Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| sesamin biosynthesis Accession ID: BioCyc:META_PWY-5469 |
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Ono E, Nakai M, Fukui Y, Tomimori N, Fukuchi-Mizutani M, Saito M, Satake H, Tanaka T, Katsuta M, Umezawa T, Tanaka Y. Formation of two methylenedioxy bridges by a Sesamum CYP81Q protein yielding a furofuran lignan, (+)-sesamin. Proc. Natl. Acad. Sci. U.S.A. 2006 Jun 27;103(26):10116–21. doi: 10.1073/pnas.0603865103.; Nakano D, Itoh C, Ishii F, Kawanishi H, Takaoka M, Kiso Y, Tsuruoka N, Tanaka T, Matsumura Y. Effects of Sesamin on Aortic Oxidative Stress and Endothelial Dysfunction in Deoxycorticosterone Acetate-Salt Hypertensive Rats. Biological & Pharmaceutical Bulletin. 2003;26(12):1701–5. doi: 10.1248/bpb.26.1701.; IKEDA S, KAGAYA M, KOBAYASHI K, TOHYAMA T, KISO Y, HIGUCHI N, YAMASHITA K. Dietary Sesame Lignans Decrease Lipid Peroxidation in Rats Fed Docosahexaenoic Acid. Journal of Nutritional Science and Vitaminology, J Nutr Sci Vitaminol. 2003;49(4):270–6. doi: 10.3177/jnsv.49.270.; Nakai M, Harada M, Nakahara K, Akimoto K, Shibata H, Miki W, Kiso Y. Novel antioxidative metabolites in rat liver with ingested sesamin. J Agric Food Chem. 2003 Mar 12;51(6):1666–70. doi: 10.1021/jf0258961. PMID: 12617602.; Ikeda S, Tohyama T, Yamashita K. Dietary sesame seed and its lignans inhibit 2,7,8-trimethyl- 2(2'-carboxyethyl)-6-hydroxychroman excretion into urine of rats fed gamma-tocopherol. J Nutr. 2002 May;132(5):961–6. doi: 10.1093/jn/132.5.961. PMID: 11983822.; Utsunomiya T, Chavali SR, Zhong WW, Forse RA. Effects of sesamin-supplemented dietary fat emulsions on the ex vivo production of lipopolysaccharide-induced prostanoids and tumor necrosis factor a in rats. The American Journal of Clinical Nutrition. 2000 Sep;72(3):804–8. doi: 10.1093/ajcn/72.3.804. |
| 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. |
| (4S)-carvone biosynthesis Accession ID: BioCyc:META_PWY-7443 |
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Ishida T. Biotransformation of terpenoids by mammals, microorganisms, and plant-cultured cells. Chem Biodivers. 2005 May;2(5):569–90. doi: 10.1002/cbdv.200590038. PMID: 17192005.; Duetz WA, Bouwmeester H, van Beilen JB, Witholt B. Biotransformation of limonene by bacteria, fungi, yeasts, and plants. Applied Microbiology and Biotechnology. 2003 Mar 15;61(4):269–77. doi: 10.1007/s00253-003-1221-y.; Wagner K, Elmadfa I. Biological Relevance of Terpenoids. Ann Nutr Metab. 2003;47(3-4):95–106. doi: 10.1159/000070030.; MARUYAMA T, ITO M, KIUCHI F, HONDA G. Molecular Cloning, Functional Expression and Characterization of d-Limonene Synthase from Schizonepeta tenuifolia. Biological & Pharmaceutical Bulletin. 2001;24(4):373–7. doi: 10.1248/bpb.24.373.; van der Werf MJ, van der Ven C, Barbirato F, Eppink MH, de Bont JA, van Berkel WJ. Stereoselective carveol dehydrogenase from Rhodococcus erythropolis DCL14. A novel nicotinoprotein belonging to the short chain dehydrogenase/reductase superfamily. J Biol Chem. 1999 Sep 10;274(37):26296–304. doi: 10.1074/jbc.274.37.26296. PMID: 10473585.; Bouwmeester, Gershenzon, Konings, Croteau. Biosynthesis of the monoterpenes limonene and carvone in the fruit of caraway. I. Demonstration Of enzyme activities and their changes with development . Plant Physiol. 1998 Jul;117(3):901–12. PMID: 9662532; PMCID: PMC34944.; Gershenzon J, Maffei M, Croteau R. Biochemical and Histochemical Localization of Monoterpene Biosynthesis in the Glandular Trichomes of Spearmint (Mentha spicata). Plant Physiol. 1989 Apr 01;89(4):1351–7. doi: 10.1104/pp.89.4.1351. |
