Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| triacylglycerol degradation Accession ID: BioCyc:META_LIPAS-PWY |
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Henry SA, Kohlwein SD, Carman GM. Metabolism and regulation of glycerolipids in the yeast Saccharomyces cerevisiae. Genetics. 2012 Feb;190(2):317–49. PMID: 22345606; PMCID: PMC3276621.; Heier C, Taschler U, Rengachari S, Oberer M, Wolinski H, Natter K, Kohlwein SD, Leber R, Zimmermann R. Identification of Yju3p as functional orthologue of mammalian monoglyceride lipase in the yeast Saccharomyces cerevisiae. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2010 Sep;1801(9):1063–71. doi: 10.1016/j.bbalip.2010.06.001.; Rajakumari S, Daum G. Multiple Functions as Lipase, Steryl Ester Hydrolase, Phospholipase, and Acyltransferase of Tgl4p from the Yeast Saccharomyces cerevisiae. Journal of Biological Chemistry. 2010 May;285(21):15769–76. doi: 10.1074/jbc.m109.076331.; Rajakumari S, Daum G. Janus-faced Enzymes Yeast Tgl3p and Tgl5p Catalyze Lipase and Acyltransferase Reactions. MBoC. 2010 Feb 15;21(4):501–10. doi: 10.1091/mbc.e09-09-0775.; Czabany T, Athenstaedt K, Daum G. Synthesis, storage and degradation of neutral lipids in yeast. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2007 Mar;1771(3):299–309. doi: 10.1016/j.bbalip.2006.07.001.; Eastmond PJ. SUGAR-DEPENDENT1Encodes a Patatin Domain Triacylglycerol Lipase That Initiates Storage Oil Breakdown in GerminatingArabidopsisSeeds. 2006 Feb 10;18(3):665–75. doi: 10.1105/tpc.105.040543.; Kurat CF, Natter K, Petschnigg J, Wolinski H, Scheuringer K, Scholz H, Zimmermann R, Leber R, Zechner R, Kohlwein SD. Obese Yeast: Triglyceride Lipolysis Is Functionally Conserved from Mammals to Yeast. Journal of Biological Chemistry. 2006 Jan;281(1):491–500. doi: 10.1074/jbc.m508414200.; Athenstaedt K, Daum G. Tgl4p and Tgl5p, Two Triacylglycerol Lipases of the Yeast Saccharomyces cerevisiae Are Localized to Lipid Particles. Journal of Biological Chemistry. 2005 Nov;280(45):37301–9. doi: 10.1074/jbc.m507261200.; Holm C, Osterlund T, Laurell H, Contreras JA. Molecular mechanisms regulating hormone-sensitive lipase and lipolysis. Annu Rev Nutr. 2000;20():365–93. doi: 10.1146/annurev.nutr.20.1.365. PMID: 10940339.; Athenstaedt K, Zweytick D, Jandrositz A, Kohlwein SD, Daum G. Identification and Characterization of Major Lipid Particle Proteins of the Yeast Saccharomyces cerevisiae. J Bacteriol. 1999 Oct 15;181(20):6441–8. doi: 10.1128/jb.181.20.6441-6448.1999.; Osterlund T, Danielsson B, Degerman E, Contreras JA, Edgren G, Davis RC, Schotz MC, Holm C. Domain-structure analysis of recombinant rat hormone-sensitive lipase. Biochem J. 1996 Oct 15;319 ( Pt 2)():411–20. PMID: 8912675; PMCID: PMC1217784.; Fredrikson G, Strålfors P, Nilsson NO, Belfrage P. Hormone-sensitive lipase of rat adipose tissue. Purification and some properties. Journal of Biological Chemistry. 1981 Jun;256(12):6311–20. doi: 10.1016/s0021-9258(19)69164-7.; Vaughan M, Berger JE, Steinberg D. Hormone-sensitive Lipase and Monoglyceride Lipase Activities in Adipose Tissue. Journal of Biological Chemistry. 1964 Feb;239(2):401–9. doi: 10.1016/s0021-9258(18)51692-6. |
| coumarin biosynthesis (via 2-coumarate) Accession ID: BioCyc:META_PWY-5176 |
