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Update Reaction DB
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refers to #54.

Enables synthrophic Acetate oxidation via Wood-Ljungdahl pathway. Tested
for _Syntrophaceticus schinkii_ (Refseq accession: GCF_000946815.1)
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@Waschina
Waschina committed Feb 11, 2021
1 parent f656f94 commit 35da59e
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Showing 11 changed files with 52 additions and 17 deletions.
7 changes: 6 additions & 1 deletion dat/corrections_seed_reactionDB.tsv
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Expand Up @@ -2238,7 +2238,7 @@ rxn10430 > [SW] direction changed according to MetaCyc https://metacyc.org/MET

rxn90057 = -4:cpd00067:0:0:"H+";-2:cpd11620:0:0:"Reducedferredoxin";2:cpd11621:0:0:"Oxidizedferredoxin";1:cpd11640:0:0:"H2";2:cpd00067:1:0:"H+" [JZ] rxn05759 can be reversible when linked to membrane potential http://dx.doi.org/10.1038/nrmicro1931 ECHAF ferredoxin hydrogenase (chemiosmosis)
rxn90058 = -3:cpd00067:0:0:"H+";-1:cpd02935:0:0:"CoM-S-S-CoB";-1:cpd08702:0:0:"Dihydromethanophenazine";1:cpd02246:0:0:"CoM";1:cpd02817:0:0:"HTP";1:cpd08701:0:0:"Methanophenazine";2:cpd00067:1:0:"H+" [JZ] rxn03126 can be reversible when linked to membrane potential http://dx.doi.org/10.1038/nrmicro1931 Coenzyme B:coenzyme M:methanophenazine oxidoreductase (chemiosmosis)
rxn90059 = -2:cpd00067:0:0:"H+";-1:cpd08701:0:0:"Methanophenazine";-1:cpd11640:0:0:"H2";1:cpd08702:0:0:"Dihydromethanophenazine";2:cpd00067:1:0:"H+" [JZ] rxn16961 can be reversible when linked to membrane potential http://dx.doi.org/10.1038/nrmicro1931 hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase (chemiosmosis)
rxn90059 < -2:cpd00067:0:0:"H+";-1:cpd08701:0:0:"Methanophenazine";-1:cpd11640:0:0:"H2";1:cpd08702:0:0:"Dihydromethanophenazine";2:cpd00067:1:0:"H+" [JZ] rxn16961 can be reversible when linked to membrane potential http://dx.doi.org/10.1038/nrmicro1931 hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase (chemiosmosis)
rxn15961 > [JZ] direction changed according to MetaCyc + Thauer2008 https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-7733 http://dx.doi.org/10.1038/nrmicro1931
rxn90060 > -1:cpd28763:1:0:"(2,1-beta-D-fructan)";-9:cpd00001:1:0:"H2O";9:cpd00082:1:0:"D-Fructose";1:cpd02298:1:0:"1F-beta-D-Fructosylsucrose" [SW] New reaction for inulin/fructan degradation step 1 https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=3.2.1.153-RXN inulinase fructan beta-(2,1)-fructosidase (extracellular)
rxn23749 > -1:cpd00001:0:0:"H2O";-1:cpd02298:0:0:"1F-beta-D-Fructosylsucrose";1:cpd00076:0:0:"Sucrose";1:cpd00082:0:0:"D-Fructose" [SW] Reaction needed for 1-Kestotriose degradation https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-1841
Expand Down Expand Up @@ -2338,3 +2338,8 @@ rxn10480 -1:cpd00067:1:0:"H+";-1:cpd00204:0:0:"CO";1:cpd00204:1:0:"CO";1:cpd00
rxn03641 > [SW] Corrected according to MetaCyc https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-8889
rxn03642 > [SW] Corrected according to MetaCyc https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-20447
rxn14087 -1:cpd00308:0:0:"Malonate";-1:cpd11494:0:0:"Acetyl-ACP";1:cpd00029:0:0:"Acetate";1:cpd11492:0:0:"Malonyl-acyl-carrierprotein-" [SW] Mass and charge balanced

rxn15620 > [SW] Corrected according to MetaCyc https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-15105
rxn15621 > [SW] Corrected according to MetaCyc https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-15105
rxn14350 > [SW] Corrected according to MetaCyc https://metacyc.org/META/NEW-IMAGE?object=ERYTHRONOLIDE-SYNTHASE-RXN&&redirect=T
rxn14196 > [SW] Corrected according to MetaCyc https://metacyc.org/META/NEW-IMAGE?object=ERYTHRONOLIDE-SYNTHASE-RXN&&redirect=T
1 change: 1 addition & 0 deletions dat/env/env_highH2.tsv
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Expand Up @@ -7,3 +7,4 @@ rxn09184 <
rxn06696 >
rxn10519 >
rxn10517 >
rxn90059 >
Binary file modified dat/full.model.RDS
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6 changes: 3 additions & 3 deletions dat/gapseq_reactions.html
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Large diffs are not rendered by default.

