Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| urea cycle Accession ID: BioCyc:HUMAN_PWY-4984 |
|
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. |
| biotin-carboxyl carrier protein assembly Accession ID: BioCyc:HUMAN_PWY0-1264 |
- | |
| superpathway of methionine degradation Accession ID: BioCyc:HUMAN_PWY-5328 |
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| UMP biosynthesis Accession ID: BioCyc:HUMAN_PWY-5686 |
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| 1,4-dihydroxy-6-naphthoate biosynthesis II Accession ID: BioCyc:META_PWY-7371 |
|
Mahanta N, Fedoseyenko D, Dairi T, Begley TP. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J Am Chem Soc. 2013 Oct 16;135(41):15318–21. PMID: 24083939; PMCID: PMC3855536.; Li X, Apel D, Gaynor EC, Tanner ME. 5'-Methylthioadenosine Nucleosidase Is Implicated in Playing a Key Role in a Modified Futalosine Pathway for Menaquinone Biosynthesis in Campylobacter jejuni. Journal of Biological Chemistry. 2011 Jun;286(22):19392–8. doi: 10.1074/jbc.m111.229781.; HIRATSUKA T, ITOH N, SETO H, DAIRI T. Enzymatic Properties of Futalosine Hydrolase, an Enzyme Essential to a Newly Identified Menaquinone Biosynthetic Pathway. Bioscience, Biotechnology, and Biochemistry. 2009 May 23;73(5):1137–41. doi: 10.1271/bbb.80906.; Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science. 2008 Sep 19;321(5896):1670–3. doi: 10.1126/science.1160446. PMID: 18801996. |
| 1,4-dihydroxy-6-naphthoate biosynthesis I Accession ID: BioCyc:META_PWY-7374 |
|
Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17;52(37):6525–36. PMID: 23972005; PMCID: PMC3813303.; Li X, Apel D, Gaynor EC, Tanner ME. 5'-Methylthioadenosine Nucleosidase Is Implicated in Playing a Key Role in a Modified Futalosine Pathway for Menaquinone Biosynthesis in Campylobacter jejuni. Journal of Biological Chemistry. 2011 Jun;286(22):19392–8. doi: 10.1074/jbc.m111.229781.; HIRATSUKA T, ITOH N, SETO H, DAIRI T. Enzymatic Properties of Futalosine Hydrolase, an Enzyme Essential to a Newly Identified Menaquinone Biosynthetic Pathway. Bioscience, Biotechnology, and Biochemistry. 2009 May 23;73(5):1137–41. doi: 10.1271/bbb.80906.; Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science. 2008 Sep 19;321(5896):1670–3. doi: 10.1126/science.1160446. PMID: 18801996. |
| methylaspartate cycle Accession ID: BioCyc:META_PWY-6728 |
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Khomyakova M, Bükmez Ö, Thomas LK, Erb TJ, Berg IA. A methylaspartate cycle in haloarchaea. Science. 2011 Jan 21;331(6015):334–7. doi: 10.1126/science.1196544. PMID: 21252347. |
| CO2 fixation into oxaloacetate (anaplerotic) Accession ID: BioCyc:META_PWYQT-4429 |
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Sánchez R, Flores A, Cejudo FJ. Arabidopsis phosphoenolpyruvate carboxylase genes encode immunologically unrelated polypeptides and are differentially expressed in response to drought and salt stress. Planta. 2006 Apr;223(5):901–9. doi: 10.1007/s00425-005-0144-5. PMID: 16283377.; 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. |
| 2-aminoethylphosphonate biosynthesis Accession ID: BioCyc:META_PWY-6839 |