| heme degradation IV Accession ID: BioCyc:META_PWY-7843 |
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Ouellet YH, Ndiaye CT, Gagné SM, Sebilo A, Suits MDL, Jubinville É, Jia Z, Ivancich A, Couture M. An alternative reaction for heme degradation catalyzed by the Escherichia coli O157:H7 ChuS protein: Release of hematinic acid, tripyrrole and Fe(III). Journal of Inorganic Biochemistry. 2016 Jan;154():103–13. doi: 10.1016/j.jinorgbio.2015.11.002. |
| heme degradation II Accession ID: BioCyc:META_PWY-7845 |
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Wegele R, Tasler R, Zeng Y, Rivera M, Frankenberg-Dinkel N. The Heme Oxygenase(s)-Phytochrome System of Pseudomonas aeruginosa. Journal of Biological Chemistry. 2004 Oct;279(44):45791–802. doi: 10.1074/jbc.m408303200. |
| superpathway of aromatic compound degradation via 2-hydroxypentadienoate Accession ID: BioCyc:META_PWY-6954 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Kasai D, Fujinami T, Abe T, Mase K, Katayama Y, Fukuda M, Masai E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J Bacteriol. 2009 Nov;191(21):6758–68. PMID: 19717587; PMCID: PMC2795304.; Takenaka S, Sato T, Koshiya J, Murakami S, Aoki K. Gene cloning and characterization of a deaminase from the 4-amino-3-hydroxybenzoate-assimilating Bordetella sp. strain 10d. FEMS Microbiol Lett. 2009 Sep;298(1):93–8. doi: 10.1111/j.1574-6968.2009.01699.x. PMID: 19594622.; Harwood CS, Parales RE. The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol. 1996;50():553–90. doi: 10.1146/annurev.micro.50.1.553. PMID: 8905091.; Kukor JJ, Olsen RH. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J Bacteriol. 1991 Aug;173(15):4587–94. doi: 10.1128/jb.173.15.4587-4594.1991.; Menn FM, Zylstra GJ, Gibson DT. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene. 1991 Jul 31;104(1):91–4. doi: 10.1016/0378-1119(91)90470-v. PMID: 1916282.; Kishore G, Sugumaran M, Vaidyanathan CS. Metabolism of DL-(+/-)-phenylalanine by Aspergillus niger. J Bacteriol. 1976 Oct;128(1):182–91. doi: 10.1128/jb.128.1.182-191.1976.; Wheelis ML, Stanier RY. The genetic control of dissimilatory pathways in Pseudomonas putida. Genetics. 1970 Oct;66(2):245–66. PMID: 5525301; PMCID: PMC1212492. |
| taxol biosynthesis Accession ID: BioCyc:META_PWY-5660 |
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Long RM, Croteau R. Preliminary assessment of the C13-side chain 2'-hydroxylase involved in Taxol biosynthesis. Biochemical and Biophysical Research Communications. 2005 Dec;338(1):410–7. doi: 10.1016/j.bbrc.2005.08.119.; Chau M, Croteau R. Molecular cloning and characterization of a cytochrome P450 taxoid 2alpha-hydroxylase involved in Taxol biosynthesis. Arch Biochem Biophys. 2004 Jul 01;427(1):48–57. doi: 10.1016/j.abb.2004.04.016. PMID: 15178487.; Chau M, Jennewein S, Walker K, Croteau R. Taxol biosynthesis: Molecular cloning and characterization of a cytochrome P450 taxoid 7 beta-hydroxylase. Chem Biol. 2004 May;11(5):663–72. doi: 10.1016/j.chembiol.2004.02.025. PMID: 15157877.; Jennewein S, Rithner CD, Williams RM, Croteau R. Taxoid metabolism: Taxoid 14beta-hydroxylase is a cytochrome P450-dependent monooxygenase. Arch Biochem Biophys. 