Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| conversion of succinate to propanoate Accession ID: BioCyc:META_PWY0-43 |
- | |
| palmatine biosynthesis Accession ID: BioCyc:META_PWY-5470 |
- | |
| berberine biosynthesis Accession ID: BioCyc:META_PWY-3901 |
|
Samanani N, Park SU, Facchini PJ. Cell type-specific localization of transcripts encoding nine consecutive enzymes involved in protoberberine alkaloid biosynthesis. Plant Cell. 2005 Mar;17(3):915–26. PMID: 15722473; PMCID: PMC1069708.; Ikezawa N, Tanaka M, Nagayoshi M, Shinkyo R, Sakaki T, Inouye K, Sato F. Molecular Cloning and Characterization of CYP719, a Methylenedioxy Bridge-forming Enzyme That Belongs to a Novel P450 Family, from cultured Coptis japonica Cells. Journal of Biological Chemistry. 2003 Oct;278(40):38557–65. doi: 10.1074/jbc.m302470200.; Bock A, Wanner G, Zenk MH. Immunocytological localization of two enzymes involved in berberine biosynthesis. Planta. 2002 Nov;216(1):57–63. doi: 10.1007/s00425-002-0867-5. PMID: 12430014.; Facchini PJ. A |
| nopaline degradation Accession ID: BioCyc:META_NOPALINEDEG-PWY |
|
Cho K, Fuqua C, Martin BS, Winans SC. Identification of Agrobacterium tumefaciens genes that direct the complete catabolism of octopine. J Bacteriol. 1996 Apr;178(7):1872–80. doi: 10.1128/jb.178.7.1872-1880.1996.; Zanker H, Lurz G, Langridge U, Langridge P, Kreusch D, Schröder J. Octopine and nopaline oxidases from Ti plasmids of Agrobacterium tumefaciens: molecular analysis, relationship, and functional characterization. J Bacteriol. 1994 Aug;176(15):4511–7. doi: 10.1128/jb.176.15.4511-4517.1994. |
| pyruvate fermentation to acetate and alanine Accession ID: BioCyc:META_PWY-5096 |
|
Sakuraba H, Ohshima T. Novel energy metabolism in anaerobic hyperthermophilic archaea: a modified Embden-Meyerhof pathway. Journal of Bioscience and Bioengineering. 2002 May;93(5):441–8. doi: 10.1016/s1389-1723(02)80090-1.; Ward DE, Kengen SWM, van der Oost J, de Vos WM. Purification and Characterization of the Alanine Aminotransferase from the Hyperthermophilic Archaeon Pyrococcus furiosus and Its Role in Alanine Production. J Bacteriol. 2000 May;182(9):2559–66. doi: 10.1128/jb.182.9.2559-2566.2000.; de Vos WM, Kengen SW, Voorhorst WG, van der Oost J. Sugar utilization and its control in hyperthermophiles. Extremophiles. 1998 Aug;2(3):201–5. doi: 10.1007/s007920050061. PMID: 9783166. |
| succinate to cytochrome bo oxidase electron transfer Accession ID: BioCyc:META_PWY0-1329 |
- | |
| peptidoglycan cross-bridge biosynthesis II (E. faecium) Accession ID: BioCyc:META_PWY-6461 |
|
Veiga P, Erkelenz M, Bernard E, Courtin P, Kulakauskas S, Chapot-Chartier M. Identification of the Asparagine Synthase Responsible for |
| 2-aminoethylphosphonate degradation II Accession ID: BioCyc:META_PWY-6832 |
|
Borisova SA, Christman HD, Metcalf MEM, Zulkepli NA, Zhang JK, van der Donk WA, Metcalf WW. Genetic and Biochemical Characterization of a Pathway for the Degradation of 2-Aminoethylphosphonate in Sinorhizobium meliloti 1021. Journal of Biological Chemistry. 2011 Jun;286(25):22283–90. doi: 10.1074/jbc.m111.237735. |
| retinoate biosynthesis I Accession ID: BioCyc:META_PWY-6872 |
|
