Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
L-arginine biosynthesis I (via L-ornithine)

Accession ID: BioCyc:MSMI420247_ARGSYN-PWY		 -
N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis

Accession ID: BioCyc:GCF_000013425_PWY0-1587		 -
UMP biosynthesis I

Accession ID: BioCyc:GCF_000013425_PWY-5686		 -
inosine-5'-phosphate biosynthesis I

Accession ID: BioCyc:GCF_000013425_PWY-6123		 -
N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis

Accession ID: BioCyc:COLLINSAERO_PWY0-1587		 -
inosine-5'-phosphate biosynthesis I

Accession ID: BioCyc:COLLINSAERO_PWY-6123		 -
UMP biosynthesis I

Accession ID: BioCyc:COLLINSAERO_PWY-5686		 -
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis

Accession ID: BioCyc:HUMAN_PWY-7211		 -
gluconeogenesis

Accession ID: BioCyc:HUMAN_PWY66-399
  • 10.1002/dmrr.217
  • 10.1146/annurev.nutr.19.1.379
 Radziuk J, Pye S. Hepatic glucose uptake, gluconeogenesis and the regulation of glycogen synthesis. Diabetes Metab Res Rev. 2001 Jul;17(4):250–72. doi: 10.1002/dmrr.217. PMID: 11544610.; Nordlie RC, Foster JD, Lange AJ. Regulation of glucose production by the liver. Annu Rev Nutr. 1999;19():379–406. doi: 10.1146/annurev.nutr.19.1.379. PMID: 10448530.
superpathway of pyrimidine ribonucleotides de novo biosynthesis

Accession ID: BioCyc:HUMAN_PWY0-162		 -
leucine degradation

Accession ID: BioCyc:HUMAN_LEU-DEG2-PWY
  • 10.1128/jb.118.1.112-120.1974
 Massey LK, Conrad RS, Sokatch JR. Regulation of Leucine Catabolism in Pseudomonas putida. J Bacteriol. 1974 Apr;118(1):112–20. doi: 10.1128/jb.118.1.112-120.1974.
urea cycle

Accession ID: BioCyc:META_PWY-4984
  • 10.1146/annurev.ge.20.120186.002243
 Jackson MJ, Beaudet AL, O'Brien WE. Mammalian urea cycle enzymes. Annu Rev Genet. 1986;20():431–64. doi: 10.1146/annurev.ge.20.120186.002243. PMID: 3545062.
superpathway of the 3-hydroxypropanoate cycle

Accession ID: BioCyc:META_PWY-7024
  • 10.1016/s0021-9258(19)75797-4
  • 10.1073/pnas.0908356106
  • 10.1111/j.1432-1033.1993.tb18074.x
  • 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.; STRAUSS G, FUCHS G. Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle. European Journal of Biochemistry. 1993 Aug;215(3):633–43. doi: 10.1111/j.1432-1033.1993.tb18074.x.; 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.
3-hydroxypropanoate cycle

Accession ID: BioCyc:META_PWY-5743
  • 10.1016/s0021-9258(19)75797-4
  • 10.1111/j.1432-1033.1993.tb18074.x
 STRAUSS G, FUCHS G. Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle. European Journal of Biochemistry. 1993 Aug;215(3):633–43. doi: 10.1111/j.1432-1033.1993.tb18074.x.; 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.
partial TCA cycle (obligate autotrophs)

Accession ID: BioCyc:META_PWY-5913
  • 10.1128/jb.94.4.972-983.1967
 Smith AJ, London J, Stanier RY. Biochemical Basis of Obligate Autotrophy in Blue-Green Algae and Thiobacilli. J Bacteriol. 1967 Oct;94(4):972–83. doi: 10.1128/jb.94.4.972-983.1967.
biotin-carboxyl carrier protein assembly

Accession ID: BioCyc:META_PWY0-1264		 -
UMP biosynthesis I

Accession ID: BioCyc:META_PWY-5686
  • 10.1146/annurev.arplant.57.032905.105421
 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.
2-oxobutanoate degradation I

Accession ID: BioCyc:META_PWY-5130
  • 10.1042/bj2340295
 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.
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 demethylmenaquinol-8 biosynthesis I

Accession ID: BioCyc:META_PWY-5861
  • 10.1016/0014-5793(81)80080-4
 Heide L, Leistner E. Enzymatic synthesis of the coenzyme a ester of o-succinylbenzoic acid, an intermediate in menaquinone (vitamin K2) biosynthesis. FEBS Letters. 1981 Jun 15;128(2):201–4. doi: 10.1016/0014-5793(81)80080-4.