PathWhiz

PathWhiz ID	Pathway	Meta Data
PW127284 View Pathway	disease UMP Synthase Deficiency (Orotic Aciduria) Homo sapiens Orotic aciduria, also known as UMP synthase deficiency, is an autosomal recessive disorder of pyrimidine metabolism caused by a defective uridine monophosphate synthetase (UMPS). UMPS is a multifunctional protein which carries out the functions of both orotate phosphoribosyltransferase (OPRT) and orotidine 5'-phosphate decarboxylase (ODC). UMPS catalyzes the conversion of orotic acid into uridine monophosphate (UMP) which is a nucleotide incorporated into ribonucleic acid (RNA). This disease is characterized by a very large accumulation of orotic acid in the urine, occasionally causing urinary obstruction. Symptoms of the disease include megaloblastic anemia as well as retarded growth and development. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Ray Kruger Created On: November 29, 2022 at 16:03 Last Updated: November 29, 2022 at 16:03
PW002026 View Pathway	metabolic Uracil Degradation III Escherichia coli Uracil is a pyrimidine nucleobase found in RNA, and can be used as a source of nitrogen for E. coli. There are at least three pathways through which uracil is degraded. This one begins with uracil, which originates from purine degradation. The putative monooxygenase enzyme rutA catalyzes the breakdown of uracil into peroxyaminoacrylate, using FMNH2 as a cofactor. Peroxyaminoacrylate is then broken down into both carbamic acid and 3-aminoacrylate following the addition of a water molecule by the putative isochorismatase family protein rutB. Carbamic acid can then spontaneously, with the addition of a hydrogen ion, split into an ammonium ion and a molecule of carbon dioxide. 3-aminoacrylate, on the other hand, is catalyzed by the UPF0076 protein rutC to form 2-aminoacrylic acid. This compound enters into a reaction catalyzed by protein rutD, which adds a water molecule and hydrogen ion and forms malonic semialdehyde with ammonium being a byproduct. Finally, the putative NADH dehydrogenase/NAD(P)H nitroreductase rutE complex converts malonic semialdehyde into hydroxypropionic acid, which is then used to form other necessary chemicals. The ammonium ions produced will be the important source of nitrogen for the bacteria. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Ana Marcu Created On: October 01, 2015 at 14:20 Last Updated: October 01, 2015 at 14:20
PW123529 View Pathway	metabolic Uracil Degradation III Pseudomonas aeruginosa Uracil is a pyrimidine nucleobase found in RNA, and can be used as a source of nitrogen for E. coli. There are at least three pathways through which uracil is degraded. This one begins with uracil, which originates from purine degradation. The putative monooxygenase enzyme rutA catalyzes the breakdown of uracil into peroxyaminoacrylate, using FMNH2 as a cofactor. Peroxyaminoacrylate is then broken down into both carbamic acid and 3-aminoacrylate following the addition of a water molecule by the putative isochorismatase family protein rutB. Carbamic acid can then spontaneously, with the addition of a hydrogen ion, split into an ammonium ion and a molecule of carbon dioxide. 3-aminoacrylate, on the other hand, is catalyzed by the UPF0076 protein rutC to form 2-aminoacrylic acid. This compound enters into a reaction catalyzed by protein rutD, which adds a water molecule and hydrogen ion and forms malonic semialdehyde with ammonium being a byproduct. Finally, the putative NADH dehydrogenase/NAD(P)H nitroreductase rutE complex converts malonic semialdehyde into hydroxypropionic acid, which is then used to form other necessary chemicals. The ammonium ions produced will be the important source of nitrogen for the bacteria. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Ana Marcu Created On: August 12, 2019 at 22:26 Last Updated: August 12, 2019 at 22:26
PW012928 View Pathway	metabolic Urate Degradation to Glyoxylate Arabidopsis thaliana Purine nucleotides are eventually degraded to ammonia and carbon dioxide. This pathway begins in the peroxisome and follows the degradation a urate intermediate to glyoxylate. The last three steps take place in the endoplasmic reticulum. First, uricase converts urate into 5-hydroxyisourate. Steps two and three are catalyzed by the bifunctional enzyme S-allantoin synthase: the conversion of 5-hydroxyisourate into 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (OHCU) and the conversion of OHCU into S-allantoin. Fourth, allantoinase requires zinc ion as a cofactor to catalyze the conversion of S-allantoin into allantoate. Next allantoate must be transported out of the peroxisome and into the endoplasmic reticulum. Fifth, allantoate amidohydrolase catalyzes the conversion of allantoate into S-ureidoglycine. This enzyme is a homodimer and requires manganese ion as a cofactor. Sixth, ureidoglycine aminohydrolase requires a manganese ion as a cofactor to catalyze the conversion of S-ureidoglycine into S-ureidoglycolate. Seventh, ureidoglycolate amidohydrolase catalyzes the conversion of S-ureidoglycolate into glyoxylate. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Carin Li Created On: February 24, 2017 at 21:30 Last Updated: February 24, 2017 at 21:30
PW012915 View Pathway	metabolic Urate Degradation to Ureidoglycolate Arabidopsis thaliana Purine nucleotides are eventually degraded to ammonia and carbon dioxide. This pathway begins in the peroxisome and follows the degradation a urate intermediate to S-ureidoglycolate. The last two steps take place in the endoplasmic reticulum. First, uricase converts urate into 5-hydroxyisourate. Steps two and three are catalyzed by the bifunctional enzyme S-allantoin synthase: the conversion of 5-hydroxyisourate into 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (OHCU) and the conversion of OHCU into S-allantoin. Fourth, allantoinase requires zinc ion as a cofactor to catalyze the conversion of S-allantoin into allantoate. Next allantoate must be transported out of the peroxisome and into the endoplasmic reticulum. Fifth, allantoate amidohydrolase catalyzes the conversion of allantoate into S-ureidoglycine. This enzyme is a homodimer and requires manganese ion as a cofactor. Sixth, ureidoglycine aminohydrolase requires a manganese ion as a cofactor to catalyze the conversion of S-ureidoglycine into S-ureidoglycolate. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Carin Li Created On: February 24, 2017 at 15:48 Last Updated: February 24, 2017 at 15:48
PW088338 View Pathway	metabolic Urea Cycle Rattus norvegicus Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Ana Marcu Created On: August 10, 2018 at 13:58 Last Updated: August 10, 2018 at 13:58
PW000162 View Pathway	metabolic Urea Cycle Homo sapiens Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: WishartLab Created On: August 19, 2013 at 12:04 Last Updated: August 19, 2013 at 12:04
PW064668 View Pathway	metabolic Urea Cycle Mus musculus Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Carin Li Created On: January 22, 2018 at 00:16 Last Updated: January 22, 2018 at 00:16
PW088243 View Pathway	metabolic Urea Cycle Bos taurus Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Ana Marcu Created On: August 10, 2018 at 11:44 Last Updated: August 10, 2018 at 11:44
PW122235 View Pathway	metabolic Urea Cycle 55555 Candida albicans BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: September 20, 2018 at 16:51 Last Updated: September 20, 2018 at 16:51