# =================================================================================== # # ======================== Sulfolobus acidocaldarius DSM 639 ======================== # # ================================= Metabolic Model ================================= # # =============================== by Julia Helmecke ================================= # # =================================================================================== # # ================================ Biomass reactions ================================ # Biomass_proteins : 0.494893238251923 L-alanine + 0.0516395661067052 L-cysteine + 0.431651645446408 L-aspartate + 0.605007018920633 L-glutamate + 0.380279277530342 L-phenylalanine + 0.596245730880198 glycine + 0.114318636405612 L-histidine + 0.808429220373108 L-isoleucine + 0.663312476730654 L-lysine + 0.910189541818674 L-leucine + 0.194253084594749 L-methionine + 0.428417141033406 L-asparagine + 0.348974900037551 L-proline + 0.202325282564588 L-glutamine + 0.406478763275655 L-arginine + 0.621770189617581 L-serine + 0.434351753478131 L-threonine + 0.692633962387648 L-valine + 0.0878238263443284 L-tryptophan + 0.411161763143175 L-tyrosine --> 1 proteins Biomass_dna : 0.981216947939492 dAMP + 0.570130823971746 dCMP + 0.98731594128481 dTMP + 0.571556018292988 dGMP --> 1 dna Biomass_rna : 0.539012767167705 AMP + 0.886981375268245 CMP + 0.513203881906041 UMP + 1.0158725365655 GMP --> 1 rna Biomass_lipids : 0.581152075875215 sn-glycerol_1-phosphate + 0.076790996409253 saturated_glycolipidcaldarchaeol + 0.067456446745159 saturated_inositolcaldarchaeol + 0.0575813970628881 saturated_inositolcalditolcaldarchaeol + 0.047183098259274 saturated_sulfoglycolipidcaldarchaeol + 0.1428263331767 2,3-bis-O-phytanyl-sn-glycerol + 0.0642460469407317 saturated_calditolcaldarchaeol + 0.0434865989522339 saturated_inositolglycolipidcaldarchaeol + 0.165196964340583 UDP-N-acetyl-alpha-D-glucosamine + 0.0963079388560158 CDP-archaeol --> 1 lipids #Biomass_soluble : 0.136822058671214 NAD+ + 0.121956707564035 NADPH + 0.136615007978316 NADH + 0.122121847561892 NADP+ + 0.14511537020208 representative_quinone + 0.0004 coenzyme_A + 0.217276311332393 tetrahydrosulfopterin + 0.000198266694292366 pyridoxal_5'-phosphate + 0.00025714475950488 FAD + 0.215276159732262 thiamin_diphosphate + 0.0575526341110376 coenzyme_B12 + 1.03128263880641 putrescine + 0.625897983660883 spermidine + 8.18629921316567E-08 biotin + 0.0756 trehalose + 0.0189 beta-D-glucose --> 1 soluble Biomass_soluble : 0.150504264538336 NAD+ + 0.134152378320439 NADPH + 0.150276508776148 NADH + 0.134334032318081 NADP+ + 0.159626907222287 representative_quinone + 0.0004 coenzyme_A + 0.0119501971232816 tetrahydrosulfopterin + 0.000198266694292366 pyridoxal_5'-phosphate + 0.00025714475950488 FAD + 0.236803775705488 thiamin_diphosphate + 0.000194355245392974 coenzyme_B12 + 1.13441090268706 putrescine + 0.688487782026971 spermidine + 8.18629921316567E-08 biotin + 0.0756 trehalose --> 1 soluble Biomass_DSM639_Glc : 0.648107103 proteins + 0.008263 dna + 0.08042359881 rna + 0.075 lipids + 0.032 soluble + 0.1562063882 glycogen + 43.86 ATP + 43.86 H2O --> 43.86 ADP + 43.86 phosphate + 43.86 H+ Biomass_MW001_Glc : 0.5839156825 proteins + 0.004576 dna + 0.04918205193 rna + 0.075 lipids + 0.032 soluble + 0.2553264739 glycogen + 43.86 ATP + 43.86 H2O --> 43.86 ADP + 43.86 phosphate + 43.86 H+ Biomass_DSM639_Cas : 0.6019596902 proteins + 0.004483 dna + 0.0729912773 rna + 0.075 lipids + 0.032 soluble + 0.2135662547 glycogen + 43.86 ATP + 43.86 H2O --> 43.86 ADP + 43.86 phosphate + 43.86 H+ Biomass_MW001_Cas : 0.6648622657 proteins + 0.010835 dna + 0.06431511771 rna + 0.075 lipids + 0.032 soluble + 0.1529876241 glycogen + 43.86 ATP + 43.86 H2O --> 43.86 ADP + 43.86 phosphate + 43.86 H+ Biomass_NGAM : 1 ATP + 1 H2O --> 1 ADP + 1 phosphate + 1 H+ # # ================================ transporter ================================ # # --- carbon exporter --- # T_sink_glycogen : 1 glycogen --> # T_sink_trehalose : 1 trehalose --> # T_sink_galactose : 1 UDP-alpha-D-galactose --> # T_sink_dTDP-rhamnose : 1 dTDP-beta-L-rhamnose --> # T_sink_GDP-mannose : 1 GDP-alpha-D-mannose --> # T_sink_ADP-glucose : 1 ADP-alpha-D-glucose --> # T_sink_UDP-glucose : 1 UDP-alpha-D-glucose --> # # --- carbon transporter --- # T_ex_beta-D-glucose : 1 beta-D-glucose_ex <=> # T_ABC_beta-D-glucose : 1 beta-D-glucose + 1 ADP + 1 phosphate <-- 1 beta-D-glucose_ex + 1 ATP + 1 H2O # T_ex_alpha-D-xylose : 1 alpha-D-xylose_ex <=> # T_ABC_alpha-D-xylose : 1 alpha-D-xylose + 1 ADP + 1 phosphate <-- 1 alpha-D-xylose_ex + 1 ATP + 1 H2O # Saci_2120-2 T_ex_L-arabinose : 1 L-arabinose_ex <=> # T_ABC_L-arabinose : 1 L-arabinose + 1 ADP + 1 phosphate <-- 1 L-arabinose_ex + 1 ATP + 1 H2O # Saci_2120-2 T_ex_D-ribose : 1 D-ribose_ex <=> # T_ABC_D-ribose : 1 D-ribose + 1 ADP + 1 phosphate <-- 1 D-ribose_ex + 1 ATP + 1 H2O # T_ex_beta-D-galactose : 1 beta-D-galactose_ex <=> # T_ABC_beta-D-galactose : 1 beta-D-galactose + 1 ADP + 1 phosphate <-- 1 beta-D-galactose_ex + 1 ATP + 1 H2O # T_ex_glycolaldehyde : 1 glycolaldehyde_ex <=> # T_ABC_glycolaldehyde : 1 glycolaldehyde + 1 ADP + 1 phosphate <-- 1 glycolaldehyde_ex + 1 ATP + 1 H2O # T_ex_D-sorbitol : 1 D-sorbitol_ex <=> # T_ABC_D-sorbitol : 1 D-sorbitol + 1 ADP + 1 phosphate <-- 1 D-sorbitol_ex + 1 ATP + 1 H2O # T_ex_dextrin : 1 dextrin_ex <=> # T_ex_glycogen : 1 glycogen_ex <=> # T_ex_starch : 1 starch_ex <=> # T_ex_pullulan : 1 pullulan_ex <=> # T_ex_sucrose : 1 sucrose_ex <=> # T_ABC_sucrose : 1 sucrose + 1 ADP + 1 phosphate <-- 1 sucrose_ex + 1 ATP + 1 H2O # T_ex_beta-maltose : 1 beta-maltose_ex <=> # T_ABC_beta-maltose : 1 beta-maltose + 1 ADP + 1 phosphate <-- 1 beta-maltose_ex + 1 ATP + 1 H2O # Saci_1163-6 T_ex_maltotriose : 1 maltotriose_ex <=> # T_ABC_maltotriose : 1 maltotriose + 1 ADP + 1 phosphate <-- 1 maltotriose_ex + 1 ATP + 1 H2O # T_ex_glycerol : 1 glycerol_ex <=> # T_ABC_glycerol : 1 glycerol + 1 ADP + 1 phosphate <-- 1 glycerol_ex + 1 ATP + 1 H2O # T_ex_(S)-malate : 1 (S)-malate_ex <=> # T_ABC_(S)-malate : 1 (S)-malate + 1 ADP + 1 phosphate <-- 1 (S)-malate_ex + 1 ATP + 1 H2O # T_ex_succinate : 1 succinate_ex <=> # T_ABC_succinate : 1 succinate + 1 ADP + 1 phosphate <-- 1 succinate_ex + 1 ATP + 1 H2O # T_ex_fumarate : 1 fumarate_ex <=> # T_ABC_fumarate : 1 fumarate + 1 ADP + 1 phosphate <-- 1 fumarate_ex + 1 ATP + 1 H2O # T_ex_D-gluconate : 1 D-gluconate_ex <=> # T_ABC_D-gluconate : 1 D-gluconate + 1 ADP + 1 phosphate <-- 1 D-gluconate_ex + 1 ATP + 1 H2O # # --- amino acid transporter --- # T_sink_L-alanine : 1 L-alanine --> # T_sink_glycine : 1 glycine --> # T_sink_L-valine : 1 L-valine --> # T_sink_L-lysine : 1 L-lysine --> # T_ex_L-alanine : 1 L-alanine_ex <=> # T_MFS_L-alanine : 1 L-alanine + 2 H+ <-- 1 L-alanine_ex + 2 H+_pp T_ex_L-arginine : 1 L-arginine_ex <=> # T_ABC_L-arginine : 1 L-arginine + 1 ADP + 1 phosphate <-- 1 L-arginine_ex + 1 ATP + 1 H2O # T_ex_L-asparagine : 1 L-asparagine_ex <=> # T_ABC_L-asparagine : 1 L-asparagine + 1 ADP + 1 phosphate <-- 1 L-asparagine_ex + 1 ATP + 1 H2O # T_ex_L-aspartate : 1 L-aspartate_ex <=> # #T_ABC_L-aspartate : 1 L-aspartate + 1 ADP + 1 phosphate <-- 1 L-aspartate_ex + 1 ATP + 1 H2O # T_MFS_L-aspartate : 1 L-aspartate + 2 H+ <-- 1 L-aspartate_ex + 2 H+_pp T_ex_L-cysteine : 1 L-cysteine_ex <=> # T_ABC_L-cysteine : 1 L-cysteine + 1 ADP + 1 phosphate <-- 1 L-cysteine_ex + 1 ATP + 1 H2O # T_ex_L-glutamate : 1 L-glutamate_ex <=> # #T_ABC_L-glutamate : 1 L-glutamate + 1 ADP + 1 phosphate <-- 1 L-glutamate_ex + 1 ATP + 1 H2O # T_MFS_L-glutamate : 1 L-glutamate + 2 H+ <=> 1 L-glutamate_ex + 2 H+_pp # T_ex_L-glutamine : 1 L-glutamine_ex <=> # T_ABC_L-glutamine : 1 L-glutamine + 1 ADP + 1 phosphate <-- 1 L-glutamine_ex + 1 ATP + 1 H2O # T_ex_glycine : 1 glycine_ex <=> # T_MFS_glycine : 1 glycine + 2 H+ <-- 1 glycine_ex + 2 H+_pp T_ex_L-histidine : 1 L-histidine_ex <=> # T_ABC_L-histidine : 1 L-histidine + 1 ADP + 1 phosphate <-- 1 L-histidine_ex + 1 ATP + 1 H2O # T_ex_L-isoleucine : 1 L-isoleucine_ex <=> # #T_ABC_L-isoleucine : 1 L-isoleucine + 1 ADP + 1 phosphate <-- 1 L-isoleucine_ex + 1 ATP + 1 H2O # T_MFS_L-isoleucine : 1 L-isoleucine + 2 H+ <-- 1 L-isoleucine_ex + 2 H+_pp T_ex_L-lysine : 1 L-lysine_ex <=> # T_ABC_L-lysine : 1 L-lysine + 1 ADP + 1 phosphate <-- 1 L-lysine_ex + 1 ATP + 1 H2O # Saci_0448 T_ex_L-leucine : 1 L-leucine_ex <=> # #T_ABC_L-leucine : 1 L-leucine + 1 ADP + 1 phosphate <-- 1 L-leucine_ex + 1 ATP + 1 H2O # T_MFS_L-leucine : 1 L-leucine + 2 H+ <-- 1 L-leucine_ex + 2 H+_pp T_ex_L-methionine : 1 L-methionine_ex <=> # #T_ABC_L-methionine : 1 L-methionine + 1 ADP + 1 phosphate <-- 1 L-methionine_ex + 1 ATP + 1 H2O # T_MFS_L-methionine : 1 L-methionine + 2 H+ <-- 1 L-methionine_ex + 2 H+_pp T_ex_L-proline : 1 L-proline_ex <=> # #T_ABC_L-proline : 1 L-proline + 1 ADP + 1 phosphate <-- 1 L-proline_ex + 1 ATP + 1 H2O # T_MFS_L-proline : 1 L-proline + 2 H+ <-- 1 L-proline_ex + 2 H+_pp T_ex_L-phenylalanine : 1 L-phenylalanine_ex <=> # #T_ABC_L-phenylalanine : 1 L-phenylalanine + 1 ADP + 1 phosphate <-- 1 L-phenylalanine_ex + 1 ATP + 1 H2O # T_MFS_L-phenylalanine : 1 L-phenylalanine + 2 H+ <-- 1 L-phenylalanine_ex + 2 H+_pp T_ex_L-serine : 1 L-serine_ex <=> # T_ABC_L-serine : 1 L-serine + 1 ADP + 1 phosphate <-- 1 L-serine_ex + 1 ATP + 1 H2O # T_ex_L-threonine : 1 L-threonine_ex <=> # #T_ABC_L-threonine : 1 L-threonine + 1 ADP + 1 phosphate <-- 1 L-threonine_ex + 1 ATP + 1 H2O # T_MFS_L-threonine : 1 L-threonine + 2 H+ <-- 1 L-threonine_ex + 2 H+_pp T_ex_L-tyrosine : 1 L-tyrosine_ex <=> # #T_ABC_L-tyrosine : 1 L-tyrosine + 1 ADP + 1 phosphate <-- 1 L-tyrosine_ex + 1 ATP + 1 H2O # T_MFS_L-tyrosine : 1 L-tyrosine + 2 H+ <-- 1 L-tyrosine_ex + 2 H+_pp T_ex_L-valine : 1 L-valine_ex <=> # T_ABC_L-valine : 1 L-valine + 1 ADP + 1 phosphate <-- 1 L-valine_ex + 1 ATP + 1 H2O # T_MFS_L-valine : 1 L-valine + 2 H+ <-- 1 L-valine_ex + 2 H+_pp T_ex_L-pyroglutamate : 1 L-pyroglutamate_ex <=> # T_MFS_L-pyroglutamate : 1 L-pyroglutamate + 2 H+ <=> 1 L-pyroglutamate_ex + 2 H+_pp # # --- nucleobase cation symporter --- # T_ex_uracil : 1 uracil_ex <=> # T_MFS_uracil : 1 uracil + 1 H+ <=> 1 uracil_ex + 1 H+_pp # # --- other transporter --- # T_ex_CO2 : 1 CO2_ex <=> # T_trans_CO2 : 1 CO2 <=> 1 CO2_ex # T_ex_H+ : 1 H+_ex <=> # T_trans_H+ : 1 H+ <=> 1 H+_ex # T_ex_H2O : 1 H2O_ex <=> # T_trans_H2O : 1 H2O <=> 1 H2O_ex # T_ex_oxygen : 1 oxygen_ex <=> # T_trans_oxygen : 1 oxygen <=> 1 oxygen_ex # T_ex_phosphate : 1 phosphate_ex <=> # T_MFS_phosphate : 1 phosphate + 1 H+ <-- 1 phosphate_ex + 1 H+_pp # Saci_0265 T_ex_ammonium-sulfate : 1 ammonium_sulfate_ex <=> # T_trans_ammonium-sulfate : 1 ammonium_sulfate <=> 1 ammonium_sulfate_ex # T_ex_ammonia : 1 ammonia_ex <=> # T_trans_ammonia : 1 ammonia <=> 1 ammonia_ex # Saci_0883 T_ex_urea : 1 urea_ex <=> # T_trans_urea : 1 urea <=> 1 urea_ex # T_ex_carbon-monoxide : 1 carbon_monoxide_ex <=> # T_trans_carbon-monoxide : 1 carbon_monoxide <=> 1 carbon_monoxide_ex # T_ex_Fe3+ : 1 Fe3+_ex <=> # T_ABC_Fe3+ : 1 Fe3+ + 1 ADP + 1 phosphate <-- 1 Fe3+_ex + 1 ATP + 1 H2O # Saci_1220-2 T_ex_cobalt : 1 Co2+_ex <=> # T_ABC_cobalt : 1 Co2+ + 1 ADP + 1 phosphate <-- 1 Co2+_ex + 1 ATP + 1 H2O # Saci_1809-10 T_trans_cobalt : 1 Co2+ <-- 1 Co2+_ex # T_ex_copper : 1 Cu+_ex <=> # T_ABC_copper : 1 Cu+ + 1 ADP + 1 phosphate <-- 1 Cu+_ex + 1 ATP + 1 H2O # T_ex_sulfate : 1 sulfate_ex <=> # T_trans_sulfate : 1 sulfate + 1 ADP + 1 phosphate <-- 1 sulfate_ex + 1 ATP + 1 H2O # T_ex_hydrogen-sulfide : 1 hydrogen_sulfide_ex <=> # T_trans_hydrogen-sulfide : 1 hydrogen_sulfide <=> 1 hydrogen_sulfide_ex # T_ex_coenzyme-B12 : 1 coenzyme_B12_ex <=> # T_ABC_coenzyme-B12 : 1 coenzyme_B12 + 1 ADP + 1 phosphate <-- 1 coenzyme_B12_ex + 1 ATP + 1 H2O # Saci_1220-2 # --- unidentified exporter --- # # JHE The fate of D-sedoheptulose-7-phosphate is still unclear, since the noPPP is incomplete (Brasen2014) # T_sink_D-sedoheptulose-7-phosphate : 1 D-sedoheptulose_7-phosphate --> # T_sink_dialurate : 1 dialurate --> # T_sink_orotate : 1 orotate --> # # --- experimentally verified exporter --- # T_sink_stickland-tyr_4-hydroxyphenylacetate : 1 4-hydroxyphenylacetate --> # tyrosine stickland T_sink_stickland-phe_2-hydroxyphenylacetate : 1 2-hydroxyphenylacetate --> # phenylalanine stickland T_sink_stickland-leu_3-methylbutanoate : 1 3-methylbutanoate --> # leucine stickland T_sink_stickland-leu_3-methyl-2-butenoate : 1 3-methyl-2-butenoate --> T_sink_stickland-ile_2-methylbutanoate : 1 2-methylbutanoate --> # isoleucine stickland T_sink_stickland-ile_2-methyl-2-butenoate : 1 2-methyl-2-butenoate --> # isoleucine stickland T_sink_stickland-val_2-methylpropanoate : 1 2-methylpropanoate --> # valine stickland # T_sink_stickland-val_3-hydroxyisovalerate : 1 3-hydroxyisovalerate --> # ================================ conversion reactions ================================ # #conv_redox_FMN_1.5.1.36_FMNREDUCT-RXN-NAD : 1 FMNH2 + 1 NAD+ <=> 1 H+ + 1 FMN + 1 NADH# conv_redox_FAD_1.5.1.36_RXN-13750_WOP : 1 FADH2 + 1 NAD+ <=> 1 H+ + 1 NADH + 1 FAD # Saci_1722 conv_redox_thioredoxin_1.8.1.9_THIOREDOXIN-REDUCT-NADPH-RXN : 1 H+ + 1 NADP+ + 1 reduced_thioredoxin <=> 1 NADPH + 1 oxidized_thioredoxin # Saci_1169 #hypothesis_ferredoxin_conversion : 1 H+ + 1 ADP + 1 reduced_ferredoxin <=> 1 ATP + 1 oxidized_ferredoxin # conv_redox_CoA-dis_1.8.1.14_COA-DISULFIDE-REDUCTASE-NADH-RXN-NAD : 2 coenzyme_A + 1 NAD+ <-- 1 CoA-disulfide + 1 H+ + 1 NADH # Saci_0149 conv_redox_CoA-dis_1.8.1.14_COA-DISULFIDE-REDUCTASE-NADH-RXN-NADP : 2 coenzyme_A + 1 NADP+ <-- 1 CoA-disulfide + 1 H+ + 1 NADPH # Saci_0149 conv_redox_ferredoxin_1.18.1.3_1.18.1.3-RXN : 1 NAD+ + 1 H+ + 2 reduced_ferredoxin <=> 1 NADH + 2 oxidized_ferredoxin # Saci_2287 conv_redox_dihydroxyacetone-P_1.1.5.3_GLYC3PDEHYDROG-RXN : 1 sn-glycerol_3-phosphate + 1 representative_quinone --> 1 representative_quinol + 1 dihydroxyacetone_phosphate # Saci_2032 conv_redox_hydrogen-peroxide_1.11.1.15_RXN0-5468 : 1 hydrogen_peroxide + 1 reduced_thioredoxin --> 2 H2O + 1 oxidized_thioredoxin # Saci_2227 conv_ammonia__spontaneous_RXN-11811 : 1 ammonia + 1 H2O <=> 1 ammonium + 1 OH- # conv_H2O__spontaneous_H2O-dissociation : 1 H2O <=> 1 H+ + 1 OH- # conv_hydrogen-carbonate__spontaneous_4.2.1.1_RXN0-5224 : 1 hydrogen_carbonate + 1 H+ <=> 1 CO2 + 1 H2O # conv_hydrolysis_ammonium-sulfate_spontaneous : 1 ammonium_sulfate + 1 H2O --> 1 ammonium + 1 sulfate # conv_hydrolysis_PPPi_3.6.1.1_BS383385 : 2 H2O + 1 PPPi <=> 3 phosphate # Saci_0955 conv_hydrolysis_diphosphate_3.6.1.1_INORGPYROPHOSPHAT-RXN : 1 diphosphate + 1 H2O <=> 2 phosphate # Saci_0955 conv_hydrolysis_acetyl-P_3.6.1.7_BS165360 : 1 acetyl_phosphate + 1 H2O --> 1 acetate + 1 phosphate # Saci_1420 conv_hydrolysis_carbamoyl-P_3.6.1.7_BS93363 : 1 carbamoyl-phosphate + 1 H2O --> 1 carbamate + 1 phosphate # Saci_1420 conv_hydrolysis_2PG_3.6.1.7_BS165362 : 1 1,3-bisphospho-D-glycerate + 1 H2O --> 1 3-phospho-D-glycerate + 1 phosphate # Saci_1420 # conv_carb__5.1.3.