%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Here begins the description of the metabolic network of Aquifex aeolicus %%%%%%Core carbon metabolism, including CO2 fixation (rTCA + partial WL), gluconeogenesis and the pentose phosphate pathway %%%Folate CO2 uptake and reduction through a partial Wood-Ljungdahl pathway GENE_ASSOCIATION:( peg.724 and peg.726 ) PROTEIN_ASSOCIATION:fdoG+fdoI SUBSYSTEM: Formate_dehydrogenase PROTEIN_CLASS: 1.2.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.724 and peg.726 ) PROTEIN_ASSOCIATION:fdoG+fdoI SUBSYSTEM: NONE PROTEIN_CLASS: 1.2.2.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.724 and peg.726 ) PROTEIN_ASSOCIATION:fdoG+fdoI SUBSYSTEM: NONE PROTEIN_CLASS: 1.2.2.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: Gapfill_RB PROTEIN_ASSOCIATION: Gapfill_RB SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1202 PROTEIN_ASSOCIATION:peg.1202 SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: 6.3.3.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:Gapfill_RB PROTEIN_ASSOCIATION:Gapfill_RB SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: 6.3.4.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1319 PROTEIN_ASSOCIATION:folD SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: 3.5.4.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1319 PROTEIN_ASSOCIATION:folD SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: 1.5.1.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1002 PROTEIN_ASSOCIATION:metF SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: 1.5.1.20 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1002 PROTEIN_ASSOCIATION:metF SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: 1.5.1.20 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1262 PROTEIN_ASSOCIATION:purU SUBSYSTEM: One-carbon_metabolism_by_folates PROTEIN_CLASS: 3.5.1.10 $\mathrm{FLUX\_VALUE}$ %%%rTCA cycle as main carbon-fixation pathway GENE_ASSOCIATION:GAP_FILLING_RB PROTEIN_ASSOCIATION:GAP_FILLING_RB SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 1.2.7.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1029 ) or ( peg.1063 and peg.1064 ) or ( peg.1124 ) ) PROTEIN_ASSOCIATION:peg.1029 SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 6.4.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1162 ) or ( peg.1236 ) ) PROTEIN_ASSOCIATION:peg.1162 SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 1.1.1.37 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1171 ) or ( peg.1235 ) ) PROTEIN_ASSOCIATION:fumX SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 4.2.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.403 and peg.430 ) or ( peg.430 and peg.467 ) ) PROTEIN_ASSOCIATION:peg.403+frdA SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 1.3.99.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.403 and peg.430 ) or ( peg.430 ) or ( peg.430 and peg.467 ) ) PROTEIN_ASSOCIATION:peg.403+frdA SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 1.3.99.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.403 and peg.430 ) or ( peg.430 ) or ( peg.430 and peg.467 ) ) PROTEIN_ASSOCIATION:peg.403+frdA SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 1.3.99.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1312 PROTEIN_ASSOCIATION:peg.1312 SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 6.2.1.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 1.2.7.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1029 ) or ( peg.1063 and peg.1064 ) or ( peg.1124 ) ) PROTEIN_ASSOCIATION:peg.1029 SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 6.4.1.7 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1060 PROTEIN_ASSOCIATION:icd SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 1.1.1.42 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1237 PROTEIN_ASSOCIATION:aco SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 4.2.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1237 PROTEIN_ASSOCIATION:aco SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 4.2.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION:ccs SUBSYSTEM: rTCA_Cycle PROTEIN_CLASS: 6.2.1.18 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION:ccl SUBSYSTEM: NONE PROTEIN_CLASS: 4.1.3.34 $\mathrm{FLUX\_VALUE}$ %%%Gluconeogenesis, starting with synthesis of PEP from pyruvate GENE_ASSOCIATION:peg.1483 PROTEIN_ASSOCIATION:ppsA SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 2.7.9.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.353 PROTEIN_ASSOCIATION:eno SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 4.2.1.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1381 ) or ( peg.395 ) ) PROTEIN_ASSOCIATION:pgmA SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 5.4.2.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.94 PROTEIN_ASSOCIATION:pgk SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 2.7.2.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.739 PROTEIN_ASSOCIATION:gap SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 1.2.1.12 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.261 PROTEIN_ASSOCIATION:timA SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 5.3.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.975 PROTEIN_ASSOCIATION:fba SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 4.1.2.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1186 PROTEIN_ASSOCIATION:pfkA SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 2.7.1.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.530 PROTEIN_ASSOCIATION:pgi SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 5.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.530 PROTEIN_ASSOCIATION:pgi SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 5.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.530 PROTEIN_ASSOCIATION:pgi SUBSYSTEM: Gluconeogenesis PROTEIN_CLASS: 5.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: 6.2.1.1 $\mathrm{FLUX\_VALUE}$ %Acetate appendage to gluconeogenesis GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: 1.2.1.3 $\mathrm{FLUX\_VALUE}$ %%%Pentose phosphate pathway GENE_ASSOCIATION:peg.1223 PROTEIN_ASSOCIATION:tktA SUBSYSTEM: Pentose_phosphate_pathway PROTEIN_CLASS: 2.2.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.95 PROTEIN_ASSOCIATION:talC SUBSYSTEM: Pentose_phosphate_pathway PROTEIN_CLASS: 2.2.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1223 PROTEIN_ASSOCIATION:tktA SUBSYSTEM: Pentose_phosphate_pathway PROTEIN_CLASS: 2.2.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.676 PROTEIN_ASSOCIATION:peg.676 SUBSYSTEM: Pentose_phosphate_pathway PROTEIN_CLASS: 5.1.3.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.790 PROTEIN_ASSOCIATION:rpiB SUBSYSTEM: Pentose_phosphate_pathway PROTEIN_CLASS: 5.3.1.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1136 PROTEIN_ASSOCIATION:prs SUBSYSTEM: Pentose_phosphate_pathway PROTEIN_CLASS: 2.7.6.1 $\mathrm{FLUX\_VALUE}$ %The function of the next six reactions is uncertain, all are appendages within the PPP subnetwork GENE_ASSOCIATION:peg.115 PROTEIN_ASSOCIATION:deoC SUBSYSTEM: Deoxyribose_and_Deoxynucleoside_Catabolism PROTEIN_CLASS: 4.1.2.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1015 PROTEIN_ASSOCIATION:mutT SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 3.6.1.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.362 PROTEIN_ASSOCIATION:gsdA SUBSYSTEM: Pentose_phosphate_pathway PROTEIN_CLASS: 1.1.1.49 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.362 PROTEIN_ASSOCIATION:gsdA SUBSYSTEM: Formaldehyde_assimilation:_Ribulose_monophosphate_pathway PROTEIN_CLASS: 1.1.1.49 $\mathrm{FLUX\_VALUE}$ SUBSYSTEM: PROTEIN_CLASS: 2.7.1.12 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.363 PROTEIN_ASSOCIATION:gnd SUBSYSTEM: Formaldehyde_assimilation:_Ribulose_monophosphate_pathway PROTEIN_CLASS: 1.1.1.44 $\mathrm{FLUX\_VALUE}$ %%%Amino sugar and nucleotide sugar biosynthesis (important inputs to peptidoglycan and lipolysaccharide biosynthesis) %%Pathway to UDP-N-acetylglusamine GENE_ASSOCIATION:peg.223 PROTEIN_ASSOCIATION:glmS SUBSYSTEM: Formaldehyde_assimilation:_Ribulose_monophosphate_pathway PROTEIN_CLASS: 2.6.1.16 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.366 PROTEIN_ASSOCIATION:pmu SUBSYSTEM: Sialic_Acid_Metabolism PROTEIN_CLASS: 5.4.2.10 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.438 PROTEIN_ASSOCIATION:glmU SUBSYSTEM: Sialic_Acid_Metabolism PROTEIN_CLASS: 2.3.1.157 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.438 PROTEIN_ASSOCIATION:glmU SUBSYSTEM: Sialic_Acid_Metabolism PROTEIN_CLASS: 2.7.7.23 $\mathrm{FLUX\_VALUE}$ %An appendage reaction attaching an isoprene tail to N-acetylglusamine GENE_ASSOCIATION:peg.379 PROTEIN_ASSOCIATION:rfe SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Another appendage reaction GENE_ASSOCIATION:peg.742 PROTEIN_ASSOCIATION:galE SUBSYSTEM: NONE PROTEIN_CLASS: 5.1.3.7 $\mathrm{FLUX\_VALUE}$ %%%UDP-glucose units for input to lipolysaccharide GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 5.4.2.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1183 PROTEIN_ASSOCIATION:galF SUBSYSTEM: Sucrose_Metabolism PROTEIN_CLASS: 2.7.7.9 $\mathrm{FLUX\_VALUE}$ %Two more appendage reactions GENE_ASSOCIATION:peg.742 PROTEIN_ASSOCIATION:galE SUBSYSTEM: N-linked_Glycosylation_in_Bacteria PROTEIN_CLASS: 5.1.3.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.17 PROTEIN_ASSOCIATION:nsd SUBSYSTEM: Lipid_A-Ara4N_pathway_(_Polymyxin_resistance_) PROTEIN_CLASS: 1.1.1.22 $\mathrm{FLUX\_VALUE}$ %%%Other carbon metabolism, often miscelaneous disconnected subnetworks %%Mannose metabolism, whose role is unclear. Possibly related to lipolysaccharide, whose patwhays are also generally uncertain. GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: 5.3.1.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.508 PROTEIN_ASSOCIATION:mpg SUBSYSTEM: Mannose_Metabolism PROTEIN_CLASS: 5.4.2.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.508 PROTEIN_ASSOCIATION:mpg SUBSYSTEM: Mannose_Metabolism PROTEIN_CLASS: 2.7.7.13 $\mathrm{FLUX\_VALUE}$ SUBSYSTEM: PROTEIN_CLASS: 4.2.1.47 $\mathrm{FLUX\_VALUE}$ %%An appendage network of inositol metabolism, role unclear GENE_ASSOCIATION:peg.1222 PROTEIN_ASSOCIATION:peg.1222 SUBSYSTEM: Di-Inositol-Phosphate_biosynthesis PROTEIN_CLASS: 5.5.1.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1375 PROTEIN_ASSOCIATION:peg.1375 SUBSYSTEM: Inositol_catabolism PROTEIN_CLASS: 3.1.3.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1375 PROTEIN_ASSOCIATION:peg.1375 SUBSYSTEM: Inositol_catabolism PROTEIN_CLASS: 3.1.3.