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corrected compartment for dehalogentation reactions
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- pce/tce dehalogenation reactions should take part outside the cytosol
- refers 0a77c68 and #211
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@jotech
jotech committed May 9, 2024
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4 changes: 2 additions & 2 deletions dat/corrections_seed_reactionDB.tsv
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Expand Up @@ -2688,5 +2688,5 @@ rxn90124 > -1:cpd28763:0:0:"Inulin";-11:cpd00001:0:0:"H2O";11:cpd00082:0:0:"D-F

rxn27362 -1:cpd00067:1:0:"H+";-1:cpd00047:0:0:"Formate";-1:cpd00180:1:0:"Oxalate";1:cpd00067:0:0:"H+";1:cpd00047:1:0:"Formate";1:cpd00180:0:0:"Oxalate" [SW] Charge-neutral antiport oxalate formate antiporter

rxn03790 > -1:cpd04166:0:0:"PCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:0:0:"Cl-";1:cpd04167:0:0:"TCE";1:cpd00067:0:0:"H+";1:cpd15500:0:0:"Menaquinone 8" [JZ] corrected direction, added missing electron carrier and changed wrong protonation https://biocyc.org/reaction?orgid=SMUL&id=1.97.1.8-RXN pcerd tetrachloroethene reductive dehalogenase
rxn03791 > -1:cpd04167:0:0:"TCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:0:0:"Cl-";1:cpd04168:0:0:"DCE";1:cpd00067:0:0:"H+";1:cpd15500:0:0:"Menaquinone 8" [JZ] corrected direction, added missing electron carrier and changed wrong protonation https://biocyc.org/reaction?orgid=SMUL&id=TCEREDCHLOR-RXN tcerd trichloroethene reductive dehalogenase
rxn03790 > -1:cpd04166:1:0:"PCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:1:0:"Cl-";1:cpd04167:1:0:"TCE";1:cpd00067:1:0:"H+";1:cpd15500:0:0:"Menaquinone 8" [JZ] corrected direction, added missing electron carrier and changed wrong protonation https://biocyc.org/reaction?orgid=SMUL&id=1.97.1.8-RXN pcerd tetrachloroethene reductive dehalogenase
rxn03791 > -1:cpd04167:1:0:"TCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:1:0:"Cl-";1:cpd04168:1:0:"DCE";1:cpd00067:1:0:"H+";1:cpd15500:0:0:"Menaquinone 8" [JZ] corrected direction, added missing electron carrier and changed wrong protonation https://biocyc.org/reaction?orgid=SMUL&id=TCEREDCHLOR-RXN tcerd trichloroethene reductive dehalogenase
1 change: 1 addition & 0 deletions dat/medium_prediction_rules.tsv
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Expand Up @@ -25,6 +25,7 @@ CO2 cpd00011 "CALVIN-PWY" | "CODH-PWY" | "PWY-5789" | "PWY-7784" | "LWP-GS" | "M
H2 cpd11640 "CODH-PWY" | "LWP-GS" | "METHANOGENESIS-PWY" | "PWY-7867" 100 FALSE Ljungdahl-Wood pathway, methanogenesis Inorganics
Photons cpd11632 "PWY-101" 50 FALSE photosynthesis light reactions Inorganics
