Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
acetate utilization

Accession ID: BioCyc:CALBI_ACETATEUTIL2-PWY
  • 10.1002/yea.1081
  • 10.1016/0378-1097(90)90432-p
 Liu LM, Li Y, Chen J. [Application of a metabolic-pathway-analysis based breeding strategy enhances the production of pyruvate by Torulopsis glabrata]. Wei Sheng Wu Xue Bao. 2005 Feb;45(1):77–80. PMID: 15847168.; Rodrigues F, Zeeman AM, Cardoso H, Sousa MJ, Steensma HY, Côrte-Real M, Leão C. Isolation of an acetyl-CoA synthetase gene (ZbACS2) from Zygosaccharomyces bailii. Yeast. 2004 Mar;21(4):325–31. doi: 10.1002/yea.1081. PMID: 15042592.; Sheridan R, Ratledge C, Chalk PA. Pathways to acetyl-CoA formation in Candida albicans. FEMS Microbiol Lett. 1990 May;57(1-2):165–9. doi: 10.1016/0378-1097(90)90432-p. PMID: 2199302.
acetyl-CoA degradation to acetate

Accession ID: BioCyc:LEISH_PWY3IU-16
  • 10.1016/j.pt.2007.02.004
  • 10.1073/pnas.95.6.3036
 Opperdoes FR, Coombs GH. Metabolism of Leishmania: proven and predicted. Trends Parasitol. 2007 Apr;23(4):149–58. doi: 10.1016/j.pt.2007.02.004. PMID: 17320480.; Van Hellemond JJ, Opperdoes FR, Tielens AGM. Trypanosomatidae produce acetate via a mitochondrial acetate:succinate CoA transferase. Proc. Natl. Acad. Sci. U.S.A. 1998 Mar 17;95(6):3036–41. doi: 10.1073/pnas.95.6.3036.
NAD biosynthesis II (from tryptophan)

Accession ID: BioCyc:LEISH_NADSYN-PWY		 -
asparagine biosynthesis

Accession ID: BioCyc:LEISH_PWY3IU-401
  • 10.1016/j.pt.2007.02.004
 Opperdoes FR, Coombs GH. Metabolism of Leishmania: proven and predicted. Trends Parasitol. 2007 Apr;23(4):149–58. doi: 10.1016/j.pt.2007.02.004. PMID: 17320480.
fatty acid activation

Accession ID: BioCyc:LEISH_PWY-5143		 -
fatty acid β-oxidation

Accession ID: BioCyc:LEISH_PWY3IU-1054
  • 10.1016/0166-6851(96)02710-7
  • 10.1016/j.bbamcr.2006.08.019
 Michels PAM, Bringaud F, Herman M, Hannaert V. Metabolic functions of glycosomes in trypanosomatids. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2006 Dec;1763(12):1463–77. doi: 10.1016/j.bbamcr.2006.08.019.; Wiemer EA, IJlst L, van Roy J, Wanders RJ, Opperdoes FR. Identification of 2-enoyl coenzyme A hydratase and NADP(+)-dependent 3-hydroxyacyl-CoA dehydrogenase activity in glycosomes of procyclic Trypanosoma brucei. Mol Biochem Parasitol. 1996 Nov 12;82(1):107–11. doi: 10.1016/0166-6851(96)02710-7. PMID: 8943154.
anthranilate degradation III (anaerobic)

Accession ID: BioCyc:TRYPANO_2AMINOBENZDEG-PWY		 -
fatty acid β-oxidation II (core pathway)

Accession ID: BioCyc:TRYPANO_PWY-5136		 -
ethanol degradation IV (peroxisomal)

Accession ID: BioCyc:TRYPANO_PWY66-162		 -
purine nucleotides de novo biosynthesis II

