Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| 1D-myo-inositol hexakisphosphate biosynthesis III (Spirodela polyrrhiza) Accession ID: BioCyc:META_PWY-4661 |
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Stevenson-Paulik J, Bastidas RJ, Chiou S, Frye RA, York JD. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc. Natl. Acad. Sci. U.S.A. 2005 Aug 17;102(35):12612–7. doi: 10.1073/pnas.0504172102.; Raboy V. myo-Inositol-1,2,3,4,5,6-hexakisphosphate. Phytochemistry. 2003 Nov;64(6):1033–43. doi: 10.1016/s0031-9422(03)00446-1. PMID: 14568069.; Brearley CA, Hanke DE. Inositol phosphates in the duckweed Spirodela polyrhiza L. Biochem J. 1996 Feb 15;314 ( Pt 1)():215–25. PMID: 8660286; PMCID: PMC1217028.; Brearley CA, Hanke DE. Metabolic evidence for the order of addition of individual phosphate esters in the myo-inositol moiety of inositol hexakisphosphate in the duckweed Spirodela polyrhiza L. Biochem J. 1996 Feb 15;314 ( Pt 1)():227–33. PMID: 8660287; PMCID: PMC1217029.; Stephens LR, Irvine RF. Stepwise phosphorylation of myo-inositol leading to myo-inositol hexakisphosphate in Dictyostelium. Nature. 1990 Aug 09;346(6284):580–3. doi: 10.1038/346580a0. PMID: 2198472. |
| allantoin degradation to glyoxylate III Accession ID: BioCyc:META_PWY-5705 |
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Cusa E, Obradors N, Baldoma` L, Badi´a J, Aguilar J. Genetic Analysis of a Chromosomal Region Containing Genes Required for Assimilation of Allantoin Nitrogen and Linked Glyoxylate Metabolism in Escherichia coli. J Bacteriol. 1999 Dec 15;181(24):7479–84. doi: 10.1128/jb.181.24.7479-7484.1999.; Bongaerts GP, Vogels GD. Uric acid degradation by Bacillus fastidiosus strains. J Bacteriol. 1976 Feb;125(2):689–97. doi: 10.1128/jb.125.2.689-697.1976. |
| allantoin degradation to glyoxylate I Accession ID: BioCyc:META_PWY-5694 |
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Cooper TG, Gorski M, Turoscy V. A cluster of three genes responsible for allantoin degradation in Saccharomyces cerevisiae. Genetics. 1979 Jun;92(2):383–96. PMID: 385448; PMCID: PMC1213965.; Campbell LL. THE MECHANISM OF ALLANTOIN DEGRADATION BY A PSEUDOMONAS. J Bacteriol. 1954 Nov;68(5):598–603. doi: 10.1128/jb.68.5.598-603.1954. |
| UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing) Accession ID: BioCyc:META_PWY-6387 |
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Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev. 2008 Mar;32(2):168–207. doi: 10.1111/j.1574-6976.2008.00104.x. PMID: 18266853. |
| pyrimidine deoxyribonucleosides degradation Accession ID: BioCyc:META_PWY-7181 |
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| 2-nitrobenzoate degradation II Accession ID: BioCyc:META_PWY-5648 |
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Chauhan A, Jain RK. Degradation of o-Nitrobenzoate via Anthranilic Acid (o-Aminobenzoate) by Arthrobacter protophormiae: A Plasmid-Encoded New Pathway. Biochemical and Biophysical Research Communications. 2000 Jan;267(1):236–44. doi: 10.1006/bbrc.1999.1949. |
| α-linolenate biosynthesis II (cyanobacteria) Accession ID: BioCyc:META_PWY-7598 |
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Sakamoto T, Los DA, Higashi S, Wada H, Nishida I, Ohmori M, Murata N. Cloning of omega 3 desaturase from cyanobacteria and its use in altering the degree of membrane-lipid unsaturation. Plant Mol Biol. 1994 Oct;26(1):249–63. doi: 10.1007/bf00039536. PMID: 7524725. |
| α-linolenate biosynthesis I (plants and red algae) Accession ID: BioCyc:META_PWY-5997 |
