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Merge pull request #4 from Marius-uni/fix/charges
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Fix/charges
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@Marius-uni
Marius-uni authored Sep 1, 2022
2 parents 44c5340 + 4062b2d commit 47c998e
Showing 1 changed file with 18 additions and 18 deletions.
36 changes: 18 additions & 18 deletions curation/Reaction-SBtab.tsv
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Expand Up @@ -698,7 +698,7 @@ R_CAT_m Catalase 2.0 M_h2o2_m <=> 2.0 M_h2o_m + M_o2_m m FALSE (WBGene00013220)
R_CAt7r calcium / sodium antiporter (1:3), reversible 3.0 M_na1_e + M_ca2_c <=> M_ca2_e + 3.0 M_na1_c ec TRUE (WBGene00003567) or (WBGene00003566) PW107
R_CBIAT_c ATP:cobinamide Cobeta-adenosyltransferase M_atp_c + M_cbi_c <=> M_pppi_c + M_h_c + M_adocbi_c c FALSE (WBGene00016144) PW005 R07268 "[CHECKME] substrate and product only appear in this reaction; pathway moved from cobinamide metabolism to porphyrin and chlorophyll metabolism" lenov
R_CBLAT_c Cob(I)alamin adenosyltransferase M_atp_c + M_cbl1_c <=> M_pppi_c + M_h_c + M_adocbl_c c FALSE (WBGene00016144) PW006
R_CBPS_c carbamoyl-phosphate synthetase (glutamine-hydrolysing) M_h2o_c + M_hco3_c + M_gln__L_c + 2.0 M_atp_c <=> M_cbp_c + M_pi_c + 4.0 M_h_c + M_glu__L_c + 2.0 M_adp_c c FALSE (WBGene00004259) PW043 "RHEA:18633;RHEA:20013;RHEA:24296"
R_CBPS_c carbamoyl-phosphate synthetase (glutamine-hydrolysing) M_h2o_c + M_hco3_c + M_gln__L_c + 2.0 M_atp_c <=> M_cbp_c + M_pi_c + 2.0 M_h_c + M_glu__L_c + 2.0 M_adp_c c FALSE (WBGene00004259) PW043 "RHEA:18633;RHEA:20013;RHEA:24296"
R_CDPDAGtm cdp-diacylglycerol transport to mitochndria M_cdpdag_c <=> M_cdpdag_m cm FALSE PW056 [DELETION] Dupe of R_TCM0195 jpnh
R_CeCRNtm O-cerotoylcarnitine transport into mitochondria via diffusion M_carn26_0__L_c <=> M_carn26_0__L_m cm FALSE (WBGene00000996 ) PW106
R_CGLYt3_2_ Cys-Gly transport in via proton symport 2.0 M_h_e + M_cgly_e <=> 2.0 M_h_c + M_cgly_c ec FALSE (WBGene00003878) or (ND) PW107
Expand Down Expand Up @@ -1444,7 +1444,7 @@ R_FBA2_c R_FBA2_c M_f1p_c <=> M_dhap_c + M_glyald_c c TRUE (WBGene00011474) PW02
R_FBA2_n R_FBA2_n M_f1p_n <=> M_dhap_n + M_glyald_n n TRUE (WBGene00011474) PW020 RHEA:14729
R_fe2_e fe2 te <=> M_fe2_e e TRUE PW111
R_FK_c fucokinase M_atp_c + M_fuc_L_c <=> M_fuc1p_L_c + M_h_c + M_adp_c c FALSE (WBGene00007745) PW025 Changed M_fuc1p__L_c into M_fuc1p_L_c lenov
R_FKYNH_c Arylformamidase M_Lfmkynr_c + M_h2o_c <=> M_Lkynr_c + M_for_c + 3.0 M_h_c c FALSE (WBGene00017051) PW072
R_FKYNH_c Arylformamidase M_Lfmkynr_c + M_h2o_c <=> M_Lkynr_c + M_for_c + M_h_c c FALSE (WBGene00017051) PW072