-_RXN-14815 : 1 alpha-D-mannose_6-phosphate <=> 1 beta-D-mannose_6-phosphate # conv_carb__5.3.1.8_BS1025 : 1 D-allose <=> 1 D-psicose # Saci_0151 conv_carb__5.3.1.8_BS388478 : 1 aldehydo-D-talose <=> 1 D-tagatose # Saci_0151 conv_carb__5.3.1.8_BS401241 : 1 L-allose <=> 1 L-psicose # Saci_0151 conv_carb__5.3.1.8_MANNPISOM-RXN : 1 alpha-D-mannose_6-phosphate <=> 1 beta-D-fructofuranose_6-phosphate # Saci_0151 conv_carb_spontaneous_5.1.3.3_ALDOSE-1-EPIMERASE-RXN : 1 alpha-D-glucose <=> 1 beta-D-glucose # Saci_2185 conv_pyroglutamate_spontaneous : 1 L-glutamate --> 1 L-pyroglutamate + 1 H2O conv_pyroglutamate-ex_spontaneous : 1 L-glutamate_ex --> 1 L-pyroglutamate_ex + 1 H2O # ================================ core metabolism ================================ # # --- branched entner-doudoroff // special glycolysis up to acetyl-CoA # core_ed_both_1.1.1.47,1.1.1.359_GLUCOSE-1-DEHYDROGENASE-NAD-RXN : 1 beta-D-glucose + 1 NAD+ <=> 1 D-glucono-1,5-lactone + 1 NADH + 1 H+ # Saci_1079 core_ed_both_3.1.1.17_GLUCONOLACT-RXN : 1 D-glucono-1,5-lactone + 1 H2O <=> 1 D-gluconate + 1 H+ # Saci_1674 core_ed_both_4.2.1.39,4.2.1.140_GLUCONATE-DEHYDRATASE-RXN : 1 D-gluconate <=> 1 2-dehydro-3-deoxy-D-gluconate + 1 H2O # Saci_0885 core_ed_non_4.1.2.14,4.1.2.55_DHDOGALDOL-RXN : 1 2-dehydro-3-deoxy-D-gluconate <=> 1 D-glyceraldehyde + 1 pyruvate # Saci_0225 core_ed_non_1.2.99.8_GLYCERALDEHYDE-DEHYDRO-RXN : 1 oxidized_ferredoxin + 1 D-glyceraldehyde + 1 H2O <=> 1 reduced_ferredoxin + 1 D-glycerate + 1 H+ # Saci_2269-71 core_ed_non_2.7.1.165_GKI-RXN : 1 ATP + 1 D-glycerate --> 1 2-phospho-D-glycerate + 1 ADP # Saci_0113 core_ed_semi_2.7.1.45,2.7.1.178_DEOXYGLUCONOKIN-RXN : 1 2-dehydro-3-deoxy-D-gluconate + 1 ATP --> 1 2-dehydro-3-deoxy-D-gluconate_6-phosphate + 1 ADP # Saci_0226 core_ed_semi_4.1.2.55_KDPGALDOL-RXN : 1 2-dehydro-3-deoxy-D-gluconate_6-phosphate <=> 1 D-glyceraldehyde_3-phosphate + 1 pyruvate # Saci_0225 core_ed_semi_1.2.1.9_1.2.1.9-RXN : 1 D-glyceraldehyde_3-phosphate + 1 NADP+ + 1 H2O --> 1 H+ + 1 3-phospho-D-glycerate + 1 NADPH # Saci_0227 direction from Brasen2014 core_ed_semi_5.4.2.12_3PGAREARR-RXN : 1 2-phospho-D-glycerate <=> 1 3-phospho-D-glycerate # Saci_0837 core_ed_both_4.2.1.11_2PGADEHYDRAT-RXN : 1 2-phospho-D-glycerate <=> 1 phosphoenolpyruvate + 1 H2O # Saci_1377 core_ed_both_2.7.1.40_PEPDEPHOS-RXN : 1 ATP + 1 pyruvate <-- 1 ADP + 1 phosphoenolpyruvate # Saci_1648 direction from Brasen2014 core_ed_both_1.2.7.1_PYRUFLAVREDUCT-RXN : 1 coenzyme_A + 1 pyruvate + 2 oxidized_ferredoxin --> 2 H+ + 1 acetyl-CoA + 1 CO2 + 2 reduced_ferredoxin # Saci_2250-3 # --- emden meyerhof parnas --- # core_emp__1.2.1.59_GAPDHSYNEC-RXN : 1 NAD+ + 1 D-glyceraldehyde_3-phosphate + 1 phosphate <=> 1 H+ + 1 1,3-bisphospho-D-glycerate + 1 NADH # Saci_1356 core_emp__2.7.2.3_PHOSGLYPHOS-RXN : 1 ATP + 1 3-phospho-D-glycerate <=> 1 ADP + 1 1,3-bisphospho-D-glycerate # Saci_1355 core_emp__5.3.1.1_TRIOSEPISOMERIZATION-RXN : 1 D-glyceraldehyde_3-phosphate <=> 1 dihydroxyacetone_phosphate # Saci_0117 core_emp__4.1.2.13_F16ALDOLASE-RXN : 1 fructose_1,6-bisphosphate <=> 1 dihydroxyacetone_phosphate + 1 D-glyceraldehyde_3-phosphate # Saci_0671 core_emp__3.1.3.11_F16BDEPHOS-RXN : 1 fructose_1,6-bisphosphate + 1 H2O --> 1 beta-D-fructofuranose_6-phosphate + 1 phosphate # Saci_0671 core_emp__5.3.1.9_PGLUCISOM-RXN : 1 beta-D-glucose_6-phosphate <=> 1 beta-D-fructofuranose_6-phosphate # Saci_0151 core_emp__5.3.1.9_GLUCOSE-6-PHOSPHATE-1-EPIMERASE-RXN : 1 alpha-D-glucose_6-phosphate <=> 1 beta-D-glucose_6-phosphate # Saci_0151 core_emp__5.4.2.2,5.4.2.6_PHOSPHOGLUCMUT-RXN : 1 alpha-D-glucose_1-phosphate <=> 1 alpha-D-glucose_6-phosphate # Saci_0806 #core_emp__3.6.1.1_GLUCOSE-1-PHOSPHAT-RXN : 1 H2O + 1 alpha-D-glucose_1-phosphate <=> 1 phosphate + 1 beta-D-glucose # nsb core_emp__3.1.3.9_BR15946 : 1 beta-D-glucose_6-phosphate + 1 H2O --> 1 beta-D-glucose + 1 phosphate # Saci_0930 core_emp__2.7.1.1_GLUCOKIN-RXN : 1 ATP + 1 beta-D-glucose--> 1 ADP + 1 beta-D-glucose_6-phosphate # Saci_0424 # --- citric acid cycle --- # core_cac_01_2.3.3.1,2.3.3.16_CITRATE-RE-SYNTHASE-RXN : 1 acetyl-CoA + 1 oxaloacetate + 1 H2O --> 1 citrate + 1 coenzyme_A # Saci_0243 core_cac_02_4.2.1.3_BS18707 : 1 H2O + 1 cis-aconitate <=> 1 citrate # Saci_1214 core_cac_03_4.2.1.3_BS18708 : 1 D-threo-isocitrate <=> 1 H2O + 1 cis-aconitate # Saci_1214 core_cac_04_1.1.1.42,1.1.1.286_RXN-7969 : 1 NAD+ + 1 D-threo-isocitrate --> 1 H+ + 1 2-oxoglutarate + 1 CO2 + 1 NADH # Saci_2375 core_cac_06_1.2.7.3,1.2.7.11_2-OXOGLUTARATE-SYNTHASE-RXN : 1 2-oxoglutarate + 1 coenzyme_A + 2 oxidized_ferredoxin --> 2 H+ + 1 CO2 + 1 succinyl-CoA + 2 reduced_ferredoxin # Saci_2306-7 core_cac_07_6.2.1.5_SUCCCOASYN-RXN : 1 ATP + 1 coenzyme_A + 1 succinate <=> 1 ADP + 1 phosphate + 1 succinyl-CoA # Saci_1265-6 core_cac_08_1.3.5.1_SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN : 1 succinate + 1 representative_quinone <=> 1 fumarate + 1 representative_quinol # Saci_0979-82 core_cac_09_4.2.1.2_FUMHYDR-RXN : 1 (S)-malate <=> 1 fumarate + 1 H2O # Saci_0122 core_cac_10_1.1.1.37_MALATE-DEH-RXN-NAD : 1 (S)-malate + 1 NAD+ <=> 1 oxaloacetate + 1 H+ + 1 NADH # Saci_0246 # --- oxidative phosphorylation // according to Schäfer et al. (1999), Gleissner et al. (1994)# core_oxp_redox_1.6.5.3_RXN0-5330 : 1 NADH + 1 H+ + 1 representative_quinone <=> 1 NAD+ + 1 representative_quinol # Saci_2338-46 core_oxp_redox_1.10.3.13_doxABCDE_TRANS-RXN-240 : 0.5 oxygen + 1 representative_quinol + 4 H+ --> 1 H2O + 1 representative_quinone + 2 H+_pp # Saci_2087-9, Saci_0097-8, Saci_1861 core_oxp_ATP-syn_3.6.3.14_ATPSYN-RXN : 1 ADP + 1 phosphate + 4 H+_pp --> 1 ATP + 1 H2O + 4 H+ # Saci_1545-52 # --- glyoxylate cycle --- // according to Uhrigshardt et al. (2001)# core_glyox__4.1.3.1_ISOCIT-CLEAV-RXN : 1 D-threo-isocitrate <=> 1 glyoxylate + 1 succinate # Saci_2191 core_glyox__4.1.3.2,2.3.3.9_MALSYN-RXN : 1 acetyl-CoA + 1 glyoxylate + 1 H2O --> 1 coenzyme_A + 1 (S)-malate # Saci_2190 # --- anaplerotic reactions // conversion between C4 and C3# core_anap__2.7.9.2_PEPSYNTH-RXN : 1 ATP + 1 pyruvate + 1 H2O --> 1 AMP + 1 phosphoenolpyruvate + 1 phosphate # Saci_1417, Saci_2106 core_anap__4.1.1.32_4.1.1.32-RXN : 1 GTP + 1 oxaloacetate <=> 1 CO2 + 1 GDP + 1 phosphoenolpyruvate # Saci_1100 core_anap__4.1.1.31_PEPCARBOX-RXN : 1 oxaloacetate + 1 phosphate <-- 1 hydrogen_carbonate + 1 phosphoenolpyruvate # Saci_0059 # core_anap__6.4.1.1_PYRUVATE-CARBOXYLASE-RXN : 1 hydrogen_carbonate + 1 pyruvate + 1 ATP --> 1 H+ + 1 phosphate + 1 ADP + 1 oxaloacetate # core_anap__1.1.1.40,1.1.1.38_MALIC-NADP-RXN : 1 (S)-malate + 1 NADP+ <=> 1 CO2 + 1 NADPH + 1 pyruvate # Saci_2154 core_anap__1.1.1.40,4.1.1.3_OXALODECARB-RXN : 1 oxaloacetate + 1 H+ --> 1 CO2 + 1 pyruvate # Saci_2154 # --- pentose phosphate pathway (PPP) ---# core_ppp__5.3.1.9,5.3.1.6_RIB5PISOM-RXN : 1 D-ribose_5-phosphate <=> 1 D-ribulose_5-phosphate # Saci_1301 core_ppp__2.2.1.1_2TRANSKETO-RXN : 1 D-erythrose_4-phosphate + 1 D-xylulose_5-phosphate <=> 1 beta-D-fructofuranose_6-phosphate + 1 D-glyceraldehyde_3-phosphate # Saci_0180 core_ppp__2.2.1.1_1TRANSKETO-RXN : 1 D-sedoheptulose_7-phosphate + 1 D-glyceraldehyde_3-phosphate <=> 1 D-ribose_5-phosphate + 1 D-xylulose_5-phosphate # Saci_0180 core_ppp__4.1.2.13_SEDOBISALDOL-RXN : 1 D-erythrose_4-phosphate + 1 dihydroxyacetone_phosphate <=> 1 D-sedoheptulose-1,7-bisphosphate # Saci_0671 core_ppp__3.1.3.11_SEDOHEPTULOSE-BISPHOSPHATASE-RXN : 1 D-sedoheptulose-1,7-bisphosphate + 1 H2O --> 1 phosphate + 1 D-sedoheptulose_7-phosphate # Saci_0671 # --- reverse ribulose-monophosphate pathway (RuMP) //-> formaldehyd assimilation // PMID 16278835# core_rump__5.3.1.27_R12-RXN : 1 hexulose_6-phosphate <=> 1 beta-D-fructofuranose_6-phosphate # Saci_0747 core_rump__4.1.2.43_R10-RXN : 1 hexulose_6-phosphate <=> 1 formaldehyde + 1 D-ribulose_5-phosphate # Saci_0802 # --- carbon fixation // 3-hydroxypropanoate/4-hydroxybutanate cycle // JHE Hügler et al. (2003)# core_carbon-fixation__6.3.4.15_BIOTINLIG-RXN : 1 |BCCP-monomers| + 1 biotin + 1 ATP <=> 1 AMP + 1 |biotin-BCCP-monomer| + 1 diphosphate # Saci_1641 core_carbon-fixation_BCCP-dimerisation_spontaneous_RXN-7101 : 2 |biotin-BCCP-monomer| <=> 1 |biotin-BCCP-dimer| # spontaneous core_carbon-fixation__6.3.4.14_BIOTIN-CARBOXYL-RXN : 1 ATP + 1 hydrogen_carbonate + 1 |biotin-BCCP-dimer| <=> 1 ADP + 1 phosphate + 1 H+ + 1 |carboxy-biotin-BCCP-dimer| # Saci_0260 core_carbon-fixation__6.4.1.2_RXN0-5055 : 1 |carboxy-biotin-BCCP-dimer| + 1 H2O + 1 ATP + 1 acetyl-CoA --> 1 |biotin-BCCP-dimer| + 1 malonyl-CoA + 1 ADP + 1 phosphate + 1 H+ # Saci_0260-2 core_carbon-fixation__1.2.1.75_RXN-8963 : 1 3-oxopropanoate + 1 coenzyme_A + 1 NADP+ <=> 1 malonyl-CoA + 1 NADPH + 1 H+ # Saci_2370 core_carbon-fixation__1.1.1.298_RXN-8974 : 1 3-hydroxypropanoate + 1 NADP+ <=> 1 3-oxopropanoate + 1 NADPH + 1 H+ # Saci_1623 core_carbon-fixation__6.2.1.36_RXN-9086 : 1 3-hydroxypropanoate + 1 ATP + 1 coenzyme_A --> 1 3-hydroxypropanoyl-CoA + 1 AMP + 1 diphosphate # Saci_2235 core_carbon-fixation__4.2.1.116_RXN-6383 : 1 3-hydroxypropanoyl-CoA <=> 1 acryloyl-CoA + 1 H2O # Saci_1633, Saci_2063 core_carbon-fixation__1.3.1.84_RXN-9087 : 1 NADP+ + 1 propanoyl-CoA <=> 1 acryloyl-CoA + 1 NADPH + 1 H+ # Saci_0911, Saci_1115, Saci_2205 core_carbon-fixation__6.4.1.3_PROPIONYL-COA-CARBOXY-RXN : 1 ATP + 1 hydrogen_carbonate + 1 propanoyl-CoA --> 1 ADP + 1 (S)-methylmalonyl-CoA + 1 phosphate # Saci_0262 core_carbon-fixation__5.1.99.1_METHYLMALONYL-COA-EPIM-RXN : 1 (S)-methylmalonyl-CoA <=> 1 (R)-methylmalonyl-CoA # Saci_0923 core_carbon-fixation__5.4.99.2_Methylmalonyl-CoA-mutase : 1 (R)-methylmalonyl-CoA <=> 1 succinyl-CoA # Saci_0924 core_carbon-fixation__1.2.1.75,1.2.1.76_RXN-8891 : 1 coenzyme_A + 1 NADP+ + 1 succinate_semialdehyde <=> 1 NADPH + 1 H+ + 1 succinyl-CoA # Saci_2147, Saci_2370 core_carbon-fixation__1.1.1.B47_4-HYDROXYBUTYRATE-DEHYDROGENASE-RXN : 1 4-hydroxybutanoate + 1 NADP+ <=> 1 NADPH + 1 H+ + 1 succinate_semialdehyde # Saci_2145, Saci_2224 core_carbon-fixation__6.2.1.40_RXN-9092 : 1 4-hydroxybutanoate + 1 ATP + 1 coenzyme_A --> 1 4-hydroxybutanoyl-CoA + 1 AMP + 1 diphosphate # Saci_1184 core_carbon-fixation__4.2.1.120_RXN-8890 : 1 4-hydroxybutanoyl-CoA <=> 1 vinylacetyl-CoA + 1 H2O # Saci_1103, Saci_2143 core_carbon-fixation__5.3.3.3_VINYLACETYL-COA-DELTA-ISOMERASE-RXN : 1 vinylacetyl-CoA <=> 1 crotonyl-CoA # Saci_1103, Saci_2143 core_carbon-fixation__4.2.1.17_BS402361 : 1 4-hydroxybutanoyl-CoA <=> 1 crotonyl-CoA + 1 H2O# Saci_2285-6 core_carbon-fixation__4.2.1.17_4.2.1.150_RXN-11667 : 1 (S)-3-hydroxybutanoyl-CoA <=> 1 H2O + 1 crotonyl-CoA # Saci_2285-6 core_carbon-fixation__1.1.1.157,1.1.1.35_3-HYDROXYBUTYRYL-COA-DEHYDROGENASE-RXN : 1 NADP+ + 1 (S)-3-hydroxybutanoyl-CoA <=> 1 acetoacetyl-CoA + 1 NADPH + 1 H+ # Saci_1078 core_carbon-fixation__2.3.1.9_ACETYL-COA-ACETYLTRANSFER-RXN : 2 acetyl-CoA <=> 1 acetoacetyl-CoA + 1 coenzyme_A # Saci_0963, Saci_1728, Saci_2209, Saci_2232, Saci_2288 # --- 2-methylcitrate cycle ---# core_2-methylcitrate-cycle__2.3.3.5,2.3.3.16_2-METHYLCITRATE-SYNTHASE-RXN : 1 H2O + 1 propanoyl-CoA + 1 oxaloacetate <=> 1 H+ + 1 (2S,3S)-2-methylcitrate + 1 coenzyme_A # Saci_0243 core_2-methylcitrate-cycle__4.2.1.79_2-METHYLCITRATE-DEHYDRATASE-RXN : 1 (2S,3S)-2-methylcitrate <=> 1 H2O + 1 cis-2-methylaconitate # Saci_0245 core_2-methylcitrate-cycle__4.2.1.99_4.2.1.99-RXN : 1 (2R,3S)-2-methylisocitrate <=> 1 H2O + 1 cis-2-methylaconitate # Saci_1214 core_2-methylcitrate-cycle__4.1.3.30_METHYLISOCITRATE-LYASE-RXN : 1 (2R,3S)-2-methylisocitrate --> 1 pyruvate + 1 succinate # Saci_0244 JHE direction assumed # --- sulfur metabolism // no sulfur oxidization according to Chen et al. (2005)# core_sulf__2.8.1.1_THIOSULFATE-SULFURTRANSFERASE-RXN : 1 thiosulfate + 1 hydrogen_cyanide <=> 1 sulfite + 1 thiocyanate + 1 H+ # Saci_2198 core_sulf__1.8.7.1_SULFITE-REDUCTASE-FERREDOXIN-RXN : 1 hydrogen_sulfide + 3 oxidized_ferredoxin + 3 H2O <-- 1 sulfite + 3 reduced_ferredoxin + 6 H+ # Saci_2201 core_sulf__2.7.7.4_SULFATE-ADENYLYLTRANS-RXN : 1 ATP + 1 sulfate <=> 1 adenosine_5'-phosphosulfate + 1 diphosphate # Saci_2203 core_sulf__2.7.1.25_ADENYLYLSULFKIN-RXN : 1 adenosine_5'-phosphosulfate + 1 ATP <=> 1 ADP + 1 3'-phosphoadenylyl-sulfate # nsb core_sulf__1.8.4.8_1.8.4.8-RXN : 1 adenosine_3',5'-bisphosphate + 1 sulfite + 1 oxidized_thioredoxin <=> 2 H+ + 1 3'-phosphoadenylyl-sulfate + 1 reduced_thioredoxin # Saci_2202 core_sulf__1.8.5.4_BS417675 : 1 hydrogen_sulfide + 1 representative_quinone <=> 1 S0 + 1 representative_quinol # Saci_0331 core_sulf__3.1.3.7_325-BISPHOSPHATE-NUCLEOTIDASE-RXN : 1 adenosine_3',5'-bisphosphate + 1 H2O --> 1 AMP + 1 phosphate # nsb # ================================ amino acid synthesis ================================ # aa_glu__1.4.1.4_GLUTAMATE-DEHYDROGENASE-NADP+-RXN-NADP : 1 L-glutamate + 1 H2O + 1 NADP+ <=> 1 H+ + 1 2-oxoglutarate + 1 ammonia + 1 NADPH # Saci_0155 aa_glu__3.5.2.9_5-OXOPROLINASE-ATP-HYDROLYSING-RXN : 1 ATP + 2 H2O + 1 L-pyroglutamate --> 1 phosphate + 1 L-glutamate + 1 ADP # Saci_2041-2 aa_gln__6.3.1.2_GLUTAMINESYN-RXN : 1 ammonia + 1 ATP + 1 L-glutamate <=> 1 ADP + 1 L-glutamine + 1 phosphate # Saci_0558, Saci_1483, Saci_2141 # --- Synthesis with LysW as carrier protein // [Ouchi2013] // PWY-3081 aa_lys__2.3.3.14_HOMOCITRATE-SYNTHASE-RXN : 1 acetyl-CoA + 1 2-oxoglutarate + 1 H2O --> 1 (2R)-homocitrate + 1 coenzyme_A # Saci_1304 aa_lys__spontaneous_RXN3O-1983 : 1 (2R)-homocitrate --> 1 cis-homoaconitate + 1 H2O # spontaneous aa_lys__spontaneous_4.2.1.36,4.2.1.114_HOMOACONITATE-HYDRATASE-RXN : 1 (1R,2S)-homoisocitrate <=> 1 cis-homoaconitate + 1 H2O # spontaneous aa_lys__1.1.1.87,1.1.1.286_RXN-7970 : 1 NAD+ + 1 (1R,2S)-homoisocitrate --> 1 H+ + 1 2-oxoadipate + 1 CO2 + 1 NADH # Saci_2375 aa_lys__2.6.1.39_2-AMINOADIPATE-AMINOTRANSFERASE-RXN : 1 L-2-aminoadipate + 1 2-oxoglutarate <-- 1 2-oxoadipate + 1 L-glutamate # Saci_1014 forced dir aa_lys__1.4.1.4_BS371741 : 1 2-oxoadipate + 1 NADPH + 1 ammonia <=> 1 L-2-aminoadipate + 1 NADP+ + 1 H2O # Saci_0155 aa_lys_LysX_6.3.2.43_RXN-15002 : 1 L-2-aminoadipate + 1 ATP + 1 [LysW] --> 1 phosphate + 1 ADP + 1 [LysW]-alpha-aminoadipate + 1 H+ # Saci_0754 aa_lys_LysZ_2.7.2.