Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| hydrogen oxidation II (aerobic, NAD) Accession ID: BioCyc:META_PWY-5382 |
- | |
| pyrimidine deoxyribonucleotides de novo biosynthesis I Accession ID: BioCyc:META_PWY-7184 |
|
Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57():805–36. doi: 10.1146/annurev.arplant.57.032905.105421. PMID: 16669783. |
| pyrimidine deoxyribonucleotide phosphorylation Accession ID: BioCyc:META_PWY-7197 |
|
Katahira R, Ashihara H. Profiles of pyrimidine biosynthesis, salvage and degradation in disks of potato (Solanum tuberosum L.) tubers. Planta. 2002 Sep;215(5):821–8. doi: 10.1007/s00425-002-0806-5. PMID: 12244448. |
| superpathway of L-lysine degradation Accession ID: BioCyc:META_PWY-5327 |
|
Zabriskie TM, Jackson MD. Lysine biosynthesis and metabolism in fungi. Nat Prod Rep. 2000 Feb;17(1):85–97. doi: 10.1039/a801345d. PMID: 10714900.; 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.; Deana R. Substrate specificity of a dicarboxyl-CoA: dicarboxylic acid coenzyme A transferase from rat liver mitochondria. Biochem Int. 1992 Mar;26(4):767–73. PMID: 1610380.; 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-lysine degradation IV Accession ID: BioCyc:META_PWY-5280 |
|
Revelles O, Espinosa-Urgel M, Fuhrer T, Sauer U, Ramos JL. Multiple and Interconnected Pathways for |
| acetate and ATP formation from acetyl-CoA I Accession ID: BioCyc:META_PWY0-1312 |
- | |
| tetrahydrofolate biosynthesis Accession ID: BioCyc:META_PWY-6614 |
- | |
| superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) Accession ID: BioCyc:META_PWY-5910 |
|
Rodríguez-Concepción M, Boronat A. Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. A metabolic milestone achieved through genomics. Plant Physiol. 2002 Nov;130(3):1079–89. PMID: 12427975; PMCID: PMC1540259.; Okada K, Saito T, Nakagawa T, Kawamukai M, Kamiya Y. Five geranylgeranyl diphosphate synthases expressed in different organs are localized into three subcellular compartments in Arabidopsis. Plant Physiol. 2000 Apr;122(4):1045–56. PMID: 10759500; PMCID: PMC58939. |
| superpathway of L-methionine biosynthesis (transsulfuration) Accession ID: BioCyc:META_PWY-5347 |
- | |
| lactose and galactose degradation I Accession ID: BioCyc:META_LACTOSECAT-PWY |
|
Bissett DL, Wenger WC, Anderson RL. Lactose and D-galactose metabolism in Staphylococcus aureus. II. Isomerization of D-galactose 6-phosphate to D-tagatose 6-phosphate by a specific D-galactose-6-phosphate isomerase. Journal of Biological Chemistry. 1980 Sep;255(18):8740–4. doi: 10.1016/s0021-9258(18)43562-4.; Bissett DL, Anderson RL. Lactose and D-galactose metabolism in Staphylococcus aureus. IV. Isolation and properties of a class I D-ketohexose-1,6-diphosphate aldolase that catalyzes the cleavage of D-tagatose 1,6-diphosphate. Journal of Biological Chemistry. 1980 Sep;255(18):8750–5. doi: 10.1016/s0021-9258(18)43564-8.; Bissett DL, Anderson RL. Lactose and D-galactose metabolism in Staphylococcus aureus. III. Purification and properties of D-tagatose-6-phosphate kinase. Journal of Biological Chemistry. 1980 Sep;255(18):8745–9. doi: 10.1016/s0021-9258(18)43563-6.; Bissett DL, Anderson RL. Lactose and D-galactose metabolism in Staphylococcus aureus: Pathway of D-galactose 6-phosphate degradation. Biochemical and Biophysical Research Communications. 1973 May;52(2):641–7. doi: 10.1016/0006-291x(73)90761-4.; Hengstenberg W, Egan JB, Morse ML. Carbohydrate transport in Staphylococcus aureus. V. The accumulation of phosphorylated carbohydrate derivatives, and evidence for a new enzyme-splitting lactose phosphate. Proc Natl Acad Sci U S A. 1967 Jul;58(1):274–9. PMID: 4292101; PMCID: PMC335629. |
