Pathways Knowlegdes

Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit

Pathway DOIs Note
pyruvate to cytochrome bo oxidase electron transfer

Accession ID: BioCyc:ECO_PWY-7544
  • 10.1016/s0021-9258(17)39135-4
 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.
(R)-acetoin biosynthesis I

Accession ID: BioCyc:YEAST_PWY-5938		 -
(R)-acetoin biosynthesis I

Accession ID: BioCyc:CAULO_PWY-5938		 -
pyruvate fermentation to (R)-acetoin I

Accession ID: BioCyc:AGRO_PWY-5938		 -
(R)-acetoin biosynthesis I

Accession ID: BioCyc:CORYNE_PWY-5938		 -
kaempferol gentiobioside biosynthesis

Accession ID: BioCyc:META_PWY-7143
  • 10.1007/s11103-011-9815-8
  • 10.1016/j.foodchem.2012.07.043
  • 10.1016/j.phytochem.2005.07.013
  • 10.1016/j.phytochem.2009.07.027
  • 10.1016/j.phytochem.2011.07.020
  • 10.1039/c2mb25038a
  • 10.1093/pcp/pcm138
  • 10.1093/pcp/pcp088
  • 10.1177/1934578x1000501213
  • 10.1186/1749-8546-7-10
  • 10.1271/bbb.70028
  • 10.2147/ijn.s33670
 Lei Y, Chen J, Zhang W, Fu W, Wu G, Wei H, Wang Q, Ruan J. In vivo investigation on the potential of galangin, kaempferol and myricetin for protection of D-galactose-induced cognitive impairment. Food Chem. 2012 Dec 15;135(4):2702–7. doi: 10.1016/j.foodchem.2012.07.043. PMID: 22980861.; Liu L, Xie Y, Song Z, Shang S, Chen X. Influence of dietary flavonoids on the glycation of plasma proteins. Mol Biosyst. 2012 Aug;8(8):2183–7. doi: 10.1039/c2mb25038a. PMID: 22710272.; Luo H, Jiang B, Li B, Li Z, Jiang BH, Chen YC. Kaempferol nanoparticles achieve strong and selective inhibition of ovarian cancer cell viability. Int J Nanomedicine. 2012;7():3951–9. PMID: 22866004; PMCID: PMC3410694.; Guo AJ, Choi RC, Zheng KY, Chen VP, Dong TT, Wang Z, Vollmer G, Lau DT, Tsim KW. Kaempferol as a flavonoid induces osteoblastic differentiation via estrogen receptor signaling. Chinese Medicine. 2012 Apr 30;7(1):10. doi: 10.1186/1749-8546-7-10.; Saito N, Tatsuzawa F, Toki K, Shinoda K, Shigihara A, Honda T. The blue anthocyanin pigments from the blue flowers of Heliophila coronopifolia L. (Brassicaceae). Phytochemistry. 2011 Dec;72(17):2219–29. doi: 10.1016/j.phytochem.2011.07.020. PMID: 21903230.; Bollina V, Kushalappa AC, Choo TM, Dion Y, Rioux S. Identification of metabolites related to mechanisms of resistance in barley against Fusarium graminearum, based on mass spectrometry. Plant Mol Biol. 2011 Nov;77(4-5):355–70. doi: 10.1007/s11103-011-9815-8. PMID: 21830145.; Iwashina T, Yamaguchi M, Nakayama M, Onozaki T, Yoshida H, Kawanobu S, Ono H, Okamura M. Kaempferol Glycosides in the Flowers of Carnation and their Contribution to the Creamy White Flower Color. Natural Product Communications. 2010 Dec;5(12). doi: 10.1177/1934578x1000501213.; 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.
heme b biosynthesis I (aerobic)

Accession ID: BioCyc:META_HEME-BIOSYNTHESIS-II
  • 10.1007/s00253-003-1432-2
  • 10.1093/nar/gkh033
  • 10.1099/00221287-148-8-2273
  • 10.1101/gr.2050304
  • 10.1186/gb-2004-6-1-r2
 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.
tetrapyrrole biosynthesis II (from glycine)