2003 May 15;413(2):262–70. doi: 10.1016/s0003-9861(03)00090-0. PMID: 12729625.; Walker K, Fujisaki S, Long R, Croteau R. Molecular cloning and heterologous expression of the C-13 phenylpropanoid side chain-CoA acyltransferase that functions in Taxol biosynthesis. Proc Natl Acad Sci U S A. 2002 Oct 01;99(20):12715–20. PMID: 12232048; PMCID: PMC130526.; Walker K, Long R, Croteau R. The final acylation step in Taxol biosynthesis: Cloning of the taxoid C13-side-chain N -benzoyltransferase from Taxus. Proc. Natl. Acad. Sci. U.S.A. 2002 Jun 27;99(14):9166–71. doi: 10.1073/pnas.082115799.; Jennewein S, Rithner CD, Williams RM, Croteau RB. Taxol biosynthesis: taxane 13 alpha-hydroxylase is a cytochrome P450-dependent monooxygenase. Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13595–600. PMID: 11707604; PMCID: PMC61086.; Walker K, Croteau R. Taxol biosynthesis: Molecular cloning of a benzoyl- CoA:taxane 2a-O-benzoyltransferase cDNA fromTaxusand functional expression inEscherichia coli. Proc. Natl. Acad. Sci. U.S.A. 2000 Nov 28;97(25):13591–6. doi: 10.1073/pnas.250491997.; Wildung MR, Croteau R. A cDNA Clone for Taxadiene Synthase, the Diterpene Cyclase That Catalyzes the Committed Step of Taxol Biosynthesis. Journal of Biological Chemistry. 1996 Apr;271(16):9201–4. doi: 10.1074/jbc.271.16.9201. |
| phycoviolobilin biosynthesis Accession ID: BioCyc:META_PWY-7578 |
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Blot N, Wu X, Thomas J, Zhang J, Garczarek L, Böhm S, Tu J, Zhou M, Plöscher M, Eichacker L, Partensky F, Scheer H, Zhao K. Phycourobilin in Trichromatic Phycocyanin from Oceanic Cyanobacteria Is Formed Post-translationally by a Phycoerythrobilin Lyase-Isomerase. Journal of Biological Chemistry. 2009 Apr;284(14):9290–8. doi: 10.1074/jbc.m809784200.; Zhao KH, Deng MG, Zheng M, Zhou M, Parbel A, Storf M, Meyer M, Strohmann B, Scheer H. Novel activity of a phycobiliprotein lyase: both the attachment of phycocyanobilin and the isomerization to phycoviolobilin are catalyzed by the proteins PecE and PecF encoded by the phycoerythrocyanin operon. FEBS Lett. 2000 Mar 03;469(1):9–13. doi: 10.1016/s0014-5793(00)01245-x. PMID: 10708746. |
| phycocyanobilin biosynthesis Accession ID: BioCyc:META_PWY-5917 |
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Frankenberg N, Mukougawa K, Kohchi T, Lagarias JC. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell. 2001 Apr;13(4):965–78. PMID: 11283349; PMCID: PMC135530. |
| nitrogen fixation I (ferredoxin) Accession ID: BioCyc:META_N2FIX-PWY |
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Eady RR, Smith BE, Cook KA, Postgate JR. Nitrogenase of Klebsiella pneumoniae. Purification and properties of the component proteins. Biochem J. 1972 Jul;128(3):655–75. PMID: 4344006; PMCID: PMC1173817.; Vandecasteele J, Burris RH. Purification and Properties of the Constituents of the Nitrogenase Complex from Clostridium pasteurianum. J Bacteriol. 1970 Mar;101(3):794–801. doi: 10.1128/jb.101.3.794-801.1970. |
| colchicine biosynthesis Accession ID: BioCyc:META_PWY-5846 |
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| eupatolitin 3-O-glucoside biosynthesis Accession ID: BioCyc:META_PWY-7157 |