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Eckert H, La Vallee B, Schweiger BJ, Kinney AJ, Cahoon EB, Clemente T. Co-expression of the borage Delta 6 desaturase and the Arabidopsis Delta 15 desaturase results in high accumulation of stearidonic acid in the seeds of transgenic soybean. Planta. 2006 Oct;224(5):1050–7. doi: 10.1007/s00425-006-0291-3. PMID: 16718484.; Wallis JG, Browse J. Mutants of Arabidopsis reveal many roles for membrane lipids. Prog Lipid Res. 2002 May;41(3):254–78. doi: 10.1016/s0163-7827(01)00027-3. PMID: 11814526. |
| ammonia assimilation cycle II Accession ID: BioCyc:META_PWY-6964 |
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Miflin BJ, Habash DZ. The role of glutamine synthetase and glutamate dehydrogenase in nitrogen assimilation and possibilities for improvement in the nitrogen utilization of crops. J Exp Bot. 2002 Apr;53(370):979–87. doi: 10.1093/jexbot/53.370.979. PMID: 11912240. |
| L-glutamine biosynthesis I Accession ID: BioCyc:META_GLNSYN-PWY |
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| vancomycin resistance II Accession ID: BioCyc:META_PWY-6455 |
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Dutta I, Reynolds PE. The vanC-3 vancomycin resistance gene cluster of Enterococcus flavescens CCM 439. J Antimicrob Chemother. 2003 Mar;51(3):703–6. doi: 10.1093/jac/dkg131. PMID: 12615874.; Dutka-Malen S, Molinas C, Arthur M, Courvalin P. Sequence of the vanC gene of Enterococcus gallinarum BM4174 encoding a D-alanine:D-alanine ligase-related protein necessary for vancomycin resistance. Gene. 1992 Mar 01;112(1):53–8. doi: 10.1016/0378-1119(92)90302-6. PMID: 1551598. |
| (+)-secoisolariciresinol diglucoside biosynthesis Accession ID: BioCyc:META_PWY-7487 |
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Ghose K, Selvaraj K, McCallum J, Kirby CW, Sweeney-Nixon M, Cloutier SJ, Deyholos M, Datla R, Fofana B. Identification and functional characterization of a flax UDP-glycosyltransferase glucosylating secoisolariciresinol (SECO) into secoisolariciresinol monoglucoside (SMG) and diglucoside (SDG). BMC Plant Biol. 2014 Mar 28;14():82. PMID: 24678929; PMCID: PMC3986616.; Setchell KD, Brown NM, Zimmer-Nechemias L, Wolfe B, Jha P, Heubi JE. Metabolism of secoisolariciresinol-diglycoside the dietary precursor to the intestinally derived lignan enterolactone in humans. Food Funct. 2014 Mar;5(3):491–501. PMID: 24429845; PMCID: PMC3996458.; Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Gupta VS. Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns. BMC Genomics. 2012 May 08;13():175. PMID: 22568875; PMCID: PMC3412749.; Yonekura-Sakakibara K, Hanada K. An evolutionary view of functional diversity in family 1 glycosyltransferases. Plant J. 2011 Apr;66(1):182–93. doi: 10.1111/j.1365-313x.2011.04493.x. PMID: 21443631.; Hemmati S, von Heimendahl CB, Klaes M, Alfermann AW, Schmidt TJ, Fuss E. Pinoresinol-lariciresinol reductases with opposite enantiospecificity determine the enantiomeric composition of lignans in the different organs of Linum usitatissimum L. Planta Med. 2010 Jun;76(9):928–34. doi: 10.1055/s-0030-1250036. PMID: 20514607.; Adolphe JL, Whiting SJ, Juurlink BH, Thorpe LU, Alcorn J. Health effects with consumption of the flax lignan secoisolariciresinol diglucoside. Br J Nutr. 2010 Apr;103(7):929–38. doi: 10.1017/s0007114509992753. PMID: 20003621.; Pan JY, Chen SL, Yang MH, Wu J, Sinkkonen J, Zou K. An update on lignans: natural products and synthesis. Nat Prod Rep. 2009 Oct;26(10):1251–92. doi: 10.1039/b910940d. PMID: 19779640.; Noguchi A, Fukui Y, Iuchi-Okada A, Kakutani S, Satake H, Iwashita T, Nakao M, Umezawa T, Ono E. Sequential glucosylation of a furofuran lignan, (+)-sesaminol, by Sesamum indicum UGT71A9 and UGT94D1 glucosyltransferases. The Plant Journal. 