Pathways Knowlegdes

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Pathway DOIs Note
superpathway of b heme biosynthesis from glycine

Accession ID: BioCyc:META_PWY-5920
  • 10.1007/s00253-003-1432-2
  • 10.1093/nar/gkh033
  • 10.1099/00221287-148-8-2273
  • 10.1101/gr.2050304
  • 10.1186/gb-2004-6-1-r2
 Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biology. 2004 Dec 22;6(1):r2. doi: 10.1186/gb-2004-6-1-r2.; Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery. Genome Res. 2004 Apr 12;14(5):917–24. doi: 10.1101/gr.2050304.; Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 01;32(Database issue):D311–4. PMID: 14681421; PMCID: PMC308767.; Frankenberg N, Moser J, Jahn D. Bacterial heme biosynthesis and its biotechnological application. Applied Microbiology and Biotechnology. 2003 Dec 01;63(2):115–27. doi: 10.1007/s00253-003-1432-2.; Panek H, O'Brian MR. A whole genome view of prokaryotic haem biosynthesis. Microbiology (Reading). 2002 Aug;148(Pt 8):2273–82. doi: 10.1099/00221287-148-8-2273. PMID: 12177321.
superpathway of CMP-sialic acids biosynthesis

Accession ID: BioCyc:META_PWY-6145
  • 10.1016/j.pep.2004.02.013
  • 10.1021/bi048606d
  • 10.1021/ja021309g
  • 10.1074/jbc.272.39.24319
  • 10.1093/glycob/cwt018
 Gurung MK, Ræder IL, Altermark B, Smalås AO. Characterization of the sialic acid synthase from Aliivibrio salmonicida suggests a novel pathway for bacterial synthesis of 7-O-acetylated sialic acids. Glycobiology. 2013 Jul;23(7):806–19. doi: 10.1093/glycob/cwt018. PMID: 23481098.; Murkin AS, Chou WK, Wakarchuk WW, Tanner ME. Identification and mechanism of a bacterial hydrolyzing UDP-N-acetylglucosamine 2-epimerase. Biochemistry. 2004 Nov 09;43(44):14290–8. doi: 10.1021/bi048606d. PMID: 15518580.; Blume A, Ghaderi D, Liebich V, Hinderlich S, Donner P, Reutter W, Lucka L. UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase, functionally expressed in and purified from Escherichia coli, yeast, and insect cells. Protein Expression and Purification. 2004 Jun;35(2):387–96. doi: 10.1016/j.pep.2004.02.013.; Chou WK, Hinderlich S, Reutter W, Tanner ME. Sialic acid biosynthesis: stereochemistry and mechanism of the reaction catalyzed by the mammalian UDP-N-acetylglucosamine 2-epimerase. J Am Chem Soc. 2003 Mar 05;125(9):2455–61. doi: 10.1021/ja021309g. PMID: 12603133.; Stäsche R, Hinderlich S, Weise C, Effertz K, Lucka L, Moormann P, Reutter W. A bifunctional enzyme catalyzes the first two steps in N-acetylneuraminic acid biosynthesis of rat liver. Molecular cloning and functional expression of UDP-N-acetyl-glucosamine 2-epimerase/N-acetylmannosamine kinase. J Biol Chem. 1997 Sep 26;272(39):24319–24. doi: 10.1074/jbc.272.39.24319. PMID: 9305888.
superpathway of bacteriochlorophyll a biosynthesis

Accession ID: BioCyc:META_PWY-5529
  • 10.1073/pnas.97.12.6908
  • 10.1146/annurev.genet.31.1.61
 Gough SP, Petersen BO, Duus JØ. Anaerobic chlorophyll isocyclic ring formation inRhodobacter capsulatusrequires a cobalamin cofactor. Proc. Natl. Acad. Sci. U.S.A. 2000 Jun 06;97(12):6908–13. doi: 10.1073/pnas.97.12.6908.; Suzuki JY, Bollivar DW, Bauer CE. Genetic analysis of chlorophyll biosynthesis. Annu Rev Genet. 1997;31():61–89. doi: 10.1146/annurev.genet.31.1.61. PMID: 9442890.
tetrapyrrole biosynthesis II (from glycine)

Accession ID: BioCyc:META_PWY-5189
  • 10.1016/j.abb.2008.02.015
 Heinemann IU, Jahn M, Jahn D. The biochemistry of heme biosynthesis. Archives of Biochemistry and Biophysics. 2008 Jun;474(2):238–51. doi: 10.1016/j.abb.2008.02.015.
CMP-N-acetylneuraminate biosynthesis II (bacteria)

