Merge branch 'develop' into fix/perox_cofactor_trans

SysBioChalmers · Oct 7, 2023 · 739cbd2 · 739cbd2
2 parents 4030753 + 0c8bdd1
commit 739cbd2
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Showing 3 changed files with 7 additions and 28 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -230,11 +230,12 @@ 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"
+"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"
 "MAR07788"	""	"FADH2tx"	""	""	""	"FADH2tx"	"MNXR99212"	"HMR_7788"	"RCR20202"	""	0	""	""	"HMR_7788"
 "MAR04915"	""	"COAtp"	""	"r0864"	""	"COAtp"	"MNXR96815"	"HMR_4915"	"RCR20004"	""	0	""	""	"HMR_4915"
 "MAR07771"	""	"NADtpu"	""	""	""	"NADtx"	"MNXR101881"	"HMR_7771"	"RCR20023"	""	0	""	""	"HMR_7771"
 "MAR07782"	""	"ADPtx"	""	""	""	"ADPtx"	"MNXR95484"	"HMR_7782"	"RCR20201"	""	0	""	""	"HMR_7782"
 "MAR07783"	""	"AMPtp"	""	""	""	"AMPtp"	"MNXR95830"	"HMR_7783"	"RCR20046"	""	0	""	""	"HMR_7783"
-"MAR07790"	""	"FADtx"	""	""	""	"FADtx"	"MNXR99217"	"HMR_7790"	"RCR20203"	""	0	""	""	"HMR_7790"
+"MAR07790"	""	"FADtx"	""	""	""	"FADtx"	"MNXR99217"	"HMR_7790"	"RCR20203"	""	0	""	""	"HMR_7790"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -82735,26 +82735,6 @@
       - subsystem:
           - "Phenylalanine, tyrosine and tryptophan biosynthesis"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR03940"
-      - name: "L-Phenylalanine,tetrahydrobiopterin:oxygen oxidoreductase (4-hydroxylating)"
-      - metabolites: !!omap
-          - MAM01698c: 1
-          - MAM02040c: 1
-          - MAM02630c: -1
-          - MAM02724c: -1
-          - MAM02978c: -1
-          - MAM03101c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000171759"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.14.16.1"
-      - references: "PMID:3298976;PMID:4074362"
-      - subsystem:
-          - "Phenylalanine, tyrosine and tryptophan biosynthesis"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04214"
       - name: "L-tryptophan:oxygen 2,3-oxidoreductase (decyclizing)"
@@ -222975,7 +222955,6 @@
       - eccodes: "4.99.1.1"
       - references: "PMID:7983009;PMID:11175906;PMID:11215517;PMID:11853551;PMID:11947230;PMID:1624416;PMID:182145;PMID:2310748;PMID:3196293;PMID:3702737;PMID:406931;PMID:6425295;PMID:7309736;PMID:8818224;PMID:9712849;PMID:9808757"
       - subsystem:
-          - "Heme synthesis"
           - "Porphyrin metabolism"
       - confidence_score: 0
     - !!omap
@@ -225514,7 +225493,7 @@
       - eccodes: "1.3.3.4"
       - references: "PMID:8771201"
       - subsystem:
-          - "Heme synthesis"
+          - "Porphyrin metabolism"
       - confidence_score: 0
     - !!omap
       - id: "MAR01645"
@@ -270121,7 +270100,7 @@
       - eccodes: ""
       - references: "PMID:21749716"
       - subsystem:
-          - "Heme synthesis"
+          - "Porphyrin metabolism"
       - confidence_score: 0
     - !!omap
       - id: "MAR11317"
@@ -271603,7 +271582,7 @@
       - eccodes: ""
       - references: "PMID:21749716"
       - subsystem:
-          - "Heme synthesis"
+          - "Porphyrin metabolism"
