Pathways Knowlegdes

Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit

Pathway DOIs Note
superpathway of L-citrulline metabolism

Accession ID: BioCyc:META_PWY-5004		 -
glyoxylate assimilation

Accession ID: BioCyc:META_PWY-5744
  • 10.1016/s0021-9258(19)75797-4
  • 10.1073/pnas.0908356106
  • 10.1074/jbc.m201030200
  • 10.1128/jb.00659-06
 Zarzycki J, Brecht V, Müller M, Fuchs G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO 2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. U.S.A. 2009 Dec 15;106(50):21317–22. doi: 10.1073/pnas.0908356106.; Friedmann S, Alber BE, Fuchs G. Properties of Succinyl-Coenzyme A:d-Citramalate Coenzyme A Transferase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle ofChloroflexus aurantiacus. J Bacteriol. 2006 Sep 15;188(18):6460–8. doi: 10.1128/jb.00659-06.; Herter S, Fuchs G, Bacher A, Eisenreich W. A Bicyclic Autotrophic CO2 Fixation Pathway in Chloroflexus aurantiacus. Journal of Biological Chemistry. 2002 Jun;277(23):20277–83. doi: 10.1074/jbc.m201030200.; 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.
formaldehyde oxidation II (glutathione-dependent)

Accession ID: BioCyc:META_PWY-1801
  • 10.1021/bi00117a025
  • 10.1074/jbc.m600996200
 Gonzalez CF, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko AV, Yakunin AF. Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem. 2006 May 19;281(20):14514–22. doi: 10.1074/jbc.m600996200. PMID: 16567800.; Gutheil WG, Holmquist B, Vallee BL. Purification, characterization, and partial sequence of the glutathione-dependent formaldehyde dehydrogenase from Escherichia coli: a class III alcohol dehydrogenase. Biochemistry. 1992 Jan 21;31(2):475–81. doi: 10.1021/bi00117a025. PMID: 1731906.
glycolysis V (Pyrococcus)

Accession ID: BioCyc:META_P341-PWY
  • 10.1016/s0021-9258(17)32474-2
  • 10.1016/s1389-1723(02)80090-1
  • 10.1042/bj20021472
 Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MW, De Vos WM, Van Der Oost J. The unique features of glycolytic pathways in Archaea. Biochem J. 2003 Oct 15;375(Pt 2):231–46. PMID: 12921536; PMCID: PMC1223704.; Sakuraba H, Ohshima T. Novel energy metabolism in anaerobic hyperthermophilic archaea: a modified Embden-Meyerhof pathway. Journal of Bioscience and Bioengineering. 2002 May;93(5):441–8. doi: 10.1016/s1389-1723(02)80090-1.; Kengen SW, de Bok FA, van Loo ND, Dijkema C, Stams AJ, de Vos WM. Evidence for the operation of a novel Embden-Meyerhof pathway that involves ADP-dependent kinases during sugar fermentation by Pyrococcus furiosus. Journal of Biological Chemistry. 1994 Jul;269(26):17537–41. doi: 10.1016/s0021-9258(17)32474-2.
glycocholate metabolism (bacteria)

Accession ID: BioCyc:META_PWY-6518
  • 10.1194/jlr.r500013-jlr200
 Ridlon JM, Kang DJ, Hylemon PB: Bile salt biotransformations by human intestinal bacteria. J Lipid Res. 2006 Feb;47(2):241-59. doi: 10.1194/jlr.R500013-JLR200. Epub 2005 Nov 18.
UDP-α-D-xylose biosynthesis

Accession ID: BioCyc:META_PWY-4821
  • 10.1007/s00425-004-1471-7
  • 10.1007/s11103-004-7795-7
  • 10.1099/mic.0.040758-0
  • 10.1104/pp.009654
 Gu X, Lee SG, Bar-Peled M. Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase. Microbiology (Reading). 2011 Jan;157(Pt 1):260–9. PMID: 20847005; PMCID: PMC3068629.; Pattathil S, Harper AD, Bar-Peled M. Biosynthesis of UDP-xylose: characterization of membrane-bound AtUxs2. Planta. 2005 Jun;221(4):538–48. doi: 10.1007/s00425-004-1471-7. PMID: 15655675.; Bindschedler LV, Wheatley E, Gay E, Cole J, Cottage A, Bolwell GP. Characterisation and expression of the pathway from UDP-glucose to UDP-xylose in differentiating tobacco tissue. Plant Mol Biol. 2005 Jan;57(2):285–301. doi: 10.1007/s11103-004-7795-7. PMID: 15821883.; Harper AD, Bar-Peled M. Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms. Plant Physiol. 2002 Dec;130(4):2188–98. PMID: 12481102; PMCID: PMC166730.
cardiolipin biosynthesis I

