Pathways

PathWhiz ID Pathway Meta Data

PW122514

Pw122514 View Pathway
metabolic

Propionate

Bacteroides vulgatus

PW122512

Pw122512 View Pathway
metabolic

Phenylalanine Metabolism

Danio rerio
Phenylalanine is one of the 22 proteinogenic amino acids present in organisms, specifically its L-isomer. It is an alpha-amino acid, meaning the side chain is present on the first, or alpha, carbon of the compound. In this case, the side chain is a benzyl group, and as this is inert and hydrophobic, leading the amino acid itself to be neutral and non-polar. Phenylalanine is also an essential amino acid in zebrafish, meaning that they can not be synthesized de novo by the organism, and instead must be obtained from food sources, including supplements if necessary. L-henylalanine can come from phenylalanine biosynthesis, and can be converted by phenylalanine hydroxylase to L-tyrosine. L-tyrosine can then be used in tyrosine metabolism. L-phenylalanine can also be converted to and from phenylpyruvic acid in the mitochondria by either aspartae aminotransferase or tyrosine transaminase. It can also be converted to phenylpyruvic acid in a non-reversible reaction catalyzed by amine oxidase. Phenylpyruvic acid can be converted to ortho-hydroxyphenylacetc acid by 4-hydroxyphenylpyruvate dioxygenase which removes a carbon atom from the structure and alters some bonds. It can also be reversibly converted to enol-phenylpyruvate by phenylpyruvate tautomerase. Finally, L-phenylalanine can be converted to phenylethylamine by aromatic-L-amino-acid decarboxylase, which removes a carbon dioxide molecule. From here, phenylethylamine is converted reversibly to phenylacetaldehyde by either a primary amine oxidase or monoamine oxidase. Phenylacetaldehyde is then converted reversibly to phenylacetic acid by aldehyde dehydrogenase, forming the final product of the pathway.

PW122511

Pw122511 View Pathway
metabolic

Nicotinate and Nicotinamide Metabolism

Xenopus laevis
Nicotinate, also called nicotinic acid or niacin, is a form of vitamin B3 that is primarily obtained through whole and processed, as well as fortified foods. Another form of vitamin B3 is nicotinamide or niacinamide, which is also obtained in trace amounts from dietary sources. Nicotinamide is critically important in the structure of NAD(H) and NADP(H), which are both used as coenzymes in oxidation-reduction reactions such as the citric acid cycle and the electron transport chain. L-aspartic acid from the aspartate metabolism pathway can be converted into iminoaspartic acid by a putative L-aspartate dehydrogenase, removing a hydrogen ion from it. After this, a quinolinate synthase, whose protein is currently unknown in Xenopus laevis, converts it to quinolinic acid, which can also be obtained from the tryptophan metabolism pathway. Quinolinic acid can interact with carboxylating nicotinate-nculeotide pyrophosphorylase, which converts it to nicotinate beta-D-ribonucleotide. This can then be converted to nicotinate D-ribonucleoside by a cytosolic 5'-nucleotidase, adding a water molecule and removing a phosphate. This nicotinate D-ribonucleoside can then be converted back to nicotinate beta-D-ribonucleotide by a nicotinamide riboside kinase, or converted to and from nicotinic acid by purine nucleoside phosphorylase. Nicotinate beta-D-ribonucleotide can alternatively be converted straight to and from nicotinic acid by nicotinate phosphoribosyltransferase. Nicotinate beta-D-ribonucleotide can also be converted to and from nicotinic acid adenine dinucleotide by nicotinamide-nucleotide adenylyltransferase. This can then be converted back by a nucleotide diphosphatase. The nicotinic acid adenine dinucleotide is then converted to NAD by glutamine-dependent NAD synthetase. NAD can be converted to NADP by NAD kinase 2 in the mitochondria, which can be converted to and from NAD by a NAD+ transhydrogenase, also in the mitochondria. NAD can also be converted to nicotinamide ribotide by a nucleotide diphosphatase, which can then be converted to and from NAD by nicotinamide-nucleotide adenylyltransferase. Nicotinamide ribotide can form nicotinamide riboside via catalysis by a cytosolic purine 5'-nucleotidase, which can be returned to nicotinamide ribotide by a ribon. It can also be converted to nicotinamide by a purine nucleoside phosphorylase, which removes ribose 1-phosphate from it. Nicotinamide ribotide can also be directly converted to and from nicotinamide by nicotinamide phosphoribosyltransferase which removes phosphoribosyl pyrophosphate from it. Additionally, NADP and nicotinic acid can form nicotinamide and nicotinic acid adenine dinucleotide phosphate, catalyzed by 2'-phospho-cyclic-ADP-ribose transferase. Nicotinamide can finally have a methyl group added to it by nicotinamide N-methyltransferase, forming 1-methylnicotinamide, which can then interact with aldehyde oxidase 5, forming either N1-methyl-4-pyridone-3-carboxamide or N1-methyl-2-pyridone-5-carboxamide, which are the final products of this pathway.

