Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| superpathway of b heme biosynthesis from glycine Accession ID: BioCyc:META_PWY-5920 |
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Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biology. 2004 Dec 22;6(1):r2. doi: 10.1186/gb-2004-6-1-r2.; Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery. Genome Res. 2004 Apr 12;14(5):917–24. doi: 10.1101/gr.2050304.; Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 01;32(Database issue):D311–4. PMID: 14681421; PMCID: PMC308767.; Frankenberg N, Moser J, Jahn D. Bacterial heme biosynthesis and its biotechnological application. Applied Microbiology and Biotechnology. 2003 Dec 01;63(2):115–27. doi: 10.1007/s00253-003-1432-2.; Panek H, O'Brian MR. A whole genome view of prokaryotic haem biosynthesis. Microbiology (Reading). 2002 Aug;148(Pt 8):2273–82. doi: 10.1099/00221287-148-8-2273. PMID: 12177321. |
| CDP-diacylglycerol biosynthesis I Accession ID: BioCyc:META_PWY-5667 |
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Larson TJ, Lightner VA, Green PR, Modrich P, Bell RM. Membrane phospholipid synthesis in Escherichia coli. Identification of the sn-glycerol-3-phosphate acyltransferase polypeptide as the plsB gene product. Journal of Biological Chemistry. 1980 Oct;255(19):9421–6. doi: 10.1016/s0021-9258(19)70579-1. |
| anaerobic energy metabolism (invertebrates, mitochondrial) Accession ID: BioCyc:META_PWY-7384 |
|
Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu R, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiol Mol Biol Rev. 2012 Jun;76(2):444–95. doi: 10.1128/mmbr.05024-11.; Tielens AG, Rotte C, van Hellemond JJ, Martin W. Mitochondria as we don't know them. Trends Biochem Sci. 2002 Nov;27(11):564–72. doi: 10.1016/s0968-0004(02)02193-x. PMID: 12417132.; Van Hellemond JJ, Klockiewicz M, Gaasenbeek CPH, Roos MH, Tielens AGM. Rhodoquinone and Complex II of the Electron Transport Chain in Anaerobically Functioning Eukaryotes. Journal of Biological Chemistry. 1995 Dec;270(52):31065–70. doi: 10.1074/jbc.270.52.31065.; Grieshaber MK, Hardewig I, Kreutzer U, Pörtner HO. Physiological and metabolic responses to hypoxia in invertebrates. Rev Physiol Biochem Pharmacol. 1994;125():43–147. doi: 10.1007/bfb0030909. PMID: 7984874.; Campbell T, Rubin N, Komuniecki R. Succinate-dependent energy generation in Ascaris suum mitochondria. Molecular and Biochemical Parasitology. 1989 Feb;33(1):1–12. doi: 10.1016/0166-6851(89)90036-4.; Saz HJ, Pietrzak SM. Phosphorylation associated with succinate decarboxylation to propionate in Ascaris mitochondria. Archives of Biochemistry and Biophysics. 1980 Jul;202(2):388–95. doi: 10.1016/0003-9861(80)90442-7. |
| superpathway of (R,R)-butanediol biosynthesis Accession ID: BioCyc:META_P125-PWY |
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| superpathway of 2,3-butanediol biosynthesis Accession ID: BioCyc:META_PWY-6396 |
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| L-threonine degradation III (to methylglyoxal) Accession ID: BioCyc:META_THRDLCTCAT-PWY |
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Epperly BR, Dekker EE. Inactivation of Escherichia coli L-threonine dehydrogenase by 2,3-butanedione. Evidence for a catalytically essential arginine residue. J Biol Chem. 1989 Nov 05;264(31):18296–301. PMID: 2681195.; Boylan SA, Dekker EE. L-threonine dehydrogenase. Purification and properties of the homogeneous enzyme from Escherichia coli K-12. Journal of Biological Chemistry. 1981 Feb;256(4):1809–15. doi: 10.1016/s0021-9258(19)69880-7.; Komatsubara S, Murata K, Kisumi M, Chibata I. Threonine degradation by Serratia marcescens. J Bacteriol. 1978 Aug;135(2):318–23. doi: 10.1128/jb.135.2.318-323.1978.; Higgins IJ, Turner JM, Willetts AJ. Enzyme mechanism of aminoacetone metabolism by micro-organisms. Nature. 1967 Aug 19;215(5103):887–8. doi: 10.1038/215887a0. PMID: 4292865. |
| superpathway of (R,R)-butanediol biosynthesis Accession ID: BioCyc:LEISH_P125-PWY |
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| superpathway of (R,R)-butanediol biosynthesis Accession ID: BioCyc:TRYPANO_P125-PWY |
