Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| D-galactose degradation I (Leloir pathway) Accession ID: BioCyc:META_PWY-6317 |
|
Frey PA. The Leloir pathway: a mechanistic imperative for three enzymes to change the stereochemical configuration of a single carbon in galactose. The FASEB Journal. 1996 Mar;10(4):461–70. doi: 10.1096/fasebj.10.4.8647345. |
| methane oxidation to methanol II Accession ID: BioCyc:META_PWY-6742 |
|
Shiemke AK, Cook SA, Miley T, Singleton P. Detergent Solubilization of Membrane-Bound Methane Monooxygenase Requires Plastoquinol Analogs as Electron Donors. Archives of Biochemistry and Biophysics. 1995 Aug;321(2):421–8. doi: 10.1006/abbi.1995.1413. |
| superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis Accession ID: BioCyc:META_PWY-7328 |
|
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.; Samuel G, Reeves P. Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Carbohydr Res. 2003 Nov 14;338(23):2503–19. doi: 10.1016/j.carres.2003.07.009. PMID: 14670712. |
| glucose and glucose-1-phosphate degradation Accession ID: BioCyc:ECO_GLUCOSE1PMETAB-PWY |
- | |
| NADH to cytochrome bo oxidase electron transfer II Accession ID: BioCyc:META_PWY0-1567 |
|
Unden G, Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1997 Jul;1320(3):217–34. doi: 10.1016/s0005-2728(97)00034-0.; Tran QH, Bongaerts J, Vlad D, Unden G. Requirement for the Proton-Pumping NADH Dehydrogenase I of Escherichia Coli in Respiration of NADH to Fumarate and Its Bioenergetic Implications. European Journal of Biochemistry. 1997 Feb;244(1):155–60. doi: 10.1111/j.1432-1033.1997.00155.x.; Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Neijssel OM. Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain. J Bacteriol. 1993 May;175(10):3020–5. doi: 10.1128/jb.175.10.3020-3025.1993.; Ingledew WJ, Poole RK. The respiratory chains of Escherichia coli. Microbiol Rev. 1984 Sep;48(3):222–71. doi: 10.1128/mr.48.3.222-271.1984. |
| coenzyme M biosynthesis I Accession ID: BioCyc:META_P261-PWY |
|
Rein U, Gueta R, Denger K, Ruff J, Hollemeyer K, Cook AM. Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA. Microbiology (Reading). 2005 Mar;151(Pt 3):737–47. doi: 10.1099/mic.0.27548-0. PMID: 15758220.; Graupner M, White RH. The first examples of (S)-2-hydroxyacid dehydrogenases catalyzing the transfer of the pro-4S hydrogen of NADH are found in the archaea. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 2001 Jul;1548(1):169–73. doi: 10.1016/s0167-4838(01)00220-5.; Graupner M, Xu H, White RH. Identification of an Archaeal 2-Hydroxy Acid Dehydrogenase Catalyzing Reactions Involved in Coenzyme Biosynthesis in Methanoarchaea. J Bacteriol. 2000 Jul;182(13):3688–92. doi: 10.1128/jb.182.13.3688-3692.2000. |
| glycogen degradation I Accession ID: BioCyc:META_GLYCOCAT-PWY |
|
Dauville´e D, Kinderf IS, Li Z, Kosar-Hashemi B, Samuel MS, Rampling L, Ball S, Morell MK. Role of the Escherichia coli glgX Gene in Glycogen Metabolism. J Bacteriol. 2005 Feb 15;187(4):1465–73. doi: 10.1128/jb.187.4.1465-1473.2005. |
| UDP-α-D-glucose biosynthesis I Accession ID: BioCyc:META_PWY-7343 |
|
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.; Kamogawa A, Kurahashi K. Purification and properties of uridinediphosphate glucose pyrophosphorylase from Escherichia coli K12. J Biochem. 1965 Jun;57(6):758–65. doi: 10.1093/oxfordjournals.jbchem.a128142. PMID: 4284510. |