| chorismate biosynthesis I Accession ID: BioCyc:META_ARO-PWY |
|
Bentley R, Haslam E. The Shikimate Pathway — A Metabolic Tree with Many Branche. Critical Reviews in Biochemistry and Molecular Biology. 1990 Jan;25(5):307–84. doi: 10.3109/10409239009090615. |
| glycolate and glyoxylate degradation I Accession ID: BioCyc:ECO_GLYCOLATEMET-PWY |
|
Zelcbuch L, Razo-Mejia M, Herz E, Yahav S, Antonovsky N, Kroytoro H, Milo R, Bar-Even A. An In Vivo Metabolic Approach for Deciphering the Product Specificity of Glycerate Kinase Proves that Both E. coli’s Glycerate Kinases Generate 2-Phosphoglycerate. PLoS ONE. 2015 Mar 30;10(3):e0122957. doi: 10.1371/journal.pone.0122957. |
| superpathway of S-adenosyl-L-methionine biosynthesis Accession ID: BioCyc:ECO_MET-SAM-PWY |
- | |
| superpathway of L-threonine biosynthesis Accession ID: BioCyc:ECO_THRESYN-PWY |
|
Chassagnole C, Raïs B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J. 2001 Jun 01;356(Pt 2):415–23. PMID: 11368768; PMCID: PMC1221852.; Shames SL, Ash DE, Wedler FC, Villafranca JJ. Interaction of aspartate and aspartate-derived antimetabolites with the enzymes of the threonine biosynthetic pathway of Escherichia coli. Journal of Biological Chemistry. 1984 Dec;259(24):15331–9. doi: 10.1016/s0021-9258(17)42554-3.; Cohen GN, Hirsch M. THREONINE SYNTHASE, A SYSTEM SYNTHESIZING |
| pyrimidine deoxyribonucleotides de novo biosynthesis I Accession ID: BioCyc:ECO_PWY-7184 |
- | |
| N10-formyl-tetrahydrofolate biosynthesis Accession ID: BioCyc:ECO_1CMET2-PWY |
- | |
| tetrahydrofolate biosynthesis Accession ID: BioCyc:ECO_PWY-6614 |
- | |
| superpathway NAD/NADP - NADH/NADPH interconversion Accession ID: BioCyc:YEAST_PWY-7245 |
|
Feng Y, Li W, Li J, Wang J, Ge J, Xu D, Liu Y, Wu K, Zeng Q, Wu JW, Tian C, Zhou B, Yang M. Structural insight into the type-II mitochondrial NADH dehydrogenases. Nature. 2012 Nov 15;491(7424):478–82. doi: 10.1038/nature11541. PMID: 23086143.; Gossmann TI, Ziegler M, Puntervoll P, de Figueiredo LF, Schuster S, Heiland I. NAD+ biosynthesis and salvage – a phylogenetic perspective. The FEBS Journal. 2012 Apr 04;279(18):3355–63. doi: 10.1111/j.1742-4658.2012.08559.x.; Lu S, Lin S. Phosphate-responsive Signaling Pathway Is a Novel Component of NAD+ Metabolism in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2011 Apr;286(16):14271–81. doi: 10.1074/jbc.m110.217885.; Miyagi H, Kawai S, Murata K. Two Sources of Mitochondrial NADPH in the Yeast Saccharomyces cerevisiae. Journal of Biological Chemistry. 2009 Mar;284(12):7553–60. doi: 10.1074/jbc.m804100200.; Koch-Nolte F, Haag F, Guse AH, Lund F, Ziegler M. Emerging Roles of NAD + and Its Metabolites in Cell SignalingA report on the NAD2008 symposium, Hamburg, Germany, 14 to 17 September 2008. Sci. Signal. 2009 Feb 10;2(57). doi: 10.1126/scisignal.257mr1.; Bieganowski P, Seidle HF, Wojcik M, Brenner C. Synthetic Lethal and Biochemical Analyses of NAD and NADH Kinases in Saccharomyces cerevisiae Establish Separation of Cellular Functions. Journal of Biological Chemistry. 2006 Aug;281(32):22439–45. doi: 10.1074/jbc.m513919200.; Minard KI, McAlister-Henn L. Sources of NADPH in Yeast Vary with Carbon Source. Journal of Biological Chemistry. 