Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| rosamicin biosynthesis Accession ID: BioCyc:META_PWY-7677 |
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Iizaka Y, Higashi N, Ishida M, Oiwa R, Ichikawa Y, Takeda M, Anzai Y, Kato F. Function of cytochrome P450 enzymes RosC and RosD in the biosynthesis of rosamicin macrolide antibiotic produced by Micromonospora rosaria. Antimicrob Agents Chemother. 2013 Mar;57(3):1529–31. PMID: 23274670; PMCID: PMC3591866. |
| UDP-α-D-xylose biosynthesis Accession ID: BioCyc:META_PWY-4821 |
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Gu X, Lee SG, Bar-Peled M. Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase. Microbiology (Reading). 2011 Jan;157(Pt 1):260–9. PMID: 20847005; PMCID: PMC3068629.; Pattathil S, Harper AD, Bar-Peled M. Biosynthesis of UDP-xylose: characterization of membrane-bound AtUxs2. Planta. 2005 Jun;221(4):538–48. doi: 10.1007/s00425-004-1471-7. PMID: 15655675.; Bindschedler LV, Wheatley E, Gay E, Cole J, Cottage A, Bolwell GP. Characterisation and expression of the pathway from UDP-glucose to UDP-xylose in differentiating tobacco tissue. Plant Mol Biol. 2005 Jan;57(2):285–301. doi: 10.1007/s11103-004-7795-7. PMID: 15821883.; Harper AD, Bar-Peled M. Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms. Plant Physiol. 2002 Dec;130(4):2188–98. PMID: 12481102; PMCID: PMC166730. |
| methymycin, neomethymycin and novamethymycin biosynthesis Accession ID: BioCyc:META_PWY-7422 |
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Zhang Q, Sherman DH. Isolation and Structure Determination of Novamethymycin, a New Bioactive Metabolite of the Methymycin Biosynthetic Pathway in Streptomyces venezuelae. J. Nat. Prod. 2001 Oct 19;64(11):1447–50. doi: 10.1021/np010146r. |
| 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. |
| nystatin biosynthesis Accession ID: BioCyc:META_PWY-7624 |
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Brautaset T, Sekurova ON, Sletta H, Ellingsen TE, StrLm AR, Valla S, Zotchev SB. Biosynthesis of the polyene antifungal antibiotic nystatin in Streptomyces noursei ATCC 11455: analysis of the gene cluster and deduction of the biosynthetic pathway. Chem Biol. 2000 Jun;7(6):395–403. doi: 10.1016/s1074-5521(00)00120-4. PMID: 10873841. |
| tylosin biosynthesis Accession ID: BioCyc:META_PWY-7415 |
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Fouces R, Mellado E, Díez B, Barredo JL. The tylosin biosynthetic cluster from Streptomyces fradiae: genetic organization of the left region. Microbiology (Reading). 1999 Apr;145 ( Pt 4)():855–68. doi: 10.1099/13500872-145-4-855. PMID: 10220165.; Baltz RH, Seno ET. Properties of Streptomyces fradiae Mutants Blocked in Biosynthesis of the Macrolide Antibiotic Tylosin. Antimicrob Agents Chemother. 1981 Aug;20(2):214–25. doi: 10.1128/aac.20.2.214. |
| 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 menaquinol-12 biosynthesis Accession ID: BioCyc:META_PWY-5898 |
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Miller P, Rabinowitz A, Taber H. Molecular cloning and preliminary genetic analysis of the men gene cluster of Bacillus subtilis. J Bacteriol. 1988 Jun;170(6):2735–41. doi: 10.1128/jb.170.6.2735-2741.1988.; Bentley R, Meganathan R. Biosynthesis of vitamin K (menaquinone) in bacteria. Microbiol Rev. 1982 Sep;46(3):241–80. doi: 10.1128/mr.46.3.241-280.1982. |
| plastoquinol-9 biosynthesis II Accession ID: BioCyc:META_PWY-6978 |
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Pfaff C, Glindemann N, Gruber J, Frentzen M, Sadre R. Chorismate Pyruvate-Lyase and 4-Hydroxy-3-solanesylbenzoate Decarboxylase Are Required for Plastoquinone Biosynthesis in the Cyanobacterium Synechocystis sp. PCC6803. Journal of Biological Chemistry. 2014 Jan;289(5):2675–86. doi: 10.1074/jbc.m113.511709.; Sadre R, Pfaff C, Buchkremer S. Plastoquinone-9 biosynthesis in cyanobacteria differs from that in plants and involves a novel 4-hydroxybenzoate solanesyltransferase. Biochem J. 2012 Mar 15;442(3):621–9. doi: 10.1042/bj20111796. PMID: 22166075. |