| glycogen degradation I Accession ID: BioCyc:ECO_GLYCOCAT-PWY |
|
Alonso-Casaju´s N, Dauville´e D, Viale AM, Mun~oz FJ, Baroja-Ferna´ndez E, Mora´n-Zorzano MT, Eydallin G, Ball S, Pozueta-Romero J. Glycogen Phosphorylase, the Product of the glgP Gene, Catalyzes Glycogen Breakdown by Removing Glucose Units from the Nonreducing Ends in Escherichia coli. J Bacteriol. 2006 Jul 15;188(14):5266–72. doi: 10.1128/jb.01566-05.; Dippel R, Boos W. The Maltodextrin System ofEscherichia coli: Metabolism and Transport. J Bacteriol. 2005 Dec 15;187(24):8322–31. doi: 10.1128/jb.187.24.8322-8331.2005.; Dauville´e D, Kinderf IS, Li Z, Kosar-Hashemi B, Samuel MS, Rampling L, Ball S, Morell MK. Role of the Escherichia coli glgX Gene in Glycogen Metabolism. J Bacteriol. 2005 Feb 15;187(4):1465–73. doi: 10.1128/jb.187.4.1465-1473.2005. |
| nitrate reduction VIIIb (dissimilatory) Accession ID: BioCyc:META_PWY0-1573 |
|
Tran QH, Bongaerts J, Vlad D, Unden G. Requirement for the Proton-Pumping NADH Dehydrogenase I of Escherichia Coli in Respiration of NADH to Fumarate and Its Bioenergetic Implications. European Journal of Biochemistry. 1997 Feb;244(1):155–60. doi: 10.1111/j.1432-1033.1997.00155.x.; Wallace BJ, Young IG. Role of quinones in electron transport to oxygen and nitrate in Escherichia coli. Studies with a ubiA- menA- double quinone mutant. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1977 Jul;461(1):84–100. doi: 10.1016/0005-2728(77)90071-8. |
| colanic acid building blocks biosynthesis Accession ID: BioCyc:META_COLANSYN-PWY |
|
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.; Whitfield C. Biosynthesis and Assembly of Capsular Polysaccharides in Escherichia coli. Annu. Rev. Biochem. 2006 Jun 01;75(1):39–68. doi: 10.1146/annurev.biochem.75.103004.142545.; Andrianopoulos K, Wang L, Reeves PR. Identification of the Fucose Synthetase Gene in the Colanic Acid Gene Cluster of Escherichia coli K-12. J Bacteriol. 1998 Feb 15;180(4):998–1001. doi: 10.1128/jb.180.4.998-1001.1998. |
| glucose and glucose-1-phosphate degradation Accession ID: BioCyc:META_GLUCOSE1PMETAB-PWY |
- | |
| colanic acid building blocks biosynthesis Accession ID: BioCyc:ECO_COLANSYN-PWY |
|
Whitfield C. Biosynthesis and Assembly of Capsular Polysaccharides in Escherichia coli. Annu. Rev. Biochem. 2006 Jun 01;75(1):39–68. doi: 10.1146/annurev.biochem.75.103004.142545. |
| glycogen biosynthesis I (from ADP-D-Glucose) Accession ID: BioCyc:ECO_GLYCOGENSYNTH-PWY |
- | |
| UDP-α-D-glucose biosynthesis I Accession ID: BioCyc:ECO_PWY-7343 |
|
Kamogawa A, Kurahashi K. Purification and properties of uridinediphosphate glucose pyrophosphorylase from Escherichia coli K12. J Biochem. 1965 Jun;57(6):758–65. doi: 10.1093/oxfordjournals.jbchem.a128142. PMID: 4284510. |
| NADH to cytochrome bd oxidase electron transfer II Accession ID: BioCyc:META_PWY0-1568 |
|
Unden G, Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1997 Jul;1320(3):217–34. doi: 10.1016/s0005-2728(97)00034-0.; Tran QH, Bongaerts J, Vlad D, Unden G. Requirement for the Proton-Pumping NADH Dehydrogenase I of Escherichia Coli in Respiration of NADH to Fumarate and Its Bioenergetic Implications. European Journal of Biochemistry. 1997 Feb;244(1):155–60. doi: 10.1111/j.1432-1033.1997.00155.x.; Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Neijssel OM. Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain. J Bacteriol. 1993 May;175(10):3020–5. doi: 10.1128/jb.175.10.3020-3025.1993.; Cotter PA, Chepuri V, Gennis RB, Gunsalus RP. Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. J Bacteriol. 1990 Nov;172(11):6333–8. doi: 10.1128/jb.172.11.6333-6338.1990.; Ingledew WJ, Poole RK. The respiratory chains of Escherichia coli. Microbiol Rev. 1984 Sep;48(3):222–71. doi: 10.1128/mr.48.3.222-271.1984. |
