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Showing 21 - 30 of 110297 pathways
PathBank ID Pathway Chemical Compounds Proteins

SMP0012089

Pw012952 View Pathway
Metabolite

Photosynthesis

Arabidopsis thaliana
Photosynthesis involves the transfer and harvesting of energy from sunlight and the fixation of carbon dioxide into carbohydrates. This process occurs in higher plants, including Arabidopsis thaliana. Oxygenic photosynthesis requires water, which acts as an electron donor molecule. The reactions which involve the trapping of sunlight are known as "light reactions", and result in the production of NADPH, adenosine triphosphate, and molecular oxygen. The "dark reactions" are known as the Calvin cycle, and involve the use of the products of the light reactions to fix carbon dioxide and produce carbohydrates. Photosynthesis begins with photosystem II, located in the thylakoid membrane within chloroplasts, which captures light energy to transfer electrons from water to plastoquinone. This process generates oxygen as well as a proton gradient used to synthesize ATP. The D1/D2 (psbA/psbD) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. Next, the cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI). Plastoquinol shuttles electrons from PSII to cytochrome b6-f complex. Plastocyanin shuttles electrons from cytochrome b6-f complex to PSI. Photosystem I is a plastocyanin-ferredoxin oxidoreductase which uses light energy to transfer an electron from the donor P700 chlorophyll pair to the electron acceptors A0, A1, FX, FA and FB in turn. The function of PSI is to produce the NADPH necessary for the reduction of CO2 in the Calvin-Benson cycle. Finally, the proton gradient allows ATPase to synthesize ATP from ADP. The light-independent Calvin-Benson cycle consist of nine reactions that take place in the chloroplast stroma. Beginning with the enzyme RuBisCO, D-ribulose-1,5-bisphosphate is converted into 3-phosphoglyceric acid. It requires magnesium ion as a cofactor. Next, chloroplastic glyceraldehyde 3-phosphate dehydrogenase catalyzes the conversion of glyceric acid 1,3-biphosphate into D-glyceraldehyde 3-phosphate. Then triose-phosphate isomerase catalyzes the conversion of D-glyceraldehyde 3-phosphate into dihydroxyacetone phosphate. Next, the enzyme fructose-bisphosphate aldolase catalyzes the conversion of dihydroxyacetone phosphate into fructose 1,6-bisphosphate. Then fructose-1,6-bisphosphatase catalyzes the conversion of fructose 1,6-bisphosphate into fructose-6-phosphate. It requires magnesium ion as a cofactor. Next, transketolase catalyzes the conversion of fructose-6-phosphate into xylulose 5-phosphate. It requires a divalent metal cation and thiamine diphosphate as cofactors. Then the enzyme ribulose-phosphate 3-epimerase is catalyzes the interconverson of xylulose 5-phosphate and D-ribulose 5-phosphate. Lastly, phosphoribulokinase catalyzes the conversion of D-ribulose 5-phosphate to regenerate D-ribulose-1,5-bisphosphate. An alternative pathway intersects the Calvin-Benson cycle providing another route to synthesize D-ribulose 5-phosphate and D-xylulose 5-phosphate, which both feed back into the main cycle, from dihydroxyacetone phosphate. This subpathway begins with the predicted enzyme sedoheptulose-1,7-bisphosphate aldolase theorized to catalyze the converson of glycerone phosphate and D-erythrose 4-phosphate into sedoheptulose-1,7-bisphosphate. Next, sedoheptulose-1,7-bisphosphatase catalyzes the conversion of sedoheptulose-1,7-bisphosphate into D-sedoheptulose 7-phosphate. Next, transketolase catalyzes the converson of D-sedoheptulose 7-phosphate into D-ribose 5-phosphate and D-xylulose 5-phosphate (which feeds back into the main cycle). Lastly, ribose-5-phosphate isomerase is the probable enzyme that catalyzes the interconverson of D-ribose 5-phosphate and D-ribulose 5-phosphate. D-ribulose 5-phosphate feeds back into the main cycle.