R_FLDR_c Flavodoxin--NADP(+) reductase M_h_c + M_nadph_c + M_etfox_c <=> M_nadp_c + M_etfrd_c c FALSE (WBGene00001485) PW040
R_FMNAT_c FAD synthetase 2.0 M_h_c + M_atp_c + M_fmn_c <=> M_ppi_c + M_fad_c c FALSE (WBGene00011271) PW040 "RHEA:17237;RHEA:17237"
R_FOLABCCte Folate transport M_h2o_c + M_atp_c + M_fol_c <=> M_pi_c + M_h_c + M_adp_c + M_fol_e c FALSE ( WBGene00003411 or WBGene00000022 or WBGene00000020 or WBGene00000421 or WBGene00000023 or WBGene00018982 or WBGene00003407 or WBGene00003408 or WBGene00003407 or WBGene00003408 or WBGene00003996 or WBGene00003412) PW111 added rxn name jpnh
Expand Down Expand Up @@ -1498,7 +1498,7 @@ R_GLCAASE4_c R_GLCAASE4_c M_h2o_c + M_cs_a_deg2_c <=> M_cs_a_deg3_c + M_glcur_c
R_GLCt1r glucose transport (uniport) M_glc_bD_e <=> M_glc_bD_c ec TRUE (WBGene00019979) or (WBGene00019207) PW107
R_GLGNS1 glycogen synthase M_ggn_c + 4.0 M_udpg_c <=> 4.0 M_h_c + 4.0 M_udp_c + M_glygn1_c c FALSE (WBGene00001793) "PW019;PW053" RHEA:18549 Changed the stoichiometry of UDP-glucose from 3 to 4, update name, added group. lenov
R_GLNLASE_c R_GLNLASE_c M_gullac_c + M_h2o_c <=> M_guln_c + M_h_c c TRUE PW045 replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism
R_GLNS_c Glutamate--ammonia ligase M_nh3_c + M_glu__L_c + M_atp_c <=> M_pi_c + M_h_c + M_gln__L_c + M_adp_c c FALSE (WBGene00001604) or (WBGene00001602) or (WBGene00001606) or (WBGene00001607) or (WBGene00001603) or (WBGene00001603) or (WBGene00001603) PW073 "RHEA:16169;RHEA:16169;RHEA:16169"
R_GLNS_c Glutamate--ammonia ligase M_nh4_c + M_glu__L_c + M_atp_c <=> M_pi_c + M_h_c + M_gln__L_c + M_adp_c c FALSE (WBGene00001604) or (WBGene00001602) or (WBGene00001606) or (WBGene00001607) or (WBGene00001603) or (WBGene00001603) or (WBGene00001603) PW073 "RHEA:16169;RHEA:16169;RHEA:16169"
R_GLU5K_c Glutamate 5-kinase M_glu__L_c + M_atp_c <=> M_glu5p_c + M_adp_c c FALSE (WBGene00011938) PW081 "RHEA:14877;RHEA:19541"
R_GLU5K_m Glutamate 5-kinase M_glu__L_m + M_atp_m <=> M_glu5p_m + M_adp_m m FALSE (WBGene00011938) PW081 "RHEA:14877;RHEA:19541"
R_GLUCYS_c Glutamate--cysteine ligase M_cys__L_c + M_glu__L_c + M_atp_c <=> M_pi_c + 2.0 M_h_c + M_glucys_c + M_adp_c c FALSE WBGene00001527 or WBGene00017084 PW070 RHEA:13285
Expand Down Expand Up @@ -1529,7 +1529,7 @@ R_GLYC3Ptm glycerol-3-phosphate shuttle M_glyc3p_c <=> M_glyc3p_m cm FALSE ND PW
R_GLYCEROL_1_PHOSPHATASE_RXN_c Glycerol-1-phosphatase M_h2o_c + M_glyc3p_c <=> M_glyc_c + M_pi_c c TRUE PW052
R_Glycine_transport Glycine transport M_gly_c <=> M_gly_e ce TRUE ND PW107
