Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| C4 photosynthetic carbon assimilation cycle, PEPCK type Accession ID: BioCyc:META_PWY-7117 |
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Studer AJ, Gandin A, Kolbe AR, Wang L, Cousins AB, Brutnell TP. A Limited Role for Carbonic Anhydrase in C4 Photosynthesis as Revealed by a ca1ca2 Double Mutant in Maize. Plant Physiol. 2014 Jun;165(2):608–17. PMID: 24706552; PMCID: PMC4044840.; Wang Y, Bräutigam A, Weber AP, Zhu XG. Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis. J Exp Bot. 2014 Jul;65(13):3567–78. PMID: 24609651; PMCID: PMC4085956.; Rowlett RS. Structure and catalytic mechanism of ß-carbonic anhydrases. Subcell Biochem. 2014;75():53–76. doi: 10.1007/978-94-007-7359-2_4. PMID: 24146374.; Monti SM, De Simone G, Dathan NA, Ludwig M, Vullo D, Scozzafava A, Capasso C, Supuran CT. Kinetic and anion inhibition studies of a ß-carbonic anhydrase (FbiCA 1) from the C4 plant Flaveria bidentis. Bioorganic & Medicinal Chemistry Letters. 2013 Mar;23(6):1626–30. doi: 10.1016/j.bmcl.2013.01.087.; Pick TR, Bräutigam A, Schlüter U, Denton AK, Colmsee C, Scholz U, Fahnenstich H, Pieruschka R, Rascher U, Sonnewald U, Weber AP. Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell. 2011 Dec;23(12):4208–20. PMID: 22186372; PMCID: PMC3269860.; LUDWIG M. Carbonic anhydrase and the molecular evolution of C4 photosynthesis. Plant Cell & Environment. 2011 Jul;35(1):22–37. doi: 10.1111/j.1365-3040.2011.02364.x.; Tems U, Burnell JN. Characterization and expression of the maize ß-carbonic anhydrase gene repeat regions. Plant Physiol Biochem. 2010 Dec;48(12):945–51. doi: 10.1016/j.plaphy.2010.09.005. PMID: 20933433.; Tetu SG, Tanz SK, Vella N, Burnell JN, Ludwig M. The Flaveria bidentis ß-Carbonic Anhydrase Gene Family Encodes Cytosolic and Chloroplastic Isoforms Demonstrating Distinct Organ-Specific Expression Patterns. Plant Physiol. 2007 May 11;144(3):1316–27. doi: 10.1104/pp.107.098152.; Bailey KJ, Gray JE, Walker RP, Leegood RC. Coordinate Regulation of Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase by Light and CO2 during C4 Photosynthesis. Plant Physiol. 2007 Mar 02;144(1):479–86. doi: 10.1104/pp.106.093013.; Carnal NW, Agostino A, Hatch MD. Photosynthesis in Phosphoenolpyruvate Carboxykinase-Type C4 Plants: Mechanism and Regulation of C4 Acid Decarboxylation in Bundle Sheath Cells. Archives of Biochemistry and Biophysics. 1993 Nov;306(2):360–7. doi: 10.1006/abbi.1993.1524.; Murakami H, Sly WS. Purification and characterization of human salivary carbonic anhydrase. Journal of Biological Chemistry. 1987 Jan;262(3):1382–8. doi: 10.1016/s0021-9258(19)75797-4. |
| superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis Accession ID: BioCyc:META_PWY-7211 |
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Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57():805–36. doi: 10.1146/annurev.arplant.57.032905.105421. PMID: 16669783. |
| superpathway of L-methionine salvage and degradation Accession ID: BioCyc:META_PWY-5328 |
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Finkelstein JD. Methionine metabolism in mammals. The Journal of Nutritional Biochemistry. 1990 May;1(5):228–37. doi: 10.1016/0955-2863(90)90070-2.; Paxton R, Scislowski PW, Davis EJ, Harris RA. Role of branched-chain 2-oxo acid dehydrogenase and pyruvate dehydrogenase in 2-oxobutyrate metabolism. Biochem J. 1986 Mar 01;234(2):295–303. PMID: 3718468; PMCID: PMC1146565. |
| 2-carboxy-1,4-naphthoquinol biosynthesis Accession ID: BioCyc:ECO_PWY-5837 |
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| N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis Accession ID: BioCyc:ECO_PWY0-1587 |
