diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 80ca45d6..5524225a 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -230,6 +230,7 @@ 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" @@ -237,4 +238,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "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" \ No newline at end of file diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index bcdc71e0..295314c8 100644 --- 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 index 914232dd..34c5374f 100644 --- 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"