| superpathway of menaquinol-9 biosynthesis Accession ID: BioCyc:META_PWY-5845 |
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Bentley R, Meganathan R. Biosynthesis of vitamin K (menaquinone) in bacteria. Microbiol Rev. 1982 Sep;46(3):241–80. doi: 10.1128/mr.46.3.241-280.1982. |
| superpathway of plastoquinol biosynthesis Accession ID: BioCyc:META_PWY-5864 |
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Soll J, Schultz G, Joyard J, Douce R, Block MA. Localization and synthesis of prenylquinones in isolated outer and inner envelope membranes from spinach chloroplasts. Archives of Biochemistry and Biophysics. 1985 Apr;238(1):290–9. doi: 10.1016/0003-9861(85)90167-5. |
| L-arginine degradation VIII (arginine oxidase pathway) Accession ID: BioCyc:META_ARGDEG-IV-PWY |
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Vanderbilt AS, Gaby NS, Rodwell VW. Intermediates and enzymes between alpha-ketoarginine and gamma-guanidinobutyrate in the L-arginine catabolic pathway of Pseudomonas putida. Journal of Biological Chemistry. 1975 Jul;250(14):5322–9. doi: 10.1016/s0021-9258(19)41184-8. |
| 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. |
| toluene degradation IV (aerobic) (via catechol) Accession ID: BioCyc:META_PWY-5178 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Johnson DR, Park J, Kukor JJ, Abriola LM. Effect of carbon starvation on toluene degradation activity by toluene monooxygenase-expressing bacteria. Biodegradation. 2006 Oct;17(5):437–45. doi: 10.1007/s10532-005-9014-x. PMID: 16477358.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2. |
| ubiquinol-6 biosynthesis from 4-aminobenzoate (yeast) Accession ID: BioCyc:META_PWY-7230 |
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Xie LX, Ozeir M, Tang JY, Chen JY, Jaquinod S, Fontecave M, Clarke CF, Pierrel F. Overexpression of the Coq8 Kinase in Saccharomyces cerevisiae coq Null Mutants Allows for Accumulation of Diagnostic Intermediates of the Coenzyme Q6 Biosynthetic Pathway. Journal of Biological Chemistry. 2012 Jul;287(28):23571–81. doi: 10.1074/jbc.m112.360354.; Ozeir M, Mühlenhoff U, Webert H, Lill R, Fontecave M, Pierrel F. Coenzyme Q biosynthesis: Coq6 is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency. Chem Biol. 2011 Sep 23;18(9):1134–42. doi: 10.1016/j.chembiol.2011.07.008. PMID: 21944752.; Marbois B, Xie LX, Choi S, Hirano K, Hyman K, Clarke CF. para-Aminobenzoic Acid Is a Precursor in Coenzyme Q6 Biosynthesis in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2010 Sep;285(36):27827–38. doi: 10.1074/jbc.m110.151894.; Pierrel F, Hamelin O, Douki T, Kieffer-Jaquinod S, Mühlenhoff U, Ozeir M, Lill R, Fontecave M. Involvement of mitochondrial ferredoxin and para-aminobenzoic acid in yeast coenzyme Q biosynthesis. Chem Biol. 2010 May 28;17(5):449–59. doi: 10.1016/j.chembiol.2010.03.014. PMID: 20534343.; Tauche A, Krause-Buchholz U, Rödel G. Ubiquinone biosynthesis in Saccharomyces cerevisiae: the molecular organization of O-methylase Coq3p depends on Abc1p/Coq8p. FEMS Yeast Res. 2008 Dec;8(8):1263–75. doi: 10.1111/j.1567-1364.2008.00436.x. PMID: 18801050.; Padilla S, Tran UC, Jiménez-Hidalgo M, López-Martín JM, Martín-Montalvo A, Clarke CF, Navas P, Santos-Ocaña C. Hydroxylation of demethoxy-Q6 constitutes a control point in yeast coenzyme Q6 biosynthesis. Cellular and Molecular Life Sciences. 2008 Nov 11;66(1):173. doi: 10.1007/s00018-008-8547-7.; Tran UC, Clarke CF. Endogenous synthesis of coenzyme Q in eukaryotes. Mitochondrion. 2007 Jun;7():S62–71. doi: 10.1016/j.mito.2007.03.007.; Barros MH, Nobrega FG. YAH1 of Saccharomyces cerevisiae: a new essential gene that codes for a protein homologous to human adrenodoxin. Gene. 1999 Jun 11;233(1-2):197–203. doi: 10.1016/s0378-1119(99)00137-7. PMID: 10375636.; Manzella L, Barros MH, Nobrega FG. ARH1 of Saccharomyces cerevisiae: a new essential gene that codes for a protein homologous to the human adrenodoxin reductase. Yeast. 1998 Jun 30;14(9):839–46. doi: 10.1002/(sici)1097-0061(19980630)14:9<839::aid-yea283>3.0.co;2-a. PMID: 9818721. |