25 changes: 25 additions & 0 deletions dat/media/MM_anaerobic_Acetate.csv
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@@ -0,0 +1,25 @@
compounds,name,maxFlux
cpd00001,H2O,1000
cpd00029,Acetate,100
cpd11640,H2,0
cpd00009,Phosphate,100
cpd00030,Mn2+,100
cpd00034,Zn2+,100
cpd00048,Sulfate,100
cpd00058,Cu2+,100
cpd00063,Ca2+,100
cpd00067,H+,100
cpd00099,Cl-,100
cpd00149,Co2+,100
cpd00205,K+,100
cpd00254,Mg,100
cpd00531,Hg2+,100
cpd00971,Na+,100
cpd01012,Cd2+,100
cpd01048,Arsenate,100
cpd10515,Fe2+,100
cpd10516,fe3,0.01
cpd11595,chromate,100
cpd00013,NH3,100
cpd11574,Molybdate,100
cpd00244,Ni2+,100
9 changes: 6 additions & 3 deletions dat/seed_Enzyme_Class_Reactions_Aliases_unique_edited.tsv
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Expand Up @@ -1032,7 +1032,7 @@ rxn05938|rxn07824|rxn10951|rxn13974|rxn14178|rxn20651 rxn05938|rxn07824|rxn10951
rxn16328|rxn22375 1.2.7.10 Enzyme Class
rxn05940|rxn14178|rxn17398 rxn05940|rxn12777|rxn14178 1.2.7.2 Enzyme Class
rxn14048|rxn17399|rxn31312 rxn05939|rxn14048 1.2.7.3 Enzyme Class
rxn07189|rxn15962|rxn16153|rxn16164|rxn17208|rxn33372 rxn07189|rxn07824 1.2.7.4 Enzyme Class
rxn07189|rxn16153|rxn16164|rxn17208|rxn33372 rxn07189|rxn07824 1.2.7.4 Enzyme Class
rxn07190|rxn07191|rxn17209 rxn07190 1.2.7.5 Enzyme Class
rxn07191|rxn17211 rxn07191 1.2.7.6 Enzyme Class
rxn05940|rxn13962|rxn14109|rxn14152|rxn17212 rxn13962|rxn14109|rxn14152 1.2.7.7 Enzyme Class
Expand Down Expand Up @@ -2956,7 +2956,7 @@ rxn00755 rxn00755 2.8.2.6 Enzyme Class
rxn03088 rxn03088 2.8.2.7 Enzyme Class
rxn06101|rxn14032|rxn19888 rxn06101|rxn14032 2.8.2.8 Enzyme Class
rxn02941 rxn02941 2.8.2.9 Enzyme Class
rxn00990|rxn01056|rxn03641|rxn04713|rxn07623|rxn07671|rxn07886|rxn08254|rxn09174|rxn14349|rxn16143|rxn20020 rxn04713|rxn07671|rxn07886|rxn14349 2.8.3.- Enzyme Class
rxn00990|rxn01056|rxn03641|rxn04713|rxn07623|rxn07671|rxn07886|rxn08254|rxn09174|rxn14349|rxn20020 rxn04713|rxn07671|rxn07886|rxn14349 2.8.3.- Enzyme Class
rxn00677|rxn01056|rxn03798 rxn00677|rxn01056|rxn03798 2.8.3.1 Enzyme Class
rxn00972|rxn19317 rxn00972 2.8.3.10 Enzyme Class
rxn02120|rxn02257 rxn02120|rxn02257 2.8.3.11 Enzyme Class
Expand Down Expand Up @@ -4213,7 +4213,7 @@ rxn01316 4.1.3.19 Enzyme Class
rxn00330|rxn33881 rxn00330 4.1.3.2 Enzyme Class
rxn00202 4.1.3.21 Enzyme Class
rxn00234 rxn00177|rxn00234|rxn02257 4.1.3.22 Enzyme Class
rxn00177|rxn00331|rxn00682 rxn00331 4.1.3.24 Enzyme Class
rxn00331|rxn00682 rxn00331 4.1.3.24 Enzyme Class
rxn00177 rxn00177 4.1.3.25 Enzyme Class
rxn02987|rxn06638|rxn07879 rxn02987|rxn06638|rxn07879 4.1.3.26 Enzyme Class
rxn00726|rxn00727|rxn33991 rxn00726|rxn00727 4.1.3.27 Enzyme Class
Expand Down Expand Up @@ -4371,6 +4371,8 @@ rxn03236|rxn13714|rxn24515 rxn03236|rxn13714 4.2.1.96 Enzyme Class
rxn03233 rxn03233 4.2.1.97 Enzyme Class
rxn02908|rxn03510 rxn02908|rxn03510 4.2.1.98 Enzyme Class
rxn03061|rxn33768 rxn03061 4.2.1.99 Enzyme Class
rxn03440 4.2.1.148 Enzyme Class
rxn16142 4.2.1.153 Enzyme Class
rxn21843|rxn21844|rxn21845 4.2.2.- Enzyme Class
rxn06170|rxn19906 rxn06170 4.2.2.1 Enzyme Class
rxn18938 4.2.2.10 Enzyme Class
Expand Down Expand Up @@ -4762,6 +4764,7 @@ rxn05068|rxn05069 rxn05068|rxn05069 5.3.99.8 Enzyme Class
rxn04757|rxn04760|rxn26507 rxn04757 5.3.99.9 Enzyme Class
rxn02391|rxn20062 rxn02391 5.4.1.1 Enzyme Class
rxn03512|rxn04052 rxn03512|rxn04052 5.4.1.2 Enzyme Class
rxn16143 5.4.1.3 Enzyme Class
rxn01106|rxn01216|rxn18917|rxn33847 rxn01106|rxn01216 5.4.2.1 Enzyme Class
rxn01485|rxn32446 rxn01485 5.4.2.10 Enzyme Class
rxn01106|rxn18917|rxn33847 rxn01106 5.4.2.11 Enzyme Class
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