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Kim J, Dunaway-Mariano D. Phosphoenolpyruvate mutase catalysis of phosphoryl transfer in phosphoenolpyruvate: kinetics and mechanism of phosphorus-carbon bond formation. Biochemistry. 1996 Apr 09;35(14):4628–35. doi: 10.1021/bi952944k. PMID: 8605214.; Bowman ED, McQueney MS, Scholten JD, Dunaway-Mariano D. Purification and characterization of the Tetrahymena pyriformis P-C bond forming enzyme phosphoenolpyruvate phosphomutase. Biochemistry. 1990 Jul 31;29(30):7059–63. doi: 10.1021/bi00482a016. PMID: 2121271.; Barry RJ, Bowman E, McQueney M, Dunaway-Mariano D. Elucidation of the 2-aminoethylphosphonate biosynthetic pathway in Tetrahymena pyriformis. Biochemical and Biophysical Research Communications. 1988 May;153(1):177–82. doi: 10.1016/s0006-291x(88)81205-1.; Horiguchi M. Biosynthesis of 2-aminoethylphosphonic acid in cell-free preparations from tetrahymena. Biochimica et Biophysica Acta (BBA) - General Subjects. 1972 Jan;261(1):102–13. doi: 10.1016/0304-4165(72)90319-4. |
| L-glutamine biosynthesis III Accession ID: BioCyc:META_PWY-6549 |
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Taylor L, Nunes-Nesi A, Parsley K, Leiss A, Leach G, Coates S, Wingler A, Fernie AR, Hibberd JM. Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content. Plant J. 2010 May 01;62(4):641–52. doi: 10.1111/j.1365-313x.2010.04179.x. PMID: 20202167. |
| cyanate degradation Accession ID: BioCyc:META_CYANCAT-PWY |
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Qian D, Jiang L, Lu L, Wei C, Li Y. Biochemical and Structural Properties of Cyanases from Arabidopsis thaliana and Oryza sativa. PLoS ONE. 2011 Mar 31;6(3):e18300. doi: 10.1371/journal.pone.0018300.; Rowlett RS, Tu C, McKay MM, Preiss JR, Loomis RJ, Hicks KA, Marchione RJ, Strong JA, Donovan GS, Chamberlin JE. Kinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana. Arch Biochem Biophys. 2002 Aug 15;404(2):197–209. doi: 10.1016/s0003-9861(02)00243-6. PMID: 12147257.; Fett JP, Coleman JR. Characterization and expression of two cDNAs encoding carbonic anhydrase in Arabidopsis thaliana. Plant Physiol. 1994 Jun;105(2):707–13. PMID: 7520589; PMCID: PMC159412.; 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. |
| cis-genanyl-CoA degradation Accession ID: BioCyc:META_PWY-6672 |
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Förster-Fromme K, Jendrossek D. Catabolism of citronellol and related acyclic terpenoids in pseudomonads. Applied Microbiology and Biotechnology. 2010 May 20;87(3):859–69. doi: 10.1007/s00253-010-2644-x. |
| naphthalene degradation (anaerobic) Accession ID: BioCyc:META_PWY-7620 |
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Estelmann S, Blank I, Feldmann A, Boll M. Two distinct old yellow enzymes are involved in naphthyl ring reduction during anaerobic naphthalene degradation. Mol Microbiol. 2015 Jan;95(2):162–72. doi: 10.1111/mmi.12875. PMID: 25424741.; Eberlein C, Estelmann S, Seifert J, von Bergen M, Müller M, Meckenstock RU, Boll M. Identification and characterization of 2-naphthoyl-coenzyme A reductase, the prototype of a novel class of dearomatizing reductases. Mol Microbiol. 2013 Jun;88(5):1032–9. doi: 10.1111/mmi.12238. PMID: 23646996.; Mouttaki H, Johannes J, Meckenstock RU. Identification of naphthalene carboxylase as a prototype for the anaerobic activation of non-substituted aromatic hydrocarbons. Environ Microbiol. 2012 Oct;14(10):2770–4. doi: 10.1111/j.1462-2920.2012.02768.x. PMID: 22564331.; Bergmann FD, Selesi D, Meckenstock RU. Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47. Arch Microbiol. 2011 Apr;193(4):241–50. doi: 10.1007/s00203-010-0667-4. PMID: 21221530. |
| anaerobic energy metabolism (invertebrates, mitochondrial) Accession ID: BioCyc:META_PWY-7384 |