PW122510

Pw122510 View Pathway
metabolic

Lipoic Acid Metabolism

Xenopus laevis
Lipoic acid is a compound derived from octanoic acid that is used as a cofactor in at least five enzyme systems, and is present in at least small amounts in most foods.However, these sources are covalently bound to other molecules, and aren't usable. Due to this, supplements of lipoic acid are synthesized chemically rather than obtained through natural sources. This pathway takes place entirely in the mitochondria, and begins with octanoyl bound to an acyl-carrier protein (ACP) from fatty acid biosynthesis. It can interact with lipoyl synthase to form lipoyl-ACP, after which it interacts with putative lipoyl transease in order to form protein N6-(lipoyl)lysine. Octanoyl-ACP can also interact with those enzymes in the opposite order, first the putative lipoyltransferase 2, forming protein N6-(octanoyl)lysine, and then lipoyl synthase to form protein N6-(lipoyl)lysine. At the same time, lipoic acid can form lipoyl-AMP after a reaction that exists in other organisms, and is likely present in Xenopus laevis, and the lipoyl-AMP can then interact with lipoyltransferase 1 to form the protein N6-(lipoyl)lysine. As all branches of the pathway produce this, it is the final and only product of this pathway.

PW122509

Pw122509 View Pathway
metabolic

Lipoic Acid Metabolism

Danio rerio
Lipoic acid is a compound derived from octanoic acid that is used as a cofactor in at least five enzyme systems, and is present in at least small amounts in most foods.However, these sources are covalently bound to other molecules, and aren't usable. Due to this, supplements of lipoic acid are synthesized chemically rather than obtained through natural sources. This pathway takes place entirely in the mitochondria, and begins with octanoyl bound to an acyl-carrier protein (ACP) from fatty acid biosynthesis. It can interact with lipoyl synthase to form lipoyl-ACP, after which it interacts with putative lipoyl transease in order to form protein N6-(lipoyl)lysine. Octanoyl-ACP can also interact with those enzymes in the opposite order, first the putative lipoyltransferase 2, forming protein N6-(octanoyl)lysine, and then lipoyl synthase to form protein N6-(lipoyl)lysine. At the same time, lipoic acid can form lipoyl-AMP after a reaction that likely exists in Danio rerio but is unknown, and the lipoyl-AMP can then interact with lipoyltransferase 1 to form the protein N6-(lipoyl)lysine. As all branches of the pathway produce this, it is the final and only product of this pathway.

PW122506

Pw122506 View Pathway
metabolic

Camalexin Biosynthesis

Arabidopsis thaliana
Camalexin is a compound produced by Arabadopsis thaliana, used in plant defense. Its accumulation is induced by contact with parasites, and it inhibits the growth of those parasites. Synthesis of camalexin starts with L-tryptophan, which reacts using tryptophan N-monooxygenases 1 and 2 to form N-hydroxy-L-tryptophan. This then reacts using the same enzyme to form N,N-dihydroxy-L-tryptophan, which spontaneously forms (E)-indol-3-ylacetaldoxime. (E)-indol-3-ylacetaldoxime reversibly reacts with a indoleacetaldoxime dehydratase enzyme to form (Z)-indol-3-ylacetaldoxime, its isomer. The isomer then loses a water molecule via indoleacetaldoxime dehydratase again, forming 3-indoleacetonitrile. Another reaction with indoleacetaldoxime dehydratase forms 2-hydroxy-2-(1H-indol-3-yl0acetonitrile, which then reacts one final time with the indoleacetaldoxime dehydratase enzyme to lose a water molecule and form dehydro(indole-3-yl)acetonitrile. At this point, a glutatione molecule is added using glutatione S-transferase F6 to form (glutation-S-yl)(1H-indol-3-yl)acetonitrile. A water molecule is added by gamma-glutamyl peptidases 1 and 3, as well as glutathione hydrolase 3, forming L-glutamic acid as a side product, as well as (L-cysteinylglycin-S-yl)(1H-indol-3-yl)acetonitrile. An unknown enzyme then catalyzes a reaction that adds a water molecule and removes a glycine, forming 2-(cystein-S-yl)-2-(1H-indol-3-yl)-acetonitrile. Then, in a reaction using bifunctional dihydrocamalexate synthase/camalexin synthase, an oxygen molecule is added, a hydrogen ion, hydrogen cyanide molecule and water molecule are removed, and (R)-dihydrocamalexate is formed. Finally, the same enzyme catalyzes the formation of camalexin, the final product of this pathway.

