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added chlorobenzene degradation reactions
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- added gapseq reactions matching the chlorobenzene degradation pathways
  from metacyc
- testing if chlorobenze degradation works in fba models needs to be
  done
- refers #211
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@jotech
jotech committed May 9, 2024
1 parent deb77f2 commit 2d739a5
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Showing 4 changed files with 14 additions and 4 deletions.
5 changes: 5 additions & 0 deletions dat/corrections_seed_reactionDB.tsv
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Expand Up @@ -2690,3 +2690,8 @@ rxn27362 -1:cpd00067:1:0:"H+";-1:cpd00047:0:0:"Formate";-1:cpd00180:1:0:"Oxala

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

rxn25906 TRUE
rxn25907 TRUE
rxn25893 TRUE
rxn25894 TRUE
3 changes: 3 additions & 0 deletions dat/nutrients.tsv
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Expand Up @@ -491,6 +491,9 @@ cpd04073 Vanillate C8H7O4 -1 MNXM982
cpd04098 Arsenite H2AsO3 -1 MNXM658
cpd04099 Phosphonate H2O3P -1 MNXM1683
cpd04136 p-Xylene C8H10 0 MNXM3685
cpd04166 Tetrachloroethene C2Cl4 0 MNXM3102
cpd04167 Trichloroethene C2HCl3 0 MNXM1198
cpd04168 Dichloroethene C2H2Cl2 0 MNXM149903
cpd04446 m-Xylene C8H10 0 MNXM3300
cpd04533 Isoamyl alcohol C5H12O 0 MNXM1670
cpd04534 3-Methylbutanal C5H10O 0 MNXM1711
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2 changes: 2 additions & 0 deletions dat/seed_Enzyme_Class_Reactions_Aliases_unique_edited.tsv
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Expand Up @@ -607,6 +607,7 @@ rxn04597|rxn04598 rxn04597|rxn04598 1.14.12.19 Enzyme Class
rxn14170 rxn14170 1.14.12.20 Enzyme Class
rxn16399 1.14.12.21 Enzyme Class
rxn03714|rxn16354|rxn21900 1.14.12.22 Enzyme Class
rxn04646|rxn25906|rxn04671|rxn25893 1.14.12.26 Enzyme Class
rxn02526 rxn02526 1.14.12.3 Enzyme Class
rxn02427|rxn02428|rxn17067 rxn02427|rxn02428 1.14.12.4 Enzyme Class
rxn03139 rxn03139 1.14.12.5 Enzyme Class
Expand Down Expand Up @@ -1086,6 +1087,7 @@ rxn90056|rxn90054 1.3.1.110 Enzyme Class
rxn43871|rxn90082 1.3.1.114 Enzyme Class
rxn19220|rxn41945 1.3.1.115 Enzyme Class
rxn41554|rxn90081 1.3.1.116 Enzyme Class
rxn04647|rxn25907|rxn04672|rxn25894 1.3.1.119 Enzyme Class
rxn01268 rxn01268 1.3.1.12 Enzyme Class
rxn01269 rxn01269 1.3.1.13 Enzyme Class
rxn01361 rxn01361 1.3.1.14 Enzyme Class
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8 changes: 4 additions & 4 deletions dat/seed_reactions_corrected.tsv
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Expand Up @@ -22603,8 +22603,8 @@ rxn25889 RXN-9850.c RXN-9850.c (1) cpd00010[0] + (1) cpd22729[0] <=> (1) cpd0008