-_RXN-5182 : 1 [LysW]-alpha-aminoadipate + 1 ATP --> 1 ADP + 1 [LysW]-alpha-aminoadipate-phosphate # Saci_0751 aa_lys_LysY_1.2.1.-_RXN-5183 : 1 NADPH + 1 [LysW]-alpha-aminoadipate-phosphate + 1 H+ --> 1 NADP+ + 1 [LysW]-alpha-aminoadipate-semialdehyde + 1 phosphate # Saci_0750 aa_lys_LysJ_2.6.1.-_RXN-5184 : 1 2-oxoglutarate + 1 [LysW]-L-lysine <=> 1 L-glutamate + 1 [LysW]-alpha-aminoadipate-semialdehyde # Saci_0755 aa_lys_LysK_3.5.1.-_RXN-5185 : 1 [LysW]-L-lysine + 1 H2O --> 1 [LysW] + 1 L-lysine # Saci_0756 # --- Synthesis with LysW as carrier protein // [Ouchi2013] // PWY-7400 aa_orn_LysX_6.3.2.43_6.3.2.M4_RXN-15003 : 1 L-glutamate + 1 ATP + 1 [LysW] --> 1 phosphate + 1 ADP + 1 [LysW]-L-glutamate + 1 H+ # Saci_0754 aa_orn_LysZ_2.7.2.-_RXN-15005 : 1 [LysW]-L-glutamate + 1 ATP --> 1 [LysW]-L-glutamate_5-phosphate + 1 ADP # Saci_0751 aa_orn_LysY_1.2.1.-_RXN-15006 : 1 [LysW]-L-glutamate_5-phosphate + 1 H+ + 1 NADPH --> [LysW]-L-glutamate_5-semialdehyde + 1 NADP+ + 1 phosphate # Saci_0750 aa_orn_LysJ_2.6.1.-_RXN-15007 : 1 [LysW]-L-glutamate_5-semialdehyde + 1 L-glutamate <=> [LysW]-L-ornithine + 1 2-oxoglutarate # Saci_0755 aa_orn_LysK_3.5.1.-_RXN-15004 : 1 [LysW]-L-ornithine + 1 H2O --> [LysW] + 1 L-ornithine # Saci_0756 aa_arg_oro_6.3.5.5_CARBPSYN-RXN : 2 ATP + 1 L-glutamine + 1 hydrogen_carbonate + 1 H2O --> 2 ADP + 1 carbamoyl-phosphate + 1 L-glutamate + 1 phosphate # Saci_1619-20 aa_arg_ureacyc_2.1.3.3_ORNCARBAMTRANSFER-RXN : 1 carbamoyl-phosphate + 1 L-ornithine <=> 1 L-citrulline + 1 phosphate # Saci_1408 aa_arg_ureacyc_6.3.4.5_ARGSUCCINSYN-RXN : 1 ATP + 1 L-aspartate + 1 L-citrulline <=> 1 AMP + 1 L-arginino-succinate + 1 diphosphate # Saci_1617 aa_arg_ureacyc_4.3.2.1_ARGSUCCINLYA-RXN : 1 L-arginino-succinate <=> 1 L-arginine + 1 fumarate # Saci_1618 aa_arg_ureacyc_3.5.3.1_ARGINASE-RXN : 1 H2O + 1 L-arginine --> 1 urea + 1 L-ornithine # Saci_0863, Saci_2134 aa_pro__4.3.1.12_ORNITHINE-CYCLODEAMINASE-RXN : 1 L-ornithine --> 1 L-proline + 1 ammonia # Saci_2372 aa_ile__2.3.1.182_RXN-7743 : 1 acetyl-CoA + 1 pyruvate + 1 H2O <=> 1 coenzyme_A + 1 (R)-citramalate # Saci_2325 aa_ile__4.2.1.35_R-2-METHYLMALATE-DEHYDRATASE-RXN : 1 (R)-citramalate --> 1 (2R,3S)-3-methylmalate # Saci_1214? aa_ile__1.1.1.85_RXN-7745 : 1 NAD+ + 1 (2R,3S)-3-methylmalate <=> 1 H+ + 1 2-oxobutanoate + 1 NADH + 1 CO2 # Saci_0600 aa_ile__2.2.1.6_ACETOOHBUTSYN-RXN : 1 2-oxobutanoate + 1 pyruvate --> 1 2-hydroxy-2-ethyl-3-oxobutanoate + 1 CO2 # Saci_1137, Saci_1561, Saci_2255, Saci_2281 aa_ile__1.1.1.86_ACETOOHBUTREDUCTOISOM-RXN : 1 2,3-dihydroxy-3-methylpentanoate + 1 NAD+ <=> 1 2-hydroxy-2-ethyl-3-oxobutanoate + 1 NADH + 1 H+ # Saci_1559 aa_ile__4.2.1.9_DIHYDROXYMETVALDEHYDRAT-RXN : 1 2,3-dihydroxy-3-methylpentanoate --> 1 (S)-3-methyl-2-oxopentanoate + 1 H2O # Saci_1715 aa_ile__2.6.1.42_BRANCHED-CHAINAMINOTRANSFERILEU-RXN : 1 2-oxoglutarate + 1 L-isoleucine <=> 1 (S)-3-methyl-2-oxopentanoate + 1 L-glutamate # Saci_1507 aa_val-leu__2.2.1.6_ACETOLACTSYN-RXN : 2 pyruvate --> 1 (S)-2-acetolactate + 1 CO2 # Saci_1137, Saci_1561, Saci_2255, Saci_2281 aa_val-leu__1.1.1.86,1.1.1.382_ACETOLACTREDUCTOISOM-RXN : 1 (R)-2,3-dihydroxy-3-methylbutanoate + 1 NAD+ <=> 1 (S)-2-acetolactate + 1 NADH + 1 H+ # Saci_1559 aa_val-leu__4.2.1.9_DIHYDROXYISOVALDEHYDRAT-RXN : 1 (R)-2,3-dihydroxy-3-methylbutanoate --> 1 3-methyl-2-oxobutanoate + 1 H2O # Saci_1715 aa_val__2.6.1.42_BRANCHED-CHAINAMINOTRANSFERVAL-RXN : 1 2-oxoglutarate + 1 L-valine <=> 1 3-methyl-2-oxobutanoate + 1 L-glutamate # Saci_1507 aa_leu__2.3.3.13_2-ISOPROPYLMALATESYN-RXN : 1 3-methyl-2-oxobutanoate + 1 acetyl-CoA + 1 H2O --> 1 (2S)-2-isopropylmalate + 1 coenzyme_A # Saci_0940 aa_leu__4.2.1.33_RXN-13163 : 1 (2R,3S)-3-isopropylmalate <=> 1 (2S)-2-isopropylmalate # Saci_0252-3 aa_leu__4.2.1.33_BR413 : 1 (2R,3S)-3-isopropylmalate <=> 1 2-isopropylmaleate + 1 H2O # Saci_0252-3 aa_leu__1.1.1.85_RXN-13158 : 1 (2R,3S)-3-isopropylmalate + 1 NAD+ <=> 1 H+ + 1 4-methyl-2-oxopentanoate + 1 CO2 + 1 NADH # Saci_0600 aa_leu__2.6.1.42_BRANCHED-CHAINAMINOTRANSFERLEU-RXN : 1 2-oxoglutarate + 1 L-leucine <=> 1 4-methyl-2-oxopentanoate + 1 L-glutamate # Saci_1507 aa_asp__2.6.1.1_ASPAMINOTRANS-RXN : 1 2-oxoglutarate + 1 L-aspartate <=> 1 L-glutamate + 1 oxaloacetate # Saci_1428 aa_ala__2.6.1.1,2.6.1.2_ALANINE-AMINOTRANSFERASE-RXN : 1 2-oxoglutarate + 1 L-alanine <=> 1 L-glutamate + 1 pyruvate # Saci_1837 aa_ala__1.4.1.1,1.4.1.8_BR33794 : L-alanine + H2O + NAD+ <=> pyruvate + NH3 + NADH + H+ # Saci_1013 aa_thr__2.7.2.4_ASPARTATEKIN-RXN : 1 ATP + 1 L-aspartate <=> 1 ADP + 1 L-aspartyl-4-phosphate # Saci_1412 aa_thr__1.2.1.11_ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN : 1 L-aspartate-semialdehyde + 1 NADP+ + 1 phosphate <=> 1 L-aspartyl-4-phosphate + 1 NADPH + 1 H+ # Saci_1411 aa_thr__1.1.1.3_HOMOSERDEHYDROG-RXN-NADP : 1 L-homoserine + 1 NADP+ <=> 1 L-aspartate-semialdehyde + 1 H+ + 1 NADPH # Saci_1412, Saci_1636 aa_thr__2.7.1.39_HOMOSERKIN-RXN : 1 ATP + 1 L-homoserine --> 1 ADP + 1 O-phospho-L-homoserine # Saci_0972 aa_thr__4.2.3.1_THRESYN-RXN : 1 O-phospho-L-homoserine + 1 H2O --> 1 phosphate + 1 L-threonine # Saci_1023, Saci_1413 aa_ser__1.1.1.95_PGLYCDEHYDROG-RXN : 1 3-phospho-D-glycerate + 1 NAD+ <=> 1 3-phospho-hydroxypyruvate + 1 NADH + 1 H+ # Saci_1368 aa_ser__2.6.1.52_PSERTRANSAM-RXN : 1 2-oxoglutarate + 1 3-phospho-L-serine <=> 1 3-phospho-hydroxypyruvate + 1 L-glutamate # Saci_1369 aa_ser__3.1.3.16,3.1.3.3_RXN0-5114 : 1 3-phospho-L-serine + 1 H2O --> 1 phosphate + 1 L-serine # Saci_0545, Saci_0884 aa_gly__2.1.2.1_GLYOHMETRANS-RXN : 1 L-serine + 1 tetrahydrosulfopterin <=> 1 glycine + 1 5,10-methylene-tetrahydrosulfopterin + 1 H2O # Saci_1358 aa_cys__2.3.1.30_SERINE-O-ACETTRAN-RXN : 1 acetyl-CoA + 1 L-serine --> 1 O-acetyl-L-serine + 1 coenzyme_A # Saci_1488? aa_cys__2.5.1.47_ACSERLY-RXN : 1 O-acetyl-L-serine + 1 hydrogen_sulfide <=> 1 acetate + 1 L-cysteine # Saci_1475 aa_his_HisG_2.4.2.17_ATPPHOSPHORIBOSYLTRANS-RXN : 1 1-(5-phospho-beta-D-ribosyl)-ATP + 1 diphosphate <=> 1 ATP + 1 5-phospho-alpha-D-ribose_1-diphosphate # Saci_1575 aa_his_HisI_3.6.1.31_HISTPRATPHYD-RXN : 1 1-(5-phospho-beta-D-ribosyl)-ATP + 1 H2O --> 1 1-(5-phospho-D-ribosyl)-AMP + 1 diphosphate # Saci_1580 aa_his_HisJ_3.5.4.19_HISTCYCLOHYD-RXN : 1 1-(5-phospho-D-ribosyl)-AMP + 1 H2O --> 1 1-(5-phospho-beta-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide # Saci_1582 aa_his_HisA_5.3.1.16_PRIBFAICARPISOM-RXN : 1 1-(5-phospho-beta-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide <=> 1 phosphoribulosylformimino-AICAR-P # Saci_1576 aa_his_HisHF_2.4.2.-_4.1.3.-_4.3.1.B2_GLUTAMIDOTRANS-RXN : 1 L-glutamine + 1 phosphoribulosylformimino-AICAR-P --> 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + 1 D-erythro-imidazole-glycerol-phosphate + 1 L-glutamate # Saci_1578/81 aa_his_HisB_4.2.1.19_IMIDPHOSDEHYD-RXN : 1 D-erythro-imidazole-glycerol-phosphate --> 1 imidazole_acetol-phosphate + 1 H2O # Saci_1577 aa_his_HisC_2.6.1.9_HISTAMINOTRANS-RXN : 1 L-glutamate + 1 imidazole_acetol-phosphate <=> 1 2-oxoglutarate + 1 L-histidinol-phosphate # Saci_0454, Saci_1574 aa_his_HisN_3.1.3.15_HISTIDPHOS-RXN : 1 L-histidinol-phosphate + 1 H2O --> 1 histidinol + 1 phosphate # nsb aa_his_HisD_1.1.1.23_BS371011 : 1 histidinol + 1 NAD+ --> 1 histidinal + 1 NADH + 1 H+ # Saci_1579 aa_his_HisD_1.1.1.23_BS187855 : 1 H2O + 1 histidinal + 1 NAD+ --> 1 H+ + 1 L-histidine + 1 NADH # Saci_1579 # --- shikimate pathway // for phe, trp, tyr aa_shiki_AroA_2.5.1.54_DAHPSYN-RXN : 1 D-erythrose_4-phosphate + 1 phosphoenolpyruvate + 1 H2O --> 1 3-deoxy-D-arabino-heptulosonate-7-phosphate + 1 phosphate # Saci_0183 aa_shiki_AroB_4.2.3.4_3-DEHYDROQUINATE-SYNTHASE-RXN : 1 3-deoxy-D-arabino-heptulosonate-7-phosphate --> 1 3-dehydroquinate + 1 phosphate # Saci_0184 aa_shiki_AroD_4.2.1.10_3-DEHYDROQUINATE-DEHYDRATASE-RXN : 1 3-dehydroquinate <=> 1 3-dehydroshikimate + 1 H2O # Saci_0189 aa_shiki_AroE_1.1.1.25_RXN-7968-NADP : 1 shikimate + 1 NADP+ <=> 1 3-dehydroshikimate + 1 H+ + 1 NADPH # Saci_0185 aa_shiki_AroK_2.7.1.71_SHIKIMATE-KINASE-RXN : 1 ATP + 1 shikimate --> 1 ADP + 1 shikimate-3-phosphate # Saci_0187 aa_shiki_AroA_2.5.1.19_2.5.1.19-RXN : 1 phosphoenolpyruvate + 1 shikimate-3-phosphate <=> 1 5-enolpyruvyl-shikimate-3-phosphate + 1 phosphate # Saci_0188 aa_shiki_AroC_4.2.3.5_CHORISMATE-SYNTHASE-RXN : 1 5-enolpyruvyl-shikimate-3-phosphate --> 1 chorismate + 1 phosphate # Saci_0186 aa_trp_TrpEG_4.1.3.27_ANTHRANSYN-RXN : 1 chorismate + 1 L-glutamine <=> 1 anthranilate + 1 L-glutamate + 1 pyruvate # Saci_1425-6 aa_trp_TrpD_2.4.2.18_PRTRANS-RXN : 1 N-(5-phosphoribosyl)-anthranilate + 1 diphosphate <-- 1 anthranilate + 1 5-phospho-alpha-D-ribose_1-diphosphate # Saci_1423 aa_trp_TrpF_5.3.1.24_PRAISOM-RXN : 1 N-(5-phosphoribosyl)-anthranilate --> 1 1-(o-carboxyphenylamino)-1'-deoxyribulose_5'-phosphate # Saci_1424 aa_trp_TrpC_4.1.1.48_IGPSYN-RXN : 1 1-(o-carboxyphenylamino)-1'-deoxyribulose_5'-phosphate --> 1 CO2 + 1 (1S,2R)-1-C-(indol-3-yl)glycerol_3-phosphate + 1 H2O # Saci_1427 aa_trp_TrpAB_4.2.1.20_RXN0-2381 : 1 (1S,2R)-1-C-(indol-3-yl)glycerol_3-phosphate <=> 1 indole + 1 D-glyceraldehyde_3-phosphate # Saci_1421-2 aa_trp_TrpAB_4.2.1.20_RXN0-2382 : 1 L-serine + 1 indole --> 1 L-tryptophan + 1 H2O # Saci_1421-2 aa_phe-tyr_PheA_4.2.1.51,5.4.99.5_CHORISMATEMUT-RXN : 1 chorismate <=> 1 prephenate # Saci_0712 aa_phe__4.2.1.51_PREPHENATEDEHYDRAT-RXN : 1 prephenate --> 1 CO2 + 1 2-oxo-3-phenylpropanoate + 1 H2O # Saci_0712 aa_phe__2.6.1.1,2.6.1.5_PHEAMINOTRANS-RXN : 1 L-glutamate + 1 2-oxo-3-phenylpropanoate <=> 1 2-oxoglutarate + 1 L-phenylalanine # Saci_1428, Saci_1837 aa_tyr_TyrA_1.3.1.13_PREPHENATEDEHYDROG-RXN : 1 NADP+ + 1 prephenate --> 1 H+ + 1 CO2 + 1 NADPH + 1 4-hydroxyphenylpyruvate # Saci_0182 aa_tyr_cof-CQ_2.6.1.5_TYRAMINOTRANS-RXN : 1 2-oxoglutarate + 1 L-tyrosine <=> 1 L-glutamate + 1 4-hydroxyphenylpyruvate # Saci_1837 aa_asn_tRNA_6.1.1.-_6.1.1.23_RXN490-3616 : 1 ATP + 1 L-aspartate + 1 |ASN-tRNAs| --> 1 AMP + 1 diphosphate + 1 |L-aspartyl-tRNAAsn| # Saci_0768 aa_asn_tRNA_6.3.5.6_6.3.5.6-RXN : 1 ATP + 1 L-glutamine + 1 H2O + 1 |L-aspartyl-tRNAAsn| --> 1 ADP + 1 L-glutamate + 1 phosphate + 2 H+ + 1 |Charged-ASN-tRNAs| # Saci_0769 aa_asn__3.1.1.29_RXN-12460 : 1 H2O + 1 |Charged-ASN-tRNAs| --> 1 L-asparagine + 2 H+ + 1 |ASN-tRNAs| # Saci_0770 aa_met__2.5.1.48_O-SUCCHOMOSERLYASE-RXN : 1 L-cysteine + 1 O-succinyl-L-homoserine <=> 1 L-cystathionine + 1 succinate # Saci_0971 aa_met__2.5.1.48_CYSPH-RXN : 1 L-cysteine + 1 O-phospho-L-homoserine --> 1 L-cystathionine + 1 phosphate # Saci_0971 aa_met__4.4.1.8_CYSTATHIONINE-BETA-LYASE-RXN : 1 L-cystathionine + 1 H2O --> 1 ammonia + 1 L-homocysteine + 1 pyruvate # Saci_0971 aa_met_cof-sulfopterin_2.1.1.14_HOMOCYSMET-RXN : 1 5-methyl-tetrahydrosulfopterin + 1 L-homocysteine --> 1 tetrahydrosulfopterin + 1 L-methionine # Saci_0827 aa_met_cof-sam_2.1.1.13_HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN : 1 L-homocysteine + 1 S-adenosyl-L-methionine --> 1 S-adenosyl-L-homocysteine + 1 L-methionine # Saci_0828 aa_met_salvage_5.3.1.23_5.3.1.23-RXN : 1 S-methyl-5-thio-alpha-D-ribose_1-phosphate <=> 1 5-methylthioribulose_1-phosphate # Saci_0539 aa_met_salvage_4.2.1.109_R145-RXN : 1 5-methylthioribulose_1-phosphate --> 1 5-(methylthio)-2,3-dioxopentyl_1-phosphate + 1 H2O # JHE needed? aa_met_salvage_3.1.3.77_3.1.3.77-RXN : 1 5-(methylthio)-2,3-dioxopentyl_1-phosphate + 1 H2O --> 1 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + 1 phosphate # JHE needed? aa_met_salvage_1.13.11.54_R147-RXN : 1 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + 1 oxygen --> 1 2-oxo-4-methylthiobutanoate + 1 formate # JHE needed? aa_met_salvage_2.6.1.57_RXN-7708 : 1 2-oxo-3-phenylpropanoate + 1 L-methionine <=> 1 L-phenylalanine + 1 2-oxo-4-methylthiobutanoate # JHE needed? # --- other amino acids --- # aa_beta-alanine__1.4.3.21_RXN-6381 : 1 H2O + 1 oxygen + 1 propane-1,3-diamine --> 1 hydrogen_peroxide + 1 ammonium + 1 3-aminopropanal # Saci_2182 aa_beta-alanine__1.2.1.19,1.2.1.4_RXN-6382 : 14 H+ + 7 H2O + 1 3-aminopropanal + 3 NAD+ --> 2 NADH + 8 beta-alanine # Saci_1857 aa_beta-alanine__2.6.1.19,2.6.1.55_BS353590 : beta-alanine + 2-oxoglutarate <=> 3-oxopropanoate + L-glutamate # Saci_1028 # ================================ biosynthesis of polysaccharides ================================ # syn_glycogen__2.4.1.21_GLYCOGENSYN-RXN : 1 ADP-alpha-D-glucose --> 1 ADP + 1 glycogen # Saci_1201 # Trehalose biosynthesis [Empadinhas2006]; trehalose as compatible solute [Martins1997]# syn_trehalose_TreX_3.2.1.68_3.2.1.196_RXN-4301 : 1 glycogen <=> 1 maltodextrin # Saci_1439 syn_trehalose_TreY_5.4.99.15_5.4.99.15-RXN : 1 maltodextrin <=> 1 maltooligosyl-trehalose # Saci_1436 syn_trehalose_TreZ_3.2.1.141_RXN : 1 maltooligosyl-trehalose <=> 1 trehalose # Saci_1440 syn_galactose__5.1.3.2_UDPGLUCEPIM-RXN : 1 UDP-alpha-D-glucose <=> 1 UDP-alpha-D-galactose # Saci_0761 syn_GDP-mannose__5.4.2.8_PHOSMANMUT-RXN : 1 alpha-D-mannose_1-phosphate <=> 1 alpha-D-mannose_6-phosphate # Saci_0806 syn_GDP-mannose__2.7.7.13_2.7.7.13-RXN : 1 GTP + 1 alpha-D-mannose_1-phosphate <=> 1 GDP-alpha-D-mannose + 1 diphosphate # Saci_0196;Saci_0196 syn_ADP-glucose__2.7.7.27_GLUC1PADENYLTRANS-RXN : 1 ATP + 1 alpha-D-glucose_1-phosphate <=> 1 ADP-alpha-D-glucose + 1 diphosphate # Saci_1199 syn_UDP-glucose__2.7.7.9_GLUC1PURIDYLTRANS-RXN : 1 alpha-D-glucose_1-phosphate + 1 UTP <=> 1 diphosphate + 1 UDP-alpha-D-glucose # Saci_1199 syn_rhamnose__2.7.7.24_DTDPGLUCOSEPP-RXN : 1 alpha-D-glucose_1-phosphate + 1 dTTP <=> 1 dTDP-alpha-D-glucose + 1 diphosphate # Saci_2366 syn_rhamnose__4.2.1.46_DTDPGLUCDEHYDRAT-RXN : 1 dTDP-alpha-D-glucose --> 1 H2O + 1 dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose # Saci_1704 syn_rhamnose__5.1.3.13_DTDPDEHYDRHAMEPIM-RXN : 1 dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose --> 1 dTDP-4-dehydro-beta-L-rhamnose # Saci_1706 syn_rhamnose__1.1.1.133_DTDPDEHYRHAMREDUCT-RXN : 1 dTDP-beta-L-rhamnose + 1 NADP+ <=> 1 NADPH + 1 dTDP-4-dehydro-beta-L-rhamnose + 1 H+ # Saci_2310 # ================================ degradation pathways ================================ # # --- monosaccharides --- # degra-carb_galactose__1.1.1.21_RXN-12078 : 1 NADP+ + 1 galactitol <=> 1 NADPH + 1 H+ + 1 beta-D-galactose # Saci_2254 degra-carb_galactose__1.1.1.