PW122504

Pw122504 View Pathway
metabolic

Terpenoid Backbone Biosynthesis

Arabidopsis thaliana
Terpenoids are a class of organic compounds made up of 5 carbon isoprene units. There are two pathways, melvalonate and MEP/DOXP, that synthesize the terpenoid backbone components. Both of these create isopentenyl pyrophosphate, which may then react using isopentenyl diphosphate isomerase in the chloroplast to form dimethylallylprophosphate. This molecule is also produced by the MEP/DOXP pathway. Isopentenyl pyrophosphate and dimethylallylprophosphate can react with geranylphosphate synthase in the mitochondrion to form geranyl-pyrophosphate, the main compound used in monoterpenoid biosynthesis. Geranyl-pyrophosphate may also react again with isopentenyl pyrophosphate using solanesyl diphosphate synthase 2 in the chloroplast to form solanesyl pyrophosphate, a potential end product of this pathway. Alternately, they can react with (2E,6E)-farnesyl diphosphate synthase, also in the mitochondrion, to form farnesyl phosphate. Farnesyl pyrophosphate may then be used as the main precursor in the sesquiterpenoid and triterpenoid biosynthesis pathways. It may also react with geranylgeranyl pyrophosphate 6 in the mitochondrion to form geranylgeranyl pyrophosphate. Geranylgeranyl pyrophosphate can react with isopentenyl pyrophosphate, catalyzed by solanesyl diphosphate syntahse 2, again in the chloroplast, to form solanesyl pyrophosphate. Aside this reaction, it can be converted by geranylgeranyl dehydrogenase in the chloroplast to form phytyl pyrophosphate, another end product of this pathway. Farnesyl pyrophosphate can additionally react using an undecaprenyl pyrophosphate synthetase family protein as a catalyst in order to form dehydrolichol pyrophosphate, or with the protein farnesyltransferase complex, which will add a protein-cysteine to the farnesyl pyrophosphate, which in turn loses its pyrophosphate group. The S-farnesyl protein then reacts with either CAAX prenyl protease 1 or 2 in the endoplasmic reticulum membrane to form protein C-terminal S-farnesyl-L-cysteine. This complex then reacts using protein-S-isoprenylcysteine O-methyltransferase B, still in the endoplasmic reticulum membrane, to form protein-C-terminal S-farnesyl-L-cysteine methyl ester. This reaction may be reversed by isoprenylcysteine alpha-carbonyl methylesterase, yet again in the endoplasmic reticulum membrane. Alternately, through an as of yet unknown reaction, the protein may be removed, as well as several other structure changes, leaving farnesylcysteine. In the lysosome, farnesylcysteine can be catalyzed by farnesylcysteine to remove the cysteine group, leaving behind farnesal. Then, a NAD-binding Rossman-fold superfamily protein can catalyze its transformation into farnesol. Finally, within the chloroplast, farnesol can be catalyzed by farnesol kinase to form farnesyl phosphate, the final product of this pathway.

PW122503

Pw122503 View Pathway
metabolic

Mevalonate Pathway

Arabidopsis thaliana
The mevalonate pathway, also known as the isoprenoid pathway, plays an essential role in creating the chemicals needed for many plants to function. This pathway, combined with the MEP/DOXP pathway give many plants their scents, such as cinnamon and ginger, and are responsible for the red colour in tomatoes. The pathway begins with acetyl-CoA, having come from the glycolysis pathway. Acetyl-CoA immediately becomes acetoacetyl-CoA through the enzyme acetyl-CoA acetyltransferase 1/2. Combined, acetoacetyl-CoA and acetyl-CoA react with hydroxymethylglutaryl-CoA synthase to create 3-hydroxy-3methylglutaryl-CoA. From here, this compound is catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 and becomes (R)-mevalonate. Mevalonate is paired with mevalonate kinase to produce mevalonic acid-5P. In turn, mevalonic acid-5P reacts with phosphomevalonate kinase, and entering the peroxisome and becoming (R)-mevalonic acid-5-pyrophosphate. Remaining in the peroxisome, diphosphomevalonate decarboxylase MVD1 is used alongside (R)-mevalonic acid-5-pyrophosphate to create isopentenyl pyrophosphate, bringing the pathway into the chloroplast. Dimethylallylpyrophosphate is produced after isopentenyl pyrophosphate and isopentenyl diphosphate delta-isomerase II team up to catalyze it. Dimethylallylpyrophosphate then joins forces with isopentenyl again, this time adding geranylgeranyl pyrophosphate synthase 6 and moving into the mitochondria to produce geranyl-PP. This is followed by monoterpenoid biosynthesis.