rxn25890 RXN-9850.x RXN-9850.x (1) cpd00010[0] + (1) cpd22729[0] <=> (1) cpd00086[0] + (1) cpd03164[0] -1:cpd00010:0:0:"CoA";-1:cpd00067:0:0:"H+";-1:cpd22729:0:0:"3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestanoyl CoA";1:cpd00086:0:0:"Propionyl-CoA";1:cpd03164:0:0:"Chenodeoxycholoyl-CoA" 0 (1) cpd00010[0] + (1) cpd00067[0] + (1) cpd22729[0] <=> (1) cpd00086[0] + (1) cpd03164[0] (1) CoA[0] + (1) H+[0] + (1) 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestanoyl CoA[0] <=> (1) Propionyl-CoA[0] + (1) Chenodeoxycholoyl-CoA[0] = = -5.25 1.09 cpd00010;cpd00067;cpd00086;cpd03164;cpd22729 OK 1 rxn25889 HB rxn25889 not.assessed
rxn25891 RXN-9851.x RXN-9851.x (1) cpd00033[0] + (1) cpd03164[0] <=> (1) cpd00010[0] + (1) cpd03243[0] -1:cpd00033:0:0:"Glycine";-1:cpd03164:0:0:"Chenodeoxycholoyl-CoA";1:cpd00010:0:0:"CoA";2:cpd00067:0:0:"H+";1:cpd03243:0:0:"Chenodeoxyglycocholate" 0 (1) cpd00033[0] + (1) cpd03164[0] => (1) cpd00010[0] + (2) cpd00067[0] + (1) cpd03243[0] (1) Glycine[0] + (1) Chenodeoxycholoyl-CoA[0] => (1) CoA[0] + (2) H+[0] + (1) Chenodeoxyglycocholate[0] > > -5.29 1.26 cpd00010;cpd00033;cpd00067;cpd03164;cpd03243 OK 0 HB not.assessed
rxn25892 RXN-9852.x RXN-9852.x (1) cpd00210[0] + (1) cpd03164[0] <=> (1) cpd00010[0] + (1) cpd03246[0] -1:cpd00210:0:0:"Taurine";-1:cpd03164:0:0:"Chenodeoxycholoyl-CoA";1:cpd00010:0:0:"CoA";2:cpd00067:0:0:"H+";1:cpd03246:0:0:"Taurochenodeoxycholate" 0 (1) cpd00210[0] + (1) cpd03164[0] => (1) cpd00010[0] + (2) cpd00067[0] + (1) cpd03246[0] (1) Taurine[0] + (1) Chenodeoxycholoyl-CoA[0] => (1) CoA[0] + (2) H+[0] + (1) Taurochenodeoxycholate[0] > > -5.29 1.26 cpd00010;cpd00067;cpd00210;cpd03164;cpd03246 OK 1 rxn14228 HB rxn14228 approved
rxn25893 RXN-9853.c RXN-9853.c (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd20653[0] <=> (1) cpd00003[0] + (1) cpd22735[0] -1:cpd00004:0:0:"NADH";-1:cpd00007:0:0:"O2";-1:cpd00067:0:0:"H+";-1:cpd20653:0:0:"1,3-Dichlorobenzene";1:cpd00003:0:0:"NAD";1:cpd22735:0:0:"1,3-dichlorobenzene dihydrodiol" 0 (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd00067[0] + (1) cpd20653[0] => (1) cpd00003[0] + (1) cpd22735[0] (1) NADH[0] + (1) O2[0] + (1) H+[0] + (1) 1,3-Dichlorobenzene[0] => (1) NAD[0] + (1) 1,3-dichlorobenzene dihydrodiol[0] > > -71.1 1.92 cpd00003;cpd00004;cpd00007;cpd00067;cpd20653;cpd22735 OK 0 not.assessed
rxn25894 RXN-9854.c RXN-9854.c (1) cpd00003[0] + (1) cpd22735[0] <=> (1) cpd00004[0] + (1) cpd01878[0] -1:cpd00003:0:0:"NAD";-1:cpd22735:0:0:"1,3-dichlorobenzene dihydrodiol";1:cpd00004:0:0:"NADH";1:cpd00067:0:0:"H+";1:cpd01878:0:0:"3,5-Dichlorocatechol" 0 (1) cpd00003[0] + (1) cpd22735[0] => (1) cpd00004[0] + (1) cpd00067[0] + (1) cpd01878[0] (1) NAD[0] + (1) 1,3-dichlorobenzene dihydrodiol[0] => (1) NADH[0] + (1) H+[0] + (1) 3,5-Dichlorocatechol[0] > > -11.78 2.08 cpd00003;cpd00004;cpd00067;cpd01878;cpd22735 OK 0 not.assessed
