2.0 2012-05-31 10:27:35 -0600 2015-09-13 12:56:08 -0600 ECMDB00595 M2MDB000153 Hydrogen carbonate Bicarbonate is a simple single carbon molecule that plays surprisingly important roles in diverse biological processes. It is an anion that consists of one central carbon atom surrounded by three oxygen atoms in a trigonal planar arrangement, with a hydrogen atom attached to one of the oxygens. The bicarbonate ion carries a negative one formal charge and is the conjugate base of carbonic acid, H2CO3. The carbonate radical is an elusive and strong one-electron oxidant. Bicarbonate in equilibrium with carbon dioxide constitutes the main physiological buffer in cells. The bicarbonate-carbon dioxide pair stimulates the oxidation, peroxidation and nitration of several biological targets. The carbonate radical has also been proposed to be responsible for the stimulatory effects of the bicarbonate-carbon dioxide pair on oxidations mediated by hydrogen peroxide/transition metal ions. The ultimate precursor of the carbonate radical anion being bicarbonate, carbon dioxide, peroxymonocarbonate or complexes of transition metal ions with bicarbonate-derived species remains a matter of debate. Bicarbonate Bicarbonate (HCO3-) Bicarbonate anion Bicarbonate ion Bicarbonate ion (HCO31-) Bicarbonate ions Bicarbonic acid Bicarbonic acid (HCO3-) Bicarbonic acid anion Bicarbonic acid ion Bicarbonic acid ion (HCO31-) Bicarbonic acid ions Carbonate Carbonate (HCO31-) Carbonate ion (HCO31-) Carbonic acid Carbonic acid (HCO31-) Carbonic acid ion (HCO31-) CO3-2 CO32- CO<SUB>3</SUB><SUP>-2</SUP> CO<SUB>3</SUB><SUP>2-</SUP> HCO3 HCO3- HCO<SUB>3</SUB> HCO<SUB>3</SUB><SUP>-</SUP> Hydrocarbonate(1-) Hydrocarbonic acid(1-) Hydrogen carbonate Hydrogen carbonate (HCO3-) Hydrogen carbonate anion Hydrogen carbonate ion Hydrogen carbonate ion (HCO3-) Hydrogen carbonic acid Hydrogen carbonic acid (HCO3-) Hydrogen carbonic acid anion Hydrogen carbonic acid ion Hydrogen carbonic acid ion (HCO3-) Hydrogencarbonate Hydrogencarbonic acid Hydrogentrioxocarbonate Hydrogentrioxocarbonic acid Monohydrogen carbonate Monohydrogen carbonic acid CHO3 61.0168 60.992568898 carbonic acid carbonic acid 71-52-3 OC([O-])=O InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1 BVKZGUZCCUSVTD-UHFFFAOYSA-M Solid Cytosol logp 0.60 ALOGPS logs 0.57 ALOGPS solubility 2.31e+02 g/l ALOGPS melting_point 720 oC logp 0.25 ChemAxon pka_strongest_acidic 6.05 ChemAxon iupac carbonic acid ChemAxon average_mass 61.0168 ChemAxon mono_mass 60.992568898 ChemAxon smiles OC([O-])=O ChemAxon formula CHO3 ChemAxon inchi InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1 ChemAxon inchikey BVKZGUZCCUSVTD-UHFFFAOYSA-M ChemAxon polar_surface_area 57.53 ChemAxon refractivity 9.5 ChemAxon polarizability 4.23 ChemAxon rotatable_bond_count 0 ChemAxon acceptor_count 3 ChemAxon donor_count 2 ChemAxon physiological_charge -1 ChemAxon formal_charge 0 ChemAxon Reductive carboxylate cycle (CO2 fixation) ec00720 Alanine, aspartate and glutamate metabolism ec00250 Nitrogen metabolism The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction and dissimilatory nitrate reduction both for conversion to ammonia, and denitrification. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions, producing gaseous nitrogen compounds (N2, NO and N2O) to the atmosphere. Nitrate can be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK or a nitrate / nitrite transporter NarU. Nitrate is then reduced by a Nitrate Reductase resulting in the release of water, an acceptor and a Nitrite. Nitrite can also be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK Nitrite can be reduced a NADPH dependent nitrite reductase resulting in water and NAD and Ammonia. Nitrite can interact with hydrogen ion, ferrocytochrome c through a cytochrome c-552 ferricytochrome resulting in the release of ferricytochrome c, water and ammonia Another process by which ammonia is produced is by a reversible reaction of hydroxylamine with a reduced acceptor through a hydroxylamine reductase resulting in an acceptor, water and ammonia. Water and carbon dioxide react through a carbonate dehydratase resulting in carbamic acid. This compound reacts spontaneously with hydrogen ion resulting in the release of carbon dioxide and ammonia. Carbon dioxide can interact with water through a carbonic anhydrase resulting in hydrogen carbonate. This compound interacts with cyanate and hydrogen ion through a cyanate hydratase resulting in a carbamic acid. Ammonia can be metabolized by reacting with L-glutamine and ATP driven glutamine synthetase resulting in ADP, phosphate and L-glutamine. The latter compound reacts with oxoglutaric acid and hydrogen ion through a NADPH dependent glutamate synthase resulting in the release of NADP and L-glutamic acid. L-glutamic acid reacts with water through a NADP-specific glutamate dehydrogenase resulting in the release of oxoglutaric acid, NADPH, hydrogen ion and ammonia. PW000755 ec00910 Metabolic Purine metabolism ec00230 Pyrimidine metabolism The metabolism of pyrimidines begins with L-glutamine interacting with water molecule and a hydrogen carbonate through an ATP driven carbamoyl phosphate synthetase resulting in a hydrogen ion, an ADP, a phosphate, an L-glutamic acid and a carbamoyl phosphate. The latter compound interacts with an L-aspartic acid through a aspartate transcarbamylase resulting in a phosphate, a hydrogen ion and a N-carbamoyl-L-aspartate. The latter compound interacts with a hydrogen ion through a dihydroorotase resulting in the release of a water molecule and a 4,5-dihydroorotic acid. This compound interacts with an ubiquinone-1 through a dihydroorotate dehydrogenase, type 2 resulting in a release of an ubiquinol-1 and an orotic acid. The orotic acid then interacts with a phosphoribosyl pyrophosphate through a orotate phosphoribosyltransferase resulting in a pyrophosphate and an orotidylic acid. The latter compound then interacts with a hydrogen ion through an orotidine-5 '-phosphate decarboxylase, resulting in an release of carbon dioxide and an Uridine 5' monophosphate. The Uridine 5' monophosphate process to get phosphorylated by an ATP driven UMP kinase resulting in the release of an ADP and an Uridine 5--diphosphate. Uridine 5-diphosphate can be metabolized in multiple ways in order to produce a Deoxyuridine triphosphate. 