From aee34657ba8a5e8b5eee4f0ba4a8d849ae0c3fab Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 10:53:59 +1000 Subject: [PATCH 01/14] fix/inisitol_kinases removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index a1a77c5..5d1e43a 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -1724,17 +1724,17 @@ R_MHISTDMT protein-N6-methyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase M_akg R_MHPGLUT_c 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase M_hcys__L_c + M_mhpglu_c <=> M_met__L_c + M_hpglu_c c TRUE PW082 R_MI13456PK_c 1D-myo-Inositol 1,3,4,5,6-pentakisphosphate kinase M_atp_c + M_mi13456p_c <=> M_h_c + M_adp_c + M_minohp_c c FALSE (WBGene00012466) PW029 RHEA:20313 added rxn name jpnh R_MI13456PK_n 1D-myo-Inositol 1,3,4,5,6-pentakisphosphate kinase M_atp_n + M_mi13456p_n <=> M_h_n + M_adp_n + M_minohp_n n FALSE (WBGene00012466) PW029 RHEA:20313 added rxn name jpnh -R_MI1345PK_c 1D-myo-Inositol 1,3,4,5,6-pentakisphosphate phosphotransferase 2.0 M_h_c + M_adp_c + M_mi13456p_c <=> M_atp_c + M_mi1345p_c c FALSE (WBGene00014081) PW029 added rxn name jpnh -R_MI1345PK_n 1D-myo-Inositol 1,3,4,5,6-pentakisphosphate phosphotransferase 2.0 M_h_n + M_adp_n + M_mi13456p_n <=> M_atp_n + M_mi1345p_n n FALSE (WBGene00014081) PW029 added rxn name jpnh +R_MI1345PK_c 1D-myo-Inositol 1,3,4,5,6-pentakisphosphate phosphotransferase M_h_c + M_adp_c + M_mi13456p_c <=> M_atp_c + M_mi1345p_c c FALSE (WBGene00014081) PW029 added rxn name jpnh +R_MI1345PK_n 1D-myo-Inositol 1,3,4,5,6-pentakisphosphate phosphotransferase M_h_n + M_adp_n + M_mi13456p_n <=> M_atp_n + M_mi1345p_n n FALSE (WBGene00014081) PW029 added rxn name jpnh R_MI1345PP_c D-myo-Inositol 1,3,4,5-tetrakisphosphate 5-phosphohydrolase M_h2o_c + M_mi1345p_c <=> M_pi_c + M_mi134p_c c TRUE (WBGene00007620) or (WBGene00002146) or (WBGene00015278) PW029 "RHEA:19797;RHEA:11392" added rxn name jpnh R_MI1346PK_c inositol-tetrakisphosphate 5-kinase M_atp_c + M_mi1346p_c <=> M_h_c + M_adp_c + M_mi13456p_c c FALSE PW029 R_MI134PK_c inositol-1,3,4-trisphosphate 5/6-kinase M_atp_c + M_mi134p_c <=> M_h_c + M_adp_c + M_mi1346p_c c FALSE PW029 -R_MI1456PK_c D-myo-Inositol 1,3,4,5-tetrakisphosphate kinase M_atp_c + M_mi1456p_c <=> 2.0 M_h_c + M_adp_c + M_mi13456p_c c FALSE (WBGene00014081) PW029 added rxn name jpnh -R_MI1456PK_n D-myo-Inositol 1,3,4,5-tetrakisphosphate kinase M_atp_n + M_mi1456p_n <=> 2.0 M_h_n + M_adp_n + M_mi13456p_n n FALSE (WBGene00014081) PW029 added rxn name jpnh -R_MI145P6K_c Inositol-polyphosphate multikinase M_atp_c + M_mi145p_c <=> 2.0 M_h_c + M_adp_c + M_mi1456p_c c FALSE (WBGene00014081) PW029 -R_MI145P6K_n Inositol-polyphosphate multikinase M_atp_n + M_mi145p_n <=> 2.0 M_h_n + M_adp_n + M_mi1456p_n n TRUE (WBGene00014081) PW029 set to reversible janna -R_MI145PK_c 1D-myo-inositol-trisphosphate 3-kinase M_atp_c + M_mi145p_c <=> 2.0 M_h_c + M_adp_c + M_mi1345p_c c TRUE (WBGene00020631) or (WBGene00014081) or (WBGene00021260) or (WBGene00009262) or (WBGene00002979) PW029 RHEA:11020 set to reversible janna -R_MI145PK_n 1D-myo-inositol-trisphosphate 3-kinase M_atp_n + M_mi145p_n <=> 2.0 M_h_n + M_adp_n + M_mi1345p_n n TRUE (WBGene00014081) or (WBGene00021260) or (WBGene00009262) PW029 set to reversible janna +R_MI1456PK_c D-myo-Inositol 1,3,4,5-tetrakisphosphate kinase M_atp_c + M_mi1456p_c <=> M_h_c + M_adp_c + M_mi13456p_c c FALSE (WBGene00014081) PW029 added rxn name jpnh +R_MI1456PK_n D-myo-Inositol 1,3,4,5-tetrakisphosphate kinase M_atp_n + M_mi1456p_n <=> M_h_n + M_adp_n + M_mi13456p_n n FALSE (WBGene00014081) PW029 added rxn name jpnh +R_MI145P6K_c Inositol-polyphosphate multikinase M_atp_c + M_mi145p_c <=> M_h_c + M_adp_c + M_mi1456p_c c FALSE (WBGene00014081) PW029 +R_MI145P6K_n Inositol-polyphosphate multikinase M_atp_n + M_mi145p_n <=> M_h_n + M_adp_n + M_mi1456p_n n TRUE (WBGene00014081) PW029 set to reversible janna +R_MI145PK_c 1D-myo-inositol-trisphosphate 3-kinase M_atp_c + M_mi145p_c <=> M_h_c + M_adp_c + M_mi1345p_c c TRUE (WBGene00020631) or (WBGene00014081) or (WBGene00021260) or (WBGene00009262) or (WBGene00002979) PW029 RHEA:11020 set to reversible janna +R_MI145PK_n 1D-myo-inositol-trisphosphate 3-kinase M_atp_n + M_mi145p_n <=> M_h_n + M_adp_n + M_mi1345p_n n TRUE (WBGene00014081) or (WBGene00021260) or (WBGene00009262) PW029 set to reversible janna R_MI145PP_c Inositol-1,4,5-trisphosphate 5-phosphatase M_h2o_c + M_mi145p_c <=> M_pi_c + M_mi14p_c c TRUE (WBGene00007620) or (WBGene00002146) or (WBGene00015278) PW029 "RHEA:19797;RHEA:11392" R_MITOIMPORT0001 Fatty acid import by diffusion (C4:0) M_but_c <=> M_but_m cm TRUE PW132 SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi R_MITOIMPORT0002 Fatty acid import by diffusion (C6:0) M_fa6_0_c <=> M_fa6_0_m cm TRUE PW132 SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi From 461df81d62a30408c398cc0d2017c36a026817eb Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 10:57:36 +1000 Subject: [PATCH 02/14] fix/Phosphotransferases removed 1 Proton to balance the reaction/transferase activity --- curation/Reaction-SBtab.tsv | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 5d1e43a..7645a8b 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -1791,15 +1791,15 @@ R_NDP3_c Guanosine-diphosphatase M_h2o_c + M_gdp_c <=> M_pi_c + M_h_c + M_gmp_c R_NDP3_m Guanosine-diphosphatase M_h2o_m + M_gdp_m <=> M_pi_m + M_h_m + M_gmp_m m FALSE (WBGene00017244) PW042 RHEA:36799 R_NDP7_c R_NDP7_c M_h2o_c + M_udp_c <=> M_pi_c + M_h_c + M_ump_c c FALSE (WBGene00044355 or WBGene00017244) or WBGene00003254 or WBGene00010697 PW043 "RHEA:36799;RHEA:36799;RHEA:36799" R_NDP7_m R_NDP7_m M_h2o_m + M_udp_m <=> M_pi_m + M_h_m + M_ump_m m FALSE (WBGene00017244) PW043 RHEA:36799 -R_NDPK2_c ATP:UDP phosphotransferase M_atp_c + M_udp_c <=> M_h_c + M_adp_c + M_utp_c c TRUE (WBGene00019899) or (WBGene00018851) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set reversibility=TRUE" "jpnh; janna" -R_NDPK2_m ATP:UDP phosphotransferase M_atp_m + M_udp_m <=> M_h_m + M_adp_m + M_utp_m m TRUE (WBGene00019899) or (WBGene00021692) PW043 "added name to rxn; set to reversible" "jpnh; janna" -R_NDPK2_n ATP:UDP phosphotransferase M_atp_n + M_udp_n <=> M_h_n + M_adp_n + M_utp_n n TRUE (WBGene00019899) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" -R_NDPK3_c ATP:CDP phosphotransferase M_atp_c + M_cdp_c <=> M_h_c + M_adp_c + M_ctp_c c TRUE (WBGene00019899) or (WBGene00018851) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" -R_NDPK3_m ATP:CDP phosphotransferase M_atp_m + M_cdp_m <=> M_h_m + M_adp_m + M_ctp_m m TRUE (WBGene00019899) or (WBGene00021692) PW043 "added name to rxn; set to reversible" "jpnh; janna" -R_NDPK3_n ATP:CDP phosphotransferase M_atp_n + M_cdp_n <=> M_h_n + M_adp_n + M_ctp_n n TRUE (WBGene00019899) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" -R_NDPK4_c ATP:dTDP phosphotransferase M_atp_c + M_dtdp_c <=> M_h_c + M_adp_c + M_dttp_c c TRUE (WBGene00019899) or (WBGene00018851) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" -R_NDPK4_m ATP:dTDP phosphotransferase M_atp_m + M_dtdp_m <=> M_h_m + M_adp_m + M_dttp_m m TRUE (WBGene00019899) or (WBGene00021692) PW043 "added name to rxn; set to reversible" "jpnh; janna" -R_NDPK4_n ATP:dTDP phosphotransferase M_atp_n + M_dtdp_n <=> M_h_n + M_adp_n + M_dttp_n n TRUE (WBGene00019899) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK2_c ATP:UDP phosphotransferase M_atp_c + M_udp_c <=> M_adp_c + M_utp_c c TRUE (WBGene00019899) or (WBGene00018851) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set reversibility=TRUE" "jpnh; janna" +R_NDPK2_m ATP:UDP phosphotransferase M_atp_m + M_udp_m <=> M_adp_m + M_utp_m m TRUE (WBGene00019899) or (WBGene00021692) PW043 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK2_n ATP:UDP phosphotransferase M_atp_n + M_udp_n <=> M_adp_n + M_utp_n n TRUE (WBGene00019899) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK3_c ATP:CDP phosphotransferase M_atp_c + M_cdp_c <=> M_adp_c + M_ctp_c c TRUE (WBGene00019899) or (WBGene00018851) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK3_m ATP:CDP phosphotransferase M_atp_m + M_cdp_m <=> M_adp_m + M_ctp_m m TRUE (WBGene00019899) or (WBGene00021692) PW043 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK3_n ATP:CDP phosphotransferase M_atp_n + M_cdp_n <=> M_adp_n + M_ctp_n n TRUE (WBGene00019899) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK4_c ATP:dTDP phosphotransferase M_atp_c + M_dtdp_c <=> M_adp_c + M_dttp_c c TRUE (WBGene00019899) or (WBGene00018851) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK4_m ATP:dTDP phosphotransferase M_atp_m + M_dtdp_m <=> M_adp_m + M_dttp_m m TRUE (WBGene00019899) or (WBGene00021692) PW043 "added name to rxn; set to reversible" "jpnh; janna" +R_NDPK4_n ATP:dTDP phosphotransferase M_atp_n + M_dtdp_n <=> M_adp_n + M_dttp_n n TRUE (WBGene00019899) or (WBGene00009119) or (WBGene00021692) PW043 RHEA:44640 "added name to rxn; set to reversible" "jpnh; janna" R_NDPK5_c ATP:dGDP phosphotransferase M_dgdp_c + M_atp_c <=> M_dgtp_c + M_adp_c c TRUE (WBGene00019899) or (WBGene00018851) or (WBGene00009119) or (WBGene00021692) PW042 RHEA:44640 set to reversible janna R_NDPK5_m R_NDPK5_m M_dgdp_m + M_atp_m <=> M_dgtp_m + M_adp_m m TRUE (WBGene00019899) or (WBGene00021692) PW042 set to reversible janna R_NDPK5_n R_NDPK5_n M_dgdp_n + M_atp_n <=> M_dgtp_n + M_adp_n n TRUE (WBGene00019899) or (WBGene00009119) or (WBGene00021692) PW042 RHEA:44640 set to reversible janna From fb4f9e045e350195f26afd33a47c76cf671ce7c6 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 11:17:34 +1000 Subject: [PATCH 03/14] fix/NADS2_c,NADS2_m removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 7645a8b..ee90778 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -1778,8 +1778,8 @@ R_NADPPPS_m R_NADPPPS_m M_pi_m + M_nad_m <=> M_h2o_m + M_nadp_m m FALSE (WBGene R_nadptm nadptm M_nadp_m <=> M_nadp_c mc TRUE PW111 R_NADS1_c NAD(+) synthetase M_nh3_c + M_dnad_c + M_atp_c <=> M_ppi_c + M_h_c + M_amp_c + M_nad_c c FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" R_NADS1_m NAD(+) synthetase M_nh3_m + M_dnad_m + M_atp_m <=> M_ppi_m + M_h_m + M_amp_m + M_nad_m m FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" -R_NADS2_c NAD(+) synthetase (glutamine-hydrolysing) M_h2o_c + M_dnad_c + M_gln__L_c + M_atp_c <=> M_ppi_c + 2.0 M_h_c + M_glu__L_c + M_amp_c + M_nad_c c FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" -R_NADS2_m NAD(+) synthetase (glutamine-hydrolysing) M_h2o_m + M_dnad_m + M_gln__L_m + M_atp_m <=> M_ppi_m + 2.0 M_h_m + M_glu__L_m + M_amp_m + M_nad_m m FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" +R_NADS2_c NAD(+) synthetase (glutamine-hydrolysing) M_h2o_c + M_dnad_c + M_gln__L_c + M_atp_c <=> M_ppi_c +M_h_c + M_glu__L_c + M_amp_c + M_nad_c c FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" +R_NADS2_m NAD(+) synthetase (glutamine-hydrolysing) M_h2o_m + M_dnad_m + M_gln__L_m + M_atp_m <=> M_ppi_m + M_h_m + M_glu__L_m + M_amp_m + M_nad_m m FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" R_nadtm nadtm M_nad_m <=> M_nad_c mc TRUE PW111 R_NADtn NAD transport, nuclear through pores M_nad_n <=> M_nad_c nc TRUE PW108 R_NADTRHD_c NAD(P)(+) transhydrogenase (AB-specific) M_nadph_c + M_nad_c <=> M_nadh_c + M_nadp_c c FALSE (WBGene00003778) PW036 From 7e4be1e47e4f9dd5ce582e41bafc0859f5f0d9fa Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 11:18:23 +1000 Subject: [PATCH 04/14] fix/NADK_c removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index ee90778..5548d7c 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -1770,7 +1770,7 @@ R_NADDP_n NAD+ pyrophosphatase M_h2o_n + M_nad_n <=> M_nmn_n + 2.0 M_h_n + M_am R_NADH_DEHYDROG_A_RXN_8_m NADH dehydrogenase (ubiqui 8) 5.0 M_h_m + M_q8_m + M_nadh_m <=> 4.0 M_h_i + M_q8h2_m + M_nad_m m FALSE (WBGene00019401 and WBGene00021800 and WBGene00009051 and WBGene00013406 and WBGene00020636 and WBGene00015810 and WBGene00013237 and WBGene00006463 and WBGene00007684 and WBGene00021849 and WBGene00007192 and WBGene00017508 and WBGene00021839 and WBGene00022169 and WBGene00013308 and WBGene00003061 and WBGene00010326 and WBGene00021562 and WBGene00012166 and WBGene00010957 and WBGene00010967 and WBGene00010963 and WBGene00010958 and WBGene00010966 and WBGene00010961 and WBGene00010959 and WBGene00009992 and WBGene00001520 and WBGene00012376 and WBGene00016393 and WBGene00003831 and WBGene00008414 and WBGene00009712 and WBGene00022380 and WBGene00008225 and WBGene00007880) PW007 "RHEA:11356;RHEA:29091;RHEA:29091;RHEA:11356;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:11356" replaced aerobic respiration with oxidative phosphorylation lenov R_NADH_DEHYDROG_A_RXN_9_m NADH dehydrogenase (ubiqui 9) 5.0 M_h_m + M_q9_m + M_nadh_m <=> 4.0 M_h_i + M_q9h2_m + M_nad_m m FALSE (WBGene00019401 and WBGene00021800 and WBGene00009051 and WBGene00013406 and WBGene00020636 and WBGene00015810 and WBGene00013237 and WBGene00006463 and WBGene00007684 and WBGene00021849 and WBGene00007192 and WBGene00017508 and WBGene00021839 and WBGene00022169 and WBGene00013308 and WBGene00003061 and WBGene00010326 and WBGene00021562 and WBGene00012166 and WBGene00010957 and WBGene00010967 and WBGene00010963 and WBGene00010958 and WBGene00010966 and WBGene00010961 and WBGene00010959 and WBGene00009992 and WBGene00001520 and WBGene00012376 and WBGene00016393 and WBGene00003831 and WBGene00008414 and WBGene00009712 and WBGene00022380 and WBGene00008225 and WBGene00007880) PW007 "RHEA:11356;RHEA:29091;RHEA:29091;RHEA:11356;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:29091;RHEA:11356" replaced aerobic respiration with oxidative phosphorylation lenov R_nadhtm nadhtm M_nadh_m <=> M_nadh_c mc TRUE PW111 -R_NADK_c NAD(+) kinase M_atp_c + M_nad_c <=> 2.0 M_h_c + M_adp_c + M_nadp_c c FALSE (WBGene00022307) PW036 +R_NADK_c NAD(+) kinase M_atp_c + M_nad_c <=> M_h_c + M_adp_c + M_nadp_c c FALSE (WBGene00022307) PW036 R_nadphtm nadphtm M_nadph_m <=> M_nadph_c mc TRUE PW111 R_NADPHtn NADPH transport, nuclear through pores M_nadph_n <=> M_nadph_c nc TRUE PW108 R_NADPPPS_c R_NADPPPS_c M_pi_c + M_nad_c <=> M_h2o_c + M_nadp_c c FALSE (WBGene00011879) or (WBGene00017427) or (WBGene00022770) or (WBGene00008936) or (WBGene00011262) or (WBGene00018696) or (WBGene00010411) or (WBGene00013646) or (WBGene00022246) or (WBGene00022245) or (WBGene00022379) or (WBGene00015161) or (WBGene00022181) or (WBGene00007331) or (WBGene00007328) or (WBGene00009146) or (WBGene00008801) or (WBGene00008804) or (WBGene00008802) or (WBGene00004023) or (WBGene00004020) or (WBGene00016152) or (WBGene00020471) PW036 "RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017" From 7f549534c1fba433de032f68941afbd4d67284a2 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 11:53:24 +1000 Subject: [PATCH 05/14] fix/NADS1_c,NADS1_m changed nh3 to nh4 because of ph + reaction found on expasy --- curation/Reaction-SBtab.