	0	""	""	"HMR_6401"
 "MAR03940"	"R01795"	"PHETHPTOX"	"R01795C"	"r0399"	""	"r0399"	"MNXR102632;MNXR107174"	"HMR_3940"	"RCR11388"	""	0	""	"RHEA:30787"	"HMR_3940"
 "MAR07785"	""	"ATPtx"	""	""	""	"ATPtx"	"MNXR96140"	"HMR_7785"	"RCR20040"	""	0	""	""	"HMR_7785"
 "MAR07775"	""	"NADHtpu"	""	""	""	"NADHtpu;NADtpu"	"MNXR101881"	"HMR_7775"	"RCR20024"	""	0	""	""	"HMR_7775"

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -32657,14 +32657,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM02397c"
-      - name: "lipoyl-[ACP]"
-      - compartment: "c"
-      - formula: "C19H33N2O8PRS3"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02398c"
       - name: "lipoyl-AMP"
@@ -100713,49 +100705,6 @@
       - subsystem:
           - "Lipoic acid metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR06400"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01098c: 2
-          - MAM02039c: -5
-          - MAM02040c: 6
-          - MAM02397c: 1
-          - MAM02471c: 2
-          - MAM02554c: 7
-          - MAM02555c: -7
-          - MAM02643c: -1
-          - MAM02681c: 2
-          - MAM02682c: -2
-          - MAM02877c: -2
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000121897 or ENSG00000175536"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "2.8.1.8;2.3.1.181"
-      - references: ""
-      - subsystem:
-          - "Lipoic acid metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR06401"
-      - name: "lipoyl-[acp]:protein N6-lipoyltransferase"
-      - metabolites: !!omap
-          - MAM00184c: 1
-          - MAM00209c: 1
-          - MAM01350c: -1
-          - MAM02397c: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000175536"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "2.3.1.181"
-      - references: ""
-      - subsystem:
-          - "Lipoic acid metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR06402"
       - name: "octanoyl-[acp]:protein N6-octanoyltransferase"

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -4080,7 +4080,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02396n"	"MAM02396"	""	"C06315"	"HMDB0005082"	"CHEBI:6499"	"5280915"	"LMFA03040002"	""	""	"C06315"	"MNXM12130"	"m02396n"	"m02396n"
 "MAM02396x"	"MAM02396"	""	"C06315"	"HMDB0005082"	"CHEBI:6499"	"5280915"	"LMFA03040002"	""	""	"C06315"	"MNXM12130"	"m02396p"	"m02396p"
 "MAM02396r"	"MAM02396"	""	"C06315"	"HMDB0005082"	"CHEBI:6499"	"5280915"	"LMFA03040002"	""	""	"C06315"	"MNXM12130"	"m02396r"	"m02396r"
-"MAM02397c"	"MAM02397"	""	"C16239"	""	""	""	""	""	""	"M02397"	"MNXM19093"	"m02397c"	"m02397c"
 "MAM02398c"	"MAM02398"	""	"C16238"	""	""	"23724672"	""	"CE5656"	""	"CE5656"	"MNXM2392"	"m02398c"	"m02398c"