1.-Uridine 5-diphosphate interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in the release of a water molecule and an oxidized thioredoxin and an dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 2.-Uridine 5-diphosphate interacts with a reduced NrdH glutaredoxin-like protein through a Ribonucleoside-diphosphate reductase 1 resulting in a release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 3.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate. The latter compound interacts with a reduced flavodoxin through ribonucleoside-triphosphate reductase resulting in the release of an oxidized flavodoxin, a water molecule and a Deoxyuridine triphosphate 4.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in the release of a water molecule, an oxidized flavodoxin and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 5.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP then interacts with a reduced NrdH glutaredoxin-like protein through a ribonucleoside-diphosphate reductase 2 resulting in the release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 6.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. The deoxyuridine triphosphate then interacts with a water molecule through a nucleoside triphosphate pyrophosphohydrolase resulting in a release of a hydrogen ion, a phosphate and a dUMP. The dUMP then interacts with a methenyltetrahydrofolate through a thymidylate synthase resulting in a dihydrofolic acid and a 5-thymidylic acid. Then 5-thymidylic acid is then phosphorylated through a nucleoside diphosphate kinase resulting in the release of an ADP and thymidine 5'-triphosphate. PW000942 ec00240 Metabolic Carbon fixation in photosynthetic organisms ec00710 Pyruvate metabolism ec00620 Methane metabolism ec00680 Propanoate metabolism Starting from L-threonine, this compound is deaminated through a threonine deaminase resulting in a hydrogen ion, a water molecule and a (2z)-2-aminobut-2-enoate. The latter compound then isomerizes to a 2-iminobutanoate, This compound then reacts spontaneously with hydrogen ion and a water molecule resulting in a ammonium and a 2-Ketobutyric acid. The latter compound interacts with CoA through a pyruvate formate-lyase / 2-ketobutyrate formate-lyase resulting in a formic acid and a propionyl-CoA. Propionyl-CoA can then be processed either into a 2-methylcitric acid or into a propanoyl phosphate. Propionyl-CoA interacts with oxalacetic acid and a water molecule through a 2-methylcitrate synthase resulting in a hydrogen ion, a CoA and a 2-Methylcitric acid.The latter compound is dehydrated through a 2-methylcitrate dehydratase resulting in a water molecule and cis-2-methylaconitate. The latter compound is then dehydrated by a bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase resulting in a water molecule and methylisocitric acid. The latter compound is then processed by 2-methylisocitrate lyase resulting in a release of succinic acid and pyruvic acid. Succinic acid can then interact with a propionyl-CoA through a propionyl-CoA:succinate CoA transferase resulting in a propionic acid and a succinyl CoA. Succinyl-CoA is then isomerized through a methylmalonyl-CoA mutase resulting in a methylmalonyl-CoA. This compound is then decarboxylated through a methylmalonyl-CoA decarboxylase resulting in a release of Carbon dioxide and Propionyl-CoA. ropionyl-CoA interacts with a phosphate through a phosphate acetyltransferase / phosphate propionyltransferase resulting in a CoA and a propanoyl phosphate. Propionyl-CoA can react with a phosphate through a phosphate acetyltransferase / phosphate propionyltransferase resulting in a CoA and a propanoyl phosphate. The latter compound is then dephosphorylated through a ADP driven acetate kinase/propionate kinase protein complex resulting in an ATP and Propionic acid. Propionic acid can be processed by a reaction with CoA through a ATP-driven propionyl-CoA synthetase resulting in a pyrophosphate, an AMP and a propionyl-CoA. PW000940 ec00640 Metabolic Fatty acid biosynthesis The fatty acid biosynthesis starts from acetyl-CoA reacting either with a holo-[acp] through a 3-oxoacyl-[acp] synthase 3 resulting in an acetyl-[acp] or react with hydrogen carbonate through an ATP driven acetyl-CoA carboxylase resulting in a malonyl-CoA. Malonyl-CoA reacts with a holo-acp] through a malonyl-CoA-ACP transacylase resulting in a malonyl-[acp]. This compound can react with a KASI protein resulting in an acetyl-[acp]. A malonyl-[acp] can also react with an acetyl-[acp] through KASI and KASII or with acetyl-CoA through a beta-ketoacyl-ACP synthase to produce an acetoacetyl-[acp]. An acetoacetyl-[acp] is also known as a 3-oxoacyl-[acp]. A 3-oxoacyl-[acp] is reduced through a NDPH mediated 3-oxoacyl-[acp] reductase resulting in a (3R)-3-hydroxyacyl-[acp] (R3 hydroxydecanoyl-[acp]) which can either join the fatty acid metabolism, be dehydrated by an 3R-hydroxymyristoyl-[acp] dehydratase to produce a trans-2-enoyl-[acp] or be dehydrated by a hydroxydecanoyl-[acp] to produce a trans-delta2 decenoyl-[acp]. Trans-2-enoyl-[acp] is