Napoli JL. Physiological insights into all-trans-retinoic acid biosynthesis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):152–67. doi: 10.1016/j.bbalip.2011.05.004.; Moffa DJ, Lotspeich FJ, Krause RF. Preparation and Properties of Retinal-oxidizing Enzyme from Rat Intestinal Mucosa. Journal of Biological Chemistry. 1970 Jan;245(2):439–47. doi: 10.1016/s0021-9258(18)63410-6. |
| pyruvate fermentation to acetate IV Accession ID: BioCyc:META_PWY-5485 |
- | |
| spermidine biosynthesis I Accession ID: BioCyc:META_BSUBPOLYAMSYN-PWY |
|
Li Y, Hess S, Pannell LK, Tabor CW, Tabor H. In vivo mechanism-based inactivation of S -adenosylmethionine decarboxylases from Escherichia coli , Salmonella typhimurium , and Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2001 Aug 28;98(19):10578–83. doi: 10.1073/pnas.181341198.; Hamasaki-Katagiri N, Tabor CW, Tabor H. Spermidine biosynthesis in Saccharomyces cerevisae: polyamine requirement of a null mutant of the SPE3 gene (spermidine synthase). Gene. 1997 Mar 10;187(1):35–43. doi: 10.1016/s0378-1119(96)00660-9. PMID: 9073064. |
| phosphate acquisition Accession ID: BioCyc:META_PWY-6348 |
|
Lin W-, Lin S-, Chiou T-. Molecular regulators of phosphate homeostasis in plants. Journal of Experimental Botany. 2009 Jan 23;60(5):1427–38. doi: 10.1093/jxb/ern303.; Bozzo GG, Raghothama KG, Plaxton WC. Purification and characterization of two secreted purple acid phosphatase isozymes from phosphate-starved tomato (Lycopersicon esculentum) cell cultures. European Journal of Biochemistry. 2002 Dec;269(24):6278–86. doi: 10.1046/j.1432-1033.2002.03347.x. |
| spermidine biosynthesis II Accession ID: BioCyc:META_PWY-6559 |
|
Hanfrey CC, Pearson BM, Hazeldine S, Lee J, Gaskin DJ, Woster PM, Phillips MA, Michael AJ. Alternative Spermidine Biosynthetic Route Is Critical for Growth of Campylobacter jejuni and Is the Dominant Polyamine Pathway in Human Gut Microbiota. Journal of Biological Chemistry. 2011 Dec;286(50):43301–12. doi: 10.1074/jbc.m111.307835.; Deng X, Lee J, Michael AJ, Tomchick DR, Goldsmith EJ, Phillips MA. Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J Biol Chem. 2010 Aug 13;285(33):25708–19. PMID: 20534592; PMCID: PMC2919134.; Lee J, Sperandio V, Frantz DE, Longgood J, Camilli A, Phillips MA, Michael AJ. An Alternative Polyamine Biosynthetic Pathway Is Widespread in Bacteria and Essential for Biofilm Formation in Vibrio cholerae. Journal of Biological Chemistry. 2009 Apr;284(15):9899–907. doi: 10.1074/jbc.m900110200. |
| 10,13-epoxy-11-methyl-octadecadienoate biosynthesis Accession ID: BioCyc:META_PWY-7691 |
|
Lemke RA, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellström H, Coon JJ, Donohue TJ. Synthesis and scavenging role of furan fatty acids. Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3450–7. PMID: 25092314; PMCID: PMC4143029. |
| pyruvate fermentation to acetate I Accession ID: BioCyc:META_P142-PWY |
|
Boynton ZL, Bennett GN, Rudolph FB. Cloning, sequencing, and expression of genes encoding phosphotransacetylase and acetate kinase from Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol. 1996 Aug;62(8):2758–66. doi: 10.1128/aem.62.8.2758-2766.1996. |