       - confidence_score: 0
     - !!omap
       - id: "MAR11407"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -803,7 +803,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08088"	"R04188"	"3AIBTm"	""	""	""	"3AIBTm"	"MNXR108721;MNXR94851"	"HMR_8088"	"RCR11385"	""	0	""	"RHEA:13993"	"HMR_8088"
 "MAR08787"	"R00923"	"MMCDm"	""	""	""	"MMCDm"	"MNXR101656"	"HMR_8787"	"RCR11386"	""	0	""	"RHEA:21396"	"HMR_8787"
 "MAR03743"	""	""	"RE2117M"	""	""	"RE2117M"	"MNXR103611"	"HMR_3743"	"RCR11387"	""	0	""	""	"HMR_3743"
-"MAR03940"	"R01795"	"PHETHPTOX"	"R01795C"	"r0399"	""	"r0399"	"MNXR102632;MNXR107174"	"HMR_3940"	"RCR11388"	""	0	""	"RHEA:30787"	"HMR_3940"
 "MAR04214"	"R00678"	"TRPO2"	"R00678C"	"r0169"	""	"TRPO2"	"MNXR104944"	"HMR_4214"	"RCR11389"	""	0	""	"RHEA:24536"	"HMR_4214"
 "MAR04216"	"R01958"	"FKYNH"	"R01958C"	"r0454"	""	"FKYNH"	"MNXR99596"	"HMR_4216"	"RCR11390"	""	0	""	""	"HMR_4216"
 "MAR04218"	"R03936"	"LFORKYNHYD"	"R03936C"	"r0646"	""	"LFORKYNHYD"	"MNXR101060;MNXR108539"	"HMR_4218"	"RCR11391"	""	0	""	""	"HMR_4218"
@@ -956,7 +955,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06889"	""	""	"RE3201C"	""	""	"RE3201C"	"MNXR103829"	"HMR_6889"	"RCR11479"	""	0	""	""	"HMR_6889"
 "MAR07628"	"R00690"	""	""	""	""	"HMR_7628"	"MNXR106645"	"HMR_7628"	"RCR11480"	""	0	""	"RHEA:10712"	"HMR_7628"
 "MAR07756"	"R02540"	""	""	""	""	"HMR_7756"	"MNXR95813"	"HMR_7756"	"RCR11481"	""	0	""	"RHEA:64820"	"HMR_7756"
-"MAR08539"	"R07211"	"PHETHPTOX2"	""	""	""	"PHETHPTOX2"	"MNXR102633"	"HMR_8539"	"RCR11482"	""	0	""	"RHEA:20273"	"HMR_8539"
+"MAR08539"	"R07211"	"PHETHPTOX2"	""	""	""	"PHETHPTOX2"	"MNXR102633"	"HMR_8539"	"RCR11482"	""	0	""	"RHEA:20273"	"HMR_8539;MAR03940"
 "MAR08794"	"R02539"	"PACCOAL"	""	""	""	"PACCOAL"	"MNXR102315"	"HMR_8794"	"RCR11483"	""	0	""	"RHEA:20956"	"HMR_8794"
 "MAR08795"	"R02576"	"PHACCOAGLNAC"	""	""	""	"PHACCOAGLNAC"	"MNXR102611"	"HMR_8795"	"RCR11484"	""	0	""	"RHEA:21844"	"HMR_8795"
 "MAR08796"	"R05841"	""	""	""	""	"HMR_8796"	"MNXR102612"	"HMR_8796"	"RCR11485"	""	0	"RHEA:27851"	"RHEA:27850"	"HMR_8796"
@@ -4527,7 +4526,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04834"	"R05046"	""	"R05046C"	"r0776"	""	"r0776"	"MNXR105382"	"HMR_4834"	"RCR14690"	""	0	""	""	"HMR_4834"
 "MAR04835"	"R05048"	""	"R05048C"	"r0777"	""	"r0777"	"MNXR105383"	"HMR_4835"	"RCR13860"	""	0	""	""	"HMR_4835"
 "MAR04836"	"R05048"	""	"R05048C"	"r0778"	""	"r0778"	"MNXR105383"	"HMR_4836"	"RCR13861"	""	0	""	""	"HMR_4836"
-"MAR08538"	"R04734"	"THBPT4ACAMDASE"	""	""	""	"THBPT4ACAMDASE"	"MNXR104802"	"HMR_8538"	"RCR10142"	""	0	""	"RHEA:11920"	"HMR_8538"
+"MAR08538"	"R04734"	"THBPT4ACAMDASE"	""	""	""	"THBPT4ACAMDASE"	"MNXR104802"	"HMR_8538"	"RCR10142"	""	0	""	"RHEA:11920"	"HMR_8538;MAR03940"
 "MAR08738"	"R04286"	"PTHPSn"	""	""	""	"PTHPSn"	"MNXR103331"	"HMR_8738"	"RCR14691"	""	0	""	"RHEA:22048"	"HMR_8738"
 "MAR08739"	"R08208"	"SPRn"	""	""	""	"SPRn"	"MNXR104500"	"HMR_8739"	"RCR14692"	""	0	""	"RHEA:32627"	"HMR_8739"
 "MAR08740"	""	"DIGALSGALSIDEtg"	""	""	""	"DHPR2"	"MNXR97459"	"HMR_8740"	"RCR13862"	""	0	""	""	"HMR_8740"