reduced by a NADH driven enoyl-[acp] reductase resulting in a 2,3,4-saturated fatty acyl-[acp]. This product then reacts with malonyl-[acp] through KASI and KASII resulting in a holo-acyl carrier protein and a 3- oxoacyl-[acp]. Trans-delta2 decenoyl-[acp] reacts with a 3-hydroxydecanoyl-[acp] dehydrase producing a cis-delta 3-decenoyl-ACP. This product then reacts with KASI to produce a 3-oxo-cis-delta5-dodecenoyl-[acp], which in turn is reduced by a NADPH driven 3-oxoacyl-[acp] resulting in a 3R-hydroxy cis delta5-dodecenoyl-acp. This product is dehydrated by a (3R)-hydroxymyristoyl-[acp] dehydratase resulting in a trans-delta 3- cis-delta 5-dodecenoyl-[acp] which in turn is reduced by a NADH driven enoyl-[acp] reductase resulting in a cis-delta5-dodecenoyl-acp which goes into fatty acid metabolism PW000900 ec00061 Metabolic Tetracycline biosynthesis ec00253 Microbial metabolism in diverse environments ec01120 ABC transporters ec02010 Metabolic pathways eco01100 arginine metabolism The metabolism of L-arginine starts with the acetylation of L-glutamic acid resulting in a N-acetylglutamic acid while releasing a coenzyme A and a hydrogen ion. N-acetylglutamic acid is then phosphorylated via an ATP driven acetylglutamate kinase which yields a N-acetyl-L-glutamyl 5-phosphate. This compound undergoes a NDPH dependent reduction resulting in N-acetyl-L-glutamate 5-semialdehyde. This compound reacts with L-glutamic acid through a acetylornithine aminotransferase / N-succinyldiaminopimelate aminotransferase to produce a N-acetylornithine which is then deacetylated through a acetylornithine deacetylase which yield an ornithine. L-glutamine is used to synthesize carbamoyl phosphate through the interaction of L-glutamine, water, ATP, and hydrogen carbonate. This reaction yields ADP, L-glutamic acid, phosphate, and hydrogen ion. Carbamoyl phosphate and ornithine are used to catalyze the production of citrulline through an ornithine carbamoyltransferase. Citrulline reacts with L-aspartic acid through an ATP dependent enzyme, argininosuccinate synthase to produce pyrophosphate, AMP and argininosuccinic acid. Argininosussinic acid is then lyase to produce L-arginine and fumaric acid. L-arginine can be metabolized into succinic acid by two different sets of reactions: 1. Arginine reacts with succinyl-CoA through a arginine N-succinyltransferase resulting in N2-succinyl-L-arginine while releasing CoA and Hydrogen Ion. N2-succinyl-L-arginine is then dihydrolase to produce a N2-succinyl-L-ornithine through a N-succinylarginine dihydrolase. This compound in turn reacts with oxoglutaric acid through succinylornithine transaminase resulting in L-glutamic acid and N2-succinyl-L-glutamic acid 5-semialdehyde. This compoud in turn reacts with a NAD dependent dehydrogenase resulting in N2-succinylglutamate while releasing NADH and hydrogen ion. N2-succinylglutamate reacts with water through a succinylglutamate desuccinylase resulting in L-glutamic acid and a succinic acid. The succinic acid is then incorporated in the TCA cycle 2.Argine reacts with carbon dioxide and a hydrogen ion through a biodegradative arginine decarboxylase, resulting in Agmatine. This compound is then transformed into putrescine by reacting with water and an agmatinase, and releasing urea. Putrescine can be metabolized by reaction with either l-glutamic acid or oxoglutaric acid. If putrescine reacts with L-glutamic acid, it reacts through an ATP mediated gamma-glutamylputrescine producing a hydrogen ion, ADP, phosphate and gamma-glutamyl-L-putrescine. This compound is reduced by interacting with oxygen, water and a gamma-glutamylputrescine oxidoreductase resulting in ammonium, hydrogen peroxide and 4-gamma-glutamylamino butanal. This compound is dehydrogenated through a NADP mediated reaction lead by gamma-glutamyl-gamma-aminobutaryaldehyde dehydrogenase resulting in hydrogen ion, NADPH and 4-glutamylamino butanoate. In turn, the latter compound reacts with water through a gamma-glutamyl-gamma-aminobutyrate hydrolase resulting in L-glutamic acid and Gamma aminobutyric acid. On the other hand, if putrescine reacts with oxoglutaric acid through a putrescine aminotransferase, it results in L-glutamic acid, and a 4-aminobutyraldehyde. This compound reacts with water through a NAD dependent gamma aminobutyraldehyde dehydrogenase resulting in hydrogen ion, NADH and gamma-aminobutyric acid. Gamma Aaminobutyric acid reacts with oxoglutaric acid through 4-aminobutyrate aminotransferase resulting in L-glutamic acid and succinic acid semialdehyde. This compound in turn can react with with either NADP or NAD to result in the production of succinic acid through succinate-semialdehyde dehydrogenase or aldehyde dehydrogenase-like protein yneI respectively. Succinic acid can then be integrated in the TCA cycle. L-arginine is eventua lly metabolized into succinic acid which then goes to the TCA cycle PW000790 Metabolic fatty acid elongation -- saturated This pathway shows the reactions that constitute one turn of a cycle that lengthens the chain of an acyl-ACP molecule by two carbons. The pathway is fed acetoacetyl-ACP, produces from malonyl acp, acetyl coa and 3-oxoacyl acp synthase 3. The products of multiple turns of this cycle that are drawn off to become components of fatty acid-containing compounds such as phospholipids, lipid A, and lipoproteins are the saturated fatty acids , lauric (dodecanoic), myristic (tetradecanoic), palmitic (hexadecanoic), and stearic (octadecanoic) acids. E. coli also contains unsaturated fatty acids. These are formed by a pathway that branches at the level of the 10-carbon intermediate. The final step of the cycle, the reductase, once thought