-_1.1.1.12_RXN-12079 : 1 NAD+ + 1 galactitol <=> 1 H+ + 1 L-xylo-3-hexulose + 1 NADH # Saci_2130 degra-carb_galactose__1.1.1.-_RXN-12080 : 1 NADPH + 1 H+ + 1 L-xylo-3-hexulose <=> 1 NADP+ + 1 D-sorbitol # Saci_2130 degra-carb_sorbitol__3.1.3.25_3.1.3.50_SORBITOL-6-PHOSPHATASE-RXN : 1 H2O + 1 D-sorbitol_6-phosphate --> 1 phosphate + 1 D-sorbitol # Saci_0930 degra-carb_sorbitol__1.1.1.14_RXN-7644 : 1 NAD+ + 1 D-sorbitol <=> 1 keto-D-fructose + 1 NADH + 1 H+ # Saci_0410 degra-carb_sorbitol_spontaneous_RXN-14515 : 1 keto-D-fructose --> 1 beta-D-fructofuranose # # --- Weimberg pathway for xylose and arabinose --- # Wagner2017 # GDH from SSO // glucose, galactose, xylose, L-arabinose; both NAD+ and NADP+; 69% identity to Saci (E=0); conserved binding sites# # GDH has higher activity on pentoses with NADP and higher activity on glucose with NAD #degra-carb_arabinose__1.1.1.47_1.1.1.376_RXN-8774-NAD : 1 L-arabinose + 1 NAD+ --> 1 H+ + 1 L-arabinono-1,4-lactone + 1 NADH # Saci_1079 degra-carb_arabinose__1.1.1.47_1.1.1.376_RXN-8774-NADP : 1 L-arabinose + 1 NADP+ --> 1 H+ + 1 L-arabinono-1,4-lactone + 1 NADPH # Saci_1079 degra-carb_arabinose__3.1.1.17_L-arabinose : 1 L-arabinono-1,4-lactone + 1 H2O <=> 1 L-arabinonate # Saci_1674 degra-carb_arabinose__4.2.1.25,4.2.1.140_L-ARABINONATE-DEHYDRATASE-RXN : 1 L-arabinonate --> 1 2-dehydro-3-deoxy-L-arabinonate + 1 H2O # Saci_0885: Wagner2017 degra-carb_arabinose__4.1.2.18_4.1.2.18-RXN : 1 2-dehydro-3-deoxy-L-arabinonate --> 1 glycolaldehyde + 1 pyruvate # Saci_0225: Wagner2017 degra-carb_arabinose_4.2.1.43_BR3395 : 1 2-dehydro-3-deoxy-L-arabinonate --> 1 2,5-dioxopentanoate + 1 H2O # Saci_1938: Wagner2017 #degra-of-pentoses_4.1.2.18_BR349 : 1 2-dehydro-3-deoxy-L-arabinonate <=> 1 pyruvate + 1 glycolaldehyde # Saci_0225 #degra-carb_xylose__1.1.1.47_1.1.1.359_RXN-14641-NAD : 1 alpha-D-xylose + 1 NAD+ --> 1 H+ + 1 D-xylonolactone + 1 NADH # Saci_1079 degra-carb_xylose__1.1.1.47_1.1.1.359_RXN-14641-NADP : 1 alpha-D-xylose + 1 NADP+ --> 1 H+ + 1 D-xylonolactone + 1 NADPH # Saci_1079 degra-carb_xylose__3.1.1.17_RXN-12246 : 1 D-xylonolactone + 1 H2O <=> 1 D-xylonate # Saci_1674 degra-carb_xylose_KDX_4.2.1.82,4.2.1.140_XYLONATE-DEHYDRATASE-RXN : 1 D-xylonate --> 1 2-dehydro-3-deoxy-D-arabinonate + 1 H2O # Saci_0885: Wagner2017 degra-carb_xylose_KGSA_4.2.1.141_RXN-8777 : 1 2-dehydro-3-deoxy-D-arabinonate --> 1 H2O + 1 2,5-dioxopentanoate # Saci_1939: Wagner2017 degra-carb_xylose-arabinose__1.2.1.26_25-DIOXOVALERATE-DEHYDROGENASE-RXN : 1 NADP+ + 1 H2O + 1 2,5-dioxopentanoate --> 1 2-oxoglutarate + 1 NADPH + 1 H+ # Saci_1700 # Wagner2017 stated that the aldolase-dependant Dahms pathway is not used in Saci degra-carb_xylose__4.1.2.28_4.1.2.28-RXN : 1 2-dehydro-3-deoxy-D-arabinonate --> 1 glycolaldehyde + 1 pyruvate # Saci_0225 degra-carb_xylose__2.7.1.17_XYLULOKIN-RXN : 1 D-xylulose + 1 ATP <=> 1 H+ + 1 D-xylulose_5-phosphate + 1 ADP # Saci_1058 degra-carb_ribose_2.7.1.15_BR47755 : ATP + D-ribose --> ADP + D-ribose_5-phosphate # Saci_0272 degra-carb_galactose__1.1.1.47_1.1.1.359_RXN-14234-NAD : 1 beta-D-galactose + 1 NAD+ --> 1 H+ + 1 D-galactono-1,5-lactone + 1 NADH # Saci_1079 degra-carb_galactose__1.1.1.47_1.1.1.359_RXN-14234-NADP : 1 beta-D-galactose + 1 NADP+ --> 1 H+ + 1 D-galactono-1,5-lactone + 1 NADPH # Saci_1079 degra-carb_galactose__3.1.1.17_BS381743 : 1 D-galactono-1,5-lactone + 1 H2O <=> 1 D-galactonate # degra-carb_galactonate__4.2.1.6_4.2.1.140_GALACTONDEHYDRAT-RXN : 1 D-galactonate --> 1 2-dehydro-3-deoxy-D-galactonate + 1 H2O # Saci_0885 degra-carb_galactonate__2.7.1.178_DEHYDDEOXGALACTKIN-RXN : 1 2-dehydro-3-deoxy-D-galactonate + 1 ATP --> 1 H+ + 1 ADP + 1 2-dehydro-3-deoxy-D-galactonate_6-phosphate # Saci_0226 degra-carb_galactonate__4.1.2.55_4.1.2.21_DEHYDDEOXPHOSGALACT-ALDOL-RXN : 1 pyruvate + 1 D-glyceraldehyde <=> 1 2-dehydro-3-deoxy-D-galactonate_6-phosphate # Saci_0225 degra-carb_galactonate__3.1.1.25_GALACTONOLACTONASE-RXN : 1 D-galactono-1,4-lactone + 1 H2O <=> 1 D-galactonate # Saci_2140 # --- di-/trisaccharides // Grogan (1989)# degra-carb_sucrose__3.2.1.20_BS370071 : 1 sucrose + 1 H2O <=> 1 beta-D-fructofuranose + 1 alpha-D-glucose # Saci_1160 degra-carb_fructose__2.7.1.1_FRUCTOKINASE-RXN : 1 beta-D-fructofuranose + 1 ATP --> 1 beta-D-fructofuranose_6-phosphate + 1 ADP # Saci_0424 degra-carb_maltotriose__3.2.1.20_RXN0-5183 : 1 maltotriose + 1 H2O --> 1 alpha-D-glucose + 1 beta-maltose # Saci_1160 degra-carb_beta-maltose__3.2.1.20_MALTDEG-RXN : 1 beta-maltose + 1 H2O --> 2 beta-D-glucose # Saci_1160 degra-carb_trehalose_TreH_3.2.1.28_BS259712 : 1 trehalose + 1 H2O <=> 1 alpha-D-glucose # Saci_1816 # --- polysaccharides // Grogan (1989), Choi and Cha (2015)# degra-carb_starch-ex__3.2.1.1_3.2.1.41_amylopullanase : 1 starch_ex + 0.3 H2O_ex <=> 0.3 beta-D-glucose_ex + 0.2 beta-maltose_ex + 0.1 maltotriose_ex # Saci_1200;Saci_1162 degra-carb_dextrin-ex__3.2.1.1_3.2.1.41_amylopullanase : 1 dextrin_ex + 0.3 H2O_ex <=> 0.3 beta-D-glucose_ex + 0.2 beta-maltose_ex + 0.1 maltotriose_ex # Saci_1200;Saci_1162 degra-carb_glycogen-ex__3.2.1.1_3.2.1.3_glycogen-hydrolase-extra : 1 glycogen_ex + 0.2 H2O_ex <=> 0.2 beta-maltose_ex + 0.2 maltotriose_ex # Saci_1200 #degra-carb_glycogen__2.4.1.1_GLYCOPHOSPHORYL-RXN : 1 glycogen + 1 phosphate <=> 0.5 alpha-D-glucose_1-phosphate + 0.5 alpha-limit_dextrin # degra-carb_glycogen__3.2.1.196_ID? : 1 glycogen + 1 H2O --> 0.5 beta-maltose # Saci_1439 #degra-carb_glycogen__3.2.1.33_3.2.1.33-RXN : 1 alpha-limit_dextrin + 1 H2O <=> 1 beta-D-glucose # degra-carb_pullulan-ex__3.2.1.1_amylopullanase : 1 pullulan_ex + 0.25 H2O_ex <=> 0.2 beta-D-glucose_ex + 0.1 beta-maltose_ex + 0.2 maltotriose_ex # Saci_1200 # --- other --- # degra-carb_formate__1.2.1.2_1.2.1.2-RXN : 1 formate + 1 NAD+ <=> 1 H+ + 1 CO2 + 1 NADH # Saci_0320;Saci_0320 degra-carb_glycolaldehyde__1.2.1.21_GLYCOLALD-DEHYDROG-RXN : 1 NAD+ + 1 H2O + 1 glycolaldehyde <=> 1 H+ + 1 NADH + 1 glycolate # Saci_1857 degra-carb_glycolaldehyde__3.1.3.18_GPH-RXN : 1 H2O + 1 2-phosphoglycolate --> 1 phosphate + 1 glycolate # Saci_1518 degra-carb_glycolaldehyde__1.1.99.14_1.1.1.26_GLYCOLATEDEHYDRO-RXN : 1 glycolate + 1 NAD+ <=> 1 glyoxylate + 1 NADH + 1 H+ # Saci_1885, Saci_0206 degra-carb_acetaldehyd__1.2.1.4_RXN0-3962 : 1 acetaldehyde + 1 NADP+ + 1 H2O --> 1 H+ + 1 acetate + 1 NADPH # Saci_1857 degra-carb_acetate__6.2.1.1_ACETATE--COA-LIGASE-RXN : 1 coenzyme_A + 1 ATP + 1 acetate <=> 1 AMP + 1 diphosphate + 1 acetyl-CoA # Saci_2298 degra-carb_glycerol__2.7.1.30_GLYCEROL-KIN-RXN : 1 glycerol + 1 ATP <=> 1 sn-glycerol_3-phosphate + 1 ADP # Saci_2033, Saci_1117 JHE MW2000 SNP in Saci_2033 FS!! # --- mono- and diaromatic rings --- # degra-carb_parathion__3.1.8.1_ARYLDIALKYL-PHOSPHATASE-RXN : 1 parathion + 1 H2O --> 1 diethylthiophosphate + 1 4-nitrophenol # Saci_2140 degra-carb_paraoxon__3.1.8.1_RXN-8746 : 1 paraoxon + 1 H2O --> 1 diethylphosphate + 1 4-nitrophenol + 2 H+ # Saci_2140 degra-carb_phenyl-acetate__3.1.1.2_ARYLESTERASE-RXN : 1 phenyl_acetate + 1 H2O --> 1 H+ + 1 acetate + 1 phenol # not genome-based (40); Saci_2140; not genome-based (10) Saci_2140 degra-carb_nitrophenyl-acetate__3.1.1.2_BS12514 : 1 4-nitrophenyl_acetate + 1 H2O --> 1 4-nitrophenol + 1 acetate # not genome-based (40); Saci_2140; not genome-based (10) Saci_2140 # ====== amino acid degradation ====== # degra-aa_asn__3.5.1.1_ASPARAGHYD-RXN : 1 L-asparagine + 1 H2O --> 1 ammonia + 1 L-aspartate # Saci_0402 degra-aa_asp__1.4.3.16_BS258998 : 1 L-aspartate + 1 H2O + 1 oxygen --> 1 oxaloacetate + 1 ammonia + 1 hydrogen_peroxide # Saci_0549 degra-aa_cys__2.8.1.7_RXN0-308 : 1 L-cysteine + 1 |L-Cysteine-Desulfurases| --> 1 L-alanine + 1 |Persulfurated-L-cysteine-desulfurases| # Saci_0024 degra-aa_gln__1.4.1.13_GLUTAMATESYN-RXN : 2 L-glutamate + 1 NADP+ <-- 1 2-oxoglutarate + 1 L-glutamine + 1 NADPH + 1 H+ # Saci_2320-1 #degra-aa_gln__3.5.1.2_GLUTAMIN-RXN : 1 L-glutamine + 1 H2O --> 1 L-glutamate + 1 ammonium # 3.5.1.2: (8) degra-aa_glu__2.6.1.19_GABATRANSAM-RXN : 1 2-oxoglutarate + 1 4-aminobutanoate <=> 1 L-glutamate + 1 succinate_semialdehyde # Saci_1028 degra-aa_glu__1.1.1.95_BS187992 : 1 2-oxoglutarate + 1 NADH + 1 H+ <=> 1 (R)-2-hydroxyglutarate + 1 NAD+ # Saci_1368 #degra-aa_glu__2.8.3.12_RXN-1082 : 1 acetyl-CoA + 1 (R)-2-hydroxyglutarate <=> 1 (R)-2-hydroxyglutaryl-CoA + 1 acetate # #degra-aa_glu__4.2.1.B26_RXN-1083 : 1 (R)-2-hydroxyglutaryl-CoA --> 1 (E)-glutaconyl-CoA + 1 H2O # #degra-aa_glu__1.3.8.6_GLUTACONYL-COA-DECARBOXYLASE-RXN : 1 (E)-glutaconyl-CoA <=> 1 CO2 + 1 crotonyl-CoA # degra-aa_lys__1.8.1.4_2-KETO-ADIPATE-DEHYDROG-RXN : 1 NAD+ + 1 2-oxoadipate + 1 coenzyme_A <=> 1 H+ + 1 glutaryl-CoA + 1 NADH + 1 CO2 # Saci_0338 degra-aa_lys__1.3.8.6_BS413390 : 1 glutaryl-CoA + 1 FAD <=> 1 crotonyl-CoA + 1 CO2 + 1 FADH2 # Saci_2217 #degra-aa_lys__6.4.1.2_BS380476 : 1 ATP + 1 butanoyl-CoA + 1 hydrogen_carbonate + 1 H+ <=> 1 ADP + 1 glutaryl-CoA + 1 phosphate # rel: 15 #degra-aa_lys__1.3.99.32_GLUTARYL-COA-DEHYDROG-RXN : 1 FAD + 1 glutaryl-CoA <=> 1 (E)-glutaconyl-CoA + 1 FADH2 # degra-aa_arg__2.6.1.11,2.6.1.13,2.6.1.19_BS380017 : L-ornithine + 2-oxoglutarate <=> L-glutamate + L-glutamate_5-semialdehyde # Saci_1028 degra-aa_arg__1.2.1.88_RXN-14116 : 1 NAD+ + 1 H2O + 1 L-glutamate_5-semialdehyde --> 1 H+ + 1 NADH + 1 L-glutamate # Saci_0166 degra-aa_met__4.4.1.11_RXN-14301 : L-methionine --> methanethiol + 2-aminobut-2-enoate + H+ # Saci_0971 degra-aa_met__3.5.99.7,4.3.1.19,4.4.1.1,4.4.1.2_BR50837 : 2-aminobut-2-enoate <=> 2-iminobutanoate # Saci_0713 degra-aa_met__3.5.99.10,3.5.99.7,4.3.1.19,4.4.1.1,4.4.1.2_BR49538 : 2-iminobutanoate + H2O <=> 2-oxobutanoate + ammonia # Saci_0713 degra-aa_met__4.1.99.1,4.4.1.1,4.4.1.11,4.4.1.6,4.4.1.8_BS19054 : S-methyl-L-cysteine + H2O <=> pyruvate + ammonia + methanethiol # Saci_0971 degra-aa_met__1.8.3.4_BR37036 : methanethiol + oxygen + H2O --> formaldehyde + hydrogen_sulfide + hydrogen_peroxide # Saci_0305 degra-aa_ser__4.3.1.17_BR50833 : L-serine --> aminoacrylate + H2O # Saci_0713 degra-aa_ser__4.3.1.17_BR50834 : aminoacrylate <=> 2-iminopropanoate # Saci_0713 degra-aa_ser__3.5.99.10_BR50835 : 2-iminopropanoate + H2O <=> pyruvate + ammonia # Saci_1195 # JHE Stickland reactions #degra-aa_phe_stickland_2.6.1.58_2.6.1.58-RXN : 1 L-phenylalanine + 1 pyruvate <=> 1 2-oxo-3-phenylpropanoate + 1 L-alanine # degra-aa_phe_stickland_1.2.7.8_BS359419 : 1 2-oxo-3-phenylpropanoate + 1 oxidized_ferredoxin + 1 coenzyme_A <=> 1 reduced_ferredoxin + 1 phenylacetyl-CoA + 1 CO2 # Saci_2229 degra-aa_phe_stickland_6.2.1.30_6.2.1.13_RXN-10819 : 1 coenzyme_A + 1 phenylacetate + 1 ATP <=> 1 phosphate + 1 phenylacetyl-CoA + 1 AMP # Saci_2290, Saci_0025 degra-aa_phe_stickland_1.14.14.54_RXN-12489 : 1 H+ + 1 NADH + 1 oxygen + 1 phenylacetate --> 1 NAD+ + 1 H2O + 1 2-hydroxyphenylacetate # Saci_2294 #degra-aa_phe_stickland_1.14.13.