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1375 PROTEIN_ASSOCIATION:peg.1375 SUBSYSTEM: Di-Inositol-Phosphate_biosynthesis PROTEIN_CLASS: 3.1.3.25 $\mathrm{FLUX\_VALUE}$ %%Next an uncertain sequence of reactions involving glyoxylate, inserted to reincorporate glycolaldehyde created during thiamin and folate biosynthesis. Includes several gap-fills, and glycolaldehyde may instead be reincorporated through other interconversions, or expelled as waste. GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.2.1.21 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1226 PROTEIN_ASSOCIATION:peg.1226 SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.3.15 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1226 PROTEIN_ASSOCIATION:peg.1226 SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1226 PROTEIN_ASSOCIATION:peg.1226 SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 4.1.3.1 $\mathrm{FLUX\_VALUE}$ %An appendage associated with the glyoxylate subnetwork GENE_ASSOCIATION:peg.938 PROTEIN_ASSOCIATION:gph SUBSYSTEM: Glycolate,_glyoxylate_interconversions PROTEIN_CLASS: 3.1.3.18 $\mathrm{FLUX\_VALUE}$ %%A lactate appendage reaction. GENE_ASSOCIATION:peg.514 PROTEIN_ASSOCIATION:ldhA SUBSYSTEM: Fermentations:_Lactate PROTEIN_CLASS: 1.1.1.28 $\mathrm{FLUX\_VALUE}$ %%An appendage reaction that in some other organisms leads to serine, but not here GENE_ASSOCIATION:peg.1324 PROTEIN_ASSOCIATION:serA SUBSYSTEM: Serine_Biosynthesis PROTEIN_CLASS: 1.1.1.95 $\mathrm{FLUX\_VALUE}$ %%A disconnected subnetwork involving glycogen GENE_ASSOCIATION:peg.510 PROTEIN_ASSOCIATION:glgA SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.21 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.507 PROTEIN_ASSOCIATION:glgP SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.1 $\mathrm{FLUX\_VALUE}$ %%Disconnected maltose metabolism GENE_ASSOCIATION:peg.512 PROTEIN_ASSOCIATION:malM SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.512 PROTEIN_ASSOCIATION:malM SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.512 PROTEIN_ASSOCIATION:malM SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.512 PROTEIN_ASSOCIATION:malM SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.25 $\mathrm{FLUX\_VALUE}$ %Disconnected glycerate reactions GENE_ASSOCIATION:peg.29 PROTEIN_ASSOCIATION:hibD SUBSYSTEM: D-galactarate,_D-glucarate_and_D-glycerate_catabolism PROTEIN_CLASS: 1.1.1.60 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.29 PROTEIN_ASSOCIATION:hibD SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.60 $\mathrm{FLUX\_VALUE}$ %%Tartrate appendage from oxaloacetate GENE_ASSOCIATION:( ( peg.1171 ) or ( peg.1235 ) ) PROTEIN_ASSOCIATION:fumX SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.32 $\mathrm{FLUX\_VALUE}$ %%%%%% Amino acid biosynthesis, organized by sub-networks %%% Glycine, serine and cysteine synthesis through partial Wood-Ljungdahl pathway %Changed original SEED reaction (Added H+ at input) to account for changed composition of cpd11830 GENE_ASSOCIATION:( peg.1021 and peg.771 ) PROTEIN_ASSOCIATION:gcvT+peg.771 SUBSYSTEM: Glycine_cycle PROTEIN_CLASS: 2.1.2.10 $\mathrm{FLUX\_VALUE}$ %Changed SEED reaction (removed H+ at input) to account for changed composition of cpd11830 GENE_ASSOCIATION:( ( peg.1323 ) or ( peg.772 ) ) PROTEIN_ASSOCIATION:peg.1323 SUBSYSTEM: Glycine_cycle PROTEIN_CLASS: 1.4.4.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1323 and peg.771 and peg.772 ) or ( peg.521 ) or ( peg.771 and peg.772 ) ) PROTEIN_ASSOCIATION:peg.1323+peg.771+peg.772 SUBSYSTEM: Glycine_cycle PROTEIN_CLASS: 1.8.1.4 $\mathrm{FLUX\_VALUE}$ %Serine GENE_ASSOCIATION:peg.351 PROTEIN_ASSOCIATION:glyA SUBSYSTEM: Glycine_cycle PROTEIN_CLASS: 2.1.2.1 $\mathrm{FLUX\_VALUE}$ %Cysteine GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.30 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1087 PROTEIN_ASSOCIATION:cysM SUBSYSTEM: NONE PROTEIN_CLASS: 2.5.1.47 $\mathrm{FLUX\_VALUE}$ %%%Amino acids one or two amination reactions removed from TCA intermediates: Alanine, Glutamate/Glutamine, and Aspartate/Asparagine SUBSYSTEM: Alanine_biosynthesis PROTEIN_CLASS: 1.4.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1092 PROTEIN_ASSOCIATION:gltB SUBSYSTEM: Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis PROTEIN_CLASS: 1.4.1.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.89 PROTEIN_ASSOCIATION:glnA SUBSYSTEM: Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis PROTEIN_CLASS: 6.3.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1365 PROTEIN_ASSOCIATION:peg.1365 SUBSYSTEM: Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis PROTEIN_CLASS: 2.6.1.1 $\mathrm{FLUX\_VALUE}$ %Next reaction may be possible to eliminate, nadB also used to initiate nicotinamide pathway, strange to also use O2 to interconvert aspartate and oxaloacetate GENE_ASSOCIATION:peg.549 PROTEIN_ASSOCIATION:nadB SUBSYSTEM: NONE PROTEIN_CLASS: 1.4.3.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis PROTEIN_CLASS: 6.3.5.4 $\mathrm{FLUX\_VALUE}$ %%%Synthesis of branched chain amino acids: valine, leucine, isoleucine %%Valine GENE_ASSOCIATION:( peg.1286 and peg.334 ) PROTEIN_ASSOCIATION:ilvH+ilvB SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 2.2.1.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1286 and peg.334 ) PROTEIN_ASSOCIATION:ilvH+ilvB SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 2.2.1.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.868 PROTEIN_ASSOCIATION:ilvC SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 1.1.1.86 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.868 PROTEIN_ASSOCIATION:ilvC SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 1.1.1.86 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.585 PROTEIN_ASSOCIATION:ilvD SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 4.2.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1118 ) or ( peg.1316 ) ) PROTEIN_ASSOCIATION:ilvE SUBSYSTEM: Branched_chain_amino_acids_biosynthesis PROTEIN_CLASS: 2.6.1.42 $\mathrm{FLUX\_VALUE}$ %%Leucine synthesis from 2-oxoisovalerate (branching from valine synthesis) GENE_ASSOCIATION:peg.1446 PROTEIN_ASSOCIATION:peg.1446 SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 2.3.3.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.656 and peg.979 ) PROTEIN_ASSOCIATION:leuC+leuD SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 4.2.1.33 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.656 and peg.979 ) PROTEIN_ASSOCIATION:leuC+leuD SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 4.2.1.33 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.182 PROTEIN_ASSOCIATION:leuB SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 1.1.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1118 ) or ( peg.1316 ) ) PROTEIN_ASSOCIATION:ilvE SUBSYSTEM: Branched_chain_amino_acids_biosynthesis PROTEIN_CLASS: 2.6.1.42 $\mathrm{FLUX\_VALUE}$ %%Isoleucine synthesis via citramalate GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 2.3.1.182 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.656 and peg.979 ) PROTEIN_ASSOCIATION:leuC+leuD SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 4.2.1.33 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.656 and peg.979 ) PROTEIN_ASSOCIATION:leuC+leuD SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 4.2.1.33 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.182 PROTEIN_ASSOCIATION:leuB SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 1.1.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1286 and peg.334 ) PROTEIN_ASSOCIATION:ilvH+ilvB SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 2.2.1.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.868 PROTEIN_ASSOCIATION:ilvC SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 1.1.1.86 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.868 PROTEIN_ASSOCIATION:ilvC SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 1.1.1.86 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.585 PROTEIN_ASSOCIATION:ilvD SUBSYSTEM: Branched-Chain_Amino_Acid_Biosynthesis PROTEIN_CLASS: 4.2.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1118 ) or ( peg.1316 ) ) PROTEIN_ASSOCIATION:ilvE SUBSYSTEM: Branched_chain_amino_acids_biosynthesis PROTEIN_CLASS: 2.6.1.42 $\mathrm{FLUX\_VALUE}$ %%%Homoserine pathway initiating threonine, methionine and lysine synthesis GENE_ASSOCIATION:peg.800 PROTEIN_ASSOCIATION:lysC SUBSYSTEM: Threonine_and_Homoserine_Biosynthesis PROTEIN_CLASS: 2.7.2.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1299 PROTEIN_ASSOCIATION:asd SUBSYSTEM: Threonine_and_Homoserine_Biosynthesis PROTEIN_CLASS: 1.2.1.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1258 PROTEIN_ASSOCIATION:thrA SUBSYSTEM: Threonine_and_Homoserine_Biosynthesi PROTEIN_CLASS: 1.1.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1258 PROTEIN_ASSOCIATION:thrA SUBSYSTEM: Threonine_and_Homoserine_Biosynthesis PROTEIN_CLASS: 1.1.1.3 $\mathrm{FLUX\_VALUE}$ %%Threonine synthesis from homoserine GENE_ASSOCIATION:peg.911 PROTEIN_ASSOCIATION:thrB SUBSYSTEM: Methionine_Biosynthesis PROTEIN_CLASS: 2.7.1.39 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.315 ) or ( peg.439 ) ) PROTEIN_ASSOCIATION:peg.315 SUBSYSTEM: Threonine_and_Homoserine_Biosynthesis PROTEIN_CLASS: 4.2.3.1 $\mathrm{FLUX\_VALUE}$ %%Methionine synthesis from homoserine, with first two reactions inserted as gapfills. Multiple connections from homoserine to are possible, with sulfur transfer/insertion enzymes known to have broad affinity. GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: Methionine_Biosynthesis PROTEIN_CLASS: 2.3.1.31 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: Methionine_Biosynthesis PROTEIN_CLASS: 2.5.1.49 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1187 PROTEIN_ASSOCIATION:metE SUBSYSTEM: Methionine_Biosynthesis PROTEIN_CLASS: 2.1.1.14 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1187 PROTEIN_ASSOCIATION:metE SUBSYSTEM: Methionine_Biosynthesis PROTEIN_CLASS: 2.1.1.13 $\mathrm{FLUX\_VALUE}$ %%Lysine synthesis from aspartate 4-semialdehyde, proceeding via DAP pathway GENE_ASSOCIATION:peg.795 PROTEIN_ASSOCIATION:dapA SUBSYSTEM: Lysine_Biosynthesis_DAP_Pathway PROTEIN_CLASS: 4.2.1.52 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.638 PROTEIN_ASSOCIATION:dapB SUBSYSTEM: Lysine_Biosynthesis_DAP_Pathway PROTEIN_CLASS: 1.3.1.26 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.205 PROTEIN_ASSOCIATION:peg.205 SUBSYSTEM: Lysine_Biosynthesis_DAP_Pathway PROTEIN_CLASS: 2.6.1.83 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1275 PROTEIN_ASSOCIATION:dapF SUBSYSTEM: Lysine_Biosynthesis_DAP_Pathway PROTEIN_CLASS: 5.1.1.7 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.841 PROTEIN_ASSOCIATION:lysA SUBSYSTEM: Lysine_Biosynthesis_DAP_Pathway PROTEIN_CLASS: 4.1.1.20 $\mathrm{FLUX\_VALUE}$ %Lysine metabolism appendage GENE_ASSOCIATION:( ( peg.1134 ) or ( peg.336 ) ) PROTEIN_ASSOCIATION:peg.1134 SUBSYSTEM: Lysine_degradation PROTEIN_CLASS: 5.4.3.2 $\mathrm{FLUX\_VALUE}$ %%Sequence to arginine from ornithine (through partial urea cycle) GENE_ASSOCIATION:peg.678 PROTEIN_ASSOCIATION:argJ SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 2.3.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1432 PROTEIN_ASSOCIATION:argB SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 2.7.2.