rxn25893 RXN-9853.c RXN-9853.c (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd20653[0] <=> (1) cpd00003[0] + (1) cpd22735[0] -1:cpd00004:0:0:"NADH";-1:cpd00007:0:0:"O2";-1:cpd00067:0:0:"H+";-1:cpd20653:0:0:"1,3-Dichlorobenzene";1:cpd00003:0:0:"NAD";1:cpd22735:0:0:"1,3-dichlorobenzene dihydrodiol" 0 (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd00067[0] + (1) cpd20653[0] => (1) cpd00003[0] + (1) cpd22735[0] (1) NADH[0] + (1) O2[0] + (1) H+[0] + (1) 1,3-Dichlorobenzene[0] => (1) NAD[0] + (1) 1,3-dichlorobenzene dihydrodiol[0] > > -71.1 1.92 cpd00003;cpd00004;cpd00007;cpd00067;cpd20653;cpd22735 OK 0 approved
rxn25894 RXN-9854.c RXN-9854.c (1) cpd00003[0] + (1) cpd22735[0] <=> (1) cpd00004[0] + (1) cpd01878[0] -1:cpd00003:0:0:"NAD";-1:cpd22735:0:0:"1,3-dichlorobenzene dihydrodiol";1:cpd00004:0:0:"NADH";1:cpd00067:0:0:"H+";1:cpd01878:0:0:"3,5-Dichlorocatechol" 0 (1) cpd00003[0] + (1) cpd22735[0] => (1) cpd00004[0] + (1) cpd00067[0] + (1) cpd01878[0] (1) NAD[0] + (1) 1,3-dichlorobenzene dihydrodiol[0] => (1) NADH[0] + (1) H+[0] + (1) 3,5-Dichlorocatechol[0] > > -11.78 2.08 cpd00003;cpd00004;cpd00067;cpd01878;cpd22735 OK 0 approved
rxn25895 RXN-9861.c RXN-9861.c (1) cpd02243[0] <=> (1) cpd22750[0] -1:cpd00067:0:0:"H+";-1:cpd02243:0:0:"2-Chloro-cis,cis-muconate";1:cpd22750:0:0:"(+)-2-chloromuconolactone" 0 (1) cpd00067[0] + (1) cpd02243[0] <=> (1) cpd22750[0] (1) H+[0] + (1) 2-Chloro-cis,cis-muconate[0] <=> (1) (+)-2-chloromuconolactone[0] = = 0.52 1.35 cpd00067;cpd02243;cpd22750 OK 0 not.assessed
rxn25896 RXN-9864.c RXN-9864.c (1) cpd00007[0] + (1) cpd00024[0] + (1) cpd19792[0] <=> (1) cpd00011[0] + (1) cpd00036[0] + (1) cpd00040[0] + (1) cpd02134[0] -1:cpd00007:0:0:"O2";-1:cpd00024:0:0:"2-Oxoglutarate";-1:cpd19792:0:0:"MCPA";1:cpd00011:0:0:"CO2";1:cpd00036:0:0:"Succinate";1:cpd00040:0:0:"Glyoxalate";1:cpd02134:0:0:"4-Chloro-2-methylphenol" 0 (1) cpd00007[0] + (1) cpd00024[0] + (1) cpd19792[0] => (1) cpd00011[0] + (1) cpd00036[0] + (1) cpd00040[0] + (1) cpd02134[0] (1) O2[0] + (1) 2-Oxoglutarate[0] + (1) MCPA[0] => (1) CO2[0] + (1) Succinate[0] + (1) Glyoxalate[0] + (1) 4-Chloro-2-methylphenol[0] > > -118.1 0.87 cpd00007;cpd00011;cpd00024;cpd00036;cpd00040;cpd02134;cpd19792 OK 0 not.assessed
rxn25897 RXN-9866.c 4-chloro-2-methylphenol hydroxylase (1) cpd00005[0] + (1) cpd00007[0] + (1) cpd02134[0] <=> (1) cpd00001[0] + (1) cpd00006[0] + (1) cpd02260[0] -1:cpd00005:0:0:"NADPH";-1:cpd00007:0:0:"O2";-1:cpd00067:0:0:"H+";-1:cpd02134:0:0:"4-Chloro-2-methylphenol";1:cpd00001:0:0:"H2O";1:cpd00006:0:0:"NADP";1:cpd02260:0:0:"5-Chloro-3-methylcatechol" 0 (1) cpd00005[0] + (1) cpd00007[0] + (1) cpd00067[0] + (1) cpd02134[0] => (1) cpd00001[0] + (1) cpd00006[0] + (1) cpd02260[0] (1) NADPH[0] + (1) O2[0] + (1) H+[0] + (1) 4-Chloro-2-methylphenol[0] => (1) H2O[0] + (1) NADP[0] + (1) 5-Chloro-3-methylcatechol[0] > > -95.83 1.31 cpd00001;cpd00005;cpd00006;cpd00007;cpd00067;cpd02134;cpd02260 OK 0 not.assessed
Expand All @@ -22616,8 +22616,8 @@ rxn25902 RXN-9873.c 3-Chloro-3,5-cyclohexadiene-l,2-diol-1-carboxylate dehydroge