R_Glycogenin_Exchange_reactions_c Glycogenin transport M_HC02136_c <=> c TRUE PW111 Replaces the demand from extracellular compartment lenov
R_GLYCOGENIN_GLUCOSYLTRANSFERASE_RXN_c glycogenin self-glycosylation M_udpg_c + M_HC02136_c <=> M_udp_c + M_glucosyl_glycogenin_c c FALSE (WBGene00006863) or (WBGene00012020) "PW019;PW053" "RHEA:23360;RHEA:56560" "Added to the group PW053; Explicit glycogenin could be omitted on the left - to be coordinated with R_RCC0046" lenov
R_GLYCOGENIN_GLUCOSYLTRANSFERASE_RXN_c glycogenin self-glycosylation M_udpg_c + M_HC02136_c <=> M_udp_c + M_glucosyl_glycogenin_c + M_h_c c FALSE (WBGene00006863) or (WBGene00012020) "PW019;PW053" "RHEA:23360;RHEA:56560" "Added to the group PW053; Explicit glycogenin could be omitted on the left - to be coordinated with R_RCC0046" lenov
R_GLYCOPHOSPHORYL_RXN_c glycogen phosphorylase 3 M_pi_c + M_glygn2_c <=> 3 M_g1p_c + M_ldex_c c FALSE (WBGene00020696) "PW019;PW053" Changed M_glygn3_c into M_glygn2_c, changed stoichiometry to produce 3 G1P, added group lenov
R_GLYCPDIESTER_RXN_c Glycerophosphodiester phosphodiesterase M_h2o_c + M_g3pc_c <=> M_chol_c + M_glyc3p_c + M_h_c c FALSE (WBGene00011644) or (WBGene00011929) or (WBGene00010092) or (WBGene00020446) or (WBGene00022532) PW056
R_GLYCtm glycerol transport M_glyc_c <=> M_glyc_m cm TRUE ND PW106
Expand Down Expand Up @@ -1560,7 +1560,7 @@ R_GTHO_c Glutathione reductase (NADPH) M_nadp_c + 2.0 M_gthrd_c <=> M_gthox_c +
R_GTHO_m Glutathione reductase (NADPH) M_nadp_m + 2.0 M_gthrd_m <=> M_gthox_m + M_h_m + M_nadph_m m TRUE (WBGene00008117) or (WBGene00014028) PW070 "RHEA:11740;RHEA:11740"
R_GTHP_c glutathione peroxidase M_h2o2_c + 2.0 M_gthrd_c <=> 2.0 M_h2o_c + M_gthox_c c TRUE (WBGene00019846) or (WBGene00007517) or (WBGene00007516) or (WBGene00022377) or (WBGene00011045) or (WBGene00018850) or (WBGene00009165) PW070 "RHEA:16833;RHEA:16833;RHEA:16833" set to reversible janna
R_GTHP_m glutathione peroxidase M_h2o2_m + 2.0 M_gthrd_m <=> 2.0 M_h2o_m + M_gthox_m m TRUE (WBGene00018850) PW070 set to reversible janna
R_GTHS_c glutathione synthetase M_glucys_c + M_gly_c + M_atp_c <=> M_pi_c + 2.0 M_h_c + M_adp_c + M_gthrd_c c FALSE (WBGene00010941) PW070 RHEA:13557
R_GTHS_c glutathione synthetase M_glucys_c + M_gly_c + M_atp_c <=> M_pi_c + M_h_c + M_adp_c + M_gthrd_c c FALSE (WBGene00010941) PW070 RHEA:13557
R_GTPCI_c GTP cyclohydrolase I M_h2o_c + M_gtp_c <=> M_ahdt_c + M_for_c + M_h_c c TRUE (WBGene00000298) PW091 RHEA:17473
R_GTPCI_n GTP cyclohydrolase I M_h2o_n + M_gtp_n <=> M_ahdt_n + M_for_n + M_h_n n TRUE (WBGene00000298) PW091 RHEA:17473
R_GTPtn GTP diffusion in nucleus M_gtp_c <=> M_gtp_n cn TRUE PW108