Accession ID: BioCyc:META_PWY-5189
  • 10.1016/j.abb.2008.02.015
 Heinemann IU, Jahn M, Jahn D. The biochemistry of heme biosynthesis. Archives of Biochemistry and Biophysics. 2008 Jun;474(2):238–51. doi: 10.1016/j.abb.2008.02.015.
quercetin gentiotetraside biosynthesis

Accession ID: BioCyc:META_PWY-7137
  • 10.1002/biot.200700084
  • 10.1016/j.phytochem.2005.07.013
  • 10.1016/s0014-5793(03)01265-1
  • 10.1016/s0031-9422(00)00235-1
  • 10.1016/s0031-9422(03)00300-5
  • 10.1016/s1360-1385(00)01720-9
  • 10.1093/pcp/pcm138
  • 10.1093/pcp/pcp088
  • 10.1104/pp.110.161430
  • 10.1111/j.1365-313x.2005.02383.x
  • 10.2174/187220807780809445
 Dixon RA, Pasinetti GM. Flavonoids and isoflavonoids: from plant biology to agriculture and neuroscience. Plant Physiol. 2010 Oct;154(2):453–7. PMID: 20921162; PMCID: PMC2948995.; 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.; Ververidis F, Trantas E, Douglas C, Vollmer G, Kretzschmar G, Panopoulos N. Biotechnology of flavonoids and other phenylpropanoid-derived natural products. Part I: Chemical diversity, impacts on plant biology and human health. Biotechnol J. 2007 Oct;2(10):1214–34. doi: 10.1002/biot.200700084. PMID: 17935117.; Lee ER, Kang GH, Cho SG. Effect of flavonoids on human health: old subjects but new challenges. Recent Pat Biotechnol. 2007;1(2):139–50. doi: 10.2174/187220807780809445. PMID: 19075837.; 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.; Morita Y, Hoshino A, Kikuchi Y, Okuhara H, Ono E, Tanaka Y, Fukui Y, Saito N, Nitasaka E, Noguchi H, Iida S. Japanese morning glory dusky mutants displaying reddish-brown or purplish-gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase, due to 4-bp insertions in the gene. The Plant Journal. 2005 Mar 15;42(3):353–63. doi: 10.1111/j.1365-313x.2005.02383.x.; Kaminaga Y, Nagatsu A, Akiyama T, Sugimoto N, Yamazaki T, Maitani T, Mizukami H. Production of unnatural glucosides of curcumin with drastically enhanced water solubility by cell suspension cultures of Catharanthus roseus. FEBS Lett. 2003 Dec 04;555(2):311–6. doi: 10.1016/s0014-5793(03)01265-1. PMID: 14644434.; Wink M. Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective. Phytochemistry. 2003 Sep;64(1):3–19. doi: 10.1016/s0031-9422(03)00300-5. PMID: 12946402.; Harborne JB, Williams CA. Advances in flavonoid research since 1992. Phytochemistry. 2000 Nov;55(6):481–504. doi: 10.1016/s0031-9422(00)00235-1. PMID: 11130659.; 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.
(R)-acetoin biosynthesis I

