Skip to content

Commit

Permalink
added dehalogenation reactions
Browse files Browse the repository at this point in the history 
- enabled pce/tce/dce reductive dehalogenase reactions
  • Loading branch information
@jotech
jotech committed Apr 19, 2024
1 parent 8d4088a commit 0a77c68
Show file tree
Hide file tree
Showing 6 changed files with 11 additions and 6 deletions.
3 changes: 3 additions & 0 deletions dat/corrections_seed_reactionDB.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2687,3 +2687,6 @@ rxn29776 > -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd28763:1:0:"Inulin"
rxn90124 > -1:cpd28763:0:0:"Inulin";-11:cpd00001:0:0:"H2O";11:cpd00082:0:0:"D-Fructose";1:cpd00027:0:0:"D-Glucose" [JZ] inulinase, intracellular https://www.vmh.life/#reaction/INULINASE inulinase inulinase, intracellular

rxn27362 TRUE

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
1 change: 1 addition & 0 deletions dat/custom_pwy.tbl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,3 +50,4 @@ ISOBILE-BIOSYN iso-bile acids biosynthesis (NADH or NADPH dependent) iso-bile ac
|ARGDEGRAD-PWY2| L-arginine degradation V (arginine deiminase pathway) L-arginine degradation V (arginine deiminase pathway),L-arginine dihydrolase pathway,L-arginine deiminase degradation |THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|Amino-Acid-Degradation|,|Proteinogenic-Amino-Acids-Degradation|,|ARGININE-DEG| |TAX-2157|,|TAX-2759|,|TAX-2| ORNCARBAMTRANSFER-RXN,RXN-14196,RXN0-5222,ARGININE-DEIMINASE-RXN 2.1.3.3,2.7.2.2,,3.5.3.6 ORNCARBAMTRANSFER-RXN ornithine carbamoyltransferase, catabolic;carbamate kinase;cyanase;arginine deiminase 4 2 False True RXN0-5222
|PWY-8017-2| L-tryptophan degradation XIII (reductive Stickland reaction) L-tryptophan degradation XIII (reductive Stickland reaction),L-tryptophan reductive fermentation,L-tryptophan fermentation |Degradation|,|Amino-Acid-Degradation|,|Proteinogenic-Amino-Acids-Degradation|,|TRYPTOPHAN-DEG|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Energy-Metabolism|,|Fermentation|,|Amino-Acid-Fermentation|,|Stickland-Reductive| |TAX-2| RXN-19885,INDOLELACTATE-DEHYDROGENASE-RXN,TRYPTOPHAN-AMINOTRANSFERASE-RXN,RXN-19895,RXN-19896 1.3.8.15,1.1.1.110,2.6.1.1/2.6.1.27,2.8.3.17,4.2.1.175 (indolyl)propenoate reducatse;indole-3-pyruvate reductase;L-tryptophan transaminase;(indol-3-yl)-acryloyl-CoA:(indol-3-yl)-(R)-lactate CoA-transferase;(indol-3-yl)-(R)-lactoyl-CoA dehydratase False True
|ARGDEGRAD-PWY2| L-arginine degradation V (arginine deiminase pathway) L-arginine degradation V (arginine deiminase pathway),L-arginine dihydrolase pathway,L-arginine deiminase degradation |Super-Pathways|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|Amino-Acid-Degradation|,|Proteinogenic-Amino-Acids-Degradation|,|ARGININE-DEG| |TAX-2157|,|TAX-2759|,|TAX-2| ORNCARBAMTRANSFER-RXN,RXN-14196,RXN0-5222,ARGININE-DEIMINASE-RXN 2.1.3.3,,,3.5.3.6 ORNCARBAMTRANSFER-RXN ornithine carbamoyltransferase, catabolic;carbamate kinase;cyanase;arginine deiminase 4 2 False True RXN0-5222
|PCEDEG-PWY2| tetrachloroethene degradation II tetrachloroethene degradation,PCE degradation,perchloroethene degradation |THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|CHLORINATED-COMPOUNDS-DEG| |TAX-2| TCEREDCHLOR-RXN,1.97.1.8-RXN 1.21.99.M1/1.21.99.5,1.21.99.5 trichloroethene-reductive dehalogenase;tetrachloroethene reductive dehalogenase 2 2 False True
1 change: 1 addition & 0 deletions dat/medium_prediction_rules.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ O2 cpd00007 rxn05747 | rxn09272 | rxn08288 | rxn00145 12.5 FALSE Reactions from
CO2 cpd00011 "CALVIN-PWY" | "CODH-PWY" | "PWY-5789" | "PWY-7784" | "LWP-GS" | "METHANOGENESIS-PWY" 25 FALSE CO2 fixation, methanogenesis Inorganics
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