Metabolic

SMP0012094

Pw012957 View Pathway
Metabolite

Calvin-Benson Cycle

Arabidopsis thaliana
Photosynthesis involves the transfer and harvesting of energy from sunlight and the fixation of carbon dioxide into carbohydrates. This process occurs in higher plants, including Arabidopsis thaliana. Oxygenic photosynthesis requires water, which acts as an electron donor molecule. The reactions which involve the trapping of sunlight are known as "light reactions", and result in the production of NADPH, adenosine triphosphate, and molecular oxygen. The "dark reactions" are known as the Calvin cycle, and involve the use of the products of the light reactions to fix carbon dioxide and produce carbohydrates. The light-independent Calvin-Benson cycle consist of nine reactions that take place in the chloroplast stroma. Beginning with the enzyme RuBisCO, D-ribulose-1,5-bisphosphate is converted into 3-phosphoglyceric acid. It requires magnesium ion as a cofactor. Next, chloroplastic glyceraldehyde 3-phosphate dehydrogenase catalyzes the conversion of glyceric acid 1,3-biphosphate into D-glyceraldehyde 3-phosphate. Then triose-phosphate isomerase catalyzes the conversion of D-glyceraldehyde 3-phosphate into dihydroxyacetone phosphate. Next, the enzyme fructose-bisphosphate aldolase catalyzes the conversion of dihydroxyacetone phosphate into fructose 1,6-bisphosphate. Then fructose-1,6-bisphosphatase catalyzes the conversion of fructose 1,6-bisphosphate into fructose-6-phosphate. It requires magnesium ion as a cofactor. Next, transketolase catalyzes the conversion of fructose-6-phosphate into xylulose 5-phosphate. It requires a divalent metal cation and thiamine diphosphate as cofactors. Then the enzyme ribulose-phosphate 3-epimerase is catalyzes the interconverson of xylulose 5-phosphate and D-ribulose 5-phosphate. Lastly, phosphoribulokinase catalyzes the conversion of D-ribulose 5-phosphate to regenerate D-ribulose-1,5-bisphosphate. An alternative pathway intersects the Calvin-Benson cycle providing another route to synthesize D-ribulose 5-phosphate and D-xylulose 5-phosphate, which both feed back into the main cycle, from dihydroxyacetone phosphate. This subpathway begins with the predicted enzyme sedoheptulose-1,7-bisphosphate aldolase theorized to catalyze the converson of glycerone phosphate and D-erythrose 4-phosphate into sedoheptulose-1,7-bisphosphate. Next, sedoheptulose-1,7-bisphosphatase catalyzes the conversion of sedoheptulose-1,7-bisphosphate into D-sedoheptulose 7-phosphate. Next, transketolase catalyzes the converson of D-sedoheptulose 7-phosphate into D-ribose 5-phosphate and D-xylulose 5-phosphate (which feeds back into the main cycle). Lastly, ribose-5-phosphate isomerase is the probable enzyme that catalyzes the interconverson of D-ribose 5-phosphate and D-ribulose 5-phosphate. D-ribulose 5-phosphate feeds back into the main cycle.

Metabolic

SMP0121012

Pw122279 View Pathway
Metabolite

Kidney Function - Distal Convoluted Tubule

Homo sapiens
The distal convoluted tubule of the nephron is the part of the kidney between the loop of henle and the collecting duct. When renin is released from the kidneys, it causes the activation of angiotensin I in the blood circulation which is cleaved to become angiotensin II. Angiotensin II stimulates the release of aldosterone from the adrenal cortex and release of vasopressin from the posterior pituitary gland. When in the circulation, vasopressin eventually binds to receptors on epithelial cells in the distal convoluted tubule. This causes vesicles that contain aquaporins to fuse with the plasma membrane. Aquaporins are proteins that act as water channels once they have bound to the plasma membrane. As a result, the permeability of the distal convoluted tubule changes to allow for water reabsorption back into the blood circulation. In addition, sodium, chlorine, and calcium are also reabsorbed back into the systemic circulation via their respective channels and exchangers. However, aldosterone is a major regulator of the reabsorption of these ions as well, as it changes the permeability of the distal convoluted tubule to these ions. As a result, a high concentration of sodium, chlorine, and calcium in the blood vessels occurs. The reabsorption of ions and water increases blood fluid volume and blood pressure.

