Pathways Knowlegdes

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Pathway DOIs Note
glycolysis

Accession ID: BioCyc:HUMAN_PWY66-400
  • 10.1101/gad.189365.112
 Dang CV. Links between metabolism and cancer. Genes Dev. 2012 May 01;26(9):877–90. PMID: 22549953; PMCID: PMC3347786.
superpathway of N-acetylneuraminate degradation

Accession ID: BioCyc:META_P441-PWY
  • 10.1177/00220345960750080701
 Byers HL, Homer KA, Beighton D. Utilization of sialic acid by viridans streptococci. J Dent Res. 1996 Aug;75(8):1564–71. doi: 10.1177/00220345960750080701. PMID: 8906124.
1-butanol autotrophic biosynthesis (engineered)

Accession ID: BioCyc:META_PWY-6886
  • 10.1016/0005-2728(77)90041-x
  • 10.1016/j.ymben.2011.04.004
  • 10.1038/nsmb.1559
  • 10.1093/oxfordjournals.jbchem.a121813
 Lan EI, Liao JC. Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng. 2011 Jul;13(4):353–63. doi: 10.1016/j.ymben.2011.04.004. PMID: 21569861.; 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.; Inui H, Miyatake K, Nakano Y, Kitaoka S. Purification and some properties of short chain-length specific trans-2-enoyl-CoA reductase in mitochondria of Euglena gracilis. J Biochem. 1986 Oct;100(4):995–1000. doi: 10.1093/oxfordjournals.jbchem.a121813. PMID: 3102464.; 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.
formaldehyde assimilation III (dihydroxyacetone cycle)

Accession ID: BioCyc:META_P185-PWY		 -
glycolysis III (from glucose)

Accession ID: BioCyc:META_ANAGLYCOLYSIS-PWY
  • 10.1007/bf03356097
  • 10.1016/s0378-1097(03)00642-6
  • 10.1101/gad.189365.112
 Dang CV. Links between metabolism and cancer. Genes Dev. 2012 May 01;26(9):877–90. PMID: 22549953; PMCID: PMC3347786.; Hansen T, Schönheit P. ATP-dependent glucokinase from the hyperthermophilic bacterium Thermotoga maritima represents an extremely thermophilic ROK glucokinase with high substrate specificity. FEMS Microbiol Lett. 2003 Sep 26;226(2):405–11. doi: 10.1016/s0378-1097(03)00642-6. PMID: 14553940.; Selig M, Xavier KB, Santos H, Schönheit P. Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyperthermophilic archaea and the bacterium Thermotoga. Arch Microbiol. 1997 Apr;167(4):217–32. doi: 10.1007/bf03356097. PMID: 9075622.
sucrose biosynthesis I (from photosynthesis)

Accession ID: BioCyc:META_SUCSYN-PWY
  • 10.1104/pp.106.083634
  • 10.1146/annurev.arplant.50.1.27
  • 10.1371/journal.pgen.1001263
 Cho YH, Yoo SD. Signaling role of fructose mediated by FINS1/FBP in Arabidopsis thaliana. PLoS Genet. 2011 Jan 06;7(1):e1001263. PMID: 21253566; PMCID: PMC3017112.; Dai N, Petreikov M, Portnoy V, Katzir N, Pharr DM, Schaffer AA. Cloning and expression analysis of a UDP-galactose/glucose pyrophosphorylase from melon fruit provides evidence for the major metabolic pathway of galactose metabolism in raffinose oligosaccharide metabolizing plants. Plant Physiol. 2006 Sep;142(1):294–304. PMID: 16829585; PMCID: PMC1557607.; Flugge UI. PHOSPHATE TRANSLOCATORS IN PLASTIDS. Annu Rev Plant Physiol Plant Mol Biol. 1999 Jun;50():27–45. doi: 10.1146/annurev.arplant.50.1.27. PMID: 15012202.
heterolactic fermentation