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
Expand Down
6 changes: 3 additions & 3 deletions dat/seed_metabolites_edited.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4085,9 +4085,9 @@ cpd04162 MNXM49278 Dexylosylpradimicin C Dexylosylpradimicin C C34H34N2O14 694 M
cpd04163 MNXM77916 Pradimicin C Pradimicin C C39H42N2O18 826 ModelSEED 0 1 0 null 0 -501.82 6.4319 44:2.24;47:9.51;14:10.09;35:12.5;55:13.09;10:7.16 55:-3.74;35:-3.73;58:-3.51;47:-3.81;14:-3.88;50:8.68 null null null COc1cc(O)c2c(c1)C(=O)c1c(C2=O)cc2c(c1O)c1c([C@@H]([C@H]2O)O[C@@H]2O[C@H](C)[C@@H]([C@@H]([C@H]2O)O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O)O)[NH3+])cc(c(c1O)C(=O)N[CH](C(=O)[O-])C)C IHIIRQILYAXIOH-NUVDETJMSA-M 8351 InChI=1S/C39H42N2O18/c1-10-5-17-23(30(48)20(10)36(52)41-11(2)37(53)54)22-15(8-16-24(31(22)49)27(45)14-6-13(55-4)7-18(42)21(14)26(16)44)28(46)34(17)58-39-33(51)35(25(40)12(3)57-39)59-38-32(50)29(47)19(43)9-56-38/h5-8,11-12,19,25,28-29,32-35,38-39,42-43,46-51H,9,40H2,1-4H3,(H,41,52)(H,53,54)/p-1/t11-,12-,19-,25+,28+,29+,32-,33-,34+,35+,38+,39+/m1/s1 C06786
cpd04164 MNXM49277 Dexylosylbenanomicin A Dexylosylbenanomicin A C34H32NO15 694 ModelSEED -1 1 0 null 0 -416.81 5.8651 16:13.31;42:9.45;14:7.18;10:10.07;47:2.54;37:12.61 50:-3.47;37:-3.74;45:-3.51;16:-3.49;42:-3.81;10:-3.88 null null null COc1cc(O)c2c(c1)C(=O)c1c(C2=O)cc2c(c1O)c1c([C@@H]([C@H]2O)O[C@@H]2O[C@H](C)[C@@H]([C@@H]([C@H]2O)O)O)cc(c(c1O)C(=O)N[CH](C(=O)[O-])C)C PRUXMUKWYBVNMB-OVAHQGMASA-L 4472 InChI=1S/C34H33NO15/c1-9-5-16-21(27(41)18(9)32(45)35-10(2)33(46)47)20-14(26(40)31(16)50-34-30(44)29(43)23(37)11(3)49-34)8-15-22(28(20)42)25(39)13-6-12(48-4)7-17(36)19(13)24(15)38/h5-8,10-11,23,26,29-31,34,36-37,40-44H,1-4H3,(H,35,45)(H,46,47)/p-2/t10?,11-,23+,26+,29+,30-,31+,34+/m1/s1 C06787
cpd04165 MNXM43425 Benanomicin A Benanomicin A C39H40NO19 826 ModelSEED -1 1 0 null 0 -537.07 6.44987 47:9.45;10:7.18;55:12.98;35:12.45;14:10.07;44:2.54 35:-3.74;55:-3.74;58:-3.51;19:-3.49;47:-3.81;14:-3.88 null null null COc1cc(O)c2c(c1)C(=O)c1c(C2=O)cc2c(c1O)c1c([C@@H]([C@H]2O)O[C@@H]2O[C@H](C)[C@@H]([C@@H]([C@H]2O)O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O)O)O)cc(c(c1O)C(=O)N[CH](C(=O)[O-])C)C GOYUMGXIFMGKFN-FWFMMWRZSA-L 3010 InChI=1S/C39H41NO19/c1-10-5-17-23(30(48)20(10)36(52)40-11(2)37(53)54)22-15(8-16-24(31(22)49)27(45)14-6-13(55-4)7-18(41)21(14)26(16)44)28(46)34(17)58-39-33(51)35(25(43)12(3)57-39)59-38-32(50)29(47)19(42)9-56-38/h5-8,11-12,19,25,28-29,32-35,38-39,41-43,46-51H,9H2,1-4H3,(H,40,52)(H,53,54)/p-2/t11?,12-,19-,25+,28+,29+,32-,33-,34+,35+,38+,39+/m1/s1 C06788
cpd04166 MNXM3102 PCE PCE C2Cl4 164 ModelSEED 0 1 0 null 0 6.52 2.08306 null null null ClC(=C(Cl)Cl)Cl CYTYCFOTNPOANT-UHFFFAOYSA-N HMDB41980 17300;15216;26890;9471 InChI=1S/C2Cl4/c3-1(4)2(5)6 C06789 TETRACHLOROETHENE
cpd04167 MNXM1198 TCE TCE C2HCl3 130 ModelSEED 0 1 0 null 0 5.86 1.22611 null null null ClC=C(Cl)Cl XSTXAVWGXDQKEL-UHFFFAOYSA-N HMDB29593 16602;15257;27099;9686 InChI=1S/C2HCl3/c3-1-2(4)5/h1H C06790 TRICHLOROETHENE
cpd04168 MNXM149903 trans-1,2-Dichloroethene trans-1,2-Dichloroethene C2H2Cl2 96 ModelSEED 0 1 0 null 0 7.12 1.34201 null null null Cl/C=C/Cl KFUSEUYYWQURPO-OWOJBTEDSA-N 18882;29027;10701;18808 InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+ C06791 TRANS-12-DCE