Accession ID: BioCyc:TRYPANO_PWY-841		 -
pyridine nucleotide cycling

Accession ID: BioCyc:TRYPANO_PYRNUCYC-PWY		 -
thiamin (vitamin B1) biosynthesis

Accession ID: BioCyc:CALBI_PWY3B3-661
  • 10.1002/biof.5520110136
  • 10.1002/yea.916
  • 10.1007/s00253-006-0464-9
  • 10.1016/0304-4165(83)90022-3
  • 10.1016/0304-4165(87)90089-4
  • 10.1016/s0021-9258(18)43843-4
  • 10.1016/s0167-4838(98)00069-7
  • 10.1016/s0378-1119(97)00354-5
  • 10.1021/ja012708z
  • 10.1021/ja030261j
  • 10.1021/ja061413o
  • 10.1038/nchembio867
  • 10.1080/00362178185380461
  • 10.1128/jb.172.10.6145-6147.1990
  • 10.1248/bpb.23.108
  • 10.2478/s11658-007-0055-5
 Kowalska E, Kozik A. The genes and enzymes involved in the biosynthesis of thiamin and thiamin diphosphate in yeasts. Cellular & Molecular Biology Letters. 2008 Apr 10;13(2):271–82. doi: 10.2478/s11658-007-0055-5.; Bettendorff L, Wirtzfeld B, Makarchikov AF, Mazzucchelli G, Frédérich M, Gigliobianco T, Gangolf M, De Pauw E, Angenot L, Wins P. Discovery of a natural thiamine adenine nucleotide. Nat Chem Biol. 2007 Apr;3(4):211–2. doi: 10.1038/nchembio867. PMID: 17334376.; Nosaka K. Recent progress in understanding thiamin biosynthesis and its genetic regulation in Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. 2006 Jul 07;72(1):30–40. doi: 10.1007/s00253-006-0464-9.; Chatterjee A, Jurgenson CT, Schroeder FC, Ealick SE, Begley TP. Thiamin Biosynthesis in Eukaryotes: Characterization of the Enzyme-Bound Product of Thiazole Synthase from Saccharomyces cerevisiae and Its Implications in Thiazole Biosynthesis. J. Am. Chem. Soc. 2006 May 11;128(22):7158–9. doi: 10.1021/ja061413o.; Zeidler J, Sayer BG, Spenser ID. Biosynthesis of vitamin B1 in yeast. Derivation of the pyrimidine unit from pyridoxine and histidine. Intermediacy of urocanic acid. J Am Chem Soc. 2003 Oct 29;125(43):13094–105. doi: 10.1021/ja030261j. PMID: 14570482.; Rodríguez-Navarro S, Llorente B, Rodríguez-Manzaneque MT, Ramne A, Uber G, Marchesan D, Dujon B, Herrero E, Sunnerhagen P, Pérez-Ortín JE. Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Yeast. 2002 Sep 23;19(14):1261–76. doi: 10.1002/yea.916.; Zeidler J, Ullah N, Gupta RN, Pauloski RM, Sayer BG, Spenser ID. 2‘-Hydroxypyridoxol, a Biosynthetic Precursor of Vitamins B6 and B1 in Yeast. J. Am. Chem. Soc. 2002 Apr 06;124(17):4542–3. doi: 10.1021/ja012708z.; Tanaka K, Tazuya K, Yamada K, Kumaoka H. Biosynthesis of thiamin under anaerobic conditions in Saccharomyces cerevisiae. Biofactors. 2000;11(1-2):121–2. doi: 10.1002/biof.5520110136. PMID: 10705981.; TANAKA K, TAZUYA K, YAMADA K, KUMAOKA H. Biosynthesis of Thiamin under Anaerobic Conditions in Saccharomyces cerevisiae. Biological & Pharmaceutical Bulletin. 2000;23(1):108–11. doi: 10.1248/bpb.23.108.; Hohmann S, Meacock PA. Thiamin metabolism and thiamin diphosphate-dependent enzymes in the yeast Saccharomyces cerevisiae: genetic regulation. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 1998 Jun;1385(2):201–19. doi: 10.1016/s0167-4838(98)00069-7.; Singleton CK. Identification and characterization of the thiamine transporter gene of Saccharomyces cerevisiae. Gene. 1997 Oct 15;199(1-2):111–21. doi: 10.1016/s0378-1119(97)00354-5. PMID: 9358046.; Tazuya K, Azumi C, Yamada K, Kumaoka H. Pyrimidine moiety of thiamin is biosynthesized from pyridoxine and histidine in Saccharomyces cerevisiae. Biochem Mol Biol Int. 1995 Jul;36(4):883–8. PMID: 8528151.; Nosaka K, Nishimura H, Kawasaki Y, Tsujihara T, Iwashima A. Isolation and characterization of the THI6 gene encoding a bifunctional thiamin-phosphate pyrophosphorylase/hydroxyethylthiazole kinase from Saccharomyces cerevisiae. Journal of Biological Chemistry. 1994 Dec;269(48):30510–6. doi: 10.1016/s0021-9258(18)43843-4.; Tazuya K, Azumi C, Yamada K, Kumaoka H. Origin of the N-1, C-2 and C-2' atoms of the pyrimidine moiety of thiamin in Saccharomyces cerevisiae. Biochem Mol Biol Int. 1994 Jul;33(4):769–74. PMID: 7981664.; Tazuya K, Yamada K, Kumaoka H. Pyridoxine is a precursor of the pyrimidine moiety of thiamin in Saccharomyces cerevisiae. Biochem Mol Biol Int. 1993 Aug;30(5):893–9. PMID: 8220238.; Kawasaki Y, Nosaka K, Kaneko Y, Nishimura H, Iwashima A. Regulation of thiamine biosynthesis in Saccharomyces cerevisiae. J Bacteriol. 1990 Oct;172(10):6145–7. doi: 10.1128/jb.172.10.6145-6147.1990.; Tazuya K, Yamada K, Nakamura K, Kumaoka H. The origin of the sulfur atom of thiamin. Biochimica et Biophysica Acta (BBA) - General Subjects. 1987 Apr;924(1):210–5. doi: 10.1016/0304-4165(87)90089-4.; Tazuya K, Yamamoto M, Hayashiji M, Yamada K, Kumaoka H. Biosynthesis of thiamin. Precursor of C-5, C-6, and hydroxymethyl carbon atoms of the pyrimidine moiety in a eucaryote. Biochem Int. 1986 May;12(5):661–8. PMID: 3089223.; Yamada K, Yamamoto M, Hayashiji M, Tazuya K, Kumaoka H. Biosynthesis of thiamin. The precursor of the five-carbon unit of the thiazole moiety. Biochem Int. 1985 Apr;10(4):689–94. PMID: 3896243.; YAMAADA K, MORISAKI M, KUMAOKA H. Different biosynthetic pathways of the pyrimidine moiety of thiamin in procaryotes and eucaryotes. Biochimica et Biophysica Acta (BBA) - General Subjects. 1983 Mar 15;756(1):41–8. doi: 10.1016/0304-4165(83)90022-3.; Ball EH, Forbes EC, Gentles JC. Unusual response of a yeast to imidazole antifungals. Sabouraudia. 1981 Dec;19(4):287–94. doi: 10.1080/00362178185380461. PMID: 7034239.
phenylacetate degradation

