From 58da84be2dae8f16a55109653fbd183de74a57a2 Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 30 Aug 2023 14:00:18 +0200 Subject: [PATCH 1/3] fix NA[c] in metabolic tasks --- data/metabolicTasks/metabolicTasks_CellfieConsensus.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt b/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt index 2a43215d..a3032fd7 100644 --- a/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt +++ b/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt @@ -220,11 +220,11 @@ 36 Synthesis of lactose glucose[g] 1 1 lactose[g] 1 1 UDP-galactose[g] 1 1 UDP[g] 1 1 H+[g] 1 1 - 37 Glycogen biosynthesis NA[c] 1 1 glycogenin G4G7[c] 1 1 + 37 Glycogen biosynthesis glycogenin[c] 1 1 glycogenin G4G7[c] 1 1 UDP-glucose[c] 11 H+[c] 11 UDP[c] 11 38 Glycogen degradation glycogenin G4G7[c] 1 1 glucose[c] 8 - Pi[c] 3 NA[c] 1 1 + Pi[c] 3 glycogenin[c] 1 1 H2O[c] 8 glucose-1-phosphate[c] 3 39 Fructose degradation (to glucose-3-phosphate) fructose[c] 1 1 D-glyceraldehyde 3-phosphate[c] 2 2 ATP[c] 2 2 ADP[c] 2 2 @@ -1137,7 +1137,7 @@ FADH2[c] 0 1 NADP+[c] 0 4 FAD[c] 0 1 CO[c] 1 1 - NA[c] 0 1 + globin[c] 0 1 182 Heme synthesis glycine[m] 16 16 heme[m] 2 2 succinyl-CoA[m] 16 18 H2O[m] 26 26 Fe2+[m] 2 2 CoA[m] 16 18 From 6f436d955b0a94ba78ebaace0883d6acc6a1cd80 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sun, 8 Oct 2023 22:44:05 +0200 Subject: [PATCH 2/3] fix: comment-out tasks 37, 38, and 181 by adding hash tag --- .../metabolicTasks_CellfieConsensus.txt | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt b/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt index a3032fd7..245a797e 100644 --- a/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt +++ b/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt @@ -220,12 +220,12 @@ 36 Synthesis of lactose glucose[g] 1 1 lactose[g] 1 1 UDP-galactose[g] 1 1 UDP[g] 1 1 H+[g] 1 1 - 37 Glycogen biosynthesis glycogenin[c] 1 1 glycogenin G4G7[c] 1 1 - UDP-glucose[c] 11 H+[c] 11 - UDP[c] 11 - 38 Glycogen degradation glycogenin G4G7[c] 1 1 glucose[c] 8 - Pi[c] 3 glycogenin[c] 1 1 - H2O[c] 8 glucose-1-phosphate[c] 3 +# 37 Glycogen biosynthesis NA[c] 1 1 glycogenin G4G7[c] 1 1 +# UDP-glucose[c] 11 H+[c] 11 +# UDP[c] 11 +# 38 Glycogen degradation glycogenin G4G7[c] 1 1 glucose[c] 8 +# Pi[c] 3 NA[c] 1 1 +# H2O[c] 8 glucose-1-phosphate[c] 3 39 Fructose degradation (to glucose-3-phosphate) fructose[c] 1 1 D-glyceraldehyde 3-phosphate[c] 2 2 ATP[c] 2 2 ADP[c] 2 2 H+[c] 2 2 @@ -1130,14 +1130,14 @@ 180 Pyridoxal-phosphate synthesis pyridoxal[c] 1 1 pyridoxal-phosphate[c] 1 1 ATP[c] 1 1 ADP[c] 1 1 H+[c] 1 1 - 181 Synthesis of bilirubin heme[c] 1 1 bilirubin[c] 1 1 - NADPH[c] 0 4 H2O[c] 0 3 - H+[c] 0 6 Fe2+[c] 0 1 - O2[c] 0 3 Fe3+[c] 0 1 - FADH2[c] 0 1 NADP+[c] 0 4 - FAD[c] 0 1 - CO[c] 1 1 - globin[c] 0 1 +# 181 Synthesis of bilirubin heme[c] 1 1 bilirubin[c] 1 1 +# NADPH[c] 0 4 H2O[c] 0 3 +# H+[c] 0 6 Fe2+[c] 0 1 +# O2[c] 0 3 Fe3+[c] 0 1 +# FADH2[c] 0 1 NADP+[c] 0 4 +# FAD[c] 0 1 +# CO[c] 1 1 +# NA[c] 0 1 182 Heme synthesis glycine[m] 16 16 heme[m] 2 2 succinyl-CoA[m] 16 18 H2O[m] 26 26 Fe2+[m] 2 2 CoA[m] 16 18 From 7ec4322578bebec2694dd18e0a61dd35c476f4c9 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sun, 8 Oct 2023 23:17:03 +0200 Subject: [PATCH 3/3] doc: add explanation why comment-off the 3 tasks --- data/metabolicTasks/metabolicTasks_CellfieConsensus.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt b/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt index 245a797e..778b9177 100644 --- a/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt +++ b/data/metabolicTasks/metabolicTasks_CellfieConsensus.txt @@ -220,10 +220,10 @@ 36 Synthesis of lactose glucose[g] 1 1 lactose[g] 1 1 UDP-galactose[g] 1 1 UDP[g] 1 1 H+[g] 1 1 -# 37 Glycogen biosynthesis NA[c] 1 1 glycogenin G4G7[c] 1 1 +# 37 Glycogen biosynthesis NA[c] 1 1 glycogenin G4G7[c] 1 1 The metabolite NA[c] in this task is conflicting with HumanGEM # UDP-glucose[c] 11 H+[c] 11 # UDP[c] 11 -# 38 Glycogen degradation glycogenin G4G7[c] 1 1 glucose[c] 8 +# 38 Glycogen degradation glycogenin G4G7[c] 1 1 glucose[c] 8 The metabolite NA[c] in this task is conflicting with HumanGEM # Pi[c] 3 NA[c] 1 1 # H2O[c] 8 glucose-1-phosphate[c] 3 39 Fructose degradation (to glucose-3-phosphate) fructose[c] 1 1 D-glyceraldehyde 3-phosphate[c] 2 2 @@ -1130,7 +1130,7 @@ 180 Pyridoxal-phosphate synthesis pyridoxal[c] 1 1 pyridoxal-phosphate[c] 1 1 ATP[c] 1 1 ADP[c] 1 1 H+[c] 1 1 -# 181 Synthesis of bilirubin heme[c] 1 1 bilirubin[c] 1 1 +# 181 Synthesis of bilirubin heme[c] 1 1 bilirubin[c] 1 1 The metabolite NA[c] in this task is conflicting with HumanGEM # NADPH[c] 0 4 H2O[c] 0 3 # H+[c] 0 6 Fe2+[c] 0 1 # O2[c] 0 3 Fe3+[c] 0 1