2005 Dec;280(48):39890–6. doi: 10.1074/jbc.m509461200.; Shi F, Kawai S, Mori S, Kono E, Murata K. Identification of ATP-NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae. The FEBS Journal. 2005 Jun 24;272(13):3337–49. doi: 10.1111/j.1742-4658.2005.04749.x.; Contreras-Shannon V, Lin A, McCammon MT, McAlister-Henn L. Kinetic Properties and Metabolic Contributions of Yeast Mitochondrial and Cytosolic NADP+-specific Isocitrate Dehydrogenases. Journal of Biological Chemistry. 2005 Feb;280(6):4469–75. doi: 10.1074/jbc.m410140200.; Strand MK, Stuart GR, Longley MJ, Graziewicz MA, Dominick OC, Copeland WC. POS5 Gene of Saccharomyces cerevisiae Encodes a Mitochondrial NADH Kinase Required for Stability of Mitochondrial DNA. Eukaryot Cell. 2003 Aug;2(4):809–20. doi: 10.1128/ec.2.4.809-820.2003.; Outten CE, Culotta VC. A novel NADH kinase is the mitochondrial source of NADPH in Saccharomyces cerevisiae. EMBO J. 2003 May 01;22(9):2015–24. PMID: 12727869; PMCID: PMC156083.; Grabowska D, Chelstowska A. The ALD6 Gene Product Is Indispensable for Providing NADPH in Yeast Cells Lacking Glucose-6-phosphate Dehydrogenase Activity. Journal of Biological Chemistry. 2003 Apr;278(16):13984–8. doi: 10.1074/jbc.m210076200.; Påhlman I, Larsson C, Averét N, Bunoust O, Boubekeur S, Gustafsson L, Rigoulet M. Kinetic Regulation of the Mitochondrial Glycerol-3-phosphate Dehydrogenase by the External NADH Dehydrogenase in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2002 Aug;277(31):27991–5. doi: 10.1074/jbc.m204079200.; Minard KI, McAlister-Henn L. Antioxidant function of cytosolic sources of NADPH in yeast. Free Radic Biol Med. 2001 Sep 15;31(6):832–43. doi: 10.1016/s0891-5849(01)00666-9. PMID: 11557322.; Kawai S, Suzuki S, Mori S, Murata K. Molecular cloning and identification of UTR1 of a yeast Saccharomyces cerevisiae as a gene encoding an NAD kinase. FEMS Microbiol Lett. 2001 Jun 25;200(2):181–4. doi: 10.1111/j.1574-6968.2001.tb10712.x. PMID: 11425472.; Overkamp KM, Bakker BM, Ko¨tter P, van Tuijl A, de Vries S, van Dijken JP, Pronk JT. In Vivo Analysis of the Mechanisms for Oxidation of Cytosolic NADH by Saccharomyces cerevisiae Mitochondria. J Bacteriol. 2000 May 15;182(10):2823–30. doi: 10.1128/jb.182.10.2823-2830.2000.; Small WC, McAlister-Henn L. Identification of a Cytosolically Directed NADH Dehydrogenase in Mitochondria of Saccharomyces cerevisiae. J Bacteriol. 1998 Aug 15;180(16):4051–5. doi: 10.1128/jb.180.16.4051-4055.1998.; Tessier WD, Meaden PG, Dickinson FM, Midgley M. Identification and disruption of the gene encoding the K(+)-activated acetaldehyde dehydrogenase of Saccharomyces cerevisiae. FEMS Microbiol Lett. 1998 Jul 01;164(1):29–34. doi: 10.1111/j.1574-6968.1998.tb13063.x. PMID: 9675847.; Wang X, Mann CJ, Bai Y, Ni L, Weiner H. Molecular Cloning, Characterization, and Potential Roles of Cytosolic and Mitochondrial Aldehyde Dehydrogenases in Ethanol Metabolism in Saccharomyces cerevisiae. J Bacteriol. 1998 Feb 15;180(4):822–30. doi: 10.1128/jb.180.4.822-830.1998.; Meaden PG, Dickinson FM, Mifsud A, Tessier W, Westwater J, Bussey H, Midgley M. The ALD6 gene of Saccharomyces cerevisiae encodes a cytosolic, Mg(2+)-activated acetaldehyde dehydrogenase. Yeast. 