diff --git a/curation/Pathway-SBtab.tsv b/curation/Pathway-SBtab.tsv index e815f2a..ede113c 100644 --- a/curation/Pathway-SBtab.tsv +++ b/curation/Pathway-SBtab.tsv @@ -145,6 +145,8 @@ PW142 cardiolipin biosynthesis added definition for new pathways wimi PW143 biosynthesis and degradation of maradolipids added definition for new pathways wimi PW144 Biosynthesis of dafachronic acids added definition for new pathways wimi PW145 PI and PIP biosynthesis added definition for new pathways wimi +PW146 NAPE and NAE biosynthesis added definition for new pathways wimi SPW001 fatty acid metabolism added definition for super pathways wimi SPW002 ascaroside metabolism added definition for super pathways wimi SPW003 lipid metabolism added definition for super pathways wimi +SPW004 central carbon metabolism added definition for super pathways wimi diff --git a/curation/Reaction-SBtab.tsv b/curation/Reaction-SBtab.tsv index a1139f2..3820d03 100644 --- a/curation/Reaction-SBtab.tsv +++ b/curation/Reaction-SBtab.tsv @@ -53,8 +53,8 @@ R_2_7_8_15_RXN_c UDP-N-acetylglucosamine—dolichyl-phosphateN-acetylglucosa R_2_MEBUCOA_FAD_RXN_c 2-methylacyl-CoA dehydrogenase M_h_c + M_fad_c + M_2mbcoa_c <=> M_fadh2_c + M_2mb2coa_c c FALSE (WBGene00019599) or (WBGene00019406) PW083 R_2_MEBUCOA_FAD_RXN_m 2-methylacyl-CoA dehydrogenase M_h_m + M_fad_m + M_2mbcoa_m <=> M_fadh2_m + M_2mb2coa_m m FALSE (WBGene00020812) or (WBGene00020366) or (WBGene00019406) or (WBGene00019599) or (WBGene00019433) PW083 RHEA:14477 transferred ckaleta's comment to here: Irreversible version of the reaction catalyzed acdh-3 jpnh;ckaleta R_2AMADPTm L-2-aminoadipate shuttle (cytosol/mitochondria) M_akg_m + M_L2aadp_c <=> M_akg_c + M_L2aadp_m mc TRUE (WBGene00011226) PW079 -R_2OXOADOX_c R_2OXOADOX_c M_2oxoadp_c + M_coa_c + M_nad_c <=> M_co2_c + M_nadh_c + M_glutcoa_c c TRUE (WBGene00020950 and WBGene00010794 and WBGene00020679) tryptophan metabolism; lysine metabolism RHEA:15045;RHEA:12188 -R_2OXOADOX_m R_2OXOADOX_m M_2oxoadp_m + M_coa_m + M_nad_m <=> M_co2_m + M_nadh_m + M_glutcoa_m m TRUE (WBGene00020679 and WBGene00014098) and WBGene00020950 and WBGene00010794 tryptophan metabolism; lysine metabolism RHEA:15045;RHEA:12188;RHEA:12188 +R_2OXOADOX_c R_2OXOADOX_c M_2oxoadp_c + M_coa_c + M_nad_c <=> M_co2_c + M_nadh_c + M_glutcoa_c c TRUE (WBGene00020950 and WBGene00010794 and WBGene00020679) PW072;PW079 RHEA:15045;RHEA:12188 +R_2OXOADOX_m R_2OXOADOX_m M_2oxoadp_m + M_coa_m + M_nad_m <=> M_co2_m + M_nadh_m + M_glutcoa_m m TRUE (WBGene00020679 and WBGene00014098) and WBGene00020950 and WBGene00010794 PW072;PW079 RHEA:15045;RHEA:12188;RHEA:12188 R_2OXOADPTm 2-oxoadipate shuttle (cytosol/mitochondria) M_akg_m + M_2oxoadp_c <=> M_akg_c + M_2oxoadp_m mc TRUE (WBGene00011226) or (ND) PW072 R_3_1_1_47_RXN_c 2-acetyl-1-alkylglycerophosphocholine esterase M_h2o_c + M_ak2gchol_c <=> M_h_c + M_ac_c + M_1alkg3pc_c c TRUE ((WBGene00003906 or WBGene00003907) or WBGene00007756) or WBGene00003047 PW056 RHEA:17777;RHEA:17777 R_3_1_1_47_RXN_n 2-acetyl-1-alkylglycerophosphocholine esterase M_h2o_n + M_ak2gchol_n <=> M_h_n + M_ac_n + M_1alkg3pc_n n TRUE (WBGene00003907) or (WBGene00003906) PW056 RHEA:17777;RHEA:17777 @@ -109,7 +109,7 @@ R_5HTRPVESSEC 5-hydroxy-L-tryptophan secretion via secretory vesicle (ATP driven R_6_PHOSPHOFRUCTO_2_KINASE_RXN_c 6-phosphofructo-2-kinase M_f6p_c + M_atp_c <=> M_f26bp_c + M_h_c + M_adp_c c TRUE (WBGene00022456) or (WBGene00019295) PW025 RHEA:17289;RHEA:15653 R_6_PHOSPHOFRUCTO_2_KINASE_RXN_n 6-phosphofructo-2-kinase M_f6p_n + M_atp_n <=> M_f26bp_n + M_h_n + M_adp_n n TRUE (WBGene00019295) PW025 RHEA:17289;RHEA:15653 R_AABTN_c 4-acetamidobutanoate amidohydrolase M_h2o_c + M_4aabutn_c <=> M_ac_c + M_4abut_c c TRUE Unknown PW081 Added Rxn Name -R_AACOAT_c Acetoacetate--CoA ligase M_acac_c + M_atp_c + M_coa_c <=> M_ppi_c + M_amp_c + M_aacoa_c c FALSE (WBGene00006351) Acyl-CoA Synthetase (ER) SPW001 RHEA:16117 +R_AACOAT_c Acetoacetate--CoA ligase M_acac_c + M_atp_c + M_coa_c <=> M_ppi_c + M_amp_c + M_aacoa_c c FALSE (WBGene00006351) PW136 SPW001 RHEA:16117 R_AACPS9_c Octanoyl Acyl-carrier protein cleavage M_ppi_c + M_amp_c + M_acp8_0_c <=> M_atp_c + M_fa8_0_c + M_ACP_c c FALSE PW060 SPW001 Updated name jpnh R_AADSACYCL_c R_AADSACYCL_c M_h2o_c + M_thp2c_c <=> M_L2aadp6sa_c c TRUE (WBGene00000115) PW079 RHEA:16185 R_AADSACYCL_m R_AADSACYCL_m M_h2o_m + M_thp2c_m <=> M_L2aadp6sa_m m TRUE (WBGene00000115) PW079 RHEA:16185 @@ -119,11 +119,11 @@ R_ABTA_m 4-aminobutyrate aminotransferase M_akg_m + M_4abut_m <=> M_sucsal_m + R_ABUTt4_2_r 4-aminobutyrate reversible transport in via sodium symport (1:2) 2.0 M_na1_e + M_4abut_e <=> 2.0 M_na1_c + M_4abut_c ec TRUE (WBGene00004910) PW107 R_ACACCT_c acetoacetyl-CoA:acetate CoA-transferase M_acac_c + M_accoa_c <=> M_ac_c + M_aacoa_c c TRUE (WBGene00007330) PW010 R01359 added KEGG ID, changed name to KEGG one; changed pathway from acetoacetate degradation (to acetyl CoA) to propanoate metabolism lenov R_ACACCT_m acetoacetyl-CoA:acetate CoA-transferase M_acac_m + M_accoa_m <=> M_ac_m + M_aacoa_m m TRUE (WBGene00007330) PW010 R01359 added KEGG ID, changed name to KEGG one; changed pathway from acetoacetate degradation (to acetyl CoA) to propanoate metabolism lenov -R_ACACT1_c Acetyl-CoA C-acetyltransferase 2.0 M_accoa_c <=> M_coa_c + M_aacoa_c c TRUE (WBGene00002183) or (WBGene00020166) or (WBGene00020164) lysine degradation; fatty acid oxidation; valine, leucine and isoleucine degradation; propanoate metabolism; terpenoid backbone biosynthesis R00238 changed pathway from acetoacetate degradation (to acetyl CoA) to propanoate metabolism lenov -R_ACACT1_m Acetyl-CoA C-acetyltransferase 2.0 M_accoa_m <=> M_coa_m + M_aacoa_m m TRUE WBGene00020164 or WBGene00020166 or WBGene00002183 lysine degradation; fatty acid oxidation; valine, leucine and isoleucine degradation; propanoate metabolism; terpenoid backbone biosynthesis R00238 changed pathway from acetoacetate degradation (to acetyl CoA) to propanoate metabolism lenov +R_ACACT1_c Acetyl-CoA C-acetyltransferase 2.0 M_accoa_c <=> M_coa_c + M_aacoa_c c TRUE (WBGene00002183) or (WBGene00020166) or (WBGene00020164) PW080;PW062;PW083;PW010;PW001 R00238 changed pathway from acetoacetate degradation (to acetyl CoA) to PW010 lenov +R_ACACT1_m Acetyl-CoA C-acetyltransferase 2.0 M_accoa_m <=> M_coa_m + M_aacoa_m m TRUE WBGene00020164 or WBGene00020166 or WBGene00002183 PW080;PW062;PW083;PW010;PW001 R00238 changed pathway from acetoacetate degradation (to acetyl CoA) to PW010 lenov R_ACACT10_c acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase M_coa_c + M_2maacoa_c <=> M_accoa_c + M_ppcoa_c c TRUE (WBGene00009952) PW083 R_ACACT10_m acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase M_coa_m + M_2maacoa_m <=> M_accoa_m + M_ppcoa_m m TRUE (WBGene00009952) or (WBGene00015125) PW083 -R_ACALD_c Acetaldehyde dehydrogenase (acetylating) M_coa_c + M_nad_c + M_acald_c <=> M_h_c + M_nadh_c + M_accoa_c c TRUE pyrimidine metabolism; purine metabolism +R_ACALD_c Acetaldehyde dehydrogenase (acetylating) M_coa_c + M_nad_c + M_acald_c <=> M_h_c + M_nadh_c + M_accoa_c c TRUE PW043;PW042 R_ACCOAC_c Acetyl-CoA carboxylase M_hco3_c + M_atp_c + M_accoa_c <=> M_pi_c + M_h_c + M_adp_c + M_malcoa_c c TRUE WBGene00012131 or WBGene00004076 PW060 SPW001 set to reversible janna R_accoatm accoatm M_accoa_m <=> M_accoa_c mc TRUE PW111 R_ACCOAtn acetyl-CoA transport, nuclear M_accoa_c <=> M_accoa_n cn TRUE PW108 @@ -137,13 +137,13 @@ R_ACGAMPM_n Phosphoacetylglucosamine mutase M_acgam1p_n <=> M_acgam6p_n n TRUE ( R_ACHE_c Acetylcholinesterase M_ach_c + M_h2o_c <=> M_chol_c + M_h_c + M_ac_c c TRUE (WBGene00000035) or (WBGene00000037) or (WBGene00000036) or (WBGene00000038) PW056 RHEA:17561 R_ACHtn Acetylcholin transport, nuclear trhough pores M_ach_n <=> M_ach_c nc TRUE PW108 R_ACID__COA_LIGASE_GDP_FORMING_RXN_c carboxylic acid—CoA ligase (GDP-forming) M_gtp_c + M_coa_c + M_fatacid_c <=> M_pi_c + M_gdp_c + M_fataccoa_c c FALSE PW054 -R_ACITL_c ATP-citrate (pro-S-)-lyase M_cit_c + M_atp_c + M_coa_c <=> M_oaa_c + M_pi_c + M_adp_c + M_accoa_c c FALSE (WBGene00007350) or (WBGene00016995) or (WBGene00016995) or (WBGene00007150) PW023 RHEA:21160;RHEA:17661;RHEA:22120;RHEA:21160 -R_ACONITATEHYDR_RXN_c R_ACONITATEHYDR_RXN_c M_h2o_c + M_acon_C_c <=> M_icit_c c TRUE (WBGene00000041) or (WBGene00000040) tca cycle; glycine, serine and threonine metabolism; glyoxylate and dicarboxylate metabolism RHEA:10336;RHEA:10336 -R_ACONITATEHYDR_RXN_m R_ACONITATEHYDR_RXN_m M_h2o_m + M_acon_C_m <=> M_icit_m m TRUE (WBGene00000041) tca cycle; glycine, serine and threonine metabolism; glyoxylate and dicarboxylate metabolism RHEA:10336 -R_ACONT_c Aconitate hydratase M_cit_c <=> M_h2o_c + M_acon_C_c c TRUE (WBGene00000041) or (WBGene00000040) tca cycle; glycine, serine and threonine metabolism; glyoxylate and dicarboxylate metabolism RHEA:10336;RHEA:10336 -R_ACONT_m Aconitate hydratase M_cit_m <=> M_h2o_m + M_acon_C_m m TRUE (WBGene00000041) tca cycle; glycine, serine and threonine metabolism; glyoxylate and dicarboxylate metabolism RHEA:10336 +R_ACITL_c ATP-citrate (pro-S-)-lyase M_cit_c + M_atp_c + M_coa_c <=> M_oaa_c + M_pi_c + M_adp_c + M_accoa_c c FALSE (WBGene00007350) or (WBGene00016995) or (WBGene00016995) or (WBGene00007150) PW023 SPW004 RHEA:21160;RHEA:17661;RHEA:22120;RHEA:21160 +R_ACONITATEHYDR_RXN_c R_ACONITATEHYDR_RXN_c M_h2o_c + M_acon_C_c <=> M_icit_c c TRUE (WBGene00000041) or (WBGene00000040) PW023;PW074;PW030 RHEA:10336;RHEA:10336 +R_ACONITATEHYDR_RXN_m R_ACONITATEHYDR_RXN_m M_h2o_m + M_acon_C_m <=> M_icit_m m TRUE (WBGene00000041) PW023;PW074;PW030 RHEA:10336 +R_ACONT_c Aconitate hydratase M_cit_c <=> M_h2o_c + M_acon_C_c c TRUE (WBGene00000041) or (WBGene00000040) PW023;PW074;PW030 RHEA:10336;RHEA:10336 +R_ACONT_m Aconitate hydratase M_cit_m <=> M_h2o_m + M_acon_C_m m TRUE (WBGene00000041) PW023;PW074;PW030 RHEA:10336 R_ACRNtm O-acetylcarnintine transport into mitochondria via diffusion M_acrn_c <=> M_acrn_m cm FALSE (WBGene00000996 ) or (ND) PW106 -R_ACS_c acetate--CoA ligase M_atp_c + M_coa_c + M_ac_c <=> M_ppi_c + M_amp_c + M_accoa_c c FALSE (WBGene00007969) glycolysis and gluconeogenesis; pyruvate metabolism; tca cycle; glyoxylate and dicarboxylate metabolism RHEA:23176;RHEA:23176 +R_ACS_c acetate--CoA ligase M_atp_c + M_coa_c + M_ac_c <=> M_ppi_c + M_amp_c + M_accoa_c c FALSE (WBGene00007969) PW018;PW022;PW023;PW030 RHEA:23176;RHEA:23176 R_ACYLCOASYN_RXN_c 2,3,4-saturated fatty acyl-CoA synthetase M_atp_c + M_coa_c + M_fatacid_c <=> M_ppi_c + M_amp_c + M_fataccoa_c c FALSE (WBGene00009218) PW038 R_ACYLCOASYN_RXN_m 2,3,4-saturated fatty acyl-CoA synthetase M_atp_m + M_coa_m + M_fatacid_m <=> M_ppi_m + M_amp_m + M_fataccoa_m m FALSE (WBGene00009218) PW038 R_ACYLCOASYNTMITO0001 Acyl-CoA-synthethase (C4:0) M_atp_m + M_coa_m + M_but_m <=> M_ppi_m + M_amp_m + M_btcoa_m m FALSE WBGene00009221 or WBGene00019920 or WBGene00011173 or WBGene00011174 Acyl-CoA conversion (mitochondrial) SPW001 [CHECKME] Replacement for reaction R_RXN909_123_m wimi @@ -161,7 +161,7 @@ R_ADNK1_m Adenosine kinase M_atp_m + M_adn_m <=> M_h_m + M_amp_m + M_adp_m m FA R_ADNtm adenosine facilated transport in mitochondria M_adn_c <=> M_adn_m cm TRUE (WBGene00001320) or (WBGene00010701) or (ND) PW106 R_ADPSUGPPHOSPHAT_RXN_c ADP-sugar diphosphatase M_h2o_c + M_adpsug_c <=> M_amp_c + M_adaldp_c c FALSE PW034 R_ADPT_c Adenine phosphoribosyltransferase M_prpp_c + M_ade_c <=> M_ppi_c + M_amp_c c FALSE WBGene00020557 or WBGene00013690 PW042 RHEA:17973 -R_ADSK_c Adenylylsulfate kinase M_aps_c + M_atp_c <=> M_paps_c + 2.0 M_h_c + M_adp_c c TRUE (WBGene00004091) sulfur metabolism; purine metabolism set to reversible; replaced annotation sulfate activation for sulfonation with sulfur metabolism, purine metabolism janna; lenov +R_ADSK_c Adenylylsulfate kinase M_aps_c + M_atp_c <=> M_paps_c + 2.0 M_h_c + M_adp_c c TRUE (WBGene00004091) PW096;PW042 set to reversible; replaced annotation sulfate activation for sulfonation with PW096, PW042 janna; lenov R_ADSL1_c Adenylosuccinate lyase M_dcamp_c <=> M_amp_c + M_fum_c c TRUE (WBGene00011064) PW042 RHEA:16853;RHEA:23920 R_ADSL2_c Adenylosuccinate lyase M_25aics_c <=> M_aicar_c + M_fum_c c TRUE (WBGene00011064) PW042 RHEA:16853;RHEA:23920 R_ADSS_c adenylosuccinate synthetase M_asp__L_c + M_imp_c + M_gtp_c <=> M_pi_c + 2.0 M_h_c + M_dcamp_c + M_gdp_c c TRUE (WBGene00016509) or (WBGene00016509) or (WBGene00016509) PW042 20654742 RHEA:15753 added PMID and merged R_RC01135 into here; changed M_asp__L_c into M_asp_c jpnh; lenov @@ -170,14 +170,14 @@ R_AHC_c Adenosylhomocysteinase M_h2o_c + M_ahcys_c <=> M_hcys__L_c + M_adn_c c R_AHCYStn S-adenosyl-L-homocysteine nuclear transport M_ahcys_c <=> M_ahcys_n cn TRUE PW108 R_AICART_c Phosphoribosylaminoimidazolecarboxamide formyltransferase M_10fthf_c + M_aicar_c <=> M_thf_c + M_fprica_c c TRUE (WBGene00016957) PW042 R_AIRC_c Phosphoribosylaminoimidazole carboxylase M_5aizc_c + 2.0 M_h_c <=> M_air_c + M_co2_c c TRUE (WBGene00015116) PW042 RHEA:22628;RHEA:10792 -R_AKGDH_m 2-oxoglutarate dehydrogenase complex M_akg_m + M_coa_m + M_nad_m <=> M_co2_m + M_nadh_m + M_succoa_m m FALSE (WBGene00014098 and WBGene00010794 and WBGene00020950 and WBGene00020679) PW023 RHEA:15045;RHEA:12188;RHEA:12188 +R_AKGDH_m 2-oxoglutarate dehydrogenase complex M_akg_m + M_coa_m + M_nad_m <=> M_co2_m + M_nadh_m + M_succoa_m m FALSE (WBGene00014098 and WBGene00010794 and WBGene00020950 and WBGene00020679) PW023 SPW004 RHEA:15045;RHEA:12188;RHEA:12188 R_AKGMALtm alpha-ketoglutarate/malate transporter M_akg_m + M_mal__L_c <=> M_akg_c + M_mal__L_m mc TRUE WBGene00015186 or (ND) PW106 R_AKGt4_3 AKG transport via sodium symport M_akg_e + 3.0 M_na1_e <=> M_akg_c + 3.0 M_na1_c ec TRUE (WBGene00007138) PW107 R_Alanine_transport Alanine transport M_ala__L_c <=> M_ala__L_e ce TRUE PW107 replaced M_ala__L_c and M_ala__L_e with M_ala_L_c and M_ala_L_e lenov R_ALATA_L_c Alanine aminotransferase M_akg_c + M_ala__L_c <=> M_glu__L_c + M_pyr_c c TRUE (WBGene00016333) PW073 changed M_ala__L_c into M_ala_L_c lenov -R_ALCD2if_c R_ALCD2if_c M_h_c + M_nadh_c + M_acald_c <=> M_etoh_c + M_nad_c c TRUE (WBGene00010790) or (WBGene00019240) or (WBGene00021647) or (WBGene00010791) or (WBGene00017060) or (WBGene00021747) glycolysis and gluconeogenesis; pyruvate metabolism; tca cycle; glyoxylate and dicarboxylate metabolism RHEA:10736;RHEA:10740;RHEA:10736;RHEA:10740 -R_ALDD2_c R_ALDD2_c M_h2o_c + M_nad_c + M_acald_c <=> 2.0 M_h_c + M_nadh_c + M_ac_c c TRUE (WBGene00000107) or (WBGene00000108) or (WBGene00000118) or (WBGene00000110) glycolysis and gluconeogenesis; pyruvate metabolism; tca cycle; glyoxylate and dicarboxylate metabolism -R_ALDD2_m R_ALDD2_m M_h2o_m + M_nad_m + M_acald_m <=> 2.0 M_h_m + M_nadh_m + M_ac_m m TRUE (WBGene00000107 or WBGene00000108 or WBGene00000110) or WBGene00000115 glycolysis and gluconeogenesis; pyruvate metabolism; tca cycle; glyoxylate and dicarboxylate metabolism RHEA:16185 +R_ALCD2if_c R_ALCD2if_c M_h_c + M_nadh_c + M_acald_c <=> M_etoh_c + M_nad_c c TRUE (WBGene00010790) or (WBGene00019240) or (WBGene00021647) or (WBGene00010791) or (WBGene00017060) or (WBGene00021747) PW018;PW022;PW023;PW030 RHEA:10736;RHEA:10740;RHEA:10736;RHEA:10740 +R_ALDD2_c R_ALDD2_c M_h2o_c + M_nad_c + M_acald_c <=> 2.0 M_h_c + M_nadh_c + M_ac_c c TRUE (WBGene00000107) or (WBGene00000108) or (WBGene00000118) or (WBGene00000110) PW018;PW022;PW023;PW030 +R_ALDD2_m R_ALDD2_m M_h2o_m + M_nad_m + M_acald_m <=> 2.0 M_h_m + M_nadh_m + M_ac_m m TRUE (WBGene00000107 or WBGene00000108 or WBGene00000110) or WBGene00000115 PW018;PW022;PW023;PW030 RHEA:16185 R_ALDOSE_1_EPIMERASE_RXN_c Aldose 1-epimerase M_glc_aD_c <=> M_glc_bD_c c TRUE WBGene00015270 or WBGene00044734 PW020 R_AM6SAD_c Aminomuconate-semialdehyde dehydrogenase M_h2o_c + M_am6sa_c + M_nad_c <=> M_amuco_c + 2.0 M_h_c + M_nadh_c c FALSE (WBGene00000116) or (TBD) PW072 R_AMETt2m S-Adenosyl-L-methionine reversible transport, mitochondrial M_ahcys_m + M_amet_c <=> M_ahcys_c + M_amet_m mc TRUE (WBGene00008364) PW106 @@ -188,7 +188,7 @@ R_AMMONIAtm AMMONIA mitochndria transport (diffusion) M_nh3_c <=> M_nh3_m cm TRU R_AMMONIAtn AMMONIA nuclear transport (diffusion) M_nh3_c <=> M_nh3_n cn TRUE PW108 R_AMP_NUCLEOSID_RXN_c AMP nucleosidase M_h2o_c + M_amp_c <=> M_r5p_c + M_ade_c c TRUE PW042 R_AMPDA_c AMP deaminase M_h2o_c + M_amp_c <=> M_nh3_c + M_imp_c c FALSE (WBGene00016415) PW042 RHEA:14777;RHEA:14777;RHEA:14777;RHEA:14777 -R_AMPTASECG_c L-cysteinylglycine dipeptidase M_h2o_c + M_cgly_c <=> M_gly_c + M_cys__L_c c TRUE (WBGene00002249 or WBGene00002250) or WBGene00011587 gamma-glutamyl cycle; glutathione metabolism Made name more explicit lenov +R_AMPTASECG_c L-cysteinylglycine dipeptidase M_h2o_c + M_cgly_c <=> M_gly_c + M_cys__L_c c TRUE (WBGene00002249 or WBGene00002250) or WBGene00011587 gamma-glutamyl cycle;glutathione metabolism Made name more explicit lenov R_anACRNtm an O-acylcarnitine transport into mitochondria via diffusion M_acycrn_c <=> M_acycrn_m cm FALSE (WBGene00000996 ) PW106 R_APAT2_m beta-alanine:2-oxoglutarate aminotransferase M_akg_m + M_ala_B_m <=> M_msa_m + M_glu__L_m m TRUE (WBGene00001794) PW086 R00908 RHEA:23352;RHEA:13993 Added Rxn Name jpnh R_APRTO2_c N-Acetylputrescine:oxygen oxidoreductase(deaminating)(flavin-containing) M_h2o_c + M_aprut_c + M_o2_c <=> M_h2o2_c + M_nh3_c + M_n4abutn_c + M_h_c c FALSE (WBGene00017361) PW081 R04025 Added rxn name from kegg jpnh; lenov @@ -487,9 +487,9 @@ R_ASPCT_c Aspartate carbamoyltransferase M_cbp_c + M_asp__L_c <=> M_pi_c + M_h_ R_ASPDt6 D-aspartate transport via Na, H symport and K antiport M_h_e + 3.0 M_na1_e + M_asp__D_e + M_k_c <=> M_h_c + M_asp__D_c + M_k_e + 3.0 M_na1_c ec FALSE (WBGene00001620) or (WBGene00001625) PW107 replaced M_asp__D_e and M_asp__D_c with M_asp_D_e and M_asp_D_c lenov R_ASPGLUm aspartate-glutamate mitochondrial shuttle M_h_c + M_glu__L_c + M_asp__L_m <=> M_h_m + M_glu__L_m + M_asp__L_c cm TRUE WBGene00019326 PW106 Changed M_asp__L_c and M_asp__L_m into M_asp_L_c and M_asp_L_m lenov R_ASPt6 L-aspartate transport via Na, H symport and K antiport M_h_e + M_asp__L_e + 3.0 M_na1_e + M_k_c <=> M_h_c + M_asp__L_c + M_k_e + 3.0 M_na1_c ec FALSE (WBGene00001620) or (WBGene00001625) PW107 changed M_asp__L_e and M_asp__L_c into M_asp_L_e and M_asp_L_e lenov -R_ASPTA_c Aspartate aminotransferase M_oaa_c + M_glu__L_c <=> M_akg_c + M_asp__L_c c FALSE (WBGene00020146) or (WBGene00020145) or (WBGene00015771) or (WBGene00015778) alanine, aspartate and glutamate metabolism; glycine, serine and threonine metabolism RHEA:21824;RHEA:21824 [DELETION] merged into R_RC00355; changed M_asp__L_c into M_asp_c jpnh;lenov -R_ASPTA_m Aspartate aminotransferase M_oaa_m + M_glu__L_m <=> M_akg_m + M_asp__L_m m FALSE (WBGene00016652) or (WBGene00015778) alanine, aspartate and glutamate metabolism; glycine, serine and threonine metabolism RHEA:21824;RHEA:21824 changed M_asp__L_m into M_asp_L_m lenov -R_ATPH1_c Apyrase 2.0 M_h2o_c + M_atp_c <=> 2.0 M_pi_c + 3.0 M_h_c + M_amp_c c FALSE (WBGene00003254) purine metabolism; pyrimidine metabolism RHEA:36799 +R_ASPTA_c Aspartate aminotransferase M_oaa_c + M_glu__L_c <=> M_akg_c + M_asp__L_c c FALSE (WBGene00020146) or (WBGene00020145) or (WBGene00015771) or (WBGene00015778) alanine, aspartate and glutamate metabolism;PW074 RHEA:21824;RHEA:21824 [DELETION] merged into R_RC00355; changed M_asp__L_c into M_asp_c jpnh;lenov +R_ASPTA_m Aspartate aminotransferase M_oaa_m + M_glu__L_m <=> M_akg_m + M_asp__L_m m FALSE (WBGene00016652) or (WBGene00015778) alanine, aspartate and glutamate metabolism;PW074 RHEA:21824;RHEA:21824 changed M_asp__L_m into M_asp_L_m lenov +R_ATPH1_c Apyrase 2.0 M_h2o_c + M_atp_c <=> 2.0 M_pi_c + 3.0 M_h_c + M_amp_c c FALSE (WBGene00003254) PW042;PW043 RHEA:36799 R_ATPtm ADP/ATP transporter, mitochondrial M_atp_m + M_adp_c <=> M_atp_c + M_adp_m mc FALSE (WBGene00010485) or (WBGene00020140) or (WBGene00007057) or (WBGene00006439) or (ND) PW106 R_ATPtn ATP diffusion in nucleus M_atp_c <=> M_atp_n cn TRUE PW108 R_BBHOX_c γ-butyrobetaine dioxygenase M_akg_c + M_4tmeabutn_c + M_o2_c <=> M_co2_c + M_crn_c + M_succ_c c FALSE (WBGene00001522) or (WBGene00001523) PW080 RHEA:24028 @@ -644,8 +644,8 @@ R_Biomass2 Biomass2 10.0 M_h2o_c + 4.0 M_h_c + 2.0 M_nadh_c + M_outerlps_BAC_c R_biotin_Exchange_reactions_e biotin transport M_btn_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_biotin_transport biotin transport M_btn_c <=> M_btn_e ce TRUE PW107 R_BPNT_c 3′(2′),5′-bisphosphate nucleotidase M_pap_c + M_h2o_c <=> M_pi_c + M_amp_c c FALSE WBGene00044063 or WBGene00012390 PW042 -R_BPNT2_c R_BPNT2_c M_h2o_c + M_paps_c <=> M_aps_c + M_pi_c c FALSE WBGene00044063 or WBGene00012390 sulfur metabolism; purine metabolism replaced annotation sulfate activation for sulfonation with sulfur metabolism, purine metabolism lenov -R_BPNT2_m R_BPNT2_m M_h2o_m + M_paps_m <=> M_aps_m + M_pi_m m FALSE (WBGene00044063) or (WBGene00012390) sulfur metabolism; purine metabolism replaced annotation sulfate activation for sulfonation with sulfur metabolism, purine metabolism +R_BPNT2_c R_BPNT2_c M_h2o_c + M_paps_c <=> M_aps_c + M_pi_c c FALSE WBGene00044063 or WBGene00012390 PW096;PW042 replaced annotation sulfate activation for sulfonation with PW096, PW042 lenov +R_BPNT2_m R_BPNT2_m