Expand Down Expand Up @@ -1643,7 +1643,7 @@ R_Isoleucine_transport Isoleucine transport M_ile__L_c <=> M_ile__L_e ce TRUE ND
R_IZPN_c Imidazolonepropionase M_4izp_c + M_h2o_c + M_h_c <=> M_forglu_c c TRUE (WBGene00020436) PW084
R_k_e k te <=> M_k_e e TRUE PW111
R_KCCt K+-Cl- cotransport M_cl_e + M_k_e <=> M_cl_c + M_k_c ec TRUE (WBGene00019205) PW107
R_KHK_c Ketohexokinase M_fru_B_c + M_atp_c <=> M_f1p_c + M_adp_c c FALSE PW020
R_KHK_c Ketohexokinase M_fru_B_c + M_atp_c <=> M_f1p_c + M_adp_c + m_h_c c FALSE PW020
R_KYN3OX_c Kynurenine 3-monooxygenase M_Lkynr_c + M_h_c + M_nadph_c + M_o2_c <=> M_h2o_c + M_hLkynr_c + M_nadp_c c FALSE WBGene00011088 or WBGene00011089 PW072 RHEA:20545
R_L_GULONOLACTONE_OXIDASE_RXN_c L-gulonolactone oxidase M_gullac_c + M_o2_c <=> M_h2o2_c + M_lxhexll_c c FALSE PW045 replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism
R_Lact2r lactose transport (uniport) M_lac__L_e <=> M_lac__L_c ec TRUE (WBGene00008214) or (ND) PW107
Expand Down Expand Up @@ -2105,11 +2105,11 @@ R_PPM_c phosphoglucomutase M_r1p_c <=> M_r5p_c c TRUE (WBGene00012803) or (WBGen
R_PPM_n phosphoglucomutase M_r1p_n <=> M_r5p_n n TRUE (WBGene00019890) "PW027;PW042" removed PRPP biosynthesis and PW043 pathways, added PW027 lenov
R_PPNCL2_c Phosphopantothenate--cysteine ligase M_4ppan_c + M_cys__L_c + M_ctp_c <=> M_4ppcys_c + M_ppi_c + M_h_c + M_cmp_c c TRUE (WBGene00022171) PW037
R_PPPItn Inorganic triphosphate transport through nuclear pore M_pppi_c <=> M_pppi_n cn TRUE PW108
R_PPS_c Pyruvate,water dikinase M_h2o_c + M_atp_c + M_pyr_c <=> M_pep_c + M_pi_c + 3.0 M_h_c + M_amp_c c FALSE (WBGene00011893) PW018 SPW004
R_PRAGS_c Phosphoribosylamine--glycine ligase M_pram_c + M_gly_c + M_atp_c <=> M_pi_c + 2.0 M_h_c + M_gar_c + M_adp_c c TRUE (WBGene00018174) PW042 "set to reversible;Removed the redundant 5-aminoimidazole ribonucleotide biosynthesis pathway" "janna; lenov"
R_PRAIS_c phosphoribosylformylglycinamidine cyclo-ligase M_fpram_c + M_atp_c <=> M_air_c + M_pi_c + 2.0 M_h_c + M_adp_c c FALSE (WBGene00018174) PW042 Removed the redundant 5-aminoimidazole ribonucleotide biosynthesis pathway lenov
R_PRASCS_c Phosphoribosylaminoimidazole-succinocarboxamide synthetase M_5aizc_c + M_asp__L_c + M_atp_c <=> M_25aics_c + M_pi_c + 2.0 M_h_c + M_adp_c c FALSE (WBGene00015116) PW042 "RHEA:22628;RHEA:10792" "[DELETION] Incorrect stoich when using model charges. Merge with R_RC04591;change M_asp__L_c into M_asp_c" "jpnh; lenov"
R_PRFGS_c phosphoribosylformylglycinamidine synthetase M_h2o_c + M_gln__L_c + M_fgam_c + M_atp_c <=> M_pi_c + 2.0 M_h_c + M_glu__L_c + M_fpram_c + M_adp_c c FALSE (WBGene00008654) PW042 Removed the redundant 5-aminoimidazole ribonucleotide biosynthesis pathway lenov