| CDP-diacylglycerol biosynthesis I Accession ID: BioCyc:META_PWY-5667 |
|
Larson TJ, Lightner VA, Green PR, Modrich P, Bell RM. Membrane phospholipid synthesis in Escherichia coli. Identification of the sn-glycerol-3-phosphate acyltransferase polypeptide as the plsB gene product. Journal of Biological Chemistry. 1980 Oct;255(19):9421–6. doi: 10.1016/s0021-9258(19)70579-1. |
| camalexin biosynthesis Accession ID: BioCyc:META_CAMALEXIN-SYN |
|
Glawischnig E. The role of cytochrome P450 enzymes in the biosynthesis of camalexin. Biochem Soc Trans. 2006 Dec;34(Pt 6):1206–8. doi: 10.1042/bst0341206. PMID: 17073786.; Schuhegger R, Nafisi M, Mansourova M, Petersen BL, Olsen CE, Svatos A, Halkier BA, Glawischnig E. CYP71B15 (PAD3) catalyzes the final step in camalexin biosynthesis. Plant Physiol. 2006 Aug;141(4):1248–54. PMID: 16766671; PMCID: PMC1533948.; Glawischnig E, Hansen BG, Olsen CE, Halkier BA. Camalexin is synthesized from indole-3-acetaldoxime, a key branching point between primary and secondary metabolism in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2004 May 17;101(21):8245–50. doi: 10.1073/pnas.0305876101.; Naur P, Hansen CH, Bak S, Hansen BG, Jensen NB, Nielsen HL, Halkier BA. CYP79B1 from Sinapis alba converts tryptophan to indole-3-acetaldoxime. Archives of Biochemistry and Biophysics. 2003 Jan;409(1):235–41. doi: 10.1016/s0003-9861(02)00567-2.; Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, Normanly J, Chory J, Celenza JL. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev. 2002 Dec 01;16(23):3100–12. PMID: 12464638; PMCID: PMC187496.; Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA. Cytochrome P450 CYP79B2 from Arabidopsis Catalyzes the Conversion of Tryptophan to Indole-3-acetaldoxime, a Precursor of Indole Glucosinolates and Indole-3-acetic Acid. Journal of Biological Chemistry. 2000 Oct;275(43):33712–7. doi: 10.1074/jbc.m001667200.; Hull AK, Vij R, Celenza JL. Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 2000 Feb 18;97(5):2379–84. doi: 10.1073/pnas.040569997.; Zook M, Hammerschmidt R. Origin of the thiazole ring of camalexin, a phytoalexin from Arabidopsis thaliana. Plant Physiol. 1997 Feb;113(2):463–8. PMID: 9046593; PMCID: PMC158161. |
| theobromine biosynthesis II (via xanthine) Accession ID: BioCyc:META_PWY-5040 |
- | |
| thiamine salvage III Accession ID: BioCyc:META_PWY-6898 |
|
Melnick J, Lis E, Park J, Kinsland C, Mori H, Baba T, Perkins J, Schyns G, Vassieva O, Osterman A, Begley TP. Identification of the Two Missing Bacterial Genes Involved in Thiamine Salvage: Thiamine Pyrophosphokinase and Thiamine Kinase. J Bacteriol. 2004 Jun;186(11):3660–2. doi: 10.1128/jb.186.11.3660-3662.2004. |
| phospholipid remodeling (phosphatidate, yeast) Accession ID: BioCyc:META_PWY-7417 |
|