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1307 PROTEIN_ASSOCIATION:argC SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 1.2.1.38 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.16 PROTEIN_ASSOCIATION:argD SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 2.6.1.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.678 PROTEIN_ASSOCIATION:argJ SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 2.3.1.35 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1188 PROTEIN_ASSOCIATION:argF SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 2.1.3.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.792 PROTEIN_ASSOCIATION:argG SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 6.3.4.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.962 PROTEIN_ASSOCIATION:argH SUBSYSTEM: Arginine_Biosynthesis PROTEIN_CLASS: 4.3.2.1 $\mathrm{FLUX\_VALUE}$ %%Proline GENE_ASSOCIATION:peg.788 PROTEIN_ASSOCIATION:proB SUBSYSTEM: Proline_Synthesis PROTEIN_CLASS: 2.7.2.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.744 PROTEIN_ASSOCIATION:proA SUBSYSTEM: Proline_Synthesis PROTEIN_CLASS: 1.2.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.128 PROTEIN_ASSOCIATION:proC SUBSYSTEM: Proline_Synthesis PROTEIN_CLASS: 1.5.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.128 PROTEIN_ASSOCIATION:proC SUBSYSTEM: Proline_Synthesis PROTEIN_CLASS: 1.5.1.2 $\mathrm{FLUX\_VALUE}$ %%%Here starts the shikimate pathway to chorsimate, initiating synthesis of aromatic amino acids. Pathways to other compounds (e.g. cofactors) from chorismate listed elsewhere. GENE_ASSOCIATION:peg.663 PROTEIN_ASSOCIATION:pheA SUBSYSTEM: Aromatic_amino_acids_biosynthesis PROTEIN_CLASS: 2.5.1.54 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1334 PROTEIN_ASSOCIATION:peg.1334 SUBSYSTEM: Chorismate_Synthesis PROTEIN_CLASS: 4.2.3.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.14 PROTEIN_ASSOCIATION:aroD SUBSYSTEM: Common_Pathway_For_Synthesis_of_Aromatic_Compounds_(DAHP_synthase_to_chorismate) PROTEIN_CLASS: 4.2.1.10 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.626 PROTEIN_ASSOCIATION:aroE SUBSYSTEM: Common_Pathway_For_Synthesis_of_Aromatic_Compounds_(DAHP_synthase_to_chorismate) PROTEIN_CLASS: 1.1.1.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1509 PROTEIN_ASSOCIATION:aroK SUBSYSTEM: Common_Pathway_For_Synthesis_of_Aromatic_Compounds_(DAHP_synthase_to_chorismate) PROTEIN_CLASS: 2.7.1.71 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1074 PROTEIN_ASSOCIATION:aroA SUBSYSTEM: Common_Pathway_For_Synthesis_of_Aromatic_Compounds_(DAHP_synthase_to_chorismate) PROTEIN_CLASS: 2.5.1.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.68 PROTEIN_ASSOCIATION:aroC SUBSYSTEM: Common_Pathway_For_Synthesis_of_Aromatic_Compounds_(DAHP_synthase_to_chorismate) PROTEIN_CLASS: 4.2.3.5 $\mathrm{FLUX\_VALUE}$ %%Start of tryptophan sequence from chorismate. GENE_ASSOCIATION:( peg.400 and peg.424 ) PROTEIN_ASSOCIATION:trpG+trpE SUBSYSTEM: Tryptophan_synthesis PROTEIN_CLASS: 4.1.3.27 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.400 and peg.424 ) PROTEIN_ASSOCIATION:trpG+trpE SUBSYSTEM: Tryptophan_synthesis PROTEIN_CLASS: 4.1.3.27 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.151 PROTEIN_ASSOCIATION:peg.151 SUBSYSTEM: Tryptophan_synthesis PROTEIN_CLASS: 2.4.2.18 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1437 PROTEIN_ASSOCIATION:trpF SUBSYSTEM: Tryptophan_synthesis PROTEIN_CLASS: 5.3.1.24 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1238 PROTEIN_ASSOCIATION:trpC SUBSYSTEM: Tryptophan_synthesis PROTEIN_CLASS: 4.1.1.48 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1082 ) PROTEIN_ASSOCIATION:trpA SUBSYSTEM: Tryptophan_synthesis PROTEIN_CLASS: 4.1.2.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.498 ) PROTEIN_ASSOCIATION:trpB SUBSYSTEM: Tryptophan_synthesis PROTEIN_CLASS: 4.2.1.20 $\mathrm{FLUX\_VALUE}$ %%Start of tyrosine and phenylalanine sequences from chorismate via prephenate. GENE_ASSOCIATION:peg.663 PROTEIN_ASSOCIATION:pheA SUBSYSTEM: Chorismate_Synthesis PROTEIN_CLASS: 5.4.99.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.663 PROTEIN_ASSOCIATION:pheA SUBSYSTEM: Phenylalanine_synthesis PROTEIN_CLASS: 4.2.1.51 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1441 PROTEIN_ASSOCIATION:hisC SUBSYSTEM: Phenylalanine_and_Tyrosine_Branches_from_Chorismate PROTEIN_CLASS: 2.6.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1217 PROTEIN_ASSOCIATION:tyrA SUBSYSTEM: Phenylalanine_and_Tyrosine_Branches_from_Chorismate PROTEIN_CLASS: 1.3.1.12 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1217 PROTEIN_ASSOCIATION:tyrA SUBSYSTEM: Phenylalanine_and_Tyrosine_Branches_from_Chorismate PROTEIN_CLASS: 1.3.1.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1441 PROTEIN_ASSOCIATION:hisC SUBSYSTEM: Phenylalanine_and_Tyrosine_Branches_from_Chorismate PROTEIN_CLASS: 2.6.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1441 PROTEIN_ASSOCIATION:hisC SUBSYSTEM: Phenylalanine_and_Tyrosine_Branches_from_Chorismate PROTEIN_CLASS: 2.6.1.57 $\mathrm{FLUX\_VALUE}$ %%%Histidine biosynthesis GENE_ASSOCIATION:( peg.1123 and peg.802 ) PROTEIN_ASSOCIATION:hisG+peg.802 SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 2.4.2.17 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1364 PROTEIN_ASSOCIATION:hisIE SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 3.6.1.31 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1364 PROTEIN_ASSOCIATION:hisIE SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 3.5.4.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.907 PROTEIN_ASSOCIATION:hisA SUBSYSTEM: Histidine_synthesis PROTEIN_CLASS: 5.3.1.16 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.142 and peg.518 ) PROTEIN_ASSOCIATION:hisF+hisH SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 2.4.2.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.30 PROTEIN_ASSOCIATION:hisB SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 4.2.1.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1441 PROTEIN_ASSOCIATION:hisC SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 2.6.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 3.1.3.15 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.552 PROTEIN_ASSOCIATION:hisD SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 1.1.1.23 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.552 PROTEIN_ASSOCIATION:hisD SUBSYSTEM: Histidine_Biosynthesis PROTEIN_CLASS: 1.1.1.23 $\mathrm{FLUX\_VALUE}$ %%%A slightly suspicious peptidase appendage on the amino acid synthesis sub-network, as it implies potential for uptake of dipeptides. Kept in the model, but inactive. GENE_ASSOCIATION:( ( peg.1452 ) or ( peg.64 ) ) PROTEIN_ASSOCIATION:pepA SUBSYSTEM: NONE PROTEIN_CLASS: 3.4.11.2 $\mathrm{FLUX\_VALUE}$ %%%%Cofactor biosynthesis %%Nucleotides, which double as cofactors and as inputs to DNA/RNA %%Purine synthesis, first to IMP GENE_ASSOCIATION:peg.815 PROTEIN_ASSOCIATION:purF SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 2.4.2.14 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.525 PROTEIN_ASSOCIATION:purD SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 6.3.4.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.599 PROTEIN_ASSOCIATION:purN SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 2.1.2.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1273 and peg.652 and peg.768 ) PROTEIN_ASSOCIATION:purL+purS+purQ SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 6.3.5.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.544 PROTEIN_ASSOCIATION:purM SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 6.3.3.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.183 ) PROTEIN_ASSOCIATION:purK SUBSYSTEM: NONE PROTEIN_CLASS: 6.3.4.18 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.818 ) PROTEIN_ASSOCIATION:purK SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 5.4.99.18 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1465 PROTEIN_ASSOCIATION:purC SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 6.3.2.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.431 PROTEIN_ASSOCIATION:purB SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 4.3.2.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1359 PROTEIN_ASSOCIATION:purH SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 2.1.2.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1359 PROTEIN_ASSOCIATION:purH SUBSYSTEM: De_Novo_Purine_Biosynthesis PROTEIN_CLASS: 3.5.4.10 $\mathrm{FLUX\_VALUE}$ %%IMP to AMP GENE_ASSOCIATION:peg.900 PROTEIN_ASSOCIATION:purA SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 6.3.4.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.431 PROTEIN_ASSOCIATION:purB SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 4.3.2.2 $\mathrm{FLUX\_VALUE}$ %%IMP to GMP GENE_ASSOCIATION:peg.1404 PROTEIN_ASSOCIATION:guaB SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 1.1.1.205 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.176 PROTEIN_ASSOCIATION:guaA SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 6.3.5.2 $\mathrm{FLUX\_VALUE}$ %%Pyrimidine biosynthesis, first to UMP GENE_ASSOCIATION:( ( peg.1453 and peg.302 ) or ( peg.302 and peg.812 ) ) PROTEIN_ASSOCIATION:peg.1453+carA SUBSYSTEM: NONE PROTEIN_CLASS: 6.3.5.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.301 PROTEIN_ASSOCIATION:pyrB SUBSYSTEM: NONE PROTEIN_CLASS: 2.1.3.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.566 PROTEIN_ASSOCIATION:pyrC SUBSYSTEM: NONE PROTEIN_CLASS: 3.5.2.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.36 and peg.908 ) PROTEIN_ASSOCIATION:pyrD+pyrDB SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.3.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.36 and peg.908 ) PROTEIN_ASSOCIATION:pyrD+pyrDB SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.3.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.36 and peg.908 ) PROTEIN_ASSOCIATION:pyrD+pyrDB SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.3.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1325 PROTEIN_ASSOCIATION:umpS SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.2.10 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1100 PROTEIN_ASSOCIATION:pyrF SUBSYSTEM: NONE PROTEIN_CLASS: 4.1.1.23 $\mathrm{FLUX\_VALUE}$ %%From UMP to CTP via UTP GENE_ASSOCIATION:peg.504 PROTEIN_ASSOCIATION:pyrH SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.4.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.932 PROTEIN_ASSOCIATION:pyrG SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 6.3.4.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.932 PROTEIN_ASSOCIATION:pyrG SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 6.3.4.2 $\mathrm{FLUX\_VALUE}$ %%Deoxynucleotides (dTMP from dUMP) GENE_ASSOCIATION:( ( peg.1055 ) or ( peg.77 ) ) PROTEIN_ASSOCIATION:nrdF SUBSYSTEM: NONE PROTEIN_CLASS: 1.17.4.