Accession ID: BioCyc:CALBI_PWY0-321
  • 10.1002/jobm.3620360406
  • 10.1016/0045-6535(95)00301-n
 Hammer E, Kneifel H, Hofmann K, Schauer F. Enhanced excretion of intermediates of aromatic amino acid catabolism during chlorophenol degradation due to nutrient limitation in the yeast Candida maltosa. J Basic Microbiol. 1996;36(4):239–43. doi: 10.1002/jobm.3620360406. PMID: 8765083.; Kocwa-Haluch R, Lemek M. Easy and inexpensive diffusion tests for detecting the assimilation of aromatic compounds by yeast-like fungi. Part II. Assimilation of aromatic acids. Chemosphere. 1995 Dec;31(11-12):4333–9. doi: 10.1016/0045-6535(95)00301-n. PMID: 8574546.; Deshpande BS, Ambedkar SS, Sudhakaran VK, Narayanan RA, Shewale JG. Persistence of Candida sp. 115 during hydrolysis of penicillin G and metabolism of phenylacetic acid. Hindustan Antibiot Bull. 1989 Aug;31(3-4):71–5. PMID: 2486269.
asparagine biosynthesis

Accession ID: BioCyc:CALBI_ASPARAGINE-BIOSYNTHESIS
  • 10.1046/j.1365-2958.1996.d01-1715.x
 Dang V, Valens M, Bolotin-Fukuhara M, Daignan-Fornier B. Cloning of the ASN1 and ASN2 genes encoding asparagine synthetases in Saccharomyces cerevisiae: differential regulation by the CCAAT-box-binding factor. Molecular Microbiology. 1996 Nov;22(4):681–92. doi: 10.1046/j.1365-2958.1996.d01-1715.x.
NAD biosynthesis I from aspartate

Accession ID: WikiPathways:WP2484		 -
NAD salvage pathway I

Accession ID: WikiPathways:WP2486
  • 10.1002/prot.340200407
 Bork P, Koonin EV. A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity. Proteins. 1994 Dec;20(4):347–55. doi: 10.1002/prot.340200407. PMID: 7731953.
NAD salvage pathway II

Accession ID: WikiPathways:WP2487
  • 10.1098/rspb.2007.1244
 Ostrowski EA, Woods RJ, Lenski RE. The genetic basis of parallel and divergent phenotypic responses in evolving populations ofEscherichia coli. Proc. R. Soc. B. 2007 Nov 21;275(1632):277–84. doi: 10.1098/rspb.2007.1244.
Fatty Acid Oxidation

Accession ID: PathBank:SMP0000781		 -
Biosynthesis of Siderophore Group Nonribosomal Peptides

Accession ID: PathBank:SMP0000783		 -
Biotin Metabolism

Accession ID: PathBank:SMP0000785		 -