M_h2o_m + M_paps_m <=> M_aps_m + M_pi_m m FALSE (WBGene00044063) or (WBGene00012390) PW096;PW042 replaced annotation sulfate activation for sulfonation with PW096, PW042 R_BUP2_c R_BUP2_c M_h2o_c + M_3uib_c + M_h_c <=> M_co2_c + M_nh3_c + M_3aib__D_c c TRUE (WBGene00017440) PW043 Replaced M_3aib__D_c with M_3aib_D_c lenov R_BUTYRATE__COA_LIGASE_RXN_c butyrate—CoA ligase M_atp_c + M_coa_c + M_fatacid_c <=> M_ppi_c + M_amp_c + M_fataccoa_c c FALSE WBGene00011174 or WBGene00009221 or WBGene00020343 or WBGene00018152 or WBGene00013575 or WBGene00022037 or WBGene00019920 or WBGene00016716 or WBGene00011173 PW054 [DELETION] Duplicate reaction of R_ACYLCOASYN_RXN_c and general reaction of the proper cytosolic BTCoA ligase reaction R_RXN909_123_c jpnh R_C_AMCOXO_c 2-aminomuconate reductase M_h2o_c + M_amuco_c + M_h_c + M_nadh_c <=> M_nh3_c + M_2oxoadp_c + M_nad_c c FALSE PW072 @@ -729,9 +729,9 @@ R_CLBIOSYNTH0004 Phosphatidylglycerophosphatase M_h2o_m + M_1ac2acg3pg3p_m <=> M R_CLBIOSYNTH0005 CDP-diacylglycerol:phosphatidylglycerol 3-phosphatidyltransferase (mitochondrial) M_cdpdag_m + M_1ac2acg3pg_m <=> M_h_c + M_cmp_m + M_clpn_m m FALSE WBGene00017763 PW142 SPW003 [CHECKME] replaces R_RXN_8141_m wimi R_CLBIOSYNTH0006 Phospholipase A2 (CL) M_h2o_m + M_clpn_m <=> M_h_c + M_fatacid_m + M_mlclpn_m m FALSE PW142 SPW003 [CHECKME] added for cardiolipin remodeling wimi R_CLBIOSYNTH0007 monolysocardiolipin acyltransferase M_mlclpn_m + M_fataccoa_m <=> M_coa_m + M_clpn_m m FALSE WBGene00006491 PW142 SPW003 [CHECKME] added for cardiolipin remodeling wimi -R_CMPKI_RXN_c Cytidylate kinase M_atp_c + M_cmp_c <=> M_adp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) pyrimidine metabolism; purine metabolism set to reversible janna -R_CMPKI_RXN_m Cytidylate kinase M_atp_m + M_cmp_m <=> M_adp_m + M_cdp_m m TRUE (WBGene00007812) or (WBGene00009575) pyrimidine metabolism; purine metabolism set to reversible janna -R_CMPKI_RXN_n Cytidylate kinase M_atp_n + M_cmp_n <=> M_h_n + M_adp_n + M_cdp_n n TRUE (WBGene00007812) pyrimidine metabolism; purine metabolism set to reversible janna +R_CMPKI_RXN_c Cytidylate kinase M_atp_c + M_cmp_c <=> M_adp_c + M_cdp_c c TRUE (WBGene00007812) or (WBGene00009575) PW043;PW042 set to reversible janna +R_CMPKI_RXN_m Cytidylate kinase M_atp_m + M_cmp_m <=> M_adp_m + M_cdp_m m TRUE (WBGene00007812) or (WBGene00009575) PW043;PW042 set to reversible janna +R_CMPKI_RXN_n Cytidylate kinase M_atp_n + M_cmp_n <=> M_h_n + M_adp_n + M_cdp_n n TRUE (WBGene00007812) PW043;PW042 set to reversible janna R_CMPtm cmp transport to mitochndria M_cmp_c <=> M_cmp_m cm TRUE ND PW106 set to reversible janna R_CO2_Exchange_reactions_e CO2 transport M_co2_e <=> e FALSE PW111 Set directionality to FALSE` jpnh R_CO2_transport CO2 transport M_co2_c <=> M_co2_e ce TRUE ND PW107 @@ -742,8 +742,8 @@ R_COAtn coenzyme A transport, nuclear M_coa_c <=> M_coa_n cn TRUE PW108 R_CRMT_n nuclear cytidine residue C5 methylation M_cytr_n + M_amet_n <=> M_m5cytr_n + M_ahcys_n n FALSE (WBGene00013151) 25635753 There is no associated demethylation. The RNA is degraded with the methylation? lenov R_CRNATBtc Sodium-Carnitine-Chloride symporter 2.0 M_na1_e + M_cl_e + M_crn_e <=> M_cl_c + M_crn_c + 2.0 M_na1_c ec FALSE WBGene00004910 PW111 Added rxn name jpnh R_CRNtim L-carnitine transport out of mitochondria via diffusion M_crn_c <=> M_crn_m cm TRUE (WBGene00000996 ) or (ND) PW106 set to reversible -R_CS_c Citrate (si)-synthase M_oaa_c + M_h2o_c + M_accoa_c <=> M_cit_c + M_h_c + M_coa_c c FALSE (WBGene00000833) tca cycle; glyoxylate and dicarboxylate metabolism RHEA:16845 -R_CS_m Citrate (si)-synthase M_oaa_m + M_h2o_m + M_accoa_m <=> M_cit_m + M_h_m + M_coa_m m FALSE (WBGene00000833) tca cycle; glyoxylate and dicarboxylate metabolism RHEA:16845 +R_CS_c Citrate (si)-synthase M_oaa_c + M_h2o_c + M_accoa_c <=> M_cit_c + M_h_c + M_coa_c c FALSE (WBGene00000833) PW023;PW030 RHEA:16845 +R_CS_m Citrate (si)-synthase M_oaa_m + M_h2o_m + M_accoa_m <=> M_cit_m + M_h_m + M_coa_m m FALSE (WBGene00000833) PW023;PW030 RHEA:16845 R_CSND_c Cytosine deaminase M_h2o_c + M_csn_c <=> M_nh3_c + M_ura_c c TRUE PW043 R_CTPS2_c CTP synthetase M_h2o_c + M_gln__L_c + M_atp_c + M_utp_c <=> M_pi_c + 3.0 M_h_c + M_glu__L_c + M_adp_c + M_ctp_c c FALSE (WBGene00012316) PW043 RHEA:26426 R_CTPtn CTP diffusion in nucleus M_ctp_c <=> M_ctp_n cn TRUE PW108 @@ -762,7 +762,7 @@ R_Cystm Cystein reversible mitochondrial transport M_cys__L_c <=> M_cys__L_m cm R_CYSTS_c Cystathionine β-synthase M_hcys__L_c + M_ser__L_c <=> M_cyst__L_c + M_h2o_c c TRUE (WBGene00013866) or (WBGene00018783) PW082 R_CYTD_c Cytidine deaminase M_h2o_c + M_cytd_c <=> M_nh3_c + M_uri_c c TRUE (WBGene00000391) or (WBGene00000392) PW043 RHEA:13433;RHEA:16069;RHEA:13433;RHEA:16069 R_CYTD_n Cytidine deaminase M_h2o_n + M_cytd_n <=> M_nh3_n + M_uri_n n TRUE (WBGene00000391) or (WBGene00000392) PW043 RHEA:13433;RHEA:16069;RHEA:13433;RHEA:16069 -R_CYTDK1_c R_CYTDK1_c M_atp_c + M_cytd_c <=> 2.0 M_h_c + M_adp_c + M_cmp_c c FALSE WBGene00007089 or WBGene00008948 purine metabolism; pyrimidine metabolism +R_CYTDK1_c R_CYTDK1_c M_atp_c + M_cytd_c <=> 2.0 M_h_c + M_adp_c + M_cmp_c c FALSE WBGene00007089 or WBGene00008948 PW042;PW043 R_CYTDK2_c cytidine kinase M_gtp_c + M_cytd_c <=> M_h_c + M_gdp_c + M_cmp_c c TRUE PW043 Added reaction name jpnh R_CYTDt2r Cytidine transport M_h_e + M_cytd_e <=> M_h_c + M_cytd_c ec TRUE (WBGene00018716 or WBGene00014092) or (ND) PW111 Added rxn name jpnh R_CYTDtm cytidine facilated transport in mitochondria M_cytd_c <=> M_cytd_m cm TRUE (WBGene00001320) or (WBGene00010701) or (ND) PW106 @@ -770,13 +770,13 @@ R_CYTDtn cytidine transport in nucleus M_cytd_c <=> M_cytd_n cn TRUE PW108 R_cytidine_Exchange_reactions_e cytidine transport M_cytd_e <=> e TRUE PW111 [CHECK ME] compare to above reaction; Removed space from reaction ID jpnh R_cytidine_transport cytidine transport M_cytd_c <=> M_cytd_e ce TRUE ND PW107 R_CYTOCHROME_B5_REDUCTASE_RXN_c Cytochrome-b5 reductase M_nadh_c + 2.0 M_ficytb5_c <=> M_nad_c + 2.0 M_focytb5_c c FALSE PW031 [DELETION] Merged into RC00100 jpnh -R_D_PPENTOMUT_RXN_c D-deoxyribose 1,5-phosphomutase M_2dr1p_c <=> M_2dr5p_c c TRUE (WBGene00012803) pyrimidine metabolism; purine metabolism -R_DABIOSYNTH0001 DAF-36 rieske monooxygenase M_chsterol_c + M_h_c + M_nadph_c + M_o2_c <=> M_7dhchsterol_c + 2 M_h2o_c + M_nadp_c c FALSE WBGene00007536 Biosnythesis of delta7-DA PW144 -R_DABIOSYNTH0002 7-dehydrocholesterol lathosterole conversion M_7dhchsterol_c + M_h_c + M_nadph_c + M_o2_c <=> M_lthstrl_c + 2 M_h2o_c + M_nadp_c c FALSE Biosnythesis of delta7-DA PW144 -R_DABIOSYNTH0003 lathosterole reduction M_lthstrl_c + M_nad_c <=> M_lthstrone_c + M_h_c + M_nadh_c c FALSE WBGene00000979 Biosnythesis of delta7-DA PW144 [CHECKME] replaces R_dafaRXN01 wimi -R_DABIOSYNTH0004 Cytochrome P450 daf-9 producing delta7-DA M_lthstrone_c + 2 M_h_c + 3 M_nadph_c + 3 M_o2_c <=> M_d7da_c + 4 M_h2o_c + 3 M_nadp_c c FALSE WBGene00000905 Biosnythesis of delta7-DA PW144 [CHECKME] replaces R_dafaRXN02 wimi -R_DABIOSYNTH0005 HSD-1 M_chsterol_c + M_nad_c <=> M_chstenone_c + M_h_c + M_nadh_c c FALSE WBGene00012394 Biosnythesis of delta4-DA PW144 [CHECKME] replaces R_dafaRXN04 wimi -R_DABIOSYNTH0006 Cytochrome P450 daf-9 producing delta4-DA M_chstenone_c + 5 M_h_c + 3 M_o2_c + 6 M_fdxrd_c <=> M_d4da_c + 4 M_h2o_c + 6 M_fdxox_c c FALSE WBGene00000905 Biosnythesis of delta4-DA PW144 [CHECKME] replaces R_dafaRXN06 wimi +R_D_PPENTOMUT_RXN_c D-deoxyribose 1,5-phosphomutase M_2dr1p_c <=> M_2dr5p_c c TRUE (WBGene00012803) PW043;PW042 +R_DABIOSYNTH0001 DAF-36 rieske monooxygenase M_chsterol_c + M_h_c + M_nadph_c + M_o2_c <=> M_7dhchsterol_c + 2 M_h2o_c + M_nadp_c c FALSE WBGene00007536 PW144 SPW003 +R_DABIOSYNTH0002 7-dehydrocholesterol lathosterole conversion M_7dhchsterol_c + M_h_c + M_nadph_c + M_o2_c <=> M_lthstrl_c + 2 M_h2o_c + M_nadp_c c FALSE PW144 SPW003 +R_DABIOSYNTH0003 lathosterole reduction M_lthstrl_c + M_nad_c <=> M_lthstrone_c + M_h_c + M_nadh_c c FALSE WBGene00000979 PW144 SPW003 [CHECKME] replaces R_dafaRXN01 wimi +R_DABIOSYNTH0004 Cytochrome P450 daf-9 producing delta7-DA M_lthstrone_c + 2 M_h_c + 3 M_nadph_c + 3 M_o2_c <=> M_d7da_c + 4 M_h2o_c + 3 M_nadp_c c FALSE WBGene00000905 PW144 SPW003 [CHECKME] replaces R_dafaRXN02 wimi +R_DABIOSYNTH0005 HSD-1 M_chsterol_c + M_nad_c <=> M_chstenone_c + M_h_c + M_nadh_c c FALSE WBGene00012394 PW144 SPW003 [CHECKME] replaces R_dafaRXN04 wimi +R_DABIOSYNTH0006 Cytochrome P450 daf-9 producing delta4-DA M_chstenone_c + 5 M_h_c + 3 M_o2_c + 6 M_fdxrd_c <=> M_d4da_c + 4 M_h2o_c + 6 M_fdxox_c c FALSE WBGene00000905 PW144 SPW003 [CHECKME] replaces R_dafaRXN06 wimi R_DADA_c R_DADA_c M_h2o_c + M_dad_2_c <=> M_nh3_c + M_din_c c TRUE (WBGene00015551) or (WBGene00000080) or (WBGene00000079) or (WBGene00008397) or (WBGene00044764) PW042 RHEA:10120 R_DADA_n R_DADA_n M_h2o_n + M_dad_2_n <=> M_nh3_n + M_din_n n TRUE (WBGene00015551) or (WBGene00000080) or (WBGene00000079) PW042 RHEA:10120 R_DARDMT_n nuclear desoxyadenosine residue N6 demethylation M_mdadnr_n + M_akg_n + M_o2_n <=> M_dadnr_n + M_co2_n + M_succ_n n FALSE (WBGene00017304) RHEA:49524 25936839 The field is very skeptical lenov @@ -797,7 +797,7 @@ R_DEOXYINOPHOSPHOR_RXN_c R_DEOXYINOPHOSPHOR_RXN_c M_pi_c + M_din_c <=> M_hxan_c R_DEOXYINOPHOSPHOR_RXN_n R_DEOXYINOPHOSPHOR_RXN_n M_pi_n + M_din_n <=> M_hxan_n + M_2dr1p_n n TRUE (WBGene00019298) PW042 R_deoxynucbiomass_m biomass production from mitochondrial DNA 0.381 M_dadnr_m + 0.119 M_dguar_m + 0.381 M_dthyr_m + 0.119 M_dcytr_m <=> M_DNA_m m FALSE PW109 replace production of biomass from deoxynucleotides by deoxynucleotide residues lenov R_deoxynucbiomass_n biomass production from nuclear DNA 0.325 M_dadnr_n + 0.175 M_dguar_n + 0.325 M_dthyr_n + 0.175 M_dcytr_n <=> M_DNA_n n FALSE PW109 replace production of biomass from deoxynucleotides by deoxynucleotide residues lenov -R_DEOXYRIBOSE_P_ALD_RXN_c Deoxyribose-phosphate aldolase M_2dr5p_c <=> M_g3p_c + M_acald_c c TRUE (WBGene00017283) pyrimidine metabolism; purine metabolism +R_DEOXYRIBOSE_P_ALD_RXN_c Deoxyribose-phosphate aldolase M_2dr5p_c <=> M_g3p_c + M_acald_c c TRUE (WBGene00017283) PW043;PW042 R_DGR0001 Bacterial peptide degradation M_protein_BAC_c <=> 0.064161 M_lys__L_c + 0.079118 M_val__L_c + 0.05432 M_ile__L_c + 0.084235 M_leu__L_c + 0.034639 M_phe__L_c + 0.11454 M_gly_c + 0.047432 M_thr__L_c + 0.017123 M_cys__L_c + 0.049203 M_gln__L_c + 0.049203 M_glu__L_c + 0.040346 M_ser__L_c + 0.028735 M_met__L_c + 0.017713 M_his__L_c + 0.010628 M_trp__L_c + 0.04133 M_pro__L_c + 0.025782 M_tyr__L_c + 0.096044 M_ala__L_c + 0.055304 M_arg__L_c + 0.04507 M_asn__L_c + 0.04507 M_asp__L_c c FALSE ND PW110 R_DGR0002 Bacterial RNA degradation M_rna_BAC_c <=> 0.31768 M_gmp_c + 0.26761 M_amp_c + 0.21753 M_ump_c + 0.19718 M_cmp_c c FALSE ND PW110 R_DGR0003 Bacterial DNA degradation M_dna_BAC_c <=> 0.24651 M_damp_c + 0.25349 M_dgmp_c + 0.25349 M_dcmp_c + 0.24651 M_dtmp_c c FALSE ND PW110 @@ -825,7 +825,7 @@ R_DGR0024 Bacterial phosphatidate degradation 3.0 M_h2o_c + M_1ac2acglyc3p_BAC_ R_DGR0025 Bacterial phosphatidylserine uptake M_1ac2acg3ps_BAC_e <=> M_1ac2acg3ps_BAC_c ec FALSE PW110 R_DGR0026 Bacterial phosphatidylserine degradation 3.0 M_h2o_c + M_1ac2acg3ps_BAC_c <=> M_glyc_c + 3.0 M_h_c + 2.0 M_Rtotal_BAC_c + M_pser_L_c c FALSE WBGene00007419 or WBGene00044468 PW110 R_DGR0027 glycogen assimilation M_glycogen_BAC_e <=> M_glycogen_BAC_c ec FALSE PW110 -R_DGR0028 bacterial glycogen degradation 100 M_pi_c + M_glycogen_BAC_c <=> 100 M_g1p_c + 100 M_ldex_c c FALSE WBGene00020696 bacterial digestion; glycogen metabolism Replaced M_dxtrn1_c by M_ldex_c on the right. Should we keep this reaction though? Janna adds: This reaction is providing all the glucose and dextrin to the model. Have updated the stoichiometry as 0.5 units of glucose per unit of glycogen is ridiculous. Plus ldex was limiting for our worm biomass construction. lenov; janna +R_DGR0028 bacterial glycogen degradation 100 M_pi_c + M_glycogen_BAC_c <=> 100 M_g1p_c + 100 M_ldex_c c FALSE WBGene00020696 bacterial digestion;glycogen metabolism Replaced M_dxtrn1_c by M_ldex_c on the right. Should we keep this reaction though? Janna adds: This reaction is providing all the glucose and dextrin to the model. Have updated the stoichiometry as 0.5 units of glucose per unit of glycogen is ridiculous. Plus ldex was limiting for our worm biomass construction. lenov; janna R_DGR0029 dephosphorylation of thiamine pyrophosphate 2.0 M_h2o_e + M_thmpp_e <=> 2.0 M_pi_e + M_h_e + M_thm_e e FALSE PW110 R_DGTPtn dGTP diffusion in nucleus M_dgtp_c <=> M_dgtp_n cn TRUE PW108 R_DGULND_c dehydro-L-gulonate decarboxylase M_3dhguln_c + M_h_c <=> M_co2_c + M_xylu_L_c c FALSE Unknown PW033 @@ -841,7 +841,7 @@ R_DIACYLGLYKIN_RXN_c Diacylglycerol kinase M_atp_c + M_1ac2acglyc_c <=> M_adp_c R_DIACYLGLYKIN_RXN_n Diacylglycerol kinase M_atp_n + M_1ac2acglyc_n <=> M_adp_n + M_1ac2acglyc3p_n n TRUE (WBGene00000958) or (WBGene00000960) or (WBGene00019428) PW056 RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272;RHEA:10272 R_DIDPtn dIDP nuclear transport M_didp_c <=> M_didp_n cn TRUE PW108 R_DITPtn dITP nuclear transport M_ditp_c <=> M_ditp_n cn TRUE PW108 -R_DMATT_c Dimethylallyltransferase M_ipdp_c + M_dmpp_c <=> M_grdp_c + M_ppi_c c TRUE (WBGene00011058) terpenoid backbone biosynthesis; ubiquinol-9 biosynthesis +R_DMATT_c Dimethylallyltransferase M_ipdp_c + M_dmpp_c <=> M_grdp_c + M_ppi_c c TRUE (WBGene00011058) PW001;ubiquinol-9 biosynthesis R_DMHISTDMT protein-N6,N6-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase M_akg_n + M_Ndmelys_n + M_o2_n <=> M_co2_n + M_Nmelys_n + M_fald_n + M_succ_n n FALSE WBGene00020821 PW101 RHEA:42032 Histone demethylation takes place in the nucleus lenov R_DMN0001 pyridoxal phosphate demand M_pydx5p_c <=> c FALSE PW039 R_DMN0002 vitamin B12 demand (adocbl form) M_adocbl_m <=> m FALSE PW006 @@ -971,8 +971,8 @@ R_DOPAVESSEC Dopamine secretion via secretory vesicle (ATP driven) M_h2o_c + M_ 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_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) purine metabolism; pyrimidine metabolism RHEA:13517 set to reversible janna -R_DTMPK_n Thymidylate kinase M_atp_n + M_dtmp_n <=> M_adp_n + M_dtdp_n n TRUE (WBGene00011272) purine metabolism; pyrimidine metabolism RHEA:13517 set to reversible janna +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 +R_DTMPK_n Thymidylate kinase M_atp_n + M_dtmp_n <=> M_adp_n + M_dtdp_n n TRUE (WBGene00011272) PW042;PW043 RHEA:13517 set to reversible janna R_DTTPtn dTTP diffusion in nucleus M_dttp_c <=> M_dttp_n cn TRUE PW108 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 @@ -987,8 +987,8 @@ R_ECOAH8_c 3-hydroxystearoyl-dehydratase <=> M_h2o_c + M_coa18_1_2e_c c FALSE P R_ECOAH8_new_c 3-hydroxyoctadecanoyl-dehydratase M_coa18_0_3oh__S_c <=> M_h2o_c + M_coa18_1_2e_c c FALSE PW060 SPW001 R07760 [CHECK ME] Renamed reaction to better reflect the chemical name of the enzyme. Added the reactant to the reaction. This reaction should replace R_ECOAH8_c - please remove the new from !Reaction post merge jpnh 4.2.1.134 R_ECOAH9i_c Tiglyl-CoA hydratase M_h2o_c + M_2mb2coa_c <=> M_3hmbcoa_c c TRUE (WBGene00020347) or (WBGene00001156) or (WBGene00001155) or (WBGene00001154) or (WBGene00001152) or (WBGene00001150) PW083 RHEA:16105;RHEA:20724 set to reversible janna R_ECOAH9i_m Tiglyl-CoA hydratase M_h2o_m + M_2mb2coa_m <=> M_3hmbcoa_m m TRUE (WBGene00001156) or (WBGene00001155) or (WBGene00001154) or (WBGene00001152) or (WBGene00001150) or (WBGene00020347) PW083 RHEA:16105;RHEA:20724 set to reversible janna -R_ENO_c Phosphopyruvate hydratase M_2pg_c <=> M_h2o_c + M_pep_c c TRUE (WBGene00011884) or (WBGene00011884) PW018 RHEA:10164 -R_ENO_m Phosphopyruvate hydratase M_2pg_m <=> M_h2o_m + M_pep_m m TRUE (WBGene00011884) PW018 RHEA:10164 +R_ENO_c Phosphopyruvate hydratase M_2pg_c <=> M_h2o_c + M_pep_c c TRUE (WBGene00011884) or (WBGene00011884) PW018 SPW004 RHEA:10164 +R_ENO_m Phosphopyruvate hydratase M_2pg_m <=> M_h2o_m + M_pep_m m TRUE (WBGene00011884) PW018 SPW004 RHEA:10164 R_ETFCLOS_RXN_c R_ETFCLOS_RXN_c M_nadh_c + M_etfox_c <=> M_nad_c + M_etfrd_c c FALSE (WBGene00017734 and WBGene00009187) PW098 R_ETHAK_c ethanolamine kinase M_etha_c + M_atp_c <=> M_ethamp_c + M_h_c + M_adp_c c FALSE WBGene00000515 or (WBGene00000509 or WBGene00000510 or WBGene00000511 or WBGene00000512 or WBGene00000513) PW056 RHEA:12837;RHEA:12837;RHEA:12837;RHEA:12837;RHEA:13069 R_ETHERLIPIDBIOSYNTH0001 Fatty acyl-CoA reductase M_fataccoa_c + 2 M_nadph_c + 2 M_h_c <=> M_alkylR1oh_c + 2 M_nadp_c + M_coa_c c FALSE WBGene00022200 PW141 SPW003 [CHECKME] replaces nonsense reaction R_RC01998 wimi @@ -1203,7 +1203,7 @@ R_EXC0135 Vaccenic acid Exchange reactions M_vacc_e <=> e FALSE PW111 R_EXC0141 3-mercaptolactate-cysteine disulfide Exchange reactions M_mercplaccys_e <=> e FALSE PW111 R_EXC0142 phospholipid component of E. coli diet Exchange reactions M_phospholipid_BAC_e <=> e FALSE PW111 R_EXC0152 Random peptide (special aminoacid carrier) Exchange reactions M_pepX_e <=> e FALSE PW111 -R_F16BDEPHOS_RXN_c Fructose-bisphosphatase M_h2o_c + M_fdp_c <=> M_f6p_c + M_pi_c c FALSE (WBGene00001404) PW018 +R_F16BDEPHOS_RXN_c Fructose-bisphosphatase M_h2o_c + M_fdp_c <=> M_f6p_c + M_pi_c c FALSE (WBGene00001404) PW018 SPW004 R_F1PGT_c fucose-1-phosphate guanylyltransferase M_fuc1p_L_c + M_h_c + M_gtp_c <=> M_gdpfuc_c + M_ppi_c c TRUE (WBGene00044903) PW025 Changed M_fuc1p__L_c into M_fuc1p_L_c lenov R_F1PGT_n fucose-1-phosphate guanylyltransferase M_fuc1p_L_n + M_h_n + M_gtp_n <=> M_gdpfuc_n + M_ppi_n n TRUE (WBGene00044903) PW025 Changed M_fuc1p__L_c into M_fuc1p_L_c lenov R_FABIOSYNTHBRANCHEDCYTO0001 Isovaleryl-CoA ACP transacylase M_ivcoa_c + M_ACP_c <=> M_ivACP_c + M_coa_c c FALSE WBGene00009342 PW122 SPW001 [CHECKME] Reactions for biosynthesis of branched chain fatty acids wimi @@ -1438,8 +1438,8 @@ R_FAELONGSTRAIGHT0064 Acyl-CoA-thioesterase (C24:0) M_coa24_0_c + M_h2o_c <=> M_ R_FAELONGSTRAIGHT0065 Acyl-CoA-thioesterase (C26:0) M_coa26_0_c + M_h2o_c <=> M_fa26_0_c + M_coa_c + M_h_c c FALSE PW129 SPW001 [CHECKME] Reactions for fatty acid elongation of straight fatty acids wimi R_FAELONGSTRAIGHT0066 Acyl-CoA-thioesterase (C28:0) M_coa28_0_c + M_h2o_c <=> M_fa28_0_c + M_coa_c + M_h_c c FALSE PW129 SPW001 [CHECKME] Reactions for fatty acid elongation of straight fatty acids wimi R_FAELONGSTRAIGHT0067 Acyl-CoA-thioesterase (C30:0) M_coa30_0_c + M_h2o_c <=> M_fa30_0_c + M_coa_c + M_h_c c FALSE PW129 SPW001 [CHECKME] Reactions for fatty acid elongation of straight fatty acids wimi -R_FBA_c Fructose-bisphosphate aldolase M_fdp_c <=> M_dhap_c + M_g3p_c c TRUE (WBGene00017166) or (WBGene00011474) PW018 RHEA:14729;RHEA:14729;RHEA:14729 -R_FBA_n Fructose-bisphosphate aldolase M_fdp_n <=> M_dhap_n + M_g3p_n n TRUE (WBGene00011474) PW018 RHEA:14729 +R_FBA_c Fructose-bisphosphate aldolase M_fdp_c <=> M_dhap_c + M_g3p_c c TRUE (WBGene00017166) or (WBGene00011474) PW018 SPW004 RHEA:14729;RHEA:14729;RHEA:14729 +R_FBA_n Fructose-bisphosphate aldolase M_fdp_n <=> M_dhap_n + M_g3p_n n TRUE (WBGene00011474) PW018 SPW004 RHEA:14729 R_FBA2_c R_FBA2_c M_f1p_c <=> M_dhap_c + M_glyald_c c TRUE (WBGene00011474) PW020 RHEA:14729 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 @@ -1456,26 +1456,26 @@ R_FRTT_c geranylgeranyl-diphosphate synthase M_ipdp_c + M_frdp_c <=> M_ppi_c + R_FTHFCL_c 5-formyltetrahydrofolate cyclo-ligase M_h_c + M_atp_c + M_5fthf_c <=> M_pi_c + M_adp_c + M_methf_c c FALSE (WBGene00013708) PW091 R_FTHFL_c Formate--tetrahydrofolate ligase M_for_c + M_atp_c + M_thf_c <=> M_pi_c + M_adp_c + M_10fthf_c c TRUE (WBGene00019492) PW091 R_FTHFL_m Formate--tetrahydrofolate ligase M_for_m + M_atp_m + M_thf_m <=> M_pi_m + M_adp_m + M_10fthf_m m TRUE (WBGene00019492) PW091 -R_FUM_c Fumarate hydratase M_mal__L_c <=> M_h2o_c + M_fum_c c TRUE (WBGene00001503) PW023 RHEA:12460 -R_FUM_m Fumarate hydratase M_mal__L_m <=> M_h2o_m + M_fum_m m TRUE (WBGene00001503) PW023 RHEA:12460 -R_FUMAC_c Fumarylacetoacetase M_4fumacac_c + M_h2o_c <=> M_acac_c + M_h_c + M_fum_c c TRUE (WBGene00019620) phenylalanine degradation; tyrosine metabolism RHEA:10244 +R_FUM_c Fumarate hydratase M_mal__L_c <=> M_h2o_c + M_fum_c c TRUE (WBGene00001503) PW023 SPW004 RHEA:12460 +R_FUM_m Fumarate hydratase M_mal__L_m <=> M_h2o_m + M_fum_m m TRUE (WBGene00001503) PW023 SPW004 RHEA:12460 +R_FUMAC_c Fumarylacetoacetase M_4fumacac_c + M_h2o_c <=> M_acac_c + M_h_c + M_fum_c c TRUE (WBGene00019620) phenylalanine degradation;tyrosine metabolism RHEA:10244 R_FUMSO3tm Fumarate:sulfite antiport, mitochondrial M_so3_m + M_fum_c <=> M_so3_c + M_fum_m mc TRUE (WBGene00019656) or (ND) PW106 R_FUMSO4tm Fumarate:sulfate antiport, mitochondrial M_so4_m + M_fum_c <=> M_so4_c + M_fum_m mc TRUE (WBGene00019656) or (ND) PW106 R_FUMtm fumarate transport, mitochondrial M_pi_m + M_fum_c <=> M_pi_c + M_fum_m mc TRUE (WBGene00019656) or (ND) PW106 R_FUMTSULtm Fumarate:thiosulfate antiport, mitochondrial M_tsul_m + M_fum_c <=> M_tsul_c + M_fum_m mc TRUE (WBGene00019656) or (ND) PW106 -R_G1PP_c Glucose-1-phosphatase M_h2o_c + M_g1p_c <=> M_glc_aD_c + M_pi_c c FALSE PW018 -R_G3PD1_c Glycerol-3-phosphate dehydrogenase (NAD+) M_dhap_c + M_h_c + M_nadh_c <=> M_glyc3p_c + M_nad_c c TRUE (WBGene00010778) or (WBGene00009824) glycerolipid metabolism; glycerophospholipid metabolism RHEA:11092;RHEA:11092;RHEA:11092;RHEA:11092;RHEA:11092 set to reversible janna +R_G1PP_c Glucose-1-phosphatase M_h2o_c + M_g1p_c <=> M_glc_aD_c + M_pi_c c FALSE PW018 SPW004 +R_G3PD1_c Glycerol-3-phosphate dehydrogenase (NAD+) M_dhap_c + M_h_c + M_nadh_c <=> M_glyc3p_c + M_nad_c c TRUE (WBGene00010778) or (WBGene00009824) glycerolipid metabolism;glycerophospholipid metabolism RHEA:11092;RHEA:11092;RHEA:11092;RHEA:11092;RHEA:11092 set to reversible janna R_G5SD_c Glutamate-5-semialdehyde dehydrogenase M_pi_c + M_glu5sa_c + M_nadp_c <=> M_glu5p_c + M_h_c + M_nadph_c c TRUE (WBGene00011938) PW081 RHEA:14877;RHEA:19541 R_G5SD_m Glutamate-5-semialdehyde dehydrogenase M_pi_m + M_glu5sa_m + M_nadp_m <=> M_glu5p_m + M_h_m + M_nadph_m m TRUE (WBGene00011938) PW081 RHEA:14877;RHEA:19541 R_G6PDA_c glucosamine-6-phosphate deaminase M_h2o_c + M_gam6p_c <=> M_nh3_c + M_f6p_c + M_h_c c FALSE (WBGene00011399) or (WBGene00011399) or (WBGene00011399) or (WBGene00011399) PW009 R00765 added KEGG ID lenov -R_G6PDH2r_c Glucose-6-phosphate 1-dehydrogenase M_g6p_B_c + M_nadp_c <=> M_6pgl_c + M_h_c + M_nadph_c c TRUE (WBGene00007108) PW027 RHEA:15841 -R_G6PDH2r_n Glucose-6-phosphate 1-dehydrogenase M_g6p_B_n + M_nadp_n <=> M_6pgl_n + M_h_n + M_nadph_n n TRUE (WBGene00007108) PW027 RHEA:15841 -R_GALE_c UDP-galactose 4-epimerase M_udpg_c <=> M_udpgal_c c TRUE (WBGene00008132) amino sugar and nucleotide sugar metabolism; galactose metabolism RHEA:22168;RHEA:20517 Updated RXN ID and name to be consistent with NCBI, wormbase, and BIGG. Mutants have been analyzed in C. elegans and show impact on galactose metabolism. Found in cytosol and nucleus in human https://www.proteinatlas.org/ENSG00000117308-GALE/cell also Reviewed in C. elegans in https://doi.org/10.1534/genetics.117.300106 nel -R_GALK_c Galactokinase M_adgal_c + M_atp_c <=> M_gal1p_c + M_h_c + M_adp_c c FALSE (WBGene00006461) amino sugar and nucleotide sugar metabolism; galactose metabolism 28978773 Reviewed in C. elegans in https://doi.org/10.1534/genetics.117.300106 nel +R_G6PDH2r_c Glucose-6-phosphate 1-dehydrogenase M_g6p_B_c + M_nadp_c <=> M_6pgl_c + M_h_c + M_nadph_c c TRUE (WBGene00007108) PW027 SPW004 RHEA:15841 +R_G6PDH2r_n Glucose-6-phosphate 1-dehydrogenase M_g6p_B_n + M_nadp_n <=> M_6pgl_n + M_h_n + M_nadph_n n TRUE (WBGene00007108) PW027 SPW004 RHEA:15841 +R_GALE_c UDP-galactose 4-epimerase M_udpg_c <=> M_udpgal_c c TRUE (WBGene00008132) amino sugar and nucleotide sugar metabolism;galactose metabolism RHEA:22168;RHEA:20517 Updated RXN ID and name to be consistent with NCBI, wormbase, and BIGG. Mutants have been analyzed in C. elegans and show impact on galactose metabolism. Found in cytosol and nucleus in human https://www.proteinatlas.org/ENSG00000117308-GALE/cell also Reviewed in C. elegans in https://doi.org/10.1534/genetics.117.300106 nel +R_GALK_c Galactokinase M_adgal_c + M_atp_c <=> M_gal1p_c + M_h_c + M_adp_c c FALSE (WBGene00006461) amino sugar and nucleotide sugar metabolism;galactose metabolism 28978773 Reviewed in C. elegans in https://doi.org/10.1534/genetics.117.300106 nel R_GALM_c D-galactose 1-epimerase M_gal_c <=> M_adgal_c c TRUE (WBGene00015270) or (WBGene00044734) PW017 Human homolog expressed in cytosol (https://www.ncbi.nlm.nih.gov/protein/NP_620156.1). Crystal structure analyzed in C. elegans (1LUR) 10.1074/jbc.M402347200 However a BLAST of the structure sequence shows higher homology to the predicted solute carriers: WBGene00015271 or WBGene00021219 but these two don't show high homology to the human or top hits of the human -> C.eleg BLAST. I also updated the RXN ID to be consistent with BIGG;replaced pathway galactose degradation with galactose metabolism nel, lenov R_GALt1r galactose transport (uniport) M_gal_e <=> M_gal_c ec TRUE (WBGene00019979) or (WBGene00019207) or (ND) PW107 -R_GALU_c UTP--glucose-1-phosphate uridylyltransferase M_g1p_c + M_h_c + M_utp_c <=> M_ppi_c + M_udpg_c c TRUE WBGene00016996 or WBGene00010665 amino sugar and nucleotide sugar metabolism; starch and sucrose metabolism; ascorbate and aldarate metabolism; galactose metabolism FLAGGED: Need to verify localization. Wormbase reports ER, human homolog seen in nucleus and mitochondrion (https://www.proteinatlas.org/ENSG00000169764-UGP2/cell); replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism nel; replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism -R_GAPD_c Glyceraldehyde 3-phosphate dehydrogenase (phosphorylating) M_g3p_c + M_pi_c + M_nad_c <=> M_h_c + M_nadh_c + M_13dpg_c c TRUE (WBGene00001684) or (WBGene00001684) or (WBGene00001685) or (WBGene00001685) or (WBGene00001683) or (WBGene00001683) or (WBGene00001686) or (WBGene00001686) PW018 RHEA:10300;RHEA:10300;RHEA:10300;RHEA:10300 +R_GALU_c UTP--glucose-1-phosphate uridylyltransferase M_g1p_c + M_h_c + M_utp_c <=> M_ppi_c + M_udpg_c c TRUE WBGene00016996 or WBGene00010665 amino sugar and nucleotide sugar metabolism;starch and sucrose metabolism;ascorbate and aldarate metabolism;galactose metabolism FLAGGED: Need to verify localization. Wormbase reports ER, human homolog seen in nucleus and mitochondrion (https://www.proteinatlas.org/ENSG00000169764-UGP2/cell); replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism nel; replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism +R_GAPD_c Glyceraldehyde 3-phosphate dehydrogenase (phosphorylating) M_g3p_c + M_pi_c + M_nad_c <=> M_h_c + M_nadh_c + M_13dpg_c c TRUE (WBGene00001684) or (WBGene00001684) or (WBGene00001685) or (WBGene00001685) or (WBGene00001683) or (WBGene00001683) or (WBGene00001686) or (WBGene00001686) PW018 SPW004 RHEA:10300;RHEA:10300;RHEA:10300;RHEA:10300 R_GARFT_c Phosphoribosylglycinamide formyltransferase M_gar_c + M_10fthf_c <=> M_h_c + M_fgam_c + M_thf_c c TRUE (WBGene00018174) PW042 Removed the redundant 5-aminoimidazole ribonucleotide biosynthesis pathway lenov R_GCVP_RXN_c Glycine dehydrogenase (decarboxylating) M_gly_c + M_lip_gcvh_c <=> M_co2_c + M_amehl_c c FALSE (WBGene00020022 and WBGene00009918 and WBGene00008354) PW074 RHEA:24304;RHEA:24304 fixed gene associations. Cytosolic reaction real? hjs R_GCVP_RXN_m Glycine dehydrogenase (decarboxylating) M_gly_m + M_lip_gcvh_m <=> M_co2_m + M_amehl_m m FALSE (WBGene00020022 and WBGene00009918 and WBGene00008354) PW074 RHEA:24304;RHEA:24304 fixed gene association hjs @@ -1487,16 +1487,16 @@ R_GDP_KIN_RXN_n Nucleoside-diphosphate kinase M_atp_n + M_gdp_n <=> M_h_n + M_g R_GDPMNH_c GDP-mannose mannosyl hydrolase M_h2o_c + M_gdpmann_c <=> M_h_c + M_gdp_c + M_man_c c TRUE PW025 R_GF6PTA_c Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) M_f6p_c + M_gln__L_c <=> M_glu__L_c + M_gam6p_c c TRUE (WBGene00008546) or (WBGene00009035) PW032 R_GF6PTA_m Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) M_f6p_m + M_gln__L_m <=> M_glu__L_m + M_gam6p_m m TRUE (WBGene00009035) PW032 -R_GFUCS_c GDP-L-fucose synthase M_gdpddman_c + M_h_c + M_nadph_c <=> M_gdpfuc_c + M_nadp_c c TRUE (WBGene00019813) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism RHEA:18885 16650000 genes identified and cloned in C. elegans. Human homolog localized to the cytosol and nucleus (https://www.proteinatlas.org/ENSG00000104522-TSTA3/cell) nel -R_GHMT2_c glycine hydroxymethyltransferase M_ser__L_c + M_thf_c <=> M_h2o_c + M_gly_c + M_mlthf_c c TRUE (WBGene00003214) glycine, serine and threonine metabolism; folate biosynthesis RHEA:15481 -R_GHMT2_m glycine hydroxymethyltransferase M_ser__L_m + M_thf_m <=> M_h2o_m + M_gly_m + M_mlthf_m m TRUE (WBGene00003214) glycine, serine and threonine metabolism; folate biosynthesis RHEA:15481 +R_GFUCS_c GDP-L-fucose synthase M_gdpddman_c + M_h_c + M_nadph_c <=> M_gdpfuc_c + M_nadp_c c TRUE (WBGene00019813) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism RHEA:18885 16650000 genes identified and cloned in C. elegans. Human homolog localized to the cytosol and nucleus (https://www.proteinatlas.org/ENSG00000104522-TSTA3/cell) nel +R_GHMT2_c glycine hydroxymethyltransferase M_ser__L_c + M_thf_c <=> M_h2o_c + M_gly_c + M_mlthf_c c TRUE (WBGene00003214) PW074;folate biosynthesis RHEA:15481 +R_GHMT2_m glycine hydroxymethyltransferase M_ser__L_m + M_thf_m <=> M_h2o_m + M_gly_m + M_mlthf_m m TRUE (WBGene00003214) PW074;folate biosynthesis RHEA:15481 R_GHMT3_c 4-Trimethylammoniobutanal :: (3S)-3-Hydroxy-N6,N6,N6-trimethyl-L-lysine conversion M_3htmelys_c <=> M_4tmeabut_c + M_gly_c c TRUE Unknown PW101 R_GK1_c Guanylate kinase M_atp_c + M_gmp_c <=> M_adp_c + M_gdp_c c TRUE (WBGene00020190) PW042 R_GK1_m Guanylate kinase M_atp_m + M_gmp_m <=> M_h_m + M_adp_m + M_gdp_m m TRUE (WBGene00020190) PW042 -R_GLBRAN amylo-(1,4->1,6)-transglycosylase M_glygn1_c <=> M_glygn2_c c FALSE (WBGene00011409) starch and sucrose metabolism; glycogen metabolism Changed name to more explicit synonym, added group lenov +R_GLBRAN amylo-(1,4->1,6)-transglycosylase M_glygn1_c <=> M_glygn2_c c FALSE (WBGene00011409) starch and sucrose metabolism;glycogen metabolism Changed name to more explicit synonym, added group lenov R_GLCAASE4_c R_GLCAASE4_c M_h2o_c + M_cs_a_deg2_c <=> M_cs_a_deg3_c + M_glcur_c c FALSE (WBGene00013693) PW014 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) starch and sucrose metabolism; glycogen metabolism RHEA:18549 Changed the stoichiometry of UDP-glucose from 3 to 4, update name, added group. lenov +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) starch and sucrose metabolism;glycogen metabolism 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_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 @@ -1514,14 +1514,14 @@ R_GLUS_c glutamate synthase (NADH) 2.0 M_glu__L_c + M_nad_c <=> M_akg_c + M_h_c R_GLUSy_c glutamate synthase (NADPH) M_akg_c + M_h_c + M_gln__L_c + M_nadph_c <=> 2.0 M_glu__L_c + M_nadp_c c FALSE (WBGene00012326) PW073 R_GLUt2m L-glutamate reversible transport via proton symport, mitochondrial M_h_c + M_glu__L_c <=> M_h_m + M_glu__L_m cm TRUE (WBGene00018901) or (WBGene00019326) or (WBGene00008979) or (ND) PW106 R_GLUt6 Glutamate transport via Na, H symport and K antiport M_h_e + M_glu__L_e + 3.0 M_na1_e + M_k_c <=> M_h_c + M_glu__L_c + M_k_e + 3.0 M_na1_c ec FALSE (WBGene00001620) or (WBGene00001625) PW107 -R_GLUTACONYL_COA_DECARBOXYLASE_RXN_c glutaconyl-CoA decarboxylase M_h_c + M_glutaconyl_coa_c <=> M_co2_c + M_b2coa_c c FALSE lysine metabolism; lysine degradation +R_GLUTACONYL_COA_DECARBOXYLASE_RXN_c glutaconyl-CoA decarboxylase M_h_c + M_glutaconyl_coa_c <=> M_co2_c + M_b2coa_c c FALSE PW079;PW080 R_Glutamate_transport Glutamate transport M_glu__L_c <=> M_glu__L_e ce TRUE ND PW107 R_Glutamine_transport Glutamine transport M_gln__L_c <=> M_gln__L_e ce TRUE ND PW107 R_GLUTAREDOXIN_RXN_c Glutaredoxin reaction M_grxox_c + 2.0 M_E_c <=> M_grxrd_c c FALSE PW070 added rxn name; replaced M_E__c with M_E_c jpnh; lenov -R_GLUTARYL_COA_DEHYDROG_RXN_c glutaryl-CoA dehydrogenase M_h_c + M_fad_c + M_glutcoa_c <=> M_fadh2_c + M_glutaconyl_coa_c c FALSE lysine metabolism; lysine degradation -R_GLUTARYL_COA_DEHYDROGENASE_RXN_c glutaryl-CoA dehydrogenase 2.0 M_h_c + M_fad_c + M_glutcoa_c <=> M_co2_c + M_fadh2_c + M_b2coa_c c TRUE (WBGene00010052) lysine degradation; tryptophan metabolism; fatty acid oxidation -R_GLUTARYL_COA_DEHYDROGENASE_RXN_m glutaryl-CoA dehydrogenase 2.0 M_h_m + M_fad_m + M_glutcoa_m <=> M_co2_m + M_fadh2_m + M_b2coa_m m TRUE (WBGene00010052) lysine degradation; tryptophan metabolism; fatty acid oxidation -R_GLUTARYL_COA_DEHYDROGENASE_RXN_n glutaryl-CoA dehydrogenase 2.0 M_h_n + M_fad_n + M_glutcoa_n <=> M_co2_n + M_fadh2_n + M_b2coa_n n TRUE (WBGene00010052) lysine degradation; tryptophan metabolism; fatty acid oxidation +R_GLUTARYL_COA_DEHYDROG_RXN_c glutaryl-CoA dehydrogenase M_h_c + M_fad_c + M_glutcoa_c <=> M_fadh2_c + M_glutaconyl_coa_c c FALSE PW079;PW080 +R_GLUTARYL_COA_DEHYDROGENASE_RXN_c glutaryl-CoA dehydrogenase 2.0 M_h_c + M_fad_c + M_glutcoa_c <=> M_co2_c + M_fadh2_c + M_b2coa_c c TRUE (WBGene00010052) PW080;PW072;PW062 +R_GLUTARYL_COA_DEHYDROGENASE_RXN_m glutaryl-CoA dehydrogenase 2.0 M_h_m + M_fad_m + M_glutcoa_m <=> M_co2_m + M_fadh2_m + M_b2coa_m m TRUE (WBGene00010052) PW080;PW072;PW062 +R_GLUTARYL_COA_DEHYDROGENASE_RXN_n glutaryl-CoA dehydrogenase 2.0 M_h_n + M_fad_n + M_glutcoa_n <=> M_co2_n + M_fadh2_n + M_b2coa_n n TRUE (WBGene00010052) PW080;PW072;PW062 R_GluToAscrLump lump reaction from glucose to ascarylose M_glc_aD_c <=> M_ascr_c c FALSE TBD PW050 SPW002 [CHECK ME]First instance of Ascr biosynthesis wimi R_GLUVESSEC L-glutamate secretion via secretory vesicle (ATP driven) M_h2o_c + M_glu__L_c + M_atp_c <=> M_pi_c + M_h_c + M_glu__L_e + M_adp_c c FALSE (WBGene00001135) PW107 R_GLYAT_m Glycine C-acetyltransferase M_gly_m + M_accoa_m <=> M_2aobut_m + M_h_m + M_coa_m m TRUE (WBGene00012007) PW074 @@ -1529,8 +1529,8 @@ 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) starch and sucrose metabolism; glycogen metabolism RHEA:23360;RHEA:56560 Added to the group glycogen metabolism; 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) starch and sucrose metabolism; glycogen metabolism Changed M_glygn3_c into M_glygn2_c, changed stoichiometry to produce 3 G1P, added group 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) starch and sucrose metabolism;glycogen metabolism RHEA:23360;RHEA:56560 Added to the group glycogen metabolism; 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) starch and sucrose metabolism;glycogen metabolism 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 R_GLYK_c Glycerol kinase M_glyc_c + M_atp_c <=> M_glyc3p_c + 2.0 M_h_c + M_adp_c c FALSE (WBGene00020007) PW052 @@ -1540,15 +1540,15 @@ R_GLYOXII_RXN_c Hydroxyacylglutathione hydrolase M_lgt_S_c + M_h2o_c <=> M_h_c R_GLYOXII_RXN_n Hydroxyacylglutathione hydrolase M_lgt_S_n + M_h2o_n <=> M_h_n + M_lac__D_n + M_gthrd_n n FALSE (WBGene00012459) PW024 replaced M_lgt__S_n with M_lgt_S_n lenov R_GLYOXYLATE_OXIDASE_RXN_c glyoxylate oxidase M_h2o_c + M_o2_c + M_glx_c <=> M_h2o2_c + M_oxa_c + M_h_c c FALSE (WBGene00009334) PW030 R_GLYOXYLATE_OXIDASE_RXN_m glyoxylate oxidase M_h2o_m + M_o2_m + M_glx_m <=> M_h2o2_m + M_oxa_m + M_h_m m FALSE (WBGene00009334) PW030 -R_GMAND_c GDP-mannose 4,6-dehydratase M_gdpmann_c <=> M_h2o_c + M_gdpddman_c c FALSE (WBGene00000266) or (WBGene00010166) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism RHEA:23820;RHEA:23820 genes identified and cloned in C. elegans nel +R_GMAND_c GDP-mannose 4,6-dehydratase M_gdpmann_c <=> M_h2o_c + M_gdpddman_c c FALSE (WBGene00000266) or (WBGene00010166) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism RHEA:23820;RHEA:23820 genes identified and cloned in C. elegans nel R_GMP_REDUCT_RXN_c GMP reductase M_nh3_c + M_imp_c + M_nadp_c <=> M_h_c + M_gmp_c + M_nadph_c c TRUE (WBGene00017984) PW034 R_GMP_REDUCT_RXN_n GMP reductase M_nh3_n + M_imp_n + M_nadp_n <=> M_h_n + M_gmp_n + M_nadph_n n TRUE (WBGene00017984) PW034 R_GMPS2_c GMP synthetase (glutamine-hydrolysing) M_h2o_c + M_xmp_c + M_gln__L_c + M_atp_c <=> M_ppi_c + 3.0 M_h_c + M_glu__L_c + M_gmp_c + M_amp_c c FALSE (WBGene00010912) or (WBGene00010912) PW042 RHEA:11680 R_GMPtn GMP nuclear transport M_gmp_c <=> M_gmp_n cn TRUE PW108 -R_GND_c R_GND_c M_6pgc_c + M_nadp_c <=> M_co2_c + M_ru5p_D_c + M_nadph_c c TRUE (WBGene00012015) or (WBGene00012015) or (WBGene00012015) PW027 -R_GND_m R_GND_m M_6pgc_m + M_nadp_m <=> M_co2_m + M_ru5p_D_m + M_nadph_m m TRUE (WBGene00012015) PW027 -R_GND2_c R_GND2_c M_6pgc_c + M_nad_c <=> M_co2_c + M_ru5p_D_c + M_nadh_c c TRUE (WBGene00012015) or (WBGene00012015) or (WBGene00012015) PW027 -R_GND2_m R_GND2_m M_6pgc_m + M_nad_m <=> M_co2_m + M_ru5p_D_m + M_nadh_m m TRUE (WBGene00012015) PW027 +R_GND_c R_GND_c M_6pgc_c + M_nadp_c <=> M_co2_c + M_ru5p_D_c + M_nadph_c c TRUE (WBGene00012015) or (WBGene00012015) or (WBGene00012015) PW027 SPW004 +R_GND_m R_GND_m M_6pgc_m + M_nadp_m <=> M_co2_m + M_ru5p_D_m + M_nadph_m m TRUE (WBGene00012015) PW027 SPW004 +R_GND2_c R_GND2_c M_6pgc_c + M_nad_c <=> M_co2_c + M_ru5p_D_c + M_nadh_c c TRUE (WBGene00012015) or (WBGene00012015) or (WBGene00012015) PW027 SPW004 +R_GND2_m R_GND2_m M_6pgc_m + M_nad_m <=> M_co2_m + M_ru5p_D_m + M_nadh_m m TRUE (WBGene00012015) PW027 SPW004 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 @@ -1570,7 +1570,7 @@ R_Guanosine_Exchange_reactions_e Guanosine transport M_gsn_e <=> e TRUE PW111 R_Guanosine_transport Guanosine transport M_gsn_c <=> M_gsn_e ce TRUE ND PW107 [CHECK ME] Identical except H usage? jpnh. R_GUAPRT_c R_GUAPRT_c M_prpp_c + M_gua_c <=> M_ppi_c + M_gmp_c c TRUE WBGene00020557 or WBGene00013690 PW042 RHEA:17973 R_GULN3D_c L-gulonate 3-dehydrogenase M_guln_c + M_nad_c <=> M_3dhguln_c + M_h_c + M_nadh_c c TRUE (WBGene00022130) PW033 -R_GULND_c Glucuronate reductase M_guln_c + M_nadp_c <=> M_h_c + M_nadph_c + M_glcur_c c TRUE Unknown pentose and glucuronate interconversions; ascorbate and aldarate metabolism replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism lenov +R_GULND_c Glucuronate reductase M_guln_c + M_nadp_c <=> M_h_c + M_nadph_c + M_glcur_c c TRUE Unknown pentose and glucuronate interconversions;ascorbate and aldarate metabolism replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism lenov R_H2O2tn hydrogen peroxide nuclear transport M_h2o2_c <=> M_h2o2_n cn TRUE PW108 R_H2OGLYAQPt R_H2OGLYAQPt M_h2o_e + M_glyc_e <=> M_h2o_c + M_glyc_c ec TRUE (WBGene00000170 or WBGene00000175 or WBGene00000171 or WBGene00000169 or WBGene00000176) PW107 R_H2Otm H2O transport, mitochondrial M_h2o_c <=> M_h2o_m cm TRUE (WBGene00000172) or (WBGene00000174) or (ND) PW106 @@ -1582,14 +1582,14 @@ R_HCO3_NAt bicarbonate transport (Na/HCO3 cotransport) M_hco3_e + M_na1_e <=> M R_HCRNtm O-hexanoylcarnitine transport into mitochondria via diffusion M_carn6_0__L_c <=> M_carn6_0__L_m cm FALSE (WBGene00000996 ) PW106 R_HDCAFAPMtc Hexadecanoate Transport M_fa16_0_e <=> M_fa16_0_c ec TRUE (WBGene00000170 or WBGene00000175 or WBGene00000171 or WBGene00000169 or WBGene00000176) or (ND) PW107 added name; set to reversible jpnh; janna R_Heme_Exchange_reactions_e pheme transport M_pheme_e <=> e TRUE PW111 Removed space from reaction ID jpnh -R_HEX1_c beta-D-Glucokinase M_glc_bD_c + M_atp_c <=> M_g6p_B_c + 2.0 M_h_c + M_adp_c c FALSE WBGene00008780 or WBGene00010416 or WBGene00022306 amino sugar and nucleotide sugar metabolism; glycolysis and gluconeogenesis; trehalose degradation R01600 fixed the name lenov +R_HEX1_c beta-D-Glucokinase M_glc_bD_c + M_atp_c <=> M_g6p_B_c + 2.0 M_h_c + M_adp_c c FALSE WBGene00008780 or WBGene00010416 or WBGene00022306 amino sugar and nucleotide sugar metabolism;PW018;trehalose degradation R01600 fixed the name lenov R_HEX4_c D-mannose transport M_atp_c + M_man_c <=> M_man6p_c + M_h_c + M_adp_c c FALSE (WBGene00010416) or (WBGene00022306) or (WBGene00008780) PW025 R_HEX4_m D-mannose transport M_atp_m + M_man_m <=> M_man6p_m + M_h_m + M_adp_m m FALSE (WBGene00010416) PW025 R_HEX4_n D-mannose transport M_atp_n + M_man_n <=> M_man6p_n + M_h_n + M_adp_n n FALSE (WBGene00010416) or (WBGene00022306) or (WBGene00008780) PW025 R_HEX7_c Fructokinase M_fru_B_c + M_atp_c <=> M_f6p_c + 2.0 M_h_c + M_adp_c c FALSE (WBGene00008780) PW031 R_HEX7_n Fructokinase M_fru_B_n + M_atp_n <=> M_f6p_n + 2.0 M_h_n + M_adp_n n FALSE (WBGene00008780) PW031 -R_HGNTOR_c Homogentisate 1,2-dioxygenase M_hgentis_c + M_o2_c <=> M_4mlacac_c + M_h_c c FALSE (WBGene00001843) phenylalanine degradation; tyrosine metabolism RHEA:15449 -R_HGNTOR_n Homogentisate 1,2-dioxygenase M_hgentis_n + M_o2_n <=> M_4mlacac_n + M_h_n n FALSE (WBGene00001843) phenylalanine degradation; tyrosine metabolism RHEA:15449 +R_HGNTOR_c Homogentisate 1,2-dioxygenase M_hgentis_c + M_o2_c <=> M_4mlacac_c + M_h_c c FALSE (WBGene00001843) phenylalanine degradation;tyrosine metabolism RHEA:15449 +R_HGNTOR_n Homogentisate 1,2-dioxygenase M_hgentis_n + M_o2_n <=> M_4mlacac_n + M_h_n n FALSE (WBGene00001843) phenylalanine degradation;tyrosine metabolism RHEA:15449 R_HISD_c Histidine ammonia-lyase M_his__L_c <=> M_urcan_c + M_nh3_c + M_h_c c FALSE (WBGene00009813) PW084 RHEA:21232 R_HISTACET Acetyl-CoA:histone acetyltransferase M_accoa_n + M_Nlys_n <=> M_h_n + M_coa_n + M_Naclys_n n FALSE ((WBGene00008209 or WBGene00000366) or WBGene00045419 or WBGene00007029 or WBGene00020596 or WBGene00044069 or WBGene00014123 or WBGene00010537 or WBGene00021636) or WBGene00007914 PW101 RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948;RHEA:45948 Histone acetylation takes place in the nucleus lenov R_HISTDIMET histone-L-lysine N6-methyltransferase (acting on monomethylated residues) M_Nmelys_n + M_amet_n <=> M_Ndmelys_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 Histone dimethylation takes place in the nucleus lenov @@ -1598,8 +1598,8 @@ R_Histidine_transport Histidine transport M_his__L_c <=> M_his__L_e ce TRUE ND P R_HISTONE_LYSINE_N_METHYLTRANSFERASE_RXN_n Histone-lysine N-methyltransferase M_Nlys_n + M_amet_n <=> M_Nmelys_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:1004;RHEA:10024;RHEA:10024;RHEA:10024;RHEA:10024 Histone methylation is irreversible; merged all Gene associations from different compartments; replace pathway annotation with histone modification lenov R_HKYNH_c R_HKYNH_c M_h2o_c + M_hLkynr_c <=> M_3hanthrn_c + M_h_c + M_ala__L_c c TRUE (WBGene00015802) PW072 replaced M_ala__L_c with M_ala_L_c lenov R_HMGCOAR_c Hydroxymethylglutaryl-CoA reductase (NADPH) 2.0 M_h_c + 2.0 M_nadph_c + M_hmgcoa_c <=> M_mev_R_c + M_coa_c + 2.0 M_nadp_c c TRUE (WBGene00017268) PW001 R02082 RHEA:15989 added KEGGID ms -R_HMGCOAS_c Hydroxymethylglutaryl-CoA synthase M_h2o_c + M_accoa_c + M_aacoa_c <=> M_h_c + M_coa_c + M_hmgcoa_c c TRUE (WBGene00017769) valine, leucine and isoleucine degradation; terpenoid backbone biosynthesis R01978 RHEA:10188 added KEGGID ms -R_HMGCOAS_m Hydroxymethylglutaryl-CoA synthase M_h2o_m + M_accoa_m + M_aacoa_m <=> M_h_m + M_coa_m + M_hmgcoa_m m TRUE (WBGene00017769) valine, leucine and isoleucine degradation; terpenoid backbone biosynthesis R01978 RHEA:10188 added KEGGID ms +R_HMGCOAS_c Hydroxymethylglutaryl-CoA synthase M_h2o_c + M_accoa_c + M_aacoa_c <=> M_h_c + M_coa_c + M_hmgcoa_c c TRUE (WBGene00017769) PW083;PW001 R01978 RHEA:10188 added KEGGID ms +R_HMGCOAS_m Hydroxymethylglutaryl-CoA synthase M_h2o_m + M_accoa_m + M_aacoa_m <=> M_h_m + M_coa_m + M_hmgcoa_m m TRUE (WBGene00017769) PW083;PW001 R01978 RHEA:10188 added KEGGID ms R_HMGL_c Hydroxymethylglutaryl-CoA lyase M_hmgcoa_c <=> M_acac_c + M_accoa_c c TRUE (WBGene00022150) PW083 R_HMGL_m Hydroxymethylglutaryl-CoA lyase M_hmgcoa_m <=> M_acac_m + M_accoa_m m TRUE (WBGene00022150) PW083 R_HOLO_ACP_SYNTH_RXN_c Holo-[acyl-carrier protein] synthase M_coa_c + M_apoACP_c <=> M_pap_c + M_ACP_c c FALSE (WBGene00020215) or (WBGene00012142) PW037 @@ -1631,13 +1631,13 @@ R_IMPD_c IMP dehydrogenase M_h2o_c + M_imp_c + M_nad_c <=> M_xmp_c + M_h_c + M 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_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) glycine, serine and threonine metabolism; glyoxylate and dicarboxylate metabolism RHEA:13245;RHEA:18181 -R_ISOCIT_CLEAV_RXN_n Isocitrate lyase M_icit_n <=> M_glx_n + M_succ_n n TRUE (WBGene00001564) glycine, serine and threonine metabolism; glyoxylate and dicarboxylate metabolism RHEA:13245;RHEA:18181 -R_ISOCITDEH_RXN_c Isocitrate dehydrogenase (NADP+) M_nadp_c + M_icit_c <=> M_akg_c + M_co2_c + M_nadph_c c FALSE (WBGene00010317) PW023 RHEA:19629;RHEA:19629 -R_ISOCITDEH_RXN_m Isocitrate dehydrogenase (NADP+) M_nadp_m + M_icit_m <=> M_akg_m + M_co2_m + M_nadph_m m FALSE WBGene00010317 or WBGene00007942 PW023 RHEA:19629;RHEA:19629;RHEA:19629 -R_ISOCITRATE_DEHYDROGENASE_NAD__RXN_c Isocitrate dehydrogenase (NAD+) M_nad_c + M_icit_c <=> M_akg_c + M_co2_c + M_nadh_c c FALSE (WBGene00009664) PW023 RHEA:23632 -R_ISOCITRATE_DEHYDROGENASE_NAD__RXN_m Isocitrate dehydrogenase (NAD+) M_nad_m + M_icit_m <=> M_akg_m + M_co2_m + M_nadh_m m FALSE (WBGene00016266) or (WBGene00009664) or (WBGene00009440) or (WBGene00007993) PW023 RHEA:23632;RHEA:23632 -R_ISOCITRATE_DEHYDROGENASE_NAD__RXN_n Isocitrate dehydrogenase (NAD+) M_nad_n + M_icit_n <=> M_akg_n + M_co2_n + M_nadh_n n FALSE (WBGene00009664) PW023 RHEA:23632 +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 +R_ISOCIT_CLEAV_RXN_n Isocitrate lyase M_icit_n <=> M_glx_n + M_succ_n n TRUE (WBGene00001564) PW074;PW030 RHEA:13245;RHEA:18181 +R_ISOCITDEH_RXN_c Isocitrate dehydrogenase (NADP+) M_nadp_c + M_icit_c <=> M_akg_c + M_co2_c + M_nadph_c c FALSE (WBGene00010317) PW023 SPW004 RHEA:19629;RHEA:19629 +R_ISOCITDEH_RXN_m Isocitrate dehydrogenase (NADP+) M_nadp_m + M_icit_m <=> M_akg_m + M_co2_m + M_nadph_m m FALSE WBGene00010317 or WBGene00007942 PW023 SPW004 RHEA:19629;RHEA:19629;RHEA:19629 +R_ISOCITRATE_DEHYDROGENASE_NAD__RXN_c Isocitrate dehydrogenase (NAD+) M_nad_c + M_icit_c <=> M_akg_c + M_co2_c + M_nadh_c c FALSE (WBGene00009664) PW023 SPW004 RHEA:23632 +R_ISOCITRATE_DEHYDROGENASE_NAD__RXN_m Isocitrate dehydrogenase (NAD+) M_nad_m + M_icit_m <=> M_akg_m + M_co2_m + M_nadh_m m FALSE (WBGene00016266) or (WBGene00009664) or (WBGene00009440) or (WBGene00007993) PW023 SPW004 RHEA:23632;RHEA:23632 +R_ISOCITRATE_DEHYDROGENASE_NAD__RXN_n Isocitrate dehydrogenase (NAD+) M_nad_n + M_icit_n <=> M_akg_n + M_co2_n + M_nadh_n n FALSE (WBGene00009664) PW023 SPW004 RHEA:23632 R_Isoleucine_Exchange_reactions_e Isoleucine transport M_ile__L_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Isoleucine_transport Isoleucine transport M_ile__L_c <=> M_ile__L_e ce TRUE ND PW107 R_IZPN_c Imidazolonepropionase M_4izp_c + M_h2o_c + M_h_c <=> M_forglu_c c TRUE (WBGene00020436) PW084 @@ -1649,7 +1649,7 @@ R_L_GULONOLACTONE_OXIDASE_RXN_c L-gulonolactone oxidase M_gullac_c + M_o2_c <=> R_Lact2r lactose transport (uniport) M_lac__L_e <=> M_lac__L_c ec TRUE (WBGene00008214) or (ND) PW107 R_LACTATEDH_c D-lactate dehydrogenase M_lac__D_c + M_nad_c <=> M_pyr_c + M_nadh_c + M_h_c c TRUE PW024 replaces R_DLACTDEHYDROGFAD_RXN_c lenov R_LCRNtm O-lauroylcarnitine transport into mitochondria via diffusion M_carn12_0__L_c <=> M_carn12_0__L_m cm FALSE (WBGene00000996 ) PW106 -R_LDH_L_c L-lactate dehydrogenase M_nad_c + M_lac__L_c <=> M_h_c + M_nadh_c + M_pyr_c c TRUE (WBGene00002262) or (WBGene00002262) or (WBGene00002262) PW022 RHEA:23444;RHEA:23444 +R_LDH_L_c L-lactate dehydrogenase M_nad_c + M_lac__L_c <=> M_h_c + M_nadh_c + M_pyr_c c TRUE (WBGene00002262) or (WBGene00002262) or (WBGene00002262) PW022 SPW004 RHEA:23444;RHEA:23444 R_LEUB0AT2tc R_LEUB0AT2tc M_leu__L_e + M_na1_e <=> M_leu__L_c + M_na1_c ec TRUE (WBGene00015778 or WBGene00016652) PW107 RHEA:21824;RHEA:21824 R_Leucine_Exchange_reactions_e Leucine transport M_leu__L_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Leucine_transport Leucine transport M_leu__L_c <=> M_leu__L_e ce TRUE ND PW107 @@ -1684,17 +1684,17 @@ R_Lysine_transport Lysine transport M_lys__L_c <=> M_lys__L_e ce TRUE ND PW107 R_LYStm Lysine mitochondrial transport via ornithine carrier M_h_m + M_lys__L_c <=> M_h_c + M_lys__L_m mc TRUE (WBGene00020422) or (ND) PW106 R_LYStn L-lysine transport, nuclear M_lys__L_c <=> M_lys__L_n cn TRUE PW108 R_M4CET3_c R_M4CET3_c M_m3emgacpail_c + M_1ac2acg3pe_c <=> M_mem2emgacpail_c + M_1ac2acglyc_c c FALSE (WBGene00016159) PW028 -R_MACACI_c Maleylacetoacetate isomerase M_4mlacac_c <=> M_4fumacac_c c TRUE WBGene00021817 or WBGene00001790 or WBGene00001791 phenylalanine degradation; tyrosine metabolism RHEA:14817 +R_MACACI_c Maleylacetoacetate isomerase M_4mlacac_c <=> M_4fumacac_c c TRUE WBGene00021817 or WBGene00001790 or WBGene00001791 phenylalanine degradation;tyrosine metabolism RHEA:14817 R_MALS_c malate synthase M_h2o_c + M_glx_c + M_accoa_c <=> M_h_c + M_coa_c + M_mal__L_c c TRUE (WBGene00001564) PW030 RHEA:13245;RHEA:18181 R_MALS_m malate synthase M_h2o_m + M_glx_m + M_accoa_m <=> M_h_m + M_coa_m + M_mal__L_m m TRUE (WBGene00001564) PW030 RHEA:13245;RHEA:18181 R_MALSO3tm Malate:sulfite antiport, mitochondrial M_so3_m + M_mal__L_c <=> M_so3_c + M_mal__L_m mc TRUE (WBGene00019656) or (ND) PW106 R_MALSO4tm Malate:sulfate antiport, mitochondrial M_so4_m + M_mal__L_c <=> M_so4_c + M_mal__L_m mc TRUE (WBGene00019656) or (ND) PW106 R_MALSULtm malate:thiosulfate antiport, mitochondrial M_tsul_m + M_mal__L_c <=> M_tsul_c + M_mal__L_m mc TRUE (WBGene00019656) or (ND) PW106 R_MALtm malate transport, mitochondrial M_pi_m + M_mal__L_c <=> M_pi_c + M_mal__L_m mc TRUE (WBGene00019656) or (ND) PW106 -R_MAN1PT_c Mannose-1-phosphate guanylyltransferase M_man1p_c + M_h_c + M_gtp_c <=> M_gdpmann_c + M_ppi_c c TRUE (WBGene00021628) or (WBGene00016583) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism RHEA:15229 Human homolog shows localization in the nucleus (https://www.proteinatlas.org/ENSG00000173540-GMPPB/cell) nel -R_MAN1PT_n Mannose-1-phosphate guanylyltransferase M_man1p_n + M_h_n + M_gtp_n <=> M_gdpmann_n + M_ppi_n n TRUE (WBGene00021628) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism (set to reversible, janna)Human homolog shows localization in the nucleus (https://www.proteinatlas.org/ENSG00000173540-GMPPB/cell) nel -R_MAN6PI_c Mannose-6-phosphate isomerase M_man6p_c <=> M_f6p_c c TRUE (WBGene00015464) or (WBGene00014013) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism -R_MAN6PI_n Mannose-6-phosphate isomerase M_man6p_n <=> M_f6p_n n TRUE (WBGene00015464) or (WBGene00014013) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism +R_MAN1PT_c Mannose-1-phosphate guanylyltransferase M_man1p_c + M_h_c + M_gtp_c <=> M_gdpmann_c + M_ppi_c c TRUE (WBGene00021628) or (WBGene00016583) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism RHEA:15229 Human homolog shows localization in the nucleus (https://www.proteinatlas.org/ENSG00000173540-GMPPB/cell) nel +R_MAN1PT_n Mannose-1-phosphate guanylyltransferase M_man1p_n + M_h_n + M_gtp_n <=> M_gdpmann_n + M_ppi_n n TRUE (WBGene00021628) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism (set to reversible, janna)Human homolog shows localization in the nucleus (https://www.proteinatlas.org/ENSG00000173540-GMPPB/cell) nel +R_MAN6PI_c Mannose-6-phosphate isomerase M_man6p_c <=> M_f6p_c c TRUE (WBGene00015464) or (WBGene00014013) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism +R_MAN6PI_n Mannose-6-phosphate isomerase M_man6p_n <=> M_f6p_n n TRUE (WBGene00015464) or (WBGene00014013) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism R_MANt1r mannose transport (uniport) M_man_e <=> M_man_c ec TRUE (WBGene00019979) or (WBGene00019207) or (ND) PW107 R_MARBIOSYNTH0001 Trehalose acyl transferase M_tre_c + M_fataccoa_c <=> M_lmar_c + M_coa_c c FALSE PW143 SPW003 [CHECKME] added maradolipid biosynthesis and degradation wimi R_MARBIOSYNTH0002 Lysomarado acyl transferase M_lmar_c + M_fataccoa_c <=> M_mar_c + M_coa_c c FALSE PW143 SPW003 [CHECKME] added maradolipid biosynthesis and degradation wimi @@ -1702,11 +1702,11 @@ R_MARBIOSYNTH0003 Marado hydrolase M_mar_c + M_h2o_c <=> M_lmar_c + M_fatacid_c R_MARBIOSYNTH0004 Lysomarado hydrolase M_lmar_c + M_h2o_c <=> M_tre_c + M_fatacid_c + M_h_c c FALSE PW143 SPW003 [CHECKME] added maradolipid biosynthesis and degradation wimi R_MCD_m malonyl-CoA decarboxylase M_h_m + M_malcoa_m <=> M_co2_m + M_accoa_m m FALSE (WBGene00009439) PW038 R00233 added KEGG ID lenov R_MCRNtm O-Myristoylcarnitine transport into mitochondria via diffusion M_carn14_0__L_c <=> M_carn14_0__L_m cm FALSE (WBGene00000996 ) PW106 -R_MDH_c Malate dehydrogenase M_nad_c + M_mal__L_c <=> M_oaa_c + M_h_c + M_nadh_c c TRUE (WBGene00018491) or (WBGene00018491) tca cycle; alanine, aspartate and glutamate metabolism; glyoxylate and dicarboxylate metabolism; glycolysis and gluconeogenesis RHEA:21432;RHEA:21432 -R_MDH_m Malate dehydrogenase M_nad_m + M_mal__L_m <=> M_oaa_m + M_h_m + M_nadh_m m TRUE WBGene00018491 or WBGene00003162 tca cycle; alanine, aspartate and glutamate metabolism; glyoxylate and dicarboxylate metabolism; glycolysis and gluconeogenesis RHEA:21432;RHEA:21432;RHEA:21432 -R_ME1_c Malate dehydrogenase (oxaloacetate decarboxylating) M_nad_c + M_mal__L_c <=> M_co2_c + M_nadh_c + M_pyr_c c TRUE PW018 -R_ME2_c Malate dehydrogenase (oxaloacetate decarboxylating) (NADP+) M_nadp_c + M_mal__L_c <=> M_co2_c + M_nadph_c + M_pyr_c c TRUE (WBGene00012983) PW018 -R_ME2_m Malate dehydrogenase (oxaloacetate decarboxylating) (NADP+) M_nadp_m + M_mal__L_m <=> M_co2_m + M_nadph_m + M_pyr_m m TRUE (WBGene00012983) PW018 +R_MDH_c Malate dehydrogenase M_nad_c + M_mal__L_c <=> M_oaa_c + M_h_c + M_nadh_c c TRUE (WBGene00018491) or (WBGene00018491) PW023;alanine, aspartate and glutamate metabolism;PW030;PW018 RHEA:21432;RHEA:21432 +R_MDH_m Malate dehydrogenase M_nad_m + M_mal__L_m <=> M_oaa_m + M_h_m + M_nadh_m m TRUE WBGene00018491 or WBGene00003162 PW023;alanine, aspartate and glutamate metabolism;PW030;PW018 RHEA:21432;RHEA:21432;RHEA:21432 +R_ME1_c Malate dehydrogenase (oxaloacetate decarboxylating) M_nad_c + M_mal__L_c <=> M_co2_c + M_nadh_c + M_pyr_c c TRUE PW018 SPW004 +R_ME2_c Malate dehydrogenase (oxaloacetate decarboxylating) (NADP+) M_nadp_c + M_mal__L_c <=> M_co2_c + M_nadph_c + M_pyr_c c TRUE (WBGene00012983) PW018 SPW004 +R_ME2_m Malate dehydrogenase (oxaloacetate decarboxylating) (NADP+) M_nadp_m + M_mal__L_m <=> M_co2_m + M_nadph_m + M_pyr_m m TRUE (WBGene00012983) PW018 SPW004 R_METAT_c Methionine adenosyltransferase M_h2o_c + M_met__L_c + M_atp_c <=> M_pi_c + M_ppi_c + M_h_c + M_amet_c c FALSE (WBGene00006416) or (WBGene00015540) or (WBGene00015538) or (WBGene00008205) PW082 R00177 RHEA:21080;RHEA:21080;RHEA:21080;RHEA:21080 22939621 lenov 2.5.1.6 R_METB0AT2tc R_METB0AT2tc M_met__L_e + M_na1_e <=> M_met__L_c + M_na1_c ec TRUE (WBGene00015778 or WBGene00016652 or WBGene00004905) PW107 RHEA:21824;RHEA:21824 R_Methionine_Exchange_reactions_e Methionine transport M_met__L_e <=> e TRUE PW111 Removed space from reaction ID jpnh @@ -1714,8 +1714,8 @@ R_Methionine_transport Methionine transport M_met__L_c <=> M_met__L_e ce TRUE ND R_METHYLACYLYLCOA_HYDROXY_RXN_c Methylacrylyl-CoA hydratase M_h2o_c + M_2mp2coa_c <=> M_3hibutcoa_c c TRUE (WBGene00001156) or (WBGene00020347) or (WBGene00001155) or (WBGene00001154) or (WBGene00001152) or (WBGene00001150) PW083 RHEA:16105;RHEA:20724 R_METHYLACYLYLCOA_HYDROXY_RXN_m Methylacrylyl-CoA hydratase M_h2o_m + M_2mp2coa_m <=> M_3hibutcoa_m m TRUE (WBGene00001156) or (WBGene00001155) or (WBGene00001154) or (WBGene00001152) or (WBGene00001150) or (WBGene00020347) or (WBGene00001151) PW083 RHEA:16105;RHEA:20724 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 folate biosynthesis; cysteine and methionine metabolism 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) folate biosynthesis; cysteine and methionine metabolism RHEA:11172 +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 folate biosynthesis;cysteine and methionine metabolism 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) folate biosynthesis;cysteine and methionine metabolism 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_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 @@ -1736,11 +1736,11 @@ R_MI145P6K_n Inositol-polyphosphate multikinase M_atp_n + M_mi145p_n <=> 2.0 M_ 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_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 Mitochondrial import by diffusion 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 Mitochondrial import by diffusion SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi -R_MITOIMPORT0003 Fatty acid import by diffusion (C8:0) M_fa8_0_c <=> M_fa8_0_m cm TRUE Mitochondrial import by diffusion SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi -R_MITOIMPORT0004 Fatty acid import by diffusion (C10:0) M_fa10_0_c <=> M_fa10_0_m cm TRUE Mitochondrial import by diffusion SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi -R_MITOIMPORT0005 Fatty acid import by diffusion (C12:0) M_fa12_0_c <=> M_fa12_0_m cm TRUE Mitochondrial import by diffusion SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi +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 +R_MITOIMPORT0003 Fatty acid import by diffusion (C8:0) M_fa8_0_c <=> M_fa8_0_m cm TRUE PW132 SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi +R_MITOIMPORT0004 Fatty acid import by diffusion (C10:0) M_fa10_0_c <=> M_fa10_0_m cm TRUE PW132 SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi +R_MITOIMPORT0005 Fatty acid import by diffusion (C12:0) M_fa12_0_c <=> M_fa12_0_m cm TRUE PW132 SPW001 [CHECKME] Short chain fatty acids can enter mitochondria by diffusion wimi R_MME_m Methylmalonyl-CoA epimerase M_mmcoa_R_m <=> M_mmcoa_S_m m TRUE (WBGene00008415) PW001;PW010 R_MMM2_m Methylmalonyl-CoA mutase M_mmcoa_R_m <=> M_succoa_m m TRUE WBGene00014202 PW001;PW010 RHEA:22888 R_MMSAD3_m Malonate-semialdehyde dehydrogenase (acetylating) M_msa_m + M_coa_m + M_nad_m <=> M_co2_m + M_nadh_m + M_accoa_m m FALSE (WBGene00000114) PW038;PW010 R00705 RHEA:20804;RHEA:22992;RHEA:22988 added name to rxn; added KEGG ID jpnh; lenov @@ -1991,16 +1991,16 @@ R_PALMITOLEICBETAOX0012 3-ketothiolase (C12:1(5Z,3O), mitochondrial) M_coa12_1_5 R_PALMITOLEICBETAOX0013 Enoyl-CoA delta isomerase (C10:1(3Z), mitochondrial) M_coa10_1_3z_m <=> M_coa10_1_2e_m m FALSE WBGene00001153 PW116 SPW001 [CHECKME] Detailed replacement for lumped reaction R_RMC0088 wimi R_Pantothenate_Exchange_reactions_e Pantothenate transport M_pnto_R_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Pantothenate_transport Pantothenate transport M_pnto_R_c <=> M_pnto_R_e ce TRUE ND PW107 -R_PC_m Pyruvate carboxylase M_hco3_m + M_atp_m + M_pyr_m <=> M_oaa_m + M_pi_m + 2.0 M_h_m + M_adp_m m FALSE (WBGene00004258) PW023 RHEA:20844 +R_PC_m Pyruvate carboxylase M_hco3_m + M_atp_m + M_pyr_m <=> M_oaa_m + M_pi_m + 2.0 M_h_m + M_adp_m m FALSE (WBGene00004258) PW023 SPW004 RHEA:20844 R_PCLAD_c Aminocarboxymuconate-semialdehyde decarboxylase M_cmusa_c + M_h_c <=> M_co2_c + M_am6sa_c c FALSE (WBGene00022104) PW072 RHEA:16557 R_PCRNtm O-Palmitoylcarnitine transport into mitochondria via diffusion M_carn16_0__L_c <=> M_carn16_0__L_m cm FALSE WBGene00000996 or WBGene00008320 PW106 -R_PDE4_c 3′,5′-cyclic-GMP phosphodiesterase M_h2o_c + M_35cgmp_c <=> M_h_c + M_gmp_c c FALSE (WBGene00016328) or (WBGene00003966) or (WBGene00011433) or (WBGene00020114) or (WBGene00022389) or (WBGene00008443) or (WBGene00011146) nucleotide interconversion; purine metabolism RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653 -R_PDE4_m 3′,5′-cyclic-GMP phosphodiesterase M_h2o_m + M_35cgmp_m <=> M_h_m + M_gmp_m m FALSE (WBGene00003966) nucleotide interconversion; purine metabolism -R_PDE4_n 3′,5′-cyclic-GMP phosphodiesterase M_h2o_n + M_35cgmp_n <=> M_h_n + M_gmp_n n FALSE (WBGene00016328) or (WBGene00003966) or (WBGene00011433) or (WBGene00020114) or (WBGene00022389) nucleotide interconversion; purine metabolism RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653 -R_PDH_m pyruvate dehydrogenase M_coa_m + M_nad_m + M_pyr_m <=> M_co2_m + M_nadh_m + M_accoa_m m FALSE (WBGene00010794 and WBGene00007824 and WBGene00009082 and WBGene00015413 and WBGene00011510) glycolysis and gluconeogenesis; pyruvate metabolism; tca cycle; glyoxylate and dicarboxylate metabolism RHEA:19189;RHEA:17017;RHEA:15045;RHEA:19189 -R_PEPCARBOX_RXN_c Phosphoenolpyruvate carboxylase M_oaa_c + M_pi_c + M_h_c <=> M_co2_c + M_h2o_c + M_pep_c c TRUE PW018 -R_PEPCK_c Phosphoenolpyruvate carboxykinase (GTP) M_oaa_c + M_gtp_c <=> M_co2_c + M_pep_c + M_gdp_c c TRUE (WBGene00021043) or (WBGene00011232) or (WBGene00019151) PW018 set to reversible janna -R_PEPCK_m Phosphoenolpyruvate carboxykinase (GTP) M_oaa_m + M_gtp_m <=> M_co2_m + M_pep_m + M_gdp_m m FALSE (WBGene00021043) PW018 +R_PDE4_c 3′,5′-cyclic-GMP phosphodiesterase M_h2o_c + M_35cgmp_c <=> M_h_c + M_gmp_c c FALSE (WBGene00016328) or (WBGene00003966) or (WBGene00011433) or (WBGene00020114) or (WBGene00022389) or (WBGene00008443) or (WBGene00011146) nucleotide interconversion;PW042 RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653 +R_PDE4_m 3′,5′-cyclic-GMP phosphodiesterase M_h2o_m + M_35cgmp_m <=> M_h_m + M_gmp_m m FALSE (WBGene00003966) nucleotide interconversion;PW042 +R_PDE4_n 3′,5′-cyclic-GMP phosphodiesterase M_h2o_n + M_35cgmp_n <=> M_h_n + M_gmp_n n FALSE (WBGene00016328) or (WBGene00003966) or (WBGene00011433) or (WBGene00020114) or (WBGene00022389) nucleotide interconversion;PW042 RHEA:14653;RHEA:14653;RHEA:14653;RHEA:14653 +R_PDH_m pyruvate dehydrogenase M_coa_m + M_nad_m + M_pyr_m <=> M_co2_m + M_nadh_m + M_accoa_m m FALSE (WBGene00010794 and WBGene00007824 and WBGene00009082 and WBGene00015413 and WBGene00011510) PW018;PW022;PW023;PW030 RHEA:19189;RHEA:17017;RHEA:15045;RHEA:19189 +R_PEPCARBOX_RXN_c Phosphoenolpyruvate carboxylase M_oaa_c + M_pi_c + M_h_c <=> M_co2_c + M_h2o_c + M_pep_c c TRUE PW018 SPW004 +R_PEPCK_c Phosphoenolpyruvate carboxykinase (GTP) M_oaa_c + M_gtp_c <=> M_co2_c + M_pep_c + M_gdp_c c TRUE (WBGene00021043) or (WBGene00011232) or (WBGene00019151) PW018 SPW004 set to reversible janna +R_PEPCK_m Phosphoenolpyruvate carboxykinase (GTP) M_oaa_m + M_gtp_m <=> M_co2_m + M_pep_m + M_gdp_m m FALSE (WBGene00021043) PW018 SPW004 R_PEPCPSBIOSYNTH0001 CDP-choline 1,2-diacyl-sn-glycerol phosphocholine transferase M_cdpchol_c + M_1ac2acglyc_c <=> M_h_c + M_cmp_c + M_1ac2acg3pc_c c FALSE WBGene00009057 or WBGene00013024 PW139 SPW003 [CHECKME] Replaces R_RC01321 & R_RXN_5781_c wimi R_PEPCPSBIOSYNTH0002 CDP-ethanolamine 1,2-diacyl-sn-glycerol phosphoethanolamine transferase M_cdpea_c + M_1ac2acglyc_c <=> M_h_c + M_cmp_c + M_1ac2acg3pe_c c FALSE WBGene00009057 or WBGene00013024 PW139 SPW003 [CHECKME] Replaces R_ETHANOLAMINEPHOSPHOTRANSFERASE_RXN_c & R_RC02057 wimi R_PEPCPSBIOSYNTH0003 phosphatidylcholine-serine O-phosphatidyltransferase M_ser__L_c + M_1ac2acg3pc_c <=> M_chol_c + M_1ac2acg3ps_c c FALSE WBGene00013920 PW139 SPW003 [CHECKME] Replaces R_RXN_10638_c wimi @@ -2029,26 +2029,26 @@ 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) amino sugar and nucleotide sugar metabolism; glycolysis and gluconeogenesis 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) amino sugar and nucleotide sugar metabolism; glycolysis and gluconeogenesis RHEA:16109;RHEA:16109 +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) amino sugar and nucleotide sugar metabolism;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) amino sugar and nucleotide sugar metabolism;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) amino sugar and nucleotide sugar metabolism; glycolysis and gluconeogenesis; fructose and mannose metabolism RHEA:11816;RHEA:11816 -R_PGI_m Glucose-6-phosphate isomerase M_g6p_B_m <=> M_f6p_m m TRUE (WBGene00013597) amino sugar and nucleotide sugar metabolism; glycolysis and gluconeogenesis; fructose and mannose metabolism RHEA:11816;RHEA:11816 -R_PGK_c Phosphoglycerate kinase M_atp_c + M_3pg_c <=> M_adp_c + M_13dpg_c c TRUE (WBGene00020185) PW018 RHEA:14801 -R_PGL_c 6-phosphogluconolactonase M_h2o_c + M_6pgl_c <=> M_6pgc_c + M_h_c c TRUE (WBGene00013301) PW027 -R_PGM_c Phosphoglycerate mutase M_3pg_c <=> M_2pg_c c TRUE (WBGene00019001) PW018 RHEA:15901 +R_PGI_c Glucose-6-phosphate isomerase M_g6p_B_c <=> M_f6p_c c TRUE (WBGene00013597) amino sugar and nucleotide sugar metabolism;PW018;fructose and mannose metabolism RHEA:11816;RHEA:11816 +R_PGI_m Glucose-6-phosphate isomerase M_g6p_B_m <=> M_f6p_m m TRUE (WBGene00013597) amino sugar and nucleotide sugar metabolism;PW018;fructose and mannose metabolism RHEA:11816;RHEA:11816 +R_PGK_c Phosphoglycerate kinase M_atp_c + M_3pg_c <=> M_adp_c + M_13dpg_c c TRUE (WBGene00020185) PW018 SPW004 RHEA:14801 +R_PGL_c 6-phosphogluconolactonase M_h2o_c + M_6pgl_c <=> M_6pgc_c + M_h_c c TRUE (WBGene00013301) PW027 SPW004 +R_PGM_c Phosphoglycerate mutase M_3pg_c <=> M_2pg_c c TRUE (WBGene00019001) PW018 SPW004 RHEA:15901 R_PHEAMINOTRANS_DEG_RXN_c Aromatic amino acid transferase M_glu__L_c + M_phpyr_c <=> M_akg_c + M_phe__L_c c TRUE (WBGene00020146) or (WBGene00020145) or (WBGene00015778) or (WBGene00015771) or (WBGene00009628) PW076 RHEA:21824;RHEA:21824 [DELETION] Dupe of R_RXN909_57_c jpnh R_PHEAMINOTRANS_DEG_RXN_m Aromatic amino acid transferase M_glu__L_m + M_phpyr_m <=> M_akg_m + M_phe__L_m m TRUE (WBGene00016652) or (WBGene00015778) PW076 RHEA:21824;RHEA:21824 [DELETION] Dupe of R_RXN909_57_m jpnh R_PHEMEABCte R_PHEMEABCte M_h2o_c + M_atp_c + M_pheme_c <=> M_pi_c + M_h_c + M_adp_c + M_pheme_e c FALSE WBGene00003412 PW107 R_PHEMEe release of heme into the blood M_pheme_c <=> M_pheme_e ce TRUE WBGene00019830 or WBGene00009493 PW107 R_PHEMEtm Heme transport to cytosol M_pheme_m <=> M_pheme_c mc TRUE ND PW106 -R_PHENYLALANINE_4_MONOOXYGENASE_RXN_c Phenylalanine 4-monooxygenase M_phe__L_c + M_thbpt_c + M_o2_c <=> M_thbpt4acam_c + M_tyr__L_c c FALSE (WBGene00006600) or (WBGene00000296) or (WBGene00000240) alanine, aspartate and glutamate metabolism; tyrosine biosynthesis RHEA:20309;RHEA:18201;RHEA:20273;RHEA:16709 -R_PHENYLALANINE_4_MONOOXYGENASE_RXN_n Phenylalanine 4-monooxygenase M_phe__L_n + M_thbpt_n + M_o2_n <=> M_thbpt4acam_n + M_tyr__L_n n FALSE (WBGene00000240) alanine, aspartate and glutamate metabolism; tyrosine biosynthesis RHEA:20273;RHEA:16709 +R_PHENYLALANINE_4_MONOOXYGENASE_RXN_c Phenylalanine 4-monooxygenase M_phe__L_c + M_thbpt_c + M_o2_c <=> M_thbpt4acam_c + M_tyr__L_c c FALSE (WBGene00006600) or (WBGene00000296) or (WBGene00000240) alanine, aspartate and glutamate metabolism;tyrosine biosynthesis RHEA:20309;RHEA:18201;RHEA:20273;RHEA:16709 +R_PHENYLALANINE_4_MONOOXYGENASE_RXN_n Phenylalanine 4-monooxygenase M_phe__L_n + M_thbpt_n + M_o2_n <=> M_thbpt4acam_n + M_tyr__L_n n FALSE (WBGene00000240) alanine, aspartate and glutamate metabolism;tyrosine biosynthesis RHEA:20273;RHEA:16709 R_Phenylalanine_Exchange_reactions_e Phenylalanine transport M_phe__L_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Phenylalanine_transport Phenylalanine transport M_phe__L_c <=> M_phe__L_e ce TRUE ND PW107 R_PHOSPHAGLYPSYN_RXN_c CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase M_glyc3p_c + M_cdpdag_c <=> M_h_c + M_cmp_c + M_1ac2acg3pg3p_c c FALSE (WBGene00021677) PW056 RHEA:12593;RHEA:12593 [DELETION] Dupe of R_RC01801 jpnh R_PHOSPHATIDATE_PHOSPHATASE_RXN_c Phosphatidate phosphatase M_h2o_c + M_1ac2acglyc3p_c <=> M_pi_c + M_1ac2acglyc_c c FALSE (WBGene00018756) PW056 -R_PHOSPHOGLUCMUT_RXN_c Phosphoglucomutase M_g1p_c <=> M_g6p_A_c c TRUE WBGene00019890 or WBGene00012803 amino sugar and nucleotide sugar metabolism; galactose metabolism; glycolysis and gluconeogenesis; starch and sucrose metabolism +R_PHOSPHOGLUCMUT_RXN_c Phosphoglucomutase M_g1p_c <=> M_g6p_A_c c TRUE WBGene00019890 or WBGene00012803 amino sugar and nucleotide sugar metabolism;galactose metabolism;PW018;starch and sucrose metabolism R_PHOSPHOLIPASE_C_RXN_c Phospholipase C M_h2o_c + M_1ac2acg3pc_c <=> M_cholp_c + M_1ac2acglyc_c + M_h_c c FALSE (WBGene00004037) or (WBGene00004039) PW056 RHEA:33179;RHEA:33179 replaced pathway phospholipases by glycerophospholipid metabolism lenov R_Pi_Exchange_reactions_e Pi transport M_pi_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Pi_transport Phosphate transport M_pi_c <=> M_pi_e ce TRUE ND PW107 @@ -2085,9 +2085,9 @@ R_PItn phosphate transport, nuclear M_pi_n <=> M_pi_c nc TRUE PW108 R_PMEVK_c Phosphomevalonate kinase M_5pmev_c + M_atp_c <=> M_5dpmev_c + M_h_c + M_adp_c c TRUE (WBGene00009335) PW001 R03245 added KEGGID, ChEBI ms R_PMPOXI_RXN_m pyridoxal 5′-phosphate synthase M_h2o_m + M_o2_m + M_pyam5p_m <=> M_h2o2_m + M_nh3_m + M_h_m + M_pydx5p_m m FALSE (WBGene00018996) PW039 R_PMTFATPtc R_PMTFATPtc M_atp_c + M_coa_c + M_fa16_0_e <=> M_ppi_c + M_amp_c + M_coa16_0_c c FALSE (WBGene00017012 or WBGene00009218) PW107 -R_PNANM_c Phosphomannomutase M_man1p_c <=> M_man6p_c c TRUE (WBGene00009925) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism -R_PNANM_m Phosphomannomutase M_man1p_m <=> M_man6p_m m TRUE (WBGene00009925) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism -R_PNANM_n Phosphomannomutase M_man1p_n <=> M_man6p_n n TRUE (WBGene00009925) amino sugar and nucleotide sugar metabolism; fructose and mannose metabolism +R_PNANM_c Phosphomannomutase M_man1p_c <=> M_man6p_c c TRUE (WBGene00009925) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism +R_PNANM_m Phosphomannomutase M_man1p_m <=> M_man6p_m m TRUE (WBGene00009925) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism +R_PNANM_n Phosphomannomutase M_man1p_n <=> M_man6p_n n TRUE (WBGene00009925) amino sugar and nucleotide sugar metabolism;fructose and mannose metabolism 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 @@ -2097,15 +2097,15 @@ R_PPA_m Inorganic pyrophosphatase M_h2o_m + M_ppi_m <=> 2.0 M_pi_m + M_h_m m TR R_PPA_n Inorganic pyrophosphatase M_h2o_n + M_ppi_n <=> 2.0 M_pi_n + M_h_n n TRUE (WBGene00007548) PW007 R_PPA2_c Triphosphatase M_h2o_c + M_pppi_c <=> M_pi_c + M_ppi_c c TRUE Unknown PW007 R_PPCDC_c Phosphopantothenoylcysteine decarboxylase M_4ppcys_c + M_h_c <=> M_co2_c + M_pan4p_c c TRUE (WBGene00009138) PW037 -R_PPCK_c Phosphoenolpyruvate carboxykinase (ATP) M_oaa_c + M_atp_c <=> M_co2_c + M_pep_c + M_h_c + M_adp_c c FALSE (WBGene00019151) PW018 +R_PPCK_c Phosphoenolpyruvate carboxykinase (ATP) M_oaa_c + M_atp_c <=> M_co2_c + M_pep_c + M_h_c + M_adp_c c FALSE (WBGene00019151) PW018 SPW004 R_PPCOAC_c Propionyl-CoA carboxylase M_hco3_c + M_atp_c + M_ppcoa_c <=> M_pi_c + 2.0 M_h_c + M_adp_c + M_mmcoa_S_c c FALSE (WBGene00018701 and WBGene00017864) PW001;PW010 RHEA:23720 R_PPCOAC_m Propionyl-CoA carboxylase M_hco3_m + M_atp_m + M_ppcoa_m <=> M_pi_m + 2.0 M_h_m + M_adp_m + M_mmcoa_S_m m FALSE (WBGene00018701 and WBGene00017864) PW001;PW010 RHEA:23720 R_PPItn Inorganic diphosphate transport through nuclear pore M_ppi_c <=> M_ppi_n cn TRUE PW108 -R_PPM_c phosphoglucomutase M_r1p_c <=> M_r5p_c c TRUE (WBGene00012803) or (WBGene00019890) pentose phosphate pathway; purine metabolism removed PRPP biosynthesis and pyrimidine metabolism pathways, added pentose phosphate pathway lenov -R_PPM_n phosphoglucomutase M_r1p_n <=> M_r5p_n n TRUE (WBGene00019890) pentose phosphate pathway; purine metabolism removed PRPP biosynthesis and pyrimidine metabolism pathways, added pentose phosphate pathway lenov +R_PPM_c phosphoglucomutase M_r1p_c <=> M_r5p_c c TRUE (WBGene00012803) or (WBGene00019890) PW027;PW042 removed PRPP biosynthesis and PW043 pathways, added PW027 lenov +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 +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 @@ -2124,8 +2124,8 @@ R_Proton_Exchange_reactions_e Proton transport M_h_e <=> e TRUE PW111 Re R_Proton_transport Proton transport M_h_c <=> M_h_e ce TRUE PW107 R_PRPNCOAHYD_c 3-Hydroxypropionyl-CoA hydro-lyase M_h2o_c + M_prpncoa_c <=> M_3hpcoa_c c TRUE (WBGene00001150) PW086 R02963 Added Rxn Name jpnh R_PRPNCOAHYD_m 3-Hydroxypropionyl-CoA hydro-lyase M_h2o_m + M_prpncoa_m <=> M_3hpcoa_m m TRUE (WBGene00001155 or WBGene00001156) or (WBGene00020347 or WBGene00001150) or WBGene00001152 PW086;PW010 R02963 RHEA:16105;RHEA:20724 Added Rxn Name jpnh -R_PRPPS_c ribose-phosphate diphosphokinase M_r5p_c + M_atp_c <=> M_prpp_c + 2.0 M_h_c + M_amp_c c TRUE (WBGene00020107) purine metabolism; pentose phosphate pathway set to reversible; changed the pathway annotation janna; lenov -R_PRPPS_n ribose-phosphate diphosphokinase M_r5p_n + M_atp_n <=> M_prpp_n + 2.0 M_h_n + M_amp_n n TRUE (WBGene00020107) purine metabolism; pentose phosphate pathway set to reversible; changed the pathway annotation lenov +R_PRPPS_c ribose-phosphate diphosphokinase M_r5p_c + M_atp_c <=> M_prpp_c + 2.0 M_h_c + M_amp_c c TRUE (WBGene00020107) PW042;PW027 set to reversible; changed the pathway annotation janna; lenov +R_PRPPS_n ribose-phosphate diphosphokinase M_r5p_n + M_atp_n <=> M_prpp_n + 2.0 M_h_n + M_amp_n n TRUE (WBGene00020107) PW042;PW027 set to reversible; changed the pathway annotation lenov R_PSERT_c Phosphoserine aminotransferase M_akg_c + M_pser_L_c <=> M_3php_c + M_glu__L_c c TRUE (WBGene00009177) PW074 [DELETION] Same reaction as R_RC04173 jpnh 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 @@ -2146,14 +2146,14 @@ 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 RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157;RHEA:18157 +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_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 R_PYRIDOXKIN_RXN_c pyridoxal kinase M_atp_c + M_pydx_c <=> M_h_c + M_adp_c + M_pydx5p_c c FALSE (WBGene00019008) PW039 RHEA:10224 R_PYRIDOXKIN_RXN_m pyridoxal kinase M_atp_m + M_pydx_m <=> M_h_m + M_adp_m + M_pydx5p_m m FALSE (WBGene00019008) PW039 RHEA:10224 -R_PYRROLINECARBDEHYDROG_RXN_c 1-pyrroline-5-carboxylate dehydrogenase 2.0 M_h2o_c + M_1pyr5c_c + M_nad_c <=> M_h_c + M_glu__L_c + M_nadh_c c TRUE (WBGene00000112) arginine and proline metabolism; alanine, aspartate and glutamate metabolism -R_PYRROLINECARBDEHYDROG_RXN_m 1-pyrroline-5-carboxylate dehydrogenase 2.0 M_h2o_m + M_1pyr5c_m + M_nad_m <=> M_h_m + M_glu__L_m + M_nadh_m m TRUE (WBGene00000112) arginine and proline metabolism; alanine, aspartate and glutamate metabolism +R_PYRROLINECARBDEHYDROG_RXN_c 1-pyrroline-5-carboxylate dehydrogenase 2.0 M_h2o_c + M_1pyr5c_c + M_nad_c <=> M_h_c + M_glu__L_c + M_nadh_c c TRUE (WBGene00000112) arginine and proline metabolism;alanine, aspartate and glutamate metabolism +R_PYRROLINECARBDEHYDROG_RXN_m 1-pyrroline-5-carboxylate dehydrogenase 2.0 M_h2o_m + M_1pyr5c_m + M_nad_m <=> M_h_m + M_glu__L_m + M_nadh_m m TRUE (WBGene00000112) arginine and proline metabolism;alanine, aspartate and glutamate metabolism R_PYRt2m pyruvate mitochondrial transport via proton symport M_h_c + M_pyr_c <=> M_h_m + M_pyr_m cm TRUE ND PW111 R_QUILSYN_c Quinolinate Synthase M_cmusa_c <=> M_h2o_c + M_quln_c c FALSE PW036 R_r0941 Bicarbonate Exchange reactions M_hco3_c <=> M_hco3_m cm TRUE PW111 @@ -2213,7 +2213,7 @@ R_RC00678 L-tryptophan:oxygen 2,3-oxidoreductase (decyclizing) M_trp__L_c + M_o R_RC00685 L-Tryptophan decarboxy-lyase M_h_c + M_trp__L_c <=> M_co2_c + M_trypta_c c FALSE WBGene00000239 or WBGene00015467 or WBGene00001839 or WBGene00006562 PW072 RHEA:14345;RHEA:12272;RHEA:18533 R_RC00698 L-phenylalanine:oxygen oxidoreductase (decarboxylating) M_phe__L_c + M_o2_c <=> M_co2_c + M_h2o_c + M_pad_c c TRUE WBGene00021401 PW075 R_RC00699 L-phenylalanine carboxy-lyase (phenylethylamine-forming) M_h_c + M_phe__L_c <=> M_co2_c + M_peamn_c c FALSE WBGene00000239 or WBGene00015467 or WBGene00001839 or WBGene00006562 PW075 RHEA:14345;RHEA:12272;RHEA:18533 -R_RC00711 Acetaldehyde:NADP+ oxidoreductase M_h2o_c + M_nadp_c + M_acald_c <=> 2.0 M_h_c + M_nadph_c + M_ac_c c FALSE WBGene00000111 PW018 +R_RC00711 Acetaldehyde:NADP+ oxidoreductase M_h2o_c + M_nadp_c + M_acald_c <=> 2.0 M_h_c + M_nadph_c + M_ac_c c FALSE WBGene00000111 PW018 SPW004 R_RC00731 L-Tyrosine:oxygen oxidoreductase 2.0 M_tyr__L_c + M_o2_c <=> 2.0 M_34dhphe_c c FALSE WBGene00015332 or WBGene00010661 or WBGene00009001 or WBGene00016419 or WBGene00021553 or WBGene00022231 PW077 R_RC00748 ethanolamine-phosphate phosphate-lyase (deaminating) (acetaldehyde-forming) M_h2o_c + M_ethamp_c <=> M_pi_c + M_acald_c + M_nh4_c c FALSE WBGene00020139 PW056 R_RC00751 L-threonine acetaldehyde-lyase (glycine-forming) M_thr__L_c <=> M_gly_c + M_acald_c c TRUE WBGene00011291 PW074 @@ -2232,7 +2232,7 @@ R_RC00996 L-threonine ammonia-lyase (2-oxobutanoate-forming) M_thr__L_c <=> M_2o R_RC01000 2-Hydroxybutyrate:NAD+ oxidoreductase M_nad_c + M_2hb_c <=> M_h_c + M_nadh_c + M_2obut_c c TRUE WBGene00002262 PW010 RHEA:23444;RHEA:23444 R_RC01005 UDPglucose:dolichyl-phosphate beta-D-glucosyltransferase M_udpg_c + M_dolp_c <=> M_udp_c + M_dolglcp_c c FALSE WBGene00019276 PW011 R_RC01010 Glycerone phosphate phosphohydrolase M_h2o_c + M_dhap_c <=> M_dha_c + M_pi_c c FALSE WBGene00013646 or ((WBGene00009146 or WBGene00014076 or WBGene00007328 or WBGene00007331) or (WBGene00020471 or WBGene00015161 or WBGene00011262) or WBGene00022379 or WBGene00008531) or (WBGene00206373 or WBGene00008802 or WBGene00008801 or WBGene00022246 or WBGene00004020 or WBGene00016152 or WBGene00004023 or WBGene00018696 or WBGene00011879 or WBGene00022181) PW052 RHEA:15017;RHEA:15017;RHEA:15017;RHEA:15017 -R_RC01016 methylglyoxal synthase M_dhap_c <=> M_pi_c + M_mthgxl_c c FALSE Unknown PW022 +R_RC01016 methylglyoxal synthase M_dhap_c <=> M_pi_c + M_mthgxl_c c FALSE Unknown PW022 SPW004 R_RC01041 Glycerol:NADP+ oxidoreductase M_glyald_c + M_h_c + M_nadph_c <=> M_glyc_c + M_nadp_c c TRUE WBGene00012722 or WBGene00016985 PW052 R_RC01054 ADP-ribose ribophosphohydrolase M_h2o_c + M_adprib_c <=> M_r5p_c + 2.0 M_h_c + M_amp_c c FALSE WBGene00003579 or WBGene00003583 PW042 R_RC01055 uracil hydro-lyase M_r5p_c + M_ura_c <=> M_h2o_c + M_psd5p_c c TRUE WBGene00020765 PW043 @@ -2280,7 +2280,7 @@ R_RC01687 (5-L-glutamyl)-peptide:taurine 5-glutamyltransferase M_gthrd_c + M_ta R_RC01704 long-chain-aldehyde dehydrogenase M_h2o_c + M_hxdcal_c + M_nad_c <=> 2.0 M_h_c + M_nadh_c + M_fa16_0_c c TRUE WBGene00000110 PW057 R_RC01710 Pyridoxamine:oxygen oxidoreductase (deaminating) M_h2o_c + M_o2_c + M_pydam_c <=> M_h2o2_c + M_pydx_c + M_nh4_c c FALSE WBGene00018996 PW039 R_RC01711 Pyridoxine:oxygen oxidoreductase (deaminating) M_o2_c + M_pydxn_c <=> M_h2o2_c + M_pydx_c c FALSE WBGene00018996 PW039 -R_RC01737 ATP:D-Gluconate 6-phosphotransferase M_atp_c + M_glcn_c <=> M_6pgc_c + M_h_c + M_adp_c c FALSE WBGene00017818 PW027 +R_RC01737 ATP:D-Gluconate 6-phosphotransferase M_atp_c + M_glcn_c <=> M_6pgc_c + M_h_c + M_adp_c c FALSE WBGene00017818 PW027 SPW004 R_RC01752 D-Glyceraldehyde:NAD+ oxidoreductase M_h2o_c + M_glyald_c + M_nad_c <=> 2.0 M_h_c + M_nadh_c + M_glyc_R_c c TRUE (WBGene00000108 or WBGene00000110) or WBGene00000118 PW052 R_RC01758 L-Arabitol:NAD+ 1-oxidoreductase M_h_c + M_nadh_c + M_arab__L_c <=> M_nad_c + M_abt_c c TRUE WBGene00012722 PW033 R_RC01759 L-Arabitol:NADP+ 1-oxidoreductase M_h_c + M_nadph_c + M_arab__L_c <=> M_nadp_c + M_abt_c c TRUE WBGene00012722 PW033 @@ -2291,9 +2291,9 @@ R_RC01795 L-Phenylalanine,tetrahydrobiopterin:oxygen oxidoreductase (4-hydroxyla R_RC01814 L-Tryptophan,tetrahydrobiopterin:oxygen oxidoreductase (5-hydroxylating) (Dihydrobiopterin forming) M_trp__L_c + M_thbpt_c + M_o2_c <=> M_h2o_c + M_5htrp_c + M_dhbpt_c c FALSE WBGene00006600 PW072 R_RC01815 L-Tyrosine,tetrahydrobiopterin:oxygen oxidoreductase (3-hydroxylating) (Dihydrobiopterin forming) M_tyr__L_c + M_thbpt_c + M_o2_c <=> M_h2o_c + M_34dhphe_c + M_dhbpt_c c FALSE WBGene00000296 PW077 RHEA:20309;RHEA:18201 R_RC01816 anthranilate 3-monooxygenase M_h_c + M_thbpt_c + M_o2_c + M_anth_c <=> M_h2o_c + M_3hanthrn_c + M_dhbpt_c c FALSE Unknown PW072 -R_RC01829 Sedoheptulose 1,7-bisphosphate D-glyceraldehyde-3-phosphate-lyase M_s17bp_c <=> M_dhap_c + M_e4p_c c TRUE WBGene00017166 or WBGene00011474 PW027 RHEA:14729;RHEA:14729;RHEA:14729 -R_RC01843 ATP:Sedoheptulose 7-phosphate 1-phosphotransferase M_s7p_c + M_atp_c <=> M_h_c + M_adp_c + M_s17bp_c c FALSE WBGene00008230 or WBGene00022199 PW027 RHEA:16109;RHEA:16109 -R_RC01844 ATP:sedoheptulose 7-phosphate M_atp_c + M_sedh_c <=> M_s7p_c + M_h_c + M_adp_c c TRUE WBGene00012017 PW027 +R_RC01829 Sedoheptulose 1,7-bisphosphate D-glyceraldehyde-3-phosphate-lyase M_s17bp_c <=> M_dhap_c + M_e4p_c c TRUE WBGene00017166 or WBGene00011474 PW027 SPW004 RHEA:14729;RHEA:14729;RHEA:14729 +R_RC01843 ATP:Sedoheptulose 7-phosphate 1-phosphotransferase M_s7p_c + M_atp_c <=> M_h_c + M_adp_c + M_s17bp_c c FALSE WBGene00008230 or WBGene00022199 PW027 SPW004 RHEA:16109;RHEA:16109 +R_RC01844 ATP:sedoheptulose 7-phosphate M_atp_c + M_sedh_c <=> M_s7p_c + M_h_c + M_adp_c c TRUE WBGene00012017 PW027 SPW004 R_RC01878 Cytidine aminohydrolase M_h2o_c + M_h_c + M_cytd_c <=> M_uri_c + M_nh4_c c FALSE WBGene00000391 or WBGene00000392 PW043 RHEA:13433;RHEA:16069;RHEA:13433;RHEA:16069 R_RC01896 xylitol dehydrogenase (D-xyulose-forming) M_xylt_c + M_nad_c <=> M_xylu_D_c + M_h_c + M_nadh_c c TRUE WBGene00011003 or WBGene00011004 PW033 R_RC01903 L-arabinitol 4-dehydrogenase M_nad_c + M_abt_c <=> M_xylu_L_c + M_h_c + M_nadh_c c TRUE Unknown PW033 @@ -2330,7 +2330,7 @@ R_RC02478 UDP-glucuronate-androsterone glucuronyltransferase M_udpglcur_c + M_a R_RC02485 Deoxycytidine aminohydrolase M_h2o_c + M_h_c + M_dcyt_c <=> M_duri_c + M_nh4_c c FALSE WBGene00000391 or WBGene00000392 PW043 RHEA:13433;RHEA:16069;RHEA:13433;RHEA:16069 R_RC02497 dihydrotestosterone:NADP+ delta4-oxidoreductase M_h_c + M_nadph_c + M_tststerone_c <=> M_nadp_c + M_5adtststerone_c c FALSE WBGene00007102 or WBGene00009635 PW049 R_RC02529 aminoacetone:oxygen oxidoreductase (deaminating) M_h2o_c + M_o2_c + M_aact_c <=> M_h2o2_c + M_mthgxl_c + M_nh4_c c FALSE WBGene00000138 PW074 -R_RC02531 Lactaldehyde:NAD+ 1-oxidoreductase M_nad_c + M_lald_D_c <=> M_h_c + M_nadh_c + M_mthgxl_c c TRUE WBGene00012722 PW022 +R_RC02531 Lactaldehyde:NAD+ 1-oxidoreductase M_nad_c + M_lald_D_c <=> M_h_c + M_nadh_c + M_mthgxl_c c TRUE WBGene00012722 PW022 SPW004 R_RC02532 4-[(1R)-2-Amino-1-hydroxyethyl]-1,2-benzenediol:oxygen oxidoreductase (deaminating) (flavin-containing) M_h2o_c + M_o2_c + M_nrpphr_c <=> M_h2o2_c + M_34dhmald_c + M_nh4_c c FALSE WBGene00000138 PW077 R_RC02535 3,4-dihydroxyphenetylamine,ascorbate:oxygen oxidoreductase (beta-hydroxylating) M_dopa_c + M_o2_c + M_ascb__L_c <=> M_dhdascb_c + M_h2o_c + M_nrpphr_c c FALSE WBGene00006541 PW077 R_RC02556 Deoxyadenosine aminohydrolase M_h2o_c + M_h_c + M_dad_2_c <=> M_din_c + M_nh4_c c FALSE WBGene00015551 or WBGene00016632 PW042 @@ -2342,9 +2342,9 @@ R_RC02695 4-Hydroxyphenylacetaldehyde:NAD+ oxidoreductase M_h2o_c + M_nad_c + R_RC02697 4-Hydroxyphenylacetaldehyde:NADP+ oxidoreductase M_h2o_c + M_nadp_c + M_4hoxpacd_c <=> 2.0 M_h_c + M_nadph_c + M_4hphac_c c TRUE WBGene00000111 PW077 R_RC02731 D-Fructose-2,6-bisphosphate 2-phosphohydrolase M_h2o_c + M_f26bp_c <=> M_f6p_c + M_pi_c c FALSE WBGene00022456 or WBGene00019295 PW025 RHEA:17289;RHEA:15653 R_RC02737 trehalose 6-phosphate synthase M_g6p_A_c + M_udpg_c <=> M_h_c + M_udp_c + M_tre6p_c c FALSE WBGene00006602 or WBGene00006603 PW019 RHEA:18889;RHEA:18889 ms -R_RC02739 alpha-D-Glucose 6-phosphate ketol-isomerase (producing beta-D-Glucose 6-phosphate) M_g6p_A_c <=> M_g6p_B_c c TRUE WBGene00013597 PW018 RHEA:11816;RHEA:11816 +R_RC02739 alpha-D-Glucose 6-phosphate ketol-isomerase (producing beta-D-Glucose 6-phosphate) M_g6p_A_c <=> M_g6p_B_c c TRUE WBGene00013597 PW018 SPW004 RHEA:11816;RHEA:11816 R_RC02743 (5-L-Glutamyl)-L-cysteine 5-glutamyltransferase (cyclizing) M_glucys_c <=> M_5oxpro_c + M_cys__L_c c FALSE WBGene00016629 PW070 -R_RC02750 2-Deoxy-D-ribose 5-phosphate + ADP = Deoxyribose + ATP M_atp_c + M_2doxrib_c <=> M_h_c + M_adp_c + M_2dr5p_c c FALSE WBGene00008548 PW027 +R_RC02750 2-Deoxy-D-ribose 5-phosphate + ADP = Deoxyribose + ATP M_atp_c + M_2doxrib_c <=> M_h_c + M_adp_c + M_2dr5p_c c FALSE WBGene00008548 PW027 SPW004 R_RC02778 Trehalose-6-phosphate phosphohydrolase M_h2o_c + M_tre6p_c <=> M_tre_c + M_pi_c c FALSE WBGene00001649 PW019 RHEA:23420 ms R_RC02869 S-adenosylmethioninamine:spermidine 3-aminopropyltransferase M_ametam_c + M_spmd_c <=> M_5mta_c + M_h_c + M_sprm_c c FALSE WBGene00012909 PW082 R_RC02902 UDP-glucuronate-retinol glucuronyltransferase M_udpglcur_c + M_retn_c <=> M_udp_c + M_retnglc_c c FALSE WBGene00015371 or WBGene00016959 or WBGene00017334 or WBGene00018789 or WBGene00019181 or WBGene00019235 or WBGene00019379 or WBGene00007072 or WBGene00020594 or WBGene00020593 or WBGene00020592 or WBGene00019232 or WBGene00019233 or WBGene00008097 or WBGene00013901 or WBGene00007422 or WBGene00013900 or WBGene00019515 or WBGene00007073 or WBGene00019516 or WBGene00007885 or WBGene00007455 or WBGene00007650 or WBGene00016762 or WBGene00015692 or WBGene00015695 or WBGene00015694 or WBGene00021709 or WBGene00013903 or WBGene00011340 or WBGene00021464 or WBGene00018543 or