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| (R)-acetoin biosynthesis I Accession ID: BioCyc:ANTHRA_PWY-5938 |
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| superpathway of (R,R)-butanediol biosynthesis Accession ID: BioCyc:BSUB_P125-PWY |
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| (S)-acetoin biosynthesis Accession ID: BioCyc:CORYNE_PWY-6389 |
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| myricetin gentiobioside biosynthesis Accession ID: BioCyc:META_PWY-7140 |
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Vepsäläinen S, Koivisto H, Pekkarinen E, Mäkinen P, Dobson G, McDougall GJ, Stewart D, Haapasalo A, Karjalainen RO, Tanila H, Hiltunen M. Anthocyanin-enriched bilberry and blackcurrant extracts modulate amyloid precursor protein processing and alleviate behavioral abnormalities in the APP/PS1 mouse model of Alzheimer's disease. The Journal of Nutritional Biochemistry. 2013 Jan;24(1):360–70. doi: 10.1016/j.jnutbio.2012.07.006.; Fiori J, Naldi M, Bartolini M, Andrisano V. Disclosure of a fundamental clue for the elucidation of the myricetin mechanism of action as amyloid aggregation inhibitor by mass spectrometry. Electrophoresis. 2012 Nov;33(22):3380–6. doi: 10.1002/elps.201200186. PMID: 22961751.; Chobot V, Hadacek F. Exploration of pro-oxidant and antioxidant activities of the flavonoid myricetin. Redox Report. 2011 Nov;16(6):242–7. doi: 10.1179/1351000211y.0000000015.; Kumar D, Kumar S, Gupta J, Arya R, Gupta A. A review on chemical and biological properties of Cayratia trifolia Linn. (Vitaceae). Pharmacogn Rev. 2011 Jul;5(10):184–8. PMID: 22279376; PMCID: PMC3263053.; Owens DK, McIntosh CA. Identification, recombinant expression, and biochemical characterization of a flavonol 3-O-glucosyltransferase clone from Citrus paradisi. Phytochemistry. 2009 Jul;70(11-12):1382–91. doi: 10.1016/j.phytochem.2009.07.027. PMID: 19733370.; Masada S, Terasaka K, Oguchi Y, Okazaki S, Mizushima T, Mizukami H. Functional and structural characterization of a flavonoid glucoside 1,6-glucosyltransferase from Catharanthus roseus. Plant Cell Physiol. 2009 Aug;50(8):1401–15. doi: 10.1093/pcp/pcp088. PMID: 19561332.; Oguchi Y, Masada S, Kondo T, Terasaka K, Mizukami H. Purification and characterization of UDP-glucose : curcumin glucoside 1,6-glucosyltransferase from Catharanthus roseus cell suspension cultures. Plant Cell Physiol. 2007 Nov;48(11):1635–43. doi: 10.1093/pcp/pcm138. PMID: 17940060.; TAHARA S. A Journey of Twenty-Five Years through the Ecological Biochemistry of Flavonoids. Bioscience, Biotechnology, and Biochemistry. 2007 Jun 23;71(6):1387–404. doi: 10.1271/bbb.70028.; Martens S, Mithöfer A. Flavones and flavone synthases. Phytochemistry. 2005 Oct;66(20):2399–407. doi: 10.1016/j.phytochem.2005.07.013. PMID: 16137727.; Vogt T, Jones P. Glycosyltransferases in plant natural product synthesis: characterization of a supergene family. Trends Plant Sci. 2000 Sep;5(9):380–6. doi: 10.1016/s1360-1385(00)01720-9. PMID: 10973093. |
| pyruvate to cytochrome bo oxidase electron transfer Accession ID: BioCyc:META_PWY-7544 |
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Carter K, Gennis RB. Reconstitution of the Ubiquinone-dependent pyruvate oxidase system of Escherichia coli with the cytochrome o terminal oxidase complex. Journal of Biological Chemistry. 1985 Sep;260(20):10986–90. doi: 10.1016/s0021-9258(17)39135-4. |
| superpathway of anaerobic energy metabolism (invertebrates) Accession ID: BioCyc:META_PWY-7389 |
|
Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu R, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiol Mol Biol Rev. 2012 Jun;76(2):444–95. doi: 10.1128/mmbr.05024-11.; Fukuda W, Fukui T, Atomi H, Imanaka T. First Characterization of an Archaeal GTP-Dependent Phosphoenolpyruvate Carboxykinase from the Hyperthermophilic Archaeon Thermococcus kodakaraensis KOD1. J Bacteriol. 2004 Jul 15;186(14):4620–7. doi: 10.1128/jb.186.14.4620-4627.2004.; Tielens AG, Rotte C, van Hellemond JJ, Martin W. Mitochondria as we don't know them. Trends Biochem Sci. 2002 Nov;27(11):564–72. doi: 10.1016/s0968-0004(02)02193-x. PMID: 12417132.; Van Hellemond JJ, Klockiewicz M, Gaasenbeek CPH, Roos MH, Tielens AGM. Rhodoquinone and Complex II of the Electron Transport Chain in Anaerobically Functioning Eukaryotes. Journal of Biological Chemistry. 1995 Dec;270(52):31065–70. doi: 10.1074/jbc.270.52.31065. |