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Curini M, Cravotto G, Epifano F, Giannone G. Chemistry and biological activity of natural and synthetic prenyloxycoumarins. Curr Med Chem. 2006;13(2):199–222. doi: 10.2174/092986706775197890. PMID: 16472213.; Lacy A, O'Kennedy R. Studies on coumarins and coumarin-related compounds to determine their therapeutic role in the treatment of cancer. Curr Pharm Des. 2004;10(30):3797–811. doi: 10.2174/1381612043382693. PMID: 15579072.; Fylaktakidou KC, Hadjipavlou-Litina DJ, Litinas KE, Nicolaides DN. Natural and synthetic coumarin derivatives with anti-inflammatory/ antioxidant activities. Curr Pharm Des. 2004;10(30):3813–33. doi: 10.2174/1381612043382710. PMID: 15579073.; Oba K, Conn EE, Canut H, Boudet AM. Subcellular Localization of 2-(beta-d-Glucosyloxy)-Cinnamic Acids and the Related beta-glucosidase in Leaves of Melilotus alba Desr. Plant Physiol. 1981 Dec;68(6):1359–63. PMID: 16662108; PMCID: PMC426103.; Poulton JE, McRee DE, Conn EE. Intracellular Localization of Two Enzymes Involved in Coumarin Biosynthesis in Melilotus alba. Plant Physiol. 1980 Feb 01;65(2):171–5. doi: 10.1104/pp.65.2.171.; Gestetner B, Conn EE. The 2-hydroxylation of trans-cinnamic acid by chloroplasts from Melilotus alba desr. Archives of Biochemistry and Biophysics. 1974 Aug;163(2):617–24. doi: 10.1016/0003-9861(74)90522-0.; Kleinhofs A, Haskins FA, Gorz HJ. Ultraviolet-induced isomerization of beta-D-glucosyl omicron-hydroxycinnamic acid on filter paper. J Chromatogr. 1966 Apr;22(1):184–6. doi: 10.1016/s0021-9673(01)97086-4. PMID: 5921806.; Haskins FA, Williams LG, Gorz HJ. Light-Induced Trans to Cis Conversion of ß-d-Glucosyl o-Hydroxycinnamic Acid in Melilotus alba Leaves. Plant Physiol. 1964 Sep 01;39(5):777–81. doi: 10.1104/pp.39.5.777.; Stoker JR. The biosynthesis of coumarin in Melilotus alba. Biochemical and Biophysical Research Communications. 1963 Dec;14(1):17–20. doi: 10.1016/0006-291x(63)90203-1.; Stoker JR, Bellis DM. The Biosynthesis of Coumarin in Melilotus Alba. Journal of Biological Chemistry. 1962 Jul;237(7):2303–5. doi: 10.1016/s0021-9258(19)63437-x.; Kosuge T. Studies on the identity of bound coumarin in sweet clover. Archives of Biochemistry and Biophysics. 1961 Nov;95(2):211–8. doi: 10.1016/0003-9861(61)90137-0.; KOUKOL J, CONN EE. The metabolism of aromatic compounds in higher plants. IV. Purification and properties of the phenylalanine deaminase of Hordeum vulgare. J Biol Chem. 1961 Oct;236():2692–8. PMID: 14458851.; Kosuge T, Conn EE. The Metabolism of Aromatic Compounds in Higher Plants. Journal of Biological Chemistry. 1959 Aug;234(8):2133–7. doi: 10.1016/s0021-9258(18)69879-5. |
| thiosulfate oxidation I (to tetrathionate) Accession ID: BioCyc:META_THIOSULFOX-PWY |
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Hensen D, Sperling D, Trüper HG, Brune DC, Dahl C. Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Molecular Microbiology. 2006 Sep 25;62(3):794–810. doi: 10.1111/j.1365-2958.2006.05408.x. |
| ajugose biosynthesis I (galactinol-dependent) Accession ID: BioCyc:META_PWY-5342 |