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1055 ) or ( peg.77 ) ) PROTEIN_ASSOCIATION:nrdF SUBSYSTEM: NONE PROTEIN_CLASS: 1.17.4.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1055 ) or ( peg.77 ) ) PROTEIN_ASSOCIATION:nrdF SUBSYSTEM: NONE PROTEIN_CLASS: 1.17.4.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1055 ) or ( peg.77 ) ) PROTEIN_ASSOCIATION:nrdF SUBSYSTEM: NONE PROTEIN_CLASS: 1.17.4.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.504 PROTEIN_ASSOCIATION:pyrH SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.4.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.458 ) SUBSYSTEM: NONE PROTEIN_CLASS: 2.1.1.148 $\mathrm{FLUX\_VALUE}$ %%Purine substitution interconversions %I sequence GENE_ASSOCIATION:peg.396 PROTEIN_ASSOCIATION:hpt SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 2.4.2.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.248 PROTEIN_ASSOCIATION:peg.248 SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 3.6.1.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1491 PROTEIN_ASSOCIATION:cmk SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.1.48 $\mathrm{FLUX\_VALUE}$ %X sequence GENE_ASSOCIATION:peg.248 PROTEIN_ASSOCIATION:peg.248 SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 3.6.1.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.396 PROTEIN_ASSOCIATION:hpt SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.2.8 $\mathrm{FLUX\_VALUE}$ %G sequence GENE_ASSOCIATION:peg.248 PROTEIN_ASSOCIATION:peg.248 SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 3.6.1.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.146 PROTEIN_ASSOCIATION:peg.146 SUBSYSTEM: MLST PROTEIN_CLASS: 2.7.4.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.588 PROTEIN_ASSOCIATION:spoT SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.6.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: 3.6.1.11 or 3.6.1.40 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: 3.1.7.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.396 PROTEIN_ASSOCIATION:hpt SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 2.4.2.7 $\mathrm{FLUX\_VALUE}$ %A sequence GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: 3.6.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.65 PROTEIN_ASSOCIATION:kad SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.4.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.65 PROTEIN_ASSOCIATION:kad SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 2.7.4.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: 2.4.2.7 $\mathrm{FLUX\_VALUE}$ %Gapfill to reincorporate adenosine produced in SAH to homocysteine conversion (which itself reinitiates SAM chemistry) GENE_ASSOCIATION: Gapfill_RB PROTEIN_ASSOCIATION: Gapfill_RB SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %%Pyrimidine substitution interconversions %U sequence GENE_ASSOCIATION:peg.248 PROTEIN_ASSOCIATION:peg.248 SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 3.6.1.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1498 PROTEIN_ASSOCIATION:uraP SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.4.2.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1024 and peg.1219 and peg.404 ) or ( peg.497 and peg.529 ) ) PROTEIN_ASSOCIATION:peg.1024+peg.1219+peg.404 SUBSYSTEM: tRNA_processing PROTEIN_CLASS: 4.2.1.70 $\mathrm{FLUX\_VALUE}$ %C sequence GENE_ASSOCIATION:peg.1119 PROTEIN_ASSOCIATION:dcd SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 3.5.4.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1491 PROTEIN_ASSOCIATION:cmk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.14 $\mathrm{FLUX\_VALUE}$ %%Deoxynucleotide substitution interconversions %A sequence GENE_ASSOCIATION:peg.65 PROTEIN_ASSOCIATION:kad SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 2.7.4.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.146 PROTEIN_ASSOCIATION:peg.146 SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.4.8 $\mathrm{FLUX\_VALUE}$ %U sequence GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.167 ) or ( peg.248 ) ) PROTEIN_ASSOCIATION:dut SUBSYSTEM: Nudix_proteins_(nucleoside_triphosphate_hydrolases) PROTEIN_CLASS: 3.6.1.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1119 PROTEIN_ASSOCIATION:dcd SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 3.5.4.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.580 PROTEIN_ASSOCIATION:surE SUBSYSTEM: NONE PROTEIN_CLASS: 3.1.3.5 $\mathrm{FLUX\_VALUE}$ %C sequence GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1491 PROTEIN_ASSOCIATION:cmk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.14 $\mathrm{FLUX\_VALUE}$ %G sequence GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.146 PROTEIN_ASSOCIATION:peg.146 SUBSYSTEM: MLST PROTEIN_CLASS: 2.7.4.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.248 PROTEIN_ASSOCIATION:peg.248 SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 3.6.1.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1328 PROTEIN_ASSOCIATION:peg.1328 SUBSYSTEM: Purine_conversions PROTEIN_CLASS: 3.1.5.1 $\mathrm{FLUX\_VALUE}$ %T sequence GENE_ASSOCIATION:peg.677 PROTEIN_ASSOCIATION:tmk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1108 PROTEIN_ASSOCIATION:ndk SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 2.7.4.6 $\mathrm{FLUX\_VALUE}$ %Disconnected dITP reaction GENE_ASSOCIATION:peg.248 PROTEIN_ASSOCIATION:peg.248 SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 3.6.1.19 $\mathrm{FLUX\_VALUE}$ %%% %%Nicotinamide synthesis GENE_ASSOCIATION:peg.549 PROTEIN_ASSOCIATION:nadB SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 1.4.3.16 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1313 PROTEIN_ASSOCIATION:nadA SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.605 PROTEIN_ASSOCIATION:nadC SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 2.4.2.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.733 PROTEIN_ASSOCIATION:peg.733 SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 6.3.4.21 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.27 PROTEIN_ASSOCIATION:peg.27 SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 2.7.7.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.669 PROTEIN_ASSOCIATION:nadE SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 6.3.1.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.669 PROTEIN_ASSOCIATION:nadE SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 6.3.5.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.632 PROTEIN_ASSOCIATION:peg.632 SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.1.23 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.27 PROTEIN_ASSOCIATION:peg.27 SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.7.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.632 PROTEIN_ASSOCIATION:peg.632 SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 2.7.1.23 $\mathrm{FLUX\_VALUE}$ %Appendage reaction GENE_ASSOCIATION:peg.695 PROTEIN_ASSOCIATION:pncA SUBSYSTEM: NAD_and_NADP_cofactor_biosynthesis_global PROTEIN_CLASS: 3.5.1.19 $\mathrm{FLUX\_VALUE}$ %%CoA synthesis GENE_ASSOCIATION:peg.1367 PROTEIN_ASSOCIATION:panB SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 2.1.2.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1200 ) or ( peg.868 ) ) PROTEIN_ASSOCIATION:peg.1200 SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 1.1.1.169 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.348 PROTEIN_ASSOCIATION:panD SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 4.1.1.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1475 PROTEIN_ASSOCIATION:panC SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 6.3.2.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1336 PROTEIN_ASSOCIATION:peg.1336 SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 2.7.1.33 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.573 PROTEIN_ASSOCIATION:dfp SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 6.3.2.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.573 PROTEIN_ASSOCIATION:dfp SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 6.3.2.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.573 PROTEIN_ASSOCIATION:dfp SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 4.1.1.36 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.189 PROTEIN_ASSOCIATION:kdtB SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 2.7.7.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1376 PROTEIN_ASSOCIATION:peg.1376 SUBSYSTEM: Coenzyme_A_Biosynthesis PROTEIN_CLASS: 2.7.1.24 $\mathrm{FLUX\_VALUE}$ %%%Biotin synthesis. First the synthesis of pimeloyl-ACP through a fatty acid biosynthesis analog, followed by its conversion to biotin. %This sequence starts with a tentative gapfilled reaction, also used by E.coli, in which a methyl ester of malonyl-ACP is generated, to ensure internal production of pimelate. The sequence following the gapfilled reaction reuses fatty acid biosynthesis machinery for a sequence of chain lengthening steps. A possible alternative completion would be the oxidative cleavage of longer acyl-ACP chains as used by B.subtillis. GENE_ASSOCIATION:Gapfill_RB PROTEIN_ASSOCIATION:bioC SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 4.2.1.58 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 4.2.1.58 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:Gapfill_RB PROTEIN_ASSOCIATION:bioH SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Two additional gapfills to reincorporate methanol, via formaldehyde, as formate. GENE_ASSOCIATION:Gapfill_RB PROTEIN_ASSOCIATION:Gapfill_RB SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:Gapfill_RB PROTEIN_ASSOCIATION:Gapfill_RB SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Start of the sequence leading from pimeloyl-ACP to biotin GENE_ASSOCIATION:peg.450 PROTEIN_ASSOCIATION:bioF SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: 2.3.1.47 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.132 PROTEIN_ASSOCIATION:bioA SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: 2.6.1.62 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.407 PROTEIN_ASSOCIATION:bioD SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: 6.3.3.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.682 PROTEIN_ASSOCIATION:bioB SUBSYSTEM: NONE PROTEIN_CLASS: 2.8.1.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.412 PROTEIN_ASSOCIATION:birA SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: 6.2.1.