R_PPS_c Pyruvate,water dikinase M_h2o_c + M_atp_c + M_pyr_c <=> M_pep_c + M_pi_c + 2.0 M_h_c + M_amp_c c FALSE (WBGene00011893) PW018 SPW004
R_PRAGS_c Phosphoribosylamine--glycine ligase M_pram_c + M_gly_c + M_atp_c <=> M_pi_c + M_h_c + M_gar_c + M_adp_c c TRUE (WBGene00018174) PW042 "set to reversible;Removed the redundant 5-aminoimidazole ribonucleotide biosynthesis pathway" "janna; lenov"
R_PRAIS_c phosphoribosylformylglycinamidine cyclo-ligase M_fpram_c + M_atp_c <=> M_air_c + M_pi_c + M_h_c + M_adp_c c FALSE (WBGene00018174) PW042 Removed the redundant 5-aminoimidazole ribonucleotide biosynthesis pathway lenov
R_PRASCS_c Phosphoribosylaminoimidazole-succinocarboxamide synthetase M_5aizc_c + M_asp__L_c + M_atp_c <=> M_25aics_c + M_pi_c + M_h_c + M_adp_c c FALSE (WBGene00015116) PW042 "RHEA:22628;RHEA:10792" "[DELETION] Incorrect stoich when using model charges. Merge with R_RC04591;change M_asp__L_c into M_asp_c" "jpnh; lenov"
R_PRFGS_c phosphoribosylformylglycinamidine synthetase M_h2o_c + M_gln__L_c + M_fgam_c + M_atp_c <=> M_pi_c + M_h_c + M_glu__L_c + M_fpram_c + M_adp_c c FALSE (WBGene00008654) PW042 Removed the redundant 5-aminoimidazole ribonucleotide biosynthesis pathway lenov
R_PROAKGOX1_c proline,2-oxoglutarate-4-dioxygenase M_akg_c + M_pro__L_c + M_o2_c <=> M_co2_c + M_4hpro_LT_c + M_succ_c c TRUE (WBGene00003963 and WBGene00001077) or (WBGene00003963 and WBGene00004025) or WBGene00015773 or WBGene00077688 or WBGene00004026 or WBGene00012815 PW081 "RHEA:18945;RHEA:18945"
R_PROB0AT2tc R_PROB0AT2tc M_pro__L_e + M_na1_e <=> M_pro__L_c + M_na1_c ec TRUE (WBGene00015778 or WBGene00016652) PW107 "RHEA:21824;RHEA:21824"
R_PROCOLLAGEN_LYSINE_5_DIOXYGENASE_RXN_c Procollagen-lysine 5-dioxygenase M_akg_c + M_o2_c + M_pcollglys_c <=> M_co2_c + M_succ_c + M_pcollg5hlys_c c TRUE (WBGene00002497) PW089 "RHEA:16569;RHEA:12637;RHEA:12576"
Expand All @@ -2130,7 +2130,7 @@ R_PSERT_c Phosphoserine aminotransferase M_akg_c + M_pser_L_c <=> M_3php_c + M_
R_PSFLIPm phosphatidylserine flippase M_h2o_c + M_atp_c + M_1ac2acg3ps_c <=> M_pi_c + 2.0 M_h_c + M_adp_c + M_1ac2acg3ps_m c FALSE (WBGene00013034) or (ND) PW106
R_PTHPS_c 6-pyruvoyltetrahydropterin synthase M_ahdt_c <=> M_6pthp_c + M_pppi_c c FALSE (WBGene00015010) PW091 RHEA:22048
R_PTHPS_n 6-pyruvoyltetrahydropterin synthase M_ahdt_n <=> M_6pthp_n + M_pppi_n n FALSE (WBGene00015010) PW091 RHEA:22048
R_PTPAT_c Pantetheine-phosphate adenylyltransferase M_pan4p_c + M_atp_c <=> M_ppi_c + M_dpcoa_c c FALSE (WBGene00022031) PW037
R_PTPAT_c Pantetheine-phosphate adenylyltransferase M_pan4p_c + M_atp_c + M_h_c <=> M_ppi_c + M_dpcoa_c c FALSE (WBGene00022031) PW037