| mandelate degradation to acetyl-CoA Accession ID: BioCyc:META_PWY-6957 |
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Ca´mara B, Bielecki P, Kaminski F, dos Santos VM, Plumeier I, Nikodem P, Pieper DH. A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate. J Bacteriol. 2007 Mar;189(5):1664–74. doi: 10.1128/jb.01192-06.; Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt PC, Kenyon GL. Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli. Biochemistry. 1990 Oct 23;29(42):9856–62. doi: 10.1021/bi00494a015. PMID: 2271624. |
| L-malate degradation II Accession ID: BioCyc:META_PWY-7686 |
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Landete JM, Ferrer S, Monedero V, Zúñiga M. Malic enzyme and malolactic enzyme pathways are functionally linked but independently regulated in Lactobacillus casei BL23. Appl Environ Microbiol. 2013 Sep;79(18):5509–18. PMID: 23835171; PMCID: PMC3754186. |
| coenzyme A biosynthesis II (eukaryotic) Accession ID: BioCyc:META_PWY-7851 |
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Ruiz A, González A, Muñoz I, Serrano R, Abrie JA, Strauss E, Ariño J. Moonlighting proteins Hal3 and Vhs3 form a heteromeric PPCDC with Ykl088w in yeast CoA biosynthesis. Nat Chem Biol. 2009 Dec;5(12):920–8. doi: 10.1038/nchembio.243. PMID: 19915539.; Rubio S, Larson TR, Gonzalez-Guzman M, Alejandro S, Graham IA, Serrano R, Rodriguez PL. An Arabidopsis mutant impaired in coenzyme A biosynthesis is sugar dependent for seedling establishment. Plant Physiol. 2006 Mar;140(3):830–43. PMID: 16415216; PMCID: PMC1400581.; Leonardi R, Zhang YM, Rock CO, Jackowski S. Coenzyme A: back in action. Prog Lipid Res. 2005 Mar;44(2-3):125–53. doi: 10.1016/j.plipres.2005.04.001. PMID: 15893380.; Ruiz A, Muñoz I, Serrano R, González A, Simón E, Ariño J. Functional characterization of the Saccharomyces cerevisiae VHS3 gene: a regulatory subunit of the Ppz1 protein phosphatase with novel, phosphatase-unrelated functions. J Biol Chem. 2004 Aug 13;279(33):34421–30. doi: 10.1074/jbc.m400572200. PMID: 15192104.; Kupke T, Hernández-Acosta P, Culiáñez-Macià FA. 4'-Phosphopantetheine and Coenzyme A Biosynthesis in Plants. Journal of Biological Chemistry. 2003 Oct;278(40):38229–37. doi: 10.1074/jbc.m306321200.; Steinbacher S, Hernández-Acosta P, Bieseler B, Blaesse M, Huber R, Culiáñez-Macià FA, Kupke T. Crystal structure of the plant PPC decarboxylase AtHAL3a complexed with an ene-thiol reaction intermediate. J Mol Biol. 2003 Mar 14;327(1):193–202. doi: 10.1016/s0022-2836(03)00092-5. PMID: 12614618.; Ariño J. Novel protein phosphatases in yeast. European Journal of Biochemistry. 2002 Feb 15;269(4):1072–7. doi: 10.1046/j.0014-2956.2002.02753.x.; de Nadal E, Clotet J, Posas F, Serrano R, Gomez N, Ariño J. The yeast halotolerance determinant Hal3p is an inhibitory subunit of the Ppz1p Ser/Thr protein phosphatase. Proc. Natl. Acad. Sci. U.S.A. 1998 Jun 23;95(13):7357–62. doi: 10.1073/pnas.95.13.7357. |
| thymine degradation Accession ID: BioCyc:META_PWY-6430 |
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Tsai CS, Axelrod B. Catabolism of Pyrimidines in Rape Seedlings. Plant Physiol. 1965 Jan;40(1):39–44. PMID: 16656066; PMCID: PMC550236.; Evans WR, Axelrod B. Pyrimidine metabolism in germinating seedlings. Plant Physiol. 1961 Jan;36(1):9–13. PMID: 16655478; PMCID: PMC406080. |
| L-tryptophan degradation XII (Geobacillus) Accession ID: BioCyc:META_PWY-6505 |
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Liu X, Dong Y, Li X, Ren Y, Li Y, Wang W, Wang L, Feng L. Characterization of the anthranilate degradation pathway in Geobacillus thermodenitrificans NG80-2. Microbiology (Reading). 2010 Feb;156(Pt 2):589–95. doi: 10.1099/mic.0.031880-0. PMID: 19942660. |