Physiological

SMP0002334

Pw002417 View Pathway
Metabolite

Tetrahydrofolate Biosynthesis

Saccharomyces cerevisiae
The biosynthesis of tetrahydrofolate begins with guanosine triphosphate interacting with water through GTP-cyclohydrlase resulting in the release of a formic acid, a hydrogen ion and a dihydroneopterin triphosphate. The latter compound then reacts with water in a spontaneous reaction resulting in the release of pyrophosphate, hydrogen ion and dihydroneopterinphosphate. Dihydroneopterin phosphate then reacts spontaneously with water resulting in the release of phosphate and 7,8-dihydroneopterin. This compound reacts wuth a folic acid synthesis enzyme resulting in the release of glycoaldehyde and 6-hydroxymethyl-7,8-dihydropterin. The latter compound is then diphosphorylated through an ATP driven folic acid synthesis resulting in the release of AMP, a hydrogen ion and 6-hydroxymethyl-7,8-dihydropterin diphosphate. This compound reacts with p-Aminobenzoic acid that is release from chorismate, the reaction happens through a folic acid synthesis resulting in the pyrophosphate and 7,8-dihydropteric acid. The latter compound reacts with glutamic acid through an ATP driven folic acid synthesis 3 resulting in the release of hydrogen ion, a phosphate, ADP and a 7,8-dihydrofolate monoglutamate. The latter compound reacts with a hydrogen ion through a NADPH through a dihydrofolate reductase resulting in the release of NADP and tetrahydrofolate. This compound can also be a result of 5,10 methenyltetrahydrofolic acid reacting with water through a mitochondrials c1-tetrahydrofolate synthase which releases a 10-formyltetrahydrofolate. This compound in turn reacts with a 5-phosphoribosyl-N-formylglycinamide through a glycinamide ribotide transformylase resulting in the release of a tetrahydrofolate and a 5'phosphoribosyl-N-fromylglycinamide.

Metabolic

SMP0002304

Pw002377 View Pathway
Metabolite

TCA Cycle

Saccharomyces cerevisiae
Citric acid cycle (also known as tricarboxylic acid cycle (TCA) and Krebs cycle) contains series of reactions that involved enzyme catalyzation which are essential for all living cells that require oxygen for cellular respiration. In mitochondria (for eukaryotes), TCA cycle begins with acetyl-CoA and oxaloacetic acid (oxaloacetate) be catalyzed to form citric acid (citrate) by citrate synthase 3. Then, 3-isopropylmalate dehydratase with cofactor 4Fe-4S can catalyze citrate to form cis-aconitic acid as the intermediate compound and catalyze cis-aconitic acid to form isocitric acid. Many TCA cycle intermediates are the precursors for other molecules' synthesis; and NADH (from NAD+) is the major energy that is produced by oxidative steps of the TCA cycle.

Metabolic

SMP0002114

Pw002102 View Pathway
Metabolite

Ribose Degradation

Escherichia coli
Escherichia coli can utilize the monosaccharide D-ribose as the sole source of carbon and energy for the cell. A high-affinity ABC transport system transports D-ribose into the cell as unphosphorylated beta-D-ribopyranose. Ribose pyranase converts between the furanose and pyranose forms of beta-D-ribose. D-ribofuranose converts between the alpha and beta anomers quickly and spontaneously. Ribokinase converts D-ribose to the pentose phosphate pathway intermediate, D-ribose 5-phosphate, which can enter the central metabolism pathways to meet the cells needs.