rxn25903 RXN-9874.c 5-Chloro-3,5-cyclohexadiene-l,2-diol-1-carboxylate dehydrogenase (1) cpd00003[0] + (1) cpd22738[0] <=> (1) cpd00004[0] + (1) cpd00011[0] + (1) cpd01586[0] -1:cpd00003:0:0:"NAD";-1:cpd22738:0:0:"5-chloro-3,5-cyclohexadiene-l,2-diol-1-carboxylate";1:cpd00004:0:0:"NADH";1:cpd00011:0:0:"CO2";1:cpd01586:0:0:"4-Chlorocatechol" 0 (1) cpd00003[0] + (1) cpd22738[0] => (1) cpd00004[0] + (1) cpd00011[0] + (1) cpd01586[0] (1) NAD[0] + (1) 5-chloro-3,5-cyclohexadiene-l,2-diol-1-carboxylate[0] => (1) NADH[0] + (1) CO2[0] + (1) 4-Chlorocatechol[0] > > -12.52 2.06 cpd00003;cpd00004;cpd00011;cpd01586;cpd22738 OK 0 not.assessed
rxn25904 RXN-9875.c RXN-9875.c (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd22740[0] <=> (1) cpd00003[0] + (1) cpd22741[0] -1:cpd00004:0:0:"NADH";-1:cpd00007:0:0:"O2";-1:cpd00067:0:0:"H+";-1:cpd22740:0:0:"1,2,4,5-tetrachlorobenzene";1:cpd00003:0:0:"NAD";1:cpd22741:0:0:"1,2,4,5-tetrachlorobenzene dihydrodiol" 0 (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd00067[0] + (1) cpd22740[0] => (1) cpd00003[0] + (1) cpd22741[0] (1) NADH[0] + (1) O2[0] + (1) H+[0] + (1) 1,2,4,5-tetrachlorobenzene[0] => (1) NAD[0] + (1) 1,2,4,5-tetrachlorobenzene dihydrodiol[0] > > -69.57 2.21 cpd00003;cpd00004;cpd00007;cpd00067;cpd22740;cpd22741 OK 0 not.assessed
rxn25905 RXN-9876.c RXN-9876.c (1) cpd22741[0] <=> (1) cpd00099[0] + (1) cpd09310[0] -1:cpd22741:0:0:"1,2,4,5-tetrachlorobenzene dihydrodiol";1:cpd00067:0:0:"H+";1:cpd00099:0:0:"Cl-";1:cpd09310:0:0:"3,4,6-Trichlorocatechol" 0 (1) cpd22741[0] <=> (1) cpd00067[0] + (1) cpd00099[0] + (1) cpd09310[0] (1) 1,2,4,5-tetrachlorobenzene dihydrodiol[0] <=> (1) H+[0] + (1) Cl-[0] + (1) 3,4,6-Trichlorocatechol[0] = = 1e+07 1e+07 cpd00067;cpd00099;cpd09310;cpd22741 OK 0 HB not.assessed
rxn25906 RXN-9878.c RXN-9878.c (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd10027[0] <=> (1) cpd00003[0] + (1) cpd22742[0] -1:cpd00004:0:0:"NADH";-1:cpd00007:0:0:"O2";-1:cpd00067:0:0:"H+";-1:cpd10027:0:0:"o-Dichlorobenzene";1:cpd00003:0:0:"NAD";1:cpd22742:0:0:"1,2-dichlorobenzene dihydrodiol" 0 (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd00067[0] + (1) cpd10027[0] => (1) cpd00003[0] + (1) cpd22742[0] (1) NADH[0] + (1) O2[0] + (1) H+[0] + (1) o-Dichlorobenzene[0] => (1) NAD[0] + (1) 1,2-dichlorobenzene dihydrodiol[0] > > -71.1 1.92 cpd00003;cpd00004;cpd00007;cpd00067;cpd10027;cpd22742 OK 0 not.assessed
rxn25907 RXN-9879.c RXN-9879.c (1) cpd00003[0] + (1) cpd22742[0] <=> (1) cpd00004[0] + (1) cpd22743[0] -1:cpd00003:0:0:"NAD";-1:cpd22742:0:0:"1,2-dichlorobenzene dihydrodiol";1:cpd00004:0:0:"NADH";1:cpd00067:0:0:"H+";1:cpd22743:0:0:"3,4-dichlorocatechol" 0 (1) cpd00003[0] + (1) cpd22742[0] => (1) cpd00004[0] + (1) cpd00067[0] + (1) cpd22743[0] (1) NAD[0] + (1) 1,2-dichlorobenzene dihydrodiol[0] => (1) NADH[0] + (1) H+[0] + (1) 3,4-dichlorocatechol[0] > > -11.78 2.08 cpd00003;cpd00004;cpd00067;cpd22742;cpd22743 OK 0 not.assessed