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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.; 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.; Grieshaber MK, Hardewig I, Kreutzer U, Pörtner HO. Physiological and metabolic responses to hypoxia in invertebrates. Rev Physiol Biochem Pharmacol. 1994;125():43–147. doi: 10.1007/bfb0030909. PMID: 7984874.; Campbell T, Rubin N, Komuniecki R. Succinate-dependent energy generation in Ascaris suum mitochondria. Molecular and Biochemical Parasitology. 1989 Feb;33(1):1–12. doi: 10.1016/0166-6851(89)90036-4.; Saz HJ, Pietrzak SM. Phosphorylation associated with succinate decarboxylation to propionate in Ascaris mitochondria. Archives of Biochemistry and Biophysics. 1980 Jul;202(2):388–95. doi: 10.1016/0003-9861(80)90442-7. |
| L-arginine biosynthesis II (acetyl cycle) Accession ID: BioCyc:META_ARGSYNBSUB-PWY |
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Cunin R, Glansdorff N, Piérard A, Stalon V. Biosynthesis and metabolism of arginine in bacteria. Microbiol Rev. 1986 Sep;50(3):314–52. doi: 10.1128/mr.50.3.314-352.1986. |
| superpathway of L-citrulline metabolism Accession ID: BioCyc:META_PWY-5004 |
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| glyoxylate assimilation Accession ID: BioCyc:META_PWY-5744 |
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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: |
| superpathway of menaquinol-8 biosynthesis II Accession ID: BioCyc:META_PWY-6263 |
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Li X, Apel D, Gaynor EC, Tanner ME. 5'-Methylthioadenosine Nucleosidase Is Implicated in Playing a Key Role in a Modified Futalosine Pathway for Menaquinone Biosynthesis in Campylobacter jejuni. Journal of Biological Chemistry. 2011 Jun;286(22):19392–8. doi: 10.1074/jbc.m111.229781.; HIRATSUKA T, ITOH N, SETO H, DAIRI T. Enzymatic Properties of Futalosine Hydrolase, an Enzyme Essential to a Newly Identified Menaquinone Biosynthetic Pathway. Bioscience, Biotechnology, and Biochemistry. 2009 May 23;73(5):1137–41. doi: 10.1271/bbb.80906.; Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science. 2008 Sep 19;321(5896):1670–3. doi: 10.1126/science.1160446. PMID: 18801996.; 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. |
| superpathway of menaquinol-8 biosynthesis III Accession ID: BioCyc:META_PWY-7992 |
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Mahanta N, Fedoseyenko D, Dairi T, Begley TP. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J Am Chem Soc. 2013 Oct 16;135(41):15318–21. PMID: 24083939; PMCID: PMC3855536.; Li X, Apel D, Gaynor EC, Tanner ME. 5'-Methylthioadenosine Nucleosidase Is Implicated in Playing a Key Role in a Modified Futalosine Pathway for Menaquinone Biosynthesis in Campylobacter jejuni. Journal of Biological Chemistry. 2011 Jun;286(22):19392–8. doi: 10.1074/jbc.m111.229781.; HIRATSUKA T, ITOH N, SETO H, DAIRI T. Enzymatic Properties of Futalosine Hydrolase, an Enzyme Essential to a Newly Identified Menaquinone Biosynthetic Pathway. Bioscience, Biotechnology, and Biochemistry. 2009 May 23;73(5):1137–41. doi: 10.1271/bbb.80906.; Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science. 2008 Sep 19;321(5896):1670–3. doi: 10.1126/science.1160446. PMID: 18801996. |
| superpathway of chorismate metabolism Accession ID: BioCyc:META_ALL-CHORISMATE-PWY |
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Keating TA, Marshall CG, Walsh CT. Reconstitution and characterization of the Vibrio cholerae vibriobactin synthetase from VibB, VibE, VibF, and VibH. Biochemistry. 2000 Dec 19;39(50):15522–30. doi: 10.1021/bi0016523. PMID: 11112538. |