Metabolic

SMP0000958

Pw000941 View Pathway
Metabolite

Starch and Sucrose Metabolism

Escherichia coli
The metabolism of starch and sucrose begins with D-fructose interacting with a D-glucose in a reversible reaction through a maltodextrin glucosidase resulting in a water molecule and a sucrose. D-fructose is phosphorylated through an ATP driven fructokinase resulting in the release of an ADP, a hydrogen ion and a Beta-D-fructofuranose 6-phosphate. This compound can also be introduced into the cytoplasm through either a mannose PTS permease or a hexose-6-phosphate:phosphate antiporter. The Beta-D-fructofuranose 6-phosphate is isomerized through a phosphoglucose isomerase resulting in a Beta-D-glucose 6-phosphate. This compound can also be incorporated by glucose PTS permease or a hexose-6-phosphate:phosphate antiporter. The beta-D-glucose 6 phosphate can also be produced by a D-glucose being phosphorylated by an ATP-driven glucokinase resulting in a ADP, a hydrogen ion and a Beta-D-glucose 6 phosphate. The beta-D-glucose can produce alpha-D-glucose-1-phosphate by two methods: 1.-Beta-D-glucose is isomerized into an alpha-D-Glucose 6-phosphate and then interacts in a reversible reaction through a phosphoglucomutase-1 resulting in a alpha-D-glucose-1-phosphate. 2.-Beta-D-glucose interacts with a putative beta-phosphoglucomutase resulting in a Beta-D-glucose 1-phosphate. Beta-D-glucose 1-phosphate can be incorporated into the cytoplasm through a glucose PTS permease. This compound is then isomerized into a Alpha-D-glucose-1-phosphate The beta-D-glucose can cycle back into a D-fructose by first interacting with D-fructose in a reversible reaction through a Polypeptide: predicted glucosyltransferase resulting in the release of a phosphate and a sucrose. The sucrose then interacts in a reversible reaction with a water molecule through a maltodextrin glucosidase resulting in a D-glucose and a D-fructose. Alpha-D-glucose-1-phosphate can produce glycogen in by two different sets of reactions: 1.-Alpha-D-glucose-1-phosphate interacts with a hydrogen ion and an ATP through a glucose-1-phosphate adenylyltransferase resulting in a pyrophosphate and an ADP-glucose. The ADP-glucose then interacts with an amylose through a glycogen synthase resulting in the release of an ADP and an Amylose. The amylose then interacts with 1,4-α-glucan branching enzyme resulting in glycogen 2.- Alpha-D-glucose-1-phosphate interacts with amylose through a maltodextrin phosphorylase resulting in a phosphate and a glycogen. Alpha-D-glucose-1-phosphate can also interacts with UDP-galactose through a galactose-1-phosphate uridylyltransferase resulting in a galactose 1-phosphate and a Uridine diphosphate glucose. The UDP-glucose then interacts with an alpha-D-glucose 6-phosphate through a trehalose-6-phosphate synthase resulting in a uridine 5'-diphosphate, a hydrogen ion and a Trehalose 6- phosphate. The latter compound can also be incorporated into the cytoplasm through a trehalose PTS permease. Trehalose interacts with a water molecule through a trehalose-6-phosphate phosphatase resulting in the release of a phosphate and an alpha,alpha-trehalose.The alpha,alpha-trehalose can also be obtained from glycogen being metabolized through a glycogen debranching enzyme resulting in a the alpha, alpha-trehalose. This compound ca then be hydrated through a cytoplasmic trehalase resulting in the release of an alpha-D-glucose and a beta-d-glucose. Alpha-D-glucose-1-phosphate can be metabolized to produce dTDP-Beta-L-rhamnose. This happens by Alpha-D-glucose-1-phosphate reacting with a dTTP and a hydrogen ion through a dTDP-glucose pyrophosphorylase resulting in the release of a pyrophosphate and a dTDP-alpha-D-glucose. This coumpound in turn reacts with a dTDP-glucose 4,6-dehydratase resulting in the release of a water molecule and a dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose. The latter compound reacts with a dTDP-4-dehydrorhamnose 3,5-epimerase resulting in the release of a dTDP-4-dehydro-beta-L-rhamnose. This compound in turn gets metabolized by a NADPH dependent dTDP-4-dehydrorhamnose reductase resulting in a release of a NADP and a dTDP-beta-L-rhamnose Glycogen is then metabolized by reacting with a phosphate through a glycogen phosphorylase resulting in a alpha-D-glucose-1-phosphate and a dextrin. The dextrin is then hydrated through a glycogen phosphorylase-limit dextrin α-1,6-glucohydrolase resulting in the release of a debranched limit dextrin and a maltotetraose. This compound can also be incorporated into the cytoplasm through a maltose ABC transporter. The maltotetraose interacts with a phosphate through a maltodextrin phosphorylase releasing a alpha-D-glucose-1-phosphate and a maltotriose. The maltotriose can also be incorporated through a maltose ABC transporter. The maltotriose can then interact with water through a maltodextrin glucosidase resulting in a D-glucose and a D-maltose. D-maltose can also be incorporated through a maltose ABC transporter The D-maltose can then interact with a maltotriose through a amylomaltase resulting in a maltotetraose and a D-glucose. The D-glucose is then phosphorylated through an ATP driven glucokinase resulting in a hydrogen ion, an ADP and a Beta-D-glucose 6-phosphate