Accession ID: BioCyc:META_PWY-5668
  • 10.1128/jb.108.1.219-226.1971
 Short SA, White DC. Metabolism of Phosphatidylglycerol, Lysylphosphatidylglycerol, and Cardiolipin of Staphylococcus aureus. J Bacteriol. 1971 Oct;108(1):219–26. doi: 10.1128/jb.108.1.219-226.1971.
superpathway of chorismate metabolism

Accession ID: BioCyc:META_ALL-CHORISMATE-PWY
  • 10.1021/bi0016523
 Keating TA, Marshall CG, Walsh CT. Reconstitution and characterization of the Vibrio cholerae vibriobactin synthetase from VibB, VibE, VibF, and VibH. Biochemistry. 2000 Dec 19;39(50):15522–30. doi: 10.1021/bi0016523. PMID: 11112538.
phosphatidylglycerol biosynthesis II (non-plastidic)

Accession ID: BioCyc:META_PWY4FS-8
  • 10.1111/j.1365-313x.2006.02790.x
 Xu C, Yu B, Cornish AJ, Froehlich JE, Benning C. Phosphatidylglycerol biosynthesis in chloroplasts of Arabidopsis mutants deficient in acyl-ACP glycerol-3- phosphate acyltransferase. Plant J. 2006 Jul;47(2):296–309. doi: 10.1111/j.1365-313x.2006.02790.x. PMID: 16774646.
rhamnogalacturonan type I degradation II (bacteria)

Accession ID: BioCyc:META_PWY-6771
  • 10.1002/prot.20410
  • 10.1016/j.bbrc.2006.07.034
  • 10.1016/j.jmb.2006.04.047
  • 10.1128/aem.00147-07
 Ochiai A, Itoh T, Kawamata A, Hashimoto W, Murata K. Plant Cell Wall Degradation by Saprophytic Bacillus subtilis Strains: Gene Clusters Responsible for Rhamnogalacturonan Depolymerization. Appl Environ Microbiol. 2007 Jun 15;73(12):3803–13. doi: 10.1128/aem.00147-07.; Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochemical and Biophysical Research Communications. 2006 Sep;347(4):1021–9. doi: 10.1016/j.bbrc.2006.07.034.; Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K. A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J Mol Biol. 2006 Jul 14;360(3):573–85. doi: 10.1016/j.jmb.2006.04.047. PMID: 16781735.; Zhang R, Minh T, Lezondra L, Korolev S, Moy SF, Collart F, Joachimiak A. 1.6 Å crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins. 2005 May 19;60(3):561–5. doi: 10.1002/prot.20410.
glycerol and glycerophosphodiester degradation

Accession ID: BioCyc:META_PWY0-381		 -
superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism

Accession ID: BioCyc:META_PWY-6358
  • 10.1038/320631a0
 Irvine RF, Letcher AJ, Heslop JP, Berridge MJ. The inositol tris/tetrakisphosphate pathway--demonstration of Ins(1,4,5)P3 3-kinase activity in animal tissues. Nature. 1986 Apr;320(6063):631–4. doi: 10.1038/320631a0. PMID: 3010126.
superpathway of phosphatidylcholine biosynthesis