2008 Jan 31;54(3):415–27. doi: 10.1111/j.1365-313x.2008.03428.x.; Berim A, Ebel R, Schneider B, Petersen M. UDP-glucose:(6-methoxy)podophyllotoxin 7-O-glucosyltransferase from suspension cultures of Linum nodiflorum. Phytochemistry. 2008 Jan;69(2):374–81. doi: 10.1016/j.phytochem.2007.07.030. PMID: 17870138.; Geisler-Lee J, Geisler M, Coutinho PM, Segerman B, Nishikubo N, Takahashi J, Aspeborg H, Djerbi S, Master E, Andersson-Gunnerås S, Sundberg B, Karpinski S, Teeri TT, Kleczkowski LA, Henrissat B, Mellerowicz EJ. Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Plant Physiol. 2006 Mar;140(3):946–62. PMID: 16415215; PMCID: PMC1400564.; von Heimendahl CB, Schäfer KM, Eklund P, Sjöholm R, Schmidt TJ, Fuss E. Pinoresinol-lariciresinol reductases with different stereospecificity from Linum album and Linum usitatissimum. Phytochemistry. 2005 Jun;66(11):1254–63. doi: 10.1016/j.phytochem.2005.04.026. PMID: 15949826.; SUZUKI S, UMEZAWA T, SHIMADA M. Stereochemical Diversity in Lignan Biosynthesis ofArctium lappaL. Bioscience, Biotechnology, and Biochemistry. 2002 Jan;66(6):1262–9. doi: 10.1271/bbb.66.1262.; Ichiba S, Shimizu N, Kawasaki S, Aoe M, Kajitani N, Hara K, Ando H, Teramoto S. [A case of malignant lymphoma arising from chest wall in chronic empyema]. Kyobu Geka. 1991 Aug;44(9):739–42. PMID: 1956133. |
| diphyllin biosynthesis Accession ID: BioCyc:META_PWY-6820 |
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Hemmati S, Schneider B, Schmidt TJ, Federolf K, Alfermann AW, Fuss E. Justicidin B 7-hydroxylase, a cytochrome P450 monooxygenase from cell cultures of Linum perenne Himmelszelt involved in the biosynthesis of diphyllin. Phytochemistry. 2007 Nov;68(22-24):2736–43. doi: 10.1016/j.phytochem.2007.10.025. PMID: 17997463. |
| protein SAMPylation and SAMP-mediated thiolation Accession ID: BioCyc:META_PWY-7887 |
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Hepowit NL, de Vera IMS, Cao S, Fu X, Wu Y, Uthandi S, Chavarria NE, Englert M, Su D, S?ll D, Kojetin DJ, Maupin-Furlow JA. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. The FEBS Journal. 2016 Oct;283(19):3567–86. doi: 10.1111/febs.13819. |
| mAGP Accession ID: BioCyc:META_PWY-6397 |
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Grzegorzewicz AE, Ma Y, Jones V, Crick D, Liav A, McNeil MR. Development of a microtitre plate-based assay for lipid-linked glycosyltransferase products using the mycobacterial cell wall rhamnosyltransferase WbbL. 2008 Dec 01;154(12):3724–30. doi: 10.1099/mic.0.2008/023366-0.; Birch HL, Alderwick LJ, Bhatt A, Rittmann D, Krumbach K, Singh A, Bai Y, Lowary TL, Eggeling L, Besra GS. Biosynthesis of mycobacterial arabinogalactan: identification of a novel a(1?3) arabinofuranosyltransferase. Molecular Microbiology. 2008 Aug 05;69(5):1191–206. doi: 10.1111/j.1365-2958.2008.06354.x.; Belánová M, Dianisková P, Brennan PJ, Completo GC, Rose NL, Lowary TL, Mikusová K. Galactosyl transferases in mycobacterial cell wall synthesis. J Bacteriol. 2008 Feb;190(3):1141–5. PMID: 18055597; PMCID: PMC2223555.; Mikus?ova´ K, Bela´n?ova´ M, Kordula´kova´ J, Honda K, McNeil MR, Mahapatra S, Crick DC, Brennan PJ. Identification of a Novel Galactosyl Transferase Involved in Biosynthesis of the Mycobacterial Cell Wall. J Bacteriol. 2006 Sep 15;188(18):6592–8. doi: 10.1128/jb.00489-06.; Mills JA, Motichka K, Jucker M, Wu HP, Uhlik BC, Stern RJ, Scherman MS, Vissa VD, Pan F, Kundu M, Ma YF, McNeil M. Inactivation of the Mycobacterial Rhamnosyltransferase, Which Is Needed for the Formation of the Arabinogalactan-Peptidoglycan Linker, Leads to Irreversible Loss of Viability. Journal of Biological Chemistry. 2004 Oct;279(42):43540–6. doi: 10.1074/jbc.m407782200.; Crick DC, Mahapatra S, Brennan PJ. Biosynthesis of the arabinogalactan-peptidoglycan complex of Mycobacterium tuberculosis. Glycobiology. 2001 Sep;11(9):107R–118R. doi: 10.1093/glycob/11.9.107r. PMID: 11555614. |