Metabolic

SMP0000974

Pw000958 View Pathway
Metabolite

Secondary Metabolites: Methylerythritol Phosphate and Polyisoprenoid Biosynthesis

Escherichia coli
The biosynthesis of isoprenoids starts with a D-glyceraldehyde 3-phosphate interacting with a hydrogen ion through a 1-deoxyxylulose-5-phosphate synthase resulting in a carbon dioxide and 1-Deoxy-D-xylulose. The latter compound then interacts with a hydrogen ion through a NADPH driven 1-deoxy-D-xylulose 5-phosphate reductoisomerase resulting in a NADP and a 2-C-methyl-D-erythritol 4-phosphate. The latter compound then interacts with a cytidine triphosphate and a hydrogen ion through a 4-diphosphocytidyl-2C-methyl-D-erythritol synthase resulting in a pyrophosphate and a 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound is then phosphorylated through an ATP driven 4-diphosphocytidyl-2-C-methylerythritol kinase resulting in a release of an ADP, a hydrogen ion and a 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound then interacts with a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase resulting in the release of a 2-C-methyl-D-erythritol-2,4-cyclodiphosphate resulting in the release of a cytidine monophosphate and 2-C-methyl-D-erythritol-2,4-cyclodiphosphate. The latter compound then interacts with a reduced flavodoxin through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase resulting in the release of a water molecule, a hydrogen ion, an oxidized flavodoxin and a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The compound 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate can interact with an NADPH,a hydrogen ion through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase resulting in a NADP, a water molecule and either a Dimethylallylpyrophosphate or a Isopentenyl pyrophosphate. These two last compounds can be are isomers that can be produced through a isopentenyl diphosphate isomerase. Dimethylallylpyrophosphate interacts with the isopentenyl pyrophosphate through a geranyl diphosphate synthase / farnesyl diphosphate synthase resulting in a pyrophosphate and a geranyl--PP. The latter compound interacts with a Isopentenyl pyrophosphate through a geranyl diphosphate synthase / farnesyl diphosphate synthase resulting in the release of a pyrophosphate and a farnesyl pyrophosphate. The latter compound interacts with isopentenyl pyrophosphate either through a undecaprenyl diphosphate synthase resulting in a release of a pyrophosphate and a di-trans,octa-cis-undecaprenyl diphosphate or through a octaprenyl diphosphate synthase resulting in a pyrophosphate and an octaprenyl diphosphate