to be catalyzed by two enzymes, has been shown to be catalyzed by a single enzyme, FabI, that can use either NADH or NADPH as a cofactor. However, the activity with NADH was over 17-fold higher than with NADPH, The production of acetoacetyl-acp is provided for context. Acetoacetyl-acp reacts spontaneously to produce a 3-oxoacyl acp. This compound will undergo the cycles of the elongation. The first step is converting the oxoacyl acp into a (3R) 3-hydroxyacyl(acp) through a 3-oxoacyl[acp] reductase.This second step converts the hydroxyacyl into a trans 2 enoyl acp through a protein complex conformed of a hydroxomyristoyl dehydratase and a hydroxydecanoyl dehydratase. The third step can be reached through two different reactions with a enoyl-acp reductase, involving NADPH or NADH. This leads to the production of a 2,3,4-saturated fatty acyl acp. For the final step the 2,3,4 fatty acyl acp is turned into a oxoacyl acp through a 3-oxoacyl acp synthase protein complex. This concludes one cycle. PW000798 Metabolic palmitate biosynthesis Palmitate is synthesized by stepwise condensation of C2 units to a growing acyl chain. Each elongation cycle results in the addition of two carbons to the acyl chain, and consists of four separate reactions. The pathway starts with acetyl-CoA interacting with hydrogen carbonate through an ATP driven acetyl-CoA carboxylase resulting in a phosphate, an ADP , a hydrogen ion and a malonyl-CoA. The latter compound interacts with a holo-[acp] through a malonyl-CoA-ACP transacylase resulting in a CoA and a malonyl-[acp]. This compound interacts with hydrogen ion, acetyl-CoA through a KASIII resulting in a CoA, carbon dioxide and an acetoacetyl-[acp]. The latter compound interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxybutanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a crotonyl-[acp](2). The crotonyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a butyryl-[acp](3). The butyryl-[acp] interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-hexanoyl-[acp](4). The 3-oxo-hexanoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxyhexanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans hex-2-enoyl-[acp](2). The trans hex-2-enoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a hexanoyl-[acp](3). The hexanoyl-[acp] interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-octanoyl-[acp](4). The 3-oxo-octanoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxyoctanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans oct-2-enoyl-[acp](2). The trans oct-2-enoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a octanoyl-[acp](3). The octanoyl-[acp] interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-decanoyl-[acp](4). The 3-oxo-decanoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxydecanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans-delta2-decenoyl-[acp](2). The a trans-delta2-decenoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a decanoyl-[acp](3). The decanoyl-[acp] interacts with a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-dodecanoyl-[acp](4). The 3-oxo-dodecanoyl-[acp ]interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxydodecanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans dodec-2-enoyl-[acp](2). The trans dodec-2-enoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a dodecanoyl-[acp](3). This compound can either react with water spontaneously resulting in a hydrogen ion, a holo-[acp] and a dodecanoic acid or it interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-myristoyl-[acp](4). The 3-oxo-myristoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (3R) 3-Hydroxymyristoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans tetradec-2-enoyl-[acp](2). This compound interacts with a hydrogen ion, through a NADH-driven KASI resulting in a NAD and a myristoyl-[acp]. Myristoyl-[acp] with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-palmitoyl-[acp](4). The 3-oxo-palmitoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (3R) 3-Hydroxypalmitoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans hexadecenoyl-[acp](2). The trans hexadecenoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a palmitoyl-[acp](3). Palmitoyl then reacts with water spontaneously resulting in a hydrogen ion, a holo-[acp] and palmitic acid. No integral membrane protein required for long chain fatty acid uptake has been identified in E. coli. The transport of long chain fatty acids across the cytoplasmic membrane is dependent on fatty acyl-CoA synthetase. An energised membrane is necessary for fatty acid transport and it has been suggested that uncharged fatty acids flip across the inner membrane by diffusion. PW000797 Metabolic purine nucleotides de novo biosynthesis The biosynthesis of purine nucleotides is a complex process that begins with a phosphoribosyl pyrophosphate. This compound interacts with water and L-glutamine through a amidophosphoribosyl transferase resulting in a pyrophosphate, L-glutamic acid and a 5-phosphoribosylamine. The latter compound proceeds to interact with a glycine through an ATP driven phosphoribosylamine-glycine ligase resulting in the addition of glycine to the compound. This reaction releases an ADP, a phosphate, a hydrogen ion and a N1-(5-phospho-β-D-ribosyl)glycinamide. The latter compound interacts with formic acid, through an ATP driven phosphoribosylglycinamide formyltransferase 2 resulting in a phosphate, an ADP, a hydrogen ion and a 5-phosphoribosyl-N-formylglycinamide. The latter compound interacts with L-glutamine, and water through an ATP-driven phosphoribosylformylglycinamide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion, a L-glutamic acid and a 