Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
L-homoserine biosynthesis

Accession ID: BioCyc:META_HOMOSERSYN-PWY
  • 10.1042/0264-6021:3560415
 Chassagnole C, Raïs B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J. 2001 Jun 01;356(Pt 2):415–23. PMID: 11368768; PMCID: PMC1221852.
L-lysine biosynthesis I

Accession ID: BioCyc:META_DAPLYSINESYN-PWY
  • 10.1016/s0021-9258(18)64502-8
  • 10.1016/s0021-9258(18)97014-6
  • 10.1021/jm100349s
 Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808–12. doi: 10.1021/jm100349s. PMID: 20503968.; Farkas W, Gilvarg C. The Reduction Step in Diaminopimelic Acid Biosynthesis. Journal of Biological Chemistry. 1965 Dec;240(12):4717–22. doi: 10.1016/s0021-9258(18)97014-6.; Kindler SH, Gilvarg C. N-Succinyl-l-a, e-diaminopimelic Acid Deacylase. Journal of Biological Chemistry. 1960 Dec;235(12):3532–5. doi: 10.1016/s0021-9258(18)64502-8.
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation

Accession ID: BioCyc:META_PWY-6604
  • 10.1016/s0021-9258(18)65732-1
  • 10.1016/s0021-9258(18)71290-8
  • 10.1016/s0021-9258(18)71291-x
  • 10.1096/fasebj.9.9.7601336
 Thorpe C, Kim JP. Structure and mechanism of action of the Acyl-CoA dehydrogenases 1. The FASEB Journal. 1995 Jun;9(9):718–25. doi: 10.1096/fasebj.9.9.7601336.; Hauge JG, Crane FL, Beinert H. ON THE MECHANISM OF DEHYDROGENATION OF FATTY ACYL DERIVATIVES OF COENZYME A. Journal of Biological Chemistry. 1956 Apr;219(2):727–33. doi: 10.1016/s0021-9258(18)65732-1.; Green DE, Mii S, Mahler HR, Bock RM. STUDIES ON THE FATTY ACID OXIDIZING SYSTEM OF ANIMAL TISSUES. Journal of Biological Chemistry. 1954 Jan;206(1):1–12. doi: 10.1016/s0021-9258(18)71290-8.; MAHLER HR. Studies on the fatty acid oxidizing system of animal tissues. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J Biol Chem. 1954 Jan;206(1):13–26. PMID: 13130522.
L-asparagine degradation I

Accession ID: BioCyc:META_ASPARAGINE-DEG1-PWY		 -
trehalose degradation II (cytosolic)

Accession ID: BioCyc:META_PWY0-1182
  • 10.1128/aem.70.5.2771-2778.2004
 Jules M, Guillou V, Franc¸ois J, Parrou J. Two Distinct Pathways for Trehalose Assimilation in the YeastSaccharomyces cerevisiae. Appl Environ Microbiol. 2004 May;70(5):2771–8. doi: 10.1128/aem.70.5.2771-2778.2004.
superpathway of anaerobic energy metabolism (invertebrates)

Accession ID: BioCyc:META_PWY-7389
  • 10.1016/s0968-0004(02)02193-x
  • 10.1074/jbc.270.52.31065
  • 10.1128/jb.186.14.4620-4627.2004
  • 10.1128/mmbr.05024-11
 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 tetrahydrofolate biosynthesis

Accession ID: BioCyc:META_PWY-6612		 -
glutaryl-CoA degradation

Accession ID: BioCyc:META_PWY-5177
  • 10.1111/j.1432-1033.1993.tb17593.x
 KOCH J, EISENREICH W, BACHER A, FUCHS G. Products of enzymatic reduction of benzoyl-CoA, a key reaction in anaerobic aromatic metabolism. European Journal of Biochemistry. 1993 Feb;211(3):649–61. doi: 10.1111/j.1432-1033.1993.tb17593.x.
κ-carrageenan degradation

Accession ID: BioCyc:META_PWY-6821
  • 10.1111/j.1432-1033.1981.tb05084.x
 McLEAN MW, WILLIAMSON FB. Neocarratetraose 4-O-Monosulphate ß-Hydrolase from Pseudomonas carrageenovora. European Journal of Biochemistry. 1981 Jan;113(3):447–56. doi: 10.1111/j.1432-1033.1981.tb05084.x.
formaldehyde assimilation I (serine pathway)

Accession ID: BioCyc:META_PWY-1622
  • 10.1016/s0021-9258(18)96350-7
  • 10.1128/mmbr.60.2.439-471.1996
 Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Rev. 1996 Jun;60(2):439–71. doi: 10.1128/mr.60.2.439-471.1996.; Kallen RG, Jencks WP. The Mechanism of the Condensation of Formaldehyde with Tetrahydrofolic Acid. Journal of Biological Chemistry. 1966 Dec;241(24):5851–63. doi: 10.1016/s0021-9258(18)96350-7.
ketolysis

Accession ID: BioCyc:META_PWY66-368		 -
glycolate and glyoxylate degradation I

Accession ID: BioCyc:META_GLYCOLATEMET-PWY		 -
ppGpp biosynthesis

Accession ID: BioCyc:META_PPGPPMET-PWY
  • 10.1021/bi00618a007
 Heinemeyer EA, Richter D. Characterization of the guanosine 5'-triphosphate 3'-diphosphate and guanosine 5'-diphosphate 3'-diphosphate degradation reaction catalyzed by a specific pyrophosphorylase from Escherichia coli. Biochemistry. 1978 Dec 12;17(25):5368–72. doi: 10.1021/bi00618a007. PMID: 365225.
methanogenesis from H2 and CO2

Accession ID: BioCyc:META_METHANOGENESIS-PWY
  • 10.1111/j.1432-1033.1997.00919.x
 Vorholt JA, Thauer RK. The Active Species of ‘CO2’ Utilized by Formylmethanofuran Dehydrogenase from Methanogenic Archaea. European Journal of Biochemistry. 1997 Sep;248(3):919–24. doi: 10.1111/j.1432-1033.1997.00919.x.
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I

Accession ID: BioCyc:ECO_P4-PWY		 -
pyrimidine deoxyribonucleotide phosphorylation

Accession ID: BioCyc:ECO_PWY-7197		 -
L-lysine biosynthesis I

Accession ID: BioCyc:ECO_DAPLYSINESYN-PWY		 -
superpathway of glycol metabolism and degradation

Accession ID: BioCyc:ECO_GLYCOL-GLYOXDEG-PWY		 -
ppGpp biosynthesis

Accession ID: BioCyc:ECO_PPGPPMET-PWY
  • 10.1021/bi00618a007
 Heinemeyer EA, Richter D. Characterization of the guanosine 5'-triphosphate 3'-diphosphate and guanosine 5'-diphosphate 3'-diphosphate degradation reaction catalyzed by a specific pyrophosphorylase from Escherichia coli. Biochemistry. 1978 Dec 12;17(25):5368–72. doi: 10.1021/bi00618a007. PMID: 365225.
ketolysis

Accession ID: BioCyc:HUMAN_PWY66-368
  • 10.1016/j.plefa.2003.11.001
 Fukao T, Lopaschuk GD, Mitchell GA. Pathways and control of ketone body metabolism: on the fringe of lipid biochemistry. Prostaglandins Leukot Essent Fatty Acids. 2004 Mar;70(3):243–51. doi: 10.1016/j.plefa.2003.11.001. PMID: 14769483.