Pathways Knowlegdes

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Pathway DOIs Note
tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde

Accession ID: BioCyc:LEISH_PWY-5651		 -
tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde

Accession ID: BioCyc:TRYPANO_PWY-5651		 -
tryptophan degradation via kynurenine

Accession ID: BioCyc:CALBI_TRYPTOPHAN-DEGRADATION-1
  • 10.1002/jobm.19740140508
  • 10.1016/s0014-5793(02)02585-1
  • 10.1271/bbb.69.2358
 TSAI S, TSAI L, LI Y. An IsolatedCandida albicansTL3 Capable of Degrading Phenol at Large Concentration. Bioscience, Biotechnology, and Biochemistry. 2005 Jan;69(12):2358–67. doi: 10.1271/bbb.69.2358.; Panozzo C, Nawara M, Suski C, Kucharczyk R, Skoneczny M, Bécam A, Rytka J, Herbert CJ. Aerobic and anaerobic NAD+ metabolism in Saccharomyces cerevisiae. FEBS Letters. 2002 Mar 22;517(1-3):97–102. doi: 10.1016/s0014-5793(02)02585-1.; Teuscher G, Karczewski P, Weide H. [Catabolism of tryptophan by Candida guilliermondii, strain H17]. Z Allg Mikrobiol. 1974;14(5):429–33. doi: 10.1002/jobm.3630140508. PMID: 4408763.
superpathway of phenylalanine, tyrosine and tryptophan biosynthesis

Accession ID: BioCyc:CALBI_COMPLETE-ARO-PWY		 -
tryptophan biosynthesis

Accession ID: BioCyc:CALBI_TRPSYN-PWY
  • 10.1002/(sici)1097-0061(200004)16:6<553::aid-yea554>3.0.co;2-7
  • 10.1016/s0021-9258(17)43193-0
  • 10.1128/ec.5.5.816-824.2006
  • 10.1128/jb.175.4.1061-1068.1993
  • 10.1128/mmbr.55.3.349-370.1991
 Kingsbury JM, Goldstein AL, McCusker JH. Role of Nitrogen and Carbon Transport, Regulation, and Metabolism Genes for Saccharomyces cerevisiae Survival In Vivo. Eukaryot Cell. 2006 May;5(5):816–24. doi: 10.1128/ec.5.5.816-824.2006.; Toyn JH, Gunyuzlu PL, White WH, Thompson LA, Hollis GF. A counterselection for the tryptophan pathway in yeast: 5-fluoroanthranilic acid resistance. Yeast. 2000 Apr;16(6):553–60. doi: 10.1002/(sici)1097-0061(200004)16:6<553::aid-yea554>3.0.co;2-7. PMID: 10790693.; Graf R, Mehmann B, Braus GH. Analysis of feedback-resistant anthranilate synthases from Saccharomyces cerevisiae. J Bacteriol. 1993 Feb;175(4):1061–8. doi: 10.1128/jb.175.4.1061-1068.1993.; Braus GH. Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. Microbiol Rev. 1991 Sep;55(3):349–70. doi: 10.1128/mr.55.3.349-370.1991.; Zalkin H, Paluh JL, van Cleemput M, Moye WS, Yanofsky C. Nucleotide sequence of Saccharomyces cerevisiae genes TRP2 and TRP3 encoding bifunctional anthranilate synthase: indole-3-glycerol phosphate synthase. Journal of Biological Chemistry. 1984 Mar;259(6):3985–92. doi: 10.1016/s0021-9258(17)43193-0.
IAA biosynthesis I

Accession ID: BioCyc:LEISH_PWY-581		 -
tRNA charging pathway

Accession ID: BioCyc:LEISH_TRNA-CHARGING-PWY		 -
tryptophan degradation

Accession ID: BioCyc:LEISH_PWY3IU-46
  • 10.1111/j.1550-7408.1992.tb01329.x
 LEELAYOOVA S, MARBURY D, RAINEY PM, MACKENZIE NE, HALL JE. In Vitro Tryptophan Catabolism by Leishmania donovani donovani Promastigotes. The Journal of Protozoology. 1992 Mar;39(2):350–8. doi: 10.1111/j.1550-7408.1992.tb01329.x.
NAD biosynthesis II (from tryptophan)

Accession ID: BioCyc:TRYPANO_NADSYN-PWY		 -
NAD biosynthesis (from tryptophan)

Accession ID: BioCyc:CALBI_NADSYN-PWY
  • 10.1016/j.tibs.2006.11.006
  • 10.1111/j.1567-1364.2007.00231.x
  • 10.1128/jb.139.3.883-888.1979
 Li YF, Bao WG. Why do some yeast species require niacin for growth? Different modes of NAD synthesis. FEMS Yeast Res. 2007 Aug;7(5):657–64. doi: 10.1111/j.1567-1364.2007.00231.x. PMID: 17425674.; Belenky P, Bogan KL, Brenner C. NAD+ metabolism in health and disease. Trends Biochem Sci. 2007 Jan;32(1):12–9. doi: 10.1016/j.tibs.2006.11.006. PMID: 17161604.; Chaffin WL, Barton RA, Jacobson EL, Jacobson MK. Nicotinamide adenine dinucleotide metabolism in Candida albicans. J Bacteriol. 1979 Sep;139(3):883–8. doi: 10.1128/jb.139.3.883-888.1979.
tryptophan degradation I (via anthranilate)