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 5548d7c..8969d87 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -1776,8 +1776,8 @@ R_NADPHtn NADPH transport, nuclear through pores M_nadph_n <=> M_nadph_c nc TRUE R_NADPPPS_c R_NADPPPS_c M_pi_c + M_nad_c <=> M_h2o_c + M_nadp_c c FALSE (WBGene00011879) or (WBGene00017427) or (WBGene00022770) or (WBGene00008936) or (WBGene00011262) or (WBGene00018696) or (WBGene00010411) or (WBGene00013646) or (WBGene00022246) or (WBGene00022245) or (WBGene00022379) or (WBGene00015161) or (WBGene00022181) or (WBGene00007331) or (WBGene00007328) or (WBGene00009146) or (WBGene00008801) or (WBGene00008804) or (WBGene00008802) or (WBGene00004023) or (WBGene00004020) or (WBGene00016152) or (WBGene00020471) PW036 "RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017" R_NADPPPS_m R_NADPPPS_m M_pi_m + M_nad_m <=> M_h2o_m + M_nadp_m m FALSE (WBGene00044044) or (WBGene00010411) or (WBGene00013654) PW036 R_nadptm nadptm M_nadp_m <=> M_nadp_c mc TRUE PW111 -R_NADS1_c NAD(+) synthetase M_nh3_c + M_dnad_c + M_atp_c <=> M_ppi_c + M_h_c + M_amp_c + M_nad_c c FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" -R_NADS1_m NAD(+) synthetase M_nh3_m + M_dnad_m + M_atp_m <=> M_ppi_m + M_h_m + M_amp_m + M_nad_m m FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" +R_NADS1_c NAD(+) synthetase M_nh4_c + M_dnad_c + M_atp_c <=> M_ppi_c + M_h_c + M_amp_c + M_nad_c c FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" +R_NADS1_m NAD(+) synthetase M_nh4_m + M_dnad_m + M_atp_m <=> M_ppi_m + M_h_m + M_amp_m + M_nad_m m FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" R_NADS2_c NAD(+) synthetase (glutamine-hydrolysing) M_h2o_c + M_dnad_c + M_gln__L_c + M_atp_c <=> M_ppi_c +M_h_c + M_glu__L_c + M_amp_c + M_nad_c c FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" R_NADS2_m NAD(+) synthetase (glutamine-hydrolysing) M_h2o_m + M_dnad_m + M_gln__L_m + M_atp_m <=> M_ppi_m + M_h_m + M_glu__L_m + M_amp_m + M_nad_m m FALSE (WBGene00007698) PW036 "RHEA:24384;RHEA:24384" R_nadtm nadtm M_nad_m <=> M_nad_c mc TRUE PW111 From 4ac8f08db720902f0dbe568ed3267e6cc837a975 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 12:21:35 +1000 Subject: [PATCH 06/14] fix/PFK_c PFK_n RXN909_109_c RXN909_109_m removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 8969d87..6b1b641 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -2029,8 +2029,8 @@ R_PEROXID_RXN_c Peroxidase M_h2o2_c + M_donor_h2_c <=> 2.0 M_h2o_c + M_acceptor R_PEROXID_RXN_m Peroxidase M_h2o2_m + M_donor_h2_m <=> 2.0 M_h2o_m + M_acceptor_m m TRUE (WBGene00011530) or (WBGene00022743) or (WBGene00021845) PW098 RHEA:56136 [CHECKME] this reaction is generic and looks disconnected lenov R_PEROXID_RXN_n Peroxidase M_h2o2_n + M_donor_h2_n <=> 2.0 M_h2o_n + M_acceptor_n n TRUE (WBGene00017968) or (WBGene00019970) or (WBGene00016700) PW098 [CHECKME] this reaction is generic and looks disconnected lenov R_PETHCT_c ethanolamine-phosphate cytidylyltransferase M_ethamp_c + M_h_c + M_ctp_c <=> M_ppi_c + M_cdpea_c c TRUE (WBGene00021352) or (WBGene00016531) PW056 set to reversible janna -R_PFK_c 6-phosphofructokinase M_f6p_c + M_atp_c <=> M_fdp_c + 2.0 M_h_c + M_adp_c c FALSE (WBGene00022199) or (WBGene00008230) "PW031;PW018" "RHEA:16109;RHEA:16109" -R_PFK_n 6-phosphofructokinase M_f6p_n + M_atp_n <=> M_fdp_n + 2.0 M_h_n + M_adp_n n FALSE (WBGene00022199) or (WBGene00008230) "PW031;PW018" "RHEA:16109;RHEA:16109" +R_PFK_c 6-phosphofructokinase M_f6p_c + M_atp_c <=> M_fdp_c + M_h_c + M_adp_c c FALSE (WBGene00022199) or (WBGene00008230) "PW031;PW018" "RHEA:16109;RHEA:16109" +R_PFK_n 6-phosphofructokinase M_f6p_n + M_atp_n <=> M_fdp_n + M_h_n + M_adp_n n FALSE (WBGene00022199) or (WBGene00008230) "PW031;PW018" "RHEA:16109;RHEA:16109" R_PGCD_c Phosphoglycerate dehydrogenase M_nad_c + M_3pg_c <=> M_3php_c + M_h_c + M_nadh_c c TRUE (WBGene00007836) PW074 set to reversible janna R_PGI_c Glucose-6-phosphate isomerase M_g6p_B_c <=> M_f6p_c c TRUE (WBGene00013597) "PW031;PW018;PW025" "RHEA:11816;RHEA:11816" R_PGI_m Glucose-6-phosphate isomerase M_g6p_B_m <=> M_f6p_m m TRUE (WBGene00013597) "PW031;PW018;PW025" "RHEA:11816;RHEA:11816" @@ -2916,8 +2916,8 @@ R_RXN66_321_c R_RXN66_321_c M_h_c + M_nadph_c + M_chlstol_c <=> M_lthstrl_c + R_RXN909_10_m ubiquinol-cytochrome c reductase 2.0 M_h_m + M_q9h2_m + 2.0 M_cytc_m <=> 4.0 M_h_i + M_q9_m + 2.0 M_cytc_red_m m FALSE (WBGene00009739 and WBGene00020181 and WBGene00011679 and WBGene00018963 and WBGene00000869 and WBGene00000829 and WBGene00002162 and WBGene00012094 and WBGene00019937) PW007 RHEA:11484 "added name; replaced aerobic respiration with oxidative phosphorylation" "jpnh; lenov" R_RXN909_107_c Glycerol:NAD+ oxidoreductase M_glyald_c + M_h_c + M_nadh_c <=> M_glyc_c + M_nad_c c TRUE (WBGene00012722) PW052 set to reversible janna R_RXN909_108_m D-Glyceraldehyde:NAD+ oxidoreductase 2.0 M_h_m + M_nadh_m + M_glyc_R_m <=> M_h2o_m + M_glyald_m + M_nad_m m FALSE (WBGene00000115) PW052 RHEA:16185 added rxn name jpnh -R_RXN909_109_c ATP:(R)-glycerate 3-phosphotransferase M_atp_c + M_glyc_R_c <=> 2.0 M_h_c + M_adp_c + M_3pg_c c FALSE (WBGene00015733) PW052 -R_RXN909_109_m ATP:(R)-glycerate 3-phosphotransferase M_atp_m + M_glyc_R_m <=> 2.0 M_h_m + M_adp_m + M_3pg_m m FALSE (WBGene00015733) PW052 +R_RXN909_109_c ATP:(R)-glycerate 3-phosphotransferase M_atp_c + M_glyc_R_c <=> M_h_c + M_adp_c + M_3pg_c c FALSE (WBGene00015733) PW052 +R_RXN909_109_m ATP:(R)-glycerate 3-phosphotransferase M_atp_m + M_glyc_R_m <=> M_h_m + M_adp_m + M_3pg_m m FALSE (WBGene00015733) PW052 R_RXN909_110_c sucrose glucohydrolase M_h2o_c + M_sucr_c <=> M_glc_aD_c + M_fru_B_c c FALSE (WBGene00019895) or (WBGene00017071) PW020 R_RXN909_112_c alkaline phosphatase M_ahdt_c + 3.0 M_h2o_c <=> M_dhnpt_c + 3.0 M_pi_c + 3.0 M_h_c c TRUE (WBGene00013646) PW091 R_RXN909_113_c R_RXN909_113_c M_m2emgacpail_c + M_1ac2acg3pe_c <=> M_em2emgacpail_c + M_1ac2acglyc_c c FALSE (WBGene00016159) PW028 From 7633dfd1df28e347138681c497c32d85b7011604 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 13:26:48 +1000 Subject: [PATCH 07/14] fix/CoA-Fatty acid ligase removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 6b1b641..438c805 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -2925,13 +2925,13 @@ R_RXN909_114_c L-Cysteine:2-oxoglutarate aminotransferase M_akg_c + M_cys__L_c R_RXN909_114_m L-Cysteine:2-oxoglutarate aminotransferase M_akg_m + M_cys__L_m <=> M_mercppyr_m + M_glu__L_m m TRUE (WBGene00016652) or (WBGene00015778) PW082 "RHEA:21824;RHEA:21824" R_RXN909_115_c 3-mercaptopyruvate sulfurtransferase M_mercppyr_c + M_cyan_c <=> M_h_c + M_pyr_c + M_tcynt_c c FALSE WBGene00008409 or WBGene00010380 or WBGene00010383 or WBGene00017387 or WBGene00022006 or WBGene00022007 or WBGene00011307 PW082 "RHEA:16881;RHEA:16881" R_RXN909_117_m L-3-amino-isobutanoate:2-oxoglutarate aminotransferase M_glu__L_m + M_mmtsa_m <=> M_akg_m + M_3aib_m m FALSE (WBGene00001794) PW083 "RHEA:23352;RHEA:13993" -R_RXN909_118_c myristate:CoA ligase M_atp_c + M_coa_c + M_fa14_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa14_0_c c FALSE (WBGene00016716) or (WBGene00018579) or (WBGene00009221) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) or (WBGene00013575) or (WBGene00018152) PW136 SPW001 -R_RXN909_118_m