Accession ID: BioCyc:META_PWY-6139
  • 10.1007/s00253-008-1643-7
  • 10.1007/s12010-008-8144-0
  • 10.1016/j.bioorg.2005.01.005
  • 10.1016/j.pep.2004.02.013
  • 10.1021/bi048606d
  • 10.1021/ja021309g
  • 10.1074/jbc.272.39.24319
 Mizanur RM, Pohl NL. Bacterial CMP-sialic acid synthetases: production, properties, and applications. Appl Microbiol Biotechnol. 2008 Oct;80(5):757–65. doi: 10.1007/s00253-008-1643-7. PMID: 18716769.; Santi-Gadelha T, Rocha BAM, Oliveira CC, Aragão KS, Marinho ES, Gadelha CAA, Toyama MH, Pinto VPT, Nagano CS, Delatorre P, Martins JL, Galvani FR, Sampaio AH, Debray H, Cavada BS. Purification of a PHA-Like Chitin-binding Protein from Acacia farnesiana Seeds: A Time-dependent Oligomerization Protein. Applied Biochemistry and Biotechnology. 2008 Feb 20;150(1):97. doi: 10.1007/s12010-008-8144-0.; Tanner ME. The enzymes of sialic acid biosynthesis. Bioorg Chem. 2005 Jun;33(3):216–28. doi: 10.1016/j.bioorg.2005.01.005. PMID: 15888312.; Murkin AS, Chou WK, Wakarchuk WW, Tanner ME. Identification and mechanism of a bacterial hydrolyzing UDP-N-acetylglucosamine 2-epimerase. Biochemistry. 2004 Nov 09;43(44):14290–8. doi: 10.1021/bi048606d. PMID: 15518580.; Blume A, Ghaderi D, Liebich V, Hinderlich S, Donner P, Reutter W, Lucka L. UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase, functionally expressed in and purified from Escherichia coli, yeast, and insect cells. Protein Expression and Purification. 2004 Jun;35(2):387–96. doi: 10.1016/j.pep.2004.02.013.; Chou WK, Hinderlich S, Reutter W, Tanner ME. Sialic acid biosynthesis: stereochemistry and mechanism of the reaction catalyzed by the mammalian UDP-N-acetylglucosamine 2-epimerase. J Am Chem Soc. 2003 Mar 05;125(9):2455–61. doi: 10.1021/ja021309g. PMID: 12603133.; Stäsche R, Hinderlich S, Weise C, Effertz K, Lucka L, Moormann P, Reutter W. A bifunctional enzyme catalyzes the first two steps in N-acetylneuraminic acid biosynthesis of rat liver. Molecular cloning and functional expression of UDP-N-acetyl-glucosamine 2-epimerase/N-acetylmannosamine kinase. J Biol Chem. 1997 Sep 26;272(39):24319–24. doi: 10.1074/jbc.272.39.24319. PMID: 9305888.
Metabolism

Accession ID: Reactome:R-BTA-1430728		 -
Amino acid and derivative metabolism

Accession ID: Reactome:R-BTA-71291
  • 10.1007/978-1-4757-0734-2_8
  • 10.1146/annurev.bi.44.070175.004441
  • 10.1177/014860719001400405
 Häussinger D. Liver glutamine metabolism. JPEN J Parenter Enteral Nutr. 1990 Jul;14(4 Suppl):56S–62S. doi: 10.1177/014860719001400405. PMID: 2205732.; Owen OE, Reichard GA, Patel MS, Boden G. Energy metabolism in feasting and fasting. Adv Exp Med Biol. 1979;111():169–88. doi: 10.1007/978-1-4757-0734-2_8. PMID: 371355.; Felig P. Amino acid metabolism in man. Annu Rev Biochem. 1975;44():933–55. doi: 10.1146/annurev.bi.44.070175.004441. PMID: 1094924.
Thyroxine biosynthesis

Accession ID: Reactome:R-BTA-209968
  • 10.1159/000180686
 Köhrle J, Brabant G, Hesch RD. Metabolism of the thyroid hormones. Horm Res. 1987;26(1-4):58–78. doi: 10.1159/000180686. PMID: 3297964.
Thyroxine biosynthesis

Accession ID: Reactome:R-CEL-209968
  • 10.1159/000180686
 Köhrle J, Brabant G, Hesch RD. Metabolism of the thyroid hormones. Horm Res. 1987;26(1-4):58–78. doi: 10.1159/000180686. PMID: 3297964.
Metabolism

Accession ID: Reactome:R-CFA-1430728		 -
Metabolism of amine-derived hormones

Accession ID: Reactome:R-DME-209776
  • 10.1017/s1462399406000068
  • 10.1046/j.1365-201x.2000.00596.x
  • 10.1159/000180686
 Ruddick JP, Evans AK, Nutt DJ, Lightman SL, Rook GA, Lowry CA. Tryptophan metabolism in the central nervous system: medical implications. Expert Rev Mol Med. 2006 Aug 31;8(20):1–27. doi: 10.1017/s1462399406000068. PMID: 16942634.; Flatmark T. Catecholamine biosynthesis and physiological regulation in neuroendocrine cells. Acta Physiol Scand. 2000 Jan;168(1):1–17. doi: 10.1046/j.1365-201x.2000.00596.x. PMID: 10691773.; Köhrle J, Brabant G, Hesch RD. Metabolism of the thyroid hormones. Horm Res. 1987;26(1-4):58–78. doi: 10.1159/000180686. PMID: 3297964.
Metabolism