-_# #degra-aa_tyr_stickland_2.6.1.44_2.6.1.51_RXN3O-4157 : 1 pyruvate + 1 L-tyrosine --> 1 4-hydroxyphenylpyruvate + 1 L-alanine # degra-aa_tyr_stickland_1.2.7.8_RXN-14474 : 1 4-hydroxyphenylpyruvate + 1 coenzyme_A + 1 oxidized_ferredoxin <=> 1 4-Hydroxyphenylacetyl-CoA + 1 CO2 + 1 reduced_ferredoxin + 1 H+ # Saci_2229 degra-aa_tyr_stickland_6.2.1.30_BS400041 : 1 coenzyme_A + 1 4-hydroxyphenylacetate + 1 ATP <=> 1 AMP + 1 diphosphate + 1 4-Hydroxyphenylacetyl-CoA # Saci_2290 degra-aa_thr__4.3.1.19_THREDEHYD-RXN : 1 L-threonine --> 1 2-oxobutanoate + 1 ammonia # Saci_0713 degra-aa_thr__1.1.1,1.1.1.85_RXN-7745 : (2R,3S)-3-Methylmalate + NAD+ <=> 2-oxobutanoate + CO2 + NADH # Saci_0600 degra-aa_thr__4.2.1.35_RXN-7744 : (2Z)-2-methylbut-2-enedioate + H2O <=> (2R,3S)-3-Methylmalate # Saci_0252-3 degra-aa_thr__4.2.1.35_BR415 : (2R)-2-hydroxy-2-methylbutanedioate <=> (2Z)-2-methylbut-2-enedioate + H2O # Saci_0252-3 degra-aa_thr__2.3.1.182,2.3.3.13_BR48833 : acetyl-CoA + pyruvate + H2O <=> coenzyme_A + (2R)-2-hydroxy-2-methylbutanedioate # Saci_2325 degra-aa_ile_stickland_1.2.7.7_BS359414 : 1 (S)-3-methyl-2-oxopentanoate + 1 coenzyme_A + 1 oxidized_ferredoxin --> 1 2-methylbutanoyl-CoA + 1 CO2 + 1 reduced_ferredoxin # Saci_2250-3 #degra-aa_ile__1.2.1.25_2KETO-3METHYLVALERATE-RXN : 1 (S)-3-methyl-2-oxopentanoate + 1 NAD+ + 1 coenzyme_A --> 1 H+ + 1 NADH + 1 CO2 + 1 2-methylbutanoyl-CoA # degra-aa_ile_stickland_1.3.8.4_BS425198 : 1 FAD + 1 2-methylbutanoyl-CoA <=> 1 (E)-2-methylcrotonoyl-CoA + 1 FADH2 # Saci_1033, Saci_1069 degra-aa_ile__4.2.1.17_TIGLYLCOA-HYDROXY-RXN : 1 2-methyl-3-hydroxybutyryl-CoA <=> 1 (E)-2-methylcrotonoyl-CoA + 1 H2O # Saci_2285-6 degra-aa_ile__1.1.1.35_1.1.1.178-RXN : 1 2-methyl-3-hydroxybutyryl-CoA + 1 NAD+ <=> 1 NADH + 1 H+ + 1 2-methylacetoacetyl-CoA # Saci_2208 degra-aa_ile__2.3.1.9_METHYLACETOACETYLCOATHIOL-RXN : 1 2-methylacetoacetyl-CoA + 1 coenzyme_A <=> 1 acetyl-CoA + 1 propanoyl-CoA # Saci_0963, Saci_1728, Saci_2209, Saci_2232, Saci_2288 degra-aa_ile_stickland_6.2.1.13,6.2.1.B11_BS425944 : 1 ATP + 1 2-methylbutanoate + 1 coenzyme_A <=> 1 ADP + 1 phosphate + 1 2-methylbutanoyl-CoA # Saci_0025 degra-aa_ile_stickland_6.2.1.13_BS412980 : 1 ATP + 1 2-methyl-2-butenoate + 1 coenzyme_A <=> 1 ADP + 1 phosphate + 1 (E)-2-methylcrotonoyl-CoA # Saci_0025 degra-aa_leu_stickland_1.2.7.7_R08566 : 1 4-methyl-2-oxopentanoate + 1 coenzyme_A + 2 oxidized_ferredoxin --> 1 isovaleryl-CoA + 1 CO2 + 2 reduced_ferredoxin + 1 H+ # Saci_2250-3 #degra-aa_leu__1.2.7.7_2KETO-4METHYL-PENTANOATE-DEHYDROG-RXN : 1 NAD+ + 1 4-methyl-2-oxopentanoate + 1 coenzyme_A --> 1 H+ + 1 isovaleryl-CoA + 1 NADH + 1 CO2 # Saci_2250-3 degra-aa_leu_stickland_1.3.8.4,1.3.8.7_RXN-14264 : 1 FAD + 1 isovaleryl-CoA <=> 1 3-methylcrotonyl-CoA + 1 FADH2 # Saci_1033, Saci_1069 degra-aa_leu_stickland_6.2.1.13_BS169 : 1 ATP + 1 3-methylbutanoate + 1 coenzyme_A <=> 1 ADP + 1 phosphate + 1 isovaleryl-CoA # Saci_0025 degra-aa_leu_stickland_6.4.1.4_METHYLCROTONYL-COA-CARBOXYLASE-RXN : 1 3-methylcrotonyl-CoA + 1 hydrogen_carbonate + 1 ATP --> 1 ADP + 1 phosphate + 1 3-methylglutaconyl-CoA # Saci_0260-2 degra-aa_leu_stickland_4.2.1.18_METHYLGLUTACONYL-COA-HYDRATASE-RXN : 1 (S)-3-hydroxy-3-methylglutaryl-CoA <=> 1 3-methylglutaconyl-CoA + 1 H2O # Saci_1109 degra-aa_leu_stickland_4.2.1.17_R04137 : 1 3-hydroxyisovaleryl-CoA <=> 1 3-methylcrotonyl-CoA + 1 H2O # Saci_2285-6 degra-aa_leu_stickland_6.2.1.13,6.2.1.B11_BS167 : 1 ATP + 1 3-hydroxyisovalerate + 1 coenzyme_A <=> 1 ADP + 1 phosphate + 1 3-hydroxyisovaleryl-CoA # Saci_0025 degra-aa_leu_stickland_6.2.1.13_BS400563 : 1 ATP + 1 3-methyl-2-butenoate + 1 coenzyme_A <=> 1 ADP + 1 phosphate + 1 3-methylcrotonyl-CoA # Saci_0025 degra-aa_val_stickland_1.2.7.7_1.2.7.7-RXN : 2 H+ + 1 coenzyme_A + 1 3-methyl-2-oxobutanoate + 2 oxidized_ferredoxin <=> 1 CO2 + 1 isobutanoyl-CoA + 2 reduced_ferredoxin # Saci_2250-3 degra-aa_val_stickland_6.2.1.13,6.2.1.B11_BS167 : 1 ATP + 1 2-methylpropanoate + 1 coenzyme_A <=> 1 ADP + 1 phosphate + 1 isobutanoyl-CoA # Saci_0025 degra-aa_val__1.3.8.4_MEPROPCOA-FAD-RXN : 1 FAD + 1 isobutanoyl-CoA <=> 1 methylacryloyl-CoA + 1 FADH2 # Saci_1033, Saci_1069 degra-aa_val__4.2.1.17_METHYLACYLYLCOA-HYDROXY-RXN : 1 (S)-3-hydroxy-isobutanoyl-CoA <=> 1 methylacryloyl-CoA + 1 H2O # Saci_2286 degra-aa_val__3.1.2.4_3-HYDROXYISOBUTYRYL-COA-HYDROLASE-RXN : 1 (S)-3-hydroxy-isobutanoyl-CoA + 1 H2O --> 1 (S)-3-hydroxy-isobutanoate + 1 coenzyme_A # nsb degra-aa_val__1.1.1.31_3-HYDROXYISOBUTYRATE-DEHYDROGENASE-RXN : 1 NAD+ + 1 (S)-3-hydroxy-isobutanoate <=> 1 H+ + 1 (S)-methylmalonate-semialdehyde + 1 NADH # Saci_0385 degra-aa_val__1.2.1.27_RXN-11213 : 1 NAD+ + 1 coenzyme_A + 1 H2O + 1 (S)-methylmalonate-semialdehyde --> 1 hydrogen_carbonate + 1 propanoyl-CoA + 1 H+ + 1 NADH # nsb # JHE Teufel Pathway [Teufel2010] degra-aa_phe_PaaABCDE_1.14.13.149_RXN0-2042 : 1 NADPH + 1 H+ + 1 phenylacetyl-CoA + 1 oxygen --> 1 H2O + 1 NADP+ + 1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA # Saci_1770-1 degra-aa_phe_PaaG_5.3.3.18_RXN0-6510 : 1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA <=> 1 2-oxepin-2(3H)-ylideneacetyl-CoA # Saci_2285-6 degra-aa_phe_PaaZ_3.3.2.12_RXNMETA-12671 : 1 H2O + 1 2-oxepin-2(3H)-ylideneacetyl-CoA --> 1 3-oxo-5,6-didehydrosuberyl-CoA_semialdehyde # Saci_1070 degra-aa_phe_PaaZ_1.2.1.91_RXNMETA-12672 : 1 3-oxo-5,6-didehydrosuberyl-CoA_semialdehyde + 1 NADP+ + 1 H2O <=> 1 3-oxo-5,6-didehydrosuberyl-CoA + 1 NADPH + 1 H+ # nsb degra-aa_phe_PaaJ_2.3.1.174_2.3.1.223_RXN0-6512 : 1 2,3-didehydroadipyl-CoA + 1 acetyl-CoA <=> 1 3-oxo-5,6-didehydrosuberyl-CoA + 1 coenzyme_A # Saci_1114 degra-aa_phe_PaaF_4.2.1.17_RXN0-6513 : 1 3-hydroxyadipyl-CoA <=> 1 H2O + 1 2,3-didehydroadipyl-CoA # Saci_2285-6 degra-aa_phe_PaaH_1.1.1.35_RXN0-2044 : 1 NAD+ + 1 3-hydroxyadipyl-CoA <=> 1 H+ + 1 NADH + 1 3-oxoadipyl-CoA # Saci_1109, Saci_2208, Saci_2218 degra-aa_phe_PaaJ_2.3.1.174_RXN-3641 : 1 succinyl-CoA + 1 acetyl-CoA <-- 1 coenzyme_A + 1 3-oxoadipyl-CoA # Saci_1114 #degra-aa_shikimate__4.2.1.-_DHSHIKIMATE-DEHYDRO-RXN : 1 3-dehydroshikimate --> 1 protocatechuate + 1 H2O # # --- phe degra --- # degra-aa_phe__4.2.1.96_BS2138 : 1 4a-hydroxy-tetrahydrosulfopterin <=> 1 7,8-dihydrosulfopterin + 1 H2O # Saci_2299 #degra-aa_phe__1.14.16.1_PHENYLALANINE-4-MONOOXYGENASE-RXN : 1 tetrahydrosulfopterin + 1 L-phenylalanine + 1 oxygen --> 1 L-tyrosine + 1 4a-hydroxy-tetrahydrosulfopterin # other__pyruvate-oxidation-pathway_1.2.5.1_RXN-11496 : 1 pyruvate + 1 H2O + 1 representative_quinone --> 1 acetate + 1 CO2 + 1 representative_quinol # Saci_1935 # --- dipeptides --- # degra-aa_dipeptide_gly-pro_3.4.13.9_RXN0-6988 : 1 glycyl-L-proline + 1 H2O --> 1 L-proline + 1 glycine # Saci_1480 # ================================ cofactor biosynthesis ================================ # # --- 4-aminobenzoate // needed for sulfopterin biosynthesis# cof_aminobenzoate__2.6.1.85_PABASYN-RXN : 1 L-glutamine + 1 chorismate <=> 1 4-amino-4-deoxychorismate + 1 L-glutamate # nsb cof_aminobenzoate__4.1.3.38_ADCLY-RXN : 1 4-amino-4-deoxychorismate <=> 1 pyruvate + 1 H+ + 1 4-aminobenzoate # nsb # --- sulfopterin and tetrahydrosulfopterin biosynthesis // sulfopterin = a structurally modified folate# cof_sulfopterin__3.5.4.16_GTP-CYCLOHYDRO-I-RXN : 1 GTP + 1 H2O <=> 1 7,8-dihydroneopterin_3'-triphosphate + 1 formate # Saci_1481 cof_sulfopterin__3.6.1.67_H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN : 1 7,8-dihydroneopterin_3'-triphosphate + 1 H2O --> 1 7,8-dihydroneopterin_3'-phosphate + 1 diphosphate # nsb cof_sulfopterin__3.6.1.-_DIHYDRONEOPTERIN-MONO-P-DEPHOS-RXN : 1 7,8-dihydroneopterin_3'-phosphate + 1 H2O --> 1 7,8-dihydroneopterin + 1 phosphate # nsb cof_sulfopterin__4.1.2.25_H2NEOPTERINALDOL-RXN : 1 7,8-dihydroneopterin <=> 1 glycolaldehyde + 1 6-hydroxymethyl-7,8-dihydropterin # Saci_1101 cof_sulfopterin__2.7.6.3_H2PTERIDINEPYROPHOSPHOKIN-RXN : 1 6-hydroxymethyl-7,8-dihydropterin + 1 ATP --> 1 (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl_diphosphate + 1 AMP + 1 H+ # Saci_1101, Saci_0939 cof_sulfopterin__2.5.1.15_H2PTEROATESYNTH-RXN : 1 (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl_diphosphate + 1 4-aminobenzoate <=> 1 diphosphate + 1 H2O + 1 7,8-dihydropteroate # Saci_0932 cof_sulfopterin__unknown_sulfopterin-conv : 1 7,8-dihydropteroate + 1 NADPH <=> 1 sulfopterin # JHE BRENDA; theoretical PW cof_sulfopterin__1.5.1.3,1.5.1.33_BS259283 : 1 H+ + 1 sulfopterin + 2 NADPH <=> 1 tetrahydrosulfopterin + 2 NADP+ # Saci_1102 cof_sulfopterin__2.1.2.11_RXN-2881 : 1 formaldehyde + 1 tetrahydrosulfopterin <=> 1 H2O + 1 5,10-methylene-tetrahydrosulfopterin # Saci_0948 cof_sulfopterin__2.1.2.10_GCVMULTI-RXN : 1 NAD+ + 1 glycine + 1 tetrahydrosulfopterin <=> 1 NADH + 1 ammonium + 1 CO2 + 1 5,10-methylene-tetrahydrosulfopterin # Saci_1383 cof_sulfopterin__2.1.2.10_RXN-6321 : 1 H2O + 1 5,10-methenyltetrahydrosulfopterin --> 1 H+ + 1 5-formyl-tetrahydrosulfopterin # Saci_1383 JHE changed dir cof_sulfopterin__6.3.3.2_5-FORMYL-THF-CYCLO-LIGASE-RXN : 1 5-formyl-tetrahydrosulfopterin + 1 ATP --> 1 5,10-methenyltetrahydrosulfopterin + 1 ADP + 1 phosphate # Saci_0447 cof_sulfopterin__1.5.1.6_FORMYLTETRAHYDROFOLATE-DEHYDROGENASE-RXN : 1 10-formyl-tetrahydrosulfopterin + 1 H2O + 1 NADP+ --> 1 NADPH + 1 H+ + 1 CO2 + 1 tetrahydrosulfopterin # nsb cof_sulfopterin__1.5.1.20_1.5.1.20-RXN : 1 5-methyl-tetrahydrosulfopterin + 1 NAD+ <=> 1 5,10-methylene-tetrahydrosulfopterin + 1 NADH + 1 H+ # nsb # --- archaeosine // missing link# #cof_archaeosine__4.1.2.50_RXN0-5507 : 1 7,8-dihydroneopterin_triphosphate + 1 H2O --> 1 acetaldehyde + 1 6-carboxy-5,6,7,8-tetrahydropterin + 1 PPPi # cof_archaeosine__4.2.3.12_BR48350 : 1 7,8-dihydroneopterin_3'-triphosphate <=> 1 6-pyruvoyl_tetrahydropterin + 1 PPPi # Saci_0934 cof_archaeosine__4.1.2.50_BS418339 : 1 6-pyruvoyl_tetrahydropterin + 1 H2O <=> 1 6-carboxy-5,6,7,8-tetrahydropterin + 1 acetaldehyde + 1 PPPi # Saci_0934 cof_archaeosine__4.3.99.3_RXN0-6575 : 2 H+ + 1 6-carboxy-5,6,7,8-tetrahydropterin + 1 S-adenosyl-L-methionine --> 1 ammonia + 1 5'-deoxyadenosine + 1 7-carboxy-7-deazaguanine + 1 L-methionine # Saci_1604 cof_archaeosine__6.3.4.20_RXN-12093 : 1 ammonia + 1 ATP + 1 7-carboxy-7-deazaguanine --> 1 preQ0 + 1 ADP + 1 phosphate + 1 H2O # Saci_0280 cof_archaeosine__2.4.2.48_RXN-12144 : 1 preQ0 + 1 |Guanine15-in-tRNA| --> 1 guanine + 1 |tRNA-PreQ0| # Saci_0659 cof_archaeosine__2.6.1.97_RXN-12145 : 1 L-glutamine + 1 H2O + 1 |tRNA-PreQ0| --> 1 L-glutamate + 1 |tRNA-archaeosine| # Saci_0280 # --- quinone biosynthesis // for Biomass // isoprenoid chain is suggested to be inlcuded early (Zhou 1989) but there is no clear evidence on the subject# cof_quinone__1.13.11.27_4-HYDROXYPHENYLPYRUVATE-DIOXYGENASE-RXN : 1 4-hydroxyphenylpyruvate + 1 oxygen <=> 1 homogentisate + 1 CO2 # Saci_2059-60 cof_quinone__1.2.3.1_R02657 : homogentisate + hydrogen_peroxide <=> gentisaldehyde + oxygen + H2O # Saci_2269-71 cof_quinone__unknown_unknown03 : 1 NAD+ + 1 gentisaldehyde <=> 1 H+ + 1 NADH + 1 benzothiophen-4,7-quinone # cof_quinone__unknown_unknown04 : 1 benzothiophen-4,7-quinone <=> 1 H2O + 1 benzothiophen-4,7-diol # cof_quinone__unknown_unknown-prenyltransferase : 1 benzothiophen-4,7-diol + 1 (2E,6E)-farnesyl_diphosphate + 3 isopentenyl_diphosphate --> 1 prenylated_1,4-benzothiophen-4,7-diol + 4 diphosphate # cof_quinone__1.3.7.11_prenylated-benzothiophendiol-reduction : 1 prenylated_1,4-benzothiophen-4,7-diol + 6 NADH + 6 H+ --> 1 reduced_prenylated_1,4-benzothiophen-4,7-diol + 6 NAD+ # Saci_0986 cof_quinone__2.5.1.47_O-ACETYLHOMOSERINE-THIOL-LYASE-RXN : 1 O-acetyl-L-homoserine + 1 methanethiol <=> 1 acetate + 1 L-methionine # Saci_1475 cof_quinone__2.5.1.47_ACETYLHOMOSER-CYS-RXN : 1 O-acetyl-L-homoserine + 1 hydrogen_sulfide <=> 1 acetate + 1 L-homocysteine # Saci_1475 cof_quinone__unknown_unknown05 : 1 methanethiol + 2 NAD+ + 1 reduced_prenylated_1,4-benzothiophen-4,7-diol <=> 2 H+ + 1 caldariellaquinone + 2 NADH # cof_quinone__unknown_unknown06 : 1 S-adenosyl-L-methionine + 2 NAD+ + 1 reduced_prenylated_1,4-benzothiophen-4,7-diol <=> 1 sulfolobusquinone + 2 H+ + 2 NADH + 1 S-adenosyl-L-homocysteine # # --- quinonpool // according to Elling2016 cof_quinone_quinonepool : 0.9 caldariellaquinone + 0.1 sulfolobusquinone <=> 1 representative_quinone # #cof_quinone_quinonepool : 0.83 caldariellaquinone + 0.17 sulfolobusquinone <=> 1 representative_quinone # according to Trincone1989 # --- coenzyme A biosythesis // for Biomass# cof_coa_vitamine-B5_2.1.2.11_3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN : 1 3-methyl-2-oxobutanoate + 1 5,10-methylene-tetrahydrosulfopterin + 1 H2O <=> 1 2-dehydropantoate + 1 tetrahydrosulfopterin # Saci_0948 cof_coa_vitamine-B5_1.1.1.169_2-DEHYDROPANTOATE-REDUCT-RXN : 1 (R)-pantoate + 1 NADP+ <=> 1 2-dehydropantoate + 1 NADPH + 1 H+ # nsb cof_coa_vitamine-B5_2.7.1.169_RXN-11782 : 1 (R)-pantoate + 1 ATP <=> 1 H+ + 1 ADP + 1 (R)-4-phosphopantoate # Saci_0950 cof_coa_vitamine-B5_6.3.2.36_RXN-11781 : 1 (R)-4-phosphopantoate + 1 beta-alanine + 1 ATP --> 1 AMP + 1 diphosphate + 1 (R)-4'-phosphopantothenate + 1 H+ # Saci_0949 cof_coa__6.3.2.5_P-PANTOCYSLIG-RXN : 1 (R)-4'-phosphopantothenate + 1 CTP + 1 L-cysteine <=> 1 CMP + 1 diphosphate + 1 R-4'-phosphopantothenoyl-L-cysteine # Saci_0458 cof_coa__4.1.1.36_P-PANTOCYSDECARB-RXN : 1 R-4'-phosphopantothenoyl-L-cysteine --> 1 CO2 + 1 4'-phosphopantetheine # Saci_0458 cof_coa__2.7.7.3_PANTEPADENYLYLTRAN-RXN : 1 ATP + 1 4'-phosphopantetheine <=> 1 3'-dephospho-CoA + 1 diphosphate # Saci_1611-2 cof_coa__2.7.1.24_DEPHOSPHOCOAKIN-RXN : 1 ATP + 1 3'-dephospho-CoA --> 1 ADP + 1 coenzyme_A # Saci_1286 cof_coa__2.7.1.33_PANTOTHENATE-KIN-RXN : 1 ATP + 1 (R)-pantothenate --> 1 (R)-4'-phosphopantothenate + 1 ADP # Saci_2123 # --- NAD biosynthesis --- # #cof_nad__1.4.3.16_L-ASPARTATE-OXID-RXN : 1 L-aspartate + 1 oxygen --> 1 hydrogen_peroxide + 1 2-iminosuccinate # Saci_0549 cof_nad__1.4.3.16_BS413426 : 1 L-aspartate + 1 fumarate <=> 1 2-iminosuccinate + 1 succinate # Saci_0549 cof_nad__2.5.1.72_QUINOLINATE-SYNTHA-RXN : 1 dihydroxyacetone_phosphate + 1 2-iminosuccinate --> 1 phosphate + 1 quinolinate + 2 H2O # Saci_0023 cof_nad__2.4.2.19_QUINOPRIBOTRANS-RXN : 1 5-phospho-alpha-D-ribose_1-diphosphate + 1 quinolinate --> 1 CO2 + 1 beta-nicotinate_D-ribonucleotide + 1 diphosphate # Saci_0547 JHE SNP in MW2000 cof_nad__2.7.7.1,18_NICONUCADENYLYLTRAN-RXN : 1 ATP + 1 beta-nicotinate_D-ribonucleotide <=> 1 nicotinate_adenine_dinucleotide + 1 diphosphate # Saci_0300 cof_nad__6.3.1.5_BR147 : 1 H+ + 1 ATP + 1 nicotinate_adenine_dinucleotide + 1 L-glutamine + 1 H2O --> 1 AMP + 1 diphosphate + 1 NAD+ + 1 L-glutamate # Saci_0009 cof_nad__2.7.1.23_NAD-KIN-RXN : 1 ATP + 1 NAD+ --> 1 ADP + 1 NADP+ # Saci_0027 # cof_nad__3.1.4.1_BS73730 : 1 NADP+ + 1 H2O --> 1 NAD+ + 1 phosphate # cof_nad_salvage_2.4.2.11_beta-nicotinate-phosphoribosyltransferase : 1 diphosphate + 1 beta-nicotinate_D-ribonucleotide <=> 1 5-phospho-alpha-D-ribose_1-diphosphate + 1 beta-nicotinate # # cof_nad_salvage_3.2.2.5_NADNUCLEOSID-RXN : 1 NAD+ + 1 H2O --> 1 ADP-D-ribose + 1 nicotinamide + 1 H+ # cof_nad_salvage_3.6.1.13_RXN0-1441 : 1 ADP-D-ribose + 1 H2O --> 1 AMP + 1 D-ribose_5-phosphate # Saci_0013 # cof_nad_salvage_4.2.1.136_RXN0-6727 : 1 ADP + 1 (S)-NADHX --> 1 AMP + 1 NADH + 1 phosphate # Saci_0057 # cof_nad_salvage_3.6.1.22_BS141282 : 1 NADP+ + 1 H2O --> 