myristate:CoA ligase M_atp_m + M_coa_m + M_fa14_0_m <=> M_ppi_m + M_h_m + M_amp_m + M_coa14_0_m m FALSE (WBGene00009221) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) PW120 -R_RXN909_119_c laurate:CoA-ligase M_atp_c + M_coa_c + M_fa12_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa12_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) or (WBGene00013575) or (WBGene00018152) PW136 SPW001 -R_RXN909_120_c caprate:CoA-ligase M_atp_c + M_coa_c + M_fa10_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa10_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 -R_RXN909_121_c octanoate:CoA-ligase M_atp_c + M_coa_c + M_fa8_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa8_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 -R_RXN909_122_c Hexanoate CoA-ligase M_atp_c + M_coa_c + M_fa6_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa6_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 added rxn name jpnh -R_RXN909_123_c butyrate:CoA-ligase M_atp_c + M_coa_c + M_but_c <=> M_ppi_c + M_h_c + M_amp_c + M_btcoa_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 Added extra genes from (R_BUTYRATE__COA_LIGASE_RXN_c) which is marked for deletion jpnh +R_RXN909_118_c myristate:CoA ligase M_atp_c + M_coa_c + M_fa14_0_c <=> M_ppi_c + M_amp_c + M_coa14_0_c c FALSE (WBGene00016716) or (WBGene00018579) or (WBGene00009221) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) or (WBGene00013575) or (WBGene00018152) PW136 SPW001 +R_RXN909_118_m myristate:CoA ligase M_atp_m + M_coa_m + M_fa14_0_m <=> M_ppi_m + M_amp_m + M_coa14_0_m m FALSE (WBGene00009221) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) PW120 +R_RXN909_119_c laurate:CoA-ligase M_atp_c + M_coa_c + M_fa12_0_c <=> M_ppi_c + M_amp_c + M_coa12_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) or (WBGene00013575) or (WBGene00018152) PW136 SPW001 +R_RXN909_120_c caprate:CoA-ligase M_atp_c + M_coa_c + M_fa10_0_c <=> M_ppi_c + M_amp_c + M_coa10_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 +R_RXN909_121_c octanoate:CoA-ligase M_atp_c + M_coa_c + M_fa8_0_c <=> M_ppi_c + M_amp_c + M_coa8_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 +R_RXN909_122_c Hexanoate CoA-ligase M_atp_c + M_coa_c + M_fa6_0_c <=> M_ppi_c + M_amp_c + M_coa6_0_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 added rxn name jpnh +R_RXN909_123_c butyrate:CoA-ligase M_atp_c + M_coa_c + M_but_c <=> M_ppi_c + M_amp_c + M_btcoa_c c FALSE (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 Added extra genes from (R_BUTYRATE__COA_LIGASE_RXN_c) which is marked for deletion jpnh R_RXN909_130_n histone-L-lysine N6-methyltransferase (acting on dimethylated residues) M_Ndmelys_n + M_amet_n <=> M_Ntmelys_n + M_h_n + M_ahcys_n n FALSE (WBGene00011729 or WBGene00003040 or (WBGene00016603 or WBGene00019584) or WBGene00004782 or WBGene00019883 or WBGene00018023 or WBGene00003220 or WBGene00021515 or (WBGene00021474 or WBGene00010067 or WBGene00012302 or WBGene00010120 or WBGene00022512) or WBGene00016313 or WBGene00004781) or (WBGene00019690 or WBGene00020006 or WBGene00021282 or WBGene00008062 or WBGene00022431 or WBGene00008206) PW101 "RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024" Added all the GeneAssociation that were in cytoplasm lenov R_RXN909_132_c S-Adenosyl-L-methionine M_peplys_c + M_amet_c <=> M_pmllys_c + M_h_c + M_ahcys_c c FALSE (WBGene00016313) PW080 RHEA:10024 R_RXN909_132_n S-Adenosyl-L-methionine M_peplys_n + M_amet_n <=> M_pmllys_n + M_h_n + M_ahcys_n n FALSE (WBGene00004781) or (WBGene00021515) or (WBGene00016313) or (WBGene00004782) PW080 "RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024" From 44bde5fd4603ff846f9b25f817d5ae2993ad839c Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 13:33:36 +1000 Subject: [PATCH 08/14] fix/R_RXN909_20_c R_RXN909_20_n removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 438c805..8811bbf 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -2979,8 +2979,8 @@ R_RXN909_194_c R_RXN909_194_c M_h2o_c + M_fecost_c <=> M_etoh_c + M_dsmsterol_c R_RXN909_195_c R_RXN909_195_c 2.0 M_h_c + M_ddsmsterol_c <=> M_7dhchsterol_c c FALSE PW047 R_RXN909_196_c R_RXN909_196_c M_lthstrl_c + M_5mthf_c <=> M_lphol_c + M_thf_c c FALSE (WBGene00019198) PW047 19531354 abraham R_RXN909_197_c R_RXN909_197_c M_lphol_c <=> M_amchb_c c FALSE PW047 -R_RXN909_20_c propionyl-CoA synthetase M_ppa_c + M_atp_c + M_coa_c <=> M_ppi_c + M_h_c + M_amp_c + M_ppcoa_c c FALSE (WBGene00007969) PW086 R00925 "RHEA:23176;RHEA:23176" Added Rxn name jpnh -R_RXN909_20_n propionyl-CoA synthetase M_ppa_n + M_atp_n + M_coa_n <=> M_ppi_n + M_h_n + M_amp_n + M_ppcoa_n n FALSE (WBGene00007969) PW086 R00925 "RHEA:23176;RHEA:23176" Added Rxn name jpnh +R_RXN909_20_c propionyl-CoA synthetase M_ppa_c + M_atp_c + M_coa_c <=> M_ppi_c + M_amp_c + M_ppcoa_c c FALSE (WBGene00007969) PW086 R00925 "RHEA:23176;RHEA:23176" Added Rxn name jpnh +R_RXN909_20_n propionyl-CoA synthetase M_ppa_n + M_atp_n + M_coa_n <=> M_ppi_n + M_amp_n + M_ppcoa_n n FALSE (WBGene00007969) PW086 R00925 "RHEA:23176;RHEA:23176" Added Rxn name jpnh R_RXN909_200_c phosphoethanolamine N-methyltransferase M_ethamp_c + M_amet_c <=> M_methamp_c + M_h_c + M_ahcys_c c FALSE (WBGene00022781) PW056 removed pathway N-methyltransferases lenov R_RXN909_204_c R_RXN909_204_c 2.0 M_h2o_c + M_nadp_c + M_ddsmsterol_c <=> M_h_c + M_nadph_c + M_o2_c + M_chlstol_c c FALSE PW047 R_RXN909_205_c R_RXN909_205_c 2.0 M_h2o_c + M_nad_c + M_ddsmsterol_c <=> M_h_c + M_nadh_c + M_o2_c + M_chlstol_c c FALSE PW047 From ec1c549c1030cb6189e54786d999b1623c1bde4c Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 13:36:32 +1000 Subject: [PATCH 09/14] fix/coA+fatty acid reactions removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 8811bbf..3bc8a65 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -2952,13 +2952,13 @@ R_RXN909_174_m glutamic phenylpyruvic aminotransferase M_glu__L_m + M_2kmb_m <= R_RXN909_175_c purine-nucleoside phosphorylase M_rnam_c + M_pi_c <=> M_r1p_c + M_h_c + M_ncam_c c TRUE (WBGene00019298) PW036 set to reversible janna R_RXN909_175_n purine-nucleoside phosphorylase M_rnam_n + M_pi_n <=> M_r1p_n + M_h_n + M_ncam_n n TRUE (WBGene00019298) PW036 set to reversible janna R_RXN909_18_c L-1-Pyrroline-3-hydroxy-5-carboxylate hydrolytic ring opening M_1p3h5c_c + M_h2o_c <=> M_4hglusa_c c FALSE PW081 R04443 Added a name to the reaction jpnh -R_RXN909_180_c arachidoyl-CoA synthase M_atp_c + M_coa_c + M_fa20_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa20_0_c c FALSE (WBGene00022037) or (WBGene00008669) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 -R_RXN909_181_c Behenoyl-CoA synthase M_atp_c + M_coa_c + M_fa22_0_c <=> M_coa22_0_c + M_ppi_c + M_h_c + M_amp_c c FALSE (WBGene00009218) or (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 +R_RXN909_180_c arachidoyl-CoA synthase M_atp_c + M_coa_c + M_fa20_0_c <=> M_ppi_c + M_amp_c + M_coa20_0_c c FALSE (WBGene00022037) or (WBGene00008669) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 +R_RXN909_181_c Behenoyl-CoA synthase M_atp_c + M_coa_c + M_fa22_0_c <=> M_coa22_0_c + M_ppi_c + M_amp_c c FALSE (WBGene00009218) or (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 R_RXN909_182_c R_RXN909_182_c M_h2o_c + M_camp_c <=> M_h_c + M_amp_c c FALSE (WBGene00016328) or (WBGene00003966) or (WBGene00011433) or (WBGene00020114) or (WBGene00022389) or (WBGene00008443) or (WBGene00011146) PW034 "RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653" R_RXN909_182_m R_RXN909_182_m M_h2o_m + M_camp_m <=> M_h_m + M_amp_m m FALSE (WBGene00003966) PW034 R_RXN909_182_n R_RXN909_182_n M_h2o_n + M_camp_n <=> M_h_n + M_amp_n n FALSE (WBGene00016328) or (WBGene00003966) PW034 RHEA:14653 -R_RXN909_183_c lignoceroyl-CoA synthase M_atp_c + M_coa_c + M_fa24_0_c <=> M_coa24_0_c + M_ppi_c + M_h_c + M_amp_c c FALSE (WBGene00009218) or (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 -R_RXN909_184_c cerotoyl-CoA synthase M_atp_c + M_coa_c + M_fa26_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa26_0_c c FALSE (WBGene00009218) or (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 +R_RXN909_183_c lignoceroyl-CoA synthase M_atp_c + M_coa_c + M_fa24_0_c <=> M_coa24_0_c + M_ppi_c + M_amp_c c FALSE (WBGene00009218) or (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 +R_RXN909_184_c cerotoyl-CoA synthase M_atp_c + M_coa_c + M_fa26_0_c <=> M_ppi_c+ M_amp_c + M_coa26_0_c c FALSE (WBGene00009218) or (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00018579) PW136 SPW001 R_RXN909_185_c adenylate kinase M_atp_c + M_amp_c <=> 2.0 M_adp_c c TRUE WBGene00008458 or (WBGene00009531 or WBGene00002879) PW042 RHEA:12973 set reversibility=TRUE janna R_RXN909_185_m adenylate kinase M_atp_m + M_amp_m <=> 2.0 M_adp_m m TRUE (WBGene00014058) or (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973 set to reversible janna R_RXN909_185_n adenylate kinase M_atp_n + M_amp_n <=> 2.0 M_adp_n n TRUE (WBGene00002879) PW042 RHEA:12973 set to reversible janna From d346d6356a3ceb6f54117e2ad0e734eb0a4c0120 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 13:43:59 +1000 Subject: [PATCH 10/14] fix/ntp transferases removed 1 Proton to balance the reaction/ntp transferase activity --- curation/Reaction-SBtab.tsv | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 3bc8a65..4bee577 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -3023,24 +3023,24 @@ R_RXN909_241_c (5-L-glutamyl)-L-amino-acid gamma-glutamyl cyclotransferase (5-ox R_RXN909_242_c glutathione:L-serine 5-glutamyltransferase M_h_c + M_ser__L_c + M_gthrd_c <=> M_gluser_c + M_cgly_c c FALSE PW070 added rxn name jpnh R_RXN909_243_c R_RXN909_243_c M_didp_c + M_atp_c <=> M_ditp_c + M_adp_c c FALSE (WBGene00009119) PW042 RHEA:44640 R_RXN909_243_n R_RXN909_243_n M_didp_n + M_atp_n <=> M_ditp_n + M_adp_n n FALSE (WBGene00009119) PW042 RHEA:44640 -R_RXN909_244_c ATP:GDP phosphotransferase M_atp_c + M_idp_c <=> M_h_c + M_itp_c + M_adp_c c TRUE WBGene00019899 or WBGene00021692 or WBGene00009119 PW042 RHEA:44640 set to reversible janna -R_RXN909_244_n R_RXN909_244_n M_atp_n + M_idp_n <=> M_h_n + M_itp_n + M_adp_n n TRUE (WBGene00009119) PW042 RHEA:44640 set to reversible janna +R_RXN909_244_c ATP:GDP phosphotransferase M_atp_c + M_idp_c <=> M_itp_c + M_adp_c c TRUE WBGene00019899 or WBGene00021692 or WBGene00009119 PW042 RHEA:44640 set to reversible janna +R_RXN909_244_n R_RXN909_244_n M_atp_n + M_idp_n <=> M_itp_n + M_adp_n n TRUE (WBGene00009119) PW042 RHEA:44640 set to reversible janna R_RXN909_246_c R_RXN909_246_c M_h2o_c + M_itp_c <=> M_ppi_c + M_imp_c + M_h_c c FALSE (WBGene00001823) PW042 "RHEA:23996;RHEA:44644" R_RXN909_246_n R_RXN909_246_n M_h2o_n + M_itp_n <=> M_ppi_n + M_imp_n + M_h_n n FALSE (WBGene00001823) PW042 "RHEA:23996;RHEA:44644" R_RXN909_247_c R_RXN909_247_c M_pi_c + M_dad_2_c <=> M_h2o_c + M_damp_c c TRUE WBGene00017775 or WBGene00012423 or WBGene00022201 PW042 set to reversible janna R_RXN909_247_n R_RXN909_247_n M_pi_n + M_dad_2_n <=> M_h2o_n + M_damp_n n TRUE (WBGene00022201) PW042 set to reversible janna -R_RXN909_248_c R_RXN909_248_c M_damp_c + M_atp_c <=> M_h_c + M_dadp_c + M_adp_c c TRUE WBGene00008458 or (WBGene00009531 or WBGene00014058 or WBGene00002879) PW042 RHEA:12973 set to reversible janna -R_RXN909_248_m R_RXN909_248_m M_damp_m + M_atp_m <=> M_h_m + M_dadp_m + M_adp_m m TRUE (WBGene00014058) or (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973 set to reversible janna -R_RXN909_248_n R_RXN909_248_n M_damp_n + M_atp_n <=> M_h_n + M_dadp_n + M_adp_n n TRUE (WBGene00002879) PW042 RHEA:12973 set to reversible janna +R_RXN909_248_c R_RXN909_248_c M_damp_c + M_atp_c <=> M_dadp_c + M_adp_c c TRUE WBGene00008458 or (WBGene00009531 or WBGene00014058 or WBGene00002879) PW042 RHEA:12973 set to reversible janna +R_RXN909_248_m R_RXN909_248_m M_damp_m + M_atp_m <=> M_dadp_m + M_adp_m m TRUE (WBGene00014058) or (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973 set to reversible janna +R_RXN909_248_n R_RXN909_248_n M_damp_n + M_atp_n <=> M_dadp_n + M_adp_n n TRUE (WBGene00002879) PW042 RHEA:12973 set to reversible janna R_RXN909_249_c R_RXN909_249_c M_pi_c + M_h_c + M_imp_c <=> M_h2o_c + M_idp_c c TRUE (WBGene00044355 or WBGene00017244) or WBGene00003254 or WBGene00010697 PW042 "RHEA:36799;RHEA:36799;RHEA:36799" set to reversible janna -R_RXN909_251_c R_RXN909_251_c M_gtp_c + M_cmp_c <=> M_h_c + M_gdp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) "PW042;PW043" -R_RXN909_251_n R_RXN909_251_n M_gtp_n + M_cmp_n <=> M_h_n + M_gdp_n + M_cdp_n n TRUE (WBGene00007812) "PW042;PW043" +R_RXN909_251_c R_RXN909_251_c M_gtp_c + M_cmp_c <=> M_gdp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) "PW042;PW043" +R_RXN909_251_n R_RXN909_251_n M_gtp_n + M_cmp_n <=> M_gdp_n + M_cdp_n n TRUE (WBGene00007812) "PW042;PW043" R_RXN909_252_c R_RXN909_252_c M_ctp_c + M_cmp_c <=> 2.0 M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) PW043 R_RXN909_252_n R_RXN909_252_n M_ctp_n + M_cmp_n <=> 2.0 M_cdp_n n TRUE (WBGene00007812) PW043 R_RXN909_253_c R_RXN909_253_c M_utp_c + M_cmp_c <=> M_udp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) PW043 R_RXN909_253_n R_RXN909_253_n M_utp_n + M_cmp_n <=> M_udp_n + M_cdp_n n TRUE (WBGene00007812) PW043 -R_RXN909_254_c R_RXN909_254_c M_datp_c + M_cmp_c <=> M_h_c + M_dadp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) "PW042;PW043" -R_RXN909_254_n R_RXN909_254_n M_datp_n + M_cmp_n <=> M_h_n + M_dadp_n + M_cdp_n n TRUE (WBGene00007812) "PW042;PW043" +R_RXN909_254_c R_RXN909_254_c M_datp_c + M_cmp_c <=> M_dadp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) "PW042;PW043" +R_RXN909_254_n R_RXN909_254_n M_datp_n + M_cmp_n <=> M_dadp_n + M_cdp_n n TRUE (WBGene00007812) "PW042;PW043" R_RXN909_255_c R_RXN909_255_c M_dctp_c + M_cmp_c <=> M_dcdp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) PW043 R_RXN909_255_n R_RXN909_255_n M_dctp_n + M_cmp_n <=> M_dcdp_n + M_cdp_n n TRUE (WBGene00007812) PW043 R_RXN909_256_c R_RXN909_256_c M_dgtp_c + M_cmp_c <=> M_dgdp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) "PW042;PW043" @@ -3049,8 +3049,8 @@ R_RXN909_259_c R_RXN909_259_c M_atp_c + M_thm_c <=> M_thmpp_c + M_amp_c c FALSE R_RXN909_26_c 3-hydroxyisobutyrate dehydrogenase M_nad_c + M_3hmp_c <=> M_h_c + M_nadh_c + M_mmtsa_c c FALSE (WBGene00019978) or (WBGene00010035) or (WBGene00001158) or (WBGene00001157) or (WBGene00007129) PW083 R_RXN909_26_m 3-hydroxyisobutyrate dehydrogenase M_nad_m + M_3hmp_m <=> M_h_m + M_nadh_m + M_mmtsa_m m TRUE (WBGene00001157) or (WBGene00010035) or (WBGene00001158) or (WBGene00007129) or (WBGene00000181) or (WBGene00019978) or (WBGene00007122) PW083 Added extra genes from R_3_HYDROXYISOBUTYRATE_DEHYDROGENASE_RXN_m, set to reversible -> revise later jpnh R_RXN909_260_c (5-L-glutamyl)-L-amino-acid gamma-glutamyl cyclotransferase (5-oxoproline-forming) M_gluasp_c <=> M_5oxpro_c + M_asn__L_c c FALSE (WBGene00016629) PW071 "added rxn name; replaced M_asn__L_c by M_asn_L_c" "jpnh; lenov" -R_RXN909_261_c ATP:dGMP phosphotransferase M_h_c + M_dgdp_c + M_adp_c <=> M_atp_c + M_dgmp_c c TRUE (WBGene00020190) PW042 set to reversible janna -R_RXN909_261_m R_RXN909_261_m M_h_m + M_dgdp_m + M_adp_m <=> M_atp_m + M_dgmp_m m TRUE (WBGene00020190) PW042 set to reversible janna +R_RXN909_261_c ATP:dGMP phosphotransferase M_dgdp_c + M_adp_c <=> M_atp_c + M_dgmp_c c TRUE (WBGene00020190) PW042 set to reversible janna +R_RXN909_261_m R_RXN909_261_m M_dgdp_m + M_adp_m <=> M_atp_m + M_dgmp_m m TRUE (WBGene00020190) PW042 set to reversible janna R_RXN909_266_c R_RXN909_266_c M_gpail_c + M_coa16_0_c <=> M_gacpail_c + M_coa_c c FALSE (WBGene00022447) PW028 R_RXN909_268_c R_RXN909_268_c M_h2o_c + M_deg9_c <=> M_deg10_c + M_glcur_c c FALSE (WBGene00013693) PW016 [CHECK ME] Deg9 and 10 only appear in this reaction R_RXN909_27_c R_RXN909_27_c M_2doxrib_c + M_atp_c <=> 2.0 M_h_c + M_adp_c + M_2dr5p_c c FALSE (WBGene00008548) PW043 From c08fe25581334202416387ff92e2eb9b7057e321 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 13:47:21 +1000 Subject: [PATCH 11/14] fix/XYLULOKIN_RXN removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 4bee577..7df4607 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -3654,8 +3654,8 @@ R_Water_transport Water transport M_h2o_c <=> M_h2o_e ce TRUE ND PW107 R_XAND_c Xanthine dehydrogenase M_h2o_c + M_xan_c + M_nad_c <=> M_h_c + M_urate_c + M_nadh_c c TRUE (WBGene00010083) PW042 R_XPPT_c Xanthine-guanine phosphoribosyltransferase M_xmp_c + M_ppi_c <=> M_xan_c + M_prpp_c c TRUE WBGene00013690 PW042 RHEA:17973 R_XYLt D-xylose reversible transport M_xyl_D_e <=> M_xyl_D_c ec TRUE (WBGene00019979) or (WBGene00019207) or (ND) PW107 -R_XYLULOKIN_RXN_c Xylulokinase M_xylu_D_c + M_atp_c <=> M_xu5p_D_c + 2.0 M_h_c + M_adp_c c TRUE (WBGene00011147) PW027 SPW004 -R_XYLULOKIN_RXN_n Xylulokinase M_xylu_D_n + M_atp_n <=> M_xu5p_D_n + 2.0 M_h_n + M_adp_n n TRUE (WBGene00011147) PW027 SPW004 +R_XYLULOKIN_RXN_c Xylulokinase M_xylu_D_c + M_atp_c <=> M_xu5p_D_c + M_h_c + M_adp_c c TRUE (WBGene00011147) PW027 SPW004 +R_XYLULOKIN_RXN_n Xylulokinase M_xylu_D_n + M_atp_n <=> M_xu5p_D_n +M_h_n + M_adp_n n TRUE (WBGene00011147) PW027 SPW004 R_XYLUR_c L-xylulose reductase M_xylu_L_c + M_h_c + M_nadph_c <=> M_xylt_c + M_nadp_c c TRUE (WBGene00000984) PW033 RHEA:17025 set to reversible janna R_XYLUR_n L-xylulose reductase M_xylu_L_n + M_h_n + M_nadph_n <=> M_xylt_n + M_nadp_n n TRUE (WBGene00000984) PW033 RHEA:17025 set to reversible janna R_zn2_e zn2 te <=> M_zn2_e e TRUE PW111 From 1ddb5dea4a7aa356dbeaa384ee7851c51e6bdbb3 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 14:19:42 +1000 Subject: [PATCH 12/14] fix/TMDK1_c TRIOK_c URIK1_c removed 1 Proton to balance the reaction/found on uniprot --- curation/Reaction-SBtab.tsv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 7df4607..b50dfdb 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -3585,7 +3585,7 @@ R_TKT2_c D-Fructose 6-phosphate:D-glyceraldehyde-3-phosphate glycolaldehyde tran R_TKT2_m D-Fructose 6-phosphate:D-glyceraldehyde-3-phosphate glycolaldehyde transferase M_e4p_m + M_xu5p_D_m <=> M_f6p_m + M_g3p_m m TRUE (WBGene00012713) PW027 SPW004 "RHEA:13457;RHEA:13457" R_TKT2_n D-Fructose 6-phosphate:D-glyceraldehyde-3-phosphate glycolaldehyde transferase M_e4p_n + M_xu5p_D_n <=> M_f6p_n + M_g3p_n n TRUE (WBGene00008506) PW027 SPW004 R_TMABADH_c 4-trimethylammoniobutyraldehyde dehydrogenase M_4tmeabut_c + M_h2o_c + M_nad_c <=> 2.0 M_h_c + M_4tmeabutn_c + M_nadh_c c FALSE (WBGene00000108 or WBGene00000110) or WBGene00000118 PW080 -R_TMDK1_c Thymidine kinase M_atp_c + M_thymd_c <=> 2.0 M_h_c + M_adp_c + M_dtmp_c c FALSE (WBGene00006568) "PW042;PW043" "RHEA:19129;RHEA:19129" +R_TMDK1_c Thymidine kinase M_atp_c + M_thymd_c <=> M_h_c + M_adp_c + M_dtmp_c c FALSE (WBGene00006568) "PW042;PW043" "RHEA:19129;RHEA:19129" R_TMDS_c Thymidylate synthase M_dump_c + M_mlthf_c <=> M_dtmp_c + M_dhf_c c TRUE (WBGene00022455) PW043 R_TMDS_n Thymidylate synthase M_dump_n + M_mlthf_n <=> M_dtmp_n + M_dhf_n n TRUE (WBGene00022455) PW043 R_TMLYSOX_c Trimethyllysine dioxygenase M_akg_c + M_tmlys_c + M_o2_c <=> M_co2_c + M_3htmelys_c + M_succ_c c FALSE (WBGene00001522) or (WBGene00001523) PW080 RHEA:24028 @@ -3596,7 +3596,7 @@ R_TRANS_PENTAPRENYLTRANSFERASE_RXN_c hexaprenyl-diphosphate synthase[(2E,6E)-far R_TRDR_n Thioredoxin reductase (NADPH) M_h_n + M_nadph_n + M_trdox_n <=> M_nadp_n + M_trdrd_n n FALSE (WBGene00015553) PW093 RHEA:20345 R_TREHALA_RXN_c "α,α-trehalase" M_h2o_c + M_tre_c <=> 2.0 M_glc_bD_c c TRUE (WBGene00006610) or (WBGene00006609) or (WBGene00006608) or (WBGene00006611) or (WBGene00006607) PW026 "RHEA:32675;RHEA:32675;RHEA:32675;RHEA:32675;RHEA:32675;RHEA:32675;RHEA:32675" ms R_TREHALA_RXN_m "α,α-trehalase" M_h2o_m + M_tre_m <=> 2.0 M_glc_bD_m m TRUE (WBGene00006610) or (WBGene00006608) PW026 "RHEA:32675;RHEA:32675;RHEA:32675;RHEA:32675" ms -R_TRIOK_c Triokinase M_glyald_c + M_atp_c <=> M_g3p_c + 2.0 M_h_c + M_adp_c c FALSE PW020 +R_TRIOK_c Triokinase M_glyald_c + M_atp_c <=> M_g3p_c + M_h_c + M_adp_c c FALSE PW020 R_TRPHYDRO2_c Tryptophan 5-monooxygenase M_trp__L_c + M_thbpt_c + M_o2_c <=> M_thbpt4acam_c + M_5htrp_c c FALSE (WBGene00006600) PW072 R_Tryptophan_Exchange_reactions_e Tryptophan transport M_trp__L_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Tryptophan_transport Tryptophan transport M_trp__L_c <=> M_trp__L_e ce TRUE ND PW107 @@ -3631,7 +3631,7 @@ R_Urea_transport Urea transport M_urea_c <=> M_urea_e ce TRUE ND PW107 R_Uridine_Exchange_reactions_e Uridine transport M_uri_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Uridine_transport Uridine transport M_uri_c <=> M_uri_e ce TRUE ND PW107 R_URIH_c Uridine nucleosidase M_h2o_c + M_uri_c <=> M_ura_c + M_rib_D_c c TRUE "PW042;PW043" -R_URIK1_c Uridine kinase M_atp_c + M_uri_c <=> 2.0 M_h_c + M_adp_c + M_ump_c c FALSE WBGene00007089 or WBGene00008948 "PW042;PW043" +R_URIK1_c Uridine kinase M_atp_c + M_uri_c <=> M_h_c + M_adp_c + M_ump_c c FALSE WBGene00007089 or WBGene00008948 "PW042;PW043" R_URIK2_c GTP:uridine 5'-phosphotransferase M_gtp_c + M_uri_c <=> M_h_c + M_gdp_c + M_ump_c c TRUE PW043 R_URIt2r Uridine transport M_h_e + M_uri_e <=> M_h_c + M_uri_c ec TRUE (WBGene00018716 or WBGene00014092) or (ND) PW107 Added name jpnh R_Uritn uridine transport in nucleus M_uri_c <=> M_uri_n cn TRUE PW108 From 7ff4985b15aea96ff588a59b5b8bcee4ba85caa9 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 14:44:07 +1000 Subject: [PATCH 13/14] fix/multiple kinases removed 1 Proton to balance the reaction/kinase activity --- curation/Reaction-SBtab.tsv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index b50dfdb..22d0155 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -968,7 +968,7 @@ R_DOPAENT4tc dopamine transport M_h_e + M_dopa_e <=> M_h_c + M_dopa_c ec TRUE ( R_DOPAQNISO1_c R_DOPAQNISO1_c M_dopaqn_c <=> M_h_c + M_2c23dh56dhoxin_c c FALSE PW077 R_DOPAt4_2_r Dopamine reversible transport in via sodium symport (1:2) M_dopa_e + 2.0 M_na1_e <=> M_dopa_c + 2.0 M_na1_c ec TRUE (WBGene00000934) PW107 R_DOPAVESSEC Dopamine secretion via secretory vesicle (ATP driven) M_h2o_c + M_dopa_c + M_atp_c <=> M_pi_c + M_h_c + M_dopa_e + M_adp_c c FALSE (WBGene00000295) PW107 RHEA:20309 -R_DPCOAK_c Dephospho-CoA kinase M_atp_c + M_dpcoa_c <=> 2.0 M_h_c + M_adp_c + M_coa_c c FALSE (WBGene00022031) or (WBGene00011500) PW037 +R_DPCOAK_c Dephospho-CoA kinase M_atp_c + M_dpcoa_c <=> M_h_c + M_adp_c + M_coa_c c FALSE (WBGene00022031) or (WBGene00011500) PW037 R_DPMVD_c Diphosphomevalonate decarboxylase M_5dpmev_c + M_atp_c <=> M_ipdp_c + M_co2_c + M_pi_c + M_adp_c c TRUE (WBGene00012984) PW001 R01121 added KEGGID, ChEBI ms R_DTDPtn dTDP nuclear transport M_dtdp_c <=> M_dtdp_n cn TRUE PW108 R_DTMPK_c Thymidylate kinase M_atp_c + M_dtmp_c <=> M_adp_c + M_dtdp_c c TRUE (WBGene00011272) "PW042;PW043" RHEA:13517 set to reversible janna @@ -978,7 +978,7 @@ R_DUDPtn dUDP nuclear transport M_dudp_c <=> M_dudp_n cn TRUE PW108 R_DUMPtn dUMP nuclear transport M_dump_c <=> M_dump_n cn TRUE PW108 R_DURAD_c Dihydropyrimidine dehydrogenase (NADP+) M_h_c + M_ura_c + M_nadph_c <=> M_56dura_c + M_nadp_c c TRUE (WBGene00016103) PW043 RHEA:18093 set to reversible janna R_DURAD2_c R_DURAD2_c M_h_c + M_thym_c + M_nadph_c <=> M_56dthm_c + M_nadp_c c TRUE (WBGene00016103) PW043 RHEA:18093 set to reversible janna -R_DURIK1_c Deoxyuridine kinase M_atp_c + M_duri_c <=> 2.0 M_h_c + M_adp_c + M_dump_c c FALSE (WBGene00006568) PW043 "RHEA:19129;RHEA:19129" Added reaction name jpnh +R_DURIK1_c Deoxyuridine kinase M_atp_c + M_duri_c <=> M_h_c + M_adp_c + M_dump_c c FALSE (WBGene00006568) PW043 "RHEA:19129;RHEA:19129" Added reaction name jpnh R_DURItn deoxyuridine transport in nucleus M_duri_c <=> M_duri_n cn TRUE PW108 R_DUTPDP_c dUTP pyrophosphatase M_h2o_c + M_dutp_c <=> M_ppi_c + M_h_c + M_dump_c c FALSE WBGene00001823 or WBGene00010609 PW043 "RHEA:23996;RHEA:44644" [DELETION] Dupe of R_RXN909_4_c jpnh R_DUTPDP_m dUTP pyrophosphatase M_h2o_m + M_dutp_m <=> M_ppi_m + M_h_m + M_dump_m m FALSE (WBGene00010609) PW043 @@ -1552,7 +1552,7 @@ R_GND2_m R_GND2_m M_6pgc_m + M_nad_m <=> M_co2_m + M_ru5p_D_m + M_nadh_m m TRUE R_GRTT_c geranyltranstransferase M_ipdp_c + M_grdp_c <=> M_ppi_c + M_frdp_c c TRUE (WBGene00011058) PW001 R08528 "(JANNA: restored M_frdp_c as was blocked after this change; can look in more detail at pathway including M_ct_frdp_c later) added KEGGID, ChEBI; change to M_ct_frdp_c from M_frdp_c" ms R_GSHTRAN_RXN_c Glutathione transferase M_RX_c + M_gthrd_c <=> M_HX_c + M_S_Substituted_Glutathione_c c FALSE (WBGene00017054) or (WBGene00014251) or (WBGene00001758) or (WBGene00001758) or (WBGene00001784) or (WBGene00001752) or (WBGene00001753) or (WBGene00001750) or (WBGene00001786) or (WBGene00001751) or (WBGene00001754) or (WBGene00001755) or (WBGene00001756) or (WBGene00001749) or (WBGene00016204) or (WBGene00016204) or (WBGene00001792) or (WBGene00001771) or (WBGene00001773) PW070 "RHEA:16437;RHEA:24424;RHEA:15969;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437" R_GSHTRAN_RXN_m Glutathione transferase M_RX_m + M_gthrd_m <=> M_HX_m + M_S_Substituted_Glutathione_m m FALSE (WBGene00017054) or (WBGene00001752) or (WBGene00001753) or (WBGene00001754) or (WBGene00001755) or (WBGene00001771) PW070 "RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437;RHEA:16437" -R_GSNK_m R_GSNK_m M_atp_m + M_gsn_m <=> 2.0 M_h_m + M_gmp_m + M_adp_m m FALSE PW042 +R_GSNK_m Guanosine Kinase M_atp_m + M_gsn_m <=> M_h_m + M_gmp_m + M_adp_m m FALSE PW042 R_GSNt2r Guanosine transport M_h_e + M_gsn_e <=> M_h_c + M_gsn_c ec TRUE (WBGene00018716 or WBGene00014092) or (ND) PW107 [CHECK ME] Identical except H usage? jpnh. R_GSNtm guanosine facilated transport in mitochondria M_gsn_c <=> M_gsn_m cm TRUE (WBGene00001320) or (WBGene00010701) or (ND) PW106 R_GTHDH_c Glutathione dehydrogenase (ascorbate) M_dhdascb_c + 2.0 M_gthrd_c <=> M_gthox_c + M_h_c + M_ascb__L_c c FALSE PW070 "[DELETION] Merged into R_RC01108; replaced M_ascb__L_c with M_ascb__L_c" "jpnh; lenov" @@ -1628,7 +1628,7 @@ R_ILETA_c Isoleucine transaminase M_akg_c + M_ile__L_c <=> M_3mop_c + M_glu__L_ R_ILETA_m Isoleucine transaminase M_akg_m + M_ile__L_m <=> M_3mop_m + M_glu__L_m m TRUE (WBGene00012855) PW083 Corrected gene association ckaleta 2.6.1.42 R_IMPC_c IMP cyclohydrolase M_h2o_c + M_imp_c <=> M_fprica_c c TRUE (WBGene00016957) PW042 R_IMPD_c IMP dehydrogenase M_h2o_c + M_imp_c + M_nad_c <=> M_xmp_c + M_h_c + M_nadh_c c TRUE (WBGene00020682) PW042 -R_INSK_c Inosine kinase M_atp_c + M_ins_c <=> 2.0 M_h_c + M_imp_c + M_adp_c c FALSE PW042 +R_INSK_c Inosine kinase M_atp_c + M_ins_c <=> M_h_c + M_imp_c + M_adp_c c FALSE PW042 R_INSt2 R_INSt2 M_h_e + M_ins_e <=> M_h_c + M_ins_c ec TRUE (WBGene00018716 or WBGene00014092) or (ND) PW107 R_IPDDI_c "Isopentenyl-diphosphate δ-isomerase" M_ipdp_c <=> M_dmpp_c c TRUE (WBGene00019460) PW001 R01123 added KEGGID, ChEBI ms R_ISOCIT_CLEAV_RXN_m Isocitrate lyase M_icit_m <=> M_glx_m + M_succ_m m TRUE (WBGene00001564) "PW074;PW030" "RHEA:13245;RHEA:18181" @@ -1716,7 +1716,7 @@ R_METHYLACYLYLCOA_HYDROXY_RXN_m Methylacrylyl-CoA hydratase M_h2o_m + M_2mp2coa R_METrRNAtm Met tRNA transport M_mettrna_c <=> M_mettrna_m cm TRUE PW111 R_METS_c 5-methyltetrahydrofolate--homocysteine S-methyltransferase M_hcys__L_c + M_5mthf_c <=> M_met__L_c + M_thf_c c TRUE WBGene00010988 and WBGene00006510 "PW091;PW082" "RHEA:23908;RHEA:11172" R_METS_n 5-methyltetrahydrofolate--homocysteine S-methyltransferase M_hcys__L_n + M_5mthf_n <=> M_met__L_n + M_thf_n n TRUE (WBGene00010988) "PW091;PW082" RHEA:11172 -R_MEVK1_c Mevalonate kinase M_mev_R_c + M_atp_c <=> M_5pmev_c + 2.0 M_h_c + M_adp_c c TRUE (WBGene00021534) PW001 R02245 added KEGGID ms +R_MEVK1_c Mevalonate kinase M_mev_R_c + M_atp_c <=> M_5pmev_c + M_h_c + M_adp_c c TRUE (WBGene00021534) PW001 R02245 added KEGGID ms R_mg2_e mg2 te <=> M_mg2_e e TRUE PW111 R_MGCH_c Methylglutaconyl-CoA hydratase M_hmgcoa_c <=> M_h2o_c + M_3mgcoa_c c TRUE (WBGene00001154) PW083 R_MGCH_m Methylglutaconyl-CoA hydratase M_hmgcoa_m <=> M_h2o_m + M_3mgcoa_m m TRUE (WBGene00001154) PW083 @@ -2091,7 +2091,7 @@ R_PNANM_n Phosphomannomutase M_man1p_n <=> M_man6p_n n TRUE (WBGene00009925) "PW R_PNKIN_RXN_c R_PNKIN_RXN_c M_atp_c + M_pydxn_c <=> M_h_c + M_adp_c + M_pdx5p_c c FALSE (WBGene00019008) PW039 RHEA:10224 R_PNKIN_RXN_m R_PNKIN_RXN_m M_atp_m + M_pydxn_m <=> M_h_m + M_adp_m + M_pdx5p_m m FALSE (WBGene00019008) PW039 RHEA:10224 R_PNPOXI_RXN_m "pyridoxal 5′-phosphate synthase" M_o2_m + M_pdx5p_m <=> M_h2o2_m + M_pydx5p_m m FALSE (WBGene00018996) PW039 -R_PNTK_c Pantothenate kinase M_pnto_R_c + M_atp_c <=> M_4ppan_c + 2.0 M_h_c + M_adp_c c FALSE WBGene00004068 or WBGene00006862 PW037 RHEA:16373 +R_PNTK_c Pantothenate kinase M_pnto_R_c + M_atp_c <=> M_4ppan_c + M_h_c + M_adp_c c FALSE WBGene00004068 or WBGene00006862 PW037 RHEA:16373 R_PPA_c Inorganic pyrophosphatase M_h2o_c + M_ppi_c <=> 2.0 M_pi_c + M_h_c c TRUE (WBGene00007548) or (WBGene00008149) PW007 RHEA:24576 R_PPA_m Inorganic pyrophosphatase M_h2o_m + M_ppi_m <=> 2.0 M_pi_m + M_h_m m TRUE (WBGene00007548) or (WBGene00008149) PW007 RHEA:24576 R_PPA_n Inorganic pyrophosphatase M_h2o_n + M_ppi_n <=> 2.0 M_pi_n + M_h_n n TRUE (WBGene00007548) PW007 @@ -2146,7 +2146,7 @@ R_pydx_e Pyridoxaltransport M_pydx_e <=> e TRUE PW111 R_pydxn_e Pyridoxine transport M_pydxn_e <=> e TRUE PW111 R_pydxnt Pyridoxine transport M_pydxn_c <=> M_pydxn_e ce TRUE ND PW107 R_pydxt Pyridoxal transport M_pydx_c <=> M_pydx_e ce TRUE ND PW107 -R_PYK_c Pyruvate kinase M_pep_c + 2.0 M_h_c + M_adp_c <=> M_atp_c + M_pyr_c c FALSE (WBGene00009126) or (WBGene00014001) PW018 SPW004 "RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157" +R_PYK_c Pyruvate kinase M_pep_c +M_h_c + M_adp_c <=> M_atp_c + M_pyr_c c FALSE (WBGene00009126) or (WBGene00014001) PW018 SPW004 "RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157" R_PYNP2_c Uridine phosphorylase M_pi_c + M_uri_c <=> M_r1p_c + M_ura_c c TRUE (WBGene00022817) PW043 "RHEA:24388;RHEA:16037;RHEA:22824" R_PYRAMKIN_RXN_c R_PYRAMKIN_RXN_c M_atp_c + M_pydam_c <=> M_h_c + M_adp_c + M_pyam5p_c c FALSE (WBGene00019008) PW039 RHEA:10224 R_PYRAMKIN_RXN_m R_PYRAMKIN_RXN_m M_atp_m + M_pydam_m <=> M_h_m + M_adp_m + M_pyam5p_m m FALSE (WBGene00019008) PW039 RHEA:10224 @@ -2163,7 +2163,7 @@ R_R146_RXN_c 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase ( R_R147_RXN_c Acireductone dioxygenase (Fe(2+)-requiring) M_dhmtp_c + M_o2_c <=> M_for_c + M_h_c + M_2kmb_c c FALSE (WBGene00009636) PW082 R_r2408 Mitochondrial Carrier (MC) TCDB:2.A.29.19.1 M_h_c + M_orn_c + M_his__L_m <=> M_h_m + M_orn_m + M_his__L_c cm FALSE (WBGene00015186) PW106 R_r2472 Glycerol 3-phosphate transport CM M_glyc3p_c + M_pi_m <=> M_glyc3p_m + M_pi_c cm FALSE PW111 added rxn name jpnh -R_RBFK_c ATP-dependent riboflavin kinase M_atp_c + M_ribflv_c <=> 2.0 M_h_c + M_adp_c + M_fmn_c c FALSE (WBGene00011224) PW040 +R_RBFK_c ATP-dependent riboflavin kinase M_atp_c + M_ribflv_c <=> M_h_c + M_adp_c + M_fmn_c c FALSE (WBGene00011224) PW040 R_RC00078 Fe(II):oxygen oxidoreductase 4.0 M_h_c + M_o2_c + 4.0 M_fe2_c <=> 2.0 M_h2o_c + 4.0 M_fe3_c c FALSE WBGene00001500 or WBGene00001501 PW005 "RHEA:11148;RHEA:11148" R_RC00089 ATP diphosphate-lyase (cyclizing, 3',5'-cyclic-AMP-forming) M_atp_c <=> M_ppi_c + M_camp_c c FALSE (WBGene00000068 or WBGene00000071) or WBGene00000069 PW042 RHEA:15389 R_RC00100 NADH:ferricytochrome-b5 oxidoreductase M_h_c + M_nadh_c + 2.0 M_ficytb5_c <=> M_nad_c + 2.0 M_focytb5_c c TRUE (WBGene00020267 or WBGene00020268) PW098 RHEA:46680 From d80128f34ef82b1f5e7403030fe37ae4c5694345 Mon Sep 17 00:00:00 2001 From: Marius-uni Date: Wed, 31 Aug 2022 14:53:13 +1000 Subject: [PATCH 14/14] fix/multiple kinases removed 1 Proton to balance the reaction/kinase activity --- curation/Reaction-SBtab.tsv | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index 22d0155..7bd8809 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -2588,8 +2588,8 @@ R_RE00548 riboflavin-5-phosphate phosphohydrolase (acid optimum) M_h2o_e + M_fm R_RE10092 carbonate hydro-lyase (carbon-dioxide-forming) M_co2_e + M_h2o_e <=> M_hco3_e + M_h_e e TRUE WBGene00000283 PW098 RHEA:10748 Changed pathway annotation from nitrogen metabolism to miscellaneous lenov R_Riboflavin_Exchange_reactions_e Riboflavin transport M_ribflv_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Riboflavin_transport Riboflavin transport M_ribflv_c <=> M_ribflv_e ce TRUE WBGene00044637 or WBGene00021626 PW107 -R_RIBOKIN_RXN_c Ribokinase M_atp_c + M_rib_D_c <=> M_r5p_c + 2.0 M_h_c + M_adp_c c FALSE (WBGene00008548) PW027 SPW004 -R_RIBOKIN_RXN_m Ribokinase M_atp_m + M_rib_D_m <=> M_r5p_m + 2.0 M_h_m + M_adp_m m FALSE (WBGene00008548) PW027 SPW004 +R_RIBOKIN_RXN_c Ribokinase M_atp_c + M_rib_D_c <=> M_r5p_c + M_h_c + M_adp_c c FALSE (WBGene00008548) PW027 SPW004 +R_RIBOKIN_RXN_m Ribokinase M_atp_m + M_rib_D_m <=> M_r5p_m + M_h_m + M_adp_m m FALSE (WBGene00008548) PW027 SPW004 R_RIBONUCLEOSIDE_DIP_REDUCTII_RXN_c R_RIBONUCLEOSIDE_DIP_REDUCTII_RXN_c M_cdp_c + M_nrdh_ox_c <=> M_h2o_c + M_dcdp_c + M_nrdh_rd_c c FALSE PW043 R_RM00081 Ferrocytochrome-c:oxygen oxidoreductase 8.0 M_h_m + M_o2_m + 4.0 M_focytC_m <=> 2.0 M_h2o_m + 4.0 M_h_c + 4.0 M_ficytC_m m FALSE (WBGene00010964 and WBGene00010965 and WBGene00010962) and WBGene00000371 and WBGene00012553 and WBGene00006519 and WBGene00022170 and WBGene00017926 and WBGene00009161 PW007 "RHEA:11436;RHEA:11436;RHEA:11436" R_RM00130 ATP:dephospho-CoA 3-phosphotransferase M_atp_m + M_dpcoa_m <=> M_h_m + M_adp_m + M_coa_m m FALSE WBGene00011500 or WBGene00022031 PW037 @@ -2791,9 +2791,9 @@ R_RXN_12623_c N,N'-diacetylchitobiose synthase M_h2o_c + M_chdex_c <=> M_chtbs_ R_RXN_12624_c chitotriose synthase M_h2o_c + M_chdex_c <=> M_chttr_c c FALSE (WBGene00000503) PW021 R_RXN_12625_c "N,N'-diacetylchitobioseβ-N-acetylglucosaminidase" M_h2o_c + M_chtbs_c <=> 2.0 M_acgam_c c FALSE (WBGene00020509) PW021 R_RXN_12626_c "chitotriose β-N-acetylglucosaminidase" M_h2o_c + M_chttr_c <=> M_acgam_c + M_chtbs_c c FALSE (WBGene00020509) PW021 -R_RXN_1685_c alpha-D-glucokinase M_glc_aD_c + M_atp_c <=> M_g6p_A_c + 2.0 M_h_c + M_adp_c c FALSE (WBGene00008780) or (WBGene00022306) or (WBGene00010416) PW018 SPW004 -R_RXN_1685_m alpha-D-glucokinase M_glc_aD_m + M_atp_m <=> M_g6p_A_m + 2.0 M_h_m + M_adp_m m FALSE (WBGene00010416) PW018 SPW004 why only one hexokinase associated? Are the two others not in mitochondria? -R_RXN_1685_n alpha-D-glucokinase M_glc_aD_n + M_atp_n <=> M_g6p_A_n + 2.0 M_h_n + M_adp_n n FALSE (WBGene00008780) or (WBGene00022306) or (WBGene00010416) PW018 SPW004 +R_RXN_1685_c alpha-D-glucokinase M_glc_aD_c + M_atp_c <=> M_g6p_A_c + M_h_c + M_adp_c c FALSE (WBGene00008780) or (WBGene00022306) or (WBGene00010416) PW018 SPW004 +R_RXN_1685_m alpha-D-glucokinase M_glc_aD_m + M_atp_m <=> M_g6p_A_m + M_h_m + M_adp_m m FALSE (WBGene00010416) PW018 SPW004 why only one hexokinase associated? Are the two others not in mitochondria? +R_RXN_1685_n alpha-D-glucokinase M_glc_aD_n + M_atp_n <=> M_g6p_A_n + M_h_n + M_adp_n n FALSE (WBGene00008780) or (WBGene00022306) or (WBGene00010416) PW018 SPW004 R_RXN_2881_c Non enzymatic 5,10-Methylenetetrahydrofolate production M_thf_c + M_fald_c <=> M_h2o_c + M_mlthf_c c TRUE PW091 added rxn name jpnh R_RXN_2961_c Non enzymatic 5,10-Methylenetetrahydrofolate production M_hmgth_c <=> M_fald_c + M_gthrd_c c TRUE PW091 added rxn name jpnh R_RXN_3521_c L-ascorbate:hydrogen-peroxide oxidoreductase M_h2o2_c + 4.0 M_h_c + 2.0 M_ascb__L_c <=> 2.0 M_h2o_c + 2.0 M_mdascb_c c FALSE PW070 "added rxn name; replaced M_ascb__L_c with M_ascb__L_c" "jpnh; lenov" @@ -3053,8 +3053,8 @@ R_RXN909_261_c ATP:dGMP phosphotransferase M_dgdp_c + M_adp_c <=> M_atp_c + M R_RXN909_261_m R_RXN909_261_m M_dgdp_m + M_adp_m <=> M_atp_m + M_dgmp_m m TRUE (WBGene00020190) PW042 set to reversible janna R_RXN909_266_c R_RXN909_266_c M_gpail_c + M_coa16_0_c <=> M_gacpail_c + M_coa_c c FALSE (WBGene00022447) PW028 R_RXN909_268_c R_RXN909_268_c M_h2o_c + M_deg9_c <=> M_deg10_c + M_glcur_c c FALSE (WBGene00013693) PW016 [CHECK ME] Deg9 and 10 only appear in this reaction -R_RXN909_27_c R_RXN909_27_c M_2doxrib_c + M_atp_c <=> 2.0 M_h_c + M_adp_c + M_2dr5p_c c FALSE (WBGene00008548) PW043 -R_RXN909_27_m R_RXN909_27_m M_2doxrib_m + M_atp_m <=> 2.0 M_h_m + M_adp_m + M_2dr5p_m m FALSE (WBGene00008548) PW043 +R_RXN909_27_c R_RXN909_27_c M_2doxrib_c + M_atp_c <=> M_h_c + M_adp_c + M_2dr5p_c c FALSE (WBGene00008548) PW043 +R_RXN909_27_m R_RXN909_27_m M_2doxrib_m + M_atp_m <=> M_h_m + M_adp_m + M_2dr5p_m m FALSE (WBGene00008548) PW043 R_RXN909_270_c R_RXN909_270_c M_h2o_c + M_cs_d_deg3_c <=> M_cs_d_deg4_c + M_glcur_c c FALSE (WBGene00013693) PW014 R_RXN909_271_c R_RXN909_271_c M_h2o_c + M_cs_c_deg2_c <=> M_cs_c_deg3_c + M_glcur_c c FALSE (WBGene00013693) PW014 R_RXN909_272_c R_RXN909_272_c M_h2o_c + M_ap4a_c <=> M_h_c + M_atp_c + M_amp_c c FALSE (WBGene00003581) PW034 RHEA:32039