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Peterbauer T, Mach L, Mucha J, Richter A. Functional expression of a cDNA encoding pea (Pisum sativum L.) raffinose synthase, partial purification of the enzyme from maturing seeds, and steady-state kinetic analysis of raffinose synthesis. Planta. 2002 Sep;215(5):839–46. doi: 10.1007/s00425-002-0804-7. PMID: 12244450.; Peterbauer T, Mucha J, Mach L, Richter A. Chain Elongation of raffinose in pea seeds. Isolation, characterization, and molecular cloning of mutifunctional enzyme catalyzing the synthesis of stachyose and verbascose. J Biol Chem. 2002 Jan 04;277(1):194–200. doi: 10.1074/jbc.m109734200. PMID: 11675396. |
| demethylmenaquinol-4 biosynthesis Accession ID: BioCyc:META_PWY-7997 |
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Tonhosolo R, Gabriel HB, Matsumura MY, Cabral FJ, Yamamoto MM, D'Alexandri FL, Sussmann RAC, Belmonte R, Peres VJ, Crick DC, Wunderlich G, Kimura EA, Katzin AM. Intraerythrocytic stages of Plasmodium falciparum biosynthesize menaquinone. FEBS Letters. 2010 Oct 29;584(23):4761–8. doi: 10.1016/j.febslet.2010.10.055. |
| TCA cycle VII (acetate-producers) Accession ID: BioCyc:META_PWY-7254 |
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Mullins EA, Francois JA, Kappock TJ. A Specialized Citric Acid Cycle Requiring Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase (AarC) Confers Acetic Acid Resistance on the Acidophile Acetobacter aceti. J Bacteriol. 2008 Jul 15;190(14):4933–40. doi: 10.1128/jb.00405-08. |
| (7Z,10Z,13Z)-hexadecatrienoate biosynthesis Accession ID: BioCyc:META_PWY-7590 |
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Browse J, Warwick N, Somerville CR, Slack CR. Fluxes through the prokaryotic and eukaryotic pathways of lipid synthesis in the '16:3' plant Arabidopsis thaliana. Biochem J. 1986 Apr 01;235(1):25–31. PMID: 3741384; PMCID: PMC1146643. |
| L-tryptophan degradation X (mammalian, via tryptamine) Accession ID: BioCyc:META_PWY-6307 |
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Yu A, Granvil CP, Haining RL, Krausz KW, Corchero J, Küpfer A, Idle JR, Gonzalez FJ. The Relative Contribution of Monoamine Oxidase and Cytochrome P450 Isozymes to the Metabolic Deamination of the Trace Amine Tryptamine. The Journal of Pharmacology and Experimental Therapeutics. 2003 Feb;304(2):539–46. doi: 10.1124/jpet.102.043786.; Mousseau DD. Tryptamine: a metabolite of tryptophan implicated in various neuropsychiatric disorders. Metab Brain Dis. 1993 Mar;8(1):1–44. doi: 10.1007/bf01000528. PMID: 8098507.; Susilo R, Höfle G, Rommelspacher H. Degradation of tryptamine in pig brain: Identification of a new condensation product. Biochemical and Biophysical Research Communications. 1987 Nov;148(3):1045–52. doi: 10.1016/s0006-291x(87)80237-1.; Yamada J, Sugimoto Y, Horisaka K. Determination of endogeneous indoleacetic acid and tryptophol in mouse brain by high performance liquid chromatography with fluorometric detection. Life Sci. 1983 Nov 14;33(20):2043–7. doi: 10.1016/0024-3205(83)90744-0. PMID: 6645790.; Jaeger CB, Teitelman G, Joh TH, Albert VR, Park DH, Reis DJ. Some neurons of the rat central nervous system contain aromatic-L-amino-acid decarboxylase but not monoamines. Science. 