PW122502

Pw122502 View Pathway
metabolic

MEP/DOXP Pathway

Arabidopsis thaliana
The DOXP/MEP pathway, also known as the non-mevalonate pathway, plays an essential role in creating the chemicals needed for many plants to function. This pathway, combined with the MEP/DOXP pathway give many plants their scents, such as cinnamon and ginger, and are responsible for the red colour in tomatoes. Terpenoids, also called isoprenoids, are a substantial yet varied class of organic chemicals that occur naturally. Plant terpenoids have aromatic qualities and are used for this and their role in traditional herbal remedies. The pathway begins with D-glyceraldehyde 3-phosphate, which is produced through glycolysis. Together with pyruvic acid and the enzyme 1-deoxy-D-xylulose 5-phosphate synthase 1, these are catalyzed into 1-deoxy-xylulose 5-phosphate. From there, 1-deoxy-xylulose 5-phosphate teams up with 1-deoxy-D-xylulose 5-phosphate reductoisomerase to create 2-c-methyl-D-erythritol 4-phosphate. Moving along in the chloroplast, after being produced through 2-c-methyl-D-erythritol 4-phosphate and the enzyme 2-c-methyl-D-erythritol 4-phosphate cytidyltransferase,4-cytidine 5'-diphospho)-2-C-methyl-D-erythritol is catalyzed by 4-diphosphocytidyl-2-c-methyl-D-erythritol kinase to create 2-phospho-4-(cytidine 5'-diphospho)-2-c-methyl-D-erythritol. After that, 2-c-methyl-D-erythritol 2,4-cyclodiphosphate synthase uses the newly produced 2-phospho-4-(cytidine 5'-diphospho)-2-c-methyl-D-erythritol to create 2-c-methyl-D-erythritol-2,4-cyclodiphosphate. This compound is then joined with 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase to become 1-hydroxy-2-methyl-2-butenyl 4-diphosphate. This compound gets busy soon after its inception, branching off into two separate reactions: first reacting with 4-hydroxy-3-methylbut-2-enyl diphosphate reductase to create isopentenyl pyrophosphate, then reacting with the same enzyme to create dimethylallylpyrophosphate. Dimethylallylpyrophosphate is then looped into another reaction with isopentenyl-diphosphate delta-isomerase II, recreating isopentenyl pyrophosphate. It also reacts with geranylgeranyl pyrophosphate synthase 6, bringing the pathway into the mitochondrion to create geranyl pyrophosphate. This is later followed by a monoterpenoid biosynthesis pathway.

PW122501

Pw122501 View Pathway
metabolic

Triterpenoid Biosynthesis

Arabidopsis thaliana
Triterpenoids have 30 carbons and six isoprene units. They are derived from (S)-2,3-epoxysqualene. They may contain rings or be acyclic, depending on the bonds formed by the loss of the diphosphate group. First, the terpenoid backbone is synthesized, producing farnesyl pyrophosphate. Two molecules of farnesyl pyrophosphate then join together to form presqualene diphosphate, catalyzed by squalene synthase 1. Then, the same enzyme removes the pyrophosphate group and replaces it with a hydrogen ion, forming squalene. Squalene then undergoes oxidation of one of its bonds via squlene monooxygenase 1, to form (S)-2,3-epoxysqualene. This may then proceed to the steroid biosynthesis pathway or may react with an isomerase or lyase to form a chair-chair-chair-boat triterpenoid. Similarly, squalene may interact with an isomerase or lyase to form a chair-chair-chair-chair triterpenoid. After the backbone is complete, (S)-2,3-epoxysqualene can interact with many enzymes in order to form the triterpenoids. It can interact with camelliol C synthase to form camelliol C, thalianol synthase to form thalianol, baruol synthase to form baruol, tirucalladienol synthase to form tirucalla-7,24-dien-3-beta-ol, amyrun synthase LUP2 to form lupeol, alpha- and beta-amyrin synthases to form alpha- and beta-amyrin respectively. It can also interact with lupan-3beta,20-diol synthase to add a water molecule to form lupan-3beta,20-diol, alpha- and beta-seco-amyrin synthases to form alpha- and beta-seco-amyrin respectively, marneral synthase to form marneral, and finally arabidiol synthase to add a water molecule and form arabidiol.