Pathways Knowlegdes

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Pathway DOIs Note
pyruvate fermentation to butanol II (engineered)

Accession ID: BioCyc:META_PWY-6883
  • 10.1016/j.ymben.2011.04.004
  • 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.; 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.
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.
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.
detoxification of reactive carbonyls in chloroplasts

Accession ID: BioCyc:ARA_PWY-6786
  • 10.1016/j.jmb.2009.07.023
  • 10.1074/jbc.m110.202226
 Yamauchi Y, Hasegawa A, Taninaka A, Mizutani M, Sugimoto Y. NADPH-dependent Reductases Involved in the Detoxification of Reactive Carbonyls in Plants. Journal of Biological Chemistry. 2011 Mar;286(9):6999–7009. doi: 10.1074/jbc.m110.202226.; Simpson PJ, Tantitadapitak C, Reed AM, Mather OC, Bunce CM, White SA, Ride JP. Characterization of two novel aldo-keto reductases from Arabidopsis: expression patterns, broad substrate specificity, and an open active-site structure suggest a role in toxicant metabolism following stress. J Mol Biol. 2009 Sep 18;392(2):465–80. doi: 10.1016/j.jmb.2009.07.023. PMID: 19616008.
glycerol degradation to butanol

Accession ID: BioCyc:ECOO157_PWY-7003		 -
glycerol degradation to butanol

Accession ID: BioCyc:10403S_RAST_PWY-7003		 -
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.
superpathway of Clostridium acetobutylicum solventogenic fermentation

Accession ID: BioCyc:META_PWY-6594
  • 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
  • 10.1128/mmbr.50.4.484-524.1986
 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.; Jones DT, Woods DR. Acetone-butanol fermentation revisited. Microbiol Rev. 1986 Dec;50(4):484–524. doi: 10.1128/mr.50.4.484-524.1986.; 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.
detoxification of reactive carbonyls in chloroplasts

Accession ID: BioCyc:META_PWY-6786
  • 10.1016/j.jmb.2009.07.023
  • 10.1074/jbc.m110.202226
 Yamauchi Y, Hasegawa A, Taninaka A, Mizutani M, Sugimoto Y. NADPH-dependent Reductases Involved in the Detoxification of Reactive Carbonyls in Plants. Journal of Biological Chemistry. 2011 Mar;286(9):6999–7009. doi: 10.1074/jbc.m110.202226.; Simpson PJ, Tantitadapitak C, Reed AM, Mather OC, Bunce CM, White SA, Ride JP. Characterization of two novel aldo-keto reductases from Arabidopsis: expression patterns, broad substrate specificity, and an open active-site structure suggest a role in toxicant metabolism following stress. J Mol Biol. 2009 Sep 18;392(2):465–80. doi: 10.1016/j.jmb.2009.07.023. PMID: 19616008.
butanol and isobutanol biosynthesis (engineered)

Accession ID: BioCyc:META_PWY-7396
  • 10.1016/j.femsyr.2005.03.001
  • 10.1186/1754-6834-6-68
 Branduardi P, Longo V, Berterame NM, Rossi G, Porro D. A novel pathway to produce butanol and isobutanol in Saccharomyces cerevisiae. Biotechnology for Biofuels and Bioproducts. 2013 May 04;6(1):68. doi: 10.1186/1754-6834-6-68.; Villas-Bôas SG, Kesson M, Nielsen J. Biosynthesis of glyoxylate from glycine in Saccharomyces cerevisiae. FEMS Yeast Res. 2005 May;5(8):703–9. doi: 10.1016/j.femsyr.2005.03.001. PMID: 15851099.
glycerol degradation to butanol

Accession ID: BioCyc:META_PWY-7003
  • 10.1007/s00253-011-3629-0
  • 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
 Malaviya A, Jang YS, Lee SY. Continuous butanol production with reduced byproducts formation from glycerol by a hyper producing mutant of Clostridium pasteurianum. Appl Microbiol Biotechnol. 2012 Feb;93(4):1485–94. doi: 10.1007/s00253-011-3629-0. PMID: 22052388.; 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.
pyruvate fermentation to butanol I

Accession ID: BioCyc:META_PWY-6583
  • 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
  • 10.1128/mmbr.50.4.484-524.1986
 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.; Jones DT, Woods DR. Acetone-butanol fermentation revisited. Microbiol Rev. 1986 Dec;50(4):484–524. doi: 10.1128/mr.50.4.484-524.1986.; 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.
alkylnitronates degradation