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Thiaville PC, El Yacoubi B, Perrochia L, Hecker A, Prigent M, Thiaville JJ, Forterre P, Namy O, Basta T, de Crécy-Lagard V. Cross kingdom functional conservation of the core universally conserved threonylcarbamoyladenosine tRNA synthesis enzymes. Eukaryot Cell. 2014 Sep;13(9):1222–31. PMID: 25038083; PMCID: PMC4187629.; Deutsch C, El Yacoubi B, de Crécy-Lagard V, Iwata-Reuyl D. Biosynthesis of Threonylcarbamoyl Adenosine (t6A), a Universal tRNA Nucleoside. Journal of Biological Chemistry. 2012 Apr;287(17):13666–73. doi: 10.1074/jbc.m112.344028. |
| cyanate degradation Accession ID: BioCyc:ECO_CYANCAT-PWY |
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| inosine-5'-phosphate biosynthesis I Accession ID: BioCyc:ECO_PWY-6123 |
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Zhang Y, Morar M, Ealick SE. Structural biology of the purine biosynthetic pathway. Cellular and Molecular Life Sciences. 2008 Aug 19;65(23):3699–724. doi: 10.1007/s00018-008-8295-8.; Meyer E, Kappock TJ, Osuji C, Stubbe J. Evidence for the Direct Transfer of the Carboxylate of N5-Carboxyaminoimidazole Ribonucleotide (N5-CAIR) To Generate 4-Carboxy-5-aminoimidazole Ribonucleotide Catalyzed by Escherichia coli PurE, an N5-CAIR Mutase. Biochemistry. 1999 Feb 18;38(10):3012–8. doi: 10.1021/bi9827159.; He B, Smith JM, Zalkin H. Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR. J Bacteriol. 1992 Jan;174(1):130–6. doi: 10.1128/jb.174.1.130-136.1992. |
| aspartate biosynthesis Accession ID: BioCyc:YEAST_ASPBIO-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.; Huet C, Menendez J, Gancedo C, François JM. Regulation of pyc1 encoding pyruvate carboxylase isozyme I by nitrogen sources in Saccharomyces cerevisiae. European Journal of Biochemistry. 2000 Dec;267(23):6817–23. doi: 10.1046/j.1432-1033.2000.01779.x. |
| L-valine degradation I Accession ID: BioCyc:ARA_VALDEG-PWY |
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Schuster J, Binder S. The mitochondrial branched-chain aminotransferase (AtBCAT-1) is capable to initiate degradation of leucine, isoleucine and valine in almost all tissues in Arabidopsis thaliana. Plant Mol Biol. 2005 Jan;57(2):241–54. doi: 10.1007/s11103-004-7533-1. PMID: 15821880.; Taylor NL, Heazlewood JL, Day DA, Millar AH. Lipoic acid-dependent oxidative catabolism of alpha-keto acids in mitochondria provides evidence for branched-chain amino acid catabolism in Arabidopsis. Plant Physiol. 2004 Feb;134(2):838–48. PMID: 14764908; PMCID: PMC344558.; Diebold R, Schuster J, Däschner K, Binder S. The branched-chain amino acid transaminase gene family in Arabidopsis encodes plastid and mitochondrial proteins. Plant Physiol. 2002 Jun;129(2):540–50. PMID: 12068099; PMCID: PMC161671.; Fujiki Y, Sato T, Ito M, Watanabe A. Isolation and characterization of cDNA clones for the e1beta and E2 subunits of the branched-chain alpha-ketoacid dehydrogenase complex in Arabidopsis. J Biol Chem. 2000 Feb 25;275(8):6007–13. doi: 10.1074/jbc.275.8.6007. PMID: 10681595.; Gerbling H, Gerhardt B. Oxidative decarboxylation of branched-chain 2-oxo Fatty acids by higher plant peroxisomes. Plant Physiol. 1988 Sep;88(1):13–5. PMID: 16666252; PMCID: PMC1055516. |
| cyanate degradation Accession ID: BioCyc:ARA_CYANCAT-PWY |