Metabolic

SMP0002039

Pw002025 View Pathway
Metabolite

Oleic Acid Oxidation

Escherichia coli
The process of oleic acid B-oxidation starts with a 2-trans,5-cis-tetradecadienoyl-CoA that can be either be processed by an enoyl-CoA hydratase by interacting with a water molecules resulting in a 3-hydroxy-5-cis-tetradecenoyl-CoA, which can be oxidized in the fatty acid beta-oxidation. On the other hand 2-trans,5-cis-tetradecadienoyl-CoA can become a 3-trans,5-cis-tetradecadienoyl-CoA through a isomerase. This results interact with a water molecule through a acyl-CoA thioesterase resulting in a hydrogen ion, a coenzyme A and a 3,5-tetradecadienoate

Metabolic

SMP0000939

Pw000922 View Pathway
Metabolite

Sulfur Metabolism

Escherichia coli
The sulfur metabolism pathway starts in three possible ways. The first is the uptake of sulfate through an active transport reaction via a sulfate transport system containing an ATP-binding protein which hydrolyses ATP. Sulfate is converted by the sulfate adenylyltransferase enzymatic complex to adenosine phosphosulfate through the addition of adenine from a molecule of ATP, along with one phosphate group. Adenosine phosphosulfate is further converted to phoaphoadenosine phosphosulfate through an ATP hydrolysis and dehydrogenation reaction by the adenylyl-sulfate kinase. Phoaphoadenosine phosphosulfate is finally dehydrogenated and converted to sulfite by phosphoadenosine phosphosulfate reductase. This reaction requires magnesium, and adenosine 3',5'-diphosphate is the bi-product. A thioredoxin is also oxidized. Sulfite can also be produced from the dehydrogenation of cyanide along with the conversion of thiosulfate to thiocyanate by the thiosulfate sulfurtransferase enzymatic complex. Sulfite next undergoes a series of reactions that lead to the production of pyruvic acid, which is a precursor for pathways such as gluconeogenesis. The first reaction in this series is the conversion of sulfite to hydrogen sulfide through hygrogenation and the deoxygenation of sulfite to form a water molecule. The reaction is catalyzed by the sulfite reductase [NADPH] flavoprotein alpha and beta components. Siroheme, 4Fe-4S, flavin mononucleotide, and FAD function as cofactors or prosthetic groups. Hydrogen sulfide next undergoes dehydrogenation in a reversible reaction to form L-Cysteine and acetic acid, via the cysteine synthase complex and the coenzyme pyridoxal 5'-phosphate. L-Cysteine is dehydrogenated and converted to 2-aminoacrylic acid (a bronsted acid) and hydrogen sulfide(which may be reused) by a larger enzymatic complex composed of cysteine synthase A/B, protein malY, cystathionine-β-lyase, and tryptophanase, along with the coenzyme pyridoxal 5'-phosphate. 2-aminoacrylic acid isomerizes to 2-iminopropanoate, which along with a water molecule and a hydrogen ion is lastly converted to pyruvic acid and ammonium in a spontaneous fashion. The second possible initial starting point for sulfur metabolism is the import of taurine(an alternate sulfur source) into the cytoplasm via the taurine ABC transporter complex. Taurine, oxoglutaric acid, and oxygen are converted to sulfite by the alpha-ketoglutarate-dependent taurine dioxygenase. Carbon dioxide, succinic acid, and aminoacetaldehyde are bi-products of this reaction. Sulfite next enters pyruvic acid synthesis as already described. The third variant of sulfur metabolism starts with the import of an alkyl sulfate into the cytoplasm via an aliphatic sulfonate ABC transporter complex which hydrolyses ATP. The alkyl sulfate is dehydrogenated and along with oxygen is converted to sulfite and an aldehyde by the FMNH2-dependent alkanesulfonate monooxygenase enzyme. Water and flavin mononucleotide(which is used in a subsequent reaction as a prosthetic group) are also produced. Sulfite is next converted to pyruvic acid by the process already described.

Metabolic
Showing 21 - 30 of 110297 pathways