1997 Nov;13(14):1319–27. doi: 10.1002/(sici)1097-0061(199711)13:14<1319::aid-yea183>3.0.co;2-t. PMID: 9392076.; Wang X, Bai Y, Ni L, Weiner H. Saccharomyces cerevisiae aldehyde dehydrogenases. Identification and expression. Adv Exp Med Biol. 1997;414():277–80. doi: 10.1007/978-1-4615-5871-2_32. PMID: 9059631.; Loftus TM, Hall LV, Anderson SL, McAlister-Henn L. Isolation, characterization, and disruption of the yeast gene encoding cytosolic NADP-specific isocitrate dehydrogenase. Biochemistry. 1994 Aug 16;33(32):9661–7. doi: 10.1021/bi00198a035. PMID: 8068643.; DE VRIES S, VAN WITZENBURG R, GRIVELL LA, MARRES CAM. Primary structure and import pathway of the rotenone-insensitive NADH-ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae. European Journal of Biochemistry. 1992 Feb;203(3):587–92. doi: 10.1111/j.1432-1033.1992.tb16587.x.; MARRES CAM, de VRIES S, GRIVELL LA. Isolation and inactivation of the nuclear gene encoding the rotenone-insensitive internal NADH: ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae. European Journal of Biochemistry. 1991 Feb;195(3):857–62. doi: 10.1111/j.1432-1033.1991.tb15775.x.; de VRIES S, GRIVELL LA. Purification and characterization of a rotenone-insensitive NADH: Q6 oxidoreductase from mitochondria of Saccharomyces cerevisiae. European Journal of Biochemistry. 1988 Sep;176(2):377–84. doi: 10.1111/j.1432-1033.1988.tb14292.x.; Bruinenberg PM. The NADP(H) redox couple in yeast metabolism. Antonie Van Leeuwenhoek. 1986;52(5):411–29. doi: 10.1007/bf00393469. PMID: 3789705. |
| tetrapyrrole biosynthesis I (from glutamate) Accession ID: BioCyc:ARA_PWY-5188 |
|
Von Wettstein D, Gough S, Kannangara CG. Chlorophyll Biosynthesis. Plant Cell. 1995 Jul;7(7):1039–57. PMID: 12242396; PMCID: PMC160907.; Warren MJ, Scott AI. Tetrapyrrole assembly and modification into the ligands of biologically functional cofactors. Trends Biochem Sci. 1990 Dec;15(12):486–91. doi: 10.1016/0968-0004(90)90304-t. PMID: 2077690. |
| superpathway of proto- and siroheme biosynthesis Accession ID: BioCyc:ARA_PWYQT-62 |
|
Nagai S, Koide M, Takahashi S, Kikuta A, Aono M, Sasaki-Sekimoto Y, Ohta H, Takamiya K, Masuda T. Induction of isoforms of tetrapyrrole biosynthetic enzymes, AtHEMA2 and AtFC1, under stress conditions and their physiological functions in Arabidopsis. Plant Physiol. 2007 Jun;144(2):1039–51. PMID: 17416636; PMCID: PMC1914178.; Raux-Deery E, Leech HK, Nakrieko KA, McLean KJ, Munro AW, Heathcote P, Rigby SE, Smith AG, Warren MJ. Identification and characterization of the terminal enzyme of siroheme biosynthesis from Arabidopsis thaliana: a plastid-located sirohydrochlorin ferrochelatase containing a 2FE-2S center. J Biol Chem. 2005 Feb 11;280(6):4713–21. doi: 10.1074/jbc.m411360200. PMID: 15545265.; Leustek T, Smith M, Murillo M, Singh DP, Smith AG, Woodcock SC, Awan SJ, Warren MJ. Siroheme biosynthesis in higher plants. Analysis of an S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferase from Arabidopsis thaliana. J Biol Chem. 1997 Jan 31;272(5):2744–52. doi: 10.1074/jbc.272.5.2744. PMID: 9006913.; Narita S, Tanaka R, Ito T, Okada K, Taketani S, Inokuchi H. Molecular cloning and characterization of a cDNA that encodes protoporphyrinogen oxidase of Arabidopsis thaliana. Gene. 1996 Dec 05;182(1-2):169–75. doi: 10.1016/s0378-1119(96)00545-8. PMID: 8982084.; Sakakibara H, Takei K, Sugiyama T. Isolation and characterization of a cDNA that encodes maize uroporphyrinogen III methyltransferase, an enzyme involved in the synthesis of siroheme, which is prosthetic group of nitrite reductase. Plant J. 1996 Nov;10(5):883–92. doi: 10.1046/j.1365-313x.1996.10050883.x. PMID: 8953249. |