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine. The latter compound interacts with an ATP driven phosphoribosylformylglycinamide cyclo-ligase resulting in a release of ADP, a phosphate, a hydrogen ion and a 5-aminoimidazole ribonucleotide. The latter compound interacts with a hydrogen carbonate through an ATP driven N5-carboxyaminoimidazole ribonucleotide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion and a N5-carboxyaminoimidazole ribonucleotide.The latter compound then interacts with a N5-carboxyaminoimidazole ribonucleotide mutase resulting in a 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate. This compound interacts with an L-aspartic acid through an ATP driven phosphoribosylaminoimidazole-succinocarboxamide synthase resulting in a phosphate, an ADP, a hydrogen ion and a SAICAR. SAICAR interacts with an adenylosuccinate lyase resulting in a fumaric acid and an AICAR. AICAR interacts with a formyltetrahydrofolate through a AICAR transformylase / IMP cyclohydrolase resulting in a release of a tetrahydropterol mono-l-glutamate and a FAICAR. The latter compound, FAICAR, interacts in a reversible reaction through a AICAR transformylase / IMP cyclohydrolase resulting in a release of water and Inosinic acid. Inosinic acid can be metabolized to produce dGTP and dATP three different methods each. dGTP: Inosinic acid, water and NAD are processed by IMP dehydrogenase resulting in a release of NADH, a hydrogen ion and Xanthylic acid. Xanthylic acid interacts with L-glutamine, and water through an ATP driven GMP synthetase resulting in pyrophosphate, AMP, L-glutamic acid, a hydrogen ion and Guanosine monophosphate. The latter compound is the phosphorylated by reacting with an ATP driven guanylate kinase resulting in a release of ADP and a Gaunosine diphosphate. Guanosine diphosphate can be metabolized in three different ways: 1.-Guanosine diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and a Guanosine triphosphate. This compound interacts with a reduced flavodoxin protein through a ribonucleoside-triphosphate reductase resulting in a oxidized flavodoxin a water moleculer and a dGTP 2.-Guanosine diphosphate interacts with a reduced NrdH glutaredoxin-like proteins through a ribonucleoside-diphosphate reductase 2 resulting in the release of an oxidized NrdH glutaredoxin-like protein, a water molecule and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. 3.-Guanosine diphosphate interacts with a reduced thioredoxin ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. dATP: Inosinic acid interacts with L-aspartic acid through an GTP driven adenylosuccinate synthase results in the release of GDP, a hydrogen ion, a phosphate and N(6)-(1,2-dicarboxyethyl)AMP. The latter compound is then cleaved by a adenylosuccinate lyase resulting in a fumaric acid and an Adenosine monophosphate. This compound is then phosphorylated by an adenylate kinase resulting in the release of ATP and an adenosine diphosphate. Adenosine diphosphate can be metabolized in three different ways: 1.-Adenosine diphosphate is involved in a reversible reaction by interacting with a hydrogen ion and a phosphate through a ATP synthase / thiamin triphosphate synthase resulting in a hydrogen ion, a water molecule and an Adenosine triphosphate. The adenosine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in an oxidized flavodoxin, a water molecule and a dATP 2.- Adenosine diphosphate interacts with an reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, a oxidized thioredoxin and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP 3.- Adenosine diphosphate interacts with an reduced NrdH glutaredoxin-like protein through a ribonucleoside diphosphate reductase 2 resulting in a release of a water molecule, a oxidized glutaredoxin-like protein and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP PW000910 Metabolic purine nucleotides de novo biosynthesis 1435709748 PW000960 Metabolic biotin-carboxyl carrier protein assembly The assembly of a biotin-carboxyl carrier protein starts with a biotin carboxyl carrier protein monomer interacting with an ATP, and a biotin through a biotin -acetyl-coa-carboxylase ligase resulting in the release of a hydrogen ion, an AMP, a diphosphate and a biotynylated BCCP monomer. The latter compound reacts spontaneously to create a biotinylated BCCP dimer. This compound in turn reacts with a hydrogen carbonate and an ATP driven biotin carboxylase resulting in the release of ADP, a hydrogen Ion , a phosphate and a carboxylated biotinylated BCCP dimer. This complex can be degraded by reacting with water, an acetyl0CoA, and an ATP driven acetyl-CoA carboxyltransferase resulting in the release of a hydrogen ion, a phosphate, an ADP, a malonyl-CoA and a biotynylated BCCP dimer PW002067 Metabolic palmitate biosynthesis 2 Palmitate is synthesized by stepwise condensation of C2 units to a growing acyl chain. Each elongation cycle results in the addition of two carbons to the acyl chain, and consists of four separate reactions. The pathway starts with acetyl-CoA interacting with hydrogen carbonate through an ATP driven acetyl-CoA carboxylase resulting in a phosphate, an ADP , a hydrogen ion and a malonyl-CoA. The latter compound interacts with a holo-[acp] through a malonyl-CoA-ACP transacylase resulting in a CoA and a malonyl-[acp]. This compound interacts with hydrogen ion, acetyl-CoA through a KASIII resulting in a CoA, carbon dioxide and an acetoacetyl-[acp]. The latter compound interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxybutanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a crotonyl-[acp](2). The crotonyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a butyryl-[acp](3). The