Accession ID: BioCyc:LEISH_PWY-5938		 -
pyruvate fermentation to (R)-acetoin I

Accession ID: BioCyc:BSUB_PWY-5938		 -
pyruvate fermentation to (R)-acetoin I

Accession ID: BioCyc:META_PWY-5938
  • 10.1074/jbc.m003035200
  • 10.1271/bbb.65.1876
 TAKUSAGAWA Y, OTAGIRI M, UI S, OHTSUKI T, MIMURA A, OHKUMA M, KUDO T. Purification and Characterization of L-2,3-Butanediol Dehydrogenase of Brevibacterium saccharolyticum C-1012 Expressed in Escherichia coli. Bioscience, Biotechnology, and Biochemistry. 2001 Jan;65(8):1876–8. doi: 10.1271/bbb.65.1876.; González E, Fernández MR, Larroy C, Solà L, Pericàs MA, Parés X, Biosca JA. Characterization of a (2R,3R)-2,3-butanediol dehydrogenase as the Saccharomyces cerevisiae YAL060W gene product. Disruption and induction of the gene. J Biol Chem. 2000 Nov 17;275(46):35876–85. doi: 10.1074/jbc.m003035200. PMID: 10938079.
pyruvate fermentation to (S)-acetoin

Accession ID: BioCyc:META_PWY-6389		 -
L-threonine degradation II

Accession ID: BioCyc:META_THREONINE-DEG2-PWY
  • 10.1016/0304-4165(78)90324-0
  • 10.1042/bj1120657
 Dale RA. Catabolism of threonine in mammals by coupling of l-threonine 3-dehydrogenase with 2-amino-3-oxobutyrate-CoA ligase. Biochimica et Biophysica Acta (BBA) - General Subjects. 1978 Dec;544(3):496–503. doi: 10.1016/0304-4165(78)90324-0.; McGilvray D, Morris JG. Utilization of l-threonine by a species of Arthrobacter. A novel catabolic role for ‘aminoacetone synthase’. 1969 May 01;112(5):657–71. doi: 10.1042/bj1120657.
aminopropanol phosphate biosynthesis II

Accession ID: BioCyc:META_PWY-7378
  • 10.1016/s0021-9258(17)34497-6
  • 10.1016/s0021-9258(18)51462-9
  • 10.1016/s0021-9258(19)69880-7
 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.; Campbell RL, Swain RR, Dekker EE. Purification, separation, and characterization of two molecular forms of D-1-amino-2-propanol:NAD+ oxidoreductase activity from extracts of Escherichia coli K-12. Journal of Biological Chemistry. 1978 Oct;253(20):7282–8. doi: 10.1016/s0021-9258(17)34497-6.
L-threonine degradation II

Accession ID: BioCyc:ECO_THREONINE-DEG2-PWY
  • 10.1016/0304-4165(78)90324-0
  • 10.1042/bj1120657
  • 10.1128/jb.126.3.1245-1249.1976
  • 10.1128/jb.132.2.385-391.1977
  • 10.1128/jb.156.1.273-280.1983
 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.; Dale RA. Catabolism of threonine in mammals by coupling of l-threonine 3-dehydrogenase with 2-amino-3-oxobutyrate-CoA ligase. Biochimica et Biophysica Acta (BBA) - General Subjects. 1978 Dec;544(3):496–503. doi: 10.1016/0304-4165(78)90324-0.; Potter R, Kapoor V, Newman EB. Role of threonine dehydrogenase in Escherichia coli threonine degradation. J Bacteriol. 1977 Nov;132(2):385–91. doi: 10.1128/jb.132.2.385-391.1977.; Newman EB, Kapoor V, Potter R. Role of L-threonine dehydrogenase in the catabolism of threonine and synthesis of glycine by Escherichia coli. J Bacteriol. 1976 Jun;126(3):1245–9. doi: 10.1128/jb.126.3.1245-1249.1976.; McGilvray D, Morris JG. Utilization of l-threonine by a species of Arthrobacter. A novel catabolic role for ‘aminoacetone synthase’. 1969 May 01;112(5):657–71. doi: 10.1042/bj1120657.
(R)-acetoin biosynthesis I

Accession ID: BioCyc:TRYPANO_PWY-5938		 -
(S)-acetoin biosynthesis

Accession ID: BioCyc:MOB3B_PWY-6389		 -
(R)-acetoin biosynthesis I

Accession ID: BioCyc:MOB3B_PWY-5938		 -
flavonol glucosylation I

Accession ID: PlantCyc:PLANT_PWY-6360
  • 10.1016/j.phytochem.2009.07.027
 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.