From 68298e823aa6a7bf0ae001e1ad8942c3cef8f982 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 3 Dec 2024 03:08:06 +0000 Subject: [PATCH] Process GPML changes --- pathways/WP121/WP121.gpml | 162 ++++---- pathways/WP132/WP132.gpml | 247 +++++------ pathways/WP256/WP256.gpml | 122 +++--- pathways/WP275/WP275.gpml | 281 ++++++------- pathways/WP432/WP432.gpml | 26 +- pathways/WP479/WP479.gpml | 44 +- pathways/WP5053/WP5053.gpml | 797 +++++++++++++++++++----------------- pathways/WP54/WP54.gpml | 10 +- pathways/WP67/WP67.gpml | 40 +- 9 files changed, 880 insertions(+), 849 deletions(-) diff --git a/pathways/WP121/WP121.gpml b/pathways/WP121/WP121.gpml index 8b2c31f1f9..cf0700caf1 100644 --- a/pathways/WP121/WP121.gpml +++ b/pathways/WP121/WP121.gpml @@ -1,94 +1,94 @@ - + Colanic acid (or M antigen) is a type of extracellular polysaccharide. It consists of a polyanionic heteropolysaccharide that contains a nonstoichiometric combination of sugars such as D-glucose, L-fucoses, D-galactose, and D-glucuronate, which are decorated with O-acetyl and pyruvate side chains. Before assembly, the sugars must be activated in the form of nucleotide sugars. The process of assembling the colanic acid polysaccharide repeat takes place on the membrane lipid through a series of glycosyl transferases on the cytoplasmic side of the inner membrane. Once the single repeat is assembled, it is flipped to the periplasmic side and polymerized by the Wzy-dependent pathway. - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,24 +97,24 @@ - + - + - + - + - + @@ -124,7 +124,7 @@ - + @@ -133,24 +133,24 @@ - + - + - + - + - + @@ -168,7 +168,7 @@ - + @@ -182,57 +182,57 @@ - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + @@ -248,8 +248,8 @@ - - + + @@ -270,8 +270,8 @@ - - + + @@ -279,7 +279,7 @@ - + @@ -292,8 +292,8 @@ - - + + @@ -315,86 +315,86 @@ - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + diff --git a/pathways/WP132/WP132.gpml b/pathways/WP132/WP132.gpml index 32e2fa584e..3163a39b28 100644 --- a/pathways/WP132/WP132.gpml +++ b/pathways/WP132/WP132.gpml @@ -1,5 +1,5 @@ - + Cholesterol is a waxy steroid metabolite found in the cell membranes and transported in the blood plasma of all animals. It is an essential structural component of mammalian cell membranes, where it is required to establish proper membrane permeability and fluidity. In addition, cholesterol is an important component for the manufacture of bile acids, steroid hormones, and several fat-soluble vitamins. Cholesterol is the principal sterol synthesized by animals, but small quantities are synthesized in other eukaryotes, such as plants and fungi. It is almost completely absent among prokaryotes, which include bacteria. Source: [[wikipedia:Cholesterol|Wikipedia]] @@ -10,41 +10,41 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] a23 e57 f9d - + - + - + - + - + - + - + - + - + - + @@ -127,7 +127,7 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] - + @@ -141,211 +141,211 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + @@ -353,32 +353,32 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] - - + + - - + + - - + + - - + + @@ -394,42 +394,16 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] - - cholesterol biosynthetic pathway - PW:0000454 - Pathway Ontology - - - 8552601 - PubMed - Cloning and characterization of ERG25, the Saccharomyces cerevisiae gene encoding C-4 sterol methyl oxidase. - Proc Natl Acad Sci U S A - 1996 - Bard M - Bruner DA - Pierson CA - Lees ND - Biermann B - Frye L - Koegel C - Barbuch R - - - 11969204 - PubMed - Membrane-bound enzymes of cholesterol synthesis from lanosterol. - Biochem Biophys Res Commun - 2002 - Gaylor JL - - - 8663358 + + 12837764 PubMed - Characterization of yeast methyl sterol oxidase (ERG25) and identification of a human homologue. + Localization of mammalian NAD(P)H steroid dehydrogenase-like protein on lipid droplets. J Biol Chem - 1996 - Li L - Kaplan J + 2003 + Ohashi M + Mizushima N + Kabeya Y + Yoshimori T 10369263 @@ -454,17 +428,6 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] Brown SD Herman GE - - 12837764 - PubMed - Localization of mammalian NAD(P)H steroid dehydrogenase-like protein on lipid droplets. - J Biol Chem - 2003 - Ohashi M - Mizushima N - Kabeya Y - Yoshimori T - 8407863 PubMed @@ -475,6 +438,30 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] Korenaga T Ogura K + + 8663358 + PubMed + Characterization of yeast methyl sterol oxidase (ERG25) and identification of a human homologue. + J Biol Chem + 1996 + Li L + Kaplan J + + + 8552601 + PubMed + Cloning and characterization of ERG25, the Saccharomyces cerevisiae gene encoding C-4 sterol methyl oxidase. + Proc Natl Acad Sci U S A + 1996 + Bard M + Bruner DA + Pierson CA + Lees ND + Biermann B + Frye L + Koegel C + Barbuch R + 9498553 PubMed @@ -488,5 +475,19 @@ Source: [[wikipedia:Cholesterol|Wikipedia]] Horiuchi T Yoshida Y + + cholesterol biosynthetic pathway + PW:0000454 + Pathway Ontology + + + 11969204 + PubMed + Membrane-bound enzymes of cholesterol synthesis from lanosterol. + Biochem Biophys Res Commun + 2002 + Gaylor JL + + diff --git a/pathways/WP256/WP256.gpml b/pathways/WP256/WP256.gpml index f49142281b..7dea81a852 100644 --- a/pathways/WP256/WP256.gpml +++ b/pathways/WP256/WP256.gpml @@ -1,200 +1,200 @@ - + O-Acetyl-L-homoserine sulfhydrylase participates in an alternative pathway of L-homocysteine synthesis. Cysteine can then be produced by the reverse transsulfuration pathway, which involves the conversion of homocysteine to cysteine with the help of a cystathionine intermediate. This process takes place in two steps: First, cystathionine-synthase (Cys4p) catalyzes a -displacement reaction, whereby the thiol group of homocysteine replaces the hydroxyl group of serine, resulting in the formation of cystathionine. Second, cystathionine-lyase (Cys3p) catalyzes an ,-elimination reaction, which hydrolyzes cystathionine to generate cysteine, -ketobutyrate, and ammonia. - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - + + + - - + + - - + + - - + + - - + + - - + + - - - + + + - - - + + + - - - + + + - - + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - + + diff --git a/pathways/WP275/WP275.gpml b/pathways/WP275/WP275.gpml index c301b2174f..fbbdd8657f 100644 --- a/pathways/WP275/WP275.gpml +++ b/pathways/WP275/WP275.gpml @@ -1,10 +1,10 @@ - + The first five steps of arginine biosynthesis in S. cerevisiae take place in the mitochondrion (CITS: [11553611])(CITS: [Hinnebusch]). This part of the pathway is known as the acetylated derivatives cycle because the acetyl group that is added to L-glutamate in the first step of the pathway is recycled via N-acetylglutamate generated in the fifth step. The enzymes that catalyze the second and third steps are encoded by a single gene (ARG5,6) that is translated into a pre-protein which is imported into mitochondria and cleaved there to yield two enzymes, N-acetylglutamate kinase and N-acetylglutamyl-phosphate reductase (CITS: [1649049]). These enzymes form a complex with each other and with N-acetylglutamate synthase, the first enzyme in the pathway, which may have implications for regulation of their activity (CITS: [11553611]). The mitochondrial steps of the arginine biosynthesis pathway result in the formation of ornithine, which is exported to the cytoplasm by the transporter Ort1p (CITS: [8798783]). In the cytoplasm, L-ornithine is converted to L-arginine in three reactions mediated by ornithine carbamoyltransferase, arginosuccinate synthase, and argininosuccinate lyase. Transcription of genes of the arginine biosynthetic pathway, as well as of other amino acid biosynthetic pathways, is activated by the transcription factor Gcn4p under conditions of amino acid starvation (CITS: [11390663])(CITS: [Hinnebusch]). Transcription of ARG1, ARG3, ARG5,6, and ARG8 is also repressed in the presence of arginine by the ArgR/Mcm1p complex, which consists of Arg80p, Arg81p, Arg82p, and Mcm1p (CITS: [14563547]). The transcriptional activator Gcn4p interacts with subunits of the ArgR/Mcm1p repressor, allowing for fine-tuning of transcriptional control in response to arginine availability (CITS: [15289616]). SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html ktn ntr - + @@ -141,242 +141,242 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html - - - - - - - - + - - - + + + - - - - + + + + + - + - - - + + + - + - - + + + - - - - - + + + + - + - - + + + - - - - - + + + + - + - - + + + - + - - - + + + - + - - + + - + - - - + + + - - - - + + + + + - - - - - + + + + + - + - - + + + - - - - - + + + + + - + - - - + + + - + - - - + + - + - - - + + - - - - - + + + + - + - - - + + + - + - - - + + + - + - - - + + - - - - - + + + + + - + - - - + + + - - - - - + + + + + - - - - + + + + + - - - - - + + + + - + - - - + + + - + - - - + + + + + + + + + + - - - + + + @@ -392,17 +392,12 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html - - - - + + + + - - arginine biosynthetic pathway - PW:0001260 - Pathway Ontology - 12603335 PubMed @@ -415,6 +410,11 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html Stankiewicz A Crabeel M + + arginine biosynthetic pathway + PW:0001260 + Pathway Ontology + 11553611 PubMed @@ -428,3 +428,4 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html + diff --git a/pathways/WP432/WP432.gpml b/pathways/WP432/WP432.gpml index b87f10fa91..e7ac255a62 100644 --- a/pathways/WP432/WP432.gpml +++ b/pathways/WP432/WP432.gpml @@ -1,5 +1,5 @@ - + Like many other amino acids, asparagine may be utilized by S. cerevisiae as a sole source of nitrogen. Catabolism of asparagine for nitrogen involves the action of asparaginases, which hydrolyze the amide group in the side chain of asparagine. This converts asparagine to aspartate and releases an assimilable molecule of ammonia (NH3). Further nitrogen can be derived from the newly generated aspartate molecule via its reversible conversion to glutamate by aspartate aminotransferases. Glutamate, whose amino group can be hydrolyzed to release ammonia, represents one of the major sources of nitrogen for biosynthetic reactions in S. cerevisiae. SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html @@ -86,7 +86,7 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html - + @@ -101,7 +101,7 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html - + @@ -131,6 +131,16 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html + + 10640599 + PubMed + The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae. + FEMS Microbiol Rev + 2000 + ter Schure EG + van Riel NA + Verrips CT + https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=ASPARAGINE-DEG2-PWY URL @@ -143,16 +153,6 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html PW:0001083 Pathway Ontology - - 10640599 - PubMed - The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae. - FEMS Microbiol Rev - 2000 - ter Schure EG - van Riel NA - Verrips CT - diff --git a/pathways/WP479/WP479.gpml b/pathways/WP479/WP479.gpml index 92fcc4029b..ef8020df91 100644 --- a/pathways/WP479/WP479.gpml +++ b/pathways/WP479/WP479.gpml @@ -1,5 +1,5 @@ - + Chorismate, an intermediate in the synthesis of the aromatic amino acids and the vitamins, p-aminobenzoate and p-hydroxybenzoate, is synthesized by the shikimate pathway. The shikimate pathway has been found to be common to all eukaryotes and prokaryotes studied thus far (as reported in. In Saccharomyces cerevisiae the initial step is catalyzed by two deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase isoenzymes, one of which (ARO3) is feedback inhibited by phenylalanine, and the other (ARO4) by tyrosine. Both DAHP isoenzymes are derepressed by amino acid starvation (general control of amino acid biosynthesis). The 5 subsequent reactions are catalyzed by the pentafunctional arom enzyme, Aro1p. Aro1p is a mosaic of five monofunctional domains, each of which corresponds to one of five separate monofunctional E. coli enzymes. The last step of chorismate biosynthesis, before the pathway branches to synthesize different terminal products, is catalyzed by Aro2p. Description from YeastPathways. @@ -94,7 +94,7 @@ Description from YeastPathways. - + @@ -111,7 +111,7 @@ Description from YeastPathways. - + @@ -119,7 +119,7 @@ Description from YeastPathways. - + @@ -154,9 +154,9 @@ Description from YeastPathways. - - - + + + @@ -178,7 +178,7 @@ Description from YeastPathways. - + @@ -186,7 +186,7 @@ Description from YeastPathways. - + @@ -200,7 +200,7 @@ Description from YeastPathways. - + @@ -229,7 +229,7 @@ Description from YeastPathways. - + @@ -237,7 +237,7 @@ Description from YeastPathways. - + @@ -245,7 +245,7 @@ Description from YeastPathways. - + @@ -253,7 +253,7 @@ Description from YeastPathways. - + @@ -297,14 +297,6 @@ Description from YeastPathways. - - 1943992 - PubMed - Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. - Microbiol Rev - 1991 - Braus GH - https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=ARO-PWY-1 URL @@ -322,6 +314,14 @@ Description from YeastPathways. PW:0000002 Pathway Ontology + + 1943992 + PubMed + Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. + Microbiol Rev + 1991 + Braus GH + diff --git a/pathways/WP5053/WP5053.gpml b/pathways/WP5053/WP5053.gpml index ddcb35e0e7..93c7a9b24c 100644 --- a/pathways/WP5053/WP5053.gpml +++ b/pathways/WP5053/WP5053.gpml @@ -1,5 +1,5 @@ - + This pathway describes the gene signaling pathway active in the development of the ureteric collection system in human kidney development. Mutations in essential genes within this pathway can lead to development of CAKUT (congenital anomalies of the kidney and urinary tract). @@ -186,7 +186,7 @@ - + @@ -291,6 +291,8 @@ + fbd + a38 @@ -373,7 +375,7 @@ Evidence in mouse only f5a - + @@ -627,7 +629,7 @@ - diff --git a/pathways/WP54/WP54.gpml b/pathways/WP54/WP54.gpml index 4e7c70e6dd..aebcb029d3 100644 --- a/pathways/WP54/WP54.gpml +++ b/pathways/WP54/WP54.gpml @@ -1,5 +1,5 @@ - + Under conditions where optimal sources of nitrogen are unavailable, S. cerevisiae is able to utilize arginine as its sole nitrogen source. Arginine catabolism occurs in the cytosol with the hydrolysis of arginine to proline, releasing three nitrogen atoms that can be used by the cell. In the absence of oxygen, the proline ring is unable to be further degraded. The utilization of arginine as a nitrogen source is repressed if better nitrogen compounds such as ammonia, asparagine or glutamine are present. This is known as nitrogen catabolite repression (NCR). The CAR1 gene is subject to the effect of this repression which is mediated by the negative regulator Ure2p. In the presence of arginine and the absence of a preferred nitrogen source, NCR is released by the GATA transcriptional activators Gln3p and Gat1p. Unrelated to NCR, the presence of arginine also induces CAR1 and CAR2 expression by the regulators Arg80p, Arg81p and Mcm1p. The CAR genes are also activated by the globally acting transcription factors Rap1p and Abf1p. Conversely, CAR1 and CAR2 expression is repressed by the Ume6p-Sin2p-Rpd3p complex. Additionally, CAR2 expression is induced by the two positive regulators Dal81p and Dal82p as well as allophanate, a degradation product of urea. Description from [https://pathway.yeastgenome.org YeastPathways]. @@ -71,7 +71,7 @@ Description from [https://pathway.yeastgenome.org YeastPathways]. - + @@ -100,7 +100,7 @@ Description from [https://pathway.yeastgenome.org YeastPathways]. - + @@ -115,7 +115,7 @@ Description from [https://pathway.yeastgenome.org YeastPathways]. - + @@ -130,7 +130,7 @@ Description from [https://pathway.yeastgenome.org YeastPathways]. - + diff --git a/pathways/WP67/WP67.gpml b/pathways/WP67/WP67.gpml index 8b26f24547..935c2324da 100644 --- a/pathways/WP67/WP67.gpml +++ b/pathways/WP67/WP67.gpml @@ -1,5 +1,5 @@ - + The precursor to asparagine is oxaloacetate, which the AAT enzyme converts to aspartate by transferring the amino group from glutamate to oxaloacetate, producing α-ketoglutarate and aspartate. The enzyme ASN produces asparagine, AMP, glutamate, and pyrophosphate from aspartate, glutamine, and ATP. Description adapted from [https://en.wikipedia.org/wiki/Asparagine Wikipedia]. @@ -15,16 +15,16 @@ Description adapted from [https://en.wikipedia.org/wiki/Asparagine Wikipedia]. - + - + - + @@ -54,7 +54,7 @@ Description adapted from [https://en.wikipedia.org/wiki/Asparagine Wikipedia]. - + @@ -71,7 +71,7 @@ Description adapted from [https://en.wikipedia.org/wiki/Asparagine Wikipedia]. - + @@ -79,49 +79,49 @@ Description adapted from [https://en.wikipedia.org/wiki/Asparagine Wikipedia]. - + - - + + - - + + - - + + - + - + - + @@ -140,13 +140,13 @@ Description adapted from [https://en.wikipedia.org/wiki/Asparagine Wikipedia].L-asparagine biosynthesis I - classic metabolic pathway - PW:0000002 + asparagine metabolic pathway + PW:0001083 Pathway Ontology - asparagine metabolic pathway - PW:0001083 + classic metabolic pathway + PW:0000002 Pathway Ontology