R_PTRCAT1_c acetyl-CoA:putrescine N-acetyltransferase M_ptrc_c + M_accoa_c <=> 2.0 M_h_c + M_aprut_c + M_coa_c c TRUE (WBGene00008408) PW081 R01154 Added rxn name from kegg jpnh
R_PUNP1_c R_PUNP1_c M_pi_c + M_adn_c <=> M_r1p_c + M_ade_c c TRUE (WBGene00019298) PW042
R_PUNP1_n R_PUNP1_n M_pi_n + M_adn_n <=> M_r1p_n + M_ade_n n TRUE (WBGene00019298) PW042
Expand Down Expand Up @@ -2962,12 +2962,12 @@ R_RXN909_184_c cerotoyl-CoA synthase M_atp_c + M_coa_c + M_fa26_0_c <=> M_ppi_
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
R_RXN909_186_c adenylate kinase M_h_c + M_dadp_c <=> M_damp_c + M_datp_c c FALSE (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_186_m adenylate kinase M_h_m + M_dadp_m <=> M_damp_m + M_datp_m m FALSE (WBGene00014058) or (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_186_n adenylate kinase M_h_n + M_dadp_n <=> M_damp_n + M_datp_n n FALSE (WBGene00002879) PW042 RHEA:12973
R_RXN909_187_c adenylate kinase M_datp_c + M_amp_c <=> M_h_c + M_dadp_c + M_adp_c c FALSE (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_187_m adenylate kinase M_datp_m + M_amp_m <=> M_h_m + M_dadp_m + M_adp_m m FALSE (WBGene00014058) or (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_187_n adenylate kinase M_datp_n + M_amp_n <=> M_h_n + M_dadp_n + M_adp_n n FALSE (WBGene00002879) PW042 RHEA:12973
R_RXN909_186_c adenylate kinase 2.0 M_dadp_c <=> M_damp_c + M_datp_c c FALSE (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_186_m adenylate kinase 2.0 M_dadp_m <=> M_damp_m + M_datp_m m FALSE (WBGene00014058) or (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_186_n adenylate kinase 2.0 M_dadp_n <=> M_damp_n + M_datp_n n FALSE (WBGene00002879) PW042 RHEA:12973
R_RXN909_187_c adenylate kinase M_datp_c + M_amp_c <=> M_dadp_c + M_adp_c c FALSE (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_187_m adenylate kinase M_datp_m + M_amp_m <=> M_dadp_m + M_adp_m m FALSE (WBGene00014058) or (WBGene00009531) or (WBGene00002879) PW042 RHEA:12973
R_RXN909_187_n adenylate kinase M_datp_n + M_amp_n <=> M_dadp_n + M_adp_n n FALSE (WBGene00002879) PW042 RHEA:12973
R_RXN909_188_c L-Proline:NADP+ 5-oxidoreductase M_pro__L_c + M_nadp_c <=> M_1pyr5c_c + 2.0 M_h_c + M_nadph_c c TRUE (WBGene00018904) or (WBGene00010924) PW081
R_RXN909_188_m L-Proline:NADP+ 5-oxidoreductase M_pro__L_m + M_nadp_m <=> M_1pyr5c_m + 2.0 M_h_m + M_nadph_m m TRUE (WBGene00018904) or (WBGene00010924) PW081
R_RXN909_189_n R_RXN909_189_n M_h2o_n + M_adpglc_n <=> M_g1p_n + 2.0 M_h_n + M_amp_n n FALSE (WBGene00003579) PW034
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