1 H+ + 1 adenosine_3',5'-bisphosphate + 1 1-(beta-D_ribofuranosyl)nicotinamide # # cof_nad_salvage_3.6.1.22_NADPYROPHOSPHAT-RXN : 1 H2O + 1 NAD+ --> 1 H+ + 1 1-(beta-D_ribofuranosyl)nicotinamide + 1 AMP # cof_nad_salvage_2.7.7.1_2.7.7.1-RXN : 1 ATP + 1 H+ + 1 1-(beta-D_ribofuranosyl)nicotinamide <=> 1 diphosphate + 1 NAD+ # Saci_0720 # --- biotin biosynthesis --- # cof_biotin_change-reaction_01 : 1 S-adenosyl-4-methylthio-2-oxobutanoate --> 1 8-amino-7-oxononanoate # cof_biotin__2.6.1.62_DAPASYN-RXN : 1 S-adenosyl-L-methionine + 1 8-amino-7-oxononanoate <=> 1 7,8-diaminopelargonate + 1 S-adenosyl-4-methylthio-2-oxobutanoate # Saci_2137 cof_biotin__6.3.3.3_DETHIOBIOTIN-SYN-RXN : 1 CO2 + 1 ATP + 1 7,8-diaminopelargonate <=> 1 H+ + 1 dethiobiotin + 1 phosphate + 1 ADP # nsb cof_biotin__2.8.1.6_BS360047 : 1 dethiobiotin + 1 S0 --> 2 H+ + 1 biotin # Saci_0343 cof_biotin__6.3.4.15_BS398826 : 1 biotin + 1 ATP <=> 1 Biotinyl-5'-AMP + 1 diphosphate # Saci_1641 # --- flavin biosynthesis // for Biomass# cof_flavin__3.5.4.29_RXN-10055 : 1 GTP + 3 H2O --> 1 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + 2 phosphate # Saci_0819 cof_flavin__3.5.1.102_RXN-10056 : 1 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + 1 H2O --> 1 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + 1 formate # Saci_0818 cof_flavin__1.1.1.302_RXN-10057 : 1 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one + 1 NAD+ <-- 1 H+ + 1 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + 1 NADH # Saci_2164 cof_flavin__3.5.4.26_RIBOFLAVINSYNDEAM-RXN : 1 2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one + 1 H2O --> 1 ammonia + 1 5-amino-6-(5-phospho-D-ribitylamino)uracil # nsb cof_flavin__3.1.3.104_RIBOPHOSPHAT-RXN : 1 5-amino-6-(5-phospho-D-ribitylamino)uracil + 1 H2O --> 1 5-amino-6-(D-ribitylamino)uracil + 1 phosphate # nsb cof_flavin__4.1.99.12_DIOHBUTANONEPSYN-RXN : 1 D-ribulose_5-phosphate --> 1 1-deoxy-L-glycero-tetrulose_4-phosphate + 1 formate # Saci_0822 cof_flavin__2.5.1.78_LUMAZINESYN-RXN : 1 5-amino-6-(D-ribitylamino)uracil + 1 1-deoxy-L-glycero-tetrulose_4-phosphate --> 1 6,7-dimethyl-8-(1-D-ribityl)lumazine + 1 phosphate + 2 H2O # Saci_0820 cof_flavin__2.5.1.9_RIBOFLAVIN-SYN-RXN : 2 6,7-dimethyl-8-(1-D-ribityl)lumazine <=> 1 5-amino-6-(D-ribitylamino)uracil + 1 riboflavin # Saci_0821 cof_flavin__2.7.1.161_RXN-9296 : 1 CTP + 1 riboflavin --> 1 CDP + 1 FMN # Saci_1332 cof_flavin__2.7.7.2_FADSYN-RXN : 1 ATP + 1 FMN <=> 1 FAD + 1 diphosphate # Saci_1333 # --- thiamin biosynthesis // for Biomass // vitamin B1# # ThiS = Saci_1652; ThiI = Saci_2336 cof_thiamin__2.7.7.73_RXN-9789 : 1 ATP + 1 |ThiS| --> 1 diphosphate + 1 |Adenylated-ThiS| # Saci_0179 cof_thiamin__1.4.3.19_RXN-12614 : 1 oxygen + 1 glycine --> 1 hydrogen_peroxide + 1 2-iminoacetate # nsb cof_thiamin_het_unknown01 : 1 |ThiI| + 1 |Persulfurated-L-cysteine-desulfurases| <=> 1 |Persulfurated-ThiI| + 1 |L-Cysteine-Desulfurases| # cof_thiamin_het_unknown02 : 1 |Adenylated-ThiS| + 1 |Persulfurated-ThiI| <=> 1 AMP + 1 |Thiocarboxyadenylated-ThiS| + 1 |ThiI| # cof_thiamin_het_2.2.1.7_DXS-RXN : 1 D-glyceraldehyde_3-phosphate + 1 pyruvate --> 1 CO2 + 1 1-deoxy-D-xylulose_5-phosphate # Saci_0181 cof_thiamin_het_2.8.1.10_THIAZOLSYN2-RXN : 1 2-iminoacetate + 1 1-deoxy-D-xylulose_5-phosphate + 1 |Thiocarboxyadenylated-ThiS| --> 1 2-[(2R,5Z)-(2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl_phosphate + 2 H2O + 1 |ThiS| # Saci_0854 cof_thiamin_hmp_4.1.99.17_PYRIMSYN1-RXN : 1 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + 1 S-adenosyl-L-methionine --> 1 4-amino-2-methyl-5-phosphomethylpyrimidine + 1 carbon_monoxide + 1 5'-deoxyadenosine + 1 formate + 1 L-methionine # Saci_0137 cof_thiamin_hmp_2.7.4.7_PYRIMSYN3-RXN : 1 4-amino-2-methyl-5-phosphomethylpyrimidine + 1 ATP --> 1 ADP + 1 4-amino-2-methyl-5-diphosphomethylpyrimidine # Saci_0953 cof_thiamin__2.5.1.3_RXN-12611 : 1 4-amino-2-methyl-5-diphosphomethylpyrimidine + 1 2-[(2R,5Z)-(2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl_phosphate <=> 1 CO2 + 1 diphosphate + 1 thiamin_phosphate # Saci_0078 cof_thiamin__2.7.4.16_THI-P-KIN-RXN : 1 ATP + 1 thiamin_phosphate --> 1 ADP + 1 thiamin_diphosphate # Saci_0704 # --- tetrapyrrole biosynthesis // uroporphyrinogen-III is used for cobalamin biosynthesis# cof_cobalamin_tRNA_6.1.1.17_GLURS-RXN : 1 ATP + 1 L-glutamate + 1 H+ + 1 |GLT-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-GLT-tRNAs| # Saci_1519 cof_cobalamin_tetrapyrrole_1.2.1.70_GLUTRNAREDUCT-RXN : 1 (S)-4-amino-5-oxopentanoate + 1 NADP+ + 1 |GLT-tRNAs| <=> 1 NADPH + 1 |Charged-GLT-tRNAs| # Saci_0777 cof_cobalamin_tetrapyrrole_5.4.3.8_GSAAMINOTRANS-RXN : 1 (S)-4-amino-5-oxopentanoate <=> 1 5-aminolevulinate # Saci_0779 cof_cobalamin_tetrapyrrole_4.2.1.24_PORPHOBILSYNTH-RXN : 2 5-aminolevulinate <=> 1 porphobilinogen + 2 H2O # Saci_0778 cof_cobalamin_tetrapyrrole_2.5.1.61_OHMETHYLBILANESYN-RXN : 4 porphobilinogen + 1 H2O <=> 4 ammonia + 1 hydroxymethylbilane # Saci_0780 cof_cobalamin_tetrapyrrole_4.2.1.75_UROGENIIISYN-RXN : 1 hydroxymethylbilane <=> 1 uroporphyrinogen-III + 1 H2O # Saci_0781 # --- cobalamin biosynthesis // unknown sec. substrate of 6.3.1.10 --> maybe not (R)-1-amino-2-propanol_O-2-phosphate (missing enzymes)# cof_cobalamin_anaerobic_2.1.1.107_RXN-13403 : 2 S-adenosyl-L-methionine + 1 uroporphyrinogen-III --> 2 S-adenosyl-L-homocysteine + 1 precorrin-2 # Saci_0914, Saci_2200 cof_cobalamin_anaerobic_4.99.1.3_4.99.1.4_RXN-8759 : 1 Co2+ + 1 precorrin-2 --> 2 H+ + 1 cobalt-precorrin-2 # Saci_0776, Saci_0830 cof_cobalamin_anaerobic_2.1.1.151_2.1.1.130_RXN-8760 : 1 cobalt-precorrin-2 + 1 S-adenosyl-L-methionine --> 1 S-adenosyl-L-homocysteine + 1 cobalt-precorrin-3 # Saci_0395 cof_cobalamin_anaerobic_2.1.1.272_RXN-14314 : 1 H+ + 1 S-adenosyl-L-methionine + 1 cobalt-precorrin-3 <=> 1 S-adenosyl-L-homocysteine + 1 cobalt-precorrin-4 # Saci_0398 cof_cobalamin_anaerobic_2.1.1.271_RXN-8762 : 1 cobalt-precorrin-4 + 1 S-adenosyl-L-methionine --> 1 S-adenosyl-L-homocysteine + 1 cobalt-precorrin-5A # Saci_0394 cof_cobalamin_anaerobic_3.7.1.12_RXN-8763 : 1 cobalt-precorrin-5A + 1 H2O --> 1 acetaldehyde + 1 cobalt-precorrin-5B # Saci_0401 cof_cobalamin_anaerobic_2.1.1.195_RXN-8764 : 1 cobalt-precorrin-5B + 1 S-adenosyl-L-methionine --> 1 S-adenosyl-L-homocysteine + 1 cobalt-precorrin-6A # Saci_0397 cof_cobalamin_anaerobic_1.3.1.106_RXN-8765 : 1 cobalt-precorrin-6A + 1 NADPH + 1 H+ --> 1 cobalt-precorrin-6B + 1 NADP+ # nsb cof_cobalamin_anaerobic_2.1.1.196_RXN-8766 : 1 cobalt-precorrin-6B + 1 S-adenosyl-L-methionine --> 1 S-adenosyl-L-homocysteine + 1 cobalt-precorrin-7 # Saci_0396 cof_cobalamin_anaerobic_2.1.1.289_RXN-8767 : 1 cobalt-precorrin-7 + 1 S-adenosyl-L-methionine --> 1 S-adenosyl-L-homocysteine + 1 cobalt-precorrin-8 # Saci_0400 cof_cobalamin_anaerobic_5.4.99.60_RXN-8768 : 1 cobalt-precorrin-8 --> 1 cobyrinate + 1 H+ # Saci_0399 cof_cobalamin_anaerobic_6.3.5.9_6.3.5.11_RXN-8769 : 2 ATP + 1 cobyrinate + 2 L-glutamine + 2 H2O --> 2 ADP + 1 cob(II)yrinate_a,c-diamide + 2 L-glutamate + 2 phosphate # Saci_0825 cof_cobalamin__1.16.8.1_R343-RXN : 2 cob(I)yrinate_a,c-diamide + 1 FMN + 2 H+ <-- 2 cob(II)yrinate_a,c-diamide + 1 FMNH2 # nsb cof_cobalamin__2.5.1.17_R344-RXN : 1 H+ + 1 ATP + 1 cob(I)yrinate_a,c-diamide --> 1 adenosyl-cobyrinate_a,c-diamide + 1 PPPi # Saci_1571, Saci_2373 cof_cobalamin__6.3.5.10_R345-RXN : 4 ATP + 1 adenosyl-cobyrinate_a,c-diamide + 4 L-glutamine + 4 H2O --> 4 ADP + 1 adenosylcobyrate + 4 L-glutamate + 4 phosphate # Saci_0413 cof_cobalamin__6.3.1.10_RXN-6261 : 1 ATP + 1 adenosylcobyrate + 1 (R)-1-amino-2-propanol_O-2-phosphate --> 1 adenosyl-cobinamide_phosphate + 1 ADP + 1 phosphate # Saci_0411 cof_cobalamin__2.7.7.62_COBINPGUANYLYLTRANS-RXN : 1 adenosyl-cobinamide_phosphate + 1 GTP <=> 1 adenosylcobinamide-GDP + 1 diphosphate # Saci_0391 cof_cobalamin__2.7.8.26_COBALAMIN5PSYN-RXN : 1 alpha-ribazole_5'-phosphate + 1 H2O + 1 adenosylcobinamide-GDP <=> 1 phosphate + 1 GMP + 1 coenzyme_B12 + 1 H+ # Saci_0412 cof_cobalamin_aminoprop_2.7.1.177_RXN-8626 : 1 ATP + 1 L-threonine --> 1 H+ + 1 ADP + 1 L-threonine_3-O-phosphate # nsb cof_cobalamin_aminoprop_4.1.1.81_4.1.1.81-RXN : 1 H+ + 1 L-threonine_3-O-phosphate --> 1 CO2 + 1 (R)-1-amino-2-propanol_O-2-phosphate # nsb cof_cobalamin_FMN_1.13.11.79_RXN-8771 : 1 oxygen + 1 FMNH2 --> 1 dialurate + 1 5,6-dimethylbenzimidazole + 1 D-erythrose_4-phosphate # Saci_0250 cof_cobalamin_FMN_2.4.2.21_DMBPPRIBOSYLTRANS-RXN : 1 5,6-dimethylbenzimidazole + 1 beta-nicotinate_D-ribonucleotide --> 1 alpha-ribazole_5'-phosphate + 1 nicotinate # nsb cof_cobalamin__6.3.4.21_NICOTINATEPRIBOSYLTRANS-RXN : 1 H2O + 1 5-phospho-alpha-D-ribose_1-diphosphate + 1 nicotinate + 1 ATP <=> 1 beta-nicotinate_D-ribonucleotide + 1 phosphate + 1 diphosphate + 1 ADP # Saci_1470 # --- polyamines // norspermidine and norspermine not found in Saci # cof_polyamines_sama_4.1.1.50_SAMDECARB-RXN : 1 H+ + 1 S-adenosyl-L-methionine --> 1 CO2 + 1 S-adenosyl_3-(methylthio)propylamine # Saci_1568 cof_polyamines_agmatine_4.1.1.19_ARGDECARBOX-RXN : 1 L-arginine --> 1 agmatine + 1 CO2 # Saci_1363 cof_polyamines_putrescine_4.1.1.17,4.1.1.19,4.1.1.B12_ORNDECARBOX-RXN : 1 L-ornithine --> 1 putrescine + 1 CO2 # Saci_1363 cof_polyamines_putrescine_3.5.3.11_AGMATIN-RXN : 1 agmatine + 1 H2O --> 1 putrescine + 1 urea # Saci_2134, Saci_0863 cof_polyamines_spermidine_2.5.1.16_SPERMIDINESYN-RXN : 1 putrescine + 1 S-adenosyl_3-(methylthio)propylamine --> 1 S-methyl-5'-thioadenosine + 1 H+ + 1 spermidine # Saci_0643 cof_polyamines__2.4.2.28_5-METHYLTHIOADENOSINE-PHOSPHORYLASE-RXN : 1 S-methyl-5'-thioadenosine + 1 phosphate --> 1 adenine + 1 S-methyl-5-thio-alpha-D-ribose_1-phosphate # Saci_0997 cof_polyamines_spermine_2.5.1.16,2.5.1.22_BR44280 : 1 S-adenosyl_3-(methylthio)propylamine + 1 spermidine <=> 1 S-methyl-5'-thioadenosine + 1 spermine # Saci_0643 # --- carotenoid biosynthesis --- // Hemmi2003 cof_carotenoids_crtB_2.5.1.32_2.5.1.32-RXN : 2 geranylgeranyl_diphosphate --> 1 prephytoene_diphosphate + 1 diphosphate # Saci_1734 cof_carotenoids_crtB_2.5.1.32_RXNARA-8002 : 1 prephytoene_diphosphate --> 1 15-cis-phytoene + 1 diphosphate # Saci_1734 cof_carotenoids_crtI_1.3.99.31_RXN-12414 : 1 15-cis-phytoene + 4 FAD + 4 H+ <=> 1 all-trans-lycopene + 4 FADH2 # Saci_1732 cof_carotenoids_crtZ_5.5.1.19_BS415669 : 1 all-trans-lycopene <=> 1 all-trans-beta-carotene # Saci_1733 cof_carotenoids_crtY_1.14.13.129_RXN1F-152 : 1 all-trans-beta-carotene + 2 NADH + 2 oxygen + 2 H+ <=> 1 zeaxanthin + 2 NAD+ + 2 H2O # Saci_1735 # --- other cofactors --- # cof_plp_vitamin-B6_4.3.3.6_RXN-11322 : 1 D-glyceraldehyde_3-phosphate + 1 L-glutamine + 1 D-ribose_5-phosphate --> 1 L-glutamate + 1 phosphate + 1 pyridoxal_5'-phosphate + 3 H2O # Saci_1556 cof_prpp_nuc-cof-nad_2.7.6.1_PRPPSYN-RXN : 1 ATP + 1 D-ribose_5-phosphate <=> 1 AMP + 1 5-phospho-alpha-D-ribose_1-diphosphate # Saci_1282 cof_sam__2.5.1.6_S-ADENMETSYN-RXN : 1 ATP + 1 L-methionine + 1 H2O --> 1 phosphate + 1 diphosphate + 1 S-adenosyl-L-methionine # Saci_0798 cof_sah_salvage_3.3.1.1_ADENOSYLHOMOCYSTEINASE-RXN : 1 S-adenosyl-L-homocysteine + 1 H2O <=> 1 adenosine + 1 L-homocysteine # Saci_0646 # ================================ biosynthesis of lipids and other membrane components ================================ # # --- isoprenoids biosynthesis --- # Mevalonate Pathway from Jain2014 and Koga2007 lipids_isoprenoids_HMGS_2.3.3.10_HYDROXYMETHYLGLUTARYL-COA-SYNTHASE-RXN : 1 acetoacetyl-CoA + 1 acetyl-CoA + 1 H2O --> 1 (S)-3-hydroxy-3-methylglutaryl-CoA + 1 coenzyme_A # Saci_1362 lipids_isoprenoids_HMGR_1.1.1.34_1.1.1.34-RXN : 1 coenzyme_A + 1 (R)-mevalonate + 2 NADP+ <=> 1 (S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+ # Saci_1359 lipids_isoprenoids_MVK_2.7.1.36_MEVALONATE-KINASE-RXN : 1 ATP + 1 (R)-mevalonate <=> 1 ADP + 1 (R,S)-5-phosphomevalonate # Saci_2365 lipids_isoprenoids_PMK_2.7.4.2_PHOSPHOMEVALONATE-KINASE-RXN : 1 ATP + 1 (R,S)-5-phosphomevalonate <=> 1 ADP + 1 mevalonate-diphosphate # Saci_1244 lipids_isoprenoids_MDC_4.1.1.33_DIPHOSPHOMEVALONTE-DECARBOXYLASE-RXN : 1 ATP + 1 mevalonate-diphosphate --> 1 ADP + 1 CO2 + 1 isopentenyl_diphosphate + 1 phosphate # Saci_1245 lipids_isoprenoids_IPK_2.7.4.26_BR50003 : 1 ATP + 1 isopentenyl_phosphate <=> 1 ADP + 1 isopentenyl_diphosphate # rel: 0 suggested by Jain2014 lipids_isoprenoids_IDI_5.3.3.2_IPPISOM-RXN : 1 isopentenyl_diphosphate <=> 1 dimethylallyl_diphosphate # Saci_0091 lipids_isoprenoids__2.5.1.1_GPPSYN-RXN : 1 dimethylallyl_diphosphate + 1 isopentenyl_diphosphate <=> 1 geranyl_diphosphate + 1 diphosphate # lipids_isoprenoids__2.5.1.10_FPPSYN-RXN : 1 isopentenyl_diphosphate + 1 geranyl_diphosphate --> 1 (2E,6E)-farnesyl_diphosphate + 1 diphosphate # lipids_isoprenoids__2.5.1.29_FARNESYLTRANSTRANSFERASE-RXN : 1 isopentenyl_diphosphate + 1 (2E,6E)-farnesyl_diphosphate --> 1 geranylgeranyl_diphosphate + 1 diphosphate # Saci_0092 lipids_terpene__2.5.1.82_RXN-11485 : 2 isopentenyl_diphosphate + 1 geranylgeranyl_diphosphate <=> 1 all-trans-hexaprenyl_diphosphate + 2 diphosphate # Saci_0995 lipids_terpene__2.5.1.89_RXN-11488 : 7 isopentenyl_diphosphate + 1 geranylgeranyl_diphosphate <=> 7 diphosphate + 1 tri-trans,hepta-cis-undecaprenyl_diphosphate # Saci_0757 lipids_terpene__2.5.1.31_RXN-8999 : 8 isopentenyl_diphosphate + 1 (2E,6E)-farnesyl_diphosphate --> 8 diphosphate + 1 di-trans,octa-cis-undecaprenyl_diphosphate # # --- archaeol biosynthesis --- // uses sn-glycerol-1-phosphate as ether backbone [Jain2014]# lipids_synthesis__1.1.1.261_1.1.1.261-RXN-NAD : 1 sn-glycerol_1-phosphate + 1 NAD+ <-- 1 dihydroxyacetone_phosphate + 1 H+ + 1 NADH # Saci_0640 lipids_synthesis__1.1.1.261_1.1.1.261-RXN-NADP : 1 sn-glycerol_1-phosphate + 1 NADP+ <-- 1 dihydroxyacetone_phosphate + 1 H+ + 1 NADPH # Saci_0640 lipids_synthesis__2.5.1.41_2.5.1.41-RXN : 1 geranylgeranyl_diphosphate + 1 sn-glycerol_1-phosphate --> 1 diphosphate + 1 3-(O-geranylgeranyl)-sn-glycerol_1-phosphate # Saci_0728 lipids_synthesis__2.5.1.42_2.5.1.42-RXN : 1 geranylgeranyl_diphosphate + 1 3-(O-geranylgeranyl)-sn-glycerol_1-phosphate --> 1 2,3-bis-O-(geranylgeranyl)-sn-glycerol_1-phosphate + 1 diphosphate # Saci_1565 lipids_synthesis__1.3.7.11_RXN-14399 : 1 2,3-bis-O-phytanyl-sn-glycerol_1-phosphate + 8 NAD+ <-- 8 H+ + 8 NADH + 1 2,3-bis-O-(geranylgeranyl)-sn-glycerol_1-phosphate # Saci_0986 lipids_synthesis__2.7.7.67_RXN-14400 : 1 CTP + 1 2,3-bis-O-phytanyl-sn-glycerol_1-phosphate + 1 H+ --> 1 diphosphate + 1 CDP-archaeol # Saci_0897 lipids_synthesis_hydroxyarchaeol : 1 2,3-bis-O-phytanyl-sn-glycerol_1-phosphate + 1 H2O --> 1 2,3-bis-O-phytanyl-sn-glycerol + 1 phosphate # archaetidate ??? lipids_synthesis_calditol_glycosyl-transferase : 1 beta-D-glucose + 1 CDP-archaeol <=> 1 hexose-archaeol lipids_synthesis_calditol_calditol-synthase1 : 1 adenosine --> 1 deoxyadenosyl_radical # Saci_1489 [Zeng2018] lipids_synthesis_calditol_calditol-synthase2 : 1 hexose-archaeol + 1 deoxyadenosyl_radical --> 1 saturated_archaetidylcalditol + 1 adenosine # Saci_1489 [Zeng2018] lipids_synthesis_sulfolipid_3.13.1.1_RXN-1223 : 1 UDP-alpha-D-sulfoquinovopyranose + 1 H2O <-- 1 UDP-alpha-D-glucose + 1 sulfite + 1 H+ # Saci_0423 lipids_synthesis_myo-inositol_5.5.1.4_MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN : 1 beta-D-glucose_6-phosphate --> 1 1D-myo-inositol_3-monophosphate # Saci_2337 lipids_synthesis_myo-inositol_3.1.3.25_MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN : 1 1D-myo-inositol_3-monophosphate + 1 H2O --> 1 myo-inositol + 1 phosphate # Saci_0930 lipids_synthesis__2.7.8.39_RXN-14403 : 1 CDP-archaeol + 1 1D-myo-inositol_3-monophosphate --> 1 CMP + 1 saturated_archaetidylinositol_phosphate # Saci_1541 lipids_synthesis_unknown_RXN-14404 : 1 saturated_archaetidylinositol_phosphate + 1 H2O --> 1 phosphate + 1 saturated_archaetidylinositol # lipids_synthesis_caldarchaeol-phospholipid-condensation01 : 1 saturated_archaetidylinositol + 1 2,3-bis-O-phytanyl-sn-glycerol + 1 NADPH + 1 H+ --> 1 saturated_inositolcaldarchaeol + 1 NADP+ # lipids_synthesis__2.7.8.38_RXN-14405 : 1 CDP-archaeol + 1 L-serine --> 1 CMP + 1 saturated_archaetidylserine # lipids_synthesis__unknown_RXN-14406 : 1 saturated_archaetidylserine --> 1 CO2 + 1 saturated_archaetidylethanolamine # lipids_synthesis__2.7.8.-_saturated-archaetidylglycerolphosphate-synthase : 1 sn-glycerol_1-phosphate + 1 CDP-archaeol <=> 1 H+ + 1 saturated_archaetidylglycerolphosphate + 1 CMP # lipids_synthesis__3.1.3.-_saturated-archaetidylglycerolphosphate-phosphatase : 1 saturated_archaetidylglycerolphosphate + 1 H2O --> 1 saturated_archaetidylglycerol + 1 phosphate # Saci_0983 lipids_synthesis__1.3.7.11_RXN-16518 : 1 saturated_archaetidylglycerol + 16 oxidized_ferredoxin --> 1 unsaturated_archaetidylglycerol + 16 reduced_ferredoxin + 16 H+ # Saci_0986 lipids_synthesis_glycolipid_01 : 1 2,3-bis-O-phytanyl-sn-glycerol + 1 UDP-alpha-D-galactose --> 1 saturated_archaetidylgalactose + 1 UDP # lipids_synthesis_glycolipid_02 : 1 saturated_archaetidylgalactose + 1 UDP-alpha-D-glucose --> 1 saturated_archaetidylgalactosylglucose + 1 UDP # lipids_synthesis_caldarchaeol-glycolipid-condensation01 : 1 saturated_archaetidylgalactosylglucose + 1 2,3-bis-O-phytanyl-sn-glycerol + 1 NADPH + 1 H+ --> 1 saturated_glycolipidcaldarchaeol + 1 NADP+ # lipids_synthesis_sulfocaldarchaeol : 1 saturated_glycolipidcaldarchaeol + 1 3'-phosphoadenylyl-sulfate --> 1 H+ + 1 adenosine_3',5'-bisphosphate + 1 saturated_sulfoglycolipidcaldarchaeol # #lipids_synthesis_glycolipid_03 : 1 2,3-bis-O-phytanyl-sn-glycerol + 1 UDP-calditol --> 1 saturated_archaetidylcalditol + 1 UDP # lipids_synthesis_glycolipid_04 : 1 saturated_archaetidylcalditol + 1 UDP-alpha-D-glucose --> 1 saturated_archaetidylcalditylglucose + 1 UDP # lipids_synthesis_caldarchaeol-glycolipid-condensation02 : 1 saturated_archaetidylcalditylglucose + 1 2,3-bis-O-phytanyl-sn-glycerol + 1 NADPH + 1 H+ --> 1 saturated_calditolcaldarchaeol + 1 NADP+ # lipids_synthesis_caldarchaeol-inositol-glycolipid-condensation01 : 1 saturated_archaetidylgalactosylglucose + 1 saturated_archaetidylinositol + 1 NADPH + 1 H+ --> 1 saturated_inositolglycolipidcaldarchaeol + 1 NADP+ # lipids_synthesis_caldarchaeol-inositol-glycolipid-condensation02 : 1 saturated_archaetidylcalditylglucose + 1 saturated_archaetidylinositol + 1 NADPH + 1 H+ --> 1 saturated_inositolcalditolcaldarchaeol + 1 NADP+ # # --- exopolysaccharides --- # lipids_exopolysaccharides__2.6.1.16_L-GLN-FRUCT-6-P-AMINOTRANS-RXN : 1 beta-D-fructofuranose_6-phosphate + 1 L-glutamine --> 1 alpha-D-glucosamine_6-phosphate + 1 L-glutamate # Saci_2364 lipids_exopolysaccharides__5.4.2.10_5.4.2.10-RXN : 1 D-glucosamine_1-phosphate <=> 1 alpha-D-glucosamine_6-phosphate # Saci_0806 lipids_exopolysaccharides__2.3.1.157_2.3.1.157-RXN : 1 acetyl-CoA + 1 D-glucosamine_1-phosphate <=> 1 coenzyme_A + 1 N-acetyl-alpha-D-glucosamine_1-phosphate # Saci_0619 lipids_exopolysaccharides__2.7.7.23_NAG1P-URIDYLTRANS-RXN : 1 N-acetyl-alpha-D-glucosamine_1-phosphate + 1 UTP <=> 1 diphosphate + 1 UDP-N-acetyl-alpha-D-glucosamine # Saci_0619 # ================================ nucleic acid synthesis ================================ # # --- nucleic acid de novo synthesis --- # nuc_purin_de-novo_2.4.2.14_PRPPAMIDOTRANS-RXN : 1 5-phospho-beta-D-ribosylamine + 1 L-glutamate + 1 diphosphate <-- 1 L-glutamine + 1 5-phospho-alpha-D-ribose_1-diphosphate + 1 H2O # Saci_1612 nuc_purin_de-novo_6.3.4.13_GLYRIBONUCSYN-RXN : 1 5-phospho-beta-D-ribosylamine + 1 ATP + 1 glycine --> 1 5-phospho-ribosyl-glycineamide + 1 ADP + 1 phosphate # Saci_1613 nuc_purin_de-novo_2.1.2.-_GARTRANSFORMYL2-RXN : 1 5-phospho-ribosyl-glycineamide + 1 ATP + 1 formate --> 1 N2-formyl-N1-(5-phospho-beta-D-ribosyl)glycinamide + 1 ADP + 1 phosphate # Saci_0214 nuc_purin_de-novo_2.1.2.2_GART-RXN : 1 10-formyl-tetrahydrosulfopterin + 1 5-phospho-ribosyl-glycineamide <=> 1 N2-formyl-N1-(5-phospho-beta-D-ribosyl)glycinamide + 1 tetrahydrosulfopterin # nuc_purin_de-novo_6.3.5.3_FGAMSYN-RXN : 1 N2-formyl-N1-(5-phospho-beta-D-ribosyl)glycinamide + 1 ATP + 1 L-glutamine + 1 H2O <=> 1 2-(formamido)-N1-(5-phospho-beta-D-ribosyl)acetamidine + 1 ADP + 1 L-glutamate + 1 phosphate # Saci_1610; Saci_1608; Saci_0079; Saci_0704 nuc_purin_de-novo_6.3.3.1_AIRS-RXN : 1 2-(formamido)-N1-(5-phospho-beta-D-ribosyl)acetamidine + 1 ATP --> 1 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + 1 ADP + 1 phosphate # Saci_1614 nuc_purin_de-novo_4.1.1.21_AIRCARBOXY-RXN : 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate <=> 1 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + 1 CO2 # Saci_1190 nuc_purin_de-novo_6.3.2.6_SAICARSYN-RXN : 1 ATP + 1 L-aspartate + 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate --> 1 ADP + 1 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole + 1 phosphate # Saci_1607 nuc_purin_de-novo_4.3.2.2_AICARSYN-RXN : 1 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <=> 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + 1 fumarate # Saci_0706 nuc_purin_de-novo_6.3.4.23_RXN-10066 : 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + 1 ATP + 1 formate --> 1 ADP + 1 phosphoribosyl-formamido-carboxamide + 1 phosphate # Saci_0707-8 nuc_purin_de-novo_2.1.2.3_IMPCYCLOHYDROLASE-RXN : 1 IMP + 1 H2O <=> 1 phosphoribosyl-formamido-carboxamide # nsb # nuc_purin_de-novo_6.3.4.23_RXN-10066 : 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + 1 formate + 1 ATP <=> 1 phosphate + 1 5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide + 1 ADP # Saci_0708 nuc_purin_de-novo_1.1.1.205_IMP-DEHYDROG-RXN : 1 IMP + 1 NAD+ + 1 H2O <=> 1 NADH + 1 H+ + 1 XMP # nsb nuc_purin_de-novo_6.3.5.2_GMP-SYN-GLUT-RXN : 1 ATP + 1 L-glutamine + 1 H2O + 1 XMP --> 1 AMP + 1 L-glutamate + 1 GMP + 1 diphosphate # Saci_0548 nuc_purin_de-novo_6.3.4.4_ADENYLOSUCCINATE-SYNTHASE-RXN : 1 GTP + 1 IMP + 1 L-aspartate --> 1 adenylo-succinate + 1 GDP + 1 phosphate # Saci_0709 nuc_purin_de-novo_4.3.2.2_AMPSYN-RXN : 1 adenylo-succinate <=> 1 AMP + 1 fumarate # Saci_0706 nuc_pyrim_de-novo_2.1.3.2_ASPCARBTRANS-RXN : 1 carbamoyl-phosphate + 1 L-aspartate <=> 1 N-carbamoyl-L-aspartate + 1 phosphate # Saci_1595 nuc_pyrim_de-novo_3.5.2.3_DIHYDROOROT-RXN : 1 (S)-dihydroorotate + 1 H2O <=> 1 N-carbamoyl-L-aspartate # Saci_1593 nuc_pyrim_de-novo_1.3.1.14_BS413428 : 1 (S)-dihydroorotate + 1 FMN <=> 1 orotate + 1 FMNH2 # Saci_1592 nuc_pyrim_de-novo_1.3.1.14_RXN0-6491 : 1 (S)-dihydroorotate + 1 representative_quinone <=> 1 orotate + 1 representative_quinol # Saci_1592 # nuc_pyrim_de-novo_1.3.98.1_BS258661 : 1 (S)-dihydroorotate + 1 oxygen --> 1 orotate + 1 hydrogen_peroxide # nuc_pyrim_de-novo_2.4.2.10_OROPRIBTRANS-RXN : 1 orotidine_5'-phosphate + 1 diphosphate <=> 1 orotate + 1 5-phospho-alpha-D-ribose_1-diphosphate #Saci_1597 JHE MW001 deletion; ḾW2000 SNP, FS!! nuc_pyrim_de-novo_4.1.1.23_OROTPDECARB-RXN : 1 orotidine_5'-phosphate --> 1 CO2 + 1 UMP # JHE MW001 deletion Saci_1598 Saci_1598 nuc_pyrim_de-novo_2.7.4.6_UDPKIN-RXN : 1 ATP + 1 UDP <=> 1 ADP + 1 UTP # Saci_0696 nuc_pyrim_de-novo_6.3.4.2_CTPSYN-RXN : 1 ATP + 1 L-glutamine + 1 UTP + 1 H2O --> 1 ADP + 1 CTP + 1 L-glutamate + 1 phosphate # Saci_0801 # --- nucleic acid synthesis and conversion --- # nuc_purin__1.17.4.1_ADPREDUCT-RXN : 1 dADP + 1 H2O + 1 oxidized_thioredoxin <-- 2 H+ + 1 ADP + 1 reduced_thioredoxin # Saci_2220 nuc_purin__1.17.4.1_GDPREDUCT-RXN : 1 dGDP + 1 H2O + 1 oxidized_thioredoxin <-- 2 H+ + 1 GDP + 1 reduced_thioredoxin # Saci_2220 #nuc_purin__2.7.4.3_ADENYL-KIN-RXN : 1 AMP + 1 ATP <=> 2 ADP # Saci_0443 nuc_purin__2.7.4.3,2.7.4.6_RXN-14074 : 1 GTP + 1 AMP <=> 1 GDP + 1 ADP # Saci_0443 nuc_purin__2.7.4.3,2.7.4.6_CDPKIN-RXN : 1 ATP + 1 CDP <=> 1 ADP + 1 CTP # Saci_0443 nuc_purin__2.7.4.3,2.7.4.6_DCDPKIN-RXN : 1 ATP + 1 dCDP <=> 1 ADP + 1 dCTP # Saci_0443 nuc_purin__2.7.4.3,2.7.4.14_RXN-11832 : 1 ATP + 1 CMP <=> 1 ADP + 1 CDP # Saci_0443 nuc_purin__2.7.4.3_R01547 : 1 ATP + 1 dAMP <=> 1 ADP + 1 dADP # Saci_0443 nuc_purin__2.7.4.6_DADPKIN-RXN : 1 ATP + 1 dADP <=> 1 ADP + 1 dATP # Saci_0696 nuc_purin__2.7.4.6_DGDPKIN-RXN : 1 ATP + 1 dGDP <=> 1 ADP + 1 dGTP # Saci_0696 #nuc_purin__2.7.4.6_RXN-14074 : 1 GDP + 1 ADP <=> 1 GTP + 1 AMP # Saci_0696 nuc_purin__2.7.4.6_RXN-14120 : 1 ATP + 1 IDP <=> 1 ITP + 1 ADP # Saci_0696 nuc_purin__2.7.4.6_RXN-14228 : 1 ATP + 1 dIDP <=> 1 ADP + 1 dITP # Saci_0696 nuc_purin__2.7.4.8_GUANYL-KIN-RXN : 1 ATP + 1 GMP <=> 1 ADP + 1 GDP # nsb nuc_purin__3.6.1.1_3.6.4.12_RXN : 1 ATP + 1 H2O --> 1 ADP + 1 phosphate # Saci_0955 nuc_purin__3.6.1.15,3.6.1.19_BS359054 : 1 XTP + 1 H2O --> 1 XDP + 1 phosphate # Saci_0011 nuc_purin__3.6.1.15,3.6.1.19_BS373042 : 1 dGTP + 1 H2O --> 1 dGDP + 1 phosphate # Saci_0011 nuc_purin__3.6.1.15,3.6.1.19_BS384566 : 1 dADP + 1 H2O --> 1 dAMP + 1 phosphate # Saci_0011 nuc_purin__3.6.1.15,3.6.1.19_BS384600 : 1 dGDP + 1 H2O --> 1 dGMP + 1 phosphate # Saci_0011 nuc_purin__3.6.1.15,3.6.1.19_BS402613 : 1 dITP + 1 H2O --> 1 dIDP + 1 phosphate # Saci_0011 nuc_purin__3.6.1.15,3.6.1.19_RXN-14214 : 1 dATP + 1 H2O --> 1 dADP + 1 phosphate # Saci_0011 nuc_purin__3.6.1.15,3.6.1.19_RXN0-5462 : 1 GTP + 1 H2O --> 1 GDP + 1 phosphate # Saci_0011 nuc_purin__5.4.99.18_RXN0-743 : 1 N5-carboxyaminoimidazole_ribonucleotide <=> 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate # Saci_1190 nuc_purin__6.3.4.18_RXN0-742 : 1 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + 1 ATP + 1 hydrogen_carbonate --> 1 ADP + 1 N5-carboxyaminoimidazole_ribonucleotide + 1 phosphate # Saci_1191 nuc_pyrim__2.7.4.3_BS358186 : 1 UTP + 1 AMP <=> 1 UDP + 1 ADP # Saci_0443 nuc_pyrim__1.17.4.1_CDPREDUCT-RXN : 1 dCDP + 1 H2O + 1 oxidized_thioredoxin <-- 2 H+ + 1 CDP + 1 reduced_thioredoxin # Saci_2220 nuc_pyrim__1.17.4.1_UDPREDUCT-RXN : 1 dUDP + 1 H2O + 1 oxidized_thioredoxin <-- 2 H+ + 1 UDP + 1 reduced_thioredoxin # Saci_2220 nuc_pyrim__2.1.1.148_RXN-8850 : 1 dUMP + 1 5,10-methylene-tetrahydrosulfopterin + 1 NADPH + 1 H+ --> 1 NADP+ + 1 tetrahydrosulfopterin + 1 dTMP # Saci_2347 nuc_pyrim__2.7.4.14_RXN-12002 : 1 ATP + 1 UMP <=> 1 ADP + 1 UDP # Saci_0570 nuc_pyrim__2.7.4.14_RXN-14122 : 1 ATP + 1 dUMP <=> 1 ADP + 1 dUDP # Saci_0570 nuc_pyrim__2.7.4.14_RXN-7913 : 1 ATP + 1 dCMP <=> 1 ADP + 1 dCDP # Saci_0570 nuc_pyrim__2.7.4.6_DTDPKIN-RXN : 1 ATP + 1 dTDP <=> 1 ADP + 1 dTTP # Saci_0696 nuc_pyrim__2.7.4.6_DUDPKIN-RXN : 1 ATP + 1 dUDP <=> 1 ADP + 1 dUTP # Saci_0696 #nuc_pyrim__2.7.4.6_GDPKIN-RXN : 1 ATP + 1 GDP <=> 1 ADP + 1 GTP # Saci_0696 nuc_pyrim__2.7.4.9_DTMPKI-RXN : 1 ATP + 1 dTMP <=> 1 ADP + 1 dTDP # Saci_2020 nuc_pyrim__3.6.1.23_BS139757 : 1 UTP + 1 H2O --> 1 UMP + 1 diphosphate # Saci_1672 nuc_pyrim__3.5.4.13_DCTP-DEAM-RXN : 1 dCTP + 1 H2O --> 1 ammonia + 1 dUTP # Saci_1672 nuc_pyrim__3.5.4.13_RXN-14118 : 1 CTP + 1 H2O --> 1 UTP + 1 ammonium # Saci_1672 nuc_pyrim__3.6.1.15,3.6.1.19_BS141286 : 1 UDP + 1 H2O --> 1 UMP + 1 phosphate # Saci_0011 nuc_pyrim__3.6.1.15,3.6.1.19_BS141301 : 1 dUDP + 1 H2O --> 1 dUMP + 1 phosphate # Saci_0011 nuc_pyrim__3.6.1.15,3.6.1.19_BS141340 : 1 dUTP + 1 H2O --> 1 dUDP + 1 phosphate # Saci_0011 nuc_pyrim__3.6.1.15,3.6.1.19_BS384570 : 1 dCDP + 1 H2O --> 1 dCMP + 1 phosphate # Saci_0011 nuc_pyrim__3.6.1.15,3.6.1.19_BS93276 : 1 CDP + 1 H2O --> 1 CMP + 1 phosphate # Saci_0011 nuc_pyrim__3.6.1.15,3.6.1.19_RXN-12195 : 1 CTP + 1 H2O --> 1 CDP + 1 phosphate # Saci_0011 nuc_pyrim__3.6.1.15,3.6.1.19_RXN-12196 : 1 UTP + 1 H2O --> 1 phosphate + 1 UDP # Saci_0011 nuc_pyrim__3.6.1.3,3.6.1.15,3.6.1.19_RXN-14216 : 1 dCTP + 1 H2O --> 1 dCDP + 1 phosphate # Saci_0011 # --- nucleic acid salvage --- # nuc_purin_degra-nuc_1.17.1.4_RXN0-901 : 1 NAD+ + 1 xanthine + 1 H2O <=> 1 H+ + 1 urate + 1 NADH # Saci_2117 nuc_purin_salvage_3.5.4.3_GUANINE-DEAMINASE-RXN : 1 guanine + 1 H2O --> 1 ammonia + 1 xanthine # Saci_0888 nuc_purin_salvage_1.17.1.4_RXN-7682 : 1 hypoxanthine + 1 NAD+ + 1 H2O <=> 1 NADH + 1 H+ + 1 xanthine # Saci_2117 nuc_purin_salvage_2.4.2.1_ADENPHOSPHOR-RXN : 1 adenosine + 1 phosphate --> 1 adenine + 1 alpha-D-ribose-1-phosphate # Saci_1247 nuc_purin_salvage_2.4.2.1_DEOXYADENPHOSPHOR-RXN : 1 2'-deoxyadenosine + 1 phosphate <=> 1 adenine + 1 2-deoxy-alpha-D-ribose_1-phosphate # Saci_1247 nuc_purin_salvage_2.4.2.1_DEOXYGUANPHOSPHOR-RXN : 1 2'-deoxyguanosine + 1 phosphate <=> 1 2-deoxy-alpha-D-ribose_1-phosphate + 1 guanine # Saci_1247 nuc_purin_salvage_2.4.2.1_DEOXYINOPHOSPHOR-RXN : 1 2'-deoxyinosine + 1 phosphate <=> 1 2-deoxy-alpha-D-ribose_1-phosphate + 1 hypoxanthine # Saci_1247 nuc_purin_salvage_2.4.2.1_deoxyuridine : 1 phosphate + 1 2'-deoxyuridine <=> 1 2-deoxy-alpha-D-ribose_1-phosphate + 1 uracil # Saci_1247 nuc_purin_salvage_2.4.2.1_INOPHOSPHOR-RXN : 1 inosine + 1 phosphate <=> 1 hypoxanthine + 1 alpha-D-ribose-1-phosphate # Saci_1247 nuc_purin_salvage_2.4.2.1_RXN0-5199 : 1 guanosine + 1 phosphate <-- 1 guanine + 1 alpha-D-ribose-1-phosphate # Saci_1247 nuc_purin_salvage_2.4.2.1_XANTHOSINEPHOSPHORY-RXN : 1 phosphate + 1 xanthosine <=> 1 alpha-D-ribose-1-phosphate + 1 xanthine # Saci_1247 nuc_purin_salvage_2.4.2.22_XANPRIBOSYLTRAN-RXN : 1 diphosphate + 1 XMP <=> 1 5-phospho-alpha-D-ribose_1-diphosphate + 1 xanthine # Saci_0701 nuc_purin_salvage_2.4.2.28_RXN-14304 : 1 5'-deoxyadenosine + 1 phosphate <=> 1 5-deoxy-alpha-ribose_1-phosphate + 1 adenine # Saci_0997 nuc_purin_salvage_predicted : 1 ATP + 5-deoxy-alpha-ribose_1-phosphate --> 1 5-phospho-alpha-D-ribose_1-diphosphate + 1 ADP # JHE only predicted nuc_purin_salvage_2.4.2.7_ADENPRIBOSYLTRAN-RXN : 1 AMP + 1 diphosphate <-- 1 adenine + 1 5-phospho-alpha-D-ribose_1-diphosphate # Saci_0998 nuc_purin_salvage_2.4.2.7_2.4.2.8_BS354829 : 1 GMP + 1 diphosphate <-- 1 guanine + 1 5-phospho-alpha-D-ribose_1-diphosphate # Saci_0998,Saci_0925 nuc_purin_salvage_2.4.2.8_HYPOXANPRIBOSYLTRAN-RXN : 1 IMP + 1 diphosphate <-- 1 hypoxanthine + 1 5-phospho-alpha-D-ribose_1-diphosphate # Saci_0925 nuc_purin_salvage_3.1.3.5_AMP-DEPHOSPHORYLATION-RXN : 1 AMP + 1 H2O --> 1 adenosine + 1 phosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_BS64635 : 1 dGMP + 1 H2O --> 1 2'-deoxyguanosine + 1 phosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_BS73810 : 1 ADP + 1 H2O --> 1 adenosine + 1 diphosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_dAMP : 1 dAMP + 1 H2O --> 1 2'-deoxyadenosine + 1 phosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_dTMP : 1 dTMP + 1 H2O --> 1 thymidine + 1 phosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_dUMP : 1 dUMP + 1 H2O --> 1 2'-deoxyuridine + 1 phosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_RXN-7607 : 1 IMP + 1 H2O --> 1 inosine + 1 phosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_RXN-7609 : 1 GMP + 1 H2O --> 1 guanosine + 1 phosphate # Saci_0954 nuc_purin_salvage_3.1.3.5_XMPXAN-RXN : 1 H2O + 1 XMP --> 1 phosphate + 1 xanthosine # Saci_0954 nuc_purin_salvage_3.2.2.1_xanthosine : 1 xanthosine + 1 H2O --> 1 xanthine + 1 alpha-D-ribofuranose # Saci_1187 nuc_purin_salvage_3.2.2.8_R01245 : 1 adenosine + 1 H2O <=> 1 adenine + 1 beta-D-ribopyranose # Saci_1187 nuc_purin_salvage_3.2.2.8_R01677 : 1 guanosine + 1 H2O <=> 1 guanine + 1 beta-D-ribopyranose # Saci_1187 nuc_purin_salvage_3.2.2.8_R01770 : 1 inosine + 1 H2O --> 1 hypoxanthine + 1 beta-D-ribopyranose # Saci_1187 nuc_pyrim_salvage_2.4.2.9_URACIL-PRIBOSYLTRANS-RXN : 1 diphosphate + 1 UMP <=> 1 5-phospho-alpha-D-ribose_1-diphosphate + 1 uracil # Saci_0699 nuc_pyrim_salvage_3.1.3.5_BS364579 : 1 dCMP + 1 H2O <=> 1 2'-deoxycytidine + 1 phosphate # Saci_0954 nuc_pyrim_salvage_3.1.3.5_RXN-14026 : 1 CMP + 1 H2O <=> 1 cytidine + 1 phosphate # Saci_0954 nuc_pyrim_salvage_3.2.2.3_BS214506 : 1 xanthosine + 1 H2O --> 1 beta-D-ribopyranose + 1 xanthine # Saci_0159 nuc_pyrim_salvage_3.2.2.3_RXN0-361 : 1 cytidine + 1 H2O --> 1 cytosine + 1 alpha-D-ribofuranose # Saci_0159 nuc_pyrim_salvage_3.2.2.8_R02137 : 1 cytidine + 1 H2O <=> 1 cytosine + 1 beta-D-ribopyranose # Saci_1187 nuc_pyrim_salvage_3.5.4.1_CYTDEAM-RXN : 1 cytosine + 1 H2O --> 1 ammonia + 1 uracil # Saci_1072 nuc_pyrim_salvage_3.1.3.5_RXN-14025 : 1 UMP + 1 H2O --> 1 uridine + 1 phosphate # Saci_0954 nuc_pyrim_salvage_3.2.2.3_uridine : 1 uridine + 1 H2O --> 1 uracil + 1 alpha-D-ribofuranose # Saci_0159 nuc_pyrim_salvage_3.5.2.2_DIHYDROPYRIMIDINASE-RXN : 1 5,6-dihydrouracil + 1 H2O --> 1 3-ureidopropanoate # Saci_2036 nuc__salvage_5.4.2.7_PPENTOMUT-RXN : 1 alpha-D-ribose-1-phosphate <=> 1 D-ribose_5-phosphate # Saci_0806 nuc__salvage_2.7.1.15_RIBOKIN-RXN : 1 ATP + 1 alpha-D-ribofuranose --> 1 D-ribose_5-phosphate + 1 H+ + 1 ADP # Saci_0553 # ================================ tRNA charging ================================ # tRNA_TYR__6.1.1.1_TYROSINE--TRNA-LIGASE-RXN : 1 ATP + 1 H+ + 1 L-tyrosine + 1 |TYR-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-TYR-tRNAs| # Saci_0076 tRNA_TRY__6.1.1.2_TRYPTOPHAN--TRNA-LIGASE-RXN : 1 ATP + 1 H+ + 1 L-tryptophan + 1 |TRP-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-TRP-tRNAs| # Saci_0450 tRNA_THR__6.1.1.3_THREONINE--TRNA-LIGASE-RXN : 1 ATP + 1 H+ + 1 L-threonine + 1 |THR-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-THR-tRNAs| # Saci_1261 tRNA_LEU__6.1.1.4_LEUCINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-leucine + 1 H+ + 1 |LEU-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-LEU-tRNAs| # Saci_1572 tRNA_ISO__6.1.1.5_ISOLEUCINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-isoleucine + 1 H+ + 1 |ILE-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-ILE-tRNAs| # Saci_0599 tRNA_LYS__6.1.1.6_LYSINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-lysine + 1 H+ + 1 |LYS-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-LYS-tRNAs| # Saci_0067 tRNA_ALA__6.1.1.7_ALANINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-alanine + 1 H+ + 1 |ALA-tRNAs| --> 1 AMP + 1 diphosphate + 1 |Charged-ALA-tRNAs| # Saci_1455 tRNA_VAL__6.1.1.9_VALINE--TRNA-LIGASE-RXN : 1 ATP + 1 H+ + 1 L-valine + 1 |VAL-tRNAs| --> 1 AMP + 1 diphosphate + 1 |Charged-VAL-tRNAs| # Saci_1430 tRNA_MET__6.1.1.10_METHIONINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-methionine + 1 H+ + 1 |MET-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-MET-tRNAs| # Saci_1544 tRNA_SER__6.1.1.11_SERINE--TRNA-LIGASE-RXN : 1 ATP + 1 H+ + 1 L-serine + 1 |SER-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-SER-tRNAs| # Saci_1584 tRNA_ASP__6.1.1.13_ASPARTATE--TRNA-LIGASE-RXN : 1 ATP + 1 L-aspartate + 1 H+ + 1 |ASP-tRNAs| --> 1 AMP + 1 diphosphate + 1 |Charged-ASP-tRNAs| # Saci_0768 tRNA_GLY__6.1.1.14_GLYCINE--TRNA-LIGASE-RXN : 1 ATP + 1 glycine + 1 H+ + 1 |GLY-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-GLY-tRNAs| # Saci_0862 tRNA_PRO__6.1.1.15_PROLINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-proline + 1 H+ + 1 |PRO-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-PRO-tRNAs| # Saci_1553 tRNA_CYS__6.1.1.16_CYSTEINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-cysteine + 1 H+ + 1 |CYS-tRNAs| --> 1 AMP + 1 diphosphate + 1 |Charged-CYS-tRNAs| # Saci_0152 tRNA_GLU__6.1.1.18,6.3.5.7_GLUTAMINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-glutamine + 1 H+ + 1 |GLN-tRNAs| <=> 1 AMP + 1 diphosphate + 1 |Charged-GLN-tRNAs| # Saci_0361 tRNA_ARG__6.1.1.19_ARGININE--TRNA-LIGASE-RXN : 1 L-arginine + 1 ATP + 1 H+ + 1 |ARG-tRNAs| --> 1 AMP + 1 diphosphate + 1 |Charged-ARG-tRNAs| # Saci_1396 tRNA_PHE__6.1.1.20_PHENYLALANINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-phenylalanine + 1 H+ + 1 |PHE-tRNAs| --> 1 AMP + 1 diphosphate + 1 |Charged-PHE-tRNAs| # Saci_1510 tRNA_HIS__6.1.1.21_HISTIDINE--TRNA-LIGASE-RXN : 1 ATP + 1 L-histidine + 1 H+ + 1 |HIS-tRNAs| --> 1 AMP + 1 diphosphate + 1 |Charged-HIS-tRNAs| # Saci_0663 # ================================ other pathways ================================ # other___2.3.1.9_RXN-12561 : 1 acetyl-CoA + 1 propanoyl-CoA <=> 1 coenzyme_A + 1 beta-ketovaleryl-CoA # Saci_2288 other___2.5.1.46_RXN-13414 : 1 spermidine + 1 NAD+ <=> 1 dehydrospermidine + 1 NADH + 1 H+ # Saci_1316 other__jasmonic-acid-biosyn_2.3.1.16_RXN-10701 : 1 coenzyme_A + 1 OPC4-3-ketoacyl-CoA <=> 1 acetyl-CoA + 1 jasmonoyl-CoA # Saci_1114 other___6.2.1.3_LINOLENOYL-RXN : 1 Linolenoyl-CoA + 1 H2O <=> 1 coenzyme_A + 1 alpha-linolenate # Saci_2225 other___6.2.1.3_RXN-13614 : 1 decanoate + 1 ATP + 1 coenzyme_A --> 1 decanoyl-CoA + 1 AMP + 1 diphosphate # Saci_2225 other___6.2.1.3_RXN-9623 : 1 ATP + 1 coenzyme_A + 1 palmitate --> 1 AMP + 1 palmitoyl-CoA + 1 diphosphate # Saci_2225 other___6.2.1.3_RXN-9644 : 1 ATP + 1 coenzyme_A + 1 oleate --> 1 AMP + 1 oleoyl-CoA + 1 diphosphate # Saci_2225 other___6.2.1.3_RXN-9673 : 1 ATP + 1 coenzyme_A + 1 linoleate --> 1 AMP + 1 linoleoyl-CoA + 1 diphosphate # Saci_2225 other___6.2.1.3_RXN66-480 : 1 phytenate + 1 ATP + 1 coenzyme_A --> 1 phytenoyl-CoA + 1 AMP + 1 diphosphate # Saci_2225 other___6.2.1.3_RXN66-484 : 1 pristanate + 1 coenzyme_A + 1 ATP --> 1 pristanoyl-CoA + 1 diphosphate + 1 AMP # Saci_2225 other__octane-oxidation_6.2.1.3_R223-RXN : 1 ATP + 1 coenzyme_A + 1 octanoate --> 1 AMP + 1 octanoyl-CoA + 1 diphosphate # Saci_2225 other__protocat-degra-II_4.1.1.44_4-CARBOXYMUCONOLACTONE-DECARBOXYLASE-RXN : 1 2-carboxy-5-oxo-2,5-dihydrofuran-2-acetate --> 1 3-oxoadipate_enol_lactone + 1 CO2 # Saci_1814 other__metabolism-of-degra_3.5.1.87_BS189995 : 1 N-carbamoyl-L-methionine + 1 H2O --> 1 L-methionine + 1 CO2 + 1 ammonia # Saci_2132 other__metabolism-of-degra_3.5.1.87_BS389254 : 1 N-carbamoyl-L-alanine + 1 H2O --> 1 L-alanine + 1 CO2 + 1 ammonia # Saci_2132 other___2.5.1.32_RXN1F-144 : 2 geranylgeranyl_diphosphate --> 1 all-trans-phytoene + 2 diphosphate # other___3.8.1.2_BS141612 : 1 chloroacetate + 1 H2O --> 1 glycolate + 1 HCl # other___3.8.1.2_BS141613 : 1 bromoacetate + 1 H2O --> 1 glycolate + 1 HBr # #other___1.1.3.15_BS257485 : 1 glycolate + 1 oxygen --> 1 glyoxylate + 1 hydrogen_peroxide # other___1.8.4.11_1.8.4.13-RXN : 1 L-methionine + 1 oxidized_thioredoxin + 1 H2O <=> 1 reduced_thioredoxin + 1 L-methionine-(S)-S-oxide # Saci_1170 other___3.1.1.45_CARBOXYMETHYLENEBUTENOLIDASE-RXN : 1 cis-dienelactone + 1 H2O --> 1 2-maleylacetate # Saci_1718 other___3.1.1.2_BS115376 : 1 protein_S-farnesyl-L-cysteine + 1 H2O --> 1 4-nitrophenol + 1 butanoate # not genome-based (40); Saci_2140; not genome-based (10) Saci_2140 other___3.1.1.2_BS363949 : 1 tributyrin + 1 H2O <-- 1 dibutyrin + 1 butanoate # not genome-based (40); Saci_2140; not genome-based (10) Saci_2140 other__multiple-pathways_3.1.1.1_BS321404 : 1 ethanol + 1 acetyl-CoA <=> 1 butanoate + 1 coenzyme_A # Saci_1116 other___2.7.8.15_R05969 : 1 UDP-N-acetyl-alpha-D-glucosamine + 1 dolichyl_phosphate <=> 1 UMP + 1 N-acetylglucosaminyl-diphosphodolichol # Saci_0093 other___2.4.1.83_2.4.1.83-RXN : 1 dolichyl_phosphate + 1 GDP-alpha-D-mannose <=> 1 GDP + 1 dolichyl_beta-D-mannosyl_phosphate # Saci_1011;Saci_1011 other__multiple-pathways_2.3.2.2_BS370350 : 1 N-(4-nitrophenyl)-L-alpha-glutamine + 1 glutathione --> 1 4-nitroaniline + 1 5-L-glutamyl-glutathione # Saci_0425 other__multiple-pathways_2.3.2.2_R00494 : 1 glutathione + 1 H2O --> 1 L-cysteinyl-glycine + 1 L-glutamate # Saci_0425 other___2.3.1.16_RXN-13617 : 1 octanoyl-CoA + 1 acetyl-CoA <=> 1 3-oxodecanoyl-CoA + 1 coenzyme_A # Saci_1114 other___2.3.1.16_RXN-14268 : 1 lauroyl-CoA + 1 acetyl-CoA <=> 1 3-oxo-myristoyl-CoA + 1 coenzyme_A # Saci_1114 other___2.3.1.16_RXN-14274 : 1 decanoyl-CoA + 1 acetyl-CoA <=> 1 3-oxododecanoyl-CoA + 1 coenzyme_A # Saci_1114 other___2.3.1.16_RXN-14277 : 1 hexanoyl-CoA + 1 acetyl-CoA <=> 1 3-oxooctanoyl-CoA + 1 coenzyme_A # Saci_1114 other__threonine-degra-III-(to-methylglyoxal)_1.4.3.21_AMACETOXID-RXN : 1 aminoacetone + 1 oxygen + 1 H2O --> 1 ammonia + 1 hydrogen_peroxide + 1 methylglyoxal # Saci_2182 other__multiple-pathways_1.4.3.21_BS259130 : 1 tyramine + 1 H2O + 1 oxygen --> 1 4-hydroxyaceto-phenone + 1 ammonia + 1 hydrogen_peroxide # Saci_2182 other___1.4.3.21_RXN-11784 : 1 cadaverine + 1 oxygen + 1 H2O --> 1 ammonia + 1 5-aminopentanal + 1 hydrogen_peroxide # Saci_2182 other__multiple-pathways_1.4.3.21_BS259107 : 1 benzylamine + 1 H2O + 1 oxygen --> 1 benzaldehyde + 1 ammonia + 1 hydrogen_peroxide # Saci_2182 other__phenylethylamine-degra,phenylethanol-biosyn_1.4.3.21_AMINEPHEN-RXN : 1 oxygen + 1 2-phenylethylamine + 1 H2O --> 1 ammonia + 1 hydrogen_peroxide + 1 phenylacetaldehyde # Saci_2182 other__metabolism-of-degra_3.5.1.87_BS386589 : 1 N-carbamoyl-L-cysteine + 1 H2O --> 1 L-cysteine + 1 CO2 + 1 ammonia # Saci_2132 other___2.4.1.117_2.4.1.117-RXN : 1 UDP-alpha-D-glucose + 1 dolichyl_phosphate <=> 1 UDP + 1 dolichyl_beta-D-glucosyl_phosphate # Saci_1909;Saci_1909 other___2.8.3.16_RXN0-1382 : 1 formyl-CoA + 1 oxalate <=> 1 formate + 1 oxalyl-CoA # other___3.5.99.2_THIAMINASE-RXN : 1 thiamin + 1 H2O <=> 1 4-amino-2-methyl-5-pyrimidinemethanol + 1 H+ + 1 4-methyl-5-(beta-hydroxyethyl)thiazole # Saci_1230 other___3.8.1.2_BS141614 : 1 iodoacetate + 1 H2O --> 1 glycolate + 1 iodide # # other___1.2.1.24_RXN0-5293-NAD : 1 succinate_semialdehyde + 1 H2O + 1 NAD+ --> 1 H+ + 1 succinate + 1 NADH # # other___1.2.1.79_RXN0-5293-NADP : 1 succinate_semialdehyde + 1 H2O + 1 NADP+ --> 1 H+ + 1 succinate + 1 NADPH # other___1.1.1.14_L-IDITOL-2-DEHYDROGENASE-RXN : 1 L-iditol + 1 NAD+ <=> 1 H+ + 1 L-sorbose + 1 NADH # Saci_0410 other__adenosine-5'-monophosphate-recycling_5.3.1.29_RXN-8801 : 1 alpha-D-ribose_1,5-bisphosphate --> 1 D-ribulose-1,5-bisphosphate # Saci_0854 # other__2,4-dinitrotoluene-degra,valine-degra_1.2.1.27_BR29389 : 1 3-oxopropanoate + 1 coenzyme_A + 1 NADP+ --> 1 acetyl-CoA + 1 CO2 + 1 NADPH + 1 H+ # # other__2,4-dinitrotoluene-degra,valine-degra_1.2.1.27_BS189112 : 1 methylmalonate_semialdehyde + 1 coenzyme_A + 1 NAD+ --> 1 H+ + 1 propanoyl-CoA + 1 CO2 + 1 NADH # other__no-pathway_3.1.6.19_RXN-14340 : 1 (R)-secondary-alkyl_sulfate_ester + 1 H2O --> 1 H+ + 1 sulfate + 1 (S)-secondary_alcohol # not genome-based (45) 3.1.6.19: nsb (45)