Pathways Knowlegdes

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Pathway DOIs Note
superpathway of 5-aminoimidazole ribonucleotide biosynthesis

Accession ID: BioCyc:META_PWY-6277
  • 10.1128/jb.175.11.3591-3597.1993
 Nygaard P, Smith JM. Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli. J Bacteriol. 1993 Jun;175(11):3591–7. doi: 10.1128/jb.175.11.3591-3597.1993.
aspartate superpathway

Accession ID: BioCyc:META_PWY0-781
  • 10.1016/0076-6879(87)43080-2
  • 10.1016/s0021-9258(18)64502-8
  • 10.1016/s0021-9258(18)97014-6
  • 10.1016/s0083-6729(01)61003-3
  • 10.1021/jm100349s
  • 10.1042/0264-6021:3560415
  • 10.1111/j.1432-1033.1978.tb12388.x
  • 10.1128/jb.67.2.182-190.1954
 Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808–12. doi: 10.1021/jm100349s. PMID: 20503968.; 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.; Begley TP, Kinsland C, Mehl RA, Osterman A, Dorrestein P. The biosynthesis of nicotinamide adenine dinucleotides in bacteria. Vitam Horm. 2001;61():103–19. doi: 10.1016/s0083-6729(01)61003-3. PMID: 11153263.; Soda K. Microbial sulfur amino acids: an overview. Methods Enzymol. 1987;143():453–9. doi: 10.1016/0076-6879(87)43080-2. PMID: 3309561.; POWELL JT, MORRISON JF. The Purification and Properties of the Aspartate Aminotransferase and Aromatic-Amino-Acid Aminotransferase from Escherichia coli. European Journal of Biochemistry. 1978 Jun;87(2):391–400. doi: 10.1111/j.1432-1033.1978.tb12388.x.; Farkas W, Gilvarg C. The Reduction Step in Diaminopimelic Acid Biosynthesis. Journal of Biological Chemistry. 1965 Dec;240(12):4717–22. doi: 10.1016/s0021-9258(18)97014-6.; Kindler SH, Gilvarg C. N-Succinyl-l-a, e-diaminopimelic Acid Deacylase. Journal of Biological Chemistry. 1960 Dec;235(12):3532–5. doi: 10.1016/s0021-9258(18)64502-8.; Cohen GN, Hirsch M. THREONINE SYNTHASE, A SYSTEM SYNTHESIZING l -THREONINE FROM l -HOMOSERINE. J Bacteriol. 1954 Feb;67(2):182–90. doi: 10.1128/jb.67.2.182-190.1954.
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis

Accession ID: BioCyc:META_PWY-7211
  • 10.1146/annurev.arplant.57.032905.105421
 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.
5-aminoimidazole ribonucleotide biosynthesis II

Accession ID: BioCyc:ECO_PWY-6122
  • 10.1128/jb.175.11.3591-3597.1993
 Nygaard P, Smith JM. Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli. J Bacteriol. 1993 Jun;175(11):3591–7. doi: 10.1128/jb.175.11.3591-3597.1993.
L-homoserine biosynthesis

Accession ID: BioCyc:META_HOMOSERSYN-PWY
  • 10.1042/0264-6021:3560415
 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.
L-lysine biosynthesis I

Accession ID: BioCyc:META_DAPLYSINESYN-PWY
  • 10.1016/s0021-9258(18)64502-8
  • 10.1016/s0021-9258(18)97014-6
  • 10.1021/jm100349s
 Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808–12. doi: 10.1021/jm100349s. PMID: 20503968.; Farkas W, Gilvarg C. The Reduction Step in Diaminopimelic Acid Biosynthesis. Journal of Biological Chemistry. 1965 Dec;240(12):4717–22. doi: 10.1016/s0021-9258(18)97014-6.; Kindler SH, Gilvarg C. N-Succinyl-l-a, e-diaminopimelic Acid Deacylase. Journal of Biological Chemistry. 1960 Dec;235(12):3532–5. doi: 10.1016/s0021-9258(18)64502-8.
UMP biosynthesis I

Accession ID: BioCyc:META_PWY-5686
  • 10.1146/annurev.arplant.57.032905.105421
 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.
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I

Accession ID: BioCyc:ECO_P4-PWY		 -
superpathway of arginine and polyamine biosynthesis

Accession ID: BioCyc:ECO_ARG+POLYAMINE-SYN		 -
L-lysine biosynthesis I

Accession ID: BioCyc:ECO_DAPLYSINESYN-PWY		 -
L-arginine biosynthesis I (via L-ornithine)

Accession ID: BioCyc:ECO_ARGSYN-PWY		 -
UMP biosynthesis I

Accession ID: BioCyc:ECO_PWY-5686		 -
superpathway of L-methionine biosynthesis (transsulfuration)

Accession ID: BioCyc:META_PWY-5347		 -
L-arginine biosynthesis I (via L-ornithine)

Accession ID: BioCyc:META_ARGSYN-PWY
  • 10.1128/mmbr.50.3.314-352.1986
 Cunin R, Glansdorff N, Piérard A, Stalon V. Biosynthesis and metabolism of arginine in bacteria. Microbiol Rev. 1986 Sep;50(3):314–52. doi: 10.1128/mr.50.3.314-352.1986.
superpathway of pyrimidine ribonucleotides de novo biosynthesis

Accession ID: BioCyc:META_PWY0-162
  • 10.1146/annurev.arplant.57.032905.105421
 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.
5-aminoimidazole ribonucleotide biosynthesis I

Accession ID: BioCyc:ECO_PWY-6121		 -
superpathway of S-adenosyl-L-methionine biosynthesis

Accession ID: BioCyc:ECO_MET-SAM-PWY		 -
superpathway of pyrimidine ribonucleotides de novo biosynthesis

Accession ID: BioCyc:ECO_PWY0-162		 -
superpathway of L-threonine biosynthesis

Accession ID: BioCyc:ECO_THRESYN-PWY
  • 10.1016/s0021-9258(17)42554-3
  • 10.1042/0264-6021:3560415
  • 10.1128/jb.67.2.182-190.1954
 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 l -THREONINE FROM l -HOMOSERINE. J Bacteriol. 1954 Feb;67(2):182–90. doi: 10.1128/jb.67.2.182-190.1954.
superpathway of 5-aminoimidazole ribonucleotide biosynthesis

Accession ID: BioCyc:ECO_PWY-6277
  • 10.1128/jb.175.11.3591-3597.1993
 Nygaard P, Smith JM. Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli. J Bacteriol. 1993 Jun;175(11):3591–7. doi: 10.1128/jb.175.11.3591-3597.1993.