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.412 PROTEIN_ASSOCIATION:birA SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: 6.3.4.9/10/11/15 $\mathrm{FLUX\_VALUE}$ %External pimelate uptake appendage GENE_ASSOCIATION:peg.1156 PROTEIN_ASSOCIATION:bioW SUBSYSTEM: Biotin_biosynthesis PROTEIN_CLASS: 6.2.1.14 $\mathrm{FLUX\_VALUE}$ %%%Thiamin biosynthesis %First the pyrimidine branch GENE_ASSOCIATION:peg.838 PROTEIN_ASSOCIATION:thiC SUBSYSTEM: Thiamin_biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1356 PROTEIN_ASSOCIATION:thiD SUBSYSTEM: Thiamin_biosynthesis PROTEIN_CLASS: 2.7.1.49 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1356 PROTEIN_ASSOCIATION:thiD SUBSYSTEM: Thiamin_biosynthesis PROTEIN_CLASS: 2.7.4.7 $\mathrm{FLUX\_VALUE}$ %The thiazole branch GENE_ASSOCIATION:peg.499 PROTEIN_ASSOCIATION:peg.499 SUBSYSTEM: Thiamin_biosynthesis PROTEIN_CLASS: 1.4.3.19 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1510 and peg.523 ) or ( peg.1510 and peg.730 ) ) PROTEIN_ASSOCIATION:thiG+peg.523 SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Assembly and phosphorylation GENE_ASSOCIATION:peg.408 PROTEIN_ASSOCIATION:peg.408 SUBSYSTEM: Thiamin_biosynthesis PROTEIN_CLASS: 2.5.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1467 PROTEIN_ASSOCIATION:thiL SUBSYSTEM: Thiamin_biosynthesis PROTEIN_CLASS: 2.7.4.16 $\mathrm{FLUX\_VALUE}$ %%%S-adenosyl methionine and methionine metabolism, including salvage which is active as part of spermine and spermidine synthesis %Reconversion of the homocystein moiety after use in methyl group transfer. Adenosine is currently still an apendage. GENE_ASSOCIATION:( ( peg.801 ) or ( peg.854 ) ) PROTEIN_ASSOCIATION:metK SUBSYSTEM: Methionine_Biosynthesis PROTEIN_CLASS: 2.5.1.6 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.819 PROTEIN_ASSOCIATION:sahH SUBSYSTEM: Methionine_Biosynthesis PROTEIN_CLASS: 3.3.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1187 PROTEIN_ASSOCIATION:metE SUBSYSTEM: NONE PROTEIN_CLASS: 2.1.1.- $\mathrm{FLUX\_VALUE}$ %Gapfill reaction to reaminate S-Adenosyl-4-methylthio-2-oxobutanoate produced during biotin synthesis GENE_ASSOCIATION:Gapfill_RB PROTEIN_ASSOCIATION:Gapfill_RB SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Spermidine synthesis GENE_ASSOCIATION:peg.728 PROTEIN_ASSOCIATION:peg.728 SUBSYSTEM: PROTEIN_CLASS: 4.1.1.17 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.48 ) or ( peg.944 ) ) PROTEIN_ASSOCIATION:speE SUBSYSTEM: Polyamine_Metabolism PROTEIN_CLASS: 2.5.1.16 $\mathrm{FLUX\_VALUE}$ %Associated methionine salvage GENE_ASSOCIATION:peg.190 PROTEIN_ASSOCIATION:peg.190 SUBSYSTEM: Polyamine_Metabolism PROTEIN_CLASS: 4.1.1.50 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: Methionine_salvage PROTEIN_CLASS: 2.4.2.28 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1463 PROTEIN_ASSOCIATION:eif SUBSYSTEM: Methionine_Salvage PROTEIN_CLASS: 5.3.1.23 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1372 PROTEIN_ASSOCIATION:peg.1372 SUBSYSTEM: Methionine_Salvage PROTEIN_CLASS: 4.2.1.109 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1370 PROTEIN_ASSOCIATION:masA SUBSYSTEM: Methionine_Salvage PROTEIN_CLASS: 3.1.3.77 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1370 PROTEIN_ASSOCIATION:masA SUBSYSTEM: Methionine_Salvage PROTEIN_CLASS: 3.1.3.77 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1369 PROTEIN_ASSOCIATION:peg.1369 SUBSYSTEM: Methionine_Salvage PROTEIN_CLASS: 1.13.11.54 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: Methionine_salvage PROTEIN_CLASS: 2.6.1.5 or 2.6.1.57 $\mathrm{FLUX\_VALUE}$ %%%Lipoic acid synthesis, transferring octanoate from ACP directly (and only) to the H-protein of Gcv GENE_ASSOCIATION: PROTEIN_ASSOCIATION:LipM SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Sulfuration of octanoyl-GcvH to create funtional lipoic acid, using quinone for now as electron source. GENE_ASSOCIATION: PROTEIN_ASSOCIATION:LipA SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %%%Folate (THF) synthesis %Sequence from chorismate to aminobenzoate, a key precursor input to total THF synthesis GENE_ASSOCIATION:peg.400 PROTEIN_ASSOCIATION:trpG SUBSYSTEM: NONE PROTEIN_CLASS: 2.6.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 4.1.3.38 $\mathrm{FLUX\_VALUE}$ %Sequence from GTP to THF GENE_ASSOCIATION:peg.178 PROTEIN_ASSOCIATION:folE SUBSYSTEM: Pterin_biosynthesis PROTEIN_CLASS: 3.5.4.16 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.178 PROTEIN_ASSOCIATION:folE SUBSYSTEM: Pterin_biosynthesis PROTEIN_CLASS: 3.5.4.16 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.178 PROTEIN_ASSOCIATION:folE SUBSYSTEM: Pterin_biosynthesis PROTEIN_CLASS: 3.5.4.16 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.178 PROTEIN_ASSOCIATION:folE SUBSYSTEM: Pterin_biosynthesis PROTEIN_CLASS: 3.5.4.16 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 3.1.3.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 4.1.2.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.125 PROTEIN_ASSOCIATION:folK SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 2.7.6.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1028 PROTEIN_ASSOCIATION:folP SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 2.5.1.15 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1417 PROTEIN_ASSOCIATION:folC SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 6.3.2.12 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.704 PROTEIN_ASSOCIATION:udh SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 1.5.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.704 PROTEIN_ASSOCIATION:udh SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 1.5.1.3 $\mathrm{FLUX\_VALUE}$ %Two glutamate ligase appendages. THF probably has a few glutamates attached, but unclear how many. GENE_ASSOCIATION:peg.1417 PROTEIN_ASSOCIATION:folC SUBSYSTEM: Folate_Biosynthesis PROTEIN_CLASS: 6.3.2.17 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1417 PROTEIN_ASSOCIATION:folC SUBSYSTEM: NONE PROTEIN_CLASS: 6.3.2.12 $\mathrm{FLUX\_VALUE}$ %Disconnected reaction involving dihydrobiopterin GENE_ASSOCIATION:peg.37 PROTEIN_ASSOCIATION:phhB SUBSYSTEM: Pterin_biosynthesis PROTEIN_CLASS: 4.2.1.96 $\mathrm{FLUX\_VALUE}$ %%%Riboflavin synthesis %Synthesis of butanone moiety from ribulose5P, as input to lumazine synthesis GENE_ASSOCIATION:peg.254 PROTEIN_ASSOCIATION:ribA SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 4.1.99.12 $\mathrm{FLUX\_VALUE}$ %Full sequence from GTP to FAD GENE_ASSOCIATION:peg.254 PROTEIN_ASSOCIATION:ribA SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 3.5.4.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.322 PROTEIN_ASSOCIATION:peg.322 SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 3.5.4.26 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.109 ) or ( peg.322 ) ) PROTEIN_ASSOCIATION:peg.109 SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 1.1.1.193 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 3.1.3.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.104 PROTEIN_ASSOCIATION:ribH SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 2.5.1.78 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1185 PROTEIN_ASSOCIATION:ribC SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 2.5.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.110 PROTEIN_ASSOCIATION:ribF SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 2.7.1.26 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.110 PROTEIN_ASSOCIATION:ribF SUBSYSTEM: Riboflavin,_FMN_and_FAD_metabolism PROTEIN_CLASS: 2.7.7.2 $\mathrm{FLUX\_VALUE}$ %%%Porphyrin synthesis (leading to Hemes etc) %C5 pathway from glutamate GENE_ASSOCIATION:peg.850 PROTEIN_ASSOCIATION:gltX SUBSYSTEM: Porphyrin_synthesis_C5_pathway PROTEIN_CLASS: 6.1.1.17 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.893 PROTEIN_ASSOCIATION:hemA SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 1.2.1.70 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.574 PROTEIN_ASSOCIATION:gsa SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 5.4.3.8 $\mathrm{FLUX\_VALUE}$ %%Sequence from aminolevulinate to Heme A GENE_ASSOCIATION:peg.1460 PROTEIN_ASSOCIATION:hemB SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 4.2.1.24 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.196 PROTEIN_ASSOCIATION:hemC SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 2.5.1.61 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1228 PROTEIN_ASSOCIATION:peg.1228 SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 4.2.1.75 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.242 PROTEIN_ASSOCIATION:dcuP SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 4.1.1.37 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1470 PROTEIN_ASSOCIATION:hemN SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 1.3.99.22 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.3.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1398 PROTEIN_ASSOCIATION:hemG SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 1.3.3.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.661 PROTEIN_ASSOCIATION:hemH SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 4.99.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.119 PROTEIN_ASSOCIATION:ctaB SUBSYSTEM: NONE PROTEIN_CLASS: 2.5.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.118 PROTEIN_ASSOCIATION:ctaA SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Sequence to siroheme, branching from main Heme sequence at uroporphyrinogen III GENE_ASSOCIATION:peg.159 PROTEIN_ASSOCIATION:cobA SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 2.1.1.107 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.159 ) or ( peg.861 ) ) PROTEIN_ASSOCIATION:cobA SUBSYSTEM: Coenzyme_B12_biosynthesis PROTEIN_CLASS: 1.3.1.76 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.159 ) or ( peg.861 ) ) PROTEIN_ASSOCIATION:cobA SUBSYSTEM: Coenzyme_B12_biosynthesis PROTEIN_CLASS: 4.99.1.4 $\mathrm{FLUX\_VALUE}$ %Sequence to corproporphyrinogen from hydroxymethylbilane, possible appendage sidebranch off main Heme sequence GENE_ASSOCIATION: Spontaneous PROTEIN_ASSOCIATION: Spontaneous SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.242 PROTEIN_ASSOCIATION:dcuP SUBSYSTEM: Heme_and_Siroheme_Biosynthesis PROTEIN_CLASS: 4.1.1.37 $\mathrm{FLUX\_VALUE}$ %%%Vitamin B6 synthesis, via the DXP dependent pathway. Aquifex possesses the key condensation enzymes PdxJ/A, but a few gapfills of common reaction types were required GENE_ASSOCIATION:peg.739 PROTEIN_ASSOCIATION:gap SUBSYSTEM: Pyridoxin_(Vitamin_B6)_Biosynthesis PROTEIN_CLASS: 1.2.1.72 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:Gapfill_RB2010 PROTEIN_ASSOCIATION:Gapfill_RB2010 SUBSYSTEM: Pyridoxin_(Vitamin_B6)_Biosynthesis PROTEIN_CLASS: 1.1.1.290 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:Gapfill_RB2010 PROTEIN_ASSOCIATION:Gapfill_RB2010 SUBSYSTEM: Pyridoxin_(Vitamin_B6)_Biosynthesis PROTEIN_CLASS: 2.6.1.52 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.595 PROTEIN_ASSOCIATION:pdxA SUBSYSTEM: Pyridoxin_(Vitamin_B6)_Biosynthesis PROTEIN_CLASS: 1.1.1.262 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.997 PROTEIN_ASSOCIATION:pdxJ SUBSYSTEM: Pyridoxin_(Vitamin_B6)_Biosynthesis PROTEIN_CLASS: 2.6.99.