PCE cpd04166 "PCEDEG-PWY" | "PCEDEG-PWY2" 25 FALSE Reductive dehalogenation Inorganics
O2 cpd00007 "PCEDEG-PWY" | "PCEDEG-PWY2" NA FALSE Add no oxygen for anaerobic respirations Inorganics

D-Glucose cpd00027 rxn05226 | rxn08612 5 TRUE D-glucose transport via PEP:Pyr PTS Saccharides
D-Glucose cpd00027 rxn05573 | rxn08616 5 TRUE D-glucose transport in via proton symport Saccharides
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4 changes: 2 additions & 2 deletions dat/seed_reactions_corrected.tsv
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Expand Up @@ -3729,8 +3729,8 @@ rxn03785 R05492 R05492 (1) cpd00007[0] + (1) cpd02815[0] <=> (1) cpd04053[0] -1:
rxn03786 R05493 R05493 (1) cpd00007[0] + (2) cpd04363[0] <=> (2) cpd00040[0] + (2) cpd01437[0] -1:cpd00007:0:0:"O2";-2:cpd04363:0:0:"4-CPA";2:cpd00040:0:0:"Glyoxalate";2:cpd01437:0:0:"p-Chlorophenol" 0 (1) cpd00007[0] + (2) cpd04363[0] => (2) cpd00040[0] + (2) cpd01437[0] (1) O2[0] + (2) 4-CPA[0] => (2) Glyoxalate[0] + (2) p-Chlorophenol[0] > > -99.64 1.12 cpd00007;cpd00040;cpd01437;cpd04363 OK 0 approved
rxn03787 R05495 R05495 (1) cpd00001[0] + (1) cpd04383[0] <=> (1) cpd04384[0] -1:cpd00001:0:0:"H2O";-1:cpd04383:0:0:"Ethylenzene";2:cpd00067:0:0:"H+";1:cpd04384:0:0:"1-Phenylethanol" 0 (1) cpd00001[0] + (1) cpd04383[0] <=> (2) cpd00067[0] + (1) cpd04384[0] (1) H2O[0] + (1) Ethylenzene[0] <=> (2) H+[0] + (1) 1-Phenylethanol[0] = = -4.09 1.02 cpd00001;cpd00067;cpd04383;cpd04384 CI:2 0 not.assessed
rxn03789 R05498 R05498 (1) cpd04170[0] <=> (1) cpd00099[0] + (1) cpd03956[0] -1:cpd00067:0:0:"H+";-1:cpd04170:0:0:"Chloroethylene";1:cpd00099:0:0:"Cl-";1:cpd03956:0:0:"Ethylene" 0 (1) cpd00067[0] + (1) cpd04170[0] <=> (1) cpd00099[0] + (1) cpd03956[0] (1) H+[0] + (1) Chloroethylene[0] <=> (1) Cl-[0] + (1) Ethylene[0] = = 1e+07 1e+07 cpd00067;cpd00099;cpd03956;cpd04170 CI:-2 0 not.assessed
rxn03790 pcerd tetrachloroethene reductive dehalogenase (1) cpd04166[0] <=> (1) cpd00099[0] + (1) cpd04167[0] -1:cpd04166:0:0:"PCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:0:0:"Cl-";1:cpd04167:0:0:"TCE";1:cpd00067:0:0:"H+";1:cpd15500:0:0:"Menaquinone 8" 0 (1) cpd04166[0] + (1) cpd15499[0] => (1) cpd00099[0] + (1) cpd04167[0] + (1) cpd00067[0] + (1) cpd15500[0] (1) PCE[0] + (1) Menaquinol 8[0] => (1) Cl-[0] + (1) TCE[0] + (1) H+[0] + (1) Menaquinone 8[0] > = 1e+07 1e+07 cpd00067;cpd00099;cpd04166;cpd04167 CI:-2 0 corrected