Accession ID: BioCyc:TRYPANO_TRPCAT-PWY		 -
tRNA charging pathway

Accession ID: BioCyc:CALBI_TRNA-CHARGING-PWY
  • 10.1016/s0960-894x(02)00958-7
  • 10.1128/aac.00254-06
  • 10.1128/aac.48.10.3959-3967.2004
  • 10.1128/aac.49.5.2084-2092.2005
 Hasenoehrl A, Galic´ T, Ergovic´ G, Mars?ic´ N, Skerlev M, Mittendorf J, Geschke U, Schmidt A, Schoenfeld W. In Vitro Activity and In Vivo Efficacy of Icofungipen (PLD-118), a Novel Oral Antifungal Agent, against the Pathogenic Yeast Candida albicans. Antimicrob Agents Chemother. 2006 Sep;50(9):3011–8. doi: 10.1128/aac.00254-06.; Petraitiene R, Petraitis V, Kelaher AM, Sarafandi AA, Mickiene D, Groll AH, Sein T, Bacher J, Walsh TJ. Efficacy, Plasma Pharmacokinetics, and Safety of Icofungipen, an Inhibitor of Candida Isoleucyl-tRNA Synthetase, in Treatment of Experimental Disseminated Candidiasis in Persistently Neutropenic Rabbits. Antimicrob Agents Chemother. 2005 May;49(5):2084–92. doi: 10.1128/aac.49.5.2084-2092.2005.; Petraitis V, Petraitiene R, Kelaher AM, Sarafandi AA, Sein T, Mickiene D, Bacher J, Groll AH, Walsh TJ. Efficacy of PLD-118, a Novel Inhibitor of Candida Isoleucyl-tRNA Synthetase, against Experimental Oropharyngeal and Esophageal Candidiasis Caused by Fluconazole-Resistant C. albicans. Antimicrob Agents Chemother. 2004 Oct;48(10):3959–67. doi: 10.1128/aac.48.10.3959-3967.2004.; Mittendorf J, Kunisch F, Matzke M, Militzer HC, Schmidt A, Schönfeld W. Novel antifungal beta-amino acids: synthesis and activity against Candida albicans. Bioorg Med Chem Lett. 2003 Feb 10;13(3):433–6. doi: 10.1016/s0960-894x(02)00958-7. PMID: 12565945.
NAD biosynthesis II (from tryptophan)

Accession ID: BioCyc:LEISH_NADSYN-PWY		 -
tryptophan degradation I (via anthranilate)

Accession ID: BioCyc:LEISH_TRPCAT-PWY		 -
tryptophan degradation

Accession ID: BioCyc:CALBI_PWY3O-214
  • 10.1002/jobm.19740140508
  • 10.1007/bf00415010
  • 10.1007/s004380050643
  • 10.1007/s004380050644
  • 10.1016/s0014-5793(02)02585-1
  • 10.1074/jbc.m211914200
  • 10.1111/j.1439-0507.2008.01626.x
  • 10.1271/bbb.69.2358
 Kruppa M. Quorum sensing and Candida albicans. Mycoses. 2009 Jan;52(1):1–10. doi: 10.1111/j.1439-0507.2008.01626.x. PMID: 18983434.; TSAI S, TSAI L, LI Y. An IsolatedCandida albicansTL3 Capable of Degrading Phenol at Large Concentration. Bioscience, Biotechnology, and Biochemistry. 2005 Jan;69(12):2358–67. doi: 10.1271/bbb.69.2358.; Dickinson JR, Salgado LEJ, Hewlins MJE. The Catabolism of Amino Acids to Long Chain and Complex Alcohols in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2003 Mar;278(10):8028–34. doi: 10.1074/jbc.m211914200.; Panozzo C, Nawara M, Suski C, Kucharczyk R, Skoneczny M, Bécam A, Rytka J, Herbert CJ. Aerobic and anaerobic NAD+ metabolism in Saccharomyces cerevisiae. FEBS Letters. 2002 Mar 22;517(1-3):97–102. doi: 10.1016/s0014-5793(02)02585-1.; Urrestarazu A, Vissers S, Iraqui I, Grenson M. Phenylalanine- and tyrosine-auxotrophic mutants of Saccharomyces cerevisiae impaired in transamination. Molecular Genetics and Genomics. 1998 Jan;257(2):230–7. doi: 10.1007/s004380050643.; Iraqui I, Vissers S, Cartiaux M, Urrestarazu A. Characterisation of Saccharomyces cerevisiae ARO8 and ARO9 genes encoding aromatic aminotransferases I and II reveals a new aminotransferase subfamily. Molecular Genetics and Genomics. 1998 Jan;257(2):238–48. doi: 10.1007/s004380050644.; Kradolfer P, Niederberger P, Hütter R. Tryptophan degradation in Saccharomyces cerevisiae: characterization of two aromatic aminotransferases. Arch Microbiol. 1982 Dec 11;133(3):242–8. doi: 10.1007/bf00415010. PMID: 6763508.; Teuscher G, Karczewski P, Weide H. [Catabolism of tryptophan by Candida guilliermondii, strain H17]. Z Allg Mikrobiol. 1974;14(5):429–33. doi: 10.1002/jobm.3630140508. PMID: 4408763.
Inner Membrane Transport

Accession ID: PathBank:SMP0000808		 -
tRNA Charging

Accession ID: PathBank:SMP0000820		 -
tRNA Charging 2

Accession ID: PathBank:SMP0000824		 -
Tryptophan Metabolism

Accession ID: PathBank:SMP0000835		 -
Trp Operon

Accession ID: PathBank:SMP0000981		 -