| superpathway of bacteriochlorophyll a biosynthesis Accession ID: BioCyc:META_PWY-5529 |
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Gough SP, Petersen BO, Duus JØ. Anaerobic chlorophyll isocyclic ring formation inRhodobacter capsulatusrequires a cobalamin cofactor. Proc. Natl. Acad. Sci. U.S.A. 2000 Jun 06;97(12):6908–13. doi: 10.1073/pnas.97.12.6908.; Suzuki JY, Bollivar DW, Bauer CE. Genetic analysis of chlorophyll biosynthesis. Annu Rev Genet. 1997;31():61–89. doi: 10.1146/annurev.genet.31.1.61. PMID: 9442890. |
| superpathway of L-threonine metabolism Accession ID: BioCyc:META_THREOCAT-PWY |
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Liu Y, Leal NA, Sampson EM, Johnson CLV, Havemann GD, Bobik TA. PduL Is an Evolutionarily Distinct Phosphotransacylase Involved in B 12 -Dependent 1,2-Propanediol Degradation by Salmonella enterica Serovar Typhimurium LT2. J Bacteriol. 2007 Mar;189(5):1589–96. doi: 10.1128/jb.01151-06.; Epperly BR, Dekker EE. Inactivation of Escherichia coli L-threonine dehydrogenase by 2,3-butanedione. Evidence for a catalytically essential arginine residue. J Biol Chem. 1989 Nov 05;264(31):18296–301. PMID: 2681195.; Boylan SA, Dekker EE. L-threonine dehydrogenase. Purification and properties of the homogeneous enzyme from Escherichia coli K-12. Journal of Biological Chemistry. 1981 Feb;256(4):1809–15. doi: 10.1016/s0021-9258(19)69880-7. |
| CDP-diacylglycerol biosynthesis I Accession ID: BioCyc:ECO_PWY-5667 |
|
Parsons JB, Rock CO. Bacterial lipids: Metabolism and membrane homeostasis. Progress in Lipid Research. 2013 Jul;52(3):249–76. doi: 10.1016/j.plipres.2013.02.002. |
| superpathway of L-threonine metabolism Accession ID: BioCyc:ECO_THREOCAT-PWY |
|
Epperly BR, Dekker EE. Inactivation of Escherichia coli L-threonine dehydrogenase by 2,3-butanedione. Evidence for a catalytically essential arginine residue. J Biol Chem. 1989 Nov 05;264(31):18296–301. PMID: 2681195.; Boylan SA, Dekker EE. Growth, enzyme levels, and some metabolic properties of an Escherichia coli mutant grown on L-threonine as the sole carbon source. J Bacteriol. 1983 Oct;156(1):273–80. doi: 10.1128/jb.156.1.273-280.1983.; Boylan SA, Dekker EE. L-threonine dehydrogenase. Purification and properties of the homogeneous enzyme from Escherichia coli K-12. Journal of Biological Chemistry. 1981 Feb;256(4):1809–15. doi: 10.1016/s0021-9258(19)69880-7. |
| L-threonine degradation III (to methylglyoxal) Accession ID: BioCyc:ECO_THRDLCTCAT-PWY |
|
Epperly BR, Dekker EE. Inactivation of Escherichia coli L-threonine dehydrogenase by 2,3-butanedione. Evidence for a catalytically essential arginine residue. J Biol Chem. 1989 Nov 05;264(31):18296–301. PMID: 2681195.; Boylan SA, Dekker EE. Growth, enzyme levels, and some metabolic properties of an Escherichia coli mutant grown on L-threonine as the sole carbon source. J Bacteriol. 1983 Oct;156(1):273–80. doi: 10.1128/jb.156.1.273-280.1983.; Boylan SA, Dekker EE. L-threonine dehydrogenase. Purification and properties of the homogeneous enzyme from Escherichia coli K-12. Journal of Biological Chemistry. 1981 Feb;256(4):1809–15. doi: 10.1016/s0021-9258(19)69880-7.; Komatsubara S, Murata K, Kisumi M, Chibata I. Threonine degradation by Serratia marcescens. J Bacteriol. 1978 Aug;135(2):318–23. doi: 10.1128/jb.135.2.318-323.1978.; Higgins IJ, Turner JM, Willetts AJ. Enzyme mechanism of aminoacetone metabolism by micro-organisms. Nature. 1967 Aug 19;215(5103):887–8. doi: 10.1038/215887a0. PMID: 4292865. |
| pyruvate to cytochrome bd oxidase electron transfer Accession ID: BioCyc:ECO_PWY-7545 |
|
Koland JG, Miller MJ, Gennis RB. Reconstitution of the membrane-bound, ubiquinone-dependent pyruvate oxidase respiratory chain of Escherichia coli with the cytochrome d terminal oxidase. Biochemistry. 1984 Jan 31;23(3):445–53. doi: 10.1021/bi00298a008. PMID: 6367818. |