butyryl-[acp] interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-hexanoyl-[acp](4). The 3-oxo-hexanoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxyhexanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans hex-2-enoyl-[acp](2). The trans hex-2-enoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a hexanoyl-[acp](3). The hexanoyl-[acp] interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-octanoyl-[acp](4). The 3-oxo-octanoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxyoctanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans oct-2-enoyl-[acp](2). The trans oct-2-enoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a octanoyl-[acp](3). The octanoyl-[acp] interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-decanoyl-[acp](4). The 3-oxo-decanoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxydecanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans-delta2-decenoyl-[acp](2). The a trans-delta2-decenoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a decanoyl-[acp](3). The decanoyl-[acp] interacts with a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-dodecanoyl-[acp](4). The 3-oxo-dodecanoyl-[acp ]interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (R) 3-Hydroxydodecanoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans dodec-2-enoyl-[acp](2). The trans dodec-2-enoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a dodecanoyl-[acp](3). This compound can either react with water spontaneously resulting in a hydrogen ion, a holo-[acp] and a dodecanoic acid or it interacts with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-myristoyl-[acp](4). The 3-oxo-myristoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (3R) 3-Hydroxymyristoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans tetradec-2-enoyl-[acp](2). This compound interacts with a hydrogen ion, through a NADH-driven KASI resulting in a NAD and a myristoyl-[acp]. Myristoyl-[acp] with a hydrogen ion, a malonyl-[acp] through a KASI resulting in a holo-[acp],carbon dioxide and a 3-oxo-palmitoyl-[acp](4). The 3-oxo-palmitoyl-[acp] interacts with a hydrogen ion through a NADPH driven 3-oxoacyl-[acyl-carrier-protein] reductase resulting in an NADP and a (3R) 3-Hydroxypalmitoyl-[acp](1). This compound is then dehydrated by a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase resulting in the release of water and a trans hexadecenoyl-[acp](2). The trans hexadecenoyl-[acp] interacts with a hydrogen ion through a NADH enoyl-[acyl-carrier-protein] reductase(NAD) resulting in NAD and a palmitoyl-[acp](3). Palmitoyl then reacts with water spontaneously resulting in a hydrogen ion, a holo-[acp] and palmitic acid. No integral membrane protein required for long chain fatty acid uptake has been identified in E. coli. The transport of long chain fatty acids across the cytoplasmic membrane is dependent on fatty acyl-CoA synthetase. An energised membrane is necessary for fatty acid transport and it has been suggested that uncharged fatty acids flip across the inner membrane by diffusion. PW002044 Metabolic propanoyl CoA degradation The degradation of propanoyl-CoA starts with propanoyl-CoA undergoing a decarboxylase reaction by reacting with hydrogen carbonate and ATP resulting in the release of a phosphate, an ADP, a hydrogen ion and an S-methylmalonyl-CoA. This compound in turn reacts through an epimerase reaction resulting in the release of a R-methylmalonyl-CoA. This compound in turn can undergo a reversible reaction through a methylmalonyl-CoA mutase resulting in the release of a succinyl-CoA. This compound can be converted back to R-methylmalonyl-CoA through a methylmalonyl-CoA mutase. Methylmalonyl-CoA can then be converted into propanoyl-CoA through a methylmalonyl CoA decarboxylase . This compound in turn reacts with a succinate through a propionyl-CoA succinate CoA transferase resulting in the release of a propanoate and a succinyl-CoA. PW002057 Metabolic purine nucleotides de novo biosynthesis 2 The biosynthesis of purine nucleotides is a complex process that begins with a phosphoribosyl pyrophosphate. This compound interacts with water and L-glutamine through a amidophosphoribosyl transferase resulting in a pyrophosphate, L-glutamic acid and a 5-phosphoribosylamine. The latter compound proceeds to interact with a glycine through an ATP driven phosphoribosylamine-glycine ligase resulting in the addition of glycine to the compound. This reaction releases an ADP, a phosphate, a hydrogen ion and a N1-(5-phospho-β-D-ribosyl)glycinamide. The latter compound interacts with formic acid, through an ATP driven phosphoribosylglycinamide formyltransferase 2 resulting in a phosphate, an ADP, a hydrogen ion and a 5-phosphoribosyl-N-formylglycinamide. The latter compound interacts with L-glutamine, and water through an ATP-driven phosphoribosylformylglycinamide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion, a L-glutamic acid and a 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine. The latter compound interacts with an ATP driven phosphoribosylformylglycinamide cyclo-ligase resulting in a release of ADP, a phosphate, a hydrogen ion and a 5-aminoimidazole ribonucleotide. The latter compound interacts with a hydrogen carbonate through an ATP driven N5-carboxyaminoimidazole ribonucleotide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion and a N5-carboxyaminoimidazole ribonucleotide(5-Phosphoribosyl-5-carboxyaminoimidazole).The latter compound then interacts with a N5-carboxyaminoimidazole ribonucleotide mutase resulting in a 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate. This compound interacts with an L-aspartic acid through an ATP driven phosphoribosylaminoimidazole-succinocarboxamide