Accession ID: Reactome:R-MMU-1430728		 -
Amino acid and derivative metabolism

Accession ID: Reactome:R-CFA-71291
  • 10.1007/978-1-4757-0734-2_8
  • 10.1146/annurev.bi.44.070175.004441
  • 10.1177/014860719001400405
 Häussinger D. Liver glutamine metabolism. JPEN J Parenter Enteral Nutr. 1990 Jul;14(4 Suppl):56S–62S. doi: 10.1177/014860719001400405. PMID: 2205732.; Owen OE, Reichard GA, Patel MS, Boden G. Energy metabolism in feasting and fasting. Adv Exp Med Biol. 1979;111():169–88. doi: 10.1007/978-1-4757-0734-2_8. PMID: 371355.; Felig P. Amino acid metabolism in man. Annu Rev Biochem. 1975;44():933–55. doi: 10.1146/annurev.bi.44.070175.004441. PMID: 1094924.
Thyroxine biosynthesis

Accession ID: Reactome:R-CFA-209968
  • 10.1159/000180686
 Köhrle J, Brabant G, Hesch RD. Metabolism of the thyroid hormones. Horm Res. 1987;26(1-4):58–78. doi: 10.1159/000180686. PMID: 3297964.
Metabolism

Accession ID: Reactome:R-DME-1430728		 -
Amino acid and derivative metabolism

Accession ID: Reactome:R-DME-71291
  • 10.1007/978-1-4757-0734-2_8
  • 10.1146/annurev.bi.44.070175.004441
  • 10.1177/014860719001400405
 Häussinger D. Liver glutamine metabolism. JPEN J Parenter Enteral Nutr. 1990 Jul;14(4 Suppl):56S–62S. doi: 10.1177/014860719001400405. PMID: 2205732.; Owen OE, Reichard GA, Patel MS, Boden G. Energy metabolism in feasting and fasting. Adv Exp Med Biol. 1979;111():169–88. doi: 10.1007/978-1-4757-0734-2_8. PMID: 371355.; Felig P. Amino acid metabolism in man. Annu Rev Biochem. 1975;44():933–55. doi: 10.1146/annurev.bi.44.070175.004441. PMID: 1094924.
Amino acid and derivative metabolism

Accession ID: Reactome:R-GGA-71291
  • 10.1007/978-1-4757-0734-2_8
  • 10.1146/annurev.bi.44.070175.004441
  • 10.1177/014860719001400405
 Häussinger D. Liver glutamine metabolism. JPEN J Parenter Enteral Nutr. 1990 Jul;14(4 Suppl):56S–62S. doi: 10.1177/014860719001400405. PMID: 2205732.; Owen OE, Reichard GA, Patel MS, Boden G. Energy metabolism in feasting and fasting. Adv Exp Med Biol. 1979;111():169–88. doi: 10.1007/978-1-4757-0734-2_8. PMID: 371355.; Felig P. Amino acid metabolism in man. Annu Rev Biochem. 1975;44():933–55. doi: 10.1146/annurev.bi.44.070175.004441. PMID: 1094924.
Thyroxine biosynthesis

Accession ID: Reactome:R-GGA-209968
  • 10.1159/000180686
 Köhrle J, Brabant G, Hesch RD. Metabolism of the thyroid hormones. Horm Res. 1987;26(1-4):58–78. doi: 10.1159/000180686. PMID: 3297964.
Metabolism of amine-derived hormones

Accession ID: Reactome:R-HSA-209776
  • 10.1017/s1462399406000068
  • 10.1046/j.1365-201x.2000.00596.x
  • 10.1159/000180686
 Ruddick JP, Evans AK, Nutt DJ, Lightman SL, Rook GA, Lowry CA. Tryptophan metabolism in the central nervous system: medical implications. Expert Rev Mol Med. 2006 Aug 31;8(20):1–27. doi: 10.1017/s1462399406000068. PMID: 16942634.; Flatmark T. Catecholamine biosynthesis and physiological regulation in neuroendocrine cells. Acta Physiol Scand. 2000 Jan;168(1):1–17. doi: 10.1046/j.1365-201x.2000.00596.x. PMID: 10691773.; Köhrle J, Brabant G, Hesch RD. Metabolism of the thyroid hormones. Horm Res. 1987;26(1-4):58–78. doi: 10.1159/000180686. PMID: 3297964.
Metabolism of amine-derived hormones

Accession ID: Reactome:R-MMU-209776
  • 10.1017/s1462399406000068
  • 10.1046/j.1365-201x.2000.00596.x
  • 10.1159/000180686
 Ruddick JP, Evans AK, Nutt DJ, Lightman SL, Rook GA, Lowry CA. Tryptophan metabolism in the central nervous system: medical implications. Expert Rev Mol Med. 2006 Aug 31;8(20):1–27. doi: 10.1017/s1462399406000068. PMID: 16942634.; Flatmark T. Catecholamine biosynthesis and physiological regulation in neuroendocrine cells. Acta Physiol Scand. 2000 Jan;168(1):1–17. doi: 10.1046/j.1365-201x.2000.00596.x. PMID: 10691773.; Köhrle J, Brabant G, Hesch RD. Metabolism of the thyroid hormones. Horm Res. 1987;26(1-4):58–78. doi: 10.1159/000180686. PMID: 3297964.