1983 Mar 11;219(4589):1233–5. doi: 10.1126/science.6131537. PMID: 6131537.; Young SN, Davis BA, Gauthier S. Precursors and metabolites of phenylethylamine, m and p-tyramine and tryptamine in human lumbar and cisternal cerebrospinal fluid. Journal of Neurology, Neurosurgery & Psychiatry. 1982 Jul 01;45(7):633–9. doi: 10.1136/jnnp.45.7.633.; Young SN, Gauthier S, Anderson GM, Purdy WC. Tryptophan, 5-hydroxyindoleacetic acid and indoleacetic acid in human cerebrospinal fluid: interrelationships and the influence of age, sex, epilepsy and anticonvulsant drugs. Journal of Neurology, Neurosurgery & Psychiatry. 1980 May 01;43(5):438–45. doi: 10.1136/jnnp.43.5.438. |
| TCA cycle II (plants and fungi) Accession ID: BioCyc:META_PWY-5690 |
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Krebs HA, Eggleston LV. Metabolism of acetoacetate in animal tissues. 1. Biochem J. 1945;39(5):408–19. PMID: 16747930; PMCID: PMC1258257.; Krebs HA, Salvin E, Johnson WA. The formation of citric and alpha-ketoglutaric acids in the mammalian body. Biochem J. 1938 Jan;32(1):113–7. PMID: 16746585; PMCID: PMC1264001.; Krebs HA, Johnson WA. Acetopyruvic acid (alphagamma-diketovaleric acid) as an intermediate metabolite in animal tissues. Biochem J. 1937 May;31(5):772–9. PMID: 16746397; PMCID: PMC1267003. |
| glycerol-3-phosphate to cytochrome bo oxidase electron transfer Accession ID: BioCyc:META_PWY0-1561 |
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Schryvers A, Lohmeier E, Weiner JH. Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. Journal of Biological Chemistry. 1978 Feb;253(3):783–8. doi: 10.1016/s0021-9258(17)38171-1.; Freedberg WB, Lin ECC. Three Kinds of Controls Affecting the Expression of the glp Regulon in Escherichia coli. J Bacteriol. 1973 Sep;115(3):816–23. doi: 10.1128/jb.115.3.816-823.1973. |
| autoinducer AI-2 biosynthesis II (Vibrio) Accession ID: BioCyc:META_PWY-6154 |
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Chen X, Schauder S, Potier N, Van Dorsselaer A, Pelczer I, Bassler BL, Hughson FM. Structural identification of a bacterial quorum-sensing signal containing boron. Nature. 2002 Jan 31;415(6871):545–9. doi: 10.1038/415545a. PMID: 11823863. |
| S-methyl-5'-thioadenosine degradation IV Accession ID: BioCyc:META_PWY0-1391 |
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Hughes JA. In vivo hydrolysis ofS-adenosyl-L-methionine inEscherichia coliincreases export of 5-methylthioribose. Can. J. Microbiol. 2006 Jun 01;52(6):599–602. doi: 10.1139/w06-008. |
| S-methyl-5'-thioadenosine degradation III Accession ID: BioCyc:META_PWY-6753 |
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Guan R, Ho M, Almo SC, Schramm VL. Methylthioinosine Phosphorylase fromPseudomonas aeruginosa. Structure and Annotation of a Novel Enzyme in Quorum Sensing. Biochemistry. 2011 Jan 25;50(7):1247–54. doi: 10.1021/bi101642d.; Ting L, Shi W, Lewandowicz A, Singh V, Mwakingwe A, Birck MR, Ringia EAT, Bench G, Madrid DC, Tyler PC, Evans GB, Furneaux RH, Schramm VL, Kim K. Targeting a Novel Plasmodium falciparum Purine Recycling Pathway with Specific Immucillins. Journal of Biological Chemistry. 2005 Mar;280(10):9547–54. doi: 10.1074/jbc.m412693200. |
| β-D-mannosyl phosphomycoketide biosynthesis Accession ID: BioCyc:META_PWY-7740 |