synthase resulting in a phosphate, an ADP, a hydrogen ion and a SAICAR. SAICAR interacts with an adenylosuccinate lyase resulting in a fumaric acid and an AICAR. AICAR interacts with a formyltetrahydrofolate through a AICAR transformylase / IMP cyclohydrolase resulting in a release of a tetrahydropterol mono-l-glutamate and a FAICAR. The latter compound, FAICAR, interacts in a reversible reaction through a AICAR transformylase / IMP cyclohydrolase resulting in a release of water and Inosinic acid. Inosinic acid can be metabolized to produce dGTP and dATP three different methods each. dGTP: Inosinic acid, water and NAD are processed by IMP dehydrogenase resulting in a release of NADH, a hydrogen ion and Xanthylic acid. Xanthylic acid interacts with L-glutamine, and water through an ATP driven GMP synthetase resulting in pyrophosphate, AMP, L-glutamic acid, a hydrogen ion and Guanosine monophosphate. The latter compound is the phosphorylated by reacting with an ATP driven guanylate kinase resulting in a release of ADP and a Gaunosine diphosphate. Guanosine diphosphate can be metabolized in three different ways: 1.-Guanosine diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and a Guanosine triphosphate. This compound interacts with a reduced flavodoxin protein through a ribonucleoside-triphosphate reductase resulting in a oxidized flavodoxin a water moleculer and a dGTP 2.-Guanosine diphosphate interacts with a reduced NrdH glutaredoxin-like proteins through a ribonucleoside-diphosphate reductase 2 resulting in the release of an oxidized NrdH glutaredoxin-like protein, a water molecule and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. 3.-Guanosine diphosphate interacts with a reduced thioredoxin ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. dATP: Inosinic acid interacts with L-aspartic acid through an GTP driven adenylosuccinate synthase results in the release of GDP, a hydrogen ion, a phosphate and N(6)-(1,2-dicarboxyethyl)AMP. The latter compound is then cleaved by a adenylosuccinate lyase resulting in a fumaric acid and an Adenosine monophosphate. This compound is then phosphorylated by an adenylate kinase resulting in the release of ATP and an adenosine diphosphate. Adenosine diphosphate can be metabolized in three different ways: 1.-Adenosine diphosphate is involved in a reversible reaction by interacting with a hydrogen ion and a phosphate through a ATP synthase / thiamin triphosphate synthase resulting in a hydrogen ion, a water molecule and an Adenosine triphosphate. The adenosine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in an oxidized flavodoxin, a water molecule and a dATP 2.- Adenosine diphosphate interacts with an reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, a oxidized thioredoxin and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP 3.- Adenosine diphosphate interacts with an reduced NrdH glutaredoxin-like protein through a ribonucleoside diphosphate reductase 2 resulting in a release of a water molecule, a oxidized glutaredoxin-like protein and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP PW002033 Metabolic cyanate degradation The cyanate degradation pathway begins with the transportation of cyanate into the cytosol through a cynX transporter. Once inside the cytosol cyanate reacts with hydrogen carbonate and a hydrogen ion through a cyanase resulting in the release of carbon dioxide and carbamate. Carbamate reacts spontaneously with hydrogen resulting in the release of ammonium and carbon dioxide. Carbon dioxide reacts with water through carbonic anhydrase resulting in the release of hydrogen ion and hydrogen carbonate. PW002099 Metabolic biotin-carboxyl carrier protein assembly PWY0-1264 mixed acid fermentation FERMENTATION-PWY gluconeogenesis I GLUCONEO-PWY arginine biosynthesis I ARGSYN-PWY cyanate degradation CYANCAT-PWY respiration (anaerobic) ANARESP1-PWY uridine-5'-phosphate biosynthesis PWY-5686 inosine-5'-phosphate biosynthesis I PWY-6123 fatty acid biosynthesis initiation I PWY-4381 methylmalonyl pathway PROPIONMET-PWY Specdb::CMs 2934 Specdb::CMs 38623 Specdb::CMs 150884 Specdb::CMs 1069431 Specdb::CMs 1069433 Specdb::CMs 1069434 Specdb::NmrOneD 268988 Specdb::NmrOneD 268989 Specdb::NmrOneD 268990 Specdb::NmrOneD 268991 Specdb::NmrOneD 268992 Specdb::NmrOneD 268993 Specdb::NmrOneD 268994 Specdb::NmrOneD 268995 Specdb::NmrOneD 268996 Specdb::NmrOneD 268997 Specdb::MsMs 23771 Specdb::MsMs 23772 Specdb::MsMs 23773 Specdb::MsMs 30569 Specdb::MsMs 30570 Specdb::MsMs 30571 Specdb::MsMs 2279483 Specdb::MsMs 2279484 Specdb::MsMs 2279485 Specdb::MsMs 3088909 Specdb::MsMs 3088910 Specdb::MsMs 3088911 HMDB00595 769 749 C00288 6504 HCO3 Bicarbonate Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. 22080510 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 Medinas DB, Cerchiaro G, Trindade DF, Augusto O: The carbonate radical and related oxidants derived from bicarbonate buffer. IUBMB Life. 2007 Apr-May;59(4-5):255-62. 17505962 Casey JR: Why bicarbonate? Biochem Cell Biol. 2006 Dec;84(6):930-9. 