Accession ID: BioCyc:META_P122-PWY
  • 10.1006/abbi.1996.0058
  • 10.1007/s00203-006-0120-x
  • 10.1016/0005-2744(80)90036-4
  • 10.1111/j.1432-1033.1983.tb07165.x
 Helanto M, Aarnikunnas J, Palva A, Leisola M, Nyyssölä A. Characterization of genes involved in fructose utilization by Lactobacillus fermentum. Arch Microbiol. 2006 Jul;186(1):51–9. doi: 10.1007/s00203-006-0120-x. PMID: 16741753.; Levy HR, Vought VE, Yin X, Adams MJ. Identification of an arginine residue in the dual coenzyme-specific glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides that plays a key role in binding NADP+ but not NAD+. Arch Biochem Biophys. 1996 Feb 01;326(1):145–51. doi: 10.1006/abbi.1996.0058. PMID: 8579362.; Stournaras C, Maurer P, Kurz G. 6-phospho-D-gluconate dehydrogenase from Pseudomonas fluorescens. Properties and subunit structure. Eur J Biochem. 1983 Feb 01;130(2):391–6. doi: 10.1111/j.1432-1033.1983.tb07165.x. PMID: 6402366.; Ben-Bassat A, Goldberg I. Purification and properties of glucose-6-phosphate dehydrogenase (NADP+/NAD+) and 6-phosphogluconate dehydrogenase (NADP+/NAD+) from methanol-grown Pseudomonas C. Biochimica et Biophysica Acta (BBA) - Enzymology. 1980 Jan;611(1):1–10. doi: 10.1016/0005-2744(80)90036-4.
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.
gluconeogenesis I

Accession ID: BioCyc:ECO_GLUCONEO-PWY
  • 10.1007/s00253-002-1202-6
  • 10.1016/j.femsre.2004.11.002
  • 10.1074/jbc.m602553200
  • 10.1128/jb.175.21.6939-6944.1993
 Hines JK, Fromm HJ, Honzatko RB. Novel Allosteric Activation Site in Escherichia coli Fructose-1,6-bisphosphatase. Journal of Biological Chemistry. 2006 Jul;281(27):18386–93. doi: 10.1074/jbc.m602553200.; Sauer U, Eikmanns BJ. The PEP—pyruvate—oxaloacetate node as the switch point for carbon flux distribution in bacteria: We dedicate this paper to Rudolf K. Thauer, Director of the Max-Planck-Institute for Terrestrial Microbiology in Marburg, Germany, on the occasion of his 65th birthday. FEMS Microbiol Rev. 2005 Sep;29(4):765–94. doi: 10.1016/j.femsre.2004.11.002.; Peng L, Shimizu K. Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement. Applied Microbiology and Biotechnology. 2003 Jan 09;61(2):163–78. doi: 10.1007/s00253-002-1202-6.; Chao YP, Patnaik R, Roof WD, Young RF, Liao JC. Control of gluconeogenic growth by pps and pck in Escherichia coli. J Bacteriol. 1993 Nov;175(21):6939–44. doi: 10.1128/jb.175.21.6939-6944.1993.
Calvin-Benson-Bassham cycle

Accession ID: BioCyc:VCHO_CALVIN-PWY		 -
superpathway of glycolysis and the Entner-Doudoroff pathway

Accession ID: BioCyc:VCHO_GLYCOLYSIS-E-D		 -
glycolysis II (from fructose 6-phosphate)

Accession ID: BioCyc:MTBCDC1551_PWY-5484		 -
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass

Accession ID: BioCyc:MTBCDC1551_GLYCOLYSIS-TCA-GLYOX-BYPASS		 -
glycolysis I (from glucose 6-phosphate)

Accession ID: BioCyc:HPY_GLYCOLYSIS		 -
glycolysis III (from glucose)

Accession ID: BioCyc:AURANTIMONAS_ANAGLYCOLYSIS-PWY		 -
Calvin-Benson-Bassham cycle

Accession ID: BioCyc:AURANTIMONAS_CALVIN-PWY		 -
superpathway of glycolysis and Entner-Doudoroff

Accession ID: BioCyc:SCO_GLYCOLYSIS-E-D		 -
Bifidobacterium shunt

Accession ID: BioCyc:SCO_P124-PWY		 -
hexitol fermentation to lactate, formate, ethanol and acetate

Accession ID: BioCyc:SCO_P461-PWY		 -
glycolysis II (from fructose 6-phosphate)

Accession ID: BioCyc:SCO_PWY-5484		 -