rxn03791 tcerd trichloroethene reductive dehalogenase (1) cpd04167[0] <=> (1) cpd00099[0] + (1) cpd04168[0] -1:cpd04167:0:0:"TCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:0:0:"Cl-";1:cpd04168:0:0:"DCE";1:cpd00067:0:0:"H+";1:cpd15500:0:0:"Menaquinone 8" 0 (1) cpd04167[0] + (1) cpd15499[0] => (1) cpd00099[0] + (1) cpd04168[0] + (1) cpd00067[0] + (1) cpd15500[0] (1) TCE[0] + (1) Menaquinol 8[0] => (1) Cl-[0] + (1) DCE[0] + (1) H+[0] + (1) Menaquinone 8[0] > = 1e+07 1e+07 cpd00067;cpd00099;cpd04167;cpd04168 CI:-2 0 corrected
rxn03790 pcerd tetrachloroethene reductive dehalogenase (1) cpd04166[0] <=> (1) cpd00099[0] + (1) cpd04167[0] -1:cpd04166:1:0:"PCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:1:0:"Cl-";1:cpd04167:1:0:"TCE";1:cpd00067:1:0:"H+";1:cpd15500:0:0:"Menaquinone 8" 0 (1) cpd04166[1] + (1) cpd15499[0] => (1) cpd00099[1] + (1) cpd04167[1] + (1) cpd00067[1] + (1) cpd15500[0] (1) PCE[1] + (1) Menaquinol 8[0] => (1) Cl-[1] + (1) TCE[1] + (1) H+[1] + (1) Menaquinone 8[0] > = 1e+07 1e+07 cpd00067;cpd00099;cpd04166;cpd04167 CI:-2 0 corrected
rxn03791 tcerd trichloroethene reductive dehalogenase (1) cpd04167[0] <=> (1) cpd00099[0] + (1) cpd04168[0] -1:cpd04167:1:0:"TCE";-1:cpd15499:0:0:"Menaquinol 8";1:cpd00099:1:0:"Cl-";1:cpd04168:1:0:"DCE";1:cpd00067:1:0:"H+";1:cpd15500:0:0:"Menaquinone 8" 0 (1) cpd04167[1] + (1) cpd15499[0] => (1) cpd00099[1] + (1) cpd04168[1] + (1) cpd00067[1] + (1) cpd15500[0] (1) TCE[1] + (1) Menaquinol 8[0] => (1) Cl-[1] + (1) DCE[1] + (1) H+[1] + (1) Menaquinone 8[0] > = 1e+07 1e+07 cpd00067;cpd00099;cpd04167;cpd04168 CI:-2 0 corrected
rxn03792 R05501 R05501 (1) cpd04167[0] <=> (1) cpd00099[0] + (1) cpd04169[0] -1:cpd00067:0:0:"H+";-1:cpd04167:0:0:"TCE";1:cpd00099:0:0:"Cl-";1:cpd04169:0:0:"cis-1,2-Dichloroethene" 0 (1) cpd00067[0] + (1) cpd04167[0] <=> (1) cpd00099[0] + (1) cpd04169[0] (1) H+[0] + (1) TCE[0] <=> (1) Cl-[0] + (1) cis-1,2-Dichloroethene[0] = = 1e+07 1e+07 cpd00067;cpd00099;cpd04167;cpd04169 CI:-2 0 not.assessed
rxn03793 R05502 R05502 (1) cpd04168[0] <=> (1) cpd00099[0] + (1) cpd04170[0] -1:cpd00067:0:0:"H+";-1:cpd04168:0:0:"trans-1,2-Dichloroethene";1:cpd00099:0:0:"Cl-";1:cpd04170:0:0:"Chloroethylene" 0 (1) cpd00067[0] + (1) cpd04168[0] <=> (1) cpd00099[0] + (1) cpd04170[0] (1) H+[0] + (1) trans-1,2-Dichloroethene[0] <=> (1) Cl-[0] + (1) Chloroethylene[0] = = 1e+07 1e+07 cpd00067;cpd00099;cpd04168;cpd04170 CI:-2 0 not.assessed
rxn03794 R05503 R05503 (1) cpd04169[0] <=> (1) cpd00099[0] + (1) cpd04170[0] -1:cpd00067:0:0:"H+";-1:cpd04169:0:0:"cis-1,2-Dichloroethene";1:cpd00099:0:0:"Cl-";1:cpd04170:0:0:"Chloroethylene" 0 (1) cpd00067[0] + (1) cpd04169[0] <=> (1) cpd00099[0] + (1) cpd04170[0] (1) H+[0] + (1) cis-1,2-Dichloroethene[0] <=> (1) Cl-[0] + (1) Chloroethylene[0] = = 1e+07 1e+07 cpd00067;cpd00099;cpd04169;cpd04170 CI:-2 0 not.assessed
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