17215880 Nakajima, Fumiaki; Arima, Toshikazu; Kikuchi, Shintaro; Hirano, Hachiro. Production of alkaline hydrogen carbonate. Jpn. Kokai Tokkyo Koho (2005), 15 pp. http://hmdb.ca/system/metabolites/msds/000/000/514/original/HMDB00595.pdf?1358462101 Cyanate hydratase P00816 CYNS_ECOLI cynS http://ecmdb.ca/proteins/P00816.xml Carbamoyl-phosphate synthase large chain P00968 CARB_ECOLI carB http://ecmdb.ca/proteins/P00968.xml Phosphoribosylaminoimidazole carboxylase ATPase subunit P09029 PURK_ECOLI purK http://ecmdb.ca/proteins/P09029.xml Carbamoyl-phosphate synthase small chain P0A6F1 CARA_ECOLI carA http://ecmdb.ca/proteins/P0A6F1.xml Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta P0A9Q5 ACCD_ECOLI accD http://ecmdb.ca/proteins/P0A9Q5.xml Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha P0ABD5 ACCA_ECOLI accA http://ecmdb.ca/proteins/P0ABD5.xml Biotin carboxyl carrier protein of acetyl-CoA carboxylase P0ABD8 BCCP_ECOLI accB http://ecmdb.ca/proteins/P0ABD8.xml Carbonic anhydrase 1 P0ABE9 CYNT_ECOLI cynT http://ecmdb.ca/proteins/P0ABE9.xml Biotin carboxylase P24182 ACCC_ECOLI accC http://ecmdb.ca/proteins/P24182.xml Carbonic anhydrase 2 P61517 CAN_ECOLI can http://ecmdb.ca/proteins/P61517.xml Threonylcarbamoyl-AMP synthase P45748 TSAC_ECOLI tsaC http://ecmdb.ca/proteins/P45748.xml Putative sulfate transporter ychM P0AFR2 YCHM_ECOLI ychM http://ecmdb.ca/proteins/P0AFR2.xml 2 Adenosine triphosphate + L-Glutamine + Water + Hydrogen carbonate >2 ADP + Carbamoylphosphate + L-Glutamate +2 Hydrogen ion + Phosphate R00575 CARBPSYN-RXN Carbon dioxide + Water <> Hydrogen ion + Hydrogen carbonate RXN0-5224 Acetyl-CoA + Adenosine triphosphate + Hydrogen carbonate <> ADP + Hydrogen ion + Malonyl-CoA + Phosphate R00742 ACETYL-COA-CARBOXYLTRANSFER-RXN Cyanate + 3 Hydrogen ion + Hydrogen carbonate >2 Carbon dioxide + Ammonium 5-Aminoimidazole ribonucleotide + Adenosine triphosphate + Hydrogen carbonate > 5-Phosphoribosyl-5-carboxyaminoimidazole + ADP + Hydrogen ion + Phosphate 2 Adenosine triphosphate + L-Glutamine + Hydrogen carbonate + Water <>2 ADP + Phosphate + L-Glutamate + Carbamoylphosphate R00575 Adenosine triphosphate + Acetyl-CoA + Hydrogen carbonate <> ADP + Phosphate + Malonyl-CoA R00742 Cyanate + Hydrogen ion + Hydrogen carbonate <> Carbon dioxide + Carbamic acid R03546 R524-RXN Adenosine triphosphate + Holo-[carboxylase] + Hydrogen carbonate + Holo-[carboxylase] <> ADP + Phosphate + Carboxybiotin-carboxyl-carrier protein + Carboxybiotin-carboxyl-carrier protein R04385 Adenosine triphosphate + 5-Aminoimidazole ribonucleotide + Hydrogen carbonate <> ADP + Phosphate + 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole R07404 Adenosine triphosphate + Acetyl-CoA + Hydrogen carbonate > Hydrogen ion + Malonyl-CoA + Phosphate + ADP ACETYL-COA-CARBOXYLTRANSFER-RXN Adenosine triphosphate + L-Glutamine + Hydrogen carbonate + Water > Hydrogen ion + Carbamoylphosphate + L-Glutamate + Phosphate + ADP CARBPSYN-RXN Phosphate + Oxalacetic acid <> Phosphoenolpyruvic acid + Hydrogen carbonate PEPCARBOX-RXN Adenosine triphosphate + Hydrogen carbonate + Propionyl-CoA > Hydrogen ion + ADP + Phosphate + (S)-Methylmalonyl-CoA PROPIONYL-COA-CARBOXY-RXN Cyanate + Hydrogen carbonate + Hydrogen ion > Carbamic acid + Carbon dioxide R524-RXN Adenosine triphosphate + Hydrogen carbonate + Ammonia > ADP + Phosphate + Carbamoylphosphate + Hydrogen ion RXN-13202 Hydrogen carbonate + Hydrogen ion <> Carbon dioxide + Water RXN0-5224 5-Aminoimidazole ribonucleotide + Adenosine triphosphate + Hydrogen carbonate > Hydrogen ion + N5-Carboxyaminoimidazole ribonucleotide + ADP + Phosphate RXN0-742 2 Adenosine triphosphate + L-Glutamine + Hydrogen carbonate + Water + Ammonia + Carbamic acid + Carboxyphosphate <>2 ADP + Phosphate + L-Glutamate + Carbamoylphosphate R00575 Cyanate + Hydrogen carbonate + 2 Hydrogen ion + Carbamic acid <> Ammonia +2 Carbon dioxide R10079 L-Threonine + Adenosine triphosphate + Hydrogen carbonate <> L-Threonylcarbamoyladenylate + Pyrophosphate + Water R10463 Carbon dioxide + Water + Phosphoenolpyruvic acid <> Hydrogen ion + Oxalacetic acid + Phosphate + Hydrogen carbonate R00345 Carbon dioxide + Water > Hydrogen carbonate PW_R002430 Hydrogen carbonate + Cyanate + Hydrogen ion + Cyanate > Carbamic acid PW_R002431 Adenosine triphosphate + Pyruvic acid + Hydrogen carbonate > Adenosine diphosphate + Phosphate + Oxalacetic acid + ADP PW_R002581 Hydrogen carbonate + Water + L-Glutamine + 2 Adenosine triphosphate >2 Adenosine diphosphate + Phosphate + L-Glutamic acid +2 Hydrogen ion + Carbamoylphosphate +2 ADP + L-Glutamate PW_R002677 Acetyl-CoA + Hydrogen carbonate + Adenosine triphosphate > Adenosine diphosphate + Phosphate + Hydrogen ion + Malonyl-CoA + ADP + Malonyl-CoA PW_R002783 5-Aminoimidazole ribonucleotide + Hydrogen carbonate + Adenosine triphosphate > N5-Carboxyaminoimidazole ribonucleotide + Adenosine diphosphate + Phosphate +2 Hydrogen ion + N5-Carboxyaminoimidazole ribonucleotide + ADP PW_R003417 a biotinylated [BCCP dimer] + Adenosine triphosphate + Hydrogen carbonate > carboxylated-biotinylated [BCCP dimer] + Hydrogen ion + ADP + Phosphate PW_R006044 Carbon dioxide + Water > Hydrogen ion + Hydrogen carbonate PW_R006122 L-Threonine + Adenosine triphosphate + Hydrogen carbonate <> L-Threonylcarbamoyladenylate + Pyrophosphate + Water Cyanate + Hydrogen ion + Hydrogen carbonate <> Carbon dioxide + Carbamic acid Acetyl-CoA + Adenosine triphosphate + Hydrogen carbonate <> ADP + Hydrogen ion + Malonyl-CoA + Phosphate Carbon dioxide + Water + Phosphoenolpyruvic acid <> Hydrogen ion + Oxalacetic acid + Phosphate + Hydrogen carbonate 2 Adenosine triphosphate + L-Glutamine + Water + Hydrogen carbonate >2 ADP + Carbamoylphosphate + L-Glutamate +2 Hydrogen ion + Phosphate Adenosine triphosphate + 5 5-Aminoimidazole ribonucleotide + Hydrogen carbonate <> ADP + Phosphate +5 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole Cyanate + Hydrogen ion + Hydrogen carbonate <> Carbon dioxide + Carbamic acid Acetyl-CoA + Adenosine triphosphate + Hydrogen carbonate <> ADP + Hydrogen ion + Malonyl-CoA + Phosphate Acetyl-CoA + Adenosine triphosphate + Hydrogen carbonate <> ADP + Hydrogen ion + Malonyl-CoA + Phosphate 2 Adenosine triphosphate + L-Glutamine + Water + Hydrogen carbonate >2 ADP + Carbamoylphosphate + L-Glutamate +2 Hydrogen ion + Phosphate