| succinate fermentation to butanoate Accession ID: BioCyc:META_PWY-5677 |
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Söhling B, Gottschalk G. Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri. J Bacteriol. 1996 Feb;178(3):871–80. doi: 10.1128/jb.178.3.871-880.1996.; 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. |
| sesamin biosynthesis Accession ID: BioCyc:META_PWY-5469 |
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Ono E, Nakai M, Fukui Y, Tomimori N, Fukuchi-Mizutani M, Saito M, Satake H, Tanaka T, Katsuta M, Umezawa T, Tanaka Y. Formation of two methylenedioxy bridges by a Sesamum CYP81Q protein yielding a furofuran lignan, (+)-sesamin. Proc. Natl. Acad. Sci. U.S.A. 2006 Jun 27;103(26):10116–21. doi: 10.1073/pnas.0603865103.; Nakano D, Itoh C, Ishii F, Kawanishi H, Takaoka M, Kiso Y, Tsuruoka N, Tanaka T, Matsumura Y. Effects of Sesamin on Aortic Oxidative Stress and Endothelial Dysfunction in Deoxycorticosterone Acetate-Salt Hypertensive Rats. Biological & Pharmaceutical Bulletin. 2003;26(12):1701–5. doi: 10.1248/bpb.26.1701.; IKEDA S, KAGAYA M, KOBAYASHI K, TOHYAMA T, KISO Y, HIGUCHI N, YAMASHITA K. Dietary Sesame Lignans Decrease Lipid Peroxidation in Rats Fed Docosahexaenoic Acid. Journal of Nutritional Science and Vitaminology, J Nutr Sci Vitaminol. 2003;49(4):270–6. doi: 10.3177/jnsv.49.270.; Nakai M, Harada M, Nakahara K, Akimoto K, Shibata H, Miki W, Kiso Y. Novel antioxidative metabolites in rat liver with ingested sesamin. J Agric Food Chem. 2003 Mar 12;51(6):1666–70. doi: 10.1021/jf0258961. PMID: 12617602.; Ikeda S, Tohyama T, Yamashita K. Dietary sesame seed and its lignans inhibit 2,7,8-trimethyl- 2(2'-carboxyethyl)-6-hydroxychroman excretion into urine of rats fed gamma-tocopherol. J Nutr. 2002 May;132(5):961–6. doi: 10.1093/jn/132.5.961. PMID: 11983822.; Utsunomiya T, Chavali SR, Zhong WW, Forse RA. Effects of sesamin-supplemented dietary fat emulsions on the ex vivo production of lipopolysaccharide-induced prostanoids and tumor necrosis factor a in rats. The American Journal of Clinical Nutrition. 2000 Sep;72(3):804–8. doi: 10.1093/ajcn/72.3.804. |
| L-glutamate degradation VII (to butanoate) Accession ID: BioCyc:META_GLUDEG-II-PWY |
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Buckel W. Unusual enzymes involved in five pathways of glutamate fermentation. Applied Microbiology and Biotechnology. 2001 Oct 01;57(3):263–73. doi: 10.1007/s002530100773.; 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.; Buckel W, Barker HA. Two Pathways of Glutamate Fermentation by Anaerobic Bacteria. J Bacteriol. 1974 Mar;117(3):1248–60. doi: 10.1128/jb.117.3.1248-1260.1974.; 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. |
| L-tyrosine biosynthesis IV Accession ID: BioCyc:META_PWY-6134 |
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McGee MM, Greengard O, Knox WE. Liver phenylalanine hydroxylase activity in relation to blood concentrations of tyrosine and phenylalanine in the rat. Biochem J. 1972 May;127(4):675–80. PMID: 4265522; PMCID: PMC1178765. |
| pyruvate fermentation to propanoate I Accession ID: BioCyc:META_P108-PWY |
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Swick RW, Wood HG. THE ROLE OF TRANSCARBOXYLATION IN PROPIONIC ACID FERMENTATION. Proc Natl Acad Sci U S A. 1960 Jan;46(1):28–41. PMID: 16590594; PMCID: PMC285006. |