Accession ID: BioCyc:META_PWY4FS-5
  • 10.1016/j.febslet.2004.04.015
  • 10.1104/pp.88.4.1338
 Tasseva G, Richard L, Zachowski A. Regulation of phosphatidylcholine biosynthesis under salt stress involves choline kinases in Arabidopsis thaliana. FEBS Lett. 2004 May 21;566(1-3):115–20. doi: 10.1016/j.febslet.2004.04.015. PMID: 15147879.; Datko AH, Mudd SH. Enzymes of Phosphatidylcholine Synthesis in Lemna, Soybean, and Carrot. Plant Physiol. 1988 Dec 01;88(4):1338–48. doi: 10.1104/pp.88.4.1338.
L-carnitine biosynthesis

Accession ID: BioCyc:META_PWY-6100
  • 10.1016/j.ab.2006.04.007
  • 10.1016/j.mam.2004.06.006
  • 10.1016/s0021-9258(17)34915-3
  • 10.1016/s0021-9258(17)40983-5
  • 10.1042/0264-6021:3610417
 van Vlies N, Wanders RJ, Vaz FM. Measurement of carnitine biosynthesis enzyme activities by tandem mass spectrometry: differences between the mouse and the rat. Anal Biochem. 2006 Jul 01;354(1):132–9. doi: 10.1016/j.ab.2006.04.007. PMID: 16707092.; Steiber A, Kerner J, Hoppel CL. Carnitine: a nutritional, biosynthetic, and functional perspective. Mol Aspects Med. 2004 Oct;25(5-6):455–73. doi: 10.1016/j.mam.2004.06.006. PMID: 15363636.; Vaz FM, Wanders RJ. Carnitine biosynthesis in mammals. Biochem J. 2002 Feb 01;361(Pt 3):417–29. PMID: 11802770; PMCID: PMC1222323.; Hulse JD, Ellis SR, Henderson LM. Carnitine biosynthesis. beta-Hydroxylation of trimethyllysine by an alpha-ketoglutarate-dependent mitochondrial dioxygenase. Journal of Biological Chemistry. 1978 Mar;253(5):1654–9. doi: 10.1016/s0021-9258(17)34915-3.; Kaufman RA, Broquist HP. Biosynthesis of carnitine in Neurospora crassa. Journal of Biological Chemistry. 1977 Nov;252(21):7437–9. doi: 10.1016/s0021-9258(17)40983-5.
superpathway of glyoxylate bypass and TCA

Accession ID: BioCyc:META_TCA-GLYOX-BYPASS
  • 10.1038/179988a0
  • 10.1038/291381a0
 Baldwin JE, Krebs H. The evolution of metabolic cycles. Nature. 1981 Jun 04;291(5814):381–2. doi: 10.1038/291381a0. PMID: 7242661.; KORNBERG HL, KREBS HA. Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle. Nature. 1957 May 18;179(4568):988–91. doi: 10.1038/179988a0. PMID: 13430766.
butane degradation

Accession ID: BioCyc:META_PWY-7780
  • 10.1099/13500872-145-5-1173
 Arp DJ. Butane metabolism by butane-grown 'Pseudomonas butanovora'. Microbiology (Reading). 1999 May;145 ( Pt 5)():1173–80. doi: 10.1099/13500872-145-5-1173. PMID: 10376833.
coral bioluminescence

Accession ID: BioCyc:META_PWY-7914		 -
2'-deoxy-α-D-ribose 1-phosphate degradation

Accession ID: BioCyc:META_PWY-7180		 -
oxygenic photosynthesis

Accession ID: BioCyc:META_PHOTOALL-PWY
  • 10.1016/0005-2728(77)90041-x
  • 10.1038/nsmb.1559
 Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W. Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride. Nature Structural & Molecular Biology. 2009 Feb 15;16(3):334–42. doi: 10.1038/nsmb.1559.; Knaff DB, Malkin R, Clark Myron J, Stoller M. The role of plastoquinone and ß-carotene in the primary reaction of plant Photosystem II. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1977 Mar;459(3):402–11. doi: 10.1016/0005-2728(77)90041-x.
eupatolitin 3-O-glucoside biosynthesis

Accession ID: BioCyc:META_PWY-7157
  • 10.1002/pca.1014
  • 10.1002/rcm.1697
  • 10.1016/j.phytochem.2009.04.017
  • 10.1126/science.177.4048.528
  • 10.1242/jeb.204.14.2571
  • 10.1515/znc-2007-5-603
  • 10.3390/molecules15031562
 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.