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FABRE N, REITER IM, BECUWE-LINKA N, GENTY B, RUMEAU D. Characterization and expression analysis of genes encoding a and ß carbonic anhydrases in Arabidopsis. Plant Cell & Environment. 2007 Mar 02;30(5):617–29. doi: 10.1111/j.1365-3040.2007.01651.x.; Sunderhaus S, Dudkina NV, Jänsch L, Klodmann J, Heinemeyer J, Perales M, Zabaleta E, Boekema EJ, Braun H. Carbonic Anhydrase Subunits Form a Matrix-exposed Domain Attached to the Membrane Arm of Mitochondrial Complex I in Plants. Journal of Biological Chemistry. 2006 Mar;281(10):6482–8. doi: 10.1074/jbc.m511542200.; Perales M, Parisi G, Fornasari MS, Colaneri A, Villarreal F, González-Schain N, Echave J, Gómez-Casati D, Braun HP, Araya A, Zabaleta E. Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I. Plant Mol Biol. 2004 Dec;56(6):947–57. doi: 10.1007/s11103-004-6324-z. PMID: 15821992.; Parisi G, Perales M, Fornasari MS, Colaneri A, González-Schain N, Gómez-Casati D, Zimmermann S, Brennicke A, Araya A, Ferry JG, Echave J, Zabaleta E. Gamma carbonic anhydrases in plant mitochondria. Plant Mol Biol. 2004 May;55(2):193–207. doi: 10.1007/s11103-004-0149-7. PMID: 15604675.; Rowlett RS, Tu C, McKay MM, Preiss JR, Loomis RJ, Hicks KA, Marchione RJ, Strong JA, Donovan GS, Chamberlin JE. Kinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana. Arch Biochem Biophys. 2002 Aug 15;404(2):197–209. doi: 10.1016/s0003-9861(02)00243-6. PMID: 12147257.; Hewett-Emmett D, Tashian RE. Functional diversity, conservation, and convergence in the evolution of the alpha-, beta-, and gamma-carbonic anhydrase gene families. Mol Phylogenet Evol. 1996 Feb;5(1):50–77. doi: 10.1006/mpev.1996.0006. PMID: 8673298.; Fett JP, Coleman JR. Characterization and expression of two cDNAs encoding carbonic anhydrase in Arabidopsis thaliana. Plant Physiol. 1994 Jun;105(2):707–13. PMID: 7520589; PMCID: PMC159412.; Kim HJ, Bracey MH, Bartlett SG. Nucleotide sequence of a gene encoding carbonic anhydrase in Arabidopsis thaliana. Plant Physiol. 1994 May;105(1):449. PMID: 8029363; PMCID: PMC159376.; Majeau N, Coleman JR. Correlation of Carbonic Anhydrase and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Expression in Pea. Plant Physiol. 1994 Apr;104(4):1393–9. PMID: 12232176; PMCID: PMC159305.; Raines CA, Horsnell PR, Holder C, Lloyd JC. Arabidopsis thaliana carbonic anhydrase: cDNA sequence and effect of CO2 on mRNA levels. Plant Mol Biol. 1992 Dec;20(6):1143–8. doi: 10.1007/bf00028900. PMID: 1463847. |
| methylmalonyl pathway Accession ID: BioCyc:LEISH_PROPIONMET-PWY |
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| valine degradation I Accession ID: BioCyc:LEISH_VALDEG-PWY |
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Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Böhme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM. The genome of the African trypanosome Trypanosoma brucei. Science. 2005 Jul 15;309(5733):416–22. doi: 10.1126/science.1112642. PMID: 16020726. |
| superpathway of histidine, purine, and pyrimidine biosynthesis Accession ID: BioCyc:TRYPANO_PRPP-PWY |
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| inosine-5'-phosphate biosynthesis I Accession ID: BioCyc:TRYPANO_PWY-6123 |
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| urea cycle Accession ID: BioCyc:VCHO_PWY-4984 |
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| UMP biosynthesis II Accession ID: BioCyc:VCHO_PWY-7790 |
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| L-arginine biosynthesis I (via L-ornithine) Accession ID: BioCyc:VCHO_ARGSYN-PWY |
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| UMP biosynthesis Accession ID: BioCyc:SHIGELLA_PWY-5686 |
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| uridine-5'-phosphate biosynthesis Accession ID: BioCyc:PLASMO_PWY-5686 |
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| pyrimidine ribonucleotides de novo biosynthesis Accession ID: BioCyc:PLASMO_PWY0-162 |
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