Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| superpathway of histidine, purine and pyrimidine biosynthesis Accession ID: BioCyc:CALBI_PRPP-PWY |
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| homoserine biosynthesis Accession ID: BioCyc:CALBI_HOMOSERSYN-PWY |
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Schlösser T, Gätgens C, Weber U, Stahmann KP. Alanine : glyoxylate aminotransferase of Saccharomyces cerevisiae-encoding gene AGX1 and metabolic significance. Yeast. 2004 Jan 15;21(1):63–73. doi: 10.1002/yea.1058. PMID: 14745783.; Mountain HA, Byström AS, Larsen JT, Korch C. Four major transcriptional responses in the methionine/threonine biosynthetic pathway of Saccharomyces cerevisiae. Yeast. 1991 Nov;7(8):781–803. doi: 10.1002/yea.320070804. PMID: 1789001.; Yamagata S. O-Acetylhomoserine sulfhydrylase of the fission yeast Schizosaccharomyces pombe: partial purification, characterization, and its probable role in homocysteine biosynthesis. J Biochem. 1984 Nov;96(5):1511–23. doi: 10.1093/oxfordjournals.jbchem.a134980. PMID: 6526818. |
| purine nucleotides de novo biosynthesis Accession ID: BioCyc:CALBI_DENOVOPURINE2-PWY |
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Rodriguez-Suarez R, Xu D, Veillette K, Davison J, Sillaots S, Kauffman S, Hu W, Bowman J, Martel N, Trosok S, Wang H, Zhang L, Huang LY, Li Y, Rahkhoodaee F, Ransom T, Gauvin D, Douglas C, Youngman P, Becker J, Jiang B, Roemer T. Mechanism-of-action determination of GMP synthase inhibitors and target validation in Candida albicans and Aspergillus fumigatus. Chem Biol. 2007 Oct;14(10):1163–75. doi: 10.1016/j.chembiol.2007.09.009. PMID: 17961828.; Rolfes RJ. Regulation of purine nucleotide biosynthesis: in yeast and beyond. Biochem Soc Trans. 2006 Nov;34(Pt 5):786–90. doi: 10.1042/bst0340786. PMID: 17052198.; Köhler GA, White TC, Agabian N. Overexpression of a cloned IMP dehydrogenase gene of Candida albicans confers resistance to the specific inhibitor mycophenolic acid. J Bacteriol. 1997 Apr;179(7):2331–8. doi: 10.1128/jb.179.7.2331-2338.1997.; Poulter RT, Rikkerink EH. Genetic analysis of red, adenine-requiring mutants of Candida albicans. J Bacteriol. 1983 Dec;156(3):1066–77. doi: 10.1128/jb.156.3.1066-1077.1983. |
| asparagine degradation Accession ID: BioCyc:CALBI_ASPARAGINE-DEG1-PWY |
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Kil J, Kim G, Park I. Extraction of Extracellular |
| aspartate biosynthesis Accession ID: BioCyc:CALBI_ASPBIO-PWY |
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| salvage pathways of purine nucleosides Accession ID: BioCyc:CALBI_P121-PWY |
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Rolfes RJ. Regulation of purine nucleotide biosynthesis: in yeast and beyond. Biochem Soc Trans. 2006 Nov;34(Pt 5):786–90. doi: 10.1042/bst0340786. PMID: 17052198.; Challa A, Johnson S, Robertson K, Gunasekaran M. Properties of adenosine deaminase from Candida albicans. J Basic Microbiol. 1999;39(2):97–101. doi: 10.1002/(sici)1521-4028(199905)39:2<97::aid-jobm97>3.0.co;2-n. PMID: 10335602. |
| aspartate degradation Accession ID: BioCyc:CALBI_MALATE-ASPARTATE-SHUTTLE-PWY |
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| tRNA charging pathway Accession ID: BioCyc:CALBI_TRNA-CHARGING-PWY |
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Hasenoehrl A, Galic´ T, Ergovic´ G, Mars?ic´ N, Skerlev M, Mittendorf J, Geschke U, Schmidt A, Schoenfeld W. In Vitro Activity and In Vivo Efficacy of Icofungipen (PLD-118), a Novel Oral Antifungal Agent, against the Pathogenic Yeast Candida albicans. Antimicrob Agents Chemother. 2006 Sep;50(9):3011–8. doi: 10.1128/aac.00254-06.; Petraitiene R, Petraitis V, Kelaher AM, Sarafandi AA, Mickiene D, Groll AH, Sein T, Bacher J, Walsh TJ. Efficacy, Plasma Pharmacokinetics, and Safety of Icofungipen, an Inhibitor of Candida Isoleucyl-tRNA Synthetase, in Treatment of Experimental Disseminated Candidiasis in Persistently Neutropenic Rabbits. Antimicrob Agents Chemother. 2005 May;49(5):2084–92. doi: 10.1128/aac.49.5.2084-2092.2005.; Petraitis V, Petraitiene R, Kelaher AM, Sarafandi AA, Sein T, Mickiene D, Bacher J, Groll AH, Walsh TJ. Efficacy of PLD-118, a Novel Inhibitor of Candida Isoleucyl-tRNA Synthetase, against Experimental Oropharyngeal and Esophageal Candidiasis Caused by Fluconazole-Resistant C. albicans. Antimicrob Agents Chemother. 2004 Oct;48(10):3959–67. doi: 10.1128/aac.48.10.3959-3967.2004.; Mittendorf J, Kunisch F, Matzke M, Militzer HC, Schmidt A, Schönfeld W. Novel antifungal beta-amino acids: synthesis and activity against Candida albicans. Bioorg Med Chem Lett. 2003 Feb 10;13(3):433–6. doi: 10.1016/s0960-894x(02)00958-7. PMID: 12565945. |