rxn25906 RXN-9878.c RXN-9878.c (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd10027[0] <=> (1) cpd00003[0] + (1) cpd22742[0] -1:cpd00004:0:0:"NADH";-1:cpd00007:0:0:"O2";-1:cpd00067:0:0:"H+";-1:cpd10027:0:0:"o-Dichlorobenzene";1:cpd00003:0:0:"NAD";1:cpd22742:0:0:"1,2-dichlorobenzene dihydrodiol" 0 (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd00067[0] + (1) cpd10027[0] => (1) cpd00003[0] + (1) cpd22742[0] (1) NADH[0] + (1) O2[0] + (1) H+[0] + (1) o-Dichlorobenzene[0] => (1) NAD[0] + (1) 1,2-dichlorobenzene dihydrodiol[0] > > -71.1 1.92 cpd00003;cpd00004;cpd00007;cpd00067;cpd10027;cpd22742 OK 0 approved
rxn25907 RXN-9879.c RXN-9879.c (1) cpd00003[0] + (1) cpd22742[0] <=> (1) cpd00004[0] + (1) cpd22743[0] -1:cpd00003:0:0:"NAD";-1:cpd22742:0:0:"1,2-dichlorobenzene dihydrodiol";1:cpd00004:0:0:"NADH";1:cpd00067:0:0:"H+";1:cpd22743:0:0:"3,4-dichlorocatechol" 0 (1) cpd00003[0] + (1) cpd22742[0] => (1) cpd00004[0] + (1) cpd00067[0] + (1) cpd22743[0] (1) NAD[0] + (1) 1,2-dichlorobenzene dihydrodiol[0] => (1) NADH[0] + (1) H+[0] + (1) 3,4-dichlorocatechol[0] > > -11.78 2.08 cpd00003;cpd00004;cpd00067;cpd22742;cpd22743 OK 0 approved
rxn25908 RXN-9881.c RXN-9881.c (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd10107[0] <=> (1) cpd00003[0] + (1) cpd22744[0] -1:cpd00004:0:0:"NADH";-1:cpd00007:0:0:"O2";-1:cpd00067:0:0:"H+";-1:cpd10107:0:0:"1,2,3-Trichlorobenzene";1:cpd00003:0:0:"NAD";1:cpd22744:0:0:"1,2,3-trichlorobenzene dihydrodiol" 0 (1) cpd00004[0] + (1) cpd00007[0] + (1) cpd00067[0] + (1) cpd10107[0] => (1) cpd00003[0] + (1) cpd22744[0] (1) NADH[0] + (1) O2[0] + (1) H+[0] + (1) 1,2,3-Trichlorobenzene[0] => (1) NAD[0] + (1) 1,2,3-trichlorobenzene dihydrodiol[0] > > -69.88 2.07 cpd00003;cpd00004;cpd00007;cpd00067;cpd10107;cpd22744 OK 0 not.assessed
rxn25909 RXN-9882.c RXN-9882.c (1) cpd00003[0] + (1) cpd22744[0] <=> (1) cpd00004[0] + (1) cpd22745[0] -1:cpd00003:0:0:"NAD";-1:cpd22744:0:0:"1,2,3-trichlorobenzene dihydrodiol";1:cpd00004:0:0:"NADH";1:cpd00067:0:0:"H+";1:cpd22745:0:0:"3,4,5-trichlorocatechol" 0 (1) cpd00003[0] + (1) cpd22744[0] => (1) cpd00004[0] + (1) cpd00067[0] + (1) cpd22745[0] (1) NAD[0] + (1) 1,2,3-trichlorobenzene dihydrodiol[0] => (1) NADH[0] + (1) H+[0] + (1) 3,4,5-trichlorocatechol[0] > > -13 2.32 cpd00003;cpd00004;cpd00067;cpd22744;cpd22745 OK 0 not.assessed
rxn25910 RXN-9884.c RXN-9884.c (1) cpd00007[0] + (1) cpd22743[0] <=> (1) cpd22746[0] -1:cpd00007:0:0:"O2";-1:cpd22743:0:0:"3,4-dichlorocatechol";2:cpd00067:0:0:"H+";1:cpd22746:0:0:"2,3-dichloro-cis,cis-muconate" 0 (1) cpd00007[0] + (1) cpd22743[0] => (2) cpd00067[0] + (1) cpd22746[0] (1) O2[0] + (1) 3,4-dichlorocatechol[0] => (2) H+[0] + (1) 2,3-dichloro-cis,cis-muconate[0] > > -94.76 1.81 cpd00007;cpd00067;cpd22743;cpd22746 OK 0 not.assessed
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