cpd04166 MNXM3102 PCE Tetrachloroethene C2Cl4 164 ModelSEED 0 1 0 null 0 6.52 2.08306 null null null ClC(=C(Cl)Cl)Cl CYTYCFOTNPOANT-UHFFFAOYSA-N HMDB41980 17300;15216;26890;9471 InChI=1S/C2Cl4/c3-1(4)2(5)6 C06789 TETRACHLOROETHENE
cpd04167 MNXM1198 TCE Trichloroethene C2HCl3 130 ModelSEED 0 1 0 null 0 5.86 1.22611 null null null ClC=C(Cl)Cl XSTXAVWGXDQKEL-UHFFFAOYSA-N HMDB29593 16602;15257;27099;9686 InChI=1S/C2HCl3/c3-1-2(4)5/h1H C06790 TRICHLOROETHENE
cpd04168 MNXM149903 DCE Dichloroethene C2H2Cl2 96 ModelSEED 0 1 0 null 0 7.12 1.34201 null null null Cl/C=C/Cl KFUSEUYYWQURPO-OWOJBTEDSA-N 18882;29027;10701;18808 InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+ C06791 TRANS-12-DCE
cpd04169 MNXM3235 cis-1,2-Dichloroethene cis-1,2-Dichloroethene C2H2Cl2 96 ModelSEED 0 1 0 null 0 7.12 1.34201 null null null Cl/C=C\Cl KFUSEUYYWQURPO-UPHRSURJSA-N 28805;10455;18623 InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1- C06792 DICHLOROETHENE
cpd04170 MNXM2007 Chloroethylene Chloroethylene C2H3Cl 62 ModelSEED 0 1 0 null 0 9.47 0.718267 null null null ClC=C BZHJMEDXRYGGRV-UHFFFAOYSA-N 39417 28509;27293;9990 InChI=1S/C2H3Cl/c1-2-3/h2H,1H2 C06793 VINYL-CHLORIDE
cpd04171 MNXM55652 Granaticin Granaticin C22H20O10 444 ModelSEED 0 1 0 null 0 10000000 10000000 16:14.65;11:9.73;9:12.5;30:18.92;15:11.45 9:-4.04;26:-3.54;11:-3.8;16:-3.32;13:-2.94;15:-3.79 null null null O=C1C[C@H]2[C@@H](O1)C1=C([C@@H](O2)C)C(=O)c2c(C1=O)c(O)c1c(c2O)[C@]2(O)[C@H](C[C@H]1O[C@@H]2C)O QBQXQYSJPWXZJL-NWVAQQJZSA-N 5533 InChI=1S/C22H20O10/c1-5-11-15(21-8(30-5)4-10(24)32-21)19(27)13-14(17(11)25)20(28)16-12(18(13)26)7-3-9(23)22(16,29)6(2)31-7/h5-9,21,23,26,28-29H,3-4H2,1-2H3/t5?,6-,7-,8+,9-,21-,22-/m1/s1 C06799 CPD-13960
Expand Down
4 changes: 2 additions & 2 deletions dat/seed_reactions_corrected.tsv
View file
Original file line number Diff line number Diff line change
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 R05499 R05499 (1) cpd04166[0] <=> (1) cpd00099[0] + (1) cpd04167[0] -1:cpd00067:0:0:"H+";-1:cpd04166:0:0:"PCE";1:cpd00099:0:0:"Cl-";1:cpd04167:0:0:"TCE" 0 (1) cpd00067[0] + (1) cpd04166[0] <=> (1) cpd00099[0] + (1) cpd04167[0] (1) H+[0] + (1) PCE[0] <=> (1) Cl-[0] + (1) TCE[0] = = 1e+07 1e+07 cpd00067;cpd00099;cpd04166;cpd04167 CI:-2 0 not.assessed
rxn03791 R05500 R05500 (1) cpd04167[0] <=> (1) cpd00099[0] + (1) cpd04168[0] -1:cpd00067:0:0:"H+";-1:cpd04167:0:0:"TCE";1:cpd00099:0:0:"Cl-";1:cpd04168:0:0:"trans-1,2-Dichloroethene" 0 (1) cpd00067[0] + (1) cpd04167[0] <=> (1) cpd00099[0] + (1) cpd04168[0] (1) H+[0] + (1) TCE[0] <=> (1) Cl-[0] + (1) trans-1,2-Dichloroethene[0] = = 1e+07 1e+07 cpd00067;cpd00099;cpd04167;cpd04168 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
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
Expand Down
2 changes: 1 addition & 1 deletion docs/conf.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
# -- Project information -----------------------------------------------------

project = 'gapseq'
copyright = '2023, Johannes Zimmermann and Silvio Waschina'
copyright = '2024, Johannes Zimmermann and Silvio Waschina'
author = 'Johannes Zimmermann and Silvio Waschina'


Expand Down

1 comment on commit 0a77c68

@jotech
Copy link
Owner Author

@jotech jotech commented on 0a77c68 Apr 23, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

refers #211

Please sign in to comment.