| arginine biosynthesis Accession ID: BioCyc:CALBI_ARGSYNBSUB-PWY |
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| glutamine degradation Accession ID: BioCyc:CALBI_GLUTAMINEFUM-PWY |
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ter Schure EG, van Riel NA, Verrips CT. The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae. FEMS Microbiol Rev. 2000 Jan;24(1):67–83. doi: 10.1111/j.1574-6976.2000.tb00533.x. PMID: 10640599.; Soberón M, González A. Glutamine degradation through the omega-amidase pathway in Saccharomyces cerevisiae. J Gen Microbiol. 1987 Jan;133(1):9–14. doi: 10.1099/00221287-133-1-9. PMID: 3309146. |
| pyrimidine ribonucleotides de novo biosynthesis Accession ID: BioCyc:CALBI_PWY0-162 |
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Zameitat E, Gojkovic Z, Knecht W, Piškur J, Löffler M. Biochemical characterization of recombinant dihydroorotate dehydrogenase from the opportunistic pathogenic yeast Candida albicans. The FEBS Journal. 2006 Jun 19;273(14):3183–91. doi: 10.1111/j.1742-4658.2006.05327.x.; Brand A, MacCallum DM, Brown AJP, Gow NAR, Odds FC. Ectopic Expression of URA3 Can Influence the Virulence Phenotypes and Proteome of Candida albicans but Can Be Overcome by Targeted Reintegration of URA3 at the RPS10 Locus. Eukaryot Cell. 2004 Aug;3(4):900–9. doi: 10.1128/ec.3.4.900-909.2004.; Jong AY, Ma JJ. Saccharomyces cerevisiae nucleoside-diphosphate kinase: Purification, characterization, and substrate specificity. Archives of Biochemistry and Biophysics. 1991 Dec;291(2):241–6. doi: 10.1016/0003-9861(91)90129-7.; Denis-Duphil M. Pyrimidine biosynthesis in Saccharomyces cerevisiae: the ura2 cluster gene, its multifunctional enzyme product, and other structural or regulatory genes involved in de novo UMP synthesis. Biochem. Cell Biol. 1989 Sep 01;67(9):612–31. doi: 10.1139/o89-094.; Kelly R, Miller SM, Kurtz MB, Kirsch DR. Directed Mutagenesis in Candida albicans: One-Step Gene Disruption To Isolate ura3 Mutants. Molecular and Cellular Biology. 1987 Jan 01;7(1):199–208. doi: 10.1128/mcb.7.1.199-208.1987. |
| asparagine biosynthesis Accession ID: BioCyc:CALBI_ASPARAGINE-BIOSYNTHESIS |
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Dang V, Valens M, Bolotin-Fukuhara M, Daignan-Fornier B. Cloning of the ASN1 and ASN2 genes encoding asparagine synthetases in Saccharomyces cerevisiae: differential regulation by the CCAAT-box-binding factor. Molecular Microbiology. 1996 Nov;22(4):681–92. doi: 10.1046/j.1365-2958.1996.d01-1715.x. |
| NAD biosynthesis I from aspartate Accession ID: WikiPathways:WP2484 |
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| Glycolysis and gluconeogenesis Accession ID: WikiPathways:WP144 |
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| Glycolysis and gluconeogenesis Accession ID: WikiPathways:WP157 |
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Bricker DK, Taylor EB, Schell JC, Orsak T, Boutron A, Chen Y, Cox JE, Cardon CM, Van Vranken JG, Dephoure N, Redin C, Boudina S, Gygi SP, Brivet M, Thummel CS, Rutter J. A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila , and Humans. Science. 2012 Jul 06;337(6090):96–100. doi: 10.1126/science.1218099. |
| Glycolysis and gluconeogenesis Accession ID: WikiPathways:WP1027 |
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Bricker DK, Taylor EB, Schell JC, Orsak T, Boutron A, Chen Y, Cox JE, Cardon CM, Van Vranken JG, Dephoure N, Redin C, Boudina S, Gygi SP, Brivet M, Thummel CS, Rutter J. A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila , and Humans. Science. 2012 Jul 06;337(6090):96–100. doi: 10.1126/science.1218099. |
| Amino acid transport defects (IEMs) Accession ID: WikiPathways:WP5029 |
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Arriza J, Fairman W, Wadiche J, Murdoch G, Kavanaugh M, Amara S. Functional comparisons of three glutamate transporter subtypes cloned from human motor cortex. J. Neurosci. 1994 Sep 01;14(9):5559–69. doi: 10.1523/jneurosci.14-09-05559.1994. |
| Biochemical pathways: part I Accession ID: WikiPathways:WP3604 |
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Michal G. On representation of metabolic pathways. Biosystems. 1998 Jun;47(1-2):1–7. doi: 10.1016/s0303-2647(98)00019-7. PMID: 9715748. |
| Urea cycle and metabolism of amino groups Accession ID: WikiPathways:WP497 |
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| AtMetExpress overview Accession ID: WikiPathways:WP3622 |
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Sumner LW, Lei Z, Nikolau BJ, Saito K. Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Nat Prod Rep. 2015 Feb;32(2):212–29. doi: 10.1039/c4np00072b. PMID: 25342293. |