WBGene00007946 or WBGene00009255 or WBGene00044286 or WBGene00017315 or WBGene00017332 or WBGene00017333 or WBGene00017329 or WBGene00013905 or WBGene00017331 or WBGene00017336 or WBGene00017959 or WBGene00008485 or WBGene00008486 or WBGene00021372 or WBGene00015141 or WBGene00011006 or WBGene00015965 or WBGene00007070 or WBGene00013906 or WBGene00011564 or WBGene00015369 or WBGene00018931 or WBGene00020182 or WBGene00012013 or WBGene00011452 or WBGene00011453 or WBGene00009450 or WBGene00011238 or WBGene00013904 or WBGene00007402 or WBGene00018206 or WBGene00010904 or WBGene00015449 or WBGene00015577 or WBGene00008583 or WBGene00015739 or WBGene00019234 or WBGene00020587 PW069 RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032 @@ -2466,10 +2466,10 @@ R_RC07218 Cholesterol 25-hydroxylase M_h_c + M_nadph_c + M_o2_c + M_chsterol_ R_RC07296 choloyl-CoA hydrolase M_h2o_c + M_cholcoa_c <=> M_h_c + M_coa_c + M_cholate_c c FALSE WBGene00017781 PW066 R_RC07324 1D-myo-inositol-3-phosphate lyase (isomerizing) M_g6p_A_c <=> M_mi3p_D_c c FALSE WBGene00012148 PW029 replaced streptomycin biosynthesis with inositol phosphate metabolism lenov R_RC07372 oxysterol 7alpha-hydroxylase (acting on 27-hydroxycholesterol) M_h_c + M_nadph_c + M_o2_c + M_xol27oh_c <=> M_h2o_c + M_nadp_c + M_xoltri27_c c FALSE TBD PW066 -R_ETHERLIPIDREMODEL0001 Plasmenylethanolamine 2-acylhydrolase M_h2o_c + M_1alken2acg3pe_c <=> M_h_c + M_Rtotal6_c + M_alken2gpe_c c FALSE WBGene00009801 or WBGene00012319 PW065 +R_ETHERLIPIDREMODEL0001 Plasmenylethanolamine 2-acylhydrolase M_h2o_c + M_1alken2acg3pe_c <=> M_h_c + M_Rtotal6_c + M_alken2gpe_c c FALSE WBGene00009801 or WBGene00012319 PW065 SPW003 R_RC07380 Lysoplasmalogen ethanolamine phosphohydrolase M_h2o_c + M_alken2gpe_c <=> M_ethamp_c + M_h_c + M_1alkenglyc_c c TRUE WBGene00020195 or WBGene00007753 or WBGene00007755 or WBGene00008776 PW065 R_RC07385 O-1-Alk-1-enyl-2-acyl-sn-glycero-3-phosphoethanolamine phosphatidohydrolase M_h2o_c + M_1alken2acg3pe_c <=> M_etha_c + M_h_c + M_alkenac2gp_c c TRUE WBGene00004040 or (WBGene00017316 or WBGene00020256 or WBGene00013080) PW065 RHEA:14445 -R_ETHERLIPIDREMODEL0002 Plasmanylcholine 2-acylhydrolase M_h2o_c + M_1alk2acg3pc_c <=> M_h_c + M_1alkg3pc_c + M_Rtotal6_c c FALSE WBGene00009801 or WBGene00012319 PW065 +R_ETHERLIPIDREMODEL0002 Plasmanylcholine 2-acylhydrolase M_h2o_c + M_1alk2acg3pc_c <=> M_h_c + M_1alkg3pc_c + M_Rtotal6_c c FALSE WBGene00009801 or WBGene00012319 PW065 SPW003 R_RC07641 hydrogen-carbonate:ammonia amido-ligase (ADP-forming, carbamate-phosphorylating) M_hco3_c + 2.0 M_atp_c + M_nh4_c <=> M_cbp_c + M_pi_c + 2.0 M_h_c + 2.0 M_adp_c c FALSE WBGene00004259 PW043 RHEA:18633;RHEA:20013;RHEA:24296 R_RC07759 very-long-chain 3-oxoacyl-CoA reductase M_h_c + M_nadph_c + M_coa18_0_3o_c <=> M_nadp_c + M_coa18_0_3oh__S_c c TRUE WBGene00002891 PW060 SPW001 RHEA:48680 R_RC07933 DELTA6-fatty-acid desaturase M_o2_c + 2.0 M_focytb5_c + M_coa18_3_9z12z15z_c <=> 2.0 M_h2o_c + 2.0 M_ficytb5_c + M_strdnccoa_c c FALSE WBGene00001395 PW061 @@ -2495,8 +2495,8 @@ R_RC08759 cholestanetriol 26-monooxygenase M_nadp_c + M_xoltetrol_c <=> M_h_c + R_RC08761 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoate,NADPH:oxygen oxidoreductase (26-hydroxylating) M_nadph_c + M_o2_c + M_thcholst_c <=> M_h2o_c + M_nadp_c + M_thcholstoic_c c FALSE WBGene00000905 PW066 RHEA:34631 R_RC09035 acyl-CoA:1-acyl-sn-glycero-3-phosphoserine O-acyltransferase M_Rtotal2coa_c + M_1acg3ps_c <=> M_coa_c + M_1ac2acg3ps_c c TRUE WBGene00020115 or WBGene00016934 or WBGene00007446 or WBGene00013995 PW056 RHEA:12937;RHEA:33191;RHEA:32995 R_RC09036 K13510 lysophosphatidylcholine acyltransferase / lyso-PAF acetyltransferase [EC:2.3.1.23 2.3.1.67]; K13512 lysophospholipid acyltransferase [EC:2.3.1.23 2.3.1.-]; K13513 lysocardiolipin and lysophospholipid acyltransferase [EC:2.3.1.- 2.3.1.51]; K13514 lysophosphatidylglycerol acyltransferase 1 [EC:2.3.1.-]; K13519 lysophospholipid acyltransferase [EC:2.3.1.51 2.3.1.23 2.3.1.-] M_Rtotal2coa_c + M_lpglyc_c <=> M_coa_c + M_1ac2acg3pg_c c TRUE WBGene00020264 or WBGene00022646 or WBGene00044631 or WBGene00019465 or WBGene00008581 PW056 -R_RC09085 ADP:alpha-D-glucose 6-phosphotransferase M_glc_aD_c + M_adp_c <=> M_g6p_A_c + M_h_c + M_amp_c c FALSE WBGene00016810 PW018 -R_RC09086 ADP:beta-D-glucose 6-phosphotransferase M_glc_bD_c + M_adp_c <=> M_g6p_B_c + M_h_c + M_amp_c c FALSE WBGene00016810 PW018 +R_RC09085 ADP:alpha-D-glucose 6-phosphotransferase M_glc_aD_c + M_adp_c <=> M_g6p_A_c + M_h_c + M_amp_c c FALSE WBGene00016810 PW018 SPW004 +R_RC09086 ADP:beta-D-glucose 6-phosphotransferase M_glc_bD_c + M_adp_c <=> M_g6p_B_c + M_h_c + M_amp_c c FALSE WBGene00016810 PW018 SPW004 R_RC09319 glycoprotein 6-alpha-L-fucosyltransferase (acting on nm2masn) M_gdpfuc_c + M_nm2masn_c <=> M_h_c + M_gdp_c + M_fnm2masn_c c FALSE WBGene00001508 PW011 RHEA:12985 R_RC09371 S-adenosyl-L-methionine:hydrogen-selenide Se-methyltransferase M_seln_c + M_amet_c <=> M_h_c + M_ahcys_c + M_metsel_c c FALSE WBGene00013151 or WBGene00014228 PW088 RHEA:52808 R_RC09752 GDP:alpha-D-glucose 1-phosphate guanylyltransferase M_pi_c + M_gdpg_c <=> M_g1p_c + M_h_c + M_gdp_c c TRUE WBGene00015678 PW025 RHEA:30387 @@ -2506,7 +2506,7 @@ R_RC10059 NADP+:L-tyrosine oxidoreductase (iodinating) M_tyr__L_c + 2.0 M_nadp_c R_RC10065 ATP:1D-myo-inositol-1,4,5-trisphosphate 3,6-phosphotransferase 2.0 M_atp_c + M_mi145p_c <=> 2.0 M_h_c + 2.0 M_adp_c + M_mi13456p_c c TRUE WBGene00014081 PW029 R_RC10306 S-adenosyl-L-methionine:2-(3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] methyltransferase 3.0 M_amet_c + M_caphis_c <=> 3.0 M_h_c + 3.0 M_ahcys_c + M_pdipht_c c TRUE WBGene00007194 PW099 R_RC10633 NAD-dependent histone deacetylase M_h2o_c + M_nad_c + M_Naclys_c <=> M_ncam_c + M_Nlys_c + M_ac_adprib_c c TRUE WBGene00004800 or WBGene00004801 or WBGene00004802 or WBGene00004803 PW035 RHEA:43636;RHEA:43636;RHEA:43636;RHEA:43636 -R_RCC0001 citrate hydro-lyase (cis-aconitate-forming) M_cit_c <=> M_icit_c c TRUE WBGene00000040 PW023 RHEA:10336 +R_RCC0001 citrate hydro-lyase (cis-aconitate-forming) M_cit_c <=> M_icit_c c TRUE WBGene00000040 PW023 SPW004 RHEA:10336 R_RCC0005 maintenance atp M_h2o_c + M_atp_c <=> M_pi_c + M_h_c + M_adp_c c FALSE PW098 R_RCC0010 5-(methylthio)-2,3-dioxopentyl-phosphate phosphohydrolase (isomerizing); 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate-forming) M_dkmpp_c + M_h2o_c + M_o2_c <=> M_for_c + M_pi_c + 2.0 M_h_c + M_2kmb_c c FALSE WBGene00010286 and (WBGene00009636 or WBGene00020149) PW082 R_RCC0018 melanine biosynthesis (merged) 2.0 M_dopaqn_c + 0.5 M_o2_c <=> M_co2_c + M_h2o_c + M_34dhphe_c + M_ind56qn_c c FALSE WBGene00015332 or WBGene00010661 or WBGene00009001 or WBGene00016419 or WBGene00021553 or WBGene00022231 PW077 @@ -2523,8 +2523,8 @@ R_RCC0039 mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase (acting on nm3masn) R_RCC0040 beta-N-acetylglucosaminidase (acting on nm3masn) M_h2o_c + M_nm3masn_c <=> M_acgam_c + M_m3masn_c c FALSE WBGene00015767 or WBGene00012663 or WBGene00021766 or WBGene00013497 PW011 R_RCC0041 beta-N-acetylglucosaminidase (acting on nm2masn) M_h2o_c + M_nm2masn_c <=> M_acgam_c + M_m2masn_c c FALSE WBGene00015767 or WBGene00012663 or WBGene00021766 or WBGene00013497 PW011 R_RCC0042 beta-N-acetylglucosaminidase (acting on fnm2masn) M_h2o_c + M_fnm2masn_c <=> M_acgam_c + M_fm2masn_c c FALSE WBGene00015767 or WBGene00012663 or WBGene00021766 or WBGene00013497 PW011 -R_RCC0045 Debranching enzyme activity M_h2o_c + M_ldex_c <=> M_glc_bD_c + M_ggn_c c FALSE WBGene00011050 starch and sucrose metabolism; glycogen metabolism RHEA:55988 Changed name, replaced M_dxtrn2_c by M_ldex_c, replaced M_dxtrn3_c by M_ggn_c, fixed the stoichiometry, added group lenov -R_RCC0046 dextrin phosphorylase 8 M_pi_c + M_ggn_c <=> 8 M_g1p_c + M_HC02136_c c FALSE WBGene00020696 starch and sucrose metabolism; glycogen metabolism Replaced M_dxtrn3_c by M_ggn_c. Changed stoichiometry to produce 8 G1P. Added M_HC02136_c on the right, but coordinate with reaction R_GLYCOGENIN_GLUCOSYLTRANSFERASE_RXN_c, added group +R_RCC0045 Debranching enzyme activity M_h2o_c + M_ldex_c <=> M_glc_bD_c + M_ggn_c c FALSE WBGene00011050 starch and sucrose metabolism;glycogen metabolism RHEA:55988 Changed name, replaced M_dxtrn2_c by M_ldex_c, replaced M_dxtrn3_c by M_ggn_c, fixed the stoichiometry, added group lenov +R_RCC0046 dextrin phosphorylase 8 M_pi_c + M_ggn_c <=> 8 M_g1p_c + M_HC02136_c c FALSE WBGene00020696 starch and sucrose metabolism;glycogen metabolism Replaced M_dxtrn3_c by M_ggn_c. Changed stoichiometry to produce 8 G1P. Added M_HC02136_c on the right, but coordinate with reaction R_GLYCOGENIN_GLUCOSYLTRANSFERASE_RXN_c, added group R_RCC0050 D-bifunctional protein M_h2o_c + M_nad_c + M_cholcoads_c <=> M_h_c + M_nadh_c + M_cholcoaone_c c TRUE WBGene00000988 or WBGene00000991 or WBGene00017123 PW066 R_RCC0051 poly(ADP-ribose) glycohydrolase (PARG) M_h2o_c + M_polyadprib_c <=> M_adprib_c c FALSE WBGene00004051 or WBGene00004052 PW035 RHEA:52216;RHEA:52216 R_RCC0061 DELTA12-fatty-acid desaturase M_o2_c + M_coa18_1_9z_c + 2.0 M_focytb5_c <=> 2.0 M_h2o_c + 2.0 M_ficytb5_c + M_coa18_2_9z12z_c c FALSE WBGene00001394 PW061 @@ -2550,7 +2550,7 @@ R_RCC0102 fatty-acid--CoA ligase (fa17p0iso) M_atp_c + M_coa_c + M_fa16_0_15me R_RCC0127 fatty-acid--CoA ligase (Rtotal6) M_atp_c + M_coa_c + M_Rtotal6_c <=> M_ppi_c + M_amp_c + M_Rtotal6coa_c c FALSE WBGene00011174 or WBGene00009221 or WBGene00020343 or WBGene00018152 or WBGene00013575 or WBGene00022037 or WBGene00019920 or WBGene00016716 or WBGene00011173 PW057 R_RCC0129 fatty-acid--CoA ligase (Rtotal3) M_atp_c + M_coa_c + M_Rtotal3_c <=> M_ppi_c + M_amp_c + M_Rtotal3coa_c c FALSE WBGene00011174 or WBGene00009221 or WBGene00020343 or WBGene00018152 or WBGene00013575 or WBGene00022037 or WBGene00019920 or WBGene00016716 or WBGene00011173 PW057 R_RCC0130 fatty-acid--CoA ligase (vacc) M_atp_c + M_coa_c + M_vacc_c <=> M_ppi_c + M_amp_c + M_coa18_1_11z_c c FALSE WBGene00011174 or WBGene00009221 or WBGene00020343 or WBGene00018152 or WBGene00013575 or WBGene00022037 or WBGene00019920 or WBGene00016716 or WBGene00011173 PW057 -R_RCC0131 methylglyoxal synthase M_g3p_c <=> M_pi_c + M_mthgxl_c c FALSE Unknown PW022 +R_RCC0131 methylglyoxal synthase M_g3p_c <=> M_pi_c + M_mthgxl_c c FALSE Unknown PW022 SPW004 R_RCC0134 (S) 3-hydroxybutyryl-CoA hydrolase M_h2o_c + M_3hbcoa_c <=> M_h_c + M_coa_c + M_S3hb_c c FALSE WBGene00017301 PW046 RHEA:20888;RHEA:20888 R_RCC0136 synthesis of peptide with asparagine M_asn__L_c <=> M_Asn_X_Ser_Thr_c c FALSE PW011 R_RCC0139 GTP:alpha-D-glucose-1-phosphate guanylyltransferase M_g1p_c + M_h_c + M_gtp_c <=> M_ppi_c + M_gdpg_c c TRUE WBGene00016583 or WBGene00021628 PW025 RHEA:15229 @@ -2588,15 +2588,15 @@ 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 -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 +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_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 R_RM00138 inorganic triphosphatase (mitochondrial) M_h2o_m + M_pppi_m <=> M_pi_m + M_ppi_m + M_h_m m FALSE Unknown PW098 R_RM00161 ATP:FMN adenylyltransferase M_h_m + M_atp_m + M_fmn_m <=> M_ppi_m + M_fad_m m FALSE WBGene00011271 PW040 RHEA:17237;RHEA:17237 -R_RM00197 (R)-Lactate:ferricytochrome-c 2-oxidoreductase M_lac__D_m + 2.0 M_ficytC_m <=> 2.0 M_h_m + M_pyr_m + 2.0 M_focytC_m m FALSE WBGene00009334 PW022 -R_RM00199 ATP:pyruvate,water phosphotransferase M_h2o_m + M_atp_m + M_pyr_m <=> M_pep_m + M_pi_m + 2.0 M_h_m + M_amp_m m FALSE WBGene00011893 PW022 +R_RM00197 (R)-Lactate:ferricytochrome-c 2-oxidoreductase M_lac__D_m + 2.0 M_ficytC_m <=> 2.0 M_h_m + M_pyr_m + 2.0 M_focytC_m m FALSE WBGene00009334 PW022 SPW004 +R_RM00199 ATP:pyruvate,water phosphotransferase M_h2o_m + M_atp_m + M_pyr_m <=> M_pep_m + M_pi_m + 2.0 M_h_m + M_amp_m m FALSE WBGene00011893 PW022 SPW004 R_RM00243 L-glutamate:NAD+ oxidoreductase (deaminating) M_h2o_m + M_glu__L_m + M_nad_m <=> M_akg_m + M_h_m + M_nadh_m + M_nh4_m m TRUE WBGene00014095 PW073 R_RM00245 L-Glutamate 5-semialdehyde:NAD+ oxidoreductase M_h2o_m + M_glu5sa_m + M_nad_m <=> 2.0 M_h_m + M_glu__L_m + M_nadh_m m FALSE WBGene00000112 PW081 R_RM00248 L-Glutamate:NADP+ oxidoreductase (deaminating) M_h2o_m + M_glu__L_m + M_nadp_m <=> M_akg_m + M_h_m + M_nadph_m + M_nh4_m m TRUE WBGene00014095 PW073 @@ -2612,7 +2612,7 @@ R_RM00533 Sulfite:oxygen oxidoreductase M_h2o_c + M_so3_c + M_o2_m <=> M_h2o2_ R_RM00549 riboflavin kinase M_atp_m + M_ribflv_m <=> M_h_m + M_adp_m + M_fmn_m m FALSE WBGene00011224 PW040 R_RM00585 L-Serine:pyruvate aminotransferase M_ser__L_m + M_pyr_m <=> M_hpyr_m + M_ala__L_m m TRUE WBGene00011767 PW074 RHEA:22852;RHEA:24248 R_RM00708 (S)-1-pyrroline-5-carboxylate:NADP+ oxidoreductase 2.0 M_h2o_m + M_1pyr5c_m + M_nadp_m <=> M_h_m + M_glu__L_m + M_nadph_m m FALSE WBGene00000112 PW073 -R_RM00711 Acetaldehyde:NADP+ oxidoreductase M_h2o_m + M_nadp_m + M_acald_m <=> 2.0 M_h_m + M_nadph_m + M_ac_m m FALSE WBGene00000111 PW018 +R_RM00711 Acetaldehyde:NADP+ oxidoreductase M_h2o_m + M_nadp_m + M_acald_m <=> 2.0 M_h_m + M_nadph_m + M_ac_m m FALSE WBGene00000111 PW018 SPW004 R_RM00716 N6-(L-1,3-Dicarboxypropyl)-L-lysine:NADP+ oxidoreductase (L-lysine-forming) M_akg_m + M_h_m + M_lys__L_m + M_nadph_m <=> M_h2o_m + M_nadp_m + M_saccrp__L_m m TRUE WBGene00019819 PW080 [DELETION] Uncharge balanced version of R_SACCD3_m jpnh R_RM00781 sulfur dioxygenase M_h2o_m + M_o2_m + M_s_m <=> M_so3_m + 2.0 M_h_m m FALSE WBGene00007886 PW096 R_RM00842 sn-Glycerol-3-phosphate:NAD+ 2-oxidoreductase M_dhap_m + M_h_m + M_nadh_m <=> M_glyc3p_m + M_nad_m m TRUE WBGene00010778 PW056 RHEA:11092;RHEA:11092;RHEA:11092;RHEA:11092 @@ -2627,14 +2627,14 @@ R_RM01393 hydroxypyruvate decarboxylase M_hpyr_m + M_h_m <=> M_co2_m + M_gcald_ R_RM01465 L-Threonine:NAD+ oxidoreductase M_thr__L_m + M_nad_m <=> M_2aobut_m + M_h_m + M_nadh_m m TRUE WBGene00017262 PW074 R01465 8407827 [DELETION] Merge into R_THRD_m, as this version is stoichiometrically unbalanced. R_THRD_m is the same reaction, but with 2+ involved. jpnh 1.1.1.103 R_RM01492 ATP:cob(I)alamin Co-beta-adenosyltransferase M_h_m + M_atp_m + M_cbl1_m <=> M_adocbl_m + M_pppi_m m TRUE WBGene00016144 or WBGene00013577 PW006 R_RM01608 3-hydroxypropionate dehydrogenase M_3hpp_m + M_nad_m <=> M_msa_m + M_h_m + M_nadh_m m TRUE Unknown PW086 -R_RM01736 (R)-S-Lactoylglutathione hydrolase M_h2o_m + M_lgt_S_m <=> M_h_m + M_lac__D_m + M_gthrd_m m FALSE WBGene00012459 PW022 +R_RM01736 (R)-S-Lactoylglutathione hydrolase M_h2o_m + M_lgt_S_m <=> M_h_m + M_lac__D_m + M_gthrd_m m FALSE WBGene00012459 PW022 SPW004 R_RM01868 (S)-dihydroorotate:qui oxidoreductase M_dhor_S_c + M_q_m <=> M_orot_c + M_qh2_m cm FALSE WBGene00020932 PW043 RHEA:30187 R_RM01875 Thiosulfate:thiol sulfurtransferase M_gthox_m + M_so3_m + M_h2s_m <=> M_tsul_m + 2.0 M_gthrd_m m TRUE Unknown PW096 R_RM02016 NADPH:oxidized-thioredoxin oxidoreductase M_h_m + M_nadph_m + M_trdox_m <=> M_nadp_m + M_trdrd_m m FALSE WBGene00015553 or (WBGene00014028) PW043 RHEA:20345;RHEA:11740 R_RM02050 (R)-3-Amino-2-methylpropanoate:pyruvate aminotransferase M_pyr_m + M_3aib__D_m <=> M_2mop_m + M_ala__L_m m TRUE WBGene00020382 PW043 R_RM02055 Phsophatidyl-L-serine carboxy-lyase M_h_m + M_1ac2acg3ps_m <=> M_co2_m + M_1ac2acg3pe_m m FALSE WBGene00015159 PW056 RHEA:20828 [DELETION] Replaced by R_PEPCPSBIOSYNTH0005 R_RM02161 Ubiquinol:ferricytochrome-c oxidoreductase 2.0 M_h_m + 2.0 M_ficytC_m + M_qh2_m <=> 4.0 M_h_c + 2.0 M_focytC_m + M_q_m m TRUE WBGene00002162 and WBGene00000829 and WBGene00000869 and (WBGene00020757 or WBGene00012158 or WBGene00011679) and WBGene00012094 and WBGene00020181 and (WBGene00009739 or WBGene00019937) and WBGene00019007 PW007 RHEA:11484 -R_RM02164 Succinate:ubiqui oxidoreductase M_succ_m + M_q_m <=> M_fum_m + M_qh2_m m FALSE ((WBGene00015391 or WBGene00016392) and WBGene00006433) and WBGene00003225 and WBGene00009353 PW023 RHEA:40523;RHEA:40523;RHEA:40523 +R_RM02164 Succinate:ubiqui oxidoreductase M_succ_m + M_q_m <=> M_fum_m + M_qh2_m m FALSE ((WBGene00015391 or WBGene00016392) and WBGene00006433) and WBGene00003225 and WBGene00009353 PW023 SPW004 RHEA:40523;RHEA:40523;RHEA:40523 R_RM02300 S-Aminomethyldihydrolipoylprotein:(6S)-tetrahydrofolate aminomethyltransferase (ammonia-forming) M_h2o_m + M_methf_m <=> M_h_m + M_5fthf_m m TRUE WBGene00017765 PW095 RHEA:16945 R_RM02301 5-Formyltetrahydrofolate cyclo-ligase (ADP-forming) M_atp_m + M_5fthf_m <=> M_pi_m + M_adp_m + M_methf_m m FALSE WBGene00013708 PW095 R_RM02313 N6-(L-1,3-Dicarboxypropyl)-L-lysine:NAD+ oxidoreductase M_h2o_m + M_nad_m + M_saccrp__L_m <=> M_L2aadp6sa_m + M_h_m + M_glu__L_m + M_nadh_m m TRUE WBGene00019819 PW080 [DELETION] Uncharge balanced version of R_1_5_1_9_RXN_m jpnh @@ -2642,7 +2642,7 @@ R_RM02433 L-cysteate:2-oxoglutarate aminotransferase M_akg_m + M_Lcyst_m <=> M_ R_RM02480 Cytochrome c apocytochrome-c-lyase M_pheme_m + M_apocytc_m <=> M_focytC_m m TRUE WBGene00011527 PW005 RHEA:22648 R_RM02488 Glutaryl-CoA:(acceptor) 2,3-oxidoreductase (decarboxylating) M_h_m + M_glutcoa_m + M_etfox_m <=> M_co2_m + M_b2coa_m + M_etfrd_m m FALSE WBGene00010052 PW057 R_RM02529 aminoacetone:oxygen oxidoreductase(deaminating) M_h2o_m + M_o2_m + M_aact_m <=> M_h2o2_m + M_mthgxl_m + M_nh4_m m FALSE WBGene00000138 PW074 -R_RM02530 glyoxalase-1 M_gthrd_m + M_mthgxl_m <=> M_lgt_S_m m TRUE WBGene00006448 PW022 +R_RM02530 glyoxalase-1 M_gthrd_m + M_mthgxl_m <=> M_lgt_S_m m TRUE WBGene00006448 PW022 SPW004 R_RM02565 p-Cumic alcohol:NADP+ oxidoreductase M_betald_m + M_h2o_m + M_nad_m <=> 2.0 M_h_m + M_nadh_m + M_glyb_m m FALSE WBGene00000115 PW074 RHEA:16185 R_RM02566 p-Cumic alcohol:NADP+ oxidoreductase M_betald_m + M_h2o_m + M_nadp_m <=> 2.0 M_h_m + M_nadph_m + M_glyb_m m FALSE WBGene00000115 PW074 RHEA:16185 R_RM02661 2-methylpropanoyl-CoA:(acceptor) 2,3-oxidoreductase M_ibcoa_m + M_etfox_m <=> M_2mp2coa_m + M_etfrd_m m TRUE (WBGene00016943 or WBGene00015894 or WBGene00019433) or WBGene00017874 PW083 @@ -2720,7 +2720,7 @@ R_RM08774 Ubiqui biosynthesis methyltransferase COQ5 M_amet_m + M_2np6mobq_m <= R_RM08775 Ubiqui biosynthesis COQ7 M_h_m + M_nadph_m + M_o2_m + M_me2np6mobq_m <=> M_h2o_m + M_nadp_m + M_2npmhobq_m m FALSE WBGene00000536 PW004 R_RM08781 methyltransferase COQ3 M_amet_m + M_2npmhobq_m <=> M_h_m + M_ahcys_m + M_q9_m m FALSE WBGene00000763 PW004 RHEA:44452;RHEA:44380 R_RM10151 Thiosulfate oxidation (cytochrome c reducing) 5.0 M_h2o_m + M_tsul_m + 8.0 M_ficytC_m <=> 2.0 M_so4_m + 10.0 M_h_m + 8.0 M_focytC_m m FALSE WBGene00017121 or WBGene00013854 PW096 -R_RMC0001 isocitrate hydro-lyase (cis-aconitate-forming) M_cit_m <=> M_icit_m m TRUE WBGene00000041 PW023 RHEA:10336 +R_RMC0001 isocitrate hydro-lyase (cis-aconitate-forming) M_cit_m <=> M_icit_m m TRUE WBGene00000041 PW023 SPW004 RHEA:10336 R_RMC0004 ATP phosphohydrolase M_pi_m + 4.0 M_h_i + M_adp_m <=> M_h2o_m + 3.0 M_h_m + M_atp_m m FALSE ((WBGene00010419 or WBGene00012040) and WBGene00000229 and WBGene00022089 and WBGene00019061 and (WBGene00017982 or WBGene00019880 or WBGene00022582) and WBGene00000230 and WBGene00010960 and (WBGene00000207 or WBGene00000206) and WBGene00022336 and WBGene00007385 and WBGene00011015 and WBGene00011273 and (WBGene00000210 or WBGene00000209)) and (WBGene00013025 and (WBGene00006921 or WBGene00004959) and WBGene00006920 and WBGene00010130 and WBGene00006917 and WBGene00006918 and WBGene00006919 and (WBGene00018698 or WBGene00020507) and (WBGene00006916 or WBGene00006914 or WBGene00006915 or WBGene00006768) and (WBGene00006911 or WBGene00006910 or WBGene00006913 or WBGene00006912) and WBGene00009882 and WBGene00021952) PW007 RHEA:57720;RHEA:57720 R_RMC0005 ATP phosphohydrolase M_pi_m + 3.0 M_h_i + M_adp_m <=> M_h2o_m + 2.0 M_h_m + M_atp_m m FALSE ((WBGene00010419 or WBGene00012040) and WBGene00000229 and WBGene00022089 and WBGene00019061 and (WBGene00017982 or WBGene00019880 or WBGene00022582) and WBGene00000230 and WBGene00010960 and (WBGene00000207 or WBGene00000206) and WBGene00022336 and WBGene00007385 and WBGene00011015 and WBGene00011273 and (WBGene00000210 or WBGene00000209)) and (WBGene00013025 and (WBGene00006921 or WBGene00004959) and WBGene00006920 and WBGene00010130 and WBGene00006917 and WBGene00006918 and WBGene00006919 and (WBGene00018698 or WBGene00020507) and (WBGene00006916 or WBGene00006914 or WBGene00006915 or WBGene00006768) and (WBGene00006911 or WBGene00006910 or WBGene00006913 or WBGene00006912) and WBGene00009882 and WBGene00021952) PW007 RHEA:57720;RHEA:57720 R_RMC0006 NADH:ubiqui oxidoreductase 5.0 M_h_m + M_nadh_m + M_q_m <=> 4.0 M_h_c + M_nad_m + M_qh2_m m FALSE (WBGene00010959 and WBGene00010961 and WBGene00010966 and WBGene00010963 and WBGene00010967 and WBGene00010957 and WBGene00010958) and (WBGene00009992 and (WBGene00001520 or WBGene00006463) and WBGene00020417 and WBGene00003831 and WBGene00021562 and WBGene00012376 and WBGene00020636 and WBGene00003061 and WBGene00021839 and WBGene00009051) and (WBGene00009294 and WBGene00013406 and WBGene00007880 and WBGene00013308 and WBGene00009740 and WBGene00021849 and WBGene00021800 and WBGene00019401 and (WBGene00018151 or WBGene00013237) and WBGene00016393) and (WBGene00009712 and WBGene00007684 and WBGene00012166 and WBGene00016118 and WBGene00014086 