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:Gapfill_RB2010 PROTEIN_ASSOCIATION:Gapfill_RB2010 SUBSYSTEM: Pyridoxin_(Vitamin_B6)_Biosynthesis PROTEIN_CLASS: 1.4.3.5 $\mathrm{FLUX\_VALUE}$ %Appendage to hydroxythreonine GENE_ASSOCIATION:( ( peg.315 ) or ( peg.439 ) ) PROTEIN_ASSOCIATION:peg.315 SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.3.1 $\mathrm{FLUX\_VALUE}$ %%%Menaquinone synthesis (DMK7). This subsystem include many gapfills, but Aquifex has been experimentally shown to possess DMK-7. GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 5.4.4.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 2.2.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 4.2.99.20 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 4.2.1.113 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 6.2.1.26 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 4.1.3.36 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 3.1.2.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: Menaquinone_synthesis PROTEIN_CLASS: 2.5.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.245 ) or ( peg.886 ) ) PROTEIN_ASSOCIATION:peg.245 SUBSYSTEM: NONE PROTEIN_CLASS: 2.1.1.- $\mathrm{FLUX\_VALUE}$ %Disconnected ubiquinone reactions. Not clear if these are real, as it has been shown Aquifes uses (mainly?) (de-methyl)menaquinone rather than ubiquinone. GENE_ASSOCIATION:peg.39 PROTEIN_ASSOCIATION:ubiA SUBSYSTEM: Ubiquinone_Biosynthesis PROTEIN_CLASS: 2.5.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1122 ) or ( peg.386 ) ) PROTEIN_ASSOCIATION:peg.1122 SUBSYSTEM: Ubiquinone_Biosynthesis PROTEIN_CLASS: 4.1.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.245 ) or ( peg.886 ) ) PROTEIN_ASSOCIATION:peg.245 SUBSYSTEM: Ubiquinone_Biosynthesis PROTEIN_CLASS: 2.1.1.- $\mathrm{FLUX\_VALUE}$ %A disconnected phyloquinone reaction, possibly of relevance as the DMK7 form Aquifex uses has a few saturated bonds at the end of the isoprene tail. GENE_ASSOCIATION:( ( peg.1020 ) or ( peg.245 ) or ( peg.886 ) ) PROTEIN_ASSOCIATION:peg.1020 SUBSYSTEM: Menaquinone_and_Phylloquinone_Biosynthesis PROTEIN_CLASS: 2.1.1.- $\mathrm{FLUX\_VALUE}$ %%%A disconnected CoB:CoM reaction. Genes code for a heterodisulfide reductase, possibly related to the glycine cycle GENE_ASSOCIATION:( peg.287 and peg.288 and peg.289 and peg.290 and peg.292 and peg.293 ) PROTEIN_ASSOCIATION:peg.287+peg.288+peg.289+hdrA+hdrC+hdrB SUBSYSTEM: Methanogenesis PROTEIN_CLASS: 1.8.98.1 $\mathrm{FLUX\_VALUE}$ %%%%%%Cellular encapsulation %%%The DOXP pathway for synthesis of isoprenoids, used as membrane tails/anchors for quinones and heme, and to transport peptidoglycan across the membrane GENE_ASSOCIATION:peg.613 PROTEIN_ASSOCIATION:peg.613 SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.2.1.7 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.297 PROTEIN_ASSOCIATION:peg.297 SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 1.1.1.267 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.922 PROTEIN_ASSOCIATION:peg.922 SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.7.7.60 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.637 PROTEIN_ASSOCIATION:peg.637 SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.7.1.148 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.667 PROTEIN_ASSOCIATION:peg.667 SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 4.6.1.12 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1076 PROTEIN_ASSOCIATION:gcpE SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1206 PROTEIN_ASSOCIATION:lytB SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 1.17.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1206 PROTEIN_ASSOCIATION:lytB SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 1.17.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1206 PROTEIN_ASSOCIATION:lytB SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 1.17.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1206 PROTEIN_ASSOCIATION:lytB SUBSYSTEM: DOXP_branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 1.17.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.528 ) or ( peg.621 ) ) PROTEIN_ASSOCIATION:ispA SUBSYSTEM: Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.5.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.528 ) or ( peg.621 ) ) PROTEIN_ASSOCIATION:ispA SUBSYSTEM: Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.5.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.528 ) or ( peg.621 ) ) PROTEIN_ASSOCIATION:ispA SUBSYSTEM: Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.5.1.29 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.528 ) or ( peg.621 ) ) PROTEIN_ASSOCIATION:ispA SUBSYSTEM: Isoprenoid_Biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.528 ) or ( peg.621 ) ) PROTEIN_ASSOCIATION:ispA SUBSYSTEM: Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.5.1.33 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.528 ) or ( peg.621 ) ) PROTEIN_ASSOCIATION:ispA SUBSYSTEM: Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.5.1.30 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.528 ) or ( peg.621 ) ) PROTEIN_ASSOCIATION:ispA SUBSYSTEM: Isoprenoid_Biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %%Adding 8 isopentenyl groups to generate the undecaprenyl tail to transport peptidoglycan building blocks through the membrane GENE_ASSOCIATION:peg.870 PROTEIN_ASSOCIATION:peg.870 SUBSYSTEM: Mevalonate_Branch_of_Isoprenoid_Biosynthesis PROTEIN_CLASS: 2.5.1.31 $\mathrm{FLUX\_VALUE}$ %%%Phospholipid membrane synthesis %%Synthesis of the glycerol 3-phopshate backbones to which the fatty acid tails (synthesized below) are later attached. %Reactions are redundant, with 5 different reducants included by SEED for the reduction from glycerone to glycerol. GENE_ASSOCIATION:peg.1135 PROTEIN_ASSOCIATION:gspA SUBSYSTEM: Glycerol_and_Glycerol-3-phosphate_Uptake_and_Utilization PROTEIN_CLASS: 1.1.1.94 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1135 PROTEIN_ASSOCIATION:gspA SUBSYSTEM: Glycerol_and_Glycerol-3-phosphate_Uptake_and_Utilization PROTEIN_CLASS: 1.1.1.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1138 PROTEIN_ASSOCIATION:glpC SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.99.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1138 PROTEIN_ASSOCIATION:glpC SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.99.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1138 PROTEIN_ASSOCIATION:glpC SUBSYSTEM: Glycerol_and_Glycerol-3-phosphate_Uptake_and_Utilization PROTEIN_CLASS: 1.1.99.5 $\mathrm{FLUX\_VALUE}$ %Two appendage reactions from glycerol 3-phosphate, to glycerol and to UDP-glycerol. GENE_ASSOCIATION:peg.321 PROTEIN_ASSOCIATION:glpK SUBSYSTEM: Glycerol_and_Glycerol-3-phosphate_Uptake_and_Utilization PROTEIN_CLASS: 2.7.1.30 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.959 PROTEIN_ASSOCIATION:peg.959 SUBSYSTEM: Teichoic_and_lipoteichoic_acids_biosynthesis PROTEIN_CLASS: 2.7.7.39 $\mathrm{FLUX\_VALUE}$ %%Attaching pantetheine to ACP GENE_ASSOCIATION:peg.571 PROTEIN_ASSOCIATION:acpS SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.7.8.7 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.244 PROTEIN_ASSOCIATION:cysQ SUBSYSTEM: Inorganic_Sulfur_Assimilation PROTEIN_CLASS: 3.1.3.7 $\mathrm{FLUX\_VALUE}$ %%Sequence generating malonyl-ACP from HCO3 and acetyl-CoA GENE_ASSOCIATION:( peg.412 and peg.954 ) PROTEIN_ASSOCIATION:birA+accB SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 6.3.4.14 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.329 and peg.839 ) PROTEIN_ASSOCIATION:accD+accA SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 6.4.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ %%Main fatty acid synthesis sequences, starting with transfer of acetyl from CoA to ACP, followed by sequential chain lengthening reactions (via malonyl-insertions). GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.38 $\mathrm{FLUX\_VALUE}$ %Basic pathway to unsaturated, even carbon number FA's. GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 4.2.1.58 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ %The synthesis of n-7 unsaturated FA's with even numbered chain lengths, starting from isomerization of trans-2-decenoyl-ACP to cis-3-decenoyl-ACP GENE_ASSOCIATION:GAPFILL_RB2010 PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ %The synthesis of n-9 unsaturated FA's with even numbered chain lengths, starting from isomerization of trans-2-dodecenoyl-ACP to cis-3-dodecenoyl-ACP GENE_ASSOCIATION:GAPFILL_RB2010 PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ %Here start the synthesis of saturated FA's of uneven chain lengths from propionyl-CoA. First step is synthesis of prop-CoA from butanoate. SUBSYSTEM: PROTEIN_CLASS: 1.2.7.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.38 $\mathrm{FLUX\_VALUE}$ %First malonyl insertion from Mal-Coa, and so on. GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 4.2.1.58 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ %Here begins the synthesis of n-8 unsaturated FA's of uneven chain lenghts, starting from isomerization of Undec-2-enoyl-ACP GENE_ASSOCIATION:GAPFILL_RB2010 PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.100 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 2.3.1.85 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: Fatty_Acid_Biosynthesis_FASII PROTEIN_CLASS: 1.3.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1193 and peg.763 ) PROTEIN_ASSOCIATION:fabF+fabH SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.43 PROTEIN_ASSOCIATION:fabZ SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.0 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1085 PROTEIN_ASSOCIATION:fabI SUBSYSTEM: NONE PROTEIN_CLASS: 1.3.1.0 $\mathrm{FLUX\_VALUE}$ %Here start the outflows from FA's to lipids, starting with transformations of acyl-ACP to acyl-CoA. GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.2 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.618 PROTEIN_ASSOCIATION:fabD SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %%Here start the phospholipid assembly sequences, including three classes of generic ester and ether syntheses, whose generic tails are subsequently replace by known fatty acids and alcohols. %A generic phospho-ester-lipid sequence, adding two generic acyl-groups (from R-COOH) that are later replaced in the final global ester-lipid synthesis reaction. GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.480 and peg.764 ) PROTEIN_ASSOCIATION:peg.480+plsX SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.15 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1425 ) or ( peg.697 ) ) PROTEIN_ASSOCIATION:aas SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.51 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.871 PROTEIN_ASSOCIATION:cds SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.7.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1036 ) or ( peg.1492 ) or ( peg.668 ) or ( peg.867 ) ) PROTEIN_ASSOCIATION:peg.1036 SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.8.