 "MAM02399c"	"MAM02399"	""	""	""	""	"53481572"	""	"CE2102"	""	"CE2102"	"MNXM60228"	"m02399c"	"m02399c"
 "MAM02401c"	"MAM02401"	""	"C03127"	""	"CHEBI:29160"	""	""	""	""	"M02401"	"MNXM89832"	"m02401c"	"m02401c"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -1666,10 +1666,8 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06397"	""	""	"RE2882C"	""	""	"HMR_6397"	""	"HMR_6397"	"RCR10619"	""	0	""	""	"HMR_6397"
 "MAR06398"	"R07770"	""	"R07770C"	""	""	"RE1944C"	"MNXR101081"	"HMR_6398"	"RCR14489"	""	0	""	"RHEA:12913"	"HMR_6398"
 "MAR06399"	"R07771"	""	"R07771C"	""	""	"HMR_6399"	"MNXR111358"	"HMR_6399"	"RCR14490"	""	0	""	"RHEA:20473"	"HMR_6399"
-"MAR06400"	"R07768"	""	"R07768C"	""	""	"HMR_6400"	"MNXR111356"	"HMR_6400"	"RCR11944"	""	0	""	""	"HMR_6400"
-"MAR06401"	"R07769"	""	"R07769C"	""	""	"HMR_6401"	"MNXR111357"	"HMR_6401"	"RCR11945"	""	0	""	""	"HMR_6401"
-"MAR06402"	"R07766"	""	"R07766C"	""	""	"HMR_6402"	"MNXR111354"	"HMR_6402"	"RCR11946"	""	0	""	"RHEA:17665"	"HMR_6402"
-"MAR06403"	"R07767"	""	"R07767C"	""	""	"HMR_6403"	"MNXR111355"	"HMR_6403"	"RCR11947"	""	0	""	"RHEA:16585"	"HMR_6403"
+"MAR06402"	"R07766;R07769"	""	"R07766C;R07769C"	""	""	"HMR_6402;HMR_6401"	"MNXR111354"	"HMR_6402;HMR_6401"	"RCR11946;RCR11945"	""	0	"RHEA:17666"	"RHEA:17665"	"HMR_6402;HMR_6401;MAR06401"
+"MAR06403"	"R07767;R07768"	""	"R07767C;R07768C"	""	""	"HMR_6403;HMR_6400"	"MNXR111355"	"HMR_6403;HMR_6400"	"RCR11947;RCR11948"	""	0	"RHEA:16586"	"RHEA:16585"	"HMR_6403;HMR_6400;MAR06400"
 "MAR06404"	"R08550"	""	"R08550C"	""	""	"HMR_6404"	"MNXR112089"	"HMR_6404"	"RCR14491"	""	0	""	""	"HMR_6404"
 "MAR02472"	""	"HMR_2472"	"RE3109C"	""	""	"HMR_2472"	""	"HMR_2472"	"RCR11948"	""	0	""	""	"HMR_2472"
 "MAR02475"	""	"RE3110C"	"RE3110C"	""	""	"RE3110C"	"MNXR103792"	"HMR_2475"	"RCR11949"	""	0	""	""	"HMR_2475"
@@ -4063,7 +4061,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR01702"	""	""	""	"r1012"	""	""	"MNXR105423"	"HMR_1702"	"RCR20518"	""	0	""	""	"HMR_1702"
 "MAR01703"	"R08739"	""	""	""	"R-HSA-193452"	"HMR_1703"	"MNXR124748"	"HMR_1703"	"RCR13627"	""	0	""	""	"HMR_1703"
 "MAR01704"	""	""	""	""	"R-HSA-193369"	"HMR_1704"	"MNXR124227"	"HMR_1704"	"RCR13628"	""	0	""	""	"HMR_1704"
-"MAR01706"	"R04809"	""	""	""	"R-HSA-193535"	"HMR_1706"	"MNXR123029"	"HMR_1706"	"RCR13629"	""	0	""	""	"HMR_1706"
+"MAR01706"	"R04809"	""	""	""	"R-HSA-193535"	"HMR_1706"	"MNXR123029"	"HMR_1706"	"RCR13629"	""	0	"RHEA:47409"	"RHEA:47408"	"HMR_1706"
 "MAR01708"	"R04810"	""	""	"r1021"	"R-HSA-193508"	"HMR_1708"	"MNXR124228"	"HMR_1708"	"RCR13630"	""	0	""	""	"HMR_1708"
 "MAR01710"	"R04811"	""	""	""	"R-HSA-193533"	"HMR_1710"	"MNXR109135"	"HMR_1710"	"RCR13631"	""	0	""	""	"HMR_1710"
 "MAR01716"	"R03974"	""	"RE1835X"	""	""	"RE1835X"	"MNXR103559"	"HMR_1716"	"RCR14626"	""	0	""	"RHEA:31511"	"HMR_1716"