and WBGene00008414 and WBGene00013094 and WBGene00015810 and WBGene00010326 and WBGene00022169 and WBGene00018361) 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 @@ -2743,7 +2743,7 @@ R_RMC0133 branched-chain 2-oxo acid dehydrogenase M_coa_m + M_nad_m + M_2obut_ R_RMC0154 Propionyl-CoA:carnitine O-propionyltransferase II M_coa_m + M_pcrn_m <=> M_crn_m + M_ppcoa_m m FALSE WBGene00011122 PW010 R_RMC0155 electron transfer flavoprotein M_fadh2_m + M_etfox_m <=> M_fad_m + M_etfrd_m m FALSE PW098 R_RMC0182 rhodoqui-9 biosynthesis M_h2o_m + M_q9_m + 3.0 M_nad_m + M_nh4_m <=> M_co2_m + 4.0 M_h_m + 3.0 M_nadh_m + M_rq9_m m FALSE Unknown PW004 -R_RMC0183 fumarate reductase M_fum_m + M_rq9h2_m <=> M_succ_m + M_rq9_m m FALSE WBGene00018610 PW023 +R_RMC0183 fumarate reductase M_fum_m + M_rq9h2_m <=> M_succ_m + M_rq9_m m FALSE WBGene00018610 PW023 SPW004 R_RMC0184 NADH:rhodoqui oxidoreductase 5.0 M_h_m + M_nadh_m + M_rq9_m <=> 4.0 M_h_c + M_nad_m + M_rq9h2_m m FALSE (WBGene00010959 and WBGene00010961 and WBGene00010966 and WBGene00010963 and WBGene00010967 and WBGene00010957 and WBGene00010958) and (WBGene00009992 and (WBGene00001520 or WBGene00006463) and WBGene00020417 and WBGene00003831 and WBGene00021562 and WBGene00012376 and WBGene00020636 and WBGene00003061 and WBGene00021839 and WBGene00009051) and (WBGene00009294 and WBGene00013406 and WBGene00007880 and WBGene00013308 and WBGene00009740 and WBGene00021849 and WBGene00021800 and WBGene00019401 and (WBGene00018151 or WBGene00013237) and WBGene00016393) and (WBGene00009712 and WBGene00007684 and WBGene00012166 and WBGene00016118 and WBGene00014086 and WBGene00008414 and WBGene00013094 and WBGene00015810 and WBGene00010326 and WBGene00022169 and WBGene00018361) 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 FALSE R_rnasynth_m RNA polymerisation in mitochondria 0.406 M_h2o_m + 0.406 M_atp_m + 0.381 M_datp_m + 0.119 M_gtp_m + 0.381 M_utp_m + 0.119 M_ctp_m <=> 0.406 M_pi_m + M_ppi_m + 0.406 M_h_m + 0.406 M_adp_m + 0.381 M_adnr_m + 0.119 M_guar_m + 0.381 M_urir_m + 0.119 M_cytr_m m FALSE ((WBGene00009658 or WBGene00011791 or WBGene00012528) and WBGene00001596 and WBGene00014115) and (WBGene00012999 and WBGene00008781 and WBGene00000123 and WBGene00016140 and WBGene00004411 and WBGene00017300 and WBGene00013680) PW044 RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:11332;RHEA:11332 replace the generic production of DNA to represent each nucleotide residue lenov R_rnasynth_n RNA polymerisation in nucleus 0.406 M_h2o_n + 0.731 M_atp_n + 0.175 M_gtp_n + 0.325 M_utp_n + 0.175 M_ctp_n <=> 0.406 M_pi_n + M_ppi_n + 0.406 M_h_n + 0.406 M_adp_n + 0.325 M_adnr_n + 0.175 M_guar_n + 0.325 M_urir_n + 0.175 M_cytr_n n FALSE ((WBGene00009658 or WBGene00011791 or WBGene00012528) and WBGene00001596 and WBGene00014115) and (WBGene00012999 and WBGene00008781 and WBGene00000123 and WBGene00016140 and WBGene00004411 and WBGene00017300 and WBGene00013680) PW044 RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:21248;RHEA:11332;RHEA:11332 replace the generic production of DNA to represent each nucleotide residue lenov @@ -2759,9 +2759,9 @@ R_RNTR1_c R_RNTR1_c M_atp_c + M_etfrd_c <=> M_h2o_c + M_datp_c + M_etfox_c c FA R_RNTR2_c R_RNTR2_c M_gtp_c + M_etfrd_c <=> M_h2o_c + M_dgtp_c + M_etfox_c c FALSE PW042 R_RNTR3_c R_RNTR3_c M_ctp_c + M_etfrd_c <=> M_h2o_c + M_dctp_c + M_etfox_c c FALSE PW043 R_RNTR4_c R_RNTR4_c M_utp_c + M_etfrd_c <=> M_h2o_c + M_dutp_c + M_etfox_c c FALSE PW043 -R_RPE_c ribulose phosphate 3-epimerase M_ru5p_D_c <=> M_xu5p_D_c c TRUE (WBGene00017272) PW027 -R_RPI_c Ribose 5-phosphate epimerase M_r5p_c <=> M_ru5p_D_c c TRUE (WBGene00015101) PW027 RHEA:14657 -R_RPI_m Ribose 5-phosphate epimerase M_r5p_m <=> M_ru5p_D_m m TRUE (WBGene00015101) PW027 RHEA:14657 +R_RPE_c ribulose phosphate 3-epimerase M_ru5p_D_c <=> M_xu5p_D_c c TRUE (WBGene00017272) PW027 SPW004 +R_RPI_c Ribose 5-phosphate epimerase M_r5p_c <=> M_ru5p_D_c c TRUE (WBGene00015101) PW027 SPW004 RHEA:14657 +R_RPI_m Ribose 5-phosphate epimerase M_r5p_m <=> M_ru5p_D_m m TRUE (WBGene00015101) PW027 SPW004 RHEA:14657 R_Rthioredtn Red Thioredoxin nuclear transport (diffusion) M_trdrd_c <=> M_trdrd_n cn TRUE PW108 R_RXN_10841_c NADP-retinol dehydrogenase M_nadp_c + M_retinol_c <=> M_h_c + M_nadph_c + M_retinal_c c TRUE (WBGene00000967) or (WBGene00000982) or (WBGene00000976) or (WBGene00007780) or (WBGene00010063) PW069 RHEA:19257;RHEA:10736;RHEA:10740 R_RXN_10938_c R_RXN_10938_c M_h2o_c + M_1ac2acg3pi3p5p_c <=> M_pi_c + 2.0 M_h_c + M_1ac2acg3pi3p_c c FALSE PW029 @@ -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 -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 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 +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_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 @@ -2832,12 +2832,11 @@ R_RXN_7592_c Formylisoglutamine degradation to Isoglutamine M_for_isogln_c + M_ R_RXN_7593_c Non enzymatic Isoglutamine degradation to 4-Oxoglutaramate M_4izp_c + M_h2o_c + 2.0 M_h_c + M_o2_c <=> M_nh3_c + M_4ogm_c + M_for_c c FALSE PW084 R_RXN_7594_c non-enzymatic hydrolysis of Oxoglutamarate M_h2o_c + M_4ogm_c <=> M_akg_c + M_nh3_c + M_h_c c TRUE PW084 R_RXN_7605_c 5-Methyltetrahydrofolate:Adenosyl-L-homocysteine S-methyltransferase M_amet_c + M_thf_c <=> M_h_c + M_ahcys_c + M_5mthf_c c TRUE PW082 -R_RXN_7667_c glucosyl-glycogenin self-glycosylation 7 M_udpg_c + M_glucosyl_glycogenin_c <=> M_ggn_c + 7 M_udp_c c FALSE (WBGene00006863) or (WBGene00012020) starch and sucrose metabolism; glycogen metabolism RHEA:23360;RHEA:56560 Changed the stoichiometry of UDP-glucose from 1 to 8, update name, added group. lenov +R_RXN_7667_c glucosyl-glycogenin self-glycosylation 7 M_udpg_c + M_glucosyl_glycogenin_c <=> M_ggn_c + 7 M_udp_c c FALSE (WBGene00006863) or (WBGene00012020) starch and sucrose metabolism;glycogen metabolism RHEA:23360;RHEA:56560 Changed the stoichiometry of UDP-glucose from 1 to 8, update name, added group. lenov R_RXN_7719_m dihydrolipoyl-dehydrogenase M_nad_m + M_bcaadh_m <=> M_h_m + M_nadh_m + M_bcaalip_m m FALSE (WBGene00010794) PW083 RHEA:15045 updated !Name to be more descriptive (was just !Reaction copied) hjs -R_RXN_7904_c long-chain-fatty-acid—CoA ligase M_atp_c + M_coa_c + M_fatacid_c <=> M_ppi_c + M_amp_c + M_fataccoa_c c FALSE Fatty Acid beta-Oxidation (cytosol) [DELETION] Merge into R_ACYLCOASYN_RXN_c jpnh R_RXN_7908_c 4a-hydroxytetrahydrobiopterin dehydratase M_thbpt4acam_c <=> M_h2o_c + M_dhbpt_c c FALSE (WBGene00020397) PW091 RHEA:11920 added rxn name jpnh R_RXN_7908_m 4a-hydroxytetrahydrobiopterin dehydratase M_thbpt4acam_m <=> M_h2o_m + M_dhbpt_m m FALSE (WBGene00020397) PW091 RHEA:11920 added rxn name jpnh -R_RXN_7909_c 5,6,7,8-tetrahydrobiopterin:NAD+ oxidoreductase M_h_c + M_dhbpt_c + M_nadh_c <=> M_thbpt_c + M_nad_c c TRUE (WBGene00011398) folate biosynthesis; alanine, aspartate and glutamate metabolism added rxn name jpnh +R_RXN_7909_c 5,6,7,8-tetrahydrobiopterin:NAD+ oxidoreductase M_h_c + M_dhbpt_c + M_nadh_c <=> M_thbpt_c + M_nad_c c TRUE (WBGene00011398) folate biosynthesis;alanine, aspartate and glutamate metabolism added rxn name jpnh R_RXN_8162_c R_RXN_8162_c 2.0 M_h2o_c + M_nad_c + M_thp2c_c <=> M_h_c + M_nadh_c + M_L2aadp_c c TRUE (WBGene00000115) PW079 RHEA:16185 R_RXN_8162_m R_RXN_8162_m 2.0 M_h2o_m + M_thp2c_m + M_nad_m <=> M_L2aadp_m + M_h_m + M_nadh_m m TRUE (WBGene00000115) PW079 RHEA:16185 R_RXN_821_c Proline dehydrogenase M_pro__L_c + M_fad_c <=> M_1pyr5c_c + M_fadh2_c c FALSE (WBGene00007197) PW081 @@ -2868,14 +2867,14 @@ R_RXN_969_c R_RXN_969_c M_glyclt_c + M_o2_c <=> M_h2o2_c + M_glx_c c FALSE (WBG R_RXN_969_n R_RXN_969_n M_glyclt_n + M_o2_n <=> M_h2o2_n + M_glx_n n FALSE (WBGene00018286) PW030 R_RXN_9779_c phosphatidylinositol-4,5-bisphosphate 4-phosphatase M_h2o_c + M_1ac2acg3pi4p5p_c <=> M_pi_c + M_1ac2acg3pi5p_c c FALSE WBGene00022167 PW029 R_RXN_982_c arsenate reductase (glutaredoxin) M_aso4_c + M_grxrd_c <=> M_h2o_c + M_aso3_c + M_grxox_c c FALSE PW070 replaced arsenate detoxification by glutathione metabolism lenov -R_RXN_9927_2 Glycerol-3-phosphate dehydrogenase M_glyc3p_c + M_q9_m <=> M_dhap_c + M_q9h2_m cm FALSE (WBGene00013049) or (WBGene00009824) or (WBGene00012031) glycerolipid metabolism; glycerophospholipid metabolism RHEA:11092 +R_RXN_9927_2 Glycerol-3-phosphate dehydrogenase M_glyc3p_c + M_q9_m <=> M_dhap_c + M_q9h2_m cm FALSE (WBGene00013049) or (WBGene00009824) or (WBGene00012031) glycerolipid metabolism;glycerophospholipid metabolism RHEA:11092 R_RXN_9969_c di-trans,poly-cis-polyprenyl diphosphate synthase[(2E,6E)-farnesyl diphosphate specific] 13.0 M_ipdp_c + M_frdp_c <=> 13.0 M_ppi_c + M_dtpcpprd_c c TRUE (WBGene00044025) PW001 R06447 added KEGGID, ChEBI ms R_RXN_9969_n di-trans,poly-cis-polyprenyl diphosphate synthase[(2E,6E)-farnesyl diphosphate specific] 13.0 M_ipdp_n + M_frdp_n <=> 13.0 M_ppi_n + M_dtpcpprd_n n TRUE (WBGene00044025) PW001 R06447 added KEGGID, ChEBI ms R_RXN_9970_c R_RXN_9970_c M_h2o_c + M_dtpcpprd_c <=> M_dtpcppr_c + M_ppi_c c FALSE PW001 R_RXN_9971_c R_RXN_9971_c M_dtpcppr_c + M_h_c + M_nadph_c <=> M_nadp_c + M_dolichol_c c FALSE PW001 R_RXN0_2161_m L-Seryl-tRNA(Sec) formation M_ser__L_m + M_atp_m + M_trnasec_m <=> M_ppi_m + M_amp_m + M_sertrna_sec_m m FALSE WBGene00005663 or WBGene00005662 PW082 RHEA:12292;RHEA:42580 added name; replaced M_SEC__tRNAs_m by M_trnasec_m and M_sertrna_LPAREN_sec_RPAREN__m by M_sertrna_sec_m; fixed gene assication jpnh; lenov R_RXN0_276_c S-(hydroxymethyl)glutathione dehydrogenase M_nad_c + M_hmgth_c <=> M_Sfglutth_c + M_h_c + M_nadh_c c TRUE WBGene00019240 or WBGene00021747 PW091 set to reversible janna -R_RXN0_308_c cysteine desulfurase M_cys__L_c + M_cysdesase_c <=> M_ala__L_c + M_prot_scyst_c c FALSE (WBGene00015021) molybdenum cofactor biosynthesis; alanine, aspartate and glutamate metabolism replaced M_ala__L_c with M_ala_L_c lenov +R_RXN0_308_c cysteine desulfurase M_cys__L_c + M_cysdesase_c <=> M_ala__L_c + M_prot_scyst_c c FALSE (WBGene00015021) molybdenum cofactor biosynthesis;alanine, aspartate and glutamate metabolism replaced M_ala__L_c with M_ala_L_c lenov R_RXN0_5114_m O-phospho-L-serine phosphohydrolase M_h2o_m + M_pser_L_m <=> M_pi_m + M_ser__L_m m TRUE (WBGene00013379) PW074 added name to rxn; replaced M_pser__L_m with M_pser_L_m jpnh; lenov R_RXN0_5224_c Bicarbonate formation (cytosol) M_co2_c + M_h2o_c <=> M_hco3_c + M_h_c c TRUE (WBGene00000282) or (WBGene00000281) or (WBGene00077690) or (WBGene00000284) or (WBGene00000245) or (WBGene00000279) or (WBGene00000280) or (WBGene00000283) or (WBGene00013805) PW098 RHEA:10748;RHEA:10748;RHEA:10748;RHEA:10748;RHEA:10748;RHEA:10748;RHEA:10748 Updated rxn name jpnh R_RXN0_5224_m Bicarbonate formation (mitochondrial) M_co2_m + M_h2o_m <=> M_hco3_m + M_h_m m TRUE WBGene00000245 or WBGene00000282 PW098 RHEA:10748 Updated rxn name jpnh @@ -2915,9 +2914,6 @@ R_RXN66_28_c R_RXN66_28_c M_h_c + M_nadph_c + M_dsmsterol_c <=> M_nadp_c + M_c R_RXN66_281_c squalene synthase M_psqldp_c + M_h_c + M_nadph_c <=> M_sql_c + M_ppi_c + M_nadp_c c FALSE PW002 R_RXN66_321_c R_RXN66_321_c M_h_c + M_nadph_c + M_chlstol_c <=> M_lthstrl_c + M_nadp_c c FALSE (WBGene00018718) PW047 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_101_m (S)-hydroxyhexanoyl-CoA:NAD+ oxidoreductase M_nad_m + M_coa6_0_3oh__S_m <=> M_h_m + M_nadh_m + M_coa6_0_3o_m m TRUE (WBGene00007129 or WBGene00010035 or WBGene00001157 or WBGene00001158 or WBGene00019978) or (WBGene00020347 or WBGene00001150) Fatty Acid beta-Oxidation (mitochondria) [DELETION] Merge into R_RXN909_100_m jpnh -R_RXN909_102_c butanoyl-CoA:acetyl-CoA C-butanoyltransferase M_accoa_c + M_btcoa_c <=> M_coa_c + M_coa6_0_3o_c c TRUE (WBGene00009952) fatty acid biosynthesis; fatty acid oxidation [DELETION] Merge into R_RXN909_103_c; which is same reaction with better gene annotation jpnh -R_RXN909_102_m butanoyl-CoA:acetyl-CoA C-butanoyltransferase M_accoa_m + M_btcoa_m <=> M_coa_m + M_coa6_0_3o_m m TRUE (WBGene00015125 or WBGene00009952) or (WBGene00020164 or WBGene00020166 or WBGene00002183) fatty acid biosynthesis; fatty acid oxidation [DELETION] Dupe of R_RXN909_103_m jpnh 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 @@ -2929,21 +2925,21 @@ 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) Acyl-CoA Synthetase (ER) 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) Fatty Acid beta-Oxidation (mitochondria) -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) Acyl-CoA Synthetase (ER) 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) Acyl-CoA Synthetase (ER) 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) Acyl-CoA Synthetase (ER) 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) Acyl-CoA Synthetase (ER) 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) Acyl-CoA Synthetase (ER) 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_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_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 R_RXN909_135_c R_RXN909_135_c M_lys__L_c + M_peptide_c <=> M_peplys_c c FALSE PW099 R_RXN909_136_c dopamine beta-hydroxylase M_tym_c + M_h_c + M_o2_c + M_ascb__L_c <=> M_dhdascb_c + M_h2o_c + M_octpam_c c FALSE (WBGene00006541) PW077 replaced M_ascb__L_c with M_ascb__L_c; replaced octopamine biosynthesis by tyrosine metabolism lenov R_RXN909_137_c peroxiredoxin M_h2o2_c + M_trdrd_c <=> 2.0 M_h2o_c + M_trdox_c c FALSE (WBGene00011110) or (WBGene00006434) PW093 RHEA:10008 -R_RXN909_139_c stearoyl-CoA synthase M_atp_c + M_coa_c + M_fa18_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa18_0_c c FALSE (WBGene00018579) or (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) Acyl-CoA Synthetase (ER) SPW001 -R_RXN909_139_m stearoyl-CoA synthase M_atp_m + M_coa_m + M_fa18_0_m <=> M_ppi_m + M_h_m + M_amp_m + M_coa18_0_m m FALSE (WBGene00009221) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) Fatty Acid beta-Oxidation (mitochondria) wimi +R_RXN909_139_c stearoyl-CoA synthase M_atp_c + M_coa_c + M_fa18_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa18_0_c c FALSE (WBGene00018579) or (WBGene00016716) or (WBGene00009221) or (WBGene00018579) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) or (WBGene00020343) or (WBGene00022037) or (WBGene00008669) PW136 SPW001 +R_RXN909_139_m stearoyl-CoA synthase M_atp_m + M_coa_m + M_fa18_0_m <=> M_ppi_m + M_h_m + M_amp_m + M_coa18_0_m m FALSE (WBGene00009221) or (WBGene00019920) or (WBGene00011173) or (WBGene00011174) PW120 wimi R_RXN909_15_c (2S,3S)-3-hydroxy-2-methylbutanoyl-CoA:NAD+ oxidoreductase M_nad_c + M_3hmbcoa_c <=> M_h_c + M_nadh_c + M_2maacoa_c c TRUE (WBGene00019978) or (WBGene00010035) or (WBGene00001158) or (WBGene00001157) or (WBGene00007129) or (WBGene00000181) PW083 R_RXN909_15_m (2S,3S)-3-hydroxy-2-methylbutanoyl-CoA:NAD+ oxidoreductase M_nad_m + M_3hmbcoa_m <=> M_h_m + M_nadh_m + M_2maacoa_m m TRUE WBGene00000181 or (WBGene00007129 or WBGene00010035 or WBGene00001157 or WBGene00001158 or WBGene00019978) PW083 R_RXN909_150_c R_RXN909_150_c M_em2emgacpail_c + M_dolmanp_c <=> M_mem2emgacpail_c + M_h_c + M_dolp_c c FALSE PW028 @@ -2956,13 +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) Acyl-CoA Synthetase (ER) 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) Acyl-CoA Synthetase (ER) SPW001 +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_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) Acyl-CoA Synthetase (ER) 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) Acyl-CoA Synthetase (ER) 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_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_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 @@ -3037,18 +3033,18 @@ R_RXN909_248_c R_RXN909_248_c M_damp_c + M_atp_c <=> M_h_c + M_dadp_c + M_adp_c 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_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) purine metabolism; pyrimidine metabolism -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) purine metabolism; pyrimidine metabolism +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_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) purine metabolism; pyrimidine metabolism -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) purine metabolism; pyrimidine metabolism +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_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) purine metabolism; pyrimidine metabolism -R_RXN909_256_n R_RXN909_256_n M_dgtp_n + M_cmp_n <=> M_dgdp_n + M_cdp_n n TRUE (WBGene00007812) purine metabolism; pyrimidine metabolism +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 +R_RXN909_256_n R_RXN909_256_n M_dgtp_n + M_cmp_n <=> M_dgdp_n + M_cdp_n n TRUE (WBGene00007812) PW042;PW043 R_RXN909_259_c R_RXN909_259_c M_atp_c + M_thm_c <=> M_thmpp_c + M_amp_c c FALSE (WBGene00014027) PW041 RHEA:11576 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 @@ -3082,7 +3078,7 @@ R_RXN909_290_c R_RXN909_290_c M_MGn_c + M_gdpfuc_c <=> M_MGnF6_c + M_h_c + M_gd R_RXN909_290_m R_RXN909_290_m M_MGn_m + M_gdpfuc_m <=> M_MGnF6_m + M_h_m + M_gdp_m m FALSE (WBGene00001508) PW112 RHEA:12985 R_RXN909_291_c R_RXN909_291_c M_man5_c + M_uacgam_c <=> M_man5Gn_c + M_h_c + M_udp_c c FALSE (WBGene00001639) or (WBGene00001637) or (WBGene00001638) PW011 RHEA:11456 R_RXN909_291_n R_RXN909_291_n M_man5_n + M_uacgam_n <=> M_man5Gn_n + M_h_n + M_udp_n n FALSE (WBGene00001639) PW011 -R_RXN909_292_c R_RXN909_292_c 2.0 M_h2o_c + M_man5Gn_c <=> M_MGn_c + 2.0 M_man_c c FALSE (WBGene00010284) n-glycan biosynthesis; core modifications of n-glycans +R_RXN909_292_c R_RXN909_292_c 2.0 M_h2o_c + M_man5Gn_c <=> M_MGn_c + 2.0 M_man_c c FALSE (WBGene00010284) n-glycan biosynthesis;core modifications of n-glycans R_RXN909_294_c R_RXN909_294_c M_h2o_c + M_MGnF6_c <=> M_acgam_c + M_MMF6_c c FALSE (WBGene00015767) PW112 R_RXN909_294_m R_RXN909_294_m M_h2o_m + M_MGnF6_m <=> M_acgam_m + M_MMF6_m m FALSE (WBGene00015767) PW112 R_RXN909_295_c R_RXN909_295_c M_MMF6_c + M_gdpfuc_c <=> M_mmf3f6_c + M_h_c + M_gdp_c c FALSE (WBGene00001505) PW112 RHEA:24444 @@ -3168,35 +3164,27 @@ R_RXN909_56_c R_RXN909_56_c M_2hyoxplac_c + M_h_c + M_nadh_c + M_o2_c <=> M_h R_RXN909_57_c L-Phenylalanine:2-oxoglutarate aminotransferase M_akg_c + M_phe__L_c <=> M_glu__L_c + M_phpyr_c c TRUE (WBGene00020146) or (WBGene00020145) or (WBGene00015778) or (WBGene00015771) or (WBGene00009628) PW076 rn:R00694 RHEA:21824;RHEA:21824 Added Genes from deprecated R_PHEAMINOTRANS_DEG_RXN_c jpnh R_RXN909_57_m L-Phenylalanine:2-oxoglutarate aminotransferase M_akg_m + M_phe__L_m <=> M_glu__L_m + M_phpyr_m m TRUE (WBGene00009628) or (WBGene00016652) or (WBGene00015778) PW076 rn:R00694 RHEA:21824;RHEA:21824 Added Genes from deprecated R_PHEAMINOTRANS_DEG_RXN_m jpnh R_RXN909_58_c R_RXN909_58_c M_gpail_c + M_coa16_0_c <=> M_gacpail_c + M_coa_c c FALSE PW028 -R_RXN909_59_c (S)-3-Hydroxybutanoyl-CoA hydro-lyase M_h2o_c + M_b2coa_c <=> M_3hbcoa_c c TRUE (WBGene00001156) or (WBGene00020347) or (WBGene00001155) or (WBGene00001154) or (WBGene00001152) or (WBGene00001150) tryptophan metabolism; fatty acid oxidation RHEA:16105;RHEA:20724 +R_RXN909_59_c (S)-3-Hydroxybutanoyl-CoA hydro-lyase M_h2o_c + M_b2coa_c <=> M_3hbcoa_c c TRUE (WBGene00001156) or (WBGene00020347) or (WBGene00001155) or (WBGene00001154) or (WBGene00001152) or (WBGene00001150) PW072;PW062 RHEA:16105;RHEA:20724 R_RXN909_6_c 2'-Deoxyinosine-5'-triphosphate pyrophosphohydrolase M_h2o_c + M_ditp_c <=> M_dimp_c + M_ppi_c + M_h_c c TRUE (WBGene00001823) PW042 RHEA:23996;RHEA:44644 R_RXN909_6_n 2'-Deoxyinosine-5'-triphosphate pyrophosphohydrolase M_h2o_n + M_ditp_n <=> M_dimp_n + M_ppi_n + M_h_n n TRUE (WBGene00001823) PW042 RHEA:23996;RHEA:44644 -R_RXN909_60_c (S)-3-Hydroxybutanoyl-CoA:NAD+ oxidoreductase M_nad_c + M_3hbcoa_c <=> M_h_c + M_nadh_c + M_aacoa_c c TRUE (WBGene00019978) or (WBGene00010035) or (WBGene00001158) or (WBGene00001157) or (WBGene00007129) tryptophan metabolism; fatty acid oxidation -R_RXN909_60_m (S)-3-Hydroxybutanoyl-CoA:NAD+ oxidoreductase M_nad_m + M_3hbcoa_m <=> M_h_m + M_nadh_m + M_aacoa_m m TRUE (WBGene00010035) or (WBGene00001158) or (WBGene00007129) or (WBGene00001157) tryptophan metabolism; fatty acid oxidation -R_RXN909_61_c Palmitate:CoA ligase M_atp_c + M_coa_c + M_fa16_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa16_0_c c FALSE (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00013575) or (WBGene00018152) fatty acid biosynthesis; fatty acid oxidation -R_RXN909_61_m Palmitate:CoA ligase M_atp_m + M_coa_m + M_fa16_0_m <=> M_ppi_m + M_h_m + M_amp_m + M_coa16_0_m m FALSE (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00009221) fatty acid biosynthesis; fatty acid oxidation -R_RXN909_63_m Palmitoyl-CoA:oxygen 2-oxidoreductase M_h_m + M_fad_m + M_coa16_0_m <=> M_fadh2_m + M_coa16_1_2e_m m TRUE (WBGene00020812) or (WBGene00020366) or (WBGene00019406) Fatty Acid beta-Oxidation (mitochondria) RHEA:14477 [DELETION] Dupe of R_RXN909_62_m jpnh -R_RXN909_66_c (S)-3-Hydroxyhexadecanoyl-CoA:NAD+ oxidoreductase M_nad_c + M_coa16_0_3oh__S_c <=> M_h_c + M_nadh_c + M_coa16_0_3o_c c TRUE (WBGene00020347) or (WBGene00001150) fatty acid biosynthesis; fatty acid oxidation [DELETION] Dupe of R_RXN909_65_c which has better annotation jpnh -R_RXN909_66_m (S)-3-Hydroxyhexadecanoyl-CoA:NAD+ oxidoreductase M_nad_m + M_coa16_0_3oh__S_m <=> M_h_m + M_nadh_m + M_coa16_0_3o_m m TRUE (WBGene00007129 or WBGene00010035 or WBGene00001157) or (WBGene00020347 or WBGene00001150) fatty acid biosynthesis; fatty acid oxidation [DELETION] Dupe of R_RXN909_65_m which has better annotation +R_RXN909_60_c (S)-3-Hydroxybutanoyl-CoA:NAD+ oxidoreductase M_nad_c + M_3hbcoa_c <=> M_h_c + M_nadh_c + M_aacoa_c c TRUE (WBGene00019978) or (WBGene00010035) or (WBGene00001158) or (WBGene00001157) or (WBGene00007129) PW072;PW062 +R_RXN909_60_m (S)-3-Hydroxybutanoyl-CoA:NAD+ oxidoreductase M_nad_m + M_3hbcoa_m <=> M_h_m + M_nadh_m + M_aacoa_m m TRUE (WBGene00010035) or (WBGene00001158) or (WBGene00007129) or (WBGene00001157) PW072;PW062 +R_RXN909_61_c Palmitate:CoA ligase M_atp_c + M_coa_c + M_fa16_0_c <=> M_ppi_c + M_h_c + M_amp_c + M_coa16_0_c c FALSE (WBGene00008669) or (WBGene00022037) or (WBGene00020343) or (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00018579) or (WBGene00018579) or (WBGene00009221) or (WBGene00016716) or (WBGene00013575) or (WBGene00018152) PW124;PW062 +R_RXN909_61_m Palmitate:CoA ligase M_atp_m + M_coa_m + M_fa16_0_m <=> M_ppi_m + M_h_m + M_amp_m + M_coa16_0_m m FALSE (WBGene00011174) or (WBGene00011173) or (WBGene00019920) or (WBGene00009221) fatty acid biosynthesis;PW062 R_RXN909_67_c R_RXN909_67_c M_gacpail_c + M_dolmanp_c <=> M_mgacpail_c + M_h_c + M_dolp_c c FALSE (WBGene00007189) PW028 -R_RXN909_73_c (S)-3-hydroxydodecanoyl-CoA:NAD+ oxidoreductase M_nad_c + M_coa12_0_3oh__S_c <=> M_h_c + M_nadh_c + M_coa12_0_3o_c c TRUE (WBGene00020347) or (WBGene00001150) fatty acid biosynthesis; fatty acid oxidation [DELETION] Merge into R_RXN_909_72_c jpnh -R_RXN909_73_m (S)-3-hydroxydodecanoyl-CoA:NAD+ oxidoreductase M_nad_m + M_coa12_0_3oh__S_m <=> M_h_m + M_nadh_m + M_coa12_0_3o_m m TRUE (WBGene00007129 or WBGene00010035 or WBGene00001157 or WBGene00001158 or WBGene00019978) or (WBGene00020347 or WBGene00001150) fatty acid biosynthesis; fatty acid oxidation [DELETION] Merge into R_RXN_909_72_m jpnh R_RXN909_78_c R_RXN909_78_c M_mgacpail_c + M_1ac2acg3pe_c <=> M_emgacpail_c + M_1ac2acglyc_c c FALSE (WBGene00021840) PW028 R_RXN909_79_c R_RXN909_79_c M_emgacpail_c + M_dolmanp_c <=> M_memgacpail_c + M_h_c + M_dolp_c c FALSE (WBGene00020375) PW028 -R_RXN909_8_m R_RXN909_8_m M_q9_m + M_succ_m <=> M_q9h2_m + M_fum_m m FALSE (WBGene00006433 and WBGene00009353 and WBGene00003225 and WBGene00016392 and WBGene00015391) PW023 RHEA:40523;RHEA:40523;RHEA:40523 +R_RXN909_8_m R_RXN909_8_m M_q9_m + M_succ_m <=> M_q9h2_m + M_fum_m m FALSE (WBGene00006433 and WBGene00009353 and WBGene00003225 and WBGene00016392 and WBGene00015391) PW023 SPW004 RHEA:40523;RHEA:40523;RHEA:40523 R_RXN909_80_c R_RXN909_80_c M_memgacpail_c + M_dolmanp_c <=> M_m2emgacpail_c + M_h_c + M_dolp_c c FALSE PW028 -R_RXN909_89_m (S)-hydroxydecanoyl-CoA:NAD+ oxidoreductase M_nad_m + M_coa10_0_3oh__S_m <=> M_h_m + M_nadh_m + M_coa10_0_3o_m m TRUE (WBGene00007129 or WBGene00010035 or WBGene00001157 or WBGene00001158 or WBGene00019978) or (WBGene00020347 or WBGene00001150) Fatty Acid beta-Oxidation (mitochondria) [DELETION] merge into R_RXN909_88_m jpnh -R_RXN909_9_m R_RXN909_9_m M_q8_m + M_succ_m <=> M_q8h2_m + M_fum_m m FALSE (WBGene00006433 and WBGene00009353 and WBGene00003225 and WBGene00016392 and WBGene00015391) PW023 RHEA:40523;RHEA:40523;RHEA:40523 -R_RXN909_92_c Octanoyl-CoA:oxygen 2-oxidoreductase M_h_c + M_fad_c + M_coa8_0_c <=> M_fadh2_c + M_coa8_1_2e_c c FALSE (WBGene00019599) or (WBGene00019406) Fatty Acid beta-Oxidation (cytosol) [DELETION] No longer required, replaced by peroxisomal beta-oxidation wimi -R_RXN909_95_m R_RXN909_95_m M_nad_m + M_coa8_0_3oh__S_c <=> M_h_m + M_nadh_m + M_coa8_0_3o_m m TRUE (WBGene00007129 or WBGene00010035 or WBGene00001157 or WBGene00001158 or WBGene00019978) or (WBGene00020347 or WBGene00001150) Fatty Acid beta-Oxidation (mitochondria) [DELETION] Merge into R_RXN909_94_m jpnh +R_RXN909_9_m R_RXN909_9_m M_q8_m + M_succ_m <=> M_q8h2_m + M_fum_m m FALSE (WBGene00006433 and WBGene00009353 and WBGene00003225 and WBGene00016392 and WBGene00015391) PW023 SPW004 RHEA:40523;RHEA:40523;RHEA:40523 R_RXtm RX transport M_RX_c <=> M_RX_m cm TRUE PW111 R_SACCD3_c Saccharopine dehydrogenase (NADP+, L-lysine forming) M_akg_c + 5.0 M_h_c + M_lys__L_c + M_nadph_c <=> M_h2o_c + M_saccrp__L_c + M_nadp_c c FALSE (WBGene00019819) PW079 replaced M_saccrp__L_c with M_saccrp_L_c lenov R_SACCD3_m Saccharopine dehydrogenase (NADP+, L-lysine forming) M_akg_m + 5.0 M_h_m + M_lys__L_m + M_nadph_m <=> M_h2o_m + M_saccrp__L_m + M_nadp_m m TRUE (WBGene00019819) PW079 Set to reversible, as per kegg jpnh -R_SADT_c Sulfate adenylyltransferase M_so4_c + M_atp_c + M_h_c <=> M_aps_c + M_ppi_c c TRUE (WBGene00004091) sulfur metabolism; purine metabolism set to reversible; replaced annotation sulfate activation for sulfonation with sulfur metabolism, purine metabolism janna; lenov +R_SADT_c Sulfate adenylyltransferase M_so4_c + M_atp_c + M_h_c <=> M_aps_c + M_ppi_c c TRUE (WBGene00004091) PW096;PW042 set to reversible; replaced annotation sulfate activation for sulfonation with PW096, PW042 janna; lenov R_SARCOX_RXN_c sarcosine oxidase M_h2o_c + M_sarcs_c + M_o2_c <=> M_h2o2_c + M_gly_c + M_fald_c c FALSE (WBGene00015783) PW074 R_SARCOX_RXN_m sarcosine oxidase M_h2o_m + M_sarcs_m + M_o2_m <=> M_h2o2_m + M_gly_m + M_fald_m m FALSE (WBGene00015783) PW074 R_SecrRNAtm Sec tRNA transport M_trnasec_c <=> M_trnasec_m cm TRUE PW111 replaced M_SEC__tRNAs_c and M_SEC__tRNAs_m by M_trnasec_c and M_trnasec_m lenov -R_SELNPS_c Selenide,water dikinase M_h2o_c + M_seln_c + M_atp_c <=> M_selnp_c + M_pi_c + M_h_c + M_amp_c c FALSE (WBGene00012867) selenocompound metabolism; cysteine and methionine metabolism RHEA:18737 +R_SELNPS_c Selenide,water dikinase M_h2o_c + M_seln_c + M_atp_c <=> M_selnp_c + M_pi_c + M_h_c + M_amp_c c FALSE (WBGene00012867) selenocompound metabolism;cysteine and methionine metabolism RHEA:18737 R_SERAT_c serine O-acetyltransferase M_ser__L_c + M_accoa_c <=> M_acser_c + M_coa_c c FALSE PW082 R_SERINE__PYRUVATE_AMINOTRANSFERASE_RXN_c serine—pyruvate transaminase M_ser__L_c + M_pyr_c <=> M_hpyr_c + M_ala__L_c c FALSE (WBGene00011767) PW074 RHEA:22852;RHEA:24248 [DELETION] Dupe of R_RC00585 lenov R_SERINE__PYRUVATE_AMINOTRANSFERASE_RXN_m serine—pyruvate transaminase M_ser__L_m + M_pyr_m <=> M_hpyr_m + M_ala__L_m m FALSE (WBGene00011767) PW074 RHEA:22852;RHEA:24248 [DELETION] Dupe of R_RM00585 lenov @@ -3219,7 +3207,7 @@ R_SNK0056 Protein N6,N6-dimethyl-L-lysine sink M_Ndmelys_n <=> n FALSE PW101 R_SNK0069 Phosphoglycolic acid sink M_2pglyc_c <=> c FALSE PW030 R_SNK0070 acetylhistone sink M_Naclys_n <=> n FALSE PW101 Changed cytopl to nucl rather than removing lenov R_SNK0071 non-methylated histone sink M_Nlys_n <=> n FALSE PW101 Changed cytopl to nucl rather than removing lenov -R_SNK0074 beta-fructose 2,6-bisphosphate sink M_f26bp_c <=> c FALSE PW018 +R_SNK0074 beta-fructose 2,6-bisphosphate sink M_f26bp_c <=> c FALSE PW018 SPW004 R_SNK1002 Peptide histidine sink M_caphis_c <=> c FALSE PW099 R_SNK1003 Peptide diphtine sink M_pdipht_c <=> c FALSE PW099 R_SO4HCOtex sulfate transport via bicarbonate countertransport 2.0 M_hco3_c + M_so4_e <=> 2.0 M_hco3_e + M_so4_c ce FALSE (WBGene00017464) PW107 @@ -3263,14 +3251,14 @@ R_SSAL_c Succinate-semialdehyde dehydrogenase M_h2o_c + M_sucsal_c + M_nad_c < R_SSAL_m Succinate-semialdehyde dehydrogenase M_h2o_m + M_sucsal_m + M_nad_m <=> 2.0 M_h_m + M_nadh_m + M_succ_m m TRUE (WBGene00000113) PW073 R_SUCCt2m succinate transport, mitochondrial M_pi_m + M_succ_c <=> M_pi_c + M_succ_m mc TRUE (WBGene00019656) or (ND) PW106 R_SUCCt4_2 succinate transport via sodium symport M_succ_e + 2.0 M_na1_e <=> M_succ_c + 2.0 M_na1_c ec TRUE (WBGene00003517) or (WBGene00003519) or (WBGene00003518) PW107 -R_SUCOAS_m Succinate--CoA ligase (ADP-forming) M_atp_m + M_coa_m + M_succ_m <=> M_pi_m + M_adp_m + M_succoa_m m TRUE (WBGene00007350 or WBGene00017759) and WBGene00009812 PW023 RHEA:17661;RHEA:22120;RHEA:17661;RHEA:22120;RHEA:17661 -R_SUCOAS1_m Succinate--CoA ligase (GDP-forming) M_gtp_m + M_coa_m + M_succ_m <=> M_pi_m + M_gdp_m + M_succoa_m m TRUE (WBGene00007350 or WBGene00017759) and WBGene00016844 PW023 RHEA:17661;RHEA:22120;RHEA:22120;RHEA:17661;RHEA:22120 +R_SUCOAS_m Succinate--CoA ligase (ADP-forming) M_atp_m + M_coa_m + M_succ_m <=> M_pi_m + M_adp_m + M_succoa_m m TRUE (WBGene00007350 or WBGene00017759) and WBGene00009812 PW023 SPW004 RHEA:17661;RHEA:22120;RHEA:17661;RHEA:22120;RHEA:17661 +R_SUCOAS1_m Succinate--CoA ligase (GDP-forming) M_gtp_m + M_coa_m + M_succ_m <=> M_pi_m + M_gdp_m + M_succoa_m m TRUE (WBGene00007350 or WBGene00017759) and WBGene00016844 PW023 SPW004 RHEA:17661;RHEA:22120;RHEA:22120;RHEA:17661;RHEA:22120 R_SULFITE_OXIDASE_RXN_c Sulfite oxidase M_h2o_c + M_so3_c + M_o2_c <=> M_h2o2_c + M_so4_c c FALSE (WBGene00010397) PW096 replaced sulfite oxidation with Sulfur metabolism lenov R_SULFITE_OXIDASE_RXN_m Sulfite oxidase M_h2o_m + M_so3_m + M_o2_m <=> M_h2o2_m + M_so4_m m FALSE (WBGene00010397) PW096 replaced sulfite oxidation with Sulfur metabolism lenov R_T4HCINNMFM_m R_T4HCINNMFM_m M_34hpl_m <=> M_h2o_m + M_T4hcinnm_m m FALSE Unknown PW003 -R_TALA_c Transaldolase M_s7p_c + M_g3p_c <=> M_e4p_c + M_f6p_c c TRUE (WBGene00021286) PW027 RHEA:17053 -R_TALA_m Transaldolase M_s7p_m + M_g3p_m <=> M_e4p_m + M_f6p_m m TRUE (WBGene00021286) PW027 RHEA:17053 -R_TALA_n Transaldolase M_s7p_n + M_g3p_n <=> M_e4p_n + M_f6p_n n TRUE (WBGene00021286) PW027 RHEA:17053 +R_TALA_c Transaldolase M_s7p_c + M_g3p_c <=> M_e4p_c + M_f6p_c c TRUE (WBGene00021286) PW027 SPW004 RHEA:17053 +R_TALA_m Transaldolase M_s7p_m + M_g3p_m <=> M_e4p_m + M_f6p_m m TRUE (WBGene00021286) PW027 SPW004 RHEA:17053 +R_TALA_n Transaldolase M_s7p_n + M_g3p_n <=> M_e4p_n + M_f6p_n n TRUE (WBGene00021286) PW027 SPW004 RHEA:17053 R_TCE0333 Adenine transport M_ade_e <=> M_ade_c ec TRUE ND PW105 R_TCE0342 Bicarbonate and Chloride transport 2.0 M_hco3_c + M_cl_e <=> 2.0 M_hco3_e + M_cl_c ce FALSE ND PW105 R_TCE0346 Sodium and Selenate transport 3.0 M_na1_e + M_sel_e <=> 3.0 M_na1_c + M_sel_c ec TRUE ND PW105 @@ -3494,7 +3482,7 @@ R_TCM0183 Glyoxylate transport M_glx_c <=> M_glx_m cm TRUE ND PW105 R_TCM0189 Uridine transport M_uri_c <=> M_uri_m cm TRUE ND PW105 R_TCM0190 Acetate transport M_ac_c <=> M_ac_m cm TRUE ND PW105 R_TCM0192 beta-Alanine transport M_ala_B_c <=> M_ala_B_m cm TRUE ND PW105 -R_TCM0195 CDP diacylglycerol transport M_cdpdag_c <=> M_cdpdag_m cm TRUE ND CL biosynthesis +R_TCM0195 CDP diacylglycerol transport M_cdpdag_c <=> M_cdpdag_m cm TRUE ND PW142 R_TCM0199 dUDP and dATP transport M_datp_c + M_dudp_m <=> M_datp_m + M_dudp_c cm FALSE ND PW105 R_TCM0200 dUDP and dGTP transport M_dgtp_c + M_dudp_m <=> M_dgtp_m + M_dudp_c cm FALSE ND PW105 R_TCM0206 dTDP and dADP transport M_dadp_m + M_dtdp_c <=> M_dadp_c + M_dtdp_m mc FALSE WBGene00016588 PW105 @@ -3590,19 +3578,19 @@ R_Threonine_transport Threonine transport M_thr__L_c <=> M_thr__L_e ce TRUE ND P R_THYM_PHOSPH_RXN_c Thymidine phosphorylase M_pi_c + M_thymd_c <=> M_thym_c + M_2dr1p_c c TRUE PW043 R_Thymine_Exchange_reactions_e Thymine transport M_thym_e <=> e TRUE PW111 Removed space from reaction ID jpnh R_Thymine_transport Thymine transport M_thym_c <=> M_thym_e ce TRUE ND PW107 -R_TKT1_c Transketolase M_s7p_c + M_g3p_c <=> M_xu5p_D_c + M_r5p_c c TRUE (WBGene00012713) or (WBGene00008506) PW027 RHEA:13457;RHEA:13457 -R_TKT1_m Transketolase M_s7p_m + M_g3p_m <=> M_xu5p_D_m + M_r5p_m m TRUE (WBGene00012713) PW027 RHEA:13457;RHEA:13457 -R_TKT1_n Transketolase M_s7p_n + M_g3p_n <=> M_xu5p_D_n + M_r5p_n n TRUE (WBGene00008506) PW027 -R_TKT2_c D-Fructose 6-phosphate:D-glyceraldehyde-3-phosphate glycolaldehyde transferase M_e4p_c + M_xu5p_D_c <=> M_f6p_c + M_g3p_c c TRUE (WBGene00012713) or (WBGene00008506) PW027 RHEA:13457;RHEA:13457 -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 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 +R_TKT1_c Transketolase M_s7p_c + M_g3p_c <=> M_xu5p_D_c + M_r5p_c c TRUE (WBGene00012713) or (WBGene00008506) PW027 SPW004 RHEA:13457;RHEA:13457 +R_TKT1_m Transketolase M_s7p_m + M_g3p_m <=> M_xu5p_D_m + M_r5p_m m TRUE (WBGene00012713) PW027 SPW004 RHEA:13457;RHEA:13457 +R_TKT1_n Transketolase M_s7p_n + M_g3p_n <=> M_xu5p_D_n + M_r5p_n n TRUE (WBGene00008506) PW027 SPW004 +R_TKT2_c D-Fructose 6-phosphate:D-glyceraldehyde-3-phosphate glycolaldehyde transferase M_e4p_c + M_xu5p_D_c <=> M_f6p_c + M_g3p_c c TRUE (WBGene00012713) or (WBGene00008506) PW027 SPW004 RHEA:13457;RHEA:13457 +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) purine metabolism; pyrimidine metabolism RHEA:19129;RHEA:19129 +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_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 R_TMLYSOX_n Trimethyllysine dioxygenase M_akg_n + M_tmlys_n + M_o2_n <=> M_co2_n + M_3htmelys_n + M_succ_n n FALSE (WBGene00001522) or (WBGene00001523) PW080 RHEA:24028 -R_TPI_c Triosephosphate isomerase M_g3p_c <=> M_dhap_c c TRUE (WBGene00006601) glycolysis and gluconeogenesis; sucrose degradation RHEA:18585;RHEA:17937 +R_TPI_c Triosephosphate isomerase M_g3p_c <=> M_dhap_c c TRUE (WBGene00006601) PW018;sucrose degradation RHEA:18585;RHEA:17937 R_TRANS_OCTAPRENYLTRANSTRANSFERASE_RXN_c all-trans-nonaprenyl-diphosphate synthase[geranyl-diphosphate specific] 7.0 M_ipdp_c + M_grdp_c <=> 7.0 M_ppi_c + M_nonadp_c c FALSE (WBGene00000761) PW003 R_TRANS_PENTAPRENYLTRANSFERASE_RXN_c hexaprenyl-diphosphate synthase[(2E,6E)-farnesyl-diphosphate specific] 3.0 M_ipdp_c + M_frdp_c <=> 3.0 M_ppi_c + M_hexdp_c c TRUE (WBGene00000761) PW001 R09245 added KEGGID ms 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 @@ -3627,11 +3615,11 @@ R_UDP_GLUCURONATE_DECARBOXYLASE_RXN_c UDP-glucuronate decarboxylase M_udpglcur_c R_UDP_N_ACETYLGLUCOSAMINE_4_EPIMERASE_RXN_c UDP-N-acetylglucosamine 4-epimerase M_uacgam_c <=> M_udpacgal_c c FALSE (WBGene00008132) PW032 RHEA:22168;RHEA:20517 R_UDP_N_ACETYLGLUCOSAMINE_4_EPIMERASE_RXN_m UDP-N-acetylglucosamine 4-epimerase M_uacgam_m <=> M_udpacgal_m m FALSE (WBGene00008132) PW032 RHEA:22168;RHEA:20517 R_UDPGNP_c R_UDPGNP_c M_h2o_c + M_udpglcur_c <=> M_h_c + M_udp_c + M_glcur_c c FALSE (WBGene00015371 or WBGene00016959 or WBGene00017334 or WBGene00018789 or WBGene00019181 or WBGene00019235 or WBGene00019379 or WBGene00007072 or WBGene00020594 or WBGene00020593 or WBGene00020592 or WBGene00019232 or WBGene00019233 or WBGene00008097 or WBGene00013901 or WBGene00007422 or WBGene00013900 or WBGene00019515 or WBGene00007073 or WBGene00019516 or WBGene00007885 or WBGene00007455 or WBGene00007650 or WBGene00016762 or WBGene00015692 or WBGene00015695 or WBGene00015694 or WBGene00021709 or WBGene00013903 or WBGene00011340 or WBGene00021464 or WBGene00018543 or WBGene00007946 or WBGene00009255 or WBGene00044286 or WBGene00017315 or WBGene00017332 or WBGene00017333 or WBGene00017329 or WBGene00013905 or WBGene00017331 or WBGene00017336 or WBGene00017959 or WBGene00008485 or WBGene00008486 or WBGene00021372 or WBGene00015141 or WBGene00011006 or WBGene00015965 or WBGene00007070 or WBGene00013906 or WBGene00011564 or WBGene00015369 or WBGene00018931 or WBGene00020182 or WBGene00012013 or WBGene00011452 or WBGene00011453 or WBGene00009450 or WBGene00011238 or WBGene00013904 or WBGene00007402 or WBGene00018206 or WBGene00010904 or WBGene00015449 or WBGene00015577 or WBGene00008583 or WBGene00015739 or WBGene00019234 or WBGene00020587) and (WBGene00013693) PW045 RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032;RHEA:21032 replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism -R_UGD_RXN_c UDP-glucose 6-dehydrogenase M_h2o_c + 2.0 M_nad_c + M_udpg_c <=> M_udpglcur_c + 3.0 M_h_c + 2.0 M_nadh_c c TRUE (WBGene00005022) amino sugar and nucleotide sugar metabolism; starch and sucrose metabolism; ascorbate and aldarate metabolism; galactose metabolism RHEA:23596 replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism lenov -R_UGLT_c UDP-galactose--hexose-1-phosphate uridylyltransferase M_gal1p_c + M_udpg_c <=> M_g1p_c + M_udpgal_c c TRUE (WBGene00014203) amino sugar and nucleotide sugar metabolism; galactose metabolism [ADDITIONAL CURATION BY JANNA 18/01/2018 CORRECTED TO CYTOSOLIC WAS WRONGLY MITOCHONDRIAL]Corrected reaction name. Only cytosolic in human (https://www.proteinatlas.org/ENSG00000213930-GALT/cell). C. elegans enzyme activity was studied (https://www.ncbi.nlm.nih.gov/pubmed/19858195). Reviewed in C. elegans in https://doi.org/10.1534/genetics.117.300106 nel -R_UMPKI_RXN_c ATP:UMP phosphotransferase M_atp_c + M_ump_c <=> M_adp_c + M_udp_c c TRUE (WBGene00009575) or (WBGene00007812) pyrimidine metabolism; purine metabolism set to be reversible janna -R_UMPKI_RXN_m R_UMPKI_RXN_m M_atp_m + M_ump_m <=> M_adp_m + M_udp_m m FALSE purine metabolism; pyrimidine metabolism -R_UMPKI_RXN_n ATP:UMP phosphotransferase M_atp_n + M_ump_n <=> M_adp_n + M_udp_n n TRUE (WBGene00007812) pyrimidine metabolism; purine metabolism set to reversible janna +R_UGD_RXN_c UDP-glucose 6-dehydrogenase M_h2o_c + 2.0 M_nad_c + M_udpg_c <=> M_udpglcur_c + 3.0 M_h_c + 2.0 M_nadh_c c TRUE (WBGene00005022) amino sugar and nucleotide sugar metabolism;starch and sucrose metabolism;ascorbate and aldarate metabolism;galactose metabolism RHEA:23596 replaced L-ascorbate biosynthesis with ascorbate and aldarate metabolism lenov +R_UGLT_c UDP-galactose--hexose-1-phosphate uridylyltransferase M_gal1p_c + M_udpg_c <=> M_g1p_c + M_udpgal_c c TRUE (WBGene00014203) amino sugar and nucleotide sugar metabolism;galactose metabolism [ADDITIONAL CURATION BY JANNA 18/01/2018 CORRECTED TO CYTOSOLIC WAS WRONGLY MITOCHONDRIAL]Corrected reaction name. Only cytosolic in human (https://www.proteinatlas.org/ENSG00000213930-GALT/cell). C. elegans enzyme activity was studied (https://www.ncbi.nlm.nih.gov/pubmed/19858195). Reviewed in C. elegans in https://doi.org/10.1534/genetics.117.300106 nel +R_UMPKI_RXN_c ATP:UMP phosphotransferase M_atp_c + M_ump_c <=> M_adp_c + M_udp_c c TRUE (WBGene00009575) or (WBGene00007812) PW043;PW042 set to be reversible janna +R_UMPKI_RXN_m R_UMPKI_RXN_m M_atp_m + M_ump_m <=> M_adp_m + M_udp_m m FALSE PW042;PW043 +R_UMPKI_RXN_n ATP:UMP phosphotransferase M_atp_n + M_ump_n <=> M_adp_n + M_udp_n n TRUE (WBGene00007812) PW043;PW042 set to reversible janna R_UPPN_c β-ureidopropionase M_h2o_c + M_cala_c + M_h_c <=> M_co2_c + M_nh3_c + M_ala_B_c c TRUE (WBGene00017440) PW043 R_UPPRT_c Uracil phosphoribosyltransferase M_ppi_c + M_ump_c <=> M_prpp_c + M_ura_c c TRUE (WBGene00020036) or (WBGene00011559) or (WBGene00008131) PW043 RHEA:10380;RHEA:11596 R_UPPRT_m Uracil phosphoribosyltransferase M_ppi_m + M_ump_m <=> M_prpp_m + M_ura_m m TRUE (WBGene00011559) PW043 RHEA:10380;RHEA:11596 @@ -3642,8 +3630,8 @@ R_Urea_Exchange_reactions_e Urea transport M_urea_e <=> e FALSE PW111 Re 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 purine metabolism; pyrimidine metabolism -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 purine metabolism; pyrimidine metabolism +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_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 @@ -3666,18 +3654,18 @@ 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 -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 +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_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 -R_ETHERLIPIDREMODEL0003 Plasmenylethanolamine 2-acyl tansferase M_fataccoa_c + M_alken2gpe_c <=> M_coa_c + M_1alken2acg3pe_c c FALSE SPW003 -R_ETHERLIPIDREMODEL0004 Plasmenylcholine 2-acyl tansferase M_fataccoa_c + M_1alkg3pc_c <=> M_coa_c + M_1alk2acg3pc_c c FALSE SPW003 -R_NAPEBIOSYNTH0001 M_1ac2acg3pe_c + M_1ac2acg3pc_c <=> M_nape_c + M_2acg3pc_c c RHEA:45188 -R_NAPEBIOSYNTH0002 M_nape_c + M_h2o_c <=> M_nae_c + M_1ac2acglyc3p_c c RHEA:33159 -R_NAPEBIOSYNTH0003 M_nape_c + M_h2o_c <=> M_pnae_c + M_1ac2acglyc_c c -R_NAPEBIOSYNTH0004 M_pnae_c + M_h2o_c <=> M_nae_c + M_pi_c c -R_NAPEBIOSYNTH0005 M_nape_c + M_h2o_c <=> M_lnape_c + M_fatacid_c + M_h_c c RHEA:45460 -R_NAPEBIOSYNTH0006 M_lnape_c + M_h2o_c <=> M_gpnae_c + M_fatacid_c c -R_NAPEBIOSYNTH0007 M_gpnae_c + M_h2o_c <=> M_glyc_c + M_nae_c c -R_NAPEBIOSYNTH0008 M_h2o_c + M_nae_c <=> M_etha_c + M_h_c + M_fatacid_c c +R_ETHERLIPIDREMODEL0003 Plasmenylethanolamine 2-acyl tansferase M_fataccoa_c + M_alken2gpe_c <=> M_coa_c + M_1alken2acg3pe_c c FALSE PW065 SPW003 +R_ETHERLIPIDREMODEL0004 Plasmenylcholine 2-acyl tansferase M_fataccoa_c + M_1alkg3pc_c <=> M_coa_c + M_1alk2acg3pc_c c FALSE PW065 SPW003 +R_NAPEBIOSYNTH0001 M_1ac2acg3pe_c + M_1ac2acg3pc_c <=> M_nape_c + M_2acg3pc_c c PW146 SPW003 RHEA:45188 +R_NAPEBIOSYNTH0002 M_nape_c + M_h2o_c <=> M_nae_c + M_1ac2acglyc3p_c c PW146 SPW003 RHEA:33159 +R_NAPEBIOSYNTH0003 M_nape_c + M_h2o_c <=> M_pnae_c + M_1ac2acglyc_c c PW146 SPW003 +R_NAPEBIOSYNTH0004 M_pnae_c + M_h2o_c <=> M_nae_c + M_pi_c c PW146 SPW003 +R_NAPEBIOSYNTH0005 M_nape_c + M_h2o_c <=> M_lnape_c + M_fatacid_c + M_h_c c PW146 SPW003 RHEA:45460 +R_NAPEBIOSYNTH0006 M_lnape_c + M_h2o_c <=> M_gpnae_c + M_fatacid_c c PW146 SPW003 +R_NAPEBIOSYNTH0007 M_gpnae_c + M_h2o_c <=> M_glyc_c + M_nae_c c PW146 SPW003 +R_NAPEBIOSYNTH0008 M_h2o_c + M_nae_c <=> M_etha_c + M_h_c + M_fatacid_c c PW146 SPW003