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.230 PROTEIN_ASSOCIATION:peg.230 SUBSYSTEM: NONE PROTEIN_CLASS: 3.1.3.27 $\mathrm{FLUX\_VALUE}$ %Next the global ester-lipid synthesis, releasing the placeholder acyl-groups and incorporating known stoichiometric ratios of FA's into ester-lipids. GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Next the phospho-ether-lipid synthesis series, starting with reduction of acyl-CoA to alcohol groups that are later attached to glycerone group. GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Here starts the sequence of ether-lipid synthesis, first attaching generic alkyl groups (from R-OH) to a glycerone moiety that are later replaced by stoichiometric distributions of known alcoholos in global ether-lipid reactions. GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Synthesis of glycerol-mono-ethers (GME), starting with three head-group modification reactions of generic alkyl-glycerol moiety and finally a global synthesis reaction that replaces R-OH with correct alcohol distribution GENE_ASSOCIATION:peg.871 PROTEIN_ASSOCIATION:cds SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.7.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1036 ) or ( peg.1492 ) or ( peg.668 ) or ( peg.867 ) ) PROTEIN_ASSOCIATION:peg.1036 SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.8.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.230 PROTEIN_ASSOCIATION:peg.230 SUBSYSTEM: NONE PROTEIN_CLASS: 3.1.3.27 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Synthesis of glycerol-di-ethers (GDE), starting with three head-group modification reactions of generic dialkyl-glycerol moiety and finally a global synthesis reaction that replaces R-OH with correct alcohol distribution GENE_ASSOCIATION:peg.871 PROTEIN_ASSOCIATION:cds SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.7.41 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1036 ) or ( peg.1492 ) or ( peg.668 ) or ( peg.867 ) ) PROTEIN_ASSOCIATION:peg.1036 SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.8.5 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.230 PROTEIN_ASSOCIATION:peg.230 SUBSYSTEM: NONE PROTEIN_CLASS: 3.1.3.27 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %%%Peptidoglycan synthesis, starting with some precursors, then the main sequence and finally membrane transport and final assembly %%D-glutamate and D-alanine-D-alanine synthesis GENE_ASSOCIATION:peg.237 PROTEIN_ASSOCIATION:murI SUBSYSTEM: Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis PROTEIN_CLASS: 5.1.1.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1268 PROTEIN_ASSOCIATION:alr SUBSYSTEM: Alanine_biosynthesis PROTEIN_CLASS: 5.1.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.381 PROTEIN_ASSOCIATION:ddlA SUBSYSTEM: NONE PROTEIN_CLASS: 6.3.2.4 $\mathrm{FLUX\_VALUE}$ %%Here starts the main sequence to peptidoglycan from N-acetylglucosamine and PEP GENE_ASSOCIATION:peg.894 PROTEIN_ASSOCIATION:murA SUBSYSTEM: NONE PROTEIN_CLASS: 2.5.1.7 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.374 ) or ( peg.380 ) ) PROTEIN_ASSOCIATION:peg.374 SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.158 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.952 PROTEIN_ASSOCIATION:murC SUBSYSTEM: NONE PROTEIN_CLASS: 6.3.2.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1436 PROTEIN_ASSOCIATION:murD SUBSYSTEM: NONE PROTEIN_CLASS: 6.3.2.9 $\mathrm{FLUX\_VALUE}$ %Continuation of peptidoglycan synthesis via the diaminopimelate branch, the only branch in Aquifex and standard branch for gram-negative bacteria. GENE_ASSOCIATION:peg.1212 PROTEIN_ASSOCIATION:murE SUBSYSTEM: Methicillin_resistance_in_Staphylococci PROTEIN_CLASS: 6.3.2.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.578 PROTEIN_ASSOCIATION:murF SUBSYSTEM: NONE PROTEIN_CLASS: 6.3.2.10 $\mathrm{FLUX\_VALUE}$ %Here start of the transmembrane transport and assembly sequence, beginning with attachment the undecaprenyl isoprene tail and a second N-acetylglucosamine group. GENE_ASSOCIATION:peg.40 PROTEIN_ASSOCIATION:mraY SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.8.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.817 PROTEIN_ASSOCIATION:murG SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.227 $\mathrm{FLUX\_VALUE}$ %Final peptidoglycan polymerization reaction, which also detaches the undecaprenyl isoprene tail. GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Closing the undecaprenyl isoprene cycle, dephosphorylation undecaprenyl from -PP to -P form which can then reinitiate transport of next peptidoglycan monomer subunit. GENE_ASSOCIATION:peg.1523 PROTEIN_ASSOCIATION:bacA SUBSYSTEM: Teichoic_and_lipoteichoic_acids_biosynthesis PROTEIN_CLASS: 3.6.1.27 $\mathrm{FLUX\_VALUE}$ %%%Lipopolysaccharide synthesis. This sub-systems contains the single largest number of gap-fills of all Aquifex sub-systems. Synthesis of a few precursor inputs is listed next, followed by the complete assembly sequence. %The octulosonate (C8) precursor from Ribulose-5P (via Arabinose-5P). GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 5.3.1.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.71 PROTEIN_ASSOCIATION:kdsA SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.5.1.55 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1504 PROTEIN_ASSOCIATION:peg.1504 SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 3.1.3.45 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.489 PROTEIN_ASSOCIATION:kpsU SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.7.7.38 $\mathrm{FLUX\_VALUE}$ %The heptose (C7) precursor from sedoheptulose-7P. GENE_ASSOCIATION:peg.631 PROTEIN_ASSOCIATION:gmhA SUBSYSTEM: LOS_core_oligosaccharide_biosynthesis PROTEIN_CLASS: 5.-.-.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.147 ) or ( peg.411 ) ) PROTEIN_ASSOCIATION:peg.147 SUBSYSTEM: LOS_core_oligosaccharide_biosynthesis PROTEIN_CLASS: 2.7.-.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 3.1.-.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.147 ) or ( peg.411 ) ) PROTEIN_ASSOCIATION:peg.147 SUBSYSTEM: LOS_core_oligosaccharide_biosynthesis PROTEIN_CLASS: 2.7.-.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.250 PROTEIN_ASSOCIATION:rfaD SUBSYSTEM: LOS_core_oligosaccharide_biosynthesis PROTEIN_CLASS: 5.1.3.20 $\mathrm{FLUX\_VALUE}$ %A mannose (C6) precursor from Glucose-1P GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.7.24 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.46 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 5.1.3.13 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 1.1.1.133 $\mathrm{FLUX\_VALUE}$ %Full lipopolysaccharide synthesis and assembly from UDP-GlcNAc, starting with Lipid A synthesis. GENE_ASSOCIATION:peg.437 PROTEIN_ASSOCIATION:lpxA SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.3.1.129 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1229 PROTEIN_ASSOCIATION:envA SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 3.5.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.392 PROTEIN_ASSOCIATION:lpxD SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.3.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 3.6.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1000 PROTEIN_ASSOCIATION:lpxB SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.4.1.182 $\mathrm{FLUX\_VALUE}$ %Here begins the modification of the basic Lipid A unit, first adding few saccharides to KDO-Lipid IV, then additional fatty acid anchors for anchoring into the membrane, and finally a series of sugar groups as part of LPS core assembly GENE_ASSOCIATION:peg.1153 PROTEIN_ASSOCIATION:peg.1153 SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.7.1.130 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.238 PROTEIN_ASSOCIATION:kdtA SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.-.-.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.238 PROTEIN_ASSOCIATION:kdtA SUBSYSTEM: KDO2-Lipid_A_biosynthesis PROTEIN_CLASS: 2.-.-.- $\mathrm{FLUX\_VALUE}$ %Adding fatty acid membrane anchors to KDO-Lipid IV GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.3.1.- $\mathrm{FLUX\_VALUE}$ %Final LPS core assembly sequence adding a series of sugar groups GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.113 PROTEIN_ASSOCIATION:peg.113 SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.-.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.- $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:INITIAL_GAP_FILLING_SEED PROTEIN_ASSOCIATION:INITIAL_GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 2.4.1.56 $\mathrm{FLUX\_VALUE}$ %%%%%%Global cellular replication, including protein synthesis, DNA/RNA replication and total biomass reaction. GENE_ASSOCIATION:( ( peg.837 and peg.741 and peg.519 and peg.520 and peg.608 and peg.1164 and peg.693 and peg.1201 and peg.1393 and peg.255 and peg.604 and peg.1213 and peg.185 and peg.8 and peg.9 and peg.10 and peg.11 and peg.12 and peg.13 and peg.1311 and peg.1474 and peg.1170 and peg.138 and peg.67 and peg.558 and peg.765 and peg.222 and peg.97 and peg.98 and peg.265 and peg.659 and peg.49 and peg.51 and peg.226 and peg.3 and peg.4 and peg.5 and peg.6 and peg.7 and peg.877 and peg.341 and peg.664 and peg.665 and peg.57 and peg.59 and peg.60 and peg.61 and peg.62 and peg.1343 and peg.1344 and peg.1345 and peg.902 and peg.850 and peg.1488 and peg.991 and peg.1305 and peg.1306 and peg.169 and peg.1224 and peg.1482 and peg.1414 and peg.1351 and peg.645 and peg.1141 and peg.1142 and peg.1143 and peg.1144 and peg.1145 and peg.1146 and peg.1147 and peg.1148 and peg.1149 and peg.1150 and peg.1151 and peg.1339 and peg.1231 ) or ( peg.837 and peg.741 and peg.1271 and peg.1272 and peg.608 and peg.1164 and peg.693 and peg.1201 and peg.1393 and peg.255 and peg.604 and peg.1213 and peg.185 and peg.8 and peg.9 and peg.10 and peg.11 and peg.12 and peg.13 and peg.1311 and peg.1474 and peg.1170 and peg.138 and peg.67 and peg.558 and peg.765 and peg.222 and peg.97 and peg.98 and peg.265 and peg.659 and peg.49 and peg.51 and peg.226 and peg.3 and peg.4 and peg.5 and peg.6 and peg.7 and peg.877 and peg.341 and peg.664 and peg.665 and peg.57 and peg.59 and peg.60 and peg.61 and peg.62 and peg.1343 and peg.1344 and peg.1345 and peg.902 and peg.850 and peg.1488 and peg.991 and peg.1305 and peg.1306 and peg.169 and peg.1224 and peg.1482 and peg.1414 and peg.1351 and peg.645 and peg.1141 and peg.1142 and peg.1143 and peg.1144 and peg.1145 and peg.1146 and peg.1147 and peg.1148 and peg.1149 and peg.1150 and peg.1151 and peg.1339 and peg.1231 ) or ( peg.837 and peg.741 and peg.519 and peg.520 and peg.608 and peg.1164 and peg.693 and peg.1201 and peg.1393 and peg.1227 and peg.604 and peg.1213 and peg.185 and peg.8 and peg.9 and peg.10 and peg.11 and peg.12 and peg.13 and peg.1311 and peg.1474 and peg.1170 and peg.138 and peg.67 and peg.558 and peg.765 and peg.222 and peg.97 and peg.98 and peg.265 and peg.659 and peg.49 and peg.51 and peg.226 