| glycogen biosynthesis I (from ADP-D-Glucose) Accession ID: BioCyc:META_GLYCOGENSYNTH-PWY |
|
Ball S, Colleoni C, Cenci U, Raj JN, Tirtiaux C. The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis. J Exp Bot. 2011 Mar;62(6):1775–801. doi: 10.1093/jxb/erq411. PMID: 21220783.; BAUM H, GILBERT GA. A simple method for the preparation of crystalline potato phosphorylase and Q-enzyme. Nature. 1953 May 30;171(4361):983–4. doi: 10.1038/171983a0. PMID: 13063502. |
| nitrate reduction VIIIb (dissimilatory) Accession ID: BioCyc:ECO_PWY0-1573 |
|
Tran QH, Bongaerts J, Vlad D, Unden G. Requirement for the Proton-Pumping NADH Dehydrogenase I of Escherichia Coli in Respiration of NADH to Fumarate and Its Bioenergetic Implications. European Journal of Biochemistry. 1997 Feb;244(1):155–60. doi: 10.1111/j.1432-1033.1997.00155.x.; Wallace BJ, Young IG. Role of quinones in electron transport to oxygen and nitrate in Escherichia coli. Studies with a ubiA- menA- double quinone mutant. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1977 Jul;461(1):84–100. doi: 10.1016/0005-2728(77)90071-8. |
| NADH to cytochrome bd oxidase electron transfer II Accession ID: BioCyc:ECO_PWY0-1568 |
|
Unden G, Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1997 Jul;1320(3):217–34. doi: 10.1016/s0005-2728(97)00034-0.; Tran QH, Bongaerts J, Vlad D, Unden G. Requirement for the Proton-Pumping NADH Dehydrogenase I of Escherichia Coli in Respiration of NADH to Fumarate and Its Bioenergetic Implications. European Journal of Biochemistry. 1997 Feb;244(1):155–60. doi: 10.1111/j.1432-1033.1997.00155.x.; Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Neijssel OM. Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain. J Bacteriol. 1993 May;175(10):3020–5. doi: 10.1128/jb.175.10.3020-3025.1993.; Cotter PA, Chepuri V, Gennis RB, Gunsalus RP. Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. J Bacteriol. 1990 Nov;172(11):6333–8. doi: 10.1128/jb.172.11.6333-6338.1990.; Ingledew WJ, Poole RK. The respiratory chains of Escherichia coli. Microbiol Rev. 1984 Sep;48(3):222–71. doi: 10.1128/mr.48.3.222-271.1984. |
| NADH to cytochrome bo oxidase electron transfer II Accession ID: BioCyc:ECO_PWY0-1567 |
|
Unden G, Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1997 Jul;1320(3):217–34. doi: 10.1016/s0005-2728(97)00034-0.; Tran QH, Bongaerts J, Vlad D, Unden G. Requirement for the Proton-Pumping NADH Dehydrogenase I of Escherichia Coli in Respiration of NADH to Fumarate and Its Bioenergetic Implications. European Journal of Biochemistry. 1997 Feb;244(1):155–60. doi: 10.1111/j.1432-1033.1997.00155.x.; Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Neijssel OM. Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain. J Bacteriol. 1993 May;175(10):3020–5. doi: 10.1128/jb.175.10.3020-3025.1993.; Ingledew WJ, Poole RK. The respiratory chains of Escherichia coli. Microbiol Rev. 1984 Sep;48(3):222–71. doi: 10.1128/mr.48.3.222-271.1984. |