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DB correction: aromonatic amino acid decarboxylases
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... and transporters for amine products.
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@Waschina
Waschina committed Jul 28, 2023
1 parent e3210c0 commit 0386575
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Showing 4 changed files with 27 additions and 12 deletions.
13 changes: 12 additions & 1 deletion dat/corrections_seed_reactionDB.tsv
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Expand Up @@ -1215,7 +1215,6 @@ rxn05687 > [SW] ptrc:H+ symport only described for import https://metacyc.org/
rxn10560 < H+-coupled transport w/o chemical transformation of transported molecule should work only in the direction where protons are imported. transport
rxn12526 < H+-coupled transport w/o chemical transformation of transported molecule should work only in the direction where protons are imported. transport
rxn12527 < H+-coupled transport w/o chemical transformation of transported molecule should work only in the direction where protons are imported. transport
rxn12533 < H+-coupled transport w/o chemical transformation of transported molecule should work only in the direction where protons are imported. transport
rxn12567 < H+-coupled transport w/o chemical transformation of transported molecule should work only in the direction where protons are imported. transport
rxn12586 < H+-coupled transport w/o chemical transformation of transported molecule should work only in the direction where protons are imported. transport
rxn12597 < H+-coupled transport w/o chemical transformation of transported molecule should work only in the direction where protons are imported. transport
Expand Down Expand Up @@ -2646,3 +2645,15 @@ rxn46031 < -1:cpd00067:0:0:"H+";-1:cpd01202:0:0:"Phloretate";-1:cpd27005:0:0:"E
rxn90117 = -1:cpd01202:0:0:"Phloretate";-1:cpd00067:0:0:"H+";1:cpd01202:1:0:"Phloretate";1:cpd00067:1:0:"H+" [SW] Transport reaction for Phloretate Phloretate-transport Phloretate-transport

rxn41427 > -3:cpd00067:0:0:"H+";-1:cpd00239:0:0:"H2S";-1:cpd00346:0:0:"L-Aspartate4-semialdehyde";-2:cpd11620:0:0:"Reducedferredoxin";1:cpd00001:0:0:"H2O";1:cpd00135:0:0:"Homocysteine";2:cpd11621:0:0:"Oxidizedferredoxin" [SW] Key-reaction in a methionine bionsynthetic pathway. MetaCyc ID PWY-7977 https://metacyc.org/META/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=RXN-19380 asd-S-transferase L-aspartate semialdehyde sulfurtransferase
rxn32690 TRUE [SW] duplicate reaction to rxn00484
rxn09326 TRUE [SW] duplicate reaction to rxn05663
rxn09709 TRUE [SW] duplicate reaction to rxn05663
rxn34411 TRUE [SW] duplicate reaction to rxn05663
rxn32036 TRUE [SW] duplicate reaction to rxn32033
rxn32039 TRUE [SW] duplicate reaction to rxn32033
rxn31860 TRUE [SW] duplicate reaction to rxn14082
rxn31864 TRUE [SW] duplicate reaction to rxn14082

rxn90118 = -1:cpd00067:1:0:"H+";-1:cpd00318:0:0:"Tryptamine";1:cpd00318:1:0:"Tryptamine";1:cpd00067:0:0:"H+" [SW] Tryptamine-proton Antiport to ensure charge-neutral transport transport tryptamine-proton-antiporter Tryptamine transport via proton antiport
rxn05686 TRUE [SW] Reaction is not charge neutral (tranport of net-charge 2)
rxn90119 = -1:cpd00067:1:0:"H+";-1:cpd00374:0:0:"Tyramine";1:cpd00374:1:0:"Tyramine";1:cpd00067:0:0:"H+" [SW] Tyramine-proton Antiport to ensure charge-neutral transport transport Tyramine-proton-antiporter Tyramine transport via proton antiport
3 changes: 2 additions & 1 deletion dat/nutrients.tsv
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Expand Up @@ -187,7 +187,7 @@ cpd00266 Carnitine C7H15NO3 0 MNXM173
cpd00268 Thiosulfate HO3S2 -1 MNXM323
cpd00269 2-Oxoadipate C6H6O5 -2 MNXM263
cpd00274 Citrulline C6H13N3O3 0 MNXM211
cpd00276 GLUM C6H14NO5 1 MNXM533
cpd00276 D-Glucosamine C6H14NO5 1 MNXM533
cpd00277 Deoxyguanosine C10H13N5O4 0 MNXM647
cpd00280 D-Galacturonate C6H9O7 -1 MNXM48464
cpd00281 GABA C4H9NO2 0 MNXM192
Expand All @@ -209,6 +209,7 @@ cpd00311 Guanosine C10H13N5O5 0 MNXM401
cpd00312 Histamine C5H10N3 1 MNXM635
cpd00313 Quercetin C15H9O7 -1 MNXM620
cpd00314 D-Mannitol C6H14O6 0 MNXM615
cpd00318 Tryptamine C10H13N2 1 MNXM806
cpd00320 D-Aspartate C4H6NO4 -1 MNXM974
cpd00322 L-Isoleucine C6H13NO2 0 MNXM231
cpd00324 Methanethiol CH4S 0 MNXM652
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1 change: 1 addition & 0 deletions dat/seed_Enzyme_Class_Reactions_Aliases_unique_edited.tsv
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Expand Up @@ -4180,6 +4180,7 @@ rxn16805 4.1.1.94 Enzyme Class
rxn20838 4.1.1.99 Enzyme Class
rxn41263 4.1.1.110 Enzyme Class
rxn11132 4.1.1.101 Enzyme Class
rxn00484 4.1.1.105 Enzyme Class
rxn01202|rxn01203|rxn01334|rxn01619|rxn02351|rxn03458|rxn03884|rxn03920|rxn15748|rxn15750|rxn23641|rxn26038|rxn26435 rxn01202|rxn01203|rxn01619|rxn02351|rxn03458|rxn03643|rxn03920 4.1.2.- Enzyme Class
rxn01296|rxn05998|rxn06250|rxn20170|rxn31668 rxn01296|rxn05998|rxn06250|rxn13959 4.1.2.10 Enzyme Class
rxn01935|rxn05998|rxn06250|rxn19917|rxn31668 rxn01935|rxn05998|rxn06250|rxn13959 4.1.2.11 Enzyme Class
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