Henry SA, Kohlwein SD, Carman GM. Metabolism and regulation of glycerolipids in the yeast Saccharomyces cerevisiae. Genetics. 2012 Feb;190(2):317–49. PMID: 22345606; PMCID: PMC3276621.; Ayciriex S, Le Guédard M, Camougrand N, Velours G, Schoene M, Leone S, Wattelet-Boyer V, Dupuy JW, Shevchenko A, Schmitter JM, Lessire R, Bessoule JJ, Testet E. YPR139c/LOA1 encodes a novel lysophosphatidic acid acyltransferase associated with lipid droplets and involved in TAG homeostasis. Mol Biol Cell. 2012 Jan;23(2):233–46. PMID: 22090344; PMCID: PMC3258169.; Rajakumari S, Daum G. Multiple Functions as Lipase, Steryl Ester Hydrolase, Phospholipase, and Acyltransferase of Tgl4p from the Yeast Saccharomyces cerevisiae. Journal of Biological Chemistry. 2010 May;285(21):15769–76. doi: 10.1074/jbc.m109.076331.; Rajakumari S, Daum G. Janus-faced Enzymes Yeast Tgl3p and Tgl5p Catalyze Lipase and Acyltransferase Reactions. MBoC. 2010 Feb 15;21(4):501–10. doi: 10.1091/mbc.e09-09-0775.; Petschnigg J, Wolinski H, Kolb D, Zellnig G, Kurat CF, Natter K, Kohlwein SD. Good Fat, Essential Cellular Requirements for Triacylglycerol Synthesis to Maintain Membrane Homeostasis in Yeast. Journal of Biological Chemistry. 2009 Nov;284(45):30981–93. doi: 10.1074/jbc.m109.024752.; Jain S, Stanford N, Bhagwat N, Seiler B, Costanzo M, Boone C, Oelkers P. Identification of a Novel Lysophospholipid Acyltransferase in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2007 Oct;282(42):30562–9. doi: 10.1074/jbc.m706326200.; Boumann HA, Gubbens J, Koorengevel MC, Oh CS, Martin CE, Heck AJ, Patton-Vogt J, Henry SA, de Kruijff B, de Kroon AI. Depletion of phosphatidylcholine in yeast induces shortening and increased saturation of the lipid acyl chains: evidence for regulation of intrinsic membrane curvature in a eukaryote. Mol Biol Cell. 2006 Feb;17(2):1006–17. PMID: 16339082; PMCID: PMC1356607.; Kurat CF, Natter K, Petschnigg J, Wolinski H, Scheuringer K, Scholz H, Zimmermann R, Leber R, Zechner R, Kohlwein SD. Obese Yeast: Triglyceride Lipolysis Is Functionally Conserved from Mammals to Yeast. Journal of Biological Chemistry. 2006 Jan;281(1):491–500. doi: 10.1074/jbc.m508414200.; Athenstaedt K, Daum G. Tgl4p and Tgl5p, Two Triacylglycerol Lipases of the Yeast Saccharomyces cerevisiae Are Localized to Lipid Particles. Journal of Biological Chemistry. 2005 Nov;280(45):37301–9. doi: 10.1074/jbc.m507261200.; Wagner S, Paltauf F. Generation of glycerophospholipid molecular species in the yeast Saccharomyces cerevisiae. Fatty acid pattern of phospholipid classes and selective acyl turnover at sn-1 and sn-2 positions. Yeast. 1994 Nov;10(11):1429–37. doi: 10.1002/yea.320101106.; Nagiec MM, Wells GB, Lester RL, Dickson RC. A suppressor gene that enables Saccharomyces cerevisiae to grow without making sphingolipids encodes a protein that resembles an Escherichia coli fatty acyltransferase. Journal of Biological Chemistry. 1993 Oct;268(29):22156–63. doi: 10.1016/s0021-9258(20)80661-9.; Brown P. The Board of Nursing explains guidelines, rules and advisory opinions. Wash Nurse. 1991 Nov;21(8):15–6. PMID: 1767529.; Cullis PR, De Kruijff B. The polymorphic phase behaviour of phosphatidylethanolamines of natural and synthetic origin. A 31P NMR study. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1978 Oct;513(1):31–42. doi: 10.1016/0005-2736(78)90109-8.; LANDS WE. LIPID METABOLISM. Annu Rev Biochem. 1965;34():313–46. doi: 10.1146/annurev.bi.34.070165.001525. PMID: 14321173.; LANDS WE. Metabolism of glycerolipids. 2. The enzymatic acylation of lysolecithin. J Biol Chem. 1960 Aug;235():2233–7. PMID: 14413818. |