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Matsunaga I, Bhatt A, Young DC, Cheng TY, Eyles SJ, Besra GS, Briken V, Porcelli SA, Costello CE, Jacobs WR, Moody DB. Mycobacterium tuberculosis pks12 produces a novel polyketide presented by CD1c to T cells. J Exp Med. 2004 Dec 20;200(12):1559–69. PMID: 15611286; PMCID: PMC2211992. |
| S-methyl-5'-thioadenosine degradation II Accession ID: BioCyc:META_PWY-6756 |
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Della Ragione F, Takabayashi K, Mastropietro S, Mercurio C, Oliva A, Russo GL, Della Pietra V, Borriello A, Nobori T, Carson DA, Zappia V. Purification and Characterization of Recombinant Human 5'-Methylthioadenosine Phosphorylase: Definite Identification of Coding cDNA. Biochemical and Biophysical Research Communications. 1996 Jun;223(3):514–9. doi: 10.1006/bbrc.1996.0926. |
| protein N-glycosylation initial phase (eukaryotic) Accession ID: BioCyc:META_MANNOSYL-CHITO-DOLICHOL-BIOSYNTHESIS |
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Helenius A, Aebi M. Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem. 2004;73():1019–49. doi: 10.1146/annurev.biochem.73.011303.073752. PMID: 15189166.; Chantret I, Dancourt J, Dupré T, Delenda C, Bucher S, Vuillaumier-Barrot S, Ogier de Baulny H, Peletan C, Danos O, Seta N, Durand G, Oriol R, Codogno P, Moore SE. A deficiency in dolichyl-P-glucose:Glc1Man9GlcNAc2-PP-dolichyl alpha3-glucosyltransferase defines a new subtype of congenital disorders of glycosylation. J Biol Chem. 2003 Mar 14;278(11):9962–71. doi: 10.1074/jbc.m211950200. PMID: 12480927.; Burda P, Aebi M. The dolichol pathway of N-linked glycosylation. Biochimica et Biophysica Acta (BBA) - General Subjects. 1999 Jan;1426(2):239–57. doi: 10.1016/s0304-4165(98)00127-5.; Runge KW, Robbins PW. A new yeast mutation in the glucosylation steps of the asparagine-linked glycosylation pathway. Formation of a novel asparagine-linked oligosaccharide containing two glucose residues. Journal of Biological Chemistry. 1986 Nov;261(33):15582–90. doi: 10.1016/s0021-9258(18)66754-7. |
| NADH to cytochrome bo oxidase electron transfer I Accession ID: BioCyc:META_PWY0-1335 |
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| Lipid A-core biosynthesis (E. coli K-12) Accession ID: BioCyc:META_LIPA-CORESYN-PWY |
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Raetz CRH, Whitfield C. Lipopolysaccharide Endotoxins. Annu. Rev. Biochem. 2002 Jun;71(1):635–700. doi: 10.1146/annurev.biochem.71.110601.135414. |
| chitin derivatives degradation Accession ID: BioCyc:META_PWY-6906 |
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Hunt DE, Gevers D, Vahora NM, Polz MF. Conservation of the chitin utilization pathway in the Vibrionaceae. Appl Environ Microbiol. 2008 Jan;74(1):44–51. PMID: 17933912; PMCID: PMC2223224.; Park JK, Wang LX, Roseman S. Isolation of a glucosamine-specific kinase, a unique enzyme of Vibrio cholerae. J Biol Chem. 2002 May 03;277(18):15573–8. doi: 10.1074/jbc.m107953200. PMID: 11850417. |
| reductive acetyl coenzyme A pathway I (homoacetogenic bacteria) Accession ID: BioCyc:META_CODH-PWY |
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Diekert G, Wohlfarth G. Metabolism of homocetogens. Antonie Van Leeuwenhoek. 1994;66(1-3):209–21. doi: 10.1007/bf00871640. PMID: 7747932. |