and peg.3 and peg.4 and peg.5 and peg.6 and peg.7 and peg.877 and peg.341 and peg.664 and peg.665 and peg.57 and peg.59 and peg.60 and peg.61 and peg.62 and peg.1343 and peg.1344 and peg.1345 and peg.902 and peg.850 and peg.1488 and peg.991 and peg.1305 and peg.1306 and peg.169 and peg.1224 and peg.1482 and peg.1414 and peg.1351 and peg.645 and peg.1141 and peg.1142 and peg.1143 and peg.1144 and peg.1145 and peg.1146 and peg.1147 and peg.1148 and peg.1149 and peg.1150 and peg.1151 and peg.1339 and peg.1231 ) or ( peg.837 and peg.741 and peg.1271 and peg.1272 and peg.608 and peg.1164 and peg.693 and peg.1201 and peg.1393 and peg.1227 and peg.604 and peg.1213 and peg.185 and peg.8 and peg.9 and peg.10 and peg.11 and peg.12 and peg.13 and peg.1311 and peg.1474 and peg.1170 and peg.138 and peg.67 and peg.558 and peg.765 and peg.222 and peg.97 and peg.98 and peg.265 and peg.659 and peg.49 and peg.51 and peg.226 and peg.3 and peg.4 and peg.5 and peg.6 and peg.7 and peg.877 and peg.341 and peg.664 and peg.665 and peg.57 and peg.59 and peg.60 and peg.61 and peg.62 and peg.1343 and peg.1344 and peg.1345 and peg.902 and peg.850 and peg.1488 and peg.991 and peg.1305 and peg.1306 and peg.169 and peg.1224 and peg.1482 and peg.1414 and peg.1351 and peg.645 and peg.1141 and peg.1142 and peg.1143 and peg.1144 and peg.1145 and peg.1146 and peg.1147 and peg.1148 and peg.1149 and peg.1150 and peg.1151 and peg.1339 and peg.1231 ) ) PROTEIN_ASSOCIATION:lysU+cysS+peg.519+peg.520+RpmE+thrS+trpS+pheT+rpsB+leuS+rpsU+tyrS+gatA+rpsS+rplV+rpsC+rplP+rpmC+rpsQ+mesJ+fmt+aspS+rpmH+rpmB+rpmI+rpmF+serS+peg.97+rpsP+proS+glyQ+rpsF+rpsR+ileS+rpsJ+rplC+rplD+rplW+rplB+metG+gatB+rplT+pheS+rplQ+rpsD+rpsK+rpsM+rpmJ+rplA+rplJ+rplL+alaS+gltX+gatC+valS+rplM+rpsI+rpsO+rpsT+glyS+rplI+rplS+argS+rplU+rplO+rpmD+rpsE+rplR+rplF+rpsH+rpsN+rplE+rplX+rplN+rpmG+rpmA SUBSYSTEM: Macromolecule biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.715 and peg.703 and peg.234 and peg.1308 and peg.1221 and peg.468 and peg.559 and peg.453 and peg.455 and peg.1290 and peg.686 and peg.1045 and peg.50 and peg.978 ) PROTEIN_ASSOCIATION:gyrB+dnaE+dnaA+dnaN+peg.1221+topA+rep+xcpC+ligA+dnaX+gyrA+dnaG+ssb+lig SUBSYSTEM: Macromolecule biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1043 and peg.1044 and peg.1346 and peg.1347 and peg.853 and peg.660 and peg.193 and peg.58 ) PROTEIN_ASSOCIATION:trmD+rpoD+rpoB+rpoC+peg.853+rnc+nusA+rpoA SUBSYSTEM: Macromolecule biosynthesis PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:UNIVERSAL PROTEIN_ASSOCIATION:UNIVERSAL SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %%%%%%Energy metabolism, including sulfur, reactive oxygen, cyanide and other inorganic conversions GENE_ASSOCIATION:( peg.1105 and peg.1106 and peg.1107 and peg.139 and peg.141 and peg.1412 and peg.1413 and peg.478 and peg.482 ) PROTEIN_ASSOCIATION:peg.1105+peg.1106+atpH+atpE+atpB+atpD+peg.1413+atpC+atpA SUBSYSTEM: NONE PROTEIN_CLASS: 3.6.3.14, $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.752 PROTEIN_ASSOCIATION:cysD SUBSYSTEM: Inorganic_Sulfur_Assimilation PROTEIN_CLASS: 2.7.1.25 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1516 and peg.1519 and peg.1520 ) PROTEIN_ASSOCIATION:coxC+peg.1519+peg.1520 SUBSYSTEM: NONE PROTEIN_CLASS: 1.9.3.1, $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.158 and peg.165 ) or ( peg.583 ) ) PROTEIN_ASSOCIATION:nirB+narB SUBSYSTEM: NONE PROTEIN_CLASS: 1.7.1.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1050 PROTEIN_ASSOCIATION:sodA SUBSYSTEM: Protection_from_Reactive_Oxygen_Species PROTEIN_CLASS: 1.15.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.162 PROTEIN_ASSOCIATION:cynS SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.104 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.752 PROTEIN_ASSOCIATION:cysD SUBSYSTEM: Inorganic_Sulfur_Assimilation PROTEIN_CLASS: 2.7.7.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1257 and peg.1330 ) PROTEIN_ASSOCIATION:peg.1257+peg.1330 SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.365 PROTEIN_ASSOCIATION:trxB SUBSYSTEM: pyrimidine_conversions PROTEIN_CLASS: 1.8.1.9 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1081 PROTEIN_ASSOCIATION:ppa SUBSYSTEM: NONE PROTEIN_CLASS: 3.6.1.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1516 ) or ( peg.1519 and peg.1520 ) ) PROTEIN_ASSOCIATION:coxC SUBSYSTEM: Terminal_cytochrome_C_oxidases PROTEIN_CLASS: 1.9.3.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.158 ) or ( peg.583 ) ) PROTEIN_ASSOCIATION:nirB SUBSYSTEM: NONE PROTEIN_CLASS: 1.7.1.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: 4.2.1.104 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB PROTEIN_ASSOCIATION:GAP_FILLING_RB SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.469 and peg.470 and peg.471 and peg.949 ) or ( peg.563 ) ) PROTEIN_ASSOCIATION:peg.469+peg.470+hoxZ+cydA SUBSYSTEM: NONE PROTEIN_CLASS: 1.18.99.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.563 PROTEIN_ASSOCIATION:peg.563 SUBSYSTEM: NONE PROTEIN_CLASS: 1.18.99.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.323 and peg.416 and peg.417 and peg.963 and peg.964 and peg.965 and peg.966 and peg.967 and peg.968 and peg.969 and peg.970 and peg.971 ) PROTEIN_ASSOCIATION:nuoG+nuoF+nuoE+peg.963+peg.964+peg.965+peg.966+peg.967+peg.968+peg.969+peg.970+peg.971 SUBSYSTEM: NONE PROTEIN_CLASS: 1.6.5.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.323 and peg.416 and peg.417 and peg.963 and peg.964 and peg.965 and peg.966 and peg.967 and peg.968 and peg.969 and peg.970 and peg.971 ) PROTEIN_ASSOCIATION:nuoG+nuoF+nuoE+peg.963+peg.964+peg.965+peg.966+peg.967+peg.968+peg.969+peg.970+peg.971 SUBSYSTEM: NONE PROTEIN_CLASS: 1.6.5.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.174 ) or ( peg.949 and peg.950 ) ) PROTEIN_ASSOCIATION:soxF SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.174 ) or ( peg.34 and peg.35 ) or ( peg.949 and peg.950 ) ) PROTEIN_ASSOCIATION:soxF SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.165 PROTEIN_ASSOCIATION:narB SUBSYSTEM: NONE PROTEIN_CLASS: 1.7.99.4 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.158 ) or ( peg.165 ) ) PROTEIN_ASSOCIATION:nirB SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_RB2010 PROTEIN_ASSOCIATION:GAP_FILLING_RB2010 SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.403 and peg.430 ) or ( peg.430 and peg.467 ) ) PROTEIN_ASSOCIATION:peg.403+frdA SUBSYSTEM: NONE PROTEIN_CLASS: Undetermined $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.859 and peg.858 and peg.857 ) PROTEIN_ASSOCIATION:dmsA+peg.858+dmsC SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.859 and peg.858 and peg.857 ) PROTEIN_ASSOCIATION:dmsA+peg.858+dmsC SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.859 and peg.858 and peg.857 ) PROTEIN_ASSOCIATION:dmsA+peg.858+dmsC SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.859 and peg.858 and peg.857 ) PROTEIN_ASSOCIATION:dmsA+peg.858+dmsC SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.1561 PROTEIN_ASSOCIATION:peg.1561 SUBSYSTEM: NONE PROTEIN_CLASS: 2.7.9.3 $\mathrm{FLUX\_VALUE}$ %%%%%%Transport reactions GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.164 PROTEIN_ASSOCIATION:nasA SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.90 PROTEIN_ASSOCIATION:amtB SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.782 PROTEIN_ASSOCIATION:peg.782 SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.746 PROTEIN_ASSOCIATION:czcD SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1399 and peg.1400 and peg.732 ) PROTEIN_ASSOCIATION:pstS+pstC+pstB SUBSYSTEM: NONE PROTEIN_CLASS: TC-3.A.1.7 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.164 PROTEIN_ASSOCIATION:nasA SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.875 PROTEIN_ASSOCIATION:feoB SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.324 PROTEIN_ASSOCIATION:peg.324 SUBSYSTEM: NONE PROTEIN_CLASS: 1.A.11 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.782 PROTEIN_ASSOCIATION:peg.782 SUBSYSTEM: NONE PROTEIN_CLASS: 3.A.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1120 and peg.72 ) PROTEIN_ASSOCIATION:modA+modC SUBSYSTEM: NONE PROTEIN_CLASS: TC-3.A.1.8 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.782 PROTEIN_ASSOCIATION:peg.782 SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.1500 and peg.1501 ) or ( peg.447 ) ) PROTEIN_ASSOCIATION:peg.1500+scbA SUBSYSTEM: NONE PROTEIN_CLASS: TC-3.A.1.15 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( peg.1053 and peg.1054 ) PROTEIN_ASSOCIATION:peg.1053+peg.1054 SUBSYSTEM: NONE PROTEIN_CLASS: TC-2.A.37 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:( ( peg.570 ) or ( peg.706 ) ) PROTEIN_ASSOCIATION:peg.570 SUBSYSTEM: NONE PROTEIN_CLASS: 1.A.1 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.782 PROTEIN_ASSOCIATION:peg.782 SUBSYSTEM: NONE PROTEIN_CLASS: TC-3.A.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.746 PROTEIN_ASSOCIATION:czcD SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.782 PROTEIN_ASSOCIATION:peg.782 SUBSYSTEM: NONE PROTEIN_CLASS: TC-3.A.3 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:UNIVERSAL PROTEIN_ASSOCIATION:UNIVERSAL SUBSYSTEM: NONE PROTEIN_CLASS: TC-2.A.53 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:UNIVERSAL PROTEIN_ASSOCIATION:UNIVERSAL SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:UNIVERSAL PROTEIN_ASSOCIATION:UNIVERSAL SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: 3.A.1.15 $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:GAP_FILLING_SEED PROTEIN_ASSOCIATION:GAP_FILLING_SEED SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:SPONTANEOUS PROTEIN_ASSOCIATION:SPONTANEOUS SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:UNIVERSAL PROTEIN_ASSOCIATION:UNIVERSAL SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:UNIVERSAL PROTEIN_ASSOCIATION:UNIVERSAL SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %Two glutamate transport reactions, made inactive because Aquifex is an autotroph not known to grow on glutamate. GENE_ASSOCIATION:peg.928 PROTEIN_ASSOCIATION:gltP SUBSYSTEM: NONE PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION:peg.928 PROTEIN_ASSOCIATION:gltP SUBSYSTEM: NONE PROTEIN_CLASS: 2.A.23 $\mathrm{FLUX\_VALUE}$ %An odd dipeptide transport reaction also made inactive. Aquifex is an autotroph not known to use organics, let alone something as complex as dipeptides. GENE_ASSOCIATION:( ( peg.1009 ) or ( peg.1058 ) or ( peg.352 ) ) PROTEIN_ASSOCIATION:oppA SUBSYSTEM: NONE PROTEIN_CLASS: TC-3.A.1.5 $\mathrm{FLUX\_VALUE}$ %%%%%%Exchange reactions GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$ %%%A drain for 5-deoxyadenosine, a byproduct created in the synthesis of several cofactors. No plausible gapfill reaction could be included to reincorporate this compound. This is the only organic exchange reaction in the model. GENE_ASSOCIATION: PROTEIN_ASSOCIATION: SUBSYSTEM: S_ PROTEIN_CLASS: $\mathrm{FLUX\_VALUE}$