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Khan AL, Hussain J, Hamayun M, Gilani SA, Ahmad S, Rehman G, Kim YH, Kang SM, Lee IJ. Secondary metabolites from Inula britannica L. and their biological activities. Molecules. 2010 Mar 10;15(3):1562–77. PMID: 20336001; PMCID: PMC6257271.; Schlangen K, Miosic S, Castro A, Freudmann K, Luczkiewicz M, Vitzthum F, Schwab W, Gamsjäger S, Musso M, Halbwirth H. Formation of UV-honey guides in Rudbeckia hirta. Phytochemistry. 2009 May;70(7):889–98. doi: 10.1016/j.phytochem.2009.04.017. PMID: 19477473.; Guinot P, Gargadennec A, Valette G, Fruchier A, Andary C. Primary flavonoids in marigold dye: extraction, structure and involvement in the dyeing process. Phytochem Anal. 2008 Jan;19(1):46–51. doi: 10.1002/pca.1014. PMID: 17654539.; Papaioannou P, Lazari D, Karioti A, Souleles C, Heilmann J, Hadjipavlou-Litina D, Skaltsa H. Phenolic compounds with antioxidant activity from Anthemis tinctoria L. (Asteraceae). Z Naturforsch C J Biosci. 2007 May;62(5-6):326–30. doi: 10.1515/znc-2007-5-603. PMID: 17708435.; Parejo I, Jáuregui O, Viladomat F, Bastida J, Codina C. Characterization of acylated flavonoid- O -glycosides and methoxylated flavonoids from Tagetes maxima by liquid chromatography coupled to electrospray ionization tandem mass spectrometry. Rapid Comm Mass Spectrometry. 2004 Oct 27;18(23):2801–10. doi: 10.1002/rcm.1697.; Kevan PG, Chittka L, Dyer AG. Limits to the salience of ultraviolet: lessons from colour vision in bees and birds. J Exp Biol. 2001 Jul;204(Pt 14):2571–80. doi: 10.1242/jeb.204.14.2571. PMID: 11511673.; Li S, Mao W, Cao X, Liang S, Ding Z, Li N. Inhibition of rat lens aldose reductase by quercetagetin and patuletin. Yan Ke Xue Bao. 1991 Mar;7(1):29–30, 33. PMID: 1843126.; Thompson WR, Meinwald J, Aneshansley D, Eisner T. Flavonols: pigments responsible for ultraviolet absorption in nectar guide of flower. Science. 1972 Aug 11;177(4048):528–30. doi: 10.1126/science.177.4048.528. PMID: 5050486. |
| nitrate reduction I (denitrification) Accession ID: BioCyc:META_DENITRIFICATION-PWY |
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Knowles R. Denitrification. Microbiol Rev. 1982 Mar;46(1):43–70. doi: 10.1128/mr.46.1.43-70.1982.; Delwiche CC, Bryan BA. Denitrification. Annu Rev Microbiol. 1976;30():241–62. doi: 10.1146/annurev.mi.30.100176.001325. PMID: 10827. |
| 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis Accession ID: BioCyc:ARA_PWY-6890 |
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Ajjawi I, Tsegaye Y, Shintani D. Determination of the genetic, molecular, and biochemical basis of the Arabidopsis thaliana thiamin auxotroph th1. Archives of Biochemistry and Biophysics. 2007 Mar;459(1):107–14. doi: 10.1016/j.abb.2006.11.011. |
| phytochromobilin biosynthesis Accession ID: BioCyc:ARA_PWY-7170 |
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Emborg TJ, Walker JM, Noh B, Vierstra RD. Multiple heme oxygenase family members contribute to the biosynthesis of the phytochrome chromophore in Arabidopsis. Plant Physiol. 2006 Mar;140(3):856–68. PMID: 16428602; PMCID: PMC1400562. |
| 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis Accession ID: BioCyc:SHIGELLA_PWY-6890 |
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| 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis Accession ID: BioCyc:ECOL199310_PWY-6890 |
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| 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis Accession ID: BioCyc:AGRO_PWY-6890 |
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| 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis Accession ID: BioCyc:AURANTIMONAS_PWY-6890 |
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| 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis Accession ID: BioCyc:BSUB_PWY-6890 |
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