Accession ID: BioCyc:META_PWY-723
  • 10.1007/bf00446519
  • 10.1016/0003-9861(72)90181-6
  • 10.1016/0005-2744(78)90289-9
  • 10.1016/s0021-9258(17)32932-0
  • 10.1016/s0021-9258(19)40804-1
  • 10.1016/s0021-9258(19)68821-6
  • 10.1016/s0021-9258(19)81274-7
  • 10.1042/bj1040103
  • 10.1074/jbc.271.39.24096
  • 10.1128/aem.64.3.1029-1033.1998
  • 10.1128/jb.175.8.2379-2392.1993
 Gorlatova N, Tchorzewski M, Kurihara T, Soda K, Esaki N. Purification, Characterization, and Mechanism of a Flavin Mononucleotide-Dependent 2-Nitropropane Dioxygenase from Neurospora crassa. Appl Environ Microbiol. 1998 Mar;64(3):1029–33. doi: 10.1128/aem.64.3.1029-1033.1998.; Colandene JD, Garrett RH. Functional Dissection and Site-directed Mutagenesis of the Structural Gene for NAD(P)H-Nitrite Reductase in Neurospora crassa. Journal of Biological Chemistry. 1996 Sep;271(39):24096–104. doi: 10.1074/jbc.271.39.24096.; Exley GE, Colandene JD, Garrett RH. Molecular cloning, characterization, and nucleotide sequence of nit-6, the structural gene for nitrite reductase in Neurospora crassa. J Bacteriol. 1993 Apr;175(8):2379–92. doi: 10.1128/jb.175.8.2379-2392.1993.; Prodouz KN, Garrett RH. Neurospora crassa NAD(P)H-nitrite reductase. Studies on its composition and structure. Journal of Biological Chemistry. 1981 Sep;256(18):9711–7. doi: 10.1016/s0021-9258(19)68821-6.; Greenbaum P, Prodouz KN, Garrett RH. Preparation and some properties of homogeneous Neurospora crassa assimilatory NADPH-nitrite reductase. Biochimica et Biophysica Acta (BBA) - Enzymology. 1978 Sep;526(1):52–64. doi: 10.1016/0005-2744(78)90289-9.; Kido T, Soda K, Suzuki T, Asada K. A new oxygenase, 2-nitropropane dioxygenase of Hansenula mrakii. Enzymologic and spectrophotometric properties. Journal of Biological Chemistry. 1976 Nov;251(22):6994–7000. doi: 10.1016/s0021-9258(17)32932-0.; Kido T, Yamamoto T, Soda K. Microbial assimilation of alkyl nitro compounds and formation of nitrite. Arch Microbiol. 1975 Dec 31;106(3):165–9. doi: 10.1007/bf00446519. PMID: 1217935.; Vega J, Garrett R. Siroheme: a prosthetic group of the Neurospora crassa assimilatory nitrite reductase. Journal of Biological Chemistry. 1975 Oct;250(20):7980–9. doi: 10.1016/s0021-9258(19)40804-1.; Lafferty MA, Garrett RH. Purification and Properties of the Neurospora crassa Assimilatory Nitrite Reductase. Journal of Biological Chemistry. 1974 Dec;249(23):7555–67. doi: 10.1016/s0021-9258(19)81274-7.; Prakash O, Sadana JC. Purification, characterization and properties of nitrite reductase of Achromobacter fischeri. Archives of Biochemistry and Biophysics. 1972 Feb;148(2):614–32. doi: 10.1016/0003-9861(72)90181-6.; Pateman JA, Rever BM, Cove DJ. Genetic and biochemical studies of nitrate reduction in Aspergillus nidulans. Biochem J. 1967 Jul;104(1):103–11. PMID: 4382427; PMCID: PMC1270550.
glycerol degradation to butanol

Accession ID: BioCyc:CLOSSAC_PWY-7003		 -
detoxification of reactive carbonyls in chloroplasts

Accession ID: PlantCyc:ARA_PWY-6786
  • 10.1016/j.jmb.2009.07.023
  • 10.1074/jbc.m110.202226
 Yamauchi Y, Hasegawa A, Taninaka A, Mizutani M, Sugimoto Y. NADPH-dependent Reductases Involved in the Detoxification of Reactive Carbonyls in Plants. Journal of Biological Chemistry. 2011 Mar;286(9):6999–7009. doi: 10.1074/jbc.m110.202226.; Simpson PJ, Tantitadapitak C, Reed AM, Mather OC, Bunce CM, White SA, Ride JP. Characterization of two novel aldo-keto reductases from Arabidopsis: expression patterns, broad substrate specificity, and an open active-site structure suggest a role in toxicant metabolism following stress. J Mol Biol. 2009 Sep 18;392(2):465–80. doi: 10.1016/j.jmb.2009.07.023. PMID: 19616008.
detoxification of reactive carbonyls in chloroplasts

Accession ID: PlantCyc:WHEATA_PWY-6786		 -
fatty acid α-oxidation I (plants)

Accession ID: PlantCyc:WHEATD_PWY-2501		 -
detoxification of reactive carbonyls in chloroplasts

Accession ID: PlantCyc:WHEATD_PWY-6786		 -
fatty acid α-oxidation I (plants)

Accession ID: PlantCyc:BOLERACEA_CAPITATA_PWY-2501		 -
fatty acid α-oxidation I (plants)

Accession ID: PlantCyc:CACUMINATA_PWY-2501		 -